74bc4b62-efca-4bad-aa97-fb198e192772 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001009494 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:High coverage whole genome sequencing data (total: 22; median coverage: ~56X; range: 27X – 82X) from fresh frozen postmortem tissues harvested from patients who participated in the CASCADE rapid autopsy program and died of metastatic castration resistant prostate cancer.
| EGAD00001009491 | EGA
Project description:High-coverage whole genome sequencing data (median coverage: 23.5X, range: 14.14X-32.62X)) from white blood cells of the patients from isolated buffy coat of the blood drawn postmortem from patients who participated in the CASCADE rapid autopsy program and died of metastatic castration resistant prostate cancer.
| EGAD00001009493 | EGA
Project description:RNA-Seq data from 20 fresh-frozen postmortem samples from three patients who participated in the CASCADE rapid autopsy program and died of metastatic castration resistant prostate cancer.
| EGAD00001009492 | EGA
Project description:Next generation sequencing platforms have become essential tools for understanding DNA in a wide range of contexts. Their success heavily relies on the accuracy, sensitivity and specificity of methods used to discern differences between the reference genome and genomes under investigation. Here we compare the relative performances of five popular single nucleotide variant callers with and without their associated recommended hard filtering criteria. We compare: FreeBayes; the Genome Analysis Toolkit’s Haplotype Caller and Unified Genotyper; SAMtools; and VarScan. We tailor this comparison to suit smaller projects with modest sample numbers (n = 10) and coverage (~10X) to fill a current gap in the literature. Other comparison studies are generally applicable only to larger projects in model species, where there is access to large amounts of sequencing data and curated callsets for base and variant quality score recalibration. We estimated the accuracy, sensitivity and specificity of each pipeline according to the genotype concordance rate and number with the “truth” dataset for 10 canine samples. The truth dataset was defined as genotypes obtained from the CanineHD BeadChip array. Whole genome sequencing data was performed on the Illumina HiSeq2000 or HiSeq2500 platform as 100-101 base pair, paired end reads to an average sample coverage of 10.3X. Apart from GATK Haplotype Caller, applying recommended hard filters did not improve the performance of genotyping concordance at the tested levels of minimum coverage. The default VarScan pipeline with no additional filters applied (VarScan uses SAMtools mpileup, without base alignment quality computation) generally outperformed other callers in terms of accuracy, sensitivity and specificity. The results of this study demonstrate that hard filtering of variant calls from low-powered genome studies can impair accuracy, sensitivity and specificity of callsets and provides some benchmark performance metrics on a range of low coverage levels.
2018-08-31 | GSE117010 | GEO
Project description:High-coverage TAC-seq expression
| PRJNA431607 | ENA
Project description:The prostate gland is one of the last internal organs to deteriorate during human decomposition. However, the effect of postmortem interval (PMI) on the mRNA and lncRNA expression and splicing is yet to be investigated in detail. The current study aims to identify the functional role of postmortem gene induction and pathway activation in prostate tissues with respect to the PMI gradient. The cadaver samples that were used in this study were collected during forensic autopsies and preserved at -20°C within the morgue at the University of Pavia (Pavia, Italy). After RNA extraction, total RNA sequencing was performed on Illumina’s NovaSeq 6000 using paired-ended sequencing approach. StringTie was used to perform expression level for mRNAs and lncRNAs by calculating FPKM. Additionally, mRNAs/lncRNAs differential expression analysis was performed by DESeq2. rMATS (version 4.1.1) was used to identify alternative splicing events and analyze differential alternative splicing events between samples having high and low PMI. Pathway analysis of the differentially expressed genes demonstrated the enrichment of FoxO signaling, aldosterone-regulated sodium reabsorption and adipocytokine signaling pathways in prostate tissue with high PMI. Gene Set Enrichment Analysis (GSEA) indicated the positive enrichment of genes belonging from protein export, proteasome, ferroptosis, and citric acid cycle in high PMI group. A comprehensive detection of alternative splicing events (ASEs) at the cellular level in postmortem prostate tissue was performed to reveal skipped exon events to be most prominent ASE in high PMI group followed by retained intron events. Our study implies that the transcription machinery remains active in prostate tissue even after five days postmortem.
2026-01-14 | GSE291070 | GEO
Project description:Studies exploring the transcriptome of stress and its effects on meat quality are very limited, particularly in goats. Fifty-four male Spanish goats (8-mo old; BW = 29.7 ± 2.03 kg) were randomly subjected to one of three treatments (TRT; n = 18 goats / treatment): (i) transported for 180 min, (ii) transported for 30 min, or (iii) held in pens (control) to analyze the transcriptome of stress and meat quality in goats using RNA-seq technology. Blood samples were collected before and after treatment, and meat samples were collected after humane slaughter for stress hormone, meat quality (Longissimus dorsi), and transcriptomic analysis. Plasma epinephrine concentrations were higher (P < 0.01) in 180 min and 30 min groups compared to the control group; however, norepinephrine concentrations were not affected by the treatment. Muscle glycogen concentrations (15 min postmortem) were lower (P < 0.01) in both 30 min and 180 min groups compared to the control group. Calpastatin levels were higher (P < 0.01) in 180 min and 30 min groups than the control group. Warner-Bratzler shear force values of loin chops were the highest in the 180 min group (4 ± 0.15, kg), lowest in the control group (3.51 ± 0.10, kg), and intermediate in the 30 min group (3.78 ± 0.09, kg; P < 0.01) both at day 1 and day 6 aging time. Additionally, desmin levels of day 6 samples were lowest in the control group, highest in 180 min group, and intermediate in 30 min group (P < 0.05). RNA-seq results showed that a total of 10,633 genes were differentially expressed (5,194 up regulated; 5,439 down regulated) among all comparisons (blood and day 1 and day 6 muscle samples). Among these differentially expressed genes (DEGs), KLF9, AMPK, FOXO3, PTX3, GADD45, PTPN1, CASP7, MAPK4, HSPA12A, and JAK-STAT were probably associated with the effects of stress on skeletal muscle proteins and involved in biological process such as cellular response to corticosteroid stimulus, endoplasmic reticulum stress, insulin resistance, DNA repair, apoptosis, MAPK cascade and regulation of proteolysis. The KEGG analysis revealed that AMPK and JAK-SAT signaling pathways and autophagy were among the top 20 enriched pathways in our treatment comparisons. The results provide an understanding of the genes and pathways involved in stress responses and related changes in postmortem muscle metabolism and meat quality characteristics in goats.
2022-08-14 | GSE210823 | GEO