Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

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

Attributes by original data submitter

Sample

source_name
mouse embryonic stem cell
genotype
Usp16 WT
cell line
V6.5
cell type
mouse embryonic stem cell
passages
15-20
strain
C57BL/6
chip antibody
Millipore, AP132

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-Seq samples, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody as elaborated in supplemetal methods. For RNA-Seq, TRIzol is used for total RNA purification and RNA samples are subjected to protocol as described in supplemental methods. For ChIP-Seq samples, NEB Next DNA sample prep reagents (New England Biolabs, E6000S/L) were used for end repair, dA-tailing, and adaptor ligation (custom adaptors from Hudson Alpha GSL). The entire volume ligated product was PCR amplified for 15 cycles using Invitrogen's Pfx DNA polymerase using the custom adaptors designed to allow for 96 unique indexes. Size selection was performed on 2% agarose gel. The final library quality was examined by Qubit and Bioanalysis, and real time PCR was performed using KAPA's library quantification kit for Illumina. Each library was diluted to 12.5 pM and clustered using a cBot. Each library was sequenced over 1/6th of a HiSeq 2000 lane following standard Illumina protocols for paired end 50 bp sequencing. For RNA-Seq samples, cDNA library was constructed with TruSeq library generation kits (Illumina). The cDNA ends were repaired, A-tailed, and adaptor ligated for indexing. The cDNA library was then quantitated by real time PCR in a Roche LightCycler 480 with the Kapa Biosystems kit for library quantitation (Kapa Biosystems) prior to cluster generation. Clusters were then generated to yield approximately 725-825 K clusters/mm2 and the density and quality were determined after the first base addition. Paired end 2 x 50bp sequencing runs were performed for all samples.

Sequencing Platform

instrument_model
Illumina Genome Analyzer

mm10

Number of total reads
19921156
Reads aligned (%)
37.8
Duplicates removed (%)
64.3
Number of peaks
449 (qval < 1E-05)

mm9

Number of total reads
19921156
Reads aligned (%)
37.7
Duplicates removed (%)
64.7
Number of peaks
459 (qval < 1E-05)

Base call quality data from DBCLS SRA