Supplemental Tables 1 and 2 For: ANALYSIS OF GENE EXPRESSION, COPY NUMBER AND PALINDROME FORMATION WITH A DT40 ENRICHED CDNA MICROARRAY By Neiman et al. In DT40 Handbook, Ed. JM Buerstedde Table 1 This is a Microsoft Excel spreadsheet with two worksheets. The first lists genes with RNA over-expressed in DT40 cells relative to normal bursa, and the second lists underexpressed genes. Data are based on microarray results shown in Figure 1A in the chapter Column A; Unique clone ID number on the chicken 13K cDNA microarray Column B: Genbank accession number Column C: Clone ID number from original source Column D: Annotation available from original source at time array was constructed. Column E: Additional annotation obtained by BLAST search at time of array construction when no annotation was available from original source Column F: Log2 fluorescence signal ratio Cy-5 (DT40) /Cy-3(Normal Bursa). Table 2 This is a Microsoft Excel spreadsheet listing the genes which were amplified or deleted in common, by array CGH, in three clones from a parental DT40 cell culture with a many year chronic passage history in this laboratory. The overall array CGH results are given in Venn diagrams in Figure 5 in the chapter Column A; Unique clone ID number on the chicken 13K cDNA microarray Column B: Chromsome on which clone sequence is located (draft chicken genomic sequence Feb 2005) Column C: Sequence number on chromosome for EST sequence of clone Column D: Genbank accession number. Column E: Clone ID number from original source. Column F: Annotation available from original source at time array was constructed. Column G: Additional annotation obtained by BLAST search at time of array construction when no annotation was available from original source Columns H,I,J: Log2 fluorescence signal ratio Cy-5 (DT40) /Cy-3(Normal Bursa) for triplicate array CGH assays with DT40 Clone # 3 DNA vs. reference normal bursa DNA Columns K,L,M: Log2 fluorescence signal ratio Cy-5 (DT40) /Cy-3(Normal Bursa) for triplicate array CGH assays with DT40 Clone # 7 DNA vs. reference normal bursa DNA Columns N,O,P: Log2 fluorescence signal ratio Cy-5 (DT40) /Cy-3(Normal Bursa) for triplicate array CGH assays with DT40 Clone # 8 DNA vs. reference normal bursa DNA How to obtain further information regarding the clones on the 13K Chicken cDNA microarray ------------------------------------------------------------------------In order to obtain more information about a particular clone represented on the Chicken13k array, users are encouraged to search the following web sites, as appropriate for the clone's source using either a clone name, source ID or GenBank Accession number for the given clone. UMIST Clones (clones whose Array Ids are of the form "C00041...") Web site: http://www.chick.umist.ac.uk Click on "ID Search". Enter a list of one or more Clone Names or EST Ids in the text pane as indicated. Click on "Search" DKFZ Clones (clones whose Array Ids are of the form "DKFZ426..."): Web site: http://swallow.gsf.de/dt40Est.html Click on "View Data Files" Enter the source_id value (e.g. dkfz426_10a5r1) Be sure to use the source_id column values, not the id column values. All letters in the source_ids are lower case, and each source_id has an 'r1' suffix. DT40 Clones (clones whose Array Ids are of the form "DT40subNB..."): Website: http://www.ncbi.nlm.nih.gov Search "Nucleotides" using the GenBank Accession Number (i.e. BE139972) Pat-clones and pgn1c Clones (clones whose Array Ids are of the form "pat_..."): Web site: http://www.chickest.udel.edu Click on "Search By Clone ID" Type in the Clone ID (e.g. 'pat.pk0023.e5.f' or 'pgn1c.pk002.b19') NB: this is case sensitive. Use lower case for ALL entries. Select a Library (if relevant, otherwise leave on default setting "Any Type") Click on "Search" On the resulting page, click on either "BLASTX Hits" or "BLASTN Hits" Obtaining Clones represented on the Chicken13k Array -------------------------------------------------------Inquiries about access to clones on the 13K chicken cDNA microarray should be addressed to: UMIST clones: via Web Form: http://www.ark-genomics.org/order/cloneorder.html DKFZ clones: Jean-Marie Buerstedde, PhD Director, GSF-Institute for Molecular Radiobiology e-mail: buersted@gsf.de DT40 clones: Jeffrey Delrow, PhD Staff Scientist & Manager Genomics Resource Fred Hutchinson Cancer Research Center e-mail: jdelrow@fhcrc.org Pat & PGN1C clones: Joan Burnside, PhD Professor Delaware Biotechnology Institute e-mail: joan@udel.edu