Transcriptome of short RNA fraction in Rickettsia conorii
Ontology highlight
ABSTRACT:
ORGANISM(S): Rickettsia conorii str. Malish 7
SUBMITTER: AurM-CM-)lie RenvoisM-CM-)
PROVIDER: E-GEOD-27647 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Comparisons of gene expression profiles between ovaries of before (day 0) and after eyestalk ablation (days 1, 4 and 7) of domesticated 14-month-old black tiger shrimp (Penaeus monodon) were made using a cDNA microarray. Differentially expressed genes were identified through the microarray analysis, and the microarray results were confirmed by real-time PCR. Selected genes were further characterized. A cDNA microarray consisting of 5,568 features was constructed from EST libraries of P. monodon. RNA samples were extracted from the ovaries of before (day 0) and after eyestalk ablation at days 1, 4 and 7 from shrimp from the Shrimp Genetic Improvement Center, Thailand. The RNA was converted into cDNA by indirect aminoallyl-cDNA labelling method (LabelStar Array, Qiagen). aa-cDNA from day 0 samples were coupled with Cy3 dye as a reference, and those from days 1, 4 and 7 were coupled with Cy5 dye.
2012-05-01 | E-GEOD-29025 | biostudies-arrayexpress
Project description:Comparisons of gene expression profiles from testis of wild and domesticated male brooders were made through a cDNA microarray in the black tiger shrimp (Penaeus monodon). Differentially expressed genes were identified through the microarray analysis, and the microarray results were confirmed by real-time PCR. Selected genes were further characterized. A cDNA microarray was constructed from the EST libraries of P. monodon, consisting of 5,568 features. RNA samples were extracted from testes of pooled juveniles (4 month-old, pooled from n=114), broodstocks from West and East sides of Thailand, and domesticated broodstocks of 10-, 14-, and 18-month old. The RNA from testis of pooled juveniles was labeled with Cy3 dye as a reference and those of the broodstocks were labeled with Cy5 dye.
2012-05-11 | E-GEOD-21890 | biostudies-arrayexpress
Project description:Comparisons of gene expression profiles between testis and ovary of juvenile and wild brooders were made through a cDNA microarray in the black tiger shrimp (Penaeus monodon). Differentially expressed genes were identified through the microarray analysis, and the microarray results were confirmed by real-time PCR. Selected genes were further characterized. A cDNA microarray was constructed from the EST libraries of P. monodon, consisting of 5,568 features. RNA samples were extracted from both testes and ovaries of pooled juveniles (4 month-old, pooled from n=114 ), individual juvenile and broodstocks from West sides of Thailand. The RNA from ovaries were labeled with Cy3 dye as a reference and those of testes were labeled with Cy5 dye.
2011-05-27 | E-GEOD-22090 | biostudies-arrayexpress
Project description:Identification of testis-relevant genes using in silico analysis from testes ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon) A total of 4,803 ESTs from the testis library were unidirectionally sequenced and analyzed in silico using a customizable data analysis package, ESTplus. A total of 2,702 unique sequences from 424 contigs and 2,278 singletons were identified. Approximately, 1,134 sequences from the total of 2,702 unique sequences (contigs and singletons) are homologous to genes with known functions. Some of which (mago nashi, insulin-degrading enzyme, actin-depolymerizing factor) are related to testicular development in studies of other organisms. Moreover, the sequences were further characterized according to the gene ontology categories (41% biological process, 24% molecular function, 35% cellular component). By comparing with the EST libraries of other tissues, a total of 1,579 possible testis-specific ESTs were identified. Some of these testis-specific ESTs, such as Phospholipase A2 and Matrix Metalloproteinases, have functions relevant to testicular development. In addition, novel ESTs (621 ESTs) that have never been identified in any ESTs from the Penaeidae family were found in this study. Through cDNA microarray analysis, some of testis-specific ESTs were preferentially expressed in testes to ovary; one of which was a saposin homolog. Therefore, saposin was further characterized by real-time PCR and its full-length sequence was obtained by RACE-PCR. A cDNA microarray was constructed from the EST libraries of P. monodon, consisting of 5,376 features (1,125 features were amplified from testis EST libraries). RNA samples were extracted from testes and ovaries of juveniles (4 month-old, pooled from n=112 and n=98 for testes and ovaries, respectively) and broodstocks from Andaman Sea. The RNA from ovary was labeled with Cy3 dye as a reference and that from testes was labeled with Cy5 dye.
2010-11-04 | E-GEOD-19037 | biostudies-arrayexpress
Project description:To investigate the contribution of small non-coding RNAs, including microRNAs, to stress response in C. elegans, we examined their expression changes using Illumina deep-sequencing technology. Stress conditions we examined include heat shock, Pseudomonas aeruginosa (PA-14) and L1 arrest. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Total RNAs were purified from wild-type young adult animals that were exposed to each stress condition, and used for cDNA library preparation for small RNAs. As for the L1 arrest sample, first wild-type embryos were collected and cultured without a food source in M9 buffer for 48 hrs with rotation, and then RNAs purified from L1 animals in a developmentally arrested state were used for the library preparation. These cDNA libraries established were sequenced with Illumina Genome Analyzer II.
2010-12-02 | E-GEOD-25739 | biostudies-arrayexpress
Project description:A growing body of evidence in mammalian cells indicates that secreted vesicles can be used to mediate intercellular communication processes by transferring various bioactive molecules, including mRNAs and microRNAs. Based on these findings, we decided to analyze whether T. cruzi-derived extracellular vesicles contain RNA molecules and performed a deep sequencing and genome-wide analysis of a size-fractioned cDNA library (16M-bM-^@M-^S40 nt) from extracellular vesicles secreted by noninfective epimastigote and infective metacyclic trypomastigote forms. Our data show that the small RNAs contained in these extracellular vesicles originate from multiple sources, including tRNAs. In addition, our results reveal that the variety and expression of small RNAs are different between parasite stages, suggesting diverse functions. Taken together, these observations call attention to the potential regulatory functions that these RNAs might play once transferred between parasites and/or to mammalian host cells. Small RNAs profiles (16-40 nt) of epimastigote-derived extracellular vesicles, metacyclic trypomastigote-derived extracellular vesicles and metacyclic trypomastigote parental cells.
2014-07-15 | E-GEOD-54111 | biostudies-arrayexpress
Project description:miRNA profiling of curcumin treated Y79 cells with untreated Y79 cells (control). Aim of the study to see whether any oncogenes or tumor suppressor genes are regulated on curcumin treatment in Y79 cells. Agilent one-color experiment,Organism: Human ,Agilent-019118 Human miRNA Microarray 2.0 G4470B , Labeling kit: Agilent miRNA labeling reagent and Hybridization Kit Cat # 5190-0408
2010-04-01 | E-GEOD-21126 | biostudies-arrayexpress
Project description:To understand how microRNAs are involved in stress response, we examined their expression changes in C. elegans animals that were exposed to stress conditions, including heat shock, oxidation, hypoxia and starvation. Total RNAs were purified from young adult animals that were exposed to each stress, and used for cDNA library preparation for small RNAs. In this experiment, spe-9(hc88), a temperature sensitive sterile mutant, that were cultured at 23dC, was used in order to avoid the effect from developing embryos. Stress conditions we examined include: Heat shock (32M-BM-0C, 6 hrs), Recovery from heat shock (6 hrs recovery at 23M-BM-0C after heat shock treatment at 32M-BM-0C for 6 hrs), Hypoxia (0.01%, 6 hrs), Oxidation (Juglone 750 M-NM-<M, 6 hrs), Starvation (complete food deprivation, 12 hrs). In addition to these stress conditions, RNAs were prepared from normally cultured, untreated animals at three time points, 0 hr (baseline), 6 hrs (as controls for heat shock, hypoxia and oxidation) and 12 hrs (as controls for heat shock recovery and starvation) after starting stress exposure. These cDNA libraries established were sequenced with Illumina Genome Analyzer II.
2012-02-04 | E-GEOD-35529 | biostudies-arrayexpress
Project description:Purpose: MicroRNAs (miRNAs) are ubiquitous components of endogenous plant transcriptome. miRNAs are small, single-stranded and ~21 nt long RNAs which regulate gene expression at the post-transcriptional level and are known to play essential roles in various aspects of plant development and growth. Previously, a number of miRNAs have been identified in potato through in silico analysis and deep sequencing approach. However, identification of miRNAs through deep sequencing approach was limited to a few tissue types and developmental stages. This study reports the identification and characterization of potato miRNAs in three different vegetative tissues and four stages of tuber development by high throughput sequencing. Results: Small RNA libraries were constructed from leaf, stem, root and four early developmental stages of tuberization and subjected to deep sequencing, followed by bioinformatics analysis. A total of 89 conserved miRNAs (belonging to 33 families), 147 potato-specific miRNAs (with star sequence) and 112 candidate potato-specific miRNAs (without star sequence) were identified. The digital expression profiling based on TPM (Transcripts Per Million) and qRT-PCR analysis of conserved and potato-specific miRNAs revealed that some of the miRNAs showed tissue specific expression (leaf, stem and root) while a few demonstrated tuberization stage-specific expressions. Targets were predicted for identified conserved and potato-specific miRNAs, and predicted targets of four conserved miRNAs, miR160, miR164, miR172 and miR171, which are ARF16 (Auxin Response Factor 16), NAM (NO APICAL MERISTEM), RAP1 (Relative to APETALA2 1) and HAIRY MERISTEM (HAM) respectively, were experimentally validated using 5M-bM-^@M-2RLM-RACE (RNA ligase mediated rapid amplification of cDNA ends). Gene ontology (GO) analysis for potato-specific miRNAs was also performed to predict their potential biological functions. Conclusions: We report a comprehensive study of potato miRNAs at genome-wide level by high-throughput sequencing and demonstrate that these miRNAs have tissue and/or developmental stage specific expression profile. Also, predicted targets of conserved miRNAs were experimentally confirmed for the first time in potato. Our findings indicate the existence of extensive and complex small RNA population in this crop and suggest their important role in pathways involved in diverse biological processes, including tuber developmental process. Total seven (Leaf, Root, Stem, Potato Tuber stage 0(PT0),Potato Tuber stage 1(PT1),Potato Tuber stage 2(PT2),Potato Tuber stage 3(PT3) ) small RNA libraries were consctructed and sequenced by deep sequencing using Illumina GAIIx.
2014-01-09 | E-GEOD-52599 | biostudies-arrayexpress
Project description:microRNAs (miRNAs) have been reported as key regulators in the post-transcriptional process in eukaryotic cells. In insects most of the studies have been reported in holometabolans while only recently two hemimetabolansM-BM- (Locusta migratoria and Acyrthosiphonpisum) have had their miRNAs identified. Therefore, the study on miRNAs of the evolutionarily basal hemimetabolanM-BM- Blattella germanica, may provide valuable insights on the structural and functional evolution of miRNAs. Small RNA libraries of the cockroach B. germanica were built from the whole body of the last instar nymph, and the adult ovaries. The high throughput Solexa sequencing resulted in approximately 11 and 8 million reads for the whole-body andM-BM- ovaries, respectively. Bioinformatic analyses identified 38 known miRNAs as well as 11 known miRNA*s. We also found 411 miRNA candidates conserved in other insects and 1017 candidates specific of B. germanica. The positive correlation between Solexa data and real-time quantitative PCR showed that reads can be used as quantitative method. Novel miRNA candidates were validated by decreasing levels of expression in dicer-1 RNAi knockdown individuals. The comparison of the two libraries indicates that whole-body nymph contain more known miRNAs than ovaries, whereas the adult ovaries are enriched with novel miRNA candidates. Our study has identified many known miRNAs and novel miRNA candidates in the basal hemimetabolan insect B. germanica, and most of the specific sequences were found in ovaries. Deep sequencing data reflect miRNA abundance and Dicer-1 RNAi assay is a reliable method to validate novel miRNAs. Small RNAs were sequenced whole body of the last instar nymph and adult ovaries of the cockroach Blattella germanica.
2011-01-01 | E-GEOD-22892 | biostudies-arrayexpress