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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from fibroblasts BjhTERT-RhoA-KO and PC3 tumor cells after cocultivation and before

ABSTRACT: Gene expression analysis of BJhTERT RhoA-KO and PC3 mRFP was performed before and after six days confrontation in co-cultivation. Analyses of original and control fibroblasts was also performed. To identify molecules that may mediate the tumor promoting effect of RhoA knock out fibroblasts, we performed gene expression analysis of BJhTERT RhoA-KO and PC3 mRFP cells before the confrontation and then after six days after it, using Affymetrix Whole Transcript Assay platform. Four days old fibroblast monolayer was confronted with PC3 mRFP tumor cells, plated in ratio 1:30 to number of plated fibroblasts. After six days of confrontation cells were sorted by FACS (Fluorescence-activated cell sorting). Total RNA was isolated from each confronted and non-confronted cells with kit. Then 150 ng of total RNA were used for transcriptomic analysis.for RNA extraction and hybridization on Affymetrix microarrays

ORGANISM(S): Homo sapiens

SUBMITTER: Tatiana Pavlova

PROVIDER: E-GEOD-83913 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from fibroblasts BjhTERT-RhoA-KO and PC3 tumor cells after cocultivation and before

Project description:Gene expression analysis of BJhTERT RhoA-KO and PC3 mRFP was performed before and after six days confrontation in co-cultivation. Analyses of original and control fibroblasts was also performed. To identify molecules that may mediate the tumor promoting effect of RhoA knock out fibroblasts, we performed gene expression analysis of BJhTERT RhoA-KO and PC3 mRFP cells before the confrontation and then after six days after it, using Affymetrix Whole Transcript Assay platform.

2016-07-01 | GSE83913 | GEO

Increased Rho GTPase activity is associated with decreased tumor inhibitory activity of immortalized fibroblasts

Project description:Clone (Whirly) of human BJhTERT (human foreskin cell line) cells exposed to PC3 mRFP cells Clones (Whirly) of human BJhTERT (human foreskin cell line) cells exposed to PC3 mRFP cells were analyzed with Affymetrix Whole Target (WT) Assay (GeneTitan plate format Gene ST 1.1)

2014-04-17 | E-GEOD-56832 | biostudies-arrayexpress

Drosophila melanogaster selection lines confronted with Aspergillus nidulans

Project description:Experimental evolution was conducted using Drosophila melanogaster populations that developed as larvae on breeding substrate that was infested with Aspergillus nidulans wild type, A. nidulans toxin-impaired mutant strain delta-laeA, the mycotoxin sterigmatocystin, or on fungi and toxin free substrate. Overall population were reared under these conditions for 11 generations, where after each confrontation generation one relaxation generation (fungi and toxin free breeding substrate) was conducted. Nine generations after the last selection treatment, first instar larvae were confronted with 3 days old A. nidulans wild type colonies or control conditions. 24 hours after confrontation start larvae were collected. For each biological replicate 52 larvae were collected from 4 independent confrontation units, balanced design. Three populations per selection regime were conducted, resulting in: 2 conditions x 4 selection regimes x 3 biological replicates (equal to fly population) = 24 samples. Selection regimes: sCO= control; sWT= A. nidulans wild type; sLA= A. nidulans mutant strain; sST= Sterigmatocystin. confrontation condition: cCO= control; cWT= A. nidulans wild type.

2020-05-09 | E-MTAB-9011 | biostudies-arrayexpress

The inhibition of tumor cell proliferation and motility by fibroblasts is both contact and soluble factor dependent

Project description:Clone (Whirly) of human BJhTERT (human foreskin cell line) cells exposed to PC3 mRFP cells

2014-04-17 | GSE56832 | GEO

Urinary bladder in constant darkness: time course

Project description:Analysis of urinary bladder in wild-type C57BL/6 females sacrificed every 4 hours at six time points under constant darkness after acclimation for 2 weeks under 12-hour light and 12-hour dark conditions. Results provide insight into circadian gene expression patterns in normal urinary bladder. Analysis of urinary bladder in wild-type C57BL/6 females sacrificed every 4 hours at six time points (n=2 for each time (CT 0, 4, 8, 12 and 20)) under constant darkness after acclimation for 2 weeks under 12-hour light and 12-hour dark conditions.

2012-04-30 | E-GEOD-35795 | biostudies-arrayexpress

Homo sapiens

Project description:Expression data from fibroblasts BjhTERT-RhoA-KO and PC3 tumor cells after cocultivation and before

| PRJNA327397 | ENA

Gene expression profiles of human immature dendritic cells co-cultivated with Aspergillus fumigatus, Candida albicans and LPS

Project description:In a whole-transcriptome study, cellular responses of DCs confronted with the fungi A. fumigatus, C. albicans or the bacterial cell wall component LPS were investigated. Therefore DCs of four independent donors were harvested after 6 and 12 hours co-culture with A. fumigatus, C. albicans and LPS and analyzed with Affymetrix whole genome expression arrays. In general, transcriptomic analysis revealed a clustering of the A. fumigatus and C. albicans stimulated DCs. However, LPS and fungi-dependent gene expression showed more common similarities compared to the untreated control. Stimulation with LPS induced a differential regulation of 2793 and 2863 genes after 6 /12h, while confrontation with A. fumigatus and C. albicans resulted in 743/1076 and 1729/974 differentially regulated genes, respectively. Kruppel-like factor 4 (KLF4) was identified as the only transcription factor that was down-regulated in DCs by both fungi but induced by stimulation with LPS. Human DCs were generated from 4 independent, healthy blood donors. moDCs were either left untreated or co-cultivated with Aspergillus fumigatus 46645 germ tubes or Candida albicans SC5314 (MOI1) and or LPS (1µg/ml) for 6h.

2015-06-23 | E-GEOD-69723 | biostudies-arrayexpress

Epstein-Barr Virus (EBV)-positive B-cell strain, 28-2: Low v. High latent membrane protein 1 (LMP1)-mRFP expression (miRNA)

Project description:Expression of miRNAs in an EBV-positive B-cell strain, 28-2. 28-2 are infected with a derivative of the B-958 strain of EBV, which expresses eGFP constitutively and LMP1 fused to mRFP from its native promoter. Single cells were sorted by flow cytometry for their levels of LMP1-mRFP (5% expressing the lowest levels of LMP1-mRFP or 5% expressing the highest levels of LMP1-mRFP) Two-condition experiment: Low v. High LMP1-mRFP expression. Biological replicates: 3 Low LMP1-mRFP, 3 High LMP1-mRFP. Samples were normalized to the expression of miRNAs in a pool of unsorted 28-2 cells.

2012-02-01 | E-GEOD-33972 | biostudies-arrayexpress

Epstein-Barr Virus (EBV)-positive B-cell strain, 28-2: Low v. High latent membrane protein 1 (LMP1)-mRFP expression

Project description:Expression of mRNAs in an EBV-positive B-cell strain, 28-2. 28-2 are infected with a derivative of the B-958 strain of EBV, which expresses eGFP constitutively and LMP1 fused to mRFP from its native promoter. Single cells were sorted by flow cytometry for their levels of LMP1-mRFP (5% expressing the lowest levels of LMP1-mRFP or 5% expressing the highest levels of LMP1-mRFP) Two-condition experiment: Low v. High LMP1-mRFP expression. Biological replicates: 3 Low LMP1-mRFP, 3 High LMP1-mRFP. Samples were normalized to the expression of mRNAs in a pool of unsorted 28-2 cells.

2012-02-01 | E-GEOD-33673 | biostudies-arrayexpress

RNA-seq experiment of Drosophila melanogaster larvae reared on Aspergillus nidulans infested breeding substrate

Project description:Drosophila melanogaster larvae and filamentous fungi both utilise organic material. Here they compete for resources. Filamentous fungi can defend themselves and their substrate from predation respectively competition by the production and excretion of secondary metabolites, including substances with antibiotic and insecticidal properties. To analyse the traits that enables D. melanogaster larvae to reduce the harmful effects of fungal secondary metabolites and to develop on fungal infested substrate we confronted larvae with a toxin-producing wild type of Aspergillus nidulans, with a toxin-production-impaired mutant strain of A. nidulans, and with sterigmatocystin, a highly toxic metabolite of A. nidulans. Early first instar larvae were transferred to breeding substrate inhabited by fungal colonies respectively inoculated with the purified mycotoxin or controls. After 3, 6, 12, and 24 hours of confrontation larvae were collected and samples prepared for whole transcriptome shotgun sequencing.

2017-12-01 | E-MTAB-5344 | biostudies-arrayexpress

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