|
| Status |
Public on Dec 17, 2014 |
| Title |
KE09_1278_2 |
| Sample type |
RNA |
| |
|
| Source name |
RNA, Hu1278
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: Hu1278
genotype: mit1D::kan
treatment: untreated
|
| Treatment protocol |
Cells were grown to mid-log phase in YES containing 5 µM of drug (HMS-I1, HMS-I2) (dissolved in DMSO, final DMSO concentration 0.4%) and 10 µg/ml G418.
|
| Growth protocol |
Haploid Schizosaccharomyces pombe cells were grown in YES (yeast extract with supplements) medium at 32 °C and maintained in log phase during experiments
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with hot acid phenol and chloroform. Briefly, cells were harvested by centrifugation at RT, resuspended in TES (10 mM TrisHCl pH7.5, 10 mM EDTA and 0.5% SDS) and transferred to preheated acid phenol (65 °C). After a 45 min shaking incubation at 65 °C, RNA was isolated by phenol-chloroform extraction.
|
| Label |
biotin
|
| Label protocol |
The RNA was purified using an RNeasy mini-kit (Qiagen) and tested for quality control with an Agilent 2200 Tape-station (Agilent). For each sample 150 nanograms of pure RNA was then used for labeling (Ambion Expr. Label)
|
| |
|
| Hybridization protocol |
Hybridised to Affymetrix GeneChip S. pombe Tiling 1.0FR Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.
|
| Scan protocol |
Scanned at the Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.
|
| Description |
RNA from mit1∆
|
| Data processing |
Data were normalized with ‘quantile normalization plus scaling’ using the Tiling Analysis Software (TAS) 1.1, 2004 genome assembly, log2 scale, target intensity: 100, band width:100
Results files in BAR formats were generated using Affymetrix Tiling Analysis Software (TAS) v1.1. and contain log2 values for each probe. F: forward strand, R: reverse strand
|
| |
|
| Submission date |
Apr 30, 2014 |
| Last update date |
Dec 17, 2014 |
| Contact name |
Karl Ekwall |
| E-mail(s) |
karl.ekwall@ki.se
|
| Phone |
+46 8 6089133
|
| Organization name |
Karolinska Inst
|
| Street address |
Alfred Nobels Alle 7
|
| City |
Stockholm |
| ZIP/Postal code |
S-141 89 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL7715 |
| Series (1) |
| GSE57207 |
An in vivo screen identifies compounds that disrupt heterochromatin integrity |
|
