Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 67
Release date: Mar 17 2018
Last update date: Nov 30 2018
Access: Public
Dataset link Compendium of CD8+ T cell Data

Experimental Protocol


CD8+ T cell data was combined from the Kaech, Goldrath, Pereira and various other laboratories to create a CD8+ T cell sequencing data compendium across multiple assay types. Cells were collected in the context of infection (primarily LCMV) at Naive (day 0), Effector (day 8 or day 10), or Memory (day 30+) time points, or in 'Special' culture conditions corresponding primarily to ChIP-seq of transcription factors. Additional subsetted samples from the Effector timepoint, Memory Precursors (KLRG1lo IL7Rhi) and Terminal Effectors (KLRG1hi IL7Rlo) were also collected. Samples were analyzed by using ChIP-seq, ATAC-seq, and RNA-seq specific pipelines. ChIP-seq and ATAC-seq were first trimmed for adapters and low quality sequences with cutadapt, and subsequently aligned with bowtie2 v2.3.3.1 using `--very-sensitive-local` mode, `--no-mixed --nodiscordant`. ATAC-seq data additionally used `--maxins 2000`. ATAC-seq reads were shifted per the original Buenrostro protocol by +4/-5 bases, and filtered to remove mitochondrial mapping reads. ChIP-seq and ATAC-seq data were then called for peaks using MACS2 v2.1.0. ATAC-seq peaks were called using `--nomodel --shift -100 --extsize 200 --broad`. For H3K4me1 and H3K27me3 ChIP-seq data, `--broad --nomodel --broad-cutoff 0.1` was used. For H3K27ac and H3K4me3 ChIP-seq data, default (narrowPeak) settings were used. ChIP-seq data used control (input) data as available. ChIP-seq and ATAC-seq signal tracks were made using deepTools bamCoverage with `--binSize 5 --smoothLength 15 --normalizeTo1x 2150570000 --extendReads 200` for visualization. For RNA-seq data, kallisto v0.42 was used to quantify transcript counts directly from fastq files. All data was aligned to the Ensembl GRCm38 (mm10) reference genome, appending chromosome names with 'chr' for maximal compatibility with downstream tools. Finally, all sample annotation, counts, and peak data were combined into an R package `ctlcon`, available at "https://bitbucket.com/robert_amezquita/ctlcon" with additional processed datasets and information. contributor: Pereira & Goldrath Labs (Histone mods and ATAC) contributor: Haining, Egawa, Li, Zhao, Cantor, Kallies, Groner, Vella, Xue Labs (ChIP-seq of TFs) The re-analyzed data is linked as Series supplementary file and the details (including sample-to-file associations, SRR accessions of the re-analyzed raw data etc.) are included in the 'readme_re-analyzed_samples.txt'.

Repositories


GEO

GSE111902

ENA

SRP135862

BioProject

PRJNA438595

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Contact


Robert Amezquita