Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1259372 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The RNA-seq data provided here were collected in order to examine the effect of identified coding and non-coding genomic aberrations on gene expression, as part of the publication ‘Whole-genome sequencing of chronic lymphocytic leukemia (CLL) identifies subgroups with distinct biological and clinical features’ by Robbe et al, Nat Gen, 2022.
2022-10-31 | E-MTAB-12124 | biostudies-arrayexpress
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc
Project description:Nucleic acids in wastewater provide a rich source of data for detection and surveillance of microbes. We have longitudinally collected 116 RNA samples from a wastewater treatment plant in Berlin/Germany, from March 2021 to July 2022, and 24 DNA samples from May to July 2022. We tracked human astroviruses, enteroviruses, noroviruses and adenoviruses over time to the level of strains or even individual nucleotide variations, showing how detailed human pathogens can be observed using wastewater. For respiratory pathogens, a broad enrichment panel enabled us to detect waves of RSV, influenza, or common cold coronaviruses in high agreement with clinical data. By applying a profile Hidden Markov Model-based search for novel viruses, we identified more than 100 thousand novel transcript assemblies likely not belonging to known virus species, thus substantially expanding our knowledge of virus diversity. Phylogenetic analysis is shown for bunyaviruses and parvoviruses. Finally, we identify Hundreds of novel protein sequences for CRISPR-associated proteins such as Transposase B, a class of small RNA-guided DNA editing enzymes. Taken together, we present a longitudinal and deep investigation into wastewater-derived genomic sequencing data that underlines the value of sewage surveillance for public health, planetary virome research, and biotechnological potential.
2023-04-13 | GSE228220 | GEO
Project description:Investigation of whole genome gene expression level changes in Prochlorococcus from environmental samples. The diel gene expression analyzed in this study is further described in Muñoz-Marin, M., Duhamel, S., Björkman, K., Magasin, J., Díez, J., Karl, D.M., Garcia-Fernandez, J.M., 2021. ISME J. (to be submitted).
2022-08-23 | GSE154594 | GEO
Project description:Salivary glands are recognised targets of SARS-CoV-2 infection, with viral RNA and protein detected in both major and minor glandular tissue; however, the transcriptional response of salivary gland epithelium and stroma to infection remains poorly characterised. Here, we present a bulk RNA sequencing dataset from major (parotid, submandibular) and minor salivary gland samples obtained at autopsy from individuals with confirmed COVID-19 and controls. Transcriptomic profiling reveals dysregulated innate immune signalling, interferon response pathways, or glandular epithelial stress responses in COVID-19 compared to control tissue, with differences observed between both major and minor gland compartments; gland-specific features were identified. These data provide a tissue-level transcriptional resource for investigating salivary gland pathology in acute COVID-19 and its potential contribution to oral manifestations of infection and post-acute sequelae. Manuscripts to site: Huang N, Pérez P,...Warner BM, Byrd KM. SARS-CoV-2 infection of the oral cavity and saliva. Nat Med. 2021 May;27(5):892-903. doi: 10.1038/s41591-021-01296-8. Epub 2021 Mar 25. PMID: 33767405; PMCID: PMC8240394; Stein SR, ...et al., ...Hewitt SM, Kleiner DE, Chertow DS. SARS-CoV-2 infection and persistence in the human body and brain at autopsy. Nature. 2022 Dec;612(7941):758-763. doi: 10.1038/s41586-022-05542-y. Epub 2022 Dec 14. PMID: 36517603; PMCID: PMC9749650.
2026-08-10 | GSE337369 | GEO
Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
| 2612481 | ecrin-mdr-crc
Project description:For the purpose of Covid-19 antibody testing, the human plasma samples acquired over a period of 310 days from August 18, 2021, to June 22, 2022, were subjected to DIA- LC-MS proteomics analysis.
2024-11-01 | PXD046562 | JPOST Repository
Project description:For the purpose of Covid-19 antibody testing, the human plasma samples acquired over a period of 310 days from August 18, 2021, to June 22, 2022, were subjected to DIA- LC-MS proteomics analysis.
2025-03-26 | PXD062242 | JPOST Repository