Similar studies for GEO DataSets (Select 200066718) - GEO DataSets

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Items: 20

Select item 2000667181.

Identification of small non-coding RNAs in zebrafish

(Submitter supplied) MicroRNAs (miRNAs) are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes, namely developmental timing, cell differentiation, cell proliferation, immune response and infection. For this reason, their identification is essential to understand eukaryotic biology. more...

Organism:: Danio rerio

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

Platform:: GPL19872
12 Samples

Download data: TXT

Series

Accession:: GSE66718

ID:: 200066718

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Select item 2000804002.

Small RNA sequencing of human prostate cancer samples

(Submitter supplied) We sequenced the small RNA transcriptome of prostate cancer at different stages and generated a quantified catalogue of 3927 small non-coding RNAs (sncRNAs) detected in normal and malignant prostate tissue. From these sncRNAs less than half are microRNAs. The remaining sncRNAs represent stable sncRNAs species that originate from snoRNA, tRNA and other sncRNAs.

Organism:: Homo sapiens

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

Platform:: GPL9052
11 Samples

Download data: TXT

Series

Accession:: GSE80400

ID:: 200080400

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Select item 2000997693.

Global gene repression by Dicer-independent tRNA fragments

(Submitter supplied) We have performed RNA sequencing after tRNA/tRF overexpression

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
4 Samples

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Series

Accession:: GSE99769

ID:: 200099769

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Select item 2001197714.

Genome-wide identification and characterization of transfer RNA-derived small RNAs in Plasmodium falciparum

(Submitter supplied) In this study, we performed deep sequencing and bioinformatics analyses of short RNAs from Plasmodium falciparum parasites to identify and characterize novel type of small RNAs. A total of 14,828,877 raw reads were produced from small RNA libraries. We detected a new type of small RNA from tranfer RNA known as tRFs.

Organism:: Plasmodium falciparum 3D7

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

Platform:: GPL17634
1 Sample

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Series

Accession:: GSE119771

ID:: 200119771

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Select item 2001541655.

tRNA-seq and YAMAT-seq profiling the expressions of tRNA-derived fragments and tRNAs in plants

(Submitter supplied) Here, we apply tRNA-seq and YAMAT-seq to profile the expressions of tRFs and tRNAs in plants. We provide a high-quality expression atlas of tRFs and tRNAs in Arabidopsis and rice, and uncover complex tRF population and the dynamic expressions of tRNA genes in plants.

Organism:: Glycine max; Hordeum vulgare; Triticum aestivum; Sorghum bicolor; Setaria italica; Zea mays; Arabidopsis thaliana

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

7 related Platforms
13 Samples

Download data: TXT, XLSX

Series

Accession:: GSE154165

ID:: 200154165

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Select item 2001246086.

Quantification of tRNA-derived fragments in Arabidopsis and rice

(Submitter supplied) Here, we adopt a method that combines tRNA-seq and cp-RNA-seq to identify and quantify tRFs and tRNAs in plants. We provide a high-quality expression atlas of tRFs and tRNAs in Arabidopsis and rice, and uncovers complex tRFs repertoire and the dynamic expressions of tRNA genes in plants.

Organism:: Arabidopsis thaliana; Oryza sativa

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

Platforms:: GPL23013 GPL21785
24 Samples

Download data: XLSX

Series

Accession:: GSE124608

ID:: 200124608

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Select item 2001065117.

A novel class of tRNA-derived small non-coding RNAs in response to myocardial hypertrophy and contribute to intergenerational inheritance

(Submitter supplied) tRNA-derived fragments (tRFs) have served as new class of non-coding RNA and played important role in regulating cellular RNA processing and protein translation, which was also proved have function on the intergenerational effects of paternal disease. However, there was no study reported the influence of tRFs on myocardial hypertrophy. In the current study, we explore the hypothesis that tRFs in response to myocardial hypertrophy and contribute to intergenerational inheritance.We used isoproterenol induced myocardial hypertrophy rat model. more...

Organism:: Rattus norvegicus

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

Platform:: GPL14844
6 Samples

Download data: FA

Series

Accession:: GSE106511

ID:: 200106511

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Select item 2000574148.

Characterization of Sus scrofa small RNA sequences present in both female and male gonads

(Submitter supplied) We used deep sequencing to characterize 3 families of sRNAs (piRNAs, miRNAs, and tRFs) present in Sus scrofa gonads and focused on the sRNA fraction present in both male and female gonads. Of the sequences detected in the testes, 2.6% of piRNAs, 9% of miRNAs, and 10% of tRFs were also present in the ovaries. Notably, the majority of the shared piRNAs mapped to the introns of ribosomal RNAs and were derived from clustered loci. more...

Organism:: Sus scrofa

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

Platform:: GPL15064
2 Samples

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Series

Accession:: GSE57414

ID:: 200057414

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Select item 2001398979.

Small non-coding RNA discovery and profiling with sRNAtools based on high-throughput sequencing

(Submitter supplied) Small non-coding RNAs (sncRNAs) are generated from different genomic loci and have important roles in biological processes, such as cell proliferation and regulation of gene expression. Next-generation sequencing (NGS) has provided an unprecedented opportunity to discover and quantify diverse kinds of sncRNAs, such as tRFs (tRNA-derived small RNA fragments), phasiRNAs (phased, secondary, small interfering RNAs), piRNAs and plant specific 24-nt short interfering RNAs (siRNAs). more...

Organism:: Populus deltoides

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

Platform:: GPL20012
11 Samples

Download data: TXT

Series

Accession:: GSE139897

ID:: 200139897

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Select item 20013888910.

Dysregulation of different classes of tRNA fragments in chronic lymphocytic leukemia

(Submitter supplied) We analyzed small RNA sequencing data from CD5+/CD19+ B cells of a cohort of indolent and aggressive CLL patients compared with CD19+ B-cells of healthy donors. We identified tsRNA signatures in indolent and aggressive CLL vs. normal B-cells; we also found a drastic dysregulation of the expression of mature tRFs in CLL.

Organism:: Homo sapiens

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

Platform:: GPL16791
28 Samples

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Series

Accession:: GSE138889

ID:: 200138889

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Select item 20023178511.

The serum small non-coding RNA (SncRNA) landscape as a molecular biomarker of age associated muscle dysregulation and insulin resistance in older adults.

(Submitter supplied) Small noncoding RNAs (sncRNAs) are implicated in age-associated pathologies, including sarcopenia and insulin resistance (IR). This study aimed to characterise the wider circulating sncRNA transcriptome of older individuals and associations with sarcopenia and IR. Total RNA was used for sncRNA expression including miRNAs, transfer RNAs (tRNAs), tRNA-associated fragments (tRFs) and piwi-interacting RNAs (piRNAs) was measured in serum from 21 healthy and 21 sarcopenic women matched for age (mean 78.9 years) and HOMA2-IR from the Hertfordshire Sarcopenia Study. more...

Organism:: Homo sapiens

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

Platform:: GPL16791
43 Samples

Download data: TXT

Series

Accession:: GSE231785

ID:: 200231785

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Select item 20013919112.

tRNA-derived fragments and microRNAs in the maternal-fetal interface of a mouse maternal-immune-activation autism model

(Submitter supplied) We analyzed the small RNA composition of mouse placenta/decidua to determine whether there are specific differences in small RNAs during fetal development and in response to maternal immune activation.

Organism:: Mus musculus

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

Platform:: GPL19057
84 Samples

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Series

Accession:: GSE139191

ID:: 200139191

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Select item 20006360513.

Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement

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

Organism:: Homo sapiens

Type:: Expression profiling by array; Other

Platforms:: GPL11154 GPL10558
102 Samples

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Series

Accession:: GSE63605

ID:: 200063605

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Select item 20006360414.

YBX1 HITS-CLIP

(Submitter supplied) In order to identify YBX1 binding sites on endogenous RNA, we performed HITS-CLIP on endogenous YBX1

Organism:: Homo sapiens

Type:: Other

Platform:: GPL11154
3 Samples

Download data: FA

Series

Accession:: GSE63604

ID:: 200063604

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Select item 20006359715.

YBX1 small-RNA HITS-CLIP

(Submitter supplied) In order to identify YBX1 binding sites on tRNA fragments, we performed small-RNA HITS-CLIP on endogenous YBX1

Organism:: Homo sapiens

Type:: Other

Platform:: GPL11154
3 Samples

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Series

Accession:: GSE63597

ID:: 200063597

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Select item 20006356516.

YBX1-dependent LNA-tRF-mediated modulation of transcript stability

(Submitter supplied) In order to identify YBX1-dependent targets that are modulated upon changing the levels of endogenous tRFs, we used transient transfection of antisense locked-nucleic acids (LNAs) against tRFAsp, tRFGly, tRFGlu, and tRFTyr followed by alpha-amanitine treatment, RNA extraction at time points 0 and 8hr post-treatment, and transcriptomic profiling.

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL10558
48 Samples

Download data: TXT

Series

Accession:: GSE63565

ID:: 200063565

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Select item 20006356417.

YBX1-dependent LNA-tRF-mediated modulation of gene expression

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL10558
24 Samples

Download data: TXT

Series

Accession:: GSE63564

ID:: 200063564

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Select item 20006356318.

YBX1-dependent LNA-tRF-mediated modulation of gene expression under hypoxia

(Submitter supplied) In order to test whether inhibition of tRFs induced under hypoxia would counteract the YBX1-dependent reduction of target transcripts, we used transient transfection of antisense locked-nucleic acids (pooled LNAs) against tRFAsp, tRFGly, tRFGlu, and tRFTyr under hypoxia followed by microarray profiling.

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL10558
8 Samples

Download data: TXT

Series

Accession:: GSE63563

ID:: 200063563

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Select item 20006356219.

YBX1-dependent hypoxia-induced modulation of gene expression

(Submitter supplied) In order to identify YBX1-dependent targets that are modulated under hypoxic conditions, we used control and YBX1 knockdown cells grown under normoxia and hypoxia to profile gene expression levels.

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL10558
16 Samples

Download data: TXT

Series

Accession:: GSE63562

ID:: 200063562

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Select item 20011490420.

Differential expression of human tRNA genes drives the abundance of tRNA-derived fragments

(Submitter supplied) The human genome encodes hundreds of tRNA genes but their individual contribution to the tRNA pool is not fully understood. Deep sequencing of tRNA transcripts (tRNA-Seq) can estimate tRNA abundance at single gene resolution, but tRNA structures and post-transcriptional modifications impair these analyses. Here we present a bioinformatics strategy to investigate differential tRNA gene expression and use it to compare tRNA-Seq datasets from cultured human cells and human brain. more...

Organism:: Homo sapiens

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

Platform:: GPL11154
8 Samples

Download data: XLS

Series

Accession:: GSE114904

ID:: 200114904

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