title: Illumina Genome Analyzer II (Trypanosoma brucei brucei x gambiense 414)

status: Public on Sep 29 2010

last: GEO

country: USA

organism: Trypanosoma brucei brucei x Trypanosoma gambiense 414

technology: high-throughput sequencing

distribution: virtual


title: Illumina Genome Analyzer II (Trypanosoma brucei brucei x gambiense 181)

organism: Trypanosoma brucei brucei x Trypanosoma gambiense 181


title: Illumina Genome Analyzer II (Salmonella enterica subsp. enterica serovar Typhimurium)


title: Illumina Genome Analyzer II (Bemisia tabaci)

status: Public on Sep 27 2010

organism: Bemisia tabaci


title: GenoExplorer human microRNA array

status: Public on Feb 15 2011

city: Phoenix

first: Julianna

last: Ross

state: AZ

department: Cancer and Cell Biology

institute: Translational Genomics Research Institute

organism: Homo sapiens

technology: spotted oligonucleotide

description:
The chips are coated with patented polymers used for DNA probe attachment. The biochips covalently immobilized amine-modified DNA oligonucleotide probes for use in microarray analysis.

The array contains probes in triplicate for 678 validated human mature miRNAs and an additional 473 validated human pre-miRNAs, and positive and negative control probes.

distribution: custom-commercial


title: 454 GS FLX (Chlamydomonas reinhardtii)

status: Public on Sep 24 2010

organism: Chlamydomonas reinhardtii


title: TIGR NSF rice oligonucleotide microarray A

status: Public on Sep 30 2010

city: Orono

first: Benildo

middle: G

last: de los Reyes

state: ME

address: 5735 Hitchner Hall

department: School of Biology and Ecology

institute: University of Maine

organism: Oryza sativa Japonica Group

description:
NSF-45K array.
About 45,000 oligonucleotides corresponding to ORFs encoded by the Nipponbare genome were printed on two separate glass slides (A and B).

distribution: non-commercial

manufacturer: The Institute for Genomic Research (TIGR)

first: Myoung-Ryoul

last: Park

first: Kil-Young

last: Yun

first: Venura

last: Herath

first: Song-Joong

manufacture_protocol: Oligonucleotides (~60-mer) corresponding to ORFs in the Nipponbare genomic sequence were synthesized and printed on amine-coated glass slides by TIGR. Microarray slides were purchased through the NSF rice oligonucleotide microarray project (UC Davis).


title: Illumina Genome Analyzer (Cunninghamia lanceolata)

status: Public on Sep 20 2010

organism: Cunninghamia lanceolata


title: TIGR NSF rice oligonucleotide microarray B


title: NimbleGen mouse 385K Refseq and miRNA promoter tiling, 1 of 2-array set (2007-07-27_MM8_promoters_miRNA)

city: Los Angeles

first: Yi

last: Sun

state: CA

address: 635, Charles E. Young Dr. South

department: Molecular and Medical Pharmacology

institute: UCLA

organism: Mus musculus

technology: in situ oligonucleotide

description:
Annotation in this record based on NCBI mouse build 36 (mm8).
native array description file:  2007-07-27_MM8_promoters_miRNA_1.ndf
native array description file: 2007-07-27_MM8_promoters_miRNA_1.pos

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


title: NimbleGen mouse 385K Refseq and miRNA promoter tiling, 2 of 2-array set (2007-07-27_MM8_promoters_miRNA)

description:
Annotation in this record based on NCBI mouse build 36 (mm8).
native array description file:  2007-07-27_MM8_promoters_miRNA_2.ndf
native array description file:  2007-07-27_MM8_promoters_miRNA_2.pos


title: Agilent pre-release murine 12K miRNA arrays (array design ID 018077)

city: St. Louis

first: Seth

middle: Daniel

last: Crosby

state: MO

address: 660 S. Euclid

department: Genetics

institute: Washington Univeristy School of Medicine

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


title: UTHSC/Kotb Streptococcus pyogenes 2.3K v2

status: Public on Sep 22 2010

city: Cincinnati

first: Rita

last: Kansal

state: OH

address: 3235 Eden Avenue

institute: University Of Cincinnati

organism: Streptococcus pyogenes

manufacturer: Molecular Resource Center, University of Tennessee Health Science Center

manufacture_protocol: This oligonucleotide microarray displays probes representing M1 core ORFeome in addition to ORFs representing various M1, M3, M18, and S. dysgalactiae prophages. The microarray was an expansion of one described previously (GEO Platform GPL7661). Oligomers (70mers) were printed in the Molecular Resource Center, UTHSC by the use of MicroGrid II (Genomic Solutions). Additional 70mers, representing M1T1-specific prophages and prophage 3396 of S. dysgalactiae, were designed in batch according to the same design criteria applied for the other oligomers (Oligo Wiz 2.0, URL: http://www.cbs.dtu.dk/services/OligoWiz) and obtained from Integrated DNA Technologies.


title: HG18_Aug09_HD2.3_Custom_Promoter (NimbleGen)

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description:
HG18
The array tiles 23550 RefSeq genes from -3000 to +7000 relative to the TSS, with a mean probe spacing of 75bp

manufacture_protocol: see the NimbleGen website


title: FGP Eschscholzia californica 11K v1.0

status: Public on Sep 21 2010

city: Gainesville

first: Andre

last: Chanderbali

state: FL

address: Museum Road

institute: Univrsity of Florida

organism: Eschscholzia californica

manufacture_protocol: See manufacturer's website


title: febit human miRBase v11

status: Public on Sep 23 2010

city: Homburg

first: Andreas

last: Keller

address: Building 60

country: Germany

institute: Saarland University

distribution: commercial

manufacture_protocol:
MicroRNAs (miRNAs) are endogenous, non-coding RNAs that play a fundamental role in gene regulation and have critical functions across various biological processes. Pairing to mRNAs of protein-coding genes, They direct posttranscriptional repression by altering the stability or translational efficiency of their target mRNAs.
Recent studies indicate that miRNAs are involved in the development of human malignancies, suggesting that they represent a promising new class of cancer biomarkers. Identifying miRNAs involved in specific cancers could provide useful diagnostic information, allow disease classification and reveal potential treatment targets.
MPEA: On-Chip Labeling for Highest Sensitivity
Enzymatic labeling assay requires minimal sample amount
In addition to the standard hybridization of pre-labeled RNA, the microfluidic Geniom Biochip enables a highly sensitive enzymatic labeling protocol.
MPEA benefits
* Higher sensitivity and specificity
* miRNA hybridization without preceding treatment like enrichment, PCR -based amplification or labeling eliminates potential bias
* High discriminatory power
* Minimal amount of sample RNA needed (more than or equal 20 ng total RNA)
* Easy to use protocol for Geniom RT Analyzer
The unique Microfluidic Primer Extension Assay (MPEA) uses unlabeled miRNAs for hybridization. In a second step, Klenow fragment of DNA polymerase I is added directly into the channels of the microfluidic chip, where the specific elongation of the bound miRNAs takes place.
The method combines the specificity of a hybridization assay with the discriminatory power of an enzymatic extension and reduces the required sample amount to a minimum.
Details provided at www.febit.com


title: SWEGENE H_v2.1.1_27k

status: Public on Sep 22 2007

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

first: Ake

last: Borg

manufacture_protocol: Arrays were produced by the Swegene DNA micro array resource center at Lund University by using probes from Operon. Probes were recovered in Corning Universal Spotting Solution and printed on amino-silane-coated glass slides (UltraGAPS from Corning) using a MicroGrid2 robot (BioRobotics).


title: Agilent-023956 S. mutans UA159-140509

city: Braunschweig

first: Xiaoli

last: Xue

address: Inhoffenstr. 7

department: Cell Biology

institute: Helmholtz Center for Infection Research

organism: Streptococcus mutans UA159


title: MM6 385K Whole Genome Tiling array

status: Public on Dec 30 2010

city: Lausanne

first: Charlotte

middle: N.

last: Henrichsen

address: Quartier Sorge

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

description:
mm6 genome assembly
native array description file: 2005-06-03_MM6_WG_CGH.ndf
native array description file: 2005-06-03_MM6_WG_CGH.pos

manufacture_protocol: see NimbleGen


title: PFGRC Staphylococcus_aureus_full_genome_RT-PCR

city: Rockville

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

organism: Staphylococcus aureus

technology: RT-PCR

description: Full genome Staphylococcus aureus qRT-PCR

first: Marcus

last: Jones

first: Qiang

first: Tatiana

last: Dracheva


title: NimbleGen mouse 385K whole genome tiling set26 (2006-07-17_MM8Tiling_Set26 out of a 37-array set)

description:
Annotation in this record based on NCBI mouse build 36 (mm8).
native array description file:  2006-07-17_MM8Tiling_Set26.ndf
native array description file:  2006-07-17_MM8Tiling_Set26.pos


title: Ehuxleyi_Coccolithovirus_V3

status: Public on Nov 21 2011

city: Bergen

first: António

last: Pagarete

address: Thormøhlensgate 53 A & B

department: Department of Biology

country: Norway

institute: University of Bergen

organism:
Emiliania huxleyi
Emiliania huxleyi virus 86
Emiliania huxleyi virus 163

manufacture_protocol: This oligonucleotide microarray displays probes representing Emiliania huxleyi EST's as well as Coccolithovirus genomic sequences (from both EhV-86 and EhV163). Array with 21420 features, in 35 zones, with 3844 biosequences representing 3844 reporters and 0 composite sequences, with surface type aminosilane. Microarray slides (Corning GAPS II Amino-propyl-silane) were printed using Array Jet AJ120 microarray spotter. Oligonucleotides were printed at 20 uM concentration in 50% glycerol with a 0.2 mm pitch, 1 drop per spot. The array is designed in 5 replicate metarows (each contains 3936 spots with 70 base oligomers).


title: Agilent Eichler Homo sapiens 4-plex 210k v1.0

city: Cambridge

first: Peter

last: Sudmant

state: MA

address: 77 Massachusetts Ave

institute: MIT

description: Human genome UCSC hg18.

manufacture_protocol: See manufacturer web site (www.agilent.com).


title: [Mitochip_2] Affymetrix Human Mitochondrial Resequencing Array 2.0

city: Santa Clara

last: Affymetrix

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

manufacture_protocol: see manufacturer's web site


title: Hs-OperonV2-vW2 Human oligonucleotide array

city: Baltimore

first: Sheelu

last: Varghese

address: 655 W Baltimore Street

department: surgery

institute: University of Maryland, Baltimore

manufacturer: Advanced Technology Center (ATC) at the National Cancer Institute (NCI), Gaithersburg, MD

manufacture_protocol: Oligos are arrayed in a glass slide


title: Agilent Mycobacterium tuberculosis Whole Genome Oligo Microarray (8x15K)_condensed

city: Changchun

first: Lu

last: Yu

address: Xi'an Road 5333

country: China

institute: Jilin university

organism: Mycobacterium tuberculosis H37Rv

description: The Platform data table reflects a condensed representation of the array's replicate features.

last: Guo

manufacture_protocol: Refer to manufacturer's website (www.agilent.com).


title: UniversityPadova_Ruditapes philippinarum_4x44K_v1.0

status: Public on Aug 24 2012

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

organism: Ruditapes philippinarum

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


title: Illumina Genome Analyzer II (Pseudomonas putida KT2440)

status: Public on Sep 16 2010

last: GEO

organism: Pseudomonas putida KT2440


title: NimbleGen Mus musculus 385K MM8_60mer_expr

city: Zhunan Town

first: Chiou-Hwa

last: Yuh

state: Miaoli County

address: No. 35 Keyan Road

department: Division of Molecular and Genomic medicine

country: Taiwan

institute: National Health Research Institutes

description:
NimbleGen design name MM8_60mer_expr, NimbleGen design ID 5045, catalog number: A4543-00-01  Mus musculus 385K Array,  for 42,586 genes and there are 9 probes per gene.
Expression design for Mouse from mm8.  Each NM refseq entry (18879) has three probes, each XM entry (6751) has at least 2 (1861 have a third probe).The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are linked below as supplementary files.

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


title: VIMSS Desulfovibrio vulgaris Hildenborough 3.4K

city: Berkeley

first: Adam

middle: P.

last: Arkin

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

first: Arkin

middle: P

last: Adam

first: Marcin

last: Joachimiak

manufacture_protocol: Thompson, D., Beliaev, A., Giometti, C., Tollaksen, S.,Khare, T., Lies, D., Nealson, K., Lim, H., Yates, J., Brandt, C. Tiedje, J., and Zhou, J. 2002. Transcriptional and Proteomic Analysis of a Ferric Uptake Regulator (Fur) Mutant of Shewanella oneidensis: Possible Involvement of Fur in Energy Metabolism, Transcriptional Regulation, and Oxidative Stress. Appl. Environ. Microbiol. 68:881-892.


title: Human_Cancer MicroRNA Array_v1.0

status: Public on Sep 11 2010

city: Chicago

first: Jingjing

last: Wu

state: IL

address: 303 E. Chicago Avenue

department: pathology

institute: northwestern university

first: Jianjun

last: Wei

manufacture_protocol: In this array, each miRNA is targeted by two oligos, each that hybridizes a half molecule of miRNA to form a RNA/DNA duplex. After target miRNA and oligos are matched, the joint is ligated by DNA ligase. Then the ligated molecules are amplificated via T7 trancription into RNA in the presence of biotin-UTP which can be used for hybridization.


title: NimbleGen_Magnaporthe grisea_38K_NC/ChIP_080229

status: Public on Sep 10 2010

city: Columbus

first: Soonok

last: Kim

address: 2021 Coffey Rd.

department: Plant Pathology

institute: The Ohio State University

organism: Pyricularia grisea

description: ChIP chip design for Magnaporthe grisea 5 (rice blast) non-codding regions.  Sequences from the Broad Institute.  42bp interval.

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


title: AB SOLiD System 3.0 (Drosophila melanogaster)

status: Public on Sep 18 2010

organism: Drosophila melanogaster


title: Frankia alni ACN14a whole genome microarray [2008-05-19_RDKK060_Faln_60mer_expr]

status: Public on Sep 12 2010

city: Kagohima

first: Ken-ichi

last: Kucho

address: Korimoto 1-21-35

country: Japan

institute: Kagoshima University

organism: Frankia alni ACN14a

first: Nicole

last: Alloisio

first: Clothilde

last: Queiroux

first: Pascale

last: Fournier

first: Petar

last: Pujic

first: Claudine

last: Médigue

first: Masatoshi

last: Yamaura

first: Kentaro

last: Kakoi

first: Philippe

last: Normand

manufacture_protocol: See manufacturer's web site (http://www.nimblegen.com/products/exp/index.html)


title: Frankia alni ACN14a whole genome microarray [2007-06-20_Frankia_expr]


title: Prevotella ruminicola whole genome array

status: Public on Sep 15 2010

city: Urbana

first: Carl

middle: James

last: Yeoman

address: 1207 W Gregory ave

department: Institute for Genomic Biology

institute: University of Illinois

organism: Xylanibacter ruminicola 23

middle: J

first: JongNam

first: Mark

last: Morrison

first: Issac

middle: K

last: Cann

first: Roderick

middle: I

last: Mackie

manufacture_protocol: Oligos were printed using agilents inkjet technology


title: Chr. Hansen A/S_Bifidobacterium animalis subsp lactis BB12_1689_v1.0

city: Cadorago

first: Martin

middle: Bastian

last: Pedersen

state: CO

address: Via Manzoni 29

department: R&D

institute: Sacco Srl

organism: Bifidobacterium animalis subsp. lactis

first: Christel

last: Garrigues

middle: B

manufacture_protocol: DNA oligos were purchased from Bioneer Corporation at 50nmol synthesis scale with BioRP purification and in lyophilized state (Daedeok-gu, Daejeon, South Korea). Oligos were dissolved at 10uM in 50% DMSO and printed in 4 replicates on UltraGAPS slides (Corning B.V., Schiphol-Rijk, The Netherlands) using a Genpak ARRAY 21 arrayer (Genetix Ltd., Hampshire, United Kingdom) with 16 SMP3 pins, (TeleChem International Inc., Sunnyvale, CA) giving a spot diameter of 100-120mm. Washing was performed between each print cycle for 20s in water followed by 20s in 70% ethanol. The relative humidity was kept at 48 ± 5% by placing a water bath at the appropriate temperature below the air inlet of the arrayer. The oligos were cross-linked to the surface using a Stratalinker 1800 UV Crosslinker set at 70mJ/cm2 (Stratagene). Printed arrays were stored in aluminium pouches with five arrays each and silica gel to remove humidity.


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

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

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

first: Stefano

last: Cagnin

first: Beniamina

last: Pacchioni

first: Caterina

last: Millino

first: Barbara

last: Celegato

first: Cristiano

last: De Pitta'

first: Lucia

last: Tombolan

first: Francesco

last: Chemello

first: Paolo

last: Laveder

first: Camilla

last: Bean

last: Martinati

last: Martini

manufacture_protocol: This set consists of 13,439 70mer oligonucleotides (Operon V1.1) designed on Mouse Unigene clusters, mainly in the 3'-terminal region. Each oligonucleotide is spotted by our robotic station Biorobotics Microgrid II, in two replicates on a MICROMAX glass slide SuperChip I (Cat No MPS696) provided by PerkinElmer Life Sciences Inc. The deposition is qualitatively assessed by a scan of the spotted slide at 10 micron resolution, using a GSI Lumonics scanner and a protocol that allows the detection of spotted features through the salts derived from the dried solution in which oligonucleotides are dissolved. Microarray slides that meet the quality standards, are washed as recommended by the supplier and the glass slides are stored, ready for use, in the dark under deep vacuum. Probe annotation was updated, respect to Operon annotation, by scanning oligo sequences in three databases: ENSEMBL (version 56), RefSeq (version 38) and UniGene (version 183).


title: Ambion mirVana™ miRNA Probe Set 1564V2 Oct06_IZKF (condensed)

city: Wuerzburg

first: Burkhard

middle: Gerhard

last: Kneitz

address: Oberdürrbacher Str. 6

department: Klinik und Poliklinik für Urologie und Kinderurologie

institute: University of Wuerzburg

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description:
support = Nexterion® Slide E, coating = epoxy

The Platform data table reflects a condensed representation of the array's quadruplicate features.  The full array layout representing all of the individual features is linked as a supplementary file at the foot of this record.

manufacturer: Laboratory for microarray applications, IZKF, University of Wuerzburg

first: Susanne

manufacture_protocol:
1. Oligos are arrayed in 96 well plates. Each well contains 500 pmol of 42–46 nucleotides (nt) long oligos and consist of an 18–24 nt segment that targets a specific known human, mouse, or rat miRNA, plus spacer and attachment sequences for coupling to the surface of the microarray slide
2. Add  3 x SSC + 1.5 M Betaine (in Rnase-free water) to 10 uM
3. Seal plates and wrap them in saran wrap
4. Let it resuspend in a humid chamber on a shaker (60 rpm) over night
5. Centrifuge plates at 2000 rpm for 3 minutes.
6. Rearray 10 µL into 384-well, V-bottom plates
7. Centrifuge plates at 2000 rpm for 3 minutes.
8. 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 15 minutes before next cassette is needed to begin centrifugation
9. After the print run is completed, allow plates to dry through passive evaporation in a protected environment
10. Spots are printed in quadruplicates
11. For each subsequent preparation of these plates for a print run, add water to the wells instead of print 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 each dip


title: [Bovine] Affymetrix Bovine Genome Array [CDF: Brainarray Version 12, Bovine_Bt_REFSEQ]

status: Public on Sep 17 2010

city: Jouy-en-Josas

first: Nuria

last: Mach

state: Ile de France

address: Rue de Vilvert

department: Animal Genetics and Integrative Biology (GABI)

country: France

institute: INRA

organism: Bos taurus

description: This identical to GPL2112 but a custom CDF environment was used to extract data (CDF: Bovine_Bt_REFSEQ). The CDF can be found at the Web link below.

relation: Alternative to: GPL2112 (Alternative CDF [official])


title: LC_MRA-1001_miRHuman_12.0_080901

city: North Chicago

first: Dominik

middle: M

last: Duelli

address: 3333 Green Bay Road

department: Pathology

institute: Rosalind Franklin University of Medicine and Science

organism: Homo sapiens

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 (Sus scrofa)

last: GEO

organism: Sus scrofa


title: CombiMatrix_Prokaryotic_4x2K_design 6809

status: Public on Sep 09 2010

city: Beaverton

first: Maria

last: Smit

state: OR

address: 20000 NW Walker Rd

department: Environmental and Biomolecular Systems

institute: Oregon Health and Science University

organism:
Bacteria
Archaea

description: Prokaryotic (bacteria and archaea) microorganisms known to be present in aquatic and soil habitats of the Northern Hemisphere.

manufacture_protocol:
The custom oligonucleotide microarray is synthesized on a semiconductor using an electrochemical synthesis process. Each oligonucleotide probe (spot) is synthesized on a platinum electrode that is independently controlled by the synthesizer’s computer. Synthesis is based on established phosphoramidite chemistry and occurs at thousands of sites simultaneously according to a computer algorithm that activates only specified electrodes. Since physical photolithographic masks, mechanical micromirrors, or inkjet technologies are not involved in the process, all probes can be easily changed without extra time or cost.
The oligonucleotides are synthesized in a proprietary porous reaction layer that coats the surface of the semiconductor, and acts to covalently attach the oligonucleotide to the surface of the chip.


title: Aspergillus nidulans 12K version 1

status: Public on Sep 08 2010

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

organism: Aspergillus nidulans

manufacture_protocol: For details see http://pfgrc.jcvi.org/index.php/microarray/array_description/aspergillus_nidulans/version1.html


title: Haloferax volcanii DS2 tiled array

first: Chuck

last: Daniels

address: 484 West 12th Avenue

department: Microbiology

institute: The Ohio State Uinversity

organism: Haloferax volcanii DS2

manufacture_protocol: The oligonucleotide microarray is composed of 259616 25 mer perfect match (PM) oligonucleotides and 259616 corresponding mismatch (MM) controls.  Sequences are based on the updated version of the H. volcanii genome sequence released April 2007 by The Institute for Genomic Research (Dr. J. Eisen personal communication) and publically available at http://archaea.ucsc.edu/cgi-bin/hgGateway?db=haloVolc1


title: DUMRU Mouse 12K v1.0

city: Waurn Ponds

first: Sean

last: McGee

state: Victoria

address: 75 Pigdons Rd

department: Metolic Research Unit, School of Medicine

country: Australia

institute: Deakin University

organism: Mus musculus

technology: other

description: ONLY CLONES OF INTEREST HAVE BEEN SEQUENCED AND IDENTIFIED

manufacturer: Deakin University, Metabolic Research Unit

manufacture_protocol:
1. Individual cDNA clones were randomly selected from a mouse skeletal muscle cDNA library (5?-Stretch Plus, Clontech, Palo Alto, CA, USA) using a BioPick automated colony picker (BioRobotics Woburn, MA, USA)
2. The cDNA inserts were PCR amplified using primers and conditions recommended by the library manufacturer (Clonetch) and the PCR products were visualized by agarose gel electrophoresis but not sequenced and hence each clone identity remained unknown
3. Amplified cDNAs were then purified using an ArrayIT PCR Purification Kit and resuspended in 30µl of ArrayIt spotting solution (TeleChem International, Sunnyvale, USA)
4. 5µl of resuspended cDNA was transferred to 384 well Uniplates (Whatman Inc, Clifton, USA)
5. cDNA was printed onto 40 microarray slides using an SDDC2 robotic arrayer (Engineering Services Inc, Toronto, Canada)
6. The arrayer was set up to print 32 cDNA spots per cycle with ArrayIt Stealth SMP3 quill tipped microarray pins (TeleChem, International Inc, Sunnyvale, USA)
7. Spacing between cDNA spots was 200 microns
8. Each pin drew 0.25µl of cDNA, tapped a blotting slide twice and deposited approximately 0.6nl on each SuperAmine microarray glass slide (TeleChem International, Sunnyvale, USA)
9. Pins were washed in distilled water and air-dried automatically between cycles
10. Humidity was kept between 55 and 65% during printing
11. Slides were stored at 35% humidity for 36 hours to dry before fixing
12. cDNA was fixed to the slides using the following procedures.
13. Slides were placed in an oven at 80oC for 1 hour, and then allowed to cool to room temperature
14. Slides were placed DNA side down in a humidity chamber (Sigma, St Louis, USA) for 60 seconds to rehydrate the DNA before snap drying them on a heating block set to >100oC
15. cDNA was fixed to the glass slide by UV cross-linking at 60mJ
16. Slides were washed with constant agitation in the following separate solutions: 0.2% SDS, water, water, boiling water, and again in 0.2% SDS, water, water for 2 minutes
17. Immediately after the last wash, slides were dried by centrifugation at 800xg for 5 minutes
18. Slides were then stored until ready for hybridisation experiments


title: University of Florida Bacillus subtilis 9K array version 1

city: Merritt Island

first: Wayne

middle: L

last: Nicholson

address: 505 Odyssey Way, Rm. 201-B

department: Microbiology and Cell Science

institute: University of Florida

organism: Bacillus subtilis

technology: spotted DNA/cDNA

manufacture_protocol: Glass microarray slides (Eurogentec) were spotted in duplicate with 4,096 PCR products, each representing an annotated B. subtilis ORF.


title: Affymetrix Human Genome U133 Plus 2.0 Array [CDF: HGU133Plus2_Hs_REFSEQ_12.1.0]

city: Stanford

first: Ash

middle: A

last: Alizadeh

address: 269 Campus Drive, CCSR 1145c

department: Medicine, Divisions of Hematology and of Oncology

institute: Stanford University School of Medicine

description: This is identical to GPL570 but a custom CDF environment was used to extract data [BrainArray HGU133Plus2_Hs_REFSEQ v12.1.0].

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

manufacture_protocol: See manufacturer's web site: http://www.affymetrix.com/support/technical/byproduct.affx?product=hg-u133-plus


title: [ChlpnV1a520166F] IHBI-C&T Chlamydia 2K v1.0_custom

city: Brisbane

first: Ashkan

last: Amirshahi

state: QLD

address: 60 Musk ave, Kelvin Grove

department: Infectious diseases

institute: Institute of Health and Biomedical Innovation (IHBI)

organism:
Chlamydia trachomatis
Chlamydia pneumoniae CWL029

description: The custom Affymetrix microarray was designed from the genomes of the human pathogens Chlamydia pneumoniae CWL029 and Chlamydia trachomatis serovar D.

manufacture_protocol: The 2K microarray chip was designed with 11 sets of 15-mer oligonucleotide per defined open reading frame. Match and mismatched probes were generated using homologous sequences between the two defined species. Each gene-specific probe was designed to bind to the corresponding transcripts generated by the prokaryotic progenitors. Internal Affymetrix-specific controls for human, mouse, Escherichia coli and Bacillus sequences were included on the array for verification of hybridisation specificities. Proprietary Affymetrix hardware, software and spotting protocols were used in the construction of the custom array.


title: JCVI PFGRC Streptococcus pneumoniae 21K v6 array designed primarily based on strain TIGR4 [full array version]

status: Public on Sep 07 2010

city: New Haven

first: Jonathan

last: Thomas

state: CT

address: 60 College St.

institute: Yale University

organism: Streptococcus pneumoniae

manufacturer: JCVI/Pathogen Functional Genomics Resource Center

manufacture_protocol: 6QSP, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Streptococcus pneumoniae 21K v7 array designed primarily based on strain TIGR4 [full array version]


title: Stintzi Lab Campylobacter jejuni 2.4k array, version 5.0

city: Ottawa

first: Alain

last: Stintzi

state: Ontario

address: 451 Smyth road

department: Biochemistry, Microbiology and Immunology

country: Canada

institute: University of Ottawa

organism: Campylobacter jejuni

manufacture_protocol: A set of 3,308 oligonucleotides were designed with Primer 3 (code available at http://www.genomewi.mit.edu/genome_software/other/primer3.htm) to amplify, via PCR, an internal fragment from each of the 1,654 predicted open reading frames (ORFs) identified in the annotated genomic sequence of C. jejuni NCTC 11168. Genomic DNA (20 ng) was used as a template in the first round of PCR amplifications with standard methods in a 96-well plate format. The PCR products were analyzed by agarose gel electrophoresis. Successful PCR products were reamplified to reduce the amount of residual genomic DNA carried over from the first PCR. PCRs without product or with incorrectly sized products were performed again by modifying the reaction conditions or by designing new primers.   DNA fragments were obtained for approximately 98% of the ORFs. PCR products were purified with the Millipore PCR96 cleanup kit and quantified with the PicoGreen double-stranded DNA quantitation reagent from Molecular Probes. They were diluted in a 50% dimethyl sulfoxide solution at a concentration of 75 ng/µl and rearrayed into a 384-well format. They were then printed on aminosilane-coated glass microscope slides (CMT GAPS-II; Corning Inc., Corning, N.Y.) with an arrayer robot (Molecular Dynamic). Finally, the DNA fragments were immobilized onto the slides by baking at 80°C for 4 h.


title: MEEBO_38.5K_Mus musculus_spotted_oligo_array

city: Santiago

first: Leonardo

middle: Ignacio

last: Pavez

state: Santiago

address: Av Manuel Montt #948

country: Chile

institute: Universidad de Las Américas

manufacture_protocol: Microarrays were produced by Microarrays, Inc. (www.microarrays.com) using high precision robotics and amine-coated glass slides from Genexprex.


title: MIT-KI zebrafish Zv7+8 15K CGH v1.0

city: Cambridge

first: Sebastian

last: Hoersch

address: 77 Massachusetts Avenue (E18-366)

department: David H. Koch Institute for Integrative Cancer Research at MIT

institute: Massachusetts Institute of Technology

organism: Danio rerio

description:
This genomic 15K CGH array was custom designed against zebrafish (Danio rerio) genome assembly danRef5/Zv7 (available at: http://hgdownload.cse.ucsc.edu/goldenPath/danRer5/bigZips/) on the basis of a database of seven million genomic probe sequences provided by Agilent. Probe sequences were later re-mapped with respect to genome assembly danRer6/Zv8 (http://hgdownload.cse.ucsc.edu/goldenPath/danRer6/bigZips/). During this process, probes were annotated with respect to the quality of their mapping to the Zv8 assembly - see table columns 'Zv8:ProbeRemapped' and 'Zv8:ProbeRemappedQualityCode'. The quality code is defined as follows:
Primary code:
A: Perfect match over entire probe sequence
B: Probe sequence matches contiguously with 1 mismatch (BLAT blockCount=1)
C: Probe sequence matches contiguously with 2-5 mismatches (BLAT blockCount=1)
X: No match for probe sequence in genomic (Zv8) BLAT results => probe not used under Zv8.
Z: Best BLAT match worse than per code C => probe not used under Zv8
Primary code qualifiers (suffixes):
' = duplicate matches (quality A,B,C) within under 50K
^ = duplicate matches (quality A,B,C) within 50K-250K
(Longer intervals than 250K between duplicate matches led to rejection => primary code Z)
+ = several matches (4-10), regardless of location and quality
# = many matches (>10), regardless of location and quality

first: GuangJun

last: Zhang

first: Adam

last: Amsterdam

first: Charles

last: Whittaker

first: Jacqueline

last: Lees

first: Nancy

last: Hopkins

manufacture_protocol:
Agilent (http://www.agilent.com) proprietary.
http://www.chem.agilent.com/Library/technicaloverviews/Public/5988-8171en.pdf  ("Agilent SurePrint Technology Content centered microarray design enabling speed and flexibility")


title: Agilent Mycobacterium tuberculosis Whole Genome Oligo Microarray (8x15K)

status: Public on Sep 03 2010

city: Changchun

first: Lu

last: Yu

address: Xi'an Road 5333

institute: Jilin university

organism:
Mycobacterium tuberculosis CDC1551
Mycobacterium tuberculosis H37Rv

last: Guo

manufacture_protocol: Refer to manufacturer's website (www.agilent.com).


title: 454 GS (Drosophila melanogaster)

status: Public on Sep 02 2010

last: GEO

organism: Drosophila melanogaster


title: 2007-03-13_Henikoff_Dros_ChIP_1

city: Montpellier

first: Giacomo

last: Cavalli

email: itys.comet@bric.ku.dk, benjamin.leblanc@igh.cnrs.fr, frederic.bantignies@igh.cnrs.fr, giacomo.cavalli@igh.cnrs.fr

address: 141 rue de la Cardonille

institute: Institute of Human Genetics

description:
Tiling array mapping euchromatic regions of the Drosophila melanogaster genome (Flybase release 4). Chip 1 of 3 of a NimbleGen platform (DesignID=5385) originally designed by Henikoff and Mito (GEO accession: GPL3352).
Whole chromosome 3R mapped with 219005 isothermal probes with an average oligonucleotide length of 50bp and an average inter-oligo spacing of 120bp. The 3R chromosome sequence was unchanged from FlyBase release 4 to FlyBase release 5 and thus release 4 coordinates also corresponds to release 5 coordinates  for this chromosome.
Other probes provide dense tiling of Chr 2L proximal, Chr X proximal and distal, first part of Chr 4, and Bithorax complex (BXC1).


title: Salmonella enterica STv7S_MMCC (uncondensed)

status: Public on Sep 06 2010

city: Boston

first: Richelle

middle: C.

last: Charles

address: 55 Fruit Street, Gray 504

department: Infectious Diseases

institute: Massachussetts General Hospital

organism: Salmonella enterica

manufacture_protocol: Custom-made Salmonella array.


title: Nimblegen Naegleria gruberi 385K array, v1.0

status: Public on Sep 01 2010

city: Berkeley

first: Lillian

last: Fritz-Laylin

state: CA

address: 345 LSA, UC Berkeley MCB

department: MCB

institute: UC Berkeley

organism: Naegleria gruberi

description:
NimbleGen design name 080519_N_gruberi_UCBerk_LFL_expr, NimbleGen design ID 2451.   Array consists of 182,813 probes corresponding to 15,777 gene models predicted on the N.gruberi genome sequence version 1.0 (http://genome.jgi-psf.org/Naegr1/Naegr1.home.html), and an additional 963 orfs identified in intergenic regions (these orf ids can also be accessed via http://genome.jgi-psf.org/Naegr1/Naegr1.home.html).  Each gene is represented by 11 60-mer probes, and each probe set is replicated twice on the array.  The design includes control probes.

Oligonucleotide sequences are available in the supplementary 'GPL10350_080519_N_gruberi_UCBerk_LFL_expr.ndf' file.

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


title: WashU_crypto_ver2_array

status: Public on Sep 04 2010

city: Lynchburg

first: Michael

middle: S

last: Price

state: VA

address: 1971 University Blvd.

department: Biology & Chemistry

institute: Liberty University

organism: Cryptococcus neoformans

manufacturer: Washington University at Saint Louis Genome Center

manufacture_protocol:
The v1.0 array represents an effort to generate an array useful for all of the currently predicted genes in serotype D. This set includes all the C. neoformans genes that were manually annotated by The Institute for Genome Research using a combination of automated gene prediction, homology, and EST data (Loftus et al, 2005). The set also includes all genes predicted by the TWINSCAN software (Korf, Flicek, Duan, and Brent, 2001; Tenney, Brown, Vasquez, Lodge, Doering, and Brent, 2004) that are not already included in the TIGR set. The gene list generated from these two sources was used to choose a set of oligos for each gene using ArrayOligoSelector, and the final oligo for each gene was chosen to primarily optimize homology to genes predicted in serotype A, and secondarily by proximity to the 3' end of the coding sequence. Oligonucleotide sequences, sources, physical characteristics, and TIGR annotations (where applicable) are in a spreadsheet linked under Array Specific Information at the left. The TWINSCAN database used in this work may be similarly accessed.
The revised array includes all of the content from the previous array, as well as new probes designed for:
* 3,075 serotype A genes that did not match (≤2 mismatches) any probe in the previous probe set
* 477 serotype D genes (B3501 or JEC21) that did not match (≤2 mismatches) any probe in the previous probe set
* 48 mating locus genes – the array now represents both mating types of both serotypes


title: Adelaide Microarray Facility CompuGen OligoLibrary Mouse 22k V2.1

city: Darlinghurst

first: Renee

last: Rogers

state: NSW

address: 384 Victoria Street

institute: Garvan Institute of Medical Research

manufacturer: Adelaide Microarray Facility, University of Adelaide, Australia

manufacture_protocol: CompuGen Mouse OligoLibrary V2.0 comprising 21,991 65-mers representing 21,587 unique genes. Additional locally made control plate spotted. Spots printed onto Corning CMT-GAPS slides using a 4x16 pinhead robot. Each print head printed an array of 480 spots arranged as a 24 rows by 20 columns (23040 features per array). This spotting layout is version 2.1. See www.microarray.adelaide.edu.au for printing details.


title: Agilent Human 244K Alternative Splicing Oligo Custom Microarray

city: Toronto

first: Qun

last: Pan

address: 160 College St.

institute: University of Toronto

description:
A microarray platform to profile alternative splicing levels for 5782 cassette-type alternative exons.
Abridged Platform data table (35k of 244k rows) reflects the data discussed in accompanying publication.

first: Vidisha

last: Tripathi

middle: D

last: Ellis

first: Zhen

last: Shen

first: David

middle: Y

last: Song

first: Andrew

middle: T

last: Watt

first: Susan

last: Freier

first: C.

last: Frank Bennett

first: Alok

last: Sharma

first: Paula

last: Bubulya

first: Benjamin

last: Blencowe

first: Supriya

middle: G

last: Prasanth

first: Kannanganattu

middle: V

manufacture_protocol: 60-mer ink-jet Agilent microarray


title: Affymetrix E. coli Antisense Genome Array

first: Henry

middle: H

last: Lee

address: 36 Cummington St

department: Biomedical Engineering

institute: Boston University

organism: Escherichia coli K-12

relation: Alternative to: GPL199 (Alternative CDF [official])

manufacture_protocol: see manufacturer's web site


title: LFGC miRNA NCODEV1

city: Berlin

first: Oleg

last: Tchernitsa

address: Chariteplatz 1

department: Institute of Pathology

institute: Charite

organism:
Homo sapiens
Rattus norvegicus

last: Chernitsa

first: Alexander

last: Gross

manufacture_protocol: Microarrays was constructed using the NCODETM multi-species microarray probe set V1 (Invitrogen, CA, USA). Oligos were spotted at a concentration of 30µM on epoxy treated slides (Corning®, NY, USA) using the MicroGrid compact microarrayer (Genomic Solutions, Ann Arbor, USA) equipped with a MicroSpot 2500 quill pins. Every oligo was spotted twice. After spotting slides were rinsed in milliQ and dryed.


title: Affymetrix GeneChip Rat Genome 230 2.0 Array (CDF:rat2302daiplusv6.cdf)

city: Amsterdam

first: Xiaolian

last: Yuan

state: North Holland

address: Science Park 904

department: Microarray department

country: Netherlands

institute: Amsterdam University

organism: Rattus norvegicus

description:
This platform is identical to GPL1355 but a custom CDF (rat2302daiplusv6.cdf) was used to extract data.
Probes were re-annotated according to de Leeuw et al., 2008 (PMID: 18710586), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix.

relation: Alternative to: GPL1355 (Alternative CDF [official])

manufacture_protocol: See manufacturer's web site.


title: Arabidopsis thaliana SNP-tiling array AtSNPtile ver. 2

city: Chicago

first: Justin

last: Borevitz

department: Ecology and Evolution

institute: University of Chicago

organism: Arabidopsis thaliana

description: This array contains both SNP probes and tiling probes. SNP probes interrogate ~250K SNPs obtained from resequencing of 20 diverse A. thaliana strains (Clark et al. 2007). Each SNP is interrogated by the middle base of four 25mer probes, representing 2 alleles on 2 strands. Tiling probes interrogate ~1.5M unique sequences tiled along the A. thaliana genome with ~35 bp resolution. The reference genome for the array design is Columbia-0. The array is based on The Arabidopsis Information Resource (TAIR) genome release TAIR9.

first: Susanna

last: Atwell

first: Yu

last: Huang

first: Bjarni

middle: J

last: Vilhjálmsson

first: Glenda

last: Willems

first: Matthew

last: Horton

first: Yan

last: Li

first: Dazhe

last: Meng

last: Platt

first: Aaron

last: Tarone

first: Tina

last: Hu

first: Rong

last: Jiang

first: Wayan

last: Muliyati

first: Xu

last: Zhang

first: Muhammad

last: Ali Amer

first: Ivan

last: Baxter

last: Brachi

first: Joanne

last: Chory

first: Caroline

last: Dean

first: Marilyne

last: Debieu

first: Juliette

last: de Meaux

first: Joseph

middle: R

last: Ecker

first: Nathalie

last: Faure

first: Joel

last: Kniskern

first: Jonathan

last: Jones

first: Todd

last: Michael

first: Adnane

last: Nemri

first: Fabrice

last: Roux

middle: E

last: Salt

first: Chunlao

last: Tang

first: Marco

last: Todesco

first: Brian

last: Traw

first: Detlef

last: Weigel

first: Paul

last: Marjoram

middle: O

first: Joy

last: Bergelson

first: Magnus

last: Nordborg


title: UBEC Operon Array Ready E. coli Oligonucleotide set 1.0 [Oligo ID version]

city: Birmingham

last: Turan

address: University of Birmingham, Edgbaston

country: United Kingdom

institute: University of Birmingham

organism: Escherichia coli

description: Alternative version of GPL1246 [this version based on unique oligo ids].

manufacture_protocol: The 70-mer oligonucleotide array was constructed, containing 6112 oligonucleotides that sampled chromosomal genes identified in the genome sequences of E. coli strains K-12 MG1655, O157:H7 VT2 Sakai, and O157:H7 EDL933 and plasmid genes from the two genome-sequenced O157:H7 strains (the Operon Array Ready E. coli Oligonucleotide set 1.0, Qiagen- Operon, Hilden, Germany). 12 positive and 12 negative control oligonucleotides were also included. The oligonucleotides were resuspended in 3 X SSC buffer and printed on to Corning GAPS II slides (Corning B.V Life Sciences, Schiphol-Rijk, Netherlands ) using a Biorobotics Microgrid TAS array printer. Amersham Lucidea array controls (Amersham Biosciences Ltd, Little Chalfont, UK) were printed in each subarray. After printing, slides were briefly rehydrated in steam, dried at 100oC, and UV-cross-linked according to the manufacturer's instructions. Slides were stored desiccated and in the dark until use.


title: NHRI Human 46K cDNA array

city: Miaoli County

first: Chieh Hua

last: Lin

address: 35, Keyan Road, Zhunan Town

department: Division of Biostatistics and Bioinformatics

institute: National Health Research Institutes

organism: Homo sapiens

manufacture_protocol: The NHRI human cDNA microarray contains 46,657 cDNA clones (IMAGE consortium), representing approximately 26,000 unique Unigene clusters. We fabricated cDNA microarrays essentially following protocols as described by Michael B. Eisen and Patrick O. Brown with minor modification. Briefly, the purified cDNA products were resuspended in spotting solution containing 50% dimethyl sulfoxide. The final concentration of each probe was around 0.2 to 0.5 mg/ml. These probes were robotically arrayed onto aminosilane-coated UltraGAPS glass microarray slides (Corning) using a home-made robotic microarray spotter. In addition to the human cDNA probes, a series of control DNA probes from the Lucidea Universal ScoreCard (Amersham Bioscience) were also included for quality assessment of the microarray experiment. In total, there are 49,152 probes spotted on a single microarray slide.


title: NimbleGen Human 12x135K array v1.0 HG17

city: Seattle

first: Andy

last: Itsara

state: WA

address: Foege Building S-250, Box 355065, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington School of Medicine

description:
Annotation in this record based on HG17, NCBI human build 35.
Custom array-CGH was targeted to all predicted CNVs in asthma trios along with a genomic backbone.

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


title: NimbleGen Human 12x135K array v1.0 HG18

description:
Annotation in this record based on HG18, NCBI human build 36.
Custom array-CGH was targeted to all predicted CNVs in asthma trios along with a genomic backbone.


title: NimbleGen 2.1M HD2 Arabidopsis HD2 Custom Array

city: Ikoma

first: Soichi

last: Inagaki

state: Nara

address: 8916-5, Takayama-cho

department: Graduate School of Biological Sciences

institute: Nara Institute of Science and Technology

description:
The 2.1M HD2 array is custom-made by NimbleGen.
The array covers entire genome of A. thaliana.
BUILD: TAIR genome release TAIR8
Accession numbers of genome sequences used to make HD2 array:
chromosome 1:NC_003070.6
chromosome 2:NC_003071.4
chromosome 3:NC_003074.5
chromosome 4:NC_003075.4
chromosome 5:NC_003076.5

NimbleGen description files linked below:
2008-08-06_RDKK096_Atha_CGH_HX1a.ndf
2008-08-06_RDKK096_Atha_CGH_HX1a.pos


title: NimbleGen_Schmidtea mediterranea_385k array

city: Urbana

first: Phillip

last: Newmark

address: C609 CLSL, 601 S. Goodwin Ave.

department: Cell and Developmental Biology

institute: University of Illinois, Urbana-Champaign

organism: Schmidtea mediterranea

description:
NimbleGen design name 2007-11-06_Smed_ESTs_4_expr, NimbleGen design ID 6642.  An expression design for 16,797 ESTs from Schmidtea mediterranea with ten 60-mer probes per gene.  Each probe is replicated twice.  The design includes random GC and other control probes.
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf file is linked below as supplementary file.

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


title: UNIS_S COELICOLOR_SCo3_8149

status: Public on Apr 30 2008

city: Manchester

first: Giles

last: Velarde

address: MIB

institute: University of Manchester

organism: Streptomyces coelicolor

manufacture_protocol:
1. Arrays are printed in 12X4 blocks using a Genetix QArray2 high-throughput spotting robot with tungsten split pins at room temperature, 45% Humidity and a spotting buffer containg 150mM PO4/0.005% SDS/Tween20.
2. After printing, the arrays stay on the platform in the printing chamber overnight (printing starts in early afternoon).
3. Next day the oligo arrays are cross linked at 600 mJ/cm2.


title: VUMC MACF human 5K BAC v37

status: Public on Aug 03 2010

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

description:
- clones were mapped to the UCSC July 2003 Freeze of the Human Golden Path (NCBI build 34)
- oncobacs were mapped using their overgo-primers and are available via www.ensembl.org

last: van den Ijssel

first: Bauke

last: Ylstra

manufacture_protocol: as described in: Carvalho et al (J. Clin. Path.,2004, vol. 57, 644-646). DNA from the 1 Mb resolution Sanger BAC clone set, the OncoBac set, and in house clones of interest, supplemented with clones from the Children’s Hospital Oakland Research Institute (CHORI), amounting to a total of 4678 clones with known chromosomal positions, was isolated according to the CHORI protocol. Amplification of the DNA was done by ligation mediated polymerase chain reaction (PCR) according to Snijders et al. (Nat. Genet.,2001, vol.29, 263-264) and PCR clones were purified using Montage PCR μ96 filter plates (Millipore BV, Amsterdam, the Netherlands). Clones were spotted in triplicate at a concentration of 1 μg/µl, in 150 mM sodium phosphate (pH 8.5), on CodeLink™ slides (Amersham BioSciences, Roosendaal, the Netherlands), using an Omnigrid 100 microarrayer (Genomic Solutions, Ann Arbor, MI, USA) equipped with SMP3 pins (TeleChem International, Sunnyvale, CA, USA). After printing slides were processed and blocked prior to use according to the manufacturer’s protocol.


title: Mouse 33K cDNA array

status: Public on Sep 20 2010

city: Roma

first: Francesca

last: Amati

address: Via Montpellier 1

department: Biomedicine and Prevention

institute: University of Rome Tor Vergata

organism: Mus musculus

manufacturer: MICROARRAY  FACILITY Albert Einstein College of Medicine of Yeshiva University (http://microarray1k.aecom.yu.edu/)

manufacture_protocol: The arrays are printed under rigorous clean-room conditions and quality control is employed all along the way, starting with preparation of the printing material as well as during the actual printing and finally with post-printing tests that include a sample chip hybridization. All cDNA products are tested on Agarose gel to assure quality and concentration of PCR products. During array printing, sample slides are inspected to assure proper performance of pen tips. After printing sample slides are dye stained to help quantitate the concentration of the deposited products and then a test hybridization is performed. Print plates are barcode scanned and a print file is computer generated while printing to assure error-free spot ID. Each slide is uniquely numbered so as to permit documented traceability starting from the manufacturing batch of the blank slide, to the printing location while on the printer, to the environmental conditions during printing and actual content spotted, to the individual who purchased the array & performed the hybridization and submitted it for scanning.  Incorporated into all of our standard arrays is a set of bacterial DNA spots that can be used to calibrate hybridization results. Four bacterial DNA spots are printed in each pen domain of every chip as a minimum. These spots can be used as negative controls as is, or, if appropriate bacterial DNA is spiked into each of the probe samples, can be used to equilibrate ratios for each pen domain, or for ratio gain adjustment when spiked in appropriate ratios. The Oligo arrays have an additional set of 384 control spots consisting of 12 positive and 12 negative controls each replicated 16 times.


title: Illumina Genome Analyzer (Drosophila yakuba)

status: Public on Sep 30 2010

last: GEO

organism: Drosophila yakuba