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Sample GSM2670945 Query DataSets for GSM2670945
Status Public on Jun 01, 2018
Title A_SMAD4_WT_1
Sample type SRA
Source name Colon
Organism Mus musculus
Characteristics strain: C57BL/6J
tissue: Colon epithelia
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 2500
Description SMAD4_WT
Colon epithelium from Smad4ΔLrig1 and from Smad4+ control mice was isolated. Total RNA was isolated from these tissues using RNeasy kit (Qiagen).
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
Organization name Vanderbilt University
Street address D2300 MCN 1161 21st Ave
City Nashville
State/province TN
ZIP/Postal code 37232
Country USA
Platform ID GPL17021
Series (1)
GSE100082 Smad4 pathways modulate induction of the chemokine Ccl20 and repress inflammation-induced carcinogenesis in mouse colon
BioSample SAMN07247076
SRA SRX2922338

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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