Perturb-seq dataset
We performed a systematic, genome-wide investigation of enhancer regions in colorectal cancer (CRC). We identified 12,117 putative enhancer regions using H3K27ac and H3Kme1 ChIP-seq and ATAC-seq. We performed scRNA-seq in HT29 and SW480 (MSS CRC cell lines) using the Parse Biosciences WT-mega kit with CRISPRi/dCas9 inhibition of these regions (Perturb-seq). The Parse split-pipe pipeline was used to demultiplex the raw fastq files into the processed files (mtx files for genes and gRNA) for each cell line.
- 08/04/2024
- 2 samples
- DAC: EGAC50000000023
- Technology: Illumina NovaSeq 6000
- NPUNCU DUO:0000018 (version: 2021-02-23)not for profit, non commercial use onlyThis data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use.
- GS DUO:0000022 (version: 2021-02-23)geographical restrictionThis data use modifier indicates that use is limited to within a specific geographic region.
- US DUO:0000026 (version: 2021-02-23)user specific restrictionThis data use modifier indicates that use is limited to use by approved users.
- PS DUO:0000027 (version: 2021-02-23)project specific restrictionThis data use modifier indicates that use is limited to use within an approved project.
- IS DUO:0000028 (version: 2021-02-23)institution specific restrictionThis data use modifier indicates that use is limited to use within an approved institution.
- GRU DUO:0000042 (version: 2021-02-23)general research useThis data use permission indicates that use is allowed for general research use for any research purpose.
ICR Cancer Genomics Cell Line Data Policy
Please contact Janet Nwaoshai (janet.nwaoshai@icr.ac.uk) and Richard Houlston (richard.houlston@icr.ac.uk) for the full policy details and data access agreement.
Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.
| Study ID | Study Title | Study Type |
|---|---|---|
| EGAS50000000256 | Cancer Genomics |
This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.
| ID | File Type | Size | Located in | |
|---|---|---|---|---|
| EGAF50000092443 | fastq.gz | 121.4 GB | ||
| EGAF50000092444 | fastq.gz | 89.9 GB | ||
| EGAF50000092445 | fastq.gz | 139.4 GB | ||
| EGAF50000092446 | fastq.gz | 198.1 GB | ||
| EGAF50000092447 | fastq.gz | 179.5 GB | ||
| EGAF50000092448 | fastq.gz | 129.6 GB | ||
| EGAF50000092449 | fastq.gz | 143.3 GB | ||
| EGAF50000092450 | fastq.gz | 105.1 GB | ||
| EGAF50000092451 | fastq.gz | 141.5 GB | ||
| EGAF50000092452 | fastq.gz | 104.8 GB | ||
| EGAF50000092453 | fastq.gz | 107.2 GB | ||
| EGAF50000092454 | fastq.gz | 143.6 GB | ||
| EGAF50000092455 | fastq.gz | 140.0 GB | ||
| EGAF50000092456 | fastq.gz | 103.0 GB | ||
| EGAF50000092457 | fastq.gz | 106.3 GB | ||
| EGAF50000092458 | fastq.gz | 145.7 GB | ||
| EGAF50000092459 | fastq.gz | 149.6 GB | ||
| EGAF50000092460 | fastq.gz | 105.1 GB | ||
| EGAF50000092461 | fastq.gz | 96.9 GB | ||
| EGAF50000092462 | fastq.gz | 132.1 GB | ||
| EGAF50000092463 | fastq.gz | 104.4 GB | ||
| EGAF50000092464 | fastq.gz | 76.7 GB | ||
| EGAF50000092465 | fastq.gz | 155.9 GB | ||
| EGAF50000092466 | fastq.gz | 107.3 GB | ||
| EGAF50000092467 | mtx | 505.1 MB | ||
| EGAF50000092468 | mtx | 18.2 GB | ||
| EGAF50000092469 | txt | 1.4 MB | ||
| EGAF50000092470 | mtx | 1.3 GB | ||
| EGAF50000092471 | txt | 2.2 MB | ||
| EGAF50000092472 | mtx | 16.3 GB | ||
| 30 Files (3.1 TB) | ||||