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| Status |
Public on Feb 14, 2018 |
| Title |
m6A-irCLIP rep1 |
| Sample type |
SRA |
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| Source name |
WT CD4+ T cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: CD4+ T cells
antibody: m6A, Synaptic Systems, 202 003
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| 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
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| 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.
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| Submission date |
Nov 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Howard Chang |
| E-mail(s) |
howchang@stanford.edu
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| Organization name |
Stanford University School of Medicine
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| Department |
Dermatology
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| Lab |
Chang Lab
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| Street address |
269 Campus Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE107055 |
m6A-irCLIP of mouse CD4+ T cell RNA |
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| Relations |
| SRA |
SRX3403567 |
| BioSample |
SAMN08045089 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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