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
cerebral cortex
cell line
CD-1
tissue
cerebral cortex
cell type
Mouse neural stem cell

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed using 107 mouse neural stem cells per reaction. Cells were dissociated by treatment with Accutase and cross-linked in 1% (vol/vol) formaldehyde for 10 min at RT with rotation. Then, 0.125 M glycine was used to quench the cross-linking reaction. Cells were pelleted and washed with ice-cold PBS. Next, nuclei were isolated and a Bioruptor sonicator (Diagenode) was used to shear chromatin DNA. Either 5 ml of OLIG2 antibody (AB9610, Chemicon) or 5 ml of normal rabbit IgG (#2729, Cell Signaling) was added to Dynabeads Protein A (Invitrogen) beads and incubated for 3 h at 4 °C with rotation. Then, the Dynabeads-antibody complexes were incubated with sheared chromatin DNA overnight at 4 °C. After immunoprecipitation, the precipitated complex was treated with RNase A and Proteinase K, and incubated at 65 °C overnight to reverse crosslinks. The ChIP-Seq library was constructed by using DNA SMART ChIP-Seq Kit according to the manufacturer's instructions (Clontech) and was sequenced on the Illumina HiSeq 2000 Sequencer.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
40574139
Reads aligned (%)
92.9
Duplicates removed (%)
11.4
Number of peaks
559 (qval < 1E-05)

mm9

Number of total reads
40574139
Reads aligned (%)
92.8
Duplicates removed (%)
11.4
Number of peaks
544 (qval < 1E-05)

Base call quality data from DBCLS SRA