Illumina HiSeq 4000 paired end sequencing; Genome-wide binding sites of NF90/ILF3 in K562 erythroleukemia cells
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
No description
Antigen
NA
Cell type
Cell type Class
Blood
Cell type
K-562
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Chronic Myelogenous
Attributes by original data submitter
Sample
ENA first public
2018-03-01
ENA last update
2017-09-04
ENA-CHECKLIST
ERC000011
External Id
SAMEA104279661
INSDC center alias
Pulmonary and Critical Care Medicine, Stanford University School of Medicine
INSDC center name
Pulmonary and Critical Care Medicine, Stanford University School of Medicine
INSDC first public
2018-03-01T17:01:49Z
INSDC last update
2017-09-04T10:29:58Z
INSDC status
public
Submitter Id
E-MTAB-6042:NF90_K562_ChIPSeq
broker name
ArrayExpress
cell line
K562
cell type
lymphoblast
common name
human
disease
chronic myelogenous leukemia
organism part
bone marrow
sample name
E-MTAB-6042:NF90_K562_ChIPSeq
sex
female
Sequenced DNA Library
library_name
NF90_K562_ChIPSeq_p
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were harvested and crosslinked in 1% formaldehyde for 10 minutes at room temperature. Cell pellets were re-suspended in hypotonic buffer (20 mM HEPES, 10 mM KCl, 1mM EDTA, 10% glycerol) supplemented with Pierce Protease Inhibitor Tablets (Thermo Fisher), placed on ice for 10 minutes and centrifuged to remove cytoplasmic supernatant. Chromatin was released from nuclear pellet with mild chemical lysis with Radio-immunoprecipitation assay buffer (RIPA) containing 0.1% SDS and 1% Triton-X-100. Protein-bound chromatin was sheared with mechanical sonication (Branson 250 Sonifier) at 35% output with 20 second pulses for 30 cycles to obtain chromatin fragments of high resolution at 200 – 500 bps. Successful chromatin fragmentation was assayed by reverse cross-linking, and electrophoresis through 0.8% agarose gel to confirm enrichment of small chromatin fragments at the target range. K562 erythroleukemia cells were grown in RPMI1640 media supplemented with 10% fetal bovine serum and Antibiotic-Antimycolic 100X (Life Technologies). Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with with monoclonal antibody to NF90 (BD mAB DRBP76 #612155). Libraries were prepared according to Bravo automatic library preparation.