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SRP096878
Drosophila melanogaster
28 Downloadable Samples
Illumina HiSeq 2500
Description
Y-chromosome aneuploidy strains were generated for 2 distinct Y chromosomes (Ycongo and Yohio), and expression profile analyzed by RNA-seq. Overall design: CONTRAST 1: X^X (control) vs X^XYohio; CONTRAST 2: X^X (control) vs X^XYcongo; CONTRAST 3: X^Y (control) vs X^YYohio; CONTRAST 4: X^Y (control) vs X^YYcongo.
Publication Title
The Y Chromosome Modulates Splicing and Sex-Biased Intron Retention Rates in <i>Drosophila</i>.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Macaca mulatta
- 6 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
Circadian regulation of gene expression in central and peripheral tissue has been studied in mice. The biomedical implications of this findings led us to the development of a model in which to study the circadian mechanisms underlying primate physiology.
Publication Title
Twenty-four-hour rhythmic gene expression in the rhesus macaque adrenal gland.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
HIF-1A and HIF-2A regulate both overlapping and unique target genes in response to hypoxia.
Publication Title
The hypoxia-associated factor switches cells from HIF-1α- to HIF-2α-dependent signaling promoting stem cell characteristics, aggressive tumor growth and invasion.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 15 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Copy number variation in Y chromosome multicopy genes is linked to a paternal parent-of-origin effect on CNS autoimmune disease in female offspring.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The prevalence of some autoimmune diseases (AID) is greater in females compared with males, notwithstanding that disease severity is often greater in males. The reason for this sexual dimorphism (SD) is unknown, but may reflect negative selection of Y chromosome (ChrY) bearing sperm during spermatogenesis or male fetuses early in the course of conception/pregnancy. Previously, we showed that the SD in experimental autoimmune encephalomyelitis (EAE) is associated with copy number variation (CNV) in ChrY multicopy genes. Here, we test the hypothesis that CNV in ChrY multicopy genes influences the paternal parent-of-origin effect on EAE susceptibility in female mice. We show that C57BL/6J consomic strains of mice possessing an identical ChrX and CNV in ChrY multicopy genes exhibit a female biased sex-ratio and sperm head abnormalities, consistent with X-Y intragenomic conflict arising from an imbalance in CNV between homologous ChrX:ChrY multicopy genes. These males also display paternal transmission of EAE to female offspring and differential loading of miRNAs within the sperm nucleus. These findings provide evidence for a genetic mechanism at the level of the male gamete that contributes to the SD in EAE and paternal parent-of-origin effects in female mice, raising the possibility that a similar mechanism may contribute to the SD in MS.
Publication Title
Copy number variation in Y chromosome multicopy genes is linked to a paternal parent-of-origin effect on CNS autoimmune disease in female offspring.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 72 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
We applied a meta-analysis of datasets from seven different microarray studies on lung cancer for differentially expressed genes related to survival time (under 2 y and over 5 y). Systematic bias adjustment in the datasets was performed by distance-weighted discrimination (DWD). We identified a gene expression signature consisting of 64 genes that is highly predictive of which stage I lung cancer patients may benefit from more aggressive therapy.
Publication Title
A gene expression signature predicts survival of patients with stage I non-small cell lung cancer.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
We generated iPSc from skin fibroblasts of two MPSIIIB patients (P1 and P2). MPSIIIB-associated cell defects were prominent in undifferentiated iPSc, in neural stem cells and in their neuronal progeny.
Publication Title
Modeling neuronal defects associated with a lysosomal disorder using patient-derived induced pluripotent stem cells.
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples- Danio rerio
- 30 Downloadable Samples
- Illumina HiSeq 2500
Description
After an acclimatization period with increasing temperature (from 27 to 35째C; ~1째C increment/day), adult zebrafish males were exposed to 35째C for 14 days and injected with the cytostatic agent busulfan (single intraperitoneal injection after 7 days at 35째C; 40 mg/Kg). Then, fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection (i.e. 10 dpi) and the recovery of endogenous spermatogenesis ~14 dpi. Total RNA was isolated from (1) testes of untreated adult control zebrafish, (2) germ cell-depleted, and (3) testis tissue at the beginning of the recovery period, and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples, 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples
Publication Title
Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: follicle-stimulating hormone, retinoic acid and androgens.
Sample Metadata Fields
Specimen part, Subject
View Samples- Danio rerio
- 10 Downloadable Samples
- IlluminaHiSeq2500
Description
Fsh-mediated regulation of zebrafish spermatogenesis includes modulating the expression of testicular growth factors. Here, we study if and how two Sertoli cell-derived Fsh-responsive growth factors, anti-Müllerian hormone (Amh; inhibiting steroidogenesis and germ cell differentiation) and insulin-like growth factor 3 (Igf3; stimulating germ cell differentiation), cooperate in regulating spermatogonial development. In dose response and time course experiments with primary testis tissue cultures, Fsh upregulated igf3 transcript levels and down-regulated amh transcript levels; igf3 transcript levels were more rapidly up-regulated and responded to lower Fsh concentrations than were required to decrease amh mRNA levels. Quantification of immunoreactive Amh and Igf3 on testis sections showed that Fsh increased slightly Igf3 staining but decreased clearly Amh staining. Studying the direct interaction of the two growth factors showed that Amh compromised Igf3-stimulated proliferation of type A (both undifferentiated [Aund] and differentiating [Adiff]) spermatogonia. Also the proliferation of those Sertoli cells associated with Aund spermatogonia was reduced by Amh. To gain more insight into how Amh inhibits germ cell development, we examined Amh-induced changes in testicular gene expression by RNA sequencing. The majority (69%) of the differentially expressed genes was down-regulated by Amh, including several stimulators of spermatogenesis, such as igf3 and steroidogenesis-related genes. At the same time, Amh increased the expression of inhibitory signals, such as inha and id3, or facilitated prostaglandin E2 (PGE2) signaling. Evaluating one of the potentially inhibitory signals, we indeed found in tissue culture experiments that PGE2 promoted the accumulation of Aund at the expense of Adiff and B spermatogonia. Our data suggest that an important aspect of Fsh bioactivity in stimulating spermatogenesis is implemented by restricting the different inhibitory effects of Amh and by counterbalancing them with stimulatory signals, such as Igf3 Overall design: 10 samples in total were analyzed: 5 biological replicates from control testis samples and 5 biological replicates from Amh-treated testis samples (all co-incubated with 11KT)
Publication Title
Antagonistic regulation of spermatogonial differentiation in zebrafish (Danio rerio) by Igf3 and Amh.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Gene expression profiling was carried out in Huh-7.5 cells in which miR-27a was over- or under-expressed. Transfection of cells with pre-miR-27a and pre-miR-control, or anti-miR-27a and anti-miR-control enabled down- and up-regulated genes to be determined, respectively.
Publication Title
MicroRNA-27a regulates lipid metabolism and inhibits hepatitis C virus replication in human hepatoma cells.
Sample Metadata Fields
Cell line, Treatment
View Samples