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GSE65570
Homo sapiens
15 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Altered integrin expression patterns shown by microarray in human cutaneous melanoma.
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples- Homo sapiens
- 15 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Metastatic process is considered the predominant cause of melanoma-specific death, decreasing survival dramatically, and resulting in difficulties in the effective treatment. Large variety of molecular pathways associated with disease development and progression suggests that no individual molecular alteration is crucial in these processes per se.
Publication Title
Altered integrin expression patterns shown by microarray in human cutaneous melanoma.
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples- Homo sapiens
- 8 Downloadable Samples
Illumina HiSeq 2500
Description
In this study, we analyzed how non-coding double stranded RNA (dsRNAs) act as a damage associated molecular pattern (DAMP) in the skin, and how the human cathelicidin AMP LL-37 might influence growth factor production in response to this DAMP. Overall design: Each sample''s RNA was isolated form a single biological source of P6 NHEKs. In total there are 4 samples (non-replicates); Control (PBS treated), 1.75uM LL-37 treated, 0.1ug/ml Poly(I:C) treated, and co-treated with 1.75uM LL-37 and 0.1ug/ml Poly(I:C).
Publication Title
Non-coding Double-stranded RNA and Antimicrobial Peptide LL-37 Induce Growth Factor Expression from Keratinocytes and Endothelial Cells.
Sample Metadata Fields
Cell line, Treatment, Subject, Time
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
The Notch signalling pathway plays fundamental roles in diverse developmental processes in metazoans, where it is important in driving cell fate and directing differentiation of various cell types. However, we still have limited knowledge about the role of Notch in early preimplantation stages of mammalian development, or how it interacts with other signalling pathways active at these stages such as Hippo. By using genetic and pharmacological tools in vivo, together with image analysis of single embryos and pluripotent cell culture, we have found that Notch is active from the 4-cell stage. Transcriptomic analysis in single morula identified novel Notch targets, such as early naïve pluripotency markers or transcriptional repressors such as TLE4. Our results reveal a previously undescribed role for Notch in driving transitions during the gradual loss of potency that takes place in the early mouse embryo prior to the first lineage decisions. Overall design: Transcriptomic analysis comparing single Rbpj mutant and control mouse morulae. RNA was isolated from individual E2.5 embryos from two litters. 3 mutant and 3 control embryos were used for analysis.
Publication Title
Transitions in cell potency during early mouse development are driven by Notch.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This data set is intended as a public resource documenting the identity of roughly 10,000 genes that are abundantly expressed in the mouse cochlea. The data have many uses, including for making comparisons with proteomics studies, and for comparisons of expression profiles with other mouse strains and with other species. The CBA/CaJ strain was chosen because of its lack of known vulnerabilities to premature cochlear degeneration or to extreme reactions to cochlear stresses. It may therefore be considered a normal mouse. No experimental manipulations were done on the mice of this study. Contamination of the results by genes expressed in the surrounding petrous bone and from those in blood cells was minimized.
Publication Title
Immunocytochemical traits of type IV fibrocytes and their possible relations to cochlear function and pathology.
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 12 Downloadable Samples
- Affymetrix Zebrafish Genome Array (zebrafish)
Description
Brains are sexually dimorphic in adult zebrafish. We dissected brains from young and old, adult zebrafish, from both males and females.
Publication Title
Gene expression changes in aging zebrafish (Danio rerio) brains are sexually dimorphic.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
Single cell RNA-seq is a powerful methodology, but with important limitations. In particular, the process of enzymatic separation of cells at 37O C can be expected to result in artifact changes in gene expression patterns. We here describe a dissociation method that uses protease from a psychrophilic microorganism with high activity in the cold. The entire procedure is carried out at 6O C or colder, where mammalian transcriptional machinery is largely inactive. To test this method we carry out single cell RNA-seq on about 9,000 cells, comparing the results of the cold method with a method using 37O C incubations for multiple times. We show that the cold active protease method results in a great reduction in gene expression artifacts. Overall design: Whole mouse post natal day 1 kidney cells were dissassociated by either a cold active protease or an enzyme cocktail for varying lengths of time. The gene expression profiles of the four groups of cells were determined by drop-seq / RNA-seq.
Publication Title
Psychrophilic proteases dramatically reduce single-cell RNA-seq artifacts: a molecular atlas of kidney development.
Sample Metadata Fields
Subject
View Samples- Bos taurus
- 40 Downloadable Samples
- Illumina Genome Analyzer II
Description
Rift Valley Fever Virus (RVFV), a negative-stranded RNA virus, is the etiological agent of the vector-borne zoonotic disease, Rift Valley Fever (RVF). In both humans and livestock, protective immunity can be achieved through vaccination. Earlier and more recent vaccine trials in cattle and sheep demonstrated a strong neutralizing antibody and total IgG response induced by the RVFV vaccine, MP-12. From previous work, protective immunity in sheep and cattle vaccinates normally occurs from 7 to 21 days after inoculation with MP-12. While the serology and protective response induced by MP-12 has been studied, little attention has been paid to the underlying molecular and genetic events occurring prior to the serologic immune response. To address this, we isolated RNA from whole blood from vaccinates over a time course of 21 days before and after inoculation during a recent vaccine trial with MP-12. This RNA time course was deeply sequenced by RNASeq and bioinformatically analyzed. Our results revealed time-dependent activation or repression of numerous gene ontologies and pathways related to immune response and regulation. Additional analyses identified a correlative relationship between specific genes related to immune activity and protective immunity prior to serologic detection of antibody response. These data provide an important proof of concept for identifying molecular and genetic components underlying the immune response to vaccination and protection prior to serologic detection. Overall design: Experimental Animals: Healthy, 4 – 6 month old Bos taurus heifer and steer calves were used in the present study. The calves were seronegative to both bovine viral diarrhea and bovine leukemia virus by antigen capture enzyme-linked immunosorbent assay (ELISA) analyses done at the Texas Veterinary Medical Diagnostic Laboratory, College Station, Texas and had no detectable neutralizing antibodies to RVFV by PRNT80 at the time of vaccination. The animal experiments were performed under an Institutional Animal Care and Use Committee approved protocol #2010-192. Vaccines: The authentic recombinant MP-12 (MP12) is an attenuated RVFV vaccine prepared for use in humans by the U. S. Army Medical Research Institute of Infectious Diseases. Vaccines were propagated and prepared at University of Texas Medical Branch in Galveston, TX. Experimental Design: The calves were housed in an ABSL2 Ag biocontainment facility where they were randomized into test groups and acclimated to the facility for 14 days. Animals were inoculated either subcutaneously (s.c.) or intramuscularly (i.m.) with 1x105 PFU of MP-12 (3 animals in each group). Whole blood was collected prior to inoculation on Days 0 through 7, 10, 14, 21 and preserved for serum neutralization studies (PRNT) or total RNA purification for RNASeq analysis. Experimentally determined PRNT values were used to determine the “serologic response status” for animals “unvaccinated”, “vaccinated, not protected”, or “vaccinated, protected” with animals having a serum dilution ration of >1:80 being considered protected. Only RNA samples that met the minimum quality and quantity thresholds were used for the sequencing analysis. Rectal temperatures were recorded each time blood was collected and their health status was documented daily. At the end of the respective studies, the calves were euthanized with pentobarbital sodium (120 mg/kg i.v.). All calves were healthy and clinically normal at the termination of the respective studies. Morrill, John C., Richard C. Laughlin, Nandadeva Lokugamage, Jing Wu, Roberta Pugh, Pooja Kanani, L. Garry Adams, Shinji Makino, C. J. Peters. Immunogenicity of a Recombinant Rift Valley Fever MP-12 Vaccine Candidate in Calves. Vaccine. 2013. doi:10.1016/j.vaccine.2013.08.003. 238. Morrill, John C., Richard C. Laughlin, Nandadeva Lokugamage, Roberta Pugh, Elena Sbrana, William J. Weise, L. Garry Adams, Shinji Makino and C. J. Peters.. Safety and Immunogenicity of Recombinant Rift Valley Fever MP-12 Vaccine Candidates in Sheep. Vaccine 10.1016/j.vaccine.2012.10.118, 2012.
Publication Title
Correlative Gene Expression to Protective Seroconversion in Rift Valley Fever Vaccinates.
Sample Metadata Fields
Specimen part, Subject, Time
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
The Hox complex consists of 39 genes arranged in 4 clusters of flanking genes and 13 paralogous groups in mammals. To assess the functional redundancy of Hox abdominal-B genes during renal development, we used a modified recombineering strategy to simultaneous introduce frameshift mutations into the Hox9, Hox10, and Hox11 flanking genes of the HoxA, HoxC, and HoxD paralogous groups. We performed RNA seq on whole kidneys at E18.5 in triplicates for representative genotypes including: wild type; Hoxa9,10,11-/- HoxC9,10,11+/-, Hoxa9,10,11+/- HoxC9,10,11-/-, Hoxa9,10,11-/- HoxC9,10,11-/-. Our results suggest that the loss of Hox function results in a partial metanephric to mesonephric transformation, with tubules co-expressing markers of both proximal tubules and collecting ducts, as well as markers of mesonephric-derived epididymis tubules. Overall design: mRNA profiles were generated by performing RNA-seq on whole kidneys at E18.5 in triplicates for Hox mutant genotypes including: 1) wild type; 2) Hoxa9,10,11-/- HoxC9,10,11+/-, 3) Hoxa9,10,11+/- HoxC9,10,11-/-, and 4) Hoxa9,10,11-/- HoxC9,10,11-/- by deep sequencing using Illumina Hi-Seq 2500
Publication Title
Disruption of Hox9,10,11 function results in cellular level lineage infidelity in the kidney.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
Cultured epidermal keratinocyte controls used for IFNg, TNFa and IL1 treatment.
Publication Title
Unique keratinocyte-specific effects of interferon-gamma that protect skin from viruses, identified using transcriptional profiling.
Sample Metadata Fields
No sample metadata fields
View Samples