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| Status |
Public on Jul 18, 2024 |
| Title |
OFO1003V2 |
| Sample type |
SRA |
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| Source name |
iPSC-derived forebrain organoids
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| Organism |
Homo sapiens |
| Characteristics |
cell type: iPSC-derived forebrain organoids
disease: opioid use disorder
treatment: PBS
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| Growth protocol |
We generated 3-D iPSC-derived forebrain organoids. Briefly, pre-patterned floating embryonic bodies (EBs) formed from intact iPSC colonies were embedded in matrigel and cultured with 1x N2, 1x NEAA and 1x Glutamax (Invitrogen, Grand Island, NY), 1 μM SB431542, and 1 μM CHIR99021 (Selleckchem, Carlsbad, CA) for 7 days. On day 14, organoids were mechanically dissociated from the matrigel and cultured in a bioreactor (16). Culture medium from days 14-70 consisted of DMEM/F12 medium supplemented with 1x N2, 1x B27, 1x NEAA and 1x Glutamax, 1x 2-metabptoethanol, 100x penicillin-streptomycin solution, and 2.5 μg/ml insulin (Sigma-Aldrich, St Louis, MO). The medium was changed every other day. From day 70 onward, supplementing media with 20 ng/ml BDNF, 20 ng/ml GDNF (Peprotech, Rocky Hill, NJ), 0.2 mM L-Ascorbic Acid, and 0.5 mM cAMP (Sigma-Aldrich, St Louis, MO) was used.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Drug treatment was conducted at 83-90 days of forebrain organoid differentiation and at 28-34 days of forebrain neuron differentiation. The concentrations of oxycodone (50 µg/L) and buprenorphine (2 ng/mL) used to perform these experiments were selected to fall within the range of blood drug concentrations in patients taking standard clinical doses of these two drugs. 3-D iPSC-derived brain organoids were cultured in the bioreactors with the drugs for seven days, and the medium was changed daily.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Fastq files were mapped to the UCSC hg19 reference genome using STAR
gene-level counts were obtained from the alignment using featureCounts from the SubRead package.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include gene counts for each sample
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| Submission date |
Aug 01, 2022 |
| Last update date |
Jul 18, 2024 |
| Contact name |
Hu Li |
| Organization name |
Mayo Clinic
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| Street address |
200 1st St SW
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| City |
Rochester |
| ZIP/Postal code |
55905 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE210206 |
Single cell transcriptomics reveals distinct transcriptional responses to oxycodone and buprenorphine by iPSC-derived brain organoids from patients with opioid use disorder |
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| Relations |
| BioSample |
SAMN30078948 |
| SRA |
SRX16750043 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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