|
| Status |
Public on Nov 27, 2023 |
| Title |
Cdx1 mutant organoid line 1: transduced with Ppard-targetting dual guide RNAs, treated with 4-hydroxytamoxifen |
| Sample type |
SRA |
| |
|
| Source name |
Primary murine organoids from distal small intestine
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Primary murine organoids from distal small intestine
cell type: Intestinal epithelial cells
genotype: Lgr5creERT2; Rosa26 LSL-Cas9-eGFP/+; ROSA26tdTomato
time: long-term organoid culture seeded with adult intestinal stem cells
treatment: transduced with Ppard-targetting dual guide RNAs, treated with 4-hydroxytamoxifen
organoid type: Cdx1 mutant organoid line 1
|
| Growth protocol |
Single intestinal epithelial cells were FACs sorted into matrigel-coated plates, and cultured into organoids as described in Sato et al. Nature 2009. Organoids were propagated for several passages prior to collection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Organoids were washed with PBS and resuspended in TRI reagent containing 1% 2-Mercaptoethanol. RNA was extracted using Direct-zol RNA Miniprep Plus (Zymo Research).
Prepared by Novogene
Illumina, PE150, 20M Paired Reads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
kallisto v. 0.46.0 with standard parameters in paired-end mode was used to obtain abundance measurements from the fastq files
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include transcript length and effective length as well as estimated counts and TPM values for each sample.
|
| |
|
| Submission date |
Apr 29, 2022 |
| Last update date |
Nov 27, 2023 |
| Contact name |
Rachel Klapper Zwick |
| E-mail(s) |
Rachel.Zwick@ucsf.edu
|
| 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 |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE201858 |
Epithelial zonation along the mammalian small intestine defines five discrete metabolic domains [Mouse_bulkRNA-seq] |
| GSE201859 |
Epithelial zonation along the mammalian small intestine defines five discrete metabolic domains |
|
| Relations |
| BioSample |
SAMN27622673 |
| SRA |
SRX15046687 |
