Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Human colon carcinoma cell line treated with bafilomycin A1

ABSTRACT: Analysis of mRNA expression changes in human colon carcinoma cell lines (HCT116 H2B-GFP) after treatment bafilomycin A1. mRNA expression analysis of HCT116 H2B-GFP treated with bafilomycin A1 compared to untreated HCT116 H2B-GFP. Four biological replicates were performed for treated samples.

ORGANISM(S): Homo sapiens

SUBMITTER: Milena DÃ¼rrbaum

PROVIDER: E-GEOD-47836 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Unique features of the transcriptional response to model aneuploidy in human cells.

Dürrbaum Milena M Kuznetsova Anastasia Yurievna AY Passerini Verena V Stingele Silvia S Stoehr Gabriele G Storchová Zuzana Z

BMC genomics 20140218

<h4>Background</h4>Aneuploidy, a karyotype deviating from multiples of a haploid chromosome set, affects the physiology of eukaryotes. In humans, aneuploidy is linked to pathological defects such as developmental abnormalities, mental retardation or cancer, but the underlying mechanisms remain elusive. There are many different types and origins of aneuploidy, but whether there is a uniform cellular response to aneuploidy in human cells has not been addressed so far.<h4>Results</h4>Here we evalua ...[more]

PMID: 24548329

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Project description:We sought to determine which gene transcripts are enriched in Wnt-responsive adrenocortical mouse cells compared to the entire adrenocortical mouse cell population in vivo. To this end, we employed transgenic reporter mice that label Wnt-responsive cells with GFP expression (TCF/Lef:H2B-GFP mice) or label all adrenocortical cells with GFP expression (Sf1:eGFP mice). GFP-positive adrenocortical cells were obtained from 6-week-old male TCF/Lef:H2B-GFP mice and Sf1:eGFP mice independently. 10 adrenals per genotype per sort were minced and digested by incubation in DMEM:F12 containing 0.1% collagenase/ 0.01% DNaseI solution for 1 h at 37Â°C. A single cell suspension was obtained following mechanical dispersion, filtration through a 40 micron nylon cell strainer, centrifugation at 1500rpm for 5 min followed by re-suspension in sterile 1X PBS containing 10% cosmic calf serum and 10Î¼g/mL Propidium iodide. 10,000-50,000 viable GFP-positive cells were isolated via FACS using a BD FACSAria III cell sorter. RNA was extracted using an RNeasy Micro Kit (Qiagen) from 4 independent sorts per genotype. cDNA were prepared according to the NuGen WT-Pico V2 kit protocol from 5 ng total RNA (Ovation PicoSL WTA System V2 P/N 3312). Biotinylated single-stranded cDNA were prepared from 3ug of cDNA (Encore Biotin Module P/N 4200-12, 4200-60, 4200-A01). Targets were assayed on the Mouse Gene ST 1.1 strip arrays using the Affymetrix Gene Atlas system (software version 1.0.4.267). One TCF/Lef:H2B-GFP array was deemed low-quality and discarded. Two-sample T-tests were used to compare the two groups of samples. We also supply a supplementary file holding the data and some statistical analysis, as well as probe-set annotation that we used at that time (users may wish to obtain new annotation though). We analyzed only 28944 probe-sets with category "main", "---", and "flmrna->unmapped" according to Affymetrix annotation. GFP-positive adrenocortical cells were obtained from 6-week-old male TCF/Lef:H2B-GFP mice and Sf1:eGFP mice independently. 10 adrenals per genotype per sort were minced and digested by incubation in DMEM:F12 containing 0.1% collagenase/ 0.01% DNaseI solution for 1 h at 37Â°C. A single cell suspension was obtained following mechanical dispersion, filtration through a 40 micron nylon cell strainer, centrifugation at 1500rpm for 5 min followed by re-suspension in sterile 1X PBS containing 10% cosmic calf serum and 10Î¼g/mL Propidium iodide. 10,000-50,000 viable GFP-positive cells were isolated via FACS using a BD FACSAria III cell sorter. RNA was extracted using an RNeasy Micro Kit (Qiagen) from 4 independent sorts per genoytpe. cDNA were prepared according to the NuGen WT-Pico V2 kit protocol from 5 ng total RNA (Ovation PicoSL WTA System V2 P/N 3312). Biotinylated single-stranded cDNA were prepared from 3ug of cDNA (Encore Biotin Module P/N 4200-12, 4200-60, 4200-A01). Targets were assayed on the Mouse Gene ST 1.1 strip arrays using the Affymetrix Gene Atlas system (software version 1.0.4.267).

Dataset Information

Human colon carcinoma cell line treated with bafilomycin A1

Publications

Unique features of the transcriptional response to model aneuploidy in human cells.

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