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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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