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E-MEXP-1304
Arabidopsis thaliana
52 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
In most organisms biological processes are partitioned, or phased to specific times over the day through interactions between external cycles of temperature (thermocycles) and light (photocycles), and the endogenous circadian clock. This orchestration of biological activities is achieved in part through an underlying transcriptional network. To understand how thermocycles, photocycles and the circadian clock interact to control time of day specific transcript abundance in Arabidopsis thaliana, we conducted four diurnal and three circadian two-day time courses using Affymetrix GeneChips (ATH1). All time courses were carried out with seven-day-old seedlings grown on agar plates under thermocycles (HC, hot/cold) and/or photocycles (LD, light/dark), or continuous conditions (LL, continuous light; DD, continuous dark, HH, continuous hot). Whole seedlings (50-100), including roots, stems and leaves were collected every four hours and frozen in liquid nitrogen. The four time courses interrogating the interaction between thermocycles, photocycles and the circadian clock were carried out as two four-day time courses. Four-day time courses were divided into two days under diurnal conditions, and two days under circadian conditions of continuous light and temperature. Thermocycles of 12 hours at 22C (hot) and 12 hours at 12C (cold) were used in this study. The two time courses interrogating photoperiod were conducted under short days (8 hrs light and 16 hrs dark) or long days (16 hrs light and 8 hrs dark) under constant temperature. In addition, the photoperiod time courses were in the Landsberg erecta (ler) accession, in contrast to the other time courses that are in the Columbia (col) background. The final time course interrogated circadian rhythmicity in seedlings grown completely in the dark (etiolated). Dark grown seedlings were synchronized with thermocycles, and plants were sampled under the circadian conditions of continuous dark and temperature.
Publication Title
Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules.
Sample Metadata Fields
Age, Time
View Samples- Arabidopsis thaliana
- 35 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Arabidopsis thaliana circadian and light signaling mutants have long hypocotyls under light/dark cycles. In order to determine if aberrant hypocotyl growth is due to time of day specific miss-expression of growth associated transcripts we conducted time course microarray experiments in the lux-2, lhy and phyB-9 mutants. The mutants and their parental genotypes were grown on plates under either intermediate days (12 hours light and 12 hours dark) for lux-2, or short day (8 hrs of light and 16 hrs of dark) for lhy and phyB-9, for seven days and tissue was collected every four hours over one day.
Publication Title
A circadian and light transcriptional network orchestrates plant growth
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Goal of this study was to compare transcriptional changes in CTL cells compared to Tc17 cells
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 36 Downloadable Samples
Illumina HiSeq 1500
Description
The goal was to characterize gene expression profiles of HSPCs in mice during Bordetella pertussis infection. Mice were immunized with acellular or whole cell pertussis vaccines. HSPCs were isolated by flow cytometric sorting and RNA was prepared for library prep and RNA seq analysis.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Cell line, Treatment
View Samples- Mus musculus
- 32 Downloadable Samples
- Illumina HiSeq 1500
Description
Total transcriptome analysis of naive or vaccinated murine lungs, post-challenge with Bordatella pertussis. Mice were immunized with PBS, whole cell pertussis vaccine, acellular pertussis vaccine, and RTX (adenylate cyclase toxoid) vaccine. The mice were then infected with B. pertussis and at 1 or 6/9 days post-challenge total lung RNA was purified for RNA-seq analysis.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Disease, Cell line, Treatment
View Samples- Homo sapiens
- 24 Downloadable Samples
- Illumina HiSeq 2500
Description
Infection of mammalian cells with vesicular stomatitis virus (VSV) results in the inhibition of cellular gene expression. This host shut-off is achieved through viral mediated inhibition of cellular gene expression at multiple levels including transcription, mRNP nuclear-cytoplasmic export, and translation. To interrogate the effects of VSV infection on translation, we infected HeLa cells at MOI 10 for 2 or 6 hours and performed polysome profiling and deep sequenced total cytoplasmic mRNA as well as monosome- and polysome-associated mRNAs. Our data support a model where viral mRNA abundance contributes to host shut-off by dominating the pool of cytoplasmic mRNA.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment, Time
View Samples- Mus musculus
- 14 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
12 C57BL/6 mice were infected orogastrically with the H. pylori strain SS1. After 6 and 12 months, 3 non-infected and 3 infected mice were sacrificed and stomachs isolated. Gastric tissues were disaggregated and total RNA were isolated by TRIzol extraction and then purified on RNeasy minicolumns. After synthesis of the first cDNA strand (In vitrogen), the double-stranded cDNA was obtained and used to produce biotin-labeled cRNA (Enzo Diagnostic). FRagmented cRNA was hybridized to GeneChip Mouse expression array 430A (Affymetrix).
Publication Title
Interferon gamma-signature transcript profiling and IL-23 upregulation in response to Helicobacter pylori infection.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Subject, Time
View Samples- Saccharomyces cerevisiae
- 14 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Yeast knockout strains were constructed by the Yeast Deletion Project. Three biological replicates were analyzed for each strain. 5 ml cultures were inoculated at OD600 = 0.2 from saturated overnight cultures and grown to mid-log phase (OD600 = 0.6 - 0.8) in YPD media 37 or in phosphate-depleted media 38 at 30C. Cells were harvested by centrifugation and washed with nuclease-free water (Ambion). Total RNA was isolated immediately after harvest using the Ribopure Yeast RNA Isolation Kit (Ambion). 5 mg of total RNA was used to generate labeled probes with standard Affymetrix protocols.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Pseudomonas aeruginosa
- 10 Downloadable Samples
- Affymetrix Pseudomonas aeruginosa Array (paeg1a)
Description
Effect of acyl-HSL signal or ectopic lasR, rhlR, or rpoS expression on the advancement of quorum sensing gene expression during the logarithmic phase of growth
Publication Title
Early Activation of Quorum Sensing in Pseudomonas aeruginosa Reveals the Architecture of a Complex Regulon
Sample Metadata Fields
Compound
View Samples- Homo sapiens
- 10 Downloadable Samples
- Illumina HiSeq 2500
Description
Cells were transfected with control, TIF-IA, or UBF siRNAs prior to transfection of no DNA or dsDNA. The impact of TIF-IA depletion on gene expression and the impact of TIF-IA and UBF depletion on dsDNA-induced gene expression were assayed.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples