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Sample GSM5672441 Query DataSets for GSM5672441
Status Public on Mar 01, 2023
Title intestinal organoids, AA_D1#1
Sample type SRA
 
Source name intestinal organoids, AA_D1
Organism Mus musculus
Characteristics tissue: intestinal organoids
strain: C57BL/6
treatment: AA
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 Id4_AA-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 SAMN22892751
SRA SRX12972791

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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