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Sample GSM4195023 Query DataSets for GSM4195023
Status Public on Dec 01, 2019
Title ChIP-seq AML12 shCtrl-1
Sample type SRA
 
Source name AML12 shCtrl
Organism Mus musculus
Characteristics cell line: AML12
lentivirus: shCtrl
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 SAMN13412277
SRA SRX7228386

Supplementary file Size Download File type/resource
GSM4195023_shCtrl-1.bigwig 182.8 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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