|
| Status |
Public on Jan 01, 2022 |
| Title |
96hpi - mock - replicate 2 |
| 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: 96h
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 |
96m2
|
| 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 |
SAMN19299273 |
| SRA |
SRX10957038 |
