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Status
Public on Mar 02, 2009
Title
LU/IBL_D.rerio_44k_015747
Technology type
in situ oligonucleotide
Distribution
custom-commercial
Organism
Danio rerio Manufacturer
Agilent
Manufacture protocol
the arrays were produced according to manufacturer's protocol, check website: http://www.chem.agilent.com/en-US/products/instruments/dnamicroarrays/pages/default.aspx
Catalog number
none
Support
glass
Coating
aminosilane
Description
The micro-array slides were custom designed by Agilent Technologies. The slides contain in total 43.371 probes of a 60 oligonucleotide length. Of these probes a total of 21.496 probes were identical to the probes present on the Agilent probe set that is commercially available under catalog number 013223_D. Most of the additional probes were designed using the eArray software from Agilent Technologies (https://earray.chem.agilent.com/earray/ ). Settings used were based on the following settings: base composition methodology, best probe methodology and design with 3’ bias. The Agilent D.rerio transcriptome was used as a reference database. A small number of probes were manually designed based on knowledge of particular polymorphisms for genes encoding protein families such as 14-3-3 proteins, chitinase-like proteins and Toll-like receptors in order to obtain gene-specific probes.
Contributor(s)
Meijer AH , Spaink HP Submission date
Dec 04, 2008
Last update date
Jan 18, 2013
Contact name
Anna Magdalena Zakrzewska
E-mail(s)
ania.zakrzewska@gmail.com Phone
020-6923990
Fax
-
URL
http://- Organization name
University of Leiden
Department
IBL
Lab
A. Meijer
Street address
Wassenaarseweg 64
City
Leiden
ZIP/Postal code
2333 AL
Country
Netherlands
Samples (232)
GSM351279 , GSM351346 , GSM351347 , GSM351348 , GSM351349 , GSM351350
GSM351351 ,
GSM351384 ,
GSM351385 ,
GSM351386 ,
GSM351387 ,
GSM351388 ,
GSM351390 ,
GSM351391 ,
GSM351392 ,
GSM351394 ,
GSM351395 ,
GSM351396 ,
GSM351397 ,
GSM351398 ,
GSM351399 ,
GSM351400 ,
GSM351425 ,
GSM351426 ,
GSM351480 ,
GSM351482 ,
GSM351484 ,
GSM351485 ,
GSM351487 ,
GSM351489 ,
GSM351495 ,
GSM351497 ,
GSM351498 ,
GSM351499 ,
GSM351501 ,
GSM351504 ,
GSM368915 ,
GSM368916 ,
GSM368917 ,
GSM368918 ,
GSM381145 ,
GSM381147 ,
GSM381148 ,
GSM381150 ,
GSM381152 ,
GSM381154 ,
GSM381156 ,
GSM381158 ,
GSM381162 ,
GSM381166 ,
GSM381171 ,
GSM381174 ,
GSM381583 ,
GSM381599 ,
GSM381600 ,
GSM381601 ,
GSM381602 ,
GSM381603 ,
GSM382228 ,
GSM382229 ,
GSM382231 ,
GSM382238 ,
GSM382241 ,
GSM382243 ,
GSM382245 ,
GSM382247 ,
GSM384921 ,
GSM384922 ,
GSM384923 ,
GSM384924 ,
GSM384925 ,
GSM384926 ,
GSM384927 ,
GSM385001 ,
GSM385003 ,
GSM474849 ,
GSM474850 ,
GSM474851 ,
GSM474852 ,
GSM474859 ,
GSM475956 ,
GSM475977 ,
GSM475992 ,
GSM657489 ,
GSM657490 ,
GSM657491 ,
GSM657492 ,
GSM657493 ,
GSM657494 ,
GSM657495 ,
GSM657496 ,
GSM657502 ,
GSM657503 ,
GSM657504 ,
GSM657505 ,
GSM657506 ,
GSM657507 ,
GSM657508 ,
GSM657509 ,
GSM657510 ,
GSM657511 ,
GSM657512 ,
GSM657513 ,
GSM657514 ,
GSM694418 ,
GSM696168 ,
GSM696187 ,
GSM696307 ,
GSM696316 ,
GSM696317 ,
GSM1051337 ,
GSM1051338 ,
GSM1051339 ,
GSM1051340 ,
GSM1051341 ,
GSM1051342 ,
GSM1051343 ,
GSM1051344 ,
GSM1051345 ,
GSM1051346 ,
GSM1051347 ,
GSM1051348 ,
GSM1051349 ,
GSM1051350 ,
GSM1051351 ,
GSM1051352 ,
GSM1051353 ,
GSM1051354 ,
GSM1051355 ,
GSM1051356 ,
GSM1051357 ,
GSM1051358 ,
GSM1051359 ,
GSM1051360 ,
GSM1051361 ,
GSM1051362 ,
GSM1051363 ,
GSM1051364 ,
GSM1051365 ,
GSM1051366 ,
GSM1051367 ,
GSM1051368 ,
GSM1051369 ,
GSM1051370 ,
GSM1051371 ,
GSM1051372 ,
GSM1051373 ,
GSM1051374 ,
GSM1051375 ,
GSM1051376 ,
GSM1051377 ,
GSM1051378 ,
GSM1051379 ,
GSM1051380 ,
GSM1051381 ,
GSM1051382 ,
GSM1051383 ,
GSM1051384 ,
GSM1051385 ,
GSM1051386 ,
GSM1051387 ,
GSM1051388 ,
GSM1051389 ,
GSM1051390 ,
GSM1051391 ,
GSM1051392 ,
GSM1051393 ,
GSM1051394 ,
GSM1051395 ,
GSM1051396 ,
GSM1051397 ,
GSM1051398 ,
GSM1051399 ,
GSM1051400 ,
GSM1051401 ,
GSM1051402 ,
GSM1051403 ,
GSM1051404 ,
GSM1051405 ,
GSM1051406 ,
GSM1051407 ,
GSM1051408 ,
GSM1051409 ,
GSM1051410 ,
GSM1051411 ,
GSM1051412 ,
GSM1051413 ,
GSM1051414 ,
GSM1051415 ,
GSM1051416 ,
GSM1051417 ,
GSM1051418 ,
GSM1051419 ,
GSM1051420 ,
GSM1051421 ,
GSM1051422 ,
GSM1051423 ,
GSM1051424 ,
GSM1051425 ,
GSM1051426 ,
GSM1051427 ,
GSM1051428 ,
GSM1051429 ,
GSM1051430 ,
GSM1051431 ,
GSM1051432 ,
GSM1051433 ,
GSM1051434 ,
GSM1051435 ,
GSM1051436 ,
GSM1051437 ,
GSM1051438 ,
GSM1051439 ,
GSM1051440 ,
GSM1051441 ,
GSM1051442 ,
GSM1051443 ,
GSM1051444 ,
GSM1051445 ,
GSM1051446 ,
GSM1051447 ,
GSM1051448 ,
GSM1051449 ,
GSM1051450 ,
GSM1051451 ,
GSM1051452 ,
GSM1051453 ,
GSM1051454 ,
GSM1051455 ,
GSM1051456 ,
GSM1051457 ,
GSM1051458 Series (10)
GSE13994 Salmonella typhimurium infection of zebrafish embryo
GSE14782 Mycobacterium marinum chronic infection of adult zebrafish
GSE15328 Specificity of the zebrafish host transcriptome response to acute and chronic mycobacterial infection
GSE19206 Macrophage-specific gene functions in Spi1-directed innate immunity
GSE26707 Zebrafish 27hpf embryos: hdac1 mutant (hi1618) vs sibling
GSE26708 Zebrafish embryos: hdac1 Morphants vs Standard control morphants
GSE26709 Zebrafish embryos: hdac1 Morphants vs Standard control morphants at 12, 18 and 27 hpf
GSE26710 Zebrafish hdac1 mutant and morphant embryos
GSE28110 Hai1 Mediates Inflammation Through MMP9
GSE42856 Transcriptome analysis of Traf6 function in early zebrafish embryogenesis
Data table header descriptions ID SEQUENCE 60-mer nucleotide sequence of each oligo
GB_ACC GenBank Accession identifier of a gene or biological sequence
GENE_SYMBOL available gene name
DESCRIPTION additional information about the gene or sequence
SPOT_ID
Data table ID SEQUENCE GB_ACC GENE_SYMBOL DESCRIPTION SPOT_ID A_15_P100001
TATATTTCTTGATGGTTATCAACGGCTAAAGGACTGTCAACCATGTTTCTTCCGAGAGTG
EH505971 LOC793156
AY398373 MAP1 light chain 3-like protein 2 {Danio rerio;} , complete [TC291423]
A_15_P100002
GCTGAAGTCTACCGCAGTATTTCTACTGAGTTCAATAGTTTGCACTTTATGATTATGATT
NM_200289 zgc:56454
Danio rerio zgc:56454 (zgc:56454), mRNA [NM_200289];LOLannot:zgc:56454
A_15_P100003
CGTTCCAAACACCAACAGCACTATCTAATGCTTAATCTCAGTGAACGGAGGCATGACATC
-- NO INFORMATION
A_15_P100004
AAATCATCTTTCTAGAGCTAGCAGATAGCACGGTCTGACATCTACCTTCACACAAATAAT
BF717781 lyn
fd51g04.y1 Zebrafish WashU MPIMG EST Danio rerio cDNA clone IMAGE:3733302 5', mRNA sequence [BF717781];LOLannot:lyn protein
A_15_P100005
TCAGCAGGGGGCGTCATCTCAGTGTCTTCCTCAAGAAACTTTCCTGATGTAGAAATGTTT
NM_212915 spast
Danio rerio zgc:85952 (zgc:85952), mRNA [NM_212915];LOLannot:zgc:85952
A_15_P100006
ACACGCTGCATTTTCTCACAGCGCAGAAAATTTACAAAACGCGCTGCATTTTCTCACAAC
CT682462 Dr.95167
UCRH_YEAST (P00127) Ubiquinol-cytochrome C reductase complex 17 kDa protein (Mitochondrial hinge protein) (Complex III polypeptide VI) , partial (8%) [TC295755]
A_15_P100007
TGTTTGTTTGATGGAGATACGTTTAAAATCATTTTTCTGAACGTACAAACATGCTCTGGC
BC097233 zgc:114184
O13096 (O13096) Slow myotomal muscle troponin-T isoform 1S, partial (71%) [TC293411]
A_15_P100008
AACGAACACCTTTGTTTTCTCACAAAACAGTTCTGTGTTCTAATCTTGGTGTTGAAATAC
NM_213001 klhl20
Danio rerio zgc:66288 (zgc:66288), mRNA [NM_213001];LOLannot:zgc:66288
A_15_P100009
AGGATTGTTTTTTCGTTTTGAATATCGTAGCCTAAATGTTGTCTTCCATGTGAATACCAC
CF347571 wu:fb74f10
AGENCOURT_15226081 NIH_ZGC_10 Danio rerio cDNA clone IMAGE:7001776 5', mRNA sequence [CF347571];LOLannot:wu:fb74f10
A_15_P100010
AGCCTGAATGTTCGAGCGGGCACTGATATTTTGTTTTAAATAACTCCACATTTTAAAAAG
NM_213126 wu:fb66f11
Danio rerio zgc:64161 (zgc:64161), mRNA [NM_213126];LOLannot:zgc:64161
A_15_P100011
AAACTGTACCATTTCTTCAACACTAAACATTTTCTGTATGCAAAGCCAGATTACAGATGG
NM_001002497 zgc:92842
Danio rerio zgc:92842 (zgc:92842), mRNA [NM_001002497];LOLannot:zgc:92842
A_15_P100012
CTGTGAGGGAAATGTTTCGGCAGTGCTCTTCTCTGATTTTCCTACGTTAAATGATCCCTT
NM_001007415 glmnl
Danio rerio zgc:101567 (zgc:101567), mRNA [NM_001007415];LOLannot:zgc:101567
A_15_P100013
AACTGTGTGATTTGTGCAGCTACAAGCTATCTTCTGAGTAGCTTATAAATGTTTCTACAA
CK398207 si:dkey-192p21.4
AGENCOURT_17179396 NIH_ZGC_4 Danio rerio cDNA clone IMAGE:7117842 5', mRNA sequence [CK398207];LOLannot:mp:zf637-2-001473
A_15_P100014
CACTTCTGCAAAAGAGCTTCAGTGACACGGCAATGGAGGAGGCAAGGGTTGAATAATAAT
NM_001030106 si:busm1-132m23.3
Q9UKC0 (Q9UKC0) F-box protein Fbx22 (Fragment), partial (62%) [TC297168]
A_15_P100015
CTGTTACCAGAAAATGAAAAGTCTATACCTTGGATCTGTAGTTTGGGTCCAAAATGTGCT
NM_200764 trappc4
Danio rerio trafficking protein particle complex 4 (trappc4), mRNA [NM_200764];LOLannot:trafficking protein particle complex 4
A_15_P100016
AAAGCGTATTGTAGTGGACTAGATTCAGATGTTAGTAGATGTGGTTAGTAGATGTTGTGT
CK362685 Dr.90589
AGENCOURT_17185635 NIH_ZGC_4 Danio rerio cDNA clone IMAGE:7088994 5', mRNA sequence [CK362685]
A_15_P100017
GCTATGCTGAAACCAGAAATTATGTGACAGACATCGATCTGGAGGAGTTCATTAGGCTGT
-- NO INFORMATION
A_15_P100018
CCTTTGAACTGACTGGTTAATAATATGATCCTGTCTTTATAGTGTCCTTGCACCAGACAC
XM_682932 LOC559576
Q8CHD9 (Q8CHD9) MKIAA0664 protein (Fragment), partial (49%) [TC292241]
A_15_P100019
AAAGCTCTGTTTGATTATTTAAACACAGATTTGAAGGAAGATAACTATCACCCGAGTGAC
CN324195 DKEY-32M20.2
AF465485 voltage-gated calcium channel beta2 subunit {Homo sapiens;} , partial (22%) [TC277026]
A_15_P100020
ACGCTCACTGATGAAGTGTGTAAAGGAATGTTCAAGGAGGATCTCCTACAAATGCTTCGG
-- NO INFORMATION
43370 7732 Kbytes .Supplementary data files not provided
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