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| Status |
Public on Aug 04, 2020 |
| Title |
Comparison of tumor-associated YAP1 fusions identifies a recurrent set of functions critical for oncogenesis [Cut&Run ChIP-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
Several different YAP1 gene fusions have been identified in various human cancers. We performed Cut and Run Chip sequencing on human neural stem cells overexpressing either YAP1-MAMLD1, YAP1-FAM118B, YAP1-TFE3, wild type YAP1, wild type MAMLD1, wild type FAM118B, wild type TFE3, or S127/397A-YAP1 (all HA tagged at the N'terminus)
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| Overall design |
U5 human neural stem cells were transduced with pLJM1-"transgene"-PGK-Puro. 48 hrs post transduction, positive clones were selected by 72 hrs of Puromycin selection. Cells were lysed and gDNA was extracted for Cut and Run experiments 48 hrs after Puromycin selection. Used antibodies: rabbit anti-HA, mouse anti-TEAD4, rabbit Igg, mouse Igg
***Please note that no processed data was provided for the 'wild type FAM118B HA rep1' and 'wild type MAMLD1 HA rep3' samples as no peaks detected using the SEACR package. The experiment was carried out twice, which generated inconsistent results both times (i.e. one replicate gives a million peaks, other gives much lesser, or zero peaks). However, all four samples are submitted and included in the records for users who may try to analyze the data.
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| Contributor(s) |
Szulzewsky F, Holland EC, Arora S |
| Citation(s) |
32675324 |
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| Submission date |
Jan 30, 2020 |
| Last update date |
Aug 12, 2020 |
| Contact name |
Sonali Arora |
| E-mail(s) |
sarora@fredhutch.org
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| Organization name |
FHCRC
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| Street address |
1100 Fairview Ave N,
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (45)
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| This SubSeries is part of SuperSeries: |
| GSE137040 |
Comparison of tumor-associated YAP1 fusions identifies a recurrent set of functions critical for oncogenesis |
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| Relations |
| BioProject |
PRJNA604071 |
| SRA |
SRP246236 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE144581_RAW.tar |
4.2 Mb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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