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| Status |
Public on Aug 08, 2020 |
| Title |
MA003 |
| Sample type |
SRA |
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| Source name |
brain organoids generated from iPSC
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| Organism |
Homo sapiens |
| Characteristics |
agent: none
experiment site: A
organoid: FA11
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| Treatment protocol |
90-day old organoids were infected with viruses, and RNA extracted after 10 days
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| Growth protocol |
Cerebral organoids were generated as previously described (Lancaster et. al. 2013) from two iPSC lines (FA0000010 and FA0000011, for brevity called FA10 and FA11). Briefly, cells were dissociated into single cell suspensions with Accutase (Stem Cell Technologies, cat#7920) and seeded at 4,500 cells/ well in 96-well low attachment U bottom plates, using EB media (DMEM/F12 (Thermo Fisher Scientific, cat. #11330-032) supplemented with 20% Knockout Serum Replacement (Thermo Fisher Scientific, cat. #10828-028), 3% ES quality batch-tested fetal bovine serum (Thermo Fisher Scientific, cat#10439024), 1% Glutamax (Thermo Fisher Scientific, cat. #35050-038), 1x Non-Essential Amino Acids, 0.1mM 2-mercaptoethanol, 4ng/ml bFGF (R&D Systems, cat.#233FB01M), and 50uM Y-27632. Fresh medium was replaced every other day until day 6,when EB medium was replaced with Neural Induction (NI) medium (DMEM/F12, 1x N2 Supplement, 1X Glutamax, 1X NEAA and 1μg/ml Heparin (Sigma-Aldrich, cat#H3149) ) and the organoids were transferred to 60 mm or 100 mm low-attachment plates. The organoids were allowed to form neuroepithelium tissue till day 11-14, with media changed every other day. Between day 11-24, the organoids were coated with Matrigel droplets and allowed to gel by keeping them at 37°C for 30 min. Matrigel-coated organoids were transferred to differentiation media (1:1 DMEM/F12:Neurobasal, 0.5% N2 Supplement, 2% B27 Supplement without Vitamin A (Life Technologies, cat#12587010), 0.25% Insulin solution (Life Technologies, cat#12585014), 50uM 2-mercaptoethanol, 1% Glutamax, 0.5% NEAA, 1% Penicillin-Streptomycin), for 4 days, then transferred to differentiation media containing B27 Supplement with Vitamin A (Thermo Fisher Scientific, cat#17504-044). Brain organoids were cultured for an additional 60 days with medium changed every 7 days, and used for experiments at 90 days or 270 days.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Direct-zoltm RNA MicroPrep (Zymo)
TruSeq stranded/poly-A enrichment (Illumina)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
MA003_FA11_none
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| Data processing |
Paired end/2x100 bp reads, illumina novaseq 6000
Illumina Casava1.7 software used for basecalling.
Reads were pseudoaligned by Kallisto v0.44 to human reference transcriptome GRCh38.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw gene counts for each sample generated by kallisto
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| Submission date |
Aug 07, 2020 |
| Last update date |
Aug 08, 2020 |
| Contact name |
Nicole A P Lieberman |
| Organization name |
University of Washington
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| Department |
Laboratory Medicine
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| Lab |
Greninger
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| Street address |
850 Republican St S130
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98118 |
| Country |
USA |
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| Platform ID |
GPL27644 |
| Series (2) |
| GSE155884 |
Molecular features of the measles virus viral fusion complex that favor infection and spread in the brain [human] |
| GSE155886 |
Molecular features of the measles virus viral fusion complex that favor infection and spread in the brain |
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| Relations |
| BioSample |
SAMN15760247 |
| Supplementary data files not provided |
| Processed data are available on Series record |
| Raw data not provided for this record |
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