Antigen

Antigen Class

Input control

Antigen

Input control

Cell type

Cell type Class

Embryonic fibroblast

Cell type

Swiss 3T3 Cells

MeSH Description

A cell line established in 1962 from disaggregated Swiss albino mouse embryos. This fibroblast cell line is extremely popular in research.

Sample

source_name

Input, Serum-starved (72h) Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM)

cell line

Swiss 3T3

cell type

fibroblasts

antibody

none

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Chromatin immunorecipitation was performed as described (Hauser et al., Molecular and Cellular Biology, 2002) with the following modifications: chromatin-antibody complexes were pulled down using Dynabeads® protein A or G beads (Invitrogen). The following antibodies were used in the study: H3S28ph (Sigma, cat number H9908), H3K9ac (Millipore, cat number 06-942), H3K4me3 (Millipore, cat number 07-473), RNAPIIS5ph (Bethyl, cat number A300-655A), RNAPIIS2ph (Bethyl, cat number A300-654A). Immunoprecipitated DNA as well as input samples were subjected to library preparation protocol using NEBNext® Library Prep Reagent Set for Illumina (NEB). The following TrueSeq barcodes were used for the input samples: sample input_0h TTAGGC, sample input_1hA TGACCA.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

52112027

Reads aligned (%)

97.2

Duplicates removed (%)

17.5

Number of peaks

295 (qval < 1E-05)

mm9

Number of total reads

52112027

Reads aligned (%)

96.9

Duplicates removed (%)

17.4

Number of peaks

556 (qval < 1E-05)