|
| Status |
Public on Mar 07, 2024 |
| Title |
SATB2_ChIP in wild type colonic epithelium |
| Sample type |
SRA |
| |
|
| Source name |
Intestine epithelium
|
| Organism |
Mus musculus |
| Characteristics |
genotyping: Wild Type
intestine part: Colon
|
| Treatment protocol |
Epithilal tissues were collected by the EDTA method 30 days after tamoxifen injection and cross-linked with 2mM DSG and 1% formaldehye.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
50 µl of pelleted cross-linked cells were resuspended in 350 µl sarkosyl lysis buffer (0.25% sarkosyl, 1 mM DTT and protease inhibitor in RIPA buffer) and sonicated at 15% amplification by a tip sonicator (Qsonica, Q125) to obtain 200bp to 800bp chromatin fragments. Diluted lysates were incubated with TFs antibodies at 4°C overnight and were additionally incubated with 30 µl protein A/G magnetic beads. ChIPed DNA was purified with a MinElute purification kit.
Libraries were prepared using the ThruPLEX DNA-Seq Kit
Exactly followed the protocol from Takara bio, R400428. All final libraries were size selected (200-800 bp) by AMPure XP beads (Beckman, A63880) and loaded for sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
SATB2_ChIP
|
| Data processing |
All reads were trimmed with trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), and subjected to quality control with FastQC before and after adapter trimming.
Bowtie2 (Langmead and Salzberg, 2012) was used to align the two independent ChIP-Seq analyses to the mouse (mm10) genome with default parameters.
Aligned ChIP-Seq data in SAM format were transformed to BAM files and non-uniquely mapped reads were filtered-out.
Duplicate alignments were then marked and removed using Sambamba.
The merge function in samtools was used to merge the BAM files of different replicates and filter out non-uniquely mapped reads.
Deeptools bamCoverage (duplicate reads ignored, RPKM normalized) was used to generate bigWig files from BAM files.
Assembly: Mouse mm10
Supplementary files format and content: Bigwig files for visualization of TFs genomic binding peaks.
|
| |
|
| 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 |
GPL21103 |
| Series (2) |
| GSE213877 |
ChIP-seq of colonic intestine epithelium from Vil-CreER;MTA2F/F (MTA2KO), Vil-CreER;SATB2F/F(SATB2KO) and Wild Type mice |
| GSE213880 |
A MTA2-SATB2 chromatin complex restrains colonic plasticity toward small intestine by retaining HNF4A at colonic chromatin |
|
| Relations |
| BioSample |
SAMN30952507 |
| SRA |
SRX17659515 |
