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| Status |
Public on Aug 04, 2023 |
| Title |
YCCEL1-Input-2 |
| Sample type |
SRA |
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| Source name |
Human Gammaherpesvirus 4-infected gastric carcinoma cell line YCCEL1
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| Organism |
human gammaherpesvirus 4 |
| Characteristics |
host cell line: YCCEL1
host cell type: Gastric Cancer
treatment: decitabine
chip antibody: none
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, 25x10^6 cells per immunoprecipitation were collected and fixed with 1% formaldehyde for 15 min and then quenched with 0.25 M glycine for 5 min on ice. After 3 washes with 1X PBS, pellets were resuspended in 10 mL each of a series of three lysis buffers before fragmentation in Covaris ME220 sonicator (peak power 75, duty factor 25, cycles/burst 1000, average power 18.8, time 720 sec) to generate chromatin fragments roughly 200–500 bp in size as determined by DNA gel electrophoresis. Chromatin was centrifuged to clear debris and a 1:20 of this cleared chromatin was kept as standard input for comparison against immunoprecipitations. Chromatin was incubated rotating at 4°C 1h with 8 µg of antibody against CTCF (Active Motif 61311). Chromatin–antibody complexes were precipitated using 50 µL of Dynabeads Protein A (ThermoFisher, product No. 10001D) incubated rotating at 4°C overnight. DNA was purified using Promega Wizard SV Gel and PCR Clean-up Kit (product No. A9285).
Libraries for sequencing were made using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, product No. E7103) and sequenced on the NextSeq 500 (Illumina).
CTCF protein was crosslinked to the DNA. DNA is sheared by sonication and antibody precipitation pulls-down CTCF-DNA complexes. Libraries are constructed from DNA sequences which bind to CTCF.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Adapter sequences were removed using TrimGalore
Sequence alignment to the human gammaherpesvirus 4 (HHV4) NC_007605.1 was performed by Bismark
We used MACS2[72,73] software packages to call peaks using input samples as control
Assembly: Viral Genome Human gammaherpesvirus 4 NC_007605.1
Supplementary files format and content: bw
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| Submission date |
Jun 09, 2023 |
| Last update date |
Aug 04, 2023 |
| Contact name |
Sarah Alp |
| E-mail(s) |
salp@wistar.org
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| Organization name |
The Wistar Institute
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| Street address |
3601 Spruce Street
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19401 |
| Country |
USA |
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| Platform ID |
GPL33481 |
| Series (2) |
| GSE234603 |
Decitabine disrupts EBV genomic epiallele DNA methylation patterns around CTCF binding sites to increase chromatin accessibility and lytic transcription in gastric cancer [ChIP-seq] |
| GSE234658 |
Decitabine disrupts EBV genomic epiallele DNA methylation patterns around CTCF binding sites to increase chromatin accessibility and lytic transcription in gastric cancer |
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| Relations |
| BioSample |
SAMN35686358 |
| SRA |
SRX20646938 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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