|
| Status |
Public on Sep 17, 2020 |
| Title |
IPD5 |
| Sample type |
SRA |
| |
|
| Source name |
IPD_midbrain
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Idiopathic Parkinson's disease (IPD)
age at death: 79
Sex: M
pmi (h): 25
tissue: Midbrain
molecule subtype: nuclear RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The left hemi-midbrain was removed. This midbrain block was then snap-frozen at -120°C and cryosectioned at ~15 μm thickness in the transverse plane. The resulting sections were stored at -80°C. Addapted 10x Genomics protocol for nuclei isolation was used to extract the nuclei. Sorted nuclei were processed using the Chromium Next GEM Single Cell 3’ Kit v3.1 to generate the cDNA libraries
The sample was prepared for sequencing using standard Illumina protocol and sequenced on Illumina NovaSeq 6000-S2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
L18123_1_IPD5_S7
|
| Data processing |
Cell Ranger v3 mkfastq
Cell Ranger v3 count
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw UMI count matrix, gene metdata and cell metadata
|
| |
|
| Submission date |
Sep 10, 2020 |
| Last update date |
Sep 17, 2020 |
| Contact name |
Malte Spielmann |
| E-mail(s) |
spielman@molgen.mpg.de
|
| Organization name |
Max Planck Institute for Molecular Genetics
|
| Street address |
Ihnestraße 63
|
| City |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE157783 |
Single cell atlas of the human midbrain reveals cell state specific to Parkinson’s disease |
|
| Relations |
| BioSample |
SAMN16093811 |
| SRA |
SRX9104636 |
