Comparing gene discovery from Affymetrix GeneChip microarrays and Clontech PCR-select cDNA subtraction: a case study

BACKGROUND: Several high throughput technologies have been employed to identify differentially regulated genes that may be molecular targets for drug discovery. Here we compared the sets of differentially regulated genes discovered using two experimental approaches: a subtracted suppressive hybridization (SSH) cDNA library methodology and Affymetrix GeneChip(® )technology. In this "case study" we explored the transcriptional pattern changes during the in vitro differentiation of human monocytes to myeloid dendritic cells (DC), and evaluated the potential for novel gene discovery using the SSH methodology. RESULTS: The same RNA samples isolated from peripheral blood monocyte precursors and immature DC (iDC) were used for GeneChip microarray probing and SSH cDNA library construction. 10,000 clones from each of the two-way SSH libraries (iDC-monocytes and monocytes-iDC) were picked for sequencing. About 2000 transcripts were identified for each library from 8000 successful sequences. Only 70% to 75% of these transcripts were represented on the U95 series GeneChip microarrays, implying that 25% to 30% of these transcripts might not have been identified in a study based only on GeneChip microarrays. In addition, about 10% of these transcripts appeared to be "novel", although these have not yet been closely examined. Among the transcripts that are also represented on the chips, about a third were concordantly discovered as differentially regulated between iDC and monocytes by GeneChip microarray transcript profiling. The remaining two thirds were either not inferred as differentially regulated from GeneChip microarray data, or were called differentially regulated but in the opposite direction. This underscores the importance both of generating reciprocal pairs of SSH libraries, and of real-time RT-PCR confirmation of the results. CONCLUSIONS: This study suggests that SSH could be used as an alternative and complementary transcript profiling tool to GeneChip microarrays, especially in identifying novel genes and transcripts of low abundance

Measurements of the observed cross sections for exclusive light hadron production in e^+e^- annihilation at \sqrt{s}= 3.773 and 3.650 GeV

By analyzing the data sets of 17.3 pb$^{-1}$ taken at $\sqrt{s}=3.773$ GeV and 6.5 pb$^{-1}$ taken at $\sqrt{s}=3.650$ GeV with the BESII detector at the BEPC collider, we have measured the observed cross sections for 12 exclusive light hadron final states produced in $e^+e^-$ annihilation at the two energy points. We have also set the upper limits on the observed cross sections and the branching fractions for $\psi(3770)$ decay to these final states at 90% C.L.Comment: 8 pages, 5 figur

Measurements of psi(2S) decays to octet baryon-antibaryon pairs

With a sample of 14 million psi(2S) events collected by the BESII detector at the Beijing Electron Positron Collider (BEPC), the decay channels psi(2S)->p p-bar, Lambda Lambda-bar, Sigma0 Sigma0-bar, Xi Xi-bar are measured, and their branching ratios are determined to be (3.36+-0.09+-0.24)*10E-4, (3.39+-0.20+-0.32)*10E-4, (2.35+-0.36+-0.32)*10E-4, (3.03+-0.40+-0.32)*10E-4, respectively. In the decay psi(2S)->p p-bar, the angular distribution parameter alpha is determined to be 0.82+-0.17+-0.04.Comment: 8 pages, 8 figure

Search for the Rare Decays J/Psi --> Ds- e+ nu_e, J/Psi --> D- e+ nu_e, and J/Psi --> D0bar e+ e-

We report on a search for the decays J/Psi --> Ds- e+ nu_e + c.c., J/Psi --> D- e+ nu_e + c.c., and J/Psi --> D0bar e+ e- + c.c. in a sample of 5.8 * 10^7 J/Psi events collected with the BESII detector at the BEPC. No excess of signal above background is observed, and 90% confidence level upper limits on the branching fractions are set: B(J/Psi --> Ds- e+ nu_e + c.c.)<4.8*10^-5, B(J/Psi --> D- e+ nu_e + c.c.) D0bar e+ e- + c.c.)<1.1*10^-5Comment: 10 pages, 4 figure

Measurement of \psip Radiative Decays

Using 14 million psi(2S) events accumulated at the BESII detector, we report first measurements of branching fractions or upper limits for psi(2S) decays into gamma ppbar, gamma 2(pi^+pi^-), gamma K_s K^-pi^++c.c., gamma K^+ K^- pi^+pi^-, gamma K^{*0} K^- pi^+ +c.c., gamma K^{*0}\bar K^{*0}, gamma pi^+pi^- p pbar, gamma 2(K^+K^-), gamma 3(pi^+pi^-), and gamma 2(pi^+pi^-)K^+K^- with the invariant mass of hadrons below 2.9GeV/c^2. We also report branching fractions of psi(2S) decays into 2(pi^+pi^-) pi^0, omega pi^+pi^-, omega f_2(1270), b_1^\pm pi^\mp, and pi^0 2(pi^+pi^-) K^+K^-.Comment: 5 pages, 4 figure

Measurements of J/ψJ/\psi and ψ(2S)\psi(2S) decays into ΛΛˉπ0\Lambda \bar{\Lambda}\pi^0 and ΛΛˉη\Lambda \bar{\Lambda}\eta

Using 58 million $J/\psi$ and 14 million $\psi(2S)$ events collected by the BESII detector at the BEPC, branching fractions or upper limits for the decays $J/\psi$ and $\psi(2S) \to \Lambda \bar{\Lambda}\pi^0$ and $\Lambda \bar{\Lambda}\eta$ are measured. For the isospin violating decays, the upper limits are determined to be ${\cal B}(J/\psi \to \Lambda \bar{\Lambda}\pi^0)<6.4\times 10^{-5}$ and ${\cal B}(\psi(2S) \to \Lambda \bar{\Lambda}\pi^0)<4.9\times 10^{-5}$ at the 90% confidence level. The isospin conserving process $J/\psi \to \Lambda \bar{\Lambda}\eta$ is observed for the first time, and its branching fraction is measured to be ${\cal B}(J/\psi \to \Lambda \bar{\Lambda}\eta)=(2.62\pm 0.60\pm 0.44)\times 10^{-4}$, where the first error is statistical and the second one is systematic. No $\Lambda \bar{\Lambda}\eta$ signal is observed in $\psi(2S)$ decays, and ${\cal B}(\psi(2S) \to \Lambda \bar{\Lambda}\eta)<1.2\times 10^{-4}$ is set at the 90% confidence level. Branching fractions of $J/\psi$ decays into $\Sigma^+ \pi^- bar{\Lambda}$ and $\bar{\Sigma}^- \pi^+ \Lambda$ are also reported, and the sum of these branching fractions is determined to be ${\cal B}(J/\psi \to \Sigma^+\pi^- \bar{\Lambda} + c.c.)=(1.52\pm 0.08\pm 0.16)\times 10^{-3}$.Comment: 7 pages, 10 figures. Phys.Rev.D comments considere

Experimental study of ψ(2S)\psi(2S) decays to \K^+ K^- \pi^+ \pi^- \pi^0 final states

$K^+K^-\pi^+\pi^-\pi^0$ final states are studied using a sample of $14\times10^6$ $\psi(2S)$ decays collected with the Beijing Spectrometer (BESII) at the Beijing Electron-Position Collider. The branching fractions of $\psi(2S)$ decays to $K^+K^-\pi^+\pi^-\pi^0$, $\omega K^+ K^-$, $\omega f_0(1710)$, $K^{\ast}(892)^0 K^- \pi^+\pi^0+c.c.$, $K^{\ast}(892)^{+} K^- \pi^+\pi^- +c.c.$, $K^{\ast}(892)^{+} K^- \rho^0+c.c.$ and $K^{\ast}(892)^0 K^-\rho^+ + c.c.$ are determined. The first two agree with previous measurements, and the last five are first measurements.Comment: 19 pages, 9 figure

First observation of ψ(2S)→pnˉπ−+c.c.\psi(2S) \to p \bar{n} \pi^- +c.c.

Using 14 million $\psi(2S)$ events collected with the Beijing Spectrometer (BESII) at the Beijing Electron-Positron Collider, the branching fractions of $\psi(2S)$ decays to $p \bar{n} \pi^-$ and $\bar{p} n \pi^+$ and the branching fractions of the main background channels $\psi(2S) \to p \bar{n} \pi^-\pi^0$, $\psi(2S) \to \gamma\chi_{c0} \to \gamma p \bar{n} \pi^-$, $\psi(2S) \to \gamma\chi_{c2} \to \gamma p \bar{n} \pi^-$, and $\psi(2S) \to \gamma \chi_{cJ} \to \gamma p \bar{n} \pi^- \pi^0$ are determined. The contributions of the $N^{\ast}$ resonances in $\psi(2S) \to p \bar{n} \pi^- +c.c.$ are also discussed.Comment: 19 pages, 8 figures, add vertex requirement systematic erro