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Sample GSM4194651 Query DataSets for GSM4194651
Status Public on Dec 01, 2019
Title Hi-C AML12 shSafb-1 AML12
Sample type SRA
 
Source name Safb KD (shSafb)
Organism Mus musculus
Characteristics cell line: AML12
lentivirus: shSafb
Treatment protocol The shRNA lentiviruses were prepared as previously described (Fu et al., 2015). Then AML12 cells were infected with 200 μl of virus concentrate in a well of six-well-plates. Medium was changed 24 hours after transfection, and then collect cells 5 days after transfection.
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 Hi-C was carried out according to the protocol (PMID: 25497547). Briefly, Five million cells were crosslinked with 1% formaldehyde for 10min at room temperature, and then the cells were divided into two tubes, taking one tube for the subsequent experiments, the cells were permeabilized with 0.2% Igepal CA630, and then the pelleted nuclei were treated with 0.5% SDS. The chromatin was digested with 100 units of MboI overnight, the DNA ends were marked by biotinylated nucleotides, After reversal of crosslinks, the DNA was sheared to a size of 300-500bp, and then the ligated DNA was pull-down by streptavidin magnetic beads.
Illumina sequencing library were prepared according to the standard Illumina protocol.
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
Data processing Raw HiC data were processed through the HiC-Pro pipeline (PMID: 26619908) (including read mapping/binning/ICE correction).
hic files were generated using HiC-Pro script: hicpro2juicebox.sh
Genome_build: mm9
Supplementary_files_format_and_content: hic files contain the HiC contact matrix at different resolution.
 
Submission date Nov 26, 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
GSE141080 The nuclear matrix protein SAFB maintains heterochromatin architecture through RNA-dependent phase separation [Hi-C]
Relations
BioSample SAMN13392755
SRA SRX7223820

Supplementary file Size Download File type/resource
GSM4194651_Safb_1.hic 1.7 Gb (ftp)(http) HIC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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