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Sample GSM4291553 Query DataSets for GSM4291553
Status Public on Jun 21, 2021
Title PD_4_VTA
Sample type SRA
 
Source name ventral tegmental area
Organism Homo sapiens
Characteristics case number (refer to table in paper): 52
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 SAMN13955403
SRA SRX9659330

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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