|
| Status |
Public on Jul 05, 2022 |
| Title |
BS_NonLrcRep2 |
| Sample type |
SRA |
| |
|
| Source name |
Back skin IFE
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6;BL6
tissue/cell type: Back skin IFE
age: Post natal day 47
genotype: wild type (K5-tTA x pTRE-H2BGFP)
|
| Treatment protocol |
Mice were fed with doxy chow for 2 or 3 weeks before harvest.
|
| Growth protocol |
None
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Interfollicular epidermis was FACS sorted using alpha6-integrin+ and Sca1+ staining and doxycycline inducible K5tta 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 single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Interfollicular epidermis was FACS sorted using alpha6-integrin+ and Sca1+ staining and doxycycline inducible K5tta 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
Assembly: mm10-3.0.0
Supplementary files format and content: feature.tsv, barcode.tsv and matrix.mtx files for each sample
|
| |
|
| Submission date |
Jun 09, 2022 |
| Last update date |
Jul 05, 2022 |
| Contact name |
Sangeeta Ghuwalewala |
| E-mail(s) |
[email protected]
|
| Phone |
6072796894
|
| Organization name |
Cornell University
|
| Department |
Molecular Biology and Genetics
|
| Lab |
Tudorita Tumbar
|
| Street address |
107 Biotechology Building 526 Campus Road
|
| City |
ITHACA |
| State/province |
New York |
| ZIP/Postal code |
14850 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE205745 |
Epidermal basal domains organization highlights skin robustness to environmental exposure [scRNA-seq] |
| GSE205746 |
Epidermal basal domains organization highlights skin robustness to environmental exposure. |
|
| Relations |
| BioSample |
SAMN28934817 |
| SRA |
SRX15645053 |
