|
| Status |
Public on Mar 07, 2024 |
| Title |
Mouse_colonoid_Ctrl_1 |
| Sample type |
SRA |
| |
|
| Source name |
3D cultured mouse colonic organoids
|
| Organism |
Mus musculus |
| Characteristics |
genotyping: Ctrl sgRNA
intestine part: Colonic Organoid
|
| Treatment protocol |
Mouse organoid were differentiated for 4 days. Materigel was removed by Cell recovery solution, pellet organoids were resuspended in RLT lysis buffer (Qigen Kit)
|
| Growth protocol |
Mouse colonic organoids were cultured at P2. Lentivirus, contain control, Satb2, Mta2, Chd4, Gatad2a, Smarca5, Smarca4, Smarcd2 and Ctbp2 sgRNA along with Cas9, infected organoids and selected with puromycin.
|
| 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 |
A48
|
| 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 (Raw data of sample Satb2_KO1 (A1) and Satb2_KO2 (A3) were processed from GSE167283 )
|
| |
|
| 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) |
| GSE213878 |
Bulk RNA-seq of mouse colonic organoids: CRISPR functional Screening of Satb2-interact proteins (NuRD and SWI/SNF complex) |
| GSE213880 |
A MTA2-SATB2 chromatin complex restrains colonic plasticity toward small intestine by retaining HNF4A at colonic chromatin |
|
| Relations |
| BioSample |
SAMN30952552 |
| SRA |
SRX17659753 |
