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Sample GSM4437026 Query DataSets for GSM4437026
Status Public on Sep 28, 2022
Title THAP1 iPSCs C5-1
Sample type SRA
 
Source name iPSCs
Organism Homo sapiens
Characteristics cell type: iPSC differentiated mDA Neurons
genotype: THAP1 c.197_198delAG
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).
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)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
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
 
Submission date Mar 27, 2020
Last update date Sep 28, 2022
Contact name Fubo Cheng
E-mail(s) fubo.cheng@med.uni-tuebingen.de
Organization name University of Tuebingen
Department Institute of Medical Genetics and Applied Genomics
Street address Calwerstrasse 7
City Tuebingen
ZIP/Postal code 72076
Country Germany
 
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]
Relations
BioSample SAMN14468650
SRA SRX8012677

Supplementary file Size Download File type/resource
GSM4437026_THAP1_C5_1_counts.tsv.gz 1.1 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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