NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3780958 Query DataSets for GSM3780958
Status Public on Jun 30, 2019
Title Aml12_Ctrl_rep2
Sample type SRA
 
Source name AML12
Organism Mus musculus
Characteristics genotype/variation: control
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 SAMN11783924
SRA SRX5865761

Supplementary file Size Download File type/resource
GSM3780958_Ctrl_rep2_sort_200M_allValidPairs.hic 1.1 Gb (ftp)(http) HIC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap