GEO DataSets

(Submitter supplied) Human preimplantation development is a complex process involving extensive remodeling of gene expression. However, the preimplantation embryo transcriptome has only been annotated using short-read sequencing, which fails to capture full-length mRNAs and associated isoform diversity. We present a novel human embryo transcriptome using integrated long- and short-read RNA sequencing data. Our analysis reveals a total of 110,212 novel isoforms transcribed from known genes containing either a novel combination of known splice sites or at least one novel splice site, and 17,964 isoforms transcribed from completely novel genes located either in antisense direction of known genes or in intergenic space.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

73 Samples

Download data: TSV

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28352 GPL24676

83 Samples

Download data

(Submitter supplied) Human preimplantation development is a complex process involving extensive remodeling of gene expression. However, the preimplantation embryo transcriptome has only been annotated using short-read sequencing, which fails to capture full-length mRNAs and associated isoform diversity. We present a novel human embryo transcriptome using integrated long- and short-read RNA sequencing data. Our analysis reveals a total of 110,212 novel isoforms transcribed from known genes containing either a novel combination of known splice sites or at least one novel splice site, and 17,964 isoforms transcribed from completely novel genes located either in antisense direction of known genes or in intergenic space.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28352

10 Samples

Download data: GTF

(Submitter supplied) We used an combination of long-read and short-read sequencing data to explore the transcriptome of preimplantation embryo

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24198 GPL24247

21 Samples

Download data: GFF, GTF, 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) This study explores alternative splicing's role in embryo development. Using single-cell direct isoform sequencing, we detected an abundance of 3-prime partial transcripts lacking stop codons in oocytes and zygotes, potentially influencing the maternal-to-zygote transition. Long-read sequencing identified dynamic changes in 3894 transposable element loci throughout preimplantation, impacting nearby gene expression and shedding light on early embryonic transcriptional regulation.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29177

4 Samples

Download data: CSV, FASTA, GTF, XLS

(Submitter supplied) Zebrafish embryos are transcriptional silent until activation of the zygotic genome during the 10th cell cycle. Onset of transcription is followed by cellular and morphological changes involving cell speciation and gastrulation. Previous genome-wide surveys of transcriptional changes only assessed gene expression levels; however, recent studies have shown the necessity to map isoform-specific transcriptional changes. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15583

2 Samples

Download data: TDF

(Submitter supplied) mRNA seq based approach to determine the transcriptome dynamics during early development To study the mechanisms regulating this developmental event in zebrafish, we applied RNA deep sequencing technology and generated comprehensive transcriptome profiles of 6 developmental stages from oocyte to early gastrulation. We determined the expression levels of maternal and zygotic transcripts and clustered them based on expression pattern. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10658

6 Samples

Download data: BEDGRAPH, GFF

(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) 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

(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

6 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

6 Samples

Download data: BED, TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL20795 GPL16791

327 Samples

Download data: TSV, TXT

(Submitter supplied) To investigate the contribution of parental genomes to early embryogenesis, we systematically profiled the single-cell transcriptomes of human biparental and uniparental embryos from one-cell to morula stages. We observed that uniparental embryos exhibit variable and overall less activation patterns of embryonic genome activation (EGA). Comparative transcriptome analysis identified 807 maternally biased expressed genes (MBGs) and 581 paternally biased expressed genes (PBGs) in preimplantation stages. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20795

31 Samples

Download data: TXT

(Submitter supplied) To investigate the contribution of parental genomes to early embryogenesis, we systematically profiled the single-cell transcriptomes of human biparental and uniparental embryos from one-cell to morula stages. We observed that uniparental embryos exhibit variable and overall less activation patterns of embryonic genome activation (EGA). Comparative transcriptome analysis identified 807 maternally biased expressed genes (MBGs) and 581 paternally biased expressed genes (PBGs) in preimplantation stages. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20795 GPL16791

296 Samples

Download data: TSV