Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| HGDP00491.IonXpress_019.vcf.gz | Vcf | |||
| HGDP00491.IonXpress_019.vcf.gz.tbi | Vcf | |||
| HGDP00540.IonXpress_030.vcf.gz | Vcf | |||
| HGDP00540.IonXpress_030.vcf.gz.tbi | Vcf | |||
| HGDP00541.IonXpress_031.vcf.gz | Vcf |
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Project description:Advances in molecular diagnostics have enabled accurate disease diagnosis. However, the application of molecular biology technology in the field of forensic medicine, especially in forensic pathology, is still limited. Degraded samples with altered physicochemical properties pose challenges for molecular techniques. Identifying degradation-resistant, sensitive techniques is key for forensic molecular pathology. ATAC-seq maps open chromatin and is increasingly used in disease diagnosis and mechanism studies. Given forensic use of degraded DNA, we explored ATAC-seq's potential for analyzing degraded forensic samples. In a TBI model, ATAC-seq detected injury-induced chromatin changes after 2h degradation. We identified 1,432 TBI-associated loci with robust chromatin changes unaffected by degradation. These loci have potential as a panel of biomarkers for molecular diagnosis from degraded forensic samples.
2025-03-06 | GSE245683 | GEO
Project description:Forensic body fluid identification is important for crime scene reconstruction. We used Illumina HumanMethylation 450K bead array containing over the 450,000 CpG sites in 16 body fluid samples to find novel DNA methylation marker for forensic body fluid identification. Examination of genome-wide DNA methylation profiling in 16 body fluid samples
2014-07-31 | E-GEOD-55734 | biostudies-arrayexpress
Project description:Forensic body fluid identification is important for crime scene reconstruction. We used Illumina HumanMethylation 450K bead array containing over the 450,000 CpG sites in 16 body fluid samples to find novel DNA methylation marker for forensic body fluid identification.
2014-07-31 | GSE55734 | GEO
Project description:A challenge for advancing approaches to liver regeneration is loss of functional differentiation capacity when hepatocyte progenitors are maintained in culture. Recent lineage-tracing studies have shown that mature hepatocytes (MHs) convert to an immature state during chronic liver injury, and we investigated whether this conversion could be recapitulated in vitro and if such converted cells could represent a source of expandable hepatocytes. We report that a cocktail of small molecules, Y-27632, A-83-01 and CHIR99021, can convert rat and mouse MHs in vitro into proliferative bipotent cells, which we term chemically induced liver progenitors (CLiPs). CLiPs can differentiate into both MHs and biliary epithelial cells that can form functional ductal structures. CLiPs in long-term culture did not lose their proliferative capacity or their hepatic differentiation ability, and rat CLiPs were shown to extensively repopulate chronically injured liver tissue. Thus our study advances the goals of liver regenerative medicine. Transcriptomic analyses for freshly isolated MHs and cells cultured for the designated periods with or without YAC stimulation (Matrix 1). Transcriptomic analysis for CLiPs which underwent hepatic induction (Matrix 2). Transcriptomic comparison of hepatic inducibility between CLiPs at early passage and those at late passages (Matrix 3). Transcriptomic comparison between chimera-derived rat cells (designated as “2nd”) and primary rat MH-derived cells (designated as “1st”) (Matrix 4).
2016-11-15 | GSE87611 | GEO
Project description:Current molecular diagnostic techniques in forensic science are significantly hindered by DNA degradation, underscoring the urgent need for robust molecular tools with resistance to degradation. In our previous study using a murine traumatic brain injury (TBI) model, we were the first to propose the feasibility of using ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) to identify trauma-related chromatin changes under early postmortem degradation conditions (2 hours). However, its applicability to human forensic samples remains insufficiently evaluated. This study aims to systematically assess the utility of ATAC-seq in identifying chromatin accessibility changes induced by TBI in human samples, with a particular focus on its stability and reliability under late-stage postmortem degradation. Cortical brain tissues from three human TBI cases and three matched controls were collected and subjected to sampling at 0 and 24 hours postmortem. Standard ATAC-seq protocols were used for library construction and sequencing. Downstream analyses included quality control, differential accessibility analysis, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment, and transcription factor motif analysis. All 12 samples exhibited high-quality sequencing metrics. Numerous differentially accessible chromatin regions (peaks) were identified between TBI and control groups, demonstrating the sensitivity of ATAC-seq in detecting trauma-associated chromatin alterations. Notably, no significant differences were observed between samples degraded for 0 and 24 hours, indicating the method’s robustness to degradation. Enrichment analyses revealed that differential peaks were significantly associated with biological processes and pathways relevant to TBI pathology, including axon development, synaptic signaling, and neurotrophin signaling pathways. The SOX transcription factor family emerged as a dominant motif, consistent with known mechanisms of TBI pathophysiology. This study provides compelling evidence that trauma-induced chromatin accessibility changes remain stable even in degraded forensic brain tissues, including those subject to late postmortem intervals. The high sensitivity and specificity of ATAC-seq support its potential application in forensic pathology, offering both a theoretical foundation and empirical validation for its broader use in forensic diagnostics.
2026-06-04 | GSE298572 | GEO
Project description:Hyphomonas adhaerens MHS-3 Genome Sequencing
| PRJNA186164 | ENA
Project description:Hyphomonas johnsonii MHS-2 Genome Sequencing
| PRJNA186166 | ENA
Project description:A challenge for advancing approaches to liver regeneration is loss of functional differentiation capacity when hepatocyte progenitors are maintained in culture. Recent lineage-tracing studies have shown that mature hepatocytes (MHs) convert to an immature state during chronic liver injury, and we investigated whether this conversion could be recapitulated in vitro and if such converted cells could represent a source of expandable hepatocytes. We report that a cocktail of small molecules, Y-27632, A-83-01 and CHIR99021, can convert rat and mouse MHs in vitro into proliferative bipotent cells, which we term chemically induced liver progenitors (CLiPs). CLiPs can differentiate into both MHs and biliary epithelial cells that can form functional ductal structures. CLiPs in long-term culture did not lose their proliferative capacity or their hepatic differentiation ability, and rat CLiPs were shown to extensively repopulate chronically injured liver tissue. Thus our study advances the goals of liver regenerative medicine. Transcriptomic analysis for mouse CLiPs at P1 which underwent hepatic induction (Matrix 1). Transcriptomic analysis for mouse CLiPs at P11-12 which underwent hepatic induction (Matrix 2).
2016-11-15 | GSE87579 | GEO
Project description:Identifying the type and origin of biological samples left at a crime scene is crucial in forensic investigations as it can provide important clues for crime scene reconstruction and linkages between victim/perpetrator/scene. MicroRNAs (miRNAs) are considered to be more stable than mRNA due to their small size and protection by protein and have been demonstrated to be a viable tool for body fluid identification in forensic casework. To screen reliable body-fluid specific miRNAs, ten arrays were performed in five body fluids (peripheral blood, menstrual blood, saliva, semen and vaginal secretion). Two arrays were carried out for each body fluid: three samples for the first and the other two for the second (for menstrual blood, the second array detected three samples).
2020-06-25 | GSE153135 | GEO