|
| Status |
Public on Apr 17, 2014 |
| Title |
swd2.2delta cells-replica 3-FW and RV strands |
| Sample type |
RNA |
| |
|
| Source name |
swd2.2delta cells grown at 34°C for 3 hours, replica 3
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: swd2.2delta
genetic background: Sp972
|
| Growth protocol |
cells were grown in rich YES+ Adenine medium for one generation (3 hours) at 34°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from 2.10^8 cells according to the procedure described in (Wilhelm et al., 2008; Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453, 1239-1243.).
|
| Label |
biotin
|
| Label protocol |
Extracted RNA were purified using the miRNeasy mini kit (Qiagen), dosed using a nanodrop and their quality were assessed using a Bioanalyzer 2100 (Agilent). To prepare cDNAs, 250 ng of RNA were then amplified using the WT Expression Kit (Ambion). The resulting cDNAs were then dosed (nanodrop) and their quality assessed using a Bioanalyzer 2100 (Agilent). 5,5 µg of cDNAs were then fragmented and labelled using the GeneChIP WT Terminal Labelling Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
5 µg of cDNAs were then hybridized on a GeneChip S.pombe Tiling 1.0FR Array (Affymetrix), according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
strand-specific expression data from fission yeast cells lacking Swd2.2 grown for 3 hours at 34°C
|
| Data processing |
CEL files were generated using the Affymetrix GeneChip Command Console software (AGCC) 3.0
Series supplementary files contain RMA normalized data and UTR ratio
corresponds to the chromosome followed by the position on the given chromosome of the 1st nucleotide of the probe
Raw data were normalized with Partek Genomic Suite software 6.5 (Partek Inc., St. Louis, MO, US) using Robust Multiarray Average (RMA) statistical algorithm, which includes RMA background correction, quantile normalization and log2 transformation.
UTR ratios
Columns ABCDE: Gene of interest (E) with its position on the chromosome (ABCD)
Columns FGHI: Genomic positions of the 5'UTR, the coding sequence (CDS) and the 3'UTR of the gene of interest
Columns JKL: Average signal intensity recorded in swd2.2+ cells for the 5'UTR (column J), the CDS (column K) and the 3'UTR (column L) of the gene
Columns MNO: Average signal intensity recorded in swd2.2delta cells for the 5'UTR (column M), the CDS (column N) and the 3'UTR (column O) of the gene
Column P UTR ratio swd2.2+: Ratio of the average signal intensity recorded in the 3'UTR versus the CDS in swd2.2+ cells
Column Q UTR ratio swd2.2delta: Ratio of the average signal intensity recorded in the 3'UTR versus the CDS in swd2.2delta cells
Column R UTR ratio swd2.2delta/UTR ratio swd2.2+
|
| |
|
| Submission date |
May 16, 2012 |
| Last update date |
Apr 17, 2014 |
| Contact name |
Vincent Vanoosthuyse |
| E-mail(s) |
vincent.vanoosthuyse@ens-lyon.fr
|
| Phone |
0033-4-72728197
|
| Organization name |
CNRS
|
| Department |
Laboratoire de Biologie Moléculaire de la Cellule
|
| Street address |
46 allée d'Italie
|
| City |
Lyon |
| ZIP/Postal code |
69007 |
| Country |
France |
| |
|
| Platform ID |
GPL7715 |
| Series (1) |
| GSE38005 |
Comparison of genome-wide gene expression in wild-type and swd2.2delta fission yeast cells |
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