title: Agilent-017616 : S. Bayanus 44k tiling 0827

status: Public on Sep 30 2016

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

country: USA

institute: University of Washington

organism: Saccharomyces bayanus

technology: in situ oligonucleotide

description: 44k S. Bayanus tiling array

distribution: commercial

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


title: 20050609MD_PMC

organism:
Saccharomyces bayanus
Saccharomyces cerevisiae

technology: spotted oligonucleotide

description: Dunham project-SCSB-1, a multi-organism print.

distribution: non-commercial

manufacturer: Lewis-Sigler Institute Microarray Facility

manufacture_protocol:
The following parameters were used to manufacture the printed array named "20050609MD_PMC"
Printer: Arrayer 250B
Array Configuration: (columns X rows) 48 sectors ( 4 X 12 spotted) Standard 48 tip
Spot Columns per Sector: 24
Spot Rows per Sector: 12
Column Spacing: 184
Row Spacing: 156
Plate Orientation: rotated 90 degrees clockwise (P1 top-left, A1 top-right)
Printhead Dip Dynamics: top to bottom, right to left
Sector Spotting Dynamics: left to right, top to bottom
Number of Slides: 46
Plates used in this print, in order.
PLATEID PLATENAME PLATE_VISITS IS_FLIPPED
100530 70_N_SSC_1
100513 HYBRIDSC_1
100514 HYBRIDSC_2
100515 HYBRIDSC_3
100516 HYBRIDSC_4
100517 HYBRIDSC_5
100518 HYBRIDSC_6
100519 HYBRIDSC_7
100520 HYBRIDSC_8
100521 HYBRIDSC_9
100522 HYBRIDSC_10
100523 HYBRIDSC_11
100524 HYBRIDSC_12
100525 HYBRIDSC_13
100526 HYBRIDSC_14
100527 HYBRIDSC_15
100528 HYBRIDSC_16
100529 HYBRIDSC_17
100500 HYBRIDSB_1
100501 HYBRIDSB_2
100502 HYBRIDSB_3
100503 HYBRIDSB_4
100504 HYBRIDSB_5
100505 HYBRIDSB_6
100506 HYBRIDSB_7
100507 HYBRIDSB_8
100508 HYBRIDSB_9
100509 HYBRIDSB_10
100510 HYBRIDSB_11
100511 HYBRIDSB_12
100512 HYBRIDSB_13
100528 HYBRIDSC_16
100525 HYBRIDSC_13
100524 HYBRIDSC_12


title: Illumina HiSeq 2500 (Zika virus)

last: GEO

organism: Zika virus

technology: high-throughput sequencing

distribution: virtual


title: Mouse NIA 15k NCI-FCRF

city: Santiago

first: Ulises

last: Urzua

address: Independencia 1027

department: Basic and Clinical Oncology

country: Chile

institute: University of Chile

organism: Mus musculus

technology: spotted DNA/cDNA

manufacturer: Laboratory of Molecular Technology - NCI Frederick

manufacture_protocol: individual cDNAs obtained by PCR from bacterial clones; amplicons purified by column and stored in 384 plates; DNA concentration>1ug/ul; microarrays printed on poly-lysine coated, succinic anhydride treated slides with a MicroGrid BioRobotics arrayer.


title: Illumina HiSeq 2500 (Pantoea stewartii subsp. stewartii DC283)


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [CDF: HuEx10stv2_Hs_ENTREZG.cdf, Brainarray v16.0.0]

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

description: This array is identical to GPL5175 but the data were analyzed with a custom CDF environment (HuEx10stv2_Hs_ENTREZG.cdf, Brainarray v16.0.0).

distribution: custom-commercial

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

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


title: miRCURY LNA microRNA Array, v.11.0 - hsa, mmu & rno [miRBase 13.0]

status: Public on Jun 15 2017

city: Jackson

first: Damian

middle: G.

last: Romero

state: MS

address: 2500 N. State St.

department: Biochemistry

institute: University of Mississippi Medical Center

organism: Rattus norvegicus

manufacture_protocol: See manufacturers website (www.exiqon.com)


title: Illumina MiSeq (uncultured bacterium)

status: Public on Sep 27 2016

organism: uncultured bacterium


title: 20050711MD_PMC

description: Dunham project-SCSB-1-print 2, a multi-organism print.

manufacture_protocol:
The following parameters were used to manufacture the printed array named "20050711MD_PMC"
Printer: Arrayer 250B
Array Configuration: (columns X rows) 48 sectors ( 4 X 12 spotted) Standard 48 tip
Spot Columns per Sector: 24
Spot Rows per Sector: 11
Column Spacing: 184
Row Spacing: 156
Plate Orientation: rotated 90 degrees clockwise (P1 top-left, A1 top-right)
Printhead Dip Dynamics: top to bottom, right to left
Sector Spotting Dynamics: left to right, top to bottom
Number of Slides: 230
Plates used in this print, in order.
PLATEID PLATENAME PLATE_VISITS IS_FLIPPED
100530 70_N_SSC
100511 HYBRIDSB_12
100508 HYBRIDSB_9
100524 HYBRIDSC_12
100521 HYBRIDSC_9
100505 HYBRIDSB_6
100519 HYBRIDSC_7
100526 HYBRIDSC_14
100518 HYBRIDSC_6
100504 HYBRIDSB_5
100502 HYBRIDSB_3
100516 HYBRIDSC_4
100522 HYBRIDSC_10
100520 HYBRIDSC_8
100506 HYBRIDSB_7
100510 HYBRIDSB_11
100512 HYBRIDSB_13
100529 HYBRIDSC_17
100513 HYBRIDSC_1
100525 HYBRIDSC_13
100528 HYBRIDSC_16
100517 HYBRIDSC_5
100507 HYBRIDSB_8
100503 HYBRIDSB_4
100514 HYBRIDSC_2
100509 HYBRIDSB_10
100501 HYBRIDSB_2
100523 HYBRIDSC_11
100515 HYBRIDSC_3
100500 HYBRIDSB_1
100527 HYBRIDSC_15


title: Oryza sativa 3'-Tiling 300k Microarray

city: Pyeongchang

first: Dong-Keun

last: Lee

address: Pyeongchang Dae-ro, Daehwa-myeon

department: GBST

country: South Korea

institute: Seoul National University

organism: Oryza sativa

description:
Array provided by Ggbiotech (Http://www.ggbio.com); designed for cultivar Nipponbare
Submitter states that the .ngd and .ndf files are not available for this array.  Instead, text files with platform metadata and cDNA sequences have been provided.

manufacture_protocol: This microarray chip contains 27,448 genes deposited at the International Rice Genome Sequencing Project Rice Annotation Project 1 database (http://rapdb.lab.nig.ac.jp). Among the genes on the microarray, 20,507 genes are from Rice Annotation Project 1 sequences with cDNA/EST supports, and 6,941 genes are predicted without cDNA/EST supports. Ten probes per each gene are designed at the 3’ region of the gene to detect gene expression.


title: Illumina MiSeq (Ruminiclostridium thermocellum 27405)

organism: Acetivibrio thermocellus ATCC 27405


title: Illumina MiSeq (Acinetobacter baumannii ATCC 17978)

organism: Acinetobacter baumannii ATCC 17978


title: Illumina HiSeq 2500 (Fervidobacterium islandicum)

organism: Fervidobacterium islandicum


title: [Rat230_2] Affymetrix Rat Genome 230 2.0 Array [CDF: Rat2302_Rn_ENTREZG_19.0.0]

status: Public on Sep 28 2016

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

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

manufacture_protocol: See manufacturer's web site.


title: Illumina HiSeq 2500 (Salmonella enterica subsp. enterica serovar Typhimurium str. LT2)


title: Illumina HiSeq 1500 (Metallibacterium scheffleri)

status: Public on Sep 26 2016

organism: Metallibacterium scheffleri


title: Illumina HiSeq 2000 (Fusarium oxysporum)

organism: Fusarium oxysporum


title: Illumina NextSeq 500 (Amphimedon queenslandica)

organism: Amphimedon queenslandica


title: Agilent-022594 Midge Expression [Probe Name version]

status: Public on Sep 29 2016

city: Stoneville

first: JIANXIU

last: YAO

state: Mississippi

address: 141 Experiment station Rd

institute: USDA-ARS

organism: Chironomus tentans

description:
Chironomus tentans

Arrays of this design have barcodes that begin with 16022594 or 2522594.

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 MiSeq (Homo sapiens; Influenza A virus (A/Puerto Rico/8/1934(H1N1)))

organism:
Homo sapiens
Influenza A virus (A/Puerto Rico/8/1934(H1N1))


title: Illumina HiSeq 2000 (Ustilaginoidea virens)

organism: Ustilaginoidea virens


title: GeoChip 3.0 [2016]

city: Norman

first: Jizhong

last: Zhou

state: OK

address: 101 David L Boren Blvd

department: Department of Microbiology and Plant Biology

institute: University of Oklahoma

organism:
Bacteria
Archaea
Fungi
Viruses


title: Illumina HiSeq 2000 (Pantoea ananatis LMG 2665)

status: Public on Sep 22 2016

organism: Pantoea ananatis LMG 2665


title: Illumina HiSeq 2500 (Moricandia arvensis)

organism: Moricandia arvensis


title: Illumina Genome Analyzer Iix (Mus musculus)

status: Public on Sep 21 2016

organism: Mus musculus


title: Illumina HiSeq 4000 (Caulobacter crescentus NA1000)

organism: Caulobacter vibrioides NA1000


title: Illumina HiSeq 2500 (Moricandia suffruticosa)

organism: Moricandia suffruticosa


title: Illumina HiSeq 2500 (Clostridioides difficile)

organism: Clostridioides difficile


title: Ion Torrent PGM (Oryzias latipes)

organism: Oryzias latipes


title: Illumina HiSeq 2500 (Moricandia moricandioides)

organism: Moricandia moricandioides


title: Illumina NextSeq 500 (Populus tremula x Populus alba)

organism: Populus tremula x Populus alba


title: LC Sciences porcine miRNA Array (miRPig_20_LCB_140313)

city: Hangzhou

first: Xin

last: Tao

address: Shiqiao Road 145

country: China

institute: Zhejiang Academy of Agricultural Sciences

organism: Sus scrofa

description:
Part No. MRA-1013
Version No. miRPig_20_LCB_140313
Based on Sanger miRBase Release 20

manufacture_protocol: On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.


title: Agilent-046065 Mouse miRNA Microarray (miRBase release 21 miRNA ID version)

description: Grid Date: Oct-6-2014 (corresponding to miRBase release 21)

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


title: [Atdschip_expr] Affymetrix AGRONOMICS1 expression array (CDF: agronomics1_TAIR10_gene)

city: NORWICH

first: Robert

last: Sablowski

state: Norfolk

address: The John Innes Centre

department: CDB

country: United Kingdom

institute: JIC

organism: Arabidopsis thaliana

manufacture_protocol: see manufacturer's website; European AGRONOMICS project


title: Fluidigm RT-PCR array for AML human samples

city: TOULOUSE

first: DAVID

last: Laure

address: 2 avenue Hubert CURIEN

institute: Cancer Research Center of Toulouse

organism: Homo sapiens

technology: RT-PCR

description: PCR assay

manufacturer: Biomark Dynamic Arrays (Fluidigm, BioMark, Pueblo, CO, USA

manufacture_protocol: see manufacturer's website


title: Agilent-038779 UniversityPadova_Ruditapes philippinarum_8x15K_v4

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

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

country: Italy

institute: University of Padova

organism: Ruditapes philippinarum

description:
In situ long-oligonucleotide microarray
GE 8x15k oligo microarray that covers 14,805  transcripts of the Manila clam (Ruditapes philippinarum).  Illumina libraries public available produced by Passamonti et al. (2012), 454 sequences produced by Milan et al. (2011; SRX022422), and 454 sequences produced by Moreira et al. (2012; SRX100159) were assembled by using CLC Genomic Workbench 5 (default parameters). A total of 283.752 assembled contigs produced by CLC bio assembly have been annotated  through blastx similarity searches conducted against UniProtKB/SwissProt database and few protein databases available on Ensembl Genome Browser: Homo sapiens, Danio rerio, and Drosophila melanogaster. Alignments with an E-value of at most 1 E-4 were considered significant and only the best hit per contig was taken into account. In order to recover probes employed and validated in the previous versions of R. philippinarum microarray (Milan et al. 2011; Milan et al. 2014) blastn has been performed versus the “new” annotated contigs generated. In addition, probes representing transcripts  correlated to pollutants concentrations in previous study (Milan et al. 2013) have been also considered. A total of 866 probes were already employed on a previous versions of the microarray (GPL10900 and GPL15723) and maintained the same Probe ID (contig ID plus suffix _1, _2, _AS or _S). For the others transcipts probe design started with selection of 15,098 non-redundant annotated contigs to be represented onto the R. philippinarum microarray. As most sequence reads were obtained from a non directional cDNA library, sense strand orientation was inferred putatively from that of homologuous protein sequences of other species. One probe for annotated transcripts with known orientation was designed to construct a high-density oligo-DNA microarray, while two probes with both orientations were designed for contigs with ambiguous orientation. Probe design was carried out using the Agilent eArray interface [https://earray.chem.agilent.com/earray/], which applies proprietary prediction algorithms to design 60 mer oligoprobes. A total of 14,171 probes have been successfully obtained and considered for the microarray design. A total of 15,037 probes (14,171 “new” probes, and 866 probes represented in previous R. philippinarum microarray platform) representing 14,805 transcripts were successfully represented in the new DNA microarray platform. Both independent probes designed for the same transcript are named with an univocal ID; the sense probes are distinguished by suffix_S while the anti-sense probes are distinguished by suffix _AS. Oligonucleotides, 60-mer plus a “linker”, are synthesized directly on glass slide using the Agilent’s SurePrint Tecnology.

Please note that the contig are not available in any public database yet. A "txt file" with new contigs considered will be provide as supplementary file with the associated publication. In addition, we are uploading a Ruditapes philippinarum database containing all contigs obtained to date: http://compgen.bio.unipd.it/ruphibase/. However this database has not yet been updated.

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


title: Agilent-074128 Nb_101_March2015

status: Public on Sep 19 2016

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

organism: Nicotiana benthamiana

description:
Nicotiana benthamiana gene expression microarray based on N. benthamiana 1.0.1 genome annotation

Arrays of this design have barcodes that begin with 16074128 or 2574128.

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 (Imperata cylindrica)

organism: Imperata cylindrica


title: Phalanx Human lncRNA OneArray v1_lncRNA

status: Public on Sep 20 2016

city: Hsinchu City

first: Rachel

last: Huang

address: 6F., No.6, Keji 5th Rd., East Dist.

country: Taiwan

institute: Phalanx Biotech Group

manufacture_protocol: See http://www.phalanxbiotech.com/ for updated protocols


title: Illumina HiSeq 2000 (Capillipedium parviflorum)

organism: Capillipedium parviflorum


title: NanoString nCounter human

city: Spartanburg

first: Bernard

last: Omolo

state: SC

address: 800 University Way

department: Mathematics and Computer Science

institute: University of South Carolina - Upstate

technology: other


title: Illumina HiSeq 2000 (Bothriochloa ischaemum)

organism: Bothriochloa ischaemum


title: Illumina HiSeq 2000 (Solanum lycopersicum x Solanum pennellii)


title: Illumina HiSeq 2000 (Arundinella pubescens)

organism: Arundinella pubescens


title: [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array [CDF: mouse4302mmentrezgaltrabio11112cdf]

city: LYON

first: Jacqueline

last: MARVEL

address: 21 AV TONY GARNIER

institute: INSERM

manufacture_protocol: This is identical to GPL1261 but a custom cdf environment was used to extract data. The cdf can be found at the link below.


title: Illumina HiSeq 2000 (Solanum pennellii)

organism: Solanum pennellii


title: Illumina HiSeq 2000 (Arundinella nepalensis)

organism: Arundinella nepalensis


title: Illumina HiSeq 2000 (Arundinella hirta)

organism: Arundinella hirta


title: Illumina HiSeq 2000 (Arundinella fluviatilis)

organism: Arundinella fluviatilis


title: Agilent-072413 FADRU Bovine 4x45K v3 array (Feature number version)

city: Orient

first: James

last: Zhu

state: NY

department: Foreign Animal Disease Research Unit

organism:
Bos taurus
Foot-and-mouth disease virus
Human adenovirus 5

manufacture_protocol: SurePrint HD, see manufacturer's web site


title: Illumina HiSeq 2000 (Arundinella anomala)

last: GEO

organism: Arundinella anomala


title: LC Sciences A. thaliana miRNA LC_MRA-1010_miRArabidopsisT_20

first: Xunyan

last: Liu

address: Xuelin street 16#, Xiasha,

institute: Hangzhou Normal University

description: Standard Mature miRNAs based on Sanger miRBase Release 20.

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 HiSeq 2500 (Serapias vomeracea)

organism: Serapias vomeracea


title: Illumina HiSeq 2500 (Apera spica-venti)

status: Public on Sep 16 2016

organism: Apera spica-venti


title: Illumina HiSeq 2500 (Serapias vomeracea; Tulasnella calospora)

status: Public on Sep 15 2016

organism:
Serapias vomeracea
Tulasnella calospora


title: Illumina HiSeq 2500 (Corynebacterium glutamicum)

organism: Corynebacterium glutamicum


title: Illumina HiSeq 2500 (Tulasnella calospora)

organism: Tulasnella calospora


title: [bMxHERV3b520850] Affymetrix HERVV3 Array

city: Pierre Bénite

first: Jeremie

middle: FC

last: Becker

address: Centre Hospitalier Lyon Sud, Bâtiment 3F

department: Medical diagnostic Discovery department

institute: bioMérieux

organism: Homo sapiens

manufacture_protocol: Affymetrix


title: Illumina HiSeq 4000 (Trichodesmium erythraeum IMS101)

organism: Trichodesmium erythraeum IMS101


title: Illumina NextSeq 500 (Trichodesmium)

organism: Trichodesmium


title: Illumina NextSeq 500 (Trichodesmium thiebautii VI-1)

organism: Trichodesmium thiebautii VI-1


title: Illumina NextSeq 500 (Trichodesmium erythraeum 21-75)

organism: Trichodesmium erythraeum 21-75


title: Illumina NextSeq 500 (Trichodesmium erythraeum IMS101)


title: 3D-Gene Rat Oligo chip 20k V1.2.0

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

organism: Rattus norvegicus

manufacture_protocol: See manufacturer's web site


title: Agilent-030951 A. lyrata 8X60 {Probe Name version]

status: Public on Sep 14 2016

city: Kolkata

first: Malay

last: Das

state: West Bengal

address: 86/1 College Street

department: Biological Sciences

country: India

institute: Presidency University

organism: Arabidopsis lyrata

description:
Arrays of this design have barcodes that begin with 16030951 or 2530951.

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 Names.

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 4000 (Helicoverpa armigera)

organism: Helicoverpa armigera


title: Illumina HiSeq 2000 (Populus tremula)

organism: Populus tremula


title: Illumina HiSeq 2500 (Candida albicans SC5314; Homo sapiens)

organism:
Homo sapiens
Candida albicans SC5314


title: Illumina HiSeq 2000 (Propionibacterium acidipropionici)

organism: Acidipropionibacterium acidipropionici


title: CapitalBio Rat 27k long oligo array [v2]

status: Public on Sep 13 2016

city: Jinan

first: Yuchao

last: Zhang

address: 44 Wenhua Road West

institute: Shandong University

manufacture_protocol: as described in CapitalBio Labs manual


title: miRCURY LNA™ Universal RT microRNA PCR, Ready-to-Use Mouse&Rat Panel I V3

status: Public on Sep 10 2016

city: Lanzhou

first: Wenjun

last: Wei

address: 509 Nanchang Road

institute: Institute of Modern Physics, Chinese Academy of Sciences

organism: Mus musculus

description: 384 well PCR assay pannel


title: Illumina MiSeq (Xenopus laevis)

organism: Xenopus laevis


title: SurePrint G3 Rat GE 8x60K Microarray Toxplus ver.2 [Probe Name Version]

city: Kitakatsushika-gun

first: Kyosuke

last: Yamashita

state: Saitama

address: Sugito-machi Shimotakano1600

department: Tokyo

institute: Chemicals Evaluation and Research Institute Japan

description: custom rat array


title: Illumina NextSeq 500 (Trichechus manatus latirostris)

status: Public on Sep 09 2016

organism: Trichechus manatus latirostris


title: [HT_MG-430_PM] Affymetrix HT MG-430 PM Array Plate [CDF: HTMG430PM_Mm_ENTREZG.cdf, Brainarray version 17]

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH


title: Illumina MiSeq (Drosophila virilis)

organism: Drosophila virilis


title: Agilent-028911 Oryza sativa eArray-N30 [Feature Number version]

city: Bellaterra (Cerdanyola del Vallés)

first: Sonia

last: Campo

state: Barcelona

address: Parc de Recerca UAB Edifici CRAG, Campus UAB

country: Spain

institute: Center for Research in Agricultural Genomics (CRAG)

organism: Oryza sativa Japonica Group

description:
Arrays of this design have barcodes that begin with 16028911 or 2528911.

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: [HT_MG-430_PM] Affymetrix HT MG-430 PM Array Plate [CDF: htmg430pmmmentrezgaltrabio12124.cdf]


title: UCI Leptospira interrogans serovar Copenhageni Protein Microarray chip LI9 and LI10

city: Irvine

first: Carolina

last: Lessa Aquino

address: 302 MedSurge II

institute: University of California Irvine

technology: spotted peptide or protein

manufacture_protocol: The arrays were produced by in vitro transcription/translation (IVTT) reactions using plasmids encoding individual leptospire ORFs as templates, and reactions printed onto nitrocellulose-coated slides. Multiple spots consisting of reactions lacking plasmid templates ('no DNA' controls) are present on each array and used for data normalization. ORFs larger than 3kb were segmented into smaller fragments and are designated as the original ORF ID followed by segment number (example: LIC10502s2). For these cases, the protein accession number corresponds to the original full protein (in that example, the accession number provided would be the one for the full LIC10502 protein).


title: Illumina HiSeq 2000 (Escherichia coli HS)

organism: Escherichia coli HS


title: Illumina MiSeq (Drosophila pseudoobscura)

organism: Drosophila pseudoobscura


title: 3D-Gene Mouse Oligo chip 24k V1.2.0


title: 454 GS FLX Titanium (Fundulus heteroclitus)

status: Public on Sep 08 2016

organism: Fundulus heteroclitus


title: Illumina HiSeq 2500 (Mesocricetus auratus)

status: Public on Sep 06 2016

organism: Mesocricetus auratus


title: Illumina NextSeq 500 (Candida albicans)

status: Public on Sep 07 2016

organism: Candida albicans


title: Agilent-044466 Copy_of_HORSE-GENOPOLE_1351163833207 026033

status: Public on Sep 04 2016

city: jouy en josas

first: Nuria

last: Mach

address: Domaine de Vilvert

institute: INRA

organism: Equus caballus

description:
Horse Agilent + 384 equine oligo

Arrays of this design have barcodes that begin with 16044466 or 2544466.

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 (Escherichia coli 102712)

organism: Escherichia coli 102712


title: Illumina HiSeq 2000 (Escherichia coli 102651)

organism: Escherichia coli 102651


title: Illumina HiSeq 4000 (Megalobrama amblycephala)

status: Public on Sep 02 2016

organism: Megalobrama amblycephala


title: Illumina NextSeq 500 (Caenorhabditis angaria)

organism: Caenorhabditis angaria


title: Illumina HiSeq 2000 (Escherichia coli ETEC H10407)

organism: Escherichia coli ETEC H10407


title: Illumina HiSeq 1500 (Streptomyces venezuelae ATCC 10712)

organism: Streptomyces venezuelae ATCC 10712


title: Illumina HiSeq 2000 (Escherichia coli 402290)

status: Public on Oct 09 2015

organism: Escherichia coli 402290


title: OPERON CYL Calbicans 1.0

city: Hsinchu

first: Yu-Ting

last: Chen

address: No.101, Sec. 2, Guang-Fu Rd.

department: Institute of Molecular and Cellular Biology

institute: National Tsing Hua University, Taiwan

description:
Operon inc. ( Candid albicans AROS? V1.2  & Candida albicans AROS? upgrade set V1.1)
Probes were dissolved in 3X SSC at a concentration of 40 ?M. The microarrays were printed on UltraGAPS-coated slide (Corning) with a GeneMachines OmniGrid 100 Microarrayer (Diglab) using CMP#3 pin (TeleChem) according to the manufacturer?s instructions. The slides post-proceed according to Corning?s protocol. GeneMachines OminGrid operation software was used to track where samples have been printed on the slides and to exprot the Gene Array list (GAL) file.

manufacture_protocol:
See manufacturer's website
DNA Microarray Core Laboratory, Institue of Plant and Microbial Biology,  Academia Sinica, Taiwan.


title: Agilent-060464 Custom Horse plus Human v18

description:
Custom Horse plus Human v18

Arrays of this design have barcodes that begin with 16060464 or 2560464.

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-062039 RoboArbovirusChip V2

city: Ribeirao Preto

first: Victor

middle: Hugo

last: Aquino

state: Sao Paulo

address: Avenida do Cafe, s/n

department: Fculty of Pharmaceutical Sciences

country: Brazil

institute: University of Sao Paulo

organism: Viruses

description:
Arrays of this design have barcodes that begin with 16062039 or 2562039.

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 Sciences MRA-1001_miRHuman_18 (miRNA_ID version)

status: Public on Sep 03 2016

city: Houston

first: Kyle

middle: Ryan

last: Navel

state: Texas

address: 2575 W. Bellfort Ave. Ste 270

department: Sales

institute: LC Sciences

organism: Homo sapiens

description: Based on Sanger miRBase Release 18

manufacture_protocol: LC Sciences


title: Illumina NextSeq 500 (Lactococcus lactis subsp. cremoris)

organism: Lactococcus cremoris


title: Agilent-048715 RoboArboChip V1

status: Public on Sep 05 2016

description:
Arrays of this design have barcodes that begin with 16048715 or 2548715.

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-067226 Plasmodium berghei Gene Expression Custom Microarray 4x44k

status: Public on Sep 01 2016

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

institute: Genotypic Technology

organism: Plasmodium berghei

description: Agilent Custom Plasmodium berghei Gene Expression Microarray 4x44k  (067226) designed by Genotypic Technology Private Limited.


title: Illumina NextSeq 500 (Glycine max)

organism: Glycine max


title: Illumina HiSeq 2000 (Escherichia coli 401140)

organism: Escherichia coli 401140


title: Agilent-033004 USP Schistosoma mansoni 4x180K microarray

city: São Paulo

first: Leticia

last: Anderson

state: SP

address: Av. Vital Brasil, 1500

department: Parasitologia

institute: Instituto Butantan

organism: Schistosoma mansoni

description:
Chip assembly with public ESTs and 454 runs from Verjo Lab

Please note that Schistosoma mansoni is not a model organism, thus the gene information used in databases and literatures consists in Smp_XXXXXX to protein coding genes as in Ensembl database
http://metazoa.ensembl.org/Schistosoma_mansoni/Info/Index

The custom designed microarray contains 60-mer probes, of which 4,854 are Agilent control probes and 176,026 non-control probes designed to detect Schistosoma mansoni expressed transcripts. All publicly available transcript information for S. mansoni were used in the design of probes, namely 260,035 ESTs available in dbEST database (downloaded in 2010), high-throughput RNA-seq sequences from 454 Roche sequencing obtained in our laboratory (doi:10.1016/j.exppara.2011.06.010) and gene predictions from the Wellcome Trust Sanger Institute. We annotated the probes with the latest S. mansoni gene predictions from genome version ASM23792v2 available in the Ensembl Metazoa database, allowing the identification of unique probes to 9,255 Smp genes and probes to 9,079 transcripts eventually generated from the genomic strand opposite to Smp genes, noting that the Agilent cRNA labeling technology is strand specific.

Arrays of this design have barcodes that begin with 16033004 or 2533004.

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 MiSeq (Drosophila ananassae)

last: GEO

organism: Drosophila ananassae


title: Corynebacterium glutamicum array [Cg3kOLI_S10]

status: Public on Jun 20 2015

city: Bielefeld

first: Hironori

last: Taniguchi

department: Biology

country: Germany

institute: Bielefeld University

organism: Corynebacterium glutamicum ATCC 13032

manufacturer: Center for Biotechnology, Bielefeld University

manufacture_protocol: Nexterion Slide E microarrays carrying 70mer oligonucleotides (nucleotide sequence is attached as file)


title: Agilent-038994 VulCanDep1

city: Göttingen

last: Chano

address: Buesgenweg 2

department: Forest Genetics and Forest Tree Breeding

institute: University of Göttingen

organism: Pinus taeda

description:
Arrays of this design have barcodes that begin with 16038994 or 2538994.

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 (Escherichia coli O127:H6 str. E2348/69)

status: Public on May 29 2015

organism: Escherichia coli O127:H6 str. E2348/69


title: Ion Torrent PGM (Cicer arietinum)

organism: Cicer arietinum


title: Agilent Yeast 8X15K conversion (Agilent-016322)

status: Public on Feb 23 2010

city: Seattle

first: Maitreya

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

organism: Saccharomyces cerevisiae

description:
Yeast 8X15K conversion
Agilent-016322

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


title: Agilent-032491 3D7v7.1_transcriptome

status: Public on Nov 06 2013

city: New York

first: Bjorn

last: Kafsack

address: 1300 York Avenue

department: Microbiology & Immunology

institute: Weill Cornell Medicine

organism: Plasmodium falciparum

description:
Arrays of this design have barcodes that begin with 16032491 or 2532491.

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: [HTA-2_0] Affymetrix Human Transcriptome Array 2.0 [transcript (gene) version]

manufacture_protocol: See manufacturer's website.


title: Agilent-067119 OE Custom Cow lncRNA Microarray (Probe Name version)

city: Yangzhou

first: Yongjiang

last: Mao

address: No.48 East Wenhui Road

institute: Yangzhou University

organism: Bos taurus

description: The ID column represents the Agilent Feature Extraction feature number.


title: Agilent-020186 C. elegans (V2) Gene Expression Microarray (Probe Name version)

status: Public on Dec 21 2010

city: Palo Alto

last: Agilent Technologies

state: CA

institute: Agilent Technologies

organism: Caenorhabditis elegans

description:
Caenorhabditis elegans (Nematode) Oligo Microarray

Arrays of this design have barcodes that begin with 16020186 or 2520186.

*** 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 GPL10094.


title: Illumina HiSeq 2000 (Tetrahymena thermophila)

status: Public on Jun 17 2012

organism: Tetrahymena thermophila


title: nCounter Mouse PanCancer Immune Profiling Panel

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

organism: Mus musculus

manufacture_protocol:
See manufacturer's website (http://www.nanostring.com)
http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf


title: Agilent-046065 Mouse_miRNA_V19.0_Microarray (miRNA ID version)

status: Public on Nov 12 2013

description: Mouse miRBase version 19.0

relation:
Alternative to: GPL19970
Alternative to: GPL22486


title: Illumina HiSeq 4000 (Xenopus laevis)

organism: Xenopus laevis


title: Illumina HiSeq 4000 (Rattus norvegicus)

organism: Rattus norvegicus


title: Agilent-016010 S.pombe 4X44K_v3 (Feature Number version)

status: Public on Mar 31 2008

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

organism: Schizosaccharomyces pombe

description:
Agilent 60mer oligo arrays tiling entire S. pombe genome across 3 chromsomes at 300bp interval alternately from the plus and minus strand.
Choromosome locations in data table are based on assembled contigs at ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Chromosome_contigs/OLD/Sep_15_2004

first: Ke

last: Zhang

first: Kerstin

last: Mosch

first: Wolfgang

last: Fischle

middle: I

manufacture_protocol: Custom 60mer oligonucleotide microarrays based upon Agilent’s non-contact in situ synthesis process