|
| 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: 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 |
SAMN06350711 |
| SRA |
SRX2578758 |
