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SRP063416
Homo sapiens
7 Downloadable Samples
IlluminaHiSeq2000
Description
In the present study, the autologous cell based therapy for the compromised liver disease due to hepatitis B infection has been investigated. To perform this research, the HBsAg positive and nucleic acid test (NAT) positive blood samples along with healthy blood samples were utilized to generate hepatocyte-like cells (NeoHeps) from monocytes. The monocytes were sorted by MACS technology from the PBMCs so that the abundant non-monocyte cells were depleted.The isolated monocytes were cultured in two steps for 21 days. In the first step monocytes were incubated with serum supplemented IMDM medium containing cytokines like IL-3, MCSF and 2-ME for a period of six days for priming to induce plasticity in them. After six day in culture, the primed monocytes were termed as reprogrammed monocytes (RM). The reprogrammed monocytes were then differentiated for 15 days in serum supplemented IMDM medium containing mitogenic reagents like EGF, HGF and FGF-4 to generate NeoHeps.The RNA sequencing (RNASeq) of the Monocytes, RM and NeoHeps generated from both healthy and HBsAg positive blood samples were performed to analyse the kinetics of this differentiation process at the transcript level.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 2 Downloadable Samples
- IlluminaHiSeq2000
Description
Most ribosomal proteins (RP) are regarded as essential, static components that only contribute to ribosome biogenesis and protein synthesis. However, emerging evidence suggests that RNA-binding RP are dynamic and can influence cellular processes by performing “extraribosomal”, regulatory functions involving binding to select, critical target mRNAs. We report here that the RP, Rpl22, and its highly homologous paralog, Rpl22-Like1 (Rpl22l1 or Like1), play critical, extraribosomal roles in embryogenesis. Indeed, they antagonistically control morphogenesis through developmentally-regulated localization to the nucleus where they modulate splicing of the pre-mRNA encoding smad2, an essential transcriptional effector of Nodal/TGF-ß signaling. During gastrulation, Rpl22 binds to intronic sequences of smad2 pre-mRNA and induces exon 9 skipping in cooperation with hnRNP-A1. This action is opposed by its paralog, Like1, which promotes exon 9 inclusion in the mature transcript. The nuclear roles of these RP in controlling morphogenesis represent a fundamentally different and paradigm-shifting mode of action for RP.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Sus scrofa
- 12 Downloadable Samples
Affymetrix Porcine Genome Array (porcine)
Description
In the present study, Sn expressed on primary pig macrophages was crosslinked with the anti-Sn monoclonal antibody 41D3 and the mRNA expression profiles were compared, using the Affymetrix microarray technology, to macrophages incubated with the irrelevant, isotype matched, monoclonal antibody 13D12
Publication Title
The transcriptome of porcine alveolar macrophages (PAM) after antibody-mediated crosslinking of sialoadhesin (Sn, Siglec-1)
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Gallus gallus
- 4 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
We determined gene expression profiles which were induced in the chick chorio-allantoic membrane 24 h after application of recombinant human VEGF.
Publication Title
Impaired angiogenesis and tumor development by inhibition of the mitotic kinesin Eg5.
Sample Metadata Fields
No sample metadata fields
View Samples- Gallus gallus
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Human pancreatic adenocarcinoma cells were grafted on the chick chorioallantoic membrane (CAM). Human and chicken GeneChips were used simultaneously to study gene regulation during PDAC cell invasion.
Publication Title
Netrin-1 mediates early events in pancreatic adenocarcinoma progression, acting on tumor and endothelial cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 16 Downloadable Samples
- Illumina HiSeq 2000, Affymetrix Human Genome U219 Array (hgu219)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Cell-Cycle-Dependent Reconfiguration of the DNA Methylome during Terminal Differentiation of Human B Cells into Plasma Cells.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 16 Downloadable Samples
Affymetrix Human Genome U219 Array (hgu219), Illumina HiSeq 2000
Description
Molecular mechanisms underlying terminal differentiation of B-cells into plasma cells are major determinants of adaptive immunity but remain only partially understood. Here, we present the transcriptional and epigenomic landscapes of cell subsets arising from activation of human naive B-cells and differentiation into plasmablasts. Cell proliferation of activated B cells was linked to a slight decrease in DNA methylation levels but followed by a committal step in which an S-phase-synchronized differentiation switch was associated with an extensive DNA demethylation and local acquisition of 5-hydroxymethylcytosine at enhancers and genes related to plasma cell identity.
Publication Title
Cell-Cycle-Dependent Reconfiguration of the DNA Methylome during Terminal Differentiation of Human B Cells into Plasma Cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 5 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st), Illumina HiSeq 2000
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
The epigenetic processes of meiosis in male mice are broadly affected by the widely used herbicide atrazine.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 5 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st), Illumina HiSeq 2000
Description
Environmental factors such as pesticides are widely used in the agriculture of many countries and their negative impact on human health and fertility are largely unknown. There is a rapidly growing body of evidence that human reproductive health is negatively affected by the various environmental factors, including life style and exposure to the chemical compounds such as certain drugs and pesticides. Sexually reproducing organisms produce haploid gametes via a process called meiosis. Meiosis is dependent on androgen action within the testis. Pesticides and herbicides interfere with natural hormones system and are considered to be endocrine disruptors. We hypothesize that atrazine (ATZ), a herbicide used globally, adversely affects meiosis. To test this idea we used the mouse as a model organism. Mice were treated three weeks with atrazine in drinking water at concentration of 100 mg/l. To assess the molecular mechanisms of effects of ATZ on spermatogenesis we performed comparative analysis of genes expression by using Affymetrix microarray by using three biological testis samples from ATZ treated and control mice. Using a fold-change cutoff value of 1.5 and p value <0.05 (statistical Limma test (linear models test for microarray data)), we identified 51 genes that were differentially expressed in ATZ treated mice.
Publication Title
The epigenetic processes of meiosis in male mice are broadly affected by the widely used herbicide atrazine.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 4 Downloadable Samples
- Illumina ratRef-12 v1.0 expression beadchip
Description
Based on the developmental origin of health of disease hypothesis, we previously showed that prenatal 70% maternal food restriction (FR30) predisposes the offspring to development of pathologies in adulthood. In the present study, we focused on the liver gene expression profile of standard and high fat (HF)-fed FR30 adult offspring.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples