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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 25, 2020 |
| Title |
8858-1_4_79_2 |
| Sample type |
SRA |
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| Source name |
human cortical spheroids
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| Organism |
Homo sapiens |
| Characteristics |
Sex: M
iPSc line: 8858-1
deletion.status: 8858-1_4
differentiation day: 79
batch: 2
racepc1: -0.000108454
racepc2: 0.050698
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| Growth protocol |
hiPSC were cultured on inactivated mouse embryonic fibroblast feeders (EmbryoMax PMEF; Millipore) in DMEM/F12 (1:1, Life Technologies, 11330) containing 20% knockout serum (Life Technologies, 10828), 1mM non-essential amino acids (Life Technologies, 11140), 1:200 GlutaMax (Life Technologies, 35050), 0.1 mM β-mercaptoethanol (Sigma-Aldrich, M3148), 1:100 penicillin and streptomycin (Life Technologies, 15070), and 10 ng/ml FGF2 (R&D Systems, 233-FB) diluted at 0.1% BSA in DPBS (Life Technologies, 14190). hCS were generated as previously described (Pasca, 2015). Intact hiPSC cells colonies were lifted using 0.7 mg/ml dispase and transferred to ultralow-attachment plastic dishes (Corning) in hiPSC cell medium supplemented with 5 μM dorsomorphin (Sigma-Aldrich), 10 μM SB-431542 (Tocris) both of which are SMAD inhibitors, and 10 μM Y-27632 (EMD Chemicals) which is a ROCK inhibitor. From day 2 (48 hours of differentiation), the medium supplemented with dorsomorphin and SB-431542 was changed daily. From day six until day 24, neural spheroids were grown in neurobasal-A (Life Technologies, 10888) neural medium supplemented with B-27 supplement without vitamin A (Life Technologies, 12587), 1:100 GlutaMax (Life Technologies), 1:100 penicillin and streptomycin (Life Technologies) and with 20 ng/ml EGF (R&D Systems, 236-EG) and 20 ng/ml FGF2 (R&D Systems, 233-FB). From day 25 to 42, the neural medium was supplemented with 20 ng/ml BDNF (Peprotech, 450-02) and 20 ng/ml NT3 (Peprotech, 450-03) and medium was changed every other day. From day 43 onwards, hCS were maintained in unsupplemented neural medium with medium changes every four days
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| Extracted molecule |
total RNA |
| Extraction protocol |
Following extraction of total RNA, rRNA was depleted (RiboZero Gold, Illumina) and libraries were prepared using Truseq stranded RNA RiboZero Gold (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Paired end reads were mapped using STAR to hg38 with Gencode v25 annotations.
Gene expression levels were quantified using rsem (v1.3.0)
Genome_build: hg38
Supplementary_files_format_and_content: csv file containing raw counts
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| Submission date |
May 08, 2020 |
| Last update date |
Dec 26, 2020 |
| Contact name |
Aaron Gordon |
| Organization name |
UCLA
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| Department |
Neurology
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| Lab |
Geschwind
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| Street address |
695 Charles E. Young Drive South, Gonda 2306, Los Angeles, CA 90095-1761
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE150123 |
RNA sequencing of Human Cortical Organoids diffrentiated for extended periods of time |
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| Relations |
| BioSample |
SAMN14906542 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4523920_8858-1_4_79_2.csv.gz |
207.9 Kb |
(ftp)(http) |
CSV |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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