01-01-2025
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB75144 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:this is an exercise about uploading data to ENA
| PRJEB75142 | ENA
Project description:Dear Juan Francisco, Dear Pablo we finished analyzing your latest order. In short, the data looks great! Your neg. controls behave as expected and cluster tightly. The probe (JT-195) enriches for a lot of prey proteins. Many are shared with the cysteinome control. Replicates are very similar. Kind regards, Tobias *** Always reply to workflow results by using the order comments function in b-fabric! Please do NOT send emails to proteomics@ or individual people involved in workflow processing (order coach). *** 1 Downloading results packaged in a b-fabric workunits [https://fgcz-bfabric.uzh.ch/wiki/tiki-index.php?page=WorkunitDownload] 2 General data processing logic LC-MS raw data => Dia-NN => proLFQ/SAINTexpress => Interaction proteomics report |-> ScaffoldDIA 3 Workunit guidance 3.1 Dia-NN The main output of Dia-NN is called <WU#>_report.tsv and is a precursor-centric table in long format. It describes chromatographic features mapped to peptides. This file can be loaded in downstream processing tools like DIAgui [https://github.com/mgerault/DIAgui] or amica [https://github.com/tbaccata/amica] or a spread sheet calculator. For direct exploration of Dia-NN output we recommend using the so called matrix files named <WU#>_report.<level>_matrix.tsv These files summarize the main report for pr (precursor), pg (protein group), or gg (gene group) level by the maxLFQ algorithm in matrix-like tables (feature x sample). Be aware that maxLFQ estimates are tailored towards comparisons between experimental conditions (also called horizontal comparisions). They should not be used for rank sorting proteins, as estimator for the abs. amount of proteins. For this special estimators like topN or iBAQ should be used (available in DIAgui) [https://github.com/vdemichev/DiaNN] 3.2 SAINTexpress The main interaction scoring results are summarized in the interaction proteomics report. This report is named SaintExpressReport*_<WU#>.html and can be viewed in any web browser. All numbers shown in the report are extracted from the SAINTexpress output which is available as DIANN_<WU#>_data.xlsx. The list tab summarizes all bait-prey pairs scored by the ML model for the different comparisons. We judge preys by co-filtering in effect size (FoldChange) and significance dimension (BFDR). Suitable cutoffs are very experiment/data dependent, especially in the effect size dimension. We tend to use BFDR <5% and FC >1 as initial thresholds. Refiltering according to known interactions is always a good approach to arrive at meaningful candidate lists. The ORA_Bait_<baitName>_<preyName>.txt files can be used to upload candidate lists to web tools like String-DB [https://string-db.org] for network/enrichment analysis. They are always filtered according to parameters shown in the interaction proteomics report. [https://saint-apms.sourceforge.net/Main.html] 3.3 ScaffoldDIA The main output of protein identification and quantification performed by Dia-NN is also available as ScaffoldDIA formatted file (<WU#>_result.sdia). ScaffoldDIA allows to browse LC-MS datasets using a GUI. The ScaffoldDIA app can be downloaded free of charge from [https://www.proteomesoftware.com/products/scaffold-dia] and runs on all mayor (OS) platforms. Be aware that Dia-NN matrix files might be different to ScaffoldDIA outputs, since ScaffoldDIA takes the Dia-NN main report (which describes chromatographic features mapped to peptides) and recalculates protein inference, reestimate protein quantifies. The output in the app also heavily depends on the set filter options. We do NOT recommend using ScaffoldDIA exports for statistical downstream processing, but only for interactive explorative analysis.
2025-09-22 | PXD062853 | Pride
Project description:Enzootic nasal adenocarcinoma (ENA), an epithelial tumor induced in goats and sheep by enzootic nasal tumor virus (ENTV), is a chronic, progressive, contact sexually transmitted disease. This study aimed to identify novel and differentially expressed miRNAs in the tumor and para-carcinoma nasal tissues of Nanjiang yellow goats with ENA. Small RNA Illumina high-throughput sequencing was used to construct a goat nasal miRNA library; 406 known miRNAs and 29 novel miRNAs were identified. A total of 116 miRNAs were significantly differentially expressed in para-carcinoma nasal tissues and ENA (54 downregulated; 60 upregulated; 2 only expressed in control group); Target gene prediction and functional analysis revealed that 6176 non-redundancy target genes, 1792 significant GO and 97 significant KEGG pathway for 121 miRNAs (116 significant expression miRNAs and 5 star sequence) were predicted. GO and KEGG pathway analysis revealed the majority of target genes in ENA are involved in cell proliferation, signal transduction and other processes associated with cancer. This is the first large-scale identification of miRNAs in Capra hircus ENA and provides a theoretical basis for investigating the complicated miRNA-mediated regulatory networks involved in the pathogenesis and progression of ENA.
2016-01-25 | GSE65305 | GEO
Project description:This study aims to study genome wide location of HNF4a, FoxA1 and CEBPA in wild type rat liver. Please note that all raw data files for this study were replaced with new versions on 12 March 2014 because the previous versions are corrupted. The corrupted files are associated with ENA run accessions ERR215698 to ERR215705 and should not be used. The correct files are associated with ENA run accessions ERR458085 to ERR458092.
2013-08-30 | E-MTAB-1415 | biostudies-arrayexpress
Project description:We investigated wether host cell gene expression response to a bacterial infection can involve changes at alternative splicing level. To identify these events, we have analyzed the long read sequencing data to identify which transcript isoforms were altered in a human epithelial colon adenocarcinoma cell line (LoVo ATCC CCL-229) along a 0- to 10-h time-course of infection by Listeria monocytogenes strain LL195. This set is linked to a previous short-read set referenced on ENA (https://www.ebi.ac.uk/ena/browser/view/PRJEB26593).
2023-10-17 | GSE225417 | GEO
Project description:Five-vertebrate ChIP-seq reveals the evolutionary dynamics of trancription factor binding. The SRF files for this experiment can be found in the European Read Archive with study accession number ERP000054. The fastq files can be found in the raw archives and for some assays links to the ENA runs and ENA fastq files are provided.
2010-04-08 | E-TABM-722 | biostudies-arrayexpress