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Sample GSM2670960 Query DataSets for GSM2670960
Status Public on Jun 01, 2018
Title Flx_TNFa_3
Sample type SRA
 
Source name Colonocytes
Organism Mus musculus
Characteristics strain: IMCfl/fl Smad4+ colonocytes
tissue: Colonocytes
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNeasy kit (Qiagen). Processing of RNA using a TruSeq Stranded mRNA sample prep kit was conducted according to the manufacturer’s instructions (Illumina, San Diego, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description Flx_TNFa
Total RNA was isolated from colonocytes treated with or without TNF, TGFb1, and BMP2 using RNeasy kit (Qiagen)
group_Flx_TNFa_vs_Flx_Ctl_DEG.txt
Data processing Casava and bcl2fastq v2.16 were used for demultiplexing data from HiSeq2500 and HiSeq3000, seperately.
We mapped the reads to the mouse genome mm10 using TopHat-2.1.0 (Kim et al. 2013). Then, following the method of Anders (Anders et al. 2013), we counted the number of reads that fall into annotated genes by samtools-1.3.1 (Li et al. 2009) and HTSeq-0.5.4p5 (Anders et al. 2014).
Finally, we performed count-based differential expression analysis using edgeR_3.4.2 (McCarthy et al. 2012) which implements general differential analyses based on the negative binomial model.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized count values and differential expression analysis results for each Sample
 
Submission date Jun 15, 2017
Last update date May 15, 2019
Contact name Jing Zhu
E-mail(s) jing.zhu@vanderbilt.edu
Organization name Vanderbilt University
Street address D2300 MCN 1161 21st Ave
City Nashville
State/province TN
ZIP/Postal code 37232
Country USA
 
Platform ID GPL21493
Series (1)
GSE100082 Smad4 pathways modulate induction of the chemokine Ccl20 and repress inflammation-induced carcinogenesis in mouse colon
Relations
BioSample SAMN07247063
SRA SRX2922353

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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