[PDF] Top 20 Comparative analysis of sequencing technologies for single cell transcriptomics
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Comparative analysis of sequencing technologies for single cell transcriptomics
... to single-cell reaction (ground truth) (Additional file 1: Figure S1B – ...the single-cell sensitivity is computed using a logistic regres- sion model with spike-in RNA detection as a ... See full document
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Studying hematopoiesis using single-cell technologies
... high-throughput sequencing; Baso: Basophil; CLP: Common lymphoid progenitors; CMP: Common myeloid progenitors; CNVs: Copy number variations; CTCs: Circulating tumor cells; CyTOF: Cytometry by Time-Of-Flight; DC: ... See full document
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Systematic comparative analysis of single nucleotide variant detection methods from single cell RNA sequencing data
... patients. Single cells were collected and sorted from freshly dissected tu- mors as we described previously ...70-μm Cell-Strainer (BD) and cen- ...blood cell (Solarbio), the pelleted cells were re- ... See full document
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Single cell transcriptomics unveils gene regulatory network plasticity
... network analysis of single-cell data are the technical limitations inherent to the technology and the very large data ...of single-cell data ...large-scale sequencing data ... See full document
20
In silico lineage tracing through single cell transcriptomics identifies a neural stem cell population in planarians
... our analysis pipeline readily predicts the known order of epithelial lineage differentiation described by previous works [18, 20, ...and analysis pipeline to reconstruct planarian neoblast ...of ... See full document
17
Design and computational analysis of single cell RNA sequencing experiments
... in single-cell sequencing technologies and con- comitant advances in computational and statistical ...from single-cell RNA-seq, as well as other types of ... See full document
14
Single cell sequencing in stem cell biology
... by sequencing (ChIP-seq) is a widely used method for mapping histone modifications at the whole-genome ...a single-cell analysis by combining droplet and barcoding strategies ...their ... See full document
12
Single cell transcriptomics : a high resolution avenue for plant functional genomics
... a cell (referred to as ‘empty barcodes’) or one ...per cell barcode in descending order should reveal a ‘knee’ in the distribution indicative of a transition from STAMPs to background ...plots, cell ... See full document
12
Single cell sequencing: a distinct new field
... a single cell NGS-based method for aneuploidy screening in single ...array comparative genomic hybridization (array-CGH) and demonstrated that a single cell NGS-based method ... See full document
11
Single-cell transcriptomics–based MacSpectrum reveals macrophage activation signatures in diseases
... define cell lineages, signals altered during macrophage terminal maturation and activation are relatively less distinct, as we observed in this study and others have pointed out as one of the major computational ... See full document
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The single-cell sequencing: new developments and medical applications
... accurate analysis of tumor cells. Traditional sequencing methods can only detect cell populations, get the average of the signals in a group of cells, but the heterogeneity in tumor cells can be ... See full document
9
BART Seq: cost effective massively parallelized targeted sequencing for genomics, transcriptomics, and single cell analysis
... the analysis of 22 markers of early gastru- lation, housekeeping genes, and 3 RNA spike-ins, which we also validated by nested qPCR (Table 1, ...global sequencing of bulk RNA following 72 h of stimulation, ... See full document
16
Single cell expression analysis reveals anatomical and cell cycle dependent transcriptional shifts during heart development
... parameters. Cell filter, data normalization and unsupervised analysis were carried out in Seurat version 2 according to their recommended steps (Butler et ...library sequencing depth followed by log ... See full document
12
UMI count modeling and differential expression analysis for single cell RNA sequencing
... a single experiment [2, ...(ARMS) cell line (6875 cells) prepared in-house on the Chromium platform (10× ...clustering analysis (Additional file 1: Figure S2) and were included to evaluate the ... See full document
17
Comparative analysis of salivary microbiome in oral squamous cell carcinoma patients and healthy individuals using 16S rRNA sequencing
... bacterial cell rRNA in the ...gene sequencing: The use of 16S rRNA gene sequences to study bacterial phylogeny and taxonomy has been by far the most common housekeeping genetic marker used for a number of ... See full document
180
Single cell analysis of long non coding RNAs in the developing human neocortex
... rate analysis was performed by calculating for each gene and ERCC spike the number of cells out of the 276 neocortex cells that exhibited >1 normalized counts for that ...per cell. At more than eight ... See full document
17
Sensitivity to sequencing depth in single-cell cancer genomics
... Raw single-nucleotide variant (SNV) calls for the bulk datasets were obtained using the paired-sample variant- calling approach implemented in the VarDict software ...Genome Analysis Toolkit (GATK) ... See full document
11
Future medical applications of single-cell sequencing in cancer
... microarray comparative genomic hybridization (aCGH) has been in clinical use for constitutional genetic disorders for some time, its use in profiling cancers has been largely limited to basic ...DNA ... See full document
12
Structural and Functional Apple Genomics and its Application in Breeding
... new technologies proved to be useful as assembly template for transcriptome re-sequencing, new mo- lecular marker development, creation of the targeted sequencing assays such as ... See full document
7
Comparative Transcriptomics of Grapevine Powdery Mildew
... Illumina sequencing. Given the current state of the sequencing market, one is led to believe that Illumina sequencing is the cheaper and more effective ... See full document
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