|
| Status |
Public on Jan 29, 2018 |
| Title |
On the design of CRISPR-based single cell molecular screens |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
We demonstrate that vector designs for such screens that rely on cis linkage of guides and distally located barcodes suffer from swapping of intended guide-barcode associations at rates approaching 50% due to template switching during lentivirus production, greatly reducing sensitivity.
|
| |
|
| Overall design |
Experiments were conducted with FACs followed by NGS to quantify the rate of template switching. single-cell RNA-seq experiments were performed on the 10X Genomics platform for mock and doxorubicin treated MCF10a cells that had been tranduced with a CRISPR KO library (targeting tumor suppressors) that allowed for readout of the KO via a linked distal barcode using both an arrayed lentivirus production strategy and a pooled lentivirus production strategy. single-cell RNA-seq was also performed on mock and doxorubicin cells tranduced with a CRISPR KO library targeting tumor suppressors using a CROP-seq vector as the backbone.
|
| |
|
| Contributor(s) |
Hill AJ, McFaline-Figueroa JL, Shendure J, Trapnell C |
| Citation(s) |
29457792 |
| |
| Submission date |
Jan 03, 2018 |
| Last update date |
Mar 26, 2019 |
| Contact name |
Jay Shendure |
| E-mail(s) |
shendure@uw.edu
|
| Organization name |
University of Washington
|
| Department |
Genome Sciences
|
| Lab |
Shendure Lab
|
| Street address |
3720 15th Ave NE
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98105 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (13)
|
|
| Relations |
| BioProject |
PRJNA428344 |
| SRA |
SRP127963 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE108699_cs.cell_metadata.tsv.gz |
459.8 Kb |
(ftp)(http) |
TSV |
| GSE108699_cs.celldataset.rds.gz |
331.3 Mb |
(ftp)(http) |
RDS |
| GSE108699_cs.d.barcodes.tsv.gz |
23.6 Kb |
(ftp)(http) |
TSV |
| GSE108699_cs.d.genes.tsv.gz |
251.2 Kb |
(ftp)(http) |
TSV |
| GSE108699_cs.d.matrix.mtx.gz |
65.9 Mb |
(ftp)(http) |
MTX |
| GSE108699_cs.m.barcodes.tsv.gz |
24.7 Kb |
(ftp)(http) |
TSV |
| GSE108699_cs.m.genes.tsv.gz |
251.2 Kb |
(ftp)(http) |
TSV |
| GSE108699_cs.m.matrix.mtx.gz |
89.3 Mb |
(ftp)(http) |
MTX |
| GSE108699_facs_gfp_bfp_proportions.tsv.gz |
408 b |
(ftp)(http) |
TSV |
| GSE108699_initial.barcodes.tsv.gz |
29.4 Kb |
(ftp)(http) |
TSV |
| GSE108699_initial.cell_metadata.tsv.gz |
163.5 Kb |
(ftp)(http) |
TSV |
| GSE108699_initial.celldataset.rds.gz |
109.6 Mb |
(ftp)(http) |
RDS |
| GSE108699_initial.genes.tsv.gz |
251.2 Kb |
(ftp)(http) |
TSV |
| GSE108699_initial.matrix.mtx.gz |
51.6 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
Less...
More...