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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 01, 2018 |
| Title |
Smad4 pathways modulate induction of the chemokine Ccl20 and repress inflammation-induced carcinogenesis in mouse colon |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To understand the extent of Smad-mediated gene regulation in the colon, we isolated colon epithelium from Smad4ΔLrig1 and from Smad4+ control mice (either mice lacking a CreERT allele and treated with tamoxifen, or mice bearing a CreERT allele but treated with vehicle only) and analyzed the colonic epithelium by RNAseq. The ability of TGFβ1 and/or BMP2 to block TNF-mediated induction of Ccl20 from our study suggests that these Smad-mediated pathways may act as gatekeepers for induction of other inflammation-associated genes. To determine if Smad-mediated signaling blocks all or specific subsets of TNF-induced genes, we analyzed both colonocytes and mouse colonoid treated with or without TNF, TGFβ1, and BMP2 by RNA seq.
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| Overall design |
In total, three RNAseq experiments were performed and three biological replicates were used for each condition: 1. Colon epithelium from Smad4ΔLrig1 and from Smad4+ control mice was isolated. Total RNA was isolated from these tissues 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). 32~37 million 51 base pair single-end reads were generated per sample. 2. Total RNA was isolated from colonocytes treated with or without TNF, TGFβ1, and BMP2 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). 26~50 million 75 base pair paired-end reads were generated per sample. 3. Total RNA was isolated from mouse colonoid treated with or without TNF, TGFβ1, and BMP2 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). 50~72 million 75 base pair paired-end reads were generated per sample.
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| Web link |
https://www.ncbi.nlm.nih.gov/pubmed/30109253
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| Contributor(s) |
Means AL, Freeman TJ, Zhu J, Weaver CJ, Padmanabhan C, An H, Zi J, Wessinger B, Brown T, Deane NG, Chaturvedi R, Coffey RJ, Wilson KT, Washington MK, Shi C, Beauchamp RD |
| Citation(s) |
30109253, 33759564 |
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| Submission date |
Jun 15, 2017 |
| Last update date |
Aug 03, 2021 |
| 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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| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL21493 |
Illumina HiSeq 3000 (Mus musculus) |
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| Samples (30)
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| Relations |
| BioProject |
PRJNA390642 |
| SRA |
SRP109291 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE100082_DEG_P3027_S15_20_May10_2017.txt.gz |
675.9 Kb |
(ftp)(http) |
TXT |
| GSE100082_group_Flx_TGFb+BMP2_vs_Flx_Ctl_DEG.txt.gz |
984.5 Kb |
(ftp)(http) |
TXT |
| GSE100082_group_Flx_TNFa+TGFb+BMP2_vs_Flx_TNFa_DEG.txt.gz |
981.2 Kb |
(ftp)(http) |
TXT |
| GSE100082_group_Flx_TNFa_vs_Flx_Ctl_DEG.txt.gz |
959.3 Kb |
(ftp)(http) |
TXT |
| GSE100082_group_TGFb+BMP+TNF_vs_TNF_DEG.txt.gz |
685.9 Kb |
(ftp)(http) |
TXT |
| GSE100082_group_TGFb+BMP_vs_Ctl_DEG.txt.gz |
689.3 Kb |
(ftp)(http) |
TXT |
| GSE100082_group_TNF_vs_Ctl_DEG.txt.gz |
648.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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