Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell microRNA sequencing method comparison and profiling of cell lines and circulating lung tumor cells

ABSTRACT: In a stepwise approach, we evaluated available protocols before performing an analysis on circulating tumor cells of small cell lung cancer patients. We first compared 19 protocols on single MCF7 cells spiked miRExplore. Second, we analyzed MCF7 single cell equivalents of the eight best protocols. Third, we carried out single cell small RNA sequencing using the best performing protocol on 8 cell lines and 67 circulating tumor cells from seven small cell lung cancer patients.

ORGANISM(S): Homo sapiens

PROVIDER: GSE162514 | GEO | 2021/05/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories

Project description:In this study, we evaluated the feasibility of proteomics and phosphoproteomics on formalin-fixed paraffin-embedded (FFPE) lung tissue for protein extraction protocols, quantification methods, pre-analytics, and sample size. First, we compared three protocols for the extraction of proteins from FFPE tissues and used the best-performing protocol to acquire a deep proteome of lung adenocarcinoma and squamous cell carcinoma. We quantified >8,000 proteins and >14,000 phosphosites with a tandem mass tag (TMT11) approach and 6,700 proteins and 7,000 phosphosites with a microscaled TMT approach, enabling the analysis of FFPE needle biopsies with limited amounts of tissue. This is a considerable increase in coverage compared to label-free quantification techniques. We also evaluated pre-analytical variables such as the influence of fixation times and the duration of heat-assisted de-crosslinking on protein extraction efficiency and proteome coverage. Our improved workflows provide quantitative information on protein abundance and phosphosite regulation for most relevant oncogenes, tumor suppressors, and signaling pathways in lung cancer. We also present general guidelines to what proteomics and phosphoproteomics methods are best suited for different applications for retrospective cancer studies.

2021-05-05 | PXD024800 | Pride

Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects (C1HT small)

Project description:Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects (C1HT small)

| PRJNA551750 | ENA

Performance comparison of small RNA-Seq library preparation methods for biofluid samples

Project description:We report performance of six different protocols for small RNAseq library preparation and of a method utilizing sequencing of probes targeting microRNAs (HTG EdgeSeq). Recently, small RNA sequencing (small RNA-seq) has been introduced as a method for quantifying circulating microRNAs (miRNAs) and enabling their global profiling without prior knowledge of target sequences. Despite its great promise, small RNA-seq has not delivered the expected outcomes, particularly due to ligation and PCR bias introduced within the workflow. In this study, we assessed the performance of all existing approaches to the small RNA-seq of miRNAs in plasma samples: original two adapter ligation approach; single adapter ligation with subsequent circularization; polyadenylation; use of randomized adapters; and use of unique molecular identifiers (UMI). Using comprehensive set of metrics, we evaluated each protocol in terms of yield, precision, accuracy, sensitivity, and ability to detect isomiRs. Moreover, we assessed performance of targeted RNA-seq method utilizing hybridization probes across relevant metrics and together with RT-qPCR we used it as a reference for accuracy evaluation. The best results were delivered by targeted RNA-seq outperforming other methods in all relevant parameters. The protocols using randomized adapters or UMIs showed consistent good performance across all of the assessed metrics. In contrast, the polyadenylation approach generated a high percentage of discarded reads and impeded the analysis of isomiRs. The single adapter ligation with subsequent circularization failed to prevent ligation bias and the traditional two adapter ligation approach achieved the worse scores in the majority of tested metrics. To sum, we provide a comprehensive comparison that can serve as a guide for new users interested in analysis of circulating miRNAs and as a reference for further comparative studies.

2020-12-31 | GSE149513 | GEO

Circulating Microvesicles and Exosomes in Small Cell Lung Cancer by Quantitative Proteomics

Project description:Early detection of small cell lung cancer crucially demands highly reliable markers. Growing evidence suggests that extracellular vesicles carry tumor cell-specific cargo suitable as protein markers in cancer. Therefore, we isolated plasma-derived exosomes from newly diagnosed small cell lung cancer patients and investigated proteome dynamics of these exosomes aiming at improving the detection of small cell lung cancer. A total of 1,016 proteins were initially identified. After data processing and statistical analysis, several proteins were found to be differentially expressed in comparing small cell lung cancer patients and healthy individuals, indicating that circulating exosomes may encompass specific proteins with potential diagnostic attributes for small cell lung cancer. Furthermore, our data may indicate a novel tumor-suppressing role of blood coagulation and involvement of complement activation in small cell lung cancer pathogenesis.

2022-04-04 | PXD028885 | Pride

Small and large RNA sequencing of a Kras G12D mouse model of lung adenocarcinoma

Project description:Mice bearing a G12D activating mutation in Kras consistently develop lung adenocarcinomas in a manner analogous to humans. By performing small and large RNA sequencing on KrasG12D tumors from F1 hybrid mice we were able to identify genes and microRNAs differentially expressed in these tumor samples. Quantification of reads that cover single nucleotide polymorphisms that distinguish between the parental mouse strains enabled an analysis of allele specific expression and imprinting status in these tumors. mRNA and small RNA fractions of mouse lungs and lung adenocarcinomas were deep sequenced in triplicate

2013-12-09 | E-GEOD-43028 | biostudies-arrayexpress

Homo sapiens

Project description:Circulating RNAs profile in non-small cell lung cancer patients

| PRJNA286291 | ENA

Homo sapiens

Project description:Inferring Evolution and Progression of Small-Cell Lung Cancer by Single-Cell Sequencing of Circulating Tumor Cells

| PRJNA448888 | ENA

Lineage plasticity in SCLC generates non-neuroendocrine cells primed for vasculogenic mimicry

Project description:RNA-seq data characterising neuroendocrine (NE) and non-NE cells, cultured on plastic or Matrigel, extracted from small cell lung cancer circulating tumour cell derived explants.

2023-09-17 | E-MTAB-10950 | biostudies-arrayexpress

[68Ga]-NeoBOMB1 Imaging in Patients With Malignancies Known to Overexpress Gastrin Releasing Peptide Receptor (GRPR)

Project description:This was a Phase II, multi-center, open label, single dose study in patients with tumor types known to overexpress Gastrin-Releasing Peptide Receptor (GRPR), including breast, prostate, colorectal, Non-Small Cell Lung Cancer (NSCLC) and Small-Cell Lung Cancer (SCLC).

| 2288221 | ecrin-mdr-crc

RNA of Small Cell Lung Cancer Circulating Tumour Cells Derived Explants

Project description:RNA of Small Cell Lung Cancer Circulating Tumour Cells Derived Explants

| PRJEB36164 | ENA