|
| Status |
Public on Apr 14, 2021 |
| Title |
hair follicle stem cells at anagen, scRNA-Seq, Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Hair follicles
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6;CD1
tissue: Skin
age: Post natal day 32
genotype: wild type
cell type: Hair follicle stem cells
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hair follicle stem cells were FACS sorte using CD34 and K14 promoter driven H2BGFP
Single-cell 3′ cDNA libraries generation using Chromium Single Cell 3′ gel bead and library Kit v3, following the manufacturer’s protocols (10x Genomics)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Hair follicle stem cells were FACS sorted using CD34 and K14 promoter driven H2BGFP
|
| Data processing |
The raw data files were demultiplexed to generate the sample-specific FASTQ files, which were aligned to the mouse reference genome (mm10-3.0.0) using the 10X Genomics Cell Ranger pipeline (v3.1.0)
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 3.1
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
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: feature.tsv, barcode.tsv and matrix.mtx files for each sample
|
| |
|
| Submission date |
Nov 30, 2020 |
| Last update date |
Apr 14, 2021 |
| Contact name |
Tudorita Tumbar |
| E-mail(s) |
tt252@cornell.edu
|
| 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) |
| GSE162333 |
High resolution single cell transcriptomics reveals heterogeneity of self-renewing hair follicle stem cells |
|
| Relations |
| BioSample |
SAMN16955674 |
| SRA |
SRX9604968 |
