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Next Generation Sequencing facilitates to identify the differential expression genes of liver tissue from HBVN donors, HBVP donors, LF donors and transplant donors.

ABSTRACT: Next Generation Sequencing facilitates to identify the differential expression genes of liver tissue from HBVN donors, HBVP donors, LF donors and transplant donors.

PROVIDER: PRJNA923663 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23075211_1.fastq.gz	Fastqsanger.gz
	SRR23075211_2.fastq.gz	Fastqsanger.gz
	SRR23075212_1.fastq.gz	Fastqsanger.gz
	SRR23075212_2.fastq.gz	Fastqsanger.gz
	SRR23075213_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing facilitates to identify the differential expression genes of liver tissue from HBVN donors, HBVP donors, LF donors and transplant donors.

Project description:We obtained liver tissues from HBVN donors, HBVP donors, LF donors and transplant donors to rperforme next-generation sequencing (NGS). Illumina mRNA-seq sample preparation kit was used to perform paired-end library sequencing with Illumina HiSeq 2000 and sequence analysis was determined using the Illumina data analysis pipeline. Based on the comparison results，we performed the GO and KEGG pathway enrichment analysis. That might suggest the different status of HBV-infected liver from liver surgery(AST<40) and liver transplantation(AST>40).

2025-03-21 | GSE222856 | GEO

Combined Calorie and Protein Restriction in Healthy Kidney Donors Improves Kidney Outcome in Donors and Kidney Transplant Recipients

Project description:A preoperative short-term diet combining calorie and protein restriction diet given during five days before kidney donation and transplantation improves kidney outcome in live kidney donors and kidney transplant recipients, which shows that the benefits of dietary restriction on stress resistance can be induced rapidly in humans, and may be used for clinically relevant endpoints.

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Soil metagenome LF

Project description:Soil metagenome LF

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NGS in hematopoietic cell transplant recipients

Project description:Transplant-associated thrombotic microangiopathy (TA-TMA) is a life-threatening complication of allogeneic hematopoietic cell transplantation (HCT). We hypothesized that pre-transplant genetic susceptibility is evident in adult TA-TMA patients at the level of TMA-associated variants and further investigated the association of genetic variants with clinical outcomes. We studied 30 patients with TA-TMA at a median of 73 (9-540) post-transplant days, donors of 18/30 patients and 30 control non-TMA HCT recipients, without significant differences in transplant characteristics. Genomic DNA from pre-transplant peripheral blood was analyzed by targeted next generation sequencing for complement regulatory genes and ADAMTS13. Donors presented significantly lower frequency of rare variants (p=0.049) and variants in exonic/splicing/UTR regions (p=0.025), compared to TA-TMA patients. Controls also showed a significantly lower frequency of rare variants in ADAMTS13 (p=0.001), CD46 (p=0.002), CFH (p=0.010) and CFI (p=0.031). Pathogenic variants were found in ADAMTS13, CFH, CFI and CFB, while homozygous pathogenic variants in ADAMTS13 and CFB were evident in only 4 TA-TMA patients (p=0.038). Patients refractory to conventional treatment (70%) were significantly (p=0.045) enriched for variants in exonic/splicing/UTR regions compared to responders. Nineteen of 30 patients (63%) succumbed to transplant-related mortality, which was also associated with significantly (p=0.012) increased frequency of variants in exonic/splicing/UTR regions. In conclusion, increased incidence of pathogenic, rare and variants in exonic/splicing/UTR regions of TA-TMA patients suggests genetic susceptibility not evident in controls or donors. Notably, variants in exonic/splicing/UTR regions were associated with poor response and survival. Therefore, pre-transplant genomic screening may be useful to intensify monitoring and early intervention in high-risk patients.

2019-04-18 | E-MTAB-7848 | biostudies-arrayexpress

Differential transcriptomic profile of Piscirickettsia salmonis LF-89 and EM-90 during an in vivo spatial separation co-culture in Atlantic salmon

Project description:Salmonid Rickettsial Syndrome (SRS), caused by Piscirickettsia salmonis, is the most important disease in the Chilean aquaculture industry since it induces the highest mortality rates among infectious diseases. P. salmonis is a facultative intracellular bacterium comprising two genetically distinct groups (LF-89 and EM-90) in Chile. Previous data suggest that their cohabitation triggers the expression of virulence effectors, which could be related to a higher pathogenicity in salmon during a co-infection. Therefore, we evaluated whether the physical contact between two isolates from LF-89 and EM-90 was needed to activate this effect. Through a spatially separated in vivo co-culture inside Atlantic salmon followed by RNA-seq analysis, we compared the differential expressed genes (DEGs) with our previous results from an in vivo mixed co-culture. Data showed that LF-89 presented a similar virulence factor profile compared to the mixed co-culture. In contrast, EM-90 had more downregulated DEGs and the flagellar-related genes observed during mixed co-culture were absent. Hence, the synergistic effect related to increased pathogenicity to the host may be driven by the physical co-localization of both LF-89 and EM-90 P. salmonis isolates.

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Piscirickettsia salmonis LF-89 = ATCC VR-1361 isolate:Lf-89

Project description:Piscirickettsia salmonis LF-89 = ATCC VR-1361 isolate:Lf-89 Raw sequence reads

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Lung transplant

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multiFLEX-LF: A Computational Approach to Quantify the Modification Stoichiometries in Label-free Proteomics Datasets

Project description:In high-throughput LC-MS/MS-based proteomics, information about the presence and stoichiometry of post-translational modifications is normally not readily available. To overcome this problem we developed multiFLEX-LF, a computational tool that builds upon FLEXIQuant and FLEXIQuant-LF, which detect modified peptides and quantify their modification extent by monitoring the differences between observed and expected intensities of the unmodified peptides. To this end, multiFLEX-LF relies on robust linear regression to calculate the modification extent of a given peptide relative to a within-study reference. multiFLEX-LF can analyze entire label-free discovery proteomics datasets. Furthermore, to analyze modification dynamics and co-regulated modifications, the peptides of all proteins are hierarchically clustered based on their computed relative modification scores. To demonstrate the versatility of multiFLEX-LF we applied it on a cell-cycle time series dataset acquired using data-independent acquisition. The clustering of the peptides highlighted several groups of peptides with different modification dynamics across the four analyzed time points providing evidence of the kinases involved in the cell-cycle. Overall, multiFLEX-LF enables fast identification of potentially differentially modified peptides and quantification of their differential modification extent in large datasets. Additionally, multiFLEX-LF can drive large-scale investigation of modification dynamics of peptides in time series and case-control studies. multiFLEX-LF is available at https://gitlab.com/SteenOmicsLab/multiflex-lf.

2022-02-11 | PXD027970 | Pride

Transcription profiling of microdissected human transplant kidney biopsies obtained from five cadaveric and five matched live donors before transplantation

Project description:Recipients of live donor transplant kidneys (LIV) exhibit a significantly longer allograft half-life compared with cadaveric donor organs (CADs). The reasons are incompletely understood. Therefore this study sought to elucidate the genome-wide gene expression profiles in microdissected transplant kidney biopsies obtained from five cadaveric and five matched live donors before transplantation. cDNA microarrays were used to determine the transcripts in isolated glomeruli (G) and the tubulointerstitial (TI) compartment. Data were subjected to hierarchical clustering, maxT adjustment and a jackknife procedure to ensure robustness of reported findings; validation was performed by independent analysis of split biopsies and TaqMan-PCR. One hundred and thirteen sequences representing 62 unique genes (17 redundant features), and 34 ESTs separated G from TI. No difference in gene expression was found in G between LIV and CAD kidneys, but nine genes (two represented twice) and three ESTs were abundantly expressed in the CAD TI compared with LIV. The main biological function of these genes is counter regulation of oxidative stress. Promoter analysis of significant features suggested coregulated gene groups. These data suggest that CAD kidneys exhibit a distinctly different set of transcripts in the TI compartment but not in the G compartment when compared with LIV kidneys.

2005-11-09 | E-SMDB-3022 | biostudies-arrayexpress

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