By Sample Breast Luminal Epithelial Cells Track Settings
 
Breast Luminal Epithelial Cells tracks for 10 assay type(s)

Track collection: Roadmap data by sample

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  Assay Type H3K36me3  H3K4me1  Input  mRNA-Seq  H3K9me3  MeDIP-Seq  MRE-Seq  H3K27me3  Bisulfite-Seq  smRNA-Seq Assay Type  
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 Bisulfite-Seq  RM066  UCSF-UBC-USC Breast Luminal Epithelial Cells Bisulfite-Seq Donor RM066 Library A22478 EA Release 9    Data format 
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 H3K27me3  RM080  Breast Luminal Epithelial Cells H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.28 Pcnt=64)    Data format 
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 H3K36me3  RM080  Breast Luminal Epithelial Cells H3K36me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.2208 Pcnt=38)    Data format 
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 H3K4me1  RM080  Breast Luminal Epithelial Cells H3K4me1 Signal from REMC/UCSF-UBC (Hotspot_Score=0.4115 Pcnt=54)    Data format 
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 H3K9me3  RM080  Breast Luminal Epithelial Cells H3K9me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.1878 Pcnt=73)    Data format 
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 Input  RM080  UCSF-UBC-USC Breast Luminal Epithelial Cells ChIP-Seq Input Donor RM080 Library HS2797 EA Release 8    Data format 
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 MRE-Seq  RM035  Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)    Data format 
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 MRE-Seq  RM037  Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM037)    Data format 
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 MRE-Seq  RM066  Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM066)    Data format 
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 MRE-Seq  RM070  Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM070)    Data format 
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 MeDIP-Seq  RM035  Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4531 Pcnt=87 DonorID:RM035)    Data format 
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 MeDIP-Seq  RM037  Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2494 Pcnt=16 DonorID:RM037)    Data format 
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 MeDIP-Seq  RM066  Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.291 Pcnt=33 DonorID:RM066)    Data format 
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 MeDIP-Seq  RM070  Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2634 Pcnt=20 DonorID:RM070)    Data format 
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 mRNA-Seq  RM035  Breast_Luminal_Epithelial_Cells mRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)    Data format 
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 mRNA-Seq  RM080  Breast Luminal Epithelial Cell mRNA Signal from REMC/UCSF-UBC    Data format 
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 mRNA-Seq  RM084  UCSF-UBC-USC Breast Luminal Epithelial Cells mRNA-Seq Donor RM084 Library A17918 EA Release 9    Data format 
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 smRNA-Seq  RM080  BL smRNA RM080 smRNA-seq Signal from REMC/UCSF-UBC    Data format 
    
Assembly: Human Feb. 2009 (GRCh37/hg19)

Vizhub @ Wash U built this track, and Roadmap Epigenomics Consortium is responsible for its contents.

Description

These tracks are genome-wide DNA methylation maps generated by Roadmap Epigenomics Project. Each track is collection of DNA methylation experiment data on one sample type.

DNA methylation of human DNA mostly happens on cytosine bases of CpG dinucleotides. The methylated DNA usually prevent accessibility of regulatory proteins and hampers transcription, while unmethylated DNA is usually indicative of open chromatin. The MeDIP-Seq and MRE-Seq experiments are usually performed on same sample to identify genome-wide DNA methylation pattern. MeDIP-Seq (methylated DNA immunoprecipitation and sequencing) is a ChIP-based approach utilizing antibody against methylated cytosine. This method enriches methylated DNA and high read count indicates high likelihood of underlying region is methylated. The MRE-Seq (methylation restriction enzyme sequencing) uses methylation-sensitive restriction enzymes to digest DNA, and only cut at unmethylated restriction sites. The cut restriction sites will be detected by sequencing where reads aligned to a restriction site on reference genome means the restriction site is unmethylated.

The MethylC-Seq (MethylC sequencing) uses bisulfite to convert methylated cytosines to thymines before sequencing. The percentage of reads with a T versus a C indicates the percentage methylation at the cytosine. Details can be found in this paper Lister R, et al., Nature. 2009 Nov 19;462(7271):315-22. .

RRBS (Reduced-Representation-Bisulfite-Sequencing) is similar to MethylC-seq except RRBS uses restriction enzyme to fragment the genome into fragments suitably-sized for sequencing. While RRBS produces percent methylation similar to MethylC-seq, it is limited to cytosines that are within restriction fragments of a suitable size and tend to measure CpG dense regions only. Details can be found in this paper: Meissener, A. et al., Nucleic Acids Res. 2005; 33(18): 5868-5877. .

Display conventions

Each track can be turned on/off individually. Inside each track, sub-tracks are displayed in same vertical space and are overlayed with transparent colors for contrast. All tracks displays read density data in form of wiggle plots. Number of aligned reads is counted at each base pair, and a summarized value is computed for each 20 bp interval for display. Sub-tracks sharing same space use same scale.

Methods

Experimental protocols: follow this link for experimental protocols.

Data processing: EDACC carried out data processing and quality assessment. Details are fully explained here . In brief, sequencing reads were aligned with 'Pash' program to derive read density data. The read density data is prepared into 'wiggle' format files with fixed step length of 20 bp. Data in wiggle and other formats have been deposited in NCBI Gene Expression Omnibus database for public access.

Quality control: the HotSpot was one of the methods used to assess quality of MeDIP-Seq experiments. The long track name includes a "Hotspot_Score" field indicates the percentage of sequencing reads found inside hotspot regions. The "Pcnt" field shows the percentile of current experiment score in all MeDIP-Seq experiments. This value is subject to change in next Data Release. The most comprehensive and up-to-date description on QC Metrics used by the consortium can be found here .

Release Notes

The data is combination of Release II, III, IV, V, VI, VII, VIII and IX which were mapped to human reference genome version hg19. The data is production of Roadmap Epigenomics Project.

Please follow the link for Roadmap Epigenomics data access policy

Credits

These data were generated in labs from three institutions: UCSF, UBC, UCSD as part of Roadmap Epigenomics Project.

Useful links