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Zingiberales

ABSTRACT: Multiplexed exon capture in the Zingiberales including sampling from each of the 8 families enriched on a single microarray

PROVIDER: PRJNA302314 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2923340_1.fastq.gz	Fastqsanger.gz
	SRR2923340_2.fastq.gz	Fastqsanger.gz
	SRR2923370_1.fastq.gz	Fastqsanger.gz
	SRR2923370_2.fastq.gz	Fastqsanger.gz
	SRR2923760_1.fastq.gz	Fastqsanger.gz

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Zingiberales_chem_ecolog_CR_UHPLC-HRMS_neg

Project description:Set of 85 plant extracts of the Zingiberales. Includes Families: Cannacea, Costaceae, Heliconiaceae, Marantaceae, Musaceae, Zingiberacea. Collection was done by Miguel Chavez at La Selva Biological Station in Costa Rica, The samples were measured in Geneva Switzerland, within a collaboration with Jean-Luc Wolfender's Lab. User: Luis Quiros-Guerrero

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Project description:Single-cell CRISPR screens are powerful tools to understand genome function by linking genetic perturbations to transcriptome-wide phenotypes. However, since few cells can be affordably sequenced in these screens, biased sampling of cells could affect data interpretation. One potential source of biased sampling is clonal cell expansion. Here, we present a computational pipeline for clonal cell identification in single cell screens using multiplexed sgRNA barcodes. We find that the cells in each clone share transcriptional similarities and we infer the segmental copy number changes in clonal cells. These analyses suggest that clones are genetically distinct. Finally, we show that the transcriptional similarities of clonally expanded cells contribute to false positives in single-cell CRISPR screens. As a result, experimental conditions that reduce clonal expansion or computational filtering of clonal cells will improve the reliability of single-cell CRISPR screens.

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