Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Neural
Cell type
Neural progenitor cells
NA
NA

Attributes by original data submitter

Sample

source_name
neural progenitor cells
cell type
neural progenitor cells
genotype
wild type
pulldown
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed for 10 minutes with 1% Formaldehyde at room temperature and incubated for 10 min on ice in the presence of 1.25M Glycine. Cells were harvested and treated for 10 min with 10mM EDTA, 10mM TRIS, 0.5mM EGTA and 0.25% Triton X-100 and 10 min in 1mM EDTA, 10mM TRIS, 0.5mM EGTA and 200mM NaCl with subsequent nuclear lysis in 50mM HEPES, 1mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.1% SDS and 150 mM NaCl. DNA was purified with Qiagen columns for PCR Purification. Crosslinked chromatin was subjected to sonication in a Bioruptor instrument (Diagenode). ProteinA (Invitrogen) pre-cleared chromatin was either saved as input or incubated with blocked (1%CFSG, 100ng tRNA) Streptavidin-M280 (Invitrogen) magnetic beads over night at 4°C. Beads were washed and treated with RNaseA for 30 min at 37°C, Proteinase K for 3 hours at 55°C then de-crosslinked over night at 65°C.  Libraries were prepared according to the NEBnext protocol with size selection of the fragments (150-200bp) before adaptor ligation and PCR amplification with indexed primers.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
74473206
Reads aligned (%)
96.8
Duplicates removed (%)
10.6
Number of peaks
669 (qval < 1E-05)

mm9

Number of total reads
74473206
Reads aligned (%)
96.6
Duplicates removed (%)
10.6
Number of peaks
736 (qval < 1E-05)

Base call quality data from DBCLS SRA