Ontology highlight
ABSTRACT:
PROVIDER: PRJNA357494 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Polymerase Specific Error Rates and Profiles Identified by PacBio Single Molecule Sequencing
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Project description:Knowledge of the expression profile and spatial landscape of the transcriptome in individual cells is essential for understanding the rich repertoire of cellular behaviors. Here we report multiplexed error-robust fluorescence in situ hybridization (MERFISH), a single-molecule imaging approach that allows the copy numbers and spatial localizations of thousands of RNA species to be determined in single cells. Using error-robust encoding schemes to combat single-molecule labeling and detection errors, we demonstrated the imaging of 100 – 1000 unique RNA species in hundreds of individual cells. Correlation analysis of the ~10^4 – 10^6 pairs of genes allowed us to constrain gene regulatory networks, predict novel functions for many unannotated genes, and identify distinct spatial distribution patterns of RNAs that correlate with properties of the encoded proteins. A single sample is analyzed
2015-04-09 | E-GEOD-67685 | biostudies-arrayexpress
Project description:Taq Polymerase Error Rate and Profile Determined by High Coverage Single Molecule Amplicon Sequencing
| PRJEB12157 | ENA
Project description:Single-molecule level spatial distribution of MERFISH (Multiplexed error-robust fluorescence in situ hybridization) probes targeting 140 genes were analyzed on two control (non-aneurysmal) samples and three TAA samples with Thoracic aortic aneurysm (TAA).
2023-10-14 | GSE241870 | GEO
Project description:Knowledge of the expression profile and spatial landscape of the transcriptome in individual cells is essential for understanding the rich repertoire of cellular behaviors. Here we report multiplexed error-robust fluorescence in situ hybridization (MERFISH), a single-molecule imaging approach that allows the copy numbers and spatial localizations of thousands of RNA species to be determined in single cells. Using error-robust encoding schemes to combat single-molecule labeling and detection errors, we demonstrated the imaging of 100 – 1000 unique RNA species in hundreds of individual cells. Correlation analysis of the ~10^4 – 10^6 pairs of genes allowed us to constrain gene regulatory networks, predict novel functions for many unannotated genes, and identify distinct spatial distribution patterns of RNAs that correlate with properties of the encoded proteins.
2015-04-09 | GSE67685 | GEO
Project description:Single-cell transcriptomics has recently emerged as a powerful technology to explore gene expression heterogeneity amongst single cells. Here we identify two major sources of technical variability, sampling noise and global cell-to-cell variation in sequencing efficiency. We propose noise models to correct for this and after validation by single-molecule FISH experiments, we apply these models to demonstrate that growing mES cells in 2i instead of serum/LIF globally reduces gene expression variability.
2014-04-20 | GSE54695 | GEO
Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of DNA methylations in Burkholderia pseudomallei. SMRTbell™ sequencing
2014-09-15 | E-GEOD-55168 | biostudies-arrayexpress
Project description:Advances in biochemical technologies have led to a boost in the field of single cell genomics. Observation of the genome at a single cell resolution is currently achieved by pre-amplification using whole genome amplification (WGA) techniques that differ by their biochemical aspects and as a result by biased amplification of the original molecule. Several comparisons between commercially available single cell dedicated WGA kits (scWGA) were performed, however, these comparisons are costly, were only performed on selected scWGA kit and more notably, are limited by the number of analyzed cells, making them limited for reproducibility analysis. We benchmarked an economical assay to compare all commercially available scWGA kits that is based on targeted sequencing of thousands of genomic regions, including highly mutable genomic regions (microsatellites), from a large cohort of human single cells (125 cells in total). Using this approach, we could analyze the genome coverage, the reproducibility of genome coverage and the error rate of each kit. Our experimental design provides an affordable and reliable comparative assay that simulates a real single cell experiment. Results demonstrate the need for a dedicated kit selection depending on the desired single cell assay.
2017-09-24 | E-MTAB-5968 | biostudies-arrayexpress
Project description:Single molecule sequencing after WGA
| PRJDB5917 | ENA
Project description:Chromatin structure and transcription factor localization can be assayed genome-wide by sequencing genomic DNA fractionated by protein occupancy or other properties. However, current technologies involve multiple steps that introduce bias and inefficiency. Here we apply a single-molecule approach to directly sequence chromatin immunoprecipitated DNA with minimal sample manipulation. This method is accurate, compatible with just 50 picograms of DNA and should thus facilitate charting chromatin maps from limited cell populations. Application of a single-molecule approach to directly sequence chromatin immunoprecipitated DNA of the CTCF DNA binding protein.
2009-11-29 | E-GEOD-18699 | biostudies-arrayexpress