GEO DataSets

(Submitter supplied) Long-read RNA sequencing (RNA-seq) holds great potential for characterizing transcriptome variation and full-length transcript isoforms, but the relatively high error rate of current long-read sequencing platforms poses a major challenge. We present ESPRESSO, a computational tool for robust discovery and quantification of transcript isoforms from error-prone long reads. ESPRESSO jointly considers alignments of all long reads aligned to a gene and uses error profiles of individual reads to improve the identification of splice junctions and the discovery of their corresponding transcript isoforms. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24106

48 Samples

Download data: GTF, TXT

(Submitter supplied) Long-read RNA sequencing (RNA-seq) is a powerful technology for transcriptome analysis, but the relatively low throughput of current long-read sequencing platforms limits transcript coverage. We present TEQUILA-seq, a versatile, easy-to-implement, and low-cost method for targeted long-read RNA-seq. TEQUILA-seq can be broadly used for targeted sequencing of full-length transcripts in diverse biomedical research settings.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24676 GPL24106

123 Samples

Download data: GTF, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24973 GPL17021

12 Samples

Download data: TXT

(Submitter supplied) We explored changes at gene-level or transcript-level in embryonic stem cells, before and after in vitro differentiation with retinoic acid. RNA was sequenced both via Illumina short reads, and with Oxford Nanopore Technology with cDNA and direct RNA sequencing.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: TXT

(Submitter supplied) We explored changes at gene-level or transcript-level in embryonic stem cells, before and after in vitro differentiation with retinoic acid. RNA was sequenced both via Illumina short reads, and with Oxford Nanopore Technology with cDNA and direct RNA sequencing.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24973

8 Samples

Download data: TXT

(Submitter supplied) While numerous studies have described the transcriptomes of EVs in different cellular contexts, these efforts have typically relied on sequencing methods requiring RNA fragmentation, which limits interpretations on the integrity and isoform diversity of EV-encapsulated RNA populations. Furthermore, it has been assumed that mRNA signatures in EVs are likely to be fragmentation products of the cellular mRNA material, and little is known about the extent to which full-length mRNAs are present within EVs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24106

6 Samples

Download data: BED, TSV

(Submitter supplied) The NanoString experiment were conducted on 59 cell lines including 12 ovary cell lines, 12 lung cell lines, 11 colon cell lines, 10 breast cell lines, 4 pancreas cell lines, 2 prostate cell lines, 2 stomach cell lines, and 6 cell lines of 6 other types of tissues. A total of 404 probes were customized to estimate the isoform expressions of 155 cancer genes curated from the literature with more reliable isoform annotations, where each of the 155 gene contains at least two isoforms. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL26834

59 Samples

Download data: TXT

(Submitter supplied) Ongoing improvements to next generation sequencing technologies are leading to longer sequencing read lengths, but a thorough understanding of the impact of longer reads on RNA sequencing analyses is lacking. To address this issue, we generated and compared two RNA sequencing datasets of differing read lengths -- 2x75 bp (L75) and 2x262 bp (L262) -- and investigated the impact of read length on various aspects of analysis, including the performance of currently available read-mapping tools, gene and transcript quantification, and detection of allele-specific expression patterns. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15520 GPL11154

2 Samples

Download data: TXT

(Submitter supplied) Single cell RNA-seq was used to profile gene expression in 5 human lung adenocarcinoma cell lines.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

2 Samples

Download data: CSV, GFF3

(Submitter supplied) Single cell RNA-seq was used to profile gene expression in 5 human lung adenocarcinoma cell lines.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

1 Sample

Download data: CSV, GFF3

(Submitter supplied) Single cell RNA-seq was used to identify the gene expression signatures and transcript isoforms that distinguish quiescent and activated muscle stem cells in mouse.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

2 Samples

Download data: CSV, GFF3

(Submitter supplied) Single cell sequencing technology has been widely used for understanding the heterogeneity of complex tissue and for identifying novel cell types or cell states. Previous efforts of single cell profiling are mostly performed by measuring transcriptomes using single cell RNA sequencing (scRNA-seq). scRNA-seq is relatively well developed and around 500 analysis tools are currently available for performing different tasks. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: BED, CSV, MTX, TAB, TSV

(Submitter supplied) We perform full-length transcriptome analysis across 10 GC cell lines.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26180 GPL11154

20 Samples

Download data: GTF, TXT

(Submitter supplied) We report isoCirc, a long-read sequencing strategy coupled with an integrated computational pipeline to characterize full-length circular RNA (circRNA isoforms) using rolling circle amplification (RCA) followed by long-read sequencing. Applying isoCirc to 12 human tissues, we determined full-length structures and examined tissue specificities of circRNA isoforms in human transcriptomes.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24106 GPL16791

24 Samples

Download data: TXT

(Submitter supplied) New tools for improved long-read transcript assembly and coalescence with its short-read counterpart are required. Using our short- and long-read measurements from different cell lines with spiked-in standards, we systematically compared key parameters and biases in the read alignment and assembly of transcripts. We report a cDNA synthesis artifact in long-read datasets that impacts the identity and quantitation of assembled transcripts. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24973 GPL21103

8 Samples

Download data: CSV

(Submitter supplied) New tools for improved long-read transcript assembly and coalescence with its short-read counterpart are required. Using our short- and long-read measurements from different cell lines with spiked-in standards, we systematically compared key parameters and biases in the read alignment and assembly of transcripts. We report a cDNA synthesis artifact in long-read datasets that impacts the identity and quantitation of assembled transcripts. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL24106

8 Samples

Download data: CSV

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. Methods: Retinal mRNA profiles of 21-day-old wild-type (WT) and neural retina leucine zipper knockout (Nrl−/−) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

6 Samples

Download data: BAM, TXT, XLS

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24106

20 Samples

Download data: TXT

(Submitter supplied) To explore in depth and in a quantitative manner the complexity of the HIV-1 splicing landscape we used nanopore long-read cDNA (ONT) sequencing in NL4-3 HIV-1 infected primary CD4+ T cells and transfected/infected HeLa cells. Mean read lengths were between 1286 and 2626 nucleotides with maximum sizes of up to 9182 nucleotides, sufficiently long to span all possible splice junctions and to be assigned to a total of 229 exon combinations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24106

5 Samples

Download data: BED, TXT

(Submitter supplied) To explore in depth and in a quantitative manner the complexity of the HIV-1 splicing landscape we used nanopore long-read cDNA (ONT) sequencing in NL4-3 HIV-1 infected primary CD4+ T cells and transfected/infected HeLa cells. Mean read lengths were between 1286 and 2626 nucleotides with maximum sizes of up to 9182 nucleotides, sufficiently long to span all possible splice junctions and to be assigned to a total of 229 exon combinations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24106

3 Samples

Download data: BED, TXT