Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
YY1

Cell type

Cell type Class
Blood
Cell type
Lymphoblastoid cell line
Tissue
blood
Lineage
mesoderm
Description
parental cell type to lymphoblastoid cell lines

Attributes by original data submitter

Sample

source_name
HEP14_00120_YY12
cell type
Immortalized lymphoblastoid cell line (LC)
genotype/variation
YY1-mutated (p.Lys179*)
chip antibody
YY1, (H-414)X sc-1703X lot#A1414 rabbit polyclonal
chip target
YY1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation was performed as previously described (Frank et al., 2001) with some modification. Briefly, LCL were centrifuged at 150g for 5 minutes, an average of 150 x 106 LCLs were re-suspended in formaldehyde 1% in PBS for cross-linking. To stop the cross-linking reaction glycine was added to the final concentration 125 mM. Cells were re-suspended using ChIP SDS buffer (0.5% SDS, 5 mM EDTA, NaCl 100mM and 50 mM Tris-HCl at pH 8.1). Pellets were collected by centrifuging at 400g for 30 min and re-suspended in IP buffer (0.5% SDS, 5 mM EDTA, NaCl 100mM and 50 mM Tris-HCl at pH 8.6, Triton X-100 1,5%). To obtain a bulk of 300 bp DNA fragments, cells were sonicated using the Branson digital sonifier (Emerson Industrial Automation). Chromatin was quantified using Bradford protein assay (Bio-Rad). To immuno-precipitate YY1, 1 mg of total proteins was incubated with YY1 antibodies (sc-1703 or sc-281, Santa-Cruz Biotechnologies). For H3K27Ac chromatin immunoprecipitation, 100µg of proteins were immuno-precipitated using the antibody ab4729 (Abcam). Chromatin was incubated overnight with antibody at 4°C. G-Sepharose 4B (Thermo Fisher) beads were incubated with chromatin and antibodies mix for 4 hours at 4°C and followed by washes using low and high salt buffers (1% Triton X-100, 0.1% SDS, 150mM or 500mM NaCl , 2mM EDTA, 20 mM Tris-HCl ph8). Decross-linking was performed at 65°C for 3 hours. DNA was collected with QIAquick PCR Purification Kit (Qiagen). Libraries were prepared as already described (Blecher-Gonen et al., 2013) with adaptations for the automated system Biomek FX.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
32493003
Reads aligned (%)
89.2
Duplicates removed (%)
5.3
Number of peaks
2077 (qval < 1E-05)

hg38

Number of total reads
32493003
Reads aligned (%)
91.9
Duplicates removed (%)
3.8
Number of peaks
1749 (qval < 1E-05)

Base call quality data from DBCLS SRA