Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SUZ12

Cell type

Cell type Class
Lung
Cell type
Lu-130
NA
NA

Attributes by original data submitter

Sample

source_name
Lu130_Suz12_ChIPSeq
cell line
Lu130
cell type
Small cell lung cancer cell line
chip antibody
Suz12 (D39F6, Cell Signaling, rabbit monoclonal)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked with 1% formaldehyde for 10 min at room temperature and were prepared for ChIP. Briefly, cells were crosslinked with 1% formalin for 10 min, and crosslinked cell lysates underwent fragmentation by sonication and incubated with antibodies bound to protein A-sepharose beads (50% slurry) overnight at 4 ºC. The beads were washed several times and eluted with elution buffer (1% SDS, 0.1 M NaHCO3). The eluates were treated with 1.5 μg of pronase 2 hr at 42 ºC then incubated at 65 ºC over night to reverse the crosslinks. The ChIP’ed DNA was purified by phenol/chroloform treatment and precipitated with LiCl and 70% ethanol. Sample preparation for ChIP-seq was performed according to the manufacturer's instructions (Illumina). Briefly, size fractionated DNA was extracted and a single adenosine was added using Klenow exo– (3' and 5' exo minus; Illumina). Illumina adaptors were then added and DNA was subjected to 20 cycles of PCR according to manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
26519170
Reads aligned (%)
86.2
Duplicates removed (%)
7.1
Number of peaks
1134 (qval < 1E-05)

hg38

Number of total reads
26519170
Reads aligned (%)
88.6
Duplicates removed (%)
5.5
Number of peaks
908 (qval < 1E-05)

Base call quality data from DBCLS SRA