Preservation
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB49125 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR7456970_1.fastq.gz | Fastqsanger.gz | |||
| ERR7456970_2.fastq.gz | Fastqsanger.gz | |||
| ERR7456980_1.fastq.gz | Fastqsanger.gz | |||
| ERR7456980_2.fastq.gz | Fastqsanger.gz | |||
| ERR7456990_1.fastq.gz | Fastqsanger.gz |
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Project description:We developed and validated a simple method for viable cryopreservation of whole blood, without any preprocessing, Simple prEservatioN of Single cElls (SENSE), with granulocyte depletion for generating high-quality single-cell profiles. We performed rigorous in-depth characterization of the SENSE method on clinical blood samples and compared it to the conventional multistep density-gradient isolation of peripheral blood mononuclear cells (PBMCs) method. The SENSE method is an effective and simple solution for the cryopreservation of blood samples in clinics/labs and single cell profiles generation.
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Project description:In the current study, we have studied the effect of three storage and preparation protocols on two AML-derived cell lines: 1) cryopreservation of viable cells for storage in liquid nitrogen, 2) cell pellet storage in liquid nitrogen and 3) freshly SDS lysed cell lysate stored at -°80. We further studied the effect cell pellet wash with cold PBS had on the AML patient cell lysate, aiming to remove remaining contaminants from FBS and blood.
2018-01-19 | PXD008361 | Pride
Project description:The evolutional trajectory of gut microbial colonization from birth has been shown to prime for health later in life. Here, we combined cultivation-independent 16S rRNA gene sequencing and metaproteomics to investigate the functional maturation of gut microbiota in faecal samples from full-term healthy infants collected at 6 and 18 months of age. Phylogenetic analysis of the metaproteomes showed that Bifidobacterium provided the highest number of distinct protein groups. Considerable divergences between taxa abundance and protein phylogeny were observed at all taxonomic ranks. Age had a profound effect on early microbiota where compositional and functional complexity of less dissimilar communities increased with time. Comparisons of the relative abundances of proteins revealed the transition of taxon-associated saccharolytic and carbon metabolism strategies from catabolic pathways of milk and mucin-derived monosaccharides feeding acetate/propanoate synthesis to complex food sugars fuelling butyrate production. Furthermore, co-occurrence network analysis uncovered two anti-correlated modules of functional taxa. A low-connected Bifidobacteriaceae-centred guild of facultative anaerobes was succeeded by a rich club of obligate anaerobes densely interconnected around Lachnospiraceae, underpinning their pivotal roles in microbial ecosystem assemblies. Our findings establish a framework to visualize whole microbial community metabolism and ecosystem succession dynamics, proposing opportunities for microbiota-targeted health-promoting strategies early in life.
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Project description:RNAseq and LC/MS metabolomics analysis of C. difficile strain 630 grown in BHIS media with 50% (vol/vol) faecal water added, compared with control BHIS containing only the additional PBS used for prep of Faecal water. Cells grown in biological triplicates to late log phase (T=6h) prior to harvest. Goal was to determine changes in gene expression caused by exposure to Faecal water, and changes in the metabolite profile of faecal water containing medium when incubated with actively growing C. difficile cells
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Project description:Isolation and characterization of quorum quenching anaerobes
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Project description:The GeneChip Porcine Genome Array was used to identify the transcriptional response upon Salmonella typhimurium infection in three porcine intestinal sections (jejumun, ileum and colon) along a time course of 1,2 and 6 days post infection. The objetives in this study were i) characterize transcriptional changes upon S. typhimurium infection in the intestinal mucosa; ii) identify differences among porcine intestinal sections in inmune resposes against S. typhimurium; iii) identify change that could be associated to salmonellosis pathogenesis and symtomatology; and finally, iv) identify transcriptional changes that could be induced by S. typhimurium in order to get bacterial survival and successful colonization. Sixteen male and female crossbreeds weaned piglets, approximately 4 weeks of age, were used in this study. Before infection, faecal samples from each animal were analyzed to confirm that piglets were free of Salmonella. Pigs were housed in an environmentally controlled isolation facility at 25ºC and under constant light with ad libitum access to feed and water. After an acclimation period of 5 days, pigs were challenged orally with 108 cfu of Salmonella enterica serovar Typhimurium phagetype DT104 (n=12), whereas the control group (n=4) received sterile medium orally. The four non-infected control pigs were necropsied two hours prior to experimental infection. Four randomly chosen infected pigs were necropsied at 1 day post infection (dpi), 2 dpi and 6 dpi, respectively. Faecal swabs, blood and tissues samples were aseptically collected. Ileum was collected, sectioned in pieces of around 10 cm and immediately frozen in liquid nitrogen for mucosa isolation and RNA purification. To ensure the inoculated pigs were infected, faecal samples were cultured and checked for positive Salmonellae organism Four reps per treatment and tissue group except 'Ileum 1dpi' has only 3 replicates.
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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).
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