Supplemental Tables 1 and 2
For:
Genomic Instability during Myc-induced lymphomagenesis in the bursa of Fabricius
By Neiman et al.
Supplemental Table 1
This is a Microsoft Excel spreadsheet that lists genes with significant copy number change in duplicate samples of three different Myc-induced metastatic lymphomas and provides duplicate averaged Log transformed fluorescence ratios for each tumor. Data are based on microarray results summarized in Table 1 of the manuscript
First Column; Unique clone ID number on the chicken 13K cDNA microarray
Second Column: Genbank accession number
Third Column: Clone ID number from original source (see Burnside et al,,2005).
Forth Column: Annotation available from original source at time array was constructed. : Additional annotation obtained by BLAST search at time of array
construction when no annotation was available from original source.
Columns 5,6 and 7: Average Log2 fluorescence signal ratios for Tumors 1 - 3.
Table 2
This is a Microsoft Excel spreadsheet listing the genes with significant expression change during bursal lymphoma genesis. Data are based on microarray results summarized in Figure 7 in the manuscript. The data are presented in four sections labeled:
E15 vs. TF UP; for genes with at least 2 fold increase in expression in TF vs normal embryonic day 15 bursa
E15 vs. TF DOWN; for genes with at least 2 fold decreased expression in TF vs normal embryonic day 15 bursa
TF vs TUMOR UP; for genes with at least 2 fold increased expression in metastatic lymphomas vs. the reference TF sample.
TF vs. TUMOR DOWN; for genes with at least 2 fold decreases expression in metastatic tumors vs the reference TF sample.
On each worksheet the following columns are displayed:
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 (see Burnside et al,,2005).
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: Average Log2 fluorescence signal ratios for the several experimental samples.
How to obtain further information regarding the clones on the 13K Chicken cDNA microarray
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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
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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:
DT40 clones:
Jeffrey Delrow, PhD
Staff Scientist & Manager
Genomics Resource
Fred Hutchinson Cancer Research Center
e-mail:
Pat & PGN1C clones:
Joan Burnside, PhD
Professor
Delaware Biotechnology Institute
e-mail: