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GSE51724
Drosophila melanogaster
6 Downloadable Samples
Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
We used microarrays to identify genes that are differentially expressed in the absence of miR-998 expression.
Publication Title
An intronic microRNA links Rb/E2F and EGFR signaling.
Sample Metadata Fields
Specimen part
View Samples- Caenorhabditis elegans
- 12 Downloadable Samples
Illumina HiSeq 2000
Description
In animals, microRNAs frequently form families with related sequences. The functional relevance of miRNA families and the relative contribution of family members to target repression have remained, however, largely unexplored. Here, we used the C. elegans miR-58 miRNA family, comprised primarily of four highly abundant members: miR-58.1, miR-80, miR-81 and miR-82, as a model to investigate the redundancy of miRNA family members and their impact on target expression in an in vivo setting. Overall design: RNA was extracted from different miR-58 family mutants (mir-58.1, mir-80; mir-58.1 and mir-80; mir-58.1; mir-81-82) and wild-type Bristol C. elegans strain at late L4 stage and submitted to transcriptome sequencing with Illumina HiSeq2000. The goal was to compare miR-58 target RNA expression and system-wide perturbations across various samples.
Publication Title
Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 275 Downloadable Samples
- Affymetrix Human Gene 2.1 ST Array (hugene21st)
Description
This SuperSeries is composed of the SubSeries listed below. A subset of samples profiled in this analysis were also profiled in Series GSE68127, and GSE104066. Corresponding glomerular transcriptome data can be found under GEO ID: GSE108109.
Publication Title
Metabolic pathways and immunometabolism in rare kidney diseases.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 196 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
summary : Glomerular Transcriptome from European Renal cDNA Bank subjects and living donors. Samples included in this analysis have been previously analyzed using older CDF definitions and are included under previous GEO submissions - GSE47183 (chronic kidney disease samples), and GSE32591 (IgA nephropathy samples).
Publication Title
Metabolic pathways and immunometabolism in rare kidney diseases.
Sample Metadata Fields
Specimen part, Disease
View Samples- Homo sapiens
- 194 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
summary : Tubulointerstitial transcriptome from ERCB subjects with chronic kidney disease and living donor biopsies. Samples included in this analysis have been previously analyzed using older CDF definitions and are included under previous GEO submissions - GSE47184 (chronic kidney disease samples), and GSE32591 (IgA nephropathy samples).
Publication Title
Metabolic pathways and immunometabolism in rare kidney diseases.
Sample Metadata Fields
Specimen part, Disease
View Samples- Homo sapiens
- 169 Downloadable Samples
- Affymetrix Human Gene 2.1 ST Array (hugene21st)
Description
Tubulointerstitial transcriptome from human kidney biopsies in Neptune and ERCB. A number of samples profiled in this analysis were also profiled in Series GSE68127.
Publication Title
Metabolic pathways and immunometabolism in rare kidney diseases.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 106 Downloadable Samples
- Affymetrix Human Gene 2.1 ST Array (hugene21st)
Description
Glomerular transcriptome from human kidney biopsies in Neptune and ERCB. A subset of samples profiled in this analysis were also profiled in Series GSE68127, and in GSE104066. Corresponding tubulointerstitial transcriptome data is submitted under GEO ID: GSE108113.
Publication Title
Metabolic pathways and immunometabolism in rare kidney diseases.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 30 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Microarrays were used to determine the change in gene expression of genes involved in the CDT1/NAE pathway
Publication Title
Quantitative proteomic analysis of cellular protein modulation upon inhibition of the NEDD8-activating enzyme by MLN4924.
Sample Metadata Fields
Cell line, Treatment, Time
View Samples- Caenorhabditis elegans
- 27 Downloadable Samples
- Illumina HiSeq 2500
Description
A-to-I RNA editing is a conserved and widespread phenomenon in which adenosine (A) is converted to inosine (I) by adenosine deaminases (ADARs) in double-stranded RNA regions. Although human RNAs contain millions of A-to-I editing sites, most of these occur in noncoding regions and their function is unknown. Knockdown of ADAR enzymes in C. elegans causes defects in normal development but is not lethal as it is in human and mouse, making C. elegans an ideal organism for studying the regulatory effects of RNA editing on the transcriptome. Previous studies in C. elegans indicated competition between RNA interference (RNAi) and RNA editing mechanisms, with the observation that lack of both mechanisms can suppress defects observed when only RNA editing is absent. To study the effects of RNA editing on gene expression and function, we established a novel screen that enabled to identify thousands of RNA editing sites in non-repetitive regions in the genome. These include dozens genes that are edited at their 3’UTR region. We found that these genes are mainly germline and neuronal genes and that they are downregulated in the absence of ADAR enzymes. Moreover, we discovered that almost half of these genes are edited in a developmental-specific manner. In addition, we found that many pseudogenes and other lncRNAs are also extensively downregulated in the absence of ADARs in embryo but not L4 larva developmental stage, while this downregulation is not observed in additional knockout of RNAi. Taken together, our results suggest a role for RNA editing in normal growth and development by regulating silencing via RNAi. Overall design: RNA-seq samples were generated from: 1. wildtype (N2) at embryo stage 2. wildtype (N2) at L4 stage 3. ADAR mutant (BB21 or BB4) worms at L4 stage 4. ADAR mutant (BB21 or BB4) worms at embryo stage 5. ADAR mutant and RNAi mutant (BB23, BB24) at embryo stage RNA in high and low molecular weight fractions was extracted by mirVana kit (ambion). mRNA was sequenced from the high molecular weight fraction by means of Illumina TruSeq® RNA Sample Preparation kit automated by Agilent Bravo Automated Liquid Handling Platform. The resulting libraries were sequences with an Illumina HiSeq 2500.
Publication Title
A-to-I RNA editing promotes developmental stage-specific gene and lncRNA expression.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 18 Downloadable Samples
- Illumina HiSeq 2500
Description
To uncover genes regulated by mTORC1 and estradiol in uterine Tsc2-null LAM like cells, we performed RNAseq on uteri from 12-week old wild-type (WT) and uterine-specific Tsc2-null (KO) mice that were either untreated (intact), oopherectomized (ovx) or oopherectomized + treated with 17ß-estradiol pellets (E2) for 8 weeks. We identified genes that were both estradiol- and TSC2-mediated. Overall design: Uterine mRNA profiles of 12 week old wild type (WT) and uterine-specific Tsc2-null (KO) mice in the presence or absence of estradiol were generated using Illumina HiSeq2500
Publication Title
Estrogen maintains myometrial tumors in a lymphangioleiomyomatosis model.
Sample Metadata Fields
Age, Specimen part, Cell line, Treatment, Subject
View Samples