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Series GSE130485 Query DataSets for GSE130485
Status Public on May 01, 2019
Title THZ1-induced transcriptional changes in SMO inhibitor responsive and resistant mouse hedgehog-driven medulloblastoma cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: To assess THZ1-induced global changes of transcriptome of Hh-driven cancer
Methods: SMB56 or SMB56-shSufu cells were mouse hedgehog-driven medulloblastoma cell lines that are either responsive or resistant to SMO inhibitor (GDC-0449). They were treated with 0.1 uM THZ1 or DMSO for 8 hours. 1 uM GDC-0449 treated SMB56 cells were included as control. Gene expression profiles were generated by RNAseq, in duplicate, using Hiseq3000. The RNAseq reads were mapped to the hg19 reference genome using STAR (v2.5.3a). Expression levels for each sample were quantified to FPKM using Cufflinks (v2.2.1). Differential expression analysis was carried out using R package DESeq2 (v1.20.0)
Results: Compared to GDC-0449 treatment in SMB56 cells, THZ1 induced a robust global transcriptional downregulation in both SMB56 and SMB56-shSufu cells. When we compared the top 2000 significantly downregulated genes between THZ1-treated SMB56 and SMB56-shSufu cells, we found they had ~70% in common. GSEA reveals Hh-target genes are enriched in DMSO treated cells versus THZ1-treated ones.
Conclusions: CDK7 inhibition induced a robust and similar transcriptional downregulation in both SMB56 and SMB56-shSufu cells, with preferential targeting of Hh pathway transcriptional output.
Overall design RNAseq of SMO inhibitor responsive or resistant hedgehog-driven mouse medulloblastoma cells treated with THZ1, GDC-0449 or DMSO.
Contributor(s) Tang Y, Zhang L
Citation(s) 31182587
Submission date Apr 30, 2019
Last update date Aug 01, 2019
Contact name Yujie Tang
Organization name Shanghai Jiao Tong University School of Medicine
Street address 280 South Chong-qing Rd
City Shanghai
ZIP/Postal code 200025
Country China
Platforms (2)
GPL21273 HiSeq X Ten (Mus musculus)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (10)
GSM3740924 SMB56-DMSO-1
GSM3740925 SMB56-DMSO-2
GSM3740926 SMB56-THZ1-1
BioProject PRJNA540461
SRA SRP194252

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Supplementary file Size Download File type/resource
GSE130485_SMB56-shSufu-THZ1_DEG_COUNTS_FPKM.xlsx 2.0 Mb (ftp)(http) XLSX
GSE130485_SMB56_GDC0449_DEG_COUNTS_FPKM.xlsx 1.3 Mb (ftp)(http) XLSX
GSE130485_SMB56_THZ1_DEG_COUNTS_FPKM.xlsx 1.4 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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