Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZEB1

Cell type

Cell type Class
Neural
Cell type
NCH421k
NA
NA

Attributes by original data submitter

Sample

Alias
E-MTAB-5541:Zeb1_NCH421k
Broker name
ArrayExpress
Description
Protocols: Cells were cultured as previously described (Conti et al. 2005), using laminin as a media supplement (20ug/mL), and plated at a density of 28,000/cm2 Cells were fixed sequentially with di(N-succimidyl) glutarate and 1% formaldehyde in phosphate buffered saline and then lysed, sonicated and immunoprecipitated, as previously described (Castro et al., 2011), with an anti-ZEB1 antibody DNA libraries were prepared from 10ng of immunoprecipitated DNA according to the standard Illumina ChIP-seq protocol.
ENA checklist
ERC000011
INSDC center alias
Instituto Gulbenkian de Ciencia
INSDC center name
Instituto Gulbenkian de Ciencia
INSDC first public
2018-04-24T17:03:46Z
INSDC last update
2017-03-06T12:10:54Z
INSDC status
public
SRA accession
ERS1580349
Sample Name
ERS1580349
Title
Zeb1_NCH421k
cell_line
D4 glioblastoma derived primary cell line
cell_type
cancer stem-like cell
disease
glioblastoma multiforme
genotype
NCH421k
growth condition
media
organism
Homo sapiens
tumor grading
IV

Sequenced DNA Library

library_name
Zeb1_NCH421k_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cultured as previously described (Conti et al. 2005), using laminin as a media supplement (20ug/mL), and plated at a density of 28,000/cm2 Cells were fixed sequentially with di(N-succimidyl) glutarate and 1% formaldehyde in phosphate buffered saline and then lysed, sonicated and immunoprecipitated, as previously described (Castro et al., 2011), with an anti-ZEB1 antibody DNA libraries were prepared from 10ng of immunoprecipitated DNA according to the standard Illumina ChIP-seq protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
38579646
Reads aligned (%)
65.2
Duplicates removed (%)
33.0
Number of peaks
3025 (qval < 1E-05)

hg38

Number of total reads
38579646
Reads aligned (%)
67.1
Duplicates removed (%)
31.7
Number of peaks
3088 (qval < 1E-05)

Base call quality data from DBCLS SRA