title: 22K Human Genome Array

status: Public on Nov 30 2014

city: shanghai

first: juan

last: xu

address: 21F, 415 fengyang road

country: China

institute: endocrinology

organism: Homo sapiens

technology: spotted oligonucleotide

distribution: custom-commercial

manufacture_protocol: as described in CapitalBio Corporation Manual


title: Agilent-047718 Custom 8X60 Human array [Probe Name Version]

status: Public on May 27 2015

city: Singapore

first: Igor

middle: V

last: Kurochkin

address: 30 Biopolis street, #07-01 Matrix

country: Singapore

institute: Bioinformatics Institute, A*STAR

technology: in situ oligonucleotide

description:
Custom microarray was designed based on Agilent platform, format 8x60K (Design ID 047718).

The probes were designed against Gencode v15 database. Two probes targeted each of 22,001 lncRNA transcripts and 17,535 randomly selected protein coding targets.

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


title: Applied Biosystems Human TaqMan Low Density Array

status: Public on Jan 29 2015

city: Tampa

first: Jennifer

middle: Permuth

last: Wey

state: FL

address: 12902 Magnolia Dr

country: USA

institute: Moffitt Cancer Center

technology: RT-PCR

description: PCR assay

distribution: virtual

manufacture_protocol: see manufacturer's website


title: Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Agilent Systematic Name, collapsed probe, version)

status: Public on Mar 15 2015

city: Frederiksberg C

first: Niels

middle: Frank

last: Jensen

address: Dyrlaegevej 88, 1.

department: Faculty of Health and Medical Sciences

country: Denmark

institute: University of Copenhagen

description: Identical to GPL6480, multiple probe names have been converted to one systematic name.


title: Agilent-045089 Genotypic custom Jatropha 4x44k GE Array 045087

city: Nagoya

first: Joyce

last: Cartagena

address: Furo-cho, Chikusa-ku

country: Japan

institute: Nagoya University

organism: Jatropha curcas

description:
Arrays of this design have barcodes that begin with 16045089 or 2545089.
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: [HuGene-2_1-st] Affymetrix Human Gene 2.1 ST Array [brainarray refseq v18.0.0]

city: Milano

first: Giuseppe

last: Testa

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology & University of Milano, Italy

description: Same as GPL17692, except using the updated brainarray's updated chip definition file (refseq, version 18.0.0) found at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/18.0.0/refseq.asp

manufacture_protocol: See manufacturer's web site


title: TaqMan® Human Stem Cell Pluripotency Array (Applied Biosystems)

status: Public on Nov 29 2014

city: MADRID

first: María José

last: Pino-Barrio

state: MADRID

address: Avda Complutense, 40.

department: Hematopoietic Innovative Therapies Division.

country: Spain

institute: CIEMAT

description: The Applied Biosystems® TaqMan® Human Stem Cell Pluripotency Array is an efficient, easy-to-use micro fluidic card for the characterization of undifferentiated stem cells or their differentiated derivatives. This gene signature panel contains 90 well-defined genes validated as markers for pluripotency plus 6 endogenous controls.

distribution: commercial


title: Illumina Genome Analyzer IIx (Litchi chinensis)

status: Public on Nov 26 2014

last: GEO

organism: Litchi chinensis

technology: high-throughput sequencing


title: PIQOR (TM) Skin 2.0 Microarray, human, antisense (591)

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

country: Germany

institute: Miltenyi Biotec GmbH

technology: spotted DNA/cDNA

description: The PIQOR (TM) Skin 2.0 Microarray is composed of 1542 human specific cDNAs. These cDNAs include for each array four E. coli DNA fragments and the corresponding in vitro transcribed RNAs (spiking controls) provide a control for the labeling and hybridisation efficiency. Two negative controls are given by spotted herring sperm DNA and buffer, respectively. All features are spotted in quadruplicate. The Platform data table reflects a condensed representation of the quadruplicate features.

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio

manufacture_protocol: Defined 200-400 bp fragments of selected cDNAs were generated by RT-PCR, cloned and sequence-verified. Amplified and purified cDNA inserts were spotted in quadruplicate on PIQOR slides using a proprietary piezoelectric spotter. The PIQOR slides were coated in a 2 step process generating a surface which covalently binds DNA molecules.


title: Illumina MouseRef-8 v2.0 expression beadchip (ILMN_SYMBOL)

city: Nijmegen

first: Laurensia

last: Yuniati

address: Route 412 PO BOX  9101

department: Pediatric Oncology

country: Netherlands

institute: Radboud university medical center

organism: Mus musculus

technology: oligonucleotide beads

description:
The MouseRef-8 v2.0 Expression BeadChip offer the most up-to-date content for whole-genome expression profiling in the mouse. Featuring content derived from the National Center for Biotechnology Information Reference Sequence (NCBI RefSeq) database (Build 36, Release 22).

The official version of this platform is accession number GPL6885. This version includes ILMN_SYMBOL values in the ID column.


title: Tammar wallaby custom 13,440 spot cDNA array

status: Public on Nov 27 2014

city: Bundoora

first: Christy

last: Vander Jagt

state: Victoria

address: 5 Ring Road, LaTrobe University

department: Computational Biology

country: Australia

organism: Notamacropus eugenii

distribution: non-commercial

manufacturer: Department of Environment and Primary Industries (Victoria)

manufacture_protocol:
1. Approximately 100 pg cDNA per spot was spotted onto CMT-GAPS coated slides (Corning)
2. Slide baked for 30 minutes at 80°C
3. cDNA was then immobilised by treatment with UV light (650 x 100 Joules) in a Stratalinker (Stratagene)
4. In preparation for hybridisation, slides were re-hydrated in water at 95°C for 5 minutes, followed by ethanol for 1 minute and dried by centrifugation (Sigma 4K15 centrifuge, Sigma) at 800 rpm for 3 minutes


title: Cowpea_UP12_expression_array [110706_asp_bean_CB_expr]

city: Hangzhou

first: Pei

last: Xu

address: 198 Shiqiao Rd

department: Vegetable Institute

institute: Zhejiang Academy of Agricultural Sciences

organism: Vigna unguiculata

description:
Each probe is replicated 3 times. Ten copies of each of eight control probes derived from the yeast genome sequence with no matches to the unigene sequences were also included in the microarray.
A custom Roche NimbleGen microarray was designed based on 29,728 unigene sequences from assembly P12 of cowpea cDNAs in the HarvEST database (http://harvest.ucr.edu/). With the exception of 189 unigenes that failed to pass quality filtering for probe design, each of the unigenes was represented by a set of four 60-mer probes on the fabricated microarray. Due to high sequence similarity, 65 unigenes shared the same group of probes. Therefore, a total of 29,471 unigenes, 26,156 of which were functionally annotated, were represented on the microarray, and a total of 24 microarrays (2 genotypes × 2 tissues × 2 treatments × 3 replicates) were produced for hybridization.

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


title: Illumina HiSeq 2000 (Cameraria ohridella)

status: Public on Nov 25 2014

organism: Cameraria ohridella


title: Illumina HumanMethylation450 BeadChip (v1.2, extended annotation)

city: Rotterdam

first: Martin

middle: Anne

last: Rijlaarsdam

address: Wytemaweg 80

department: Pathology

institute: Erasmus MC

description:
The Illumina annotation manifest (v1.2) for 450K array was extended. Briefly, probes close to small nuclear RNAs and microRNAs from snoRNABase and miRBase were identified, as were probes within repeats as defined by RepeatMasker (source: UCSC). Probes close to the transcription start site (TSS) of imprinted genes were also identified (geneimprint.com / igc.otago.ac.nz). Known imprinting control regions (ICR) were retrieved from WAMIDEX and igc.otago.ac.nz. Imprinting is indicated using the expressed allele. Illumina probe classes were extended with a number of merged categories. Where applicable the upstream (-) and downstream (+) margins reported in this manuscript are analogous to the Illumina annotation (-1500+0; -200+0). All results are based on the GRch37/hg19 assembly. also, Cross hybridizing probes and probes with a SNP at or within 10 bp of the target CpG (allele frequency >= 0.05) are indicated according to [1]. Please see the attached supplementary information for more details (start from pdf).
1. Chen, Y.A., et al., Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics, 2013. 8(2): p. 203-9.

manufacture_protocol: See manufacturer's website


title: Illumina HiSeq 2000 (Litchi chinensis)


title: Illumina HiSeq 2000 (Pararge aegeria)

organism: Pararge aegeria


title: febit-Hyphomonas neptunium15K v1.0

status: Public on Nov 24 2014

city: Marburg

last: Thanbichler

address: Hans-Meerwein-Straße 4

institute: Philipps University Marburg

organism: Hyphomonas neptunium ATCC 15444

manufacture_protocol: Probes were designed based on the published genome sequence of Hyphomonas neptunium ATCC 15444 (GenBank accession CP000158.1). Each gene was represented by up to four probes per array, resulting in up to four data points for each mRNA in the raw data file. For 181 genes, it was not possible to determine specific probes. The intensities of blank probes consisting of a single T nucleotide were used for background correction. Additional features were included as controls for the hybridization process and as positional cues. Blank and hybridization control probes were not included in the data analysis. The microarrays used in this study (Biochips) were generated on an activated three-dimensional reaction carrier consisting of a glass-silicon-glass sandwich. Features were generated by light-activated in-situ oligonucleotide synthesis employing the Geniom One platform (febit), using standard DNA synthesis reagents and 3'-phosphoramidites carrying a 5'-photolabile protective group. Prior to feature synthesis, the glass surface was activated by coating with a spacer to facilitate probe-target interaction and to avoid probe-probe interference.


title: Agilent-023740 209_DrerioAgilentCatalogV2_PlusELinneyContent

city: Durham

first: Nishad

last: Jayasundara

state: NC

address: A346, Research Drive, LSRC

department: Nicholas School of the Environment

institute: Duke University

organism: Danio rerio

description:
Redacted content from the Agilent V2 catalog array in order to make room for Elwood's neural and RA content. Custom design for Lindsey.

Arrays of this design have barcodes that begin with 16023740 or 2523740.

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: Nimblegen Streptococcus pneumoniae pan-genomic 12x135k custom design

city: Oeiras

first: Raquel

last: Sá-Leão

address: Av da República

country: Portugal

institute: ITQB António Xavier

organism: Streptococcus pneumoniae

description: The Nimblegen array contained 3-500 probes per predicted CDS and 22,739 negative control probes with a similar length distribution and CG content as the experimental probes

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


title: Legionella pneumophila Philadelphia-1 3x15K array

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

description: Legionella pneumophila Philadelphia-1 genome, including prediceted sRNA (Faucher 2010 PNAS) and sRNA found by RNA-seq (Weissenmayer, 2011 Plos ONE).

manufacture_protocol: Proprietary Light Directed Oligonucleotide Synthesis, 50-mer, on glass slide.


title: NimbleGen Bordetella 4x72K custom design expression array (genes)

status: Public on Nov 21 2014

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

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

institute: Utrecht University

organism:
Bordetella bronchiseptica
Bordetella pertussis

description:
The NimbleGen array contained 1-8 probes for all coding sequences (CDS) with an average coverage of 7.5 probes per CDS and pseudogene, 15 bp overlapping tiling probes covering both strands of the intergenic regions, and 7,304 random probes with a similar length distribution and GC content as the experimental probes. The array design was based on the genome sequence of B. pertussis Tohama I, supplemented with additional B. bronchiseptica CDS and intergenic sequences that are present in the B. pertussis strains used in this study.
110228_Bpertussis_TohamaI_HB_exp.ndf
110228_Bpertussis_TohamaI_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: Agilent-045706 SurePrint Helicoverpa zea 8x15K expression array [Feature Number version]

city: Brisbane

first: Quan

middle: Hoang

last: Nguyen

state: Queensland

address: Queensland Bioscience Precinct (Building 80) The University of Queensland. 306 Carmody Road. St

department: Australian Institute for Bioengineering and Nanotechnology

institute: The University of Queensland

organism:
Helicoverpa zea
Helicoverpa armigera nucleopolyhedrovirus

description:
Arrays of this design have barcodes that begin with 16045706 or 2545706.

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 ID column contains Feature numbers for non-control probes. Probes for spike-in controls are given the probe name.

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


title: Illumina HiSeq 2000 (Solanum lycopersicum var. cerasiforme)

status: Public on Nov 20 2014

organism: Solanum lycopersicum var. cerasiforme


title: Agilent-024241 Human Xq22_44K

city: HOUSTON

first: Christine

middle: R.

last: Beck

state: Texas

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description:
Arrays of this design have barcodes that begin with 16024241 or 2524241.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-049286 Arabidopsis thaliana Ath_8x60K_exp_validated_OakLabs_05-2013 048923

city: Uppsala

first: Emilio

last: Gutierrez Beltran

state: Sweden

address: Almas Allé 5

department: Department of Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SLU (Biocenter)

organism: Arabidopsis thaliana

description:
Arabidopsis thaliana, experimentally validated for No-0 and Col-0 by OakLabs May 2013.

Arrays of this design have barcodes that begin with 16049286 or 2549286.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Illumina HiSeq 2000 (Arabidopsis lyrata)

status: Public on Nov 19 2014

organism: Arabidopsis lyrata


title: Illumina Genome Analyzer (Penicillium oxalicum)

status: Public on Nov 18 2014

organism: Penicillium oxalicum


title: AB SOLiD 4 System (Hydra vulgaris)

organism: Hydra vulgaris


title: NimbleGen Arabidopsis Custom Probe Layout 12 x 135k [100902_Cele_CR_exptil]

city: Lubbock

first: Christopher

middle: Dale

last: Rock

state: TX

address: Flint and Main Sts.

department: Biological Sciences

institute: Texas Tech University

manufacture_protocol: genome coordinates, strand specific, variable length


title: Illumina HiSeq 2500 (Amycolatopsis mediterranei U32)

last: GEO

organism: Amycolatopsis mediterranei U32


title: Agilent-028520 Cynomolgus macaque Gene Expression microarray (FeatureNumber verstion)

city: Hachioji

first: Chiho

last: Yoshida

address: Takakura 9-1

institute: Agilent Technologies

organism: Macaca fascicularis

description:
Published Design https://earray.chem.agilent.com/earray/PublishDesignLogin.do?eArrayAction=showPreviewForLogin&publishdesignid=PD425310354
Microarray designed gene expression profiling of Cynomolgus macaque; Source: NCBI, Unigene Rrepresentative sequences.
Arrays of this design have barcodes that begin with 16028520 or 2528520.
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: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array (CDF: hugene10st_Hs_ENSGvs1500.cdf)

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

organism: Homo sapiens

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

manufacture_protocol: See manufacturer's web site.


title: Illumina HiSeq 2000 (Malus hupehensis)

status: Public on Nov 17 2014

organism: Malus hupehensis


title: Illumina MiSeq (mouse metagenome)

organism: mouse metagenome


title: Illumina HiSeq 2500 (Cicer arietinum)

organism: Cicer arietinum


title: Illumina NextSeq 500 (Caldicellulosiruptor kristjanssonii)

organism: Caldicellulosiruptor acetigenus


title: AB SOLiD 4 System (Plasmodium falciparum)

organism: Plasmodium falciparum


title: Illumina Genome Analyzer (Malus hupehensis)


title: NimbleGen Saccharomyces cerevisiae 12x135K Array [10078_Scer_EXP_HX12]

city: VTT, Espoo

first: Merja

last: Oja

address: Tietotie 2

country: Finland

institute: VTT Technical Research Centre of Finland

organism: Saccharomyces cerevisiae

description:
NimbleGen design name 10078 Scer EXP HX12.
An expression design with 12 arrays which each measures 5,777 genes from Saccharomyces cerevisiae S288C with eight 60-mer probes per gene, with three-fold technical redundancy. The design includes random GC and other control probes.
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features. The .ndf, .ngd and .ncd files are linked below as supplementary files.
100718_Scer_EXP.ndf
100718_Scer_EXP.ngd
100718_Scer_EXP_HX12.ncd


title: Illumina HiSeq 2000 (Saimiri boliviensis)

organism: Saimiri boliviensis


title: Illumina HiSeq 2500 (Phytophthora infestans)

status: Public on Nov 14 2014

organism: Phytophthora infestans


title: Broad P. falciparum 328 v1

status: Public on Nov 15 2014

city: Boston

first: Daria

last: Van Tyne

address: 243 Charles Street

institute: Harvard Medical School

technology: other

manufacture_protocol:
From Methods section of associated publication: nCounter® probe specificity is generated by designing two 50bp probes that sit next to one another, yielding 100bp total probe specificity for each gene of interest. Probe set design was carried out to maximize specificity and minimize cross-hybridization. Specifically, long direct and inverted repeats and long polynucleotide repeats were excluded, target regions were screened for cross-hybridization against the Human RefSeq mRNA database (http://www.ncbi.nlm.nih.gov/refseq/), and probes with stretches of more than 15 contiguous bases complementary to any non-target mRNA were excluded. Probes were also screened for inter- and intra-probe interactions, and were selected to have calculated melting temperatures (Tm) between 78 and 83°C, with an ideal target of 80.5°C. Finally, mismatch probes were also included in the nCounter® custom probe set, as part of the negative controls.
Custom nCounter probes


title: Illumina HiSeq 2000 (Chlorella minutissima)

status: Public on Nov 13 2014

organism: Neodesmus pupukensis


title: Wilson human antibody microarray H3/H7

city: CHICAGO

first: Patrick

middle: C

last: Wilson

state: Illinois

address: 924 E 57th street, Knapp building

department: Medicine, Rheumatology

institute: University of Chicago

technology: antibody

description:
Human monoclonal antibodies spotted.
The mAbs have been isolated from different individuals.  Some antibodies are from the same individual (i.e., the ones starting by the same 3 numbers, for example 011) but they have been cloned from different cells (we isolate single B cells by flow cytometry and clone the heavy and light chain to make the mAbs).

manufacturer: Patrick Wilson's laboratory, University of Chicago using ArrayIt technology (SpotBot3 microarrayer)

manufacture_protocol:
1. 6-8µl of each human monoclonal antibodies at 500µg/ml are deposited in a 384 wells plate (ArrayIt)
2. the same volume of 2X Printing Buffer (ArrayIt) is added in each well. Mix well.
3. antibodies are then printed, in triplicate, on SuperEpoxy treated glass slides (ArrayIt). The same set of antibody is spotted 24 times on the same slide allowing 24 samples to be applied.
4. After the run, slides are kept at 4 degres before use.


title: Phalanx Human OneArray (30968 probes)

city: Beijing

first: Jun

last: Chen

address: No.15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

description: 60 bp oligos


title: Agilent-024048 Drosophila melanogaster genome-wide tiling array (Probe name version)

status: Public on Nov 10 2014

city: Cambridge

first: Terry

middle: L.

last: Orr-Weaver

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

organism: Drosophila melanogaster


title: Customized CombiMatrix Eukaryotic 90K

city: Piacenza

first: Lorenzo

last: Bomba

state: Piacenza

address: via Emilia Parmense, 82

department: Istituto di Zootecnica

institute: Università Cattolica del Sacro Cuore

organism: Sus scrofa

manufacturer: University of Verona - Scientific and Technological Department - Plant Functional Genomics Centre

manufacture_protocol: Probes are directly synthesized on a 90k Combimatrix array by an in situ oligo synthesis system developed by Combimatrix Corporation (Mukilteo, USA) using the Combimatrix CustomArray synthesizer. Standard synthesis protocol provided by Combimatrix was used.


title: Illumina MiSeq (Thermotoga maritima MSB8)

organism: Thermotoga maritima MSB8


title: Agilent-068787 D. melanogaster Oligo Microarray 8x60K v1

status: Public on Nov 12 2014

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

institute: Miltenyi Biotec GmbH

description:
8x60K expression array for D. melanogaster based on the design of 021791 (4x44K v2)

Arrays of this design have barcodes that begin with 16068787 or 2568787.

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 HiSeq 2000 (Brassica carinata x Brassica napus)

status: Public on Nov 07 2014

organism: Brassica carinata x Brassica napus


title: Illumina HiSeq 2000 (Methylobacterium extorquens AM1)

organism: Methylorubrum extorquens AM1


title: Agilent-027763 Amp and URv2 (Probe name version)


title: Ion Torrent PGM (Caenorhabditis elegans)

organism: Caenorhabditis elegans


title: Spectral Genomics Constitutional Chip v4

status: Public on Nov 06 2014

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

institute: CHU Nice

manufacturer: Spectral Genomics (now part of Perkin Elmer)

manufacture_protocol: Spectral Genomics Constitutionnal Chip v4. This array was provided by Perkin Elmer


title: Agilent-016047 Maize Gene Expression Microarray 4x44K (Feature Number)

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Zea mays

description:
This Agilent 60mer oligo microarray represents the transcriptome for Z. Mays.  It was developed in collaboration with Dr. Walbot’s lab at Stanford.

Arrays of this design have barcodes that begin with 16016047 or 2516047.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-023043 LipidomicNet_V1 014850

status: Public on Nov 05 2014

city: Helsinki

first: YOU

last: ZHOU

address: Tukholmankatu 8

institute: Minerva Institute for Medical Research

organism: Homo sapiens

description:
Whole Human Genome Microarray 4x44K

Arrays of this design have barcodes that begin with 16023043 or 2523043.

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: Duke/RG_E2F1-3-4_cust2_v1

status: Public on Nov 04 2014

city: Durham

first: Raluca

last: Gordan

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

organism: synthetic construct

manufacture_protocol: In situ oligosynthesized array with proprietary sequences that target E2F putative binding sites in genomic context, as well as all 10-mer sequences.


title: Illumina HiSeq 2500 (Homo sapiens; Sindbis virus)

status: Public on Nov 03 2014

organism:
Homo sapiens
Sindbis virus


title: Agilent Drosophila 2.0 (Agilent Design ID: 035757)

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

institute: University of Padova

description:
Arrays of this design have barcodes that begin with 16035757 or 2535757.
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 Probe Name.
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.

first: Alberto

last: Biscontin

first: Caterina

last: Da Re

first: Paola

last: Cusumano

first: Rodolfo

last: Costa


title: Exiqon miRCURY LNA microRNA array 6th generation product no. 208400 batch no. 34013 mirBase v18

city: Belfield

first: Paul

last: McGettigan

state: Co Dublin

address: Veterinary Sciences Centre, UCD

department: School of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

organism: Bos taurus


title: Illumina HiSeq 2500 (Drosophila melanogaster; Sindbis virus)

last: GEO

organism:
Drosophila melanogaster
Sindbis virus


title: Illumina HiSeq 2000 (Neisseria gonorrhoeae)

organism: Neisseria gonorrhoeae


title: Illumina HiSeq 2500 (Mus musculus; Saccharomyces cerevisiae)

organism:
Saccharomyces cerevisiae
Mus musculus


title: Agilent-021850 SurePrint G3 Human CGH Microarray (Probe Name version)

city: Palo Alto

last: Agilent Technologies

state: CA

description: *** 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 GPL9777.


title: Agilent-046842 S. vermifera and A. thaliana MPI_UL 63K array (Feature number version)

status: Public on Nov 01 2014

city: Regensburg

first: Urs

last: Lahrmann

address: Am Biopark 9

department: Project Group Personalized Tumor Therapy

institute: Fraunhofer ITEM

organism:
Arabidopsis thaliana
Serendipita vermifera

description:
Agilent-046842 Svermifera_Athal_MPI_UL
Whole transcriptome array calculated from JGI predicted genes for S. vermifera and TAIR10 release for A. thaliana.

Arrays of this design have barcodes that begin with 16046842 or 2546842.

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 NextSeq 500 (synthetic construct)


title: Affymetrix AGRONOMICS Tiling Array [CDF: agronomics1attairg version 13.0.0]

city: koeln

first: Yong

last: Xiang

address: Carl-von-Linne-Weg 10

institute: Max Planck Institute for Plant Breeding Research

organism: Arabidopsis thaliana

manufacture_protocol: In collaboration with Affymetrix, the European AGRON-OMICS project has developed a new array including probes representing both strands of the entire Arabidopsis genome. Performance comparison with the ATH1 array indicates that both microarrays yield data of comparable quality, but that the new tiling array yields expression information for significantly more genes, since the ATH1 array profiles only about 65% of >33.000 TAIR9 annotated genes. The AGRONOMICS1 arrays also carry all of the original ATH1 sense probes, thereby streamlining the integration with ATH1-based results.


title: Illumina HiSeq 2000 (Epinephelus coioides)

organism: Epinephelus coioides


title: Illumina HiSeq 2000 (Pseudomonas aeruginosa PAO1)

organism: Pseudomonas aeruginosa PAO1


title: SABiosciences PCR Array for Mouse Cytokines and Chemokines (PAMM-150Z)

city: Hamilton

first: Ali

middle: A

last: Ashkar

address: 1280 Main St. West

institute: McMaster University

organism: Mus musculus

description: SABiosciences RT² Profiler PCR array

manufacture_protocol: see manufacturer's website


title: Exiqon custom Mus musculus miRNA array

city: Toronto

first: Andrew

last: Emili

address: 160 College St #602

department: Donnelly Centre

institute: University of Toronto

manufacture_protocol: See manufacturer's website: http://www.exiqon.com/array


title: A-UMCU-BT44K-1.0

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

manufacturer: Holstege Lab, UMC Utrecht, The Netherlands

first: Dik

last: van Leenen

first: Philip

last: Lijnzaad

first: Linda

last: Bakker

first: Erik

last: Sluiters

first: Sander

last: van Hooff

first: Patrick

last: Kemmeren

first: Frank

last: Holstege

manufacture_protocol: 1. Slides are obtained from a commercial provider (Agilent) and reannotated using blat to obtain the latest gene annotations from Ensembl.


title: Tohoku_Univ_2008-02_Sinorhizobium meliloti_60mer_4plex

city: Sendai

first: Hisayuki

last: Mitsui

address: 2-1-1, Katahira, Aoba-ku

department: Graduate School of Life Sciences

institute: Tohoku University

organism: Sinorhizobium meliloti 1021

description:
2008-02-06_RDKK013_Smel_60mer_4plex.ndf
2008-02-06_RDKK013_Smel_60mer_4plex.ngd

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


title: SMD Print_HOAR

status: Public on Oct 31 2014

city: San Francisco

first: Nikoleta

last: Tsvetanova

address: 600 16th street

institute: University of California, San Francisco

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: NuGO array (human) NuGO_Hs1a520180 [nugohs1a520180hsentrezg 13.0.0 cdf version]

status: Public on Oct 30 2014

city: Freising-Weihenstephan

first: Bernhard

middle: L

last: Bader

address: Gregor-Mendel Straße 2

department: Clinical Nutritional Unit - ZIEL-Research Center for Nutrition and Food Sciences

institute: Technische Universität München

manufacture_protocol: See manufacturer's web site


title: UHN Microarray Centre Drosophila melanogaster D14k3

status: Public on May 01 2013

city: Cologne

first: Julia

last: Hoffmann

address: Joseph-Stelzmann-Str. 9b

department: Partridge

institute: MPI for Biology of Ageing

organism: Drosophila melanogaster

manufacturer: University Health Network Microarray Centre (www.microarrays,ca, Toronto, Canada)

manufacture_protocol: The arrays are printed on ChipWriter Pro (BioRad) using Stealth microarray printing pins (ArrayIT) on UltraGAPS microarray slides (Corning).


title: Agilent-030025 Texas-Adelaide Array

city: College Station

first: Sharmila

last: Ghosh

address: VMS Building, Rm 107, 4458 TAMUS

department: VIBS

institute: Texas A&M University

organism: Equus caballus

description:
WG 400K

Arrays of this design have barcodes that begin with 16030025 or 2530025.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Gene symbol version)

city: Amsterdam

first: Manon

middle: Heleen

last: Kerkhof

state: Noord Holland

address: de Boelelaan 1118

department: Obstetrics & Gynaecology

institute: VU University Medical Centre


title: Agilent-037288 Timecourse_Insect_Virus

status: Public on Mar 01 2013

city: Brisbane

first: Quan

last: Nguyen

address: Queensland Bioscience Precinct (Building 80) The University of Queensland. 306 Carmody Road. St

department: Australian Institute for Bioengineering and Nanotechnology

institute: The University of Queensland

organism:
Helicoverpa zea
Helicoverpa armigera

description:
A custom 8x60,000 SurePrint Agilent expression slide (Agilent, Santa Clara, CA)  with probes including probes for 27,400 H. zea sequences that were validated previously (Nguyen et al., 2012. PLOS ONE, 7(5), e36324) and all 134 H. armigera single-capsid nucleopolyhedrovirus (HearNPV) genes (Accession: NC_002654).
Arrays of this design have barcodes that begin with 16037288 or 2537288.


title: Agilent-016047 Maize Gene Expression Microarray 4x44K (Probe name version)

status: Public on Sep 21 2012

last: Agilent Technologies

institute: Agilent Technologies

organism: Zea mays

description: The ID column includes the Agilent Probe Names.


title: JCVI PFGRC Mycobacterium tuberculosis 3K v1 array designed primarily for gene mutantion research.

status: Public on May 22 2010

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Mycobacterium tuberculosis

description: This set includes 392 reporters, has 3360 spots distributed in 96 blocks.

manufacture_protocol: QDM, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 35, machine cycles 3797232, pen id 179, pen cycles -1, operator robin, humidity control On, humidity set point65


title: Agilent-023939 SurePrint Custom Human Chr19p CGH Microarray 60K

status: Public on May 05 2010

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

organism: Homo sapiens


title: Illumina HiSeq 2000 (Candida albicans)

status: Public on Jun 03 2012

last: GEO

organism: Candida albicans


title: 080814_HG18_Deluxe_Promoter_HX1

status: Public on Nov 30 2014

city: Rennes

first: Raphaël

last: Métivier

address: Campus de Beaulieu

institute: CNRS UMR 6290

description:
HG18
This design consists of 2.1 M probes, with a mean spacing of 99 bp, including  1) Promoter regions, from 7250 bases upstream of each TSS to 3250 bases downstream.  2) miRNA genes, starting from 15kbp upstream of the mature gene product to its 3' end.  3) CpG islands.  4) ENCODE regions.  Probes were chosen from the hg18_tiling database.
native array description file: 080814_HG18_Deluxe_Promoter_HX1.ndf
native array description file: 080814_HG18_Deluxe_Promoter_HX1.pos


title: [CytoScan750K_Array] Affymetrix CytoScan 750K Array

status: Public on May 02 2014

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

description:
#CytoScan750K_Array.cn.na32.3.annot.csv
#%create_date=2012-11-27 GMT-08:00 16:16:00
#%chip_type=CytoScan750K_Array
#%genome-species=Homo sapiens
#%genome-version=hg19
#%genome-version-ucsc=hg19
#%genome-version-ncbi=37
#%genome-version-create_date=2009-02-00
#%dbSNP_date=2010-09-23
#%dbSNP_version=132
#%dgv-date=2010-10-00
#%dgv-version=10
#%hapmap-date=2008-01-08
#%hapmap-version=23
#%netaffx-annotation-date=2012-11-05
#%netaffx-annotation-netaffx-build=32.3

#CytoScan750K_Array.na32.3.annot.csv
#%create_date=2012-11-27 GMT-08:00 16:17:00
#%chip_type=CytoScan750K_Array
#%genome-species=Homo sapiens
#%genome-version=hg19
#%genome-version-ucsc=hg19
#%genome-version-ncbi=37
#%genome-version-create_date=2009-02-00
#%dbSNP_date=2010-09-23
#%dbSNP_version=132
#%dgv-date=2010-10-00
#%dgv-version=10
#%hapmap-date=2008-01-08
#%hapmap-version=23
#%netaffx-annotation-date=2012-11-05
#%netaffx-annotation-netaffx-build=32.3

manufacture_protocol: see manufacturer's web site


title: Agilent-028282 Whole Rat Genome Microarray 4x44K v3 (Feature Number version)

status: Public on Oct 14 2011

city: Palo Alto

organism: Rattus norvegicus

description:
Whole Rat Genome Microarray 4x44K v3

Arrays of this design have barcodes that begin with 16028282 or 2528282.

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: Streptococcus mutans UA159 Affymetrix Microarray

status: Public on Jun 15 2007

city: Miami

first: Dragana

last: Ajdic

state: Florid

address: 1600 NW 10th Ave, RMSB 2023

department: Dermatology

institute: University of Miami

organism: Streptococcus mutans

manufacture_protocol: Affymetrix Microchip Manufacturing Protocol


title: Human 3.0 A1

status: Public on Jul 12 2006

city: Boston

first: Julja

last: Burchard

address: 33 Avenue Louis Pasteur

department: Computational & Systems Biology

institute: Merck & Co., Inc.

description: Oligonucleotide array on glass.  Contains 60mer probes designed against 23,000+ human genes arrayed on Agilent ink-jet arrays.

first: Amit

last: Kulkarni

first: John

last: Castle


title: Agilent-014693 Human Genome CGH Microarray 244A (Probe name version)

status: Public on Sep 01 2009

description:
This microarray is Agilent’s premium product for human DNA copy-number profiling. Over 236,000 60-mer oligonucleotide probes, specifically optimized for copy-number measurement, span coding and non-coding genomic sequences with median spacing of 7.4 kb and 16.5 kb respectively. This microarray is designed for use with Agilent’s optimized assay protocols, enabling researchers to use nanogram levels of total genomic DNA without complexity reduction.

*** 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 GPL4091.