Description
These tracks show the Iso-Seq long read alignments of marmoset cDNAs to the
genome. The data set consists eleven tissue samples from two individuals.
Display Conventions and Configuration
These track use the BAM Display Conventions and Configuration.
Methods
- Generation of Full Length cDNA and Library Preparation for Sequencing
Full-length cDNA was prepared and sequenced from total RNA isolated from various tissues of both a two year old male and a two year old female Callithrix jacchus. Iso-Seq library production was performed as per the Iso-Seq Express protocol (https://www.pacb.com/wp-content/uploads/Procedure-Checklist-IsoSeq-Express-Template-Preparation-for-Sequel-and-Sequel-II-Systems.pdf) and barcoded using barcoded adapters. One library was generated for each tissue.
- Sequencing with the PacBio Sequel II Platform
Libraries were pooled equimolar and sequenced on 3 SMRT Cell 8M on the Sequel II platform with chemistry version 2EA.
- Data Processing
Collected data was demultiplexed with lima (demultiplex barcoding), then analyzed with CCS with a requirement of 1 minimum pass and at least 0.9 identity (--minPasses 1 --min-rq 0.9). The Iso-Seq analysis pipeline was used to generate FLNC reads ensuring each has a poly-A tail, plus a single 3' and 5' primer signal for downstream analysis.
- Mapping
Resulting reads were aligned to the marmoset genome with
minimap2 2.17-r941 using the options
-t 12 -ax splice:hq -u.
Data Access
The genomic alignments are stored in a BAM file that can be obtained from the
download server.
Credits
Samples were provided from the New England Primate Research Center
by Ricardo del Rosario and Anna Newman of the Broad Institute.
Iso-Seq sequencing & FLNC analysis performed by: Evan Eichler, Alexandra
Lewis, Shwetha Murali, and Katherine Munson of the University of Washington.
References
Warren WC, Harris RA, Haukness M, Fiddes IT, Murali SC, Fernandes J, Dishuck PC, Storer JM,
Raveendran M, Hillier LW et al.
Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility.
Science. 2020 Dec 18;370(6523).
PMID: 33335035; PMC: PMC7818670
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