Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NELFE

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
NELF-E Knockdown, vehicle, GFP, NELFE
cell type
human breast cancer cells
cell line
MCF-7
chip antibody
NELFE

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
PARP-1 ChIP-seq: Following mock ADP-ribosylation in intact nuclei from MEFs as described above, the nuclei were crosslinked with 0.5% formaldehyde and clicked to biotin. Nuclei were sonicated in a water bath sonicator to a DNA fragment size distribution of 200 to 500 bp and chromatin was used for chromatin immunoprecipitation. Click-ChIP-seq: Following 8-Bu(3-yne)T-ADP-ribosylation in intact nuclei from MEFs as described above, the nuclei were crosslinked with 0.5% formaldehyde and clicked to biotin. Nuclei were sonicated in a water bath sonicator to a DNA fragment size distribution of 200 to 500 bp and bound to streptavidin-conjugated magnetic beads. Following extensive washing, the beads were collected in a magnetic field and de-crosslinked overnight at 65°C. DNA was to be sequenced was recovered by magnetic separation from the beads and purified by PCIAA extraction and ethanol precipitation. All Other ChIP-seq: Cells were sonicated in a water bath sonicator to a DNA fragment size distribution of 200 to 500 bp and chromatin was used for chromatin immunoprecipitation. After purification, 50 ng of ChIP’d DNA for each condition was used to generate libraries for sequencing, as previously described {Robertson, 2007 #41}, with some modifications. Briefly, the DNA was end-repaired and a single “A”-base overhang was added using the Klenow fragment of E. coli DNA polymerase. The A-modified DNA was ligated with Ilumina sequencing adaptors using the Illumina TruSeq DNA Sample Prep Kit. The ligated DNA (250 ± 25 bp) was size-selected by agarose gel electrophoresis and extraction, amplified by PCR, and purified using AmPure beads (Beckman Coulter). The final libraries were subjected to QC (size, purity, adapter contamination) and sequenced using an Illumina HiSeq 2000 per the manufacturer’s instructions.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
11276775
Reads aligned (%)
175.4
Duplicates removed (%)
2.4
Number of peaks
5474 (qval < 1E-05)

hg38

Number of total reads
11276775
Reads aligned (%)
176.9
Duplicates removed (%)
2.3
Number of peaks
5481 (qval < 1E-05)

Base call quality data from DBCLS SRA