title: Agilent-012795 C. elegans Oligo Microarray G2518A Option 002 (Feature Number version)

status: Public on Sep 24 2005

city: Palo Alto

last: Agilent Technologies

state: CA

country: USA

institute: Agilent Technologies

organism: Caenorhabditis elegans

technology: in situ oligonucleotide

description:
Agilent has made available a new microarray with genome-wide coverage of C. elegans with over 21,000 predicted genes from WormBase, a public C. elegans genome database.

Arrays of this design have barcodes that begin with 16012795 or 2512795.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7272.

distribution: custom-commercial

manufacture_protocol: see manufacturer's web site at http://www.agilent.com/


title: Agilent-012106 Rice Oligo Microarray G4138A (Feature Number version)

status: Public on Jan 02 2004

organism: Oryza sativa Japonica Group

description:
This array will enable researchers to simultaneously characterize thousands of rice genes associated with biological functions, growth processes, and biotic and abiotic stress response. Probes on this array are designed to selections from the extensive rice (japonica) cDNA library of Japans National Institute of Agrobiological Sciences.

Arrays of this design have barcodes that begin with 16012106 or 2512106.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7268.


title: Fundulus heteroclitus cDNA-based embryo microarray

status: Public on Apr 14 2013

city: Talence

first: angela

last: tingaud-sequeira

address: avenue des Facultés

country: France

institute: Université Bordeaux 1

organism: Fundulus heteroclitus

technology: spotted DNA/cDNA

description: Reference = Cerdà, J., Tingaud-Sequeira A., Lozano J., Otero D., Zapater C., Beck A., Kuhl H., Kreutzberger J., Kube M., Reinhardt R. Transcriptome analysis of killifish embryos.

distribution: non-commercial

manufacture_protocol: 15658 high-quality sequences were obtained from Fundulus hetoclitus embryo cDNA libraries. The final array design contained 15,658 spotted Fundulus heteroclitus specific cDNAs.


title: Agilent-013162 Whole Rat Genome Microarray G4131A (Feature Number version)

organism: Rattus norvegicus

description:
With a focus on well known rat genes and homologues to human and  mouse genes with useful annotation, Agilent's Whole Rat Genome Oligo Microarray provides researchers with a new tool for modeling human biology in the rat model organism. For researchers, this means they now have access to a microarray made up of relevant content that has been empirically validated by Agilent.

Arrays of this design have barcodes that begin with 16013162 or 2513162.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7289.


title: Agilent-011521 Human 1A Microarray G4110A  (Feature Number version)

organism: Homo sapiens

description:
Agilent's Human 1A Oligo Microarray (V2) includes over 17K 60-mer oligonucleotide probes, sourced from the Incyte Foundation Database and are designed to span conserved exons across the transcripts of the targeted full length genes. Coupled with Agilent's

Arrays of this design have barcodes that begin with 16011521 or 2511521.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7260.


title: Agilent-035111 miOVO fish V16

status: Public on Dec 31 2012

city: Rennes

first: Julien

last: Bobe

address: Campus de Beaulieu

institute: Institut National de la Recherche Agronomique

organism: Oncorhynchus mykiss

description:
Arrays of this design have barcodes that begin with 16035111 or 2535111.

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.


title: NimbleGen Mouse DNA Methylation 2.1M Economy Whole-Genome Tiling Arrays (4/4)

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

organism: Mus musculus

description:
Format: 2.1M
Format: Source: UCSC
Format: Build: MM9
Format: Probe Length: 50-75mer
Format: Median Probe Spacing: 255

manufacture_protocol: see manufacturer's website


title: NimbleGen Mouse DNA Methylation 2.1M Economy Whole-Genome Tiling Arrays (3/4)


title: Agilent-011868 Rat Oligo Microarray G4130A (Feature Number version)

description:
This microarray contains representative sequences derived from rat RefSeq, high-quality public rat mRNA accessions, homologs to human and mouse RefSeq, EST clusters determined by a leading biopharmaceutical company and the Incyte Zooseq database as well as toxicology markers determined by the National Institute of Environmental Health Sciences (NIEHS) and others. Many of the toxicology markers used in the design of this microarray were released to the public domain for the first time and will be used on this unique microarray product.

Arrays of this design have barcodes that begin with 16011868 or 2511868.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7267.


title: Agilent-033484 Populus 8x60K v2.0 (Feature Number version)

city: Athens

first: Chung-Jui

last: Tsai

state: GA

address: 120 Green Street

department: School of Forestry and Natural Resources

institute: University of Georgia

organism: Populus trichocarpa

description:
Populus transcriptome based on v2.2.
Arrays of this design have barcodes that begin with 16033484 or 2533484.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL16322.

first: Liangjiao

last: Xue

relation: Alternative to: GPL16322 (Probe Name version)


title: Combimatrix 90k TomatArray 1.0

status: Public on Feb 12 2013

city: Portici (NA)

first: Antonio

last: Di Matteo

address: Via Universita' 100 - Parco Gussone - Edificio 75

department: DiSSPAPA

country: Italy

institute: University of Naples Federico II

organism: Solanum lycopersicum

description: 20200 specific oligos (35-40mer) were designed on Tomato Gene Index Version 11 (LeGI v.11, June21, 2006) tentative consensus (TC) sequences by using the program design OligoArray 2.1 (Rouillard et al. 2003). As negative controls nine bacterial oligonucleotides sequences provided by Combimatrix were utilized. The 90K TomatArrayTM  1.0 was designed with four replicates of each probe randomly distributed across the array to allow measurement of the variability within the array. All the procedures provided were performed as indicated by Combimatrix protocols available at Combimatrix website (www.combimatrix.com)

manufacturer: University of Verona - Scientific and Technological Department - Plant Functional Genomics Centre

manufacture_protocol: Probes are directly synthesized on a 90k Combimatrix array by an in situ oligo synthesis system developed by Combimatrix Corporation (Mukilteo, USA) using the Combimatrix CustomArray synthesizer. Standard synthesis protocol provided by Combimatrix was used.


title: Agilent-011978 Mouse Microarray G4121A (Feature Number version)

description:
Mouse is the most widely used mammalian model in biological research and target identification. This microarray will enable researchers to simultaneously characterize expression activities of many thousands of mouse genes associated with various biological functions and processes. Content for this empirically validated microarray includes a comprehensive set of toxicology markers determined through collaboration with leaders in toxicogenomics including NIEHS, Toxicogenomics Research Consortium, and Paradigm Genetics

Arrays of this design have barcodes that begin with 16011978 or 2511978.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL6466.


title: NimbleGen Mouse DNA Methylation 2.1M Economy Whole-Genome Tiling Arrays (1/4)


title: [PIGTEATa520665F] Custom Affymetrix porcine QTL-region-specific microarray [FBN_PigTeat_1.5k v1]

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

organism: Sus scrofa

manufacture_protocol: see manufacturer's web site


title: Agilent-028992 Clostridium difficile R20291 expression array

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

organism: Clostridioides difficile

description:
All the features named "CDR20291_" come from the same complete sequence of R20291 with the GenBank Accession Number: FN545816.1.

Arrays of this design have barcodes that begin with 16028992 or 2528992.
DesignID: 028992

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.


title: NIA mouse 15K cDNA clones

city: clayton

first: Dave

last: Winkler

address: bayview ave

country: Australia

institute: CSIRO

first: Greg

last: Stephanopoulos

manufacture_protocol: Spotted on to glass slide


title: Agilent-TQ Cardiovascular Human Oligonucleotide Array

status: Public on Jun 30 2005

first: Jennifer

last: King

department: Cardiovascular Medicine

institute: Stanford University

technology: spotted oligonucleotide

description: Cardiovascular specific human oligonucleotide array (20433 unique probes) developed between Agilent Technologies and the Quertermous Lab at Stanford University.

middle: Y

first: Rossella

last: Ferrara

first: Raymond

last: Tabibiazar

first: Joshua

middle: M

last: Spin

first: Mary

last: Chen

first: Allan

last: Kuchinsky

first: Aditya

last: Vailaya

first: Robert

last: Kincaid

first: Andrew

last: Connolly

first: Anya

last: Tsalenko

first: David

middle: X

last: Deng

first: Peng

last: Zhang

first: Clifton

last: Watt

first: Zohar

last: Yakhini

first: Amir

last: Ben-Dor

first: Annette

last: Adler

first: Laurakay

last: Bruhn

first: Philip

last: Tsao

first: Thomas

last: Quertermous

first: Euan

middle: A

last: Ashley


title: Bakal Drosophila melanogaster 4x2k v1.0

city: Cambridge

first: Michael

last: Baym

state: MA

address: MIT 32-G572 / 32 Vassar St.

department: Mathematics

institute: MIT

organism: Drosophila melanogaster

first: Chris

last: Bakal

first: Bonnie

last: Berger

first: Norbert

last: Perrimon

manufacture_protocol: Hybridization protocol for CustomArray 4x2k, by CombiMatrix.


title: HEEBO Human 48.5K Microarrays Inc

city: Anderlecht

first: sebastien

last: floor

state: Bruxelles

address: Route de Lennik 808

country: Belgium

institute: IRIBHM - ULB


title: Agilent-026120 Cryptosporidium parvum whole genome 15K expression array v1.0

city: College Station

first: haili

last: zhang

address: Texas A&M University 4467 TAMU

department: VTPB

institute: TAMU

organism: Cryptosporidium parvum

first: Huaijun

last: Zhou

first: Guan

last: Zhu

first: Haili

manufacture_protocol: probes was in situ synthesized.


title: Agilent-012097 Human 1A Microarray (V2) G4110B (Feature Number version)

last: Agilent Technologies

description:
Agilent's Human 1A Oligo Microarray (V2) includes over 20K 60-mer oligonucleotide probes, sourced from the Incyte Foundation Database, RefSeq, and GenBank, and are designed to span conserved exons across the transcripts of the targeted full length genes. Coupled with Agilent's probe selection and validation processes, this design method gives the customer maximum confidence in data quality and prevents redundancy in gene coverage.

Arrays of this design have barcodes that begin with 16012097 or 2512097.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7264.


title: NimbleGen Mouse DNA Methylation 2.1M Economy Whole-Genome Tiling Arrays (2/4)

first: Xiwei

last: Wu


title: University of Illinois/Haifa University Spalax galili Agilent 8x15K microarray

city: Urbana

first: Mark

middle: Robert

last: Band

state: IL

address: 1201 W. Gregory Dr

department: Biotechnology

institute: University of Illinois

organism: Nannospalax galili

description: Spalax galili 8 x 15K oligo microarray

first: Aaron

last: Avivi

first: Assaf

last: Malik

first: Avraham

last: Korol

manufacture_protocol: In situ oligo synthesis


title: IRIBHM-human-miRNA(V.11.0)-Exiqon

manufacturer: Exiqon for the libriry, spotting at the IRIBHM

manufacture_protocol: The library mercury LNA microRNA ready-to-spot probes set (V11.0) from Exiqon were spotted on Corning epoxide slide using a MicroGrid II, with a humidity of 48%. The library were spotted in duplicate on each array. Spotting solution ; Pronto! Epoxide spotting solution. Probe sequences are not available


title: Exiqon microRNA Ready-to-Use PCR, Human panel I+II, V2.M

status: Public on Dec 29 2012

city: Shanghai

first: Qifeng

last: Wang

address: NO 270,Dongan Road

country: China

institute: Cancer Hospital, Fudan University

technology: RT-PCR

description:
miRCURY LNA™ Universal RT microRNA PCR, 4x Human panel I and 4x Human panel II in 384well PCR plates.
One reaction each of 742 human microRNAs and 6 reference genes.
For use with ABI 7900HT and other instruments.

distribution: virtual

manufacture_protocol: see manufacturer's website (http://www.exiqon.com/mirna-pcr-panels)


title: Custom Segment Definition for Human Exon 1.0 ST Array

status: Public on Jan 21 2013

city: Moscow

first: Pavel

last: Mazin

address: Skolkovo Innovation Center, Building 3

department: Biomed

country: Russia

institute: Skolkovo Institute of Science and Technology

description: HuEx-1_0-st array analysis with custom segment definitions. Linked supplementary file contains the probe to segment mappings for segments having uniquely mapped probes. Segments without uniquely mapped probes were not included in the analysis.

manufacture_protocol: See manufacturer's web site


title: SHEEPARRAY

city: Trieste

first: alberto

last: Pallavicini

address: via Giorgierei 5

department: Life Sciences

institute: University of Trieste

organism: Ovis aries

manufacturer: University of Verona - Department of Biotechnology - Functional Genomics Centre


title: Agilent-023386 Rattus norvegicus Array

city: Newort on tay

first: Simon

last: Plummer

address: 23 Wellgate Street

country: United Kingdom

institute: Micromatrices Associates ltd

description: Genome build: RGSC_v3.4 rn4

manufacture_protocol: See manufacturer's web site at http://www.agilent.com/.


title: TAMU Salmonella enterica Serovar Typhimurium 4.4K v 2.0

city: Dallas

first: Palmy

middle: R

last: Jesudhasan

state: TX

department: Microbiology

institute: University of Texas Southwestern Medical Center

organism: Salmonella enterica subsp. enterica serovar Typhimurium

description: grids - 48

first: Suresh

middle: D

last: Pillai

manufacture_protocol:
PFGRC_SALM, with arrayer LUCIDEA, mode
Normal, replicates 2, repeats 1, slide_dips -1, machine cycles 552382,
pen id 10113, pen cycles -1, operator Robin, humidity control On,
humidity set point 65


title: SABiosciences Human Mitochondria Energy Array

city: Portland

first: Alina

last: Maloyan

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Medicine

institute: Oregon Health and Science University

description:
Human Mitochondria Energy Array
SABiosciences RT² Profiler panel of PCR assays.


title: TaqMan Rodent MicroRNA A Array v2.0

status: Public on Dec 30 2012

city: Stanford

first: Liang

last: Wei

address: 1201 Welch Rd MSLS P328

department: Surgery

organism:
Mus musculus
Rattus norvegicus

description:
TaqMan array rodent microRNA A Card v2.0
Real-time PCR based microRNA microarrays


title: UIUC Honey bee oligo 13K v1

city: Alfenas

first: Joseana

last: Vieira

state: Minas Gerais

address: Rua Gabriel Monteiro da Silva, 700

country: Brazil

institute: Unifal-MG

organism: Apis mellifera

description:
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 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.

manufacturer: Keck Center for Comparative and Functional Genomics - University of Illinois

first: Anna

middle: C

last: G Freire

first: Angel

last: Barchuk

first: Zilá

middle: L

last: Simões

first: Ana

last: Bomtorin

first: Livia

last: Moda

manufacture_protocol: Honey bee oligonucleotide microarray v1 contains 28800 features, and a total of 13440 double spotted ss oligos. 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.


title: Illumina Genome Analyzer II (Cryptococcus neoformans)

status: Public on Dec 28 2012

last: GEO

organism: Cryptococcus neoformans

technology: high-throughput sequencing


title: Illumina HiSeq 2000 (Mycobacterium avium subsp. paratuberculosis K-10)


title: Illumina HiSeq 2000 (Blumeria graminis f. sp. hordei)

status: Public on Dec 27 2012

organism: Blumeria hordei


title: Illumina HiSeq 2000 (Dugesia japonica)

organism: Dugesia japonica


title: Agilent-012694 Whole Mouse Genome G4122A (Feature Number version)

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Designed to truly represent all known genes in the mouse genome and their resulting transcripts, Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts. Content for this microarray was generated from leading public databases, including RefSeq, RIKEN, NIA, Ensembl, RIKEN, UCSC Goldenpath, and Unigene.

Arrays of this design have barcodes that begin with 16012694 or 2512694.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7042.


title: Brucella melitensis 9.7K

first: Leslie

middle: Garry

last: Adams

address: 402 Raymond Stotzer Blvd.

department: Veterinary Pathobiology

institute: Texas A&M University

organism: Brucella melitensis bv. 1 str. 16M

manufacturer: Western Regional Center of Excellence (WRCE) Pathogen Expression Core (Arizona State University)

first: Stephen

last: Johnston

first: Mitchell

last: McGee

first: Rhonda

last: Friedberg

manufacture_protocol: A set of unique 70-base oligonucleotides representing 3,227 ORFs of B. melitensis strain 16M and unique / divergent genes from B. abortus and B. suis were designed at the Pathogen Expression Core and purchased from Sigma-Genosys (The Woodland, TX). Oligonucleotides were suspended in 3X SSC (Ambion) at the final concentration of 40 uM before robotic arraying in triplicate onto ultraGAPS coated glass slides (Corning) using a Spotarray 72 microarray printer (Perkin Elmer, Downer’s Grove, ILL). Printed slides were steamed and UV cross-linked and stored in a desiccators until use.


title: Applied Biosystems TaqMan miRNA Expression Assays A and B

status: Public on Dec 26 2012

city: Munich

first: Andreas

last: Schober

state: Bavaria

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

institute: Ludwig-Maximilians-University

description: PCR assay.

manufacture_protocol: See manufacturer's website.


title: UHN Human 10K v1

organism: Homo sapiens

manufacturer: UHN Microarray Centre (University Health Network, Ontario, Canada)

first: Zhibin

last: Lu

manufacture_protocol: 1. Acquisition of bacterial clone set—These are well characterized human ESTs, and annotations for most clones in this clone set are available in OMIM, RefSeq and/or SwissProt IDs.  2. Clone set is PCR amplified and DNA purified in working 96 well plates.  3. The purified DNA is then transferred to 384 well source plates with DNA concentration ranging from .10ug/ul to 0.25ug/ul. These are used for spotting.  4. We use high precision robots that can use up to 48 pins or print heads. H10k slides are printed using 48 pins and we use UltraGAPS slides (Corning Inc.) We are able to print up to 120 slides in each batch and batches that result in greater than 95% printing fidelity are selected for post printing quality control tests.  5. Post Printing Quality Control tests include: A real hybridization using commercially available RNA; Vector Probe labeling method; Terminal Transferase tailing method.


title: All Illumina Human expression beadchips based on nuID

city: La Jolla

first: Eric

last: Lau

address: 10901 North Torrey Pines Road, Rm 6207

department: Signal Transduction

institute: The Sanford-Burnham Medical Research Institute

technology: oligonucleotide beads

description: This platform pools probe IDs of all Illumina Human expression beadchips based on nuID. nuIDs are defnined based on probe sequence, they are universally unique. Using nuIDs will make data integration and maintenance very easier. See Bioconductor lumi package for more details of nuID annotation.


title: SA Biosciences Mouse lung gene expression array

status: Public on Dec 25 2012

city: Gary

first: Roman

last: Dziarski

state: IN

address: 3400 Broadway

institute: Indiana University School of Medicine-Northwest

organism: Mus musculus

description: Quantitative reverse transcription real-time PCR (qRT-PCR)


title: Agilent-033077 Campylobacter jejuni expression array HY_81176 (Agilent Feature Number version)

city: Helsinki

first: Heidi

middle: J

last: Hyytiäinen

address: Agnes Sjöbergin katu 2

department: Dep. of Food Hygiene and Environmental Health

country: Finland

institute: University of Helsinki

organism: Campylobacter jejuni subsp. jejuni 81-176

description:
Agilent-033077 HY_81176
Expression 81176/P3
Arrays of this design have barcodes that begin with 16033077 or 2533077.
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.

manufacture_protocol: See manufacturer's web site at http://www.agilent.com/ .


title: Agilent-034214 Ecoli E22 RegA ANTISENSE

city: Parkville

first: Matthew

last: Wakefield

state: VIC

address: 1G Royal Parade

department: Bioinformatics

institute: Walter and Eliza Hall Institute

organism: Escherichia coli E22

description:
Ecoli E22 antisense

Arrays of this design have barcodes that begin with 16034214 or 2534214.

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.

manufacture_protocol: see manufacturer's web site at http://www.agilent.com/


title: Micro-CRIBI Mouse 27K Oligo Array (Operon V1.1)

status: Public on Dec 24 2012

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

distribution: commercial

manufacturer: Microcribi - Microarray Service (CRIBI - University of Padova)

manufacture_protocol: This set consists of 13,443 70mer oligonucleotides (Operon version 1.1) designed on Mouse Unigene clusters, mainly in the 3'-terminal region. Each oligonucleotide is spotted by our robotic station Biorobotics Microgrid II, in two replicates on a MICROMAX glass slide SuperChip I (Cat No MPS696) provided by PerkinElmer Life Sciences Inc. The deposition is qualitatively assessed by a scan of the spotted slide at 10 micron resolution, using a GSI Lumonics scanner and a protocol that allows the detection of spotted features through the salts derived from the dried solution in which oligonucleotides are dissolved. Microarray slides that meet the quality standards, are washed as recommended by the supplier and the glass slides are stored, ready for use, in the dark under deep vacuum.


title: Agilent-025249 S. pombe Whole Genome ChIP-on-Chip Microarray 4x44K (Probe Name version)

city: San Francisco

first: Kyle

last: Fowler

state: California

address: 600 16th Street

institute: University of California San Francisco

organism: Schizosaccharomyces pombe

description:
Agilent-025249 Smith_Array_1

This Platform includes the probes of GPL16235, supplemented with probes for repetitive regions.

manufacture_protocol: See manufacturer's web site at http://www.agilent.com.


title: Applied Biosystems Taqman miRNA Expression Assays A and B

manufacture_protocol: Applied Biosystems


title: Illumina Hiseq 2000 (Plasmodium falciparum)

status: Public on Dec 22 2012

organism: Plasmodium falciparum


title: UF_Wang_Xfa_2x105K_version 1.0

status: Public on Dec 21 2012

city: Lake Alfred

first: Nian

last: Wang

state: Florida

address: 700 Experiment Station Road

department: Citrus Research and Education Center/Department of Microbiology and Cell Science

institute: University of Florida

organism:
Xylella fastidiosa 9a5c
Xylella fastidiosa Temecula1

manufacture_protocol: see manufacturer's web site


title: 25K human oligonucleotide array v2

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

institute: IGBMC

manufacture_protocol:
The 50 mers 5’amino modified oligonucleotides from the RNG/MRC oligonucleotide collection (see Le Brigand et al, below) (information available at http://www.microarray.fr:8080/merge/index) were diluted to a final concentration of 50 mM in 50% dimethyl sulfoxide (D-8418, Sigma), 100mM potassium phosphate (pH 8.0) and printed onto hydrogel-coated slides (Nexterion H slides, Schott, Jena, Germany) using a microGrid II arrayer (Genomic Solutions, Cambridge, UK).
Le Brigand K, Russel R, Moreillon C, et al. An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes. Nucleic Acids Research, 2006 Jul 19; 34(12):e87


title: Illumina Genome Analyzer IIx (Petaurus breviceps)

status: Public on Dec 19 2012

organism: Petaurus breviceps


title: Illumina Genome Analyzer IIx (Tadarida brasiliensis)

organism: Tadarida brasiliensis


title: Saccharomyces cerevisiae 5.8K (TI4932 60mer expr X4)

city: Bethesda

first: Maria

middle: de los Angeles

last: Jaime

state: Maryland

address: 50 South Drive, National Institutes of Health

department: NIDDK - LCDB

institute: NIH

organism: Saccharomyces cerevisiae

description:
NimbleGen 4X72k yeast microarrays (Roche NimbleGen, Inc.; Design ID A6186-00-01, TI4932 60mer expr X4)
TI4932_60mer_expr.ndf
TI4932_60mer_expr.ngd

manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.


title: Illumina HiSeq 2000 (Volvariella volvacea)

last: GEO

organism: Volvariella volvacea


title: Topic-defined PIQORTM miRXplore Microarray

city: Milano

first: Yvan

last: Torrente

address: Francesco Sforza 35

department: Neuroscience

institute: University of the Studies of Milan

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

manufacture_protocol: 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides using a customized piezoelectric spotter


title: Illumina Genome Analyzer IIx (Peromyscus leucopus)

organism: Peromyscus leucopus


title: Illumina Genome Analyzer (Nicotiana tabacum)

status: Public on Dec 20 2012

organism: Nicotiana tabacum


title: AB 5500xl Genetic Analyzer (Drosophila melanogaster)

organism: Drosophila melanogaster


title: Illumina Genome Analyzer IIx (Suncus murinus)

organism: Suncus murinus


title: Illumina Genome Analyzer IIx (Meriones unguiculatus)

organism: Meriones unguiculatus


title: Illumina Genome Analyzer IIx (Oryctolagus cuniculus)

organism: Oryctolagus cuniculus


title: AB 5500xl Genetic Analyzer (Pseudomonas chlororaphis subsp. aureofaciens 30-84)


title: Agilent-020996 USEPA Ampelisca abdita 8 x15k 60mer v1.0 (G2509F)

city: Cincinnati

first: mitch

last: kostich

state: Ohio

address: 26 W. Martin Luther King Dr

department: Office of Research and Development

institute: US Environmental Protection Agency

organism: Ampelisca abdita

manufacture_protocol: 60-mer oligonucleotides selected and printed by Agilent. Design format IS-15744-8-V1.  Design ID 020996


title: [Bovine] Affymetrix Bovine Genome Array

status: Public on May 24 2005

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Bos taurus

description:
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 GeneChip Bovine Genome Array can be used to study gene expression of over 23,000 bovine transcripts. The array is an ideal tool for researchers studying gene expression profiles in cattle. With the broadest representation of publicly available expressed sequence information, bovine researchers will be able to use this array to monitor genetic mechanisms regulating a variety of preferred traits, such as:

- Disease resistance
- Meat and dairy production
- Stress tolerance

The Bovine Genome Array was designed in close collaboration with the Bovine Research Community as part of the Affymetrix GeneChip Consortia Program.

Annotations derived from Affymetrix CSV file dated 4/01/2005

relation: Alternative to: GPL10186 (Alternative CDF)

relation: Alternative to: GPL10941 (Alternative CDF)

relation: Alternative to: GPL13706 (Alternative CDF)


title: Illumina Genome Analyzer IIx (Mesocricetus auratus)

organism: Mesocricetus auratus


title: Illumina Genome Analyzer IIx (Meles meles)

organism: Meles meles


title: Illumina Genome Analyzer IIx (Felis catus)

organism: Felis catus


title: Illumina Genome Analyzer IIx (Erinaceus europaeus)

organism: Erinaceus europaeus


title: Illumina Genome Analyzer IIx (Cavia porcellus)

organism: Cavia porcellus


title: NimbleGen custom Mouse MIRTA Array

city: Klosterneuburg

first: Florian

last: Pauler

address: Am Campus 1

country: Austria

institute: IST Austria

organism: Mus musculus

description:
Annotation in this record based on NCBI mouse build 37.
Array build is based on potentially imprinted genes, 100nt spacing

manufacture_protocol: see manufacturer's web site www.nimblegen.com


title: Illumina Genome Analyzer IIx (Chlorocebus aethiops)

organism: Chlorocebus aethiops


title: Agilent-030587 CCMC CGH plus SNP 180k Microarray

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Homo sapiens

description:
CCMC, CGH+SNP, SNP, Cancer, 180k Microarray

Arrays of this design have barcodes that begin with 16030587 or 2530587.

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.


title: Illumina Genome Analyzer IIx (Acomys cahirinus)

organism: Acomys cahirinus


title: Illumina HiSeq 2000 (Grosmannia clavigera)

status: Public on Dec 18 2012

organism: Leptographium clavigerum


title: Illumina Genome Analyzer IIx (Tamias sibiricus)

organism: Tamias sibiricus


title: Galbraith Laboratory Arabidopsis thaliana 29.1k Operon Long Oligonucleotide Microarray version 3.0 (Atq3.6.4.Z)

city: Nijmegen

first: Tom

last: Tytgat

address: Heyendaalseweg 135

department: Ecogenomics

country: Netherlands

institute: Radboud University Nijmegen

organism: Arabidopsis thaliana

manufacturer: Galbraith Laboratory, University of Arizona

manufacture_protocol: This oligonucleotide array is produced from the Operon Version 3.0 Array-Ready Oligo Set (AROS), which comprises 29110 70-mer oligonucleotides representing 26173 protein-coding genes, 28964 protein encoding gene transcripts, and 8787 microRNA precursors. AROS design is based on ATH1 release 5.0 of the TIGR Arabidopsis genome annotation database, and Release 4.0 of the miRNA Registry at the Sanger Institute. (http://ag.arizona.edu/microarray/)


title: Illumina Genome Analyzer II (Grosmannia clavigera)


title: NU Hydrangea macrophylla 12K CustomArray ver.1.0

city: Nagoya

first: Takashi

last: Negishi

state: Aichi

address: Furo-cho, Chikusa-ku

country: Japan

institute: Nagoya University Graduate School

organism: Hydrangea macrophylla

description:
oligo DNA (35 to 40-mer)
Negative control probes (derived from bacteria, plant other than H. macrophylla, and bacteriophage) were spotted on 70 spots, and factory QC probes were spotted on 326 spots. Therefore, signal data from total of 396 control spots were included in 12,396-spot data on the custom-designed H. macrophylla oligo DNA microarray.

manufacture_protocol: see manufacturer's website http://www.customarrayinc.com/html/arrays.html


title: Saccharomyces cerevisiae 6.4K array (Y6.4K), version 4 [ORF-centered]

city: Gothenburg

first: Abraham

last: Ericsson

address: Medicinaregatan 9C

department: Cell and Molecular Biology

country: Sweden

institute: Gothenburg University

organism: Saccharomyces cerevisiae

description: This is an ORF-centered version of Platform GPL4462

first: Michael

last: Thorsen

first: Erik

last: Kristiansson

first: Markus

last: Tamas

first: Olle

last: Nerman

manufacture_protocol: Microarrays are printed on GAPS II or UltraGAPS™ slides (Corning Inc.) using high-precision robotics. Printed arrays are processed following Corning's protocol and are ready-to-use. Double-spotted array containing 6,240 yeast ORFs (plus control spots totalling 6.4K).


title: Illumina Genome Analyzer IIx (Staphylococcus sp. OJ82)

organism: Staphylococcus sp. OJ82


title: Illumina HiSeq 2000 (Acinetobacter sp. ADP1)

organism: Acinetobacter baylyi


title: Illumina Genome Analyzer (Olea europaea)

organism: Olea europaea


title: SABiosciences Human (normal respiratory epithelia and lung cancer cells) miRNA PCR array assay panel

city: Frederick

first: Jigui

last: Shan

address: 430 Miller Dr

institute: NCI-Frederick

description:
PCR assay
SABiosciences Human Genome RT2 miRNA PCR Array.

manufacture_protocol: see manufacturer's website


title: Illumina Genome Analyzer IIx (Petunia x hybrida)

status: Public on Dec 17 2012

organism: Petunia x hybrida


title: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array (Brainarray CustomCDF [Hs133P_Hs_UG])

status: Public on Dec 13 2012

city: Mannheim

first: Li

last: Li

address: Theodor-Kutzer-Ufer

institute: University Heidelberg

description: Probe set definition from CustomCDF file (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp - version 10)

relation: Alternative to: GPL570 (Alternative CDF [official])

manufacture_protocol: see the Affymetrix website


title: Illumina HiSeq 2000 (Arabidopsis thaliana x Arabidopsis arenosa)


title: Agilent-015424 S. pombe Whole Genome ChIP-on-Chip Microarray 4x44K (Probe Name version - A_86_Pnnnn probes)

city: Palo Alto

last: Agilent Technologies

state: CA

institute: Agilent Technologies

organism: Schizosaccharomyces pombe

description:
S. pombe Whole Genome ChIP-on-Chip Microarray 4x44K

The ID column represents the Agilent Probe Name.

This Platform is an alternative to GPL16235, which includes Probe Names prefixed with A_93_Pnnnnnnnn. This Platform's Probe Names are prefixed with A_86_Pnnnnnnnn.

relation:
Alternative to: GPL16218
Alternative to: GPL16235


title: NimbleGen A.palmata 135K array v1.0

city: University Park

first: Nicholas

last: Polato

state: PA

address: 208 Mueller Lab

department: Biology

institute: Penn State University

organism: Acropora palmata

description: NimbleGen IRN/design name 6019040401.  A 12X 135K custom expression array design with two 60-mer probes per contig sequence and one per singleton sequence (additional probes as specified in the .ngd file). The .ndf and .ngd files are available as supplementary files.

manufacture_protocol: High-density microarray prepared with Roche NimbleGen's digital manufacturing process. See manufacturer's website at http://www.nimblegen.com/.


title: NimbleGen 120629_Olea_Populus_TU_exp

city: cankiri

first: mine

last: turktas

address: ballica campus

country: Turkey

institute: cankiri karatekin university

organism:
Populus trichocarpa
Olea europaea

description:
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are linked below as supplementary files.
Design name: 120629_Olea_Populus_TU_exp
Design ID: 572411
NimbleChip_HX12


title: Agilent-027840 Rat miRNA Microarray Rel.14.0

city: Nagareyama

first: Wataru

last: Kurihara

state: Chiba

address: Higashifukai 105

institute: Biomatrix Research Inc.

organism: Rattus norvegicus

description:
Arrays of this design have barcodes that begin with 16027840 or 2527840.

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.


title: HZAU_Tomato_12800_v.CGEP

status: Public on Dec 12 2012

city: wuhan

first: Fei

last: Guo

address: shizishan

institute: Huazhong Agricultural Univesity

organism: Solanum lycopersicum

manufacture_protocol:
1. TOM2 oligo array from tomato contain a total of 12800 elements or approximately 11860 unique elements.
2. Sixty-nine oligonucleotides sequences from unigenes were synthesized by Operon (Operon biotechnologies, Hunstville, AL).
3. Oligos were re-suspended in 12 uL of spotting buffer (3X SSC), and were spotted on Ultra Gaps Coated Slides (Corning, Lowell, MA) using a MicroGrid Pro arrayer (BioRobotics Inc., MA) with 32 MicroSpot2500 printing pins.
4. Before printing, add 5 µL of 1X Printing Buffer to each well. This can be done the night before a print run is started.


title: Nimblegen Human custom 135k tiling array hg19 (OID31380)[100915_HG19_p53_NG_CGH]

status: Public on Dec 10 2012

city: Hamburg

first: Genrich

last: Tolstonog

department: Department of Tumor Virology

institute: Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology

description:
The Nimblegen custom 135k tiling array was designed to cover 1894 genomic intervals that comprise 902 genes (coding and non-coding) and 1 kb 5'-flanking regions of 1040 full-length LINE1 (FL-L1) sequences. 812 tiling intervals cover single genes, 36 tiling intervals cover two genes, and 6 tiling intervals cover three genes. Gene coordinates including flanking regions in a length of 1500 bp were retrieved from Biomart. Annotation in this record is based on the GRCh37 release of the human reference assembly made by the GRC (The Genome Reference Consortium). The genes covered by the array were selected after pilot gene expression studies for identification of genes that are regulated dependent on mutant p53 and wt-p53 expression in human tumor cell lines.

DesignID: 534821

native array description file: 100915_HG19_p53_NG_CGH.ndf
native array description file: 100915_HG19_p53_NG_CGH.pos


title: SABiosciences Human Cancer Pathway Finder PCR assay panel

status: Public on Dec 31 2012

city: Charleston

first: Dennis

last: Watson

address: 68 President Street

institute: Medical Univeristy of South Carolina

description:
Human Cancer Pathway Finder
SABiosciences RT² Profiler panel of PCR assays.


title: Mouse Cytokine/Chemokine Array - I Wang Lab

city: Durham

first: Yun

last: Zhang

state: North Carolina

address: 308 Research Dr., C215 LSRC

department: Pharmacology and Cancer Biology

institute: Duke University

organism: Mus musculus

description: PCR assay containig 95 cytokine/chemokine genes and their receptors.

manufacturer: Self-designed by Dr. Xiao-fan Wang Lab at Department of Pharmacology and Cancer Biology at Duke University Medical Center.

manufacture_protocol: The panel mainly focus on chemokines and their receptors. It also contains some cytokines and their receptors. β-actin was used as the control gene. Most of the primers were designed using the Roche   Universal ProbeLibrary Assay Design Center (https://www.roche-applied-science.com/sis/rtpcr/upl/index.jsp?id=UP030000).


title: [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array - custom CDF ATH1121501_At_TAIRG_14.1.0)

city: Bethesda

first: GEO

last: admin


title: AB SOLiD 3 Plus System (Drosophila melanogaster)

status: Public on Dec 11 2012

last: GEO

organism: Drosophila melanogaster


title: Human miRNA Array - I Li Lab

organism: Homo sapiens

description: PCR assay containig 245 specific miRNA forward primer

manufacturer: Self-designed by Dr. Qi-jing Li Lab at Department of Immunology at Duke University Medical Center.


title: Agilent-012391 Whole Human Genome Oligo Microarray G4112A (Feature Number version)

status: Public on Nov 17 2004

description:
This single 44K formatted microarray represents a compiled view of the human genome as it is understood today. The sequence information used to design this product was derived from a broad survey of well known sources such as RefSeq, Goldenpath, Ensembl, Unigene and others. The resulting view of the human genome covers 41K unique genes and transcripts which have been verified and optimized by alignment to the human genome assembly and by Agilent's Empirical Validation process.

Arrays of this design have barcodes that begin with 16012391 or 2512391.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL6848.

manufacture_protocol: see manufacturer's web site at http://www.agilent.com/


title: Affymetrix Escherichia coli MG1655 tiling array [Ecoli_TAb520346F]

status: Public on Dec 07 2012

first: Andrei

middle: Nikolai

last: Trostel

address: 9000 Rockville Pike, Building 37, Room 5138

department: Laboratory of Molecular Biology

institute: National Institutes of Health

organism: Escherichia coli

manufacture_protocol: See manufacturer's website (www.affymetrix.com)


title: NimbleGen custom IRHS_Medtr_102K_v1

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

organism: Medicago truncatula

description: A dataset of 119,780 quality-filtered unigenes were submitted for probe design and production of the high-density microarray. One oligoprobe was selected for each sequence, based on highest hybridization specicifity. The Medtr_v1.0 chip contains a total of 102,123 predicted coding genes, transposons and microRNA genes. Annotation is based on the Mt3.5.1 version.

manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/


title: Locust 20k 60-mer oligo array

city: New Haven

first: Dejian

last: Zhao

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale School of Medicine

organism: Locusta migratoria

manufacture_protocol: Oligos are arrayed in Greiner 384-well flat-bottom plates. Each well contains 600 pmol of 70-mer oligo. Resuspend oligos in water to 20 uM and rearray 5 µL into 384-well, Genetix polystyrene V-bottom plates (cat# X6004). Allow Genetix plates to dry through passive water evaporation in a protected environment (e.g., chemical hood). Before printing, add 5 µL of 1X Printing Buffer to each well. This can be done the night before a print run is started. Seal plates with Corning seals. Incubate at 37°C for 30 minutes to aid resuspension of DNA. Shake plates near maximum rotational speed on flat-bed shaker for 1 minute. Centrifuge plates at 2000 rpm for 3 minutes. Remove seals and cover with plate lids. Place in appropriate location of plate cassette. This should be done with first plates just before print run is started to minimize evaporation time before printing. For second and third cassettes, wait until 30  Make sure plates rest behind both holding clips in the cassettes. Push plates back into the cassettes as far as they will go, putting them in the proper position for the server arm. After the print run is completed, allow plates to dry through passive evaporation in a protected environment. For each subsequent preparation of these plates for a print run, add water to the wells instead of sodium phosphate buffer.


title: Iyer Lab Human 46K cDNA microarray v2

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

manufacture_protocol:
Printed cDNA microarrays on poly L-lysine coated microscope slides using a custome-built robotic arrayer.
Each slide printed with about 47,000 sequence-verified image clones.


title: WJC hsa mmu miRNA v7.1 01 (miRNA ID)

status: Public on Dec 08 2012

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

organism:
Homo sapiens
Mus musculus

manufacturer: Wilhelm Johannsen Center for Functional Genome Research, University of Copenhagen

manufacture_protocol: Locked nucleic acid modified oligonucleotide probes were purchased from Exiqon. Probes were dissolved in printing buffer (150 mM sodium phosphate, pH 8.5) to a final concentration of 25 µM and printed in quadruples onto CodeLink slides (GE-Healthcare) using a MicroGrid TAS II (Biorobotics) at 50 % relative humidity. Printed slides were post-processed according to the slide manufacturer's instructions.


title: OSU Ezeji Clostridium beijerinckii NCIMB 8052 30K

status: Public on Dec 06 2012

city: Wooster

first: Yan

state: OH

address: 1680 Madison Avenue

department: Animal Sciences

country: USA

institute: The Ohio State University

organism: Clostridium beijerinckii NCIMB 8052

manufacture_protocol: Each array has 30,720 potential addresses for probes, of which 25,015 spots have 45-47mer probes for Clostridium beijerinckii NCIMB 8052 (Cb) genes, 4,985 features have no probe, 608 features have MYcroarray in-house QC probes and 112 features have positive control probes. Each gene is appraised by one unique probe sequence. There are 5 identical replicates of each Cb probe sequence such that a total of 5,003 Cb genes are appraised by each array. Probes are synthesized on a microscope slide, using the robust phosphoramidite chemistry refined since the 1970's for commercial oligonucleotide synthesis.


title: Illumina Genome Analyzer IIx (Oryzias melastigma)

status: Public on Dec 03 2012

organism: Oryzias melastigma


title: Agilent-025396 Bartonella_quintana

status: Public on Dec 05 2012

city: San Francisco

first: Christopher

middle: S

last: Nelson

institute: UCSF

organism: Bartonella quintana


title: [Mouse4302_Mm_ENTREZG] Affymetrix GeneChip Mouse Genome 430 2.0 Array [Brainarray Version 16]

first: Ryan

last: Dale

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

relation: Alternative to: GPL1261 (Alternative CDF [official])

manufacture_protocol:
This is identical to GPL1261 but a custom CDF environment was used to extract data [Brainarray Version 16, Mouse4302_Mm_ENTREZG].
CDF and other files can be downloaded at: (see web link below).


title: 3D-Gene Mouse miRNA Oligo Chip V17.1.0

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

manufacture_protocol: See manufacturer's web site (http://www.toray.com).


title: Illumina HiSeq 2000 (Brassica oleracea)

organism: Brassica oleracea


title: miRCURY LNA™ microRNA Array V11.0- hsa, mmu & rno

city: Tianjin, P.R.China

first: Yang

last: Rongcun

address: 94 Weijin Road, Nankai District

department: School of medicine

institute: Nankai University

organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

description: The array covers Sanger miRBase 12.0 and Exiqon miRPlus mature miRNAs.

manufacture_protocol: Exiqon's miRCURY LNA™ microRNA Array system is a complete system for global microRNA expression profiling. The system is based on the LNA™-technology, which offers unique advantages in the specific and sensitive detection of short RNA sequences.


title: INRA Sus scrofa 15K Adipose Tissue (Probe ID version)

city: saint-gilles

first: marie

last: damon

address: domaine de la prise

country: France

organism: Sus scrofa

description: a custom repertoire of 15,000 60-mer DNA probes targeting transcripts expressed in growing pig adipose tissue


title: miRCURY LNA microRNA Array, 5th generation - hsa, mmu & rno [mapped to Sus scrofa]

status: Public on Dec 01 2012

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

institute: Lund University, Sweden

description:
The original array was designed to target microRNAs found in miRBase 14.
We have then re-annotated the microRNAs to version 18 and 19.
Probes were remapped from human, mouse and rat to pig (ssc).

manufacture_protocol: See manufacturers website


title: Agilent-021643 GIS Zebrafish Array ver1.1_custom layout [PROBE NAME version]

city: Singapore

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

organism: Danio rerio

description:
Arrays of this design have barcodes that begin with 16021643 or 2521643.

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."

This is the PROBE NAME version of the array


title: Human, approximately 43,000 features, representing 32,968 unique human genes

city: Worcester

first: Mahesh

last: Appari

state: MA

address: 381 Plantation St

department: Medicine, Diabetes division

institute: University of Massachusetts Medical School - Worcester

manufacturer: Stanford Functional Genomics Facility (SFGF)

manufacture_protocol:
Print batch: SHGS, UltraGAPS 12605000B, Corning amino-silane.Feb 2006, Print Tip Type: Majer 17-4 ss
Print batch: SHGI, UltraGAPS 00305000B, Corning amino-silane.Oct2005, Print Tip Type: Majer 17-4 ss


title: Illumina Genome Analyzer IIx (Cicer arietinum)

organism: Cicer arietinum


title: Agilent-029034 Morone saxatilis ST2010B [Probe Name version]

first: Marion

last: Neely

state: SC

address: 331 Ft. Johnson Rd

department: NCCOS

institute: National Ocean Services

organism: Morone saxatilis

description:
Arrays of this design have barcodes that begin with 16029034 or 2529034.

The "Contig" information is not available in a public database because they are referring to contig assemblies of ESTs that we assembled.


title: GenoExploxer Homo sapiens 1.4K miRBASE version 13.0

city: Phoenix

first: Irene

last: Cherni

state: AZ

address: 445 N. fifth Street

department: Cancer and Cell Biology

institute: Translational Genomics Research Institute

description: The chips are coated with patented polymers used for DNA probe attachment. The biochips covalently


title: Affymetrix IST_IBB Burkholderia 15K v1.0 [CDF: BCC1sa520656F_Xspecies.CEL80]

city: Lisboa

first: Leonilde

middle: Morais

last: Moreira

address: A. Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Tecnico

organism:
Burkholderia cenocepacia J2315
Burkholderia multivorans ATCC 17616

description:
This array is identical to GPL13356, but  a custom CDF environment is used to extract data.
DNA-based probe-selection was performed using Xspecies DNA hyb CDF batchmaker v3.2, available here: http://affymetrix.arabidopsis.info/xspecies/. An optimal signal cutoff of 80 and minimum number of probes per probe set of 7 were determined empirically, resulting in the masking of 24223 of the original 226576 probes on the array and the exclusion of 156 probe sets. Bcc1sa520656F_Xspecies.CEL80.cdf is the resulting cdf file.

relation: Alternative to: GPL13356 (Alternative CDF [official])

manufacture_protocol:
See manufacturer's website (www.affymetrix.com).
The parameters chosen for the custom array design were as follows: 11-micron feature size, standard 12.8-mm array format, prokaryotic antisense target type, perfect-match probes only, full length sequence for probe selection, and eight as the minimum acceptable probes per sequence.


title: UCI Leptospira interrogans serovar Copenhageni Protein Microarray chip LI6

status: Public on Dec 04 2012

city: Irvine

first: Carolina

last: Lessa Aquino

address: 302 MedSurge II

institute: University of California Irvine

technology: spotted peptide or protein

manufacture_protocol:
The arrays were produced by in vitro transcription/translation (IVTT) reactions using plasmids encoding individual leptospire ORFs as templates, and reactions printed onto nitrocellulose-coated slides. Multiple spots consisting of reactions lacking plasmid templates ('no DNA' controls) are present on each array and used for data normalization.
ORFs larger than 3kb were segmented into smaller fragments and are designated as the original ORF ID followed by segment number (example: LIC10502-s2). For these cases, the protein accession number corresponds to the original full protein (in that example, the accession number provided would be the one for the full LIC10502 protein).


title: Genotoul/Biopuces Eurogentec Yarrowia lipolytica 6.4K oligonucleotide array v2007 [13376 row layout]

city: Thiverval-Grignon

first: Jean-Marie

last: Beckerich

address: Campus Agroparistech

organism: Yarrowia lipolytica

description: Probes are spotted in duplicate.  For a condensed version of this array, please see GPL13486

manufacture_protocol: 4x8 pin head, each pin has spotted a block of 22x19 spots. Each well is spotted in duplicate.


title: Agilent-021254 Giardia lamblia Custom 8x15K

city: Taipei

first: Chin-Hung

last: Sun

address: Department of Parasitology, College of Medicine, National Taiwan University

department: Department of Parasitology

country: Taiwan

organism: Giardia duodenalis

manufacture_protocol: see manufacturer's website


title: Affymetrix Acinetobacter baumannii GeneChip [PMDacba1a520551F]

city: Rochester

first: Paul

last: Dunman

state: NY

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

organism: Acinetobacter baumannii

manufacture_protocol: Affymetrix


title: NimbleGen Brucella ovis array 2.9K v1.0

city: Madison

first: Gary

last: Splitter

state: WI

address: 1656 Linden Dr

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

organism: Brucella ovis

manufacture_protocol: Microarray design and experimentation were made by NimbleGen Systems, INC from catalogue design for B. ovis chromosomes I (NC_009505.1) and II (NC_009504.1) with 20 probes per gene (10 perfect matches and 10 mismatches). Each probe (60 mer) was replicated three times on chip (design includes random GC probes). Triplicate samples of each strain were mixed and one chip was made per strain.


title: 24sure Homo sapiens 3K BAC v2.0

city: Brussels

first: Claudia

last: Spits

address: Laarbeeklaan 103

department: Research Group of Reproduction and Genetics

country: Belgium

institute: Vrije Universiteit Brussel

organism: Homo sapiens

manufacturer: BlueGnome Ltd, Capital Park CPC4, Fulbourn, Cambridge CB21 5XE UK, info@cambridgebluegnome.com


title: NimbleGen Brucella melitensis 3K A4357-001-01

organism: Brucella melitensis


title: Agilent-020430 Danio rerio custom 8x15k miRNA [Feature Number version]

city: Leiden

first: Annemarie

middle: H.

last: Meijer

address: Einsteinweg 55

department: Animal Sciences and Health

institute: Institute of Biology, Leiden University

description: Custom-designed Agilent zebrafish 8x15k miRNA platform. The 15k design contained a duplicate of 7604 probes of 60-oligonucleotide length. The probes consisted of 2x22 nucleotide sequences antisense to mature miRNAs separated by a spacer of 8 nucleotides (CGATCTTT) and with a second spacer with the same sequence at the end. From 7604 probes 546 were designed for left (5') and right (3') arms of the hairpins of zebrafish miRNAs  known in miRBase, while the remainder 7058 probes corresponded to predicted hairpin structures in the zebrafish genome that might include additional miRNAs but were not considered in this study

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


title: Exiqon Human 757 v10.0

city: Chicago

first: Ravand

last: Samaeekia

state: IL

department: Ben May Department of Cancer Research

institute: University of Chicago


title: Agilent Escherichia coli O157:H7 str. EDL933

city: Birmingham

first: Chrystala

last: Constantinidou

department: School of Biosciences

institute: University of Birmingham

organism: Escherichia coli O157:H7 str. EDL933

manufacture_protocol:
in-situ synthesized 60mer 8x15k oligonucleotide arrays.
Multiple probes per gene designed by OGT were screened by UBEC using RNA and genomic DNA hybridizations. Optimal probe per gene was selected and arrays were synthesized by Agilent.


title: INRA Sus scrofa 15K Adipose Tissue

institute: INRA

first: Marie

last: Damon

first: Annie

last: Vincent

first: Isabelle

last: Louveau


title: NimbleGen F verticillioides custom 14K array

city: Peoria

first: Robert

last: Butchko

address: 1815 N. University St.

institute: U.S. Dept. of Agriculture

organism: Fusarium verticillioides

description: Array designed based on large EST library (Brown et al, Analysis of 87,000 expressed sequence tags reveals alternatively spliced introns in multiple genes of the fumonisin gene cluster, Fungla Genetics and Biology, 42:848-861) and the Fusarium comparative database at the Broad Institute (http://www.broad.mit.edu/annotation/genome/fusarium_verticillioides/MultiHome.html)

manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.


title: Agilent Escherichia coli 0127:H6 E2348/69

organism: Escherichia coli O127:H6 str. E2348/69


title: Illumina HiSeq 2000 (Pteropus alecto)

status: Public on Aug 07 2012

last: GEO

organism: Pteropus alecto


title: Agilent-028679 SurePrint G3 Human Exon 4x180K Microarray (Feature Number Version)

status: Public on Sep 08 2011

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Human4x180KExon

Arrays of this design have barcodes that begin with 16028679 or 2528679.

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.

manufacture_protocol: see manufacturer's web site at http://www.agilent.com/


title: Agilent-015424 S. pombe Whole Genome ChIP-on-Chip Microarray 4x44K (Feature Number version - A_86_Pnnnn probes)

status: Public on Oct 27 2012

organism: Schizosaccharomyces pombe

description:
S. pombe Whole Genome ChIP-on-Chip Microarray 4x44K

The ID column represents the Agilent Feature Extraction feature number.

This platform is an alternative to GPL6374, which includes probe names prefixed with A_93_Pnnnnnnnn. This platform's probe names are prefixed A_86_Pnnnnnnnn.

relation:
Alternative to: GPL6374
Alternative to: GPL16383


title: Agilent-026595 Whole Chr array_18 19 21 [Feature Number Version]

status: Public on Sep 26 2011

description:
Human whole chromosomal ChIP-on-CHIP microarray. Chr 18, 19, 21. Designed by Agilent eArray: Build Number: H. sapiens, UCSC hg18, NCBI;  Advanced HD Search by Genomic Intervals;  Tm Filter: Yes;  Hm Filter: Yes.

Arrays of this design have barcodes that begin with 16026595 or 2526595.

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.


title: Agilent-015058 O. sativa (Rice) Oligo Microarray 4x44K (Feature Number version)

status: Public on Mar 05 2012

organism: Oryza sativa

description:
This array will enable researchers to simultaneously characterize thousands of rice genes associated with biological functions, growth processes, and biotic and abiotic stress response. Probes on this array are designed to selections from the extensive ric

Arrays of this design have barcodes that begin with 16015058 or 2515058.

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.

relation: Alternative to: GPL15307 (Probe Name version)


title: SMD Print_1564 hoaa Homo sapiens

status: Public on Aug 23 2012

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

manufacturer: Stanford Functional Genomics Facility, Stanford School of Medicine

manufacture_protocol: Material is transferred from microtiter plate wells to the slide surface by an automated print head


title: Agilent-027811 SurePrint G3 Human Promoter Microarray 1x1M [Feature Number Version]

description:
SurePrint G3 Human Promoter Microarray 1x1M

Arrays of this design have barcodes that begin with 16027811 or 2527811.

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.


title: HumanRef-8 v2 Expression BeadChip

status: Public on May 29 2011

first: Sherry

last: Wang

address: 21 Lower Kent Ridge Road

department: Biochemistry

institute: National University of Singapore


title: NimbleGen 2006-06-16_mouse36_deLaat tiling array

status: Public on Apr 21 2011

city: Bethesda

first: Myong-Hee

last: Sung

state: MD

address: 41 Library Dr

department: NCI

institute: NIH

organism: Mus musculus

description:
Mouse genome build mm8 (NCBI Build 36).

One oligonucleotide probe per HindIII site.

NimbleGen array description files are linked below:
2006-06-16_mouse36_deLaat.ndf
2006-06-16_mouse36_deLaat.pos

manufacture_protocol: NimbleGen custom microarray manufacture.


title: NimbleGen Human DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Array [100718_HG18_CpG_Refseq_Prom_MeDIP]

status: Public on Mar 01 2011

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
Format: 3X720K
Source: UCSC
Build: HG18, NCBI 36
Probe Length: 50-75mer
Median Probe Spacing: 104

manufacture_protocol: see manufacturer's web site


title: Agilent-026437 D. rerio (Zebrafish) Oligo Microarray V3 (Feature Number version)

status: Public on Oct 08 2011

organism: Danio rerio

description:
D. rerio (Zebrafish) Oligo Microarray V3

Arrays of this design have barcodes that begin with 16026437 or 2526437.
DesignID : 026437

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL14664.

relation: Alternative to: GPL14664 (Probe Name version)


title: Agilent-015424 S. pombe Whole Genome ChIP-on-Chip Microarray 4x44K (Probe Name version - A_93_Pnnnn probes)

status: Public on Nov 02 2012

description:
Schizosaccharomyces pombe Whole Genome ChIP-on-Chip Microarray 4x44K

The ID column represents the Agilent Probe Name.

This Platform is an alternative to GPL16383, which includes Probe Names prefixed with A_86_Pnnnnnnnn. This Platform's Probe Names are prefixed with A_93_Pnnnnnnnn.

manufacture_protocol: See manufacturer's web site at http://www.agilent.com/ .


title: Agilent-022297 Wheat Gene Expression Microarray (Feature Number version)

status: Public on May 20 2011

organism: Triticum aestivum

description:
T. aestivum (Wheat) Oligo Microarray

Arrays of this design have barcodes that begin with 16022297 or 2522297.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL13636.


title: Agilent-020449 Mosquito Gene Expression Microarray (Feature Number version)

status: Public on Feb 11 2011

organism: Anopheles gambiae

description:
A. gambiae (Mosquito) Oligo Microarray

Arrays of this design have barcodes that begin with 16020449 or 2520449.

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.


title: Agilent-024207 Schistosoma mansoni 45K array (Feature Number version)

status: Public on Sep 03 2010

city: Brisbane

first: Geoffrey

last: Gobert

address: 300 Herston Rd

country: Australia

institute: QIMR

organism: Schistosoma mansoni

description:
schisto-v1_1164838824901_1244575027696

Arrays of this design have barcodes that begin with 16024207 or 2524207.

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.


title: Agilent-021322 Horse Gene Expression Microarray [Feature Number version]

status: Public on Feb 03 2012

organism: Equus caballus

description:
E. caballus (Horse) Oligo Microarray

Arrays of this design have barcodes that begin with 16021322 or 2521322.

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.


title: Agilent-026441 Gallus gallus (Chicken) Oligo Microarray v2 (Feature Number version)

status: Public on Jun 30 2011

organism: Gallus gallus

description:
G. gallus (Chicken) Oligo Microarray v2

Arrays of this design have barcodes that begin with 16026441 or 2526441.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL15357.


title: Agilent-015067 Canine 4x44K Microarray (Feature Number version)

status: Public on Dec 22 2010

organism: Canis lupus familiaris

description:
Agilent-015067
015067_D_20060913

manufacture_protocol: See manufacturer's website.


title: Illumina HumanOmni2.5 BeadChip (hg19)

status: Public on Oct 02 2012

city: Toronto

first: Boyko

last: Kabakchiev

state: Ontario

address: 60 Murray Street, Room L3-004

department: Samuel Lunenfeld Research Institute

country: Canada

institute: Mount Sinai Hospital

description: build: hg19

manufacture_protocol: See manufacturer's website


title: Nimblegen Rat Gene Expression array [2007-07-20_Rat_X4_expr]

status: Public on Jul 02 2010

first: Inc

last: Nimblegen Systems

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Rattus norvegicus

description: Rat NCBI 6-20-07.  131,954 probes from 26,419 nr genes with 5 probes per target.  Random GC probes included.  Random probe distribution.

manufacture_protocol: As described in: http://www.nimblegen.com/products/exp/index.html


title: Agilent-023642 SurePrint G3 Human High-Resolution Discovery Microarray 1x1M (Feature Number version)

status: Public on Mar 10 2010

organism: Homo sapiens

description:
SurePrint G3 Human High-Resolution Discovery Microarray, 1x1M

Arrays of this design have barcodes that begin with 16023642 or 2523642.

Data table annotations based on build hg18:NCBI36:Mar2006.

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.


title: Agilent-014841 Human Whole Genome ChIP-on-Chip Set 244K - 24 of 25 (Feature Number version)

status: Public on Nov 12 2009

description:
Human Whole Genome ChIP-on-Chip Set 244K, 24 of 25

Arrays of this design have barcodes that begin with 16014841 or 2514841.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL9661.


title: Agilent-014840 Human Whole Genome ChIP-on-Chip Set 244K - 23 of 25 (Feature Number version)

description:
Human Whole Genome ChIP-on-Chip Set 244K, 23 of 25

Arrays of this design have barcodes that begin with 16014840 or 2514840.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL9660.


title: Agilent-014838 Human Whole Genome ChIP-on-Chip Set 244K - 21 of 25 (Feature Number version)

description:
Human Whole Genome ChIP-on-Chip Set 244K, 21 of 25

Arrays of this design have barcodes that begin with 16014838 or 2514838.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL9658.


title: Agilent-014843 Human Whole Genome ChIP-on-Chip Set 244K - 25 of 25 (Feature Number version)

description:
Human Whole Genome ChIP-on-Chip Set 244K, 25 of 25

Arrays of this design have barcodes that begin with 16014843 or 2514843.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL9662.


title: Agilent-014839 Human Whole Genome ChIP-on-Chip Set 244K - 22 of 25 (Feature Number version)

description:
Human Whole Genome ChIP-on-Chip Set 244K, 22 of 25

Arrays of this design have barcodes that begin with 16014839 or 2514839.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL9659.


title: GiLS Lepeophtheirus salmonis

status: Public on May 19 2012

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

institute: The University of Victoria

organism: Lepeophtheirus salmonis

manufacture_protocol: see eArray site; and Contigs from Yasuike et al. 2012 Genomic Resources for Sea Lice: Analysis of ESTs and Mitochondrial Genomes; The selection process was strongly biased in favor of the 3' region of consensus transcripts derived from the assembly of multiple high quality EST sequences. Oligos derived from the contigs were 60 bases in length. Each contig is represented at least twice (duplicate probes).


title: Agilent-014837 Human Whole Genome ChIP-on-Chip Set 244K - 20 of 25 (Feature Number version)

description:
Human Whole Genome ChIP-on-Chip Set 244K, 20 of 25

Arrays of this design have barcodes that begin with 16014837 or 2514837.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL9657.


title: Agilent-014836 Human Whole Genome ChIP-on-Chip Set 244K - 19 of 25 (Feature Number version)

description:
Human Whole Genome ChIP-on-Chip Set 244K, 19 of 25

Arrays of this design have barcodes that begin with 16014836 or 2514836.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL9656.


title: Agilent-014835 Human Whole Genome ChIP-on-Chip Set 244K - 18 of 25 (Feature Number version)

description:
Human Whole Genome ChIP-on-Chip Set 244K, 18 of 25

Arrays of this design have barcodes that begin with 16014835 or 2514835.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL9655.


title: Agilent-014818 Human Whole Genome ChIP-on-Chip Set 244K - 1 of 25 (Feature Number version)

description:
Human Whole Genome ChIP-on-Chip Set 244K, 1 of 25

Arrays of this design have barcodes that begin with 16014818 or 2514818.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL9638.


title: Agilent-022270 Tomato Gene Expression Microarray (Feature Number version)

status: Public on Jun 21 2010

organism: Solanum lycopersicum

description:
S. lycopersicum (Tomato) Oligo Microarray

Arrays of this design have barcodes that begin with 16022270 or 2522270.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL10571.


title: Illumina Genome Analyzer II (Glycine max)

status: Public on Nov 10 2010

organism: Glycine max