Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NOTCH1

Cell type

Cell type Class
Neural
Cell type
GSC8
NA
NA

Attributes by original data submitter

Sample

source_name
NICD_GSC8
cell line
Patient-derived neurosphere line GSC8
drug treatment
none
chip-antibody
cleaved Notch1 (Val1744) (CST, 4147, lot 4)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells was fixed in 1% formaldehyde and snap frozen in liquid nitrogen and stored at -80ºC for at least overnight. Sonication of crosslinked cells was calibrated such that DNA was sheared to between 400bp and 2000bp. ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3’ A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
19155820
Reads aligned (%)
98.9
Duplicates removed (%)
0.2
Number of peaks
249 (qval < 1E-05)

hg38

Number of total reads
19155820
Reads aligned (%)
98.9
Duplicates removed (%)
0.2
Number of peaks
108 (qval < 1E-05)

Base call quality data from DBCLS SRA