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Arabidopsis thaliana
2 Downloadable Samples
Illumina HiSeq 2000
Description
In order to gain insight into relative stability of transcripts in plants that lacked m6A, we performed global mapping of uncapped and cleaved transcripts Overall design: 2 replicates of GMUCT in Arabidopsis thaliana ecotype Col-0 ABI3:MTA (mta) plants. genome-wide mapping of uncapped and cleaved transcripts (GMUCT)
Publication Title
N<sup>6</sup>-Methyladenosine Inhibits Local Ribonucleolytic Cleavage to Stabilize mRNAs in Arabidopsis.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 37 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
To obtain a separation of the epidermal and dermal compartments in order to examine compartment specific biological mechanisms in the skin we incubated 4 mm human skin punch biopsies in ammonium thiocyanate (NH4SCN). We wanted to test 1) the histological quality of the dermo-epidermal separation obtained by different incubation times 2) the amount and quality of extractable epidermal RNA, and 3) its impact on sample RNA expression profiles assessed by large-scale gene expression microarray analysis in both normal and inflamed skin. At 30 minutes incubation, the split between dermis and epidermis was not always histologically well-defined (i.e. occurred partly intra-epidermally) but varied between subjects. Consequently, curettage along the dermal surface of the biopsy was added to the procedure. This modified method resulted in an almost perfect separation of the epidermal and dermal compartments and satisfactory amounts of high-quality RNA were obtained. Hybridization to Affymetrix HG_U133A 2.0 GeneChips showed that ammonium thiocyanate incubation had a minute effect on gene expression resulting in only one significantly downregulated gene (cystatin E/M). We conclude that epidermis can be reproducibly and almost completely separated from the dermis of 4 mm skin biopsies by 30 min incubation in 3.8% ammonium thiocyanate combined with curettage of the dermal surface, producing high-quality RNA suitable for transcriptional analysis. Our refined method of dermo-epidermal separation will undoubtedly prove valuable in the many different settings, where the epidermal and dermal compartments need to be evaluated separately.
Publication Title
Extraction of high-quality epidermal RNA after ammonium thiocyanate-induced dermo-epidermal separation of 4 mm human skin biopsies.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 9 Downloadable Samples
- IlluminaGenomeAnalyzerIIx
Description
Sequencing of 5' ends of RNA molecules from control and exosome-depleted HeLa-S3 cells. Overall design: CAGE library construction from RNA extracted from control and exosome-depleted cells.
Publication Title
Nuclear stability and transcriptional directionality separate functionally distinct RNA species.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 10 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
We used microarrays to assess differences in gene expression associated with single nucleotide polymorphisms occurred in three genes, PMA1, MDS3 and MKT1, as compared to a reference strain devoid of any mutations (Progenitor strain).
Publication Title
Cellular effects and epistasis among three determinants of adaptation in experimental populations of Saccharomyces cerevisiae.
Sample Metadata Fields
No sample metadata fields
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SRP189590- Mus musculus
- 10 Downloadable Samples
- Illumina HiSeq 2000
Description
RNA-seq with male and female juvenile and adult spinal cords Overall design: RNA was isolated from 4 week and 8 week spinal cords for sequencing
Publication Title
Age and Sex-Related Changes to Gene Expression in the Mouse Spinal Cord.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Subject
View Samples- Mus musculus
- 40 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
The transition from pregnancy to lactation is a critical event in the survival of the newborn since all the nutrient requirements of the infant are provided by milk. While milk contains numerous components, including proteins, that aid in maintaining the health of the infant, lactose and milk fat represent the critical energy providing elements of milk. Much of the research to date on mammary epithelial differentiation has focused upon expression of milk protein genes, providing a somewhat distorted view of alveolar differentiation and secretory activation. While expression of milk protein genes increases during pregnancy and at secretory activation, the genes whose expression is more tightly regulated at this transition are those that regulate lipid biosynthesis. The sterol regulatory element binding protein (SREBP) family of transcription factors is recognized as regulating fatty acid and cholesterol biosynthesis. We propose that SREBP1 is a critical regulator of secretory activation with regard to lipid biosynthesis, in a manner that responds to diet, and that the serine/threonine protein kinase Akt influences this process, resulting in a highly efficient lipid synthetic organ that is able to support the nutritional needs of the newborn.
Publication Title
Key stages in mammary gland development. Secretory activation in the mammary gland: it's not just about milk protein synthesis!
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
The goal of this study was to determine the effects of dietary selenium levels on translational control of selenoprotein synthesis in mouse liver. Overall design: Wild type mice and mice expressing a mutant Sec-tRNA gene (TrspA37G) were fed diets supplemented with 0, 0.1, or 2 ppm selenium for 6 weeks. Livers were harvested and ribosome and mRNA profiles were generated by deep-sequencing using the Illumina HiSeq 2000.
Publication Title
Translational redefinition of UGA codons is regulated by selenium availability.
Sample Metadata Fields
Age, Cell line, Treatment, Subject
View Samples- Pseudomonas aeruginosa
- 10 Downloadable Samples
- Affymetrix Pseudomonas aeruginosa Array (paeg1a)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
In vitro analysis of tobramycin-treated Pseudomonas aeruginosa biofilms on cystic fibrosis-derived airway epithelial cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 7 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
We tested the effects of the antioxidant NAC (N-Acetyl-Cysteine) on gene expression in Nkx3.1-deficient mouse prostate.
Publication Title
Antioxidant treatment promotes prostate epithelial proliferation in Nkx3.1 mutant mice.
Sample Metadata Fields
Age, Specimen part
View Samples- Pseudomonas aeruginosa
- 6 Downloadable Samples
- Affymetrix Pseudomonas aeruginosa Array (paeg1a)
Description
We grew Pseudomonas aeruginosa biofilms on CFBE41o- human airway cells in culture, and we treated these biofilms with tobramycin. Microarray analysis was performed to gain an understanding of the global transcriptional changes that occur during antibiotic treatment.
Publication Title
In vitro analysis of tobramycin-treated Pseudomonas aeruginosa biofilms on cystic fibrosis-derived airway epithelial cells.
Sample Metadata Fields
No sample metadata fields
View Samples