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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 22, 2024 |
| Title |
Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in Desmoplastic Small Round Cell Tumors [ChIP-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Desmoplastic Small Round Cell Tumor (DSRCT) is a rare, aggressive sarcoma driven by the EWSR1-WT1 chimeric transcription factor. Despite this unique oncogenic driver, DSRCT displays a polyphenotypic differentiation of unknown causality. Using single-cell multi-omics on samples from patients, we find that DSRCT tumor cells cluster into consistant subpopulations with partially overlapping lineage- and metabolism-related transcriptional programs.
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| Overall design |
ChIP-seq was performed in the JN-DSRCT-1 cell line using the GTX15249 WT1 C-terminal antibody or a rabbit isotype control. A second assay was performed in the same cell line after a 48-hour siRNA-mediated silencing using a control non-targeting siRNA or a EWSR1::WT1 siRNA, using H3K9ac or H3K27ac antibodies in both conditions.
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| Contributor(s) |
Henon C, Vibert J, Colmet-Daage L, Postel-Vinay S |
| Citation(s) |
38781959 |
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| Submission date |
May 18, 2024 |
| Last update date |
Aug 02, 2024 |
| Contact name |
Clémence Henon |
| E-mail(s) |
clemence.henon@gustaveroussy.fr
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| Organization name |
Gustave Roussy
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| Street address |
114 rue Edouard Vaillant
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| City |
Villejuif |
| ZIP/Postal code |
94800 |
| Country |
France |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (11)
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| GSM8279061 |
JN-DSRCT-1, assay_1, input |
| GSM8279062 |
JN-DSRCT, assay_1, isotype, R1, ChIP-seq |
| GSM8279063 |
JN-DSRCT, assay_1, isotype, R2, ChIP-seq |
| GSM8279064 |
JN-DSRCT, assay_1, WT1, R1, ChIP-seq |
| GSM8279065 |
JN-DSRCT, assay_1, WT1, R2, ChIP-seq |
| GSM8279066 |
JN-DSRCT-1, assay_2, siCTRL, input |
| GSM8279067 |
JN-DSRCT-1, assay_2, siEWS-WT1, input |
| GSM8279068 |
JN-DSRCT, assay_2, siCTRL, H3K27ac, ChIP-seq |
| GSM8279069 |
JN-DSRCT, assay_2, siEWS-WT1, H3K27ac, ChIP-seq |
| GSM8279070 |
JN-DSRCT, assay_2, siCTRL, H3K9ac, ChIP-seq |
| GSM8279071 |
JN-DSRCT, assay_2, siEWS-WT1, H3K9ac, ChIP-seq |
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| This SubSeries is part of SuperSeries: |
| GSE263523 |
Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in Desmoplastic Small Round Cell Tumors |
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| Relations |
| BioProject |
PRJNA1113158 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE267803_RAW.tar |
4.6 Gb |
(http)(custom) |
TAR (of BIGWIG) |
SRA Run Selector |
| Raw data are available in SRA |
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