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| Status |
Public on Oct 21, 2020 |
| Title |
TOP2B_1523_ETO |
| Sample type |
SRA |
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| Source name |
Glioma cells
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| Organism |
Homo sapiens |
| Characteristics |
chip antibody: TOP2B
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| Treatment protocol |
50x10e6 cells were treated with etoposide or DMSO, crosslinked using formaldehyde 1%.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclear extracts were isolated, chromatin fragmented using Covaris sonicator in 1mL tubes for 1min. 10 ug of antibody (TOP2A Abcam TOP2B Abcam) wasc incubated overnight. Washes with RIPA Buffer 4 times and once of TE with 50mM NaCl. Reversed crosslink and DNA purified for sequencing using phenol:chloroform:isoamyl alcohol.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Data processing |
ChIP-seq reads were aligned to the hg19 genome assembly using bwa mem.
peaks were called using macs2 with the default setting.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files were generated using macs2.
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| Submission date |
Oct 20, 2020 |
| Last update date |
Oct 21, 2020 |
| Contact name |
Junfei Zhao Zhao |
| E-mail(s) |
zjf19870628@gmail.com
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| Organization name |
Columbia University
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| Street address |
1130 St. Nicholas Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platform ID |
GPL9052 |
| Series (1) |
| GSE133263 |
TOP2B binding and enzymatic activity on promoters and introns modulates multiple oncogenes in human gliomas [ChIP-seq] |
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| Relations |
| BioSample |
SAMN16489400 |
| SRA |
SRX9318380 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4838090_TOP2B_1523_ETO_peaks.xls.gz |
12.5 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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