|
| Status |
Public on Feb 01, 2020 |
| Title |
PD10-1 |
| Sample type |
SRA |
| |
|
| Source name |
Putamen
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain
age: 71
Sex: Male
pmi: 23.5
rin: 7.3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole brains were slabbed and frozen at -80 °C. RNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen; #80224).
300 ng RNA per sample was used as inpt for library preparation using TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold rRNA Removal Kit (Illumina; #RS-122-2303).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Data were trimmed using Trimmomatic v. 0.38 in paired-end mode (PE) including clipping Illumina adapter sequences (ILLUMINACLIP) using the following specifications: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed data were aligned to GRCh38 release 94, thereby creating BAM files, using STAR v. 2.5.3a with genome index created using --sjdbOverhang 100
A count table was produced for aligned data using summarizeOverlaps from GenomicAlignments in R v. 3.5.0 using the following specifications: mode="Union", singleEnd=FALSE, ignore.strand=FALSE, fragments=TRUE
Genome_build: GRCh38 rel. 94
Supplementary_files_format_and_content: A tab-delimited text file containing raw gene counts per sample.
|
| |
|
| Submission date |
Jul 17, 2019 |
| Last update date |
Feb 01, 2020 |
| Contact name |
Rasmus Rydbirk |
| E-mail(s) |
rasmus.rydbirk@regionh.dk
|
| Phone |
+4528252902
|
| Organization name |
Bispebjerg-Frederiksberg Hospital
|
| Department |
Department of Neurology
|
| Lab |
Resarch Laboratory for Stereology and Neuroscience
|
| Street address |
Nielsine Nielsens Vej 6B, stair 11B, 2nd Floor
|
| City |
Copenhagen NW |
| State/province |
Please Select |
| ZIP/Postal code |
2400 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE134390 |
RNA-seq in putamen of Parkinson's disease patients |
|
| Relations |
| SRA |
SRX6454838 |
| BioSample |
SAMN12306274 |
