Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NELFE

Cell type

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

Attributes by original data submitter

Sample

source_name
HeLa_shINTS11_dox_NELF-E_ChIP-seq
cell line
HeLa
cell type
cervical adenocarcinoma
cell source
ATCC#CCL-2
modification
Tet-pLKO_shINTS11 stable cells
chip antibody
NELF-E [Santa Cruz #sc-377052]

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq was performed as previously described (Gardini, A. et al. 2014, Lai, F. et a.l 2015, Yue, J. et. al 2017) with slight modifications. 2 x 107 cells were crosslinked in 1% formaldehyde for 10 minutes at room temperature and quenched with 125 mM glycine. Samples were resuspended in ChIP lysis buffer (20 mM Tris-HCl, 50 mM NaCl, 0.1% SDS, 0.5% Triton-X-100, 1 mM EDTA) and sonicated in a Covaris M220 focused sonicator until chromatin fragments of 150-300 bp were produced. Protein A/G magnetic beads were bound with antibody and incubated with 1 mg of sonicated chromatin overnight. The following day, beads were washed twice with Mixed Micelle Buffer (150 mM NaCl, 1% Triton X-100, 0.2% SDS, 20 mM Tris-HCl, 5 mM EDTA, 65% sucrose), Buffer 500 (500 mM NaCl, 1% Triton X-100, 0.1% Na deoxycholate, 25 mM HEPES, 10 mM Tris-HCl, 1 mM EDTA), LiCl/detergent wash (250 mM LiCl, 0.5% Na deoxycholate, 0.5% NP-40, 10 mM Tris-HCl, 1 mM EDTA), and eluted in Decrosslinking Buffer (20 mM Tris-HCl, 300 mM NaCl, 0.5% SDS, 1 mM EDTA) at 65 °C. Eluates were treated with RNAse A for 1 hour at 37 °C and then Proteinase K for 3 hours at 56 °C. The DNA was finally purified by phenol/chloroform and eluted in 1x TE. ChIP-seq libraries were generated using the NEBNext Ultra II DNA library prep kit (New England Biolabs, #E7645S) with at least 10 ng of input DNA.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
46776879
Reads aligned (%)
90.8
Duplicates removed (%)
6.9
Number of peaks
25634 (qval < 1E-05)

hg38

Number of total reads
46776879
Reads aligned (%)
91.3
Duplicates removed (%)
6.9
Number of peaks
25681 (qval < 1E-05)

Base call quality data from DBCLS SRA