Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NELFA

Cell type

Cell type Class
Uterus
Cell type
HeLa
Primary Tissue
Cervix
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
HeLa cells
cell line
HeLa
antibody
NELF-A (A-20) (Santa Cruz, sc-23599)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
HeLa cells were grown to 0.5 million cells/ml and crosslinked with 1% formaldehyde in media for 10 minutes before glycine addition to 125 mM. After washing and lysis, cells were sonicated in RIPA buffer (50 mM Tris, pH 7.6; 150 mM NaCl; 1 mM EDTA; 0.25% sodium deoxycholate; 1% IGEPAL CA-630) on ice using a Fisher Model 550 Sonic Dismembrator. For each ChIP, sonicated supernatant from 5 million cells was incubated at 4°C overnight with 10 µg of Pol II (Santa Cruz, sc-899), NELF (sc-23599), or DSIF (sc-28678) antibody, and then 1 hr with 50 µl Protein G-Sepharose bead slurry (Sigma, P3296). Beads were washed in columns with 15 ml ice cold RIPA buffer and rinsed with 10 ml ice cold PBS. Immunocomplexes were eluted, incubated at 65°C overnight to reverse crosslinks, and treated with RNase A and Proteinase K. DNA was isolated by MinElute PCR purification kit (QIAGEN, 28004). Library preparation was performed by the University of Iowa DNA Facility using the Ovation SP Ultralow DR Multiplex System (Nugen, 8033-32) for Mondrian.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
31619578
Reads aligned (%)
29.8
Duplicates removed (%)
84.6
Number of peaks
2474 (qval < 1E-05)

hg38

Number of total reads
31619578
Reads aligned (%)
31.7
Duplicates removed (%)
83.8
Number of peaks
2756 (qval < 1E-05)

Base call quality data from DBCLS SRA