Filters
Technology
Platform
Mus musculus
2 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Investigation of whole genome gene expression level changes in OASIS KO calvaria compared to wild-type calvaria.
Publication Title
Signalling mediated by the endoplasmic reticulum stress transducer OASIS is involved in bone formation.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 1 Downloadable Sample
Description
Investigate epigenetic mechanisms contributing to stemness/pluripotency in lung cancers and potentially identify novel therapeutic targets in these malignancies.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 42 Downloadable Samples
- Illumina HiSeq 1500
Description
Nuclear reprogramming is an inefficient process with only a small proportion of cells successful converting into induced pluripotent stem (iPS) cells. However, in order to molecularly understand the process these rare intermediates need to be identified and isolated for profiling. In the context of this project we purified the rare reprogramming for three cell types (Fibroblasts, Neutrophils and Keratinocytes) by fluorescent activated cell sorting and submitted them, together with the resulting iPS cells, to RNA sequencing.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Mus musculus
- 15 Downloadable Samples
- Illumina HiSeq 2000
Description
The isolation of pure populations of mouse intestinal stem cells (ISCs) is essential to facilitate functional studies of tissue homeostasis, tissue regeneration and intestinal diseases. However, the purification of ISCs has relied predominantly on the use of transgenic reporter alleles in mice. Here, we introduce a new combinational cell surface marker mediated strategy that allows the isolation of an ISC population transcriptionally and functionally equivalent to the gold standard Lgr5-GFP ISCs. We tested the ability of three cell surface marker mediated isolated strategies (termed SM2, SM4 and SM6 according to the number of key cell surface markers used) to purify ISCs and transcriptionally compared them to established standards, Lgr5-GFP high cells and cells negative for any ISC markers (Negative). The best cell surface marker mediated strategy (SM6) allowed the isolation of ISCs from reporter free mice (SM6-WT) that were functionally and transcriptionally distinct from cells isolated from transgenic mice (SM6-TG) due to Lgr5 haploinsufficiency. Overall design: To adequately benchmark the quality of our method with the existing methods, we performed first RNA sequencing with the Lgr5-GFP strain (C57/Bl6 background) on 5 FACS purified groups: SM2, SM4, SM6, Lgr5-GFPhigh reference population and cells negative or low for all of the cell surface markers used. We also performed RNA sequencing of SM6-TG and SM6-WT cells to investigate in detail potential transcriptional differences between them.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Homo sapiens
- 2 Downloadable Samples
- Illumina HiSeq 1500
Description
Compare transcriptional profiles of naïve and primed pluripotent stem cells using high throughput RNA sequencing.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The Nuclear Factor I C (NFI-C) transcription factor has been implicated in TGF- signaling, extracellular matrix deposition and skin appendage pathologies.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Mus musculus
- 8 Downloadable Samples
- NextSeq 500
Description
Myotonic dystrophy type 1 (DM1) is an autosomal dominant, CTG microsatellite expansion disease. Transcription of the CTG repeats gives rise to CUG repeat RNA with a toxic gain-of-function. The toxic CUG RNA sequesters the muscleblind-like (MBNL) family of RNA-binding proteins and disrupts their normal cellular function causing global mis-regulation of RNA processing. Multiple approaches have been developed to target the toxic RNA; these include, but are not limited to, displacing MBNL proteins from the CUG repeats, increasing MBNL protein levels or delivery of exogenous MBNL proteins, and blocking the transcription of the CUG repeats. From a screen of diamidine molecules, we previously identified furamidine as a promising lead molecule that was shown to reduce ribonuclear foci and rescue mis-splicing of splicing reporters in a HeLa cell model of DM1. We reported that treatment of the HSALR DM1 mouse model with furamidine partially rescued the Atp2a1 and Clcn1 mis-splicing events via RT-PCR. Here, using RNA-seq examine global splicing, we report that furamidine rescued over 70 mis-splicing events in the HSALR DM1 mouse model and minimally affected gene expression. Heptamidine, in comparison, rescued ~62 events but caused significant alterations in gene expression.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Danio rerio
- 4 Downloadable Samples
- IlluminaHiSeq2500
Description
We performed RNA-sequencing on four groups of zebrafish larvae: control, Tg(Myc), Tg(Kras), Tg(Myc)&Tg(Kras) to analyze the expression of genes involved in the lipid-associated pathways.The results revealed high dynamic alterations in almost all aspects of lipid metabolism, among which, the expressions of genes involved in TG/DG/GP transformation and FA desaturation/elongation displayed intensive changes, in consistent with our observations in lipodomics profiling
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples
SRP075430- Homo sapiens
- 2 Downloadable Samples
- Illumina HiSeq 2500
Description
In order to validate our method to develop immortalized cellular models of microglia, we used RNA-seq to confirm the microglial phenotype of a representative clone (C20, a clonal population), which derived from the transformation of human primary microglia (human microglia purchased cryopreserved after purification from Sciencell, Cat. #1900). Transformation was carried out with vesicular stomatitis virus G envelop simian virus 40 large T antigen viral particles (VSVG SV40), containing the pBABE-puro SV40 LT construct (Addgene, Plasmid #13970), followed by VSVG containing the human telomerase reverse transcriptase (hTERT)-neomycin (pBABE-neo-hTERT) construct (Addgene, Plasmid #1774). Immortalized cells were selected in the presence of 2 µg/mL puromycin and 600 µg/mL neomycin. Individual clonal populations, including clone C20, were allowed to grow for approximately 4 weeks prior to further testing. In addition, we also used RNA-seq to verify the capacity of these cellsto respond to an inflammatory stimulus (TNF-a).
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
To analyse roles of HAI-1/Spint1 in intestinal tumorigenesis, we examined the effect of intestine-specific deletion of Spint1 gene on Apc(Min/+) mice. The loss of Hai-1/Spint1 significantly accelerated tumor formation in ApcMin/+ mice and shortened their survival periods.
Publication Title
Hepatocyte growth factor activator inhibitor type 1 is a suppressor of intestinal tumorigenesis.
Sample Metadata Fields
Specimen part
View Samples