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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- Arabidopsis thaliana
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
RNA-Seq experiment was done to compare cngc16 (a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated channel 16) and wild type pollen for differences in their response to a temperature stress condition. Transcriptomes were analyzed from mature pollen grains harvested at midday from plants grown under normal (control) conditions or a heat stress regime. For the stress condition, plants were grown under a diurnal cycle of hot and cold temperatures and pollen were harvested at the end of a HS period that peaked at 40 degrees Celsius.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 4 Downloadable Samples
- IlluminaHiSeq2000
Description
Exosomes are 40~120 nm diameter vesicles of endocytic origin released by most cells and important in mediating cell-cell communication. As mRNA and noncoding RNA are two main functional RNA molecules in post transcription level and involves in many bio-activities including cancer progression and metastasis, it is important to understand the coding and noncoding genes contained within exosomes released by tumour cells. This study focused on the protein coding and noncoding genes enriched in two subtypes of exosomes (A33-enriched exosomes, A33-Exos and EpCAM-enriched exosomes, EpCAM-Exos) released by human colon cancer LIM1863 cell line. With high throughput sequencing technology and bioinformatics analyses, we demonstrate 350 protein coding genes (PCGs) and 222 noncoding genes (NCGs) are commonly enriched; 56 PCGs and 202 NCGs were specifically enriched in A33-Exos and 276 PCGs and 253 NCGs were enriched unique to EpCAM-Exos. A salient finding was the significant enrichment of TPT1, ribosomal protein genes and GAS5, a tumour noncoding gene, in exosomes. We further demonstrate differentially seven expressed genes (SCARB1, SCD, TPT1, EETF1G, BCL7C, RPS3, and RAB13) by qRT-PCR. Importantly, we correlated these findings with several matched tissue-derived tumour-normal samples showed TPT1 and ribosomal protein genes were up regulated in human tumour samples. Our findings provide a new insight of functional RNA molecules in exosomes and new select non-invasive biomarker candidates for colon cancer diagnosis and prognosis.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Caenorhabditis elegans
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
Transcriptional response to plant extract
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 30 Downloadable Samples
- NextSeq 500
Description
Studies in human innate lymphoid cell (ILC) development are important in understanding the pathophysiology of immune deficiencies and providing insights into the design of immunotherapies for patients with cancer, infection, and autoimmune disease. Currently, it is unclear where and how ILCs develop in humans. The overall goal of our study is to gain a comprehensive understanding of the cellular and molecular components that regulate human ILC development and function in order to best understand how they work in physiological and pathological states.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples
SRP161648- Mus musculus
- 24 Downloadable Samples
- Illumina HiSeq 2000
Description
NKTp, NKT1, NKT2, NKT17 were flow sorted from 7 wk old female live BALB/c TBET (gfp) KN2 reporter mice and RNA sequenced
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
Affymetrix Mouse Expression 430A Array (moe430a)
Description
MEF from p8 knock-out mice were immortalized with rasV12/E1A and infected with an empty or a p8-overexpressing retroviral vector as described. Total RNA was isolated and gene expression profile was studied.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
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- Homo sapiens
- 34 Downloadable Samples
- Illumina HiSeq 4000
Description
The activity of different E2F constructs with respect to gene expression was measured. E2F constructs differed in degradability, and were doxycycline inducible. Different samples with the different E2F constructs, and with or without dox inductions were assayed for gene expression.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples