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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 28, 2024 |
| Title |
Paired CRISPR screens to map gene regulation in cis and trans (CUT&RUN) |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
In this study, we develop a scalable approach that pairs discovery of cis- and trans-acting elements to systematically decipher the gene regulatory network. We explore the regulation of the immune checkpoint PD-L1 under both basal and IFNγ-stimulated contexts. PD-L1 expression on tumor cells serves as a clinically-actionable diagnostic for immune checkpoint blockade therapy across multiple cancer types.
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| Overall design |
Cleavage Under Targets & Release Using Nuclease (CUT&RUN) for SRF, BPTF, and H3K4me3 in BxPC3 human pancreatic adenocarcinoma cells
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| Contributor(s) |
Xue X, Gajic Z, Caragine C, Legut M, Walker C, Kim J, Wang X, Yan RE, Wessels H, Lu C, Bapodra N, Gursoy G, Sanjana NE |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Feb 13, 2024 |
| Last update date |
Nov 28, 2024 |
| Contact name |
Xinhe Xue |
| E-mail(s) |
[email protected]
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| Organization name |
New York Genome Center/New York University
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| Street address |
101 Avenue of the Americas
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| City |
NEW YORK |
| State/province |
New York |
| ZIP/Postal code |
10013 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (12)
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| GSM8078018 |
BxPC3, BPTF, Replicate1, CUT&RUN |
| GSM8078019 |
BxPC3, BPTF, Replicate2, CUT&RUN |
| GSM8078020 |
BxPC3, BPTF, Replicate3, CUT&RUN |
| GSM8078021 |
BxPC3, H3K4me3, Replicate1, CUT&RUN |
| GSM8078022 |
BxPC3, H3K4me3, Replicate2, CUT&RUN |
| GSM8078023 |
BxPC3, H3K4me3, Replicate3, CUT&RUN |
| GSM8078024 |
BxPC3, IgG, Replicate1, CUT&RUN |
| GSM8078025 |
BxPC3, IgG, Replicate2, CUT&RUN |
| GSM8078026 |
BxPC3, IgG, Replicate3, CUT&RUN |
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| This SubSeries is part of SuperSeries: |
| GSE255701 |
Paired CRISPR screens to map gene regulation in cis and trans |
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| Relations |
| BioProject |
PRJNA1076336 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE255699_BxPC3_CUTRUN_BPTF_Rep123.bw |
791.7 Mb |
(ftp)(http) |
BW |
| GSE255699_BxPC3_CUTRUN_BPTF_Rep123_peaks.narrowPeak.gz |
1.1 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE255699_BxPC3_CUTRUN_H3K4me3_Rep123.bw |
198.3 Mb |
(ftp)(http) |
BW |
| GSE255699_BxPC3_CUTRUN_H3K4me3_Rep123_peaks.narrowPeak.gz |
1.9 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE255699_BxPC3_CUTRUN_IgG_Rep123.bw |
620.0 Mb |
(ftp)(http) |
BW |
| GSE255699_BxPC3_CUTRUN_IgG_Rep123_peaks.narrowPeak.gz |
46.0 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE255699_BxPC3_CUTRUN_SRF_Rep123.bw |
804.2 Mb |
(ftp)(http) |
BW |
| GSE255699_BxPC3_CUTRUN_SRF_Rep123_peaks.narrowPeak.gz |
626.3 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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