Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Naa10

Cell type

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

Attributes by original data submitter

Sample

source_name
Naa10p-ChIP_KO-mES
genotype
Naa10-/Y
cell type
Blastocyst-derived embryonic stem cell
strain
C57BL6/JF1 F1
chip antibody
rabbit polyclonal Naa10p (made in-house)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The mES cells were fixed with 1% formaldehyde for 10 min, followed by 0.125 M glycine quenching for 5 min. Cells were lysed in 1% SDS, 10 mM EDTA and 50 mM Tris-HCl (pH 8.0) and the DNA was fragmented by sonication to approximately 150-300 bp (Bioruptor, Diagenode). Immunoprecipitation was performed with 10 μg of rabbit polyclonal Naa10p for overnight at 4 °C. Antibody-bound samples were isolated by protein G agarose beads (Active Motif), washed, eluted and reverse cross-linked. ChIPed DNA was extracted by phenol/chloroform, ethanol precipitated and quantified by Qubit assay (Invitrogen). The ChIPed DNA library for NextSeq 500 sequencing was constructed using the NEBNext DNA library Prep Master Mix Set for Illumina (New England Bio Labs) according to the manufacturer's instruction. Briefly, the ChIPed DNA was blunt ended and a dA tail was added. The DNA with dA overhangs was ligated with multiplex oligos for illumina with individual index sequences (New England Bio Labs). Adaptor-ligated DNA was amplified by PCR for 12 cycles, followed by size selection using magnetic beads (KAPA Pure Beads, KAPA Biosystem). The purified DNA was quantified by Qubit assay (Invitrogen) and qualified by Agilent Bioanalyzer.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
37359262
Reads aligned (%)
72.2
Duplicates removed (%)
15.8
Number of peaks
387 (qval < 1E-05)

mm9

Number of total reads
37359262
Reads aligned (%)
72.0
Duplicates removed (%)
15.8
Number of peaks
489 (qval < 1E-05)

Base call quality data from DBCLS SRA