Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Blood
Cell type
BLaER1
NA
NA

Attributes by original data submitter

Sample

ENA first public
2020-05-08
ENA last update
2020-04-29
ENA-CHECKLIST
ERC000011
External Id
SAMEA6808374
INSDC center alias
CRG, BIST IMIM UPF
INSDC center name
CRG, BIST IMIM UPF
INSDC first public
2020-05-08T17:05:01Z
INSDC last update
2020-04-29T20:56:14Z
INSDC status
public
Submitter Id
E-MTAB-9010:H3K27ac_0h_rep1
broker name
ArrayExpress
cell line
BLaER1
cell type
B cell
common name
human
sample name
E-MTAB-9010:H3K27ac_0h_rep1

Sequenced DNA Library

library_name
H3K27ac_0h_rep1_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
BLaER1 cells at different time points after trasndifferentiation induction were fixed for 10 minutes at room temperature with 1% formaldehyde. Chromatin was sheared by using a Covaris ultrasonicator until fragments ranged from 200 to 1,000 bp. Chromatin immunoprecipitations were performed with 2 ug of chromatin and following standard procedures. BLaER1 cells were grown in RPMI 1640 medium (Gibco) supplemented with 10% inactivated Foetal Bovine Serum (Gibco), 5% Penicillin-Streptomycin (Gibco) and 5% L-Glutamine (Gibco). Cells were maintained at 37ºC in a humid atmosphere containing 5% CO2. Transdifferentiation was induced by addition of 100 nM of beta-estradiol (Calbiochem) and 10 nM of IL-3 and CSF-1 (Peprotech). Immunoprecipitated chromatin was purified with Qiagen PCR purification columns, following the manufacturer's instructions. Sequencing libraries were performed with I ug of ChIP'ped DNA with NebNext ChIP-Seq library kit, following the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
56100671
Reads aligned (%)
98.9
Duplicates removed (%)
10.3
Number of peaks
22097 (qval < 1E-05)

hg19

Number of total reads
56100671
Reads aligned (%)
98.3
Duplicates removed (%)
11.3
Number of peaks
22174 (qval < 1E-05)

Base call quality data from DBCLS SRA