Efce6694-b402-4955-8cca-65429853b4be - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001009852 | EGA |
REPOSITORIES: EGA
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Project description:Whole-exome sequencing (WES) data of tumor-normal pairs from 40 ENKTCL patients and RNA sequencing (RNA-seq) data of tumors from 20 ENKTCL patients and genetically manipulated cell line (MSN overexpression) and mouse model (MSN conventional knockout) for functional analysis of MSN.
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2024-01-11 | PXD048441 |
Project description:In this series the ocular primordium was microdissected from normal CD-1 (outbred) mouse embryos harvested days 8-10 post-coitus, corresponding to human development during the 3rd-4th weeks post-fertilization. The precise embryological age was ascertained by counting somite pairs to an accuracy of +/- 2 pairs per litter. Samples were pooled as follows: optic pit pooled from 48-50 embryos (6 litters) on 8 d.p.c. (4-8 somite pairs), optic vesicle pooled from 36-40 embryos (5 litters) on 9 d.p.c. (16-20 somite pairs), and optic cip pooled from 27-30 embryos (3 litters) on 10 d.p.c. (28-32 somite pairs). The common reference for this series was RNA collected from embryonic headfold microdissected on 8 d.p.c. RNA samples were collected from CD-1 rat embryos at equivalent somite stages for the headfold, optic vesicle, and opic cup. Keywords = embryo Keywords = eye development Keywords = mouse Keywords = rat Keywords: time-course
2004-03-11 | GSE1082 | GEO
Project description:In our study, we constructed a multicenter thyroid-cancer cohort consisting of 467 formalin-fixed paraffin-embedded (FFPE) samples, among which WES, proteome, and phosphorylated proteome analysis were conducted. Thyroid tumors consisted of 124 ATC samples, 47 PDTC samples and 177 PTC samples (including 3 biological replications).The 119 NATs were derived from tumor-adjacent tissues of 20 ATC patients and 99 PTC patients. Phosphoproteomic analysis was performed on 63 ATCs, 25 PDTCs, and 81 PTCs. 48 NAT samples were determined from tumor-adjacent tissues of 20 ATC patients and 28 PTC patients.
2025-03-16 | PXD054521 |
Project description:Purpose:The Vimentin gene plays a pivotal role in epithelial-to-mesenchymal transition (EMT) and is known to be over-expressed in the prognostically poor basal-like breast cancer subtype. Recent studies have reported Vimentin DNA methylation in association with poor clinical outcomes in other solid tumors, but not in breast cancer. We therefore quantified Vimentin DNA methylation in breast tumors and matched normal pairs in association with gene expression and survival in a cohort of 83 breast cancer patients. Materials and Methods:Vimentin methylation was quantified in 14 breast cell lines, 83 breast tumors, and 57 matched normal pairs using MALDI-TOF mass spectrometry. Gene expression data via qRT-PCR in cell lines, and oligo microarray data from breast tissues was correlated with percent methylation in the Vimentin promoter. A threshold of 20 percent average methylation was set for bivariate and multivariate tests of association between methylation and tumor subtype, tumor histopathology, and survival. Results:Vimentin was differentially methylated in luminal breast cancer cell lines, and in luminal A, luminal B and HER2+ breast tumor subtypes, but was rare in basal-like cell lines and tumors. Increased methylation was strongly correlated with decreased mRNA expression in cell lines, and had a moderate inverse correlation in breast tumors. Importantly, Vimentin methylation predicted poor overall survival independent of race, subtype, stage, nodal status or estrogen receptor positivity. Conclusion:Vimentin methylation predicts overall survival in breast cancer patients and holds promise as a prognostic biomarker for guiding treatment and prophylaxis.
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Project description:In this study we employ a strand-specific RNA-seq appoach and stranded gene expression analysis tools to identify drought responsive antisense gene loci and sense-antisense gene pairs in Populus. we generated and sequenced 28 strand-specific cDNA libraries derived from either leaf or root tissues of Populus trichocarpa plants associaed with both short-term drought (24 hours of water stress of 40% of field capacity) and long-term drought ( 25 days of water stress of 40% of field capacity) . We mapped over 71 billion nucleotides to Populus genome. Our data demonstrates that with the current sequence depth ~ 19 % of Populus genome undergoes antisense transcription subjected to drought regulation. All in all we have identified that in root tissues 524 differentially expressed antisense genes and 247 drought-responsive SA gene pairs which are significantly regulated by drought (padj <0.05). Taken all data from both drought treatments, we have identified 1185 unique drought-responsive antisense gene loci and 606 drought-responsive SA gene pairs (padj <0.05).
2019-01-06 | GSE97463 | GEO