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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jun 01, 2018 |
Title |
Ctl_L43 |
Sample type |
SRA |
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Source name |
Colonoid
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Organism |
Mus musculus |
Characteristics |
tissue: Colonoid
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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 |
L45-5 (L43 colonoid) vehicle treated Total RNA was isolated from mouse colonoid treated with or without TNF, TGFb1, and BMP2 using RNeasy kit (Qiagen) group_TNF_vs_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 |
SAMN07247084 |
SRA |
SRX2922360 |
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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