|
| 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 |
| E-mail(s) |
ndeng@stanford.edu
|
| 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)
|
|
| Relations |
| SRA |
SRP009272 |
| BioProject |
PRJNA148851 |
Less...
More...