Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Neural
Cell type
HSR-GBM1A
NA
NA

Attributes by original data submitter

Sample

source_name
DNA from glioblastoma stem cells
cell line
GBM1A
cell type
glioblastoma stem cell line

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were subjected to ChIP using MAGnify ChIP system (Invitrogen) following manufacturer’s protocol. KLF9 bound DNA was immunoprecipitated using mouse anti-FLAG M2 antibody (Sigma-Aldrich) and Dynabeads Magnetic Beads (Life Technologies). ChIP-enriched DNA was used for PCR and deep sequencing. ChIP-enriched DNA or input DNA (10ng each) was subjected to library preparation using ChIP-Seq DNA Sample Prep Kit (Illumina) following manufacturer’s protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
197596050
Reads aligned (%)
92.1
Duplicates removed (%)
78.4
Number of peaks
39185 (qval < 1E-05)

hg19

Number of total reads
197596050
Reads aligned (%)
91.4
Duplicates removed (%)
80.1
Number of peaks
40165 (qval < 1E-05)

Base call quality data from DBCLS SRA