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Series GSE94111 Query DataSets for GSE94111
Status Public on Mar 06, 2018
Title Rational targeting of RNA structure in SMN2 transcripts reverses Spinal Muscular Atrophy molecular phenotypes
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Marine natural compound homocarbonyltopsentin PK4C9 is a small TSL2-binding molecule which was identified to increase exon 7 splicing to therapeutic levels and rescue downstream molecular alterations in SMA cells. To assess the functionality of the restored SMN protein, we studied whether PK4C9 could modify SMN-mediated splicing events using RNA sequencing data from PK4C9-treated (40 microM, 24 h) vs. DMSO-treated GM03813C fibroblasts. The data was also used to find shared motifs amongst PK4C9-sensitive splicing events, in order to contribute to the description of the mechanism of action of PK4C9 and to help identify off-targets.
Overall design Examination of 4 total-RNA replicates of DMSO-treated GM03813C fibroblasts (control) and 4 replicates of PK4C9-treated (40 microM, 24 h) GM03813C fibroblasts (GM03813C is a fibroblast cell line derived from a type I SMA patient).
Contributor(s) Garcia-Lopez A, Wacker A, Tessaro F, Jonker H, Richter C, Comte A, Berntenis N, Schmucki R, Hatje K, Sciarra D, Konieczny P, Fournet G, Faustino I, Orozco M, Artero R, Goekjian P, Metzger F, Ebeling M, Joseph B, Schwalbe H, Scapozza L
Citation(s) 29795225
Submission date Jan 26, 2017
Last update date May 15, 2019
Contact name Roland Schmucki
Organization name F. Hoffmann - La Roche AG
Street address Grenzacherstrase
City Basel
ZIP/Postal code 4058
Country Switzerland
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (8)
GSM2469391 Control_FB13c1
GSM2469392 Control_FB13c2
GSM2469393 Control_SMA_01
BioProject PRJNA368964
SRA SRP097892

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE94111_PK4C9_counts.gct.gz 433.1 Kb (ftp)(http) GCT
GSE94111_PK4C9_rpkms.gct.gz 525.9 Kb (ftp)(http) GCT
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Raw data are available in SRA
Processed data are available on Series record

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