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| Status |
Public on Jan 31, 2021 |
| Title |
Epistatic transcriptional interations underlying oncogenic genetic interactions (GI) via combinatorial CROP-seq |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
In our combinatorial CRISPR screenings, we screened for tumor/growth promoting GIs between 52 tumor suppressor genes (TSGs). In this part, we systematically profiled single-cell transcriptomes of double knocking-out (DKO) and single knocking-out (SKO) cells of GI pairs identified in our GI screenings, and tried to decipher the role of transcription in the phenotypic effects of GIs.
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| Overall design |
Cell library expressing dual CROPseq-sgRNAs was constructed by infection of CROPseqGuide-Puro-sgRNAs viruses and CROPseqGuide-Blasti-sgRNAs viruses sequentially. MCF10A-Cas9-Venus-vector cells were infected with 15 different CROPseqGuide-Puro-sgRNA viruses individually. CROPseqGuide-puro-(NF1_1, PTEN_5, SMAD4_5, CASP8_5, CBFB_2, CDH1_5, RB1_3, TP53_3, NF2_2, TBX3_3, USP9X_3, TP53_4, TP53_5, hRosa26_2, CTRL0002), and selected in 1.5 µg/ml puromycin for 4 days. Cells were then frozen, and passed for the next infection of CROPseqGuide-Blasti viruses. After 24 h of infection, Blasticidin (15 ng/µl) was added for selection. 72 of different pair-wised sgRNA combinations in total were included in the CROPseq cell library. Cell library was then cultured in different media and harvested for single cell transcriptome profiling. Single cells contain different perturbations that generating single knocking-out (SKO) and double knocking_out (DKO) and Control cells.
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| Contributor(s) |
Zhao X, Powers S |
| Citation(s) |
34561273 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 CA217206 |
Multigenic copy number alterations |
The Research Foundation for SUNY, Stony Brook University |
Scott Powers |
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| |
| Submission date |
Jan 17, 2021 |
| Last update date |
Jan 13, 2023 |
| Contact name |
Robert Scott Powers |
| E-mail(s) |
scott.powers@stonybrook.edu
|
| Organization name |
Stony Brook University
|
| Department |
Pathology
|
| Lab |
Powers Lab
|
| Street address |
100 Nicolls Rd
|
| City |
Stony Brook |
| State/province |
NY |
| ZIP/Postal code |
11794 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (20)
|
| GSM5024191 |
10X gene expression library (S1_full_D0) |
| GSM5024192 |
Enrichment PCR libarary for S1_full_D0 group1 |
| GSM5024193 |
Enrichment PCR libarary for S1_full_D0 group2 |
| GSM5024194 |
Enrichment PCR libarary for S1_full_D0 group3 |
| GSM5024195 |
Enrichment PCR libarary for S1_full_D0 group4 |
| GSM5024196 |
10X gene expression library (S2_full_D6) |
| GSM5024197 |
Enrichment PCR libarary for S2_full_D6 group1 |
| GSM5024198 |
Enrichment PCR libarary for S2_full_D6 group2 |
| GSM5024199 |
Enrichment PCR libarary for S2_full_D6 group3 |
| GSM5024200 |
Enrichment PCR libarary for S2_full_D6 group4 |
| GSM5024201 |
10X gene expression library (S3_tgf_D6) |
| GSM5024202 |
Enrichment PCR libarary for S3_tgf_D6 group1 |
| GSM5024203 |
Enrichment PCR libarary for S3_tgf_D6 group2 |
| GSM5024204 |
Enrichment PCR libarary for S3_tgf_D6 group3 |
| GSM5024205 |
Enrichment PCR libarary for S3_tgf_D6 group4 |
| GSM5024206 |
10X gene expression library (S4_min_D6) |
| GSM5024207 |
Enrichment PCR libarary for S4_min_D6 group1 |
| GSM5024208 |
Enrichment PCR libarary for S4_min_D6 group2 |
| GSM5024209 |
Enrichment PCR libarary for S4_min_D6 group3 |
| GSM5024210 |
Enrichment PCR libarary for S4_min_D6 group4 |
|
| Relations |
| BioProject |
PRJNA692740 |
| SRA |
SRP302119 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE164996_S1_filtered_barcodes.tsv.gz |
29.0 Kb |
(ftp)(http) |
TSV |
| GSE164996_S1_filtered_features.tsv.gz |
297.8 Kb |
(ftp)(http) |
TSV |
| GSE164996_S1_filtered_matrix.mtx.gz |
60.2 Mb |
(ftp)(http) |
MTX |
| GSE164996_S1_protospacer_calls_per_cell.csv.gz |
51.1 Kb |
(ftp)(http) |
CSV |
| GSE164996_S1_raw_barcodes.tsv.gz |
2.4 Mb |
(ftp)(http) |
TSV |
| GSE164996_S1_raw_features.tsv.gz |
297.8 Kb |
(ftp)(http) |
TSV |
| GSE164996_S1_raw_matrix.mtx.gz |
108.8 Mb |
(ftp)(http) |
MTX |
| GSE164996_S2_filtered_barcodes.tsv.gz |
38.0 Kb |
(ftp)(http) |
TSV |
| GSE164996_S2_filtered_features.tsv.gz |
297.8 Kb |
(ftp)(http) |
TSV |
| GSE164996_S2_filtered_matrix.mtx.gz |
58.2 Mb |
(ftp)(http) |
MTX |
| GSE164996_S2_protospacer_calls_per_cell.csv.gz |
64.0 Kb |
(ftp)(http) |
CSV |
| GSE164996_S2_raw_barcodes.tsv.gz |
2.4 Mb |
(ftp)(http) |
TSV |
| GSE164996_S2_raw_features.tsv.gz |
297.8 Kb |
(ftp)(http) |
TSV |
| GSE164996_S2_raw_matrix.mtx.gz |
80.3 Mb |
(ftp)(http) |
MTX |
| GSE164996_S3_filtered_barcodes.tsv.gz |
32.0 Kb |
(ftp)(http) |
TSV |
| GSE164996_S3_filtered_features.tsv.gz |
297.8 Kb |
(ftp)(http) |
TSV |
| GSE164996_S3_filtered_matrix.mtx.gz |
56.7 Mb |
(ftp)(http) |
MTX |
| GSE164996_S3_protospacer_calls_per_cell.csv.gz |
54.9 Kb |
(ftp)(http) |
CSV |
| GSE164996_S3_raw_barcodes.tsv.gz |
2.4 Mb |
(ftp)(http) |
TSV |
| GSE164996_S3_raw_features.tsv.gz |
297.8 Kb |
(ftp)(http) |
TSV |
| GSE164996_S3_raw_matrix.mtx.gz |
77.8 Mb |
(ftp)(http) |
MTX |
| GSE164996_S4_filtered_barcodes.tsv.gz |
40.4 Kb |
(ftp)(http) |
TSV |
| GSE164996_S4_filtered_features.tsv.gz |
297.8 Kb |
(ftp)(http) |
TSV |
| GSE164996_S4_filtered_matrix.mtx.gz |
55.7 Mb |
(ftp)(http) |
MTX |
| GSE164996_S4_protospacer_calls_per_cell.csv.gz |
69.5 Kb |
(ftp)(http) |
CSV |
| GSE164996_S4_raw_barcodes.tsv.gz |
2.4 Mb |
(ftp)(http) |
TSV |
| GSE164996_S4_raw_features.tsv.gz |
297.8 Kb |
(ftp)(http) |
TSV |
| GSE164996_S4_raw_matrix.mtx.gz |
79.3 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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