title: TMV-derived Small RNAs Reveals Role for Arabidopsis thaliana RNA-dependent RNA Polymerases in Viral siRNA Biogenesis

status: Public on Mar 24 2009

city: Lubbock

first: Zhixin

last: Xie

state: TX

institute: texas tech university

summary: Using a crucifer-infecting strain of Tobacco Mosaic Virus (TMV-Cg) and Arabidopsis thaliana as a model system, we analyzed the viral small RNA profile in wild-type plants as well as rdr mutants by applying small RNA deep sequencing technology.  Over 100,000 TMV-Cg-specific small RNA reads, mostly of 21- (78.4%) and 22-nucleotide (12.9%) in size and originating predominately (79.9%) from the genomic sense RNA strand, were captured at an early infection stage, yielding the first high-resolution small RNA map for a plant virus.  The TMV-Cg genome harbored multiple, highly reproducible small RNA-generating hot spots that corresponded to regions with no apparent local hairpin-forming capacity.  Significantly, both the rdr1 and rdr6 mutants exhibited globally reduced levels of viral small RNA production as well as reduced strand bias in viral small RNA population, revealing an important role for these host RDRs in viral siRNA biogenesis.  In addition, an informatics analysis showed that a large set of host genes could be potentially targeted by TMV-Cg-derived siRNAs for posttranscriptional silencing, raising the interesting possibility for a hidden layer of widespread virus-host interactions that may contribute to viral pathogenicity and host specificity.

overall_design: Profiling of TMV-Cg derived small RNAs in systemically infected tissues of wild type (Col-0) Arabidopsis as well as the rdr1and rdr6 mutants, at 3 days post-infection.

first: Xiaopeng

last: Qi

first: Forrest

last: Bao


title: Late-term turkey embryo hatching muscle (complexus muscle) gene expression

status: Public on Jan 31 2008

city: Raleigh

first: Jean

middle: Eduardo

last: de Oliveira

state: NC

address: 2711 Founders Dr

department: Poultry Science

country: USA

institute: North Carolina State University

summary:
Turkey embryos are very sensitive to perturbations in energy metabolism because they have a wider hatching window than chicken embryos. Mortality of turkey embryos during late-term incubation is high relative to chickens, and many surviving hatchlings have compromised vitality. Intestinal maturation at hatch is also crucial to survival and post-hatch performance. The study of poultry embryo metabolism during the last stages of incubation is difficult due to many shifts and changes that occur in preparation for hatching. Microarray technology is suitable to study complex biological systems like avian late-term embryonic development. Therefore, the objectives of this study were to create a customized focused oligonucleotide microarray based on chicken genome sequences that could be used to study late-term avian metabolism and intestinal maturation, and use this array to survey turkey embryos gene expression from 20 days of incubation until hatch. The key features of this microarray are that all genes present have been annotated and gene spot replication (4) within each array chip. Microarray analysis was performed on liver, pectoral muscle, hatching muscle, and duodenum
Keywords: time course, embryo development

overall_design: Pooled samples from 6 embryos were arraged on a complete interwoven loop design where each treatment (embryonic ages 20, 22, 24, 26 and 28) was replicated 4 times (2 dye-swaps).

middle: E

first: Chistopher

middle: M

last: Ashwell

first: Peter

middle: R

last: Ferket

first: Zehava

last: Uni


title: High-throughput pyrosequencing of plant virus small RNAs

status: Public on Jul 10 2009

city: Garchinig

first: Yu

last: Wang

address: Boltzmannstrasse 1

department: High performance computing

country: Germany

institute: Leibniz Supercomputing Centre

type: Non-coding RNA profiling by high throughput sequencing

summary:
Plant virus infection involves the production of viral small RNAs (vsRNAs) with the potential to associate with distinct Argonaute (AGO)-containing silencing complexes and mediate diverse silencing effects on RNA and chromatin. We used multiplexed, high-throughput pyrosequencing to profile populations of vsRNAs from plants infected with viruses from different genera. Sense and antisense vsRNAs of 20 to 24 nucleotides (nts) spread throughout the entire viral genomes in an overlapping configuration; virtually all genomic nucleotide positions were represented in the dataset. We present evidence to suggest that every genomic position could be a putative cleavage site for vsRNA formation, although viral genomes contain specific regions that serve as preferential sources of vsRNA production. Hotspots for vsRNAs of 21-, 22-, and 24-nt usually coincide in the same genomic regions, indicating similar target affinities among Dicer-like (DCL) enzymes. In the light of our results, the overall contribution of perfectly base paired double-stranded RNA and imperfectly base paired structures within single-stranded RNA to vsRNA formation is discussed. Our census of vsRNAs extends the current view of the distribution and composition of vsRNAs in virus-infected plants, and contributes to define a more comprehensive scenario of vsRNA biogenesis and their regulatory functions in plants

Raw data files are available on our FTP site:
ftp://ftp.ncbi.nlm.nih.gov/pub/geosup/Series/GSE16996

sample_organism:
Tomato yellow leaf curl virus
Melon necrotic spot virus
Cymbidium ringspot virus
Potato virus X
Turnip mosaic virus
Pepper mild mottle virus
Tobacco rattle virus
Cucumber mosaic virus
Watermelon mosaic virus

overall_design: 10 samples examined: Arabidopsis plants infected with TRV, TuMV or CMV; Nicothiana benthamiana plants infected with CymRSV, PVX or PMMoV; Cucumis melo plants infected with MNSV, quimeric MNSV or WMV and  Solanum lycopersicum plants infected with TYLCV.

first: Livia

last: Donaire

first: Daniel

last: Gonzalez-Ibeas

first: Klaus

middle: F

last: Mayer

first: Miguel

middle: A

last: Aranda

first: Cesar

last: Llave


title: Endogenous small RNAs of meristematic and a terminally differentiated tissue of rice.

status: Public on Jun 08 2009

city: Davis

first: Venkatesan

last: Sundaresan

state: CA

address: One Shields Ave

department: Plant Biology

institute: University of California Davis

summary: To address the role of small regulatory RNAs in rice development, we generated a large data set of small RNAs from root apices (RoApx), shoot apices (ShApx), developing inflorescence (Infl) and mature leaf (Leaf). These tissues were chosen because they are expected to be rich in small RNAs and display different patterns of small RNA expression. The RoApx, ShApx, and Infl samples are expected to be enriched for meristematic tissues each of which have different fates. The Infl sample would also be expected to contain developing female gametes. In contrast, the Leaf sample is terminally differentiated and may be expected to be more transcriptionally repressed. These small RNAs comprise a total of 781,885 distinct sequences, and all of these map to at least one locus of the rice genome TIGR version 5.

overall_design: Total RNA was extracted from root apices, shoot apices, developing inflorescence and mature leaf. Three samples from each tissue were taken to represent replicates and small RNAs from these were ligated to a common 5' RNA adapter and a replicate-specific 3' adapter. These replicate samples were then identified from within single 454 data sets using the 3' adapter sequence. It should be noted that there was a strong frequency bias observed between the RNA sequence and the particular 3' adapter used in the sequencing.  This resulted in both increased or decreased read counts for the known miRNA sequences in a 3' adapter dependent fashion. Use of the three samples for each tissue as replicates is therefore problematic.

first: Cameron

last: Johnson

first: Anna

last: Kasprzewska

first: Kristin

last: Tennessen

first: John

last: Fernandes

first: Guo-Ling

first: Virginia

last: Walbot

first: Vicki

last: Vance

first: Lewis

last: Bowman


title: Late-term turkey embryo duodenum gene expression

first: Jean

last: de Oliveira

first: Chistopher

last: Ashwell

first: Peter


title: High-throughput sequencing of small RNAs from Caenorhabditis elegans

status: Public on Oct 15 2006

city: Cambridge

first: James

middle: Graham

last: Ruby

state: MA

address: 9 Cambridge Center

department: Biology

institute: Whitehead Institute for Biomedical Research and MIT

summary:
High-throughput sequencing of mixed-stage Caenorhabditis elegans small RNAs.
total RNA, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH
Keywords: high-throughput 454 sequencing

sample_organism:
Escherichia coli
Caenorhabditis elegans

platform_organism:
Escherichia coli
Caenorhabditis elegans

overall_design: Small RNAs were sequenced from mixed-stage C. elegans.


title: Late-term turkey embryo pectoralis muscle gene expression

last: Ferket

first: Zehava

last: Uni


title: Zebrafish germline small RNAs

status: Public on Apr 05 2007

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

summary:
Piwi proteins specify an animal-specific subclass of the Argonaute family, that in vertebrates are specifically expressed in germ cells. We demonstrate that zebrafish Piwi (Ziwi) is expressed in both the male and the female gonad, and is a component of a germline specifying structure, called nuage. Loss of Ziwi function results in a progressive loss of germ cells due to apoptosis during larval development. In animals that have only reduced Ziwi function, germ cells are maintained, but display abnormal levels of apoptosis in adults. In mammals, Piwi proteins have been found to associate with approximately 29-nucleotide long, testis specific RNA molecules, called piRNAs. Here we show that zebrafish piRNAs are present in both ovaries and testes. Furthermore, we show that piRNAs are modified at their 3’ end and that they are produced by a Dicer independent mechanism. Many ovarian piRNAs are derived from transposons, implicating a role for these molecules in the silencing of these repetitive elements in vertebrates.
Keywords: high-throughput 454 sequencing

overall_design: sequencing of ~30 nt small RNAs from zebrafish ovaries and testes using 454 technology


title: siRNAs 15-29 nucleotides long with 100 percent hit to Turnip mosaic virus clone GBR98

status: Public on Sep 12 2008

city: Oxford

first: Thien

middle: Xuan

last: Ho

address: Mansfield road

country: United Kingdom

institute: CEH Oxford

summary:
Mustard (Brassica juncea) was tested for Turnip mosaic virus infection. Small RNA of the plant was extracted and converted to DNA according to Ho, T., et al. (2006)  Journal of Virological Methods 136:217-223, with primers modified to contain 454 adapter nucleotide sequences. The DNA then passed quality control through Bioanalyzer and Nanodrop before sequenced by 454 Life Sciences.

Keywords: siRNA

overall_design: One sample analyzed by 454 high-throughput sequencing technology

first: Hui

last: Wang


title: siRNAs 15-29 nucleotides long with 100 percent hit to Cocksfoot streak virus

summary:
Cocksfoot grass (Dactylis glomerata) collected from Wytham, Oxford, UK, was tested for Cocksfoot streak virus infection. Small RNA of the grass was extracted and converted to DNA according to Ho, T., et al. (2008)  Biochem Biophys Res Commun. 368:433-7, with primers modified to contain 454 adapter nucleotide sequences. The DNA then passed quality control through Bioanalyzer and Nanodrop before sequenced by 454 Life Sciences.

Keywords: siRNA


title: Late-term turkey embryo liver, pectoralis muscle, hatching muscle and duodenum gene expression

summary:
Turkey embryos are very sensitive to perturbations in energy metabolism because they have a wider hatching window than chicken embryos. Mortality of turkey embryos during late-term incubation is high relative to chickens, and many surviving hatchlings have compromised vitality. Intestinal maturation at hatch is also crucial to survival and post-hatch performance. The study of poultry embryo metabolism during the last stages of incubation is difficult due to many shifts and changes that occur in preparation for hatching. Microarray technology is suitable to study complex biological systems like avian late-term embryonic development. Therefore, the objectives of this study were to create a customized focused oligonucleotide microarray based on chicken genome sequences that could be used to study late-term avian metabolism and intestinal maturation, and use this array to survey turkey embryos gene expression from 20 days of incubation until hatch. The key features of this microarray are that all genes present have been annotated and gene spot replication (4) within each array chip. Microarray analysis was performed on liver, pectoral muscle, hatching muscle, and duodenum

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Comparison of D. simulans/D. mauritiana F1 third instar male larvae hybrid expression values to pure-species parents

status: Public on Sep 13 2006

city: Durham

first: Amanda

middle: J.

last: Moehring

department: DCMB/Biology

institute: Duke University

summary:
Species often produce sterile hybrids early in their evolutionary divergence, and some evidence suggests that hybrid sterility may be associated with deviations or disruptions in gene expression.  In support of this idea, many studies have shown that a high proportion of male-biased genes are underexpressed compared to non-sex-biased genes in sterile F1 male hybrids of Drosophila species.  In this study, we examined and compared patterns of misexpression in F1 hybrid male third instar larvae of Drosophila simulans and its sibling species, D. mauritiana.  We analyzed hybrids using custom cDNA arrays we developed from RT-PCRs of spermatogenesis-related transcripts from these species and another sibling species (D. sechellia).  The results from a commercial genome-wide array and custom chip for adults of this species pair, from the custom chip and the genome-wide chip for adults of the D. simulans-D. sechellia species pair, and from the larvae of the D. simulans-D. sechellia species pair, are presented separately.
Keywords: Comparison of pure-species Drosophila expression to hybrid expression

sample_organism: Drosophila simulans x Drosophila mauritiana

platform_organism:
Drosophila mauritiana
Drosophila sechellia
Drosophila simulans

overall_design: We analyzed 11 arrays: 4 of sim-mau vs. mau, 4 of sim-mau vs. sim, and one each of self-hybridizations (sim vs. sim, sim-mau vs. sim-mau, mau vs. mau).

middle: J

first: Mohamed

last: Noor


title: Deep sequencing of Drosophila melanogaster small RNAs

status: Public on Apr 30 2008

city: Cold Spring Harbor

first: Julius

last: Brennecke

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Labs

summary:
High throughput seqeuncing of small RNAs (PAGE isolated from total RNA or Argonaute immunoprecipitates) from Drosophila melanogaster using the Illumina platform. Adapter ligation requires 5' monophosphate and 3' OH.
Full analysis of all libraries in this set is published (Czech B. et al. 2008), leading to the description of endogenous siRNAs in flies.
Keywords: Solexa sequences

sample_organism:
Drosophila melanogaster
Flock House virus

overall_design: 7 libraries; each seqeunced once


title: Drosophila Polycomb and Pleiohomeotic genomic binding in 0-16h embryos and L3 larval discs (ChIP-on-chip)

status: Public on Aug 01 2008

first: Steve

last: Russell

address: Downing Street

department: Department of Genetics

institute: University of Cambridge

type: Genome binding/occupancy profiling by genome tiling array

summary:
We have studied the linkage between the binding of Polycomb Group (PcG) proteins and the developmental regulation of gene expression using whole-genome mapping to identify sites bound by the PcG proteins, Polycomb (Pc) and Pleiohomeotic (Pho), in the Drosophila embryo and in a more restricted tissue, the imaginal discs of the third thoracic segment. Our data provide considerable support for the idea that Pho is a general component of the maintenance machinery since the majority of Pc targets are also associated with Pho binding.  We find, in general, considerable developmental stability of Pc and Pho binding at target genes and observe that Pc/Pho binding can be associated with both expressed and inactive genes. In particular, at the Hox complexes both active and inactive genes have significant Pc and Pho binding; however, in comparison to inactive genes the active Hox genes show reduced and altered binding profiles.
Keywords: ChIP-on-chip, tissue-specific binding

overall_design: We used chromatin from whole embryos and larval T3 imaginal discs (haltere and third leg) to compare genomic binding of Pc and Pho between these tissues by ChIP-on-chip. Each chromatin source was represented with at least three biological replicates (in addition, Pc embryonic material and controls were hybridised to up to three different arrays), and enrichment profiles were generated by comparison of specific and control ChIP DNA samples. For Pc target analysis the specific reaction used chromatin from the Pc-GFP fly line immunopurified using anti-GFP, and the control reaction used wild type chromatin immunopurified using anti-GFP.  For Pho analysis wild type chromatin was used with anti-Pho for the specific reaction and pre-immune antiserum for the control. Purified DNAs were then fragmented, TdT labeled and hybridized to the Affymetrix Drosophila genome Tiling Array 1.0 (reverse part number 520,054), as previously described (Manak et al. 2006).

first: Boris

last: Adryan

first: Camilla

last: Kwong

last: Manak

first: Steven

first: Robert

last: White


title: whole body

status: Public on Jan 31 2004

first: Jose

last: Ranz

address: Downing

department: Genetics

summary:
Expression profile comparison of females of D. melanogaster, D. simulans and their hybrid. RNA source: whole body.
Keywords: other

sample_organism:
Drosophila melanogaster
Drosophila simulans

first: Kalsang

last: Namgyal

first: Greg

last: Gibson

first: Daniel

middle: L

last: Hartl


title: Global expression profiling applied to the analysis of Arabidopsis stamen development

status: Public on Aug 31 2007

city: Bellaterra

first: Jose Luis

last: Riechmann

state: Barcelona

address: Campus UAB - Edifici CRAG

country: Spain

institute: Center for Research in Agricultural Genomics

summary:
To obtain detailed information about gene expression during stamen development in Arabidopsis thaliana, we compared, by microarray analysis, the gene expression profile of wild-type inflorescences to those of the floral mutants apetala3, sporocyteless/nozzle, and male sterile 1, in which different aspects of stamen formation are disrupted. These experiments led to the identification of groups of genes with predicted expression at early, intermediate and late stages of stamen development.
Additional experiments aimed at characterizing gene expression specifically during microspore formation. To this end, we compared the gene expression profiles of wild-type flowers of distinct developmental stages to those of the male sterile 1 mutant. Computational analysis of the datasets derived from this experiment led to the identification of genes that are likely involved in the control of key developmental processes during microsporogenesis.
Keywords: mutant comparison, developmental series

overall_design:
To identify genes expressed during distinct stages of stamen development at a genome-wide scale, we compared, by microarray analysis, the gene expression profiles of flowers of ap3, spl/nzz, and ms1 mutants to that of wild-type flowers. For the identification of transcripts expressed at early stages of stamen development, we dissected older flowers from inflorescences of ap3 mutant plants and the wild type and then collected the inflorescence meristem and floral buds up to early stage 10 for analysis. We refer to these tissue samples as ap3 early stages, or ap3 es. The second mutant included in our analysis, spl/nzz, shows defects at the earliest steps of sporogenesis. Thus, we expected that genes expressed in sporogenous tissues would be down-regulated in mutant flowers compared to the wild type. Lastly, we analyzed the ms1 mutant to identify genes expressed during pollen development and maturation. For both ms1and spl/nzz, as well as for the wild type, tissue samples containing the inflorescence meristem and floral buds up to stage 13 were collected for analysis.
To gain more detailed insights into the transcriptional program underlying microspore development in Arabidopsis, we made further use of the ms1 mutant, which lacks viable pollen. We collected flowers from ms1 and wild-type plants and pooled them according to their developmental stages into 7 tissue samples, where sample 1 contained mature (stage 13) flowers and subsequent samples contained successively younger flowers, with sample 7 containing the youngest floral buds and the inflorescence meristem.
Gene expression profiling experiments were done using oligonucleotide microarrays, as described previously (Wellmer et al. (2006) PLoS Genetics 2, e117. In all cases, at least three independent biological samples were used in separate hybridizations, and the dyes used for labeling of the co-hybridized samples were switched in the replicate experiments.

first: Marcio

last: Alves-Ferreira

first: Frank

last: Wellmer

first: Vijaya

last: Kumar

first: Elliot

last: Meyerowitz


title: Decapped mRNAs during Arabidopsis Early Flower Development

status: Public on Oct 10 2008

city: Pasadena

first: Yuling

last: Jiao

address: 1200 E California Blvd

institute: California Institute of Technology

summary: The composition of the transcriptome is regulated by both mRNA synthesis and degradation.  One route for mRNA decay is through 5’ decapping, which can be initiated by decapping enzymes and small RNAs.  Although decapped RNAs are an important intermediate for mRNA decay, their identity and abundance have never been studied on a large scale.  Here we present an experimental method for transcriptome-wide profiling of decapped mRNAs.  We applied the method to study the prevalence of decapped transcripts during the early stages of Arabidopsis thaliana flower development.  Decapped transcripts were identified for the majority of expressed genes, although at different levels.  By comparing decapped RNA levels with steady-state overall transcript levels, our study provides evidence for widespread decapping-mediated mRNA degradation control in numerous biological processes and for genes of varied molecular functions, implying that mRNA decapping is a dynamically regulated process.  Sequence analyses identified structural features of transcripts and cis-elements that were associated with levels of decapping.

overall_design: Four sets of biologically independent tissue samples were collect 0,1,2,3,4, and 5 days after activation of the AP1-GR fusion protein. Decapped mRNA and total mRNA of each time point from each set were co-hybridized to micoarrays. Dyes used for labeling the RNA populations derived from the individual samples were switched in the replicate experiments to reduce dye-related artefacts.


title: heads only

summary:
Expression profile comparison of the heads of females of D. melanogaster, D. simulans and their hybrid.
Keywords: other


title: Small RNAs in Chlamydomonas reinhardtii

status: Public on May 16 2007

city: Beijing

first: Yijun

last: Qi

address: No.7 Science Park Road,Zhongguancun Life Science Park

country: China

institute: National Institute of Biological Sciences, Beijing

summary:
RNA populations in Chlamydomonas reinhardtii
Keywords: Highly parallel pyrosequencing

overall_design: Small RNAs were prepared from Chlamydomonas reinhardtii total extracts,ligated to a 3' adaptor and a 5' acceptor sequentially, and then RT-PCR amplified. PCR products were reamplified using a pair of 454 cloning primers and provided to 454 Life Sciences (Branford, CT) for sequencing. For technical details, see Tao Zhao, Guanglin Li, Shijun Mi, Shan Li, Gregory J. Hannon, Xiu-Jie Wang, and Yijun Qi. 2007. A Complex System of Small RNAs in the Unicellular Green Alga Chlamydomonas reinhardtii. Genes & Development

first: Xiu-Jie

last: Wang


title: Comparison of D. simulans/D. mauritiana F1 male hybrid custom expression values to pure-species parents

first: Amanda

last: Moehring

summary:
Species often produce sterile hybrids early in their evolutionary divergence, and some evidence suggests that hybrid sterility may be associated with deviations or disruptions in gene expression.  In support of this idea, many studies have shown that a high proportion of male-biased genes are underexpressed compared to non-sex-biased genes in sterile F1 male hybrids of Drosophila species.  In this study, we examined and compared patterns of misexpression in 4 day old sterile male F1 hybrids of Drosophila simulans and its sibling species, D. mauritiana.  We analyzed hybrids using custom cDNA arrays we developed from RT-PCRs of spermatogenesis-related transcripts from these species and another sibling species (D. sechellia).  The results from a commercial genome-wide array for this species pair, from the custom chip and the genome-wide chip for the D. simulans-D. sechellia species pair, and from the larvae of these two species pairs using the custom chip, is presented separately.
Keywords: Comparison of pure-species Drosophila expression to hybrid expression

first: Mohamed

last: Noor


title: Comparison of D. simulans/D. sechellia F1 male hybrid genome-wide expression values to pure-species parents

summary:
Species often produce sterile hybrids early in their evolutionary divergence, and some evidence suggests that hybrid sterility may be associated with deviations or disruptions in gene expression.  In support of this idea, many studies have shown that a high proportion of male-biased genes are underexpressed compared to non-sex-biased genes in sterile F1 male hybrids of Drosophila species.  In this study, we examined and compared patterns of misexpression in 4 day old sterile male F1 hybrids of Drosophila simulans and its sibling species, D. sechellia.  We analyzed hybrids using genome-wide D. melanogaster arrays from the Drosophila Genome Resource Center (DGRC).  The results from a custom array (GPL4022) for this species pair, from the custom array and the genome-wide array for the D. simulans-D. mauritiana species pair, and from the larvae of these two species pairs using the custom array, are presented separately.
Keywords: Comparison of pure-species Drosophila expression to hybrid expression

sample_organism: Drosophila sechellia x Drosophila simulans

overall_design: We analyzed 11 arrays: 4 of sim-sec vs. sec, 4 of sim-sec vs. sim, and one each of self-hybridizations (sim vs. sim, sim-sec vs. sim-sec, sec vs. sec).


title: Comparison of D. simulans/D. mauritiana F1 male hybrid genome-wide expression values to pure-species parents

summary:
Species often produce sterile hybrids early in their evolutionary divergence, and some evidence suggests that hybrid sterility may be associated with deviations or disruptions in gene expression.  In support of this idea, many studies have shown that a high proportion of male-biased genes are underexpressed compared to non-sex-biased genes in sterile F1 male hybrids of Drosophila species.  In this study, we examined and compared patterns of misexpression in 4 day old sterile male F1 hybrids of Drosophila simulans and its sibling species, D. mauritiana.  We analyzed hybrids using genome-wide D. melanogaster arrays from the Drosophila Genome Resource Center (DGRC).  The results from a custom array (GPL4022) for this species pair, from the custom array and the genome-wide array for the D. simulans-D. sechellia species pair, and from the larvae of these two species pairs using the custom array, are presented separately.
Keywords: Comparison of pure-species Drosophila expression to hybrid expression


title: Drosophila life cycle

status: Public on Nov 04 2004

city: New Haven

first: Zareen

last: Gauhar

state: CT

address: 333 Cedar St, 386 NSB

institute: Yale

summary:
RNA from six developmental stages during the Drosophila life cycle (0-2hr embryos, 3-16hr embryos, larvae, pupae, male and female adults) was isolated, reverse transcribed in the presence of oligodT and random hexamers and the labeled cDNA was hybridized to these arrays.Each sample was hybridized four times, twice with Cy5 labeling and twice with Cy3 labeling.
Keywords: other


title: Comparison of D. simulans/D. sechellia third instar male larvae hybrid expression values to pure-species larvae parents

summary:
Species often produce sterile hybrids early in their evolutionary divergence, and some evidence suggests that hybrid sterility may be associated with deviations or disruptions in gene expression.  In support of this idea, many studies have shown that a high proportion of male-biased genes are underexpressed compared to non-sex-biased genes in sterile F1 male hybrids of Drosophila species.  In this study, we examined and compared patterns of misexpression in F1 hybrid male third instar larvae of Drosophila simulans and its sibling species, D. sechellia.  We analyzed hybrids using custom cDNA arrays we developed from RT-PCRs of spermatogenesis-related transcripts from these species and another sibling species (D. mauritiana).  The results from a commercial genome-wide array and custom chip for adults of this species pair, from the custom chip and the genome-wide chip for adults of the D. simulans-D. mauritiana species pair, and from the larvae of the D. simulans-D. mauritiana species pair, are presented separately.
Keywords: Comparison of pure-species Drosophila expression to hybrid expression in larvae


title: Comparison of D. simulans/D. sechellia F1 male hybrid custom expression values to pure-species parents

summary:
Species often produce sterile hybrids early in their evolutionary divergence, and some evidence suggests that hybrid sterility may be associated with deviations or disruptions in gene expression.  In support of this idea, many studies have shown that a high proportion of male-biased genes are underexpressed compared to non-sex-biased genes in sterile F1 male hybrids of Drosophila species.  In this study, we examined and compared patterns of misexpression in 4 day old sterile male F1 hybrids of Drosophila simulans and its sibling species, D. sechellia.  We analyzed hybrids using custom cDNA arrays we developed from RT-PCRs of spermatogenesis-related transcripts from these species and another sibling species (D. mauritiana).  The results from a commercial genome-wide array for this species pair, from the custom chip and the genome-wide chip for the D. simulans-D. mauritiana species pair, and from the larvae of these two species pairs using the custom chip, is presented separately.
Keywords: Comparison of pure-species Drosophila expression to hybrid expression


title: Comparison of pure-species Drosophila expression to hybrid expression

summary: This SuperSeries is composed of the SubSeries listed below.

platform_organism:
Drosophila mauritiana
Drosophila melanogaster
Drosophila sechellia
Drosophila simulans

first: Katherine

middle: C

last: Teeter


title: Transcript Specificity in Yeast Pre-mRNA Splicing Revealed by Mutations in Core Spliceosomal Components

status: Public on Apr 04 2007

city: Lexington

first: Gregg

middle: Brooks

last: Whitworth

state: VA

address: 204 West Washington St

institute: Washington and Lee Unversity

summary:
Appropriate expression of most eukaryotic genes requires the removal of introns from their pre-messenger RNAs (pre-mRNAs), a process catalyzed by the spliceosome. In higher eukaryotes a large family of auxiliary factors known as SR proteins can improve the splicing efficiency of transcripts containing suboptimal splice sites by interacting with distinct sequences present in those pre-mRNAs. The yeast Saccharomyces cerevisiae lacks functional equivalents of most of these factors; thus, it has been unclear whether the spliceosome could effectively distinguish among transcripts. To address this question, we have used a microarray-based approach to examine the effects of mutations in 18 highly conserved core components of the spliceosomal machinery. The kinetic profiles reveal clear differences in the splicing defects of particular pre-mRNA substrates. Most notably, the behaviors of ribosomal protein gene transcripts are generally distinct from other intron-containing transcripts in response to several spliceosomal mutations. However, dramatically different behaviors can be seen for some pairs of transcripts encoding ribosomal protein gene paralogs, suggesting that the spliceosome can readily distinguish between otherwise highly similar pre-mRNAs. The ability of the spliceosome to distinguish among its different substrates may therefore offer an important opportunity for yeast to regulate gene expression in a transcript-dependent fashion. Given the high level of conservation of core spliceosomal components across eukaryotes, we expect that these results will significantly impact our understanding of how regulated splicing is controlled in higher eukaryotes as well.
Keywords: time course, splicing mutant, splicing-specific microarray

overall_design: Splicing-specific microarrays were used to assay the phenotypes of 23 different conditional mutations in splicing and mRNA processing factors.  The data includes time courses of shifts to the non-permissive temperature for each factor as well as dye-flipped technical replicates of each time point.

first: Jeffrey

last: Pleiss

middle: B

first: Megan

last: Bergkessel

first: Christine

last: Guthrie


title: Breast Cancer: Invasive Ductal Carcinoma

status: Public on Dec 07 2005

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

summary:
Invasive breast cancer was histopathologically confirmed on 47 samples obtained by core or incisional biopsy.
Keywords: other

first: Jane

last: Kaiano

first: Louise

middle: D

last: Motta


title: Renormalised expression data from 1570 breast cancer related samples

status: Public on Jun 01 2013

city: London

first: Marketa

last: Zvelebil

address: 237 Fulham Road

institute: The Institute of Cancer Research

type:
Third-party reanalysis
Expression profiling by array

summary: An integration of several studies normalized to enable consistent cross-study comparisons and enrichment of the less frequent breast cancer types, enabling detection of new potential cancer driver genes.

overall_design: Raw Affymetrix CEL files were retrieved from the series GSE2034  GSE11121  GSE20194  GSE1456  GSE2603  GSE6532 GSE20437 GSE1561 GSE7390 GSE5847. Samples were then filtered with a three stage quality control resulting in the final dataset. These were subjected to RMA normalization and then placed on a log2 scale. Samples were stratified by levels of MYC expression with the top quartile defined as High and the bottom quartile defined as Low.

first: Saif

last: Ur-Rehman