|
Status |
Public on Sep 29, 2010 |
Title |
U1 vs control |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
RNA from U1 morpholino treated cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: HeLa
|
Treatment protocol |
Cells were transfected with antisense morpholino and culture for 8 hours or treated with methanol or spliceostatin A for 8 hours.
|
Growth protocol |
HeLa cells were grown in DMEM + 10% FBS in humdified incubator with 5% CO2.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extractedusing TRIzol according to manufacturer's recommendation.
|
Label |
biotin
|
Label protocol |
Labelled cDNA targets were prepared using the GeneChip WT amplified Double-Stranded cDNA Synthesis Kit and the GeneChip WT Double-Stranded DNA Terminal Labelling Kit according to the manufacturer’s directions.
|
|
|
Channel 2 |
Source name |
RNA from control morpholino treated cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: HeLa
|
Treatment protocol |
Cells were transfected with antisense morpholino and culture for 8 hours or treated with methanol or spliceostatin A for 8 hours.
|
Growth protocol |
HeLa cells were grown in DMEM + 10% FBS in humdified incubator with 5% CO2.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extractedusing TRIzol according to manufacturer's recommendation.
|
Label |
biotin
|
Label protocol |
Labelled cDNA targets were prepared using the GeneChip WT amplified Double-Stranded cDNA Synthesis Kit and the GeneChip WT Double-Stranded DNA Terminal Labelling Kit according to the manufacturer’s directions.
|
|
|
|
Hybridization protocol |
The end-labelled cDNA targets were applied to GeneChip human tiling 2.0R E arrays. Hybridization was performed using F450-001 fluidics wash and stain script on the Affymetrix GeneChip Fluidics Station 450.
|
Scan protocol |
Arrays were scanned using the Affymetrix GCS 3000 7G GeneChip Operating Software (GCOS).
|
Description |
Affected regions by U1 snRNP inhibition. Biological Rep 1-3
|
Data processing |
For tiling array analysis, we produced .BAR files from the .CEL files using the Affymetrix Tiling Analysis Software (TAS) version 1.1 to visualize on the Integrated Genome Browser (IGB).
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|
|
Submission date |
Sep 16, 2010 |
Last update date |
Sep 16, 2010 |
Contact name |
Daisuke Kaida |
E-mail(s) |
kaida@med.u-toyama.ac.jp
|
Organization name |
University of Toyama
|
Department |
Frontier Research Core for Life Sciences
|
Street address |
2630 Sugitani
|
City |
Toyama |
State/province |
Toyama |
ZIP/Postal code |
930-0194 |
Country |
Japan |
|
|
Platform ID |
GPL4914 |
Series (1) |
GSE24179 |
Transcriptome changes in splicing inhibited cells |
|