GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1110845 Query DataSets for GSM1110845
Status Public on Mar 30, 2013
Title input BrgKO
Sample type SRA
Source name input BrgKO
Organism Mus musculus
Characteristics cell line: Brgf/f-CreER infected with V5-hTopoIIa and sh mTopoIIa
cell type: Embryonic Stem Cells
genotype/variation: Brg1-/-
chip antibody: none
Treatment protocol Cells were plated on gelatin with tamoxifen or ethanol for 24 hours, and then in ES cell media for 48 hours. Cells were treated with etoposide (100 micromolar) for 10 minutes before lysing.
Growth protocol ES cells derived from Brg1f/f-actinCreER mice were maintained on a layer of mouse embryonic feeders. The cell line was infected with V5-tagged human Topoisomerase 0Iia and the endogenouse mouse Topoisomerase Iia was knocked down.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated cells and TopoIIa-DNA covalent complexes were isolated with antibody.
The ChIP DNA ends were repaired using PNK and Klenow enzyme, followed by treatment with Taq polymerase to generate a protruding 3'A base used for adaptor ligation. Following ligation of a pair of Solexa adaptors to the repaired ends, the ChIP DNA was amplified using the adaptor primers for 17 cycles and the fragments around 300 bp isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Solexa 1G Genome Analyzer following manufacturer protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description tamoxifen treatment
Data processing Mapped reads with Bowtie (version 0.12.8)
Called peaks with MACS (version 1.4.2)
Genome_build: mm9
Supplementary_files_format_and_content: bed format, peaks
Submission date Mar 29, 2013
Last update date May 15, 2019
Contact name Emily Dykhuizen
Organization name Purdue University
Department medicinal chemistry and molecular pharmacology
Lab dykhuizen
Street address 201 S. University
City West Lafayette
State/province IN
ZIP/Postal code 47907
Country USA
Platform ID GPL13112
Series (1)
GSE45625 mSWI/SNF (BAF) Complexes Facilitate Decatentation of DNA by Topoisomerase IIa
SRA SRX256952
BioSample SAMN01994497

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap