|
| Status |
Public on Jan 27, 2021 |
| Title |
SS2.16.225_B12 |
| Sample type |
SRA |
| |
|
| Source name |
dorsal root ganglion
|
| Organism |
Macaca mulatta |
| Characteristics |
animal id: C01
age(years): 5
region: Lumbar
gender: Female
cell identity: lowq/nonneuron
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Extracted DRGs were cut once longitudinally (along the nerve) followed by chopping into ~0.5 mm slices. Samples were enzymatically treated for 1 h at 37°C with triturating every 15 min. The resulting cell suspension was then run through 100 µm cell-strainers. 1 ml of 10% Optiprep was loaded under the cell suspension solution using a gel loading tip and centrifugated at 200g for 6 min with a low break. Supernatant was discarded, the cell pellet resuspended and run through a 10 µm strainer. The strainer was rinsed twice and cells were then collected by flushing the filter twice. The cells were kept on ice for 15-20 min, centrifuged for 3 min at 100 g and resuspended in 900 µl of filtered NMDG-SC/B27/12% optiprep and dispensed immediately into a WaferGen9600 Chip.
RNA libraries were prepared for sequencing using the Smart-Seq2 protocol (Picelli et al, Nat Protoc. 2014)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
SS2-16-225_expression_for_R.tab
|
| Data processing |
Read processing was essentially performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that no UMIs were analysed. and that the reads were not analysed without strand specificity and not trimmed before alignment.
Genome_build: Mmul10
Supplementary_files_format_and_content: Processed data includes raw UMI counts matrix with the assigned celltype clusters, where rows are geneIDs and columns cellIDs. Corresponding annotation text files, where rows are CellIDs and columns different annotation ( sample name, Celltype)
|
| |
|
| Submission date |
Jan 26, 2021 |
| Last update date |
Jan 28, 2021 |
| Contact name |
Sten Linnarsson |
| Organization name |
Karolinska Institutet
|
| Department |
Medical Biochemistry and Biophysics
|
| Lab |
Molecular Neurobiology
|
| Street address |
Scheeles väg 1
|
| City |
Stockholm |
| ZIP/Postal code |
171 65 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL19129 |
| Series (2) |
| GSE165553 |
Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain [SmartSeq2] |
| GSE165569 |
Single cell transcriptomics of primate sensory neurons identifies cell types associated with human chronic pain |
|
| Relations |
| BioSample |
SAMN17579168 |
| SRA |
SRX9941448 |
