Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Embryonic fibroblast
Cell type
3T3-L1
Tissue
Embryo
Cell Type
Fibroblast

Attributes by original data submitter

Sample

source_name
3T3L1
cell line
3T3L1
chip antiboy
WCE
treatment
TNF
time
2H

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The chromatin was then fragmented to a size range of ~200 to 600 bp using a Branson 250 digital sonifier (sonication conditions were separately optimized for each sample). Solubilized chromatin was then diluted and incubated with 1-2 ug antibody overnight at 4°C. Immune complexes were captured with ~ 0.02 ml protein A-sepharose, washed and eluted. Enriched chromatin was then subjected to crosslink reversal and proteinase K digestion at 65°C, phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. Isolated ChIP DNA was resuspended in RNAase treated water and quantified using the Qubit assay (Invitrogen). ChIP assays were performed using the following antibodies: H3K4me1 (Abcam ab8895, lot 38311/659352, H3K4me3 (Milipore 07-473, lot DAM1623866), H3K27ac (Active Motif 39133, lot 31610003), H3K36me3 (Abcam ab9050, lot 499302, H3K27me3 (Millipore 07-449, lot DAM1514011), H3K79me2 (Cell Signaling 9757, lot 1).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
42736277
Reads aligned (%)
91.7
Duplicates removed (%)
18.0
Number of peaks
689 (qval < 1E-05)

mm9

Number of total reads
42736277
Reads aligned (%)
91.4
Duplicates removed (%)
17.9
Number of peaks
797 (qval < 1E-05)

Base call quality data from DBCLS SRA