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Sample GSM2860293 Query DataSets for GSM2860293
Status Public on Feb 14, 2018
Title m6A-irCLIP rep1
Sample type SRA
 
Source name WT CD4+ T cells
Organism Mus musculus
Characteristics tissue: CD4+ T cells
antibody: m6A, Synaptic Systems, 202 003
Extracted molecule total RNA
Extraction protocol Cells were lysed and total RNA collected, RNA was polyA selected, and fragmented to ~30-60 nts, m6A residues were isolated by crosslinking anti-m6A antibody to fragmented RNA
RNA ligation for library construction was perfromed on affinity beads and RNA was subsequenctly transformed into dsRNA libraries using RT, cDNA circularization, and PCR amplification
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Library strategy: CLIP-seq
FASTQ files first demultiplexed by sample, PCR duplicates removed, and all adaptor sequences trimmed as previously described (PMID: 25411354)
Processed sequencing reads were mapped to mouse genome indices, RT stop positions extracted, and replciate experiments intersected to obtain highly reproducible binding sites for further analysis as per FAST-iCLIP (PMID: 25411354)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files containing RT stops of m6A-irCLIP datasets mapped to mm10 build of mouse genome.
 
Submission date Nov 17, 2017
Last update date May 15, 2019
Contact name Howard Chang
E-mail(s) howchang@stanford.edu
Organization name Stanford University School of Medicine
Department Dermatology
Lab Chang Lab
Street address 269 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL19057
Series (1)
GSE107055 m6A-irCLIP of mouse CD4+ T cell RNA
Relations
SRA SRX3403567
BioSample SAMN08045089

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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