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Arabidopsis thaliana
9 Downloadable Samples
Illumina HiSeq 2500
Description
Transcriptomic data of Arabidopsis seedlings (Col-0 and cerk1-2 mutant) treated with a 1,3-b-glucan hexasaccharide
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Age, Specimen part
View Samples
GSE2515- Mus musculus
- 6 Downloadable Samples
Affymetrix Mouse Expression 430A Array (moe430a)
Description
TEC (B6 vs Aire KO). Thymic epithelial cells from B6 strain and AIRE KO are compared.
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
screening of AtMYB44-responsive genes under 250mM NaCl treatment
Publication Title
Overexpression of AtMYB44 enhances stomatal closure to confer abiotic stress tolerance in transgenic Arabidopsis.
Alternate Accession IDs
None
Sample Metadata Fields
Compound
View Samples- Arabidopsis thaliana
- 2 Downloadable Samples
- Affymetrix Arabidopsis Genome Array (ag)
Description
Effect of JMT overexpression in global gene expression
Publication Title
Complement analysis of xeroderma pigmentosum variants.
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 6 Downloadable Samples
- Illumina HiSeq 3000
Description
The zebrafish has become a valuable model for examining ocular lens development, physiology and disease. The zebrafish cloche mutant, first described for its loss of hematopoiesis, also shows reduced eye and lens size, interruption in lens cell differentiation and a cataract likely caused by abnormal protein aggregation. To facilitate the use of the cloche mutant for studies on cataract development and prevention we characterized variation in the lens phenotype, quantified changes in gene expression by qRT-PCR and RNA-Seq and compared the ability of two promoters to drive expression of introduced proteins into the cloche lens. We found that the severity of cloche embryo lens cataract varied, while the decrease in lens diameter and retention of nuclei in differentiating lens fiber cells was constant. We found very low expression of both aB-crystallin genes (cryaba and cryabb) at 4 days post fertilization (dpf) by both qRT-PCR and RNA-Seq in cloche, cloche sibling and wildtype embryos and no significant difference in aA-crystallin (cryaa) expression. RNA-Seq analysis of 4 dpf embryos identified transcripts from 25,281 genes, with 1,329 showing statistically significantly different expression between cloche and wildtype samples. Downregulation of eight lens ß- and ?M-crystallin genes and 22 retinal related genes may reflect a general reduction in eye development and growth. Six stress response genes were upregulated. We did not find misregulation of any known components of lens development gene regulatory networks. These results suggest that the cloche lens cataract is not caused by loss of aA-crystallin or changes to lens gene regulatory networks. Instead, we propose that the cataract results from general physiological stress related to loss of hematopoiesis. Our finding that the zebrafish aA-crystallin promoter drove strong GFP expression in the cloche lens demonstrates its use as a tool for examining the effects of introduced proteins on lens crystallin aggregation and cataract prevention.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Arabidopsis thaliana
- 2 Downloadable Samples
- Illumina HiSeq 2000
Description
To investigate the effect of the expression of YlDGAT2 gene on transcriptome of Arabidopsis
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 128 Downloadable Samples
- Affymetrix Human Genome U219 Array (hgu219)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Standard of hygiene and immune adaptation in newborn infants.
Alternate Accession IDs
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 113 Downloadable Samples
- Affymetrix Human Genome U219 Array (hgu219)
Description
The prevalence of immune-mediated diseases such as allergies and autoimmune diseases is on the rise in the developed world. Microbial exposure is known to modulate the risk for these diseases. In order to explore differences in the gene expression patterns induced in utero in infants born in contrasting standards of living and hygiene, we collected umbilical cord blood RNA samples from full-term newborn infants born with normal vaginal delivery in Finland (modern society), Estonia (rapidly developing society) and the Republic of Karelia, Russia (poor economical conditions). Transcriptomic profiles were analyzed using whole genome microarrays including gender, gestational age, birth month and HLA allele genotype as confounding variables in the analysis. The data revealed that the whole blood transcriptome of Finnish and Estonian neonates differ from their Karelian counterparts. Samples from Karelian infants had an increase in transcripts associated with LPS induction and bacterial sepsis observed in 1-year-old infants in earlier studies. The results suggest exposure to toll like receptor (TLR) ligands and a more matured immune response in infants born in Petrozavodsk compared to the Finnish and Estonian infants. These results further support the concept of a conspicuous plasticity in the developing immune system: the environmental factors that play a role in the susceptibility/protection towards immune-mediated diseases begin to shape the neonatal immunity already in utero and direct the maturation of both the adaptive and the innate immune responses in accordance with the surrounding microbial milieu.
Publication Title
Standard of hygiene and immune adaptation in newborn infants.
Alternate Accession IDs
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 46 Downloadable Samples
- Sentrix Human-6 Expression BeadChip
Description
Special AT-rich binding protein 1 (SATB1) is a global chromatin organizer and a transcription factor induced by interleukin-4 (IL-4) during the early T helper 2 (Th2) cell differentiation. In this study, we investigated the role of SATB1 in T helper cell differentiation by performing gene expression profiling of human differentiating Th cells in which expression of SATB1 was downregulated by RNA interference (RNAi). Our results indicate that SATB1 is involved in the regulation of more than three hundred genes in primary human CD4+ T cells, including several IL-12 and/or IL-4 regulated factors, suggesting a role in the development or function of Th subtypes.
Publication Title
SATB1 dictates expression of multiple genes including IL-5 involved in human T helper cell differentiation.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Identification of global regulators of T-helper cell lineage specification.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
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