Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA936628 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3’ and/or 5’ end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5’ differences and in support of this we report that a 5’ isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis of miRBase shows that 5’ isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes Sequence library of miRNAs from a single sample of human foetal mesenchymal stem cells. Results tested and confirmed by northern blotting. Please note that only raw data files are available for the embryonic and neual samples and thus, directly submitted to SRA (SRX547311, SRX548700, respectively under SRP042115/PRJNA247767)
2014-08-06 | E-GEOD-58734 | biostudies-arrayexpress
Project description:human prostate cancer cell line LNCaP Raw sequence reads
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Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 |
Project description:Pseudoexfoliation syndrome (PEX) is a systemic disorder that manifests as a fluffy, proteinaceous fibrillar material throughout the body. In the eye, such deposits result in glaucoma (PEXG), due to impeding aqueous humor outflow. When a patient presents acute glaucoma, it is necessary to remove some of the aqueous fluid within the eye to relief pain and pressure. This label free proteomics dataset was collected from human donors during cataract surgery. The aqueous humor was collected during essential ophthalmic procedures that allowed paracentesis after obtaining informed consents from human subjects without collecting identifiers, but all disease and medication history were collected. The sample collection included non-glaucomatous controls (CTL-GC), those with pseudoexfoliation syndrome (PEX-GC), and synthesized GC-Globulin pure protein (GC-Pure). Approximately 50-120 ul volume of AH was collected by paracentesis and stored in -80C immediately upon acquisition until analysis. Protein extraction was carried out by homogenization of the tissue in extraction buffer (TEAB, NaCl and SDS). Protein amounts were estimated and normalized to 10 ug across experimental samples. Samples were reduced using TCEP, alkylated with iodoacetamide and digested overnight with trypsin. Untargeted liquid chromatography-mass spectrometry was performed on an Easy nLC 1000 liquid chromatograph coupled to a QExactive mass spectrometer (LC-MS/MS). Data analysis was performed using Proteome Discoverer 3.0 and Graph Pad Prism 10. Each sample was run three separate times.
Raw mass spectrometry data files were analyzed using Proteome Discoverer 3.0. The human proteome was downloaded from UniProt and used as the target database for protein identification. Max missed cleavage site was set to 2 and minimum peptide length to 6. Precursor Mass Tolerance was set to 10ppm and Fragment Mass Tolerance to 0.02 Da. Post-translational modifications for experimental proteins included oxidation, acetylation, and carbamidomethylation. The normalization was set to total peptide amount and confidence to low.
2023-12-18 | MSV000093682 | MassIVE