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Status |
Public on Dec 01, 2019 |
Title |
Hi-C AML12 shCtrl-1 |
Sample type |
SRA |
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Source name |
shCtrl AML12
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Organism |
Mus musculus |
Characteristics |
cell line: AML12 lentivirus: shCtrl
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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.
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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.
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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.
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Library strategy |
Hi-C |
Library source |
genomic |
Library selection |
other |
Instrument model |
HiSeq X Ten |
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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.
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Submission date |
Nov 26, 2019 |
Last update date |
Dec 01, 2019 |
Contact name |
Bo Wen |
E-mail(s) |
bowen75@fudan.edu.cn
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Organization name |
Fudan University
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Street address |
130 Dongan Rd.
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City |
ShangHai |
ZIP/Postal code |
200032 |
Country |
China |
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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] |
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Relations |
BioSample |
SAMN13392757 |
SRA |
SRX7223818 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4194649_Control_1.hic |
1.7 Gb |
(ftp)(http) |
HIC |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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