What is the "barcode" in your shRNAmir vectors and what information can you give about them?
The barcodes on the shRNAmir vectors (pSM2, pSMP, pGIPZ, pTRIPZ) are ~60nt unique sequences cloned into the vector downstream of the shRNA. This barcode being unique to each shRNA clone enables screening with pools of shRNA clones. The underlying concept is that by PCR amplification of integrated DNAs one can count the number of cells that contain a specific shRNA vector. This is measured by hybridizing genomic PCR products containing the barcodes to custom microarrays that contain the complement of these barcode sequences. By comparing barcode representations from cell populations treated in different ways one can assess the consequences of expressing a given individual shRNA on the cells response to the treatment. For example, if a particular shRNA provided resistance to a growth inhibitor stimulus then the representation of its associated barcode should be increased after treatment. If a given shRNA sensitized a population to a specific stress, then the relative abundance of its barcode should diminish after the stress. You can refer to the following papers: 1) Schlabach et al. , Science 319, 620 (2008); Cancer Proliferation Gene Discovery Through Functional Genomics 2) Silva et al. , Science 319, 617 (2008), Profiling Essential Genes in Human Mammary Cells by Multiplex RNAi Screening. ** Please note the pSM2 and pSMP libraries, constructs, gene sets and families and RNAintro kits have been discontinued.