(re)freezing PBMC
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1277808 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This study investigates the impact of cryopreservation and freezing media on RNA quality and gene expression profiles of peripheral blood mononuclear cells (PBMC). No significant difference in cell viability or RNA quality was observed between freshly isolated and cryopreserved cells, even after two freeze-thaw cycles. Transcriptome analysis revealed no significant differences in alignment rates or read counts across various conditions. Differential gene expression analysis identified changes between fresh and thawed samples, with a consistent downward trend of mRNA abundance in the frozen samples, but minimal changes were observed between the first and second freeze-thaw cycles. Gene set enrichment analysis showed only minor significant differences, and stress-related gene sets were not upregulated. Freezing medium appears to be the safer option compared to freezing in trizol. These results confirm that cryopreservation and thawing processes do not compromise RNA integrity or sequencing reliability in PBMC, supporting the use of cryopreserved samples for gene expression studies.
2025-06-19 | GSE299980 | GEO
Project description:Freezing causes physiological changes even in a hardy, cold-acclimated wild type. During recovery from freezing, gene expression will reflect the induction of damage-repair processes distinct from the damage-prevention associated with cold acclimation. This will be detected by observing the wild-type transcriptome at two time points during recovery from a freezing episode. The appropriate control is the unfrozen, cold-acclimated wild type. Experimenter name = Glenn Thorlby Experimenter phone = 01874 443770 Experimenter address = School of biological Sciences Experimenter address = Bourne Building Experimenter address = Royal Holloway Experimenter address = Egham Experimenter zip/postal_code = TW20 0EX Keywords: growth_condition_design;
2006-08-15 | GSE5524 | GEO
Project description:In order to obtain an insight into the mechanisms that cold resistance, we compared and analyzed the haemolymph proteome of two O. furnacalis strains, one freezing and one resistance-freezing, using 2D electrophoresis.
2024-05-21 | PXD044356 | Pride
Project description:Panagrolaimus sp. DAW1, a nematode cultured from the Antarctic, has the extraordinary physiological ability to survive total intracellular freezing throughout all of its compartments. While a few other organisms, all nematodes, have subsequently also been found to survive freezing in this manner, P. sp. DAW1 has so far shown the highest survival rates. In addition, P. sp. DAW1 is also, depending on the rate or extent of freezing, able to undergo cryoprotective dehydration. In this study, the proteome of P. sp DAW1 is explored, highlighting a number of differentially expressed proteins and pathways that appear to be involved in intracellular freezing. Among the strongest signals after being frozen is an upregulation of proteases and the downregulation of cytoskeletal and antioxidant activity, the latter possibly accumulated earlier much in the way the sugar trehalose is stored during acclimation.
2020-05-01 | PXD018121 | Pride
Project description:iPSCs, iPSC-derived neurons, PBMC-derived Monocytes, PBMC-derived Macrophages, PBMC-derived induced microglia
2018-12-05 | GSE123349 | GEO
Project description:Improvement of freezing tolerance of red clover (Trifolium pratense L.) would increase its persistence under cold climate. In this study, we assessed the freezing tolerance and compared the proteome composition of non-acclimated and cold-acclimated plants of two initial cultivars of red clover: Endure (E-TF0) and Christie (C-TF0) and of populations issued from these cultivars after three (TF3) and four (TF4) cycles of phenotypic recurrent selection for superior freezing tolerance. Through this approach, we wanted to identify proteins that are associated with the improvement of freezing tolerance in red clover. Recurrent selection performed indoor is an effective approach to improve the freezing tolerance of red clover. Significant improvement of freezing tolerance by recurrent selection was associated with differential accumulation of a small number of cold-regulated proteins that may play an important role in the determination of the level of freezing tolerance.
2016-03-15 | PXD003689 | Pride
Project description:Brassinosteroids (BRs) are growth-promoting plant hormones that play a role in abiotic stress responses, but molecular modes that enable this activity remain largely unknown. Here we show that BRs participate in the regulation of freezing tolerance. BR signaling-defective mutants of Arabidopsis thaliana were hypersensitive to freezing before and after cold acclimation. The constitutive activation of BR signaling, in contrast, enhanced freezing resistance. Evidence is provided that the BR-controlled basic helix–loop–helix transcription factor CESTA (CES) can contribute to the constitutive expression of the C-REPEAT/DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR (CBF) transcriptional regulators that control cold responsive (COR) gene expression. In addition, CBF-independent classes of BR-regulated COR genes are identified that are regulated in a BR- and CES-dependent manner during cold acclimation. A model is presented in which BRs govern different cold-responsive transcriptional cascades through the posttranslational modification of CES and redundantly acting factors. This contributes to the basal resistance against freezing stress, but also to the further improvement of this resistance through cold acclimation. We used microarray data to investigate the contribution of different pathways to cold tolerance of Arabidopsis thaliana .
2016-09-10 | GSE86605 | GEO
Project description:Our analysis of the sfr6 freezing-sensitive mutant (Knight, H., Veale, E., Warren, G. J. and Knight, M. R. (1999). Plant Cell 11, 875-886.) and cls8 (unpublished) chilling-sensitive mutant of Arabidopsis, has revealed that the expression of certain cold-regulated genes is aberrant in both these mutants. In order to understand the molecular basis of chilling and freezing stress in Arabidopsis and also to determine commonalities and differences between these 2 different physiological stress-tolerance processes, we request transcriptome analysis for both of these mutants compared to wild type in one experiment, upon cold treatment and at ambient conditions. The sfr6 mutant shows the most severe phenotype with respect to cold gene expression, but is tolerant to chilling (Knight, H., Veale, E., Warren, G. J. and Knight, M. R. (1999). Plant Cell 11, 875-886.). However, it is unable to cold acclimate and hence is sensitive to freezing. The cls8 mutant, on the other hand, has a relatively mild phenotype relative to the cold-regulated genes we have examined, but is very sensitive to chilling temperatures (15 to 10 degree centigrade). It is thus likely that in cls8 we have not yet identified the genes which are most affected, and which account for the physiological phenotype. Both sfr6 and cls8 have been fine-mapped and are close to being cloned. The cls8 mutant has an altered calcium signature in response to cold which means it is likely to be affected in early signalling, e.g. cold perception itself.We will compare the expression profiles of genes in sfr6, cls8 and Columbia (parental line for both mutants), both at ambient, and after treatment with cold (5 degrees) for 3 hours. This timepoint is designed to capture both rapidly responding genes e.g. CBF/DREB1 transcription factors, and also more slow genes e.g. COR genes (KIN1/2 and LTI78). Pilot northerns confirm that this time point is suitable.This analysis will provide new insight into 2 novel genes required for tolerance to low temperature in Arabidopsis, and additionally will determine the nature of overlap between the separate processes of chilling and freezing tolerance. Keywords: strain_or_line_design
2007-01-22 | GSE6167 | GEO
Project description:Analysis of long-term freezing on the stability of transcriptome profiles in PAXgene stabilized whole blood samples. In the present study it was tested if long-term freezing of PAXgene RNA tubes (up to one year) has an influence on the transcriptome profile of peripheral whole blood samples. Results indicated that gene expression profiles of whole blood samples stabilized with PAXgene RNA tubes remain stable for at least 1 year.
2011-07-22 | GSE24757 | GEO
Project description:Quantifiying the impact of initial cell counts on the identified HLA-DR immunopeptidome of PBMC.
2021-08-23 | PXD023032 | Pride