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-LTR-Luciferase cells
cell type
HeLa-LTR-Luciferase cells
chip antibody
Anti-NELF-E
chip antibody vendor
Millipore

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immuno-precipitations (ChIPs) were performed as described in Whyte et al. 201228 using ~100 x 106 HeLa-LTR-Luciferase cells as starting material with the exception of an additional nuclei purification step. Briefly, cells were thawed and resuspended in 1ml Buffer A (0.3M SUCROSE, 60mM KCl, 15mM NaCl, 5mM MgCl, 0.1 mM EGTA, Tris-HCl pH=7.5, 0.2mM PMSF), 1ml Buffer B (0.3M SUCROSE, 0.2% NP40, 60mM KCl, 15mM NaCl, 5mM MgCl, 0.1 mM EGTA, Tris-HCl pH=7.5, 0.2mM PMSF) was then added and incubated for 7min on ice, laid over a 8ml cushion of Buffer C (1.2M SUCROSE, 0.2% NP40, 60mM KCl, 15mM NaCl, 5mM MgCl, 0.1 mM EGTA, Tris-HCl pH=7.5, 0.2mM PMSF) and spinned for 20min at 3000rpm on 4 C. Pelleted nuclei were resuspended in 3ml Lysis buffer, incubated for 1 hour, sonicated (Misonix sonicator with the following settings: micro tip, 30sec on, 2min off, amplitude 70, 7min total sonication time). 10ng, as quantified by Qubit dsDNA HS Assay Kit (Life Technologies), of input and of immuno-precipitated-material was used for library preparation. Librairies were prepared using Illumina ChIP-Seq sample prep kit (non-multiplexed libraries) or TruSeq ChIP Sample Prep Kit (multiplexed libraries) according to manufacturer’s instructions. Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component. Data quality was assessed using fastqc from the Babraham Institute and the Illumina software SAV (Sequence Analysis Viewer). De-multiplexing and alignment were performed using Illumina's sequencing analysis software (CASAVA 1.8.2).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
250308922
Reads aligned (%)
27.4
Duplicates removed (%)
70.2
Number of peaks
20153 (qval < 1E-05)

hg38

Number of total reads
250308922
Reads aligned (%)
29.3
Duplicates removed (%)
68.3
Number of peaks
20959 (qval < 1E-05)

Base call quality data from DBCLS SRA