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Sample GSM6341644 Query DataSets for GSM6341644
Status Public on Aug 22, 2022
Title 160322_RNA1B_1
Sample type SRA
 
Source name transcriptome of blood of twin with parkinson 1 — replication 1
Organism Homo sapiens
Characteristics tissue: blood
batch: Batch 1
parkinson status: PD
Extracted molecule polyA RNA
Extraction protocol Total RNA isolation was conducted using a Direct-Zol RNA Mini-Prep Kit (ZymoResearch) according to the manufacturer's recommendations. The concentration of total RNA isolated was measured using a Quant-iT RNA BR Assay Kit and a Qubit fluorimeter (Invitrogen). RNA quality was monitored using an Experion automated electrophoresis system (Bio-Rad Laboratories).
Poly-a fraction of RNA was extracted from total RNA for RNA-seq. Sequencing libraries were prepared using NEBNext® mRNA Library Perp Reagent Set (NEB, USA). Sequencing was performed using HiSeq1500 (Illumina, USA), obtaining no less then 15 mln. reads of 50 length per library.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing 3 different pipelines were used in the process of data processing.
Fastq files for each sample were aligned to the GRCh38 genome (Gencode, release 37) using RSEM.
Ambiguous and low-quality bases were removed from the files obtained during the FASTQ sequencing process. Removal was done with AdapterRemoval V2. The trimmed files were aligned to the human reference genome GRCH38 and GRCH38.92 gene annotation using RSEM with rsem-prepare-reference and rsem-calculate-expression commands and the -star option to also generate STAR indices⁠.
Assembly: GRCH38
Supplementary files format and content: Processed data files are generated by RSEM and contain normalized and raw per gene counts.
 
Submission date Jul 17, 2022
Last update date Oct 23, 2023
Contact name Ivan Nikolaevitch Vlasov
E-mail(s) invlasov@mail.ru
Organization name Institute of Molecular Genetics of National Research Centre «Kurchatov Institute»
Lab Laboratory of Molecular Genetics of Hereditary Disease
Street address Akademika Kurchatova square, 2
City Moscow
ZIP/Postal code 123182
Country Russia
 
Platform ID GPL18460
Series (1)
GSE208347 Transcriptome Profiling Reveals Differential Expression of Circadian Behavior Genes in Peripheral Blood of Monozygotic Twins Discordant for Parkinson's Disease
Relations
BioSample SAMN29786943
SRA SRX16311488

Supplementary file Size Download File type/resource
GSM6341644_160322_HSGA.Slom_RNA_2016.RNA1.genes.results.txt.gz 2.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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