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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 (ATAC-seq) |
| 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 |
Assay for transposase-accessible chromatin with sequencing (ATAC-seq) for untreated and IFNγ-treated BxPC-3 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 (18)
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| GSM8078000 |
BxPC3,noIFNγ, Replicate4, ATAC-seq |
| GSM8078001 |
BxPC3,noIFNγ, Replicate5, ATAC-seq |
| GSM8078002 |
BxPC3,noIFNγ, Replicate6, ATAC-seq |
| GSM8078003 |
BxPC3,noIFNγ, Replicate7, ATAC-seq |
| GSM8078004 |
BxPC3,noIFNγ, Replicate8, ATAC-seq |
| GSM8078005 |
BxPC3,noIFNγ, Replicate9, ATAC-seq |
| GSM8078006 |
BxPC3,plusIFNγ, Replicate1, ATAC-seq |
| GSM8078007 |
BxPC3,plusIFNγ, Replicate2, ATAC-seq |
| GSM8078008 |
BxPC3,plusIFNγ, Replicate3, ATAC-seq |
| GSM8078009 |
BxPC3,plusIFNγ, Replicate4, ATAC-seq |
| GSM8078010 |
BxPC3,plusIFNγ, Replicate5, ATAC-seq |
| GSM8078011 |
BxPC3,plusIFNγ, Replicate6, ATAC-seq |
| GSM8078012 |
BxPC3,plusIFNγ, Replicate7, ATAC-seq |
| GSM8078013 |
BxPC3,plusIFNγ, Replicate8, ATAC-seq |
| GSM8078014 |
BxPC3,plusIFNγ, Replicate9, ATAC-seq |
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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 |
PRJNA1076337 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE255698_BxPC3_ATAC_NoIFNy.bw |
147.6 Mb |
(ftp)(http) |
BW |
| GSE255698_BxPC3_ATAC_NoIFNy_peaks.narrowPeak.gz |
2.9 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE255698_BxPC3_ATAC_PlusIFNy.bw |
148.2 Mb |
(ftp)(http) |
BW |
| GSE255698_BxPC3_ATAC_PlusIFNy_peaks.narrowPeak.gz |
3.1 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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