NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5530744 Query DataSets for GSM5530744
Status Public on Aug 27, 2021
Title Control Media - D42B
Sample type SRA
 
Source name control media
Organism blank sample
Characteristics treatment: Control Media - D42B
Treatment protocol Retinal organoid EVs from D42 were added to 6-well plates (78ug/well) containing (1.2*105 hRPCs/well) and incubated at 37°C. A second EV concentration (78ug/well) was added to each well at 48hrs and the experiment continued to 96hrs.
Growth protocol hiPSC-derived 3D retinal organoids were generated and maintained in culture as previously described [10].
human retinal progenitor cells were culutre expanded at 37C
Extracted molecule total RNA
Extraction protocol Exosomal RNA was isolated from samples 1-3, 9-11 using the RNA Isolation Midi Kit (Cat# 60800)
Total RNA was isolated for RNA seq using a RNeasy Mini Kit (Cat# 74104, Qiagen) according to the supplier’s protocol.
Barcoded total transcriptome RNA libraries were prepared by Ion Total RNA-Seq kit v2 (cat#4475936, Ion Torrent, ThermoFisher Scientific) according to manufacturer’s protocols.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina MiSeq
 
Data processing The pooled smalRNA library was sequenced on Illumina Miseq using v3 reagrents by Norgen biotek Corp
A small RNA expression profile was generated from the resulting FASTQ files using the exceRpt small RNA-seq pipeline
RNA sequencing was done using Ion PI Hi-Q OT2 200 Kit, with Ion PI Chip Kit v3
Basecalling in Proton runs used Torrent Suite with filtering for subthreshold reads and adapter sequence trimming
subopimal sequences were removed from FASTQ data by FASTX-Toolkit
Total transcriptome reads were aligned to human genome reference with Proton RNAseq Analysis Plugin tool v5.2.0.5
Genome_build: hg19(RNAseq) hg38(smallRNAseq)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
 
Submission date Aug 20, 2021
Last update date Aug 27, 2021
Contact name Stephen Redenti
E-mail(s) stephen.redenti@lehman.cuny.edu
Phone 6468725363
Organization name Lehman College, CUNY
Lab Science Hall 3402
Street address Biology Dept. , 250 Bedford Park Blvd.
City Bronx
State/province NY
ZIP/Postal code 10468
Country USA
 
Platform ID GPL27039
Series (1)
GSE182520 Human retinal organoids release extracellular vesicles that regulate gene expression in target human retinal progenitors
Relations
BioSample SAMN20886724
SRA SRX11837532

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap