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Series GSE214633 Query DataSets for GSE214633
Status Public on Oct 05, 2022
Title A flexible model for correlated count data, with application to analysis of gene expression differences in multi-condition experiments
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Detecting differences in gene expression is an important part of RNA sequencing (RNA-seq) experiments, and many statistical methods have been developed for this aim. Most differential expression analyses focus on comparing expression between two groups (e.g., treatment vs. control). But there is increasing interest in multi-condition differential expression analyses in which expression is measured in many conditions, and the aim is to accurately detect and estimate expression differences in all conditions. We show that directly modeling the RNA-seq counts in all conditions simultaneously, while also inferring how expression differences are shared across conditions, leads to greatly improved estimates of expression differences, particularly when the power to detect expression differences is low in the individual conditions (e.g., due to small sample sizes). We illustrate the potential of this new multi-condition differential expression analysis in analyzing data from a single-cell experiment for studying the effects of cytokine stimulation on gene expression. We call our new method “Poisson multivariate adaptive shrinkage,” and it is implemented in the R package poisson.mash.alpha, available at https://github.com/stephenslab/poisson.mash.alpha.
 
Overall design Droplet-based scRNA-seq on PBMCs from unstimulated mice and mice injected with various cytokines and chemokines.
 
Contributor(s) Chevrier N, Takahama M, Gruenbaum A
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Submission date Oct 02, 2022
Last update date Oct 05, 2022
Contact name Nicolas Chevrier
E-mail(s) nchevrier@uchicago.edu
Organization name The University of Chicago
Department Pritzker School of Molecular Engineering
Lab Nicolas Chevrier
Street address 5640 South Ellis Avenue
City Chicago
State/province Illinois
ZIP/Postal code 60637
Country USA
 
Platforms (1)
GPL21626 NextSeq 550 (Mus musculus)
Samples (50)
GSM6613401 PBMCs, CCL20_CXCL1, GEX
GSM6613402 PBMCs, CCL22_CXCL5, GEX
GSM6613403 PBMCs, CCL4_CCL11, GEX
Relations
BioProject PRJNA886428

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE214633_whole_cyto_annot.csv.gz 3.3 Mb (ftp)(http) CSV
GSE214633_whole_cyto_normalized.h5ad.gz 421.4 Mb (ftp)(http) H5AD
GSE214633_whole_cyto_raw.h5ad.gz 321.4 Mb (ftp)(http) H5AD
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Raw data are available in SRA
Processed data are available on Series record

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