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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 26, 2023 |
| Title |
Organoid_Expansion_Bulk_BR2 |
| Sample type |
SRA |
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| Source name |
human small intenstinal organoids
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| Organism |
Homo sapiens |
| Characteristics |
cell type: human small intenstinal organoids
genotype: MUC2-mNeonGreen; DEFA5-IRES-dsRed; CHGA-IRES-iRFP673
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from different cell populations using DNeasy Blood & Tissue kit (QIAGEN) following the manufacturer’s protocol.
CRISPR screen sequencing libraries were constructed as previously described (L. Lin, B. Holmes, M. W. Shen, D. Kammeron, N. Geijsen, D. K. Gifford, R. I. Sherwood, Comprehensive Mapping of Key Regulatory Networks that Drive Oncogene Expression. Cell Rep. 33, 108426 (2020).) Briefly, two sequential PCR reactions were performed to amplify the gRNA fragments integrated in the genomic DNA, using primers flanking the gRNA protospacers containing staggered barcodes and primers with full-length Illumina sequencing adapters. All primer sequences are listed in Table S3.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Data processing |
Reads were demultiplexed requiring a perfect match to a designed 8-nt index (Ilumina Nextera DNA adapter series) and up to 1 mismatch to a designed 3-nt to 9-nt staggered barcode residing at the beginning of the read.
gRNAs were counted by requiring a perfect match to a designed 19-nt, 20-nt, or 21-nt gRNA in the library using mageck count from MaGeCK CRISPR screen analysis toolkit (0.5.9.5)
Assembly: Custom TFome sgRNA library
Supplementary files format and content: Tab delimited files containing sgRNA read counts
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| Submission date |
Apr 13, 2023 |
| Last update date |
Oct 26, 2023 |
| Contact name |
Jeff DeMartino |
| Organization name |
Princess Maxima Center
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| Street address |
Heidelberglaan 25
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| City |
Utrecht |
| ZIP/Postal code |
3584 CS |
| Country |
Netherlands |
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| Platform ID |
GPL30173 |
| Series (2) |
| GSE229584 |
Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation [screen] |
| GSE229586 |
Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation. |
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| Relations |
| SRA |
SRX19950615 |
| BioSample |
SAMN34164183 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7165829_Organoid_Expansion_Bulk_BR2.txt.gz |
82.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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