[PDF] Top 20 UMI count modeling and differential expression analysis for single cell RNA sequencing
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UMI count modeling and differential expression analysis for single cell RNA sequencing
... corresponding UMI counts collected from the same set of cells, enabling us to dir- ectly evaluate the effects of PCR amplification in statis- tical ...our analysis revealed the necessity of controlling ... See full document
17
Scalable microfluidics for single cell RNA printing and sequencing
... expected cell type-specific expression ...gene expression than ...one cell in a microwell containing a single bead; (3) the association of a single cell-identifying ... See full document
16
Gene level differential analysis at transcript level resolution
... epithelial cell stretching dataset analysis We used a 3’ QuantSeq dataset (GEO Series GSE89024) of stretched and unstretched rat primary type I like alveolar epithelial ...ten single-end ... See full document
11
Single cell RNA sequencing to dissect the molecular heterogeneity in lupus nephritis
... Bioinformatic analysis. Single FASTQ files corresponding to up to 96 cells were demultiplexed into single cell FASTQ files by separating reads based on the Illumina Nextera index ...the ... See full document
13
Single-cell RNA-sequencing of the brain
... bulk RNA-seq, makes it feasible to assess the uniqueness of cell ...novel cell subtypes, and rare cell species in a tissue or biological condition ...specific cell subpop- ulation or ... See full document
14
Design and computational analysis of single cell RNA sequencing experiments
... that RNA content is constant, which is often not the case in single-cell analyses as RNA content will vary with cell- cycle phase, cell size, and the transcriptional dynamics of ... See full document
14
Single cell RNA sequencing of stem cell derived retinal ganglion cells
... gene expression suggests a progenitor or an early differentiation ...protein expression, implicated in the neuronal function and development, and DNA repair (Supplementary Table S2, Data Citation ...gene ... See full document
9
Statistical Methods for Gene Differential Expression Analysis of RNA-Sequencing
... 10 single- end RNA-Seq samples (Dolinay et ...compatibility count differential analysis and aggregation,’ TCCs were obtained with the kallisto pseudo option, differential ... See full document
140
Splatter: simulation of single cell RNA sequencing data
... in differential expression analyses of single-cell RNA-seq data” [19] Lun and Marioni extended the negative binomial model from the Lun ...the cell factors are replaced with a ... See full document
15
VIPER: variability preserving imputation for accurate gene expression recovery in single cell RNA sequencing studies
... on modeling and imputing log-transformed normalized gene expression data that are converted from the original count ...data. Modeling log-transformed normalized expression data assumes ... See full document
15
SCALE: modeling allele specific gene expression by single cell RNA sequencing
... a cell, amplification and sequencing bias can be captured and estimated through the spike-in ...for Analysis of Single Cell data, unpublished), which explicitly models the technical ... See full document
15
A comparison of automatic cell identification methods for single cell RNA sequencing data
... and cell populations (annotation level), in order to represent different levels of challenges in the clas- sification task and to evaluate how each classifier performs in each case (Table ...the sequencing ... See full document
19
PBMC fixation and processing for Chromium single cell RNA sequencing
... Molecular analysis of live cells, however, can be hindered by a variety of ...primary cell types, such as blood monocytes, rapidly undergo changes once isolated from whole ...stop cell ... See full document
11
Systematic comparative analysis of single nucleotide variant detection methods from single cell RNA sequencing data
... rare cell populations, uncovering regulatory re- lationships between genes, and tracking the trajectories of distinct cell lineages in development [10, ...gene expression as features, which could be ... See full document
15
SCOPE Seq: a scalable technology for linking live cell imaging and single cell RNA sequencing
... of RNA-Seq expression profiles are consistent with their fluorescent labels from live cell imaging data ...live cell im- aging data (Additional file 1: Supplementary Methods, ...and ... See full document
5
Next-generation profiling to identify the molecular etiology of Parkinson dementia
... CRH and SST were uniquely underexpressed in PD-D. Downregulation of certain hormone proteins suggests a potential hormone imbalance associated with dementia onset. CRH , SST , and PENK are underexpressed, all of which ... See full document
10
Differential gene expression analysis tools exhibit substandard performance for long non coding RNA sequencing data
... a single simulated dataset the observed false discovery proportion (FDP) is calculated as FDP = FP/(FP + TP), where FP and TP are the numbers of incorrect (false) and correct (true) rejec- tion of the null ... See full document
16
Extraction of total RNA from single oocytes and single cell mRNA sequencing of swine oocytes
... generation sequencing, single-oocyte RNA sequencing data have been generated for mice [4–6], cattle [7], goats [8], and humans ...of single oocytes are essen- tial for a fine dissection ... See full document
5
Klaus, Johannes (2017): Modeling neuronal heterotopias using iPSC derived neural stem cells, neurons and cerebral organoids derived from patients with mutations in FAT4 and DCHS1. Dissertation, LMU München: Medizinische Fakultät
... Organoids can be derived from adult stem cells, as has been demonstrated, for instance, for intestinal organoids, but a lot of protocols for the generation of organoids make use of embryonic stem cells. Using these ... See full document
116
Blood pressure signature genes and blood pressure response to thiazide diuretics: results from the PEAR and PEAR-2 studies
... performed differential expression ana- lysis using alternative tools in order to adjust the expres- sion levels for age, sex and baseline diastolic BP because we observed, for these variables, statistically ... See full document
9
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