|
| Status |
Public on Mar 07, 2024 |
| Title |
MTA2KO, Colonic epithelium, H3K27Ac-ChIP, Biological Repicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Colon
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Colon
cell type: Epithelium cells
genotype: Vil-CreER;MTA2F/F
antibody: anti-H3K27Ac
|
| Treatment protocol |
Pelleted cross-linked cells were resupended in 130 µl lysis buffer (50 mM Tris-HCl, 0.1% SDS, 10 mM EDTA and 1x Roche EDTA-free protease inhibitor) and sonicated ain a Covaris E210 sonicator at 4oC for 50 min with 5 min on/off cycles to obtain 200bp to 800bp chromatin fragments. Diluted lysates were incubated with anti-H3K27Ac 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.
|
| Growth protocol |
Colonic epithelial tissues were collected by the EDTA method 30 days after tamoxifen injection and cross-linked with 1% formaldehye.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared using the ThruPLEX DNA-Seq Kit (Rubicon Genomics, R400427). 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 |
| |
|
| 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)(version 2.4.1) was used to align the two independent ChIP-Seq analyses to the mouse (mm10) genome with default parameters.
Peaks were called using callpeak function in the MACS2 package with the following parameters (callpeak -t ChIPfile.bam -c Inputfile.bam --format Paired-end BAM --gsize M.musculs(1.87e9) -m 10 30 -q 0.001-bw 300); bigwigs made using bamCoverage function in the deeptools v3.4.3 with following the parameters (bamCoverage --binSize 25 -p 4 --normalizeUsing RPKM --extendReads $fragLength -b Chip.bam -o ChIP.bw)
Supplementary files format and content: Bigwig
Supplementary files format and content: Bed
|
| |
|
| Submission date |
Oct 19, 2023 |
| 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) |
| GSE213880 |
A MTA2-SATB2 chromatin complex restrains colonic plasticity toward small intestine by retaining HNF4A at colonic chromatin |
| GSE245751 |
H3K27Ac ChIP-seq of colonic intestine epithelium from Vil-CreER;MTA2F/F (MTA2KO) and Wild Type mice |
|
| Relations |
| BioSample |
SAMN37879669 |
| SRA |
SRX22139662 |
