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Sample GSM6468130 Query DataSets for GSM6468130
Status Public on Mar 01, 2023
Title Ana_S2
Sample type SRA
Source name Mouse back skin
Organism Mus musculus
Characteristics strain: C57BL/6;CD1
tissue: Skin
age: Post natal day 32
genotype: wild type
cell line: VE-cadherin+ lineages
treatment: none
Extracted molecule total RNA
Extraction protocol The VE-cadherin+ cells were labeled with tdTomato by injecting tamoxifen (200 μg/g) at postnatal day (PD)17, and dorsal skin was collected at PD20, PD25 and PD32. The dorsal skin was digested in collagenase and Dispase mixture as previously described (Chovatiya et al., 2021). The dead cells were removed by LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit (ThermoFisher). FACS Aria (BD Biosciences) was used for the cell sorting.
Single-cell 3′ cDNA libraries were generated using Chromium Single Cell 3′ gel bead and library Kit v3.
Libraries were generated following the manufacturer’s protocols (10x Genomics).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description tdTomato+ cells were FACS sorted from back skin of PD32 (anagen) tdTomato;Cdh5-CreERT2;Krt14-H2BGFP mice, barcoded single-cell 3′ cDNA libraries were generated using Chromium Single Cell 3′ gel bead and library Kit v3 (10x Genomics) and sequenced using an Illumina NextSeq-500.
Data processing 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 an expression matrix that was further analyzed in R using the Seurat package version 4.0
Principle Component Analysis (PCA) was performed on the gene expression matrix using the least number of principal components (PCs) that could be used to explain the majority of the variance in the data
The PCA embeddings were used by Harmony to integrated the datasets. Unsupervised shared nearest neighbor (SNN) clustering was done on the Harmony integrated Seurat object
Assembly: mm10-2020-A
Supplementary files format and content: feature.tsv, barcode.tsv and matrix.mtx files for each sample
Submission date Aug 16, 2022
Last update date Mar 01, 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
Platform ID GPL19057
Series (1)
GSE211381 "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"
BioSample SAMN30349019
SRA SRX17104650

Supplementary file Size Download File type/resource
GSM6468130_WT_Ana_S2_barcodes.tsv.gz 28.6 Kb (ftp)(http) TSV
GSM6468130_WT_Ana_S2_features.tsv.gz 254.1 Kb (ftp)(http) TSV
GSM6468130_WT_Ana_S2_matrix.mtx.gz 32.1 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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