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Sample GSM2496430 Query DataSets for GSM2496430
Status Public on Dec 03, 2017
Title AML12_HiC_shU_biological_replicate1
Sample type SRA
 
Source name AML12_HiC_shU_biological_replicate1
Organism Mus musculus
Characteristics tissue: AML12 cells
condition: HNRNPU KD (shU)
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: hicpro2juicebox.sh
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
E-mail(s) bowen75@fudan.edu.cn
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
Relations
BioSample SAMN06350710
SRA SRX2578759

Supplementary file Size Download File type/resource
GSM2496430_shU_rep1.hic 5.5 Gb (ftp)(http) HIC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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