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| Status |
Public on Nov 28, 2023 |
| Title |
Epithelial zonation along the mammalian small intestine defines five discrete metabolic domains [Mouse_bulkRNA-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Longitudinal zonation of epithelial cells across the mammalian small intestine defines five domains of nutrient absorption.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.
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| Overall design |
Intestinal organoids derived from the distal-most domain of the small intestine from adult Lgr5creERT2; Rosa26 LSL-Cas9-eGFP/+; ROSA26tdTomato mice, in which cas9-GFP is expressed in a tamoxifen-inducible manner. Sequenced organoids are either experimental Ppard (2 mutants) or Cdx1 (1 mutant) knockout organoids lines, which were transduced with dual guide RNAs targeting either gene and CRISPR-mediated gene deletion, or control lines (uninfected with virus containing dual guide RNAs with our without 4-hydroxytamoxifen treatment, or infected with dual guide RNAs but untreated with 4-hydroxytamoxifen).
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| Web link |
https://www.biorxiv.org/content/10.1101/2023.09.20.558726v1
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| Contributor(s) |
Zwick RK, Boffelli D, Klein OD |
| Citation(s) |
38321203 |
| BioProject |
PRJNA827827 |
| |
| Submission date |
Apr 29, 2022 |
| Last update date |
Jan 30, 2025 |
| Contact name |
Rachel Klapper Zwick |
| E-mail(s) |
Rachel.Zwick@ucsf.edu
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| Organization name |
University of California, San Francisco
|
| Lab |
Ophir Klein Lab
|
| Street address |
513 Parnassus Ave.
|
| City |
San Francisco |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
|
| Samples (8)
|
| GSM6077235 |
Uninfected, untreated, control organoids |
| GSM6077236 |
Uninfected, 4-hydroxytamoxifen treated, control organoids |
| GSM6077237 |
Dual guide RNA targeting Ppard infected, untreated, control organoids, 1 |
| GSM6077238 |
Dual guide RNA targeting Ppard infected, untreated, control organoids, 2 |
| GSM6077239 |
Ppard mutant organoid line 1: transduced with Ppard-targetting dual guide RNAs, treated with 4-hydroxytamoxifen, 1 |
| GSM6077240 |
Ppard mutant organoid line 1: transduced with Ppard-targetting dual guide RNAs, treated with 4-hydroxytamoxifen, 2 |
| GSM6077241 |
Dual guide RNA targeting Cdx1 infected, untreated, control organoids |
| GSM6077242 |
Cdx1 mutant organoid line 1: transduced with Ppard-targetting dual guide RNAs, treated with 4-hydroxytamoxifen |
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| This SubSeries is part of SuperSeries: |
| GSE201859 |
Epithelial zonation along the mammalian small intestine defines five discrete metabolic domains |
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