|
| Status |
Public on Nov 12, 2015 |
| Title |
6_swr1_rtt109_rrp6 |
| Sample type |
RNA |
| |
|
| Source name |
Budding yeast cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell density: Log phase (OD= 1.0)
cell cycle stage: Asynchronous
strain: swr1_rtt109_rrp6
|
| Treatment protocol |
Cultures were flash frozen with liquid nitrogen prior to RNA preparation, typically done within the couple of weeks.
|
| Growth protocol |
50ml of yeast grown in YEP + 2% glucose media at 30˚C were harvested at an OD600 of 0.8- 0.1 (log phase). All cultures were from freshly streaked strains from glycerol stocks stored at -80C. All strains were made by yeast dissections to avoid picking up growth suppressors.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed by vortexing with glass beads in the presence of hot phenol (pH 4.0) and RNA was exrtacted using multiple phenol:chloroform: isoamyl alcohol and chloroform:isoamyl alcohol extractions, followed by ethanol precipitation.
|
| Label |
Cy5
|
| Label protocol |
First-strand cDNA was purified using the MinElute PCR purification kit (Qiagen) and 5 ug were fragmented and labeled using the GeneChip WT Terminal labeling kit (Affymetrix) according to manufacturers protocol. The labelled cDNA samples were denatured in a volume of 300 ul containing 50 pM control oligonucleotide B2 (Affymetrix) and Hybridization mix (GeneChip Hybridization, Wash and Stain kit, Affymetrix) of which 250 ul were hybridized per array (S. cerevisiae yeast tiling array, Affymetrix, PN 520055).Actinomycin D- to ensure strand specificity of the tiling array data (to inhibit second strand synthesis during the amplification step).
|
| |
|
| Hybridization protocol |
Hybridizations were carried out at 45C for 16 h with 60 rpm rotation. The staining was carried out using the GeneChip Hybridization. Wash and Stain kit with fluidics protocol FS450_0001 in an Affymetrix Fluidics station
|
| Scan protocol |
standard protocol
|
| Data processing |
tilingArray package from Bioconductor; R
sup3_MR.txt and normProbeIntensity.txt.gz
sup3_MR.txt contains annotations and processed signal intensities and normProbeIntensity contains the raw probe intensities for all the arrays individually.
Please note that data from previously published work (Tan-Wong et al. 2012) is included in the processed file and includes the column names "wt_gl", "rrp6_gl", "ssu72_rrp6", "ssu72", although we have excluded the corresponding raw data for this.
|
| |
|
| Submission date |
Sep 16, 2015 |
| Last update date |
Nov 12, 2015 |
| Contact name |
Craig L Peterson |
| E-mail(s) |
craig.peterson@umassmed.edu
|
| Phone |
508-856-5858
|
| Organization name |
University of Massachusetts Medical School
|
| Department |
Program in Molecular Medicine
|
| Street address |
373 Plantation Street
|
| City |
Worcester |
| State/province |
MASSACHUSETTS |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL19774 |
| Series (2) |
| GSE73110 |
Genome-wide profiling of total RNA from mutants that affect chromatin dynamics: RTT109, SWR1, and the nuclear RNA exosome RRP6 |
| GSE73145 |
Chromatin dynamics and the RNA exosome function in concert to regulate transcriptional homeostasis |
|
