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Series GSE211381 Query DataSets for GSE211381
Status Public on Mar 01, 2023
Title "Alk1 acts in non-endothelial VE-cadherin+ perineurial cells to maintain nerve branching during hair homeostasis" and "Blood endothelial ALK1-BMP4 signaling axis regulates adult hair follicle stem cell activation"
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: To comprehensively characterize VE-cadherin expressing lineages during adult skin homeostasis, to dissect their population-specific transcriptomic heterogeneity, and to investigate role of Alk1 in these linegease in vivo.
Methods: We performed 10x genomics single-cell RNA sequencing (scRNA-seq) of FACS sorted tdTomato+ cells from tdTomato;Cdh5-CreERT2;Krt14-H2BGFP mice (for WT) or Alk1 flox flox;tdTomato;Cdh5-CreERT2 (For Alk1KO) back skin at indicated stage/genotype. FACS purified tdTomato+ single-cell suspension was processed for the barcoded single-cell 3′ cDNA libraries generation using Chromium Single Cell 3′ gel bead and library Kit v3. The final libraries were quantified using Agilent Bioanalyzer high sensitivity DNA chip and sequenced using an Illumina NextSeq-500. The raw data files were demultiplexed to generate the sample-specific FASTQ files, which were aligned to the mouse reference genome (mm10-2020-A) using the 10x Genomics Cell Ranger pipeline (v6.0.1). The raw scRNA-seq data was processed using Cell Ranger from the 10x platform to generate expression matrix for each sample that was further analyzed in R using the Seurat package version 4.0. Only high-quality cells that had between 200 and 5000 genes expressed and had under 10% of the UMIs mapped to mitochondrial genes were retained for further analysis.
Results: We obtained more than 2000 high quality cells at each stage/genotype for further analysis by Seurat pipeline
Conclusions: Obtained high quality single cell transcriptomic data to dissect cellular and molecular heterogeneity of VE-cadherin expressing endothelial and non-endothelial lineages in adult mouse back skin.
Overall design Single cell RNA-seq profiles of sorted VE-cadherin+ lineages at telogen and anagen stages from wild type (WT) mice and telogen stage of Alk1 knockout (KO) mice
Contributor(s) Tudorita T, Gopal C, Kefei Nina L
Citation(s) 37699906, 36994549
Submission date Aug 16, 2022
Last update date Sep 13, 2023
Contact name Tudorita Tumbar
Organization name Cornell University
Department Molecular biology and genetics
Lab Tumbar Lab
Street address 526 Campus Rd
City Ithaca
State/province NY
ZIP/Postal code 14853
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (6)
GSM6468127 Telo_S1
GSM6468128 Telo_S2
GSM6468129 Ana_S1
BioProject PRJNA870073

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
GSE211381_RAW.tar 153.0 Mb (http)(custom) TAR (of MTX, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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