Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Embryonic fibroblast
Cell type
NIH/3T3
Primary Tissue
Embryo
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
NIH/3T3 Tet-On® 3G cells
cell line
NIH/3T3 fibroblast cell line
transduced with
OFP-H3.3A/GFP-H3.3B
genotype
H3.3 Knockdown
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with formaldehyde treatment and chromatin fragmented to 200-300 bp by sonication. ChIP material was blunt-ended and phosphorylated with the End-it-Repair kit (EPICENTRE). Illumina genome sequencing adaptors were ligated with T4 DNA ligase (New England Biolabs) after addition of adenosine nucleotides, using exo-Klenow. Samples were PCR amplified with multiplexed Illumina genomic DNA sequencing primers. PCR products (250 to 450 bp in size) were gel-purified and submitted for Illumina deep sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
64726514
Reads aligned (%)
97.2
Duplicates removed (%)
15.1
Number of peaks
517 (qval < 1E-05)

mm9

Number of total reads
64726514
Reads aligned (%)
96.9
Duplicates removed (%)
15.0
Number of peaks
608 (qval < 1E-05)

Base call quality data from DBCLS SRA