title: Illumina HiSeq 2000 (Vicia sativa)

status: Public on Jan 30 2012

last: GEO

country: USA

organism: Vicia sativa

technology: high-throughput sequencing

distribution: virtual


title: Homo sapiens 5.1K CGH-Integragen 3

status: Public on Jan 25 2012

city: Evry

first: nathalie

last: lefort

address: 5 rue Henri Desbruères

country: France

institute: INSERM

organism: Homo sapiens

technology: spotted DNA/cDNA

distribution: non-commercial

first: Christine

last: Varela

first: Jérome

middle: A

last: Denis

last: Polentes

first: Maxime

last: Feyeux

first: Sophie

last: Aubert

first: Benoite

last: Champon

first: Geneviève

last: Piétu

first: Marc

last: Peschanski

first: Nathalie

last: Lefort

manufacture_protocol: IntegraChip genome-wide BAC arrays of 4,898 BAC clones (600-kb median spacing) were hybridized by the manufacturer, IntegraGen (Evry, France). The genomic positions of all clones on the array have been determined by BAC end sequencing. A genomic DNA labeling kit (Enzo, Farmingdale, NY) was used to label the sample DNA with Cy5 or with Cy3. The labeled products were purified with QiaQuick polymerase chain reaction (PCR) purification kits (Qiagen, Valencia, CA). After addition of tRNA (48 mg) plus a quantity of human Cot DNA (Invitrogen, Carlsbad, CA) equal to 50 times the mass of the labeled DNAs, the resulting products were concentrated by vacuum centrifugation, resuspended in 43 mL of hybridization solution (Ambion, Austin, TX) and deposited on the array under a coverslip. Hybridization in a sealed chamber (Corning Life Sciences, Acton, MA) was for 66 hours at 55_C, and then washed. Slides were scanned (Agilent Technologies, Santa Clara, CA), data were extracted with GenePix 6 (Axon InstrumentseMolecular Devices, Sunnyvale, CA), and copy number analysis was performed with GenoCensus (IntegraGen), which includes block Loess normalization.


title: Agilent 014867 GRL_Staphylococcus_aureus_V5-11K

status: Public on Jan 23 2012

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

organism: Staphylococcus aureus

technology: in situ oligonucleotide

description: 60-mers oligonucleotide probes, in-situ synthesis

distribution: custom-commercial

first: Patrice

last: Francois

first: Adrien

last: Fischer

first: Antoine

last: Huyghe

first: Jacques

last: Schrenzel

manufacture_protocol: SurePrint Technology (in situ synthesis)


title: Rodent TaqMan® Low Density miRNA Arrays A v2.0 (TLDA, Applied Biosystem).

status: Public on Jan 31 2012

city: Bethesda

first: Chon-Hwa

last: Tsai-Morris

state: Md

address: Bldg. 49, Rm 6B03, 49 Convent Drive

department: PDEGEN, NICHD, NIH

organism: Mus musculus

technology: RT-PCR

description:
Taqman microRNA assay
Real time qRT-PCR

manufacture_protocol: see manufacturer's website


title: Agilent-024699 Custom Paenibacillus vortex 8x15k array (Probe Name version)

status: Public on Jan 24 2012

city: Kfar Yona

first: Dalit

last: Roth

address: Turmus 199

department: Microbiology

country: Israel

institute: Tel Aviv University

organism: Paenibacillus vortex

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


title: UCL Streptococcus thermophilus 15K 60-mer array, Version 1, our ID Agilent-023342 LMD-9v2

city: Louvain-La-Neuve

first: Pascal

last: Hols

address: Place Croix du Sud 5

department: Institut des Sciences de la Vie

country: Belgium

institute: Université catholique de louvain

organism: Streptococcus thermophilus LMD-9


title: JCVI PFGRC Mycobacterium tuberculosis 22K v4 array designed primarily based on strain H37Rv [Probe-level version]

city: Baltimore

first: JongHee

last: Lee

state: MD

address: 1550 Orleans St. CRB2

department: Medicine

institute: Johns Hopkins Medical School

organism: Mycobacterium tuberculosis

technology: spotted oligonucleotide

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


title: Human Epigenome Microarray Platform V1.0

status: Public on Jan 26 2012

city: Stanford

first: Chih Long

last: Liu

state: CA

address: 269 Campus Drive

department: Medicine - Imm. & Rheum

institute: Stanford University

technology: spotted peptide or protein

first: ChihLong

first: Stephanie

last: Tangsombatvisit

first: Jacob

last: Rosenberg

first: Emily

middle: C

last: Gillespie

first: Ash

last: Alizadeh

first: Or

middle: P

last: Gozani

first: Paul

middle: J

last: Utz

manufacture_protocol: Synthetic peptides were custom-synthesized from the Yale Keck Biotechnology Resource Library with the sequences as described in the data table. Peptides were resuspended in 0.4 mg/ml in 0.5X phosphate-buffered saline (PBS) pH 7.4 with 2.5% glycerol and 0.025% tween-20. Custom microarrays were printed with the Bio-Rad Chip Writer Pro on ArrayIt streptavidin-coated slides, with each peptide printed in 6 replicates. Arrays were stored vacuum-packed for up to 2 months at 4 degrees Celsius before use.


title: Utz Lab Whole Protein Autoantigen Array V2.0

organism:
Escherichia coli
Gallus gallus
Homo sapiens
Bos taurus
Oryctolagus cuniculus
Mus musculus

manufacture_protocol: Whole protein or synthetic peptide antigens were purchased from commercial vendors as described in the data table.  Antigens were resuspended in 0.2 mg/ml in 1X phosphate-buffered saline (PBS) pH 7.4.  Custom microarrays were printed with the Bio-Rad Chip Writer Pro on Whatman FAST slides, with each antigen printed in 6 replicates.  Arrays were stored vacuum-packed for up to 2 months at 4 degrees Celsius before use.


title: SMD Print_1633 Saccharomyces cerevisiae SFGF:cpcc

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

organism: Saccharomyces cerevisiae

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: CapitalBio mammal microRNA V4.0

city: Shanghai

first: Wei-Zhong

last: Wu

address: Fenglin Rd 180, Xuhui district

department: Zhongshan Hospital

country: China

institute: Fudan University

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

manufacture_protocol: As described in CapitalBio mannual


title: LC Mouse_Human_12.0_090114 miRNA Array (MRA-2001)

city: Beijing

first: Xiao

last: Yang

address: 20 Dongdajie

institute: Beijing Institute of Biotechnology

organism:
Homo sapiens
Mus musculus

description:
Including:
1) All mouse mature miRNAs listed in miRBase version 12.0
2) Human mature miRNAs that are different from mouse miRNAs.

first: Shuilong

last: Guo

first: Yan

last: Teng

manufacture_protocol: Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the microfluidic chip, each detection probe consisted 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 were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes.


title: University of Padova Sparus aurata 40k array version 1 [Probe name version]

city: Faro

first: Florbela

middle: A.

last: Vieira

address: Campus de Gambelas

country: Portugal

institute: CCMAR - UALG

organism: Sparus aurata

description: GE 4x44k oligo microarray that covers 19,715 unique transcripts of the gilthead sea bream (Sparus aurata). Oligonucleotides, 60-mer plus a “linker”, are synthesized directly on glass slide using the Agilent’s SurePrint Tecnology; oligo design was carried out by Agilent and two non overlapping probes were designed for each ESTs cluster. The number of transcripts represented by two probes is 19,664 while 51 targets have only one probe; the total number of target probes in the platform is 39379. Both independent probes designed for the same transcript are named with an univocal ID and distinguished by suffix _1 or _2. Sequence and description of each gene (cluster) are available in the SAPD database (http://enne.cribi.unipd.it:5555/biomart/martview), where cluster ID corresponds to probe ID on the array. (Access to SAPD database will be free after publication. Login and password are now required and will be provided upon request).

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


title: Microarrays Inc. Rat RN1100 MI Ready Array

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

institute: ULB

organism: Rattus norvegicus

description: MI Rat ReadyArray for the rat genome features 34,717 70mer transcript probes representing genes and alternative splice products from ENSEMBL release 37 for Rattus norvegicus. Precision arrayed onto a single slide, the rat gene expression array features microarray probes from the Operon Biotechnologies' Array Ready Oligo Set version 3.0 and Operon's update of that microarray probe set.

first: Frédérick

manufacture_protocol: Manufacturing processes utilize MI proprietary technologies and intellectual property licensed through Oxford Gene Technology.


title: Food Safety Potato cDNA Microarray 4K 2.0

city: Wageningen

first: Jeroen

last: van Dijk

address: Bornsesteeg 45

country: Netherlands

institute: RIKILT, institute of food safety

organism: Solanum tuberosum

first: Kok

last: Esther

first: Scheffer

last: Stanley

manufacture_protocol: PCR fragments were purified through Sephadex G-50 columns (Sigma-Aldrich, USA) and precipitated by overnight incubation with of 1/10 V 3M sodium acetate (pH 5.2) and 1 V of isopropanol. The pellets were washed with 70% ethanol, air-dried, redissolved in 20 μl 50% DMSO-MiliQ and used for spotting. Microarrays were spotted on UltraGAPS slides (Corning) in 64 blocks containing 16 x 16 spots. Two complete microarrays were spotted per slide. As positive controls three different luciferase fragments corresponding to the 5', middle and 3' part of the cDNA, as well as the entire luciferase cDNA were spotted across the array as well as a Salmonella gene fragment as a negative control.A total of 264 controls were included. Microarrays were dried and stored at room temperature until use. Spotting quality was assessed for two of the spotted arrays in the series by staining the slides with 0.2 μM cyanine nucleic acid dye POPO-3 (Molecular probes, USA). Prior to hybridisation DNA was UV-crosslinked to the glass surface with 1500 mJ.


title: Illumina Genome Analyzer IIx (Fibroporia radiculosa TFFH 294)

last: GEO

organism: Fibroporia radiculosa TFFH 294


title: Agilent 024417 Saccharomyces bayanus and Saccharomyces cerevisiae (SMD Print_1667)

first: Barbara

last: Dunn

department: Genetics

organism:
Saccharomyces bayanus
Saccharomyces cerevisiae

manufacture_protocol: Agilent


title: EPFL 4x44k OGT MTB microarray

status: Public on Jan 20 2012

city: Lausanne

first: Ruben

last: Hartkoorn

state: Vaud

address: SV 3533 (Bâtiment SV) Station 19

department: GHI/SV

institute: EPFL

first: Stewart

middle: T

last: Cole

first: Claudia

last: Sala

first: Swapna

last: Uplekar

first: Jacques

last: Rougemont

manufacture_protocol: The OGT microarrays consist of 44000 60mer oligonucleotide probes designed to hybridise throughout the M.tuberculosis genomic DNA. (http://www.ogt.co.uk/)


title: Applied Biosystems Mouse Taqman miRNA Expression Assays A and B

city: Rochester

first: Jie

last: Dong

state: MN

address: 200 1st SW

department: Thoracic Surgery

institute: Mayo Clinic

description: Cards A and B.

manufacture_protocol: See manufacturer's website.


title: WashU C. Neformans ver2 array (locus ID)

status: Public on Feb 22 2012

city: Murfreesboro

first: Erin

last: McClelland

state: TN

address: 1301 East Main Street, P.O. Box 60

department: Biology

institute: Middle Tennessee State University

organism: Cryptococcus neoformans

description: * 3,075 serotype A genes that did not match (≤2 mismatches) any probe in the previous probe set

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:


title: UH/Williams Human 40k

status: Public on Oct 02 2012

city: Houston

first: Philip

last: Jonsson

state: TX

address: Department of Biology and Biochemistry – NSM Center for Nuclear Receptors and Cell Signaling 3605 Cullen Blvd, Science & Engineering Research Center Bldg 545

institute: University of Houston

manufacture_protocol: See manufacturer's website at http://www.microarrays.com/dna-arrays.php


title: Agilent-025302 Lessnick EWS 2.0

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

first: Stephen

middle: L

last: Lessnick

first: Wen

last: Luo


title: NimbleGen Human DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Arrays (090618_HG18_CpG_Refseq_Prom_MeDIP)

city: Duarte

first: Marc

last: Jung

address: 1500 East Duarte Street

institute: City Of Hope

description:
Format: 3X720K
Source: UCSC
Build: HG18, NCBI 36
Probe Length: 50-75mer
Median Probe Spacing: 104
090618_HG18_CpG_Refseq_Prom_MeDIP.ndf
090618_HG18_CpG_Refseq_Prom_MeDIP.pos
090618_HG18_CpG_Refseq_Prom_MeDIP.gff
090618_HG18_CpG_Refseq_Prom_MeDIP_HX3.ncd


title: SMD Print_1327 Saccharomyces cerevisiae ACATL2

last: Stanford Microarray Database


title: SMD Print_1428 Saccharomyces cerevisiae JJL1


title: EPFL 4x44k OGT MTB microarray (both strands condense version)

description: The forward and reverse strand is combined on this version of the platform. The supplementary files contain the oligonucleotide sequence for both strands and the array layout.


title: JCVI PFGRC Streptococcus mutans microarray version 2.0

city: New Orleans

first: Zezhang

middle: Tom

last: Wen

state: LA

address: 1100 Florida Avenue

department: Oral and Craniofacial Biology

institute: LSU Health Sciences Center

organism: Streptococcus mutans UA159

manufacture_protocol: Oligonucleotides were spotted.


title: SBRI_MTuberculosis_12x130K_ver2.0 (gene level)

city: Seattle

first: Kyle

last: Minch

state: WA

address: 307 Westlake Ave N.

institute: Seattle BioMed

description:
This platform is a gene level version of GPL14824
NimbleGen design name 110405_Mtuber_TR_exp_HX12.  Custom designed in house tiled array of 107,936 unique probes covering all 4000 ORFs, sense and antisense, and all intergenic regions.

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


title: Agilent-018359 TIFN_Listeria monocytogenes EGD-e_15K_v2.0

city: Groningen

first: Maarten

last: Mols

address: Nijenborgh 7

institute: University of Groningen

organism: Listeria monocytogenes EGD-e

description: Custom made Listeria monocytogenes EGD-e array (version 2)

first: Pia

middle: K

last: Nielsen

first: Ann

middle: Z

last: Andersen

first: Stijn

last: van der Veen

first: Tjakko

last: Abee

first: Birgitte

middle: H

last: Kallipolitis

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


title: NimbleGen Human Expression Array [2006-08-03_HG18_60mer_expr]

city: Kanazawa

first: Yo

last: Niida

state: Ishikawa

address: 13-1 Takaramachi

country: Japan

institute: Kanazawa Univ.

organism: Homo sapiens

description:
Design name: 2006-08-03_HG18_60mer_expr
Designid: 4542
Expression design for human (hg18; NCBI Build 36). 8 60mer probes per gene. 47633 exemplar genes representing a total of 63780 transcripts/variants.


title: Illumina Genome Analyzer (Populus yunnanensis)

status: Public on Jan 19 2012

last: GEO

organism: Populus yunnanensis


title: NIMBLE_MMCCSAL05_14028_380k

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

description: design name: MMCCSAL05_081030. This set includes 374328 (of 374433) 46~50mer oligonucleotides that hit both Typhimurium LT2 and Typhimurium 14028s, complemented with 10576 oligos that are specific for 14028s, 894 (of 900) oligos that are specific for Enteritidis PT4, and 100 duplicate spots. The probes were designed based on the Salmonella Typhimurium LT2 (NC_003197.1) and 14028s (CP001363.1: complete genome and CP001362.1: plasmid) genomes, with a moving window of about 12 bases. The PT4-specific probes were designed based on genome NC_011294. All probes (including control oligos) are represented in this file.

first: Steffen

last: Porwollik

first: Fred

last: Long

manufacture_protocol: in situ oligonucleotide


title: Illumina Genome Analyzer IIx (Saccharum officinarum)

status: Public on Jan 17 2012

organism: Saccharum officinarum


title: Illumina Genome Analyzer IIx (Neurospora crassa OR74A)

organism: Neurospora crassa OR74A


title: NanoString nCounter Human miRNA assay

city: Baltimore

first: Kenneth

middle: W

last: Witwer

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

description: hybridization array with capture probes and fluorescently barcoded detection probes

manufacture_protocol: see manufacturer's website: http://www.nanostring.com/


title: Applied Biosystems Human Taqman MicroRNA Array v3.0 (256)

description: qRT-PCR TaqMan Low-Density Array

manufacture_protocol: see manufacturer's website: http://www.appliedbiosystems.com/


title: Illumina HiSeq 2000 (Cyprinus carpio)

organism: Cyprinus carpio


title: Illumina HiSeq 2000 (Neurospora crassa OR74A)


title: Agilent Agrobacterium sp. 31749 5K custom array

status: Public on Jan 15 2012

city: Albuquerque

first: Anne

middle: M

last: Ruffing

state: NM

department: Bioenergy and Defense Technologies

institute: Sandia National Laboratories

organism: Agrobacterium sp. 31749

manufacture_protocol: see manufacturer's website


title: Agilent_038059 Plasmodium berghei_Mar2011_transcriptome

status: Public on Jan 16 2012

city: New York

first: Bjorn

middle: FC

last: Kafsack

state: NY

address: 1300 York Avenue

department: Microbiology & Immunology

institute: Weill Cornell Medicine

organism: Plasmodium berghei

description:
Arrays of this design have barcodes that begin with 16038059 or 2538059.

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.

The PlasmoDB_IDs are accession numbers for both GeneDB.org and the main community resource PlasmoDB.org


title: febit Candida albicans

status: Public on Jan 18 2012

city: PERUGIA

first: LUIGINA

last: ROMANI

address: VIA DEL GIOCHETTO

department: Department of Experimental Medicine and Biochemical Sciences

country: Italy

institute: University of Perugia

organism: Candida albicans

first: Andreas

last: Keller

manufacture_protocol: Each array on the biochip comprises 15.000 probes. These probes are 50mers and were  calculated using febit’s software package. For each gene two probes were computed. The  probe calculation relies on public available information of the Broad institute.  The intensities of blank probes which consist only of one single ”T” nucleotide are used  for background corrections. In order to have a grip on the hybridization process as well  as positioning features, additional hybridization controls are added to the array template.  Blank, labeling control and hybridization control probes are not included in the data analysis.


title: Illumina Genome Analyzer IIx (Candida albicans)


title: Agilent Custom 4 x 44K Array for Lachancea waltii

first: Sara

middle: Chloe

last: Di Rienzi

address: 1 Baylor Plaza Room 743E

department: Molecular Virology and Microbiology

institute: Baylor College of Medicine

organism: Lachancea waltii

description: Agilent Custom Oligo Microarray 4 x 44K G4497A

first: Kimberly

last: Lindstrom

first: Tobias

last: Mann

first: William

middle: S

last: Noble

last: Raghuraman

first: Bonita

last: Brewer

manufacture_protocol: Standard Agilent protocols for Agilent Custom Oligo Microarray 4 x 44K.  "SurePrint inkjet technology" prints oligo probes directly onto the slide.


title: Agilent 020458 GRL_Staphylococcus_epidermidis

status: Public on Jan 12 2012

city: Geneva

first: FRANCOIS

last: Patrice

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

institute: Genomic Research Laboratory

organism: Staphylococcus epidermidis

first: Patrice

last: Francois

first: Adrien

last: Fischer

first: Antoine

last: Huyghe

first: Jacques

last: Schrenzel

manufacture_protocol: SurePrint Technology (in situ synthesis)


title: Phytoplasma asteris OY-M DNA array

city: Bunkyo

first: Kenro

last: Oshima

state: Tokyo

institute: The University of Tokyo

organism: Candidatus Phytoplasma asteris

description: OY-M strain

manufacture_protocol:
1.About 300 bp of DNA are amplified for each gene from OY-M phytoplasma genome, purified, and resuspended to 0.1 ug/ul dH2O. The 5'-end of primer used with amplification is labeled with amino residue.
2. Add equal volume of the spotting buffer to the cDNA solution.
3. Spot to TaKaRa-Hubble Slide Glass.
4. After the print run is completed, process the fixation protocol of the glass.


title: Agilent custom Helicobacter pylori AMADID 029597

city: St Lucia

first: Jason

last: Steen

address: Carmody Road

department: IMB

country: Australia

institute: University of Queensland

organism: Helicobacter pylori


title: Illumina Genome Analyzer IIx (Mycobacterium tuberculosis)

last: GEO

organism: Mycobacterium tuberculosis


title: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array [CDF: Brainarray Version 12.1.0, hgu133plus2hsentrezg]

city: Oslo

first: Anders

middle: Erik Astrup

last: Dahm

address: Kirkeveien 166

department: Hematology

country: Norway

institute: Oslo University Hospital

description: Dai 2005, the package hgu133plus2hsentrezgcdf.db, version 12.1.0

distribution: commercial

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

manufacture_protocol: see manufacturer's web site


title: SMD Print_1324 hoj

city: Stanford

first: David

last: Fiorentino

address: 900 Blake Wilbur Drive

department: Dermatology

institute: Stanford University

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


title: Agilent-025735 custom 415K mouse CGH (Probe Name version)

city: Houston

first: Alexei

last: Protopopov

address: 1901 East Rd

department: IACS

institute: UT MD Anderson Cancer Center

organism: Mus musculus

description:
Belfer Institute for Applied Cancer Sciences.
Custom 2x415K array for mouse array-CGH, X/Y chromosomes excluded.
Probe coordinates are based on genome build UCSC mm9.

*** The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL15058

first: John

last: Zhang

first: Lynda

last: Chin

relation: Alternative to: GPL15058 (Feature Number version)


title: NimbleGen_Ralstonia solanacearum GMI1000_72k array

city: Madison

first: Lavanya

last: Babujee

address: Department of Plant Pathology

institute: UW-Madison

organism: Ralstonia pseudosolanacearum GMI1000

description: NimbleGen design name Ralstonia solanacearum GMI1000, NimbleGen design ID 13605.  An expression design for 5061 genes from Ralstonia solanacearum strain GMI1000 with 2 to 6, 40-70 mer probes per gene, with two-fold technical redundancy.The arrays also contain probes for intergenic regions with no technical replicates. The design includes random GC and other control probes.


title: Nimblegen_Ralstonia solanacearum UW551_72k array

organism: Ralstonia solanacearum UW551

description: NimbleGen design name Ralstonia solanacearum UW551, NimbleGen design ID 13052.  An expression design for 4318 genes from Ralstonia solanacearum strain UW551 with 2 to 6, 40-70 mer probes per gene, with two-fold technical redundancy.The arrays also contain probes for intergenic regions with no technical replicates. The design includes random GC and other control probes.


title: Nimblegen Human CGH 3x720K Whole-Genome Exon-Focused Array [100718_HG18_CGH_CCDS]

city: Little Rock

middle: Eli

last: Farrar

state: AR

address: 1 Children's Way, #512-10

department: Pediatrics/Hematology-Oncology

institute: University of Arkansas for Medical Sciences

organism: Homo sapiens

description:
Design_name: 100718_HG18_CGH_CCDS
Design_ID: 535163

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


title: NimbleGen S.cerevisiae CGH HX12 Array [090615_Scer_OA_CGH]

city: Cold Spring Harbor

first: Simon

middle: Robert Vincent

last: Knott

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

organism: Saccharomyces cerevisiae

description:
S. cerevisiae (release r.64).  r64 dated Feb-3-2011 at SGD, dated April 2011 at NCBI.
12plex Array
designname=090615_Scer_OA_CGH
designid=10131


title: CombiMatrix Yeast Custom Array 4x2K

status: Public on Jan 13 2012

city: Suwon-si

first: ga

middle: hee

last: shin

address: Gosaek-dong

country: South Korea

institute: Insilicogen

manufacture_protocol: CombiMatrix


title: SMD Print_1643 Run:moi

status: Public on Jan 11 2012

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)


title: SMD Print_1370 cpbl


title: SMD Print_1188 lc-54


title: Agilent-033357 Custom Phaeodactylum tricornutum Array [Phaeo_CSIRO_1]

city: Bangor

first: Sharon

middle: E.

last: Hook

state: NSW

address: Private Mail Bag 7

department: Centre for Environmental Contaminants Research

institute: CSIRO

organism: Phaeodactylum tricornutum


title: SMD Print_1162 lc-51


title: Illumina HiSeq 2000 (Sterkiella histriomuscorum)

organism: Sterkiella histriomuscorum


title: NimbleGen Homo sapiens 2.1M hg18

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

manufacture_protocol: see  manufacturer's website


title: [Tgondiia520372] Affymetrix Toxoplasma gondii Custom GeneChip (CDF: Tgondiia520372minusI_IIIsnp)

city: St Louis

first: Michael

middle: Sean

last: Behnke

state: MO

address: 660 S. Euclid Ave

department: Molecular Microbiology

institute: Washington University School of Medicine

organism: Toxoplasma gondii

description: The cdf used is the Tgondiia520372.cdf with all probes containing a type-I or type-III SNP removed.

manufacture_protocol: Affymetrix photolithographic array - 169 format.


title: FishCyHV-3_15K_v1.0

status: Public on Jan 05 2012

city: Liege

first: Leonor

last: Palmeira

address: Bd Colonster 20

department: Faculty of Veterinary Medicine

institute: University of Liege

organism:
Cyprinus carpio
Cyprinid herpesvirus 3

description: The microarray was custom designed for Agilent 8x15K slides. It targets both CyHV-3 and common carp transcripts: one 60-mer probe was designed for each of the 152 CyHV-3 ORFs; one 60-mer probe was designed for each of the 10,822 common carp transcript clusters. The common carp transcript clusters were derived from GenBank mRNA transcripts and EST sequences of Cyprinus carpio. Probe design was performed by Agilent.

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


title: IPA/Center of Molecular Medicine Human_Mouse_Rat Ambion mirVana miRNA v2.0 array

city: Bochum

first: Daniel

middle: Gilbert

last: Weber

address: Bürkle-de-la-Camp Platz 1

department: Molekulare Medizin

country: Germany

institute: IPA

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: Based on miRBase Sequence Database version is 8.0.

manufacturer: Norwegican Microarray Consortium (www.microarray.no).

middle: G

first: Oleksandr

last: Bryk

first: Thomas

last: Brüning

first: Georg

last: Johnen

manufacture_protocol: Probes of the mirVana miRNA Probe Set v2.0 (Ambion) were spotted in triplicates using Pronto! Microarray spotting solution (Corning) on CMT UltraGAPS (Corning) microarray slides.


title: RPCI Human HB21K

status: Public on Jan 07 2012

city: Buffalo

first: Amanda

last: Perez

address: Elm and Carlton Streets

institute: Roswell Park Cancer Institute

manufacture_protocol:
Isolation of BAC plasmid DNA: BAC clone plasmid DNAs, used as templates for PCR representations are prepared using a Qiagen BioRobot 3000. Each clone is retrieved from archival copies of the RPCI-11 BAC Resource, maintained at RPCI. The clones are streaked to single colony, grown overnight (16-18 hours) as 1.0ml pre-cultures in 96 deep-well plates at 37 C in a New Brunswick environmental shaker, and then re-inoculated as 2ml prep-cultures in 48 deep-well plates. After incubation, the cultures are RNase treated and prepped in the BioRobot 3000 using R.E.A.L. Prep 96 BioRobot kits (Qiagen). The BAC DNAs are resuspended in TE and serve as templates for restriction digestion and PCR amplification. We have found that Qiagen prepared DNA is of high quality and outperforms phenol:chloroform extraction methods for the highly sensitive restriction digestion and ligation steps.
Ligation of adapters: The adapters are ligated to the digested DNA by first annealing Mse-21 and Mse-12 primers. 1 ul of each digest (1 ng/ul), is added to 0.5 ul of 100 uM Mse-12 (TAACTAGCATGC), 0.5 ul of 100 uM Mse-21 (5’ aminolinker AGTGGGATTCCGCATGCTAGT) in a final volume of 7.5 ul using a thermalcycler (MJ Research). The mixture is incubated at 65 C for 1 min followed by ramping the temperature down to 15 C with a ramp-speed of 1.3 C per minute. When the temperature reaches 15 C, ligation proceeds with 1 ul of 10 mM ATP, 0.5 ul One-Phor-All-Buffer-Plus (10x) and 1 ul T4-DNA ligase (5 U/ul, Invitrogen) added to each tube and incubated at 15 C overnight.
PCR amplification: Two rounds of amplification are required to produce enough product for array generation as described in Cowell, J. K. and N. J. Nowak. 2003. High-resolution analysis of genetic events in cancer cells using bacterial artificial chromosome arrays and comparative genome hybridization. Adv Cancer Res 90:91-125. A single BAC PCR-representation produces enough printing solution for over 4,000 arrays. Preparation of DNA spotting solutions: PCR products (100 ul) are purified for printing by a series of ethanol precipitation steps, followed by resuspension of the pellets in 20 ul of 25% DMSO in H2O (final DNA concentration ~0.8 ug/ul) using a Qfill2 (Genetix). The DNA solutions are rearrayed into Genetix 384-well V-bottom plates using a Hydra 96-PP liquid handling system, and stored at 4 C until printing. We determined that DNA prepared using LM-PCR performed superiorly over other methods, including degenerate oligonucleotide primer PCR, inter Alu PCR and amplification of BAC subclones mixtures. 25% DMSO has several properties that make it an ideal solution for resuspending the amplicons. First, it acts as a denaturant, rendering the printing solution single-stranded for optimal slide binding and subsequent hybridization. Secondly, DMSO does not evaporate, so the printing solution volume is not affected by exposure to the environment during multiple print runs.
Array printing: Slides are printed using a MicroGrid ll TAS arrayer (Genomic Solutions) using 10K Microspot pins at 48% relative humidity, 22?C. We have a climate controlled, HEPA filtered room to minimize environmental changes that can affect printing. In addition, the arrayer is supplied with HEPA filtered air to further maintain a dust-free environment. We print each BAC clone in triplicate to create an array of on amino-silanated glass slides (Schott Nexterion, Type A+). The printed slides dry overnight, and are UV-crosslinked (350 mJ) in a Stratalinker 2400 (Stratagene). The slides are visually inspected and stored in a dessicated environment and are hybridized without additional treatment. Attempts at post-print processing or inclusion of pre-hybridization steps resulted in background issues that made the images difficult to analyze. We found no indication of DNA loss from the spots at any stage of the procedure when we performed hybridization in formamide buffers at 37°C (via DAPI staining).


title: SABiosciences Human Dermal Fibroblastsl PCR assay panel [PAHS-013]

status: Public on Jan 01 2012

city: Kumamoto

first: Taiji

last: Naashima

address: 1-1-1 Honjo

department: Department of Dermatology and Plastic Surgery

institute: Faculty of Life Sciences, Kumamoto University

description:
PCR assay
catalog number : PAHS-013


title: Antigen Discovery Vaccinia virus (strain WR) proteome microarray [batch VC11]

status: Public on Jan 09 2012

city: Irvine

first: David

middle: Huw

last: Davies

address: Med Surge II

department: Medicine

institute: University of California Irvine

organism: Vaccinia virus WR

description:
VC11 custom-commercial vaccinia (strain WR) proteome microarrays produced at Antigen Discovery Inc, Irvine CA.
The arrays are produced by in vitro transcription/translation (IVTT) reactions using plasmids encoding individual vaccinia ORFs as templates, and reactions printed onto nitrocellulose-coated slides.
Multiple spots consisting of reactions lacking plasmid templates ('no DNA' controls) are present on each array and used for data normalization.
The construction and QC of the arrays used in this study (batch VC11) has been described previoulsy (Hermanson et al 2011).


title: National Institute of Fruit Tree Science/Fruit Genome Research Team -Pyrus pyrifolia-ver024595

status: Public on Jan 10 2012

city: Tsukuba

first: Chikako

last: Nishitani

state: Ibaraki

institute: National Institutes of Fruit Tree Science

organism: Pyrus pyrifolia

description: Agilent design ID: 024595


title: SABiosciences Human Cell Development & Differentiation miRNA PCR ArrayHuman panel [MIHS-103Z]

description:
catalog number : MIHS-103Z
PCR assay


title: TaqMan® Rodent miRNA Card B v2.0

city: Palo Alto

middle: A

last: Rando

address: 3801 miranda ave.

department: Department of Neurology and Neurological Sciences

institute: Stanford University School of Medicine

organism:
Mus musculus
Rattus norvegicus

description: B Card Content: MicroRNAs less extensively studied (these tend to have less defined functions, be narrowly expressed, and/or be expressed at a low level).

first: Tom

last: Cheung


title: Illumina HiSeq 2000 (Fragaria x ananassa)

status: Public on Jan 03 2012

last: GEO

organism: Fragaria x ananassa


title: NimbleGen Human Expression Array [2006-10-26_Human_60mer_1in2]

status: Public on Jan 04 2012

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description:
Design name: 2006-10-26_Human_60mer_1in2
Designid: 4806

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


title: Agilent-025731 Ustilago_v1

city: Erlangen

first: Lars

middle: Matthias

last: Voll

address: Staudtstrasse 5

department: Division of Biochemistry

organism: Mycosarcoma maydis

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


title: Illumina Genome Analyzer IIx (Chlamydomonas reinhardtii)

organism: Chlamydomonas reinhardtii


title: TaqMan® Rodent miRNA card A v2.0

description: A Card Content: MicroRNAs of demonstrated interest to the research community (these tend to be functionally defined, broadly expressed and/or highly expressed).


title: NimbleGen Mus musculus MM9 Expression Array (12x135k) - no human/M.avium cross-hybridization [100216_MM9_JT_EXP_HX12]

description:
NimbleGen mouse MM9 Expression Array (12x135k); no human/M.avium cross-hybridization.
Design name: 100216_MM9_JT_EXP_HX12.
This is a mouse whole-genome 12-plex expression microarray design by NimbleGen designed from the MM9 genome.  Candidate probe sequences were verified to have no cross-hybridization to human (HG19) or Mycobacterium avium (NC_008595) targets.


title: NimbleGen_Human_2006-07-17_HG18Tiling_Set24

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

description:
genome build : hg18

native array description file : 2006-07-17_HG18Tiling_Set24.ndf
native array description file : 2006-07-17_HG18Tiling_Set24.pos


title: Illumina_BCM_HumanSNP-384 v1 BeadChip

city: houston

first: Ariel

last: Brautbar

address: 1 baylor plaza

institute: Baylor College of Medicine

technology: oligonucleotide beads

manufacture_protocol: See manufacturer's website, GoldenGate custom oligonucleotide beadarray


title: SMD Print_1561 (hoag)

status: Public on Jan 06 2012

city: Zurich

first: Michal

last: Rajski

address: Winterthurerstrasse 190

department: Institute of Physiology

institute: University of Zurich


title: NimbleGen Hox plus regions strand array [110215_PM_MM9_regions; design id: 548631]

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh, The Institute of Genetics and Cancer

description:
mm9; design id: 548631
native array description file: 110215_PM_MM9_regions.ndf
native array description file: 110215_PM_MM9_regions.pos


title: Human CGH 3x720K Whole-Genome Tiling v3.0 Array

city: Nijmegen

first: Roland

middle: P.

last: Kuiper

address: Geert Grooteplein 10

department: Human Genetics

institute: Radboud University Nijmegen Medical Centre

description:
Annotation in this record based on NCBI homo sapiens build 36.
Whole genome targeted array
090210_HG18_WG_CGH_v3.1_HX3.ndf
090210_HG18_WG_CGH_v3.1_HX3.pos
090210_HG18_WG_CGH_v3.1_HX3.ncd
090210_HG18_WG_CGH_v3.1_HX3.gff
090210_HG18_WG_CGH_v3.1_HX3_probe_locations.gff
HG18_WG_CGH_HX3_processed_columns_description.txt


title: Illumina Genome Analyzer IIx (Glycine max)

organism: Glycine max


title: Agilent-015757 Listeria monocytogenes array

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

organism: Listeria monocytogenes

manufacture_protocol: Agilent 60mer


title: NIAID Cnda -- Agilent Cryptococcus neoformans var. grubii H99 44K Oligo Microarray

first: Timothy

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

organism:
Homo sapiens
Mus musculus
Cryptococcus neoformans H99

description:
Cryptococcus neoformans var grubii H99 transcript sequences were downloaded from the BROAD Institute website for this custom array. Hybridization probe sequences(60-mer) were selected using e-Array software (Agilent): two for each of the 6,969 transcripts, one of them strongly 3-prime biased (best probe methodology) the other less so (best distribution methodology). The 13,938 unique probes were arrayed in 3 replicate, randomized, locations on the Agilent Sure-Print microarray slide, 4x44K format. Additional control probes were included as well.
Agilent designID: 025949


title: Agilent-019785 Custom Zebra Finch Microarray

city: Los Angeles

first: Austin

middle: T

last: Hilliard

state: CA

address: 610 Charles E Young Dr East

institute: UCLA

organism: Taeniopygia guttata


title: NimbleGen Matzkin Drosophila mojavensis 70K array v2.0.

city: Huntsville

first: Luciano

middle: Matias

last: Matzkin

state: Alabama

address: 301 Sparkman Drive

department: Biological Sciences

institute: University of Alabama in Huntsville

organism: Drosophila mojavensis

middle: M


title: Agilent custom 415K mouse CGH [design id 025735]

status: Public on Dec 29 2011

city: Houston

first: Alexei

last: Protopopov

address: 1901 East Rd

department: IACS

institute: UT MD Anderson Cancer Center

organism: Mus musculus

description:
Belfer Institute for Applied Cancer Sciences.
Custom 2x415K array for mouse array-CGH, X/Y chromosomes excluded.
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.
Probe coordinates are based on genome build UCSC mm9.
The ID column represents the Agilent Feature Extraction feature number.

first: John

last: Zhang

first: Lynda

last: Chin

relation: Alternative to: GPL15117 (Probe Name version)


title: NanoString nCounter miRNA expression platform (Validation 2)

status: Public on Jun 15 2011

city: Seattle

first: Muneesh

last: Tewari

address: 1100 Fairview Ave, N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

organism: Homo sapiens

technology: other

manufacture_protocol: See manufacturer's website


title: MM9 DNAMeth_HX1

status: Public on Jun 21 2011

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

description:
mm9
native array description file: 080430_MM9_Roloff_DNAMeth_HX1.ngd
native array description file: 080430_MM9_Roloff_DNAMeth_HX1.pos


title: NanoString nCounter miRNA expression platform (validation 1)


title: NanoString nCounter miRNA expression platform


title: OvineSNP50 BeadChip

city: Ames

first: Dorian

last: Garrick

state: IA

address: 2255 Kildee

institute: Iowa State University

organism: Ovis aries


title: Allergochip for asthma diagnosis

city: Perugia

first: tania

last: dottorini

address: via del Giochetto

department: Dept. Exp.Medicine and Bichem. Sci.

institute: University of Perugia

organism: Dermatophagoides pteronyssinus

manufacture_protocol:
The array contained 103 allergens printed in duplicate onto aldehyde-activated glass microscope slides (CEL Associates) using high-speed robotics (Microgrid Compact; Biorobotics). Arrays were printed at 23°C/60°C humidity and stored overnight inside the printing cabinet. Allergens (provided from Allergopharma) were initially reconstituted in PBS pH7.4 (reconstitution buffer) with a final concentration ranging form 0.4 to 40 mg/ml and after that spotted onto the arrays in the following spotting buffer PBS pH7.4, glycine pH2.4, Borate pH9.4, glycerol 10%, DTT 5mM, SDS (0.2%; 0.05%), Tween 20 (0.01%). Allergens spotting concentration ranged from 0.008 to 3 mg/ml.
Goat anti-human IgE  was spotted on 4 spots for positive control. Spotting buffer was printed on 46 spots with the aim of negative control. Internal calibration curve included 7 spots (duplicate).  103 spot data (duplicate) were printed on the array. Therefore, a total of 270 spot were included in the array.
A detailed description of the sample (allergens, stock and spotting concentration, spotting buffer) is provided upon request.


title: Dunham lab Human 16p Array H300A

status: Public on Nov 02 2010

city: Oxford

first: Richard

middle: J

last: Gibbons

state: Oxon

address: John Radcliffe Hospital,

department: MRC Molecular Haematology Unit

institute: Weatherall Institute of Molecular Medicine

manufacture_protocol: 1kb PCR products spotted on to glass slides.


title: SMD Print_1648 (Mycobacterium tuberculosis)

status: Public on Jul 09 2010

city: Ithaca

first: David

last: Russell

address: C5 171 Veterinary Medical Center

department: College of Veterinary Medicine

institute: Cornell University

organism: Mycobacterium tuberculosis


title: EXIQON miRCURY™ V8.1 LNA array

status: Public on May 31 2011

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

institute: University of Stirling

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

description:
annotated to mirbase 13
Spotted locked nucleic acid (LNA)


title: Agilent-016436 Human miRNA Microarray (Probe Name version)

status: Public on Sep 30 2009

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description: Agilent Human miRNA Microarray 8x15K (G4470A). Each microarray contains approximately 15,000 oligonucleotide probes specific for the Human miRNAs in Sanger miRBASE.

relation: Alternative to: GPL6955 (Feature Number version)


title: Taqman Homo sapiens microRNA Low density arrays (TLDA) panel A

status: Public on Mar 20 2010

city: Pittsburgh

first: Monica

last: Panelli

state: PA

address: 5117 Centre Ave

department: Hematology-Oncology

institute: Hillman Cancer Center, University of Pittsburgh

manufacture_protocol: Taqman ® microRNA Low density arrays (TLDA). The ABI Taqman® microRNA Low density arrays (TLDA, Applied Biosystems, Foster City, CA, www.appliedbiosystems.com) were selected as the platform for microRNA melanoma profiling. This platform consists of 2 arrays: TLDA panel A (377 functionally defined microRNAs) and TLDA panel B (289 microRNAs whose function is not yet completely defined) for a total of 666 microRNA assays. Each array/panel includes, among other endogenous controls, the mammalian U6 assay that is repeated four times on each card as a positive control as well as an assay unrelated to mammalian species, ath-miR159a, as negative control


title: Scophthalmus maximus 14K [DesignID: 016528]

status: Public on Aug 04 2009

city: Lugo

first: Adrian

middle: Millan

last: Perez

state: Lugo

department: Acuigen

country: Spain

institute: Universidad Santiago Compostela

organism: Scophthalmus maximus

description: DesignID: 016528

manufacturer: Facultad Veterinaria, Campus Universitario Pabellon IV 2 superior, Universidad Santiago Compostela

manufacture_protocol: An EST database from immune tissues was used to design the first high density turbot (Scophthalmus maximus) oligo-microarray with the aim of identifying candidate genes for tolerance to pathogens. Specific oligonucleotides (60mers) were successfully designed for 2716 out of 3482 unique sequences of the database.


title: UIUC/WMKCCFG Honeybee Sensory/CYP450 0.7K v1.0

status: Public on Aug 10 2007

city: Urbana

first: Hugh

last: Robertson

state: IL

address: 505 S. Goodwin Ave.

department: Entomology

country: USA

organism: Apis mellifera

description: Corning GAPS II

manufacturer: W.M. Keck Center for Comparative and Functional Genomics at University of Illinois at Urbana-Champaign

first: Kimberly

middle: K

last: Walden

first: Kevin

middle: W

last: Wanner

first: Mark

middle: R

last: Band

first: Al

middle: L

last: Bari

manufacture_protocol: Oligonucleotides (70-mer sense-strand) were designed using ArrayOligoSelector3.5 software (43, http://sourceforge.net) using default settings and the Apis mellifera genome (Assemby 2) for the following conceptual cDNA categories: 168 odorant receptors; 49 cytochrome p450s; 19 odorant binding proteins; 17 tetraspanins; 10 gustatory receptors; 10 carboxyl esterases; 7 glutathione S transferases; 6 chemosensory proteins (sensory appendage proteins); 5 lipocalins; 5 visual and non-visual opsins; 4 alpha-arrestins; 4 arrestins; 3 G-protein alpha subunits; 1 Pinocchio ortholog (a Drosophila melanogaster sensory-related protein); 1 sensory neuron membrane protein, and 4 housekeeping genes (cytoplasmic actin, EF1alpha, ribosomal protein 49, ribosomal protein S3), for a total of 313 genes. Oligonucleotides were synthesized by IDT (Coralville, IA) and 2.5 nmoles of each were aliquoted into a single 384-well plate and lyophilized.  Further preparation and microarray printing was performed by the Functional Genomics Unit at the U.I.U.C. W.M. Keck Center.  Oligonucleotides were suspended in 150 mM sodium phosphate to 25 uM and printed in neighboring duplicate spots on Corning GAPSII glass slides using a GeneMachines OmniGrid 100 microarray printer.  At least two housekeeping genes were spotted in each block of the 16-block array.  ArrayControl sense 70-mer oligonucleotides (Ambion) were diluted to 25 uM in printing buffer and printed as negative control spots. One control oligo of the 8 available was printed per block such that each control oligo was present in two different blocks per microarray.


title: Agilent-020954 Clostridium difficile Expression 15.7k array

status: Public on Apr 01 2011

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

organism: Clostridioides difficile

description:
Agilent-020954 CD_Expression-01_1_Of_1

Arrays of this design have barcodes that begin with 16020954 or 2520954.

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: [MOUSEDIVm520650] Affymetrix Mouse Diversity Genotyping Array

status: Public on Feb 09 2011

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

Below table was obtained after merging the corresponding CN or SNP annot.csv files provided by Affymetrix:

MOUSEDIVm520650.cn.na32.annot.csv
#%create_date=2011-09-20 GMT-08:00 14:37:53
#%chip_type=MOUSEDIVm520650
#%genome-species=Mus musculus
#%genome-version=mm9
#%genome-version-ucsc=mm9
#%genome-version-ncbi=37
#%genome-version-create_date=2007-07-00
#%dbSNP_date=2010-09-23
#%dbSNP_version=132
#%netaffx-annotation-date=2011-06-22
#%netaffx-annotation-netaffx-build=32

MOUSEDIVm520650.na32.annot.csv
#%create_date=2011-10-24 GMT-08:00 16:10:34
#%chip_type=MOUSEDIVm520650
#%genome-species=Mus musculus
#%genome-version=mm9
#%genome-version-ucsc=mm9
#%genome-version-ncbi=37
#%genome-version-create_date=2007-07-00
#%dbSNP_date=2010-09-23
#%dbSNP_version=132
#%netaffx-annotation-date=2011-06-22
#%netaffx-annotation-netaffx-build=32

manufacture_protocol: see manufacturer's web site


title: Agilent-016436 Human miRNA Microarray 1.0 (Feature Number version)

status: Public on Jul 21 2008

first: Robert

last: Ach

address: 5301 Stevens Creek Boulevard

department: Agilent Laboratories

description: Agilent design ID 016436.  miRNA probes were designed using Sanger miRBase, release 9.1.

first: Hui

last: Wang

first: Bo

last: Curry

relation: Alternative to: GPL8617 (Probe Name version)


title: HG17_HELP_Promoter

status: Public on Apr 01 2008

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

institute: University of Miiami

description:
Custom DNA methylation microarray for the HELP assay, designed to cover 25,626 HpaII amplifiable fragments around promoter regions and imprinted regions of the human genome. Based on the May 2004 release of the human genome.
While the data probes are the same for both the 2005-07-20_HG17_HELP_Promoter array and the 2006-10-26_HG17_HELP_Promoter array, they differ in the number of random probes included.

middle: E

first: Ari

last: Melnick

first: John

last: Greally

manufacture_protocol: See Roche NimbleGen website