|
| Status |
Public on Mar 01, 2023 |
| Title |
Alk1KO_S1 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse back skin
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Skin
age: Post natal day 25
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 PD25 (telogen) Alk1 flox/flox;tdTomato;Cdh5-CreERT2 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 |
| 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) |
| 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" |
|
| Relations |
| BioSample |
SAMN30349018 |
| SRA |
SRX17104651 |
