Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Blood
Cell type
Lymphoblastoid cells
NA
NA

Attributes by original data submitter

Sample

source_name
lymphoblastoid cell_22q11del
biomaterial_provider
166
cell line
ID00014
cell type
lymphoblastoid cell
age
34
genotype
22q11del

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Per chromatin immunoprecipitation (ChIP) 2 x 107 LCLs were crosslinked in 1% formaldehyde for 10 min at room temperature. The reaction was stopped by adding glycine to a final concentration of 0.125M and stirring for 5 min at room temperature. The cells were pelleted and washed with 1xPBS plus protease inhibitors to remove the crosslinking reagent. The cells were pelleted again and stored at minus 80 degrees until further use. On the day of the immunoprecipiation, the pellets were thawed and washed with 1xPBS plus Protease Inhibitors. The cells were pelleted and exposed to hypotonic buffer and broken with a Dounce homogenizer. The cell nuclei were pelleted and lysed in RIPA buffer. Chromatin was prepared using a Branson 250 Sonifier (7x 30 sec, 100% duty cycle). During the procedure the lysate was kept cold at all times. A sample of the chromatin lysate was set aside as Input control. The rest of the chromatin lysate was used in the ChIP experiment using the following antibodies against H3K27Ac (Abcam ab4729), H2K27me3 (Cell Signaling 9733), and CTCF (Millipore 07-729). Control IgG from the corresponding species was used as negative control. The Chromatin-antibody complexes were pulled down using Protein G Dynabeads (Life Technologies). The isolated DNA was purified and tested for successful enrichment using quantitative PCR against known loci. Illumina sequencing libraries were prepared using Illumina TruSeq adapters and the enzymes specified in 2. Libraries of the size range of 350 to 650 bp were excised from an agarose gel and cleaned up using the Qiagen gel extraction kit. Libraries were PCR amplified for 14 cycles. Four to fives libraries were pooled on one HiSeq2000 lane and sequenced using 2x100 bp.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
108049466
Reads aligned (%)
98.2
Duplicates removed (%)
40.5
Number of peaks
1794 (qval < 1E-05)

hg19

Number of total reads
108049466
Reads aligned (%)
97.6
Duplicates removed (%)
40.9
Number of peaks
884 (qval < 1E-05)

Base call quality data from DBCLS SRA