|
| Status |
Public on Mar 30, 2013 |
| Title |
input BrgWT |
| Sample type |
SRA |
| |
|
| Source name |
input BrgWT
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Brgf/f-CreER infected with V5-hTopoIIa and sh mTopoIIa
cell type: Embryonic Stem Cells
genotype/variation: wild-type
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 |
ethanol 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 |
|
| Relations |
| SRA |
SRX256951 |
| BioSample |
SAMN01994496 |
