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SRP062685
Danio rerio
2 Downloadable Samples
IlluminaHiSeq2000
Description
Differential Expression between testis and ovary in two months of fish
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 2 Downloadable Samples
- IlluminaHiSeq2000
Description
Differential expression between WT and CD82a from Morpholino-treated embyro of Danio rerio
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
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- Arabidopsis thaliana
- 8 Downloadable Samples
- Illumina HiSeq 2000
Description
Based on the pkl dP mutant phenotype, it is predicted that PKL plays a key role in regulating GA-responsive genes that are important for vegetative growth and phase transitions. To test this hypothesis, global transcriptome analysis was performed by RNA-Seq using shoots of 13d-old ga1-13 and ga1-13 pkl that were mock-treated or 10 µM GA3-treated for 24 h.
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part
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- Mus musculus
- 8 Downloadable Samples
- Illumina HiSeq 3000
Description
ADARs are RNA editing enzymes that catalyze the deamination of adenosine to inosine in double-stranded RNAs. In mammals, there are two isoforms of ADAR1 including a p110 isoform, which is constitutively and ubiquitously expressed, and a p150 isoform regulated by an IFN-inducible promoter. The mutation in ADAR1 gene causes Aicardi-Goutieres syndrome (AGS), a severe autoimmune disease in human. Furthermore, the significant decrease in RNA-editing activity was found in the p150 isoform mutant associated with AGS. In this study, we will perform transcriptome-wide analysis and identify the targets of ADAR1p150 isoform.
Publication Title
No associated publication
Sample Metadata Fields
Cell line
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- Mus musculus
- 6 Downloadable Samples
- Illumina Genome Analyzer II
Description
The data contains RNA sequencing data of embryonic stem cell derived cells.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
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
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