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Sample GSM3945651 Query DataSets for GSM3945651
Status Public on Feb 01, 2020
Title PD3-1
Sample type SRA
 
Source name Putamen
Organism Homo sapiens
Characteristics tissue: Brain
age: 70
Sex: Male
pmi: 24
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 SRX6454824
BioSample SAMN12306299

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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