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
Input-Pretreated-0h-MEF
cells
MEFs
strain
C58BL/6
genotype
H3.3-HA knock-in
chip antibody
input

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lisates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. ChIP-seq libraries were constructed using a Mondrian SP (NuGEN Technologies Inc.) and the Ovation SP Ultralow Library system (NuGEN). Fragments ranging from 250 to 450 bp were selected for single-read sequencing on a HiSeq2000 (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
17412281
Reads aligned (%)
90.2
Duplicates removed (%)
11.2
Number of peaks
391 (qval < 1E-05)

mm9

Number of total reads
17412281
Reads aligned (%)
89.9
Duplicates removed (%)
11.3
Number of peaks
449 (qval < 1E-05)

Base call quality data from DBCLS SRA