|
| Status |
Public on Nov 01, 2022 |
| Title |
15405X12 T+C2 4 (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 IntestiCult™ 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 |
15405X12_181015_A00421_0021_BHG3THDMXX_S130_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 |
SAMN23081486 |
| SRA |
SRX13121132 |
