|
| Status |
Public on Jun 21, 2021 |
| Title |
PD_5_VTA |
| Sample type |
SRA |
| |
|
| Source name |
ventral tegmental area
|
| Organism |
Homo sapiens |
| Characteristics |
case number (refer to table in paper): 53
tissue: midbrain
brain region: ventral tegmental area
disease status: Parkinson disease
age group: 3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lysis buffer is directly added to the cells after laser capture. No RNA extraction is conducted. The cell lysate is direcly used for library preparation.
Libraries for RNA-seq were prepared by using SMART-seq2 combined with Tn5 tagementation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
reads aligned to human genome with transcriptome annotation (GRCh38, ensemble 93) using STAR (version 2.6.0a).
the count number was calculated by htseq-count (version 0.10.0),
the TPM was calculated by stringtie (version 1.3.4d)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read count values for each sample
|
| |
|
| Submission date |
Jan 31, 2020 |
| Last update date |
Jun 21, 2021 |
| Contact name |
Eva Hedlund |
| E-mail(s) |
eva.hedlund@dbb.su.se
|
| Phone |
0046761130911
|
| Organization name |
Stockholm University
|
| Department |
Department of Biochemistry and Biophysics
|
| Lab |
Hedlund
|
| Street address |
Svante Arrhenius v. 16C
|
| City |
Stockholm |
| ZIP/Postal code |
106 91 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE114918 |
RNAseq of human SNc and VTA midbrain dopamine neurons isolated from post mortem material of control subjects and Parkinson's Disease patients using laser capture microdisection. |
|
| Relations |
| BioSample |
SAMN13955402 |
| SRA |
SRX9659331 |
