|
| Status |
Public on Dec 31, 2022 |
| Title |
intestinal epithelial cells, Kdm6a/b ablation, prolonged model, rep3 [KO.GTGATC] |
| Sample type |
SRA |
| |
|
| Source name |
jejunum
|
| Organism |
Mus musculus |
| Characteristics |
tissue: jejunum
cell type: intestinal epithelial cells
genotype: Kdm6a/Kdm6b knockout
time: prolonged (5 months post ablation)
Sex: Female
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the Rneasy Micro Kit (74004, QIAGEN). 250 ng of RNA per sample was used as input for library generation.
RNA libraries were prepared using the NEBNext Ultra RNA Library Prep Kit from Illumina (E7530, NEB) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, NEB). Manufacturer protocols were followed.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Prolonged_DKO_Biol_Rep3
|
| Data processing |
Basecalls performed using NovaSeq Control Software 1.7.0, RTA v3.4.4
RNA-Seq data quality was assessed using FastQC (v.0.11.5)
Alignment was performed using the STAR method (v2.4.0) (default parameters with a maximum fragment size of 2 kb)
Samtools (v1.9) was used to filter for properly paired primary alignments
Bedtools (v2.27.1) was used to remove mitochondrial reads and reads on non-chromosome contigs
Read counts on RefSeq genes were computed using featureCounts (v1.6.2).
Differential gene expression analysis was performed using the DESeq2 R package with normalizaiton to correct for library sizes
Genes with an FDR value of 0.05 or less were defined as differentially expressed
Assembly: mm9
Supplementary files format and content: comma-separated values (CSV) text files containing DESeq2 normalized read counts for each sample
Supplementary files format and content: bigwig files
|
| |
|
| Submission date |
Apr 18, 2022 |
| Last update date |
Dec 31, 2022 |
| Contact name |
Klaus H Kaestner |
| E-mail(s) |
kaestner@pennmedicine.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Department |
Department of Genetics and Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine
|
| Street address |
University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104-5156 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE200974 |
H3K27me3 demethylases maintain the transcriptional and epigenomic landscape of the intestinal epithelium [RNA-seq] |
| GSE200976 |
H3K27me3 demethylases maintain the transcriptional and epigenomic landscape of the intestinal epithelium. |
|
| Relations |
| BioSample |
SAMN27621109 |
| SRA |
SRX14891478 |
