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Sample GSM3417295 Query DataSets for GSM3417295
Status Public on Jan 04, 2019
Title sequence deletion validation (eNMU) clone 4 Bulk-seq
Sample type SRA
 
Source name K562 cell line
Organism Homo sapiens
Characteristics cell type: K562
Extracted molecule total RNA
Extraction protocol TruSeq Stranded mRNA Library Prep
RNEasy Mini Kit QIAGEN
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description two technical replicates (denoted A and B)
sequence_deletions_normalized_tpms.tsv
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.
 
Submission date Oct 04, 2018
Last update date Apr 03, 2019
Contact name Molly Gasperini
Organization name University of Washington
Department Genome Sciences
Street address 3720 15th Ave NE
City SEATTLE
State/province WA
ZIP/Postal code 98195
Country USA
 
Platform ID GPL18573
Series (1)
GSE120861 A genome-wide framework for mapping gene regulation via cellular genetic screens
Relations
BioSample SAMN10179967
SRA SRX4801139

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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