|
| Status |
Public on Aug 22, 2022 |
| Title |
160322_RNA1K_3 |
| Sample type |
SRA |
| |
|
| Source name |
transcriptome of blood of twin control 1 — replication 3
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
batch: Batch 1
parkinson status: control
|
| 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 |
National Research Center «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 |
SAMN29786935 |
| SRA |
SRX16311496 |
