|
| Status |
Public on Nov 21, 2023 |
| Title |
MES, Injury_D21 |
| Sample type |
SRA |
| |
|
| Source name |
sciatic nerve
|
| Organism |
Mus musculus |
| Characteristics |
tissue: sciatic nerve
cell type: FACS-isolated peripheral nerve MES
reporter: Pdgfrb-TdTomato
condition: 21 days post injury (dpi)
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nerves were freshly harvested in F12 medium, pooled, finely chopped and incubated in dissociation buffer (Collegenase Type II 50ul/ml, Hyaluyronidase 1:50, DNAse 2.5μg/ml) in DMEM and incubated on rotor at 37C with intermittent mixing for 30 min. Enzymes were inactivated with 5% FBS+ 2mM EDTA in PBS w/o Ca2+, Mg2+. Myelin-removal beads were used for the intact nerve sample. Cell suspension was passed through cell strainer and resuspended in 2% BSA PBS w/o Ca2+, Mg2+ and TdTomato + cells were FACS purified.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Sample 1
Pdgfrb-TdTomato+ cells at 21dpi
|
| Data processing |
Raw sequencing data was demultiplexed with the mkfastq application (CellRanger v6.1.2) (10X).
A reference genome was prepared from mm10, GENCODE Mus musculus basic gene annotation (version M16), and TdTomato exogenous transgene following 10x Genomics' instructions for custom genome builds (cellranger mkref).
The libraries were then mapped to the custom reference genome using CellRanger (v3.0.2) (10× Genomics).
The raw gene expression matrices generated with CellRanger (cellranger count) were analysed with the Seurat R package (v4.0.1)
Assembly: mm10, GRCm38, GENCODE Mus musculus basic gene annotation (version M16)
Supplementary files format and content: Filtered feature-barcode matrices produced by CellRanger (cellranger count) and CellType metadata.
|
| |
|
| Submission date |
May 24, 2023 |
| Last update date |
Nov 21, 2023 |
| Contact name |
Aurora Maurizio |
| E-mail(s) |
maurizio.aurora@hsr.it, auroramaurizio1@gmail.com
|
| Organization name |
IRCCS Ospedale San Raffaele
|
| Department |
Center for Omics Sciences (COSR)
|
| Street address |
Via Olgettina, 60
|
| City |
Milano MI |
| State/province |
Italy |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE233359 |
Structured wound angiogenesis instructs mesenchymal barrier compartments in the regenerating nerve [scRNASeq_Pdgfrb] |
| GSE233360 |
Structured wound angiogenesis instructs mesenchymal barrier compartments in the regenerating nerve |
|
| Relations |
| BioSample |
SAMN35356785 |
| SRA |
SRX20505932 |
