|
| Status |
Public on Jan 10, 2022 |
| Title |
transcriptome of blood of patient with COVID-19 101Cb |
| Sample type |
SRA |
| |
|
| Source name |
blood of patient with COVID-19 101 – replication 2
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
batch: Batch 1
survival status: deceased
sample extraction time: 12/2/2020 18:00
rna extraction time: 12/3/2020 11:00
age: 63
rin: NA
|
| Extracted molecule |
total 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.
Pipeline 1 - Fastq files for each sample were aligned to the GRCh38 genome (Gencode, release 37) using HISAT2 (v2.6.1b) with default parameters. Quality control for each sample was performed by FastQC (v0.11.9) and RSeQC (v4.0.0). Counting reads was done using featureCounts.
Pipeline 2 - Human reference genome assembly GRCh38 (hg38) and gene model annotation files were downloaded from Gencode website (https://www.gencodegenes.org/human/) directly (release 37). Adapters were removed by Cutadapt (v3.4). HISAT2 (v2.2.1) [18] was used with default parameters to building of the index of the reference genome and mapping reads to genome. Quality control for each sample was performed by FastQC (v0.11.9) and RSeQC (v4.0.0). Counts the number of sequencing reads mapping to each gene after the alignment step was done using htseq-count function from HTSeq framework (v.0.6.1).
Pipeline 3 – 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.
Genome_build: GRCH38
Supplementary_files_format_and_content: Processed count files were obtained using each of 3 pipelines and contains 3 columns with respective pipeline counts.
|
| |
|
| Submission date |
Oct 13, 2021 |
| Last update date |
Jan 10, 2022 |
| 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) |
| GSE185863 |
Transcriptomic profiles revealed down regulation of low-density lipoprotein particle receptor activity pathway in survived from severe COVID-19-19. |
|
| Relations |
| BioSample |
SAMN22249189 |
| SRA |
SRX12595830 |
