Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome comparison of active and regressed testes of Microtus duodecimcostatus

ABSTRACT: We also study the changes occurring in the testes of Mediterranean pine mice living in the wastelands during the breeding cycle. The transcriptomic analysis of active and regressed testis show that several molecular pathways that operate in Sertoli cells, involved in the control of spermatogenesis and BTB dynamics, are deregulated in the inactive gonad, and that the immuno privilege of the testes is lost during the non-breeding season.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Microtus duodecimcostatus

SUBMITTER: Miguel Burgos

PROVIDER: E-MTAB-10291 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Mediterranean Pine Vole, <i>Microtus duodecimcostatus:</i> A Paradigm of an Opportunistic Breeder.

Lao-Pérez Miguel M Massoud Diaa D Real Francisca M FM Hurtado Alicia A Ortega Esperanza E Burgos Miguel M Jiménez Rafael R Barrionuevo Francisco J FJ

Animals : an open access journal from MDPI 20210601 6

Most mammalian species of the temperate zones of the Earth reproduce seasonally, existing a non-breeding period in which the gonads of both sexes undergo functional regression. It is widely accepted that photoperiod is the principal environmental cue controlling these seasonal changes, although several exceptions have been described in other mammalian species in which breeding depends on cues such as food or water availability. We studied the circannual reproductive cycle in males of the Mediter ...[more]

PMID: 34205873

Similar Datasets

Transcriptome comparison of active, inactivating and regressed testes of Talpa occidentalis

Project description:We study the changes occurring in the testes of Talpa occidentalis during the breeding cycle. The transcriptomic analysis of active, inactivating and regressed testis show that several molecular pathways that operate in Sertoli cells, involved in the control of spermatogenesis and BTB dynamics, are deregulated in the inactive gonad, and that the immuno privilege of the testes is lost during the non-breeding season.

2021-12-31 | E-MTAB-10836 | biostudies-arrayexpress

An Ancient Transcription Factor Initiates the Burst of piRNA Production During Early Meiosis in Mouse Testes (RNA-Seq)

Project description:Animal germ cells produce PIWI-interacting RNAs (piRNAs), small silencing RNAs that suppress transposons and enable gamete maturation. Mammalian transposon-silencing piRNAs accumulate early in spermatogenesis, whereas pachytene piRNAs are produced later during post-natal spermatogenesis and account for >95% of all piRNAs in the adult mouse testis. Mutants defective for pachytene piRNA pathway proteins fail to produce mature sperm, but neither the piRNA precursor transcripts nor the trigger for pachytene piRNA production is known. Here, we show that the transcription factor A-MYB initiates pachytene piRNA production. A-MYB drives transcription of both pachytene piRNA precursor RNAs and the mRNAs for core piRNA biogenesis factors, including MIWI, the protein through which pachytene piRNAs function. A-MYB regulation of piRNA pathway proteins and piRNA genes creates a coherent feed-forward loop that ensures the robust accumulation of pachytene piRNAs. This regulatory circuit, which can be detected in rooster testes, likely predates the divergence of birds and mammals. Transcriptome and ChIP sequencing in mouse and rooster testes

2013-03-26 | E-GEOD-44654 | biostudies-arrayexpress

Expression analysis of leafy spurge crown buds during seasonal dormancy transitions after glyphosate treatments.

Project description:This submission contains the RNAseq data from a study of leafy spurge crown buds transitioning through a seasonal dormancy time course following glyphosate treatments where buds transitioned from paradoprmancy to endodormancy and then to ecodormancy. The sequences in this study were mapped to an assembled transcriptome built from sequences from this study along with sequences from : 1) A study of leafy spurge crown buds through a time course for paradormancy release induced by excision of the aerial portion of the shoot (Series GSE71317). 2) A study identical to this study but where leafy spurge plants were not treated with glyphosate (Series GSE71321). 3) A previously submitted study of leafy spurge shoots following treament with glyphosate was also used to assemble the transcriptome (Series GSE56509). This crown buds transitioning through a seasonal dormancy time course following a glyphosate treatment study has 4 biological replicates collected at each of the three dormancy states (paradormant, endodormant, and ecodormant).

2015-08-05 | E-GEOD-71406 | biostudies-arrayexpress

Expression analysis of leafy spurge crown buds during seasonal dormancy transitions.

Project description:This submission contains the RNAseq data from a study of leafy spurge crown buds transitioning through a seasonal dormancy time course where buds transitioned from paradoprmancy to endodormancy and then to ecodormancy. The sequences in this study were mapped to an assembled transcriptome built from sequences from this study along with sequences from : 1) A study of leafy spurge crown buds through a time course for paradormancy release induced by excision of the aerial portion of the shoot (Series GSE71317). 2) A study identical to this study but where leafy spurge plants were first treated with glyphosate (Series GSE71406). 3) A previously submitted study of leafy spurge shoots following treatment with glyphosate was also used to assemble the transcriptome (Series GSE56509). This crown buds transitioning through a seasonal dormancy time course study has 4 biological replicates collected at each of the three dormancy states (paradormant, endodormant, and ecodormant).

2015-08-05 | E-GEOD-71321 | biostudies-arrayexpress

Expression analysis of leafy spurge crown buds during dormancy transitions and release.

Project description:This submission contains the RNAseq data from one (just the study on paradormancy release) of several studies used to assemble the leafy spurge tranacriptome. These assembled transcrptome was built from 1) A study of leafy spurge crown buds through a time course for paradormancy release induced by excision of the aerial portion of the shoot (this study). 2) A study of leafy spurge crown buds through a seasonal dormancy time course where buds transitioned from paradoprmancy to endodormancy and then to ecodormancy (Series GSE71321). 3) A study identical to #2 above but where leafy spurge plants were first treated with glyphosate (Series GSE71406). 4) A previously submitted study (Series GSE56509) of leafy spurge shoots following treament with glyphosate was also used to assemble the transcriptome. The paradormancy study (#1) contained 4 time points (0hr, 6h, 1d, 3d) with 3 biological replicates at 0hr and 4 biological replicates at each of the other time points.

2015-08-05 | E-GEOD-71317 | biostudies-arrayexpress

To identify and study the regulation of cellulosic enzymes in a biomass degrading gut fungal isolate from horse (Piromyces sp. finn)

Project description:Here, we develop a systems-level approach leveraging powerful next generation sequencing, proteomics and phenotypic studies to rapidly obtain an integrated view of lignocellulose degradation in the earliest free living fungi RNA-seq of Piromyces grown on Glucose, Cellulose, Cellulobiose, Avicel, Filter paper, and time-course of transient glucose pulse (catabolite repression). N>=2

2016-02-12 | E-GEOD-64834 | biostudies-arrayexpress

Discovery and mechanistic studies of cytotoxic cyclotides from the medicinal herb Hybanthus enneaspermus (Linn) F. Muell

Project description:Cyclotides are a family of plant-derived peptides characterized by a ~30 amino acid cyclic backbone and a cystine knot motif. Cyclotides have diverse bioactivities, and in particular their cytotoxicity has attracted significant attention for its potential anti-cancer applications. Hybanthus enneaspermus is a medicinal herb widely used in India as a natural libido enhancer, and a previous study indicated that it may contain cyclotides. In the current study, 11 novel cyclotides and one known cyclotide (cycloviolacin O2) were identified and isolated from H. enneaspermus. Their sequences were determined using tandem MS, and NMR analysis of six of these cyclotides indicates their three-dimensional structures are similar to those of other known cyclotides. The most abundant cyclotide in this plant, hyen D, has comparable cytotoxicity against cancer cells to cycloviolacin O2, the most cytotoxic cyclotide discovered so far. Herein we provide a mechanistic insight into the mode-of-action of the novel cyclotides’ cytotoxicity. Hyen D, E, L, M, and cycloviolacin O2 preferentially interacted with model lipid membranes containing phospholipids with phosphatidylethanolamine-headgroups, as measured by surface plasmon resonance. Cyclotide-membrane interactions correlated with cytotoxicity, suggesting that membrane binding underpins cytotoxicity. Overall, this study helps broaden knowledge on the indigenous Indian herb H. enneaspermus, and reports the discovery of novel cyclotides with potent anti-cancer activity.

2020-05-13 | PXD017924 | Pride

Transcriptome Sequencing and Assembly of Canna indica Flower

Project description:Canna indica L. is an ornamental plant with petaloid staminodes and only a half fertile stamen in its flowers. The genetic basis for petaloid androecium remains unclear. In order to get comprehensive transcriptome data for further studies, RNA-Seq analysis were carried out. Two libraries from flower primordia and differentiated flowers of Canna indica were constructed and sequenced respectively, and totally 118,869 unigenes were assembled. The unigenes were aligned to the protein databases NR, NT, Swiss-Prot, KEGG, COG and GO (e-value<0.00001), and totally 67,299 unigenes were annotated. Our data constitute a preliminary basis for further studies on flower development of Canna indica. The two samples from flower primordium and differentiated flower were sequenced for transcriptome assembly, and gene expression information of the two stages was also obtained from these data.

2016-09-01 | E-GEOD-72440 | biostudies-arrayexpress

Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae), Sphyracephala beccarii

Project description:We utilized Comparative Genomic Hybridization (CGH), using probes designed from de novo assembly of a testes transcriptome, to identify genes located on the sex chromosomes and autosomes of a stalk-eyed fly, Sphyracephala beccarii. Analysis of X chromosome gene content revealed the evolution of a neo-X chromosome that originated prior to the diversification of the family. Comparison of X-linkage across three species spanning the phylogenetic breadth of the family indicates abundant chromosomal gene movement, particularly for genes expressed exclusively in the testes. Two-condition experiment, female vs. male DNA, for one species with 3 biological replicates

2015-12-11 | E-GEOD-75873 | biostudies-arrayexpress

Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae), Teleopsis quinqueguttata

Project description:We utilized Comparative Genomic Hybridization (CGH), using probes designed from de novo assembly of a testes transcriptome, to identify genes located on the sex chromosomes and autosomes of a stalk-eyed fly, Teleopsis quinqueguttata. Analysis of X chromosome gene content revealed the evolution of a neo-X chromosome that originated prior to the diversification of the family. Comparison of X-linkage across three species spanning the phylogenetic breadth of the family indicates abundant chromosomal gene movement, particularly for genes expressed exclusively in the testes. Two-condition experiment, female vs. male DNA, for one species with 3 biological replicates

2015-12-11 | E-GEOD-75872 | 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