|
| Status |
Public on May 19, 2009 |
| Title |
ML-DmBG3 cells: RNAi Mock 0 micrograms, 3 days biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
ML-DmBG3 cells: RNAi Mock 0 micrograms, 3 days
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cells: ML-DmBG3 cells (derived from central nervous system)
rnai knockdown: Mock
micrograms rnai: 0
time: 3 days
|
| Treatment protocol |
For RNAi treatment, cells were plated at 5 million cells per 3 cm well. Media was replaced with 1 ml of Express Five SFM (Invitrogen) with 1% FCS, and 10 micrograms per ml insulin. The indicated amount of dsRNA was added per well. Media was adjusted to 3 ml and 10% FCS with Schneider’s media after 2 hrs. Cells were replated as needed. Templates for dsRNA synthesis were made by PCR from cDNA templates using primers with T7 promoters (see primer table linked as a supplementary file to the Series GSE16152 record). Equal amounts of two dsRNAs against each target were used.
|
| Growth protocol |
ML-DmBG3 cells were cultured in Schneiders media with 10% FCS and 10 micrograms per ml insulin. Cells were passaged to keep them between 1 and 10 million cells per ml.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA then purified by Qiagen Rneasy Minelute columns.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
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| |
|
| Hybridization protocol |
Following fragmentation, 10 mg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
|
| Description |
Gene expression data from ML-DmBG3 cells; RNAi Mock 0 micrograms, 3 days
|
| Data processing |
The data were normalized using gc-RMA algorithms, which consist of background adjustment and quantile normalization, accounting for probe GC content; executed using the R statistical environment and the BioConductor package. Transcript levels from Rad21 and Nipped-B RNAi treatments were compared to those of Mock RNAi controls at 3 and >3 days (4 and 6 days) (N=4 per RNAi comparison; N=2 per treatment condition). A balanced 2-way ANOVA was performed on GCRMA-normalized log2 transformed signal intensities to assess gene expression variability with regard to RNAi treatment and treatment conditions (FDR ≤ 0.1).
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| |
|
| Submission date |
May 19, 2009 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Dale Dorsett |
| Organization name |
Saint Louis University School of Medicine
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
1100 South Grand Boulevard
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63104 |
| Country |
USA |
| |
|
| Platform ID |
GPL1322 |
| Series (1) |
| GSE16152 |
Effects of Nipped-B and Rad21 sister chromatid cohesin proteins on gene expression in Drosophila ML-DmBG3 cells |
|
| Relations |
| Reanalyzed by |
GSE119084 |
