Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Blood
Cell type
B cells
NA
NA

Attributes by original data submitter

Sample

ENA first public
2018-07-18
ENA last update
2017-09-22
ENA-CHECKLIST
ERC000011
External Id
SAMEA104313311
INSDC center alias
INSERM UMR1163, Laboratory of Normal and Pathological Homeostasis of the Immune System, Paris, France
INSDC center name
INSERM UMR1163, Laboratory of Normal and Pathological Homeostasis of the Immune System, Paris, France
INSDC first public
2018-07-18T17:02:36Z
INSDC last update
2017-09-22T10:19:53Z
INSDC status
public
Submitter Id
E-MTAB-5938:input
broker name
ArrayExpress
cell type
B cell
common name
human
disease
normal
genotype
wild type genotype
organism part
blood
sample name
E-MTAB-5938:input

Sequenced DNA Library

library_name
input_p
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Original B-lymphobast cells come from peripheral blood mononuclear cells (PBMC). These cells are obtained from blood samples after ficoll separation. PBMC from controls and patients were transduced with the Epstein Barr Virus (EBV) to generate the B-lymphobast cells lines. Cells were expanded and frozen. The B-lymphobast are cultured in medium composed of RPMI, Glutamine, Fetal bovin serum and penicillin-streptomycin. 2 control B-lymphoblastoid cell lines were established to stably express TTC7A_WT-3*Flag-HA-ires-EGFP. ChIP was performed using two distinct Flag antibodies: IP-1, sigma F1804 with 100*10e6 cells and IP-2, sigma F3165 with 30*10e6 cells. Cells were cultured in RPMI medium 1640+Glutamax (Gibco, ref 61870-010) supplemented with 10% (vol/vol) Fetal Bovine Serum (Gibco), sodium pyruvate (1 mM, LifeTechnologies) and penicillin and streptomycin (100U/ml each, LifeTechnologies). Cells with blocked in early G1/S phase with thymidine double blockage (2mM, 18 h first treatment, 9 h release and 15 h second treatment). Immunoprecipitated DNA (ChIP) and whole cell extracts DNA (input) were treated with RNaseA and proteinase K then purified by using Qiaquick PCR purification kit (Qiagen, 28106). TruSeq ChIP kit from Illumina was used to perform library preparation according to the manufacturer's recommendations. Briefly, IP and input DNA were first size selected using SPRIselect beads (Agencourt) in order to have fragments between 100 and 500bp after BioAnalyzer profiling. 1 to 10ng of DNA were used in a first step of end-repair followed by the adenylation of 3'-end allowing further ligation of specific Illumina adaptors required for sequencing. These adaptors contain specific indexes (barcodes) different for each sample so that library from different samples can be mixed together before sequencing. After PCR amplification (12-15 cycles), quality assessment of DNA libraries was achieved using BioAnalyzer profiling and Qubit quantification. After equimolar pooling of libraries, the final dilution was accurately quantified using Kapa library quantification kit.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
95263986
Reads aligned (%)
94.6
Duplicates removed (%)
5.8
Number of peaks
3104 (qval < 1E-05)

hg19

Number of total reads
95263986
Reads aligned (%)
93.2
Duplicates removed (%)
6.3
Number of peaks
923 (qval < 1E-05)

Base call quality data from DBCLS SRA