[PDF] Top 20 SCALE: modeling allele specific gene expression by single cell RNA sequencing
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SCALE: modeling allele specific gene expression by single cell RNA sequencing
... coordinated expression between the two ...one allele is expressed in any cell, is also referred to as stochastic ME ...stem cell scRNA-seq study by Kim et ...a gene show correlated ... See full document
15
A comparison of automatic cell identification methods for single cell RNA sequencing data
... s. Cell-BLAST, however, takes more than 75 ...of cell populations in the ...and cell populations separately ...methods scale linearly with the number of genes. However, LDA does not ... See full document
19
Design and computational analysis of single cell RNA sequencing experiments
... global scale factors assume 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, ... See full document
14
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× ...The expression of these genes differed significantly between the two clusters (FDR < ... See full document
17
Splatter: simulation of single cell RNA sequencing data
... 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 library size ... See full document
15
Visualizing Allele Specific Expression In Single Cells
... H19 expression, suggesting that variability in methylation may underlie the heterogeneity in allele specific ...bisulfite sequencing in single cells, especially in combination with ... See full document
134
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 ...a specific cell subpop- ... See full document
14
Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis
... at single cell ...epithelial cell isolation, sorting and single cell RNA ...(Neurog3 expression >0) and negative for Ngn3 (no Neurog3 expression, non-EP ... See full document
16
Scalable microfluidics for single cell RNA printing and sequencing
... during cell lysis and RNA capture. Significant loss of RNA occurs in our arrays when cells are lysed in unsealed or even imperfectly sealed arrays due to rapid diffusion of RNA molecules ... See full document
16
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
Allele-specific transcriptional elongation regulates monoallelic expression of the IGF2BP1 gene
... monoallelic expression, we selected 12 genes located near one of the 293 CTCF/H3K9me3 sites (DIAPH1, FUS1, PKP1, ARFGAP2, PCDHGA, MTHFR, LAIR1, GPR3, ARMET, NPR1, NHLRC1 and IGF2BP1) to search lymphoblastoid ... See full document
16
An in vitro ES cell imprinting model shows that imprinted expression of the Igf2r gene arises from an allele specific expression bias
... Imprinted expression is generally interpreted as an epigenetic silencing event (Solter, ...Igf2r allele maintains persistent low-level expression despite the gain of DNA methylation and repressive ... See full document
12
Functional methylome analysis of human diabetic kidney disease
... the expression of TNF, we developed site-specific methylome editing via the dCas9-Tet1 ...in expression of TNF in dCas9-Tet1CD cells with pooled DMR sgRNAs (Figure ...5D). Single-guide ... 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 ...their gene number and UMI number. The threshold ... See full document
12
Single-Cell Gene Expression Variation as A Cell-Type Specific Trait: A Study of Mammalian Gene Expression Using Single-Cell RNA Sequencing
... of gene characteristics for use in bias ...bulk RNA sequencing (Zheng et ...As). RNA secondary structure may hinder biochemical reactions and we assigned a score for the average strength of ... See full document
136
Discovering Single Nucleotide Polymorphisms Regulating Human Gene Expression Using Allele Specific Expression from RNA-seq Data
... the RNA sequencing data of 77 lymphoblastoid cell lines (LCLs) derived from unrelated European individuals ...mapped RNA sequencing of the LCLs (Lappalainen et ...each allele in ... See full document
11
Generation of a non-small cell lung cancer transcriptome microarray
... 48. Li C, Wong WH: DNA-Chip Analyzer (dChip). In The analysis of gene expression data: methods and software Edited by: Parmigiani G, Garrett ES, Irizarry R, Zeger SL. Springer, New York; 2003:120-141. 49. ... See full document
12
Going the Distance: Optimizing RNA-Seq Strategies for Transcriptomic Analysis of Complex Viral Genomes
... raw sequencing data into lists of regulated genes supported by statistical significant values (P values) corrected for multiple ...of gene annotations for the organism(s) of ...standard RNA-Seq ... See full document
9
SCOPE Seq: a scalable technology for linking live cell imaging and single cell RNA sequencing
... protein expression and localization dynamics, organelle dynamics and distribution, morphological features, up- take of foreign objects, and biomolecular ...live cell imaging and microwell-based assays for ... See full document
5
PBMC fixation and processing for Chromium single cell RNA sequencing
... Droplet-based sequencing [7], it remains to be determined what happens to cells with freezing and thawing manipulation and in unfavorable temperature and medium ...during cell fixation and the steps that ... See full document
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