Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Gonad
Cell type
Germline stem cells
NA
NA

Attributes by original data submitter

Sample

source_name
GSCs
tissue
germline stem cells (GSCs)
genotype
Kmt2bF/F
chip antibody
none (input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, cells were crosslinked and chromatin was prepared according to a previous report (Nat. Protoc. 3, 1032-1045) with modifications. For RNA-seq, total RNA was purified using Isogen (Nippon Gene), and treated with DNaseI to digest genomic DNA. ChIP-seq libraries for H3K4me3, H3K27me3 and input (replicate 1 and 2) samples were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB). Libraries for H3K9me3 and input (replicate 3 and 4) were prepared using ThruPLEX DNA-seq Kit (Takara). RNA-seq libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).

Sequencing Platform

instrument_model
Illumina HiSeq 3000

mm10

Number of total reads
85319925
Reads aligned (%)
97.9
Duplicates removed (%)
25.1
Number of peaks
809 (qval < 1E-05)

mm9

Number of total reads
85319925
Reads aligned (%)
97.7
Duplicates removed (%)
25.1
Number of peaks
925 (qval < 1E-05)

Base call quality data from DBCLS SRA