R语言 nem包 SahinRNAi2008()函数中文帮助文档(中英文对照)

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SahinRNAi2008(nem)
SahinRNAi2008()所属R语言包：nem

                                        Combinatorial Protein Knockdowns in the ERBB Signaling Pathway
                                         ERBB信号通路的组合蛋白击倒

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Sixteen RNAi knockdowns (including 3 double knockdowns) of proteins in the ERBB signaling pathway of trastuzumab resistant breast cancer cells were conducted. Reverse Phase Protein Array (RPPA) measurments for 10 signaling intermediates are available before and after EGF stimulation with 4 technical and 3 biological replicates.
十六RNA干扰击倒ERBB单抗耐药乳腺癌单元信号通路中的蛋白（包括双击倒3）进行。扭转为10个信号中间体阶段蛋白质阵列（RPPA）观测值可与4技术和3生物复制EGF刺激之前和之后。


用法----------Usage----------


data(SahinRNAi2008)



格式----------Format----------

dat.unnormalized: 408 x 17 matrix (rows = RPPA measurements for (16 KOs + MOCK) x 4 technical x 3 biological replicates, columns = 10 antibodies + 6 proteins without measurements + time) dat.normalized: 408 x 17 matrix (measurements from technical and biological replicates are quantile normalized for each RNAi experiment) map.int2node: list with names being interventions (=names of dat.normalized) and entries being node names (=column names of dat.normalized)
dat.unnormalized：408×17矩阵（行=（16科斯RPPA测量+假）×4技术×3生物复制，列= 10抗体+ 6蛋白无测量+时间）dat.normalized：408×17矩阵（测量从技术和生物复制位数为每个RNAi实验归）map.int2node名被干预（dat.normalized =名称）和条目节点名称（= dat.normalized列名列表）


Details

详情----------Details----------

The cells were lysed on ice by scraping the cells in M-PER lysis buffer (Pierce, Rockford, IL) containing protease inhibitor Complete Mini (Roche, Basel), anti-phosphatase PhosSTOP (Roche, Basel), 10 mM NaF and 1mM Na4VO3. Protein concentrations were determined with a BCA Protein Assay Reagent Kit (Pierce, Rockford, IL). Lysates were mixed 1:2 with 2 times Protein Arraying Buffer (Whatman, Brentfort, UK) to obtain a final protein concentration of 1.5 mug/muL. Briefly, these lysates were printed onto nitrocellulose coated ONCYTE-slides (Grace Bio Labs, Bend, USA) using a non-contact piezo spotter, sciFlexxarrayer S5 (Scienion, Berlin, Germany). After primary and near-infrared (NIR)-dye labeled secondary antibodies applied, spots were analysed using an Odyssey scanner (LI-COR, Lincoln, USA) and signal intensities were quantified using Odyssey 2.0 software (For detailed information and an antibody list, see Sahin et al., 2008). Since no antibody against MEK1 was available, we measured protein expression of pERK1/2, which is downstream of MEK1.
刮的M-PER裂解液中的单元，单元裂解冰（皮尔斯，罗克福德，IL），含有完整的迷你蛋白酶抑制剂（罗氏，巴塞尔），反磷酸PhosSTOP的（罗氏，巴塞尔），10毫米氟化钠和1mM Na4VO3 。用BCA蛋白测定试剂盒（皮尔斯，罗克福德，IL）进行了测定蛋白质浓度。裂解液混合2倍的蛋白质阵列缓冲（滤纸，Brentfort，英国）1:2取得最终的蛋白浓度的1.5杯/ MUL。简单地说，这些裂解印上硝化棉涂层ONCYTE幻灯片（格雷斯生物实验室，弯曲，美国），使用非接触式压电去污剂，sciFlexxarrayer五Scienion，柏林（德国）。应用于小学和近红外（NIR）的染料标记的二抗后，斑点分析奥德赛扫描仪（LI-COR公司，林肯，美国）和信号强度进行量化使用奥德赛2.0软件（有关详细信息和抗体列表看到沙欣等，2008）。由于没有对MEK1抗体，我们测量了磷酸化ERK1 / 2蛋白表达，是MEK1下游的。


参考文献----------References----------



参见----------See Also----------

BoutrosRNAi2002
BoutrosRNAi2002


举例----------Examples----------


    data("SahinRNAi2008")
    dim(dat.normalized)
    dim(dat.unnormalized)      

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注：
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