Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
EBF1

Cell type

Cell type Class
Adipocyte
Cell type
Adipose stromal cell
NA
NA

Attributes by original data submitter

Sample

source_name
hASC_anti_EBF1
cell type
Adipose stromal cell (ASC) adipocyte
chip antibody
custom-made EBF1 antibody (rabbit)
chip antibody vendor
Abmart, P.R.China

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were harvested and nuclear fractions were enriched by a brief sonication in lysis buffer . Then protein-DNA complexes were isolated with antibody. ChIP-sequencing libraries were prepared using NEBnext chip-seq library Prep master mix set (New England Biolabs, USA) from 5 ng of anti-EBF1 and anti-IgG ChIP DNA according to manufacturer's protocol.The concentration of the library was determined by Nanodrop spectrophotometer (Thermo Fisher Scientific Inc.) and 10 pmol of the DNA was applied for one flow-cell lane.samples were indexed with DNA barcodes and 3 different samples were multiplexed in one library and sequenced using Illumina HiSeq 2000 (single 36 bp reads). Barcode for IgG sample is ATTT and for EBF1 sample is GCCT in replicate 1 In replicate2, barcode for IgG sample is ACAT and for EBF1 sample is TAAT .

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
45946783
Reads aligned (%)
41.2
Duplicates removed (%)
37.6
Number of peaks
2733 (qval < 1E-05)

hg38

Number of total reads
45946783
Reads aligned (%)
42.0
Duplicates removed (%)
37.1
Number of peaks
2805 (qval < 1E-05)

Base call quality data from DBCLS SRA