|
| Status |
Public on Feb 01, 2024 |
| Title |
Sample 12-44-L002 [snRNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
brain (frontal cortex)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: brain (frontal cortex)
disease status: Healthy
genotype: APOE 3/3
age: 80
Sex: Female
treatment: nd apoe 33
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
snRNA-seq libraries were prepared from nuclei using the Chromium Next GEM Single Cell 3ʹ v.3.1 according to the manufacturer’s protocol (10x Genomics).
Nuclei were counted using with a TC20 Automated Cell Counter (Bio-Rad) and loaded into a 10x droplet generator at a concentration of 8,000 nuclei per sample. Thirteen pcr cycles were applied to generate cDNA, and 15 cycles for final library generation. The final snRNA-seq libraries were sequenced on a NovaSeq 6000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw gene counts were obtained by aligning reads to the hg38 genome (refdata-gex-GRCh38-2020-A) using CellRanger software (v.4.0.0) (10x Genomics). To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were also counted.
All subsequent analysis was implemented in Python (3.9.12) based on the Scanpy (1.9.1) single-cell data analysis package except when stated otherwise in the corresponfing manuscript.
assembly: hg38
|
| |
|
| Submission date |
Jan 25, 2024 |
| Last update date |
Feb 01, 2024 |
| Contact name |
Tony Wyss-Coray |
| Organization name |
Stanford University
|
| Department |
Neurology
|
| Street address |
290 Jane Stanford Way
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE254205 |
APOE4/4 is linked to damaging lipid droplets in Alzheimer's microglia |
|
| Relations |
| BioSample |
SAMN39609841 |
| SRA |
SRX23392017 |
