|
| Status |
Public on Sep 15, 2024 |
| Title |
VM13, scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Blood
disease: Vestibular Migraine
cell type: PBMC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PBMCs were thawed and diluted in RPMI + 10% FBS, and cells were counted. To eliminate granulocytes with extracellular DNA, we sorted cells stained in CD66. We continued to isolate the nuclei from a million cells per sample. Briefly, we centrifuged cells (300rcf 5min 4C). The supernatant was removed, replaced with 1 mL refrigerated lysis buffer, and incubated for 3 min before resuspension. The nuclei were centrifuged again (500 rcf, 4°C, 5 min). The pellet was resuspended in 1 mL Diluted Nuclei Buffer and passed through a 40 μm cell strainer. All steps were performed on ice. Nuclei were stained and counted. Nuclei were collected into 10% BSA. 1 U/mL RNase inhibitor (Sigma–Aldrich, 03335402001) was added to all final solutions
RNA libraries were generated from amplified cDNA. Pair-end sequencing for the 24 samples was performed by using a Hiseq X Illumina sequencing platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Five |
| |
|
| Description |
10 X Genomics
|
| Data processing |
The cellranger-arc mkfastq.gz function from Cell Ranger ARC V.2.0.0 was used to demultiplex Illumina’s base calling files (BCL) into a fastq.gz format for downstream analysis. FASTAQ files were analyzed using Cell Ranger ARC v.2.0.2 and aligned with GRCh38 for the human genome reference, as per 10x Genomics guidelines to generate a filtered matrix file for downstream analysis.
Assembly: GRch38
Supplementary files format and content: H5 files
|
| |
|
| Submission date |
Jun 05, 2024 |
| Last update date |
Sep 15, 2024 |
| Contact name |
Jose Antonio Lopez-Escamez |
| E-mail(s) |
jose.lopezescamez@sydney.edu.au
|
| Phone |
61423066010
|
| Organization name |
The University of Sydney
|
| Department |
Faculty of Medicine & Health, School of Medical Sciences, The Kolling Institute
|
| Lab |
Meniere Disease Neuroscience Lab
|
| Street address |
10 Westbourne St
|
| City |
St Leonards |
| State/province |
NSW |
| ZIP/Postal code |
2064 |
| Country |
Australia |
| |
|
| Platform ID |
GPL33758 |
| Series (1) |
| GSE269117 |
Multiomic-based Immune Response Profiling in Migraine, Vestibular Migraine and Meniere's Disease |
|
| Relations |
| BioSample |
SAMN41686682 |
| SRA |
SRX24807790 |
