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Sample GSM5329117 Query DataSets for GSM5329117
Status Public on Jan 01, 2022
Title 24hpi - mock - replicate 3
Sample type SRA
 
Source name retinal organoid
Organism Homo sapiens
Characteristics tissue type: Retinal organoids derived from Gibco episomal iPSC line A18945
treatment: Control
incubation period: 24h
day of organoid differentiation: 80
Treatment protocol Triplicates infected with SARS-CoV-2 and incubated for 24 and 96 hours
Growth protocol Retinal organoid generation (based on Capowski et al. 2019)
Extracted molecule total RNA
Extraction protocol TRIzol® reagent according manufacturer´s recommended protocol
NEBNext® Ultra TM II RNA Library Prep kit for Illumina®
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
 
Description 24m3
Data processing Samples were demultiplexed usign the Illumina software bcl2fastq v2.20.0
Alignment to a customized reference concatenation of human and SARS-CoV-2 genomes was done using STAR v2.7.7a
A table of read counts per gene was obtained with STAR v2.7.7a and further processing was done in the statistical software environment R v4.0.3
Genome_build: GRCh38.p13 + NC_045512.2
Supplementary_files_format_and_content: Comma Separated Values (csv) matrix file of raw counts per gene for each sample
 
Submission date May 21, 2021
Last update date Jan 01, 2022
Contact name Hans R Schöller
E-mail(s) office-schoeler@mpi-muenster.mpg.de
Organization name Max Planck Institute for Molecular Biomedicine
Department Cell and Developmental Biology
Street address Roentgenstrasse 20
City Muenster
State/province NRW
ZIP/Postal code 48149
Country Germany
 
Platform ID GPL30173
Series (1)
GSE174843 SARS-CoV-2 infects and replicates in photoreceptor and retinal ganglion cells of human retinal organoids
Relations
BioSample SAMN19299278
SRA SRX10957033

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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