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
cultured cell
cell type
mouse embryonic stem cells
strain
mixed genomic background
genotype/variation
SpenKO
clone
Clone 2
chip antibody
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were then lysed (50mM HEPES-KOH, 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) for 10 minutes at 4'C. Nuclei were lysed (100 mM Tris pH 8.0, 200mM NaCl, 1mM EDTA, 0.5 mM EGTA) for 10 minutes at room temperature. Chromatin was resuspended in sonication buffer (10 mM Tris pH 8.0, 1mM EDTA, 0.1% SDS) and sonicated using a Covaris Ultrasonicator to an average length of 220 bp. For all ChIPs, 5 million cells per replicate were incubated with 5 ug (Histone) or 7.5 ug (Oct4) antibody overnight at 4'C . Antibody-bound chromatin was incubated with Protein G Dynabeads (Invitrogen, 10004D) for 4 hours at 4'C and eluted in Tris buffer (10mM Tris pH 8.0, 10mM EDTA, 1% SDS). Crosslinks were reversed by incubation overnight at 65'C followed by treatment with 0.2 mg/mL proteinase K (Life Technologies, AM2548) and 0.2 mg/mL RNAse A (Qiagen). DNA was purified using Qiagen Minelute Columns (Qiagen, 28006). For library preparation, 4 ng ChIP DNA was incubated with transposase (Illumina, Fc-121-1030) for 10' at 55'C. DNA was then amplified using Nextera barcoding adapters and sequenced on an Illumina Nextseq (2x75 bp reads).

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
19202925
Reads aligned (%)
83.7
Duplicates removed (%)
7.6
Number of peaks
202 (qval < 1E-05)

mm9

Number of total reads
19202925
Reads aligned (%)
83.6
Duplicates removed (%)
7.7
Number of peaks
174 (qval < 1E-05)

Base call quality data from DBCLS SRA