Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Neural
Cell type
Neural Stem Cells
MeSH Description
Self-renewing cells that generate the main phenotypes of the nervous system in both the embryo and adult. Neural stem cells are precursors to both NEURONS and NEUROGLIA.

Attributes by original data submitter

Sample

source_name
PDGF Neural Stem Cells
cell type
PDGF Neural Stem Cells
genotype
H3WT

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature. Glycine was added at a final concentration of 125 mM to quench the formaldehyde. Cells were then washed twice with PBS and harvested in SDS buffer (50 mM Tris at pH 8.1, 0.5% SDS, 100 mM NaCl, 5 mM EDTA). Cells were pelleted down, resuspended in Triton-X IP buffer (100 mM Tris at pH 8.6, 0.3% SDS, 1.7% Triton X-100, and 5 mM EDTA) and the chromatin was sonicated to get the DNA fragments of <1000 bp with average DNA fragment size of 300 bp. 500 μg chromatin was used to perform chromatin immunoprecipitation (ChIP) and 10 ng of ChIP DNA was used to make library using NEBNext Ultra DNA library kit for illumine (E7370; New England Biolabs) according to supplier’s instructions. The libraries were sequenced using Illumina HiSeq2500 sequencer.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
30427365
Reads aligned (%)
98.4
Duplicates removed (%)
12.1
Number of peaks
402 (qval < 1E-05)

mm9

Number of total reads
30427365
Reads aligned (%)
98.2
Duplicates removed (%)
12.1
Number of peaks
446 (qval < 1E-05)

Base call quality data from DBCLS SRA