|
| Status |
Public on Mar 26, 2024 |
| Title |
CRISPRi human, cyno (gRNAs) |
| Sample type |
SRA |
| |
|
| Source name |
iPSC
|
| Organisms |
Macaca fascicularis; Homo sapiens |
| Characteristics |
cell type: iPSC
genotype: KRAB-dCas9
|
| Treatment protocol |
Cells were transduced with lentivirus, selected with pyromicing and then grown in doxycycline-containing medium for another 5 days
|
| Extracted molecule |
other |
| Extraction protocol |
Generate single cell suspension with Accumax, wash cells with PBS+0.04 % Bsa and also store in that buffer until use
According to the manufaterer's instructions (Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index); CG000510 Rev B)
5' scRNA-seq based on polyA priming and CRISPR libraries from the gRNA based on capture of constant gRNA region
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
other |
| Library selection |
cDNA |
| Instrument model |
NextSeq 1000 |
| |
|
| Description |
10x Genomics 5' CRISPR
|
| Data processing |
Reads were processed using the 10x CellRanger software (Version 7.0.0)
The CRISPR library was mapped to a custom reference
The GEX library was mapped to both the extended hg38 and the extended macFas6 genomes
Assembly: hg38, macFas6 (both extended by the KRAB-dCas9-coding donor plasmid)
Supplementary files format and content: Hierarchical data format 5 files and comma-separated values file
|
| |
|
| Submission date |
Aug 21, 2023 |
| Last update date |
Mar 26, 2024 |
| Contact name |
Ines Hellmann |
| E-mail(s) |
hellmann@bio.lmu.de
|
| Organization name |
Ludwig-Maximilians-Universität München
|
| Street address |
Großhaderner Straße 2
|
| City |
Planegg |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL33700 |
| Series (1) |
| GSE241293 |
Generation and characterization of inducible KRAB-dCas9 iPSCs from primates for cross-species CRISPRi |
|
| Relations |
| BioSample |
SAMN37099172 |
| SRA |
SRX21439595 |
