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Sample GSM3154502 Query DataSets for GSM3154502
Status Public on Jun 21, 2021
Title case15_Substantia_Nigra_compacta
Sample type SRA
 
Source name midbrain dopamine neurons
Organism Homo sapiens
Characteristics case number (refer to table in paper): 15
disease status: Control
neurons: SNc
Extracted molecule polyA 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 HiSeq 2000
 
Description GEO_RPKMS_LCMseq_human_SNc_VTA.txt
Data processing Base-calling using Illumina Cassava 1.7
Alignment to the human genome (hg38) performed using STAR with default parameters. RPKM were estimated using ¨rpkmforgenes¨ (Ramsköld et al., 2009).
For cases having more than 1 replicate per group, corresponding samples were averaged before the analysis so that each Case have only 1 SNc and 1 VTA.
Differential gene expression analysis was performed on the read counts using DESeq version 1.16.1. Only genes with reads in at least one third of the samples or more were considered in the analysis.
Genome_build: hg38
Supplementary_files_format_and_content: One processed data file is added providing abundance measurements (RPKM) organized as a matrix for all samples (tab-delimited txt).
 
Submission date May 25, 2018
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 GPL11154
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 SAMN09260282
SRA SRX4124857

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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