Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Fam60a

Cell type

Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA

Attributes by original data submitter

Sample

source_name
Embryonic stem cells
antibody
Fam60a

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
16374194
Reads aligned (%)
95.5
Duplicates removed (%)
10.6
Number of peaks
10079 (qval < 1E-05)

mm9

Number of total reads
16374194
Reads aligned (%)
95.3
Duplicates removed (%)
10.8
Number of peaks
9999 (qval < 1E-05)

Base call quality data from DBCLS SRA