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| Status |
Public on Sep 22, 2016 |
| Title |
Gene expression following: RNAi knockdown of grappa, lilliputian, or Suppressor of Triplolethal; induction of Cyclin-dependent kinase 9 dominant negative constructs, or ectopic expression of stand still in Drosophila melanogaster. |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We report the transcriptional profiling of Drosophila melanogaster gonadectomized adults following RNAi knockdown of grappa (gpp), lilliputian (lilli), or Suppressor of Triplolethal [Su(Tpl)], as well as induction of Dominant Negative (DN) allele of Cyclin-dependent kinase 9 (Cdk9), or ectopic expression of stand still (stil), with a three-component temperature sensitive system. We also included the transcriptional profiling of testes and ovaries of gppRNAi, lilliRNAi, and Su(Tpl)RNAi flies under permissive temperature. All data includes induced and non-induced sham controls.
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| Overall design |
We used a three-component temperature sensitive expression system by ubiquitously expressing both Gal4 [P{tubP-GAL4}LL7 (FBti0012687)] and the temperature-sensitive Gal4 repressor, Gal80ts [P{tubP-GAL80ts}7 (FBti0027798)], in the presence of one of the Gal4 UAS responsive transgenes - gppRNAi [y1 sc* v1; P{TRiP.HMS00160}attP2 (FBst0034842)], lilliRNAi [y1 sc* v1; P{TRiP.HMS01066}attP2 (FBst0034592)], Su(Tpl)RNAi [y1 sc* v1; P{TRiP.HMS00277}attP2 (FBst0033399)]. We used the same system to express the dominant negative allele of Cdk9 with P{UASp-Cdk9DN}Ifm1 and P{UASp-Cdk9DN}Ifm1, P{UASp-Cdk9DN}Cff1 (Daniel Pauli, unpublished), and ectopically express stil with w*; P{UASp-stil+}Amm (Daniel Pauli, unpublished). Both stil and Cdk9 constructs were cloned into the expression vector (i.e., UASp) and introduced into fly third chromosome by P-element mediated transformation. The Cdk9DN has a codon substitution to encode asparagine rather than aspartic acid in position 199 (D199N) in the active site of the kinase. For the gonadectomized fly samples, we used gppRNAi, lilliRNAi, Su(Tpl)RNAi, stil ectopic over expression, Cdk9DN over expression, as well as two sham control lines, i.e., w1118 (FBst0003605) and P{UASp-lacZ} (FBtp0010276), and all flies of the above lines were reared and crossed under the same protocol. Following shifts from the permissive (20 oC) to the restrictive temperature (29 oC), we removed the gonads and collected gonadectomized flies (three per sample) for single-end 50 bp PolyA+ strand-specific RNA-seq. For all the gonad samples, we used gppRNAi, lilliRNAi, Su(Tpl)RNAi, and the control line P{UASp-lacZ}, and the files were reared at the permissive temperature only. For each gonad sample, we dissected three pairs. We followed the same library and RNA-seq pipeline for all samples. In total, 192 samples were sequenced, of which 189 samples with > 2.5 million mapped reads are reported here. 93 samples are in triplicate, 92 samples are in quadruplicate, and four samples are in duplicate. There are 96 male samples (including 16 testis) and 93 female samples (including 16 ovary). Additionally, there are time-points at 0, 24, and 48 hours post temperature shift for all non-gonad samples.
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| Contributor(s) |
Yang H, Whitworth C, Pauli D, Oliver B |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Feb 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Oliver |
| E-mail(s) |
[email protected]
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| Phone |
301-204-9463
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| Organization name |
NIDDK, NIH
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| Department |
LBG
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| Lab |
Developmental Genomics
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| Street address |
50 South Drive
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platforms (1) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
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| Samples (189)
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| Relations |
| BioProject |
PRJNA310631 |
| SRA |
SRP069203 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE77492_RAW.tar |
11.9 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE77492_dmel-all-r6.04.ERCC.gtf.gz |
3.6 Mb |
(ftp)(http) |
GTF |
| GSE77492_merged.star_htseq_read_count.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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