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TranscriptomicsSingle-cell RNA counting at allele- and isoform-resolution using Smart-seq3
Large-scale sequencing of RNAs from individual cells can reveal patterns of gene, isoform and allelic expression across cell types and states. However, current single-cell RNA-sequencing (scRNA-seq) methods have limited ability to count RNAs at allele- and isoform resolution, and long-read sequencin...
ORGANISM(S): mixed sample 
2020-04-14 | E-MTAB-8735 | biostudies-arrayexpress
TranscriptomicsSingle-cell sequencing of HEK293FT cells with molecular spikes and recorded cell size
Individual HEK cells were dispensed using an F.SIGHT into individual wells while recording cell diameters. Each well contained 0.0321 pg of molecular spike-ins, a highly complex set of 264 molecular spikes, based on 11 unique spike sequences spanning different lengths (570 to 3070 nts) and GC conten...
ORGANISM(S): Homo sapiens 
2022-02-16 | E-MTAB-11433 | biostudies-arrayexpress
TranscriptomicsScalable full-transcript coverage single cell RNA sequencing of PBMCs using Smart-seq3xpress
Plate-based single-cell RNA-sequencing methods with full-transcript coverage typically excel at sensitivity but are more resource and time-consuming. Using miniaturized and streamlined Smart-seq3xpress protocol, we sequence >26,000 human peripheral blood mononuclear cells to generate a highly granu...
ORGANISM(S): Homo sapiens 
2022-05-16 | E-MTAB-11452 | biostudies-arrayexpress
TranscriptomicsOptimizing scalable full-transcript coverage single cell RNA sequencing using Smart-seq3xpress
Smart-seq3xpress was carefully optimized and >1,000 conditions were evaluated. This data submission is organized in 15 datasets that each contain fastq files, unmapped bam files, read count tables, UMI count tables and a barcode annotation file. The barcode_annotation.txt files contain the exact fac...
ORGANISM(S): Homo sapiens 
2022-05-16 | E-MTAB-11467 | biostudies-arrayexpress
TranscriptomicsDeep sequencing of synthetic RNA (complex molecular spike-in set)
A highly complex set of 264 molecular spikes, based on 11 unique spike sequences spanning different lengths (570 to 3070 nts) and GC contents (40-60%) was designed. In order to be able to precisely evaluate quantification over different expression levels, transcript lengths and GC contents, barcodes...
ORGANISM(S): synthetic construct 
2022-02-16 | E-MTAB-11448 | biostudies-arrayexpress
TranscriptomicsSingle-cell RNA sequencing with molecular spikes to determine RNA counting accuracy
Molecule counting is central to single-cell sequencing, yet no experimental strategy to evaluate counting performance exist. Here, we introduce RNA spike-ins containing inbuilt unique molecular identifiers (molecular spikes) that we use to monitor single-cell RNA counting performance across methods ...
ORGANISM(S): Homo sapiens 
2022-02-16 | E-MTAB-10372 | biostudies-arrayexpress
TranscriptomicsSingle Cell RNA-Seq of Ear Epithelial Cells from i) steady state C57BL6/N & Tcrd-GDL mice, ii) untreated and TPA-treated C57BL6/J mice, and iii) IL13Ra1-knockdown CD1 mice
This dataset contains three experiments, designed for interrogating the effect of DETC on epithelial keratinocytes: Dataset 1) steady state ear epithelial cells (live, CD45-) from C57BL6/N (n=3) and Tcrd-GDL (n=3), after DETC deletion. Dataset 2) untreated and topical TPA-treated ear epithelial ce...
ORGANISM(S): Mus musculus 
2022-12-31 | E-MTAB-10441 | biostudies-arrayexpress
TranscriptomicsHuman-Mouse Mixture experiment to estimate that contribution of Barcode swapping
Here we test the impact of barcode swapping in prime-seq. To this end we isolated RNA from human iPSCs and mouse ESCs, processed them separately using prime-seq but pooled them for cDNA amplification.
ORGANISM(S): synthetic construct 
2022-03-10 | E-MTAB-11456 | biostudies-arrayexpress
TranscriptomicsHuman-Mouse Mixture experiment to estimate that contribution of Barcode swapping
Here we test the impact of over-/under-amplification on barcode swapping in prime-seq. To this end we isolated RNA from human iPSCs and mouse ESCs, processed them separately using prime-seq but pooled them for cDNA amplification.
ORGANISM(S): Homo sapiens 
2022-03-10 | E-MTAB-11455 | biostudies-arrayexpress
TranscriptomicsBulk RNA-seq of human induced pluripotent stem cells (hIPSC) and neural progenitor cells (NPC) differentiated usind Dual SMAD inhibition using the prime-seq method
Five hiPSC lines from four individuals were differentiated to neural progenitor cells. The two cell types were compared in regards to marker gene expression of known cell type markers to show that the used bulk RNA-seq protocol, called prime-seq can capture known biological differences.
ORGANISM(S): Homo sapiens 
2021-08-01 | E-MTAB-10133 | biostudies-arrayexpress
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