|
| Status |
Public on Dec 01, 2019 |
| Title |
ChIP-seq AML12 shSafb-2 |
| Sample type |
SRA |
| |
|
| Source name |
AML12 Safb KD (shSafb)
|
| Organism |
Mus musculus |
| Characteristics |
cell line: AML12
lentivirus: shSafb
antibody: H3K9me3
|
| Treatment protocol |
Aml12 cells were collected after infected with shCtrl or shSAFB lentivirus 5 days
|
| Growth protocol |
AML12 cells were cultured in DMEM/F12 supplemented with 10% fetal bovine serum, ITS Liquid Media Supplement, and 0.1μM dexamethasone at 37 °C and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The H3K9me3 ChIP-seq was performed as described (PMID: 19151716 ).
Illumina sequencing library were prepared according to the standard Illumina protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
We aligned paired-end reads to the mm9 reference using Bowtie2.
We called broad domains using RSEG (Song and Smith, 2011), and retained regions that were more than 100 kb in size.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files contain ChIP-seq signal for each replicate.
|
| |
|
| Submission date |
Nov 27, 2019 |
| Last update date |
Dec 01, 2019 |
| Contact name |
Bo Wen |
| E-mail(s) |
bowen75@fudan.edu.cn
|
| Organization name |
Fudan University
|
| Street address |
130 Dongan Rd.
|
| City |
ShangHai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE125037 |
The Nuclear Matrix Protein SAFB Cooperates with Major Satellite RNAs to Stabilize Heterochromatin Architecture Partially through Phase Separation |
| GSE141104 |
The nuclear matrix protein SAFB maintains heterochromatin architecture through RNA-dependent phase separation [H3K9me3 ChIP-seq] |
|
| Relations |
| BioSample |
SAMN13412274 |
| SRA |
SRX7228389 |
