|
Status |
Public on Nov 28, 2021 |
Title |
D4_day_16 |
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: alpha16
|
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 |
SAMN23456862 |
SRA |
SRX13234692 |