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Enzymatic Methyl-seq (EM-seq) of doxycycline induced tumor and residual mouse primary mammary epithelial cells grown in 3D cell cultures against non-induced controls

ABSTRACT: This experiment investigates the genome wide DNA methylation landscape of residual breast cancer cells. Primary mammary epithelial cells taken from female mice with doxycycline-inducible hMyc- and Neu/Her2-oncogenes were grown in 3D organoid cultures. Upon the addition of doxycycline (200ng/mL) to the medium the expression of the oncogenes gets activated and the cells start uncontrolled proliferation resembling tumor growth. Tumor samples were taken after 5 days of oncogene induction. Subsequently, doxycycline was removed from the medium, which silences oncogene expression and results in rapid tumor regression. Residual samples reminiscent to the non-induced (normal) structures were taken after 7 days of de-induction (12 days overall). Non-induced structures were grown and sampled in parallel to the residual structures.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Mus musculus

SUBMITTER: Katharina Zirngibl

PROVIDER: E-MTAB-10979 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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RNA-seq of doxycycline induced tumor and residual mouse primary mammary epithelial cells grown in 3D cell cultures against non-induced controls

Project description:This experiment investigates the expression characteristics of residual breast cancer cells. Primary mammary epithelial cells taken from female mice with doxycycline-inducible hMyc- and Neu/Her2-oncogenes were grown in 3D organoid cultures. Upon the addition of doxycycline (200ng/mL) to the medium the expression of the oncogenes gets activated and the cells start uncontrolled proliferation resembling tumor growth. Tumor samples were taken after 5 days of oncogene induction. Subsequently, doxycycline was removed from the medium, which silences oncogene expression and results in rapid tumor regression. Residual samples reminiscent to the non-induced (normal) structures were taken after 7 days of de-induction (12 days overall). Non-induced structures were grown and sampled in parallel.

2020-12-31 | E-MTAB-8834 | biostudies-arrayexpress

Gene expression in organized and disorganized human breast epithelial cells

Project description:We have reported more than a dozen microenvironmental factors whose signaling must be integrated in order to effect an organized, functional tissue morphology. In order to identify underlying commonalities in gene transcription associated with the phenotype, we compared the gene expression of organized and disorganized epithelial cells of the HMT-3522 breast cancer progression series: the non-malignant S1 cells that form polarized spheres (‘acini’), the malignant T4-2 cells that form large tumor-like clusters, and the ‘phenotypically reverted’ T4-2 cells that polarize as a result of correction of the microenvironmental signaling. 24 samples were analyzed: 5 samples were non-malignant S1 cells that formed organized spherical structures ('acini'), 5 samples were the isogenic malignant counterpart of S1 cells, namely the T4-2 cells, which grow into disorganized large cell clusters; and 14 samples of T4-2 cells that had been treated with different reverting agents, these reverting agents cause the T4-2 cells to 'revert' in phenotype so that they resemble the structures formed by S1 cells.

2013-10-01 | E-GEOD-50444 | biostudies-arrayexpress

Identification of targets regulated by HSF1 in response to HSP90 inhibitors

Project description:A375 cells with inducible knockdown HSF1 with and without HSP90 inhibitor treatment A375 cells were seeded in 6-well plates for 3d with 100ng/ml doxycycline prior to treatment with 0.1% DMSO or 100nM HSP990 for 3h

2013-03-06 | E-GEOD-44867 | biostudies-arrayexpress

RNA-seq of DCIS-pInducer21-SOX11 cells grown in 2D and 3D

Project description:Using the pINDUCER21 system, we modified DCIS.com cells so that SOX11 is expressed at much higher levels after induction with Doxycycline (Dox) than observed with the constitutive DCIS-SOX11 cells we have used to model DCIS progression. After Dox induction of pIND21-SOX11 cells, both SOX11 and CD24 expression are significantly increased ). Higher ALDH levels are detected in pIND21-SOX11 cells, suggesting that high levels of SOX11 promotes acquisition of features associated with distinct types of cancer stem cells.

2020-09-21 | E-MTAB-9108 | biostudies-arrayexpress

Testing rescue of AR signaling by ectopic expression of mutant AR allele in the presence of MDV-3100

Project description:Genetically engineered LNCaPs overexpressing various AR alleles were treated with 0.1% DMSO or 10uM MDV3100 for 24h prior to collection This experiment is designed to see if expressing the F876L/T877A mutant AR can rescue AR signaling in the presence of MDV3100 Engineered lines were seeded in 6-well plates for 3d with 100ng/ml doxycycline prior to treatment with 0.1% DMSO or 10uM MDV3100 for 24h

2013-09-30 | E-GEOD-44924 | biostudies-arrayexpress

Gene expression profile upon IL-22 stimulation, forced expression of Hes1, or IL-22 stimulation under forced expression of Hes1, in human colon carcinoma-derived LS174T cells

Project description:A human colon carcinoma-derived cell line LS174T was modified to overexpress Hes1, a bHLH-type transcription factor, upon doxycycline addition (designated as LS174T-tetON-Hes1 cells), using the T-rex system (Invitrogen). We have previously shown that these cells can overexpress Hes1 under the control of CMV promoter (Zheng et al, Inflamm Bowel Dis, 17;2251-2260, 2011), and the amont of the overexpressed Hes1 protein reaches to the maximal level in early as 3 hours from doxycycline addition (100ng/ml), which persists for up to 24 hours. In the present experiment, LS174T-tetON-Hes1 cells were treated with recombinant human IL-22 (20ng/ml) alone, doxycycline alone (100ng/ml), co-treated by both IL-22 and doxycycline, or left untreated (Control) for 24 hours, and subjected for analysis. Experiment was done using a modified sub-line of LS174T cell (LS174T-tetON-Hes1 cells), in which overexpression of Hes1 can be induced by a Doxycycline dependent manner. Four-condition experiment, Control vs. IL-22 stimulation, Control vs Doxycycline addition (Hes1 overexpression) and Control vs IL22 stimulation+Doxycycline addition (Hes1 overexpression). Biological replicates: One for each condition, independently grown and harvested. One replicate per array.

2013-10-01 | E-GEOD-43012 | biostudies-arrayexpress

Expression data from Î²-globin let7 HeLa tet off cells treated with doxycycline

Project description:We used microarray to determine the genes whose expression was changed at six hours after doxycycline treatment Cells were transfected with Î²-globin let7 wt constructs. Two-condition experiment; HeLa tet off cells overexpressed control vs HeLa tet off cells treated with doxycycline for six hours

2016-03-15 | E-GEOD-66541 | biostudies-arrayexpress

Analysis of gene expression changes in RN2 acute myeloid leukemia (AML) cells at 24hrs and 48hrs after Ddx5 knockdown.

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.

2013-12-26 | E-GEOD-53599 | biostudies-arrayexpress

Elevating Sox2 levels deleteriously affects the growth of glioblastoma and medulloblastoma cells.

Project description:Induction of the transcription factor Sox2 from a doxycycline-inducible promoter in iSox2-DAOY medulloblastoma cells. Affymetrix microarrays were used to characterize the gene expression profile of iSox2-DAOY cells in the absence and presence of doxycycline. Human DAOY medulloblastoma cells were engineered to express epitope tagged Sox2 under the control of a doxycycline inducible promoter, to produce iSox2-DAOY cells. iSox2-DAOY cells were FACS sorted into CD133 low and high populations. The CD133 low population was cultured in the absence and presence of 0.5 Âµg/mL doxycycline for 24 hours. RNA was extracted from cells cultured without and with doxycycline, and was used for microarray analysis.

2012-08-25 | E-GEOD-36947 | biostudies-arrayexpress

Testing gene expression changes in VCaP upon depletion of the mutated ETS transcription factor ERG

Project description: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.

2014-08-27 | E-GEOD-60771 | biostudies-arrayexpress

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