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In addition, we also explored canonical pathways that are enriched using the Ingenuity Pathway Analysis (IPA) System http://www.ingenuity.com/.com/
After examining the general features of Hsp90-dependent proteome, we next determined the pathways or functions in which those proteins are enriched using the integrated database FunSpec (Robinson et al. 2002).
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** 6-7) Alternatively, B cells can be enriched using the B cell enrichment kit and manual magnet from BD according to the manufaturers instructions.
Read depth was greater and less variable among samples that had been enriched using the RNA-bait hybridization capture enrichment method.
These finished libraries were enriched using the Nimblegen SeqCap kit.
The pathway terms were enriched using the KEGG orthology based annotation system (KOBAS).
Heterozygous CD3+ T cells (termed "effector T cells" (TEFF) throughout) were enriched using the non-contact T Lymphocyte Enrichment Kit and MACS technology (both BD Biosciences).
The low-molecular-weight RNA fraction was enriched using the miRNA Isolation Kit MIRACLE (Stratagene, La Jolla, CA, USA).
The methylated fraction of genomic DNA was enriched using the methylated DNA immunoprecipitation (MeDIP) assay [31] and interrogated on human Promoter plus CpG Island Tiling Arrays with a ChIP design for CpG islands and promoter regions (n = 28,226) from HG18 using 385,020 Probes selected from CGH probe bank with a median spacing of 101bp (Roche NimbleGen, Madison, WI).
Mononuclear cells (MNC) were separated by density gradient centrifugation on Biocoll (Biochrom KG, Berlin, Germany) and CD34+ cells were enriched using the human CD34 Micro Bead Kit on a MiniMACS system according to the manufacturer's instructions (Miltenyi Biotec GmbH, Bergisch-Gladbach, Germany) as described before [9].
Regions of interest were enriched using the above methods and libraries were prepared.
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