Control track and group visibility more selectively below.
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| Common |
| Common methbase tracks for the hg38 assembly |
| ERP004221 |
| Genome-wide methylome profiling of normal breast and breast tumors |
| ERP005229 |
| Whole-genome Bisulfite Sequencing for Methylation Analysis of human monocytes |
| ERP011276 |
| 5Aza and TSA treatment of MCF7 cells (BS-seq) |
| ERP109610 |
| Bisulphite-seq to investigate the proto CpG island methylator phenotype of sessile serrated adenoma/polyps |
| ERP110208 |
| Whole genome methylation analysis of sperm and blood from young and old men. |
| ERP117337 |
| Whole genome DNA methylation analysis of sperm DNA from normozoospermic and oligoasthenoteratozoospermic men |
| ERP122363 |
| No evidence for intervention-associated DNA methylation changes in monocytes of patients with posttraumatic stress disorder or anorexia nervosa |
| ERP135121 |
| Whole Genome Bisulfite Sequencing (WGBS) of the SH-SY5Y human neuroblastoma cell line |
| SRP000941 |
| UCSD Human Reference Epigenome Mapping Project |
| SRP000996 |
| BI Human Reference Epigenome Mapping Project |
| SRP001371 |
| University of Washington Human Reference Epigenome Mapping Project |
| SRP001720 |
| Dynamic Changes in the Human Methylome During Differentiation |
| SRP003529 |
| Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells |
| SRP004775 |
| Large-scale methylation domains mark a functional subset of neuronally expressed genes |
| SRP005601 |
| Deep Sequence Analysis of the Relationship between Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells |
| SRP006728 |
| Genome-wide DNA methylation mapping in breast cancer cells (HCC1954) and normal breast cells (HMEC) |
| SRP006774 |
| Increased methylation variation in epigenetic domains across cancer types |
| SRP007820 |
| The DNA methylomes of a newborn and a centenarian |
| SRP008144 |
| Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment |
| SRP011945 |
| Base Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome |
| SRP012161 |
| Evolutionary Significance of DNA Methylation in Human and Chimpanzee Brains |
| SRP012380 |
| Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in Acute Myeloid Leukemia |
| SRP012412 |
| GSE59395: Genome-wide map of regulatory interactions in the human genome |
| SRP012499 |
| Epigenetic alterations of a DNMT3B-mutant ICF patient at base-pair resolution |
| SRP012560 |
| GSE34399: Replication Timing by Repli-seq from ENCODE/University of Washington |
| SRP013816 |
| SINE transcription by RNA polymerase III is suppressed by histone methylation but not DNA methylation |
| SRP014634 |
| Examination of four human tissue samples by MethylC-seq |
| SRP014898 |
| Human Sperm Epigenomes and Transcriptomes Reveal Novel Features of Enhancers, Sex Chromosomes, piRNAs, Gametogenesis, and Inherited Small RNAs (Bisulfite-Seq) |
| SRP015704 |
| Genome-wide mapping of nucleosome positioning and DNA methylation within Individual DNA molecules |
| SRP015742 |
| GSE40832: Whole Genome Bisulfite Sequencing by ENCODE/HAIB |
| SRP016558 |
| Epigenomic alterations in localized and advanced prostate cancer |
| SRP017236 |
| Analysis of DNA methylation dynamics at Alu elements during human B cell activation |
| SRP017645 |
| Direct ChIP-bisulfite sequencing reveals a role of H3K27me3 mediating aberrant hypermethylation of promoter CpG islands in cancer cells (ChIP-BS) |
| SRP019232 |
| Whole genome bisulfite-seq of two healthy males. |
| SRP019240 |
| Classification of cancer cell lines using a promoter-targeted liquid hybridization capture-based bisulfite sequencing approach |
| SRP021039 |
| Selective demethylation and altered gene expression are associated with ICF Syndrome in human induced pluripotent stem cells and mesenchymal stem cells |
| SRP021479 |
| Genome-wide DNA methylation aberrations in human atherosclerosis (sequencing) |
| SRP021846 |
| Age-related methylation changes are associated with altered transcriptional circuitry [Methyl-seq] |
| SRP022041 |
| Buccals are likely to be a more informative surrogate tissue than blood for epigenome-wide association studies [Bisulfite-Seq] |
| SRP022149 |
| Genome-wide parent-of-origin DNA methylation analysis [Methyl-seq] |
| SRP022160 |
| Whole-genome analysis of 5-hydroxymethylcytosines and 5-methylcytosines at base resolution in human brain |
| SRP026048 |
| Global epigenomic reconfiguration during mammalian brain development |
| SRP026604 |
| Genome-wide methylation maps for Proliferating and Senescent cells |
| SRP028600 |
| Charting a dynamic DNA methylation landscape of the human genome |
| SRP028804 |
| The DNA methylation landscape of human early embryos |
| SRP028957 |
| Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma |
| SRP029519 |
| Induction of sarcomas by mutant IDH2 |
| SRP032354 |
| whole-genome bisulfite sequencing (BS-seq) of HEK293 cells (HEK293-CT) and HEK293 cells stably over-expressing the BAHD1 gene (HEK-BAHD1) |
| SRP033201 |
| Homo sapiens Genome sequencing |
| SRP033252 |
| Genome-wide profiling of the functional DNA methylation landscape at base-pair resolution in human cancer types [BS-seq] |
| SRP033283 |
| The RON receptor tyrosine kinase promotes metastasis by triggering epigenetic reprogramming through the thymine glycosylase MBD4 (Bisulfite-Seq) |
| SRP033504 |
| Epigenome analysis of human epidermal samples with aging and sun exposure |
| SRP034700 |
| Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells [human] |
| SRP035642 |
| The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts [Whole genome bisulfite sequencing] |
| SRP037971 |
| Genome wide profiling of MBD2 binding |
| SRP038103 |
| Genome-wide methylation maps for untreated and Aza treated AML3 cells |
| SRP039676 |
| Promoter methylome and integrative transcriptome profiling identify key epigenetics-regulated genes in human HCCs [methylation] |
| SRP041025 |
| WGBS data of pediatric B-cell acute leukemias |
| SRP041720 |
| Genome-wide profiling of the DNA methylation landscape at base-pair resolution in human neurological disorders (Bisulfite-Seq) |
| SRP041822 |
| Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels [Bisulfite-Seq] |
| SRP041984 |
| Epigenetic and transcriptional aberrations in human pluripotent stem cells reflect differences in reprogramming mechanisms |
| SRP043572 |
| DNA Methylation Predictors of Gene Expression in the 1st Trimester Chorionic Villus: Implications for Prenatal Diagnosis |
| SRP045269 |
| Global loss of DNA methylation uncovers intronic enhancers in genes |
| SRP045902 |
| Resetting Transcription Factor Control Circuitry Towards Ground State Pluripotency In Human |
| SRP048844 |
| Genome-wide profiling of DNA methylation at single-base resolution based on MeDIP-bisulfite high-throughput sequencing and ridge regression (MethyC + MeDIP) |
| SRP049651 |
| Large-scale epigenetic reprogramming is punctuated late during the evolution of pancreatic cancer progression [BS-Seq] |
| SRP049710 |
| Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer |
| SRP050889 |
| Targeted CpG island methylation in human pluripotent stem cells |
| SRP052842 |
| Pleiotropic Analysis of Lung Cancer and Blood Triglycerides |
| SRP055494 |
| BLUEPRINT methylome of the HapMap cell line GM18507 (Coriell cell line NA18507) |
| SRP055862 |
| Targeted bisulfite sequencing to detect TALE-DNMT mediated targeted DNA methylation in human cells |
| SRP056034 |
| Romidepsin and azacitidine synergize in their epigenetic modulatory effects to induce apoptosis in CTCL |
| SRP056649 |
| Promoter methylomes of monochorionic twin placentas reveal intrauterine growth restriction specific methylation profiles |
| SRP056911 |
| DNA methylation in the placentas of typically developing and autistic children |
| SRP058102 |
| Analysis of DNA Methylation in replication and cell cycle arrest. |
| SRP058430 |
| Promoter targeted bisulfite sequencing reveals DNA methylation profiles associated with low sperm motility in asthenozoospermia |
| SRP059029 |
| Bisulfite sequencing coupled to target enrichment in MCF-7 |
| SRP059289 |
| Conversion of Human Gastric Epithelial Cells to Multipotent Endodermal Progenitors using Defined Small Molecules [DNA methylation] |
| SRP060353 |
| DNA Cytosine Hydroxymethylation Levels Are Distinct Among Peripheral Blood Leukocytes |
| SRP060659 |
| Integrative epigenomic analysis in MLL-AF9 acute myeloid leukemia (AML) and B-acute lymphoblastic leukemia (B-ALL) |
| SRP061225 |
| Dramatic Increase in Cell-subset Specific Methylation Accompanies Mammalian Brain Development [hairpin BS-Seq] |
| SRP061648 |
| Tumor hypoxia causes DNA hypermethylation by reducing TET activity (Bisulfite-Seq) |
| SRP063076 |
| High-dose folic acid supplementation alters the human sperm methylome and is influenced by the MTHFR C677T polymorphism |
| SRP065386 |
| DNA methylation variation of human-specific Alu repeats |
| SRP065418 |
| Obesity and Bariatric Surgery Drive Epigenetic Variation of Spermatozoa in Humans |
| SRP066123 |
| Reprogramming-associated aberrant DNA methylation determines hematopoietic differentiation capacity of human induced pluripotent stem cells |
| SRP067705 |
| Pervasive polymorphic imprinted methylation in the human placenta |
| SRP067779 |
| Novel contribution of acetylated histone variant H2A.Z in activation of neo-enhancers in prostate cancer [NOMe-seq] |
| SRP068579 |
| Reversion to naïve human pluripotency creates a new methylation landscape devoid of blastocyst or germline memory |
| SRP071738 |
| Mechanisms and disease associations of haplotype-dependent allele specific DNA methylation: Methyl-seq data for the identification of hap-ASM |
| SRP071771 |
| Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tissue-of-origin mapping from plasma DNA [WGBS] |
| SRP071891 |
| Functional Haploid Human Oocytes Generated from Polar Body Genomes (Bisulfite-Seq) |
| SRP072071 |
| study of brain methylation |
| SRP072075 |
| Epigenomic analysis of lymphocytes and fibroblasts |
| SRP072078 |
| epigenomic analysis of lung and liver |
| SRP072141 |
| stem cell epigenomics |
| SRP074177 |
| Nucleation of DNA Repair Factors by FOXA1 Links DNA Demethylation to Transcriptional Pioneering |
| SRP074852 |
| DNMT and HDAC inhibitors globally induce cryptic TSSs encoded in long terminal repeats |
| SRP075292 |
| Cumulative Impact of Polychlorinated Biphenyl and Large Chromosomal Duplications on DNA Methylation, Chromatin, and Expression of Autism Candidate Genes. |
| SRP075562 |
| ZBTB33 (Kaiso) Differentially Regulates Cell Cycle Through cyclin D1 and cyclin E1 in a Cell Specific Manner [BiSulfite-seq] |
| SRP075876 |
| Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain |
| SRP075910 |
| Global delay in nascent strand DNA methylation |
| SRP078133 |
| Comprehensive Assessment of Concordance Between Fresh-frozen and Formalin-fixed Paraffin Embedded Tumour DNA Methylation using a Targeted Sequencing Approach |
| SRP081132 |
| DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumour immunotolerance [SeqCapEpi] |
| SRP082156 |
| Cancer Associated Fibroblasts are defined by a core set of epigenome changes that contribute to the tumor phenotype [WGBS] |
| SRP082578 |
| Single-site CpG Profiling for KMT2D and HNF4A genomic region in pancreatic cancer cells. |
| SRP085035 |
| Molecular Criteria for Defining the Naive Human Pluripotent State [methylation profiling] |
| SRP089722 |
| Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling [WGBS] |
| SRP090105 |
| The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis [WGBS_Hs] |
| SRP090312 |
| S-adenosyl-methionine treatment selectively block liver cancer cell lines transformation and invasiveness by alterations of cancer- and invasion specific transcriptome and methylome (Bisulfite-Seq) |
| SRP092113 |
| Splinted Ligation Adapter Tagging, a novel library preparation for whole genome bisulphite sequencing |
| SRP093254 |
| Whole Genome Bisulfite Sequencing of HUES8 WT and HUES8 TET1/2/3 TKO hESCs |
| SRP094658 |
| Diverse Repetitive Element RNA Expression Define Epigenetic and Immunologic Features of Colon Cancer |
| SRP094721 |
| Epigenomic landscapes of hESC-derived neural rosettes |
| SRP094960 |
| Genomic profiling of human spermatogonial stem cells [WGBS] |
| SRP095006 |
| Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA Methylation by dCas9 methyltransferases (CRISPRme) [WGBS] |
| SRP096028 |
| Dental Pulp Stem Cells Model Early Life and Imprinted DNA Methylation Patterns. |
| SRP097759 |
| S-adenosylhomocysteine hydrolase participates in DNA methylation inheritance |
| SRP098648 |
| Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA [BiSulfite-seq] |
| SRP099603 |
| Enrichment methods provide a feasible approach to comprehensive and adequately powered investigations of the methylome |
| SRP100067 |
| Epigenome-wide analysis of DNA methylation in lung tissue shows concordance with blood studies and identifies tobacco smoke-inducible enhancers |
| SRP101887 |
| Neuronal brain region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability [Bisulfite-Seq] |
| SRP102997 |
| Genome-wide nucleosome occupancy and DNA methylation profiling in endometriosis cells |
| SRP103794 |
| Methylation DNA mediated KLF4 binding activity in glioblastoma cells |
| SRP103941 |
| DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A [BS-Seq] |
| SRP103943 |
| DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A [WGBS] |
| SRP104141 |
| NicE-seq: high resolution open chromatin profiling |
| SRP104305 |
| 5hmC dynamically correlated with enhancer''s activities during hES-to-Pancreatic endoderm cell differentiation (Bisulfite-Seq) |
| SRP106910 |
| Human memory CD8 T-cell effector-potential is epigenetically preserved during in vivo homeostasis |
| SRP107051 |
| Thermostable Group II intron reverse transcriptase single-stranded DNA-seq |
| SRP107225 |
| Simultaneous methylation-level assessment of hundreds of CpG sites by targeted bisulfite PCR sequencing (TBPseq) |
| SRP107857 |
| TRIM28-Regulated Transposon Repression Is Required for Human Germline Competency and Not Primed or Naive Human Pluripotency |
| SRP109843 |
| Single-cell multi-omics sequencing of human early embryos |
| SRP113417 |
| Chromatin and Transcriptional Dynamics in Adult Germline Stem Cells and Mammalian Spermatogenesis |
| SRP114449 |
| Targeted sequencing |
| SRP115893 |
| Characterization of distinct states of human naive pluripotency |
| SRP117084 |
| Transcription elongation regulates genome 3D structure |
| SRP117159 |
| Homo sapiens cultivar:PLC/PRF/5 Raw sequence reads |
| SRP124518 |
| UBE3A-mediated regulation of imprinted genes and epigenome-wide marks in human neurons |
| SRP125826 |
| Intervals of unmethylated DNA spatially co-segregate in cis and in trans [WGBS] |
| SRP125973 |
| A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs |
| SRP126139 |
| G-quadruplex structures moulds the DNA methylome |
| SRP126905 |
| Rescue of Fragile X syndrome neurons by DNA methylation editing of the FMR1 gene [methylation] |
| SRP126972 |
| Distinct Epigenetic Subtypes Are Linked to Disease Progression in Low-Risk MDS |
| SRP127667 |
| Epigenetic marks and nuclear transcriptomes of cardiac myocytes |
| SRP128919 |
| DNA methylation in hESC derived brain organoids and iPSC derived neurons, astrocytes and neural progenitors |
| SRP130768 |
| Homo sapiens bisulfite and mRNA sequencing of blood T cells and LCM collected lung cells |
| SRP131087 |
| An epigenomic approach to identifying differential overlapping and cis-acting lncRNAs in cisplatin-resistant cancer cells [BiSulfite-seq] |
| SRP131112 |
| Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots [RRBS] |
| SRP132292 |
| Genetic determinants and epigenetic effects of pioneer factor binding [WGBS] |
| SRP132785 |
| Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile (WGBS data set) |
| SRP155006 |
| Epigenomic signatures in liver and blood of Wilson disease patients include hypermethylation of liver-specific enhancers |
| SRP158279 |
| Epigenetic reprogramming at estrogen-receptor binding sites alters the 3D chromatin landscape in endocrine resistant breast cancer [WGBS] |
| SRP161745 |
| Human retinal pigment epithelium |
| SRP162996 |
| Very long intergenic non-coding RNA transcripts and expression profiles are associated to specific childhood acute lymphoblastic leukemia subtypes |
| SRP167041 |
| Homo sapiens Epigenomics |
| SRP174219 |
| Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer [Bisulfite-Seq] |
| SRP185639 |
| DNMT3B has oncogenic activity but evidence suggests that it does not promote CIMP nor cooperate with activated BRAFV600E in human intestinal cancer. (WGBS) |
| SRP186015 |
| Study of DNA methylation pattern in single basepair resolution in the human dopaminergic neurons |
| SRP186190 |
| Comparative and integrated functional genomics analysis of Klinefelter and Turner syndromes reveals network-wide effects of the sex chromosome dosage changes |
| SRP186275 |
| Bisulfite-seq profiling of the human neutrophil genome during PMA- and E. coli encounter-induced activation |
| SRP186642 |
| Genome-wide methyl-cytosine competition by DNMT and TET |
| SRP192966 |
| Gene expression, methylome and splicing of THP-1 monocytic cells and THP-1-derived macrophage |
| SRP198282 |
| Hammer-seq to measure kinetics of DNA methylation maintenance in HeLa cells |
| SRP199025 |
| Molecular mechanism of KCNJ5 gene hotspot mutation in adrenal aldosteronoma |
| SRP215940 |
| The DNA methylomes of hyper-IgM syndrome type 2 B cells provide insights into the roles of activation-induced deaminase prior to the germinal center reaction |
| SRP218776 |
| RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells |
| SRP219798 |
| Regulation of DNA Methylation at Enhancers by TET2 Finetunes Gene Transcription in ERa-Positive Breast Cancer Cells |
| SRP220467 |
| Human embryonic stem cell-derived organoidal retinoblastoma reveals cancerous origin and therapeutic target |
| SRP221227 |
| Persistent epigenetic memory impedes rescue of the telomeric phenotype in human ICF iPSCs following DNMT3B correction |
| SRP221387 |
| Genome-wide targeted methyl-seq: Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs I |
| SRP223055 |
| Tibetan humans Raw sequence reads |
| SRP223612 |
| Whole Genome Bisulfite sequencing: Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs |
| SRP224808 |
| Whole genome bisulfite sequencing of human spermatozoa reveals differentially methylated patterns from type 2 diabetic patients |
| SRP226234 |
| An ExtendedCulture System that Supports Human Primordial Germ Cell-Like Cells Survival and Initiation of DNA Methylation Erasure |
| SRP230221 |
| Chromatin dynamics reveal circadian control of human in vitro islet maturation [WGBS] |
| SRP233253 |
| Comparison of EM-seq and WGBS results |
| SRP238023 |
| Reliable tumor detection using cerebrospinal fluid cell-free DNA methylomes in pediatric medulloblastoma |
| SRP238061 |
| Increasing methylation of sperm rDNA and other repetitive elements in the aging male mammalian germline |
| SRP239226 |
| Principles of Signalling Pathway Modulation for Enhancing Human Naïve Pluripotency Induction [WGBS] |
| SRP241842 |
| REH MultiOmics |
| SRP246939 |
| Beta cell-specific CD8+ T cells maintain stem-cell memory-associated epigenetic programs during type 1 diabetes (WGBS) |
| SRP250803 |
| Genome-wide R-loop landscapes during epigenetic programming and reprogramming |
| SRP251688 |
| Signalling networks constructed by integrative analysis of multi-omics in peripheral blood mononuclear cells in systemic lupus erythematous patients |
| SRP259185 |
| Multi-omics analysis reveals divergent epigenetic regulation of gene expression and drivers of esophageal squamous cell carcinoma (WGBS) |
| SRP260840 |
| Naïve human embryonic stem cells can give rise to cells with trophoblast-like transcriptome and methylome [Bisulfite-Seq] |
| SRP261643 |
| Comprehensive epigenomic profiling of human alveolar epithelial differentiation identifies key epigenetic states and transcription factor co-regulatory networks for maintenance of distal lung identity |
| SRP265926 |
| 2-hydroxyglutarate drives whole-genome hypermethylation in kidney cancer cells with inactivated VHL |
| SRP266187 |
| Non-CG methylation and multiple epigenetic layers associate child abuse with immune and small GTPase dysregulation |
| SRP266653 |
| TNF induced inflammatory transcription dynamics and epigenetic changes |
| SRP266759 |
| DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumour immunotolerance [BS] |
| SRP267967 |
| Characterization of universal features of partially methylated domains across tissues and species |
| SRP268755 |
| Probing the signaling requirements for naïve human pluripotency by high-throughput chemical screening [WGBS] |
| SRP268783 |
| Acute depletion of CTCF rewires genome-wide chromatin accessibility |
| SRP272595 |
| WGBS analysis of various colon cancer cell lines |
| SRP273813 |
| Whole genome methylation sequencing of circulating tumor cells (CTCs) in Lung cancer. |
| SRP278588 |
| DNA methyation of intragenic CpG islands are required for differentiation from iPSC to NPC |
| SRP282493 |
| DNA methylation maintains integrity of higher order genome architecture (WGBS) |
| SRP286180 |
| Comprehensive methylome sequencing reveals prognostic epigenetic biomarkers for prostate cancer mortality |
| SRP286409 |
| H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination [Bisulfite-seq] |
| SRP286872 |
| Transient naive reprogramming corrects hiPS cells functionally and epigenetically [WGBS] |
| SRP291325 |
| Transient naive reprogramming corrects hiPS cells functionally and epigenetically [WGBS 2] |
| SRP298508 |
| Alternative splicing and the epigenome in CML remission [WGBS] |
| SRP299418 |
| cell-free DNA sequencing of plasma |
| SRP299802 |
| Acute lymphoblastic leukemia displays a distinct highly methylated genome |
| SRP304130 |
| Impact of exposures to persistent endocrine disrupting compounds on the sperm methylome in regions associated with neurodevelopmental disorders |
| SRP304684 |
| Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells [WGBS] |
| SRP308490 |
| Pan-cancer predictions of transcription factors mediating aberrant DNA methylation |
| SRP308810 |
| Genome-wide Programmable Transcriptional Memory by CRISPR-based Epigenome Editing |
| SRP308854 |
| Age-associated cryptic transcription in mammalian stem cells is linked to permissive chromatin at cryptic promoters [WGBS] |
| SRP309472 |
| Epigenetic crosstalk |
| SRP310254 |
| DNMT3A haploinsufficiency causes dichotomous DNA methylation defects at enhancers in mature human immune cells [BiSulfite-seq] |
| SRP315878 |
| Homo sapiens Epigenomics |
| SRP319892 |
| Expanding highly homogenous population of human primordial germ cell like cells in long-term and feeder-free culture condition [WGBS] |
| SRP320141 |
| Amplicon-seq of SVA methylation in human sperm |
| SRP321876 |
| Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states |
| SRP323032 |
| Mapping the glucocorticoid gene regulatory network and alterations that contribute to steroid resistance in childhood acute lymphoblastic leukemia [WGBS] |
| SRP324016 |
| Cerebrospinal fluid cell-free DNA methylomes subtyping pediatric medulloblastoma |
| SRP325428 |
| Systematic profiling of DNMT3A variants reveals protein instability mediated by the DCAF8 E3 ubiquitin ligase adaptor |
| SRP325722 |
| Chemical-based external stimulation reprograms human somatic cells into pluripotency (WGBS) |
| SRP329071 |
| Sperm methylome alterations following yoga-based lifestyle intervention in patients of primary male infertility: A pilot study |
| SRP330251 |
| Vitamin B12 regulates the transcriptomes of human ileal epithelial cells (iECs) |
| SRP332046 |
| The WGBS and ATAC-seq from human serum and amniotic cell |
| SRP332277 |
| Methyl-seq Human |
| SRP332448 |
| H3K9 dimethylation safeguards cancer cells against activation of the Interferon pathway [WGBS] |
| SRP337018 |
| whole-genome wide DNA methylation aberration in HCC |
| SRP337159 |
| Homo sapiens Epigenomics |
| SRP338853 |
| DNA methylation of MOLM-13 cells |
| SRP342964 |
| scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation |
| SRP345048 |
| Antigen cross-presentation in young tumor-bearing hosts promotes CD8 T cell terminal differentiation [WGBS] |
| SRP346999 |
| Whole genome bilsufite sequencing of sgTET2 HepG2 |
| SRP348645 |
| Transcriptomic and Epigenomic Profiles of CIC-knockout and IDH1 mutant cells [WGBS] |
| SRP352189 |
| CRISPR-based targeted haplotype-resolved assembly of a megabase region [WGBS] |
| SRP353040 |
| WGBS of control and DAC-treated tumor tissue from PDX model |
| SRP353536 |
| Transcriptome and Bisulfite sequencing of drug treated breast cancer cell lines |
| SRP353670 |
| DNA Methylation Potential Energy Landscape Analysis of MLL-rearranged Acute Myeloid Leukemia (AML) and Normal hematopoietic precursors [WGBS] |
| SRP356708 |
| Young vs Old Fibroblast WGBS |
| SRP357194 |
| HPV integration generates cellular super enhancer and functions as ecDNA to regulate genome-wide transcription |
| SRP357372 |
| WGBS and RNA-seq of HUVECs transfected with siNC or siTET2 |
| SRP358957 |
| WGBS of OLD and YOUNG primary Fibroblasts |
| SRP362494 |
| The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory (WGBS) |
| SRP367191 |
| Reduced Representation Bisulfite Sequencing (RRBS) of fluorescence-activated cell sorted (FACS) human spermatozoa stained with Chromomycin A3 (CMA3) and YO-PRO-1 (YOPRO) in fertile donors and infertile patients with short anogenital distances. |
| SRP375137 |
| DNMT3A-mediated DNA demethylation is required for hypoxia induced EMT of human cancer cells |
| SRP387154 |
| Accurate simultaneous sequencing of genetic and epigenetic bases in DNA |
| SRP389118 |
| Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation [WGBS] |
| SRP396738 |
| Highly efficient and rapid generation of human pluripotent stem cells by chemical reprogramming (WGBS) |
| SRP400466 |
| Multiplex Epigenome Editing of MECP2 to Rescue Rett Syndrome Neurons (WGBS) |
| SRP404930 |
| LN-stem, tumor stem, tumor terminally differentiated CD8 T cells from human kidney cancer |
| SRP405928 |
| Optimized bisulfite sequencing reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA [WGBS] |
| SRP436137 |
| Malignant Transformation Drives DNA Methylation Loss and Transcriptional Activation of Transposable Element Loci [WGBS] |
| SRP440514 |
| TNRC18 recognizes H3K9me3 to mediate transposable elements silencing at ERV regions [WGBS] |
| SRP450395 |
| Epigenetic therapy targets the 3D epigenome in endocrine-resistant breast cancer [WGBS] |
| SRP470181 |
| Hypermethylation of DNA impairs megakaryogenesis in delayed platelet recovery after allogeneic hematopoietic stem cell transplantation |
| SRP470337 |
| Highly cooperative chimeric super-SOX induces naïve pluripotency across species [RRBS] |
| SRP478966 |
| Epigenetic aging of seminal fluid is associated with inflammation |
|
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| Base Position |
| Chromosome position in bases. (Clicks here zoom in 3x) |
| Assembly |
| Assembly from Fragments |
| Assembly Tracks |
| Assembly identifiers, clones, and markers |
| STS Markers |
| STS Markers on Genetic (blue) and Radiation Hybrid (black) Maps |
| Scaffolds |
| GRCh38 Defined Scaffold Identifiers |
| GRC Contigs |
| Genome Reference Consortium Contigs |
FISH Clones |
| Clones Placed on Cytogenetic Map Using FISH |
| Centromeres |
| Centromere Locations |
| Chromosome Band |
| Chromosome Bands Localized by FISH Mapping Clones |
| Clone Ends |
| Mapping of clone libraries end placements |
| Exome Probesets |
| Exome Capture Probesets and Targeted Region |
| Gap |
| Gap Locations |
| GC Percent |
| GC Percent in 5-Base Windows |
| GRC Incident |
| GRC Incident Database |
| p14
GRC Patches |
| GRC Patches: Alt Haplotypes and Fix Sequences |
| Hg19 Diff |
| Contigs New to GRCh38/(hg38), Not Carried Forward from GRCh37/(hg19) |
| INSDC |
| Accession at INSDC - International Nucleotide Sequence Database Collaboration |
| LiftOver & ReMap |
| UCSC LiftOver and NCBI ReMap: Genome alignments to convert annotations to hg19 |
| LRG Regions |
| Locus Reference Genomic (LRG) / RefSeqGene Sequences Mapped to Dec. 2013 (GRCh38/hg38) Assembly |
| Mappability |
| Hoffman Lab Umap and Bismap Mappability |
| Umap |
| Single-read and multi-read mappability by Umap |
| Bismap |
| Single-read and multi-read mappability after bisulfite conversion |
| Problematic Regions |
| Problematic/special genomic regions for sequencing or very variable regions |
| GIAB Problematic Regions |
| Difficult regions from GIAB via NCBI |
| Highly Reproducible Regions |
| Highly Reproducible genomic regions for sequencing |
| Problematic Regions |
| Problematic/special genomic regions for sequencing or very variable regions |
| Recomb Rate |
| Recombination rate: Genetic maps from deCODE and 1000 Genomes |
| Recomb. 1k Genomes |
| Recombination rate: 1000 Genomes, lifted from hg19 (PR Loh) |
| Recomb. deCODE Dmn |
| Recombination rate: De-novo mutations found in deCODE samples |
| Recomb. deCODE Evts |
| Recombination events in deCODE Genetic Map (zoom to < 10kbp to see the events) |
| Recomb. deCODE Mat |
| Recombination rate: deCODE Genetics, maternal |
| Recomb. deCODE Pat |
| Recombination rate: deCODE Genetics, paternal |
| Recomb. deCODE Avg |
| Recombination rate: deCODE Genetics, average from paternal and maternal (mat for chrX) |
| RefSeq Acc |
| RefSeq Accession |
| Restr Enzymes |
| Restriction Enzymes from REBASE |
| Short Match |
| Perfect Matches to Short Sequence () |
|
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| GENCODE V47 |
| GENCODE V47 |
| NCBI RefSeq |
| RefSeq genes from NCBI |
| CCDS |
| Consensus CDS |
| CRISPR Targets |
| CRISPR/Cas9 -NGG Targets, whole genome |
| GENCODE Archive |
| GENCODE Archive |
| GENCODE V36 |
| GENCODE V36 |
| GENCODE V38 |
| GENCODE V38 |
| GENCODE V39 |
| GENCODE V39 |
| GENCODE V43 |
| GENCODE V43 |
| GENCODE V44 |
| GENCODE V44 |
| GENCODE V45 |
| GENCODE V45 |
| GENCODE V46 |
| GENCODE V46 |
| GENCODE Versions |
| Container of all new and previous GENCODE releases |
| GENCODE V20 (Ensembl 76) |
| Gene Annotations from GENCODE Version 20 (Ensembl 76) |
| All GENCODE V22 |
| All GENCODE transcripts including comprehensive set V22 |
| All GENCODE V23 |
| All GENCODE transcripts including comprehensive set V23 |
| All GENCODE V24 |
| All GENCODE transcripts including comprehensive set V24 |
| All GENCODE V25 |
| All GENCODE transcripts including comprehensive set V25 |
| All GENCODE V26 |
| All GENCODE annotations from V26 (Ensembl 88) |
| All GENCODE V27 |
| All GENCODE annotations from V27 (Ensembl 90) |
| All GENCODE V28 |
| All GENCODE annotations from V28 (Ensembl 92) |
| All GENCODE V29 |
| All GENCODE annotations from V29 (Ensembl 94) |
| All GENCODE V30 |
| All GENCODE annotations from V30 (Ensembl 96) |
| All GENCODE V31 |
| All GENCODE annotations from V31 (Ensembl 97) |
| All GENCODE V32 |
| All GENCODE annotations from V32 (Ensembl 98) |
| All GENCODE V33 |
| All GENCODE annotations from V33 (Ensembl 99) |
| All GENCODE V34 |
| All GENCODE annotations from V34 (Ensembl 100) |
| All GENCODE V35 |
| All GENCODE annotations from V35 (Ensembl 101) |
| All GENCODE V36 |
| All GENCODE annotations from V36 (Ensembl 102) |
| All GENCODE V37 |
| All GENCODE annotations from V37 (Ensembl 103) |
| All GENCODE V38 |
| All GENCODE annotations from V38 (Ensembl 104) |
| All GENCODE V39 |
| All GENCODE annotations from V39 (Ensembl 105) |
| All GENCODE V40 |
| All GENCODE annotations from V40 (Ensembl 106) |
| All GENCODE V41 |
| All GENCODE annotations from V41 (Ensembl 107) |
| All GENCODE V42 |
| All GENCODE annotations from V42 (Ensembl 108) |
| All GENCODE V43 |
| All GENCODE annotations from V43 (Ensembl 109) |
| All GENCODE V44 |
| All GENCODE annotations from V44 (Ensembl 110) |
| All GENCODE V45 |
| All GENCODE annotations from V45 (Ensembl 111) |
| All GENCODE V46 |
| All GENCODE annotations from V46 (Ensembl 112) |
| All GENCODE V47 |
| All GENCODE annotations from V47 (Ensembl 113) |
| updated
HGNC |
| HUGO Gene Nomenclature |
IKMC Genes Mapped |
| International Knockout Mouse Consortium Genes Mapped to Human Genome |
| LRG Transcripts |
| Locus Reference Genomic (LRG) / RefSeqGene Fixed Transcript Annotations |
| MANE |
| MANE Select Plus Clinical: Representative transcript from RefSeq & GENCODE |
| MGC/ORFeome Genes |
| MGC/ORFeome Full ORF mRNA Clones |
| ORFeome Clones |
| ORFeome Collaboration Gene Clones |
| MGC Genes |
| Mammalian Gene Collection Full ORF mRNAs |
| Non-coding RNA |
| RNA sequences that do not code for a protein |
| tRNA Genes |
| Transfer RNA Genes Identified with tRNAscan-SE |
| sno/miRNA |
| C/D and H/ACA Box snoRNAs, scaRNAs, and microRNAs from snoRNABase and miRBase |
|
lincRNA TUCP |
| lincRNA and TUCP transcripts |
|
lincRNA RNA-Seq |
| lincRNA RNA-Seq reads expression abundances |
| Old UCSC Genes |
| Previous Version of UCSC Genes |
| Other RefSeq |
| Non-Human RefSeq Genes |
| Pfam in GENCODE |
| Pfam Domains in GENCODE Genes |
| Prediction Archive |
| Gene Prediction Archive |
| SIB Genes |
| Swiss Institute of Bioinformatics Gene Predictions from mRNA and ESTs |
| SGP Genes |
| SGP Gene Predictions Using Mouse/Human Homology |
| Genscan Genes |
| Genscan Gene Predictions |
| Geneid Genes |
| Geneid Gene Predictions |
| AUGUSTUS |
| AUGUSTUS ab initio gene predictions v3.1 |
| new
Pseudogenes |
| Pseudogenes and Parents |
| RetroGenes V9 |
| Retroposed Genes V9, Including Pseudogenes |
| TransMap V5 |
| TransMap Alignments Version 5 |
| TransMap ESTs |
| TransMap EST Mappings Version 5 |
| TransMap RNA |
| TransMap GenBank RNA Mappings Version 5 |
| TransMap RefGene |
| TransMap RefSeq Gene Mappings Version 5 |
| TransMap Ensembl |
| TransMap Ensembl and GENCODE Mappings Version 5 |
| UCSC Alt Events |
| Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes |
| UniProt |
| UniProt SwissProt/TrEMBL Protein Annotations |
|
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|---|
| OMIM |
| Online Mendelian Inheritance in Man |
| OMIM Cyto Loci |
| OMIM Cytogenetic Loci Phenotypes - Gene Unknown |
| OMIM Genes |
| OMIM Gene Phenotypes - Dark Green Can Be Disease-causing |
| OMIM Alleles |
| OMIM Allelic Variant Phenotypes |
| AlphaMissense |
| AlphaMissense Score for all possible single-basepair mutations (zoom in for scores) |
| CADD 1.6 |
| CADD 1.6 Score for all single-basepair mutations and selected insertions/deletions |
| CADD 1.6 Ins |
| CADD 1.6 Score: Insertions - label is length of insertion |
| CADD 1.6 Del |
| CADD 1.6 Score: Deletions - label is length of deletion |
| CADD 1.6 |
| CADD 1.6 Score for all possible single-basepair mutations (zoom in for scores) |
| CADD 1.7 |
| CADD 1.7 Score for all single-basepair mutations and selected insertions/deletions |
| CADD 1.7 Ins |
| CADD 1.7 Score: Insertions - label is length of insertion |
| CADD 1.7 Del |
| CADD 1.7 Score: Deletions - label is length of deletion |
| CADD 1.7 |
| CADD 1.7 Score for all possible single-basepair mutations (zoom in for scores) |
| Cancer Gene Expr |
| Gene Expression in 33 TCGA Cancer Tissues (GENCODE v23) |
| Cancer Transc Expr |
| Transcript-level Expression in 33 TCGA Cancer Tissues (GENCODE v23) |
| Cancer Gene Expr |
| Gene Expression in 33 TCGA Cancer Tissues (GENCODE v23) |
| new
CIViC |
| CIViC - Expert & crowd-sourced cancer variant interpretation |
| ClinGen |
| ClinGen curation activities (Dosage Sensitivity and Gene-Disease Validity) |
ClinGen CNVs |
| Clinical Genome Resource (ClinGen) CNVs |
| ClinVar Variants |
| ClinVar Variants |
| Constraint scores |
| Human constraint scores |
| UKB Depl. Rank Score |
| UK Biobank / deCODE Genetics Depletion Rank Score |
| HMC |
| HMC - Homologous Missense Constraint Score on PFAM domains |
| JARVIS |
| JARVIS: score to prioritize non-coding regions for disease relevance |
|
Coriell CNVs |
| Coriell Cell Line Copy Number Variants |
| updated
COSMIC |
| Catalogue of Somatic Mutations in Cancer V101 |
|
COSMIC Regions |
| Catalogue of Somatic Mutations in Cancer V82 |
| COVID Data |
| Container of SARS-CoV-2 data |
| COVID Rare Harmful Var |
| Rare variants underlying COVID-19 severity and susceptibility from the COVID Human Genetics Effort |
| COVID GWAS v3 |
| GWAS meta-analyses from the COVID-19 Host Genetics Initiative |
| COVID GWAS v4 |
| COVID risk variants from GWAS meta-analyses by the COVID-19 Host Genetics Initiative (Rel 4, Oct 2020) |
| DECIPHER |
| DECIPHER |
| DECIPHER Population CNVs |
| DECIPHER: Population CNVs |
| DECIPHER SNVs |
| DECIPHER: Chromosomal Imbalance and Phenotype in Humans (SNVs) |
| DECIPHER CNVs |
| DECIPHER CNVs |
| Development Delay |
| Copy Number Variation Morbidity Map of Developmental Delay |
| Dosage Sensitivity |
| pHaplo and pTriplo dosage sensitivity map from Collins et al 2022 |
| GenCC |
| GenCC: The Gene Curation Coalition Annotations |
| Gene Interactions |
| Protein Interactions from Curated Databases and Text-Mining |
| GeneReviews |
| GeneReviews |
| GWAS Catalog |
| NHGRI-EBI Catalog of Published Genome-Wide Association Studies |
| HGMD public |
| Human Gene Mutation Database - Public Version Dec 2024 |
| LOVD Variants |
| LOVD: Leiden Open Variation Database Public Variants |
| new
MITOMAP |
| MITOMAP: A human mitochondrial genome database |
| Orphanet |
| Orphadata: Aggregated Data From Orphanet |
| PanelApp |
| Genomics England PanelApp Diagnostics |
|
REVEL Scores |
| REVEL Pathogenicity Score for single-base coding mutations (zoom for exact score) |
| SNPedia |
| SNPedia |
| new
Splicing Impact |
| Splicing Impact Prediction Scores and Databases |
| new
SpliceVarDB |
| SpliceVarDB: Experimentally validated splicing variants |
| SpliceAI |
| SpliceAI: Splice Variant Prediction Score |
| AbSplice Scores |
| Aberrant Splicing Prediction Scores |
| TCGA Pan-Cancer |
| TCGA Pan-Cancer mutations: 33 TCGA Cancer Projects Summary (Pan-Can 33) |
| UniProt Variants |
| UniProt/SwissProt Amino Acid Substitutions |
| updated
Variants in Papers |
| Genetic Variants mentioned in scientific publications |
| Mastermind Variants |
| Genomenon Mastermind Variants extracted from full text publications |
| new
enGenome VarChat |
| enGenome VarChat: Literature match and variant's summary |
| Avada Variants |
| Avada Variants extracted from full text publications |
|
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| dbSNP 155 |
| Short Genetic Variants from dbSNP release 155 |
| 1000 Genomes |
| 1000 Genomes Phase 3 |
| 1000G Ph3 Vars |
| 1000 Genomes Phase 3 Integrated Variant Calls from IGSR: SNVs and Indels |
| 1000 Genomes Trios |
| Thousand Genomes Project Family VCF Trios |
| Array Probesets |
| Microarray Probesets |
| dbSNP Archive |
| dbSNP Track Archive |
| All SNPs(141) |
| Simple Nucleotide Polymorphisms (dbSNP 141) |
| Common SNPs(141) |
| Simple Nucleotide Polymorphisms (dbSNP 141) Found in >= 1% of Samples |
| Flagged SNPs(141) |
| Simple Nucleotide Polymorphisms (dbSNP 141) Flagged by dbSNP as Clinically Assoc |
| Mult. SNPs(141) |
| Simple Nucleotide Polymorphisms (dbSNP 141) That Map to Multiple Genomic Loci |
| All SNPs(142) |
| Simple Nucleotide Polymorphisms (dbSNP 142) |
| Common SNPs(142) |
| Simple Nucleotide Polymorphisms (dbSNP 142) Found in >= 1% of Samples |
| Flagged SNPs(142) |
| Simple Nucleotide Polymorphisms (dbSNP 142) Flagged by dbSNP as Clinically Assoc |
| Mult. SNPs(142) |
| Simple Nucleotide Polymorphisms (dbSNP 142) That Map to Multiple Genomic Loci |
| All SNPs(144) |
| Simple Nucleotide Polymorphisms (dbSNP 144) |
| Common SNPs(144) |
| Simple Nucleotide Polymorphisms (dbSNP 144) Found in >= 1% of Samples |
| Flagged SNPs(144) |
| Simple Nucleotide Polymorphisms (dbSNP 144) Flagged by dbSNP as Clinically Assoc |
| Mult. SNPs(144) |
| Simple Nucleotide Polymorphisms (dbSNP 144) That Map to Multiple Genomic Loci |
| All SNPs(146) |
| Simple Nucleotide Polymorphisms (dbSNP 146) |
| Common SNPs(146) |
| Simple Nucleotide Polymorphisms (dbSNP 146) Found in >= 1% of Samples |
| Flagged SNPs(146) |
| Simple Nucleotide Polymorphisms (dbSNP 146) Flagged by dbSNP as Clinically Assoc |
| Mult. SNPs(146) |
| Simple Nucleotide Polymorphisms (dbSNP 146) That Map to Multiple Genomic Loci |
| All SNPs(147) |
| Simple Nucleotide Polymorphisms (dbSNP 147) |
| Common SNPs(147) |
| Simple Nucleotide Polymorphisms (dbSNP 147) Found in >= 1% of Samples |
| Flagged SNPs(147) |
| Simple Nucleotide Polymorphisms (dbSNP 147) Flagged by dbSNP as Clinically Assoc |
| Mult. SNPs(147) |
| Simple Nucleotide Polymorphisms (dbSNP 147) That Map to Multiple Genomic Loci |
| Flagged SNPs(150) |
| Simple Nucleotide Polymorphisms (dbSNP 150) Flagged by dbSNP as Clinically Assoc |
| Common SNPs(150) |
| Simple Nucleotide Polymorphisms (dbSNP 150) Found in >= 1% of Samples |
| All SNPs(150) |
| Simple Nucleotide Polymorphisms (dbSNP 150) |
| Mult. SNPs(150) |
| Simple Nucleotide Polymorphisms (dbSNP 150) That Map to Multiple Genomic Loci |
| Mult. SNPs(151) |
| Simple Nucleotide Polymorphisms (dbSNP 151) That Map to Multiple Genomic Loci |
| Flagged SNPs(151) |
| Simple Nucleotide Polymorphisms (dbSNP 151) Flagged by dbSNP as Clinically Assoc |
| All SNPs(151) |
| Simple Nucleotide Polymorphisms (dbSNP 151) |
| Common SNPs(151) |
| Simple Nucleotide Polymorphisms (dbSNP 151) Found in >= 1% of Samples |
| dbSNP 153 |
| Short Genetic Variants from dbSNP release 153 |
| dbVar Common Struct Var |
| NCBI Curated Common Structural Variants from dbVar |
| dbVar Conflict SV |
| NCBI dbVar Curated Conflict Variants |
| dbVar Common SV |
| NCBI dbVar Curated Common Structural Variants |
| DGV Struct Var |
| Database of Genomic Variants: Structural Variation (CNV, Inversion, In/del) |
| Genome In a Bottle |
| Genome In a Bottle Structural Variants and Trios |
| gnomAD Variants |
| Genome Aggregation Database (gnomAD) Genome and Exome Variants |
| gnomAD Structural Variants |
| Genome Aggregation Database (gnomAD) - Structural Variants v4.1 |
| gnomAD Rare CNV Variants |
| Genome Aggregation Database (gnomAD) - Rare CNV variants (<1% overall site frequency) v4.1 |
| gnomAD Constraint Metrics |
| Genome Aggregation Database (gnomAD) Predicted Constraint Metrics (LOEUF, pLI, and Z-scores) |
| gnomAD Mut Constraint |
| Gnocchi: Genome Aggregation Database (gnomAD) non-coding constraint of haploinsufficient variation, includes chrX |
|
gnomAD v2 |
| Genome Aggregation Database (gnomAD) Genome and Exome Variants v2.1 |
| gnomAD v3 |
| Genome Aggregation Database (gnomAD) Genome Variants v3 |
| gnomAD v3.1 |
| Genome Aggregation Database (gnomAD) Genome Variants v3.1 |
| gnomAD v3.1.1 |
| Genome Aggregation Database (gnomAD) Genome Variants v3.1.1 |
| gnomAD v4.1 |
| Genome Aggregation Database (gnomAD) Genome and Exome Variants v4.1 |
| Platinum Genomes |
| Platinum genome variants |
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| Multiple Alignment |
| Multiple Alignment on 90 human genome assemblies |
| Pairwise Alignments |
| Human Genomes, Chain/Net pairwise alignments, as mapped by the HPRC project |
| Rearrangements |
| Rearrangements including indels, inversions, and duplications |
| Short Variants |
| Short Variants |
| HPRC Variants > 3bp |
| HPRC VCF variants filtered for items size > 3bp |
| HPRC Variants <= 3bp |
| HPRC VCF variants filtered for items size <= 3bp |
| HPRC All Variants |
| HPRC variants decomposed from hprc-v1.0-mc.grch38.vcfbub.a100k.wave.vcf.gz (Liao et al 2023), no size filtering |
|
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| Human ESTs |
| Human ESTs Including Unspliced |
| Human mRNAs |
| Human mRNAs from GenBank |
| Other ESTs |
| Non-Human ESTs from GenBank |
| Other mRNAs |
| Non-Human mRNAs from GenBank |
| SIB Alt-Splicing |
| Alternative Splicing Graph from Swiss Institute of Bioinformatics |
| Spliced ESTs |
| Human ESTs That Have Been Spliced |
|
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| GTEx Gene V8 |
| Gene Expression in 54 tissues from GTEx RNA-seq of 17382 samples, 948 donors (V8, Aug 2019) |
| GTEx RNA-Seq Coverage |
| GTEx V8 RNA-Seq Read Coverage by Tissue |
| Affy Archive |
| Affymetrix Archive |
| Affy U95 |
| Alignments of Affymetrix Consensus/Exemplars from HG-U95 |
| Affy U133 |
| Alignments of Affymetrix Consensus/Exemplars from HG-U133 |
| Affy GNF1H |
| Alignments of Affymetrix Consensus/Exemplars from GNF1H |
| EPDnew Promoters |
| Promoters from EPDnew |
| GNF Atlas 2 |
| GNF Expression Atlas 2 |
|
GTEx Gene |
| Gene Expression in 53 tissues from GTEx RNA-seq of 8555 samples (570 donors) |
| GTEx Transcript |
| Transcript Expression in 53 tissues from GTEx RNA-seq of 8555 samples/570 donors |
| GWIPS-viz Riboseq |
| Ribosome Profiling from GWIPS-viz |
| miRNA Tissue Atlas |
| Tissue-Specific microRNA Expression from Two Individuals |
| Single Cell Expression |
| Single cell RNA expression levels cell types from many organs |
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| Blood (PBMC) Hao |
| Peripheral blood mononuclear cells (PBMC) from Hao et al 2020 |
| Blood PBMC Time |
| Blood PBMCs binned by time into experiment from Hao et al 2020 |
| Blood PBMC Phase |
| Blood PBMCs binned by phase of cell cycle from Hao et al 2020 |
| Blood PBMC Donor |
| Blood PBMCs binned by blood donor from Hao et al 2020 |
| Blood PBMC Cells 3 |
| Blood PBMCs binned by cell type (level 3) from Hao et al 2020 |
| Blood PBMC Cells 2 |
| Blood PBMCs binned by cell type (level 2) from Hao et al 2020 |
| Blood PBMC Cells |
| Blood (PBMCs) binned by cell type (level 1) from Hao et al 2020 |
| Colon Wang |
| Colon single cell sequencing from Wang et al 2020 |
| Colon Donor |
| Colon cells binned by organ donor from Wang et al 2020 |
| Colon Cells |
| Colon cells binned by cell type from Wang et al 2020 |
| Cortex Velmeshev |
| Cerebral cortex single cell data from Velmeshev et al 2019 |
| Cortex Sex |
| Cerebral cortex RNA binned by sex of donor from Velmeshev et al 2019 |
| Cortex Sample |
| Cerebral cortex RNA binned by biosample from Velmeshev et al 2019 |
| Cortex Donor |
| Cerebral cortex RNA binned by organ donor from Velmeshev et al 2019 |
| Cortex Diagnosis |
| Cerebral cortex RNA binned by ASD/control diagnosis from Velmeshev et al 2019 |
| Cortex Cells |
| Cerebral cortex RNA binned by cell type from Velmeshev et al 2019 |
| Cross Tissue Nuclei |
| Single Nuclei sequenced across many tissues |
| GTEx Immune Atlas |
| GTEx single nuclei immune expression |
| Cross Tissue Details |
| Cross tissue nuclei full details |
| Cross Tissue Nuclei |
| Cross tissue nuclei RNA by tissue and cell type |
|
Fetal Gene Atlas |
| Fetal Gene Atlas from Cao et al 2020 |
| Fetal Sex |
| Fetal Gene Atlas binned by sex from Cao et al 2020 |
| Fetal RT Group |
| Fetal Gene Atlas binned by RT group from Cao et al 2020 |
| Fetal Organ |
| Fetal Gene Atlas binned by organ from Cao et al 2020 |
| Fetal Lineage |
| Fetal Gene Atlas binned by cell lineage and organ from Cao et al 2020 |
| Fetal Exp |
| Fetal Gene Atlas binned by experiment id from Cao et al 2020 |
| Fetal Donor ID |
| Fetal Gene Atlas binned by donor ID from Cao et al 2020 |
| Fetal Cells |
| Fetal Gene Atlas binned by cell type from Cao et al 2020 |
| Fetal Assay |
| Fetal Gene Atlas binned by assay (cell/nucleus) from Cao et al 2020 |
| Heart Cell Atlas |
| Heart single cell RNA data from https://heartcellatlas.com |
| Heart HCA Version |
| Heart cell RNA binned by 10x chemistry version from https://heartcellatlas.org |
| Heart HCA State |
| Heart cell RNA binned by cell state from https://heartcellatlas.org |
| Heart HCA Source |
| Heart cell RNA binned by source (nucleus vs whole cell) from https://heartcellatlas.org |
| Heart HCA Sex |
| Heart cell RNA binned by sex of donor from https://heartcellatlas.org |
| Heart HCA Sample |
| Heart cell RNA binned by biosample from https://heartcellatlas.org |
| Heart HCA Region |
| Heart cell RNA binned by region of collection from https://heartcellatlas.org |
| Heart HCA Donor |
| Heart cell RNA binned by organ donor from https://heartcellatlas.org |
| Heart HCA Cells |
| Heart cell RNA binned by cell type from https://heartcellatlas.org |
| Heart HCA Age |
| Heart cell RNA binned by age group of donor from https://heartcellatlas.org |
| Ileum Wang |
| Ileum single cell sequencing from Wang et al 2020 |
| Ileum Donor |
| Ileum cells binned by organ donor from Wang et al 2020 |
| Ileum Cells |
| Ileum cells binned by cell type from Wang et al 2020 |
| Kidney Stewart |
| Kidney single cell data from Stewart et al 2019 |
| Kidney Project |
| Kidney RNA binned by project from Stewart et al 2019 |
| Kidney Experiment |
| Kidney RNA binned by Experiment from Stewart et al 2019 |
| Kidney Details |
| Kidney RNA binned by detailed cell type from Stewart et al 2019 |
| Kidney Compartment |
| Kidney RNA binned by compartment from Stewart et al 2019 |
| Kidney Cells |
| Kidney RNA binned by merged cell type from Stewart et al 2019 |
| Kidney Broad CT |
| Kidney RNA binned by broad cell type from Stewart et al 2019 |
| Liver MacParland |
| Liver single cell sequencing from MacParland et al 2018 |
| Liver Donor |
| Liver cells binned by organ donor from MacParland et al 2018 |
| Liver Cells |
| Liver cells binned by cell type from MacParland et al 2018 |
| Liver Broad |
| Liver cells binned by broad cell type from MacParland et al 2018 |
| Lung Travaglini |
| Lung cells from from Travaglini et al 2020 |
| Lung Sample FACS |
| Lung cells FACS method binned by sample from Travaglini et al 2020 |
| Lung Sample |
| Lung cells 10x method binned by sample from Travaglini et al 2020 |
| Lung Organ FACS |
| Lung cells FACS method binned by organ from Travaglini et al 2020 |
| Lung Organ |
| Lung cells 10x method binned by organ from Travaglini et al 2020 |
| Lung Mag Sel |
| Lung cells 10x method binned by magnetic.selection from Travaglini et al 2020 |
| Lung Locat FACS |
| Lung cells FACS method binned by location from Travaglini et al 2020 |
| Lung Locat |
| Lung cells 10x method binned by location from Travaglini et al 2020 |
| Lung Label FACS |
| Lung cells FACS method binned by label from Travaglini et al 2020 |
| Lung Half Det FACS |
| Lung cells FACS method binned by merged cell type from Travaglini et al 2020 |
| Lung Half Det |
| Lung cells 10x method binned by halfway detailed cell type from Travaglini et al 2020 |
| Lung Gating FACS |
| Lung cells FACS method binned by gating from Travaglini et al 2020 |
| Lung Donor FACS |
| Lung cells FACS method binned by organ donor from Travaglini et al 2020 |
| Lung Donor |
| Lung cells 10x method binned by organ donor from Travaglini et al 2020 |
| Lung Detail FACS |
| Lung cells FACS method binned by detailed cell type from Travaglini et al 2020 |
| Lung Detail |
| Lung cells 10x method binned by detailed cell type from Travaglini et al 2020 |
| Lung Compart FACS |
| Lung cells FACS method binned by compartment from Travaglini et al 2020 |
| Lung Compart |
| Lung cells 10x method binned by compartment from Travaglini et al 2020 |
| Lung Cells FACS |
| Lung cells FACS method binned by merged cell type from Travaglini et al 2020 |
| Lung Cells |
| Lung cells 10x method binned by merged cell type from Travaglini et al 2020 |
| Muscle De Micheli |
| Muscle single cell data from De Micheli et al 2020 |
| Muscle Sample |
| Muscle RNA binned by biosample from De Micheli et al 2020 |
| Muscle Cells |
| Muscle RNA binned by cell type from De Micheli et al 2020 |
| Pancreas Baron |
| Pancreas single cell sequencing from Baron et al 2016 |
| Pancreas Donor |
| Pancreas cells binned by organ donor from Baron et al 2016 |
| Pancreas Details |
| Pancreas cells binned by detailed cell type from Baron et al 2016 |
| Pancreas Cells |
| Pancreas cells binned by cell type from Baron et al 2016 |
| Pancreas Batch |
| Pancreas cells binned by batch from Baron et al 2016 |
| Placenta Vento-Tormo |
| Placenta and decidua cells from from Vento-Tormo et al 2018 |
| Placenta Stage |
| Placenta and decidua cells binned by placental stage 10x from Vento-Tormo et al 2018 |
| Placenta Mat/Fet Ss2 |
| Placenta and decidua cells binned by maternal/fetal smart-seq2 from Vento-Tormo et al 2018 |
| Placenta Mat/Fet |
| Placenta and decidua cells binned by maternal/fetal 10x from Vento-Tormo et al 2018 |
| Placenta Loc Ss2 |
| Placenta and decidua cells binned by cell location smart-seq2 from Vento-Tormo et al 2018 |
| Placenta Loc |
| Placenta and decidua cells binned by cell location 10x from Vento-Tormo et al 2018 |
| Placenta Detail Ss2 |
| Placenta and decidua cells binned by detailed cell type smart-seq2 from Vento-Tormo et al 2018 |
| Placenta Detail |
| Placenta and decidua cells binned by detailed cell type 10x from Vento-Tormo et al 2018 |
| Placenta Cells Ss2 |
| Placenta and decidua cells binned by cell type smart-seq2 from Vento-Tormo et al 2018 |
| Placenta Cells |
| Placenta and decidua cells binned by cell type 10x from Vento-Tormo et al 2018 |
| Rectum Wang |
| Rectum single cell sequencing from Wang et al 2020 |
| Rectum Donor |
| Rectum cells binned by organ donor from Wang et al 2020 |
| Rectum Cells |
| Rectum cells binned by cell type from Wang et al 2020 |
|
Skin Sole-Boldo |
| Skin single cell data from Sole-Boldo et al 2020 |
| Skin Donor |
| Skin single cell RNA binned by skin donor from Sole-Boldo et al 2020 |
| Skin Cell+Age |
| Skin single cell RNA binned by cell type and donor's age from Sole-Boldo et all 2020 |
| Skin Cell |
| Skin single cell RNA binned by cell type from Sole-Boldo et al 2020 |
| Skin Age |
| Skin single cell RNA binned by skin donor's age from Sole-Boldo et al 2020 |
| Tabula Sapiens |
| Tabula Sapiens single cell RNA data from many tissues |
| Tabula Tissue Cell |
| Tabula sapiens RNA by tissue and cell type |
| Tabula Details |
| Tabula sapiens full details view |
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| ENCODE cCREs |
| ENCODE Candidate Cis-Regulatory Elements (cCREs) combined from all cell types |
| ENCODE Regulation |
| Integrated Regulation from ENCODE |
| TF ChIP |
| Transcription Factor ChIP-seq Peaks (340 factors in 129 cell types) from ENCODE 3 |
| TF Clusters |
| Transcription Factor ChIP-seq Clusters (340 factors, 129 cell types) from ENCODE 3 |
| DNase HS |
| DNase I Hypersensitivity in 95 cell types from ENCODE |
| DNase Signal |
| DNase I Hypersensitivity Signal Colored by Similarity from ENCODE |
| DNase Clusters |
| DNase I Hypersensitivity Peak Clusters from ENCODE (95 cell types) |
|
Layered H3K27Ac |
| H3K27Ac Mark (Often Found Near Regulatory Elements) on 7 cell lines from ENCODE |
|
Layered H3K4Me3 |
| H3K4Me3 Mark (Often Found Near Promoters) on 7 cell lines from ENCODE |
|
Layered H3K4Me1 |
| H3K4Me1 Mark (Often Found Near Regulatory Elements) on 7 cell lines from ENCODE |
|
Transcription |
| Transcription Levels Assayed by RNA-seq on 9 Cell Lines from ENCODE |
| TF rPeak Clusters |
| Transcription Factor Representative Peak (rPeak) Clusters (912 factors in 1152 biosamples) from ENCODE 4 |
| CpG Islands |
| CpG Islands (Islands < 300 Bases are Light Green) |
| Unmasked CpG |
| CpG Islands on All Sequence (Islands < 300 Bases are Light Green) |
| CpG Islands |
| CpG Islands (Islands < 300 Bases are Light Green) |
| FANTOM5 |
| FANTOM5: Mapped transcription start sites (TSS) and their usage |
| TSS activity (TPM) |
| FANTOM5: TSS activity per sample (TPM) |
| TSS activity - read counts |
| FANTOM5: TSS activity per sample read counts |
| Max counts of CAGE reads |
| FANTOM5: Max counts of CAGE reads |
| Total counts of CAGE reads |
| FANTOM5: Total counts of CAGE reads |
| TSS peaks |
| FANTOM5: DPI peak, robust set |
| GeneHancer |
| GeneHancer Regulatory Elements and Gene Interactions |
| GTEx cis-eQTLs |
| GTEx fine-mapped cis-eQTLs |
| Hi-C and Micro-C |
| Comparison of Micro-C and In situ Hi-C protocols in H1-hESC and HFFc6 |
| JASPAR Transcription Factors |
| JASPAR Transcription Factor Binding Site Database |
| ORegAnno |
| Regulatory elements from ORegAnno |
| RefSeq Func Elems |
| NCBI RefSeq Functional Elements |
| ReMap ChIP-seq |
| ReMap Atlas of Regulatory Regions |
| updated
VISTA Enhancers |
| VISTA Enhancers |
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| UCSC 100 Vertebrates |
| UCSC 100 Vertebrates - 100 vertebrate genomes aligned with MultiZ by the UCSC Browser Group |
| Zoonomia 241 Placent |
| Zoonomia Alignment - 241 Placental Mammal Genomes aligned by the Zoonomia Project with Cactus |
| UCSC 30 Primates |
| UCSC 30 Primates - 30 primate genomes aligned with MultiZ by the UCSC Browser Group |
| Primate Chain/Net |
| Primate Genomes, Chain and Net Alignments |
| Placental Chain/Net |
| Non-primate Placental Mammal Genomes, Chain and Net Alignments |
| Vertebrate Chain/Net |
| Non-placental Vertebrate Genomes, Chain and Net Alignments |
| CHM13 alignments |
| CHM13 (GCA_009914755.4) v1_nfLO liftOver alignments |
| Hiller Lab 470 Mammals |
| Hiller Lab 470 Mammals - 470 mammalian genomes aligned with Multiz by Michael Hiller's Group, |
| Zoonomia+Primates 447 |
| Zoonomia+Primates 447 - 447 mammals, including 233 primates, aligned with Cactus, for Kuderna et al. 2023 |
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| RepeatMasker |
| Repeating Elements by RepeatMasker |
| Interrupted Rpts |
| Fragments of Interrupted Repeats Joined by RepeatMasker ID |
| Microsatellite |
| Microsatellites - Di-nucleotide and Tri-nucleotide Repeats |
| NuMTs Sequence |
| Nuclear mitochondrial DNA segments |
| RepeatMasker Viz. |
| Detailed Visualization of RepeatMasker Annotations |
| Segmental Dups |
| Duplications of >1000 Bases of Non-RepeatMasked Sequence |
| Self Alignment |
| Human Chained Self Alignments |
| Simple Repeats |
| Simple Tandem Repeats by TRF |
| WM + SDust |
| Genomic Intervals Masked by WindowMasker + SDust |
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