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Rattus norvegicus
12 Downloadable Samples
Affymetrix Rat Gene 1.0 ST Array (ragene10st)
Description
Androgens are required for prostate development, growth and physiology, by activating the androgen receptor (AR) upon activation by testosterone and dihydrotestosterone (DHT), the AR undergoes conformational changes, dimerizes and translocates to the cell nucleus regulation important genes releted to cell survival. Understanding the mechanisms of androgen regulation in the prostate gland is important, because the prostate is affected by several different diseases, in particular prostate cancer (PCa). Several ways exist to treat prostate cancer and promote epithelial cell death. Treatments involving androgen manipulation include surgical castration (bilateral orchiectomy), antiandrogens (usually AR antagonists), or substances that inhibit androgen synthesis (5 alpha-reductase inhibitors, gonadotrophin-releasing hormone blockers). 17 beta-estradiol exerts anti-androgen effects by blocking the hypothalamic production of gonadotropin-releasing hormone and thereby inhibiting the production of testosterone by the testes , but also acts locally via interactions with either of the estrogen receptors found in the gland. It is known that the kinetics of apoptosis are different in the rat ventral prostate (VP) of castrated rats (Cas group) and in rats subjected to 17 beta-estradiol high dose (group E2) or their combination (group Cas+E2), with an evident additive effect in the latter situation (Garcia-Florez et al, 2005).
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part
View Samples- Escherichia coli
- 4 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
Avian pathogenic Escherichia coli strains frequently cause extra-intestinal infections and are responsible for significant economic losses in the poultry industry worldwide. APEC isolates are closely related to human extraintestinal pathogenic E.coli strains and may also act as pathogens for humans. In this work, three type VI secretion systems were deleted to analyze which pathogenicity characteristics would change in the mutants, compared to wild type strain (SEPT 362).
Publication Title
The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 226 Downloadable Samples
- Affymetrix Human Gene 2.1 ST Array (hugene21st)
Description
Purpose: Black/African American (AA) women are twice as likely to be diagnosed with triple negative breast cancer (TNBC) compared to whites, an aggressive breast cancer subtype associated with poor prognosis. There are no routinely used targeted clinical therapies for TNBC; thus there is a clear need to identify prognostic markers and potential therapeutic targets. Methods: We evaluated expression of 27,016 genes in 155 treatment-naïve TN tumors from AA women in Detroit. Associations with survival were evaluated using Cox proportional hazards models adjusting for stage and age at diagnosis, and p-values were corrected using a false discovery rate. Our validation sample consisted of 158 TN tumors (54 AA) from The Cancer Genome Atlas (TCGA). Meta-analyses were performed to obtain summary estimates by combining TCGA and Detroit AA cohort results. Results: In the Detroit AA cohort, CLCA2 [Hazard ratio (HR)=1.56, 95% confidence interval (CI) 1.31-1.86, nominal p=5.1x10-7, FDR p=0.014], SPIC [HR=1.47, 95%CI 1.26-1.73, nominal p=1.8x10-6, FDR p=0.022], and MIR4311 [HR=1.57, 95% CI 1.31-1.92, nominal p=2.5x10-5, FDR p=0.022] expression were associated with overall survival. Further adjustment for treatment and breast cancer specific survival analysis did not substantially alter effect estimates. Meta-analysis with TCGA data showed that CLCA2 and SPIC were associated with overall survival for TNBC among AA women. Conclusions: We identified three potential prognostic markers for TNBC in AA women, for which SPIC may be an AA-specific prognostic marker.
Publication Title
CLCA2 expression is associated with survival among African American women with triple negative breast cancer.
Sample Metadata Fields
Age, Treatment, Race
View Samples- Homo sapiens
- 203 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
This is the expression dataset for two studies: 1) Characterization of visceral and subcutaneous adipose tissue transcriptome and biological pathways in pregnant and non-pregnant women: Evidence for pregnancy-related regional-specific differences in adipose tissue and 2) Characterization of visceral and subcutaneous adipose tissue transcriptome in pregnant women with and without spontaneous labor at term: Implication of alternative splicing in the metabolic adaptations of adipose tissue to parturition.
Publication Title
Characterization of visceral and subcutaneous adipose tissue transcriptome in pregnant women with and without spontaneous labor at term: implication of alternative splicing in the metabolic adaptations of adipose tissue to parturition.
Sample Metadata Fields
Specimen part, Disease stage, Subject
View Samples- Hordeum vulgare
- 168 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
Expression analysis was performed on total RNA from the Q21861 and SM89010 barley lines, and 75 derived doubled haploid progeny, with CI 16137 included as an internal Mla1 allele control. Samples were blocked by time-point and completely randomized within each block. For each sample, seven day old seedlings were inoculated with Blumeria graminis f. sp. hordei (Bgh) isolate 5874 (AVRa1, AVRa6, AVRa12), and first leaves were collected at 16 and 32 hours after inoculation (HAI). ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Roger Wise. The equivalent experiment is BB96 at PLEXdb.]
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part, Time
View Samples
GSE66913- Vitis riparia, Vitis hybrid cultivar
- 167 Downloadable Samples
- Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)
Description
Bud endodormancy induction response of two genotypes (Seyval a hybrid white wine grape and V. riparia, PI588259 a native north american species) was compared under long and short photoperiod. Three separate replicates (5 plants/replicate) were treated in each of 2 separate years (2007 and 2008) to generate paradormant (LD) and same aged endodormancy-induced (SD) buds for transcriptomic, proteomic and metabolomic analysis. Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval 3-19-07, 3/18/08; V. riparia 3/26/07, 3/24/08) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes they were randomized into groups for differential photoperiod treatments. On 4/30/07 and 4/28/08 LD and SD (13 h) treatments were imposed with automated photoperiod system (VRE Greenhouse Systems). Temperatures were maintained at 25/20 + 3C D/N. Three replications (5 vines/replication) were harvested between 5/07-6/07 and then again in 5/08-6/08. At 1, 3, 7, 14, 21, 28 and 42 days of differential photoperiod treatment, buds were harvested from nodes 3 to 12 (from the base of the shoot) of each separate replicate, immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein and metabolite extraction. These time points encompass early reversible phases as well as key time points during transition to irreversible endodormancy development. After photoperiod treatments and bud harvests, all pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date. Acknowledgement:This study was funded by NSF Grant DBI0604755 and funds from the South Dakota Agriculture Experiment Station. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Anne Fennell. The equivalent experiment is VV18 at PLEXdb.]
Publication Title
Short day transcriptomic programming during induction of dormancy in grapevine.
Sample Metadata Fields
Age, Specimen part
View Samples- Hordeum vulgare
- 166 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
The QxSM doubled-haploid mapping population was generated from a single Q21861 x SM89010 F1 plant (Borovkova et al. 1995; Steffenson et al. 1995). Four flats (each flat contained 75 DH lines + 4 replicates of each parent = 81 cones/flat) were grown in a completely randomized design at the ARS Cereal Disease Lab, University of Minnesota, St. Paul. The four flats were divided into two replicates of two flats each. Nine days after sowing, one flat of each replicate was inoculated (INOC) with TTKS urediniospores were suspended in Soltrol oil with an inoculum weight of 0.25 mg per flat and the other was mock-inoculated (MOCK). Each (MOCK and INOC) replicate was incubated in its own dew chamber overnight. After inoculation, replicates were placed in separate mist chambers for 16 hours in the dark, followed by lights for 5 hours, and then moved to the greenhouse for 2 hours. The growth stage of barley was first leaf unfolded (PO:0007094) and five seedlings were harvested and placed in liquid nitrogen for each line in the population within a 1.5 hour period at 24 hours after inoculation (hai). ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Roger P. Wise. The equivalent experiment is BB64 at PLEXdb.]
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Hordeum vulgare
- 144 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
A split-split-plot design with 144 experimental units (3 replications x 4 genotypes x 6 time points x 2 treatment types) was used to profile barley plants containing variants of Mla1 and Mla6 powdery mildew resistance genes in response to inoculation with the Blumeria graminis f. sp. hordei (Bgh) isolates 5874 (AvrMla1, AvrMla6). Barley leaves were harvested from inoculated and non-inoculated plants at 6 time points (0,8,16,20,24 and 32 hrs) after Bgh inoculation. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Rico Caldo. The equivalent experiment is BB10 at PLEXdb.]
Publication Title
Blufensin1 negatively impacts basal defense in response to barley powdery mildew.
Sample Metadata Fields
Specimen part, Time
View Samples- Mus musculus
- 126 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
Human cancers result from a complex series of genetic alterations resulting in heterogeneous disease states. Dissecting this heterogeneity is critical for understanding underlying mechanisms and providing opportunities for therapeutics matching the complexity. Mouse models of cancer have generally been employed to reduce this complexity and focus on the role of single genes. Nevertheless, our analysis of tumors arising in the MMTV-Myc model of mammary carcinogenesis reveals substantial heterogeneity, seen in both histological and expression phenotypes. One contribution to this heterogeneity is the substantial frequency of activating Ras mutations, the frequency of which can be changed by alterations in Myc. Additionally, we show that these Myc-induced mammary tumors exhibit even greater heterogeneity, revealed by distinct histological subtypes as well as distinct patterns of gene expression, than many other mouse models of tumorigenesis. Two of the major histological subtypes are characterized by differential patterns of cellular signaling pathways, including B-Catenin and Stat3 activities. We also demonstrate the predictive nature of this approach though examining metastatic potential. Together, these data reveal that a combination of histological and genomic analyses can uncover substantial heterogeneity in mammary tumor formation and therefore highlight aspects of tumor phenotype not evident in the population as a whole.
Publication Title
Genetic heterogeneity of Myc-induced mammary tumors reflecting diverse phenotypes including metastatic potential.
Sample Metadata Fields
No sample metadata fields
View Samples- Glycine max
- 117 Downloadable Samples
- Affymetrix Soybean Genome Array (soybean)
Description
Experimental design: 2 genotypes: PI230970 (resistant USDA Plant Introduction (PI) line containing SBR Rpp2 resistance gene) & Embrapa-48 (susceptible Brazilian cultivar) 2 treatments: Soybean rust challenge & mock infection 3 replications 10 time points: 6, 12, 18, 24, 36, 48, 72, 96, 120, 168hai TOTAL: 120 Affymetrix GeneChip(R) Soybean Genome Arrays ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Martijn van de Mortel. The equivalent experiment is GM2 at PLEXdb.]
Publication Title
Distinct biphasic mRNA changes in response to Asian soybean rust infection.
Sample Metadata Fields
Specimen part, Time
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