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| Status |
Public on Mar 26, 2023 |
| Title |
P1-DRG |
| Sample type |
SRA |
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| Source name |
dorsal root ganglion
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
Sex: not determined
age: postnatal day 1
tissue/cell type: dorsal root ganglion
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| Growth protocol |
Primary culture of SCs was maintained in DMEM containing 10% fetal bovine serum (complete medium) at 37°C under humidified 5% CO2.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v3 (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols
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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 |
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria: MT% < 20%; Cell Gene Number < Median Gene Number * 2; Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples. Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes
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| Submission date |
Mar 27, 2020 |
| Last update date |
Mar 26, 2023 |
| Contact name |
Sheng Yi |
| E-mail(s) |
syi@ntu.edu.cn
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| Organization name |
Nantong University
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| Street address |
19 Qixiu Road
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| City |
Nantong |
| State/province |
Jiangsu, China |
| ZIP/Postal code |
226001 |
| Country |
China |
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| Platform ID |
GPL25947 |
| Series (1) |
| GSE147615 |
Single-cell RNA-seq reveals the difference between Schwann cells in dorsal root ganglion and sciatic nerve |
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| Relations |
| BioSample |
SAMN14466813 |
| SRA |
SRX8010178 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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