Sample information curated by ChIP-Atlas

Antigen

Antigen Class
RNA polymerase
Antigen
RNA polymerase II

Cell type

Cell type Class
Gonad
Cell type
Germline stem cells
NA
NA

Attributes by original data submitter

Sample

source_name
genomic DNA, Cross link
genotype
Wild-type
strain
CD1 x C57BL/6
cell type
Cultured germline stem cells
chip antibody
Mouse anti-RNA Polymerase II, CTD clone 8WG16 (Millipore: 05-952)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq of crosslink samples, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibodies. For ChIP-seq of MNase samples, lysate was digested with Mnase and Histone-DNA complexes were isolated with antibodies. DNA library for ChIP-seq (both crosslink and MNase samples) was prepared with NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (NEB) and Agencourt AMPure XP (Beckman Coulter).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
15420184
Reads aligned (%)
91.1
Duplicates removed (%)
26.3
Number of peaks
12497 (qval < 1E-05)

mm9

Number of total reads
15420184
Reads aligned (%)
90.8
Duplicates removed (%)
26.5
Number of peaks
12500 (qval < 1E-05)

Base call quality data from DBCLS SRA