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| Status |
Public on Jan 04, 2019 |
| Title |
CRISPRi singleton (Null3_chr3.1742) Bulk-seq |
| Sample type |
SRA |
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| Source name |
K562 cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell type: K562
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| Extracted molecule |
total RNA |
| Extraction protocol |
TruSeq Stranded mRNA Library Prep
RNEasy Mini Kit QIAGEN
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
two technical replicates (denoted A and B)
singletons_set2_normalized_tpms.tsv
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| Data processing |
Single-cell RNA-seq datasets for the pilot screens were processed using 10x Genomics Cell Ranger 2.0.2.
Single-cell RNA-seq data for the at-scale screens was processed using 10x Genomics Cell Ranger 2.1.1.
bulkRNA-seq normalized transcripts per million (tpms) were generated using sleuth, and normalized by the sleuth 'between samples' size factors.
Genome_build: GRCh37
Supplementary_files_format_and_content: *.cds.rds, *.phenoData, *.genes.txt, *.cells.txt, and *.exprs.mtx.txt files were generated using Monocle2; *.tpms.tsv were generated using sleuth.
Supplementary_files_format_and_content: grna_groups.pilot.txt: gRNAgroup identifiers used to assign gRNA to the pilot screen and their corresponding spacer sequences.
Supplementary_files_format_and_content: grna_groups.at_scale.txt: gRNAgroup identifiers for the at-scale screen and their corresponding spacer sequences.
Supplementary_files_format_and_content: 50k_reference_cells.rds: File storing the names of the 50,000 cells used for differential expression testing for the at-scale screen (to save computational resources).
Supplementary_files_format_and_content: gene_gRNAgroup_pair_table.pilot.txt: Table of pilot screen's gene-target (gRNAgroup) pairs considered for differential expression testing (with corresponding information columns about each target and candidate target gene).
Supplementary_files_format_and_content: gene_gRNAgroup_pair_table.at_scale.txt: Table of at-scale screen's gene-target (gRNAgroup) pairs considered for differential expression testing (with corresponding information columns about each target and candidate target gene).
Supplementary_files_format_and_content: all_deg_results.pilot.txt: All differential expression results from the pilot screen (along with 'empirical p-values', which are only calculated for gRNA_groups associated with decreases in candidate target gene's expression).
Supplementary_files_format_and_content: all_deg_results.at_scale: All differential expression results from the at-scale screen (along with 'empirical p-values', which are only calculated for gRNA_groups associated with decreases in candidate target gene's expression).
Supplementary_files_format_and_content: zero_inflated_outlier_genes_to_exclude.atscale.txt: We observed that genes with a very high mean expression value relative to what you would expect given the number of cells in which they are expressed tended to show up frequently as false positives in permutation tests (these may be outliers with respect to their dispersion given that monocle uses shrinkage to estimate smoothed dispersion values when parameterizing the regression model used for differential gene expression). To avoid this source of false positives, we ignored this small set of outliers in downstream analysis.
Supplementary_files_format_and_content: zero_inflated_outlier_genes_to_exclude.pilot.txt: We observed that genes with a very high mean expression value relative to what you would expect given the number of cells in which they are expressed tended to show up frequently as false positives in permutation tests (these may be outliers with respect to their dispersion given that monocle uses shrinkage to estimate smoothed dispersion values when parameterizing the regression model used for differential gene expression). To avoid this source of false positives, we ignored this small set of outliers in downstream analysis.
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| Submission date |
Oct 04, 2018 |
| Last update date |
Apr 03, 2019 |
| Contact name |
Molly Gasperini |
| Organization name |
University of Washington
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| Department |
Genome Sciences
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| Street address |
3720 15th Ave NE
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| City |
SEATTLE |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE120861 |
A genome-wide framework for mapping gene regulation via cellular genetic screens |
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| Relations |
| BioSample |
SAMN10179975 |
| SRA |
SRX4801131 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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