|
| Status |
Public on Aug 27, 2021 |
| Title |
Control Media - D63/D90B |
| Sample type |
SRA |
| |
|
| Source name |
control media
|
| Organism |
blank sample |
| Characteristics |
treatment: Control Media - D63/D90B
|
| 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 4,5, 12,13 using the RNA Isolation Maxi Kit (Cat#60900)
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 |
SAMN20886730 |
| SRA |
SRX11837536 |
