Identification of Hundreds of Conserved and Non-conserved Human MicroRNAs
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE2708 | GEO | 2005/06/19
SECONDARY ACCESSION(S): PRJNA92359
REPOSITORIES: GEO
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Project description:Determining the expression of known and computationally predicted microRNAs by microRNA microarray in several tissues (placenta, testis, thymus, brain and prostate) Keywords: parallel sample microRNAs expression profile
2010-07-01 | E-GEOD-2708 | biostudies-arrayexpress
Project description:BackgroundMicroRNAs (miRNA) are small (20-25 nt) non-coding RNA molecules that regulate gene expression through interaction with mRNA in plants and metazoans. A few hundred miRNAs are known or predicted, and most of those are evolutionarily conserved. In general plant miRNA are different from their animal counterpart: most plant miRNAs show near perfect complementarity to their targets. Exploiting this complementarity we have developed a method for identification plant miRNAs that does not rely on phylogenetic conservation.ResultsUsing the presumed targets for the known miRNA as positive controls, we list and filter all segments of the genome of length approximately 20 that are complementary to a target mRNA-transcript. From the positive control we recover 41 (of 92 possible) of the already known miRNA-genes (representing 14 of 16 families) with only four false positives. Applying the procedure to find possible new miRNAs targeting any annotated mRNA, we predict of 592 new miRNA genes, many of which are not conserved in other plant genomes. A subset of our predicted miRNAs is additionally supported by having more than one target that are not homologues.ConclusionThese results indicate that it is possible to reliably predict miRNA-genes without using genome comparisons. Furthermore it suggests that the number of plant miRNAs have been underestimated and points to the existence of recently evolved miRNAs in Arabidopsis.
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Project description:The purpose of these experiments was to determine the 5' and 3' transcriptional termini of genes on chromosomes 21-22. Towards this end, we mapped the poly A + RNA isolated from 12 normal tissues and four cell lines. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf polyA+ RNAs from 11 tissues (Brain Frontal Lobe, Brain Hippocampus, Brain Hypothalamus, Cerebellum, Ovary, Placenta, Prostate, Testis, Fetal Kidney, Fetal Spleen, Fetal Thymus; all from BD Clontech) and 5 cell lines (GM06990, HeLaS3, HepG2, K562, tert-BJ) using the BD SMARTTM RACE cDNA amplification kit (BD Clontech Cat. No.634914). A single array with no replicates was run for each sample with a pool of ~23-24 RACE reactions per sample.
2010-05-15 | E-GEOD-17358 | biostudies-arrayexpress
Project description:Recent transcriptomic analyses have uncovered widespread occurrence of natural antisense transcripts (NATs), which are transcribed from the opposite strand of another discrete transcribed region. We describe a novel probe-design technique for DNA microarray analysis that specifically targets the complementary strand of annotated genes, and show that this technique can successfully identify novel NAT expression in normal and tumor samples. Northern and in situ hybridization analyses of selected examples (Acaa1, Aard, and Thbd) confirmed their transcription and dynamic expression in a tissue- and cell-type-specific manner. Our data highlight the importance of NAT expression in the regulation of cellular processes and in oncogenesis. The fundamental basis of the technology described in this paper is applicable to all genes and sample types for the identification of NAT expression that is not possible by conventional cDNA/EST/CAGE information. Total RNA for the mouse (C57BL/6J) microarray experiments was isolated from SL10 cells (fibroblast cell line), brain, heart, intestine, kidney, liver, lung, placenta (d.p.c. 10.5 and 13.5), spleen, stomach, testis, and thymus. Testis was from C57BL/6J males (8 to 10 weeks), placenta was from pregnant mice, and the other tissue was from both male and female mice. Unpublished data has been masked in the supplementary feature extraction files.
2010-05-06 | E-GEOD-14372 | biostudies-arrayexpress
Project description:Comparing miRNAs expression levels in chorioamniotic membranes from women at term in labor (TL), women at term not in labor (TNL) and women who deliverd preterm (PTLC). The goal was to see if miRNA levels are indicators of preterm delivery or spontaneous labor at term. A two-channel technology was used in this experiment in which a pooled reference RNA was used for competitive hybridization. The pooled reference was generated at Exiqon in Denmark from a mixture of several human tissues (placenta, thyroid, brain, adipose, spleen, liver, colon, skeletal muscle, ovary, kidney, heart, cervix, testes, esophagus, small intestine, prostate, trachea, thymus, bladder, lung).
2008-10-01 | E-TABM-469 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE15229: Massively Parallel Sequencing Identifies the MicroRNA Transcriptome of Normal and Malignant Human B cells GSE22895: Deep Sequencing of the Small RNA Transcriptome of Normal and Malignant Human B cells Identifies Hundreds of Novel MicroRNAs: microarray analysis Refer to individual Series
2010-08-25 | E-GEOD-22898 | biostudies-arrayexpress
Project description:Conserved non-protein-coding DNA elements (CNEs) often encode cis-regulatory elements and are rarely lost during evolution. However, CNE losses that do occur can be associated with phenotypic changes, exemplified by pelvic spine loss in sticklebacks. Using a computational strategy to detect complete loss of CNEs in mammalian genomes while strictly controlling for artifacts, we find >600 CNEs that are independently lost in at least two mammalian lineages, including a spinal cord enhancer near GDF11. We observed several genomic regions where multiple independent CNE loss events happened; the most extreme is the DIAPH2 locus. We show that CNE losses often involve deletions and that CNE loss frequencies are non-uniform. Similar to less pleiotropic enhancers, we find that independently lost CNEs are shorter, slightly less constrained and evolutionarily younger than CNEs without detected losses. This suggests that independently lost CNEs are less pleiotropic and that pleiotropic constraints contribute to non-uniform CNE loss frequencies. We also detected 35 CNEs that are independently lost in the human lineage and in other mammals. Our study uncovers an interesting aspect of the evolution of functional DNA in mammalian genomes. Experiments are necessary to test if these independently lost CNEs are associated with parallel phenotype changes in mammals.
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Project description:In this study we performed RNA sequencing to determine and compare the transcriptome of regulatory T cells (Tregs) present in the thymus, placenta, spleen and white adipose tissue (FAT) of pregnant mice. We further assessed how the expression of the receptor Rank in the thymic medullary epithelia affects the transcriptional program of these Treg populations. For the isolation of viable and bona fide Tregs, we first generated RankWt (wild type control mice) and RankΔFoxn1 (which lack expression of Rank in the thymic epithelia) and further crossed them to mice that express GFP from the Foxp3 promoter. Neuropilin1 was used to mark the thymic origin of the Tregs. Equal numbers of Tregs (280 cells) were sorted as CD45-CD8-CD4+GFP+Neuropilin1High cells from the thymus and placenta of RankWtFoxp3GFP/GFP and RankΔFoxn1Foxp3GFP/GFP pregnant females at E17.5 (both samples from the same female; n=4 females per genotype). Thymus Tregs from non-pregnant littermate female mice for each genotype cohort were also studied. To increase robustness, the 280 placental Tregs were purified from 5 individual placentas per pregnant female (56 Tregs/placenta). Our study is the first one to determine the transcriptome of thymus and placenta Tregs during pregnancy and reveals that, partially dependent on Rank expression in the thymic epithelia, placental-resident Tregs are molecularly distinct from thymic Tregs. In a separate experiment with different pregnant mice than those used for thymus and placenta analysis, VAT Tregs (20-30 cells) and splenic Tregs (150 cells) were sorted (both samples from the same female) by using the same mouse lines (Rank Wt and RankΔFoxn1), embryological days of analysis (E17.5) and sorting strategies.
2020-10-21 | GSE97666 | GEO
Project description:diagnosis of abnormally invasive placenta
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Project description:Amphioxus is an extant species closest to the ancestry of vertebrates. Observation of microRNA (miRNA) distribution of amphioxus would lend some hints for evolutionary research of vertebrates. In this study, using the publicly available scaffold data of the Florida amphioxus (Branchiostoma floridae) genome, we screened and characterized homologs of miRNAs that had been identified in other species. In total, 68 pieces of such homologs were obtained and classified into 33 families. Most of these miRNAs were distributed as clusters in genome. Inter-species comparison showed that many miRNAs, which had been thought as vertebrate- or mammal-specific before, were also present in amphioxus, while some miRNAs that had been considered as protostome-specific before also existed in amphioxus. Compared with ciona, amphioxus had an apparent miRNA gene expansion, but phylogenetic analysis showed that the duplicated miRNAs or clusters of amphioxus had a higher homology level than those duplicated ones in vertebrates.
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