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Sample GSM5687953 Query DataSets for GSM5687953
Status Public on Nov 01, 2022
Title 15405X11 T+C2 3 (4-OHT+Cer)
Sample type SRA
 
Source name Intestinal Organoids
Organism Mus musculus
Characteristics strain: C57BL/6
tissue/cell type: Intestinal Organoids
treatment: 4-OHT plus C2-ceramide
Treatment protocol Matured organoids were treated with vehicle, 4-OHT or 4-OHT plus C2-ceramide (4-OHT+Cer) for 48 hours
Growth protocol Intestinal organoids were cultured in IntestiCultâ„¢ Organoid Growth Medium (Stemcell Technologies)
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with RNeasy Pure mRNA Bead Kit (Qiagen, Cat. 180244)
RNA libraries were constructed using Illumina TruSeq Stranded Total RNA Library Prep Ribo-Zero Gold (Human, Mouse, Rat)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 15405X11_181015_A00421_0021_BHG3THDMXX_S129_L002
Data processing The mouse GRCm38 genome and gene feature files were downloaded from Ensembl release 94
The reference database was created using STAR version 2.6.1b with splice junctions optimized for 50 base pair reads
Reads were trimmed of adapters using cutadapt 1.16 and aligned to the reference database using STAR in two pass mode.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: FeatureCount output files combined into a tab-delmited raw count matrix
 
Submission date Nov 12, 2021
Last update date Nov 01, 2022
Contact name Ying Li
E-mail(s) li.ying@utah.edu
Phone 8015850860
Organization name University of Utah
Department NUIP
Lab Scott Summers
Street address 15 North 2030 East, Eccles Institute of Human Genetics
City Salt Lake City
State/province UT
ZIP/Postal code 84112
Country USA
 
Platform ID GPL24247
Series (2)
GSE188674 Serine Palmitoyltransferase Controls Stemness of Intestinal Progenitors [bulk RNA-Seq]
GSE188676 Serine Palmitoyltransferase Controls Stemness of Intestinal Progenitors.
Relations
BioSample SAMN23081484
SRA SRX13121131

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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