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Platform GPL4014 Query DataSets for GPL4014
Status Public on Jul 20, 2007
Title Zebrafish 33K (Compugen, MWG, Operon)
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Danio rerio
Manufacturer National Human Genome Research Institute / National Institutes of Health (NHGRI/NIH)
Manufacture protocol Microarray preparation. The 33K Zebra fish oligo array consist of three oligo sets: Compugen (with 16,512 60mers), MWG (with 14,240 50mers) and Operon (3,479 70mers). The set includes 170 positive (known house keeping gene) and 244 negative control oligos (Random sequences) to control the homogeneity and specificity of the hybridization. The 5' amine modified oligos were resuspended in 3xSSC and printed on Epoxy slides from Corning Life Sciences.
Support glass
Coating aminosilane
 
Description The zebra fish 35k chip is a combination of 16,399 60 mer oligos from Compugen http://www.labonweb.com/oligo/libraries.htm
14,067 50 mers from MWG. http://www.ocimumbio.com/web/arrays/oligo_zebrafish.asp
and 3500 70 mer oligos from Operon. http://www.operon.com/arrays/oligosets_zebra.php
To look for the genes in the Compugen/MWG original list, click here (http://magic2.nhgri.nih.gov/mcore/zebrafish_genelist.txt)
General questions or comments about this specific platform please direct to:
Abdel G. Elkahloun: abdel@mail.nih.gov (tel. 301-402-3170 )
Settara Chandrasekharappa: chandra@mail.nih.gov (tel. 301-402-2344)
 
Web link http://magic2.nhgri.nih.gov/mcore/maservice.shtml
Contributor(s) Pei W, Noushmehr H, Elkahloun AG, Feldman B
Submission date Jul 19, 2006
Last update date Jul 20, 2007
Contact name Benjamin Feldman
E-mail(s) bfeldman@mail.nih.gov
Organization name National Institutes of Health
Department National Human Genome Research Institute
Lab Feldman Lab
Street address 35 Convent Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 

Data table header descriptions
ID
GB_ACC GenBank Accession numbers (contains a mixture of GenBank, Entrez and RefSeq IDs)
ORF Entrez Gene IDs
Gene_Name RefSeq Gene Name obtained from annotation done using the known oligonucleotide sequences
Ensembl_ACC Ensembl Accession IDs
Ensembl_Gene_Name Ensembl Gene Name obtained from annotation done using the known oligonucleotide sequences
Manufacture Name Three different commercial company oligos were used in this platform. Each spot is labled either Compugen, MWG, or Operon
Annotation Date Date the dataset was last annotated using publicly available database (NCBI and Ensembl)
SPOT_ID

Data table
ID GB_ACC ORF Gene_Name Ensembl_ACC Ensembl_Gene_Name Manufacture Name Annotation Date SPOT_ID
CP1A1 AF025305 563571 similar to beta-cytoplasmic actin2 ENSDARG00000037746 Actin, cytoplasmic 1 (Beta-actin 1). [Source:Uniprot/SWISSPROT;Acc:Q7ZVI7] Compugen October 11, 2005
CP1A2 AF025305 563571 similar to beta-cytoplasmic actin2 ENSDARG00000037746 Actin, cytoplasmic 1 (Beta-actin 1). [Source:Uniprot/SWISSPROT;Acc:Q7ZVI7] Compugen October 11, 2005
CP1A3 AF030031 deltaA Compugen October 11, 2005
CP1A4 AJ317957 114418 crystallin, beta B1 ENSDARG00000004644 crystallin, beta B1 [Source:RefSeq_peptide;Acc:NP_775338] Compugen October 11, 2005
CP1A5 AF146429 30120 deltaC ENSDARG00000004595 deltaC [Source:RefSeq_peptide;Acc:NP_571019] Compugen October 11, 2005
CP1A6 AB035276 58109 vertebrate ancient long opsin Compugen October 11, 2005
CP1A7 AF006488 30141 deltaB ENSDARG00000004232 deltaB [Source:RefSeq_peptide;Acc:NP_571033] Compugen October 11, 2005
CP1A8 AJ290390 84039 beta-carotene 15,15'-monooxygenase 1 ENSDARG00000034369 beta-carotene 15,15'-monooxygenase 1 [Source:RefSeq_peptide;Acc:NP_571873] Compugen October 11, 2005
CP1A9 30269 sonic hedgehog ENSDARG00000035998 Sonic hedgehog protein precursor (SHH) (VHH-1). [Source:Uniprot/SWISSPROT;Acc:Q92008] Compugen October 11, 2005
CP1A10 AF067532 30425 paired box gene 2a Compugen October 11, 2005
CP1A11 AB006086 58027 spondin 1a ENSDARG00000010029 spondin 1a (spon1a), mRNA [Source:RefSeq_dna;Acc:NM_131515] Compugen October 11, 2005
CP1A12 AF210643 573462 similar to Retinal degradation slow 2 ENSDARG00000038018 retinal degradation slow 2 [Source:RefSeq_peptide;Acc:NP_571641] Compugen October 11, 2005
CP1A13 AB006087 58029 spondin 1b ENSDARG00000023694 spondin 1b [Source:RefSeq_peptide;Acc:NP_571592] Compugen October 11, 2005
CP1A14 AF210644 554705 hypothetical protein LOC554705 ENSDARG00000014840 retinal degradation slow 4 [Source:RefSeq_peptide;Acc:NP_571642] Compugen October 11, 2005
CP1A15 AF252546 259195 calcium/calmodulin-dependent serine protein kinase Compugen October 11, 2005
CP1A16 AY050506 373876 phosphodiesterase 6G, cGMP-specific, rod, gamma ENSDARG00000022820 phosphodiesterase 6G, cGMP-specific, rod, gamma [Source:RefSeq_peptide;Acc:NP_997964] Compugen October 11, 2005
CP1A17 AF116539 30645 invariant chain-like protein 2 ENSDARG00000036628 invariant chain-like protein 2 [Source:RefSeq_peptide;Acc:NP_571447] Compugen October 11, 2005
CP1A18 AB025312 30459 extra-ocular rhodopsin ENSDARG00000046115 Compugen October 11, 2005
CP1A19 AF260240 claudin 7 CGENXEB_456000010_0 claudin 7 [Source:ZFIN;Acc:ZDB-GENE-001103-5] Compugen October 11, 2005
CP1A20 AF109372 30435 opsin 1 (cone pigments), short-wave-sensitive 2 ENSDARG00000017274 Opsin 1, short-wave-sensitive 2 (Blue-sensitive opsin) (Blue cone photoreceptor pigment) (Opsin SWS-2). [Source:Uniprot/SWISSPROT;Acc:Q9W6A8] Compugen October 11, 2005

Total number of rows: 33640

Table truncated, full table size 3629 Kbytes.




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