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Sample GSM5704606 Query DataSets for GSM5704606
Status Public on Nov 28, 2021
Title D4_day_17
Sample type SRA
 
Source name healthy tissue from explanted lungs
Organism Homo sapiens
Characteristics cell type: primary human airway epithelial cells
gender: male
donor: 4
virus strain: na
ifn type: alpha17
Extracted molecule total RNA
Extraction protocol Total RNA was purified from hAECs using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions with preceding DNase I digestion with RNase-Free DNase Set (Qiagen). Quality and integrity of total RNA was controlled on 5200 Fragment Analyzer System (Agilent Technologies).
RNA sequencing library was generated from 50 ng total RNA using NEBNext® Single Cell/Low Input RNA Library to manufacture´s protocols.
The libraries were treated with Illumina Free Adapter Blocking and were sequenced on Illumina NovaSeq 6000 using NovaSeq 6000 S1 Reagent Kit (100 cycles, paired end run 2x 50 bp) with an average of 3 x107 reads per RNA sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description mislabelling during lib prep: day->IFN
Data processing RNA libraries were run on Illumina NovaSeq6000, basecalling was performed using Real-Time Analysis (RTA) v3.3.3
bcl files were converted to fastq files with bcl2fastq v2.20.0.422
Quality of fastq files was checked with CLC Genomics Workbench 20
FASTQ files of RNA sequencing files were imported into the Array Studio software v10.2.5.9 (QIAGEN, Cary, NC, USA) package for further data analysis.
All FASTQ files were aligned to the gene model Ensembl v96 and to the reference library Human B38 using the proprietary OmicSoft Aligner OSA62.
Genome_build: human NCBI genome build B38; Ensembl v96
Supplementary_files_format_and_content: xlsx
 
Submission date Nov 26, 2021
Last update date Nov 29, 2021
Contact name Daniel Todt
E-mail(s) daniel.todt@rub.de
Phone +492343222463
Organization name Ruhr University Bochum
Department Molecular & Medical Virology
Street address Universitätsstr. 150
City Bochum
ZIP/Postal code 44801
Country Germany
 
Platform ID GPL24676
Series (1)
GSE189613 Differential interferon-α immune signatures prevent SARS-CoV-2 infection
Relations
BioSample SAMN23456861
SRA SRX13234693

Supplementary file Size Download File type/resource
GSM5704606_D4_day_17_S28_001.xlsx 7.6 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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