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| Status |
Public on Dec 29, 2019 |
| Title |
Gene expression profiles of mouse colonic epithelial monolayer cultured in air-liquid interface |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The colonic epithelium can undergo multiple rounds of damage and repair, often in response to excessive inflammation. Our understanding of how this process occurs is limited by a lack of in vitro models that recapitulate key aspects of in vivo responses. We established a long-term, self-organizing 2D epithelial monolayer system to model the cyclic nature of epithelial alterations during injury-repair. Through RNA-seq analysis, we seek to evaluate the transcriptomic profiles of the cultured epithelial cells under select phases of “homeostasis-injury-repair” in vitro.
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| Overall design |
We performed RNA-seq on three separate sets of cultured mouse colonic monolayer samples collected at various time points after swittching to air-liquid interface (ALI) or re-submersion (Re-Sub): (1) monolayer RNA samples collected at ALId0, ALId4, ALId7, ALId14 and ALId21; (2) monolayer RNA samples collected at ALId0, ALId1, ALId2 after switching to air-liquid interface; (3) monolayer RNA samples collected at Re-Sub 0h (=ALId21), Re-Sub 8h, Re-Sub 24h and Re-Sub d7.
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| Contributor(s) |
Wang Y, Muegge BD, Stappenbeck TS |
| Citation(s) |
31708126 |
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| Submission date |
Feb 26, 2019 |
| Last update date |
Dec 29, 2019 |
| Contact name |
Thaddeus Stappnbeck |
| E-mail(s) |
stappet@ccf.org
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| Organization name |
Cleveland Clinic, Lerner Research Institute
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| Department |
Inflammation and Immunity
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| Street address |
9500 Euclid Ave
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| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44195 |
| Country |
USA |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (31)
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| GSM3629675 |
ALI day 0 culutre, replicate 1, experiment set 1 |
| GSM3629676 |
ALI day 0 culutre, replicate 2, experiment set 1 |
| GSM3629677 |
ALI day 4 culutre, replicate 1, experiment set 1 |
| GSM3629678 |
ALI day 4 culutre, replicate 2, experiment set 1 |
| GSM3629679 |
ALI day 7 culutre, replicate 1, experiment set 1 |
| GSM3629680 |
ALI day 7 culutre, replicate 2, experiment set 1 |
| GSM3629681 |
ALI day 14 culutre, replicate 1, experiment set 1 |
| GSM3629682 |
ALI day 14 culutre, replicate 2, experiment set 1 |
| GSM3629683 |
ALI day 21 culutre, replicate 1, experiment set 1 |
| GSM3629684 |
ALI day 21 culutre, replicate 2, experiment set 1 |
| GSM3629685 |
ALI day 0 culutre, replicate 1, experiment set 2 |
| GSM3629686 |
ALI day 0 culutre, replicate 2, experiment set 2 |
| GSM3629687 |
ALI day 0 culutre, replicate 3, experiment set 2 |
| GSM3629688 |
ALI day 1 culutre, replicate 1, experiment set 2 |
| GSM3629689 |
ALI day 1 culutre, replicate 2, experiment set 2 |
| GSM3629690 |
ALI day 1 culutre, replicate 3, experiment set 2 |
| GSM3629691 |
ALI day 2 culutre, replicate 1, experiment set 2 |
| GSM3629692 |
ALI day 2 culutre, replicate 2, experiment set 2 |
| GSM3629693 |
ALI day 2 culutre, replicate 3, experiment set 2 |
| GSM3629694 |
Re-Sub hour 0 culutre, replicate 1, experiment set 3 |
| GSM3629695 |
Re-Sub hour 0 culutre, replicate 2, experiment set 3 |
| GSM3629696 |
Re-Sub hour 0 culutre, replicate 3, experiment set 3 |
| GSM3629697 |
Re-Sub hour 8 culutre, replicate 1, experiment set 3 |
| GSM3629698 |
Re-Sub hour 8 culutre, replicate 2, experiment set 3 |
| GSM3629699 |
Re-Sub hour 8 culutre, replicate 3, experiment set 3 |
| GSM3629700 |
Re-Sub hour 24 culutre, replicate 1, experiment set 3 |
| GSM3629701 |
Re-Sub hour 24 culutre, replicate 2, experiment set 3 |
| GSM3629702 |
Re-Sub hour 24 culutre, replicate 3, experiment set 3 |
| GSM3629703 |
Re-Sub day 7 culutre, replicate 1, experiment set 3 |
| GSM3629704 |
Re-Sub day 7 culutre, replicate 2, experiment set 3 |
| GSM3629705 |
Re-Sub day 7 culutre, replicate 3, experiment set 3 |
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| Relations |
| BioProject |
PRJNA524283 |
| SRA |
SRP186862 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE127172_Exp1_all.genes_counts_final.txt.gz |
444.0 Kb |
(ftp)(http) |
TXT |
| GSE127172_Exp2_all.genes_counts_final.txt.gz |
417.3 Kb |
(ftp)(http) |
TXT |
| GSE127172_Exp3_all.genes_counts_final.txt.gz |
499.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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