Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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
whole cell
cell type
neural stem cell (NSC)
cell cycle stage
asynchronization
chip antibody
input

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed the same way as ChIP assay, except that DNA was recovered from the protein G complex using elution buffer (10 mM Tris at pH 8.0, 10 mM EDTA at pH 8.0, 1% SDS, 150 mM NaCL, 5 mM DTT). DNA was subsequently purified using Qiagen Mini Elute PCR purification kit. Total RNA was extracted using the miRNeasy Mini Kit (Qiagen #217004). The ChIP DNA libraries were prepared with the Ovation Ultralow DR Multiplex system (NuGEN). RNA-seq libraries were prepared with ovation RNA-seq system v2 kit (NuGEN).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
59615742
Reads aligned (%)
95.3
Duplicates removed (%)
8.8
Number of peaks
575 (qval < 1E-05)

hg38

Number of total reads
59615742
Reads aligned (%)
96.2
Duplicates removed (%)
8.3
Number of peaks
1327 (qval < 1E-05)

Base call quality data from DBCLS SRA