Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Embryonic fibroblast
Cell type
MEF
Tissue
Embryonic Fibroblast
Lineage
primaryCells
Description
Mouse Embryonic Fibroblast

Attributes by original data submitter

Sample

source_name
mouse embryonic fibroblasts
strain
129/C57 dams x CAST sires
tissue
E13.5 mouse embryo derived fibroblasts
genotype
Setdb1+/+ X/Y
shRNA
Nonsilencing
sequencing protocol
single-end
chip antibody
N/A

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, nuclei were isolated from formaldehyde crosslinked NSCs and chromatin was fragmented by sonication. Chromatin immunoprecipitation was performed with corresponding antibodies. DNA was extracted from the immunoprecipitated fraction following reverse-crosslinking. Sequencing libraries was generated with Illumina's TruSeq DNA Sample Preparation Kit according to manufacturer's instruction.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
18045204
Reads aligned (%)
92.4
Duplicates removed (%)
9.6
Number of peaks
297 (qval < 1E-05)

mm9

Number of total reads
18045204
Reads aligned (%)
92.2
Duplicates removed (%)
9.7
Number of peaks
246 (qval < 1E-05)

Base call quality data from DBCLS SRA