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Sample GSM2670953

Query DataSets for GSM2670953

Status

Public on Jun 01, 2018

Title

Flx_TNFa+TGFb+BMP2_1

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+TGFb+BMP2
Total RNA was isolated from colonocytes treated with or without TNF, TGFb1, and BMP2 using RNeasy kit (Qiagen)
group_Flx_TNFa+TGFb+BMP2_vs_Flx_TNFa_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