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| Status |
Public on Mar 05, 2018 |
| Title |
RNA-seq of Mus musculus: Th2 Late Bcl11b WT Rep 2 |
| Sample type |
SRA |
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| Source name |
Late Th2
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| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Th2 Late Bcl11b WT
chip antibody: none
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the RNAeasy Mini Kit (QIAGEN, 74104).
10 ng RNA was amplified with the Ovation RNA-Seq System V2 (7102-08, NuGEN) per manufacture’s instruction. 220 ng double stranded DNA was sonicated into 200–400 bp using Diagenode Bioruptor. cDNA was blunt-ended, ligated to Illumina adaptors, amplified, and sequenced with Illumina HiSeq system.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Basecalls performed using CASAVA 2.18
RNA-seq reads were mapped to mm10 using TopHat2 v2.0.13 using setting --bowtie-n.
ChIP-seq reads were mapped to mm10 using novoalign (Novocraft), V3.03.00 with adapter trimming (-a option).
Gene expression from RNA-Seq was quantified by RPKM (Mortazavi et al., 2008) with an in-house script based on RefSeq gene annotation.
To identify GATA3- or Bcl11b-binding peaks genome wide from the ChIP-Seq experiments, we used MACS v.1.4.2 (Zhang et al., 2008) with setting keep-dup=1 to call peaks using Input as control. Peaks were also called in Input sample alone with setting keep-dup=auto. Peaks were assigned to genes using FindNeighboringGenes (USeq, v.8.8.8; Nix et al., BMC Bioinformatics 2008)
Genome_build: mm10
Supplementary_files_format_and_content: *.rpkm.gz: zipped text file for gene expression. Columns from left to right denote RefSeq ID, RPKM, gene transcript size, number of read mapped to exons, a combination of RefSeq ID, gene symbol, etc, and reserved column for future development. bed: Columns from left to right are chromosome, start position, end position, peak name,
Supplementary_files_format_and_content: *.xls: chromosome, start of peak, end of peak, name, length, summit, tags, -10*log10(pvalue), fold_enrichment, chromsome, start of peak, stop of peak, name/rank, distance from transcription start site to middle of peak, gene symbol, Refseq id, geneChromosome, geneStart, geneStop, geneStrand, trxnStart
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| Submission date |
Jan 11, 2018 |
| Last update date |
Mar 05, 2018 |
| Contact name |
Andrew J Oler |
| E-mail(s) |
[email protected]
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| Organization name |
NIAID/NIH
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| Department |
Bioinformatics and Computational Biosciences Branch (BCBB)
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| Lab |
Computational Biology Section
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| Street address |
31 Center Drive, Room 3B62E
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE109107 |
Bcl11b- and GATA3-mediated gene regulation in Th2 cells |
| GSE109109 |
Bcl11b, a Novel GATA3-Interacting Protein, Suppresses Th1 while Limiting Th2 Cell Differentiation |
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| Relations |
| BioSample |
SAMN06764848 |
| SRA |
SRX2744884 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2931798_DF0029.rpkm.txt.gz |
484.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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