Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Embryonic fibroblast
Cell type
MEF
Tissue
Embryonic Fibroblast
Lineage
primaryCells
Description
Mouse Embryonic Fibroblast

Attributes by original data submitter

Sample

source_name
ChIP-Seq Control (Gadd45a) MEFs
strain background
C57BL/6N
genotype/variation
Control
cell type
Mouse Embryonic Fibroblasts (MEFs)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was carried out essentially as described (Schäfer et al., 2013; doi: 10.1101/gad.186916.112.) using rabbit a-HA antibody (Abcam). ChIP-seq library preparation was performed using NuGEN´s Ovation Ultralow System V2 1-16 (2014), following the manufacturer’s recommendations. Libraries were prepared from 48 ng ChIP-DNA and were amplified in 9 PCR cycles. Double bead size selection with ratios of 0.65:1 and 0.85:1 (beads:DNA ratio) was performed to enrich the library for 230-730bp fragments using Agencourt AMPure XP (Beckman Coulter). Libraries were profiled in a High Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). GADD45a libraries were pooled in equimolar ratio and sequenced on two HiSeq2500 lanes, rapid mode, single read for 68 cycles for read 1 plus 7 cycles for the index read.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
45962515
Reads aligned (%)
98.8
Duplicates removed (%)
13.7
Number of peaks
424 (qval < 1E-05)

mm9

Number of total reads
45962515
Reads aligned (%)
98.6
Duplicates removed (%)
13.7
Number of peaks
461 (qval < 1E-05)

Base call quality data from DBCLS SRA