Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA388108 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We use single molecule RNA FISH measurements of 26 genes in thousands of melanoma cells to provide an independent reference dataset to assess the performance of the DropSeq and Fluidigm single cell RNA sequencing platforms. We quantified the Gini coefficient, a measure of rare-cell expression variability, and find that the correspondence between RNA FISH and single cell RNA sequencing for Gini, unlike for mean, increases markedly with per-cell library complexity up to a threshold of ~2000 genes detected. A similar complexity threshold also allows for robust assignment of multi-genic cell states such as cell cycle phase.
2017-05-26 | GSE99330 | GEO
Project description:Comparative analysis between single-cell RNA-seq and single-molecule RNA FISH indicates that the pyrimidine nucleobase idoxuridine (IdU) globally amplifies transcriptional noise
| PRJNA1096246 | ENA
Project description:A Comparison of Single Molecule and Amplification Based Sequencing of Cancer Transcriptomes: RNA-Seq Comparison
| PRJNA79905 | ENA
Project description:Long noncoding RNAs (lncRNAs) have emerged as key players in different cellular processes and are required for diverse functions in vivo. However, fundamental aspects of lncRNA biology remain poorly characterized, including their subcellular localization, abundance and variation at a single cell resolution. Here, we used single molecule, single-cell RNA fluorescence in situ hybridization (RNA FISH) to survey 61 lncRNAs, chosen by properties such as conservation, tissue specific expression, and expression abundance, and to catalog their abundance and cellular localization patterns in three human cell types. Our lncRNAs displayed diverse sub-cellular localization patterns ranging from strictly nuclear localization to almost exclusive cytoplasmic localization, with the majority localized primarily in the nucleus. The low abundance of these lncRNAs as measured in bulk cell populations cannot be explained by high expression in a small subset of 'jackpot' cells. Simultaneous analysis of lncRNAs and mRNAs from corresponding divergently transcribed loci showed that divergent lncRNAs do not present a distinct localization pattern and are not always co-regulated with their neighbor. Overall, our study highlights important differences and similarities between lncRNAs and mRNAs. The rich set of localization patterns we observe are consistent with a broad range of potential functions for lncRNA, and assists in hypothesis generation for mechanistic studies. Here we provide the RNA-Seq expression matrix, as well as RNA-Seq raw data, which we used for comparison with RNA FISH molecule counts.
2015-01-07 | GSE57049 | GEO
Project description:Experiments to test the effect of CtBP2 inhibition on metabolism of breast cell lines. In particular, experiment 1 involves comparison between a normal breast cell line (MCF102A) and a triple-negative breast cancer cell line (MDA-MB231). Experiment 2 is a study between MDA-MB231 silenced for CtBP2 by stable RNA interference (shCtBP2 cells) compared to scramble (shCTRL cells). Experiment 3 is a comparison between a normal breast cell line (MCF102A) and a triple-negative breast cancer cell line (MDA-MB231)in the presence of the absence of small-molecule CtBP inhibitors: HIPP (400 μM) or P4 (300 μM)for 48 hours.
2021-08-31 | ST001941 | MetabolomicsWorkbench
Project description:Long noncoding RNAs (lncRNAs) have emerged as key players in different cellular processes and are required for diverse functions in vivo. However, fundamental aspects of lncRNA biology remain poorly characterized, including their subcellular localization, abundance and variation at a single cell resolution. Here, we used single molecule, single-cell RNA fluorescence in situ hybridization (RNA FISH) to survey 61 lncRNAs, chosen by properties such as conservation, tissue specific expression, and expression abundance, and to catalog their abundance and cellular localization patterns in three human cell types. Our lncRNAs displayed diverse sub-cellular localization patterns ranging from strictly nuclear localization to almost exclusive cytoplasmic localization, with the majority localized primarily in the nucleus. The low abundance of these lncRNAs as measured in bulk cell populations cannot be explained by high expression in a small subset of 'jackpot' cells. Simultaneous analysis of lncRNAs and mRNAs from corresponding divergently transcribed loci showed that divergent lncRNAs do not present a distinct localization pattern and are not always co-regulated with their neighbor. Overall, our study highlights important differences and similarities between lncRNAs and mRNAs. The rich set of localization patterns we observe are consistent with a broad range of potential functions for lncRNA, and assists in hypothesis generation for mechanistic studies. Here we provide the RNA-Seq expression matrix, as well as RNA-Seq raw data, which we used for comparison with RNA FISH molecule counts. We estimate FPKM of coding genes and lncRNAs across HeLa, human lung fibroblasts and human foreskin. This study includes data from human foreskin fibroblasts (hFF), human lung fibroblasts (hLF), and HeLa cells. An hFF sample (GSM1376178) and the hLF samples (GSM1376175-GSM1376177) were previously submitted and are available in GSE30554 as GSM759893 and GSM759890-GSM759892, respectively. The HeLa samples (GSM591670-GSM591671) were previously submitted and are available in GSE23316. The complete dataset representing: (1) the hFF Samples, including the re-analysis of the hFF Sample from GSE30554, (2) the re-analysis of the hLF Samples from GSE30554, and (3) the re-analysis of the HeLa Samples from GSE23316, is linked below as a supplementary file.
2015-01-07 | E-GEOD-57049 | biostudies-arrayexpress
Project description:Localization and Abundance Analysis of Human lncRNAs at Single Cell and Single Molecule Resolution
| PRJNA245725 | ENA
Project description:Tabula Sapiens is a single cell transcriptomic atlas of 24 human tissues and organs.
2022-05-13 | GSE201333 | GEO
Project description:We developed an amplified single-molecule RNA FISH method called clampFISH 2.0. To validate its performance, we used clampFISH 2.0 on two cell lines, WM989 A6-G3 cells and WM989 A6-G3 cells grown in vemurafenib, and across 10 genes, compared clampFISH 2.0 spot counts to the FPKM values from bulk RNA sequencing.
2022-08-23 | GSE211491 | GEO
Project description:HIV-1 eradication strategies require reactivation of all latent cells. Current methods lack effectiveness due to incomplete knowledge of proviral reactivation. We employed a single-molecule RNA-FISH (smRNA-FISH) analysis and found that proviral reactivation is highly variable, stochastic, and occurs in bursts and waves, with different kinetics in response to diverse LRAs. Approximately 1-5% of latent cells displayed stochastic reactivation even without stimulation. Through single-cell RNA-seq analysis, we identified NR4A3 and cMYC as extrinsic factors selectively associated with HIV-1 reactivation. Concomitant with HIV-1 reactivation cMYC was downregulated and NR4A3 was upregulated in both latent cell lines and primary CD4+ T-cells from aviremic patients. By inhibiting cMYC using SN-38, an active metabolite of irinotecan, we induced NR4A3 and HIV-1 expression. Our results suggest that inherent stochasticity in proviral reactivation contributes to cell-to-cell variability, which could potentially be modulated by drugs targeting cMYC and NR4A3.
2024-05-24 | GSE241207 | GEO