GEO DataSets

(Submitter supplied) In this study, a high-throughput sequencing strategy was employed to identify the mRNA involved in P. olivaceus albinism. Based on P. olivaceus genome, RNA-seq identified 21,787 know genes and 711 new genes by transcripts assembly. Of those, 235 genes exhibited significantly different expression pattern (fold change ≥2 or ≤0.5 and q-value≤0.05), including 194 down-regulated genes and 41 up-regulated genes in albino versus normally pigmented individuals. more...

Organism:

Paralichthys olivaceus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23520

6 Samples

Download data: XLS

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

Organism:

Paralichthys olivaceus

Type:

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

Platform:

GPL23520

12 Samples

Download data

(Submitter supplied) In this study, a high-throughput sequencing strategy was employed to identify the miRNAs involved in P. olivaceus albinism. High-throughput miRNA sequencing identified a total of 475 miRNAs, including 64 novel miRNAs. Furthermore, 33 differentially expressed miRNAs containing 13 up-regulated and 20 down-regulated miRNAs were identified in albino versus normally pigmented individuals (fold change ≥1.5 or ≤0.67 and p≤0.05).

Organism:

Paralichthys olivaceus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23520

6 Samples

Download data: XLS

(Submitter supplied) In the present study, four important somatotropic and reproductive tissues including brain, liver, gonad and muscle from 3 females and 3 males were used for transcriptomic analysis. A mean of 47,102,115 high quality clean reads were obtained from each library and 156, 67, 3434, and 378 differentially expressed genes in female and male were identified from brain, liver, gonad, and muscle, respectively (q < 0.05). more...

Organism:

Platichthys stellatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26946

16 Samples

Download data: FASTA, TXT

(Submitter supplied) After comparing albinism rate, T3 treatment and control larvae of 42 DAH were chosen for next high-throughput sequencing analyses of miRNA. A total of 337 miRNAs were identified via miRNA-seq and 12 miRNAs exhibited significantly differential expression patterns in D42_T3 vs D42_Con (TPM > 10, fold change ≥ 1.5 or ≤ 0.67 and q ≤ 0.05). These differentially expressed miRNAs targeted 3658 putative genes, further enriching 10 GO terms (q < 0.05).

Organism:

Paralichthys olivaceus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23520

2 Samples

Download data: FA, XLS

(Submitter supplied) After comparing albinism rate, T3 treatment and control larvae of 42 DAH were chosen for next high-throughput sequencing analyses of mRNA. RNA-seq identified 146 differentially expressed genes (DEGs) in D42_T3 versus D42_Con (|log2Foldchange| > 1 and q < 0.005), including pigmentation related genes such as the receptor tyrosine-protein kinase erbB-3, pro-opiomelanocortin A, melanotransferrin, and the growth-related gene somatotropin. more...

Organism:

Paralichthys olivaceus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24117

2 Samples

Download data: FASTA, XLS

(Submitter supplied) To invesigate the physiology roles of mir-122 in liver, we performed expression profiling of mir-122 knockout mice and the control B6/129 mice.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

7 Samples

Download data: CEL, CHP

(Submitter supplied) Background: Colorectal cancer (CRC) is one of the leading causes of cancer-related death worldwide. The roles of microRNAs (minRNAs) in mRNA destabilization and translational repression of this disease are well appreciated, their involvement in endonucleolytic cleavage of target mRNAs is poorly understood. Methods: High throughput small RNA sequencing was employed for the identification and profiling of miRNAs by six pairs of colorectal cancer tissues (CT) and their adjacent tissues (CN). more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: XLSX

(Submitter supplied) In this study, we determined the miRNA expression profile of bovine alveolar macrophages, using next-generation sequencing strategy. On an Illumina HiSeq 2000 machine, we sequenced 8 miRNA libraries, prepared from small RNA fractions of alveolar macrophages isolated from 8 different healthy animals (Bos taurus). From the data, the potential novel miRNAs were predicted, and the expression levels of the known miRNAs were determined. more...

Organism:

Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15749

8 Samples

Download data: TXT

(Submitter supplied) The semen of Small Tail Han Sheep has characteristics of high yield, high density, and good motility. To reveal the key miRNAs, mRNAs and miR-Targets regulatory mechanisms in Small Tail Han Sheep testes development, integrated analysis of miRNA and mRNA expression profiles in 2-, 6-, and 12-month-old testes were investigated by RNA-seq technology and bioinformatics methods. As the results shown: 630, 102, and 322 differentially expressed (DE) mRNAs; 5, 1 and 4 DE known miRNAs; 132, 105 and 24 DE novel miRNAs were identified in 2- vs 6-month-old, 6- vs 12-month-old, and 2- vs 12-month-old testes, respectively. more...

Organism:

Ovis aries

Type:

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

Platform:

GPL18884

18 Samples

Download data: TXT

(Submitter supplied) We conducted the genome-wide mRNA expression profiling in parallel with miRNA expression profiling using RNA samples extracted from rat incisor enamel organs, so as to refine the number of predicted gene targets for miRNA regulators.

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL6101

8 Samples

Download data: TXT

(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) Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) are the predominant etiological agents of hand, foot, and mouth disease (HFMD) and both belong to the human enterovirus A species of the Picornaviridae family. These viruses share similar genetic homology, although the clinical manifestations of HFMD caused by the two viruses have some discrepancies. Furthermore, the underlying mechanisms leading to these differences remain unclear. more...

Organism:

Macaca mulatta

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL14954

6 Samples

Download data: XLSX

(Submitter supplied) We used next-generation sequencing technology to characterize mRNA-seq and miRNA-seq of testes and ovaries of Odontobutis potamophila to elucidate the molecular mechanisms of sex determination and differentiation. We were able to find miRNA-mRNA pairs using bioinformatics analysis and miRNA prediction algorithms.

Organism:

Odontobutis potamophilus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL22871

12 Samples

Download data: FASTA, XLSX

(Submitter supplied) MiRNAs are small non-coding single stranded RNAs that play crucial roles in numerous biological processes. Vertebrate herpesviruses encode multiple viral miRNAs that modulate host and viral genes. However, the roles of viral miRNAs in invertebrates have not been fully determined. Here, we used high-throughput sequencing to analyse miRNA and mRNA expression profiles of Carassius auratus gibelio in response to infection by cyprinid herpesvirus 2 (CyHV-2). more...

Organism:

Carassius gibelio

Type:

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

Platform:

GPL22713

12 Samples

Download data: FASTA, XLSX

(Submitter supplied) Pathogen bacteria infections can lead to dynamic changes of microRNA (miRNA) and mRNA expression profiles, which may control synergistically the outcome of immune responses. To reveal the role of dynamic miRNA-mRNA regulation in Drosophila innate immune responses, we have detailedly analyzed the paired miRNA and mRNA expression profiles at three time points during Drosophila adult males with Micrococcus luteus (M. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

18 Samples

Download data: XLSX

(Submitter supplied) Purpose: to evaluate changes in the expression of microRNAs, which contribute to explain a phenotype of differential pigmentation and reduction of proliferation, in B16F1 melanoma cells exposed to analogue of tymidine BrdU or aminoacid L-Tyr Methods: Small RNAseq evaluation of the expression profiles of miRNAs in B16F1 melanoma cells exposed to BrdU (0.25 μg / mL) and L-Tyr (5 mM) for 72 h, as well as the expression by RT-qPCR of some molecular targets related with melanogenesis, cell cycle and senescence and construction of network models of regulation and co-expression of microRNAs. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17021

9 Samples

Download data: CSV

(Submitter supplied) miRNAs are key post-transcriptional regulators of gene expression. However, it is still poorly understood how miRNAs themselves are regulated, mainly due to the sparse annotation of miRNA transcription start sites (TSSs). Here, we developed a novel method for identifying active miRNA TSSs from nascent transcriptomes generated by nuclear run-on sequencing. With the least data requirement, our method demonstrated better performance than existing methods. more...

Organism:

Homo sapiens

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

14 Samples

Download data: BEDGRAPH

(Submitter supplied) Dilated cardiomyopathy (DCM) entails a broad group of diseases, acquired or genetic, that share a similar phenotype. The understanding of gene-specific pathogenetic mechanisms and the determination of the functional effects of each variant may tailor different therapeutic strategies. MicroRNAs (miRNAs) are short sequences of non-coding RNA that play an important role in the development of several cardiovascular diseases, including DCM. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL18573

15 Samples

Download data: XLSX

(Submitter supplied) In this study, we used RNA-seq to investigate the transcriptomic (mRNA and miRNA) profiles of pancreatic cancer in 10 paired tumor and normal pancreatic samples from patients

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

40 Samples

Download data: TXT