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SRP119979
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- Xenopus laevis
- 4 Downloadable Samples
Affymetrix Xenopus laevis Genome Array (xenopuslaevis)
Description
Xenopus laevis embryos were injected with alpha-amanitin to inhibit RNA polymerase II activity. Embryos were allowed to develop up to stage 10.5 (early gastrula, control and alpha-amanitin injected embryos) and subsequently collected for RNA isolation. The transcriptome profiles of alpha-amanitin injected and control embryos were compared.
Publication Title
Robust activation of a Tbox-Gsc-Otx2 gene network independent of TATA binding protein family members
Sample Metadata Fields
Compound
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
Masseter and Tibialis anterior muscles from adult female control mice to determine expression differences between muscle groups
Publication Title
Expression profiling reveals heightened apoptosis and supports fiber size economy in the murine muscles of mastication.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Arabidopsis thaliana
- 8 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Transcriptional profiling of guard cells and mesophyll cells in response to ABA treatment
Publication Title
Isolation of a strong Arabidopsis guard cell promoter and its potential as a research tool.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Compound
View Samples- Gallus gallus
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
Chick thymus is the critical site for T cell development and can be damaged by lipopolysaccharide (LPS) derived from Salmonella typhimurium, one of the most deleterious food-borne pathogens. However, the mechanisms remain unclear. Here we reported the first time-series transcriptome research of chick thymus after Salmonella LPS treatment. Overall design: 12 dUTP libraries of thymus samples of newly hatched male chicks were sequenced at 0, 12, 36 and 72 h post LPS treatment with 3 replications at each time point.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Disease stage, Treatment
View Samples- Homo sapiens
- 99 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Pediatric acute lymphoblastic leukemia (ALL) contains cytogenetically distinct subtypes that respond differently to cytotoxic drugs. Subtype classification can be also achieved through gene expression profiling. However, how to apply such classifiers to a single patient and correctly diagnose the disease subtype in an independent patient group has not been addressed. Furthermore, the underlying regulatory mechanisms responsible for the subtype-specific gene expression patterns are still largely unknown. Here, by combining three published microarray datasets (PMIDs: 12086872, 12730115, 17002788) on 535 Caucasian samples and generating a new dataset on 100 Chinese children ALL samples, we were able to 1) identify a 62-gene classifier with 97.6% accuracy from the Caucasian samples and validated it on the completely independent set of 100 Chinese samples, 2) to uncover potential regulatory networks of ALL subtypes. The classifier we identified was so far the only one that could be applied directly to a single sample and sustained validation in a large independent patient group. Our results also suggest that the etiology of ALL is largely the same among different ethnic groups, and that the transcription factor hubs in the predicted regulatory network might play important roles in regulating gene expression and development of ALL.
Publication Title
Gene expression-based classification and regulatory networks of pediatric acute lymphoblastic leukemia.
Sample Metadata Fields
Specimen part, Disease, Race
View Samples- Oryza sativa
- 14 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Ethylene plays major roles in adaptive growth of rice plants in water-saturated soil; however, ethylene signaling in rice is largely unclear. Here, we report identification and characterization of ethylene-response mutants based on distinct ethylene-response phenotypes of dark-grown rice seedlings.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 9 Downloadable Samples
- Illumina HiSeq 2000
Description
Recent studies have demonstrated that human astrocytes and fibroblasts can be directly converted into functional neurons by small molecules. However, the reported reprogramming efficiency of human fibroblasts is extremely low, resulting in limited clinical application for the treatment of neurological disorders. Here, we report that human fibroblasts can be efficiently and directly reprogrammed into functional neuron-like cells (with a yield up to 82% TUJ1-positive neuron-like cells) by serially exposing cells to a combination of small molecules. These chemically induced neurons (iNs) displayed typical neuronal morphologies and showed neuronal transcriptional networks resembling human primary embryonic brain neurons. The iNs also exhibited mature firing patterns and formed functional synapse when cultured on mouse astrocytes. Importantly, the iNs can survive, mature and integrate into local circuits after transplantation into the postnatal mouse brains. Our study provides a rapid and efficient transgene-free approach for chemically generating neuron-like cells from human fibroblasts. Further, our approach offers strategies for disease modeling and drug discovery in central nervous system disorders.
Publication Title
Rapid and Efficient Conversion of Human Fibroblasts into Functional Neurons by Small Molecules.
Sample Metadata Fields
Sex, Specimen part
View Samples