|
| Status |
Public on Mar 07, 2024 |
| Title |
MTA2_KO_3 |
| Sample type |
SRA |
| |
|
| Source name |
Intestine epithelium
|
| Organism |
Mus musculus |
| Characteristics |
genotyping: Mta2 Knock out
intestine part: Colon
|
| Treatment protocol |
Epithilal tissues were collected by EDTA method 30 days after Tamoxifen injection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Mini RNA extract kit
NEBNext® Ultra™ RNA Library Prep Kit for Illumina, following manufacturer's protocol.
Library construction performed by Novogene.co. Non-directional eukaryotic mRNA library
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Batch_1
|
| 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
Assembly: GRCm38
Supplementary files format and content: Normalized gene counts table and RPKM table
|
| |
|
| Submission date |
Sep 21, 2022 |
| Last update date |
Mar 07, 2024 |
| 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 |
GPL24247 |
| Series (2) |
| GSE213879 |
Bulk RNA-seq (>20M reads) of colonic epithelium from Vil-CreER;MTA2F/F (MTA2KO) and Wild Type mice |
| GSE213880 |
A MTA2-SATB2 chromatin complex restrains colonic plasticity toward small intestine by retaining HNF4A at colonic chromatin |
|
| Relations |
| BioSample |
SAMN30952589 |
| SRA |
SRX17659746 |
