Developmentally informed large-scale production and cryopreservation of human induced pluripotent stem cell-derived microglia
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ABSTRACT:
PROVIDER: PRJNA741234 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14905935.fastq.gz | Fastqsanger.gz | |||
| SRR14905936.fastq.gz | Fastqsanger.gz | |||
| SRR14905937.fastq.gz | Fastqsanger.gz | |||
| SRR14905938.fastq.gz | Fastqsanger.gz | |||
| SRR14905939.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: mRNA expression profiles of iPSC-derived microglia (iPSdMiG) generated with a new cutting-edge protocol were compared to human primary microglia and cortex samples, iPSC-derived microglia-like cells (iMGL), THP1 macrophages, and parental iPSCs. Methods: Library preparation was performed using the Quantseq 3’mRNA-Seq kit (Lexogen, USA). Reads were generated on a HiSeq 2500 V4 sequencer (Illumina, USA) and quality as well as adapter trimming were performed using BBDuk from BBMap. Reads were aligned to hg38 with the ensemble gene annotation version 97 using STAR and read counts were generated using featureCounts ignoring multimapping reads. Unwanted variance due to differences in library preparation and sequencing were removed using RUVSeq and subsequent differential gene expression analysis was performed with DESeq2. Transcription factor enrichment analysis was performed with ChEA3 and co-expression analysis was performed using WGCNA. Results: Overall, our iPSdMiG highly resemble human primary microglia. They have a similar expression of lineage-specific genes and cluster in close proximity in PCA. Our iPSdMiG and human primary microglia share key transcription factors driving cellular identity and co-express genes belonging to a immunity-related gene module.
2022-08-22 | GSE178846 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE24753: Genome-wide analysis of the effect of cryopreservation on peripheral blood mononuclear cells GSE24755: Genome-wide analysis of the effect of long-term cryopreservation on peripheral blood mononuclear cells GSE24757: Genome-wide analysis of the effect of long-term freezing of PAXgene Blood RNA tubes Refer to individual Series
2011-07-21 | E-GEOD-24758 | biostudies-arrayexpress
Project description:BackgroundOrchids are under threat from human activities and climate change, with populations limited to small geographic hotspots. This makes them ideal candidates for ex situ conservation. Orchid seeds are desiccation tolerant, but often have poor longevity in seed banks and cryopreservation of orchid protocorms is complex and expensive. Therefore, simple methods for large-scale storage programs are essential to store orchid seeds of different life forms. Seeds of five species representing epiphytic, lithophytic and terrestrial orchids from the Central Highlands of Madagascar were studied to find a simple and effective system of cryopreservation. The use of a vitrification solution prior to cryopreservation to improve survival was investigated, as well as the use of symbiotic and asymbiotic germination media to maximise germination after cryopreservation. Using the filter paper packet method, dried seeds were stored in vapour phase above liquid nitrogen and recovered after thawing with both symbiotic and asymbiotic media.ResultsThe study revealed that cryoprotection is not essential for the species in this study, which represented a range of lifeforms. Vitrification generally led to a decrease in germination post cryopreservation. The use of a symbiotic germination medium post cryopreservation was found to be successful in the species in which it was tested. However, the use of an asymbiotic medium was successful for all the species in this study.ConclusionsVitrification was not essential for the species in this study as the orchid seeds were already ultralow temperature and desiccation tolerant. However, further studies using more species are required to validate this approach. This may be an ecophysiological or genetic trait of these species. Therefore, this form of dry seed cryopreservation could form part of ex situ orchid seed conservation using a standard method. The methods developed here will store greater genetic diversity compared to what can be achieved with protocorms and are suitable for both asymbiotic and symbiotic recovery after cryopreservation. This will help reduce the time and cost of ex situ conservation, and help develop universal protocols for large genera, compared to custom protocols required for protocorm cryopreservation.
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Project description:cryopreservation human testicular tissue
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Project description:We report the effect of cryopreservation on isolated microglia and macrophages from the brains of rhesus monkeys. At the time of necropsy, cells were isolated from the brain and either used fresh or cryopreserved. For single cell sequencing, isolates were purified for CD11b expression and captured and processed through the 10xGenomics platform following by sequencing. We find that cryopreservation altered the expression of approximately 2% of the genes. These were not enriched for any known microglia/macrophage set of differentially regulated genes, but was enriched in immediate early genes and the acute phase pathway. Assessment of the fresh and cryopreseved cells in comparison to a prior dataset from animals with encephalitis revelaed equal ability to detect differentially expresed genes. Thus, given the practical difficulty of freshly processing microglia from human and non-human primate brains for isolation and scRNAseq processing the same day, and the ability to archive sampoles for potential use in scRNAseq experiments, cryopreservation is an optimal choice for future analysis of these important brainn cells, and likely other cell types.
2021-01-22 | GSE162663 | GEO
Project description:Analysis of cryopreservation effects on peripheral blood mononuclear cells at gene expression level. The hypothesis tested in the present study was that cryopreservation has an influence on the transcriptome profile of peripheral blood mononuclear cells. Results indicated remarkable changes in expression patterns upon cryopreservation of PBMCs, with a strong loss of signal intensities to background levels for several transcripts. Total RNA obtained from isolated peripheral blood mononuclear cells of healthy human subjects eihter cryopreserved in liqiud nitrogen (frozen) or direclty lysed in Trizol after isolation (fresh).
2011-07-21 | E-GEOD-24753 | biostudies-arrayexpress
Project description:Analysis of effect of long-term cryopreservation on peripheral blood mononuclear cells at gene expression level. The hypothesis tested in the present study was that long-term cryopreservation has an influence on the transcriptome profile of peripheral blood mononuclear cells. Results indicated remarkable changes in expression patterns upon cryopreservation of PBMCs, with decreasing signal intensities over time. Total RNA obtained from isolated peripheral blood mononuclear cells of melanoma patients cryopreserved in liqiud nitrogen from 20 to 60 months.
2011-07-21 | E-GEOD-24755 | biostudies-arrayexpress
Project description:Analysis of cryopreservation effects on peripheral blood mononuclear cells at gene expression level. The hypothesis tested in the present study was that cryopreservation has an influence on the transcriptome profile of peripheral blood mononuclear cells. Results indicated remarkable changes in expression patterns upon cryopreservation of PBMCs, with a strong loss of signal intensities to background levels for several transcripts.
2011-07-22 | GSE24753 | GEO
Project description:Analysis of effect of long-term cryopreservation on peripheral blood mononuclear cells at gene expression level. The hypothesis tested in the present study was that long-term cryopreservation has an influence on the transcriptome profile of peripheral blood mononuclear cells. Results indicated remarkable changes in expression patterns upon cryopreservation of PBMCs, with decreasing signal intensities over time.
2011-07-22 | GSE24755 | GEO
Project description:Studies on embryo cryopreservation efficiency had been focused mainly on technical and embryo factors. While structural damages can be easily evaluated, physiological damages only can be estimated by analyzing their in vitro and in vivo development to later stages. In order to determine how cryopreservation process affect embryo pre-implantory development, a transcriptional microarray study has been performed comparing gene expression of 6 days old rabbit embryos, previously vitrified or frozen and transferred into recipients rabbit females, to their in vivo counterparts. For each experimental group, control, vitrified and frozen late blastocysts, total RNA was extracted from 3 pools of approximately 10 embryos and labeled with Cy3 or Cy5 dyes. Then, six competitive hybridizations were carried out including two dye-swaps to compensate dye-bias. A specifically microarray designed to study rabbit gene expression profiling, the Rabbit 44K oligonucleotide array (Agilent Technologies), was used in this study. Identification of differentially expressed transcripts from 6 day old blastocysts was achieved using the Limma algorithm, and functional annotation was performed by Blast2GO software. Compared to 6 day old in vivo derived embryos, viable vitrified embryos only present 3 differentially expressed genes, in contrast to frozen viable embryos with 24 genes upregulated and 46 genes downregulated. These results reveal that effects of cryopreservation still remain in late blastocyst pre-implantatory gene expression, and potential damage and alterations produced by vitrification and slow-freezing procedures are differentially resolved after 3 days of in vivo development. Transcriptional microarray study that compares gene expression of viable 6 day old rabbit embryos, previosly vitrified or frozen and tranferred into recipient rabbit females, to their in vivo counterparts. Experiment 1: Control embryos vs. Vitrified embryos and Experiment 2: Control embryos vs. Frozen embryos. Biological replicates used: 3 replicates for control embryos, 3 replicates for vitrified embryos and 3 replicates for frozen embryos.
2011-09-22 | E-GEOD-32263 | biostudies-arrayexpress