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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE174696 | GEO | 2021/05/20

REPOSITORIES: GEO

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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

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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]

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

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

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Spatial Transcriptomics Using Multiplexed Deterministic Barcoding in Tissue

Project description:In this study, we present a multiplexed version of Deterministic Barcoding in Tissue (xDBiT) to acquire spatially resolved transcriptomes of nine tissue sections in parallel. New microfluidic chips were developed to spatially encode mRNAs over a total tissue area of 1.17 cm2 with spots of 50 µm×50 µm. Optimization of the biochemical protocol increased read and gene counts per spot by one order of magnitude compared with previous reports. Furthermore, the introduction of alignment markers allows seamless registration of images and spatial transcriptomic spot coordinates. Together with technological advances, we provide an open-source computational pipeline to transform raw sequencing data from xDBiT experiments into the AnnData format. The functionality of xDBiT was demonstrated by the acquisition of 16 spatially resolved transcriptomic datasets from five different murine organs, including cerebellum, liver, kidney, spleen, and heart. Factor analysis and deconvolution of xDBiT spatial transcriptomes allowed for in-depth characterization of the murine kidney.

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