Similar studies for GEO DataSets (Select 200200480) - GEO DataSets

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Items: 20

Select item 2002004801.

Small RNA sequencing of regenerating mouse hindlimb muscle and Type 1-Lang reovirus-infected mouse heart

(Submitter supplied) Small RNAs, including microRNAs, play many roles in the regulation of gene expression. We performed small RNA-sequencing on two groups of samples to catalog which microRNAs are expressed during muscle regeneration in response to chemical injury and in heart tissue in response to viral-induced myocarditis.

Organism:: Mus musculus

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL17021
12 Samples

Download data: CSV

Series

Accession:: GSE200480

ID:: 200200480

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Select item 2002097802.

Single-nucleus total RNA-sequencing of C2C12 myoblasts via in situ polyadenylation

(Submitter supplied) Current methods for single-nucleus RNA-sequencing (snRNAseq) are limited to assaying endogenously polyadenylated (A-tailed) RNA transcripts. Here we demonstrate that enzymatic in situ polyadenylation of RNAs enables detection of the full spectrum of RNAs, expanding the scope of sequencing-based single-nucleus transcriptomics to the total transcriptome. We apply standard snRNAseq and total snRNAseq to C2C12 myoblasts. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL19057
2 Samples

Download data: MTX, TSV, TXT

Series

Accession:: GSE209780

ID:: 200209780

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Select item 2002004813.

Spatial Total RNA-Sequencing of regenerating mouse hindlimb muscle and Type 1-Lang reovirus-infected mouse heart

(Submitter supplied) Spatial transcriptomics reveals the spatial context of gene expression, but current methods are limited to assaying endogenously polyadenylated (A-tailed) RNA transcripts. Here we demonstrate that enzymatic in situ polyadenylation of RNAs enables detection of the full spectrum of RNAs, expanding the scope of sequencing-based spatial transcriptomics to the total transcriptome. We apply this Spatial Total RNA-Sequencing (STRS) approach to spatially map noncoding RNAs, newly transcribed RNAs, and non-host RNAs at the tissue-scale in the study skeletal muscle regeneration and viral-induced myocarditis. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL19057 GPL30172
8 Samples

Download data: JSON, MTX, TIFF, TSV, TXT

Series

Accession:: GSE200481

ID:: 200200481

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Select item 2000255964.

Deep Transcriptional Profiling of Rice Using Illumina's Sequencing By Synthesis Technology

(Submitter supplied) Identification of all expressed transcripts in a sequenced genome is essential both for genome analysis and for realization of the goals of systems biology. We used the transcriptional profiling technologies like ‘massively parallel signature sequencing (MPSS)’ and ‘Sequencing by Synthesis’ (SBS) to develop a comprehensive expression atlas of rice (Oryza sativa cv Nipponbare). Illumina’s SBS technology can generate large amounts of sequence data in a short time at low cost compared to traditional Sanger sequencing based methods. more...

Organism:: Oryza sativa

Type:: Expression profiling by high throughput sequencing

Platform:: GPL9147
43 Samples

Download data: TXT

Series

Accession:: GSE25596

ID:: 200025596

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Select item 2000436525.

A Genome-Wide Survey of Maternal and Embryonic Transcripts during Xenopus tropicalis Development

(Submitter supplied) To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted total RNA were harvested across six developmental stages and subjected to high throughput sequencing. The maternally loaded transcriptome is highly diverse and consists of both polyadenylated and deadenylated transcripts. Many maternal genes show peak expression in the oocyte and include genes which are known to be the key regulators of events like oocyte maturation and fertilization. more...

Organism:: Xenopus tropicalis

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13741
9 Samples

Download data: CSV

Series

Accession:: GSE43652

ID:: 200043652

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Select item 2001232536.

Small RNA-seq analysis of human airway epithelium infected by Human Bocavirus 1

(Submitter supplied) Human Bocavirus 1(HBoV1), which belongs to the genus Bocaparvovirus of the family Parvoviridae, infects well differentiated human airway epithelium which is at mitotically quiescent state. To systematicaly investigate the host and viral small RNA expression after HBoV1 infection of primary human airway epithelium cultured at an air-liquid interface (HAE-ALI), small RNA-seq was applied to study the small RNA transcriptome profile of HAE-ALI infected by HBoV1.

Organism:: Homo sapiens; Human bocavirus

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL25879
3 Samples

Download data: TXT

Series

Accession:: GSE123253

ID:: 200123253

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Select item 2001023927.

Transcriptome analysis of human airway epithelium infected by Human Bocavirus 1

(Submitter supplied) Human Bocavirus 1(HBoV1), which belongs to the genus Bocaparvovirus of the family Parvoviridae, infects well differentiated human airway epithelium which is at mitotically quiescent state. To systematicaly investigate the interaction between HBoV1 and primary human airway epithelium cultured at an air-liquid interface (HAE-ALI), RNA-seq was applied to study the transcriptome profile of HAE-ALI infected by HBoV1.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
6 Samples

Download data: TXT

Series

Accession:: GSE102392

ID:: 200102392

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Select item 2002380048.

Nextflow Pipeline for Visium and H&E Data from Patient-Derived Xenograft Samples

(Submitter supplied) We designed a Nextflow DSL2-based pipeline, Spatial Transcriptomics Quantification (STQ), for simultaneous processing of 10x Genomics Visium spatial transcriptomics data and a matched hematoxylin and eosin (H&E)-stained whole slide image (WSI), optimized for Patient-Derived Xenograft (PDX) cancer specimens. Our pipeline enables the classification of sequenced transcripts for deconvolving the mouse and human species and mapping the transcripts to reference transcriptomes. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL24247
4 Samples

Download data: CSV, JPG, JSON, MTX, PNG, TSV

Series

Accession:: GSE238004

ID:: 200238004

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Select item 2000254509.

RNA polyadenylation landscape in human and mouse cells

(Submitter supplied) Alternative polyadenylation (APA) of mRNAs has emerged as an important mechanism for post-transcriptional gene regulation in higher eukaryotes. Although microarrays have recently been used to characterize APA globally, they have a number of serious limitations that prevents comprehensive and highly quantitative analysis. To better characterize APA and its regulation, we have developed a deep sequencing-based method called Poly(A) Site Sequencing (PAS-Seq) for quantitatively profiling RNA polyadenylation at the transcriptome level. more...

Organism:: Homo sapiens; Mus musculus

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL9052 GPL9185
4 Samples

Download data: PDF, TXT

Series

Accession:: GSE25450

ID:: 200025450

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Select item 20015866810.

De novo assembly of macaque gene models

(Submitter supplied) We reported an atlas of de novo-defined, full-length macaque gene models on the basis of single molecule long-read transcriptome sequencing (Iso-seq).

Organism:: Mus musculus; Macaca mulatta

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL24198 GPL26751
14 Samples

Download data: BW

Series

Accession:: GSE158668

ID:: 200158668

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Select item 20009082911.

The long non-coding RNA transcriptome of Dictyostelium discoideum development

(Submitter supplied) This study details the content and dynamics of the long non-coding transcriptome during D. discoideum development, providing an important compendium to the well-characterized protein coding transcriptome. Applying a novel sample preparation method, we isolated antisense and long intergenic non-coding RNAs in addition to mRNAs. We describe the behavior of these different classes of RNAs that have been shown to play important regulatory roles in numerous model systems. more...

Organism:: Dictyostelium discoideum

Type:: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:: GPL22784
23 Samples

Download data: TXT, XLSX

Series

Accession:: GSE90829

ID:: 200090829

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Select item 20009869812.

Coupling of microRNA-directed phasiRNA generation with alternative splicing in small RNA-mediated gene silencing

(Submitter supplied) Purpose:We aimed to characterize genome-widely the miRNA population and phasiRNA-generating genes/loci in litchi (Litchi chinensis). Multiple high throughput sequencing strategies, including sRNA sequencing, parallel analysis of RNA ends (PARE) sequencing, and strand-specific RNA-seq, were applied in combination with thorough bioinformatics analyses using a variety of computational methods.

Organism:: Litchi chinensis

Type:: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:: GPL19467 GPL23452
12 Samples

Download data: TXT

Series

Accession:: GSE98698

ID:: 200098698

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Select item 20007579213.

TT-Seq captures the human transient transcriptome

(Submitter supplied) A large portion of the genome is transcribed but many of the resulting RNAs live only transiently and can generally not be mapped. Here we develop transient transcriptome sequencing (TT-Seq), a protocol that maps transcriptionally active regions in a nearly uniform manner and allows for unbiased monitoring of cellular RNA synthesis activity. Application of TT-Seq to human K562 cells recovers stable mRNAs and long intergenic non-coding RNAs, and additionally maps over 10,000 transient RNAs including enhancer RNAs, antisense RNAs, promoter-associated upstream antisense and convergent RNAs. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:: GPL18460
12 Samples

Download data: GTF, TXT

Series

Accession:: GSE75792

ID:: 200075792

Select item 20004331614.

Next Generation Sequencing of different ovine muscle's Transcriptomes

(Submitter supplied) We report the application of single-molecule-based sequencing technology for high-throughput profiling of different ovine muscle's transcriptomes. 9.27 gigabases of sequence from two different breeds of sheep.

Organism:: Ovis aries

Type:: Expression profiling by high throughput sequencing

Platform:: GPL15670
2 Samples

Download data: TXT

Series

Accession:: GSE43316

ID:: 200043316

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Select item 20006342415.

Sequencing of First-strand cDNA Library Reveals Full-length Transcriptomes

(Submitter supplied) We developed a new method of preparing libraries for strand-specific RNA sequencing (ssRNA-Seq). It employs Direct Ligation of Adaptors to First-strand cDNA (DLAF). We compared ssRNA-Seq libraries prepared using either the DLAF and dUTP methods from mouse embryonic stem cells (mES) and libraries were sequenced from one end or both ends. We also conducted a comparison of ssRNA-Seq libraries prepared using DLAF and ScriptSeq v2 kit (Epicenter) from mouse embryonic cortex (mECx).

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:: GPL13112
32 Samples

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Series

Accession:: GSE63424

ID:: 200063424

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Select item 20017433016.

A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients

(Submitter supplied) We report the application of a novel method and analysis pipeline that sequences 3’end -enriched RNA to comprehensively map the APA landscape in lung cancer. The goals of this study are to identify the functional role of APA in determining transcriptomic heterogeneity in lung cancer and population differences in APA.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
196 Samples

Download data: XLSX

Series

Accession:: GSE174330

ID:: 200174330

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Select item 20008679117.

RNA binding protein CPEB1 remodels host and viral RNA landscapes [RNA-Seq]

(Submitter supplied) In this study, we report that HCMV infection results in widespread alternative splicing (AS), shorter 3′-untranslated regions (3′UTRs) and polyA tail lengthening in host genes and CPEB1 depletion reverses infection-related post-transcriptional changes.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Other

Platforms:: GPL15520 GPL20301
9 Samples

Download data: BEDGRAPH, XLSX

Series

Accession:: GSE86791

ID:: 200086791

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Select item 20007425018.

Transcriptome analysis of diverse cell types infected with human cytomegalovirus

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

Organism:: Homo sapiens

Type:: Expression profiling by array; Expression profiling by high throughput sequencing; Other

4 related Platforms
40 Samples

Download data: BED, BEDGRAPH, BW, CEL

Series

Accession:: GSE74250

ID:: 200074250

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20007385319.

Transcriptome analysis of diverse cell types infected with human cytomegalovirus [RNA-Seq]

(Submitter supplied) Comprehensive RNA sequencing and splicing-sensitive microarray analysis of three diverse cell types infected with human cytomegalovirus (HCMV), including primary fibroblasts (HFFs), endothelial cells (ECs), and neural progenitors (NPCs) derived from embryonic stem cells. This global analysis includes both host and viral gene expression measurements, and an in-depth assessment of alternative RNA processing events. more...