| 1 |
GPL15057 |
NimbleGen Drosophila melanogaster Whole Genome 2.1M tiling array [DesignID: 6725] |
2,157,868 |
NimbleGen Systems, Inc. |
2011-12-23 |
NimbleGen |
Drosophila melanogaster
 |
Tiling Array |
in situ oligonucleotide, NimbleGen Drosophila melanogaster Whole Genome 2.1M tiling array [DesignID: 6725], Platform annotations based on UCSC dm3 (BDGP Release 5). NimbleGen ChIP 2.1M WG-T (2.1M Drosophila melanogaster - Whole Genome Tiling Set) Design_ID = 6725 Native NimbleGen files linked below. From NimbleGen's website: * Format: 2.1M * Source: UCSC * Build: DM3 * Probe Length: 50-75mer * Median Probe Spacing: 55bp * Design Name: D. mel ChIP 2.1M WG-T Arr Del |
| 2 |
GPL14984 |
Agilent-033023 Hzea_Virus_2directions [Feature Number Version] |
180,880 |
The University of Queensland |
2011-12-08 |
Agilent Technologies |
Helicoverpa zea
 |
Oligo Array |
in situ oligonucleotide, Agilent-033023 Hzea_Virus_2directions [Feature Number Version], 29,586 H.zea transcript sequences obtained from denovo assembly were reverse transcribed and then combined with the original sequences to form a final target sequence file that contains 59,172 sequences. Based on these 59,172 sequences, eArray was used to design 3 probes per target, with the options for best distribution method and no 3' bias. Then, all probes with potential cross hybridization were removed, resulting in 153,492 probes. This probe set was divided into 3 probe groups (eArray probe format: complete, Ms-excel), each contains 60,000, 60,000 and 33,000 probes. Another probe set for 135 virus genes and 16 selected insect genes (3 probes/target), which were replicated 10 times. These four probe groups were then used to design the 4x180,000 Agilent arrays. |
| 3 |
GPL14914 |
NimbleGen D. melanogaster Gene Expression 4x72K Array [081202_DM_TW_exp] |
63,856 |
NIBOCH |
2011-11-22 |
NimbleGen |
Drosophila melanogaster
|
Oligo Array |
in situ oligonucleotide, NimbleGen D. melanogaster Gene Expression 4x72K Array [081202_DM_TW_exp], Annotation in this record based on DM4.3 genome release Probe Length: 60mer 4x72K per dot designname=081202_DM_TW_exp designid=8572 |
| 4 |
GPL14686 |
Ciona intestinalis Oligoarray ver.2 4X44k |
45,220 |
OIST |
2011-10-07 |
Agilent |
Ciona intestinalis
 |
Oligo Array |
in situ oligonucleotide, Ciona intestinalis Oligoarray ver.2 4X44k, A publicly-accessible accession ID or clone ID is not available. The microarray probes were designed by combination of some gene models and EST/cDNA information. Users can search the corresponding genemodel/EST/cDNA using the probe sequence. |
| 5 |
GPL14736 |
Agilent-023576 Helicoverpa armigera V3 44K |
43,863 |
Stockholm University |
2011-10-14 |
Agilent Technologies |
Helicoverpa armigera
 |
Oligo Array |
in situ oligonucleotide, Agilent-023576 Helicoverpa armigera V3 44K, Arrays of this design have barcodes that begin with 16023576 or 2523576. The ID column represents the Agilent Probe name. |
| 6 |
GPL14667 |
Drosophila 2 x 15K Genome Array |
32,448 |
Central China Normal University |
2011-10-04 |
Operon |
Drosophila melanogaster
|
Oligo Array |
spotted oligonucleotide, Drosophila 2 x 15K Genome Array, |
| 7 |
GPL14724 |
Washington University/Genome Sequencing Center C. elegans 23K [oligoID version] |
22,507 |
Broad Institute of MIT and Harvard |
2011-10-12 |
Genome Sequencing Center, Washington University in St. Louis |
Caenorhabditis elegans
 |
Oligo Array |
spotted oligonucleotide, Washington University/Genome Sequencing Center C. elegans 23K [oligoID version], |
| 8 |
GPL14920 |
Locust 20k 60-mer oligo array |
18,308 |
Institute of Zoology, Chinese Academy of Sciences |
2011-11-22 |
BGI Beijing |
Locusta migratoria
 |
Oligo Array |
spotted oligonucleotide, Locust 20k 60-mer oligo array, |
| 9 |
GPL14906 |
SARS_Oikopleura_WG_til |
16,685 |
Sars International Centre for Marine Molecular Biology |
2011-11-18 |
NimbleGen |
Oikopleura dioica
 |
Tiling Array |
in situ oligonucleotide, SARS_Oikopleura_WG_til, O. dioica custom-made whole genome tiling array with 2,173,626 oligonucleotide features including 13,936 random negative controls. The probes have 50-75 bases size range and cover the entire 70 Mb genome with average overlap between adjacent probes of approximately 30 bases. native array description file: SARS_Oikopleura_WG_til.ndf native array description file: SARS_Oikopleura_WG_til.pos, SARS_Oikopleura_WG_til_probe_locations.gff |
| 10 |
GPL14928 |
Agilent-030589 Enchytraeus albidus Gene Expression Array 8x15k |
15,744 |
CESAM & University of Aveiro |
2011-11-25 |
Agilent Technologies |
Enchytraeus albidus
 |
Oligo Array |
in situ oligonucleotide, Agilent-030589 Enchytraeus albidus Gene Expression Array 8x15k, E.albidus_1035probes_SSHmet+SSHpest+norm Arrays of this design have barcodes that begin with 16030589 or 2530589. Orientation: Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software." The ID column represents the Agilent Feature Extraction feature number. Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface)." To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions." |
| 11 |
GPL14756 |
Agilent-026120 Cryptosporidium parvum whole genome 15K expression array v1.0 |
15,208 |
TAMU |
2011-10-18 |
Agilent |
Cryptosporidium parvum
 |
Oligo Array |
in situ oligonucleotide, Agilent-026120 Cryptosporidium parvum whole genome 15K expression array v1.0, |
| 12 |
GPL14758 |
UIUC Honey bee oligo 13K v1 |
14,400 |
Universidade de Sao Paulo |
2011-10-18 |
Keck Center for Comparative and Functional Genomics - University of Illinois |
Apis mellifera
 |
Oligo Array |
spotted oligonucleotide, UIUC Honey bee oligo 13K v1, UIUC Honey bee oligo 13K v1 Array Protocol May 13, 2007 Array Development text by Jay D. Evans, Gene E. Robinson and Gos Micklem. This document describes the features on a first-generation oligonucleotide microarray developed for the honey bee genome. Funding for this project was provided by USDA-National Research Initiative grant AG2004-36504-14277 (G.E. Robinson, PI, M. Band, J.D. Evans, G. deGrandi Hoffman, K.P. White, Co-PIs) ?Honey Bee Applied Genomics and Development of a Whole-Genome Array?. The developmental files can be accessed at http://www.biotech.uiuc.edu/centers/Keck/Functional_genomics/Honey%20Bee%20Oligo.htm Input sequences: A total of 13,145 sequences were used to design oligos, as detailed below: 1) A set primarily from the Honey Bee Genome Sequencing Consortium ?Official Gene Set? (circa 11/2005) (N = 10620). 2) Variable exons from the antimicrobial peptide apidaecin (Genbank and Evans, J.D., unpublished) (N = 11). 3) Variable exons from the IG-family gene Dscam (N = 81). 4) miRNA precursor candidates from the bee genome (Weaver, D.B., et al., submitted) (N = 81). 5) non-OGS EST?s from a subtractive library biased toward larval genes upregulated with exposure to the bacterial pathogen Paenibacillus larvae, Evans, J.D., unpublished. RNA was derived from 1st-instar honey bee larvae challenged with bacteria as described in Evans and Pettis, 2005, Evolution, 59(10), 2270-2274 (N=81). 6) Non-OGS EST?s from the Univ. Illinois bee brain EST project (Whitfield, C. W., Band, M. R., Bonaldo, M. F., Kumar, C. G., Liu, L., Pardinas, J. R., Robertson, H. M., Bento Soares, M. & Robinson, G. E., 2002, Genome Research, 12, 555-566.) (N=2271). 7) Representative genes from viral, fungal, bacterial, and microsporidian pathogens of honey bees (all in Genbank, ID?s in fasta file) (N=22). Oligo Design: Long oligos for the array were developed by Debashis Rana and Gos Micklem (http://www.gen.cam.ac.uk/Research/micklem.htm) at Cambridge University, using a modified version of OligoArray 2.1 in an iterative process to identify unique sequences (60-69mers) from each of the described (above) bee-related genes and gene fragments. The set of oligos was selected to have as tight a melting temperature distribution as possible, and to avoid repetitive sequences and other anomalies. A total of 12,915 unique oligos were generated (see below for redundancies) representing all but three of the 13,145 source sequences. Of those three (the pathogen gene PlDNAk, the EST sequence JDEA05_1Def3, and the candidate miRNA precursor HCmir13a), the EST and miRNA were represented by 98% identical oligos in the array. Reverse strand oligos were added for 525 predictions, focusing on EST reads and transcripts predicted for bee pathogens (EST ? 415; miRNA ? 57; OGS ? 31, and pathogen ? 22). As such the final set contains 13,440 oligos (sequences in Array_fasta/Oligoset13440.txt). The design process was similar to that of the INDAC long oligo set designed for the fruit fly Drosophila melanogaster and available at: http://www.flymine.org/release-5.0/aspect.do?name=INDAC and http://www.flychip.org.uk/services/core/FL002. Oligo and Sequence Redundancy: Distinctly numbered oligos had the same or similar sequences 69 times (>59/69 nt alignment, < 2 mismatches). Different source sequences matched identical oligos (>59/69, < 2 mismatch) 100 times, 44 of which were not genes with predicted splice variants (which were redundant in OGS). 18 were gene calls with splice variants for which oligos matched each variant. 639 source sequences showed matches at the sequence level but did not have identical oligo matches. Of these 524 reflect either splice variants or shared exons (e.g., Dscam exons vs. an entire proposed transcript). 115 are not indicated as splice variants and these appear to be redundant sequences in the source files, either from multiple predictions in OGS or from unrecognized similarity between EST?s and other EST?s or OGS. Most redundancies were single pairs, although one oligo sequence was similar across 6 distinctly called oligos. Printing the Array text by Mark Band and Al Bari Oligos were synthesized by Invitrogen (San Diego, CA) and aliquoted into 384 well plates in Sodium Phosphate buffer. Final concentration of the oligos was 20 uM (micromolar). Arrays were printed on Corning UltraGAPS slides using an Omingrid 100 printing robot (Genomic Solutions, Ann Arbor Michigan) with Arrayit SMP2.5 capillary pins. Following printing slides were stored in vacuum bags purged with Argon gas. Creating the Array Design File (ADF) text by Amro Zayed To ensure that the ADF contains the latest annotation, we first blasted all Honey bee oligos against: 1) The prerelease updated version of OGS v2 (http://racerx00.tamu.edu/downloadFASTA.html - circa 4/9/2007), 2) NCBI?s gene predictions (Ref RNA) for the Honey bee (circa 4/18/2007), 3) All honey bee derived EST sequences on NCBI (circa 4/25/2007), and 4) The latest assembly of the Honey bee genome (AMEL 4.0, circa 4/25/2007). We used blastn with no filtering and we initially retained all matches with an evalue smaller than 1e-3. We then removed blast hits that had an alignment length that is > 4 bp less then the oligo length and/or had an alignment identity less than 95%. Except for the control groups and the Pathogen set, we assigned an oligo?s ?Reporter Name?, regardless of which set it was originally designed from, based on the best blast match to the above mentioned databases, assigning priority in the following order: prerelease OGS v2, NCBI?s gene predictions, EST sequence names, and AMEL 4.0 assembly location. In cases where an oligo matched more than one sequence in the prerelease OGS v2 or NCBI?s gene predictions at the same evalue, we assigned the ?Reporter Name? and corresponding database accession ID to the gene with the highest numerical value, but included the list of equally matching genes in the ?Reporter Comment? field. If an oligo matched to both prerelease OGS v2 and NCBI?s gene prediction, we assigned the ?Reporter Name? as the OGS v2 gene name followed by the definition line from NCBI?s gene prediction, in addition to assigning both accession numbers to the oligo. When an oligo matched a prerelease OGS v2 gene, we added its Drosophila ortholog as computed by C. Elsik (http://racerx00.tamu.edu/bee_resources.html) in the ?Reporter Comment?. We also used blastp to query the Honey bee gene against Drosophila melanogaster v.5.1 genes (http://flybase.bio.indiana.edu/ circa 5/1/2007), and the best match was also reported in the ?Reporter Comment?. For oligos that did not match entries in any of the above mentioned databases, we retained the original annotation information used to design the oligo. Similarly, we retained all the annotation information from the design files for the control sequences and for the Pathogen set. |
| 13 |
GPL14810 |
[Eh_Eia520620F_Ei] Affymetrix Entamoeba invadens Array |
12,483 |
National Institute of Infectious Diseases |
2011-10-28 |
Affymetrix |
Entamoeba invadens
 |
GeneChip |
in situ oligonucleotide, [Eh_Eia520620F_Ei] Affymetrix Entamoeba invadens Array, EIN_nnnn identifiers represent TIGR locus_tag |
| 14 |
GPL14830 |
ZB/SBS-NTU Plasmodium falciparum 11K v1.1 |
11,005 |
Nanyang Technological University, School of Biological Sciences |
2011-11-03 |
ZB lab/SBS-NTU |
Plasmodium falciparum
 |
Oligo Array |
spotted oligonucleotide, ZB/SBS-NTU Plasmodium falciparum 11K v1.1, |
| 15 |
GPL14831 |
ZB/SBS-NTU Plasmodium falciparum 10.4K v1.0 |
10,416 |
Nanyang Technological University, School of Biological Sciences |
2011-11-03 |
ZB lab/SBS-NTU |
Plasmodium falciparum
|
Oligo Array |
spotted oligonucleotide, ZB/SBS-NTU Plasmodium falciparum 10.4K v1.0, |
| 16 |
GPL14814 |
ZB/SBS-NTU Plasmodium chabaudi chabaudi 4K v1.0 |
4,077 |
Nanyang Technological University, School of Biological Sciences |
2011-10-31 |
ZB lab/SBS-NTU |
Plasmodium chabaudi chabaudi
 |
Oligo Array |
spotted oligonucleotide, ZB/SBS-NTU Plasmodium chabaudi chabaudi 4K v1.0, |
| 17 |
GPL14742 |
Calanus physiology microarray |
995 |
University of Connecticut |
2011-10-14 |
Printed in Mount Desert Island Biological Laboratory, Salisbury Cove, Maine |
Calanus finmarchicus
 |
Oligo Array |
spotted oligonucleotide, Calanus physiology microarray, |
| 18 |
GPL14738 |
Illumina Genome Analyzer IIx (Leishmania tarentolae) |
0 |
|
2011-10-14 |
|
Leishmania tarentolae
 |
HT Sequencing |
high-throughput sequencing, Illumina Genome Analyzer IIx (Leishmania tarentolae), |
| 19 |
GPL14739 |
Illumina Genome Analyzer IIx (Leishmania major) |
0 |
|
2011-10-14 |
|
Leishmania major
 |
HT Sequencing |
high-throughput sequencing, Illumina Genome Analyzer IIx (Leishmania major), |
| 20 |
GPL14749 |
Illumina Genome Analyzer IIx (Acropora millepora) |
0 |
|
2011-10-17 |
|
Acropora millepora
 |
HT Sequencing |
high-throughput sequencing, Illumina Genome Analyzer IIx (Acropora millepora), |
|