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Sample GSM2496429 Query DataSets for GSM2496429
Status Public on Dec 03, 2017
Title AML12_HiC_shCtrl_biological_replicate2
Sample type SRA
Source name AML12_HiC_shCtrl_biological_replicate2
Organism Mus musculus
Characteristics tissue: AML12 cells
condition: shCtrl
Treatment protocol For shRNA-based knockdown, shRNA lentiviruses were then prepared as previously described (PMID: 26603343). Then, 2.5×105 AML12 were infected with the viruses and selected puromycine for 3 days.
Growth protocol AML12 cell were kept in complete growth medium:a 1:1 mixture of Dulbecco's modified Eagle's medium and Ham's F12 medium with 0.005 mg/ml insulin, 0.005 mg/ml transferrin, 5 ng/ml selenium, and 40 ng/ml dexamethasone, 90%; fetal bovine serum, 10%.
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
Description HiC Library digested with MboI
Data processing Raw HiC data were processed through the HiC-Pro pipeline (MID: 26619908) (including read mapping/binning/ICE correction).
hic files were generated using HiC-Pro script:
Genome_build: mm9
Supplementary_files_format_and_content: hic files contain the HiC contact matrix at different resolution.
Submission date Feb 21, 2017
Last update date May 15, 2019
Contact name Bo Wen
Organization name Fudan University
Department Institutes of Biomedical Sciences
Street address 130 DongAn Road
City Shanghai
ZIP/Postal code 200032
Country China
Platform ID GPL21273
Series (2)
GSE95112 The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [Hi-C]
GSE95116 The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture
BioSample SAMN06350711
SRA SRX2578758

Supplementary file Size Download File type/resource
GSM2496429_shCtrl_rep2.hic 4.5 Gb (ftp)(http) HIC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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