|
| Status |
Public on Mar 01, 2010 |
| Title |
Autogamy_T20_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
total_RNA_from_cells
|
| Organism |
Paramecium tetraurelia |
| Characteristics |
Strain d4-2 is an entirely homozygous laboratory strain. d4-2 is a hybrid strain carrying a few genes from strain 29 in the genetic background of strain 51.
T20 = 4000 cells per mL (3% vegetative, 0% skeins, 8% fragmented macronucleus, 89% with visible anlagen)
|
| Biomaterial provider |
Mireille Bétermier - CNRS
|
| Growth protocol |
Cells were grown in a wheat grass powder (Pines International Co., Lawrence, USA) infusion medium bacterized the day before use with Klebsiella pneumoniae, and supplemented with 0.8 mg/l of beta-sitosterol (Merck, Darmstadt, FRG). Unless otherwise stated, cells were maintained at 27°C. The progression of autogamy through the different stages of nuclear reorganization was monitored by DAPI staining of cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from unwashed cell pellets using the TRIzol (Invitrogen) procedure, modified by the addition of glass beads. After the Trizol/Chloroform treatment, the supernatant was precipitated with isopropanol, the pellet was washed with ethanol and finally resuspended in DEPC-treated water. The RNA concentration was estimated by optical density at 260 and 280 nm.
|
| Label |
Cy5
|
| Label protocol |
RT stratagene FAIRPLAY microarray labeling kit
|
| |
|
| Hybridization protocol |
Microarrays were hybridized using the GeneTAC Hybstation (Genomic Solutions)
|
| Scan protocol |
The slides were scanned using GenePix 4000B scanner equipped with laser to excite Cy3 and Cy5. All slides were scanned using 100% laser power and PMT voltage auto-adjustment.
|
| Description |
The resulting 16 bit images were analysed using the GenePix Pro 6.0® software.
|
| Data processing |
The data overview and preprocessing were processed using MANGO (MicroArray Normalization tool of GodMap) software (ref1), an R script that allows the user to make a complete differential analysis of several two colour microarrays from raw data file via an overview and a preprocessing of all the slides. The morphological background was substracted. single-color normalization adjusting across arrays the quantiles of the intensities distribution was computed using the normalizeQuantiles function of the R limma package (ref2: see rawdatatrieparID.txt file submitted to GEO as a Sup Table). For each slide, an arithmetic means was calculated from the normalized values obtained for all replicate spots corresponding to each probe
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| |
|
| Submission date |
Sep 30, 2008 |
| Last update date |
Aug 24, 2009 |
| Contact name |
nicolas Agier |
| E-mail(s) |
nicolas.agier@pasteur.fr
|
| Phone |
01 69 82 37 65
|
| Organization name |
CNRS
|
| Department |
transcriptomique
|
| Lab |
plateforme GODMAP
|
| Street address |
Avenue de la terrasse
|
| City |
Gif sur Yvette |
| State/province |
Ile de France |
| ZIP/Postal code |
91198 |
| Country |
France |
| |
|
| Platform ID |
GPL7296 |
| Series (1) |
| GSE12988 |
Screening of the Paramecium tetraurelia megabase chromosome for autogamy-specific genes |
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