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SRP031608
Mus musculus
3 Downloadable Samples
Illumina HiSeq 2000
Description
Hair-related diseases are a major public-health problem, and their treatments are limited to hormone-therapies. Researchers have tried to investigate the genes and signal pathways underlying hair follicle (HF) stem cells and interaction of HFs and dermal papilla cells (DPCs) for specific targeted-therapies through microarrays, appropriate for the analysis of small genomes. Therefore, to enable a comprehensive transcriptome analysis for the large, complex transcriptomes, we performed RNA-seq using next generation sequencing (NGS). We isolated interfollicular keratinocytes (IFKs), HFs, and DPCs form C57BL/6 murine skin, transplanted combinations of these samples into nude mice, and followed up. Sustained hair growth was supported by intact HFs and DPCs. And, we identified 19 HF- and 34 DPC-specific novel genes with NGS, validated these data with quantitative real-time RT-PCR, and performed pathway analysis of these genes. In addition, HFs had a more quiescent cell-cycle pattern than did IFKs and DPCs in culture and flow cytometry (FCM). Therefore, the representative cell cycle-related gene expression in IFKs, HFs and DPCs were analyzed by NGS. These genes will allow the investigation of the interactions and signaling pathways involved in HF-related diseases and cancer, support bioengineering, and may be used as specific and novel markers of these cell types.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 8 Downloadable Samples
Illumina MouseRef-8 v2.0 expression beadchip
Description
We determined whether the changed imprinted genes are maintained or reverted to the parthenogenetic state when the reprogrammed cells are re-differentiated into specialized cell types. To address this question, we re-differentiated miPSCs into neural stem cells (miPS-NSCs) and compared them with biparental female NSCs (fNSCs) and parthenogenetic NSCs (pNSCs)
Publication Title
Conversion of genomic imprinting by reprogramming and redifferentiation.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 3 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
We generated iPSCs from human intervertebral disc cells which were obtained during spine fusion surgery of patients with spinal cord injury. The disc cell-derived iPSCs (diPSCs) showed similar characteristics to human embryonic stem cells (hESCs) and were efficiently differentiated into neural progenitor cells (NPCs) with the capability of differentiation into mature neurons in vitro. To examine whether the transplantation of NPCs derived from the diPSCs showed therapeutic effects, the NPCs were transplanted into mice at 9 days post-spinal cord injury. We detected a significant amelioration of hind limb dysfunction during the follow up recovery periods. Histological analysis at 5 weeks post-transplantation, we could identify undifferentiated human NPCs (Nestin+) as well as early (TUJ1+) and mature neurons (MAP2+) derived from the NPCs. Furthermore, the NPC transplantation demonstrated a preventive effect on the spinal cord degeneration resulting from the secondary injury. This study revealed that the intervertebral disc, a to-be-waste tissue, removed from the surgical procedure, could provide a unique opportunity to study iPSCs derived from hardly accessible somatic cells in normal situation and also be a useful therapeutic resource to generate autologous neural cells to treat patients suffering from spinal cord injury.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 584 Downloadable Samples
- Illumina humanRef-8 v2.0 expression beadchip
Description
A fundamental challenge in the post-genome era is to understand and annotate the consequences of genetic variation, particularly within the context of human tissues. We describe a set of integrated experiments designed to investigate the effects of common genetic variability on DNA methylation, mRNA expression and microRNA (miRNA) expression in four distinct human brain regions. We show that brain tissues may be readily distinguished based on methylation status or expression profile. We find an abundance of genetic cis regulation mRNA expression and show for the first time abundant quantitative trait loci for DNA CpG methylation. We observe that the largest magnitude effects occur across distinct brain regions. We believe these data, which we have made publicly available, will be useful in understanding the biological effects of genetic variation.
Publication Title
Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The functional activity of TRPM7 is essential for cell viability and growth, and its expression is up-regulated in certain pathological conditions. In order to assess the effects of TRPM7 activity on cellular gene expression, inducible HEK293 cell-lines harboring the wild-type mouse TRPM7 and a mutant lacking the kinase domain were established.
Publication Title
Alteration of the transcriptional profile of human embryonic kidney cells by transient overexpression of mouse TRPM7 channels.
Sample Metadata Fields
Cell line
View Samples- Mus musculus, Homo sapiens
- 2 Downloadable Samples
- Sentrix Human-6 Expression BeadChip
Description
Parkinson disease (PD) is a major neurodegenerative condition with several rare Mendelian forms. Oxidative stress and mitochondrial function have been implicated in the pathogenesis of PD but the molecular mechanism(s) involved in the degeneration of specific neuronal groups remains unclear. DJ-1 mutations are one cause of recessive parkinsonism, but this gene is also involved in cancer by promoting Ras signaling and suppressing PTEN-induced apoptosis. The specific function of DJ-1 is unclear, although it is responsive to oxidative stress and may play a role in the maintenance of mitochondria. Here we show that DJ-1 associates with specific RNA targets in cells and in the brain including mitochondrial genes, genes involved in glutathione metabolism and members of the PTEN/PI3K cascade. Pathogenic recessive mutants are deficient in this activity. We show that DJ-1 is sufficient for RNA binding at nanomolar concentrations in vitro and that there is some RNA sequence specificity to the association. Oxidative stress causes DJ-1 to dissociate from RNA. Using in vitro and in vivo models of mild oxidative stress, we show that DJ-1 normally suppresses translation in normal circumstances but allows translation after oxidative stress. We tested the hypothesis that these specific RNA targets are responsible for sensitivity to stress by exposing knockout flies to glutathione synthesis inhibitors and saw the predicted increased sensitivity in vivo. These data implicate a single mechanism for the pleiotropic effects of DJ-1 in different model systems, namely that the protein binds and regulates specific groups of RNA targets in an oxidationdependent manner. Furthermore, these results suggest how a small protein might both be an upstream regulator of processes important in parkinsonism and be a modifier of cancer-related processes.
Publication Title
RNA binding activity of the recessive parkinsonism protein DJ-1 supports involvement in multiple cellular pathways.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 244 Downloadable Samples
- Illumina human-6 v2.0 expression beadchip
Description
This study aimed to identify the genetic signatures associated with disease prognosis in bladder cancer. We used 165 primary bladder cancer samples, 23 recurrent non-muscle invasive tumor tissues, 58 normal looking bladder mucosae surrounding cancer and 10 normal bladder mucosae for microarray analysis. Hierarchical clustering was used to stratify the prognosis-related gene classifiers. For validation, real-time reverse-transcriptase polymerase chain reaction (RT-PCR) of top-ranked 14 genes was performed. On unsupervised hierarchical clustering using prognosis related gene-classifier, tumors were divided into 2 groups. The high risk gene signatures had significantly poor prognosis compared to low risk gene signatures (P<0.001 by the log-rank test, respectively). The prognosis-related gene classifiers correlated significantly with recurrence of non-muscle invasive bladder cancer (hazard ratio, 4.09; 95% confidence interval [CI], 1.94 to 8.64; P<0.001), and progression (hazard ratio, 23.68; 95% confidence interval [CI], 4.91 to 114.30; P<0.001), cancer-specific survival (hazard ratio, 29.25; 95% confidence interval [CI], 3.47 to 246.98; P=0.002) and overall survival (hazard ratio, 23.33; 95% confidence interval [CI], 4.97 to 109.50; P<0.001) of muscle invasive bladder cancer (p < 0.001, respectively). No patient with non-muscle invasive bladder cancer experienced cancer progression in low risk gene signature group. Prognosis-related gene classifiers validated by RT- PCR showed identical results. Prognosis related gene-classifiers provided strong predictive value for disease outcome. These gene classifiers could assist in selecting patients who might benefit from more aggressive therapeutic intervention or surveillance.
Publication Title
Predictive value of progression-related gene classifier in primary non-muscle invasive bladder cancer.
Sample Metadata Fields
Sex, Age, Specimen part, Disease stage
View Samples- Homo sapiens
- 100 Downloadable Samples
- Illumina human-6 v2.0 expression beadchip
Description
Gene expression data from 100 human hepatocellular carcinomas (HCC) were generated and analyzed as part of effort for validating prognostic gene expression signatures from previous studies. Using four different classification algorithms and leave-one-out cross-validation approaches, four different prognostic signatures were applied to test the robustness and concordance of predicted outcome in individual patients. All four tumor-derived signatures were significantly associated with prognosis and had a high rate of concordance with predicted outcomes for individual patients.
Publication Title
Sixty-five gene-based risk score classifier predicts overall survival in hepatocellular carcinoma.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 63 Downloadable Samples
- Illumina human-6 v2.0 expression beadchip
Description
Cholangiocarcinoma (CC) is an aggressive tumor that shows a poor survival rate even after resection. The present study aimed at identification of the genome-wide expressed genes related to CC oncogenesis and its sarcomatous transdifferentiation using DNA microarray technology. The differentially expressed genes in 9 cholangiocarcinoma cell lines (Choi.CK, Cho.CK, J.CK, S.CK, CK.L1, CK.L2, CK.P1, CK.P2 and CK.Y1) were analyzed in comparison with 4 kinds of cultured biliary epithelial cells (ND.1, ND.2, ND.3 and ND.4) using the Illumina Human-6 v2 BeadChip (48 K). Unsupervised hierachical clustering analysis perfectively classified the 13 cell samples into two groups, normal biliary epithelial (N) and immortalized biliary epithelial cells and CC (T) cells. We identified 120 commonly upregulated ( > 2.5 fold) genes and 340 commonly downregulated ( < 0.4-fold) genes in the two groups. Hierachical clustering analysis of sarcomatoid CC cells (S.CK) revealed 316 differentially upregulated genes (> 4-fold) and 335 downregulated genes (< 0.25-fold).) compared with 3 CC cell lines (Choi.CK, Cho.CK, and J.CK). In conclusion, these data will contribute to better understand the molecular mechanisms of oncogenesis and transdifferentiation in CC and provide the molecular targets for CC diagnosis and therapy.
Publication Title
Genome-wide expression patterns associated with oncogenesis and sarcomatous transdifferentation of cholangiocarcinoma.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 42 Downloadable Samples
- Illumina human-6 v2.0 expression beadchip
Description
Full title: Predictive Gene Signatures as Strong Prognostic Indicators of the Effectiveness of Bacillus CalmetteGurin (BCG) Immunotherapy in Primary pT1 Bladder Cancers
Publication Title
Gene signatures for the prediction of response to Bacillus Calmette-Guerin immunotherapy in primary pT1 bladder cancers.
Sample Metadata Fields
Sex, Age, Disease stage
View Samples