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

  1. 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.

  2. 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.

  3. 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.

  4. 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