Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KDM1A

Cell type

Cell type Class
Blood
Cell type
OCI-LY1
NA
NA

Attributes by original data submitter

Sample

source_name
OCI-LY1 cells (lymphoma)
cell line
OCI-Ly1
antibody
LSD1
sirna
control siRNA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Briefly OCI-Ly1 were fixed, lysed, and sonicated to generate fragments less than 400 bp. Sonicated lysates were incubated with antibodies against LSD1 (abcam 17721), BCL6 (Santa Cruz N3, sc-858), H3K4me1 (abcam, ab8895) or IgG control (abcam, ab171870) and after increasing stringency washes immunocomplexes were recovered and DNA was isolated. 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 (quantified using Qubit 2.0 fluorometer, Invitrogen) was end repaired by conversion of overhangs to phosphorylated blunt ends. A' bases were added to the 30 ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments. After adaptor ligation DNA was separated by electrophoresis and size selected by isolating a gel band of 250 ± 25bp. Size selected fragments were PCR amplified for 15cycles using Illumina genomic DNA primers 1.1 and 1.2 with the following program (30 s at 98oC, 15cycles of 10 at 98oC, 30 s at 65oC, 30 s at 72oC and 5min extension at 75oC). Q-PCR was repeated to confirm retention of relative enrichment.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
54122363
Reads aligned (%)
46.2
Duplicates removed (%)
51.0
Number of peaks
8606 (qval < 1E-05)

hg38

Number of total reads
54122363
Reads aligned (%)
47.9
Duplicates removed (%)
49.7
Number of peaks
8486 (qval < 1E-05)

Base call quality data from DBCLS SRA