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
3T3-L1 cells
strain
Swiss albino
cell type
preadipocyte cell
cell line
3T3-L1
chip-antibody
sigmal Aldrich-i5006

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde for 10 min at 37◦C; then, crude nuclei were purified. Chromatin was fragmented by sonication with a Bioruptor UCD-300 (Diagenode) to obtain fragments 200–800 bp in length. For each ChIP assay, 2–5 ug of antibodies were added and incubated at 4◦C overnight. ChIP DNA was quantified with a Qubit fluorometer using the Quant-iT dsDNA HS assay kit ChIP-seq libraries were generated following the procedue described in "TELP, a sensitive and versatile library construction method for next-generation sequencing" by Peng X, Wu J, Brunmeir R, Kim SY, Zhang Q, Ding C, Han W, Xie W, Xu F., published in Nucleic Acids Res. 2015 Mar 31;43(6):e35. doi: 10.1093/nar/gku818. Epub 2014 Sep 15.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
4384223
Reads aligned (%)
99.1
Duplicates removed (%)
0.0
Number of peaks
35 (qval < 1E-05)

mm9

Number of total reads
4384223
Reads aligned (%)
99.1
Duplicates removed (%)
0.0
Number of peaks
35 (qval < 1E-05)

Base call quality data from DBCLS SRA