Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Embryo
Cell type
E17.5 embryos
NA
NA

Attributes by original data submitter

Sample

source_name
Embryonic 17.5
cell/region
Whole brain
chip antibody
Input
differentiation status
Embryonic 17.5

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cell pellets (>10 x 10^6/n) and brain tissues were crosslinked and quenched. Samples were washed thoroughly before being subjected to lysis and sonication. Samples were then incubated with specific antibodies (7.5 μg/sample) bound to M-280 Dynabeads on a rotator at 4°C overnight. The following day, immunoprecipitates were washed, eluted and reverse crosslinked. Following RNA and protein digestion, DNA fragments were purified using a Qiagen PCR purification kit. RNA and ChIP libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
33162580
Reads aligned (%)
98.2
Duplicates removed (%)
12.2
Number of peaks
483 (qval < 1E-05)

mm9

Number of total reads
33162580
Reads aligned (%)
98.0
Duplicates removed (%)
12.2
Number of peaks
508 (qval < 1E-05)

Base call quality data from DBCLS SRA