GEO DataSets

(Submitter supplied) Rainbow trout (Oncorhynchus mykiss) is an important aquaculture fish species that is farmed worldwide, and it is also the most widely cultivated cold water fish in China. This species, a member of the salmonidae family, is an ideal model organism for studying the immune system in fish. Two phenotypes of rainbow trout are widely cultured; wild-type rainbow trout with black skin (WR_S) and yellow mutant rainbow trout with yellow skin (YR_S). more...

Organism:

Oncorhynchus mykiss

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23000

6 Samples

Download data: XLSX

(Submitter supplied) Purpose: The goal of this study is to identify the difference of immunity between wild-type and yellow mutant rainbow trout in natural flowing water pond culture environment. Methods: The transcriptomic profiles of the skin were generated by using the Hiseq™4000 sequencing platform. Results: A total of 557,976,332 clean reads were yielded from six libraries and then assembled into 38,226 genes. Using P-value of 0.05 as the threshold, 3373 differentially expressed genes (DEGs) were obtained between WR_S and YR_S rainbow trout skin including the members of HSP90, V-ATPases, GST, SUGT1, NLRP3, NOD1, TLR3, IFR3, DHX58, IFIH1, JAK1, JAK2, STAT1 and NAMPT (|log2 fold-change| ranged from 1 to 4). more...

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24430

6 Samples

Download data: TXT

(Submitter supplied) Rainbow trout (Oncorhynchus mykiss) is an important economical cold-water fish worldwide. However, infection with infectious hematopoietic necrosis virus (IHNV) has severely restricted the development of aquaculture and caused huge economic losses. Currently, little is known about the immune defense mechanisms of rainbow trout against IHNV. In this study, we detected the changes of immune parameters over different post-infection periods (6-, 12-, 24-, 48-, 72-, 96-, 120-, and 144 hours post-infection (hpi)), mRNA and miRNA expression profiles under 48 hpi (T48L) compared to control (C48L), and key immune-related genes expression patterns in rainbow trout liver following IHNV challenge through biochemical methods, RNA-seq, and qRT-PCR, and the function of miR-330-y was verified by overexpression and silencing in vitro and in vivo. more...

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23000

6 Samples

Download data: TXT

(Submitter supplied) Purpose: mRNA-Seq to reveal the differentially expression pattern of genes in innate/adaptive immune relevant pathways, and combining to the previous DNA microarray analysis to address the immunomodulatory effects of cecropin P1 transgene in rainbow trout. Methods: Total RNA were isolated from three tissues, spleen, liver and kidney, from two individuals of two families of transgenic and one family of non-transgenic fish. more...

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19277

6 Samples

Download data: FA, XLSX

(Submitter supplied) Purpose: a transcriptomic analysis was performed to extend our understanding on the immune response picture of rainbow trout exposed to I. multifiliis. Methods: Gill samples were collected from fish in each tank (control and infected group) at day 8 after infection. Total RNA was extracted using RTN350 (Sigma-Aldrich), according to the manufacturer’s instruction and subsequently, DNase treated with DNase I (Thermo Scientific, USA). more...

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23000

20 Samples

Download data: GFF, TSV, XLSX

(Submitter supplied) Cryptocaryonosis caused by Cryptocaryon irritans is one of the major diseases of large yellow croaker (Larimichthys crocea), which lead to massive economic losses annually. The pathogenesis for cryptocaryonosis has been researched by a series of transcriptome studies under different infection conditions. However, little is known about the roles of tissue-specifically expressed genes during the infection of C. more...

Organism:

Larimichthys crocea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30112

15 Samples

Download data: TXT

(Submitter supplied) Hantaan virus (HTNV), the prevalent prototype of the hantavirus in Asia, causes hemorrhagic fever with renal syndrome (HFRS) with high mortality in human being. However, the pathogenesis of HTNV infection remains elusive. Accumulating evidences indicate that non-coding RNAs (ncRNAs), including long non-coding RNA (lncRNA), circular RNA (circRNA) and microRNA (miRNA) play crucial roles in the progression of virus infection. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL21290

6 Samples

Download data: TXT

(Submitter supplied) Hantaan virus (HTNV), the prevalent prototype of the hantavirus in Asia, causes hemorrhagic fever with renal syndrome (HFRS) with high mortality in human being. However, the pathogenesis of HTNV infection remains elusive. Accumulating evidences indicate that non-coding RNAs (ncRNAs), including long non-coding RNA (lncRNA), circular RNA (circRNA) and microRNA (miRNA) play crucial roles in the progression of virus infection. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL21290

6 Samples

Download data: TXT

(Submitter supplied) Hantaan virus (HTNV), the prevalent prototype of the hantavirus in Asia, causes hemorrhagic fever with renal syndrome (HFRS) with high mortality in human being. However, the pathogenesis of HTNV infection remains elusive. Accumulating evidences indicate that non-coding RNAs (ncRNAs), including long non-coding RNA (lncRNA), circular RNA (circRNA) and microRNA (miRNA) play crucial roles in the progression of virus infection. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: TXT

(Submitter supplied) Here, we report a comprehensive analysis of dysregulated mRNAs, lncRNAs, miRNAs and circRNAs in peripheral blood of COPD patients with high-throughput RNA sequencing. We mapped about 50~80 million sequence reads per sample to the human genome. GSEA analysis showed that these dysregulated RNAs correlate with several critical biological processes such as RNA modification, and RNA metabolism. RT-qPCR (SYBR Green assays) with more clinical COPD samples were used for the validation of some dysregulated RNAs. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL24676

18 Samples

Download data: BED, TXT

(Submitter supplied) Whole-transcriptome sequencing (RNA sequencing [RNA-seq]) was performed in the viral producer cell lines iSLK-RGB BAC16,iSLK-RGB-K9 mutant and iSLK-RGB-K13 mutant cells to uncover the global landscape of long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), mRNAs and microRNAs (miRNAs) in KSHV replication mediated by vIRF1 or vFLIP.

Organism:

Homo sapiens

Type:

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

Platform:

GPL21290

9 Samples

Download data: XLS

(Submitter supplied) To identify the circRNA expression profile in laser-induced choroidal neovascularization (CNV) and controls in mice, we used circRNA microarray analysis to examine the expression of circRNAs in RPE-choroid-sclera complexes of CNV and control mice.

Organism:

Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL21826

6 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platforms:

GPL22120 GPL24741

24 Samples

Download data: TXT

(Submitter supplied) we profiled whole transcriptome in depression patients’ and healthy volunteers blood samples via microarray analysis.Differentially expressed miRNAs were selected for deep analysis. Especially the Differentially expressed genes that associated with cancer

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL24741

12 Samples

Download data: TXT

(Submitter supplied) we profiled whole transcriptome in depression patients’ and healthy volunteers blood samples via microarray analysis.Differentially expressed circRNAs, lncRNAs and mRNAs were selected for deep analysis. Especially the Differentially expressed genes that associated with cancer

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL22120

12 Samples

Download data: TXT

(Submitter supplied) Male and female germline stem cells are critical for passing genetic information from generation to generation. Accumulating evidences indicate that long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) play important roles in self-renewal and differentiation of germline stem cells. However, the mechanisms remain largely unknown. In this study, we explored the mRNAs, lncRNAs and circRNAs expression profiles of male and female germline stem cells through high-throughput sequencing.

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

6 Samples

Download data: XLSX

(Submitter supplied) In order to explore the epigenetic characteristics of hemorrhagic transformation(HT) after acute ischemic stroke, we used transcriptome sequencing technology to analyze the global transcriptome expression profile of patients with and without HT after acute ischemic stroke and to study the differential expression of messenger RNA (mRNA), long noncoding RNA (lncRNA), and circular RNA (circRNA) between HT group and non-HT group.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT

(Submitter supplied) Circulating plasma microRNAs (miRNAs) are well established as biomarkers of several diseases in humans and have recently been used as indicators of environmental exposures in fish. However, the role of plasma miRNAs in regulating acute stress responses in fish is largely unknown. Tissue and plasma miRNAs have recently been associated with excreted miRNAs in humans however external miRNAs have never been measured in fish. more...

Organism:

Oncorhynchus mykiss

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23004

18 Samples

Download data: TAB, XLSX

(Submitter supplied) Circular RNAs (circRNAs) are widely expressed in eukaryotes. However, only a subset have been functionally characterized. We identify and validate a collection of circRNAs in Drosophila, and show that depletion of the brain-enriched circRNA Edis causes hyperactivation of antibacterial innate immunity both in cultured cells and in vivo. Notably, Edis depleted flies display heightened resistance to bacterial infection and enhanced pathogen clearance. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17275

4 Samples

Download data: BED