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