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Sample GSM4557340 Query DataSets for GSM4557340
Status Public on May 07, 2021
Title PBS_HFD
Sample type SRA
 
Source name PBS_HFD_dorsal skin
Organism Mus musculus
Characteristics strain: B6
Sex: male
treatment: 48 hours post-mock-infection
diet: 60% high fat diet
tissue: Dorsal skin
Growth protocol N/A. Primary cells were used in this study.
Extracted molecule total RNA
Extraction protocol Single cells were isolated as previously described (Guerrero-Juarez, et al. Nat Commun. 2019)
Single cells were captured using the Chromium Platform (10X Genomics) and libraries were generated using Single Cell 3’ v3 chemistry. Cell capture, library preparation, quality control, and sequencing was performed at the UCI Genomics High Throughput Facility at the University of California, Irvine.
Single Cell 3’ v3 chemistry - 10X Genomics
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description mRNA from single cells
Data processing Transcripts from mice were mapped to the reference genome (GRCm38.93/mm10) using Cell Ranger Version 3.0.2
Quality control of all data sets was performed using Seurat (Version 3.0.0)
Analysis of all data sets was performed using Seurat (Version 3.0.0)
Genome_build: mm10
Genome_build: GRCm38.39
Supplementary_files_format_and_content: Seurat output
 
Submission date May 17, 2020
Last update date May 09, 2021
Contact name Maksim V Plikus
E-mail(s) plikus@uci.edu
Phone 949-824-1260
Organization name University of California, Irvine
Department Developmental and Cell Biology
Street address 845 Health Sciences Road
City Irvine
State/province California
ZIP/Postal code 92697
Country USA
 
Platform ID GPL21103
Series (1)
GSE150729 Diet-induced obesity promotes infection by impairment of the innate antimicrobial defense function of dermal adipocyte progenitors
Relations
BioSample SAMN14943472
SRA SRX8356235

Supplementary file Size Download File type/resource
GSM4557340_PBS_HFD_barcodes.tsv.gz 7.4 Kb (ftp)(http) TSV
GSM4557340_PBS_HFD_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSM4557340_PBS_HFD_matrix.mtx.gz 9.2 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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