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Series GSE33497 Query DataSets for GSE33497
Status Public on Feb 15, 2012
Title The effects on transcriptome from absence of Spt4/Supt4h by RNA-seq
Organisms Saccharomyces cerevisiae; Mus musculus; Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Summary We have done RNAseq analyses in yeast and in rat and mouse striatal neurons. The experiments in yeast examine globally the physiological effects of spt4 deletion on the transcriptome. The experiments in neurons examine the global effects of supt4 knockdown to a cellular level (i.e., 50% knockdown) that we have shown prevents toxicity of variant Htt protein by interfering with transcription of extended CAG repeats. The results of both sets of experiments indicate that absent spt4 function has limited effects on overall transcription. Moreover, the mammalian cell experiments indicate that supt4h knockdown to a cellular level that alters production of transcripts containing long CAG repeats has minimal effects on normal genes, supporting the notion that anti-supt4h measures may prove useful in combating trinucleotide repeat diseases.
Overall design RNA-seq was done for two yeast WT strain W303 and two spt4 deletion strain spt4∆ as biological repeats, and rat ST14A cells and mouse HdhQ7/Q7 cells after transfection with NC control siRNA or Supt4h siRNA
Contributor(s) Deng N, Lin R
Citation(s) 22341442
Submission date Nov 04, 2011
Last update date May 15, 2019
Contact name Ning Deng
Organization name Stanford University
Department Genetics Department
Lab Cohen Lab
Street address 300 Pasteur Drive, RmL-314
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platforms (3)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL13272 Illumina Genome Analyzer IIx (Saccharomyces cerevisiae)
GPL14844 Illumina HiSeq 2000 (Rattus norvegicus)
Samples (8)
GSM828671 Yeast WT-1
GSM828672 Yeast WT-2
GSM828673 Yeast Spt4 Del-1
SRA SRP009272
BioProject PRJNA148851

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Supplementary file Size Download File type/resource
GSE33497_RAW.tar 41.0 Gb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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