|
| Status |
Public on Nov 28, 2007 |
| Title |
deltaZFS_BioRep1 |
| Sample type |
RNA |
| |
|
| Source name |
S.pombe strain with zfs1 deficiency
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
A Schizosaccharomyces pombe zfs1 gene-targeted strain (zfs1-deficient) was used in a direct comparison with a representative wild-type strain that was originally used as the background cell type for zfs1 gene targeting
|
| Biomaterial provider |
These strains were gifts from Dr. Viesturs Simanis (École Polytechnique Fédérale De Lausanne, Lausanne, Switzerland).
|
| Growth protocol |
Strains were grown at 30°C in Edinburgh Minimal Medium (EMM) supplemented with 50 mg/l of adenine, histidine, leucine, lysine and uracil each (EMM+5S) or with SP minus leu (EMM+4S-Leu) when transformed (media and supplements were purchased from Q-biogene, Morgan, CA.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells from 1.5 ml of culture were centrifuged at 16,100 × g for 1 min at room temperature and total RNA was harvested from the cell pellet after storage at -80°C using the MasterPure yeast RNA purification kit (Epicenter, Madison, WI).
|
| Label |
biotin
|
| Label protocol |
Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.
|
| |
|
| Hybridization protocol |
5ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.
|
| Scan protocol |
Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450 with the Mini_euk2v3 protocol. Arrays were then scanned with an Affymetrix Scanner 3000. Data was obtained using the Genechip® Operating Software.
|
| Description |
Gene expression analysis was conducted using C. Elegans Genome Genechip® arrays (Affymetrix, Santa Clara, CA). Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol. For each array, 5ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450 with the Mini_euk2v3 protocol. Arrays were then scanned with an Affymetrix Scanner 3000. Data was obtained using the Genechip® Operating Software.
|
| Data processing |
The resulting files (.dat, .cel and .chp) were imported into the Rosetta Resolver system and the S. cerevisae probe sets were masked out prior to data pre-processing and error modeling (Weng et al., Bioinformatics, 2006).
|
| |
|
| Submission date |
Jun 12, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
NIEHS Microarray Core |
| E-mail(s) |
microarray@niehs.nih.gov, liuliw@niehs.nih.gov
|
| Organization name |
NIEHS
|
| Department |
DIR
|
| Lab |
Microarray Core
|
| Street address |
111 T.W. Alexander Drive
|
| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL2529 |
| Series (1) |
| GSE8122 |
Characterization of zfs1 as an mRNA binding and destabilizing protein in Schizosaccharomyces pombe |
|
