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SRP169508
Zea mays
41 Downloadable Samples
Illumina HiSeq 4000
Description
Senescence has tremendous impact on yield and nutritional quality of agricultural produce. However, scant information is available on genetic architecture of senescence in maize (Zea mays L.) despite the importance of stay-green, a delayed senescence phenotype, in this major cereal crop. We combined different approaches including co-expression networks derived from time-course transcriptome analysis of senescence and stay-green to identify unique candidate genes.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 7 Downloadable Samples
- IlluminaHiSeq2500
Description
HeLa cell culture RNASeq data was obtained to demonstrate the effectiveness of the Cas9 based DASH technique for depletion of unwanted abundant sequences.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 34 Downloadable Samples
- Illumina HiSeq 4000
Description
The activity of different E2F constructs with respect to gene expression was measured. E2F constructs differed in degradability, and were doxycycline inducible. Different samples with the different E2F constructs, and with or without dox inductions were assayed for gene expression.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Treatment
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- Arabidopsis thaliana
- 6 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Effect of geminivirus Cabbage leaf curl virus on Arabidopsis Col-0 at 12 days post-inoculation during short day conditions.
Publication Title
Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina Genome Analyzer II
Description
Gene expression profiles of bitter TRCs and profiles of sweet and umami TRCs.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Saccharomyces cerevisiae
- 6 Downloadable Samples
- Ion Torrent Proton
Description
Actively proliferating cells must constantly monitor and re-adjust their metabolic pathways to ensure phospholipid homeostasis for the replenishment of membranes and intracellular trafficking. Multiple studies have suggested that the lysine acetyltransferase NuA4 has a role in fine-tuning phospholipid metabolism in Saccharomyces cerevisiae, however the role of NuA4 in phospholipid homeostasis remains poorly defined. NuA4 mutants have increased gene expression of inositol-3-phosphate synthase, INO1 and overproduce inositol. NuA4 mutants are also display synthetic sickness with a mutant of the lipid remodeling gene SEC14. Here using a combination of genetics and transcriptional profiling, we explore the connections between NuA4, inositol and Sec14. We found that NuA4 mutants exacerbated the inositol auxotrophy of sec14-1ts. Transcriptome studies reveal that loss of the NuA4 subunit EAF1 in sec14-1ts depresses INO1 expression but not all inositol/choline responsive phospholipid genes. This suggests eaf1? cells are defective in coordinating phospholipid homeostasis beyond inositol production. In fact, we discovered that eaf1? cells have significantly lower lipid droplet levels and that inhibition of the fatty acid biosynthesis pathway increased the growth defect of sec14-1ts to a similar extent as untreated sec14-1tseaf1?. Altogether, our work identifies a role for NuA4 as a critical mediator of phospholipid metabolism, potentially as positive regulator of fatty acid biosynthesis.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples- Homo sapiens
- 4 Downloadable Samples
- IlluminaHiSeq2000
Description
Exosomes are 40~120 nm diameter vesicles of endocytic origin released by most cells and important in mediating cell-cell communication. As mRNA and noncoding RNA are two main functional RNA molecules in post transcription level and involves in many bio-activities including cancer progression and metastasis, it is important to understand the coding and noncoding genes contained within exosomes released by tumour cells. This study focused on the protein coding and noncoding genes enriched in two subtypes of exosomes (A33-enriched exosomes, A33-Exos and EpCAM-enriched exosomes, EpCAM-Exos) released by human colon cancer LIM1863 cell line. With high throughput sequencing technology and bioinformatics analyses, we demonstrate 350 protein coding genes (PCGs) and 222 noncoding genes (NCGs) are commonly enriched; 56 PCGs and 202 NCGs were specifically enriched in A33-Exos and 276 PCGs and 253 NCGs were enriched unique to EpCAM-Exos. A salient finding was the significant enrichment of TPT1, ribosomal protein genes and GAS5, a tumour noncoding gene, in exosomes. We further demonstrate differentially seven expressed genes (SCARB1, SCD, TPT1, EETF1G, BCL7C, RPS3, and RAB13) by qRT-PCR. Importantly, we correlated these findings with several matched tissue-derived tumour-normal samples showed TPT1 and ribosomal protein genes were up regulated in human tumour samples. Our findings provide a new insight of functional RNA molecules in exosomes and new select non-invasive biomarker candidates for colon cancer diagnosis and prognosis.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Caenorhabditis elegans
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
Transcriptional response to plant extract
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 59 Downloadable Samples
- Illumina HiSeq 1500
Description
A systems biology approach was used to analyze the blood transcriptomes of adults acutely infected with Chikungunya Virus. There were identified gene signatures and pathways that were associated to viral RNA amounts and to the onset of symptoms that characterize the adults' acute infection.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease
View Samples