|
| Status |
Public on Aug 26, 2024 |
| Title |
Sublibrary 8 |
| Sample type |
SRA |
| |
|
| Source name |
hiPSC sensory neurons
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: hiPSC sensory neurons
cell line: derived from ANAT001
genotype: WT Female
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Adhered sensory neurons were washed from cell culture plates with PBS and centrifuged at 500g for 5 minutes at 4°C to form a pellet. Following pellet aggregation, cells were lyzed and nuclei were isolated according to manufacture protocol for the Nuclei Isolation Kit: Nuclei EZ Prep (Sigma-Aldrich). Nuclei were then passed through a 40 µm strainer to remove cellular debris and fixed according to manufacturer protocol within the Parse Biosciences fixation kit. Fixed nuclei from each collection point were stored at -80°C in a Mr. Frosty Freezing Container (Thermo Scientific).
Sequencing libraries were generated using the Evercode Whole Transcriptome 100k v1 Kit (Parse Biosciences). Each sample used 12 of the available 48 wells of the library preparation kit, and individual nuclei were distributed evenly among wells.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Demultiplexing of sequencing libraries was performed using the Parse Biosciences Pipeline (v1.0.5p) to generate count matrices for individual samples. All downstream analysis including quality control, dimensional reduction, leiden clustering, and differential gene expression was performed within the Scanpy package (v1.9.2).
Assembly: GRCh38
Supplementary files format and content: h5ad
|
| |
|
| Submission date |
Aug 21, 2024 |
| Last update date |
Aug 26, 2024 |
| Contact name |
Vincent Truong |
| E-mail(s) |
vince@anatomic.com
|
| Phone |
6122086735
|
| Organization name |
Anatomic Incorporated
|
| Street address |
2112 Broadway ST NE, STE 135
|
| City |
Minneapolis |
| State/province |
MINNESOTA |
| ZIP/Postal code |
55413 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE275413 |
Transcriptomic analysis and high throughput functional characterization of human induced pluripotent stem cell derived sensory neurons (scRNA-Seq) |
|
| Relations |
| BioSample |
SAMN43291975 |
| SRA |
SRX25793537 |
