title: Custom TaqMan pPCR: 13 solute carrier transporters (SLCs)

status: Public on Jun 30 2013

city: Prague 10

first: Pavel

last: Soucek

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

organism: Homo sapiens

technology: RT-PCR

distribution: virtual

manufacture_protocol:
Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic
pre-designed TaqMan assays were used with protocol recommended by the producer (Life Technologies Corp., Carlsbad, CA, USA)
Assay IDs:
SLC28A1: Hs00984403_m1
SLC28A2: Hs00188407_m1
SLC28A3: Hs00910439_m1
SLC29A1: Hs01085706_m1
SLC29A2: Hs00155426_m1
SLC29A3: Hs00983219_m1
SLC22A1: Hs00427552_m1
SLC22A2: Hs01010723_m1
SLC22A3: Hs01009568_m1
SLC22A6: Hs00537914_m1
SLC22A7: Hs00198527_m1
SLC22A8: Hs01056647_m1
SLC22A11: Hs00945829_m1


title: Agilent-032660 LACGAR 032659

status: Public on Nov 03 2013

city: Madrid

first: Mónica

last: Aguado-Urda

address: Avda. Puerta de Hierro s/n

department: Animal Health

country: Spain

institute: Complutense University of Madrid

organism: Lactococcus garvieae

technology: in situ oligonucleotide

description:
Lactococcus garvieae 8831&2881 expression microarray
Arrays of this design have barcodes that begin with 16032660 or 2532660.
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.

distribution: custom-commercial

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


title: Customized CombiMatrix Eukaryotic 12K

city: Gwangju

first: Myunggi

last: Baik

address: 77 yongbong-ro buk-gu

country: South Korea

institute: chonnam university

organism: Bos taurus

technology: spotted oligonucleotide

description: A customized bovine Combimatrix microarray is an array of 35 to 40mer oligonucleotides based on bovine cDNA sequences covering 10,199 genes, and the oligonucleotide were spotted onto CombiMatrix Eukaryotic 12K platform.


title: Agilent-041573 Staph_V8

status: Public on Jun 27 2013

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

description:
lame Staph_V8

Arrays of this design have barcodes that begin with 16041573 or 2541573.

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.

Oligo sequences are proprietary and were not provided by submitter.  Probes with "_PH" designations are specific for un-annotated recently identified regions.

first: Patrice

last: François

first: Adrien

last: Fischer

first: Yann

last: Gizard

first: Antoine

last: Huyghe

first: Jacques

last: Schrenzel

manufacture_protocol: SurePrint Technology (in situ synthesis); see manufacturer's web site at http://www.agilent.com/


title: TaqMan Low-Density Array (TLDA) microfluidic cards

status: Public on Jun 29 2013

city: Barcelona

first: M. Carmen

last: López-Sabater

state: Barcelona

address: Av. Joan XXIII S/N

department: Food Science and Nutrition

institute: University of Barcelona

description: ABI Prism 7900HT sequence detection system

manufacture_protocol: see manufacturer's website


title: Agilent-024164 C. rangiferina array

status: Public on Nov 24 2013

city: Turku

first: Sini

last: Junttila

address: Tykistökatu 6 A

department: Centre for Biotechnology

country: Finland

institute: University of Turku

organism: Cladonia rangiferina

description:
Arrays of this design have barcodes that begin with 16024164 or 2524164.

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: Capitalbio 22K human genome array chip V1.0

city: Guangzhou

first: yang

last: yang

address: 58, Zhongshan Road II, Guangzhou

country: China

institute: Sun Yat-sen University

description: Description of each gene


title: Lawrence Livermore Microbial Census Array version 1

city: Livermore

first: Kevin

last: McLoughlin

state: CA

address: PO Box 808

department: Global Security

country: USA

institute: Lawrence Livermore National Laboratory

organism: synthetic construct

description:
Array design is described in Gardner S, Jaing CJ, McLoughlin KS, Slezak TR, 'A Microbial Detection Array (MDA) for Viral and Bacterial Detection', submitted to BMC Genomics, 2010.
091210_Census_CJ_EXP.ndf

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


title: Agilent-037484 suyunjin 037483 (Probe Name version)

city: Beijing

first: Fuping

last: Song

address: No 2 West Yuan-Ming-Yang Road

institute: Instititue of plant protection, CAAS

organism: Bacillus thuringiensis

description:
Arrays of this design have barcodes that begin with 16037484 or 2537484.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Illumina Genome Analyzer IIx (Bacteroides caccae ATCC 43185; Bacteroides ovatus ATCC 8483; Bacteroides thetaiotaomicron VPI-5482; Clostridium symbiosum; Collinsella aerofaciens ATCC 25986; Desulfovibrio piger GOR1; Escherichia coli str. K-12 substr. MG1655; Eubacterium rectale ATCC 33656; Marvinbryantia formatexigens DSM 14469)

status: Public on Jun 28 2013

last: GEO

organism:
[Clostridium] symbiosum
Bacteroides thetaiotaomicron VPI-5482
Bacteroides ovatus ATCC 8483
Bacteroides caccae ATCC 43185
Collinsella aerofaciens ATCC 25986
Marvinbryantia formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Agathobacter rectalis ATCC 33656
Desulfovibrio piger GOR1

technology: high-throughput sequencing


title: Agilent-032729 (Lactococcus lactis subsp. cremoris UC509.9, Lactococcus phage Tuc2009, Lactococcus phage c2)

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

organism:
Ceduovirus c2
Lactococcus phage Tuc2009
Lactococcus cremoris subsp. cremoris UC509.9

description:
uc509 gene array and tuc2009/c2 tiling array

Arrays of this design have barcodes that begin with 16032729 or 2532729.

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.

distribution: non-commercial


title: Illumina HiSeq 2000 (Oryza barthii)

status: Public on Jun 26 2013

organism: Oryza barthii


title: Illumina HiSeq 2000 (Clostridium acetobutylicum)

organism: Clostridium acetobutylicum


title: UCSF/Sil lab-Histoplasma capsulatum-G217Borfs3

status: Public on Aug 12 2013

city: San Francisco

first: Mark

last: Voorhies

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

organism: Histoplasma capsulatum

description: This is a revision of UCSF/Sil lab-Histoplasma capsulatum-G217Borfs2 (GEO accession GPL14901) adding 269 oligos and removing 425. All removed oligos correspond to spike-in controls in the original design. The new oligo IDs are prefixed with G217Borfs3 or G217Borfs4 and correspond to putative novel transcripts from two stages of analysis of whole genome tiling array data (published with a revised and expanded set of novel transcripts in BMC Microbiol. 11:216).  HistoBase-compatible genome coordinates for the targets of the new oligos are given in the Target column.  This platform differs from UCSF/Sil lab-Histoplasma capsulatum-G217Borfs4 (GPL17161) in the physical location of the spotted oligos, including a partial, redundant printing of a subset of oligos at the bottom of the array (the redundant spots are labeled as G217Borfs1.14*.Misprint).

first: Catherine

middle: K

last: Foo

first: Anita

last: Sil

manufacture_protocol: Spotted using DeRisi arrayer in Center for Advanced Technology, Genentech Hall, Mission Bay.  70-mer oligonucleotides representing each predicted gene are resuspended in 3XSSC and spotted on poly-lysine slides purchased from Erie Scientific.


title: Agilent-042118 MSU 7 - Rice

status: Public on Oct 17 2013

city: Singapore

first: Shu-Ye

last: Jiang

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory, National University of Singapore

organism: Oryza sativa

description:
MSU 7 - Rice - all.cDNA self BG

Arrays of this design have barcodes that begin with 16042118 or 2542118.

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: [atSNPtil_expr] Affymetrix Arabidopsis thaliana atsnptile1TAIR9

status: Public on Jun 21 2013

city: Wageningen

first: Wilco

last: Ligterink

address: Droevendaalsesteeg 1

department: Lab of Plant Physiology

institute: Wageningen University

organism: Arabidopsis thaliana

description:
The Platform is based on The Arabidopsis Information Resource (TAIR) genome release TAIR9.

The supplementary file 'GPL13961_atsnptile1TAIR9.txt' is a library file.

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


title: Illumina Genome Analyzer IIx (Leishmania donovani)

organism: Leishmania donovani


title: Illumina HiSeq 2000 (Oryza glaberrima)

organism: Oryza glaberrima


title: Febit Sus scrofa miRNA Custom Array 0.5K

status: Public on Jun 25 2013

city: Berlin

first: Soroush

last: Sharbati

address: Oertzenweg 19b

department: Institute of Veterinary Biochemistry

country: Germany

institute: Freie Universitaet Berlin

organism: Sus scrofa

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,R -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: University of Arizona Sus scrofa oligo array 20.4K array

manufacture_protocol: Information available at http://www.pigoligoarray.org


title: Agilent-021441 NCode Human Long Non-coding RNA microarray

status: Public on Aug 21 2013

city: Concord

first: Casey

middle: M

last: Wright

state: NSW

address: Gate 3, Hospital Road

country: Australia

institute: ADRI

organism: Homo sapiens

manufacture_protocol: This array targets 17,112 putative long noncoding RNAs and 22,074 coding RNA transcripts. 60-mer probes were designed using Agilent's probe design system and printed using Agilent SurePrint technology. Spots re 65μM in site.


title: miRXplore TM Microarray

city: Grenoble Cedex 09

first: Nadia

last: Cherradi

address: 17 Rue des Martyrs

department: iRTSV/CEA

country: France

institute: INSERM U1036

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

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


title: Illumina HiSeq 2000 (Brachypodium distachyon)

status: Public on Jun 24 2013

organism: Brachypodium distachyon


title: [HT_HG-U133A] Affymetrix HT Human Genome U133A Array [custom CDF: ENTREZ brainarray v. 16]

city: Cambridge

first: Marc

last: Mendillo

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
alternate CDF for GPL3921
The GeneChip HT Human Genome U133 Array Plate Set enables researchers to perform large-scale studies by analyzing whole-genome expression for up to 96 samples at a time. The set comprises a U133A and U133B plate, measuring expression levels for more than 33,000 well-characterized genes and UniGene clusters.

manufacture_protocol: see manufacturer's web site


title: Illumina HiSeq 2000 (Sitodiplosis mosellana)

status: Public on Jun 20 2013

organism: Sitodiplosis mosellana


title: NimbleGen Moraxella catarrhalis BBH18 4x72K custom design expression array [120126_Mcat_HB_exp]

city: Nijmegen

first: Hester

last: Bootsma

address: Kapittelweg 29

department: Pediatrics

institute: Radboud University Medical Centre

organism: Moraxella catarrhalis BBH18

description:
The Nimblegen array contained 8 probes per predicted CDS and 7,298 negative control probes with a similar length distribution and CG content as the experimental probes.

designname=120126_Mcat_HB_exp
designid=565341

native array description file: 120126_Mcat_HB_exp.ndf
native array description file: 120126_Mcat_HB_exp.ngd

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


title: Illumina MiSeq (Escherichia coli O157:H7)

organism: Escherichia coli O157:H7


title: AB SOLiD 4 System (Escherichia coli O157:H7)


title: Agilent-024142 Arthrobacter chlorophenolicus A6 (Probe Name version)

city: Lausanne

first: Silvia

middle: K.

last: Moreno-Forero

state: Vaud

address: Batiment Biophore, Unil Sorge

department: Department of Fundamental Microbiology

institute: University of Lausanne

organism: Pseudarthrobacter chlorophenolicus A6


title: NimbleGen HX3 array [091120_Candida19_CSU_ASU]

city: Rochester

first: Elena

last: Rustchenko

state: NY

address: 601 Elmwood Ave., Box 712

department: Biochemistry & Biophysics

institute: University of Rochester

organism: Candida albicans

description:
710,907 probes
Candida albicans genomic sequence from the assembly 19.
C. albicans sequence is available at Candida Genome Database http://www.candidagenome.org

manufacture_protocol: Tiling probes were in-situ synthersized 50-mers with an average probe spacing of 35 bp on each strand.  The design was tiled in an unbiased fashion across the entire genome.  Empty features on the array were filled with randomly generated probes that had G+C content and length comparable to the C. albicans probes.


title: Illumina Genome Analyzer IIx (Brachypodium distachyon)


title: NimbleGen E. coli K12 Mg1655 tiling array [ecoli_tiling_array]

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

institute: UNIST

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

description:
The high-density oligonucleotide tiling array with 371,034 oligonucleotide probes of 50-bp length that are spaced 25 bp apart across the E. coli genome

DESIGN_NAME: ecoli_tiling_array
DESIGN_ID: 1881

native array description file: ecoli_tiling_array.ndf
native array description file: ecoli_tiling_array.pos


title: Agilent Gene Expression Array for Debaryomyces hansenii 8x15K AMAMID=020612

first: Dawn

last: Thompson

address: 7 Cambridge Center

institute: Broad Institute

organism: Debaryomyces hansenii

description: Regev lab custom

manufacture_protocol: Standard Agilent protocols for Agilent 8x15K Oligo Microarrays


title: Illumina HiSeq 2000 (Mesorhizobium huakuii 7653R)

status: Public on Jun 19 2013

organism: Mesorhizobium huakuii 7653R


title: Illumina Genome Analyzer (Bacteria)

organism: Bacteria


title: Illumina HiSeq 2000 (Brucella melitensis)

organism: Brucella melitensis


title: Illumina Genome Analyzer IIx (Bacteria)


title: Lachancea kluyveri microarray

city: Lund

first: Anna

middle: Andersson

last: Rasmussen

address: Sölvegatan 23

department: Molecular Cellbiology

country: Sweden

institute: Lund University

organism: Lachancea kluyveri

description: Please note that, at the time the platform was designed, searchable accession numbers were not available for L. kluyveri. However, all oligos have exact matches in the Genolevures database (http://genolevures.org/), ie by blasting against it, and selecting Saccharomyces kluyveri as the organism (i.e.the former name of L. kluyveri) will give only one 100% hit, and thus tell exactly which gene matches each oligo.

manufacturer: The slides were produced at the Genome Technology Access Center, Washington University, St Louis. by Mark Johnston, Seth D Crosby, Chistopher S Sawyer and Paul Cliften.

manufacture_protocol: The oligonucleotides (20µM  in 3x Saline Sodium Citrate (SSC) buffer with 0.75M betaine) were printed in triplicate on epoxy coated glass slides (Corning) using a linear servo arrayer (P. Brown; Stanford University, made after the DeRisi model, http://derisilabs.ucsf.edu/). The printed slides were placed in at room temperature oven at 70% humidity for 12-14 hours.  After incubation, the slides were cross-linked using the UV Stratalinker 2400 (Stratagene) at 150 microjoules/cm2.  The processed slides were placed in a light-proof slide box and stored in a dessicant cabinet for future hybridization experiments.


title: NimbleGen Geobacter sulfurreducens KN400-v1.0

status: Public on Jun 18 2013

city: Amherst

first: Jessica

middle: Amber

last: Smith

address: 203 Morrill Science Center IVN

department: Microbiology

institute: UMASS Amherst

organism: Geobacter sulfurreducens KN400

description:
Custom 4x72k Gene Expression design for Geobacter sulfurreducens KN400 (accession number CP002031). 3328 CDS features were extracted from a GenBank file downloaded from NCBI on December 14th, 2011. 45-60mer probes were selected from the entire length of the sequences. 10 probes were selected for 3313 sequences. 15 sequences share all 10 probes with another sequence and are represented by exemplars. Probes were replicated 2 times on the array in containers BLOCK1-BLOCK2.  The remainder of the array was filled with randomly generated 45-60mer probes (GC=0.58, Tm=83, max. cycles=148).
120104_Gsulf_JW_expr.ndf
120104_Gsulf_JW_expr.ngd


title: Centro de Astrobiologia_Acidiphilium sp. PM shotgun genomic DNA microarray_17184 spots_v1.0

city: Torrejon de Ardoz

first: Patxi

last: San Martin-Uriz

state: Madrid

address: Ctra. de Ajalvir, km. 4

department: Centro de Astrobiologia

institute: Instituto Nacional de Tecnica Aeroespacial

organism: Acidiphilium sp. PM

technology: spotted DNA/cDNA

manufacturer: Centro de Astrobiologia (Instituto Nacional de Técnica Aeroespacial - Consejo Superior de Investigaciones Científicas)

manufacture_protocol:
1. Acidiphilium sp. PM was grown aerobically at 30ºC in medium described in  (San Martin-Uriz et al, 2013. Submitted).
2. A shotgun genomic DNA library of Acidiphilium sp. PM was constructed by digesting total DNA with Sau3AI. Fragments were separated by ultracentrifugation and those ranging from 2-6 kb, were ligated to BamHI-digested, Shrimp Alkaline Phosphatase-dephosporilated pBluescript II SK+ vector. Purified ligation products were then used to transform E. coli DH10B electrocompetent cells.
3. 8544 clones were picked, incubated overnight and lysed using alkaline lysis. After centrifugation, 2 µl of the plasmid-containing supernatant were used to PCR-amplify the inserts using the Expand Long Template PCR system (Roche). 84% of all PCR reactions were positive, with an average amplicon size of 2.2 kb.
4. PCR products were purified using 96-well plate DNA purification kits (TeleChem International, Inc., Sunnyvale, CA), then were spun-dried and resuspended in 1x MicroSpotting Solution Plus (Telechem International, Inc).
5. Purified PCR products were rearranged in 384-well plates with the aid of a liquid handling robot (epMotion 5075 Eppendorf, Hamburg, Germany). In this stage, controls were added. These include several Acidiphilium sp. PM genes involved in catabolism, replication, transcription and metal resistance. Several clones from a genomic library of Leishmania infantum were included as negative controls for the hybridization.
6. Finally, PCR products were printed in duplicate onto epoxy-coated slides (Telechem International, Inc.) at 21ºC and 37-44% relative humidity using a MicroGrid-TAS II Arrayer (Digilab, Inc., Holliston, MA).


title: miRCURY LNA microRNA Array, 6th generation - hsa, mmu & rno [miRBase 17.0]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: synthetic construct

description:
Exiqon miRCURY LNA microRNA array; 6th generation; batch 208402; lot 34002-28 - hsa, mmu & rno (miRBase 17.0 and miRPlus (mouse))

ArrayContents_DesignedFor=miRBase 16.0
ArrayContents_CurrentNameColumn=miRBase 17.0
ArrayContents_CurrentNameColumnCoverage=Homo sapiens and related vira:73.35%, Mus musculus and related vira:94.35%, Rattus norvegicus:99.85%

GAL file:
gal_208400,208401,208402,208420,208421,208422_lot34002-34002_hsa,mmu,rno-and-related-vira_from_mb170,miRPlus.gal

Some probes may target multiple miRNAs, in which case multiple miRNA names, accession numbers and sequences are listed separated by '/'

distribution: commercial

manufacture_protocol: See manufacturers website


title: Chromosome 3 Human BACPAC aCGH Array

city: Stockholm

first: Gustav

last: Nilsonne

state: None/Not Applicable

address: Retzius väg 8 A2:3

institute: Karolinska Institutet

organism: Homo sapiens

description: UCSC Genome Browser on Human Mar. 2006 Assembly

manufacturer: BACPAC Resources Center, Children’s Hospital Oakland, Oakland, USA (http://bacpac.chori.org/)

manufacture_protocol: A set of 174 BAC/PAC clones was selected according to several considerations: (i) DNA from all these clones was commercially available (2 × 96 deep well blocks) from BACPAC Resources Center, CHILDREN'S HOSPITAL OAKLAND, Oakland, USA; (ii) all clones were FISH mapped, at least partially sequenced and their localization was approved using UCSC database; (iii) all clones were chr3 specific and covered the whole chromosome with a resolution of ~1 Mb.


title: Plasmodium falciparum Reactive Antigens Array

city: Irvine

first: Elisabeth

last: Baum

address: Med Surge II

institute: University of California Irvine

organism: Plasmodium falciparum

technology: spotted peptide or protein

description: Catalog # 25-MA-0006

manufacture_protocol: The arrays features in vitro rapid translation/transcription (IVTT) reactions using plasmids encoding individual Plasmodium falciparum ORFs as templates, then 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.


title: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_Hs_ENST]

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

description: custom CDF: HuGene10stv1_Hs_ENST.cdf (version 13, defining probe sets for transcripts from Ensembl core database version 58)

relation: Alternative to: GPL6244 (alternative CDF [official])

manufacture_protocol: See manufacturer's web site


title: Agilent Gene Expression Array for Kluyveromyces polysporus 8x15K AMAMID=021533

organism: Vanderwaltozyma polyspora

description: Regev lab custom


title: AB SOLiD 4 System (Mycobacterium smegmatis)

last: GEO

organism: Mycolicibacterium smegmatis


title: 090209_P_tricornutum_Meth_HX1

status: Public on Jun 15 2013

city: Thuwal

first: Alaguraj

last: Veluchamy

address: Thuwal

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

organism: Phaeodactylum tricornutum

manufacture_protocol: see manufacturer's website


title: 2007-01-11_Raaij_TI216595

status: Public on Jun 17 2013

city: Wageningen

first: Xu

last: Cheng

address: Droevendaalsesteeg 1

institute: Wageningen University

organism: Pseudomonas [fluorescens] SBW25

description: NimbleGen design name 2007-01-11_Raaij_TI216595,  expression design was based on the updated genome sequence of Pseudomonas fluorescens SBW25, NC_012660.1 and associated plasmid pQBR0476 with nineteen 60-mer probe  per gene.  Each probe is replicated 3 times.  The design includes random GC and other control probes.


title: Illumina Genome Analyzer II (Puccinia striiformis f. sp. tritici 08/21)

status: Public on Jun 14 2013


title: Agilent-030294 Pices-miRNA-2

city: Woods Hole

first: Neelakanteswar

last: Aluru

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

organism: Danio rerio

description:
Arrays of this design have barcodes that begin with 16030294 or 2530294.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

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


title: Illumina Genome Analyzer II (Fragaria x ananassa)

organism: Fragaria x ananassa


title: AB 5500 Genetic Analyzer (synthetic construct)

status: Public on Jun 11 2013


title: Helicos HeliScope (Kluyveromyces lactis)

status: Public on Jun 12 2013

organism: Kluyveromyces lactis


title: Helicos HeliScope (Debaryomyces hansenii)

organism: Debaryomyces hansenii


title: Salmonella enterica subsp. enterica serovar Typhimurium Agilent-033768 SL1344-ORF

first: Robert

last: Kingsley

address: Hinxton

country: United Kingdom

institute: The wellcome Trust Sanger Institute

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

description:
Arrays of this design have barcodes that begin with 16033768 or 2533768.

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: LC_MRA-1003_miRRat_12.0_080901 (miRNA ID version)

status: Public on Jun 13 2013

city: Houston

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

organism: Rattus norvegicus

description: Rat miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 12.0

manufacture_protocol: Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://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 IIx (Ralstonia eutropha H16)

status: Public on Jun 07 2013

organism: Cupriavidus necator H16


title: UCSF Exiqon MirCury V9.2 array

status: Public on Jun 06 2013

city: San Francisco

first: Jeffrey

middle: A.

last: Bluestone

address: 513 Parnassus Ave

department: Diabetes Center

institute: UCSF

organism: Mus musculus

description: This array is the uncondensed version of GPL7724

manufacture_protocol: see manufacturers website


title: Bos taurus Species Specific Phosphorylation Array

status: Public on Jun 08 2013

city: Saskatoon

first: Erin

last: Scruten

state: Saskatchewan

address: 120 Veterinary Road

country: Canada

institute: VIDO-Intervac

organism: Bos taurus

manufacture_protocol:
Peptide derivatives (50 nmol) were dissolved in 25 μL of printing solution (70% DMSO, 25% 0.2 M sodium acetate pH 4.5, 5 % glycerol; by
vol.) and transferred into 384-well microtiterplates. Two droplets of 0.5 nL peptide solution were deposited per spot on aldehyde functionalized glass slides using the non-contact printer Nanoplotter of GESIM (Großerkmannsdorf, Germany) equipped with 8 piezoelectric NanoTips
(GESIM, Großerkmannsdorf, Germany). Printed peptide microarrays were kept at room temperature for 5 hours, washed with deionised water, quenched for 1 hour with 50% aqueous hydroxylamine, washed extensively with water followed by ethanol, and dried under a stream of nitrogen. Each block of 300 peptides was printed in triplicate on each slide. The final physical dimensions of the array were 19.5 X 19.5 mm with each peptide spot having a diameter of ~350 μm and peptide spots being 750 μm apart.


title: NimbleGen Moraxella catarrhalis BBH18 4x72K custom design GAF array (mapping)

city: Nijmegen

first: Hester

last: Bootsma

address: Kapittelweg 29

institute: Radboud University Medical Centre

organism: Moraxella catarrhalis BBH18

description:
The custom-designed Nimblegen 4x72K GAF microarray design was based on the AluI-restriction fragments of the M. catarrhalis BBH18 genome (de Vries et al., 2010 J Bacteriol 192: 3574-3583).
Nimblegen probes (50-72 nt) were designed on the 3’ and 5’ ends of all AluI fragments >70 nucleotides (nt) and in case of fragments >400 bp, spaced every ~ 200 bp on both strands. This allows mapping of the transposon insertion with a ~200 bp resolution. Of the 6,085 AluI fragments larger than 70 nt, probes could be designed for 6,003 fragments, resulting in a total of 20,078 experimental probes. In addition to three replicates of each experimental probe, the array contained 11,803 negative-control probes with a length distribution and G+C content similar to those of the experimental control probes.
Moraxella catarrhalis GAF.ndf
Moraxella catarrhalis GAF.pos


title: UCSF/Sil lab-Histoplasma capsulatum-G217Borfs4

first: Mark

last: Voorhies

address: 513 Parnassus, S472

institute: University of California

organism: Histoplasma capsulatum

description: This is a revision of UCSF/Sil lab-Histoplasma capsulatum-G217Borfs2 (GEO accession GPL14901) adding 269 oligos and removing 425. All removed oligos correspond to spike-in controls in the original design. The new oligo IDs are prefixed with G217Borfs3 or G217Borfs4 and correspond to putative novel transcripts from two stages of analysis of whole genome tiling array data (published with a revised and expanded set of novel transcripts in BMC Microbiol. 11:216).  HistoBase-compatible genome coordinates for the targets of the new oligos are given in the Target column.

first: Catherine

last: Foo

first: Anita

last: Sil

manufacture_protocol: Spotted using DeRisi arrayer in Center for Advanced Technology, Genentech Hall, Mission Bay.  70-mer oligonucleotides representing each predicted gene are resuspended in 3XSSC and spotted on poly-lysine slides purchased from Erie Scientific.


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

city: Duarte

first: Charles

last: Warden

address: 1500 East Duarte Rd

institute: City of Hope

organism: Homo sapiens

description:
Human Genome HG18
CpG Islands + RefSeq promoters

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


title: Affymetrix HT HG-U133+ PM Array Plate [CDF: HTHGU133PlusPM_Hs_ENTREZG_v15]

last: admin

relation: Alternative to: GPL13158 (Alternative CDF [official])

manufacture_protocol: see the Affymetrix website


title: Illumina HiSeq 2000 (Trichoplusia ni)

organism: Trichoplusia ni


title: 32K Mouse Genome Array

city: Xi'an

first: Min

last: Sun

address: No.1, Xinsi Road

institute: Tangdu Hospital

manufacture_protocol: as described in CapitalBio Corporation Manual


title: NimbleGen Brucella melitensis array [2006-07-27_TI224914_60mer]

city: Madison

first: Gary

last: Splitter

state: WI

address: 1656 Linden Drive

department: PBS

institute: UW-Madison

organism: Brucella melitensis

description:
The design (.ndf) file and description (.ngd) file are available as Supplementary files (at the foot of this record).
2006-07-27_TI224914_60mer.ndf
2006-07-27_TI224914_60mer.ngd
DESIGN_NAME: 2006-07-27_TI224914_60mer
DESIGN_ID: 4357

manufacture_protocol:
Microarray design and experimentation were made by NimbleGen System
B. melitensis chromosomes I (NC_003317) and II (NC_003318).  Each probe (60 mer) was replicated three times on chip.


title: NimbleGen Moraxella catarrhalis BBH18 4x72K custom design expression array (genes)

description:
The Nimblegen array contained 8 probes per predicted CDS and 7,298 negative control probes with a similar length distribution and CG content as the experimental probes.
Moraxella catarrhalis BBH18 expression.ndf
Moraxella catarrhalis BBH18 expression.ngd

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


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [HuEx-1_0-st-v2_na31_hg19]

status: Public on Jun 04 2013

city: Brussels

first: Miikka

last: Vikkula

address: 74(+5) Avenue Hippocrate

country: Belgium

institute: de Duve Institute, Université catholique de Louvain

description:
Annotation is based on human genome build hg19.
HuEx-1_0-st-v2_na31_hg19_2010-08-27

manufacture_protocol: See manufacturer's web site.


title: HiggsGibbons Human 1K HG18  v1.0

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: Histoplasma_capsulatum_G217B_ChIP_1

department: Microbiology and Immunology

description: 400K arrays comprised of 60mer oligos tiling the entire H. capsulatum genome at a frequency of one probe per 50 bp. Oligos were selected based on the objective function from PLoS biology 6:e38.

first: Sinem

last: Beyhan

first: Matias

last: Gutierrez

manufacture_protocol: see manufacturer's website.


title: NimbleGen Homo sapiens 2.1 M promoter

status: Public on Jun 16 2013

city: Berlin

first: David

last: Drews

address: Augustenburger Platz 1

institute: Charite


title: Illumina HiSeq 2000 (Shewanella piezotolerans WP3)

status: Public on Jun 10 2013

last: GEO

organism: Shewanella piezotolerans WP3


title: Illumina HiScanSQ (Melitaea cinxia)

organism: Melitaea cinxia


title: Nimblegen custom 12x135K chicken high-density multiplex microarray

status: Public on Jun 01 2013

city: East Geelong

first: Dragana

last: Stanley

state: Victoria

address: 5 Portarlington Rd

department: AAHL

institute: CSIRO

organism: Gallus gallus

description: A custom designed NimbleGen 12x135K chicken high-density multiplex microarray was used in this experiment. The microarray contained a set of 65,849 long oligonucleotides (60-75nt) based upon chicken UniGene sequence families. Each gene was represented by at least two independently designed probes and each probe was present in duplicate on the array. Each fabricated glass slide contained 12 identical arrays that could were independently hybridized.

manufacture_protocol: NimbleGen


title: Ion Torrent PGM (synthetic construct)

organism: synthetic construct


title: Illumina HiSeq 2000 (Pan paniscus)

organism: Pan paniscus


title: Illumina HiSeq 2000 (Cavia porcellus)

organism: Cavia porcellus


title: Illumina Genome Analyzer II (Monodelphis domestica)

organism: Monodelphis domestica


title: Illumina HiSeq 2000 (Listeria monocytogenes)

organism: Listeria monocytogenes


title: IQ-USP Gracilaria tenuistipitata 4.6K v1.0

city: São Paulo

first: Paulo

last: Zaini

state: São Paulo

address: Av. Prof. Lineu Prestes, 748 - Butantã

department: Bioquímica

country: Brazil

institute: Universidade de São Paulo

organism: Gracilaria tenuistipitata

manufacture_protocol: A 4,608-element DNA microarray was printed containing unique internal fragments of 1,448 CDS spotted at least in duplicate. DNA fragments ranging from 200 to 800 bp were PCR amplified from an EST library. PCR products in 50% DMSO were spotted with a Generation III Spotter (GE Healthcare, Little Chalfont, England) and kept in low humidity (<15%) until use.


title: Illumina HiSeq 2000 (Melitaea cinxia)


title: Illumina Genome Analyzer Iix (Homo sapiens)

status: Public on Jun 03 2013


title: LC Sciences Custom HessianFly, DrosophilaGenu and Mosquito miRNA array [KSU_100914]

status: Public on Jan 31 2013

first: Christoph

last: Eicken

description: Custom miRNA microarray targeting the mature miRNAs of HessianFly, DrosophilaGenu and Mosquito as determined by Next-Gen Sequencing

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 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: [miRChip1s520189F] Custom Affymetrix microRNA array

first: Andrei

last: Goga

department: Cell & Tissue Biology

organism:
Populus trichocarpa
Oryza sativa
Caenorhabditis elegans
Homo sapiens
Mus musculus
Rattus norvegicus
synthetic construct

description:
custom Affymetrix Genechip designed to miRNA probes derived from Sanger miRBase v9.2.
This array contained a total of 14215 probes, of which 672 matched to 301 unique mouse miRNAs.

manufacture_protocol: see manufacturer's web site


title: NimbleGen Human custom 135K

city: Aarhus

first: Morten

middle: Muhlig

last: Nielsen

address: Palle Juul-Jensens Bouleward 99

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

description:
Spotted 60 mer  probes, (135K 60mer probes)
Custom-commercial, Nimblegene HD2-12 platform
100917_HG18_JP_EXP.ndf

manufacture_protocol: see manufacturer's website at http://www.nimblegen.com/products/expression/custom/12x135k/index.html


title: Illumina HiSeq 2000 (Mycobacterium tuberculosis H37Rv)

organism: Mycobacterium tuberculosis H37Rv


title: Illumina Genome Analyzer II (Tetrahymena thermophila)

status: Public on Jun 05 2013

organism: Tetrahymena thermophila


title: Princeton uncultured crenarchaeote amoA gene BC014 array

city: Princeton

first: Xuefeng

last: Peng

state: NJ

address: Guyot Hall

department: Geosciences

institute: Princeton University

organism: uncultured crenarchaeote

description: Microarray targets the ammonia monooxygenase gene subunit A (amoA).

manufacture_protocol:
1.The probe oligonucleotides are printed onto Corning Ultragaps or Erie Scientific Epoxy Silane slides using a DeRisi style arrayer (DiRisi et al., 1997) and pins from Parallel Synthesis.
2.The 70-mer oligo probes (Operon Technologies) were adjusted to a concentration of 0.05 mg ml-1 in 50% DMSO and were spotted on CMT-GAPS amino silane-coated glass slides (Corning, Corning, NY).
3. After printing, the slides were baked at 80°C for 3 h and stored in the dark at room temperature under slight vacuum in a dessicator.


title: Illumina HiSeq 2000 (Eptesicus fuscus)

organism: Eptesicus fuscus


title: University of Iowa D4Z4 tiled oligonucleotide 9K microarray

city: Iowa City

first: Rolf

last: Turk

state: IA

address: 285 Newton Road, 4283CBRB

department: Molecular Physiology and Biophysics

institute: University of Iowa

organism: Homo sapiens

description: This platform consists of a tiled oligonucleotide microarray based on the GenBank D38024 sequence. This sequence corresponds with the D4Z4 repeat array, which is associated with FSHD. The location of the sequences are provided. The 60-mer oligos overlap 50%, resulting in a 30-nt resolution.

manufacturer: Oligos were manufactured by Sigma, Arrays were spotted by DNA Core University of Iowa

first: Kevin

middle: P

last: Campbell

manufacture_protocol: Oligonucleotides were spotted onto Corning UltraGAPS slides by Omnigrid 100 arrayer by the DNA Core of the University of Iowa according to their standard protocol. Oligonucleotides were designed by Rolf Turk.


title: Glasslab Neurospora crassa 10k V1

status: Public on Jul 21 2011

city: Berkeley

first: Jianping

address: 111 Koshland Hall

institute: UC Berkeley

organism: Neurospora crassa

manufacture_protocol:
Designed 70mer oligonucleotide immobilized probes using ArrayOligoSelector.
Oligomers were re-suspended in 3× SSC to a final concentration of 40 µM and spotted onto poly(L)-lysine-coated microscopic slides.

The ∼10,000 open reading frames (ORFs) were derived mainly from the Neurospora crassa databases at the Broad Institute (http://www.broadinstitute.org/annotation/genome/neurospora/MultiHome.html).


title: Affymetrix Human Exon 1.0 ST Array [CDF: HuEx_1_0_st_v2_core_na31_hg19_HB20110919_noSNPs]

first: Sergio

middle: E

last: Baranzini

address: 675 Nelson Rising Lane, Room S-215

department: Neurology

institute: University of California San Francisco

description:
Probe set data extracted from custom CDF [HuEx_1_0_st_v2_core_na31_hg19_HB20110919_noSNPs]

#%chip_type=HuEx-1_0-st-v2
#%lib_set_name=HuEx-1_0-st
#%lib_set_version=v2

#%genome-species=Homo sapiens
#%genome-version=hg19
#%genome-version-ucsc=hg19
#%genome-version-ncbi=GRCh37
#%genome-version-create_date=2009-02-00

#%netaffx-annotation-date=2010-07-15
#%netaffx-annotation-netaffx-build=31
#%netaffx-annotation-tabular-format-version=1.11
#%netaffx-annotation-data-type=probe_set

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

manufacture_protocol: See manufacturer's website.


title: CodeLink Mouse Whole Genome Bioarray (T00342)

first: Yulei

last: Shang

address: 513 Parnassus street

department: Pathology

institute: UCSF

organism: Mus musculus

description:
A total of 36,000 transcripts and ESTs representing 30,000 unique genes.
Total 300 spots for positive control and 320 spots for negative control.
spotted 30-mer oligonucleotide probe


title: Illumina HiSeq 2000 (Mus musculus domesticus x M. m. molossinus)

status: Public on Dec 05 2012


title: Helicos HeliScope (Saccharomyces cerevisiae)

organism: Saccharomyces cerevisiae


title: Agilent-017905 Oxford Gene Technology S. coelicolor whole genome 4x44K

city: Prague

first: Jiri

last: Vohradsky

address: Videnska 1083

country: Czech Republic

institute: Institute of Microbiology Czech Academy of Sciences

organism: Streptomyces coelicolor A3(2)

description: Arrays were 4x 44K feature design, which means they can have up to 44K probes per array and 4 separate arrays on each slide. This universal arrays have probes designed to each gene as well as probes tilled across the whole genom.

manufacture_protocol: see manufacturer's web site:  http://www.genomics.agilent.com/GenericB.aspx?PageType=Custom&SubPageType=Custom&PageID=2011


title: Agilent-020166 Ca21_GE_plus_tiling_2.0 (Feature Number version)

first: Aaron

last: Hernday

state: Ca

institute: UC San Francisco

organism: Candida albicans

description:
This is an expression array built off of the C. albicans genome assembly 21 orf list, with the alpha locus and additional tiling probes spanning the WOR1, WOR2, WOR3, CZF1 and EFG1 loci.  This is the same as AMADID 020128 with the exception of the additional tiling probes for mapping transcription start sites.

Arrays of this design have barcodes that begin with 16020166 or 2520166.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL16260.

relation: Alternative to: GPL16260 (Probe Name version)

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


title: Agilent-029949 Custom SurePrint G3 Human GE 8x60K Microarray [Probe Name version]

status: Public on Jun 27 2013

city: Odense C

first: Martin

middle: Jakob

last: Larsen

address: Sdr. Boulevard 29

department: Dept. of Clinical Genetics

institute: Odense University Hospital

description:
Custom SurePrint G3 Human GE 8x60K Microarray

Arrays of this design have barcodes that begin with 16029949 or 2529949.

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.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).


title: NimbleGen Moraxella catarrhalis BBH18 4x72K custom design

status: Public on May 07 2010

first: Hester

last: Bootsma

address: Kapittelweg 29

department: Pediatrics

institute: Radboud University Medical Centre

organism: Moraxella catarrhalis BBH18

description:
The Nimblegen array contained 1-118 probes per predicted CDS with an average coverage of 15 probes per CDS, probes on both strands within the CRISPR1 and CRISPR2 regions, and 1,103 negative control probes with a similar length distribution and CG content as the experimental probes.

Please note that the platform organism was updated on June 6, 2013 as per http://jb.asm.org/content/194/24/7021

first: Stefan

last: de Vries

first: Sacha

middle: A

last: van Hijum

first: Wolfgang

last: Schueler

first: Kristian

last: Riesbeck

first: John

last: Hays

first: Peter

middle: W

last: Hermans


title: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_Hs_ENTREZG_16.0.0]

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: Brainarray: HuGene10stv1_Hs_ENTREZG_16.0.0

relation: Alternative to: GPL6244 (Alternative CDF [official])

manufacture_protocol: See manufacturer's web site


title: Human 3.8k cDNA

status: Public on Jul 01 2005

first: Renato

middle: David

last: Puga

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

description:
Spotted cDNA Orestes clones and PCR amplified fragments on glass.
This set includes 664 orestes and 197 PCR amplified fragments based upon representative sequences in build 175 of the human UniGene database.
Keywords = spotted
Keywords = cDNA

first: Alex

last: Fiorini


title: Genotypic Candida albicans 15.7K

status: Public on Mar 15 2011

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

first: RAJA

middle: C

last: MUGASIMANGALAM

first: ROHIT

middle: N

last: SHUKLA

first: SHRUTI

last: SINHA

manufacture_protocol: see Agilent's website


title: Arabidopsis thaliana 43.7K Ath_Agilent_v2_Riechmann

status: Public on Jan 01 2011

city: Bellaterra

first: Jose Luis

last: Riechmann

state: Barcelona

address: Campus UAB - Edifici CRAG

country: Spain

institute: Center for Research in Agricultural Genomics

organism: Arabidopsis thaliana

first: Jose

middle: L

first: David

last: Mathog

first: Emilio

last: Centeno

manufacture_protocol: Custom-commercial array manufactured by Agilent (eArray) using its SurePrint technology (In Situ Synthesis Printing). http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/pages/gp557.aspx


title: Arabidopsis thaliana 32.7K Ath_Agilent_v1_Riechmann

status: Public on Apr 02 2010


title: Meyerowitz Lab Arabidopsis Operon Array Version 4

description: This microarray is based on the Arabidopsis Genome Oligo Set Version 1.0 and on the Arabidopsis Genome Oligo Set Version 1.0 Upgrade (Operon, Alameda, CA). These sets consist of a total of 30,194 oligonucleotides.

manufacturer: Meyerowitz laboratory at the California Institute of Technology

first: Frank

last: Wellmer

first: Elliot

last: Meyerowitz

manufacture_protocol: The oligonucleotides of the Arabidopsis Genome Oligo Set (Operon) were provided in 384-well plates. The dried DNA was resuspended in 15 ul of printing buffer (150 mM Na-phosphate pH 8.5) per well, resulting in an estimated DNA concentration of 40 uM. DNA was spotted onto poly-lysine coated glass slides with a MicroGrid II spotter (Biorobotics) using Microspot 10K quill pins (Biorobotics). After printing, the slides were processed and blocked following standard protocols.


title: Illumina Rat Ref-12 v1

city: Budapest

first: Viola

last: Tamasi

address: Nagyvarad sqr 4

department: Genetic, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

organism: Rattus norvegicus

technology: oligonucleotide beads

description: Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.

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


title: LC_MRA-1003_miRRat_12.0_080901

status: Public on May 19 2009

city: Houston

first: Christoph

last: Eicken

address: 2575 W. Bellfort

country: USA

institute: LC Sciences, LLC

description: Rat miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 12.0

relation: Alternative to: GPL17281 (miRNA ID version)

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: Rosenstiel Fundulus heteroclitus 7K array

status: Public on Apr 19 2011

city: Miami

first: Marjorie

middle: F.

last: Oleksiak

state: FL

address: 4600 Rickenbacker Causeway

department: Marine Biology and Fisheries

institute: University of Miami

organism: Fundulus heteroclitus

manufacturer: Rosenstiel School of Marine and Atmospheric Sciences, Crawford and Oleksiak Laboratories

manufacture_protocol: Amplified cDNA sequences for approximately 7,000 genes from Fundulus heteroclitus cDNA libraries were spotted onto epoxide slides (Corning) using an inkjet printer (Aj100, ArrayJet, Scotland).  Libraries were made from all 40 stages of F. heteroclitus development, immediately post-hatch whole larvae, and adult tissues.  Each slide contained four spatially separated arrays of ~7,000 spots (genes) including controls.  Average proble length was 1.5 Kb.  All spotted genes were sequenced and represent unique contigs.  Thus, even if multiple sequences were annotated identically, they were treated as different genes.  Multiple sequences with the same annotation do not contig together because: 1) they really are the same gene, but the sequences do not overlap, 2) they represent duplicate genes with different chromosomal locations, or 3) they share a high similarity (and hence are named based on this similarity) but are not the same gene.


title: Drosophila 200K high density 36mer oligo array

status: Public on Nov 04 2004

city: New Haven

first: Zareen

last: Gauhar

state: CT

address: 333 Cedar St, 386 NSB

department: Genetics

institute: Yale

organism: Drosophila melanogaster

description:
synthesized oligonucleotide array on glass.
This set includes 200,000 oligonucleotides, uniquely identified 36-mers.
Keywords = high density oligonucleotide

first: Christopher

last: Mason


title: Meyerowitz Lab Arabidopsis Operon Array Version 2

status: Public on Aug 24 2007

description: This microarray is based on the Arabidopsis Genome Oligo Set Version 1.0 (Operon, Alameda, CA). This set consists of 26,090 oligonucleotides that correspond to 22,361 annotated Arabidopsis genes (The Arabidopsis Information Resource (TAIR) genome annotation version 6).

first: Marcio

last: Alves-Ferreira

first: Vijaya

last: Kumar

middle: M


title: Illumina Genome Analyzer IIx (Bos taurus)

status: Public on Jun 27 2012

last: GEO

organism: Bos taurus


title: Arborea spruce 32K

status: Public on Dec 20 2011

city: Québec

first: John

last: MacKay

state: Québec

address: 1030, avenue de la Médecine, Pavillon C.-E. Marchand

department: Centre d'étude de la forêt

institute: Université Laval

organism:
Picea glauca
Picea sitchensis

manufacture_protocol: The sequences included in the microarray were selected on the basis of reproducible sequence quality form all of the ESTs and FL-cDNA described for P. glauca in Rigault et al. (2011) and P. sitchensis in Ralph et al. (2008) (Table 1A). To obtain a robust probe set, we selected sequences that were either detected in the two species, verified with two technologies (Sanger and 454) or were derived from a FL-cDNA (Table 1A). The probes were 70 nucleotides in length, and were designed to minimize similarity with other sequences in the dataset. Sequence similarity between the probes and known sequences in P. sitchensis and P. glauca was determined from sequence alignments. The microrray contains 25,045 probes that match with known P. glauca sequences; however, they represent 23,853 unique cDNA gene based on the most recent clustering (Rigault et al., 2011), such that 1007 genes are represented by more than one probe. The microarray consists of 33,984 spotted features including 33,024 sample spots (Invitrogen, Carlsbad, California), 240 negative buffer spots, and 480 Spot Report Alien Oligos (Agilent Technologies, Inc., Santa Clara, CA, USA). Oligonucleotides were consolidated into 384-well plates, lyophilized by speed-Vac, and resuspended in 3X SSC to a printing concentration of 30 µM. Oligos were printed on aminosilane slides (Erie, Hudson, NH, USA) with a QArrayMax microarray printer (Genetix Limited, Hampshire, UK) using 946MP2 microarray pins (ArrayIt Corp, Sunnyvale, CA, USA) in a 48-pin tool depositing ~0.5 nL per spot onto the slide. The resulting microarrays had a 4 x 12 subgrid layout with 708 spots per subgrid, each spot having approximate diameter and pitch of 90µm and 160 µm, respectively. A 280-bp GFP (green fluorescent protein) oligonucleotide was printed in subgrid corners to assist in grid alignment during image processing. The slides were crosslinked in a UV Stratalinker 2400 (Agilent Technologies, Inc.) at 300 mJ. Array quality was assessed by visual inspection and hybridization of representative slides from a print run by dye-labelled random 9-mer oligonucleotides. The quality control images were acquired via the GenePix 4200AL scanner (Molecular Devices, CA, USA) at a 10 micron resolution and quantified with the Imagene 8.0 software suite. Printing and quality control was performed by the Vancouver Prostate Centre Microarray Facility, Vancouver, Canada.


title: Agilent-021828 Unrestricted Mouse miRNA Microarray (V2) (miRNA_ID version)

status: Public on May 05 2011

city: Palo Alto

last: Agilent Technologies

state: CA

institute: Agilent Technologies

description:
Mouse miRNA Microarray 2.0

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 miRNA_ID. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL10384.


title: Agilent-014950 Human Genome CGH Microarray 4x44K (Probe Name version)

status: Public on Apr 18 2010

description:
Agilent-014950 Human Genome CGH Microarray 4x44K

*** 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 GPL5477.

manufacture_protocol: see manufacturer's web site (www.agilent.com)