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| Status |
Public on Nov 15, 2020 |
| Title |
Non-myelinating Corneal Schwann Cells scRNA-seq |
| Sample type |
SRA |
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| Source name |
Central corneal tissue
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| Organism |
Oryctolagus cuniculus |
| Characteristics |
cell type: Nonmyelinating Corneal Schwann Cells
treatment: No treatment
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| Growth protocol |
New Zealand white rabbits (NCBI:txid9986; 3.2 to 4 kg; male; Envigo, Denver, PA)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Corneal buttons from central aspect of the tissue from young adult male rabbits (after mechanical removal of endothelial cell layer and trypsin digeston for partial removal of epithelium) were dissociated into single cell suspension, filtered, centrifuged , and resuspended in ice-cold 1X PBS with 0.05% BSA and immediately processed for scRNA-seq analysis.
scRNA libraries were prepared for sequencing using Chromium system (10x Genomics; (Zheng et al., 2017)) for droplet-based single cell library generation with v3 Chromium chemistry and processed for cDNA library construction and subsequent scRNA-seq analysis (Rheaume et al., 2018)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Illumina basecall files (*.bcl) were converted to FASTQs using CellRanger v3.0.1.
FASTQ files were then aligned to the rabbit reference genome (OryCun2, version 3.0.2) and transcriptome using the CellRanger v3.0.1 with default parameters, as described in (Zheng et al., 2017)).
total UMIs per cell were divided by the count depth of that cell and multiplied by the median count depth of the dataset; the result plus a pseudo-count of 1 was then log-transformed.
Differential expression was performed using Monocle3
Genome_build: OryCun2, version 3.0.2
Supplementary_files_format_and_content: Excel files include raw counts and normalized expression (NE)
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| Submission date |
Nov 14, 2020 |
| Last update date |
Nov 15, 2020 |
| Contact name |
Royce Mohan |
| E-mail(s) |
mohan@uchc.edu
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| Phone |
860 679 2020
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| Organization name |
University of Connecticut Health Center
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| Department |
Neuroscience
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| Lab |
L4023
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| Street address |
263 Farmington Avenue
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| City |
Farmington |
| State/province |
Connecticut |
| ZIP/Postal code |
06030-3401 |
| Country |
USA |
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| Platform ID |
GPL26786 |
| Series (1) |
| GSE161487 |
Corneal Nonmyelinating Schwann Cells Illuminated by Single Cell Transcriptomics and Visualized by Protein Biomarkers |
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| Relations |
| BioSample |
SAMN16796259 |
| SRA |
SRX9509172 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4908644_Corneal_Schwann_Counts.csv.gz |
115.1 Kb |
(ftp)(http) |
CSV |
| GSM4908644_Corneal_Schwann_Norm.csv.gz |
167.7 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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