Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BCL11A

Cell type

Cell type Class
Lung
Cell type
LK-2
Primary Tissue
Lung
Tissue Diagnosis
Carcinoma Squamous Cell

Attributes by original data submitter

Sample

Alias
E-MTAB-6958:LK2_BCL11A-Sh1_SOX2
Broker name
ArrayExpress
Description
Protocols: LK-2 cells were cultured in RPMI (gibco) supplemented with 10% fetal bovine serum and 1% Penicillin/Streptomycin. ChIP-Seq was done exactly as described in (Schmidt, D., et al. ChIP-seq: Using high-throughput sequencing to discover protein-DNA interactions. Methods 48, 240-248 (2009)). Briefly 2 x 15cm plates per cell line were formaldehyde crosslinked, nuclear fraction was isolated and chromatin sonicated using Bioruptor Pico (Diagenode). Libraries were produced at the Wellcome Trust Sanger Institute sequencing facility. Each library was split into two and run on separate lanes
ENA checklist
ERC000011
INSDC center alias
UNIVERSITY OF CAMBRIDGE
INSDC center name
UNIVERSITY OF CAMBRIDGE
INSDC first public
2018-07-05T17:03:08Z
INSDC last update
2018-07-03T14:40:41Z
INSDC status
public
SRA accession
ERS2596308
Sample Name
ERS2596308
Title
LK2_BCL11A-Sh1_SOX2
cell_line
LK-2
disease
squamous cell lung carcinoma
organism
Homo sapiens
organism part
lung

Sequenced DNA Library

library_name
LK2_BCL11A-Sh1_SOX2_p
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
LK-2 cells were cultured in RPMI (gibco) supplemented with 10% fetal bovine serum and 1% Penicillin/Streptomycin. ChIP-Seq was done exactly as described in (Schmidt, D., et al. ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions. Methods 48, 240-248 (2009)). Briefly 2 x 15cm plates per cell line were formaldehyde crosslinked, nuclear fraction was isolated and chromatin sonicated using Bioruptor Pico (Diagenode). Libraries were produced at the Wellcome Trust Sanger Institute sequencing facility. Each library was split into two and run on separate lanes

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
114140318
Reads aligned (%)
178.3
Duplicates removed (%)
7.4
Number of peaks
32329 (qval < 1E-05)

hg38

Number of total reads
114140318
Reads aligned (%)
180.4
Duplicates removed (%)
7.0
Number of peaks
33816 (qval < 1E-05)

Base call quality data from DBCLS SRA