NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2694183 Query DataSets for GSM2694183
Status Public on Mar 25, 2018
Title OCEAN-C RPMI-8226
Sample type SRA
 
Source name Multiple myeloma
Organism Homo sapiens
Characteristics cell line: RPMI-8226
tissue: peripheral blood
cell type: B lymphocyte
age: 61
disease state: Multiple myeloma
gender: male
Growth protocol Cells were cultured in RPMI-1640 medium (ATCC, Catalog No. 30-2001) with 15% fetal bovine serum and air, 95%, carbon dioxide (CO2), 5% at 37℃.
Extracted molecule genomic DNA
Extraction protocol For OCEAN-C, about 5M cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Formaldehyde was quenched by 0.2M glycine. Nuclear lysates were incubated with MboI. Fragment ends were filled with biotinylated nucleotides, then ligated with T4. Nuclei were then isolated and sonicated. Sonicate was extracted with phenol–chloroform–isoamyl alcohol (25:24:1) and reverse crosslinked. DNA were purified and size selected before Illumina libraries generation
Sequencing libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645, NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
Description No treatment
Data processing Library strategy: OCEAN-C
Hi-C and OCEAN-C reads were aligned to hg19 using Bowtie2
genome build: hg19
processed data files format and content: bed files for Hi-C OCEAN-C sample with HOCIs
 
Submission date Jul 05, 2017
Last update date May 15, 2019
Contact name lumeng Jia
E-mail(s) lumeng_j@pku.edu.cn
Organization name Peking university
Street address Yiheyuan road
City Beijing
ZIP/Postal code 100871
Country China
 
Platform ID GPL20795
Series (1)
GSE100832 OCEAN-C: mapping hubs of open chromatin interactions across the genome reveals gene regulatory networks
Relations
BioSample SAMN07325864
SRA SRX2986030

Supplementary file Size Download File type/resource
GSM2694183_RPMI8226_OCEAN-C_HOCI.bed.gz 108.4 Kb (ftp)(http) BED
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