title: Affymetrix Mouse Genome 430 2.0 Array [CDF: Mm_ENTREZG_11.0.1]

status: Public on Sep 17 2009

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

organism: Mus musculus

technology: in situ oligonucleotide

description: Custom CDF (Brainarray v11.0.1); Entrez Gene

distribution: custom-commercial

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

manufacture_protocol: GPL1261 using Entrez Gene custom CDF available from:  http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/11.0.1/entrezg.download/mouse4302mmentrezgcdf_11.0.1.tar.gz


title: intergenic_v1.0

status: Public on Feb 12 2002

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

organism: Saccharomyces cerevisiae

technology: spotted DNA/cDNA

description:
Tip Configuration: Standard 16-tip
Columns per Sector: 24
Column Spacing: 173
Row Spacing: 173

distribution: non-commercial


title: Valencia yeast v2

status: Public on Dec 31 2003

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description:
Nylon macroarray (7 x 11 cm) with 6049 single spotted yeast ORF probes. Probes are PCR fragments comprising the whole ORF (5598 cases) or a 1000 bp-fragment from the ORF 3' end (451 cases).
Keywords = Yeast
Keywords = macroarray
Keywords = nylon

middle: E

last: Garcia-Martinez


title: salmonid fish version 1.0

status: Public on May 07 2004

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

organism: Oncorhynchus mykiss

description: contains 1300 rainbow trout genes spotted in 6 replicates

first: Heikki

last: Koskinen

first: Hannu

last: Mölsä

first: Kristiina

last: Vuori


title: ToxExpress GeneChip Canine Array

status: Public on Nov 03 2003

city: Philadelphia

first: David

last: Johnson

state: PA

address: 415 Curie Blv

department: Medicine

institute: University of Pennsylvania

organism: Canis lupus familiaris

description: Affymetrix Canis familiaris array.  Available commercially from GeneLogic Bethesda, MD.


title: Duke Operon Porcine 10.5K Oligo Array

status: Public on Feb 22 2006

city: Durham

first: Heather

middle: Anne

last: Himburg

state: NC

address: PO Box 90281

department: Biomedical Engineering

institute: Duke Univeristy

organism: Sus scrofa

technology: spotted oligonucleotide

manufacturer: Oligos: Operon Printed by: Duke Microarray Facility

manufacture_protocol: Operon probes are designed from The TIGR Gene Index Database SsGI Release 5.0 released 10/1/02. The Oligo set contains 10,665 70mer probes representing 10,665 Sus scrofa gene sequences with a hit to a known human, mouse, or pig transcript and some sequences containing a 3' expressed sequence tag.   Scanner used was a GenePix 4000B.


title: Duke/Wray Strongylocentrotus purpuratus 384-v1

status: Public on Nov 29 2012

first: Daniel

last: Runcie

department: Biology Department

institute: Duke University

organism: Strongylocentrotus purpuratus

technology: oligonucleotide beads

manufacture_protocol: see manufacturer's website


title: miRCURY LNA microRNA Array, v. 9.2 - all organisms

status: Public on Jun 11 2013

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

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

department: High Content Genomics and Bioinformatics

institute: IGTP

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

description: Array covering Sanger miRBase 12.0 and Exiqon miRPlus mature miRNAs.

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


title: Agilent-033077 Campylobacter jejuni expression array HY_81176 (Agilent Probe Name version)

status: Public on Dec 30 2012

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: MWG Rat Liver Array

status: Public on Oct 07 2003

city: High Point

last: MWG Biotech

address: 4170 Mendenhall Oaks Parkway, Suite 160

institute: MWG Biotech

organism: Rattus norvegicus

description: Array containing 1353 oligonucleotide probes representing rat liver genes Including 39 Replicas and 16 Arabidopsis controls. Information Sources: In NCBI/Genbank (keyword: tissue type = liver) only 272 genes had been assigned as liver specific; MWG Biotech has sequenced 1166 genes derived from libraries of liver tissue taken from 12 week old rats of different strains. Therefore, these genes, which are accessible in Genbank, could be assigned to be expressed in rat liver; Additionally, 187 genes sequenced by MWG and identified by protein homology to human or murine sequences are not accessible in Genbank (88 genes are derived from stroke-prone spontaneously hypertensive rats (SHRSP); 65 genes come from normotensive Wistar-Kyoto rats (WKY); 34 genes can be found in both strains).

distribution: commercial

manufacture_protocol: see manufacturer's web site


title: NimbleGen Saccharomyces cerevisiae 730K 090319_Scer_KH_CGH

status: Public on Mar 13 2013

city: Seattle

first: Toshio

last: Tsukiyama

state: WA

address: 1100 Fairview Ave N

department: Basic Science

institute: Fred Hutchinson Cancer Research Center

description: NimbleGen HX3 custom array containing ~700000 experimental probes tiling both the Watson and Crick strands of the S. cerevisiae genome.  Forward and Reverse probes for each location are complements of eachother

manufacture_protocol: Per standard NimbleGen protocol (see manufactures website for details)


title: Affymetrix GeneChip Mouse Genome 430 2.0 Array [AffyProbeMiner cdf (mouse4302geneccds) version 1.8.0]

status: Public on Oct 31 2012

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

manufacture_protocol: This identical to GPL1261 but an alternative cdf environment was used to extract data.


title: AB 5500 Genetic Analyzer (Haloferax volcanii)

last: GEO

organism: Haloferax volcanii

technology: high-throughput sequencing

distribution: virtual


title: Agilent-015028 Mouse Genome CGH Microarray 44K G4426B (ProbeName version), mm9

description: Same physical array as GPL11288, but with updated annotation based on NCBI37/mm9 assembly.

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


title: Illumina Genome Analyzer IIx (Escherichia coli K-12)

organism: Escherichia coli K-12


title: Arabidopsis 0.26K cDNA macroarray

status: Public on Oct 28 2012

city: Poznan

first: Agnieszka

middle: Wioletta

last: Ludwików

address: Umultowska 89

department: Biotechnology

country: Poland

institute: Adam Mickiewicz University

organism: Arabidopsis thaliana

manufacture_protocol: The A. thaliana EST probes were spotted on nylon membranes using a 384-manual spotting tool (Cirad Genomics Platform/Biotrop; Montpellier). The probes were spotted in duplicates. The membranes were rinsed in 2 x SSC buffer, dried and the DNA permanently fixed in an UV cross-linker. The control hybridization was carried out with radioactively labeled T7 primer for verification of a quality. After hybridization membrane was exposed to the PhosphorImager and the hybridized signals were analyzed by using a BioImaging analyzer.


title: Illumina Genome Analyzer (Plasmodium yoelii yoelii 17XNL)

status: Public on Oct 26 2012

organism: Plasmodium yoelii yoelii 17XNL


title: Montastraea faveolata 1.5K v1

city: Poughkeepsie

first: Jodi

last: Schwarz

address: 124 Raymond Ave

institute: Vassar College

organism: Orbicella faveolata

description: spotted amplified cDNAs

manufacture_protocol:
1.cDNAs are arrayed in Greiner 384-well flat-bottom plates.
2. Resuspend  in water
3. Allow Genetix plates to dry through passive water evaporation in a protected environment (e.g., chemical hood).
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.
5. Seal plates with Corning seals.
6. Incubate at 37°C for 30 minutes to aid resuspension of DNA.
7. Shake plates near maximum rotational speed on flat-bed shaker for 1 minute.
8. Centrifuge plates at 2000 rpm for 3 minutes.
9. 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
10. 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.
11. After the print run is completed, allow plates to dry through passive evaporation in a protected environment.
12. For each subsequent preparation of these plates for a print run, add water to the wells instead of sodium phosphate buffer. The amount of water should be decreased by 0.25 µL per print run, as this is the amount drawn up by the pin capillary during ea


title: Agilent-018970 Cyanothece custom 8x15K (Feature Number version)

status: Public on Oct 30 2012

city: St Louis

first: Thanura

last: Elvitigala

state: MO

address: 1 Brookings Drive, Campus Box 1137

institute: Washington University

organism: Crocosphaera subtropica ATCC 51142

description: AMADID 018970

manufacture_protocol: Single 60-mer oligonucleotide probes for each of the 5,304 ORFs. Spotted as triplicates on each microarray .


title: Agilent-027480 INTA_CIPF_Girasol (Probe Name version)

city: Castelar

first: Paula

last: Fernandez

state: Buenos Aires

address: N. Repetto y Los Reseros S/N

country: Argentina

institute: INTA Castelar

organism: Helianthus annuus

description:
array de H. annus del proyecto de girasol de CNIA-INTA/CIPF
Arrays of this design have barcodes that begin with 16027480 or 2527480.
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: FZ_IBT1_C. glutamicum_10K_ver2 array

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

organism: Corynebacterium glutamicum ATCC 13032

description:
C. glutamicum ATCC 13032, based on the genome sequence entry NC_006958
spotted with 70-mer oligonucleotides obtained from Operon (Cologne, Germany)


title: [Mouse430_2_Mm_ENTREZG_14.1.0] Affymetrix GeneChip Mouse Genome 430 2.0 Array [Brainarray Version 14]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Mus musculus


title: Thermo Scientific Dharmacon Mouse miRNA expression profiling platform

city: Cleveland

first: William

last: Schiemann

state: OH

address: 2103 Cornell Road, Rm 2404

institute: Case Western Reserve University

description: The Thermo Scientific Dharmacon Synthetic microRNA Reference Probe Set is an equimolar mixture of 5'-Thermo Scientific DyLight 547-labeled, single-stranded synthetic miRNAs targeting all mature human, mouse, and rat miRNA sequences in the Sanger miRBase sequence database. This internal reference provides reproducible data normalization and controls for variations due to up-stream processes (array manufacture, washing and hybridization processes, pipeting variation, etc.).


title: Illumina HiSeq 2000 (Colletotrichum gloeosporioides)

organism: Colletotrichum gloeosporioides


title: 454 GS FLX Titanium (Candida dubliniensis)

status: Public on Oct 22 2012

organism: Candida dubliniensis


title: Illumina Genome Analyzer IIx (Candida dubliniensis)


title: 454 GS FLX Titanium (Candida albicans)

organism: Candida albicans


title: Illumina HiSeq 2000 (Amborella trichopoda)

status: Public on Oct 24 2012

organism: Amborella trichopoda


title: NimbleGen Microcoleus vaginatus strains PCC 9802 and FGP-2 expression array [110728_Mvag_FGP2_PCC9802_LR_expr]

city: Berkeley

first: Lara

last: Rajeev

address: 1 Cyclotron Road

institute: Lawrence Berkeley Lab

organism:
Microcoleus vaginatus PCC 9802
Microcoleus vaginatus FGP-2

description:
The array was designed using 42499 60-mer oligonucleotide probes in triplicate that represent 6130 Microcoleus vaginatus genes (7 probes per gene), with 5461 sequences from strain PCC 9802 and 669 sequences from strain FGP-2.
designname=110728_Mvag_FGP2_PCC9802_LR_expr
designid=556551

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


title: Agilent-025320 Bovine Whole Genome Array 400K 9-8-09

city: College Station

first: Ryan

last: Doan

state: Texas

address: 4467 TAMU

institute: Texas A&M University

organism: Bos taurus

description:
Array design based on the bosTau4.0 (Baylor 4.0) assembly.

Arrays of this design have barcodes that begin with 16025320 or 2525320.

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 HiSeq 2000 (Bombyx mori)

organism: Bombyx mori


title: AB SOLiD 4 System (Bos taurus)

status: Public on Oct 23 2012


title: TUS mouse 22k v1.0

city: Noda

first: Hitoshi

last: Sasaki

state: Chiba

address: 2641 Yamazaki

department: Department of Biological Science and Technology

country: Japan

institute: Tokyo University of Science

manufacture_protocol: Each cDNA was extracted from cDNA library by Wizard SV 96 Plasmid DNA Purification System (Promega) and amplified by polymerase chain reaction (PCR) using Taq polymerase (Promega). PCR products were purified by isopropanol precipitation and resuspended in 50% DMSO, and spotted to GAPS II Coated Slides (Corning) using Micro Grid II (BioRobotics). After spotting, cDNAs were anchored to slide glasses by heat denaturation at 100°C and UV cross-linking (200 mJ).


title: Illumina HiSeq 2000 (Bemisia tabaci)

organism: Bemisia tabaci


title: Agilent-027266 Bovine CNV Dense Tiling Array V1 2-10-2010

description:
Array design based on the bosTau4.0 (Baylor 4.0) assembly.

Arrays of this design have barcodes that begin with 16027266 or 2527266.

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-024881 Bovine Whole Genome Array 400K 7-31

description:
Array design based on the bosTau4.0 (Baylor 4.0) assembly.

Arrays of this design have barcodes that begin with 16024881 or 2524881.

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: TaqMan Rodent microRNA A Card v3.0

status: Public on Oct 18 2012

city: London

first: Kim

middle: S.

last: Midwood

address: 65 Aspenlea Road

country: United Kingdom

institute: Kennedy Institute of Rheumatology

organism:
Mus musculus
Rattus norvegicus

technology: RT-PCR


title: Illumina Genome Analyzer II (Leishmania amazonensis)

status: Public on Oct 17 2012

organism: Leishmania amazonensis


title: NimbleGen C. elegans 12x135K microarrays

city: kunming

first: yi

middle: cheng

last: ma

state: Yunnan

address: No.2 North Cuihu Road

country: China

institute: Lab for Conservation and Utilization of Bio-Resources

organism: Caenorhabditis elegans

description:
NimbleGen 12x135K microarrays for gene expression analysis enable you to conveniently and simultaneously hybridize 12 samples on each slide.
100718_Cele_EXP.ndf
100718_Cele_EXP.ngd

manufacture_protocol: NimbleGen 12x135K microarrays for gene expression analysis, Source: Wormbase, Build: WS190,Probe Length: 60mer,Genes: 23,187, Probes/Target: 6


title: Applied Biosystems qPCR Custom Assays (rat)

city: Toronto

first: Stephenie

last: Prokopec

address: 661 University Avenue, Suite 510

institute: Ontario Institute for Cancer Research

organism: Rattus norvegicus

description: PCR assay


title: Illumina HiSeq 2000 (Pyronema omphalodes)

status: Public on Oct 16 2012

organism: Pyronema omphalodes


title: [S_aureus] Affymetrix S. aureus Genome Array

status: Public on Jul 09 2004

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Staphylococcus aureus

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

June 03, 2009: annotation table updated with netaffx build 28
Oct 18, 2012: annotation table updated with netaffx build 32

manufacture_protocol:
see manufacturer's web site

For comprehensive monitoring of the relative mRNA abundance of S. aureus sequences.

The GeneChip S. aureus Genome Array is useful for studying the expression of sequences in the following four strains of Staphylococcus aureus: N315 (National Institute of Technology and Evaluation, Japan), Mu50 (National Institute of Technology and Evaluation, Japan), NCTC 8325 (University of Oklahoma), and COL (TIGR).

The array contains probe sets to over 3,300 S. aureus open reading frames. Additionally, the array also contains probes to study both forward and reverse orientation of over 4,800 intergenic regions throughout the S. aureus genome.


title: Applied Biosystems Open Array Custom Assays (rat)

description: PCR assay


title: Illumina HiSeq 2000 (Human herpesvirus 5)

organism: Human betaherpesvirus 5


title: Phalanx Mouse miRNA OneArray Ver 2 (miRBase Release 15)

city: Hsinchu

first: Sean

last: Chang

address: 6F, NO.6 Technology Road 5

department: R&D

country: Taiwan

institute: PhalanxBiotech Group

description: Mouse miRNA microarray designed and annotated based on Sanger's miRBase release 15

manufacture_protocol: See http://www.phalanxbiotech.com/ for updated protocols


title: TingM Print 1

city: Chapel Hill

first: June

last: Brickey

address: 450 West Drive

institute: UNC

manufacturer: Duke University Microarray Facility (Duke Institute for Genome Sciences & Policy)

manufacture_protocol:
Oligos are arrayed in Greiner 384-well flat-bottom plates. Each well contains 600 pmol of 70-mer oligo.
GeneMachines Omnigrid arrayer is used to spot the oligos
4 replicate oligos spotted per array
16 blocks of spotted oligos, each with 20 rows x 21 columns and feature diameter of 110 microns
Oligos are obtained originally from Operon Biotechnologies, Inc. (Huntsville, AL)


title: Agilent-025866 gilthead seabream-Oct09 array

city: Castellón

first: Josep

middle: A

last: Calduch-Giner

address: Ribera de Cabanes

institute: Institute of Aquaculture Torre de la Sal (CSIC)

organism: Sparus aurata

description:
Arrays of this design have barcodes that begin with 16025866 or 2525866.

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 II (Human herpesvirus 5)

last: GEO


title: [Aoryzaea520360F] Affymetrix Aspergillus oryzae DNAchip

city: Higashihiroshima

first: Kazuhiro

last: Iwashita

state: Hiroshima

address: 3-7-1, Kagamiyama

institute: National Research Institute of Brewing

organism: Aspergillus oryzae RIB40

manufacture_protocol: see manufacturer's web site (http://www.affymetrix.com/support/technical/manuals.affx)


title: Illumina Genome Analyzer II (Xanthomonas citri subsp. citri)

status: Public on Oct 11 2012

organism: Xanthomonas citri pv. citri


title: SMD Agilent-028004

status: Public on Oct 13 2012

city: Stanford

first: Junqiang

last: Tian

address: 300 Pasteur Drive

department: Department of Urology

institute: Stanford University

organism: Homo sapiens

manufacture_protocol: Agilent


title: CME-Human-3K6_7 (condensed version of GPL6928)

status: Public on Oct 15 2012

city: Brussels

first: Claudia

last: Spits

address: Laarbeeklaan 103

department: Research Group of Reproduction and Genetics

country: Belgium

institute: Vrije Universiteit Brussel

manufacturer: MicroArray Facility, VIB, KULeuven, Herestraat 49, B-3000 Leuven, Belgium

manufacture_protocol:
1. Microgrid (Genomics Solutions, UK).
2. 384 microtiter plates (X7022, Genetix)
3. 16 MicroSpot quill pins - 10K (cat# BR001489, Genomics Solutions, UK)
4. Codelink slides (cat#: 30001100, GE Healthcare). Printing 2 arrays of 4x4 blocks on 1 microscope slide: 1. Dissolve PCR products in 125mM Phosphate buffer, 0.000125% sarcosyl at concentrations ranging between 300 ng/ul and array in 384 microtiter plates. 2. Set spotter settings for 2 arrays of 4x4 blocks printed with 16 pins: column pitch = 185 um, row pitch = 185 um; Humidity 55%; 61 spots per source visit. 3. Make sure room temperature is between 20-24 degrees Celsius. Place microtiter plates in the plate hotel with A1 in front left corner.
5. Place 60 to 120 slides on the slide-deck.
6. Start spotting early in the morning and stop spotting procedure at end of the day and remove pin set. Leave spotter overnight with vacuum and humidity settings on. Continue spotting the next morning until all plates are printed.
7. After spotting, incubate the slides in humid chamber with saturated NaCl for 24 to 72 hours.
8. Block 1%NH4OH.
9. Slides can be stored for at least 6 months in a dry-cabinet.
Support: glass Coating: aminosilane Description: The array contains BAC and PAC sequences, amplified by DOP - PCR and printed in 2 replicates.


title: Illumina Genome Analyzer II (Arabidopsis thaliana x Arabidopsis arenosa)

status: Public on Oct 08 2012


title: [scrMalariaa] Winzeler Lab Plasmodium falciparum expression array 5312 v2

city: La Jolla

first: Elizabeth

middle: Ann

last: Winzeler

address: 9500 Gilman Drive 0741

department: Pediatrics

institute: University of California San Diego

organism: Plasmodium falciparum

manufacture_protocol: Exome capture, 25bp.


title: Illumina Genome Analyzer II (Corynebacterium glutamicum ATCC 13032)

organism: Corynebacterium glutamicum ATCC 13032


title: AB SOLiD System 3.0 (Caenorhabditis elegans)


title: Illumina Genome Analyzer II (Pristionchus pacificus)

organism: Pristionchus pacificus


title: AB SOLiD System 3.0 (Pristionchus pacificus)


title: Agilent-022854 Custom Eucalyptus grandis expression array V1

status: Public on Oct 06 2012

city: Bet-Dagan

first: Ron

last: Ophir

address: POB 6

department: Fruit Tree Sciences

country: Israel

institute: Agricultire Research Organization

organism: Eucalyptus grandis

first: Einat

last: Sadot

manufacture_protocol: Expression array was designed based on 71,208 contigs published previously (Novaes, et al. 2008). Initially, we validated that all contigs did not retain “adaptor” and “vector” sequences by shell and perl scripts. We selected 24,264  long contigs (N90 =101bp) and then set the sequence orientation (sense/antisense) by running the contigs against public databases (e.g., NR (http://www.ncbi.nlm.nih.gov/), Arabidopsis (http://www.arabidopsis.org/), proteins of other plant at TAIR (http://www.arabidopsis.org/), PlantGDB (http://www.plantgdb.org) and UniRef (http://www.ebi.ac.uk/) at EBI). We filtered out for high fidelity sequences based on e-value (<1e-5) and query coverage (>85%) at least in one database or with less than 85% query coverage, but in the same orientation in all mentioned databases. The orientation of contigs that had no significant hit was defined by whether they had poly-A or poly-T. If poly-A/poly-T sequences were not detected, we set the orientation contig by open reading frame (ORF) based on the criterion that the length ratio of the forward to reverse complementary sequence ORF is greater than 10.  Probes were designed between 56 to 60 base pairs long and Tm was optimized by using OligoWIZ (Wernersson and Nielsen 2005). In addition, low complexity cross hybridization was avoided and a high priority was given to probes at the 3’ position.


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [HuEx10stv2_Hs_ENST_14.1.0]

city: Seattle

first: Aderem

last: Lab

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

description: This is identical to GPL5175 but a custom CDF environment was used to extract data. The CDF can be found at the link below.

manufacture_protocol: see manufacturer's web site


title: Agilent-029288 Hydra vulgaris 45J haep_celerav02_1.0

status: Public on Oct 07 2012

city: Kiel

first: Sören

last: Franzenburg

address: Am Botanischen Garten 1-9

department: cell- and developmental biology

institute: zoological institute Kiel

organism: Hydra vulgaris

description:
Hydra vulgaris (AEP)

Arrays of this design have barcodes that begin with 16029288 or 2529288.

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: Agendia_HN_dedicated

status: Public on Oct 10 2012

city: Amsterdam

first: Paul

last: Roepman

address: Science Park 406

country: Netherlands

institute: Agendia

manufacture_protocol: Microarrays were prepared by Agilent technologies using their Agilent SurePrint Technology. Breifly, 60-mer oligonucleotides are synthesized base-by-base in repetitive print layers on a solid glass substrate, using standard phosphoramidite chemistry.


title: LC_MRA-1002_miRMouse_15 (miRNA ID version)

city: Changchun

first: Pingsen

last: Zhao

state: Jilin

address: No. 666 Liuying Xilu

department: The research centre for canine diseases

institute: Institute of Military Veterinary Academy of Military Medical Sciences

organism: Mus musculus

description: Based on Sanger miRBase Release 15.

manufacture_protocol: Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes are made by in situ synthesis using PGR (photogenerated reagent) chemistry.


title: Illumina Genome Analyzer II (Strongyloides ratti)

organism: Strongyloides ratti


title: OPERON/QIAGEN Array-ready Oligo Set Candida albicans Version 1.1

city: Pittsburgh

first: Hassan

last: Badrane

address: 3550 Terrace Street, Scaife Hall, Room S875

department: Medicine

institute: University of Pittsburgh

organism: Candida albicans

manufacturer: University of Florida Genetics Institute, GAINSEVILLE, FL

first: Corneilus

last: Clancy

first: Ming-Hong

last: Nguyen

first: Henri

middle: V

last: Baker

first: Cecilia

middle: M

last: Lopez

manufacture_protocol: C. albicans Genome Oligo Set V1.1 (Qiagen, Valencia, CA) was resuspended at 30 µM in ArrayIt Micro Spotting Plus (Telechem, San Jose, CA) and printed on UltraGAPS slides (Corning, Corning, NY) using a Genemachine Omnigrid arrayer (Genomic Instrumentation Services, San Carlos, CA). Each slide had two replicated arrays with 6936 features, including 70mer oligonucleotides representing 5948 predicted ORFs, 318 cloned genes and random 70mer controls.


title: Illumina Genome Analyzer IIx (Caenorhabditis remanei)

status: Public on Oct 05 2012

organism: Caenorhabditis remanei


title: Illumina Genome Analyzer IIx (Caenorhabditis brenneri)

organism: Caenorhabditis brenneri


title: Illumina Genome Analyzer IIx (Caenorhabditis japonica)

organism: Caenorhabditis japonica


title: Illumina HiSeq 2000 (Tetraodon nigroviridis)

status: Public on Oct 04 2012

organism: Tetraodon nigroviridis


title: Agilent-021640 Clostridium difficile 630 Inter-Genic Array [01_Of_1]

status: Public on Oct 02 2012

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

organism: Clostridioides difficile 630

description:
Agilent-021640 CD630_Inter-Genic_01_Of_1

CHip & Chip puces

Arrays of this design have barcodes that begin with 16021640 or 2521640.

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: NIBB Xenopus laevis 4.6K

city: Higashi-hiroshima

first: Atsushi

last: Suzuki

address: Kagamiyama 1-3-1

department: Graduate School of Science

institute: Hiroshima University

organism: Xenopus laevis

manufacturer: Division of Morphogenesis, National Institute for Basic Biology, Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan.

manufacture_protocol: Microarray slide was prepared using the tentatively selected non-redundant 4608 cDNA set from the NIBB Xenopus EST cDNA library. The sequence information of arrayed cDNAs is available at both the XDB website (http://xenopus.nibb.ac.jp) and the GenBank.


title: Illumina HiSeq 1000 (Caenorhabditis briggsae)

last: GEO

organism: Caenorhabditis briggsae


title: Illumina HiSeq 2000 (Lasioglossum albipes)

status: Public on Oct 01 2012

organism: Lasioglossum albipes


title: Illumina HiSeq 2000 (Myotis davidii)

organism: Myotis davidii


title: Agilent-029535 Aspergillus nidulans FGSC A4 array [Feature Number version]

city: Ribeirão Preto

first: Ana

middle: Cristina

last: Colabardini

state: São Paulo

address: Av do Café s/n Cidade Universitária

department: Ciências Farmacêuticas

country: Brazil

institute: FCFRP-USP

organism: Aspergillus nidulans FGSC A4


title: [BradiAR1b520742] Brachypodium tiling arrray v1.0

city: Ghent

first: Stefanie

last: De Bodt

address: Technologiepark 927

institute: VIB/UGent

organism: Brachypodium distachyon

description: CDF and array design files can be accessed at http://ftp.brachypodium.org/files/Affymetrix/Current/

manufacture_protocol: The Affymetrix array design is based on the DOE-JGI genome sequence of Brachypodium distachyon accession Bd21, Illumina- and EST-based empirical transcriptome analysis, and ab initio gene predictions. A pooled cDNA library from Brachypodium distachyon was sequenced using the Illumina platform and generated ~289 million RNA-seq reads, which were mapped onto the Brachypodium genome assemblies to empirically identify exons and splice junctions (http://www.brachypodium.org/). The array design employs a perfect match (PM) probe strategy using Affymetrix’s 5 micro 49-format array platform containing ~6.5 million features. All of the oligonucleotide probes are unique, single copy sequences within the genome. The mean probe spacing is 42 bases with 95% of probe pairs <126 nucleotides apart. The probes designed for genic regions include 2,548,624 probes targeting exons and introns. On average, exons and introns are represented by 11 probes with 95% of exons or introns targeted by greater than 5 probes. The array also includes 1,062 control probes, 2,050 reporter probes, and 33,886 antigenomic surrogate mismatch probes.


title: NimbleGen B. Taurus and T. annulata 385K 080829_B_taurus_JK_EXP

city: Glasgow

first: William

last: Weir

address: Room 220, Henry Wellcome Building, Garscube Campus, Bearsden Road

department: Institute of Infection, Immunity and Inflammation

institute: University of Glasgow

organism:
Theileria annulata
Bos taurus

description:
385K expression array representing all available RefSeq RNA sequences plus additional EST sequences for Bos taurus and including all predicted coding sequences of the bovine intracellular parasite Theileria annulata. 60 mer probe array, five probes per gene, replicated in 2 blocks.
080829_B_taurus_JK_EXP.ndf
080829_B_taurus_JK_EXP.ngd

manufacture_protocol: Expression array - 1plex 385k expression array


title: Nostoc punctiforme ATCC 29133 Nimblegen expression array [090619_Npun_JM_EXP]

city: Davis

first: Douglas

middle: D

last: Risser

state: California

address: One Shields Ave

department: Microbiology

institute: UC Davis

organism: Nostoc punctiforme PCC 73102

description: Nimblegen Design ID 10188. Expression design for 7,151 genes from the Nostoc punctiforme ATCC 29133 chromosome and plasmids with 9 60 mer probe pairs per gene.

first: Francis

middle: F

last: Wong

first: John

last: Meeks

manufacture_protocol: See manufacturer's website at http://www.nimblegen.com/.


title: Affymetrix Rice Genome Array [custom affyricechipalt.cdf]

status: Public on Sep 26 2012

city: Metro Manila

first: Andrew

last: Cal

address: DAPO BOX 7777

country: Philippines

institute: International Rice Research Institute

organism: Oryza sativa

description: The custom CDF was built using affyprobe miner software (http://www.ncbi.nlm.nih.gov/pubmed/17660211, available http://discover.nci.nih.gov/affyprobeminer/). Probes were mapped to NCBI rice transcript ccds sequences, requiring perfect matches and a minimum of 5 probes per transcript.

relation: Affiliated with: GPL2025 (Alternative CDF [official])


title: UIUC/Newmark-Smed1 CombiMatrix array

city: Urbana

first: Noelle

last: James

state: IL

address: 601 S. Goodwin Ave.

department: Cell and Developmental Biology

country: USA

institute: U of IL / HHMI

organism: Schmidtea mediterranea

manufacture_protocol: 35- to 40-mer oligonucleotide probes were designed complementary to 11,521 planarian transcripts. In most cases, two unique oligos were designed per transcript. These probes were synthesized on two individual CombiMatrix “CustomArray” oligonucleotide arrays; “Smed1” contained 11,835 probes, while “Smed2” contained 11,584 probes. Most transcripts were represented on only one array. However, ~300 were duplicated between arrays.


title: UIUC/Newmark-Smed2 CombiMatrix array


title: Agilent-019943 Genotypic Technology designed Custom Mycobacterium tuberculosis h37Rv Whole Genome 8x15k GE Microarray

status: Public on Apr 19 2011

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

organism: Mycobacterium tuberculosis H37Rv

first: Raja

last: Mugasimangalam


title: JCVI Thalassiosira pseudonana 15K v1.0 [Tp_Affy1_exon]

city: Rockville

first: Ravi

last: Sanka

state: Maryland

address: 9704 Medical Center Drive

institute: JCVI

organism: Thalassiosira pseudonana

manufacture_protocol: An Affymetrix GeneChip custom array was designed to assay for gene expression according to the following specifications.   For gene and exon level analysis, a total of 524,909 probes were marked for synthesis, with an average of 16 probes per gene.  The probe sequences were designed from the sense strand, and were based upon the gene model predicted transcripts for Thalassiosira pseudonana, version 3.0.  Included on the array were 33,886 antigenomic probes for analysis pertaining to the subtraction of nonspecific hybridization.


title: Affymetrix Human Genome U133 Plus 2.0 Array [CDF: HGU133Plus2_Hs_ENSG v12.1.0]

status: Public on Apr 19 2010

city: Stockholm

first: Pekka

middle: Juhani

last: Kohonen

address: Nobelsväg 13, Box 210

department: IMM Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

organism: Homo sapiens

description: Custom CDF (Brainarray v12.1.0)

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


title: UIUC Honey bee whole genome oligo microarray

city: Las Vegas

first: Joseph

last: Margotta

address: 4505 S. Maryland Parkway

department: SOLS

institute: University of Nevada, Las Vegas

organism: Apis mellifera

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

manufacture_protocol: See manufacturer's webpage


title: Entamoeba histolytica E_his-1a520285F array (coding and non-coding regions)

status: Public on Nov 01 2010

city: Charlottesville

first: Carol

last: Gilchrist

state: VA

address: Dept. of Medicine/Division of Infectious Diseases, Building MR4, Rm 2126,PO Box 801365

institute: University of Virginia

organism: Entamoeba histolytica

manufacture_protocol: A custom generated Affymetrix platform full genome microarray (E_his-1a520285F). This array has 7,712 unique probe sets representing 9,435 open reading frames (ORFs). Due to the highly repetitive nature of the E. histolytica genome, some of the probe sets are predicted to cross-hybridize with other sequences. Probe sets that represent a single gene are labeled as (_at). Probe sets in which at least one probe may cross-hybridize with another gene(s) are labeled as (_x_at). In situations where all the probe sets for a given gene cross-hybridize with another gene(s), the probe sets are labeled as (_s_at) and additional genes that cross-hybridize with these probe sets are listed in Supplementary Table 2. This array also contains probes for intergenic non-coding regions, however, these are not included in this submission.


title: HOMIM-v.02

status: Public on May 21 2010

city: Boston

first: Bruce

last: Paster

state: MA

address: 140 Fenway

institute: The Forsyth Institute

organism: Bacteria

manufacturer: Michigan State University Research Technology Support Facility

manufacture_protocol: 16S rRNA-based oligonucleotide reverse capture probes were custom synthesized with a 5’-(C6)-amine modified base, eight spacer thymidines and 18 to 20-nucleotides of target sequence, and printed on 25 x 76 mm aldehyde-coated glass slides


title: Applied Biosystems Human TaqMan® Low Density Array

status: Public on Mar 18 2010

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: 365 human microRNAs and three endogenous controls (RNU48, RNU48 and RNU6B).

first: Norma

last: Gutierrez

first: Maria

last: Sarasquete

first: Manuel

last: Delgado

first: Fany

last: Ticona

first: Javier

last: de las Rivas

first: Encarna

last: Fermiã‘an

first: Patricia

last: Martin-Jimenez

first: Carmen

last: Chillon

first: Alberto

last: Risueã‘o

first: Jesus

last: Hernandez-Rivas

first: Ramon

last: Garcia-Sanz

first: Marcos

last: Gonzalez

last: San Miguel

manufacture_protocol: See manufacturer's website.


title: IQUSP_human_Intronic44k_v1.0

status: Public on Mar 29 2007

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

institute: Universidade de São Paulo

middle: I

first: Paulo

middle: P

last: Amaral

first: Rodrigo

last: Louro

first: Sergio

last: Verjovski-Almeida

first: Eduardo

last: Reis

manufacture_protocol: Agilent’s non-contact industrial inkjet printing process uniformly deposits oligo monomers onto specially-prepared glass slides. Custom microarrays are manufactured using Agilent’s non-contact in situ synthesis process of printing 60-mer length oligonucleotide probes, base-by-base, from digital sequence files. This is achieved with an inkjet process which delivers extremely small, accurate volumes (picoliters) of the chemicals to be spotted. Standard phosphoramidite chemistry used in the reactions allows for very high coupling efficiencies to be maintained at each step in the synthesis of the full-length oligonucleotide. Precise quantities are reproducibly deposited “on the fly.” This engineering feat is achieved without stopping to make contact with the slide surface and without introducing surface-contact feature anomalies, resulting in consistent spot uniformity and traceability.


title: Affymetrix GeneChip Human Genome U133A 2.0 Array [CDF: Brainarray Version 10, Hs133Av2_Hs_ENTREZG]

first: Kevin

last: Struhl

address: 240 Longwood Ave.

department: Biological Chemistry and Molecular Pharamcology

institute: Harvard Medical School

description: This is identical to GPL571 but a custom CDF environment was used to extract data [Brainarray Version 10]

first: Heather

last: Hirsch

first: Dimitrios

last: Iliopolous

first: Yong

last: Zhang

first: Amita

last: Joshi

first: Savina

last: Jager

first: Martha

last: Bulyk

first: Shirley

last: Liu

relation: Alternative to: GPL571 (Alternative CDF [official])

manufacture_protocol: Standard Affymetrix Protocol


title: [RaEx-1_0-st] Affymetrix Rat Exon 1.0 ST Array [probe set (exon) version]

status: Public on Nov 30 2007

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Rattus norvegicus

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

#%create_date=Mon Mar 16 20:01:52 2009 PDT
#%chip_type=RaEx-1_0-st-v1
#%lib_set_name=RaEx-1_0-st
#%lib_set_version=v1
#%genome-species=Rattus norvegicus
#%genome-version=rn4
#%genome-version-ucsc=rn4
#%genome-version-ncbi=HGSC v3.4
#%genome-version-create_date=2004-11
#%netaffx-annotation-date=2009-03-16
#%netaffx-annotation-netaffx-build=28

relation: Alternative to: GPL10112 (Alternative CDF)

manufacture_protocol: See manufacturer's web site