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Status
Public on Jul 20, 2007
Title
Zebrafish 34K (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)
Boorech J , Noushmehr H , Kirby M , Elkahloun AG , Feldman B
Submission date
Jul 20, 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
Samples (16)
GSM629521 , GSM629522 , GSM629523 , GSM629524 , GSM629525 , GSM629526
Series (1)
GSE25617
Molecular dissection of the migrating posterior lateral line primordium during early development in zebrafish
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
11-Oct-05
CP1A2
AF025305
563571
similar to beta-cytoplasmic actin2
ENSDARG00000037746
Actin, cytoplasmic 1 (Beta-actin 1). [Source:Uniprot/SWISSPROT;Acc:Q7ZVI7]
Compugen
11-Oct-05
CP1A3
AF030031
30131
deltaA
ENSDARG00000010791
deltaA [Source:RefSeq_peptide;Acc:NP_571029]
Compugen
11-Oct-05
CP1A4
AJ317957
114418
crystallin, beta B1
ENSDARG00000004644
crystallin, beta B1 [Source:RefSeq_peptide;Acc:NP_775338]
Compugen
11-Oct-05
CP1A5
AF146429
30120
deltaC
ENSDARG00000004595
deltaC [Source:RefSeq_peptide;Acc:NP_571019]
Compugen
11-Oct-05
CP1A6
AB035276
58109
vertebrate ancient long opsin
Compugen
11-Oct-05
CP1A7
AF006488
30141
deltaB
ENSDARG00000004232
deltaB [Source:RefSeq_peptide;Acc:NP_571033]
Compugen
11-Oct-05
CP1A8
AJ290390
84039
beta-carotene 15,15'-monooxygenase 1
ENSDARG00000034369
beta-carotene 15,15'-monooxygenase 1 [Source:RefSeq_peptide;Acc:NP_571873]
Compugen
11-Oct-05
CP1A9
L27585
30269
sonic hedgehog
ENSDARG00000035998
Sonic hedgehog protein precursor (SHH) (VHH-1). [Source:Uniprot/SWISSPROT;Acc:Q92008]
Compugen
11-Oct-05
CP1A10
AF067532
30425
paired box gene 2a
Compugen
11-Oct-05
CP1A11
AB006086
58027
spondin 1a
ENSDARG00000010029
spondin 1a (spon1a), mRNA [Source:RefSeq_dna;Acc:NM_131515]
Compugen
11-Oct-05
CP1A12
AF210643
573462
similar to Retinal degradation slow 2
ENSDARG00000038018
retinal degradation slow 2 [Source:RefSeq_peptide;Acc:NP_571641]
Compugen
11-Oct-05
CP1A13
AB006087
58029
spondin 1b
ENSDARG00000023694
spondin 1b [Source:RefSeq_peptide;Acc:NP_571592]
Compugen
11-Oct-05
CP1A14
AF210644
554705
hypothetical protein LOC554705
ENSDARG00000014840
retinal degradation slow 4 [Source:RefSeq_peptide;Acc:NP_571642]
Compugen
11-Oct-05
CP1A15
AF252546
259195
calcium/calmodulin-dependent serine protein kinase
Compugen
11-Oct-05
CP1A16
AY050506
373876
phosphodiesterase 6G, cGMP-specific, rod, gamma
ENSDARG00000022820
phosphodiesterase 6G, cGMP-specific, rod, gamma [Source:RefSeq_peptide;Acc:NP_997964]
Compugen
11-Oct-05
CP1A17
AF116539
30645
invariant chain-like protein 2
ENSDARG00000036628
invariant chain-like protein 2 [Source:RefSeq_peptide;Acc:NP_571447]
Compugen
11-Oct-05
CP1A18
AB025312
30459
extra-ocular rhodopsin
ENSDARG00000046115
Compugen
11-Oct-05
CP1A19
AF260240
Compugen
11-Oct-05
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
11-Oct-05
Total number of rows: 34647 Table truncated, full table size 3336 Kbytes .
Supplementary data files not provided