|
| Status |
Public on Oct 05, 2021 |
| Title |
WT Cecum rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Intestine epithelium
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wild type
tissue: Cecum
|
| Treatment protocol |
Epithilal tissues collected by EDTA method 30 days after Tamoxifen injection. Genotypes include Vil-CreER;Satb2f/f and Satb2f/f control mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Mini RNA extract kit
The library was constructed with NEBNext® Ultra™ RNA Library Prep Kit for Illumina, following manufacturer's protocol.
Library construction strategy was non-directional eukaryotic mRNA library Sequencing strategy was Pair-end 150 (PE150)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Intestinal_epithelial_normalized_counts.txt
|
| Data processing |
Adapter and low quality bases trimming (Q<20) using Trim Galore! with default parameters
Paired end alignment using STAR with defaut parameters
Generation of counts relative to genes using featureCounts with defaut paramets (unstranded mode)
Generation of normalized read counts and differential expression genes with normal shrinkage mode by DEseq2 package in Rstudio
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized gene counts table
|
| |
|
| Submission date |
Apr 15, 2020 |
| Last update date |
Oct 05, 2021 |
| Contact name |
Wei Gu |
| E-mail(s) |
wei.gu@beigene.com
|
| Phone |
13776921246
|
| Organization name |
Beigene
|
| Department |
Beigene Institute
|
| Lab |
Gu Lab
|
| Street address |
51 Rijing Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200135 |
| Country |
China |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE148692 |
Bulk RNA-seq of Intestine Epithelia (Jejunum, Ileum, Cecum and Colon) from Satb2-deficient and WT mice |
| GSE148695 |
SATB2 preserves colon stem cell identity and mediates ileum-colon conversion via enhancer remodeling |
|
| Relations |
| BioSample |
SAMN14600409 |
| SRA |
SRX8118438 |
