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Vitis vinifera
27 Downloadable Samples
Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)
Description
Global gene expression analysis of grapevine cv. Pinot Noir berries during development and ripening. Time-course comparison of samples collected at three developmental stages (stages 33, 34 and 36 according to the modified E-L system, ref: Coombe BG, Aust J Grape Wine Res 1995, 1: 104-110) during three seasons (2003, 2005 and 2006).
Publication Title
Genome-wide transcriptional analysis of grapevine berry ripening reveals a set of genes similarly modulated during three seasons and the occurrence of an oxidative burst at vèraison.
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Caenorhabditis elegans
- 4 Downloadable Samples
Illumina HiSeq 2000
Description
Deep sequencing of RNA isolated from ALT survivors in N2 genetic backgrounds (CS, NS). RNA-seq data was compared to the parental strain N2 trt-1(ok410). Total RNA was extracted from synchronized L4 stage worms.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Disease, Cell line
View Samples- Homo sapiens
- 3 Downloadable Samples
- IlluminaHiSeq2500
Description
RNA-Seq study from Caco2 cells following transduction with control shRNA and shRNA against CHD6
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples
SRP139292- Mus musculus
- 8 Downloadable Samples
- Illumina HiSeq 2500
Description
Small RNA seq following over expression of miR-218 in HepG2 cells; mRNA expression following perturbation of miR-218 in primary mouse motor neurons
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
Progranulin mutations found in frontotemporal lobar degeneration (FTLD) cases typically result in heterozygous loss-of-function. To assess the impact of PGRN deficiency on gene expression, particularly of genes associated with lipid metabolism, in the brain, we sequenced the total RNA extracted from whole brains from 7-month-old female Grn+/+, Grn+/–, and Grn–/– mice and determined the differential expression of transcripts in PRGN-deficient (Grn+/- and Grn-/-) and wild type (Grn+/+) brains.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Drosophila melanogaster
- 67 Downloadable Samples
- Illumina HiSeq 2500
Description
We evaluated how different microbial species commonly associated with laboratory-reared Drosophila melanogaster impact host biology at the level of gene expression in the dissected adult gut or the entire adult organism. We observed that guts from gnotobiotic animals associated from the embryonic stage with either zero, one or three bacterial species demonstrated indistinguishable transcriptional profiles. Additionally, we found that the gut transcriptional profiles of animals reared in the presence of the yeast Saccharomyces cerevisiae alone or in combination with bacteria could recapitulate those of conventionally-reared animals. In contrast, we found whole body transcriptional profiles of conventionally-reared animals were distinct from all of the gnotobiotic treatments tested. Our data suggest that adult flies are insensitive to the ingestion of different bacterial species but that prior to adulthood, different microbes impact the host in ways that lead to global transcriptional differences observable across the whole adult body.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Cell line, Treatment
View Samples SRP183700- Homo sapiens
- 30 Downloadable Samples
- NextSeq 500
Description
We examined skin biopsies from a diverse cohort of 23 SSc patients (including lesional forearm and non-lesional back samples) by RNA-seq. Metagenomic filtering and annotation was performed using the Integrated Metagenomic Sequencing Analysis (IMSA). Associations between microbiome composition and gene expression were analyzed using single-sample gene set enrichment analysis (ssGSEA).
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 21 Downloadable Samples
- NextSeq 500
Description
Estrogens have been shown to elicit anti-cancer effects against estrogen receptor alpha (ER)-positive breast cancer. We sought to determine the underlying mechanism of therapeutic response. Response to estrogen treatment was assessed in ER+ breast cancer models of anti-estrogen resistant disease: WHIM16 patient-derived xenografts, C7-2-HI and C4-HI murine mammary adenocarcinomas, and long-term estrogen-deprived MCF-7 cells.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 12 Downloadable Samples
- NextSeq 500
Description
Microenvironmental secreted factor screening revealed cytokines that modulate drug sensitivity in ER+ breast cancer cells. BMP4 was a top hit that is not normally expressed in ER+ breast cancer, and was found to enhance efficacy of anti-estrogens and CDK4/6i in anti-estrogen-sensitive and -resistant ER+ breast cancer cells. The anti-cancer effects of BMP4 were mediated by ALK3 and canonical BMP pathway signaling, leading to downstream p21 induction and cell cycle arrest. The clinical relevance of this phenotype was confirmed in analyses of 3 cohorts of patients with ER+ breast cancer, highlighting BMP4 pathway activation as a potential therapeutic opportunity in ER+ breast cancer.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
RNA-Seq experiment was done to compare cngc16 (a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated channel 16) and wild type pollen for differences in their response to a temperature stress condition. Transcriptomes were analyzed from mature pollen grains harvested at midday from plants grown under normal (control) conditions or a heat stress regime. For the stress condition, plants were grown under a diurnal cycle of hot and cold temperatures and pollen were harvested at the end of a HS period that peaked at 40 degrees Celsius.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Treatment
View Samples