Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of transcription in the Drosophila melanogaster testis

ABSTRACT: Identification and annotation of all the genes in the sequenced Drosophila genome is a work in progress. Wild-type testis function requires many genes and is thus of potentially high value for the identification of transcription units. We therefore undertook a survey of the repertoire of genes expressed in the Drosophila testis by computational and microarray analysis. We generated 3141 high-quality testis expressed sequence tags (ESTs). Testis ESTs computationally collapsed into 1560 cDNA set used for further analysis. Of those, 11% correspond to named genes, and 33% provide biological evidence for a predicted gene. A surprising 47% fail to align with existing ESTs and 16% with predicted genes in the current genome release. EST frequency and microarray expression profiles indicate that the testis mRNA population is highly complex and shows an extended range of transcript abundance. Furthermore, >80% of the genes expressed in the testis showed onefold overexpression relative to ovaries, or gonadectomized flies. Additionally, >3% showed more than threefold overexpression at p <0.05. Surprisingly, 22% of the genes most highly overexpressed in testis match Drosophila genomic sequence, but not predicted genes. These data strongly support the idea that sequencing additional cDNA libraries from defined tissues, such as testis, will be important tools for refined annotation of the Drosophila genome. Additionally, these data suggest that the number of genes in Drosophila will significantly exceed the conservative estimate of 13,601. Keywords: other

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE462 | GEO | 2003/07/16

SECONDARY ACCESSION(S): PRJNA85069

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Analysis of transcription in the Drosophila melanogaster testis

Project description:Identification and annotation of all the genes in the sequenced Drosophila genome is a work in progress. Wild-type testis function requires many genes and is thus of potentially high value for the identification of transcription units. We therefore undertook a survey of the repertoire of genes expressed in the Drosophila testis by computational and microarray analysis. We generated 3141 high-quality testis expressed sequence tags (ESTs). Testis ESTs computationally collapsed into 1560 cDNA set used for further analysis. Of those, 11% correspond to named genes, and 33% provide biological evidence for a predicted gene. A surprising 47% fail to align with existing ESTs and 16% with predicted genes in the current genome release. EST frequency and microarray expression profiles indicate that the testis mRNA population is highly complex and shows an extended range of transcript abundance. Furthermore, >80% of the genes expressed in the testis showed onefold overexpression relative to ovaries, or gonadectomized flies. Additionally, >3% showed more than threefold overexpression at p <0.05. Surprisingly, 22% of the genes most highly overexpressed in testis match Drosophila genomic sequence, but not predicted genes. These data strongly support the idea that sequencing additional cDNA libraries from defined tissues, such as testis, will be important tools for refined annotation of the Drosophila genome. Additionally, these data suggest that the number of genes in Drosophila will significantly exceed the conservative estimate of 13,601.

2010-06-05 | E-GEOD-462 | biostudies-arrayexpress

Identification of testis-relevant genes from testes ESTs and cDNA microarray in the black tiger shrimp

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.

2010-11-04 | GSE19037 | GEO

Identification of testis-relevant genes from testes ESTs and cDNA microarray in the black tiger shrimp

2010-11-04 | E-GEOD-19037 | biostudies-arrayexpress

Transcription profiling of Drosophila testes, heads, ovaries and whole gonadectomized males to analyze transcription patterns in the testes

Project description:In order to analyze transcription pattern in Drosophila testes, we performed competitive hybridizations of testes-derived cDNA against the cDNAs obtained from heads, ovaries, and whole gonadectomized males.

2008-05-01 | E-TABM-273 | biostudies-arrayexpress

Penaeus monodon

Project description:Identification of testis-relevant genes from testes ESTs and cDNA microarray in the black tiger shrimp

| PRJNA120643 | ENA

Differential expression of Aspergillus genes during the induction of aflatoxin biosynthesis

Project description:Gene expression analysis of A. parasiticus grown under conditions conducive and nonconductive for aflatoxin production was evaluated using glass slide microarrays containing the 753 ESTs. A complex regulatory network governs the biosynthesis of aflatoxin. While several genes involved in aflatoxin production are known, their action alone cannot account for its regulation. Arrays of clones from an Aspergillus flavus cDNA library and glass slide microarrays of ESTs were screened to identify additional genes. An initial screen of the cDNA clone arrays lead to the identification of 753 unique ESTs. Many showed sequence similarity to known metabolic and regulatory genes; however, no function could be ascribed to over 50% of the ESTs. Gene expression analysis of Aspergillus parasiticus grown under conditions conducive and non-conductive for aflatoxin production was evaluated using glass slide microarrays containing the 753 ESTs. Twenty-four genes were more highly expressed during aflatoxin biosynthesis and 18 genes were more highly expressed prior to aflatoxin biosynthesis. No predicted function could be ascribed to 18 of the 24 genes whose elevated expression was associated with aflatoxin biosynthesis. Keywords = Aspergillus Keywords = aflatoxin Keywords: time-course

2003-01-15 | GSE204 | GEO

Differential Gene Expression of Enriched Germ Cells Responding to a Short Heat Stimulus

Project description:It is well recognized that the quality of boar sperm is severely influenced by higher temperature in summer, thereby reducing the productivity of semen. cDNA microarray is a high throughput technique frequently used in genome-wide screening for specific genes related a known phenotype or disease. A testis cDNA microarray was established for the investigation of the differentially expressed genes, responding to a short heat stimulus, in enriched germ cells isolated from immature pigs where the first wave of spermatogenesis was just initiated. Two cDNA libraries were constructed from the testis tissues of two mature Duroc boars with or without whole body heat shock treatment. About 27,000 single colonies were randomly picked for one-direction sequencing. After the trimming of vector derived sequences, 22,969 high quality ESTs were obtained, which assembled into 3,207 contigs and 9,541 singletons, representing 12,748 tentative unique transcripts. A porcine testis cDNA microarray was established with single spot of the amplified cDNA plus 20 spots of positive and negative controls. We conducted a cell model experiment to screen the differentially expressed genes responding to a short heat shock. Small population of genes was up- or down-regulated with at least 1.5-fold of differences, including transcriptional factors, kinases, phosphatases, binding proteins and some transcripts with unknown functions. Further examination on these genes might contribute to a clear picture on the heat-tolerance of spermatogenesis in boar and benefit the breeding of boars with elite semen quality in all reasons. Keywords: stress response

2007-06-02 | GSE7954 | GEO

Differential expression of Aspergillus genes during the induction of aflatoxin biosynthesis

2003-01-15 | E-GEOD-204 | biostudies-arrayexpress

Macaca mulatta

Project description:Rhesus Testis cDNA 454

| PRJNA80105 | ENA

Analysis of Unannotated Equine Transcripts Identified by mRNA Sequencing

Project description:Horse-specific genes are not readily identified from available equine EST/cDNA resources due to relatively limited coverage. In addition, equine gene sets predicted in silico by Ensembl and NCBI will not identify horse specific genes since they rely on homology-based projection of gene structure annotation from other species. In this study, RNA-seq of 8 equine RNA samples representing 6 distinct tissues was performed and used to improve and refine equine gene structure annotation. The samples and RNA were collected as part of the related study E-GEOD-21925 and are described in Coleman et al 2010. Anim Genet 41 Suppl 2: 121-30 (PMID: 21070285). The RNA from these samples was re-sequenced in this experiment. The tissues were i). the articular cartilage and synovial membrane samples from a 3-year-old male pony. The left carpal joints received four LPS injections (0.5 ng) over 8 days, while the right carpal joints received control injections of PBS. ii) A cerebellum sample was collected from a 2-year-old female thoroughbred. iii) A testis sample from a 4-year-old thoroughbred. iv) A placental villous sample collected immediately post-partum from a full-term female thoroughbred foal. v) A whole embryo sample was obtained from a 34-day-old male thoroughbred conceptus. The embryo, cerebellum, testis and placental samples were of apparent normal gross morphology.

2013-07-30 | E-GEOD-46858 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data