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Benchmarking full-length transcript single cell mRNA sequencing protocols

ABSTRACT: Benchmarking full-length transcript single cell mRNA sequencing protocols

PROVIDER: PRJNA649961 | ENA |

REPOSITORIES: ENA

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Benchmarking full-length transcript single cell mRNA sequencing protocols

Project description:Here we present a performance evaluation of three different plate-based scRNA-seq protocols. Two commercially available kits; NEBNext Single Cell/ Low Input RNA Library Prep Kit (NEB), SMART-seq HT kit (Takara), and non-commercially available protocol Genome & transcriptome sequencing (G&T). We evaluated each kit based upon sensitivity, reproducibility, ease of use and price point per cell. This evaluation is specifically relevant for implementation of scRNA-seq in e.g. diagnostics, requiring high sensitivity in regards of gene detection, high reproducibility between samples, minimum hands on time and smooth sample preparation for technicians, as well as keeping a reasonable price point per patient. G&T protocol delivered the highest detection of genes per single cell, at the absolute lowest price point. Takara's kit delivered likewise high gene detection per single cell, and high reproducibility between sample, however at the absolute highest price points. Here we present pros and cons of each protocol, sequencing breast cancer cell line T47D.

2020-08-01 | GSE155506 | GEO

Long-read RNA-Seq analysis of the full-length F8 transcript in iPSCs

Project description:We repaired the variant in iPSCs derived from a patient with moderate hemophilia A. To confirm the restoration of the full-length F8 transcript in the gene-corrected iPSCs, we performed long-read RNA-Seq analysis in iPSCs with the EF1α promoter.

2023-04-24 | GSE229621 | GEO

Selective roles of vertebrate PCF11 in premature and full-length transcript termination

Project description:Selective roles of vertebrate PCF11 in premature and full-length transcript termination

| PRJNA507553 | ENA

Single-molecule, full-length transcript isoform sequencing reveals disease-associated RNA isoforms

Project description:Alternative splicing generates differing RNA isoforms that govern phenotypic complexity of eukaryotes. Its malfunction underlies many diseases, including cancer and cardiovascular diseases. Comparative analysis of RNA isoforms at the genome-wide scale has been difficult. Here, we established an experimental and computational pipeline that accurately quantifies transcript isoforms in their entire length from cDNA sequences with a full-length isoform detection accuracy of 97.6%. We generated a searchable, quantitative human transcriptome annotation with 31,025 known and 5,740 novel transcript isoforms (http://steinmetzlab.embl.de/iBrowser/). By analyzing the isoforms in the presence of RNA Binding Motif Protein 20 (RBM20) mutations associated with aggressive dilated cardiomyopathy (DCM), we identified 121 differentially expressed transcript isoforms in 107 cardiac genes. By establishing an isoform-differential expression test, our approach revealed that 11 of these genes displayed no detectable change in overall RNA expression. However, significant differences in the expression of specific isoforms in these genes was observed. These isoform specific effects demonstrate the need of analyzing RNA isoform expression levels rather than total gene expression levels.

2021-06-16 | E-MTAB-7334 | biostudies-arrayexpress

To detect full-length transcript of ts-ARFGEF1 in MCF-7 cell [captureRNA]

Project description:To detect full-length transcript of ts-ARFGEF1 in MCF-7 cell [captureRNA]

| PRJNA809825 | ENA

Full-length HLA class II sequences

Project description:Full-length HLA class II sequences

| PRJEB42469 | ENA

Selective roles of vertebrate PCF11 in premature and full-length transcript termination (mNET-seq)

Project description:Selective roles of vertebrate PCF11 in premature and full-length transcript termination (mNET-seq)

| PRJNA507556 | ENA

Selective roles of vertebrate PCF11 in premature and full-length transcript termination (ChIP-seq)

Project description:Selective roles of vertebrate PCF11 in premature and full-length transcript termination (ChIP-seq)

| PRJNA524536 | ENA

Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects

Project description:Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects

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Quantifying full-length circular RNAs in cancer

Project description:Circular RNAs (circRNAs) have been found abundantly expressed in cancer. Their resistance to exonucleases enables them to have potentially stable interactions with with different types of biomolecules. Alternative splicing can create different circRNA isoforms that have different sequences and unequal interaction potentials. The study of circRNA function thus requires knowledge of complete circRNA sequences. Here we describe psirc, a method that can identify full-length circRNA isoforms and quantify their expression levels using RNA sequencing data. We confirm the effectiveness and computational efficiency of psirc using both simulated and actual experimental data. Applying psirc on transcriptome profiles from nasopharyngeal carcinoma and normal nasopharynx samples, we discovered circRNA isoforms differentially expressed between the two groups. Compared to the assumed circular isoforms derived from linear transcript annotations, some of the alternatively spliced circular isoforms have 100 times higher expression and contain fewer microRNA response elements, demonstrating the importance of quantifying full-length circRNA isoforms.

2021-04-06 | GSE165181 | GEO

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