Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

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
CTCF HiChIP-seq
cell line
lymphoblastoid cell lines (LCLs)
disease
Systemic lupus erythematosus
race
European-American
gender
female
chip antibody
CTCF (Cell Signaling #3418, clone D31H2)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, we crosslinked 10 million Epstein-Barr Virus (EBV)-transformed B cells with 1% formaldehyde for 5 minutes followed by careful cell lysis using the truChIP Chromatin Shearing Kit (Covaris). Nuclei were isolated and fragmented using a Covaris E220e sonicator   with the following operating conditions: Peak Incident Power: 140 Watts; duty cycle: 5%; cycles per burst: 200; treatment time: 15 minutes; setpoint temperature: 6°C). Crosslinked protein/DNA was immunoprecipitated using H3K27ac (rabbit polyclonal, Abcam #ab4729, 20ug/ml)  or H3K4me1 (rabbit polyclonal, Abcam #ab8895, 20ug/ml) antibodies on Protein A + G immunomagnetic beads. Anti-acetyl histone H3 antibodies and isotype matched IgG antibodies were included as positive and negative controls, respectively. An aliquot of the fragmented chromatin, not subjected to immunoprecipitation, was also used as an input control. Chromatin crosslinks were reversed, then protein was digested with proteinase K and DNA fragments were purified using Ampure XP beads (Beckman Coulter). For HiChIP-sequencing, We crosslinked 10 million EBV-transformed B cells using 1% formaldehyde for 10 minutes at room temperature. Intact nuclei were isolated and digested using the MboI restriction enzyme for 4 hours at 37C. DNA fragment ends were filled and labeled with dCTP, dGTP, dTTP and biotin-dATP. Proximity ligation was performed at room temperature overnight. Following the in situ ligation, we fragmented the ligated chromatin as previously described64. Crosslinked protein/DNA was immunoprecipitated using antibodies to H3K27ac (rabbit polyclonal, Abcam #ab4729, 20ug/ml) and CTCF (rabbit mAb, clone D31H2, Cell Signaling #3418, 20ug/ml) and then purified by Protein A+G immunomagnetic beads. The amount of MboI enzyme, antibody, and beads are determined by the number of cells in each sample64. After immunoprecipitation, DNA was eluted from the beads by incubating at 65C for 4 hours with 5% Proteinase K. DNA was purified by Zymo DNA Clean & Concentrator Column and quantified by Qubit High Sensitivity Assay Kit. RNA was isolated from each LCL using TRIzol. DNA and RNA libraries were prepared for sequencing using standard Illumina protocols. DNA libraries were sequenced on the Illumina NextSeq 500 using 75bp single-end reads. RNA libraries were sequenced on the Illumina HiSeq 3000 using 75bp paired-end reads with 10 samples per lane, yielding 30 million reads per sample.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
92390968
Reads aligned (%)
139.1
Duplicates removed (%)
5.1
Number of peaks
15816 (qval < 1E-05)

hg38

Number of total reads
92390968
Reads aligned (%)
140.2
Duplicates removed (%)
5.0
Number of peaks
15447 (qval < 1E-05)

Base call quality data from DBCLS SRA