|
| Status |
Public on Mar 27, 2024 |
| Title |
CMV infected organoid rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Cerebral organoids generated from iPSC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Cerebral organoids generated from iPSC
experiment: 1
treatment: Inoculated with CMV Merlin
infection: CMV
|
| Treatment protocol |
The organoids were cultured for 55 days before undergoing mock or CMV infection and confirmation of cerebral differentiation of the organoid.
|
| Growth protocol |
Cerebral organoids were generated from iPSC (Lancaster and Knoblich, 2014). Embryoid bodies were generated by seeding 9,000 live iPSCs in low-bFGF hESC medium in a low-attachment 96-well U-bottom plate. The embryoid bodies were cultured for 5-7 days, with half the medium was removed and replaced with fresh media every other day. ROCK inhibitor and bFGF were only included for the first four days. Primitive neuroepithelial cell clusters were generated by transferring the embryoid bodies to a low-attachment 24-well plate and cultured for 4-5 days in neural induction medium. Every 48 hours of culture, fresh neural induction medium was added to each well. After 4-5 days of culture, the neuroepithelial tissues were embedded in Matrigel droplets and transferred to Petri dishes containing cerebral organoid differentiation medium without vitamin A. Following 48 hours of culture, the medium was replaced with fresh cerebral organoid differentiation medium without vitamin A. After 4 days in culture, the Matrigel-embedded organoids were transferred to Petri dishes containing cerebral organoid differentiation medium containing vitamin A. The Petri dishes were transferred to an orbital shaker and the medium was replaced every 3-4 days with cerebral organoid differentiation medium containing vitamin A. The organoids were cultured for 55 days before undergoing mock or CMV infection and confirmation of cerebral differentiation of the organoid.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed using the RNeasy mini kit (RNeasy Mini Kit; Qiagen) as per manufacturer’s instructions.
mRNA libraries were prepared at the Ramaciotti Centre for Genomics (UNSW University of New South Wales, Australia) using the Illumina Stranded Total RNA with RiboZero Plus kit. The libraries were sequenced using the Illumina NextSeq 500 to produce 75 bp paired end reads. R1.fastq and R2.fastq files were produced for each sample.
RNA-Seq paired end
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Merlin2
|
| Data processing |
Sequence reads were aligned to the human genome sequence (GRCh38) using Subread (version 1.6.3).
The featureCounts function of Subread was used to generate counts of reads uniquely mapped to annotated genes using the GRCh38.108 gtf file
Assembly: Ensembl homo sapiens genome (GRCh38)
Supplementary files format and content: Tab-delimited text file showing counts for each sample generated using featureCounts function of Subread.
|
| |
|
| Submission date |
Nov 12, 2022 |
| Last update date |
Mar 27, 2024 |
| Contact name |
Susan Corley |
| E-mail(s) |
s.corley@unsw.edu.au
|
| Phone |
+61 02 9385 8853
|
| Organization name |
UNSW
|
| Department |
Biotechnology & Biomolecular Sciences
|
| Lab |
Systems Biology Initiative
|
| Street address |
D26, Kensignton Campus
|
| City |
Sydney |
| State/province |
NSW |
| ZIP/Postal code |
2052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE217832 |
Human cytomegalovirus dysregulates neurodevelopmental pathways in cerebral organoids |
|
| Relations |
| BioSample |
SAMN31700527 |
| SRA |
SRX18242846 |
