|
| Status |
Public on Oct 26, 2023 |
| Title |
hSIO - ZNF800-KO [scRNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
human small intenstinal organoids
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: human small intenstinal organoids
genotype: ZNF800-/-; MUC2-mNeonGreen; DEFA5-IRES-dsRed; CHGA-IRES-iRFP670
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Organoids were removed from theCultrexBasement Membrane Extract (BME, Growth Factor Reduced, Type 2, R&D Systems), digested withTryplE(Thermo Fisher) for 10~15 mins into single cells, washed with ice-coldAdDMEM/F12 (GIBCO) and filtered into FACS tubes through cell strainer (Falcon) with Rho kinase inhibitor Y-27632 dihydrochloride (10 µM,AbmoleBioscience). Cells were co-stained with DAPI (Sigma) and DRAQ5 (Biostatus) and subjected for FACS sorting of live cells. FACS was performed on BD Influx™ cell sorter (BD Bioscience). 4,000 live cells per condition were subjected to droplet-based scRNA-seq using the 10x Genomics platform.
Libraries were prepared using the 10x Genomics Chromium 3’ Gene Expression solution v3.1
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
LX198
|
| Data processing |
Illumina output demultiplexed (bcl files) converted to fastq files using mkfastq (CellRanger v7.0.1)
Alignment, filtering, barcode and UMI counting done using cellranger count (CellRanger v7.0.1)
Assembly: Genome Reference Consortium Human Build 38 + transgene constructs (MUC2-mNeonGreen; DEFA5-IRES-dsRed; CHGA-IRES-iRFP670)
Supplementary files format and content: Per sample filtered_feature_bc_matrix output from CellRanger (v7.0.1); includes gene-barcode matrices, genes, barcodes
|
| |
|
| Submission date |
Apr 13, 2023 |
| Last update date |
Oct 26, 2023 |
| Contact name |
Jeff DeMartino |
| Organization name |
Princess Maxima Center
|
| Street address |
Heidelberglaan 25
|
| City |
Utrecht |
| ZIP/Postal code |
3584 CS |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE229585 |
Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation [scRNA-seq] |
| GSE229586 |
Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation. |
|
| Relations |
| SRA |
SRX19950539 |
| BioSample |
SAMN34164100 |
