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Sample GSM5242609 Query DataSets for GSM5242609
Status Public on Mar 03, 2023
Title AD4_Thioridazine
Sample type SRA
 
Source name retinal organoids
Organism Homo sapiens
Characteristics tissue: retinal organoids
treatment: Thioridazine (135uM)
Treatment protocol drug exposure for 24 hours (Sildenafil for 7 days)
Growth protocol adaped protocol based on Kuwahara et al., 2015
Extracted molecule polyA RNA
Extraction protocol Retinal organoids (day 200) were dissociated to single cells using the Neurosphere Dissociation kit (P) (Miltenyi Biotech) according to the manufacturer’s protocol
Chromium Single Cell 3′ Library & Gel Bead Kit, version 3 (10x Genomics)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description counts.txt
annotation.txt
embeddings.txt
Data processing scRNAseq samples were de-multiplexed and aligned to human reference genome GRCh38 before being quantified using CellRanger version 3.0
Quality control filtering was applied to remove any cells where fewer than 1000 reads or 500 genes or greater than 15% mitochondrial reads.
Genome_build: GRCh38
Supplementary_files_format_and_content: Expression matrix, cell annotations and UMAP embeddings
 
Submission date Apr 15, 2021
Last update date Mar 03, 2023
Contact name Majlinda Lako
Organization name Newcastle University
Department Institute of Genetic Medicine and Institute for Ageing
Street address International Centre for Life, Central Parkway
City Newcastle Upon Tyne
ZIP/Postal code NE1 3 BZ
Country United Kingdom
 
Platform ID GPL24676
Series (1)
GSE172138 Retinal organoids provide a suitable tool for toxicological drug screening – a comprehensive study validating well-known drug effects on retinal organoids
Relations
BioSample SAMN18747368
SRA SRX10606150

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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