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| Status |
Public on May 19, 2009 |
| Title |
Effects of Nipped-B and Rad21 sister chromatid cohesin proteins on gene expression in Drosophila ML-DmBG3 cells |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by array
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| Summary |
Effects of Nipped-B and Rad21 sister chromatid cohesin proteins on gene expression data in ML-DmBG3 cells derived from Drosophila melanogaster larval central nervous system
We examined the effects of Nipped-B and Rad21 knockdown on gene expression in BG3 cells using microarrays that measure over 18,700 transcripts to (a) determine if the effects of cohesion on E(spl)-C and invected-engrailed expression are unique, (b) look for effects of cohesin on regulators of E(spl)-C and engrailed, and (c) obtain a comprehensive view of the effects of cohesin on gene expression.
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| Overall design |
Effects of cohesin knockdown on E(spl)-C and invected-engrailed transcription vary over time, so we used two independent samples for three days after RNAi treatment, one four day and one six day sample for both Nipped-B and Rad21 knockdown, and mock RNAi controls for each time point.
For RNAi treatment, cells were plated at 5x106 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 supplementary file linked below). Equal amounts of two dsRNAs against each target were used.
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| Contributor(s) |
Siddiqui AM, Dorsett D |
| Citation(s) |
19587787 |
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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
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| Department |
Biochemistry and Molecular Biology
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| Street address |
1100 South Grand Boulevard
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| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63104 |
| Country |
USA |
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| Platforms (1) |
| GPL1322 |
[Drosophila_2] Affymetrix Drosophila Genome 2.0 Array |
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| Samples (12)
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| GSM404756 |
ML-DmBG3 cells: RNAi Mock 0 micrograms, 3 days biological rep1 |
| GSM404757 |
ML-DmBG3 cells: RNAi Mock 0 micrograms, 3 days biological rep2 |
| GSM404758 |
ML-DmBG3 cells: RNAi Mock 0 micrograms, 4 days biological rep3 |
| GSM404759 |
ML-DmBG3 cells: RNAi Mock 0 micrograms, 6 days biological rep4 |
| GSM404760 |
ML-DmBG3 cells: RNAi Rad21 40 micrograms, 3 days biological rep1 |
| GSM404761 |
ML-DmBG3 cells: RNAi Rad21 40 micrograms, 3 days biological rep2 |
| GSM404762 |
ML-DmBG3 cells: RNAi Rad21 10 micrograms, 4 days biological rep3 |
| GSM404763 |
ML-DmBG3 cells: RNAi Rad21 10 micrograms, 6 days biological rep4 |
| GSM404764 |
ML-DmBG3 cells: RNAi Nipped-B 40 micrograms, 3 days biological rep1 |
| GSM404765 |
ML-DmBG3 cells: RNAi Nipped-B 40 micrograms, 3 days biological rep2 |
| GSM404766 |
ML-DmBG3 cells: RNAi Nipped-B 10 micrograms, 4 days biological rep3 |
| GSM404767 |
ML-DmBG3 cells: RNAi Nipped-B 10 micrograms, 6 days biological rep4 |
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| Relations |
| BioProject |
PRJNA117171 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE16152_RAW.tar |
24.2 Mb |
(http)(custom) |
TAR (of CEL) |
| GSE16152_RNAiPRIMERS.txt.gz |
572 b |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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