Genomics

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BART-seq: cost-effective massively parallel targeted sequencing for genomics and transcriptomics [transcriptomics]


ABSTRACT: We report the application of a novel workflow, BART-Seq (Barcode Assembly foR Targeted Sequencing), the first highly sensitive, quantitative, and inexpensive technique for enriching selected cohorts of transcripts and genomic regions from thousands of samples in parallel, for next-generation sequencing (NGS). Multiplexing is based on a simple method for producing virtually unlimited matrices of barcoded primer sets. The method provides sample-specific amplicon labels for hundreds-fold enrichment compared to unbiased transcriptomics and genomics approaches. We demonstrated the technique by quantitative analysis of pluripotency genes in bulk cell preparations and thousands of single cells. We believe that BART-Seq will complement low-sensitivity global NGS approaches, such as droplet-based sequencing, by enabling analysis, validation, and screening of specific processes in biomedical research. Overall design: 11 selected transcripts and 4 external RNA spike-ins were co-amplified from single or multiple (2 to 32, incremented 2-fold) undifferentiated H9 human embryonic stem cells (hESCs) or BJ fibroblasts, as well as from four-fold dilution series (4-256 pg/well) of bulk RNA isolated from H9 hESCs. The amplicons are barcoded using the BART-seq method, and multiplexed for sequencing.

INSTRUMENT(S): Illumina MiSeq (Homo sapiens)

SUBMITTER: Fatma Uzbas  

PROVIDER: GSE107721 | GEO | 2018-10-01

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
GSE107721_Barcodes_Media_Comparison.csv.gz Csv
GSE107721_Barcodes_Transcriptomics.csv.gz Csv
GSE107721_RAW.tar Raw
GSE107721_Transcriptomics_Amplicons.txt.gz Txt
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