Df2b4b20-dcfb-4959-b7a3-f90df11a4899 - samples
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ABSTRACT:
PROVIDER: EGAD00001009796 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:RNAseq analysis between cell types. RNA extracted using Qiagen mini total RNA isolation protocols (Qiagen, Germany). Samples were treated with DNase (Ambion), and sample integrity verified on the Agilent Bioanalyser with the RNA Nano chip. Illumina Tru-seq paired end strand specific sequencing (Illumina, USA) was carried out by on a NextSeq-550 sequencer (Edinburgh Clinical Research Facility, Western General Hospital, Edinburgh, Scotland, UK). 500ng of Total RNA underwent ribosomal RNA depletion (rRNA) prior to purification, fragmentation, random hexamer cDNA generation and purification with AMPure XP beads (Beckman-Coulter, USA). Multiple indexing adapters were ligated to ds cDNA with subsequent hybridisation onto flow cells, and DNA fragment enrichment by 15 cycle PCR for sequencing. Completed libraries were quantified by qPCR using the KAPA Illumina Library Quantification Kit (Illumina, USA) before multiplexing in two equimolar pools and running on two flow cells on the Illumina NextSeq 550. The resulting FastQ files were mapped to the reference genome (mm9) using the Tophat alignment tool (V1) on Illumina Basespace software and reads per kilobase per million (RPKM) scores calculated.
2017-07-12 | GSE98034 | GEO
Project description:RNAseq analysis between cell types. RNA extracted using Qiagen mini total RNA isolation protocols (Qiagen, Germany). Samples were treated with DNase (Ambion), and sample integrity verified on the Agilent Bioanalyser with the RNA Nano chip. Illumina Tru-seq paired end strand specific sequencing (Illumina, USA) was carried out by on a NextSeq-550 sequencer (Edinburgh Clinical Research Facility, Western General Hospital, Edinburgh, Scotland, UK). 500ng of Total RNA underwent ribosomal RNA depletion (rRNA) prior to purification, fragmentation, random hexamer cDNA generation and purification with AMPure XP beads (Beckman-Coulter, USA). Multiple indexing adapters were ligated to ds cDNA with subsequent hybridisation onto flow cells, and DNA fragment enrichment by 15 cycle PCR for sequencing. Completed libraries were quantified by qPCR using the KAPA Illumina Library Quantification Kit (Illumina, USA) before multiplexing in two equimolar pools and running on two flow cells on the Illumina NextSeq 550. The resulting FastQ files were mapped to the reference genome (mm9) using the Tophat alignment tool (V1) on Illumina Basespace software and reads per kilobase per million (RPKM) scores calculated.
2017-12-01 | GSE101928 | GEO
Project description:RNAseq analysis between control (normoxia) and hypoxic mice +/- bacterial infection. Murine peripheral blood leukocytes (1x10^6/condition) were lysed and RNA extracted using Qiagen mini total RNA isolation protocols (Qiagen, Germany). Samples were treated with DNase (Ambion), and sample integrity verified on the Agilent Bioanalyser with the RNA Nano chip. Illumina Tru-seq paired end strand specific sequencing (Illumina, USA) was carried out by on a NextSeq-550 sequencer (Edinburgh Clinical Research Facility, Western General Hospital, Edinburgh, Scotland, UK). 500ng of Total RNA underwent ribosomal RNA depletion (rRNA) prior to purification, fragmentation, random hexamer cDNA generation and purification with AMPure XP beads (Beckman-Coulter, USA). Multiple indexing adapters were ligated to ds cDNA with subsequent hybridisation onto flow cells, and DNA fragment enrichment by 15 cycle PCR for sequencing. Completed libraries were quantified by qPCR using the KAPA Illumina Library Quantification Kit (Illumina, USA) before multiplexing in two equimolar pools and running on two flow cells on the Illumina NextSeq 550. The resulting FastQ files were mapped to the reference genome (mm9) using the Tophat alignment tool (V1) on Illumina Basespace software and reads per kilobase per million (RPKM) scores calculated.
2017-03-22 | GSE79484 | GEO
Project description:In this study, we developed an automated high-throughput proteomics sample preparation workflow (AutoDEP) with a commercially available 96-well DNA extraction plate on the Biomek i7 liquid handling system tailored for industrial microorganisms.
2025-12-23 | PXD072341 |
Project description:Evaporation of sweat on the skin surface is the major mechanism for dissipating heat in humans. The secretory capacity of sweat glands (SWGs) declines during aging, leading to heat intolerance in the elderly, but the mechanisms responsible for this decline remain incompletely understood. We investigated the molecular changes accompanying SWG aging in mice, where sweat tests confirmed a significant reduction of active SWGs in old mice relative to young mice. We first identified SWG-enriched mRNAs by comparing the transcriptome of Eda mutant Tabby mice, which lack SWGs, with that of wild-type control mice by RNA-sequencing analysis. This comparison revealed 171 mRNAs enriched in SWGs, including 47 mRNAs encoding core secretory proteins such as transcription factors, ion channels, ion transporters, and trans-synaptic signaling proteins. Among these, 28 SWG-enriched mRNAs showed significantly altered abundance in the aged footpad skin, and 11 of them, including Foxa1, Best2, Chrm3, and Foxc1 mRNAs belonged to the ‘core secretory’ category. Consistent with the changes in mRNA expression, immunohistology revealed that higher numbers of secretory cells from old SWGs express FOXC1 protein, the product of Foxc1 mRNA. In sum, our study identified mRNAs enriched in SWGs, including those that encode core secretory proteins, and changes in these mRNAs and proteins with SWG aging in mice.
2024-05-17 | GSE249782 | GEO
Project description:Evaporation of sweat on the skin surface is the major mechanism for dissipating heat in humans. The secretory capacity of sweat glands (SWGs) declines during aging, leading to heat intolerance in the elderly, but the mechanisms responsible for this decline remain incompletely understood. We investigated the molecular changes accompanying SWG aging in mice, where sweat tests confirmed a significant reduction of active SWGs in old mice relative to young mice. We first identified SWG-enriched mRNAs by comparing the transcriptome of Eda mutant Tabby mice, which lack SWGs, with that of wild-type control mice by RNA-sequencing analysis. This comparison revealed 171 mRNAs enriched in SWGs, including 47 mRNAs encoding core secretory proteins such as transcription factors, ion channels, ion transporters, and trans-synaptic signaling proteins. Among these, 28 SWG-enriched mRNAs showed significantly altered abundance in the aged footpad skin, and 11 of them, including Foxa1, Best2, Chrm3, and Foxc1 mRNAs belonged to the ‘core secretory’ category. Consistent with the changes in mRNA expression, immunohistology revealed that higher numbers of secretory cells from old SWGs express FOXC1 protein, the product of Foxc1 mRNA. In sum, our study identified mRNAs enriched in SWGs, including those that encode core secretory proteins, and changes in these mRNAs and proteins with SWG aging in mice.
2024-05-17 | GSE249783 | GEO
Project description:BACKGROUND: Cell-based regeneration therapies hold great promise and potential for new area in clinical medicine, although some obstacles still remain to be overcome for a wide range of clinical applications. One of the major impediments in this field is difficulties in large-scale production of cells of interest with reproducibility. Current protocol of cell therapy requires a long-time laborious manual process. To solve this problem, we focused on the robotics of automated and high throughput cell culture system. To date, an automated robotic cultivation of stem or progenitor cells in clinical trials has not been reported. METHODS: The system, AutoCulture®, used in this study can automatically replace the medium, centrifuge cells, split the cells, and take a photograph for their morphology. We examined the feasibility to use it in the clinical field by comparing the growth rate and the characteristics of cardiac stem cells (CSCs) cultivated by AutoCulture and the manual handling culture, which protocol is the exact same as current performing clinical trial in our institute. RESULTS: We demonstrated similar characteristics in both culture methods, in terms of growth rates, gene expression profiles, cell surface profiles by FACS, carbon hydrate structures on the cell surface, and genomic DNA stability. IMPLICATIONS: The results of this study showed that AutoCulture is feasible to cultivate human cells for regenerative medicine. An automated cell-processing machine for cell therapy will play more important role, as it will be widespread from multi-center trials to off-the-shelf cell products. The cells were cultured by manual handling or by the automatic cell culture apparatus. Total RNA was extracted from these cells at day 7 by the RNeasy Plus Mini Kit (QIAGEN). Gene expression analysis was performed using the Agilent Whole Human Genome Microarray chips G4112F (Agilent). Raw data were normalized and analyzed by GeneSpring GX11 software.
2013-03-31 | E-GEOD-44032 | biostudies-arrayexpress
Project description:Extracellular vesicles (EV) in body fluids are extensively studied as potential biomarkers for numerous diseases. Major impediments of EV-based biomarker discovery include the manual labor, and the specificity and reproducibility of EV sample preparation. To tackle this, we present an automated liquid handling workstation for the density-based separation of EV from human body fluids and compare its performance to manual handling by (in)experienced researchers. To validate automated density-based separation of EVs from human body fluids, including blood plasma and urine, we assess variation, yield and purity by mass spectrometry-based proteomics.
2023-05-10 | PXD032394 | Pride
Project description:Epidermal appendages play a key role in thermoregulation, which is crucial in maintaining the equilibrium of body temperature. The normality of eccrine sweat glands (SwGs) and hair follicles (HFs) assures homeostatic thermoregulation. However, the fate commitments of SwGs and HFs development and their key regulators are still poorly understood. To elucidate the regulatory networks and the major regulators in SwGs and HFs development, we generated a transcriptomic atlas within three tissues (dorsal back skin, front and hinder ventral foot skin) across four early development stages (embryonic (E) days E15.5 and E17.5, postnatal (P) days P1 and P3) of Mus musculus. We then applied a second-order polynomial model to fit time-course expression of genes and used likelihood ratio test (LRT) to identify temporal dynamic expressed genes. We further constructed temporal regulatory networks to investigate the master regulators during different developmental stages. We found the distinct temporally developmental patterns between dorsal back and ventral foot skin. Eight temporally dynamic expression modes were inferred, which are comprised of over 90% of the dynamic genes. Shh, Eda, Bmp2 and other previously identified factors were noted in our dominant dynamic patterns as well and temporally dynamic expressed in dorsal back and ventral foot. Combined with differentially expressed genes analysis, we highlighted 501 genes that were common in front and hinder foot, albeit uniquely enrich or depleted in dorsal back. Moreover, the integration of temporal expression models and genes regulatory networks accentuated master transcription factors functioning at specific stages in different tissues. Our findings demonstrated the temporally dynamic determinants during SwGs and HFs fate commitments and can contribute to restoring impaired SwGs and HFs clinically after hypohidrosis or burn injury.
2024-08-31 | GSE237102 | GEO