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| Status |
Public on Jun 01, 2018 |
| Title |
Flx_Ctl_2 |
| Sample type |
SRA |
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| Source name |
Colonocytes
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| Organism |
Mus musculus |
| Characteristics |
strain: IMCfl/fl Smad4+ colonocytes
tissue: Colonocytes
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
Flx_Ctl
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
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| 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
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| Submission date |
Jun 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jing Zhu |
| E-mail(s) |
jing.zhu@vanderbilt.edu
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| Organization name |
Vanderbilt University
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| Street address |
D2300 MCN 1161 21st Ave
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| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE100082 |
Smad4 pathways modulate induction of the chemokine Ccl20 and repress inflammation-induced carcinogenesis in mouse colon |
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| Relations |
| BioSample |
SAMN07247070 |
| SRA |
SRX2922348 |
| 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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