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
Fbxl19flfl_UNT_Input
cell line
Fbxl19 fl/fl
cell type
mouse embryonic stem cells
treated with
none (untreated)
antibody
input control
replicate
2
passage
13-20

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation was performed as described previously (Farcas et al., 2012) with slight modifications. Cells were fixed for 45 min with 2mM DSG (Thermo scientific) in PBS and 12.5 min with 1% formaldehyde (methanol-free, Thermo scientific). Reactions were quenched by the addition of glycine to a final concentration of 125µM. After cell lysis and chromatin extraction, chromatin was sonicated using a BioRuptor Pico sonicator (Diagenode), followed by centrifugation at 16,000×g for 20min at 4°C. 200µg chromatin diluted in ChIP dilution buffer (1% Triton-X100, 1mM EDTA, 20mM Tris-HCl (pH 8.0), 150mM NaCl) was used per IP. Chromatin was precleared with protein A Dynabeads blocked with 0.2 mg/ml BSA and 50 µg/ml yeast tRNA and incubated with the respective antibodies overnight at 4°C. Antibody-bound chromatin was purified using blocked protein A Dynabeads for 3 hours at 4°C. ChIP washes were performed as described previously (Farcas et al., 2012). ChIP DNA was eluted in ChIP elution buffer (1% SDS, 100mM NaHCO3) and reversed cross-linked overnight at 65°C with 200mM NaCl and RNase A (Sigma). The reverse cross-linked samples were treated with 20ug/ml Proteinase K and purified using ChIP DNA Clean&Concentrator™ kit (Zymo research). ChIP DNA material was sheared with BioRuptor Pico sonicator to obtain DNA fragments of average size 200-800 bp. ChIPseq libraries were prepared with 30-40ng of ChIP DNA material using NEBNext Ultra DNA Library Prep Kit.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
11979020
Reads aligned (%)
96.1
Duplicates removed (%)
6.1
Number of peaks
137 (qval < 1E-05)

mm9

Number of total reads
11979020
Reads aligned (%)
95.9
Duplicates removed (%)
6.9
Number of peaks
116 (qval < 1E-05)

Base call quality data from DBCLS SRA