|
| Status |
Public on Mar 01, 2023 |
| Title |
intestinal organoids, PGE2_D1#3 |
| Sample type |
SRA |
| |
|
| Source name |
intestinal organoids, PGE2_D1
|
| Organism |
Mus musculus |
| Characteristics |
tissue: intestinal organoids
strain: C57BL/6
treatment: PGE2
time: D1
|
| Treatment protocol |
Intestinal organoids were treated with vehicle, AA 25 µM and PGE2 50 nM for 1 Day, 3 Day and 6 Day
|
| Growth protocol |
Mouse intestinal organoids were generated from isolated mouse crypts and seeded into Matrigel using the media supplemented with in Advence DMEM (Gibco) media, recombinant murine EGF 40 ng/ml (PeproTech), recombinant murine Noggin 50 ng/ml (PeproTech), R-spondin 62.5 ng/ml (R&D Systems), N-acetyl-L-cysteine 1 uM (Sigma-Aldrich), CHIR-99021 5 uM (Tocris), Y-27632 20 ng/ml (Tocris), B27 1X (Gibco), N2 1X (Gibco)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Intestinal organoids rescued from matrigel using cell recovery solution, RNA was harvested using Trizol Reagent.
RNA libraries were prepared for sequencing using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Id9_PGE2-D1
|
| Data processing |
RNA-seq reads were implemented to trimming (cutadapt), mapping (STAR), and expression quantification (quantMode GeneCount), respectively.
Reads were mapped to Homo sapiens GRCh38.p6 (release M24)
Differential gene expression analyses were performed using DESeq2 ref. Lowly-expressed genes were filtered out from the differential expression analysis input matrix.
Limma (v3.46) was used to adjust for sequencing batch effects, prior to rlog normalization of the size-factor normalized read counts.
Genome_build: GRCh38.P6
Supplementary_files_format_and_content: tab-separated values version of raw counts of sequencing reads for all samples
|
| |
|
| Submission date |
Nov 04, 2021 |
| Last update date |
Mar 01, 2023 |
| Contact name |
Aybuke Alici |
| E-mail(s) |
garipca@cshl.edu
|
| Organization name |
Cold Spring Harbor Laboratory
|
| Street address |
1 Bungtown Rd.
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE188213 |
Epigenetic reprogramming of intestinal stemness by dietary arachidonic acid [intestinal organoids] |
| GSE210730 |
Epigenetic reprogramming of intestinal stemness by dietary arachidonic acid |
|
| Relations |
| BioSample |
SAMN22892754 |
| SRA |
SRX12972796 |
