Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BCOR

Cell type

Cell type Class
Blood
Cell type
OCI-LY1
NA
NA

Attributes by original data submitter

Sample

source_name
Human DLBCL cell line
cell line
OCI-LY1
chip antibody
BCOR

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture's instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. A' bases were added to the 3'ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments. After adapter ligation DNA was separated by electrophoresis and size selected by isolating a gel band of 250±25bp. This fragment range corresponds to a ChIP fragment range of about 158±25bp. Size selected fragments were PCR amplified for 15cycles using Illumina genomic DNA primers 1.1 and 1.2 with the following program (30s at 98oC, 15cycles of 10 at 98oC, 30s at 65oC,30s at 72oC and 5min extension at 75oC). Libraries were quantified and validated using Agilent Technologies 2100 Bioanalyser for size, concentration and purity. Q-PCR was repeated to confirm retention of relative enrichment. RNAseq: Three ug of total RNA was isolated from OCI-Ly1 cells transfected using Nucleofector 96-well Shuttle system (Lonza) with siBCL6 (HSS100968) or siNT (46-2001) (Stealth RNAi, Invitrogen) at 24hrs and 48hrs after nucleofection. RNAeasy Plus Kit (Qiagen) that included a gDNA elimination step was used for RNA isolation. RNA concentration and purity were determined using Nanodrop (Thermo Scientific) and integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Libraries were generated using mRNA-seq sample prep kit by Illumina. Briefly, mRNA was selected by two rounds of purification using magnetic polydT beads and then fragmented. First strand synthesis was performed using random oligos and SupersciptIII (Invitrogen). After second strand synthesis a 200bp paired-end library was prepared following the Illumina paired-end library preparation protocol.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
241626464
Reads aligned (%)
75.2
Duplicates removed (%)
21.7
Number of peaks
30943 (qval < 1E-05)

hg38

Number of total reads
241626464
Reads aligned (%)
78.0
Duplicates removed (%)
19.5
Number of peaks
32161 (qval < 1E-05)

Base call quality data from DBCLS SRA