Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Blood
Cell type
DG-75
Primary Tissue
Blood
Tissue Diagnosis
Malignant Lymphoma - Burkitts Type

Attributes by original data submitter

Sample

ENA first public
2019-04-05
ENA last update
2019-03-26
ENA-CHECKLIST
ERC000011
External Id
SAMEA5537263
INSDC center alias
Research Unit Gene Vectors Helmholtz Zentrum Munchen German Research Center for Environmental Health and German Center for Infection Research (DZIF), Partner site Munich, Germany
INSDC center name
Research Unit Gene Vectors Helmholtz Zentrum Munchen German Research Center for Environmental Health and German Center for Infection Research (DZIF), Partner site Munich, Germany
INSDC first public
2019-04-05T04:02:49Z
INSDC last update
2019-03-26T23:44:20Z
INSDC status
public
Submitter Id
E-MTAB-7821:Replicate 1 DG75 parental input
broker name
ArrayExpress
cell line
DG-75
cell type
B cell
common name
human
disease
Burkitts lymphoma
sample name
E-MTAB-7821:Replicate 1 DG75 parental input

Sequenced DNA Library

library_name
Replicate 1 DG75 parental input_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For immunoprecipitation two samples with 1×108 cells each were adjusted to a concentration of 5×105 cells/ml in fresh medium and were left non-induced or were induced with a final concentration of 100 ng/ml doxycycline (Sigma-Aldrich) for 15 h. 1 x 10^8 cells were adjusted to a concentration of 5 x 10^5 cells/ ml prior to chromatin preparation. Nuclei were extracted with hypotonic buffer (10 mM KCl, 340 mM Sucrose, 1.5 mM MgCl2, 10 mM Hepes pH 7.9) containing 10 % proteinase inhibitor cocktail (PIC, Roche) and lysed in RIPA buffer + 1x PIC. The chromatin was shared in a BioRuptor on wet ice (4 cycles, 5 min each, 30 on/off, high). The chromatin was immunoprecipitated with the BZ1 antibody (Young et al., 1991), 10 % input was used as a control. The precipitates were washed with different salt concentrations and the proteins were digested with proteinase K. The library construction was performed with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NWB # E7645S) and NEBNext Multiplex Oligos for Illumina (Index Primer Set 2, NEB #E7500S) starting from 8 ng DNA.

Sequencing Platform

instrument_model
Illumina HiSeq 1500

hg38

Number of total reads
42644850
Reads aligned (%)
98.7
Duplicates removed (%)
2.8
Number of peaks
1378 (qval < 1E-05)

hg19

Number of total reads
42644850
Reads aligned (%)
98.1
Duplicates removed (%)
3.8
Number of peaks
1368 (qval < 1E-05)

Base call quality data from DBCLS SRA