HEK293 Quality Control example dataset - contamination test
ABSTRACT: A simple HEK293 lysate, with two files containing a putative mycoplasma contamination, and two negative control samples, taken from Geiger etc al. (Mol Cell Proteomics. 2012 Mar;11(3):M111.014050. doi: 10.1074/mcp.M111.014050. Epub 2012 Jan 25.) [PXD002395].
Mass spectrometry-based proteomics coupled to liquid chromatography has matured into an automatized, high-throughput technology, producing data on the scale of multiple gigabytes per instrument per day. Consequently, an automated quality control (QC) and quality analysis (QA) capable of detecting measurement bias, verifying consistency, and avoiding propagation of error is paramount for instrument operators and scientists in charge of downstream analysis. We have developed an R-based QC pipeline ...[more]
Project description:Re-submission of raw data from Geiger T et. al., Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol Cell Proteomics. 2012 Mar;11(3):M111.014050. doi: 10.1074/mcp.M111.014050. Epub 2012 Jan 25.
Project description:This SuperSeries is composed of the SubSeries listed below. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Refer to individual Series
Project description:A simple HEK293 lysate, which can be used to benchmark the performance of both the LC system and the mass spectrometer. The four files uploaded here were aqcuired on different timepoints and show distinct LC column differences.
Project description:Frozen tissue specimens from primary breast tumors were collected and profiled using Affymetrix U133 plus 2 expression microarrays. A publication describing the generation of these data is not yet available. However, these data can be used alongside other Affymetrix breast tumour data sets to form large meta-cohorts for breast cancer research, as was done in Lasham et. al. J Natl Cancer Inst. 2012 Jan 18;104(2):133-146. Frozen tumor tissues comprising of >60% tumor cellularity were extracted for total RNA and hybridized on Affymetrix microarrays.
Project description:Comparative Dynamic Transcriptome Analysis (cDTA) enables global analysis of newly synthesized RNA as described in Sun et al. Genome Res. 2012 (DOI:10.1101/gr.130161.111) and reveals defects in transcription with much higher sensitivity than conventional steady-state methods. cDTA was carried out as described in Sun et al. Genome Res. 2012 (DOI:10.1101/gr.130161.111), using the S. cerevisiae heterozygous Med17/med17delta strain (Euroscarf) transfected with plasmids pRS315-SRB4 or pRS315-srb4-ts as described in Larivi̬re et al. Nature. 2012 (DOI:10.1038/nature11670), and Y40343-wildtype (Euroscarf) or Med18-FRB-KanMX6 (Euroscarf) strains. Heatshock of SRB4 and srb4-ts strains was applied for 18 or 60 minutes at 37C prior to RNA labeling as described in Sun et al. Genome Res. 2012 (DOI:10.1101/gr.130161.111). To deplete the Med18 subunit from the nucleus, anchor-away experiments were performed by rapamycin treatment (1 ug/ml in 200 mL YPD) for 18 or 60 minutes at 30C prior to RNA labeling as described in Sun et al. Mol. Cell. 2013 (DOI:10.1016/j.molcel.2013.09.010). Data analysis was as described in Sun et al. Genome Res. 2012 (DOI:10.1101/gr.130161.111).
Project description:Various anti-mycoplasma drugs have different effects on cells growth We used microarrays to detail the global programme of gene expression underlying gastric cancer cells treated with anti-mycoplasma drugs and identified distinct classes of up-regulated genes during this process. Overall design: Gastric cancer cells treated with anti-mycoplasma drugs were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain a disparate impact of gastric cancer cells treated with anti-mycoplasma drugs. To that end, we selected two cell lines of gastric cancer cell, AGS and BGC823, which were treated with four anti-mycoplasma drugs (A2PP, CIP, MYCO1 and MYCO2) separately.