title: Agilent-073748 PPCD1 CNV 17.3-34.0 (Probe Name version)

status: Public on Jun 30 2016

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

state: CA

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

country: USA

institute: Stein Eye Institute, UCLA

organism: Homo sapiens

technology: in situ oligonucleotide

description:
Array design is based on genome build hg19/GRCh37.

G4126A

distribution: custom-commercial

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


title: Wafergen Biosystems SmartChip Human lncRNA panel

status: Public on Jun 29 2016

city: Gent

first: Pieter

last: mestdagh

address: De Pintelaan 185

country: Belgium

institute: Center for Medical Genetics

technology: RT-PCR

description: PCR assay

distribution: virtual

manufacture_protocol: see manufacturer's website


title: NanoString human Cancer CNV panel, version 1

status: Public on Apr 30 2016

city: Jacksonville

first: Nadine

last: Norton

state: FL

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

technology: other

description: NanoString Cancer CNV panel of 80 known cancer genes; HG18

distribution: commercial

manufacture_protocol: See manufacturer's website (www.nanostring.com)


title: Illumina HiSeq 2000 (Manduca sexta)

status: Public on Apr 29 2016

last: GEO

organism: Manduca sexta

technology: high-throughput sequencing


title: Reverse phase protein array (RRPA)

status: Public on Jul 21 2016

city: Pittsburgh

first: Alison

middle: M

last: Nagle

state: PENNSYLVANIA

address: 204 Craft Ave

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

technology: spotted peptide or protein

manufacturer: RPPA Core Facility (MD Anderson Cancer Center, TX)


title: NanoString nCounter Human miRNA assay v2.1

city: Chicago

first: Craig

last: Horbinski

state: IL

address: 303 E Chicago Avenue

department: Pathology and Neurosurgery

institute: Northwestern University


title: Arabidopsis Genome 29k Array

city: Haikou

first: lili

last: zhang

address: longhua County，Xueyuan Road 4

country: China

institute: Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences

organism: Arabidopsis thaliana

technology: spotted oligonucleotide

manufacture_protocol: as described in CapitalBio Corporation Manual


title: Agilent-034811 Mycobacterium smegmatis str. MC2 155 8X15K array [Probe Name Version]

city: shanghai

first: qian

last: jin

address: libing road

institute: MSP

organism: Mycolicibacterium smegmatis MC2 155

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


title: Agilent-069672 S.lycopersicum Build 2.4

status: Public on Apr 28 2016

city: Coventry

first: Miriam

last: Gifford

address: Gibbet Hill Road

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

organism: Solanum lycopersicum

description:
Arrays of this design have barcodes that begin with 16069672 or 2569672.
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-054261 026652AsQuintuplicatesOn180k_new (Probe name version)

city: Hannover

first: Ralf

last: Hass

state: Germany

address: Carl-Neuberg-Str. 1

department: Gynecology

country: Germany

institute: Hannover Medical School

description:
This Microarray represents a refined version of the Whole Human Genome Oligo Microarray 4x44K v2 (Design ID 026652, Agilent Technologies), called '026652AsQuintuplicatesOn4x180k' (design ID 054261) developed in the Research Core Unit Transcriptomics of Hannover Medical School. Microarray design was defined at Agilent's eArray portal using a 4x180k design format for mRNA expression as template. All non-control probes of design ID 026652 have been selected to be printed five times onto one 180k Microarray (on-chip quintuplicates). Control probes required for proper Feature Extraction software algorithms were determined and placed automatically by eArray using recommended default settings.

all non-control probes of design 026652 (human 4x44k V2) were printed as quintuplicates as 4x180k format

Arrays of this design have barcodes that begin with 16054261 or 2554261.

relation: Alternative to: GPL19018 (Feature number version)


title: Illumina HiSeq 2000 (Vibrio coralliilyticus)

organism: Vibrio coralliilyticus


title: Illumina Genome Analyzer II (Pyrus x bretschneideri x Pyrus pyrifolia)


title: Illumina Genome Analyzer II (Pyrus x bretschneideri)

organism: Pyrus x bretschneideri


title: NCI Glycoarray-PROSTVAC a96

city: Frederick

first: Jeff

last: Gildersleeve

state: MD

address: 376 Boyles St.

institute: National Cancer Institute

organism:
Gallus gallus
Homo sapiens
Frangula alnus

description: Each slide contains 16 identical array containing 96 components printed in duplicate (192 features total)

distribution: non-commercial

manufacturer: National Cancer Institute, Chemical Glycobiology Section

manufacture_protocol: Glycoproteins and neoglycoproteins spotted onto epoxide functionalized glass slides (ArrayIt SME2) using a MicroGrid II arrayer.


title: Illumina HiSeq 2000 (Photobacterium galatheae)

organism: Photobacterium galatheae


title: NCI Glycoarray-380

organism:
Quercus alba
Gossypium hirsutum
Rhodotorula
Trypanosoma cruzi
Pandalus borealis
Oncorhynchus nerka
Gallus gallus
Homo sapiens
Bos taurus
Ovis aries
Mus musculus
Ceratonia siliqua
Megathura crenulata
Bothrops moojeni
Frangula alnus
Senegalia senegal
Pachymenia carnosa
Dermestes lardarius

description: Each slide contains 16 identical array containing 380 components printed in duplicate (760 features total)

manufacture_protocol: Glycoproteins and neoglycoproteins spotted onto epoxide functionalized glass slides (ArrayIt SMP2) using a MicroGrid II arrayer.


title: Illumina NextSeq 500 (Bacillus subtilis subsp. subtilis str. 168)


title: Illumina HiSeq 2000 (Linum usitatissimum)

status: Public on Apr 27 2016

organism: Linum usitatissimum


title: Agilent-077089 C.griseus_Refseq2015 [Feature number version]

city: hachiouji

first: yoshiyuki

last: ishii

address: takakura-cho

country: Japan

institute: Agilent

organism: Cricetulus griseus

description:
Transcript sequence from Refseq Protein coding genes 2015July

Arrays of this design have barcodes that begin with 16077089 or 2577089.

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 (Brassica juncea x Brassica oleracea)

status: Public on Apr 26 2016

organism: Brassica juncea x Brassica oleracea


title: NimbleGen Arabidopsis thaliana Gene Expression 12x135K Array [100718_Athal_TAIR9_exp; PROBE_ID]

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description:
DESIGN_ID: 535493
DESIGN_NAME: 100718_Athal_TAIR9_exp

manufacture_protocol: See manufacturer's website at http://www.nimblegen.com/


title: Agilent-031746 ISCA Human CGH 60K v2 (Probe Name version)

city: Tomsk

first: Aleksei

middle: A

last: Sleptcov

state: Tomskaya oblasty

address: 10 Naberejnaya Ushaiki

country: Russia

institute: Research Institute of Medical Genetics

description:
Agilent SureDesign
G4827A-031746
International Standard Cytogenomic Array (ISCA)
Based on genome build hg19 (GRCh37).

Arrays of this design have barcodes that begin with 16031746 or 2531746.

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


title: Illumina HiSeq 2500 (Tigriopus californicus)

organism: Tigriopus californicus


title: Illumina HiSeq 2500 (Yarrowia lipolytica)

organism: Yarrowia lipolytica


title: Illumina HiSeq 1500 (Streptococcus pyogenes)

organism: Streptococcus pyogenes


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: mogene10st_Mm_ENTREZG_17.0.0]

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Mus musculus

relation: Alternative to: GPL6246 (Alternative CDF[official])

manufacture_protocol: This is identical to GPL6246 but a custom cdf environment was used to extract data. The cdf can be found at the link below.


title: Agilent-049119 M. truncatula Medicago 8x60k Oligo Microarray

city: Göteborg

first: Cornelia

last: Spetea

address: Carl Scottbergsgata 22B

department: Biological and Environmental Sciences

country: Sweden

institute: Gothenburg University

organism: Medicago truncatula

description:
M. truncatula (Medicago) Oligo Microarray
The design 049119 is a custom design created in Apr-2013 and its 8x60K format array. Probes in this design are from design ID 022524, 4x44K catalog array.

Arrays of this design have barcodes that begin with 16049119 or 2549119.

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.


title: Illumina HiSeq 2000 (Trichophyton mentagrophytes)

status: Public on Apr 25 2016

organism: Trichophyton mentagrophytes


title: SABiosciences Human Dendritic and Antigen Presenting Cell PCR assay panel

status: Public on Apr 23 2016

city: Piracicaba

first: Bruna

last: Benso

department: Physiological Sciences

country: Brazil

institute: UNICAMP

organism: Homo sapiens

description:
PCR Array Human Inflammatory Response & Autoimmunity
SABiosciences RT² Profiler panel of PCR assays.


title: Illumina HiSeq 2500 (Vibrio fischeri ES114)

organism: Aliivibrio fischeri ES114


title: Exiqon human V3 microRNA PCR panel I+II (PROBE_ID version)

status: Public on Apr 22 2016

city: Bristol

first: Costanza

last: Emanueli

address: Research Floor Level 7, Bristol Royal Infirmary, Upper Maudlin Street

department: School of Clinical Science

institute: Bristol Heart Institute, University of Bristol

description:
PCR assay
The ID column includes the PROBE_ID. A different version of this platform with REF_ID in the ID column is assigned accession number GPL19631

manufacture_protocol: see manufacturer's website (http://www.exiqon.com/mirna-pcr-panels)


title: SRAN Human 270 v1.0

city: Springfield

first: Sophia

last: Ran

address: 801 N. Rutledge St.

department: MMICB

institute: Southern Illinois University - School of Medicine

description:
RT-qPCR assay
GoTaq Green Master Mix (Promega, WI)

manufacture_protocol: In-house human inflammatory and lymphatic-specific RT-qPCR targeted array was constructed from known and putative inflammatory and lymphatic genes. The array contains a total of 269 targets, including 67 cytokines, 57 cytokine receptors, 18 chemokines, 11 chemokines receptors, 10 known TLR4 downstream targets, 64 other inflammation-related proteins, 12 genes expressed primarily in lymphatic endothelial cells, and 32 endothelial cell associated proteins. An accession number based on CDS was identified for each gene of interest on the NCBI database (Bethesda, MD). Accession numbers were used to obtain potential primer sequences via the NIH qPrimerDepot (http://primerdepot.nci.nih.gov/) or Harvard Primerbank (http://pga.mgh.harvard.edu/primerbank/index.html). The sequence of each primer was compared against all known nucleotide sequences in the human genome using the NCBI BLAST alignment tool (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Only primers that had unique specificity to the individual target gene were used for validation. Primer DNA oligos were ordered from Integrated DNA Technology (Coralville, IA). Each primer was validated using four dilutions (1, 1:10, 1:100, and 1:1000) of human universal cDNA tested in duplicate with a final primer concentration of 0.5µM. RT-qPCR was performed with GoTaq Green Master Mix (Promega, WI) on a MasterCycle realplex PCR machine (Eppendorf, NY). The quality of each primer was confirmed by melting curve analysis and the amplification efficiency by Ct slope analysis of the four cDNA dilutions. All primer sequences are listed with the normalized Ct values.


title: Illumina HiSeq 2000 (Ceratitis capitata)

organism: Ceratitis capitata


title: Illumina HiSeq 2500 (Bactrocera dorsalis)

status: Public on Apr 21 2016

organism: Bactrocera dorsalis


title: Affymetrix GeneChip Human Genome U133 Array Set HG-U133 Plus2 based on a custom CDF (GeneAnnot version 2.1.0)

status: Public on Apr 20 2016

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Affymetrix HG-U133 Plus2 microarrays analysed with custom chip definition files based on the GeneAnnot database. For further information, see Ferrari F, Bortoluzzi S, Coppe A, Sirota A, Safran M, Shmoish M, Ferrari S, Lancet D, Danieli GA, Bicciato S.: Novel definition files for human GeneChips based on GeneAnnot. BMC Bioinformatics. 2007 Nov 15;8(1):446. We used Version 2.1.0 of custom CDF files and R packages based on GeneAnnot version 1.9 and GeneCards version 2.41, available online at http://www.xlab.unimo.it/GA_CDF/

manufacture_protocol: see manufacturer's web site


title: Agilent-040157 Zebrafish_Human miRNA v18 [miRNA_ID version]

city: West Lafayette

first: Jennifer

last: Freeman

address: 915 West State Street

institute: Purdue University

organism:
Danio rerio
Homo sapiens

description:
All zebrafish miRNA probes v18 (245) and all human miRNA probes v18 (1887)

Arrays of this design have barcodes that begin with 16040157 or 2540157.

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 miRNA_ID.

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: SRAN Human 150 v1.0

manufacture_protocol: In-house human inflammatory and lymphatic-specific RT-qPCR targeted array was constructed from known and putative inflammatory and lymphatic genes. We used an in-house array to analyze the gene expression of a total of 150 targets including 33 cytokines, 34 cytokine receptors, 11 known TLR  targets, 64 other inflammation-related proteins, 31 endothelial related transcription factors, 12 myeloid associated genes, 12 genes expressed primarily in lymphatic endothelial cells, and 23 endothelial cell associated proteins.  An accession number based on CDS was identified for each gene of interest on the NCBI database (Bethesda, MD). Accession numbers were used to obtain potential primer sequences via the NIH qPrimerDepot (http://primerdepot.nci.nih.gov/) or Harvard Primerbank (http://pga.mgh.harvard.edu/primerbank/index.html). The sequence of each primer was compared against all known nucleotide sequences in the human genome using the NCBI BLAST alignment tool (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Only primers that had unique specificity to the individual target gene were used for validation. Primer DNA oligos were ordered from Integrated DNA Technology (Coralville, IA). Each primer was validated using four dilutions (1, 1:10, 1:100, and 1:1000) of human universal cDNA tested in duplicate with a final primer concentration of 0.5µM. RT-qPCR was performed with GoTaq Green Master Mix (Promega, WI) on a MasterCycle realplex PCR machine (Eppendorf, NY). The quality of each primer was confirmed by melting curve analysis and the amplification efficiency by Ct slope analysis of the four cDNA dilutions. All primer sequences are listed with the normalized Ct values.


title: Exiqon Human miRCURY™ LNA Array (v.16.0)

city: He Fei

first: Yongfeng

last: Hong

address: Furong Road 678

institute: The Second Affiliated Hospital to Anhui Medical University

description: ArrayContents_DesignedFor: miRBase 16.0

manufacture_protocol: see manufacturere's website; http://www.exiqon.com/SEEEMS/26.asp


title: Illumina HiSeq 1000 (Oryzias latipes)

last: GEO

organism: Oryzias latipes


title: Illumina HiSeq 2500 (Cryptococcus neoformans var. grubii)

organism: Cryptococcus neoformans


title: Illumina HiSeq 2000 (Canis lupus)

status: Public on Apr 19 2016

organism: Canis lupus


title: Illumina HiSeq 2500 (Homo sapiens; Pseudomonas aeruginosa)

organism:
Pseudomonas aeruginosa
Homo sapiens


title: AB SOLiD System (Schizosaccharomyces pombe)

status: Public on Apr 15 2016

organism: Schizosaccharomyces pombe


title: Illumina HiSeq 2000 (Arabidopsis thaliana x Arabidopsis halleri)


title: Illumina MouseWG-6 v2.0 expression beadchip (Gene version)

city: Urbana

first: Junmin

last: Lee

address: 1304 W. Green St.

department: Materials Science and Engineering

institute: University of Illinois at Urbana-Chanpaign

technology: oligonucleotide beads


title: MPIIB Helicobacter pylori cDNA array [condensed version]

first: Christine

last: Josenhans

address: Carl-Neuberg-Strasse 1

department: Institute for Medical Microbiology

organism: Helicobacter pylori

technology: spotted DNA/cDNA

description: Array comprises two technical replicates for each gene


title: SABiosciences Mouse Autophagy RT2 Profiler PCR Arrays [PAMM-084Z]

status: Public on Apr 18 2016

city: New York

first: Kathryn

last: Moore

state: New York

address: 522 First Ave, Smilow 707

department: Medicine

institute: NYU Medical Center

description:
catalog number: PAMM-084Z
PCR assay
The Mouse Autophagy RT² Profiler PCR Array profiles the expression of 84 key genes involved in autophagy.


title: Affymetrix Axiom® Turkey Genotyping Array

city: Beltsville

first: Julie

last: Long

address: Powder Mill Road

institute: USDA/ARS

organism: Meleagris gallopavo

description:
The Axiom®Turkey  Genotyping Array interrogates 643,845 probesets on the array, covering 643,845 SNPs. The array development was led by Dr. Julie Long of the USDA-ARS Beltsville Agricultural Research Center under a public-private partnership with Hendrix Genetics, Aviagen, and Affymetrix. The Turkey Genome Sequencing Consortium led the efforts to sequence the turkey genome. The SNP marker discovery effort was led by Prof. Martien Groenen of the Animal Breeding and Genomics Centre at Wageningen University in the Netherlands, and was funded by USDA’s National Institute of Food and Agriculture. The SNP markers on the turkey array were selected by Dr. Curt Van Tassell of the USDA-ARS Beltsville Agricultural Research Center.
Reference genome version for which chromosome and position coordinates are given: UMD 5.0

first: Martien

last: Groenen

first: Curt

last: Van Tassell


title: Illumina HiSeq 2000 (Arabidopsis thaliana x Arabidopsis lyrata)


title: Illumina NextSeq 500 (Saccharomyces cerevisiae S288c)

status: Public on Apr 16 2016

organism: Saccharomyces cerevisiae S288C


title: 454 GS Junior (Mus musculus)


title: Agilent-075973 Rabbit Microarray V3 020908

city: Jouy-en-Josas

first: Anaïs

last: Vitorino Carvalho

address: Domaine de Vilvert

department: BDR

country: France

institute: INRA

organism: Oryctolagus cuniculus

description:
Biopuce maison pour l'analyse du transcriptome lapin

Arrays of this design have barcodes that begin with 16075973 or 2575973.

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-062560 C. albicans whole genome probe G4499A

city: Montreal

first: Walters

middle: Aji

last: Tebung

state: Quebec

address: 7141 Rue Sherbrooke Ouest

department: Chemistry and Biochemistry

country: Canada

institute: Concordia University

organism: Candida albicans

description:
Arrays of this design have barcodes that begin with 16062560 or 2562560

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-075257 Bovine Microarray FECUND INRA v2 022520

organism: Bos taurus

description:
Arrays of this design have barcodes that begin with 16075257 or 2575257.

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 (Paenibacillus amylolyticus; Xanthomonas retroflexus)

status: Public on Apr 14 2016

organism:
Paenibacillus amylolyticus
Xanthomonas retroflexus


title: Illumina HiSeq 2000 (Microbacterium oxydans; Paenibacillus amylolyticus; Stenotrophomonas rhizophila; Xanthomonas retroflexus)

organism:
Paenibacillus amylolyticus
Microbacterium oxydans
Stenotrophomonas rhizophila
Xanthomonas retroflexus


title: Illumina HiSeq 2000 (Microbacterium oxydans; Xanthomonas retroflexus)

organism:
Microbacterium oxydans
Xanthomonas retroflexus


title: Agilent-066279 Bovine_Microarray_FECUND_INRA_v1

description:
Microarray pour expression génique chez la vache

Arrays of this design have barcodes that begin with 16066279 or 2566279.

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-042300 CGH array G4884A [Feature number version]

city: Dallas

first: Jiadi

last: Wen

state: TEXAS

address: 2330 Inwood Rd

institute: UT Southwester Medical Center

organism: Homo sapiens

description:
Arrays of this design have barcodes that begin with 16042300 or 2542300

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 (Stenotrophomonas rhizophila; Xanthomonas retroflexus)

organism:
Stenotrophomonas rhizophila
Xanthomonas retroflexus


title: Illumina HiSeq 2000 (Vernicia montana)

status: Public on Apr 13 2016

organism: Vernicia montana


title: Illumina MiSeq (Gardnerella vaginalis AMD)

status: Public on Apr 11 2016

organism: Gardnerella vaginalis AMD


title: Affymetrix Cynomolgus Gene 1.0 ST

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

organism: Macaca fascicularis

description: Summarized at the transcript level


title: Ion Torrent Proton (Escherichia coli)

organism: Escherichia coli


title: Illumina HiSeq 2000 (Xanthomonas retroflexus)

organism: Xanthomonas retroflexus


title: Illumina HiSeq 2000 (Aspergillus niger)

organism: Aspergillus niger


title: [Axiom_Exome_1A] Affymetrix Axiom Exome 1A Array

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

description: Data table: Axiom_Exome_1A.na35.annot.csv


title: Illumina HiSeq 2000 (Drosophila heteroneura)

organism: Drosophila heteroneura


title: Illumina HiSeq 2000 (Drosophila hemipeza)

organism: Drosophila hemipeza


title: Illumina HiSeq 2000 (Drosophila silvestris)

organism: Drosophila silvestris


title: Agilent-027414 SurePrint G3 Mouse CGH Microarray 1x1M (PROBE NAME)

first: GEO

last: admin

organism: Mus musculus

description:
Arrays of this design have barcodes that begin with 16027414 or 2527414.

Data table annotations based on NCBI Build 37 (UCSC mm9), July 2007.

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: Agilent Solea senegalensis Aquagenet array (Feature Number version)

status: Public on Apr 08 2016

city: Campanillas

first: Rocio

last: Bautista

state: Malaga

address: C/ Severo Ochoa, 34. Parque Tecnologico

department: Edificio de Bioinnovacion

country: Spain

institute: Universidad de Malaga

organism: Solea senegalensis

description: SoleaAquagenet

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


title: Illumina Genome Analyzer (synthetic construct)

organism: synthetic construct


title: Agilent-060976 Aspergillus nidulans custom design 8x15K v1

city: CHATENAY-MALABRY

first: Claudine

last: DELOMENIE

address: 5, rue Jean-Baptiste Clément

department: Transcriptomique

institute: University Paris Sud 11

organism: Aspergillus nidulans

description:
Arrays of this design have barcodes that begin with 16060976 or 2560976.

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 2500 (Betula luminifera)

organism: Betula luminifera


title: Agilent-028982 Pseudomonas aeruginosa PAO1 and bacteriophage PaP1 8X15K array [Probe Name Version]

city: shanghai

first: qian

last: jin

address: libing road

institute: MSP

organism:
Pseudomonas aeruginosa PAO1
Pseudomonas phage PaP1

description:
Array includes sequences from Pseudomonas aeruginosa bacteriophage PaP1.

Arrays of this design have barcodes that begin with 16028982 or 2528982.

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).


title: Illumina HiSeq 2000 (Drosophila hawaiiensis)

organism: Drosophila hawaiiensis


title: Agilent-023783 S. pombe

status: Public on Apr 06 2016

city: Baltimore

first: Risa

last: Burr

address: 725 N Wolfe St, Physiology 107B

department: Cell Biology

institute: Johns Hopkins University School of Medicine

organism: Schizosaccharomyces pombe

description:
Arrays of this design have barcodes that begin with 16023783 or 2523783.

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 (Cloning vector pUC19)

last: GEO

organism: Cloning vector pUC19


title: Illumina HiSeq 2000 (Swertia japonica)

organism: Swertia japonica


title: ZB/SBS-NTU Plasmodium Rodent YBC 11.6K v1

city: Singapore

first: Regina

last: Hoo

address: 60, Nanyang Drive

department: School of Biological Science

country: Singapore

institute: Nanyang Technological University

organism:
Plasmodium berghei
Plasmodium chabaudi
Plasmodium yoelii

manufacture_protocol: Long oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350.  The 60-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biology 2003, 4:R9.


title: NimbleGen S. purpuratus expression array [2006_02_13_S_purpuratus_60mer]

status: Public on Apr 07 2016

city: Bethesda

first: Robert

middle: C

last: Angerer

address: 30 Convent Drive

institute: NIDCR

organism: Strongylocentrotus purpuratus

description: This array is based on predicted ORF from S. purpuratus genome. Nimblegen design name is 2006-02013_S_purpuratus_60mer. The design ID is 3052. There are 2 sets (blocks) of probes on each slide.

manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology.


title: Illumina HiSeq 2000 (Shewanella oneidensis)

status: Public on Apr 05 2016

organism: Shewanella oneidensis


title: Illumina HiSeq 2000 (Drosophila grimshawi)

organism: Drosophila grimshawi


title: Illumina Genome Analyzer IIx (Caulobacter vibrioides)

status: Public on Apr 04 2016

organism: Caulobacter vibrioides


title: PacBio RS (Caulobacter crescentus NA1000)

organism: Caulobacter vibrioides NA1000


title: Illumina MiSeq (Vibrio cholerae O1 biovar El Tor str. N16961)


title: PacBio RS (Caulobacter vibrioides)


title: Illumina HiSeq 2500 (unidentified herpesvirus)

organism: Herpesviridae sp.


title: Applied Biosystems (Thermo Fisher) Human Taqman MicroRNA OpenArray

first: Kenneth

middle: W

last: Witwer

state: Maryland

address: 733 N. Broadway

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University

organism: Homo sapiens


title: Ion Torrent Proton (Cucumis sativus)

status: Public on Apr 01 2016

organism: Cucumis sativus


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: mogene10stv1_75_030]

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

institute: Eurac Researc

organism: Mus musculus

description:
This Platform is identical to GPL6246 but a custom cdf environment was used to extract data.
The custom CDF and annotation file (transcript level probe sets, Ensembl 75 based) are linked below as a supplementary file.

relation: Alternative to: GPL6246 (Alternative CDF [official])

manufacture_protocol: See manufacturer's web site


title: Human Exonic Evidence Based Oligonucleotide (HEEBO) array [hoas.gal]

city: Monterrey

first: Sean-Patrick

last: Scott

state: Neuvo Leon

address: Morones Prieto 3000 Pte

department: Cellular Therapy

country: Mexico

institute: Tecnológico de Monterrey

manufacturer: The Stanford Functional Genomics Facility (SFGF)

manufacture_protocol:
see manufacturer's website
The oligonucleotide set consists of 44,544 70-mer probes that recognizes all known genes, and positive and buffer controls.


title: Exiqon human V3 microRNA PCR panel I+II

status: Public on Jan 13 2015

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description:
PCR assay

A different version of this platform with PROBE_ID in the ID column is assigned accession number GPL21760


title: IEG GeoChip 4.0 (Cai)

city: Beijing

first: Man

last: Cai

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

organism: Bacteria


title: Agilent-060762 Colletotrichum orbiculare 20131009Cob 060761 (Probe name version)

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

organism: Colletotrichum orbiculare

description:
Colletotrichum orbiculare probes only.

Arrays of this design have barcodes that begin with 16060762 or 2560762.

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


title: Illumina HiSeq 2000 (Penicillium oxalicum)

status: Public on May 27 2015

organism: Penicillium oxalicum


title: Illumina NextSeq 500 (Schmidtea mediterranea)

organism: Schmidtea mediterranea


title: CodeLink™ Mouse Whole Genome Bioarray

status: Public on Oct 12 2007

city: Seoul

first: Min Joo

last: Lee

address: Hyochangwon-gil 52, Yongsan-ku

department: Department of Biological Science

country: South Korea

institute: Sookmyung Women's University

first: M

first: K

last: Yoo

first: J

last: Park


title: UIUC Honey bee oligo 13K v1

status: Public on Feb 15 2012

city: Piracicaba

first: Ana

middle: Durvalina

last: Bomtorin

state: São Paulo

address: R Ajudante Albano 847

institute: Universidade de Sao Paulo

organism: Apis mellifera

description: UIUC Honey bee oligo 13K v1 Array Protocol May 13, 2007  Array Development text by Jay D. Evans, Gene E. Robinson and Gos Micklem.  This document describes the features on a first-generation oligonucleotide microarray developed for the honey bee genome. Funding for this project was provided by USDA-National Research Initiative grant AG2004-36504-14277 (G.E. Robinson, PI, M. Band, J.D. Evans, G. deGrandi Hoffman, K.P. White, Co-PIs) ?Honey Bee Applied Genomics and Development of a Whole-Genome Array?.  The developmental files can be accessed at  http://www.biotech.uiuc.edu/centers/Keck/Functional_genomics/Honey%20Bee%20Oligo.htm  Input sequences:  A total of 13,145 sequences were used to design oligos, as detailed below: 1) A set primarily from the Honey Bee Genome Sequencing Consortium ?Official Gene Set? (circa 11/2005) (N = 10620). 2) Variable exons from the antimicrobial peptide apidaecin (Genbank and Evans, J.D., unpublished) (N = 11). 3) Variable exons from the IG-family gene Dscam (N = 81). 4) miRNA precursor candidates from the bee genome (Weaver, D.B., et al., submitted) (N = 81). 5) non-OGS EST?s from a subtractive library biased toward larval genes upregulated with exposure to the bacterial pathogen Paenibacillus larvae, Evans, J.D., unpublished. RNA was derived from 1st-instar honey bee larvae challenged with bacteria as described in Evans and Pettis, 2005, Evolution, 59(10), 2270-2274 (N=81). 6) Non-OGS EST?s from the Univ. Illinois bee brain EST project (Whitfield, C. W., Band, M. R., Bonaldo, M. F., Kumar, C. G., Liu, L., Pardinas, J. R., Robertson, H. M., Bento Soares, M. & Robinson, G. E., 2002, Genome Research, 12, 555-566.) (N=2271). 7) Representative genes from viral, fungal, bacterial, and microsporidian pathogens of honey bees (all in Genbank, ID?s in fasta file) (N=22).  Oligo Design:  Long oligos for the array were developed by Debashis Rana and Gos Micklem (http://www.gen.cam.ac.uk/Research/micklem.htm) at Cambridge University, using a modified version of OligoArray 2.1 in an iterative process to identify unique sequences (60-69mers) from each of the described (above) bee-related genes and gene fragments. The set of oligos was selected to have as tight a melting temperature distribution as possible, and to avoid repetitive sequences and other anomalies. A total of 12,915 unique oligos were generated (see below for redundancies) representing all but three of the 13,145 source sequences. Of those three (the pathogen gene PlDNAk, the EST sequence JDEA05_1Def3, and the candidate miRNA precursor HCmir13a), the EST and miRNA were represented by 98% identical oligos in the array. Reverse strand oligos were added for 525 predictions, focusing on EST reads and transcripts predicted for bee pathogens (EST ? 415; miRNA ? 57; OGS ? 31, and pathogen ? 22). As such the final set contains 13,440 oligos (sequences in Array_fasta/Oligoset13440.txt). The design process was similar to that of the INDAC long oligo set designed for the fruit fly Drosophila melanogaster and available at: http://www.flymine.org/release-5.0/aspect.do?name=INDAC and http://www.flychip.org.uk/services/core/FL002.  Oligo and Sequence Redundancy:  Distinctly numbered oligos had the same or similar sequences 69 times (>59/69 nt alignment, < 2 mismatches). Different source sequences matched identical oligos (>59/69, < 2 mismatch) 100 times, 44 of which were not genes with predicted splice variants (which were redundant in OGS). 18 were gene calls with splice variants for which oligos matched each variant. 639 source sequences showed matches at the sequence level but did not have identical oligo matches. Of these 524 reflect either splice variants or shared exons (e.g., Dscam exons vs. an entire proposed transcript). 115 are not indicated as splice variants and these appear to be redundant sequences in the source files, either from multiple predictions in OGS or from unrecognized similarity between EST?s and other EST?s or OGS. Most redundancies were single pairs, although one oligo sequence was similar across 6 distinctly called oligos.   Printing the Array text by Mark Band and Al Bari  Oligos were synthesized by Invitrogen (San Diego, CA) and aliquoted into 384 well plates in Sodium Phosphate buffer. Final concentration of the oligos was 20 uM (micromolar). Arrays were printed on Corning UltraGAPS slides using an Omingrid 100 printing robot (Genomic Solutions, Ann Arbor Michigan) with Arrayit SMP2.5 capillary pins. Following printing slides were stored in vacuum bags purged with Argon gas.   Creating the Array Design File (ADF) text by Amro Zayed  To ensure that the ADF contains the latest annotation, we first blasted all Honey bee oligos against: 1) The prerelease updated version of OGS v2 (http://racerx00.tamu.edu/downloadFASTA.html - circa 4/9/2007), 2) NCBI?s gene predictions (Ref RNA) for the Honey bee (circa 4/18/2007), 3) All honey bee derived EST sequences on NCBI (circa 4/25/2007), and 4) The latest assembly of the Honey bee genome (AMEL 4.0, circa 4/25/2007).  We used blastn with no filtering and we initially retained all matches with an evalue smaller than 1e-3.  We then removed blast hits that had an alignment length that is > 4 bp less then the oligo length and/or had an alignment identity less than 95%.  Except for the control groups and the Pathogen set, we assigned an oligo?s ?Reporter Name?, regardless of which set it was originally designed from, based on the best blast match to the above mentioned databases, assigning priority in the following order: prerelease OGS v2, NCBI?s gene predictions, EST sequence names, and AMEL 4.0 assembly location.  In cases where an oligo matched more than one sequence in the prerelease OGS v2 or NCBI?s gene predictions at the same evalue, we assigned the ?Reporter Name? and corresponding database accession ID to the gene with the highest numerical value, but included the list of equally matching genes in the ?Reporter Comment? field.  If an oligo matched to both prerelease OGS v2 and NCBI?s gene prediction, we assigned the ?Reporter Name? as the OGS v2 gene name followed by the definition line from NCBI?s gene prediction, in addition to assigning both accession numbers to the oligo.  When an oligo matched a prerelease OGS v2 gene, we added its Drosophila ortholog as computed by C. Elsik (http://racerx00.tamu.edu/bee_resources.html) in the ?Reporter Comment?.  We also used blastp to query the Honey bee gene against Drosophila melanogaster v.5.1 genes (http://flybase.bio.indiana.edu/ circa 5/1/2007), and the best match was also reported in the ?Reporter Comment?.  For oligos that did not match entries in any of the above mentioned databases, we retained the original annotation information used to design the oligo.  Similarly, we retained all the annotation information from the design files for the control sequences and for the Pathogen set.

manufacturer: Keck Center for Comparative and Functional Genomics - University of Illinois

middle: D

first: Angel

middle: R

last: Barchuk

first: Zilá

middle: L

last: Simoes

manufacture_protocol: Honey bee oligonucleotide microarray v1 contains 28800 features, and a total of 13440 double spotted ss oligos.  Oligos were synthesized by Invitrogen (San Diego, CA) and aliquoted into 384 well plates in Sodium Phosphate buffer. Final concentration of the oligos was 20 uM (micromolar). Arrays were printed on Corning UltraGAPS slides using an Omingrid 100 printing robot (Genomic Solutions, Ann Arbor Michigan) with Arrayit SMP2.5 capillary pins. Following printing slides were stored in vacuum bags purged with Argon gas.


title: Mead Lab Human MEP RT-PCR Array

status: Public on Apr 02 2016

city: Oxford

first: Adam

last: Mead

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

description: Taqman gene expression assays (Life Technologies)

manufacture_protocol: see manufacturer's website


title: Bacillus subtilis Custom Agilent 44k v2

status: Public on Dec 01 2010

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

institute: University Medicine Greifswald

organism: Bacillus subtilis subsp. subtilis str. 168

manufacture_protocol: The arrays are produced by Agilent Technologies SurePrint technology (for details, see manufacturer's web site). Each protein coding gene of Bacillus subtilis str. 168 (GenBank record AL009126.2) is represented by 1 to 5 long oligonucleotides.


title: NimbleGen Arabidopsis thaliana Gene Expression 12x135K Array [100718_Athal_TAIR9_exp; SEQ_ID]

status: Public on Jul 26 2011

city: Madison

first: Inc

last: Nimblegen Systems

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Arabidopsis thaliana

description:
DESIGN_ID: 535493
DESIGN_NAME: 100718_Athal_TAIR9_exp

manufacture_protocol: See manufacturer's website at http://www.nimblegen.com/


title: Illumina HiSeq 2500 (Schmidtea mediterranea)

status: Public on May 05 2015

last: GEO