| 1 |
GPL279 |
SAGE:10:NlaIII:Meleagris gallopavo |
27,430 |
|
2003-03-19 |
|
Meleagris gallopavo
 |
SAGE NlaIII |
SAGE NlaIII, SAGE:10:NlaIII:Meleagris gallopavo, |
| 2 |
GPL530 |
MWG Zebrafish 14K-1 Array |
7,680 |
MWG Biotech |
2003-10-07 |
MWG Biotech |
Danio rerio
 |
Oligo Array |
spotted oligonucleotide, MWG Zebrafish 14K-1 Array, Total number of spots: 14240 (14K-1 Array: 7296; 14K-2 Array: 6944). One oligonucleotide per gene. Additional EST clustering and annotation information. NCBI zebrafish ESTs were clustered with Paracel's transcript assembler (PTA 2.5.9). ORFs were annotated using framefinder (ESTate package 0.5.0) combined with protein similarity searches using BLASTP. Databases searched included genpept (release 128) and pir nref (release 1.0). |
| 3 |
GPL531 |
MWG Zebrafish 14K-2 Array |
7,200 |
MWG Biotech |
2003-10-07 |
MWG Biotech |
Danio rerio
|
Oligo Array |
spotted oligonucleotide, MWG Zebrafish 14K-2 Array, Total number of spots: 14240 (14K-1 Array: 7296; 14K-2 Array: 6944). One oligonucleotide per gene. Additional EST clustering and annotation information. NCBI zebrafish ESTs were clustered with Paracel's transcript assembler (PTA 2.5.9). ORFs were annotated using framefinder (ESTate package 0.5.0) combined with protein similarity searches using BLASTP. Databases searched included genpept (release 128) and pir nref (release 1.0). |
| 4 |
GPL928 |
Hofmann-cichlid-brain-array |
4,688 |
Universit of Texas at Austin |
2004-01-12 |
|
Haplochromis burtoni
 |
cDNA Array |
spotted DNA/cDNA, Hofmann-cichlid-brain-array, This array is built from a Cichlid cDNA library first made in the lab of Russ Fernald. mRNA from brains of all ages and stages of the species Astatotilapia burtoni was used. colony picking, PCR amplification, and array printing have been done at Harvard's Bauer Center for Genomics Research in the lab of Hans Hofmann. the array also includes yeast control genes and a few other positive and negative controls Keywords = cichlid Keywords = brain |
| 5 |
GPL966 |
Salmonid 3600 - Feb 17 2003 |
8,736 |
University of Wisconsin - Milwaukee |
2004-01-28 |
|
Oncorhynchus mykiss,Salmo salar
 |
cDNA Array |
spotted DNA/cDNA, Salmonid 3600 - Feb 17 2003, GRASP ~3600 gene salmonid cDNA microarray Keywords = Atlantic salmon Keywords = rainbow trout Keywords = salmonid |
| 6 |
GPL1212 |
salmonid fish version 1.0 |
8,736 |
Akvaforsk |
2004-05-04 |
|
Oncorhynchus mykiss
 |
cDNA Array |
spotted DNA/cDNA, salmonid fish version 1.0, contains 1300 rainbow trout genes spotted in 6 replicates |
| 7 |
GPL1224 |
Fundulus_192gene_metabolic_array |
1,124 |
University of Miami, RSMAS |
2004-05-08 |
|
Fundulus heteroclitus
 |
cDNA Array |
spotted DNA/cDNA, Fundulus_192gene_metabolic_array, Microarrays were printed using 192 cDNAs from a F. heteroclitus cardiac library encoding essential proteins for cellular metabolism. These cDNAs were a subset of over 33,000 expressed sequences in our database, which all may be found at http://genomics.rsmas.miami.edu/funnybase/super_craw3/ (Oleksiak et al. 2001). These 192 cDNAs were amplified with amine-linked primers and printed on 3-D Link Activated slides (Surmodics Inc., Eden Prairie, MN) using a SpotArray Enterprise piezoelectric microarray printer (PerkinElmer Life Sciences Inc., Boston, MA, USA) at Louisiana State University. Slides were blocked following slide manufacturer protocols. The suite of 192 amplified cDNAs was printed as a group in spatially separated replicates (6 replicates for 178 genes, and 4 replicates for 14 genes). Four hybridization zones of these six replicate arrays were printed per slide, with each zone set separated by a hydrophobic barrier. Keywords = Fundulus Keywords = metabolism Keywords = populations Keywords = tissue-specific gene expression |
| 8 |
GPL1289 |
Chick Pineal 2004 |
9,053 |
Texas A&M University |
2004-06-14 |
|
Gallus gallus
 |
cDNA Array |
spotted DNA/cDNA, Chick Pineal 2004, The cDNA microarrays were prepared based upon approximately 4,500 PCR products from each of the two chicken pineal cDNA libraries constructed, for a total of ~9,000 ESTs. Briefly, the cDNA in plasmids from each library were PCR amplified using flanking primers (SK and T7), purified by ethanol precipitation using ammonium acetate, and placed in the wells of 96 well plates at a concentration of 50 ug/ml in 3X SSC. A GeneMachines OmniGrid microarrayer equipped with 8 Telechem SMP3 pins was used to spot the samples onto poly-L-lysine coated slides (CEL Associates). Duplicate 100 micron diameter spots were placed at intervals of 190 microns (center to center). Slides were printed in batches of 50–100. Printing was accomplished at 70 C and 60% humidity. The OmniGrid’s operating software used information on the position of the individual clones within the 96-well sample plates and the order in which the plates were used to create a file describing the position of each cDNA clone on the array for later analysis. Slides were stored desiccated at room temperature until their subsequent use. Prior to hybridization, the dried spots were hydrated gently over a steaming water bath, snap dried, and the DNA was UV cross-linked using a Stratalinker (Stratagene). Keywords = chick pineal gland Keywords = circadian oscillator |
| 9 |
GPL1318 |
[Xenopus_laevis] Affymetrix Xenopus laevis Genome Array |
15,611 |
Affymetrix, Inc. |
2004-06-30 |
Affymetrix |
Xenopus laevis
 |
GeneChip |
in situ oligonucleotide, [Xenopus_laevis] Affymetrix Xenopus laevis Genome Array, Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html The Affymetrix GeneChip Xenopus laevis Genome Array can be used to study gene expression of over 14,400 Xenopus laevis transcripts. Sequence information for this array was selected from the following public data sources: GenBank (release 135.0, April 2003), dbEST (June 2003), and UniGene (Build 36, June 2003). Probe sets on the array were designed with 16 oligonucleotide pairs to detect each transcript. This array was designed in collaboration with representative members of the Xenopus community and the National Institutes of Health. More information on the design of this array can be found at www.xenbase.org Note: The DsRed probe set is provided with permission from BD Biosciences, and BD Biosciences grants users a limited license to utilize this probe set only on the Affymetrix array. Other uses of the probe set, or other DsRed sequence or sequences requires a license from BD Biosciences. |
| 10 |
GPL1319 |
[Zebrafish] Affymetrix Zebrafish Genome Array |
15,617 |
Affymetrix, Inc. |
2004-07-01 |
Affymetrix |
Danio rerio
|
GeneChip |
in situ oligonucleotide, [Zebrafish] Affymetrix Zebrafish Genome Array, Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html The Affymetrix GeneChip Zebrafish Genome Array can be used to study gene expression of over 14,900 Danio rerio transcripts. Sequence information for this array was selected from the following public data sources: RefSeq (July 2003), GenBank (release 136.0, June 2003), dbEST (July 2003), and UniGene (Build 54, June 2003). Probe sets on the array were designed with 16 oligonucleotide pairs to detect each transcript. This array was designed in collaboration with representative members of the Zebrafish community and the National Institutes of Health. Note: The DsRed probe set is provided with permission from BD Biosciences, and BD Biosciences grants users a limited license to utilize this probe set only on the Affymetrix array. Other uses of the probe set, or other DsRed sequence or sequences requires a license from BD Biosciences. Annotations derived from Affymetrix CSV file dated 6/23/2004 |
| 11 |
GPL1461 |
Avian Innate Immunity Microarray (AIIM) |
14,877 |
University of Delaware |
2004-09-21 |
|
Gallus gallus
|
MIXTURE |
spotted DNA/cDNA, Avian Innate Immunity Microarray (AIIM), This microarray was created using all of the unique elements in 4 individual EST libraries created using various sources of macrophages. It was further supplemented with RT-PCR amplified genes of interest and clones from Peter Kaiser. Three libraries were made from peripheral blood derived macrophages: Unstimulated (Control), LPS stimulated for 2-4 hours (LPS), and INF-gamma stimulated for 2-4 hours (IFN). The fourth library was created from HD11 cell line macrophages stimulated for 0-72 hours (pmp1c). 134 additional clones were added from clones in the University of Delaware ChickEST library collections. In addition, 13 full-length cDNA clones were kindly provided by Dr. Pete Kaiser. Finally, 40 elements were amplified directly by RT-PCR from targeted genes of interest identified on the avian genome. Total, this array contains 4,959 unique elements. Keywords = Avian Keywords = innate immunity Keywords = macrophage Keywords = AIIM |
| 12 |
GPL1477 |
SAGE:17:NlaIII:Gallus gallus |
48,341 |
|
2004-10-04 |
|
Gallus gallus
|
SAGE NlaIII |
SAGE NlaIII, SAGE:17:NlaIII:Gallus gallus, This is a virtual platform for longSAGE 17 libraries generated for Gallus gallus using NlaIII as an anchor enzyme. Platform_anchor: NlaIII |
| 13 |
GPL1516 |
SA-DEV-VS1 |
21,600 |
HCMR |
2004-10-19 |
|
Sparus aurata
 |
cDNA Array |
spotted DNA/cDNA, SA-DEV-VS1, For the microarray production a cDNA library of mixed embryos/larvae of gilthead sea bream, Sparus aurata (Sarropoulou et al., in press) was used. A total of 10,176 clones were arrayed into 384 square well plates. In order to amplify the inserts culture PCR was performed as followed. The total volume of one PCR reaction was 50 µl, containing 43.5 µl reaction mix (2 µl 10x PCR Puffer, 0.04 µl 100 mM of each dATP, dCTP, dGTP and dTTP, 12.12 µl dH20), 1.5 µl of T7 and 1.5 µl of T3 primer (20 µM), 1 µl Taq polymerase (5U/µl) and 2.5 µl of culture. The PCR program utilized consisted of 1 step of 94ºC for 1 min 20 s, followed by 35 cycles of 94ºC for 1 min, 50ºC for 1 min, 72ºC for 1 min 30 s; the program terminated with a final step of 72ºC for 5min. Each reaction was performed twice; PCR products were combined, separated by agarose gel (2%) electrophoresis and visualized by transillumination in the presence of ethidium bromide (EtBr) in order to check insert size. Purification of PCR products was perfomed via the GFX-96TM Polymerase Chain Reaction (PCR) Purification Kit (Amersham Pharmacia) according to the manufacturer’s instructions. The purified products were then dried down by applying vacuum, re-eluted in 3x SSC and 1.5 M betaine to a volume of 10 ml and transferred to 384 well plates. The spotting was performed with the OmniGrid 300 robotic system configured with 48 pins. Each glass slide contains 10,176 PCR amplified inserts in duplicate. The spotted glass slides were baked at 80ºC for 2 h in order to cross-link the DNA onto the glass slide. The slides were then incubated in blocking buffer at 50°C for 30 min, washed twice with Millipore water at room temperature for 2 min and dried by spinning in an Eppendorf 5810R centrifuge for 7 min at 800 rpm. |
| 14 |
GPL1724 |
SAGE:10:NlaIII:Gallus gallus |
4,090 |
|
2004-11-30 |
|
Gallus gallus
|
SAGE NlaIII |
SAGE NlaIII, SAGE:10:NlaIII:Gallus gallus, This is a virtual platform for SAGE libraries generated for Gallus gallus using NlaIII as an anchor enzyme. Platform_anchor: NlaIII |
| 15 |
GPL1731 |
DEL-MAR 14K Integrated Systems |
19,200 |
University of Delaware |
2004-12-06 |
|
Gallus gallus
|
cDNA Array |
spotted DNA/cDNA, DEL-MAR 14K Integrated Systems, Spotted amplified cDNA array on glass. 19200 spot corresponding to 14053 different genes. liver / fat / muscle / pituitary / hypothalamus / pineal / testis / ovary / oviduct / Oligo |
| 16 |
GPL1737 |
UD 7.4K Metabolic/Somatic Systems |
7,680 |
University of Delaware |
2004-12-08 |
|
Gallus gallus
|
cDNA Array |
spotted DNA/cDNA, UD 7.4K Metabolic/Somatic Systems, Spotted amplified cDNA array on glass. 7680 spots corresponding to 7435 genes from Liver and Adipose tissue. |
| 17 |
GPL1742 |
UD_Liver_3.2K |
3,456 |
University of Delaware |
2004-12-09 |
|
Gallus gallus
|
cDNA Array |
spotted DNA/cDNA, UD_Liver_3.2K, Spotted amplified cDNA array on nylon membrane (8 x 12 cm). 3456 spots Keywords = spotted Keywords = cDNA |
| 18 |
GPL1743 |
Zebrafish nucleotide array |
15,174 |
Leiden University |
2004-12-10 |
|
Danio rerio
|
Oligo Array |
spotted oligonucleotide, Zebrafish nucleotide array, Microarrays of the MWG 14k Zebrafish Oligonucleotide Set were produced using the facilities of the Leiden Genome Technology Center (http://www.lgtc.nl). Oligonucleotides were dissolved in 150mM phosphate buffer (pH 8.5) to a concentration of 20 µM. With Omnigrid 100 (Genemachines) oligonucleotides were spotted on Codelink activated slides (Amersham Biosciences) according to the Amersham Codelink protocol and as described in (‘t Hoen et al 2003 and Meijer et al 2004). Microarrays were spotted according to the MIAME guidelines with 15.532 unique zebrafish oligonucleotides from the MWG oligonucleotide set. Ambion’s arraycontrol oligonucleotides (8 sense oligos) and 3 custom designed oligonucleotides were spotted together with the MWG oligonucleotide set. Spotted Codelink activated slides were treated with blocking solution and washed according to the manufacturer’s instructions. |
| 19 |
GPL1744 |
Chicken_Neuroendocrine_System_5K |
7,200 |
University of Maryland |
2004-12-10 |
|
Gallus gallus
|
cDNA Array |
spotted DNA/cDNA, Chicken_Neuroendocrine_System_5K, Spotted amplified cDNA array on glass. Produced with cDNA clones expressed in the chicken neuroendocrine system. Tissues used to produced the cDNA library included the hypothalamus, anterior pituitary gland, and pineal gland. 7200 spots Keywords = spotted Keywords = cDNA |
| 20 |
GPL1793 |
Rainbow trout sex differentiation cascade-related genes investigated using RT-PCR |
102 |
Institut National de la Recherche Agronomique-INRA |
2005-01-12 |
|
Oncorhynchus mykiss
|
RT-PCR |
RT-PCR, Rainbow trout sex differentiation cascade-related genes investigated using RT-PCR, Virtual platform listing sex differentiation cascade-related candidate genes investigated using RT-PCR. |
|