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Sample GSM5558483 Query DataSets for GSM5558483
Status Public on Aug 31, 2022
Title CoVinh_1
Sample type SRA
Source name AT2_organoids
Organism Homo sapiens
Characteristics cell_origin: AO24
infection: mock
tretament: CTR
Treatment protocol Organoid fragments were either mock-infected or challenged with SARS-CoV-2 (MOI 1, ) Munich/2020/984 strain). After incubation at 37° and 5 % CO2 for 30 min, medium with the respective inhibitor or carrier (PH-797804, VX-702, or DMSO only) was added.
Growth protocol For generation of adult stem cell derived lung organoids, primary cells were isolated from healthy parts of distal lung tissue obtained from lung cancer patients undergoing tumor resection surgery, cells were FACS sorted, counted and seeded in the extracellular matrix substitute. Organoids were kept in an incubator at 37°C, 5 % CO2. Upon growth for 2-3 weeks, the organoids were expanded by enzymatic digestion. Mature human lung organoids were collected on ice to remove remaining matrix.
Extracted molecule total RNA
Extraction protocol For total RNA isolation, the RNeasy Plus Mini Kit (Qiagen) was used according to the manufacturer`s instructions. Organoids were released from Cultrex with cold PBS, pelleted, and resuspended by vortexing in 350 μl RLT lysis buffer supplemented with β-mercaptoethanol. RNA was eluted in 30 µl water.
PolyA+RNA was purified  from 200 ng total RNA using Poly(A) mRNA Magnetic Isolation module Kit (NEB E7490L, New England Biolabs). The RNA Sequencing library was prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs).
The libraries were sequenced on Illumina Nextseq 2000 using NextSeq2000 P3 Reagent Kit (200 cycles, paired end run 2x 111 bp) with an average of 74.2 M reads per RNA sample.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
Data processing Reads were quality checked with package FastQC (version 0.11.4,), then trimmed using Trimgalore (version 0.4.4) with default settings.
Trimmed reads were mapped to human genome ENSEMBL hg38 release 91 and to CoV-2 genome EPI_ISL_463008_Cov2_AF, using STAR aligner (Dobin and Gingeras, 2015) with default settings.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)). Raw counts were then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)).
Genome_build: ENSMBL human hg38 release 91 genome and CoV-2 genome EPI_ISL_463008_Cov2_AF
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample.
Submission date Sep 06, 2021
Last update date Aug 31, 2022
Contact name Klaus Schughart
Phone +49-159-0483-7911
Organization name University Münster
Department Virology
Street address Von-Esmarch-Str 56
City Münster
ZIP/Postal code 48149
Country Germany
Platform ID GPL30173
Series (1)
GSE183507 Human lung AT2 cell organoids infected with CoV-2, treated with inhibitors
BioSample SAMN21242933
SRA SRX12024506

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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