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
mouse adipocyte
cell type
3T3L1
epitope
WCE
antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
anti-Ebf1 antibody (Abnova H00001879-M01) was used to pick up Ebf1- bound regions. DNA fragments were repaired to blunt ends by T4 DNA polymerase and phosphorylated with T4 Polynucleotide kinase using the END-IT kit (Epicentre). Then, a single ?A? base was added to 3? ends with Klenow (3??5? exo?, 0.3 U/µl). Double-stranded Solexa adaptors (75 bp with a ?T? overhang) were ligated to the fragments with DNA ligase (0.05 U/µl). Ligation products between 275 and 700 base pairs were gel purified on 2% agarose to remove unligated adaptors, and subjected to 18 PCR cycles. Completed libraries were quantified with PicoGreen (As decribed in PMID: 17603471).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
52862313
Reads aligned (%)
96.9
Duplicates removed (%)
24.8
Number of peaks
356 (qval < 1E-05)

mm9

Number of total reads
52862313
Reads aligned (%)
96.6
Duplicates removed (%)
24.8
Number of peaks
617 (qval < 1E-05)

Base call quality data from DBCLS SRA