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Dr Anna Asplund
Elisabet Andersen (technician), Adila Elobeid (research assistant), Sofie Gustavsson (technican), Frank Hammar (technician), Kristina Magnusson (technican), Ing-Marie Olsson (technican), Ann-Sofi Strand (technician), Sara Strömberg (PhD student), Margret Agnarsdottir (PhD student)
(i) production of tissue microarrays (TMA:s) and cell microarrays (CMA:s), (ii) handling of tissues (biobank material) and cells/cellines used for TMA production and protein extraction, (iii) sectioning of tissue- and TMA-blocks, (iv) scanning of immunohistochemically stained TMA slides (v) export and processing of generated images from TMA:s and (vi) administration and control of TMAx for automated image analysis.
Tissue specimens are selected from the pathology department and representative samples are histoprocessed and stored as paraffin blocks. The paraffin blocks are used as donor blocks for tissue microarray production. Areas of representative cell populations are selected from a hematoxylin-eosin stained tissue section representing each tissue block through visual inspection under the microscope. For the CMA cell lines are cultured in vitro, harvested and dispersed in agarose. Following histoprocessing the dispersed cells are stored in paraffin blocks to be used as templates for the CMAs. In addition protein extraction is done from cultured cell lines and fresh frozen tissues and used for Western blots.
An automated tissue arrayer, ATA-27, is used to subsequently collect cores of tissue from corresponding tissue blocks, and to assemble these into a recipient TMA block. Following sectioning, quality assured TMA sections are delivered to the Immunohistochemistry module.
The 8 TMA:s used for the Protein Atlas contain 48 selected normal tissues (48 x 3 replicates) and 20 different tumor types (17 x 12 replicates and 3 x 4 replicates). The CMAs contain cells from cell lines (47) and patient samples (12). In total 708 spots of tissues and cells are immunostained and analyzed for each antibody.
Immunostained TMA slides are scanned to generate digital images. Automated scanning is performed using 20x (tissue) or 40x (cells) magnification. Images from scanned TMA:s are separated and exported as individual TIFF files. Each TIFF file representing an immunostained tissue (1 mm diameter) or cell sample (0.6 mm diameter) is processed and stored in a database. The TIFF files representing staining of tissue specimens are also compressed into JPEG formats for manual analysis and annotation using a web based annotation software. Analysis of immunoreactivity in cells and cellines in the cell TMA is performed by automated image-analysis of the uncompressed TIFF files to generate objective expression data.
home | about hpr - organization | module 8
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