title: Illumina Genome Analyzer II (Trypanosoma brucei brucei)

status: Public on Jul 28 2010

last: GEO

country: USA

organism: Trypanosoma brucei brucei

technology: high-throughput sequencing

distribution: virtual


title: Nimblegen 4 plex - 080730 Saci DSM639 EXP X4

status: Public on Jul 31 2010

city: Emeryville

first: Robert

last: Dahl

state: CA

address: 5885 Hollis St, JBEI

department: Chemical Engineering

institute: University of California-Berkeley

organism: Sulfolobus acidocaldarius DSM 639

technology: in situ oligonucleotide

description:
Catalog number: A7985-00-01
4 plex array
http://www.nimblegen.com/products/exp/prokaryotic.html

distribution: custom-commercial

manufacture_protocol: See www.nimblegen.com


title: US Army ERDC Fathead minnow brain tissue cDNA 4K Microarray

status: Public on Jul 30 2010

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

organism: Pimephales promelas

technology: spotted DNA/cDNA

distribution: non-commercial

manufacture_protocol: Microarrays were constructed by spotting the fathead minnow cDNA library, ArrayControl™ Spot cDNAs (Ambion), and printing buffer blanks onto Ultra GAPS-coated microarray slides (Corning Inc., Corning, NY).  Spotted cDNAs were immobilized on the chip surface by applying 300 mJ of UV radiation in a Stratagene™ UV Stratalinker 2400 (Agilent Technologies, Waldbronn, Germany).


title: Ncode_Multi_Species_20141

status: Public on Jul 24 2010

city: Bethesda

first: Cynthia

last: Jawoski

state: MD

address: bldg 6, room 136

department: NEI

institute: NIH

organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

technology: spotted oligonucleotide

manufacture_protocol: provided by Invitrogen


title: Invitrogen custom fathead minnow oligonucleotide microarray

description: Arrays were printed in house with 21,000 oligonuclotide probes generated by Invitrogen.


title: Roseburia inulinivorans 5K array

city: Aberdeen

first: Gill

last: Campbell

address: Greenburn Road

department: Rowett Institute of  Nutrition and Health

country: United Kingdom

institute: University of Aberdeen

organism: Roseburia inulinivorans

description: The array has been printed in 48 blocks (4 columns and 12 rows), each block contains 324 features; 18 columns with 6 rows in triplicate at 0.20mm spacing. Mixed Arabidopsis thaliana cDNAs have been printed as landmarks in the top left corners of blocks 1,1; 1,4; 4,1; 4,4; 5,1; 5,4; 8,1; 8,4; 9,1; 9,4; 12,1 and 12,4.

manufacture_protocol: This array has been made from random genomic DNA fragments from R. inulinivorans A2-194. A total of 5500 individual colonies were picked from the library using a robotic colony picker and these were amplified by PCR using primers M13 forward and reverse. Approximately 5000 clones containing single inserts of 500 to 2500bp were identified and used for the array. Clones have been saved as glycerol stocks.


title: Nimblegen Custom 7.5K thermodynamic array V01

status: Public on Jul 27 2010

city: AUBIERE

first: Peyret

last: Pierre

address: 24, avenue des landais

country: France

institute: CNRS - Blaise Pascal University

organism:
Methylosinus trichosporium
Sphingomonas paucimobilis
Dehalococcoides mccartyi VS

description: Synthetic genes. The Platform data table reflects a condensed representation of the expression array's replicates (SEQ ID) features.

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


title: Illumina Genome Analyzer (Heliconius melpomene rosina)

organism: Heliconius melpomene rosina


title: NimbleGen Mus musculus 2M 090316_MM9_Promoter_MeDIP_HX1 tiling design

status: Public on Jul 29 2010

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

organism: Mus musculus

description: Methylation promoter tiling array using NimbleGen platform. Mouse MM9 build. Probe length 50-75bp isothermal. Tiled regions are 8200bp upstream and 3000bp downstream of 5 prime ends of genes as annotated in MM9.


title: [SBRI/Sherman]-Mtb-10368-v1.0

first: Ashley

middle: M

last: Sherrid

address: 307 Westlake Ave N

institute: Seattle Biomedical Research Institute

organism: Mycobacterium tuberculosis

manufacture_protocol:
1.Qiagen array ready oligo set version 1.0 are arrayed in 384-well V-bottom plates. Each well contains 600 pmol of 70-mer oligo.
2. Resuspend oligos in 3X SSC to 40 uM
3. Freeze plates at -20°C when not in use.
4. Before printing,thaw at 4°C. This can be done the night before a print run is started.
5. Seal plates with Corning seals.
6. Spin for 1 minute at 1000 RPM to settle condensation.
7. One plate at a time, load into microarray robot.
8. Load gal file based on Qiagen provided dataset.
9. Cover with Corning seals and refreeze oligos after print run is complete.


title: Illumina Genome Analyzer (Heliconius melpomene melpomene)

organism: Heliconius melpomene melpomene


title: DiscovArray human miRNA 13k array [HDDA]

city: San Diego

first: Andrew

last: Hinton

address: 3525 John Hopkins Ct.

department: Pediatrics

institute: UC, San Diego

organism: Homo sapiens

description:
Custom-manufactured Affymetrix GeneChip® from Ambion
The has-asg-* miRNA_ID identifiers are predicted miRs and not present in miRBase for version 9.2.

manufacture_protocol: see manufacturer's website


title: GenAu MB BCELL v4.0

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohrgasse 7

country: Austria

institute: Instutute of Molecular Pathology

description:
genomic regions of potential pax5 target genes from mm8
including IGH and surrounding genes
isothermal tiling oligos at 100bp

Native NimbelGen files (ndf, pos) linked below as supplementary files.

first: Shane

last: McManus

manufacture_protocol: as described in www.nimblegen.com


title: NKI-AVL Drosophila 4C 36K v. 2.0 (AMADID016016)

city: Amsterdam

first: Maarten

last: van Lohuizen

address: Plesmanlaan 121

department: Molecular Genetics

country: Netherlands

institute: NKI-AVL

organism: Drosophila melanogaster

manufacture_protocol: see manufacturers website (www.genomics.agilent.com)


title: EBT_UA_Daphnia magna_2.3K_version2

status: Public on Jul 23 2010

city: Gent

first: Michiel

last: Vandegehuchte

address: Jozef Plateaustraat 22

department: Applied ecology and environmental biology

country: Belgium

institute: Ghent University (UGent)

organism: Daphnia magna

manufacturer: Laboratory of Ecophysiology, Biochemistry and Toxicology, University of Antwerp

middle: B

first: Tine

last: Vandenbrouck

first: Dieter

last: De Coninck

first: Wim

last: De Coen

first: Colin

middle: R

last: Janssen

manufacture_protocol: Three D. magna cDNA libraries enriched with genes related to energy metabolism, molting and life stage specific processes have been developed by Soetaert et al. (2006 and 2007) using the suppression subtractive hybridization technique. In general, the differentially expressed genes were ligated in a TA-vector system using the pGEM-T easy vector (Promega, USA). Escherichia coli competent cells (JM109, Promega) were transformed through heat shock. Clones were amplified with vector-specific primers (M13 forward and M13 reverse) and purified by an exosap reaction. Next to these cDNA libraries, two extra cDNA fragments, corresponding to expressed sequence  tags (ESTs) from  genes  that  are  reported  to  be  sensitive to Zn, were spotted on the array: ESTs with homology to (1) ferritin (AJ292556) and (2) retinol dehydratase (DV437801) gene fragments (Poynton et al., 2007). Finally, also two ESTs with homology to putative MTs (metallothioneins) (DV437799 and DV437826) were spotted. These sequences were PCR-amplified from a D. magna cDNA sample, checked by electrophoresis, purified by Montage PCR Plate (Millipore, USA) and loaded into 384-well plates (Genetix, UK) in 50% dimethylsulfoxide at a final concentration of 50–75 ng/µL. The isolated cDNA clones from the cDNA libraries were PCR-amplified from the pGEM-T easy vector using adaptor-specific primers (nested primers, Clontech) after which the same control, purification and loading steps were performed. The cDNA fragments (average length of 415 bp) were spotted in triplicate on aminosilane-coated glass slides (Generoma microarray slides, Asper Biotech, Estonia). A set of artificial control genes (Lucidea Universal Scorecard, Amersham Biosciences, UK) was also spotted. After rehydration and drying, the  cDNA  fragments  were  cross-linked  to  the  slides  using  UV-radiation at 300 mJ (UV Stratalinker 2400, Stratagene, USA).


title: Affymetrix Human Exon 1.0 ST Array [CDF: Brainarray V 9.0, HsEx10stv2_Hs_ENTREZG]

status: Public on Nov 19 2012

first: Daniel

middle: Edward

last: Zak

address: 307 Westlake Ave N, Suite 5

description: This platform is identical to GPL5175 but a custom CDF environment was used to extract data [EntrezGene build from Brainarray Version 9.0, HsEx10stv2_Hs_ENTREZG].

relation: Alternative to: GPL5175 (Alternative CDF [official])

manufacture_protocol: see Affymetrix


title: NimbleGen Mus musculus 2.1M 2007-09-21_MM8_Deluxe_Promoter_HX1 tiling design

description: Promoter tiling array using NimbleGen platform. Mouse MM8 build. Probe length 50-75bp isothermal. Tiled regions are 8200bp upstream and 3000bp downstream of 5 prime ends of genes as annotated in MM8.


title: NimbleGen Oryzias latipes_TIGR_rel5 (GFC023) 27k array

status: Public on Jul 22 2010

city: Tsukuba

first: Emiko

last: Kitagawa

state: Ibaraki

address: Onogawa 16-1

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

organism: Oryzias latipes

description:
Species: Oryzias latipes (Japanese Medaka)
Data source: TIGR (The Institute for Genomic Research),
TIGR Oryzias latipes Gene Index (OlGI) Version 5.0
http://www.tigr.org/tdb/tgi/olgi/
Release Date: May 17, 2004
Custom array design:
2004-10-01_GFC023_Oryzia_latipes_TIGR_rel5_1in4
Oligo probe length: 60mer
Target probes: 12,849 TC (Tentative Consensus)
13,669 singleton ESTs
171 singleton ETs
Probe design on array: 26,689 (target) x7 (set/target) x1 (noreplicate)
The Platform data table is a condensed representation of the physical array.
Total targets: 26,580
Native NimbleGen files (ndf and ngd) are linked below as supplementary files.

distribution: commercial

first: Mikihiko

last: Nimura

manufacture_protocol: See Roche NimbleGen website


title: Operon Pig 14.4K genome microarray v1.0.2

city: Edmonton

first: James

middle: Michael

last: Wilkinson

state: Alberta

address: Ag/For Building

department: Agriculture, Food, and Nutritional Science

country: Canada

institute: University of Alberta

organism: Sus scrofa

manufacture_protocol: The Operon pig genome oligo set contains 10,665 70-mer probes with a hit to a known human, mouse, and pig gene transcript and some sequences containing a 3' EST. The pig genome oligo extension set contains 2,632 70-mer probes rpepresenting 2,632 gene sequences with at least one 3' EST. In total, 13,297 pig probes are included on the array (IDs start SS0). All probes were designed from The Institute of Genome Research (TIGR) Sus scrofa Gene Index (SsGI) version 5.0, released on October 1st 2002. All Transcript Consensus (TC) sequences and singleton expressed transcripts (ETs) were aligned using BLAST to known human, mouse, and pig genes. All TCs and singleton ETs with a more than 75% homology over at least 100 bases to a known human, mouse, or pig transcript and yielding a designed probe of less than or equal to 70% cross hybridization identity was included in the set. All probes were designed from the sense strand. They were also designed to have a Tm of 78°C +/- 5°C, be within 1,000 bases from the 3' end of the transcript, not have any contigous single base repeat of more than 8 bases in length, not have a potential hairpin structure with a stem length of more than 9 bases, and not have more than 20 contigous bases common to any other gene. All the component ESTs used to make the TCs were obtained from Genbank. All ESTs with the keyword 3', denoting a 3' EST, were marked and oligos designed in the same way. In addition to these pig probes, various negative controls are also included on the array. These include 10 sequences from the SpotReport Alien cDNA validation System from Stratagene (sequences designed to have no sequence homology to other genomes - IDs start Alien), 7 randomized probe sequences and 4 genes from the plant Arabidopsis thaliana (IDs start SSN), and 13 sequences from bacteria or viruses (from Affymetrix synthetic microarray sequences - IDs start NC). Probes were contact printed on glass aminosilane coated slides (Schott Nexterion) using a arraying robot and a 48 pin tool. Each subgrid on the array contains spots in a 24 row by 25 column grid. The top 12 rows in each subgrid are a repeat of the bottom 12.


title: GenAu MB BCELL v3.0

description:
genomic regions of potential pax5 target genes from mm6
including IGH
isothermal tiling oligos at 100bp

Native NimbelGen files (ndf, pos) linked below as supplementary files.


title: NimbleGen Saccharomyces cerevisiae 2007-09-04_SGD1_TT_ChIP

first: Toshio

last: Tsukiyama

address: 1100 Fairview Ave N

department: Basic Science

organism: Saccharomyces cerevisiae

description: Saccharomyces Genome Database (SGD) 2005.

manufacture_protocol: See NimbleGen for details (http://www.nimblegen.com).


title: Agilent custom Lactobacillus brevis Microarray (condensed version)

status: Public on Dec 30 2010

city: College Station

last: Winkler

state: TX

address: 3122 TAMU

institute: Texas A&M University

organism: Levilactobacillus brevis

description:
This is a custom 60-mer cDNA microarray designed to interrogate the transcriptional profile of Lactobacillus brevis.
Condensed version of the array's replicate features.  GPL10657 represents complete array.

middle: D

first: Katy

middle: C

last: Kao

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


title: NimbleGen Mouse 2006-08-03_MM8_60mer_expr tiling design

first: Jorja

last: Henikoff

description: Expression tiling array using NimbleGen platform. Mouse MM8 build (NCBI Build 36), 60mer probes, 9 probes/target, 42,586 gene targets.


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

city: Santa Clara

last: Affymetrix

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=Tue Dec  8 17:34:30 2009 PST
#%chip_type=RaGene-1_0-st-v1
#%lib_set_name=RaGene-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=2009-11-16
#%netaffx-annotation-netaffx-build=30.1

manufacture_protocol: See manufacturer's web site


title: GeneFilter Mouse Microarrays Release I (GF400)

status: Public on Jan 04 2011

city: Portland

first: Marina

last: Guizzetti

state: OR

address: 3710 SW US Veterans Hospital Rd

department: Behavioral Neuroscience

institute: Oregon Health & Science University; Portland VA Research Service

manufacture_protocol: Each spot on the membranes contains approximately 0.5ng of insert DNA from an I.M.A.G.E./LLNL cDNA clone containing the 3' end of a gene. The insert cDNA has been denatured and UV cross-linked to the positively charged membrane.


title: NimbleGen Drosophila melanogaster Whole Genome 2.1M tiling array

city: Cambridge

first: Sarah

last: Bray

address: Downing Street

department: PDN

institute: University  of Cambridge

description:
DM5_Tiling_Array
Platform annotations based on Drosophila melanogaster, BDGP Release 5, April 2006.
NimbleGen ChIP 2.1M WG-T (2.1M Drosophila melanogaster - Whole Genome Tiling Set)
Design_ID = 6725
Native NimbleGen files linked below.

From NimbleGen's website:
* Format: 2.1M
* Source: UCSC
* Build: DM5
* Probe Length: 50-75mer
* Median Probe Spacing: 55bp
* Design Name: D. mel ChIP 2.1M WG-T Arr Del

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


title: Geobacter metallireducens sense-detecting 12K oligo array

city: Amherst

first: Derek

last: Lovley

state: MA

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

department: Microbiology

institute: University of Massachusetts Amherst

organism: Geobacter metallireducens GS-15

description: each oligonucleotide is synthesized on an array of gold electrodes embedded in a silicon chip

first: Bradley

middle: L

last: Postier

first: Raymond

middle: J

last: DiDonato Jr.

manufacture_protocol: in-situ electrochemically synthesized oligonucleotide array. For reference see: Mauer et al. Electrochemically generated acid and its containment to 100 micron reaction areas for the production of DNA microarrays. PLoS ONE. 2006 Dec 20;1:e34.


title: Strain NaphS2 antisense-detecting 12K oligo array set 2

organism: delta proteobacterium NaphS2

description: each oligonucleotide is synthesized on an array of gold electrodes embedded in a silicon chip.

manufacture_protocol: In-situ electrochemically synthesized oligonucleotide array. For reference see: Mauer et al., Electrochemically generated acid and its containment to 100 micron reaction areas for the production of DNA microarrays. PLoS ONE. 2006, Dec 20;1:e34.


title: Rosetta/Merck Human RSTA Affymetrix 1.0 microarray, Custom CDF

status: Public on Jul 26 2010

first: Amit

middle: V

last: Kulkarni

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

description:
Human RSTA Affymetrix 1.0, Custom CDF microarray Merck.
Contains probesets for each transcript. Probeset is made of 4 to 20 distinct probes.

first: John

last: Castle

relation: Alternative to: GPL6793 (Alternative CDF)

manufacture_protocol: see manufacturer web site


title: [SYNG010s520477] Affymetrix Helianthus annuus 94K

status: Public on Jul 19 2011

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

organism: Helianthus annuus

manufacture_protocol: see manufacturer's web site


title: [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array

status: Public on Jul 18 2002

organism: Escherichia coli K-12

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

Has 7312 entries and was indexed 20-May-2002.
The GeneChip E. coli Antisense Genome Array can be used for examining expression of all known E. coli genes and discovering novel, uncharacterized intergenic transcripts. The array contains probe sets to detect the antisense strand of more than 4,200 known open reading frames. In addition, over 1,350 intergenic sequences can be interrogated in both directions permitting functional characterization of potentially important shorter expressed sequences.
Sequence information for probes on the array correspond to the M49 version of the E. coli Genome Project database at the University of Wisconsin.

Keywords = high density oligonucleotide array

relation: Alternative to: GPL10659 (Alternative CDF)


title: Geobacter metallireducens antisense-detecting 12K oligo array


title: Strain NaphS2 antisense-detecting 12K oligo array set 1


title: Wuerzburg Neisseria meningitidis 14.6K (ORF)

status: Public on Jul 19 2010

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

country: Germany

institute: University of Wuerzburg

organism: Neisseria meningitidis

manufacture_protocol: The oligonucleotides were synthesized by Operon technologies(Germany) and were spotted on Nexterion E epoxy silane coated slides using an OmniGrid scanner after resuspension in the recomended buffers.


title: Agilent-012391 Human

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

manufacture_protocol: Agilent


title: Townsend Lab Saccharomyces cerevisiae 6312 ORF PhD version

status: Public on Jul 17 2010

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

manufacture_protocol:
The microarrays were constructed with different length oligonucleotides synthesized (Illumina, San Diego) for 6312 ORFs.
they were robotically printed on CMT-GAPS-aminopolysilane-coated glass slides (Corning, NY)


title: SMD Print_1447

first: Donna

last: Peehl

department: Department of Urology

institute: Stanford University School of Medicine

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: SMD Print_1204 yeast YCPR


title: Plymouth Marine Laboratory CroV Microarray Version 1

status: Public on Jul 18 2010

city: Plymouth

first: Michael

middle: James

last: Allen

address: Prospect Place

institute: Plymouth Marine Laboratory

organism: Cafeteria roenbergensis virus BV-PW1

description: Cafeteria roenbergensis virus CroV

manufacture_protocol: Oligonucleotides were deposited and immobilised onto amino silane treated glass slides (Corning GAP II) using a BioRobotics MicroGrid 2 printer.


title: NimbleGen Aedes aegypti custom array

status: Public on Jul 21 2010

city: Notre Dame

first: Dongyoung

last: Shin

state: IN

address: Galvin Science building

department: Biology

institute: Universoty of Notre Dame

organism: Aedes aegypti

description: native array description file: 070904_A_aegypti_ND_expr.ndf

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


title: Human 35K OpArrays DNA microarray

city: Padua

first: Karina

last: Fincati

address: V.le G. Colombo, 3

department: Department of Biology, University of Padua

country: Italy

institute: CNR-Institute for Biomedical Technologies


title: Clostridium-EA 2018

city: Shanghai

first: Shiyuan

last: Hu

address: 300# fenglin road

country: China

institute: Institute of plant physiology and ecology, Shanghai institutes for biological sciences, Chinese academy of sciences

organism: Clostridium acetobutylicum

manufacture_protocol: The detailed protocol can be found in http://www.chem.agilent.com/EN-US/SUPPORT/Pages/default.aspx


title: NimbleGen Mouse 2.1M array [100512_MM8_CHARM_HX1]

city: Baltimore

first: Akiko

last: Doi

address: 855 N Wolfe St, Rangos 580

department: Medicine

institute: Johns Hopkins University School of Medicine

organism: Mus musculus

description: Annotation based on UCSC mouse genome assembly Feb 2006 (mm8)

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


title: Grossman Lab WGS8-9

first: Alan

middle: D.

last: Grossman

email: clee2@mit.edu, adg@mit.edu

address: 31 Ames Street, 68-530

institute: MIT

organism:
Escherichia coli
Bacillus subtilis subsp. subtilis str. 168

manufacturer: Research Technology Support Facility at Michigan State University, East Lansing, Michigan

first: Wiep

middle: K

last: Smits

manufacture_protocol: PCR products were prepared using a combination of the Sigma-Genosys Bacillus subtilis ORFmer PCR primer pairs and additional primers designed by the Grossman and Losick labs on a case-by-case basis. Products were spotted on Corning UltraGAPS aminosilane coated glass slides using a Genetix Q-Array Mini printer.


title: Illumina Genome Analyzer (Anas platyrhynchos)

status: Public on Jul 15 2010

last: GEO

organism: Anas platyrhynchos


title: UTU Chicken BursaEST 37K array

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: Gallus gallus

manufacturer: Deutsches Ressourcenzentrum für Genomforschung ( http://www.rzpd-ia.de )

manufacture_protocol: BursaEST array (from the dkfz426 cDNA library) BursalEST library construction: The bursas of 2-wk-old chicken of the inbred CB strain were excised and a cell suspension was prepared. The chicken bursa consists mainly of B cells but Ficoll gradient centrifugation was used to remove contaminating epithilial and red blood cells to achieve a B cell content of about 95% B cells. Poly-dT reverse transcribed mRNA was ligated to a linker and cloned into pSPORT1 plasmid. Average insert length was about 1.3 kb. Library is housed at RZPD (Deutsches Ressourcenzentrum für Genomforschung), Heidelberg, Germany as Chicken Bursa cDNA (number 426, or dkfz426). Sequences are submitted in GenBank under accession AJ392050-AJ3994559. The library is not normalized. Spotting the array: Plasmid DNA was grown up and PCR amplified using primers to the linker sequences at RZPD. PCR products were purified and spotted to a nylon filter macroarray in duplicate within a 4x4 subarray. The array contains 36864 (192x192) features including 14592 cDNA clones (in duplicate), spike control spots (not used in hybridizations) and empty spots. redundancy.The array can be hybridized several times and quality of spots on the array can be assesed by hybridizing with linker oligos to determine DNA content of a spot.


title: Gillichthys mirabilis cDNA microarray (Last Annotated 2/2010 by Cheryl A. Logan)

city: Pacific Grove

first: Cheryl

last: Logan

address: 120 Ocean View Blvd

institute: Stanford University

organism: Gillichthys mirabilis

manufacturer: Hopkins Marine Station, Stanford University

manufacture_protocol: This microarray consists of spotted cDNAs, generated by reverse transcribing mRNA collected from several tissues of the goby Gillichthys mirabilis. RNA was collected from liver, gill, brain and muscle tissue, extracted from individuals that had been exposed to heat, hypoxia or osmotic stress. cDNAs were directionally cloned into pTriplEx2 vector (Clontech; Mountain View, CA, USA). Plasmid libraries were transformed into E. coli and bacterial colonies were picked at random into 384-well microtiter plates and grown overnight at 37C. cDNA inserts were amplified by PCR using 1 ul of bacterial suspension in 50 ul standard PCR reactions with vector specific primers. After ethanol precipitation, and one round of washing in 70% ethanol, PCR products were prepared in 3X sodium citrate (SSC) and 1.5 mol-1 betaine, for spotting onto Fisher Scientific (Hampton, NH, USA) Gold Seal glass microscope slides. Slides were coated with poly-L-lysine.


title: Dickeya dadantii 5.8K Ech3937

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

organism: Dickeya dadantii

description: Dickeya dadantii 3937

manufacture_protocol: See Agilent Technologies website


title: Agilent Salmon Immunity and Quality 44k custom array_SIQ2

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

organism:
Oncorhynchus mykiss
Salmo salar

description:
SIQ2 (Salmon Immunity and Quality) is the second version of oligonucleotide platform for Atlantic salmon containing probes to protein encoding transcripts from Unigene, Genbank (complete cds) and Gene Index - DFCI with addition of EST from own leukocyte library. Rainbow trout sequences correspond to genes that have not been identified in salmon.

Versions SIQ2 and SIQ3 (GPL10705) contain the same array features, but different layouts.

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


title: Desulfotomaculum reducens MI-1 6.5K 080812_DR_MI-1_BLR_EXP

city: Neuchâtel

first: Pilar

last: Junier

address: Rue Emile-Argand 11

department: Institute of Biology

country: Switzerland

institute: University of Neuchâtel

organism: Desulforamulus reducens MI-1

description: whole genome expressio nORF array for Desulfotomaculum reducens MI-1;Starting number of sequences:  3423;Sequences with probes: 3258;Exemplars: 88;Sequence with no probes: 78; 2 replicates on the array


title: Mouse custom CGH oligo array 44K (022188)

status: Public on Jul 14 2010

city: Chiba

first: Takashi

last: Takabatake

state: Chiba

address: Anagawa 4-9-1, Inage-ku

institute: National Institute of Radiological Sciences

description: Chromosome coordinates correspond to mouse genome build mm9 (NCBI Build 37).

manufacture_protocol: See manufacturer's website.


title: Ucdenver Human U133plus2 [GeneNet software]

city: Aurora

first: Tzu Lip

last: Phang

address: 12700 East 19th Avenue

institute: University of Colorado, Denver

organism: Homo sapiens

description: We performed a shRNA synthetic lethality assay and used Affymetrix HGU133plus2 chip to measure the shRNA expression signals. Hybridization data was analyzed using GeneNet software (Systems Biosciences).

manufacture_protocol: Photolithography


title: Agilent-021827 Unrestricted Human 15.7K v3.0 miRNA Microarray

status: Public on Jul 20 2010

first: Zhidong

last: zhu

state: Shanghai

address: 151# Libing road

institute: shanghai biochip Co.

description:
Human miRNA Microarray 3.0

Arrays of this design have barcodes that begin with 16021827 or 2521827.

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: Mouse custom CGH oligo array 15K (024443)


title: Biodesign Inst. at ASU Escherichia coli Agilent-020097 array

city: Tempe

first: Joshua

last: Stomel

state: AZ

department: BON

institute: Biodesign Inst. at ASU

organism: Escherichia coli

description: E. coli (K12-MG1655, CFT073, O157-H7 EDL933, O157-H7 VT2-Sakai) Oligo Microarray. Arrays of this design have barcodes that begin with 16020097 or 2520097.

first: James

middle: W

last: Wilson

first: Megan

last: Leon

first: Phillip

last: Stafford

first: John

last: Chaput


title: NCode miRNA microarray 474

city: Jupiter

first: Paul

middle: J.

last: Kenny

state: FL

address: 130 Scripps Way

department: Molecular Therapeutics

institute: The Scripps Research Institute - Florida

organism: Rattus norvegicus

manufacture_protocol:
The microarray is contact-printed using microquill pins on Corning® Epoxide-Coated Glass Slides. The array specifications are: Total subarrays per slide: 3, Subarray layout: 8 blocks (4 rows × 2 columns), Block layout: 192 spots (12 rows × 16 columns), Block dimensions: 4 mm × 3 mm
Average spot diameter: 120 μm, Spot center-to-center spacing: 265 μm. The array is printed with NCode™ miRNA probes, which are unmodified oligonucleotides (34–44 bases long) containing all known mature miRNAs in the miRBase Sequence Database, Release 9.0, for human, mouse, rat, D. melanogaster, C. elegans, and Zebrafish. Species-specific probes were designed using a proprietary algorithm that generates miRNA sequences with enhanced hybridization properties. The probes provide comparable sensitivity to wild-type sequences, while offering maximum specificity for discerning between closely related miRNAs and normalized melting temperatures for uniform hybridization. Probes have been validated for their ability to distinguish between wild-type and mismatched miRNA sequences with ≥1 base mismatch.


title: NimbleGen Mouse 2.1M array [Feinberg_MM8_Me_HX1]

first: Akiko

last: Doi


title: Illumina Genome Analyzer (Blattella germanica)

status: Public on Jul 12 2010

organism: Blattella germanica


title: Ralstonia phage RSL1 Array

status: Public on Jul 13 2010

city: Nagoya

first: Manabu

last: Harada

state: aichi

address: 15-1 Nakanoshima, Ohdaka-cho, Midori-ku

department: Biosciences

institute: Filgen,Inc.

organism: Ralstonia phage phiRSL1

manufacture_protocol: CustomArray™ uses a specially modified “CMOS” semiconductor to direct the molecular assembly of a specific sequence of DNA bases in response to a digital command. Each feature on the array (a microelectrode) is digitally addressed to selectively generate acid, by means of an electrochemical reaction which, in-turn, controls the detritylation reaction during phosphoramidite synthesis. A software program is used to control the microelectrodes, and thus, the detritylation pattern applied on the chip during synthesis.


title: E. coli K12 4x44K array

city: Marburg

first: Torsten

last: Waldminghaus

address: Hans-Meerwein-Straße

department: Philipps-Universität Marburg

institute: Synmikro

organism: Escherichia coli str. K-12 substr. MG1655

description: Product code 10012

manufacture_protocol: The oligonucleotide microarray is composed of about 40,000 of 60-mer oligonucleotides.


title: Laval/Sirard_human-bovine_granulosa_2.5K_V1.0

status: Public on Jul 10 2010

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

organism:
Homo sapiens
Bos taurus

manufacturer: Marc-André Sirard' laboratory, Laval University.

manufacture_protocol: cDNA was obtained by SSH experiments (Clontech). The substractions were done on granulosa cells collected at the same time as competant versus incompetant oocytes from bovine and human tissues.competant Each clone was amplified by PCR, purified, dry-down and resuspended in H20/DMSO(50:50). The clones were spotted using a chipwritter (Virtek) on ultra-glass slides (Corning). The slides were UV treated occording to the manufacturer's protocole.


title: SMD Print_1679 (Mycobacterium tuberculosis)

status: Public on Jul 09 2010

city: Ithaca

first: David

last: Russell

state: NY

address: C5 171 Veterinary Medical Center

department: College of Veterinary Medicine

institute: Cornell University

organism: Mycobacterium tuberculosis


title: SMD Print_1009 Homo sapiens

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité


title: SMD Print_1094 Homo sapiens


title: SMD Print_996 Homo sapiens


title: UOklahoma_GeoChip_2.0

city: Montreal

first: Etienne

last: Yergeau

state: Qc

address: 6100 Royalmount Ave

department: Environmental Microbiology

institute: NRC-BRI

organism: Bacteria

description: Owing to their vast diversity and as-yet uncultivated status, detection, characterization and quantification of microorganisms in natural settings are very challenging, and linking microbial diversity to ecosystem processes and functions is even more difficult. Microarray-based genomic technology for detecting functional genes and processes has a great promise of overcoming such obstacles. Here, a novel comprehensive microarray, termed GeoChip, has been developed, containing 24 243 oligonucleotide (50 mer) probes and covering >10 000 genes in >150 functional groups involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, and organic contaminant degradation. The developed GeoChip was successfully used for tracking the dynamics of metal-reducing bacteria and associated communities for an in situ bioremediation study. This is the first comprehensive microarray currently available for studying biogeochemical processes and functional activities of microbial communities important to human health, agriculture, energy, global climate change, ecosystem management, and environmental cleanup and restoration. It is particularly useful for providing direct linkages of microbial genes/populations to ecosystem processes and functions.

first: Zhili

last: He

first: Liyou

last: Wu

first: Jizhong

last: Zhou

manufacture_protocol:
A new version of CommOligo (Li et al., 2005) with group-specific probe design features was used to design both gene- and group-specific oligonucleotide probes based on the following criteria: (i) gene-specific probes: 90% sequence identity, 20-base continuous stretch and -35 kcal/mol free energy (Liebich et al., 2006); (ii) group-specific probes: a group-specific probe has to meet the above requirements for nontarget groups, and it also has to have 96% of sequence identity, 35-base continuous stretch and -60 kcal/mol of free energy within the group (He et al., 2005). The information about the probes and their targets is available on our web site: http://ieg.ou.edu/GeoChip2.0/GeoChip2.0-info.xls
All designed probes were subsequently verified by ProbeChecker, and synthesized by MWG Biotech Inc. (High Point, NC, USA). The concentration of all oligonucleotides was adjusted to 100 pmol/l. All oligonucleotide probes and controls were arrayed onto Corning UltraGAPS (Corning, NY, USA) slides using a Microgrid II Arrayer (Genomic Solutions, Ann Arbor, MI, USA) as described previously (He et al., 2005)


title: 080814_HG18_Deluxe_Promoter_HX1

city: Research Triangle Park

first: Deepak

last: Mav

state: NC

address: 2 Davis Drive

institute: Sciome LLC

description:
Platform annotations are based on build HG18, NCBI 36
native array description file:  080814_HG18_Deluxe_Promoter_HX1.ndf
native array description file:  080814_HG18_Deluxe_Promoter_HX1.pos

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


title: Agilent custom C. albicans tiling array - antisense (Crick)

status: Public on Jul 07 2010

first: Adnane

last: Sellam

address: 6100 Royalmount

department: Anatomy and Cell Biology

institute: Adnane Sellam

organism: Candida albicans

description: Starting from sequences from the C. albicans Genome Assembly 21, we extracted a continuous series of 242,860 60-bp oligonucleotides each overlapping by 1 bp. We then eliminated 2062 probes containing stretches of 13 or more A or T nucleotides. The remaining 240,798 sequences were then used to produce sense (Watson) and antisense (Crick) whole genome tiling arrays using the Agilent Technologies eArray service (https://earray.chem.agilent.com/earray/).


title: NimbleGen Human 385 K array V1.0

status: Public on Jul 06 2010

city: Omaha

first: Himabindu

last: Ramachandrareddy

state: NE

address: 600 South 42nd st

department: Pathology and microbiology

institute: University of Nebraska Medical Center

description:
The coordinates of the genomic regions tiled on the custom chip are based on assembly hg18.
Genomic regions of genes having a critical role in B cell differentiaion were tiled

manufacture_protocol: NimbleGen manufactured a custom array by maskless array synthesis technology with 387,981 45- to 55-mer oligonucleotides tiling portions of >100 genes, chosen on the basis of their likely role in B-cell differentiation. We included as little as 10 kb surrounding the promoter for some genes; several hundred kb for others; and, for a few, only evolutionarily conserved portions of large regions. The region to be included was based in part on the genome-wide data available from T-cells, on the distance to neighboring genes, and the extent of evolutionary conservation in distant regions. Probes average 50 nt in size and overlap adjacent probes by 25 nt. Reverse strands were also tiled on the chip but displaced by 12-13 nt. A custom algorithm was used to eliminate oligonucleotides from repetitive elements likely to crosshybridize.


title: NimbleGen/SNU Rice 3'-tiling 385K array

city: Seoul

first: Ju-Seok

last: Seo

department: Dept. of Applied Biology & Chemistry

country: South Korea

institute: Seoul National University

organism: Oryza sativa

description:
The profiling was conducted with the Rice 3'Tiling Microarray designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp).
Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon and with shifting 10 bp so 10 probes cover 150 bp in the 3' region of the gene.
Genes from chloroplast (123) and mitochondria (74) and selection markers such as gfp, gus, hyg, bar, and kan are included. In total, 270,000 probes were designed with the average size of probe is 60-nt long to have its Tm value 75 to 85 °C.

first: Yeon-Ki

last: Kim

first: Baek

middle: H

last: Nahm

manufacture_protocol: The microarray was manufactured at NimbleGen inc (http://www.nimblegen.com/). Random GC probes (38,000) to monitor the hybridization efficiency and four corner fiducial controls (225) were included to assist with overlaying the grid on the image.


title: Nimblegen Rhipicephalus microplus 385K microarray

city: Brisbane

first: Manuel

middle: Rodriguez

last: Valle

state: QLD

address: 665 Fairfield road, Yeerongpilly

department: Emerging Technologies

country: Australia

institute: DEEDI

organism: Rhipicephalus microplus

manufacture_protocol: see www.nimblegen.com


title: Renji Hospital ABI Mouse TaqMan® MicroRNA Assays V2.0

city: Shanghai

last: Shen

address: 145 Shan Dong Middle Road

department: Department of Rheumatology

institute: Renji Hospital, JiaoTong University School of Medicine

organism: Mus musculus

manufacture_protocol: See manufacturer's website (http://www.appliedbiosystems.com/).


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [probe set (exon) version]

status: Public on Jul 28 2010

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

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=Tue Dec  8 17:31:33 2009 PST
#%chip_type=MoGene-1_0-st-v1
#%lib_set_name=MoGene-1_0-st
#%lib_set_version=v1
#%genome-species=Mus musculus
#%genome-version=mm9
#%genome-version-ucsc=mm9
#%genome-version-ncbi=37
#%genome-version-create_date=2007-07
#%netaffx-annotation-date=2009-11-16
#%netaffx-annotation-netaffx-build=30.1

manufacture_protocol: See manufacturer's web site


title: LC_MRA-1034_miRPrimates_10.0_070802

city: Houston

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

organism:
Lemur catta
Ateles geoffroyi
Lagothrix lagotricha
Macaca mulatta
Macaca nemestrina
Gorilla gorilla
Pan paniscus
Pan troglodytes
Pongo pygmaeus
Homo sapiens
Saguinus labiatus

description: Primates miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 10.0

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://www.mirbase.org) 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: German Cancer Research Center Operon Oligonucleotide 25K Array

city: Heidelberg

first: Stefan

middle: M

last: Pfister

address: INF 580

department: Molecular Genetics

institute: German Cancer Research Center

first: Marc

last: Remke

first: Till

last: Milde

manufacture_protocol: Spotted long oligonucleotide array produced using the Operon Human Genome Oligo Set Version 2.1 (21,329 70mer oligonucleotides, based on build #147 of the Human UniGene database). Keywords = spotted Keywords = human Keywords = long oligonucleotide Keywords = oligo Keywords = 70mer Keywords = Operon Protocol: 70mer oligonucleotides were diluted at 40 µM in FBNC buffer (G. Wrobel et al., Nucleic Acids Res 31 e67, 2003) and spotted as array duplicates using epoxy-silane coated glass slides (Schott Nexterion) and stainless steel split pins (SMP3, Telechem) at 20°C and 40% rH. Slides were dried (60' @ 60°C) and DNA was UV-crosslinked with 240 mJ/cm2 @ 254 nm. Slides were stored, sealed airtight and dry, at 4°C.


title: Agilent Custom Gene Expression Array for Kluyveromyces lactis

city: Boston

first: Alex

last: Tsankov

state: MA

address: 155 Bay State

institute: MIT

organism: Kluyveromyces lactis

manufacture_protocol: Standard Agilent protocols for Agilent Custom Oligo Microarray 8x15K G4427A


title: Agilent Custom Gene Expression Array for Saccharomyces kluyveryii

organism: Lachancea kluyveri NRRL Y-12651

description: Agilent Custom Oligo Microarray 8x15K G4427A


title: Agilent Custom Gene Expression Array for Debaryomyces hansenii

organism: Debaryomyces hansenii


title: Agilent Custom Gene Expression Array for Saccharomyces mikatae

organism: Saccharomyces mikatae


title: Agilent Custom Gene Expression Array for Kluyveromyces waltii

organism: Lachancea waltii


title: Agilent Custom Gene Expression Array for Saccharomyces paradoxus

organism: Saccharomyces paradoxus


title: Agilent Custom Gene Expression Array for Saccharomyces castellii

organism: Naumovozyma castellii


title: Agilent Custom Gene Expression Array for Yarrowia lipolytica

organism: Yarrowia lipolytica


title: Agilent Custom Gene Expression Array for Candida albicans


title: Agilent custom C. albicans tiling array - sense (Watson)

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


title: SMD Print_1224 Homo sapiens

first: Lars

last: Bullinger

organism: Homo sapiens

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


title: AB SOLiD System 3.0 (Danio rerio)

status: Public on Jul 08 2010

last: GEO

organism: Danio rerio


title: Illumina Genome Analyzer (Camponotus floridanus)

organism: Camponotus floridanus


title: Illumina Genome Analyzer (Harpegnathos saltator)

organism: Harpegnathos saltator


title: Agilent Custom Gene Expression Array for Saccharomyces bayanus

organism: Saccharomyces bayanus


title: UHN_human_single-spotted 19k cDNA array_version 8

status: Public on Jul 01 2010

first: Traute

last: Flatscher-Bader

state: Queensland

address: The University of Queensland, Upland Road, QBI Building (79)

department: The Queensland Brain Institute

institute: The University of Queensland

manufacturer: University Health Network Microarray Centre, Ontario Cancer Institute Toronto, Canada

manufacture_protocol:
Ontario Cancer Institute (OCI, Toronto, Canada) human single-spotted 19k (version 8) microarray slides, which consisted of 19,008 characterized and unknown human ESTs from Image Consortiumeach with an unique Genbank ID, were used for all hybridisations. The microarrays were printed on GAPS II or UltraGAPS™ slides (Corning Inc.) using high-precision robotics. Printed arrays are processed following Corning's protocol and were ready-to-use.
Slide specifications:
Grid Rows     12
Grid Cols     4
Rows      20
Cols      20
Grid to Grid Distance (um)    4500
Spot to Spot Distance (um)    200


title: M22K_01_UNAM-IFC_Murine_22K_oligoarray_version_v1

status: Public on Jul 04 2010

city: Cuernavaca

first: Sergio

middle: Manuel

last: Encarnación

state: Morelos

address: Av. Universidad S/N

department: Centro de Ciencias Genomicas

country: Mexico

institute: Universidad Nacional Autonoma de México

description: The custom-designed M22K_01 oligonucleotide array contains a total of 44640 entries and was last updated at 2006. The microarray 65-mer probe sets represent 22,000 transcripts derived from approximately 70% genome annotated and predicted mouse genes and their alternative spliced variants (MGI/GenBank).

manufacturer: UNAM-IFC DNA Microarray Facility and Sigma Genosys

first: Jorge

last: Ramirez-Salcedo

first: Simon

last: Guzman-Leon

first: Jose

last: Santillan-Torres

first: Lorena

last: Chavez-Gonzalez

manufacture_protocol: Mus musculus twenty two thousand 65-mer oligo library sets from Sigma Genosys (http://www.sigmaaldrich.com/life-science/custom-oligos.html) were resuspended (50 μM) in Micro Spotting solution (ArrayIt Brand Products). SuperAmine coated slides 25 × 75 mm (TeleChem International, INC) were printed in duplicate and fixed at 80 °C for 4 h.


title: UW_Rhodobacter_sphaeroides_2.4.1_385K_v2

city: Madison

first: Yann

middle: S

last: Dufour

state: WI

address: 1550 Linden Drive

department: Bacteriology

country: USA

institute: University of Wisconsin - Madison

organism: Cereibacter sphaeroides 2.4.1

description:
Oligo probes are 45bp in average, tiling the genome sequences with about 35-bp overlap between consecutive probes. Every other probe hybridizes to the reverse strand.

Native array description file: 2007-06-20_R_sphaeroides_long85_v2.ndf
Native array description file: 2007-06-20_R_sphaeroides_long85_v2.pos

manufacture_protocol: See manufacturer's web site (www.nimblegen.com)


title: Agilent-023144 Mouse Metastable Epialleles

first: Richard

last: Kellermayer

address: One Baylor Plaza

institute: Baylor College of Medicine

description:
Methylation specific amplification microarray (MSAM).
A 2x105k microarray containing probes, covering 33,404 (81% of all) SmaI intervals between 100 bp and 2.2 kb in the mouse genome (build NCBI37/mm9).

Arrays of this design have barcodes that begin with 16023144 or 2523144.

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 Custom Gene Expression Array for Candida glabrata

organism: Nakaseomyces glabratus


title: Yale University Rice SNP Array 386K

city: New Haven

first: Hang

last: He

state: CT

address: 165 Prospect St

department: MCDB

institute: Yale University

organism: Oryza sativa

description: Genome build information

manufacture_protocol: see manufacturer's web site


title: JCVI PFGRC Actinobacillus actinomycetemcomitans 15K v3 array designed primarily based on strain HK1651

city: Rockville

first: PFGRC

last: JCVI

state: MD

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Aggregatibacter actinomycetemcomitans

description: This set includes 2303 oligonucleotides, has 15552 spots distributed in 48 blocks.

manufacture_protocol: 3QAA, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Aspergillus fumigatus 22K v4 array designed primarily based on strain Af293

organism: Aspergillus fumigatus

description: This set includes 8895 oligonucleotides, has 22176 spots distributed in 48 blocks.

manufacture_protocol: 4QAF, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Mud crab 6K cDNA array version 1.0

city: Xiamen

first: zou

last: zhihua

state: Fujian

address: NO.43 Yindou road

department: Fishry college

institute: Jimei University

organism: Scylla paramamosain

manufacturer: Functional Genomics and Physiology Research Group, Institute of Aquaculture Biotechnology of Jimei University

manufacture_protocol:
1.Insert DNA of cDNA clones were PCR amplified and purified.
2.Purified insert DNA was arrayed in 96-well V-bottom plates,dried completely, re-dissolved in spotting solution (50 % DMSO) to a final concentration of 200 ng/μl.
3. Seal plates with plastics seals.
4. Incubate at 37°C for 30 minutes to aid resuspension of DNA.
5. Shake plates near maximum rotational speed on flat-bed shaker for 1 minute.
6. Centrifuge plates at 1000 rpm for 5 minutes.
7. 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 24 minutes.
8.Then the cDNAs are printed onto CapitlBio AminoSlide (CapitalBio, Beijing, China) using a PixSys5500 arrayer (Cartesian Technologies, Irvine, CA, USA) equipped with 16 (4*4) Chipmaker 2 pins (Telechem, Sunnydale, CA)


title: JCVI PFGRC Clostridium botulinum 13K v3 array designed primarily based on strain Hall

organism: Clostridium botulinum

description: This set includes 3297 oligonucleotides, has 13056 spots distributed in 48 blocks.

manufacture_protocol: 3QCB, with arrayer AUSHON


title: JCVI PFGRC Plasmodium falciparum 12K v4 array designed primarily based on strain 3D7

organism: Plasmodium falciparum

description: This set includes 5156 oligonucleotides, has 12288 spots distributed in 48 blocks.

manufacture_protocol: 4QPF, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Yale University Neurospora crassa 70-mer oligo whole genome transcription array

status: Public on Jul 03 2010

city: West Haven

first: Francesc

last: Lopez

department: Department of Genetics

organism: Neurospora crassa

manufacture_protocol:
The microarrays were constructed with 70mer oligonucleotides synthesized (Illumina, San Diego) for ORFs identified by Broad Institute (http://www.broad.mit.edu/annotation/genome/neurospora)
and were robotically printed on CMT-GAPS-aminopolysilane-coated glass slides (Corning, NY) at Yale University


title: JCVI PFGRC Campylobacter jejuni 16K v4 array designed primarily based on strain RM1221

organism: Campylobacter jejuni

description: This set includes 7147 oligonucleotides, has 16416 spots distributed in 48 blocks.

manufacture_protocol: 4QCJ, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Campylobacter jejuni 16K v4 array designed primarily based on strain RM1170


title: JCVI PFGRC Giardia lamblia 20K v3 array designed primarily based on strain WB_C6

organism: Giardia duodenalis

description: This set includes 7985 oligonucleotides, has 20160 spots distributed in 48 blocks.

manufacture_protocol: 3QGL, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Campylobacter jejuni 16K v4 array designed primarily based on strain CG8421


title: JCVI PFGRC Campylobacter jejuni 16K v4 array designed primarily based on strain 81116,_NCTC_11828


title: JCVI PFGRC Campylobacter jejuni 16K v4 array designed primarily based on strain IA3902


title: JCVI PFGRC Staphylococcus aureus 10K v3 array designed primarily based on strain N315

organism: Staphylococcus aureus

description: This set includes 3929 oligonucleotides, has 10800 spots distributed in 48 blocks.

manufacture_protocol: 3QSA, with arrayer LUCIDEA, mode Normal, replicates 2, repeats 1, slide_dips 75, machine cycles 1280640, pen id 10180, pen cycles -1, operator Jon, humidity control On, humidity set point65


title: JCVI PFGRC Chlamydia pneumoniae 13K v3 array designed primarily based on strain J138

organism: Chlamydia pneumoniae

description: This set includes 2059 oligonucleotides, has 13872 spots distributed in 48 blocks.

manufacture_protocol: 3QCP, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Campylobacter jejuni 16K v4 array designed primarily based on strain 269.97


title: JCVI PFGRC Mycobacterium tuberculosis 16K v5 array designed primarily based on strain CDC1551

organism: Mycobacterium tuberculosis

description: This set includes 4735 oligonucleotides, has 16416 spots distributed in 48 blocks.

manufacture_protocol: 5QMT, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Chlamydia pneumoniae 13K v3 array designed primarily based on strain D/UW-3/CX


title: JCVI PFGRC Campylobacter jejuni 16K v4 array designed primarily based on strain NCTC_11168


title: JCVI PFGRC Staphylococcus aureus 10K v3 array designed primarily based on strain Mu50


title: JCVI PFGRC Campylobacter jejuni 16K v4 array designed primarily based on strain 81-176


title: JCVI PFGRC Chlamydia pneumoniae 13K v3 array designed primarily based on strain AR39


title: JCVI PFGRC Vibrio cholerae 14K v1 array designed primarily based on strain Eltor_N16961

organism: Vibrio cholerae

description: This set includes 3811 oligonucleotides, has 14256 spots distributed in 72 blocks.

manufacture_protocol: QVC, with arrayer LUCIDEA, mode Normal, replicates 3, repeats 1, slide_dips 38, machine cycles 3886032, pen id 179, pen cycles -1, operator Robin, humidity control On, humidity set point65


title: JCVI PFGRC Streptococcus agalactiae 13K v3 array designed primarily based on strain NEM316

organism: Streptococcus agalactiae

description: This set includes 2771 oligonucleotides, has 13872 spots distributed in 48 blocks.

manufacture_protocol: 3QSB, with arrayer AUSHON


title: JCVI PFGRC Listeria monocytogenes 17K v5 array designed primarily based on strain EGD-e

organism: Listeria monocytogenes

description: This set includes 7704 oligonucleotides, has 17328 spots distributed in 48 blocks.

manufacture_protocol: 5QLM, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Staphylococcus aureus 16K v9 array designed primarily based on strain MSSA476

description: This set includes 4528 oligonucleotides, has 16416 spots distributed in 48 blocks.

manufacture_protocol: 9QSA, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Streptococcus agalactiae 13K v3 array designed primarily based on strain A909


title: JCVI PFGRC Streptococcus agalactiae 13K v3 array designed primarily based on strain 2603V/R


title: JCVI PFGRC Listeria monocytogenes 17K v5 array designed primarily based on strain HCC23


title: JCVI PFGRC Staphylococcus aureus 16K v9 array designed primarily based on strain MW2


title: JCVI PFGRC Staphylococcus aureus 16K v9 array designed primarily based on strain N315


title: JCVI PFGRC Listeria monocytogenes 17K v5 array designed primarily based on strain 1/2a F6854


title: JCVI PFGRC Listeria monocytogenes 17K v5 array designed primarily based on strain 4b F2365


title: JCVI PFGRC Listeria monocytogenes 17K v5 array designed primarily based on strain 4b H7858


title: JCVI PFGRC Staphylococcus aureus 16K v9 array designed primarily based on strain Mu50


title: Rosetta/Merck Human RSTA Custom Affymetrix 1.0 microarray

status: Public on Apr 30 2008

city: Seattle

first: Amit

last: Kulkarni

state: WA

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

organism: Homo sapiens

description: Contains probesets for each transcript. Probeset is made of mostly 11 distinct probes.

first: John

last: Castle

relation: Alternative to: GPL10687 (Alternative CDF)

manufacture_protocol: see manufacturer web site


title: JCVI PFGRC Staphylococcus aureus 16K v9 array designed primarily based on strain MRSA252


title: JCVI PFGRC Staphylococcus aureus 10K v3 array designed primarily based on strain COL


title: JCVI PFGRC Staphylococcus aureus 10K v3 array designed primarily based on strain MW2


title: JCVI PFGRC Staphylococcus aureus 16K v9 array designed primarily based on strain COL


title: JCVI PFGRC Pseudomonas aeruginosa 13K v3 array designed primarily based on strain PAO1

organism: Pseudomonas aeruginosa

description: This set includes 5552 oligonucleotides, has 13056 spots distributed in 48 blocks.

manufacture_protocol: 3QPA, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Chlamydia pneumoniae 13K v3 array designed primarily based on strain CWL029


title: AGENAE_PigGeneric2_9216

status: Public on May 06 2006

city: Jouy-en-Josas

first: Sylvain

last: Marthey

address: Domaine de Vilvert Bat 320

department: Animal Genetics

institute: INRA

organism: Sus scrofa

description: spotted DNA/cDNA

manufacture_protocol: as described in Institute Labs manual