Similar studies for GEO DataSets (Select 200028637) - GEO DataSets

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Items: 20

Select item 2000286371.

Discovering, evolution, biogenesis, expression and target prediction of porcine micro-RNAs: new regulatory gene expression network in different tissues.

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

Organism:: Sus scrofa

Type:: Non-coding RNA profiling by array; Expression profiling by array

6 related Platforms
90 Samples

Download data: PDF, TXT

Series

Accession:: GSE28637

ID:: 200028637

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000286362.

Identification of responsive probes for mRNA transcripts of the pig (S. scrofa) genome

(Submitter supplied) Pig mRNAs Ensembl transcripts (Ver. 56) and UniGene (Ver. 38) sequences were used to produce a dedicated microarray platform to analyze mRNAs gene expression. Based on sequence similarity we rejected UniGene features that overlapped more than 40% with an Ensembl transcript. After this filter we obtained 40,267 UniGene clusters and 19,603 Ensembl transcripts (protein coding + pseudogenes + retrotransposed elements). more...

Organism:: Sus scrofa

Type:: Expression profiling by array

Platform:: GPL13411
1 Sample

Download data: TXT

Series

Accession:: GSE28636

ID:: 200028636

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Select item 2000281403.

Evaluation of miRNA expression in 14 different tissues by the RAKE technology

(Submitter supplied) The short length of miRNAs results in a high dynamic range of melting temperatures and therefore impedes a proper selection of detection probes or optimized PCR primers. While miRNA microarrays allow for massive parallel and accurate relative measurement of all known miRNAs, they have so far been less useful as an assay for absolute quantification. Here we developed a new method based not only to the hybridization process that presents the limits before described, but integrating the hybridization to an enzymatic reaction. more...

Organism:: Sus scrofa

Type:: Non-coding RNA profiling by array

Platform:: GPL13322
28 Samples

Download data: TXT

Series

Accession:: GSE28140

ID:: 200028140

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Select item 2000281394.

Identification of the 5' end of the pig miRNA by the RAKE technology

(Submitter supplied) We applied a new computational approach to predict specie-specific and conserved miRNAs, than experimentally confirmed by a modified RNA-primed Array-based Klenow Extension (RAKE) method. We identified 489 conserved and 1,178 pig-specific novel miRNAs increasing our tally of confirmed miRNAs to 1,667 novel miRNAs. In addition, RAKE allowed the identification of miRNA isoforms (isomiRs) that we demonstrated to be differentially expressed across tissues suggesting that subtle variability in isomiR expression is regulated and biologically meaningful.

Organism:: Sus scrofa

Type:: Non-coding RNA profiling by array

Platform:: GPL13321
9 Samples

Download data: TXT

Series

Accession:: GSE28139

ID:: 200028139

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Select item 2000281385.

Identification of the 3' end of the pig miRNA by the RAKE technology [platform 2: 9003179]

Organism:: Sus scrofa

Type:: Non-coding RNA profiling by array

Platform:: GPL13320
12 Samples

Download data: TXT

Series

Accession:: GSE28138

ID:: 200028138

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Select item 2000281376.

Identification of the 3' end of the pig miRNA by the RAKE technology [platform 1: 9003467]

Organism:: Sus scrofa

Type:: Non-coding RNA profiling by array

Platform:: GPL13319
12 Samples

Download data: TXT

Series

Accession:: GSE28137

ID:: 200028137

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Select item 2000278537.

Messenger RNA transcript expression in the pig (S. scrofa)

(Submitter supplied) 90K Combimatrix gene expression microarrays were composed by 17,048 replicated probes and 963 not replicated specific for the Ensembl (Ver. 56) Transcripts (protein coding + pseudogenes + retrotransposed elements), 11,363 replicated probes specific for the UniGene clusters (Ver. 38) of length comprised between 778 nt and 1,348 nt, and 28,790 single probes specific for the remaining UniGene clusters. more...

Organism:: Sus scrofa

Type:: Expression profiling by array

Platform:: GPL13259
28 Samples

Download data: TXT

Series

Accession:: GSE27853

ID:: 200027853

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Select item 2000291018.

MicroRNAs and their isomiRs function cooperatively to target common biological pathways

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

Organism:: Homo sapiens

Type:: Expression profiling by array; Non-coding RNA profiling by array

Platforms:: GPL10558 GPL9081
20 Samples

Download data: TXT

Series

Accession:: GSE29101

ID:: 200029101

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Select item 2000291009.

MicroRNAs and their isomiRs function cooperatively to target common biological pathways (Agilent miRNA array)

(Submitter supplied) This data set is part of a larger study: Variants of microRNAs, (isomiRs) are commonly reported in deep-sequencing studies; however the functional significance of these variants remains controversial. To assess their biological relevance, we have performed ultra-deep miRNA-seq on ten adult human tissues, and created an analysis pipeline (miRNA-MATE) to align, annotate, and analyze miRNAs and their isomiRs. more...

Organism:: Homo sapiens

Type:: Non-coding RNA profiling by array

Platform:: GPL9081
6 Samples

Download data: TXT

Series

Accession:: GSE29100

ID:: 200029100

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Select item 20002904310.

MicroRNAs and their isomiRs function cooperatively to target common biological pathways (Illumina expression beadchip)

(Submitter supplied) Variants of microRNAs, (isomiRs) are commonly reported in deep-sequencing studies; however the functional significance of these variants remains controversial. To assess their biological relevance, we have performed ultra-deep miRNA-seq on ten adult human tissues, and created an analysis pipeline (miRNA-MATE) to align, annotate, and analyze miRNAs and their isomiRs. We find that isomiRs share sequence and expression characteristics with canonical miRNAs, and are generally strongly correlated with canonical miRNA expression. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL10558
14 Samples

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Series

Accession:: GSE29043

ID:: 200029043

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Select item 20002789811.

Genome-wide identification of microRNAs in larch and stage-specific modulation of eleven conserved microRNAs and their targets during somatic embryogenesi

(Submitter supplied) MicroRNAs (miRNAs) are emerging as essential regulators of biological processes. Somatic embryogenesis is one of the most important techniques for gymnosperm breeding programs, but there is little understanding of its underlying mechanism. To investigate the roles of miRNAs during somatic embryogenesis in larch, we constructed a small RNA library from somatic embryos. High-throughput sequencing of the library identified 83 conserved miRNAs from 35 families, 16 novel miRNAs, and 14 plausible miRNA candidates, with a high proportion specific to larch or gymnosperms. more...

Organism:: Larix kaempferi

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

Platform:: GPL13980
1 Sample

Download data: TXT

Series

Accession:: GSE27898

ID:: 200027898

PubMed Similar studies

Select item 20008318912.

PyMT 4 stages tumor progression microRNA sequencing

(Submitter supplied) We sequenced mammary gland samples of MMTV-PyMT mouse from 4 stages (hyperplasia at week 6, adenoma/MIN at week 8, early carcinoma at week 10, and late carcinoma with lung metastasis at week 12) during tumor progression.

Organism:: Mus musculus

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

Platform:: GPL17021
24 Samples

Download data: CSV

Series

Accession:: GSE83189

ID:: 200083189

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20001788513.

MicroRNAome of porcine prenatal and postnatal development.

(Submitter supplied) Sus scrofa (pig, or swine) is one of the most important economic animals and a close biological model for complex human diseases such as obesity and diabetes. It is therefore utterly important to decode the porcine microRNAome (miRNAome) as in the literature only a small portion of it is known. In this work, a comprehensive search for porcine microRNAs (miRNAs) by Illumina sequencing was performed in ten small RNA libraries prepared from mixtures of assorted tissues, which included those collected from fetuses to adult pigs. more...

Organism:: Sus scrofa

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

Platform:: GPL9126
10 Samples

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Series

Accession:: GSE17885

ID:: 200017885

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20002771314.

Genome-wide analysis of gene expression patterns in mir-122 knockout mice livers

(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

Series

Accession:: GSE27713

ID:: 200027713

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Select item 20006252115.

High-throughput deep sequencing reveals that microRNAs play important roles in salt adaptation of euhalophyte Salicornia europaea

(Submitter supplied) Backgroud: microRNA (miRNA) is implicated in plant development processes, playing pivotal roles in plant adaptation to environmental stresses. Salicornia europaea, a salt mash euhalophyte, is a good model plant to study salt adaptation mechanisms. It is also attractive in being vegetables, forage and oilseed that can be used for saline land reclamation and biofuel precursor production on marginal lands. more...

Organism:: Salicornia europaea

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

Platform:: GPL19315
6 Samples

Download data: FA

Series

Accession:: GSE62521

ID:: 200062521

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20007803116.

microRNA profiling of Sprague Dawley organs

(Submitter supplied) We performed deep sequencing of the miRNAs present in ~20 toxicologically relevant tissues in Sprague Dawley rats and used three independent analysis of the data to determine which miRNAs are tissue specific and tissue enriched.

Organism:: Rattus norvegicus

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

Platform:: GPL14844
458 Samples

Download data: TXT

Series

Accession:: GSE78031

ID:: 200078031

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20008019817.

Gene expression data of micro RNA from skeletal muscle sample of pig breed Duroc and Pietrain with malignant hyperthermia syndrome homozygous negative

(Submitter supplied) Gene expression data of micro RNA from skeletal muscle sample of pig breed Duroc and Pietrain at adult stage.

Organism:: synthetic construct; Sus scrofa

Type:: Non-coding RNA profiling by array

Platform:: GPL16384
20 Samples

Download data: CEL

Series

Accession:: GSE80198

ID:: 200080198

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20006826718.

Identification of conserved and species-specific microRNAs in tea plant (Camellia sinensis) by deep sequencing

(Submitter supplied) In this study, it is noticeable that 32 tea-specific miRNAs were confirmed on the base of genome survey, using deep sequencing and microarray hybridization, and many miRNAs might associate with secondary metabolites synthesis.

Organism:: Camellia sinensis

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

Platform:: GPL20107
1 Sample

Download data: TXT

Series

Accession:: GSE68267

ID:: 200068267

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20003598219.

Identifying microRNA-mRNA regulatory networks in colorectal cancer by a combination of expression profile and bioinformatics analysis

(Submitter supplied) A multi-step approach combining microarray profile and bioinformatics analysis was adopted to identify the CRC specific miRNA-mRNA regulatory network. First, differentially expressed miRNAs and mRNAs were found out in CRC samples compared with normal epithelial tissues by miRNA and mRNA microarray respectively. Secondly the target mRNAs of dysregualted miRNA were identified by a combination of Pearson correlation coefficient between the expression level of miRNAs and mRNAs and online miRNA target predicting databases. more...