Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

5 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of human seminiferous tubules from subfertile/infertile patients undergoing testicular sperm extraction as part of their treatment

ABSTRACT: 43 biopsies were obtained from subfertile/infertile patients undergoing testicular sperm extraction (TESE) as part of their treatment. Labelled cDNAs were compared to a reference normal testis RNA (Ambion).

INSTRUMENT(S): Axon-GenePix 4100A

ORGANISM(S): Homo sapiens

DISEASE(S): cryptozoospermia

SUBMITTER: Peter Ellis

PROVIDER: E-MEXP-1019 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Coordinated transcriptional regulation patterns associated with infertility phenotypes in men.

Ellis Peter J I PJ Furlong Robert A RA Conner Sarah J SJ Kirkman-Brown Jackson J Afnan Masoud M Barratt Christopher C Griffin Darren K DK Affara Nabeel A NA

Journal of medical genetics 20070511 8

<h4>Introduction</h4>Microarray gene-expression profiling is a powerful tool for global analysis of the transcriptional consequences of disease phenotypes. Understanding the genetic correlates of particular pathological states is important for more accurate diagnosis and screening of patients, and thus for suggesting appropriate avenues of treatment. As yet, there has been little research describing gene-expression profiling of infertile and subfertile men, and thus the underlying transcriptiona ...[more]

PMID: 17496197

Similar Datasets

Transcription profiling of hypergonadal mice (Gnrh1 deletion) mouse testes vs. wild-type to examine the effects of the endogenous lack of gonadotropins on apoptosis

Project description:A comparison of testis transcriptional profile in hypogonadal (hpg) mice and age-matched wild-type controls

2007-07-06 | E-MEXP-1153 | biostudies-arrayexpress

Transcription profiling of T. brucei bloodstream and procyclic forms to look at differential expression of membrane-trafficking genes

Project description:To look at differential expression of membrane-trafficking genes, we extracted RNA from exponentially growing cultures of T. brucei bloodstream (BSF) and procyclic (PCF) forms, labelled and competitively hybridised the cDNA to the microarray. 8 arrays, representing 6 BSF and 5 PCF biological replicates, as well as dye swaps were used.

2008-06-26 | E-MEXP-1529 | biostudies-arrayexpress

Transcription profiling of T. brucei cell lines over-expressing wild type RAB5A or mutant versions of RAB5A or RAB5B locked in the GTP-bound state

Project description:As a test of trypanosome transcriptome responsiveness, we analysed the effects of over-expression of the early endosome small GTPase Rab5A in procyclic form T.brucei, which results in significant augmentation of fluid phase and receptor-mediated endocytic activity (Pal et al. 2002). part 1: 2 PCFWT and 2 PCF5AWT-OE (PCF cell lines over-expressing a wildtype version of RAB5A) biological replicates, as well as dye swaps were used. part 2: 2 PCFWT and 2 PCF5AQL-OE (PCF cell lines over-expressing a mutant version of RAB5A locked in the GTP-bound state) biological replicates, as well as dye swaps were used. part 3: 2 PCFWT and 2 PCF5BQL-OE (PCF cell lines over-expressing a mutant version of RAB5B locked in the GTP-bound state) biological replicates, as well as dye swaps were used.

2008-06-26 | E-MEXP-1539 | biostudies-arrayexpress

Transcription profiling of T. brucei bloodstream forms cultured in different proportions of fetal bovine serum to investigate iron-sensing mechanisms

Project description:Bloodstream trypanosomes are sensitive to iron starvation, and upregulate ESAG6/7 transferrin receptor (TfR) mRNA and protein levels when placed in low transferrin or iron-depleted media, and adjust TfR expression to compensate for reduced endocytosis. Both observations suggest a specific transcriptional-level response resulting from an iron-sensing mechanism. The transcriptomes of BSFs cultured in different proportions of fetal bovine serum (FBS) were analysed. part 1: 4 biological replicates of SMB cells grown with 10% FBS (normal conditions) and 4 replicates of SMB cells grown with 30% FBS, as well as dye swaps, were used. part 2: 3 biological replicates of SMB cells grown with 10% FBS (normal conditions) and 3 replicates of SMB cells grown without FBS (but supplemented with 5 mg/ml BSA to simulate physiological concentrations of albumin in media with 10% FBS), as well as dye swaps were used. part 3: 3 biological replicates of SMB cells grown with 10% FBS (normal conditions) and 3 replicates of SMB cells grown without FBS (but supplemented with 5 mg/ml BSA and 0.3 mg/ml bovine holo-transferrin to simulate physiological concentrations of albumin and transferrin in media with 10% FBS), as well as dye swaps were used.

2008-06-26 | E-MEXP-1530 | biostudies-arrayexpress

Transcription profiling of T. brucei in vivo or in vitro samples, with in vitro samples either inclubated at 4oC or not to investiage the influence of culturing condtions on intracellular transport

Project description:The vast majority of molecular studies on T. brucei are carried out using in vitro cultures. Recently, whole-genome microarray analysis indicated significant differences between in vivo and in vitro cultures of the malaria parasite Plasmodium falciparum. Therefore, as an additional investigation into the influence of culturing conditions on intracellular transport we compared mRNA from bloodstream form MITat1.1 trypanosomes extracted from infected rats and from SMB cells cultured under standard conditions. 3 biological replicates of SMB cells grown under normal in vitro conditions, and 3 biological replicates of MITat1.1 cells grown in vivo in rats, as well as dye swaps were used. The method for RNA isolation from cells grown in vivo contains steps carried out at 4oC. To eliminate the possibility that differences between the in vitro an in vivo samples arise from cold-shock during isolation of MITat1.1 trypomastigotes, we also extracted RNA from SMB cultures incubated at 4oC for 1hr before RNA extractions. 3 biological replicates of SMB cells grown under normal in vitro conditions, and 3 biological replicates of SMB cells grown under normal in vitro conditions but incubated at 4oC for 1 hr before RNA extraction, as well as dye swaps were used.

2008-06-26 | E-MEXP-1540 | biostudies-arrayexpress

Transcription profiling of T. brucei treated with dithiothreitol (DTT) or tunicamycin to invoke the unfolded protein response

Project description:Transcriptome responsiveness was further tested by attempts to invoke the unfolded protein repsonse (UPR), a classic ER-based pathway stimulated by the presence of increased levels of unfolded polypeptides. The UPR is mediated via transcriptional responses in both yeast and metazoan cells, and can be reliably activated by addition of dithiothreitol (DTT). Using DTT at concentrations that invoke a UPR in mammalian cells, Arabidopsis, yeast and other systems, we found that, in T. brucei, DTT exposure led to rapid cell death. We analysed the transcriptome at 1 mM DTT, under conditions where cells remained viable, as assessed by motility. part 1: 3 biological replicates of SMB cells grown under normal conditions, and 3 replicates of SMB cells treated with 1mM DTT for 1hr, as well as dye swaps were used. part 2: 3 biological replicates of SMB cells grown under normal conditions, and 3 replicates of SMB cells treated with 1mM DTT for 4hr, as well as dye swaps were used. The UPR can also be activated by addition of tunicamycin. Using tunicamycin at concentrations that invoke a UPR in mammalian cells, Arabidopsis, yeast and other systems, we found that, in T. brucei, tunicamycin exposure efficiently inhibits trypanosome N-glycosylation and that it resulted in growth arrest over a period of up to 24 hours. We analysed the transcriptome at 5 ?g/ml tunicamycin under conditions where cells remained viable, as assessed by motility. part 3: 3 biological replicates of SMB cells grown under normal conditions, and 3 replicates of SMB cells treated with 5 ?g/ml tunicamycin for 4hr, as well as dye swaps were used. part 4: 3 biological replicates of SMB cells grown under normal conditions, and 3 replicates of SMB cells treated with 5 ?g/ml tunicamycin for 24hr, as well as dye swaps were used.

2008-06-26 | E-MEXP-1533 | biostudies-arrayexpress

RNAi knock-down of VSG in T. brucei for 1 or 3 days

Project description:As an additional strategy for investigating T. brucei transcriptome responsiveness, the mRNA of a highly important protein, the variant surface glycoprotein (VSG) the major surface protein in the bloodstream stage, was suppressed with RNAi. VSG RNAi results in arrest of cell cycle progression in the bloodstream stage. In addition, the mRNA of a highly important protein for endocytosis, the clathrin heavy chain (CLH), was suppressed with RNAi. CLH knockdown leads to a complete block to endocytosis. We hypothesized that if trypanosomes were able to sense alterations in trafficking and respond to these changes, then depletion of these ORFs by RNAi would be expected to elicit a response at the transcriptome level. part 1: 2 biological replicates of SMB cells transfected with the VSG- RNAi vector grown under normal conditions (non-induced), and 2 replicates of the same cells treated with 1 ug/ml tetracycline (induced) for 24hr, as well as dye swaps were used. part 2: 2 biological replicates of SMB cells transfected with the VSG- RNAi vector grown under normal conditions (non-induced), and 2 replicates of the same cells treated with 1 ug/ml tetracycline (induced) for 3 days, as well as dye swaps were used. part 3: 3 biological replicates of SMB cells transfected with the CLH- RNAi vector grown under normal conditions (non-induced), and 3 replicates of the same cells treated with 1 ug/ml tetracycline (induced), as well as dye swaps were used.

2008-06-26 | E-MEXP-1528 | biostudies-arrayexpress

Tissue Type-Specific Expression of the dsRNA-Binding Protein 76 and Genome-wide Elucidation of its Target mRNAs

Project description:RNA-binding proteins accompany all steps in the life of mRNAs and provide dynamic gene regulation functions for rapid adjustment to changing extra- or intracellular conditions. The association of RNA-binding proteins with their targets is regulated through changing sub-cellular distribution, post-translational modification or association with other proteins. Tissue type-specific isoform distribution and target mRNA binding patterns are major determinants of post-transcriptional gene regulation by RNA-binding proteins.We demonstrate that the dsRNA binding protein 76 (DRBP76), synonymous with nuclear factor 90, displays inherently distinct tissue type-specific sub-cellular distribution in the normal human central nervous system and in malignant brain tumors of glial origin. Altered sub-cellular localization and isoform distribution in malignant glioma indicate that tumor-specific changes in DRBP76-related gene products and their regulatory functions may contribute to the formation and/or maintenance of these tumors. To identify endogenous mRNA targets of DRBP76, we performed RNA-immunoprecipitation and genome-wide microarray analyses in HEK293 cells, and identified specific classes of transcripts encoding critical functions in cellular metabolism. Our data suggest that DRBP76 expression, isoform distribution and sub-cellular localization are profoundly disturbed upon malignant transformation in the CNS. Thus, DRBP76’s roles in co- or post-transcriptional gene regulation may contribute to the neoplastic phenotype. Keyword: RIP-chip 5 biological replicates of DRBP76 Immunoprecipitation samples, Mock Immunoprecipiation samples, Total mRNA samples were collected and analyzed using oligo microarrays. For each microarray, biological samples were labelled with Cy3 and human reference RNA was labelled with Cy5.

2010-05-04 | E-GEOD-20001 | biostudies-arrayexpress

Ribonomic analysis of human Pum1 in HeLa cells

Project description:PUF family proteins are among the best characterized regulatory RNA-binding proteins in non-mammalian species, but relatively little is known about mRNA targets or functions of mammalian PUF proteins. In this study, we used ribonomic analysis to identify and analyze mRNAs associated with ribonucleoproteins containing an endogenous human PUF protein, Pum1. Pum1 associated mRNAs were highly enriched for genes encoding proteins that function in transcriptional regulation and cell cycle/proliferation, results consistent with the post-transcriptional RNA regulon model and the proposed ancestral functions of PUF proteins in stem cell biology. Analysis of 3’UTR sequences of Pum1 associated mRNAs revealed a core Pum1 consensus sequence, UGUAHAUA. Pum1 knockdown demonstrated that Pum1 enhances decay of associated mRNAs, and re-localization of Pum1 to stress granules suggested that Pum1 functions in repression of translation. This study is the first in vivo genome-wide mRNA target identification of a mammalian PUF protein and provides direct evidence that human PUF proteins regulate stability of associated mRNAs. Comparison of Pum1 associated mRNAs to mRNA targets of PUF proteins from S. cerevisiae and Drosophila demonstrates how a well conserved RNA-binding domain and cognate binding sequence have been evolutionarily rewired to regulate the collective expression of different sets of functionally related genes. Pum1 IP, negative IP, and total IP samples were analyzed for each of 3 biological replicates. Each IP or total RNA sample was run on a separate array versus a common reference sample

2008-05-01 | E-GEOD-11301 | biostudies-arrayexpress

Coordinated posttranscriptional mRNA population dynamics during T-cell activation

Project description:Although RNA-binding proteins (RBPs) coordinate many key decisions during cell growth and differentiation, the dynamics of RNA–RBP interactions have not been extensively studied on a global basis. We immunoprecipitated endogenous ribonucleoprotein complexes containing HuR and PABP throughout a T-cell activation time course and identified the associated mRNA populations using microarrays. We used Gaussian mixture modeling as a discriminative model, treating RBP association as a discrete variable (target or not target), and as a generative model, treating RBP-association as a continuous variable (probability of association). We report that HuR interacts with different populations of mRNAs during T-cell activation. These populations encode functionally related proteins that are members of the Wnt pathway and proteins mediating T-cell receptor signaling pathways. Moreover, the mRNA targets of HuR were found to overlap with the targets of other posttranscriptional regulatory factors, indicating combinatorial interdependence of posttranscriptional regulatory networks and modules after activation. Applying HuR mRNA dynamics as a quantitative phenotype in the drug-gene-phenotype Connectivity Map, we identified candidate small molecule effectors of HuR and T-cell activation. We show that one of these candidates, resveratrol, exerts T-cell activation-dependent posttranscriptional effects that are rescued by HuR. Thus, we describe a strategy to systematically link an RBP and condition-specific posttranscriptional effects to small molecule drugs. Keywords: Timecourse, RIP, Immunoprecipitation, HuR, ELAVL1, PABP, T cell activation Timecourse experiment: 0hr, 4hr, and 12hr post-activation of Jurkat cells. Four samples collected: HuR-IP, PABP-IP, Neg-IP and Total RNA. 3 Biological replicates per condition and sample that were independently grown and harvested.

2009-08-19 | E-GEOD-11989 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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