single-cell
Dotaz
Zobrazit nápovědu
- MeSH
- buněčná membrána imunologie MeSH
- experimentální nádory imunologie MeSH
- experimenty na zvířatech MeSH
- fluorescenční protilátková technika MeSH
- hepatocelulární adenom chemicky indukované imunologie MeSH
- karcinogeny MeSH
- krysa rodu rattus MeSH
- techniky in vitro MeSH
- Check Tag
- krysa rodu rattus MeSH
The cell, as a fundamental structural, functional and biological unit, plays an essential role in living organisms. Analysis of the molecular/elemental composition of a single cell is a significant aspect of lipidomic, proteomic, metabolomic and metallomic studies aiming at understanding molecular processes in cells. Inductively coupled plasma mass spectrometry (ICP-MS) is a powerful technique which can help to elucidate the bioeffects of trace metals and their species on cellular metabolism and cell behavior. Numerous ICP-MS-based methods have already been utilized to explore elemental/species profiles. These include, e.g. time-resolved ICP-MS, electrothermal vaporization ICP-MS, laser ablation ICP-MS, chip-based microextraction techniques, HPLC/CE-ICP-MS, elemental tagging, and mass cytometry. All these methods are covered in this short review.
- MeSH
- analýza jednotlivých buněk metody MeSH
- hmotnostní spektrometrie * metody MeSH
- lidé MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
- MeSH
- buněčné linie účinky léků MeSH
- chromozomální aberace MeSH
- lidé MeSH
- methotrexát MeSH
- protinádorové látky MeSH
- Check Tag
- lidé MeSH
... Noninvasive metabolic assessment of single cells / David K. ... ... Gardner -- Laser capture microdissection for analysis of single cells / Nobuki Nakamura ... ... ... [et al.] -- Fluorescence in situ hybridization (FISH) on single cells (sex determination and chromosome ... ... Scriven and Caroline Mackie Ogilvie -- Single cell PCR for PGD : methods, strategies, and limitations ... ... Wangh -- Efficient isothermal amplification of the entire genome from single cells / Karen V. ...
Methods in molecular medicine, ISSN 1543-1894 132
xi, 182 s. : il., tab.
Single-cell RNA-seq methods can be used to delineate cell types and states at unprecedented resolution but do little to explain why certain genes are expressed. Single-cell ATAC-seq and multiome (ATAC + RNA) have emerged to give a complementary view of the cell state. It is however unclear what additional information can be extracted from ATAC-seq data besides transcription factor binding sites. Here, we show that ATAC-seq telomere-like reads counter-inituively cannot be used to infer telomere length, as they mostly originate from the subtelomere, but can be used as a biomarker for chromatin condensation. Using long-read sequencing, we further show that modern hyperactive Tn5 does not duplicate 9 bp of its target sequence, contrary to common belief. We provide a new tool, Telomemore, which can quantify nonaligning subtelomeric reads. By analyzing several public datasets and generating new multiome fibroblast and B-cell atlases, we show how this new readout can aid single-cell data interpretation. We show how drivers of condensation processes can be inferred, and how it complements common RNA-seq-based cell cycle inference, which fails for monocytes. Telomemore-based analysis of the condensation state is thus a valuable complement to the single-cell analysis toolbox.
- MeSH
- analýza jednotlivých buněk * metody MeSH
- B-lymfocyty metabolismus cytologie MeSH
- buněčný cyklus * genetika MeSH
- ChiP sekvenování metody MeSH
- chromatin * metabolismus chemie genetika MeSH
- fibroblasty metabolismus cytologie MeSH
- lidé MeSH
- sekvenování transkriptomu metody MeSH
- telomery * genetika MeSH
- vazebná místa MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Závěrečná zpráva o řešení grantu Agentury pro zdravotnický výzkum MZ ČR
nestr.
Navrhovaný projekt staví na dlouhodobém výzkumu naší skupiny v oblasti chronické lymfocytární leukémie (CLL). Projekt si klade za cíl prohloubit naše znalosti a lépe porozumět mechanismům klonální evoluce CLL buněk v průběhu onemocnění. Pro detailní charakterizaci nádorových buněk a sledování agresivních klonů v průběhu progrese onemocnění chceme využít moderní přístup analýzy na úrovni jednotlivých buněk (SCA). Budeme srovnávat transkriptomy tisíců CLL buněk získaných z opakovaných odběrů pacientů s relaps/refrakterní CLL (R/R CLL) což je onemocnění, které neodpovídá na léčbu nebo u něho dochází k progresi/relapsu dříve než za šest měsíců. R/R CLL reprezentuje významnou podskupinu onemocnění, která si zaslouží pozornost vzhledem k špatné prognóze onemocnění. Porozumění molekulárním mechanismům vedoucím k rozvoji R/R CLL umožní výběr nejvhodnější léčebné strategie, zvlášť v souvislosti s rychlým vývojem cílené léčby v poslední době.; The proposed project builds on our continuous well-established research on chronic lymphocytic leukemia (CLL). In this study, we would like to profound our knowledge to better understand the mechanisms underlying clonal evolution of CLL cells during the disease course. We will employ a challenging approach a single cell analysis (SCA) for detailed characterisation of malignant cells on single cell level with aim to monitor disease progression and to detect the most aggressive subclones of CLL. In particular, we will analyse and compare transcriptomes of thousands of CLL cells from consecutively collected samples of patients suffering from early relapsed/refractory disease (R/R CLL), which is defined by non-response to treatment or relapse within six months after therapy. Thus, R/R CLL represents a highly challenging subtype of disorder with very poor prognosis and deserves further attention. A deeper understanding of molecular mechanisms driving R/R CLL can help to select the best treatment approach, especially from the growing spectrum of targeted therapy.
- Klíčová slova
- klonální evoluce, chronic lymphocytic leukemia, clonal evolution, Chronická lymfocytární leukémie, single cell analysis, Single cell analýza,
- NLK Publikační typ
- závěrečné zprávy o řešení grantu AZV MZ ČR
Single cells are basic physiological and biological units that can function individually as well as in groups in tissues and organs. It is central to identify, characterize and profile single cells at molecular level to be able to distinguish different kinds, to understand their functions and determine how they interact with each other. During the last decade several technologies for single-cell profiling have been developed and used in various applications, revealing many novel findings. Quantitative PCR (qPCR) is one of the most developed methods for single-cell profiling that can be used to interrogate several analytes, including DNA, RNA and protein. Single-cell qPCR has the potential to become routine methodology but the technique is still challenging, as it involves several experimental steps and few molecules are handled. Here, we discuss technical aspects and provide recommendation for single-cell qPCR analysis. The workflow includes experimental design, sample preparation, single-cell collection, direct lysis, reverse transcription, preamplification, qPCR and data analysis. Detailed reporting and sharing of experimental details and data will promote further development and make validation studies possible. Efforts aiming to standardize single-cell qPCR open up means to move single-cell analysis from specialized research settings to standard research laboratories.
