Description of annotation procedure and files =============================================
In this study, the Affymetrix HGU133 Plus 2 array [HG-U133_Plus_2] was not used in a standard gene expression experiment but in a shRNA screen.
The GeneNet Human 50K lentiviral shRNA Library uses several probes of the array to measure the abundance of specific shRNAs targeting the corresponding gene. However, in contrast to a gene expression study, probes for the same gene belong to different shRNAs and should therefore be analyzed separately and not summarized. Therefore, annotation information was extracted from several sources given below and used to annotate individual shRNAs after preprocessing using MAS for background correction and RMA for normalization.
- H50_no_x_lib.dat File from GeneNet H50K software (version 3.2) giving information (e.g. sequences) of probes used for shRNA screening
- infos_probes_single_siRNA_probes_with_names.txt information about siRNAs which sequence match only a single probe: sequence of siRNA, probe, location of probe on the array, mapping to Affymetrix CDF (hgu133plus2cdf_2.4.0 and hgu133plus2probe_2.4.0 Bioconductor packages), mapping to custom CDF (ENST, version 12)
- infos_probes_multiple_siRNA_probes_with_names.txt information about siRNAs which sequence match to several probes (or several copies of probe sequence on array): sequence of siRNA, probe, location of probe on the array, mapping to Affymetrix CDF (hgu133plus2cdf_2.4.0 and hgu133plus2probe_2.4.0 Bioconductor packages), mapping to custom CDF (ENST, version 12)
- infos_probes_background_probes_with_names.txt information about probe sequences not used for shRNA screening were used to estimate background intensities
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