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

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

PROVIDER: PRJNA851440 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19770900.fastq.gz	Fastqsanger.gz
	SRR19771000.fastq.gz	Fastqsanger.gz
	SRR19770901.fastq.gz	Fastqsanger.gz
	SRR19771001.fastq.gz	Fastqsanger.gz
	SRR19770902.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 [small_scale_drug_screen]

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

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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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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.

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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.

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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

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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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