Small RNA sequencing of urine-derived ADO2-iPSCs
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ABSTRACT:
PROVIDER: PRJNA553161 | ENA |
REPOSITORIES: ENA
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Project description:Degradome sequencing of urine-derived ADO2-iPSCs
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Project description:To identify potential miRNA–mediated targets associated with osteopetrosis at the genome-wide level, two small RNA libraries and a degradome library were constructed from the ADO2-iPSCs and normal control human iPSCs (NC-iPSCs) for deep sequencing.
2021-11-03 | GSE133937 | GEO
Project description:Depleting ribosomal RNA sequencing of urine-derived ADO2-iPSCs.
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Project description:To identify potential miRNA–mediated targets associated with osteopetrosis at the genome-wide level, two small RNA libraries and a degradome library were constructed from the ADO2-iPSCs and normal control human iPSCs (NC-iPSCs) for deep sequencing.
2022-07-08 | GSE133938 | GEO
Project description:To identify potential miRNA–mediated targets associated with osteopetrosis at the genome-wide level, two small RNA libraries and a degradome library were constructed from the PS and normal control human iPSCs (NC-iPSCs) for deep sequencing.
2023-05-28 | GSE153885 | GEO
Project description:To construct comprehensive competing endogenous RNA (ceRNA) networks , depleting ribosomal RNA strand-specific libraries were constructed from the ADO2-iPSCs and normal control human iPSCs (NC-iPSCs) for deep RNA sequencing.
2021-11-03 | GSE140132 | GEO
Project description:We generated iPSCs from human urine cells (hUCs) with the aid of small molecules and autologous hUC feeders. A compound cocktail including Cyclic Pifithrin-a, a p53 inhibitor and other compounds known for benefiting reprogramming like A-83-01, CHIR99021, Thiazovivin, NaB and PD0325901 was used to aid hUC reprogramming (Plan B). Aided by this cocktail, we achieved significantly improved efficiency (170 folds more) for hUC reprogramming and iPSC generation. In addition, to enable iPSC generation in some cases that massive cell death occurred during delivering reprogramming factors, we replaced Matrigel with autologous hUCs as feeder for reprogramming and iPSC generation (Plan C). Replacing Matrigel with autologous feeder not only enhanced reprograming, but also avoided concern using animal components for human iPSC generation. These were efficient approaches to enable iPSC generation from hUCs that were otherwise difficult for reprogramming, which would be valuable for banking patient’s specific iPSCs.
2017-02-10 | GSE79134 | GEO
Project description:Background: Urine is a potential source of biomarkers for diseases of the kidneys and urinary tract. RNA, including microRNA, is present in the urine enclosed in detached cells or in extracellular vesicles (EVs) or bound and protected by extracellular proteins. Detection of cell- and disease-specific microRNA in urine may aid early diagnosis of organ-specific pathology. In this study, we applied barcoded deep sequencing to profile microRNAs in urine of healthy volunteers, and characterized the effects of sex, urine fraction (cells vs. EVs) and repeated voids by the same individuals. Results: Compared to urine-cell-derived small RNA libraries, urine-EV-derived libraries were relatively enriched with miRNA, and accordingly had lesser content of other small RNA such as rRNA, tRNA and sn/snoRNA. Unsupervised clustering of specimens in relation to miRNA expression levels showed prominent bundling by specimen type (urine cells or EVs) and by sex, as well as a tendency of repeated (first and second void) samples to neighbor closely. Likewise, miRNA profile correlations between void repeats, as well as fraction counterparts (cells and EVs from the same specimen) were distinctly higher than correlations between miRNA profiles overall. Differential miRNA expression by sex was similar in cells and EVs. Conclusions: miRNA profiling of both urine EVs and sediment cells can convey biologically important differences between individuals. However, to be useful as urine biomarkers, careful consideration is needed for biofluid fractionation and sex-specific analysis, while the time of voiding appears to be less important.
2016-01-28 | GSE72183 | GEO
Project description:As no one previously examined urine-derived cells from bladder cancer patients, we performed scRNAseq to profile the diversity of these cells and their transcriptional profiles. We used scRNAseq to compare the profiles of urine-derived cells to matched tumor cells and PBMC from bladder cancer patients.
2024-05-17 | GSE267718 | GEO
Project description:Corneal endothelial cells (CECs) are critical to maintaining clarity of the cornea. This study was initiated to develop peripheral blood mononuclear cells (PBMC)-originated induced pluripotent stem cells (iPSCs)-derived CECs. We isolated PBMC and programmed the mononuclear cells to generate iPSCs. Subsequently, the PBMC-originated iPSCs were differentiated to CECs. The morphology of differentiating iPSCs was examined at regular intervals by phase contrast microscopy. In parallel, the expression of pluripotent, and CECs-associated markers was investigated by quantitative real-time PCR (qRT-PCR). The molecular architecture of the iPSCs-derived CECs and human corneal endothelium (CE) were examined by mass spectrometry-based proteome sequencing. The PBMC-originated iPSCs expressed pluripotent-specific markers at levels similar to expression in H9 human embryonic stem cells (hESCs). Phase contrast microscopy illustrated that iPSCs-derived CECs are tightly adherent, exhibiting a hexagonal-like shape, one of the cardinal characteristics of CECs. The CECs-associated markers were expressed at many orders of magnitude higher in iPSCs-derived CECs at days 13, 20, and 30 compared to their respective levels in iPSCs. Importantly, only residual expression levels of pluripotency markers were detected in iPSCs-derived CECs. Mass spectrometry-based proteome profiling identified 10,575 proteins in iPSCs-derived CECs. In parallel, we completed proteome profiling of the human CE identifying 6345 proteins. Of these, 5763 proteins were identified in the iPSCs-derived CECs suggesting a 90.82% overlap between the iPSCs-derived CECs and human CE proteomes. Importantly, cryopreservation of iPSCs-derived CECs did not affect the tight adherence of CECs, and their hexagonal-like shape while expressing high levels of CECs-associated markers. We have successfully developed a personalized approach to generate CECs that closely mimic the molecular architecture of the human CE. To the best of our knowledge, this is the first report describing the development of PBMC-originated, iPSCs-derived CECs.
2018-06-06 | PXD009142 | Pride