Testing gene expression changes in VCaP upon depletion of the mutated ETS transcription factor ERG
ABSTRACT: VCaP cells expressing inducible shRNAs for either ERG or a non-targeting control were treated with Doxycycline for 1, 3, 7 and 10 days prior to collection This experiment is designed to see which genes and pathways are modulated by ERG knockdown VCaP cells stably expressing a Doxycycline (dox)-inducible control nontargeting shRNA (Pak4) or an ERG shRNA (2217) were exposed to 100ng/ml Dox for the noted days.
Project description:VCaP cells expressing either NTC shRNA or PRMT5 shRNA 1 or shRNA 2 were treated with 100ng/ml doxycycline for 5 days This experiment is designed to see which genes and pathways are modulated by PRMT5 knockdown in VCaP cells VCaP cells were treated with 100ng/ml doxyxycline for 3 days.
Project description:Ddx5 inhibition in RN2 cells slows cell proliferation and induces apoptosis within 48-72hrs. The aim of this analysis was to gain insight into how Ddx5 inhibition causes this outcome by analyzing gene expression changes in RN2 cells that occur at early timepoints after Ddx5 inhibition that precedes the timepoint when RN2 proliferation/cell death becomes evident in tissue culture (72hrs after inhibition). Derivatives of RN2 AML cells were prepared that encode doxycycline-inducible expression of either of two different shRNAs targeting Ddx5 (shDdx5.1322 and shDdx5.2086) or a negative control shRNA that targets Renilla Luciferase (shRen.713). Six independent cultures of each derivative RN2 cell line (shDdx5.1322, shDdx5.2086, or shRen.713) were treated with doxycycline at timepoint 0 days to induce expression of the indicated shRNA in the RN2 cells. Each shRNA is co-expressed with dsRed in a doxycycline-induced manner and flow cytometry analysis indicated that doxycycline induced expression of dsRed and the shRNA in 70-to-80% of the cells in each culture. RNA was isolated from three independent cultures of each derivative RN2 cell line at either 24hrs and 48hrs after dpxycycline treatment. Therefore this study consists of 18 samples, sequencing results from biological triplicate samples of RN2-shDdx5.1322, RN2-shDdx5.2086, and RN2-shRen.713 at 24hrs post-doxycycline and sequencing results from biological triplicate samples of RN2-shDdx5.1322, RN2-shDdx5.2086, and shRen.713 at 48hrs post-doxycycline.
Project description:MCL lines were treated with or without 100ng/ml doxycycline for 7 days This experiment is designed to see if shRNA-mediated knockdown of NIK downregulates NFKB signaling in MCL lines with mutations in upstream regulators of the alternative pathway (TRAF2 & TRAF3) MCL cells carrying inducible non-targeting control (NTC) shRNA, NIKshRNA#1 (NIKsh#1), or NIKshRNA#2 (NIKsh#2) were seeded in 6well dishes and treated for 7 days with or without 100ng/ml doxycycline.
Project description:Replicates of ChIP seq data using AR and ERG antibodies from VCaP cell lines harboring inducible shRNA constructs for PRMT5 (3 independent, sh1, sh2, sh3) and 1 non targeting control (NTC), all sample stimulated with ligand, either DHT or R1881 Overall design: AR ChIPseq in VCaP cells, 3 replicates each of DHT stimulated cells with one of 4 inducible shRNA constructs, sh1, sh2, sh3 targeting PRMT5 or NTC non targeting controls. Furthermore 2 AR ChIPseq in the same system stimulated with R1881 for targeting constructs sh1, sh2 and NTC. ERG ChIPseq 2 replicates DHT stimulated, each of sh1, sh2, sh3 constructs. Cells where induced (doxycyclin) for shRNA expression on day0, hormone starved on day3 and harvested on day5.
Project description:The goal of this project was to analyze the global gene expression profiles of RWPE1 and VCAP cells following transfection of GFP, GFP-ERG at 48 and 72hrs time points and stable ERG shRNA, scramble shRNA, respectively. Overall design: RWPE1 cells were transfected with GFP or GFP-ERG. VCAP cells were transfected with ERG lenti-shRNA or scramble shRNA. Transfections were performed in duplicate. Total cellular RNA was isolated with Trizol and quality analysed by the bioanalyser kit.
Project description:The goal of this project was to analyze the global gene expression profiles of RWPE1 and VCAP cells following transfection of GFP, GFP-ERG at 48 and 72hrs time points and stable ERG shRNA, scramble shRNA, respectively. RWPE1 cells were transfected with GFP or GFP-ERG. VCAP cells were transfected with ERG lenti-shRNA or scramble shRNA. Transfections were performed in duplicate. Total cellular RNA was isolated with Trizol and quality analysed by the bioanalyser kit.
Project description:Transcriptional profiling of human OCI-AML3 cells stably expressing inducibly Atg5 shRNA or NPM1-shRNA Goal was to determine the effects of knockdown of Atg5 or NPM1 on global ES gene expression of human Leukemia OCI-AML3 cells. Overall design: Control (Dox-) vs. inducible knock down of Atg5 (Dox+) or NPM1 (Dox+) by doxycycline. Biological replicates: 3 control replicates, Atg5-shRNA 2 replicates, NPM1-shRNA 3 replicates
Project description:Gene expression of T47D-MTVL human breast cancer cells expressing Dox-inducible shRNAs against histone H1X Stable breast cancer-derived cell lines expressing an shRNA against the histone H1X isoforms in response to doxycycline (Dox) were grown for six days in the presence or absence of Dox, and serum-starved for the last 48h for synchronization in G1, in duplicate, and RNA extracted for microarray hybridization. Cell lines used: inducible shRNA against H1X, and random shRNA-expression vector as a control.
Project description:Osteoblasts represent an important cell type playing a role in not only bone formation but also regulate hematopoiesis by secreting factor as well as via contact with hematopoietic stem cells in the bone marrow. Since Wnt signalling plays an important role in osteoblast differentiation, we were interested in looking at how canonical Wnt signalling activation in osteoblastic cells is likely to affect hematopoietic cell adhesion and regulate their fate. Endogenous Wnt signaling activation in osteoblastic SaOS2 cells was achieved by generating doxycycline (DOX) inducible antisense-APC expressing SaOS2 cells. Gene expression profiling was performed on SaOS2 cells induced with DOX (1μg/ml) for 3 days and further on DOX treated cells allowed to recover for 3 days. The results reveal changes in expression of a number of cell adhesion and extracellular matrix protein genes as well as genes involved in osteoblast differentiation. Doxycycline inducible antisense APC expressing SaOS2 cells were treated with DOX for 3 days and compared with control (untreated) cells. In addition, a set of DOX induced cells was further cultured for 3 days in absence of Dox to allow for the cells to recover and see the change in gene expression compared to Dox treated and control cells. All experiments were done in triplicates (in total 9 samples).
Project description:Gene expression of T47D-MTVL human breast cancer cells expressing Dox-inducible shRNAs against histone H1.4 (120sh) or multiple H1 variants (225sh) Overall design: Stable breast cancer-derived cell lines expressing an shRNA against one of each of the histone H1 isoforms in response to doxycycline (Dox) were grown for six days in the presence or absence of Doxicycline, RNA extracted and high-thorughput sequenced. Cell lines used: inducible shRNA against H1.4 or multiple H1 variants and random shRNA-expression vector.