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| Status |
Public on Sep 28, 2022 |
| Title |
THAP1 iPSCs C5-2 |
| Sample type |
SRA |
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| Source name |
iPSCs
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| Organism |
Homo sapiens |
| Characteristics |
cell type: iPSC differentiated mDA Neurons
genotype: THAP1 c.197_198delAG
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| Growth protocol |
Midbrain dopaminergic (mDA) neurons were differentiated from iPSCs according to the previously reported protocols (Reinhardt et al., 2013). iPSCs were first derived into neural precursor cells (NPCs) using Neurobasal / DMEM / F12 media supplemented with 10 μM SB431542 (Sigma, S4317), 1 μM Dorsomorphin (Sigma, P5499), 3 μM CHIR99021 (Axon, 1386), and 500 mM Purmorphamine (Sigma, SML0868) for 4 days. After derivation of neural epithelial structures (NESCs), SB431542 and Dorsomorphin were removed and Ascorbic Acid (150 μM, Sigma, A8960) was added to the culture media. NESCs were manually picked and enzymatically purified for a minimum of 5 passages before undergoing characterisation and being hereafter referred to as NPCs. After obtained NPCs, midbrain dopaminergic neurons were differentiated by using Neurobasal / DMEM / F12 media supplemented with 1 μM Purmorphamine, 200 μM Ascorbic Acid, and 100 ng/mL FGF8b (Peprotech, 100-25) for 8 days. From day 8 to day 9, culture media was changed to Neurobasal / DMEM / F12 supplemented with 0.5 μM Purmorphamine and 200μM Ascorbic Acid. From day 10, culture media was changed to Neurobasal / DMEM / F12 media supplemented with BDNF (10 ng/Ml; Peprotech, 450-02), GDNF (10 ng/mL; Peprotech, 450-10), TGFβ3 (1 ng/mL; Peprotech, 100-21), cAMP (500μM; Applichem, A0455) and Ascorbic Acid (200μM). The cells were maintained in this medium until the designated experimental timepoint (d45).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy mini kit (Qiagen)
Libraries were generated using NEBNext Ultra II Directional RNA library Preparation Kit for Illumina (NEB, #E7760L)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Base calling performed using Illumina bcl2fastq2 version 2.19.1
Reads quality of RNA-seq data in fastq files was assessed using QoRTs (v1.2.37)
Reads were aligned using STAR (v2.5.2b) allowing gapped alignments to account for splicing against a custom-built genome composed of the Ensembl Homo Sapiens GRCh37
Alignment quality was analyzed using samtools (v1.1) and visually inspected in the Integrative Genome Viewer (v2.4.19)
Normalized read counts for all genes were obtained using edgeR (v3.18.1)
Genome_build: hg19
Supplementary_files_format_and_content: tsv files counted mapped reads of each gene
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| Submission date |
Mar 27, 2020 |
| Last update date |
Sep 28, 2022 |
| Contact name |
Fubo Cheng |
| E-mail(s) |
fubo.cheng@med.uni-tuebingen.de
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| Organization name |
University of Tuebingen
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| Department |
Institute of Medical Genetics and Applied Genomics
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| Street address |
Calwerstrasse 7
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| City |
Tuebingen |
| ZIP/Postal code |
72076 |
| Country |
Germany |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE141278 |
Transcription regulation of SNCA by dystonia type 6 gene product THAP1 |
| GSE147633 |
Transcription regulation of SNCA by dystonia type 6 gene product THAP1 [RNA-Seq] |
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| Relations |
| BioSample |
SAMN14468649 |
| SRA |
SRX8012678 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4437027_THAP1_C5_2_counts.tsv.gz |
1.2 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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