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
Immortalized MEF
spry status
No Spry expression (Spry1,2,4 are excised)
stable transduction
None
culture condition
Serum Starved (DMEM + 0.1% FBS + 1% Pen/Strep)
treatment
No Additional
chip antibody
None (input)
input note
Input for CRE_S_me1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed using the ChIP Assay Kit (Millipore, #17-295) according to the manufacturer's instructions, with the following modifications. After cell lysis, extracts were subjected to sonication with a 60 Sonic Dismembrator (Fisher Scientific) at 4°C for 20 cycles, cycling ON for 20 seconds and OFF for 1 minute at power setting 5, leading to an average DNA size of 200 bp. Samples were pre-cleared using 200 μL of Protein A Agarose/Salmon Sperm DNA for 4 hrs at 4°C with rotation. Antibody immunoprecipitations were performed overnight at 4°C. To collect histone complexes of interest, 100 μL Protein A Agarose/Salmon Sperm DNA was added for 4 hrs at 4°C with rotation. Each wash step (“Low Salt Immune Complex Wash Buffer,” “High Salt Immune Complex Wash Buffer,” “LiCl Immune Complex Wash Buffer,” and “TE Buffer”) was performed twice. After reverse-crosslinking overnight, samples were treated with RNase A, and subsequently treated with Proteinase K. Immunoprecipitated chromatin was extracted using QIAquick PCR Purification Kit (Qiagen). 10 ng of input and ChIP material were used to prepare libraries. Libraries were prepared using the ChIP-seq DNA Sample Kit (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
47285820
Reads aligned (%)
95.9
Duplicates removed (%)
36.4
Number of peaks
496 (qval < 1E-05)

mm9

Number of total reads
47285820
Reads aligned (%)
95.6
Duplicates removed (%)
36.3
Number of peaks
638 (qval < 1E-05)

Base call quality data from DBCLS SRA