NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5624887 Query DataSets for GSM5624887
Status Public on Jan 10, 2022
Title transcriptome of blood of patient with COVID-19 126Ca
Sample type SRA
 
Source name blood of patient with COVID-19 126 – replication 1
Organism Homo sapiens
Characteristics tissue: blood
batch: Batch 1
survival status: survived
sample extraction time: 12/8/2020 17:00
rna extraction time: 12/9/2020 13:20
age: 74
rin: 8.8
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 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)
GSE185863 Transcriptomic profiles revealed down regulation of low-density lipoprotein particle receptor activity pathway in survived from severe COVID-19-19.
Relations
BioSample SAMN22249193
SRA SRX12595833

Supplementary file Size Download File type/resource
GSM5624887_126Ca.tab.gz 293.8 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap