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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 31, 2020 |
| Title |
SAMPLE 1_iPSC-derived neural cell wildtype |
| Sample type |
SRA |
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| Source name |
iPSC from bone marrow MSC
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Induced pluripotent stem cell derived neural cells
genotype/variation: wild type
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| Growth protocol |
Neural differentiation of iPSCs was performed as previously described (Chambers et al. 2012; Meents et al. 2019). iPSCs were seeded as single cells at a density of 105 cells/cm2 in presence of 10 µM Y-27632. At 80-90% confluency, neural conversion was induced by dual-SMAD inhibition: For the first five days LDN-193189 (100 nM or 1 µM, Sigma-Aldrich) and SB431542 (10 µM, Miltenyi Biotec) were added to the basal culture medium consisting of knockout DMEM/F 12 containing 15% knockout serum replacement, 1 mM L-glutamine, 100 µM non-essential amino acids, 100 µM β mercaptoethanol, 100 U/mL penicillin and 100 µg/mL streptomycin (all Thermo Fisher Scientific). To accelerate neural crest specification three small molecules (3 µM CHIR99021, 10 µM DAPT, and 10 µM SU5402, all Tocris, Bristol, United Kingdom) were added between days 2 to 10. After four days, the medium was supplemented in increasing percentages with DMEM/F 12, containing 10 ml/L N2, 20 ml/L B27 minus vitamin A supplements and 100 U/mL penicillin, 100 µg/mL streptomycin (all Thermo Fisher Scientific). N2/B27 medium was added to the basal medium at 25% between days 4-5, 50% between days 6-7 and 75% between days 8-10. On day 10, cells were dissociated using Accutase and seeded on glass coverslips coated with 50 µg/mL Poly-L-Ornithine (Sigma-Aldrich) and 5 µg/mL Laminin (Thermo Fisher Scientific) and further cultured for up to three weeks with N2/B27 medium supplemented with 20 ng/mL NGF (R&D Systems, Minneapolis, Minnesota, USA), BDNF, GDNF (all PeproTech) and 200 ng/mL L ascorbic acid (Sigma-Aldrich). Medium was changed every 3-4 days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA of iPSC-derived neural cells was isolated with the NucleoSpin RNA Plus kit (Macherey-Nagel, Düren, Germany).
QuantSeq 3´-mRNA Library Prep/Lexogen, Standard 3' Seq (SR, 50 cycles)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
DE33NGSUKBR106279_1
iPSC-derived neural cells after 27 days of differentiation
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| Data processing |
Adapter trimming and rRNA removal in raw fastq files was performed using TrimGalore (Babraham Bioinformatics, Cambridge, UK) and SortMeRNA (Kopylova et al. 2012), respectively. Reads were aligned to the human genome build GRCh38 with STAR aligner (Dobin et al. 2013). Read counts were retrieved by HTSeq-count and further analyzed with the R package DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Read counts
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| Submission date |
Nov 27, 2019 |
| Last update date |
Aug 31, 2020 |
| Contact name |
Wolfgang Wagner |
| E-mail(s) |
[email protected]
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| Phone |
+49 241 8088611
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| Organization name |
RWTH Aachen University
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| Department |
Helmholtz Institute for Biomedical Engineering
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| Lab |
Stem Cell Biology and Cellular Engineering
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| Street address |
Pauwelsstrasse 20
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| City |
Aachen |
| ZIP/Postal code |
52074 |
| Country |
Germany |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE141107 |
Gene expression - PRDM8 reveals aberrant DNA methylation in aging syndromes and is relevant for hematopoietic and neuronal differentiation. |
| GSE141108 |
PRDM8 reveals aberrant DNA methylation in aging syndromes and is relevant for hematopoietic and neuronal differentiation. |
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| Relations |
| BioSample |
SAMN13412282 |
| SRA |
SRX7228410 |
| 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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