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Multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in picolitre-sized droplets [small_scale_drug_screen]

ABSTRACT: Multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in picolitre-sized droplets [small_scale_drug_screen]

PROVIDER: PRJNA731138 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14587100.fastq.gz	Fastqsanger.gz
	SRR14587101.fastq.gz	Fastqsanger.gz
	SRR14587102.fastq.gz	Fastqsanger.gz
	SRR14587103.fastq.gz	Fastqsanger.gz
	SRR14587104.fastq.gz	Fastqsanger.gz

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Multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in picolitre-sized droplets

Project description:Multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in picolitre-sized droplets

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Multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in picolitre-sized droplets [large_scale_drug_screen]

Project description:Multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in picolitre-sized droplets [large_scale_drug_screen]

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Project description:Multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in picolitre-sized droplets [dataset 3]

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Multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in picolitre-sized droplets [large_scale_drug_screen]

Project description:K562 cells were perturbed with drug combinations for 12h in droplets. Subsequently cells were processed to generate libraries for RNA-Seq.

2021-05-20 | GSE174695 | GEO

Multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in picolitre-sized droplets [small_scale_drug_screen]

Project description:K562 cells were perturbed with drug combinations for 12h in droplets. Subsequently cells were processed to generate libraries for RNA-Seq.

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Multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in picolitre-sized droplets [dataset 3]

Project description:K562 cells were perturbed with drug combinations for 12h in droplets. Subsequently cells were processed to generate liraries for RNA-Seq.

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Multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in picolitre-sized droplets

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-05-20 | GSE174696 | GEO

Combi-seq for multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets.

Project description:Anti-cancer therapies often exhibit only short-term effects. Tumors typically develop drug resistance causing relapses that might be tackled with drug combinations. Identification of the right combination is challenging and would benefit from high-content, high-throughput combinatorial screens directly on patient biopsies. However, such screens require a large amount of material, normally not available from patients. To address these challenges, we present a scalable microfluidic workflow, called Combi-Seq, to screen hundreds of drug combinations in picoliter-size droplets using transcriptome changes as a readout for drug effects. We devise a deterministic combinatorial DNA barcoding approach to encode treatment conditions, enabling the gene expression-based readout of drug effects in a highly multiplexed fashion. We apply Combi-Seq to screen the effect of 420 drug combinations on the transcriptome of K562 cells using only ~250 single cell droplets per condition, to successfully predict synergistic and antagonistic drug pairs, as well as their pathway activities.

| S-EPMC9343464 | biostudies-literature

High complexity cellular barcoding and clonal tracing reveals stochastic and deterministic parameters of radiation resistance

Project description:It is elusive whether clonal selection of tumor cells in response to ionizing radiation (IR) is a deterministic or stochastic process. With high resolution clonal barcoding and tracking of over 400.000 HNSCC patient-derived tumor cells the clonal dynamics of tumor cells in response to IR was analysed. Fractionated IR induced a strong selective pressure for clonal reduction. This significantly exceeded uniform clonal survival probabilities indicative for a strong clone-to clone difference within tumor cells. Survival to IR is driven by a deterministic clonal selection of a smaller population which commonly survives radiation, while increased clonogenic capacity is a result of clonal competition of cells which have been selected stochastically. The ratio of these parameters is amenable to radiation sensitivity which correlates to prognostic biomarkers of HNSCC. Evidence for the existence of a rare subpopulation with an intrinsically radiation resistant phenotype was found at a frequency of 0.6-3.3%. With cellular barcoding we introduce a novel functional heterogeneity associated qualitative readout for evaluating the contribution of stochastic and deterministic clonal selection processes in response to IR.

2021-09-07 | E-MTAB-9693 | biostudies-arrayexpress

High complexity cellular barcoding and clonal tracing reveals stochastic and deterministic parameters of radiation resistance - Photon Irradiated samples

Project description:It is elusive whether clonal selection of tumor cells in response to ionizing radiation (IR) is a deterministic or stochastic process. With high resolution clonal barcoding and tracking of over 400.000 HNSCC patient-derived tumor cells the clonal dynamics of tumor cells in response to IR was analysed. Fractionated IR induced a strong selective pressure for clonal reduction. This significantly exceeded uniform clonal survival probabilities indicative for a strong clone-to clone difference. within tumor cells. Survival to IR is driven by a deterministic clonal selection of a smaller population which commonly survives radiation, while increased clonogenic capacity is a result of clonal competition of cells which have been selected stochastically. The ratio of these parameters is amenable to radiation sensitivity which correlates to prognostic biomarkers of HNSCC. Evidence for the existence of a rare subpopulation with an intrinsically radiation resistant phenotype was found at a frequency of 0.6-3.3%. With cellular barcoding we introduce a novel functional heterogeneity associated qualitative readout for evaluating the contribution of stochastic and deterministic clonal selection processes in response to IR. To analyze transcriptomic changes of HNSCC cell lines after fractionated Photon IR (5x4Gy), RNAseq analysis was performed on irradiated cells in comparison to untreated control cells (EBI submission E-MTAB-9693)

2021-08-31 | E-MTAB-10685 | biostudies-arrayexpress

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