|
| Status |
Public on Jun 30, 2019 |
| Title |
Aml12_KD_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
AML12
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: SRRM2 KD
|
| Growth protocol |
The mouse hepatocyte cell line alpha mouse liver 12 (AML12) cells were cultured in DMEM/F12 (HyClone) supplemented with 10% fetal bovine serum (FBS, Biowest), ITS Liquid Media Supplement (Sigma) and 0.1μM dexamethasone (Sigma) at 37 °C and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Biotin-DNA was isolated with strepavidin-beads
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Hi-C
|
| Data processing |
Library strategy: HiC-Seq
Raw HiC data were processed through the HiC-Pro pipeline (PMID: 26619908) (including read mapping/binning/ICE correction).
To eliminate the bias from the different sequencing depth, We random sampled the contacts of each sample to 200M, and then convert the sampled contacts to contact matrix at different resolutions by Juicer Tools
Genome_build: mm9
Supplementary_files_format_and_content: hic files contain the HiC contact matrix at different resolution.
|
| |
|
| Submission date |
May 20, 2019 |
| Last update date |
Jul 01, 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) |
| GSE131463 |
Nuclear speckles as a key regulator for the 3D genome organization [HiC] |
| GSE131466 |
Nuclear speckles as a key regulator for the 3D genome organization |
|
| Relations |
| BioSample |
SAMN11783922 |
| SRA |
SRX5865763 |
