Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Sin3a

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
NIH3T3
antibody
Sin3a

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP, cells were crosslinked in 1% Formaldehyde at room temperature at for 10 min before harvest. Chromatin was sheared to 300-500 bp and DNA-protein complexes were isolated with antibody. Precipitates were digested with RNaseA and Proteinase K and then Phenol-Chloroform purified. For ChIP-Seq, DNA was quantified using the Qubit® dsDNA HS Assay Kit (Invitrogen). 1-5 ng DNA from ChIP experiments were used for library preparation using the Illumina ChIP-Seq sample prep kit (IP-102-1001) and multiplexing oligonucelotide kit (PE-400-1001). For DNA purification steps, DNA SPRI bead (Beckman) cleanup was performed. The quality of the DNA libraries was assessed using a high sensitivity Bioanalyzer Chip (Agilent). Libraries were used for cluster generation and sequencing using HiSeq 2000 (Illumina) with 50 bp read length.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
37301253
Reads aligned (%)
89.8
Duplicates removed (%)
20.1
Number of peaks
548 (qval < 1E-05)

mm9

Number of total reads
37301253
Reads aligned (%)
89.5
Duplicates removed (%)
20.1
Number of peaks
639 (qval < 1E-05)

Base call quality data from DBCLS SRA