77f9f3ab-ed87-4ddc-a26b-ad9a374596f1 - samples
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ABSTRACT:
PROVIDER: EGAD00001005976 | EGA |
REPOSITORIES: EGA
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Project description:Whole exome sequencing FASTq files from 469 pre-treatment tumors from IMvigor210, POPLAR and IMmotion150, with matched PBMC samples.
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Project description:RNAseq fastq files from 611 bulk pre-treatment tumors from two indications: metastatic urothelial bladder cancer patients (IMvigor210) and metastatic renal cell carcinoma (IMmotion150)
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Project description:Gene expression analysis of CD8+ T cells isolated from PBMC from healthy donors was performed by using Nanostring Technology
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Project description:This article contains raw and processed data related to research published by Kra et al. [1]. There is a scarce knowledge on the proteome of peripheral blood mononuclear cells (PBMC) during the transition period in dairy cows. In human research, proteomics PBMC is used in order to gain insight into inflammatory diseases and syndromes. Dietary fats, and specifically omega-3 (n-3) FA, can moderate the immune fluctuation caused by parturition through improvements of the immune function [2]. Therefore, this study aim was to characterize the changes that may occur in proteome of PBMC during transition, as influenced by different n-3 FA supplementation. Proteomics data of PBMC was obtained from postpartum dairy cows supplemented peripartum with either encapsulated saturated fat (CTL), encapsulated flaxseed oil that is enriched with ALA (α-linolenic acid; FLX) or encapsulated fish oil that is enriched with EPA (eicosapentaenoic acid) and DHA (docosahexaenoic acid; FO).The analysis was done by liquid chromatography-mass spectrometry from PBMCs protein extraction. The cells were collected from six cows per treatment during the 1st week postpartum. Quantification of differential abundance between groups was done using MS1 intensity based label-free. Label-free quantitative shotgun proteomics was used for characterization. This novel dataset of proteomics data from PBMC contains 3807 proteins; 44, 42 and 65 were differently abundant (P ≤ 0.05 and FC ± 1.5), in FLX vs. CTL, FO vs. CTL and FLX vs. FO, respectively; these findings are discussed in our recent research article [1]. The present dataset of PBMC proteome adds new information regarding the effects of n-3 FA on the immune system, while providing reference for PBMC proteome in postpartum dairy cows.
2021-11-17 | PXD029683 | Pride
Project description:Background. We aimed to develop a gene expression-based prognostic signature for isocitrate dehydrogenase (IDH) wild-type glioblastoma using clinical trial datasets representative of glioblastoma clinical trial populations. Results. NanoString data were available from 512 patients in the discovery ATE dataset. Elastic net identified a prognostic signature of nine genes (CHEK1, GPR17, IGF2BP3, MGMT, MTHFD1L, PTRH2, SOX11, S100A9, and TFRC). Translating weighted elastic net scores to an average z-score signature conserved the prognostic value of the ATE signature. The z-score signature was prognostic for OS in the ATE dataset (P < 0.0001), as expected, and in the validation cohorts (AVAglio, P < 0.0001; GLARIUS, P = 0.021; UCLA, P = 0.0037). The signature remained prognostic following adjustment for MGMT promoter methylation status or corticosteroid use at baseline. A positive correlation between the signature and proneural/proliferative subtypes was observed in patients with MGMT non-methylated promoter status. Conclusions. The ATE signature showed prognostic value and may enable clinical trial stratification for IDH wild-type glioblastoma.
2020-06-01 | GSE149921 | GEO
Project description:Background. We aimed to develop a gene expression-based prognostic signature for isocitrate dehydrogenase (IDH) wild-type glioblastoma using clinical trial datasets representative of glioblastoma clinical trial populations. Results. NanoString data were available from 512 patients in the discovery ATE dataset. Elastic net identified a prognostic signature of nine genes (CHEK1, GPR17, IGF2BP3, MGMT, MTHFD1L, PTRH2, SOX11, S100A9, and TFRC). Translating weighted elastic net scores to an average z-score signature conserved the prognostic value of the ATE signature. The z-score signature was prognostic for OS in the ATE dataset (P < 0.0001), as expected, and in the validation cohorts (AVAglio, P < 0.0001; GLARIUS, P = 0.021; UCLA, P = 0.0037). The signature remained prognostic following adjustment for MGMT promoter methylation status or corticosteroid use at baseline. A positive correlation between the signature and proneural/proliferative subtypes was observed in patients with MGMT non-methylated promoter status. Conclusions. The ATE signature showed prognostic value and may enable clinical trial stratification for IDH wild-type glioblastoma.
2020-06-01 | GSE150604 | GEO
Project description:Background. We aimed to develop a gene expression-based prognostic signature for isocitrate dehydrogenase (IDH) wild-type glioblastoma using clinical trial datasets representative of glioblastoma clinical trial populations. Results. NanoString data were available from 512 patients in the discovery ATE dataset. Elastic net identified a prognostic signature of nine genes (CHEK1, GPR17, IGF2BP3, MGMT, MTHFD1L, PTRH2, SOX11, S100A9, and TFRC). Translating weighted elastic net scores to an average z-score signature conserved the prognostic value of the ATE signature. The z-score signature was prognostic for OS in the ATE dataset (P < 0.0001), as expected, and in the validation cohorts (AVAglio, P < 0.0001; GLARIUS, P = 0.021; UCLA, P = 0.0037). The signature remained prognostic following adjustment for MGMT promoter methylation status or corticosteroid use at baseline. A positive correlation between the signature and proneural/proliferative subtypes was observed in patients with MGMT non-methylated promoter status. Conclusions. The ATE signature showed prognostic value and may enable clinical trial stratification for IDH wild-type glioblastoma.
2020-06-01 | GSE150614 | GEO
Project description:Background. We aimed to develop a gene expression-based prognostic signature for isocitrate dehydrogenase (IDH) wild-type glioblastoma using clinical trial datasets representative of glioblastoma clinical trial populations. Results. NanoString data were available from 512 patients in the discovery ATE dataset. Elastic net identified a prognostic signature of nine genes (CHEK1, GPR17, IGF2BP3, MGMT, MTHFD1L, PTRH2, SOX11, S100A9, and TFRC). Translating weighted elastic net scores to an average z-score signature conserved the prognostic value of the ATE signature. The z-score signature was prognostic for OS in the ATE dataset (P < 0.0001), as expected, and in the validation cohorts (AVAglio, P < 0.0001; GLARIUS, P = 0.021; UCLA, P = 0.0037). The signature remained prognostic following adjustment for MGMT promoter methylation status or corticosteroid use at baseline. A positive correlation between the signature and proneural/proliferative subtypes was observed in patients with MGMT non-methylated promoter status. Conclusions. The ATE signature showed prognostic value and may enable clinical trial stratification for IDH wild-type glioblastoma.
2020-06-01 | GSE150612 | GEO