title: Saccharomyces cerevisiae 70-mer oligo DNA microarray

status: Public on Apr 16 2015

city: Peoria

first: Z Lewis

last: Liu

state: IL

address: 1815 N University

country: USA

institute: USDA-ARS

organism: Saccharomyces cerevisiae

technology: spotted oligonucleotide

description: 2 color array designed with customer requirement with universal RNA controls as described by Liu and Slininger, 2007 (J Microbiol Methods 68: 486-496)

distribution: custom-commercial

manufacture_protocol: Standard microarray print protocol by Microarray Inc.


title: Agilent-027389 Mycobacterium bovis BCG Pasteur [Probe Name Version]

status: Public on Dec 31 2014

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

organism: Mycobacterium tuberculosis variant bovis BCG

technology: in situ oligonucleotide

description:
Feature Number version of this Array is GPL13749

Arrays of this design have barcodes that begin with 16027389 or 2527389.

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


title: Agilent Platform Custom Candida  glabrata 8x15k designed by Genotypic Technology Private Limited.(AMADID: 49117)

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

organism: Nakaseomyces glabratus CBS 138

distribution: commercial


title: Agilent-021099 Bombyx mori GE 44k ccca-biased

city: Tokyo

first: Toru

last: Togawa

address: Sakurajyosui 3-25-40, Setagaya-ku

department: Integrated Sciences in Physics and Biology

country: Japan

institute: Nihon University

organism: Bombyx mori

description:
Arrays of this design have barcodes that begin with 16021099 or 2521099.
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-039723 Drosophila melanogaster expression Kim 2.0

status: Public on Jun 21 2015

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

organism: Drosophila melanogaster

manufacture_protocol: In situ oligonucleotide synthesis.


title: Illumina HiSeq 2000 (Litopenaeus vannamei)

last: GEO

organism: Penaeus vannamei

technology: high-throughput sequencing

distribution: virtual


title: NimbleGen S. cerevisiae ChIP-chip 385K Whole-Genome Tiling Array [2006-07-18_Scerevisiae_ChIP] merged Probe ID

city: MIAOLI COUNTY

first: GUNN-GUANG

last: LIOU

state: TAIWAN

address: 35 KEYAN ROAD, JHUNAN TOWN

department: INSTITUTE OF MOLECULAR AND GENOMIC MEDICINE

country: Taiwan

institute: NATIONAL HEALTH RESEARCH INSTITUTES

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


title: Agilent-068300 ArrayXS_Celegans_OakLabs_06-2014_V2

status: Public on Feb 11 2015

city: Konstanz

first: Tancred

last: Frickey

state: BW

address: Universitaetsstr. 10

department: Biology

institute: University of Konstanz

organism: Caenorhabditis elegans

description:
experimentally validated by OakLabs, MyArray strategy

Arrays of this design have barcodes that begin with 16068300 or 2568300.

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: S. Typhimurium arrays 70-mer oligos representing all LT2 annotated genes (Operon)

city: Heverlee

first: Hans

last: Steenackers

address: Kasteelpark Arenberg 20, box 2460

country: Belgium

institute: KU Leuven

organism: Salmonella enterica subsp. enterica

distribution: non-commercial

manufacture_protocol: oligonucleotides, spotted in duplicate on CodeLink Activated slides (Amersham Biosciences)


title: Lactococcus lactis ssp. cremoris MG1363 15K 60-mer array, Version 1

city: Kgs. Lyngby

first: Jun

last: Chen

state: Denmark

address: Søltofts Plads Building 221

department: Food

country: Denmark

institute: The Technical University of Denmark

organism: Lactococcus cremoris subsp. cremoris MG1363

manufacture_protocol: see manufacturer's website


title: miRCURY LNA™ microRNA Arrays (v14.0)

city: Beijing

first: Lijuan

last: Guo

address: 2 Yinghua Dongjie, Hepingli Beijing

country: China

institute: intensive care unit

organism: Homo sapiens

manufacture_protocol: see manufacturer's website (http://www.exiqon.com/microrna-microarray-analysis)


title: CIMAP Artemisia annua (cv. CIM-Arogya) microarray platform

city: Lucknow

first: Ajit

middle: K.

last: Shasany

state: Uttar Pradesh

address: P.O. CIMAP

department: Biotechnology Division

institute: CSIR-Central Institute of Medicinal and Aromatic Plants

organism: Artemisia annua

manufacturer: Ocimum Biosolutions Ltd., Hyderabad, India

first: Priya

last: Nair

first: Amita

last: Misra

first: Ashutosh

middle: K

last: Shukla

first: Suman

last: Khanuja

manufacture_protocol: Five microgram of total RNA was used for amplification using Amino Allyl MessageAmp™ II aRNA Amplification Kit from Ambion by linear transcription based RNA amplification system to produce cRNA. Briefly, mRNA was reverse transcribed with a oligo (dT) primer bearing T7 promoter at 42°C for 2 hrs and second strand cDNA synthesis was carried out at 16°C for 2 hrs. The resulting cDNA was then purified and was then transcribed with T7 RNA polymerase to generate multiple copies of aminoallyl antisense RNA (aRNA) at 37°C for 16 hrs. aRNA was then labelled with Cy3TM/Cy5TM post-labelling reactive dye pack (GE Healthcare, UK) at room temperature and unincorporated Cy3/Cy5  molecules were removed by purification process. Samples were purified using QIAGEN PCR purification kit before hybridization.


title: Custom human/mouse/rat miRNA array (miRBase 7.1)

city: Baoshan

first: Botao

last: Zhao

state: Shanghai

address: 333 Nanchen Rd

department: college of life science

institute: Shanghai University

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: Based on miRBase 7.1.


title: Agilent-031243 Clostridium perfringens pangenome

city: Wageningen

first: Yinghua

last: Xiao

address: Bornse Weilanden 9

country: Netherlands

institute: Wageningen University

organism: Clostridium perfringens

description:
TIFN C1056 project. Contains probes for ATCC13124, SM101, strain 13; incomplete: ATCC3626, F4969, JGS1495, JGS1721, JGS1987, NCTC8239; plasmids: pBCNF5603, pCP13, pCP8533etx, pCPF4969, pCPF5603, pCW3, pSM101A, pSM101B

Arrays of this design have barcodes that begin with 16031243 or 2531243.

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 scan files were dissected into the 4 slide regions  which generates a data file for each hybridization


title: Agilent-033486 LBLGC-Bvulgaris

city: Reims

first: Claire

last: Hébrard

address: Camus Moulin de la Housse

country: France

institute: Unité de Recherche Vigne et Vins de Champagne

organism: Beta vulgaris


title: Agilent-034921 LBLGC-Bvulgaris-CH3 [Probe Name version]

description:
LBLGC-Bvulgaris-CH3

Arrays of this design have barcodes that begin with 16034921 or 2534921.


title: Biovue's Human Sharpvue miRNA Primer Array Panels (A-E)

city: Shanghai

first: Ruo-Ying

last: Tan

address: 2nd Floor, 1st Building, 2140 Xietu Road,

institute: Biovue Technology (China) Ltd

technology: RT-PCR

description: Biovue's Sharpvue miRNA Primer Array Panels (A-E)

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


title: Agilent-048216 Neochlamydia S13 genome oligo microarray (Probe Name version)

status: Public on Dec 30 2014

city: Sapporo

first: Hiroyuki

last: Yamaguchi

address: N5 K12 Jo Kita-ku

institute: Hokkaido University

organism: Neochlamydia sp. S13


title: nCounter Human miRNA Expression Assay

city: Chicago

first: Yinan

last: Zheng

state: Illinois

address: 680 N Lake Shore Drive, Suite 1400

department: Department of Preventive Medicine

institute: Northwestern University

technology: other


title: Brassica 90K array

city: Wuhan

first: Yi

last: Huang

state: Hubei

address: No. 2 Xudong Second Road, Wuchang District

department: Rapeseed Genetics and Breeding

institute: Oil Crops Research Institute, Chinese Academy of Agricultural Sciences

organism:
Brassica napus
Brassica rapa
Brassica oleracea

manufacture_protocol: Plant Biotechnology Institute, National Research Council Canada (PBI-NRC); A Brassica genomics resource was developed at the Plant Biotechnology Institute, National Research Council Canada (PBI-NRC) and Agriculture and Agri-Food Canada (AAFC) in collaboration with other institutes. About 95,418 unique sequences were assembled using 781,826 EST sequences mainly from three species: B. napus, B. rapa, and B. oleracea. These unique sequences were submitted to CombiMatrix for the development of a 35-40mer oligonucleotide microarray, for which probes were synthesized in situ onto electrodes on a microchip. The customized Combimatrix Brassica array comprised 90,500 probes and was called as 90K array.


title: Illumina HiSeq 2500 (Cloning vector pUC19)

status: Public on Dec 29 2014

last: GEO

organism: Cloning vector pUC19


title: NimbleGen Bos taurus Btau4.0 3x720k whole genome tiling CGH

city: Yangling

first: Liangzhi

last: Zhang

state: Shaanxi

address: No.22 Xinong Road

department: College of Animal Science and Technology

institute: Northwest A&F University

organism: Bos taurus

description: Annotation in this record based on NCBI bos taurus Btau 4.0.

manufacture_protocol:
see manufacturer's web site www.nimblegen.com
Maskless array synthesis was used to construct isothermal arrays. Probes were selected with a median probe spacing of 3.3 kb. Probes were synthesized using an isothermal format (Tm = 76°C) and varied in length from 50 to 75 bp.


title: GAAS Sweetpotato 72k v1.0

city: Guangzhou

first: zhangying

last: wang

state: Guangdong

address: Jinying West 2nd Street 18#, Wushan Tianhe

department: Crops Research Institute

institute: Guangdong Academy of Agricultural Sciences

organism: Ipomoea batatas

description:
A total of 71,999 (32275×2 and 7449 ×1 ) in situ synthesized 60-mer oligonucleotide probes representing 39,724 sweetpotato genes were designed on the microarray.
All the EST sequences used for this array designing were retrieved from NCBI GenBank and sweetpotato gene index. However, there is abundant redundancy in these EST sequences due to the submission by different researchers. In order to eliminate redundant sequences and improve the sequence quality, The EST sequences were reassembled by using the TIGR Gene Indices Clustering Tools (TGICL). These reassembled EST sequences used for this array designing still have not been deposited in GenBank or other public-database. So we have not a publicly-accessible accession number yet.

manufacture_protocol: In-situ synthesis using Roche NimbleGen’s Maskless Array Synthesizer (MAS) system.


title: Illumina HiSeq 2000 (Shewanella decolorationis S12)

organism: Shewanella decolorationis S12


title: Agilent-035147 European eel Custom Array (Probe Name version)

status: Public on Dec 25 2014

city: Leioa

first: Ibon

last: Cancio

address: B/sarriena s/n

country: Spain

institute: UPV/EHU

organism: Anguilla anguilla

description:
Agilent-035147 Copy_of_EelRay_Gulatox_I_1309359858666

Pyrosequencing result

Arrays of this design have barcodes that begin with 16035147 or 2535147.

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-035147 European eel Custom Array (Feature Number version)


title: Autoantigen and Cytokine Protein Microarray

city: stanford

first: Jacob

last: Rosenberg

state: Ca

address: 269 Campus Drive, CCSR 2240

institute: Stanford University

technology: spotted peptide or protein

manufacture_protocol: Custom


title: Illumina HiSeq 2000 (Frankia sp. EUN1f)

status: Public on Dec 24 2014

organism: Parafrankia sp. EUN1f


title: UTSW Medical Center Autoantigen Array

city: Worcester

first: Rebecca

last: Baum

state: MA

address: 55 N Lake Ave LRB 240D

institute: University of Massachusetts Medical School

manufacturer: University of Texas Southwestern Medical Center


title: 040096 Agilent ChIP-on-Chip, 4X180K

city: Bangalore

first: Genotypic

last: technology

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

institute: Genotypic Technology

description: Microarray designed  by Genotypic Technology Private Limited. (AMADID-040096)


title: Illumina HiSeq 2000 (Frankia sp. EAN1pec)

organism: Parafrankia sp. EAN1pec


title: Illumina Genome Analyzer IIx (Bombus terrestris)

organism: Bombus terrestris


title: Agilent-034810 custom Paralichthys olivaceus 8x15k oligo DNA microarray

city: Tokyo

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

institute: Tokyo University of Marine Science and Technology

organism: Paralichthys olivaceus


title: Genotypic designed custom Agilent 4X180K buffalo (Bubalus bubalis) CpG island/promoter microarray (AMADID-037258)

organism: Bubalus bubalis


title: Illumina HiSeq 2000 (Ginkgo biloba)

organism: Ginkgo biloba


title: Illumina HiSeq 2000 (Frankia sp. EuI1c)

organism: Pseudofrankia inefficax


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

city: London

first: Dervis

middle: A

last: Salih

address: Gower St

department: Dementia Research Institute

country: United Kingdom

institute: University College London

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: Nimblegen_Oryza sativa japonica_45K

status: Public on Dec 22 2014

city: Villeurbanne

first: Benoît

last: DROGUE

state: Rhône-Alpes

address: Boulevard du 11 novembre

department: Université Lyon 1

institute: Université de Lyon

organism: Oryza sativa

description: The platform table is based on the Probe ID features. No control probes are included in this table. The .ndf file is linked below as a supplementary file.

manufacture_protocol: The custom-array design was based on a 385K  Nimblegen array format and is composed of 90,000 probes representing 45,000 genes and 201,691 oligomers corresponding to previously described copies of LTR retrotranposons available on the retrOryza database. Array characteristics: Probe length = 60 bp, 2 probes per gene (mostly). Manufacturing and processing of arrays, hybridization and scanning were performed according Nimblegen's recommendations


title: Illumina Genome Analyzer (Epinephelus coioides)

organism: Epinephelus coioides


title: Illumina MiSeq (Bacillus methanolicus)

status: Public on Dec 23 2014

organism: Bacillus methanolicus


title: Agilent-036300 Custom Paenibacillus larvae Array (Ag-P.Larvae)

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

organism: Paenibacillus larvae

first: Dieter

last: De Koker

first: Dirk

last: De Graaf


title: Meebo arrays v2

city: San Francisco

first: Feroz

last: Papa

address: 1700 4th Street

institute: University of California, San Francisco

manufacture_protocol:
Oligos are arrayed in Greiner 384-well flat-bottom plates.
Resuspend oligos in water to 20 uM and rearray 5 µL into 384-well, Genetix polystyrene V-bottom plates (cat# X6004).
Centrifuge plates at 2000 rpm for 3 minutes.
Oligos are printed on poly-l lysine slides with UCSF DeRisi Linear Servo Motor Microarrayer


title: Meebo arrays


title: Pancchip 6.1 arrays v2

manufacturer: University of Pennsylvania School of Medicine Functional Genomics Core

manufacture_protocol:
1.Oligos are arrayed in 96-well flat-bottom plates.
2. Resuspend oligos in 50μL water, diluted with equal volume of DMSO
Printed on poly-l-lysine–coated slides with an Affymetrix 417 arrayer.


title: Heebo arrays

organism: Homo sapiens

manufacture_protocol: Oligos are printed on Schott epoxy slides with major 17-4ss tips


title: Illumina HiSeq 2000 (Oikopleura dioica)

organism: Oikopleura dioica


title: Pancchip 6.1 arrays


title: Illumina HiSeq 2000 (Togninia minima)

status: Public on Dec 20 2014

organism: Phaeoacremonium minimum


title: [PhyloChip] Affymetrix G3 PhyloChip

city: Singapore

first: Gourvendu

last: Saxena

state: Singapore (General)

address: #05-02, 28 Medical Drive

department: The Singapore Centre on Environmental Life Sciences Engineering

country: Singapore

institute: National University of Singapore

organism: Bacteria

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


title: GeoChip 3.0 for Bacteria, Archaea, Eukaryota and Viruses


title: Agilent-032221 Stylophora pistillata array

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

organism: Stylophora pistillata

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


title: Agilent-029200 Unrestricted Rat miRNA v15.0  Microarray 028774 [miRBase release 16.0 miRNA ID version]

city: Kaohsiung

first: I-Hsuan

middle: Ann

last: Chen

address: 123 Ta-Pei Rd., Niao-Sung

institute: CGMH

organism: Rattus norvegicus

description:
all rat 15 probes, total 387 probe sets, on 8X15k format, 20 features per target

Arrays of this design have barcodes that begin with 16029200 or 2529200.

Grid_Date: 02-Nov-2010 (corresponding to miRBase release 16.0)


title: AB SOLiD 4 System (Phycomyces blakesleeanus)

status: Public on Dec 19 2014

last: GEO

organism: Phycomyces blakesleeanus


title: Illumina HiSeq 2000 (Methanosarcina acetivorans C2A)

organism: Methanosarcina acetivorans C2A


title: Agilent-029200 Unrestricted Rat miRNA v15.0  Microarray 028774 [Feature Number version]

description:
all rat 15 probes, total 387 probe sets, on 8X15k format, 20 features per target

Arrays of this design have barcodes that begin with 16029200 or 2529200.

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: Homo sapiens 41K (Human breast cancer_ Julie V1)

status: Public on Dec 18 2014

city: Los Angeles

first: Vasu

last: Punj

address: Biggy Street

institute: USC

technology: spotted DNA/cDNA

manufacture_protocol:
See the following reference for details:
Fox, M.S., Ares, V.X., Turek, P.J., Haqq, C. and Pera, R.A.R. (2003) Feasibility of global gene expression analysis in testicular biopsies from infertile men. Mol. Reprod. Dev., 66, 403 - 421.


title: Agilent-028004 SurePrint G3 Human GE 8x60K Microarray [GENCODE v.16 gene annotation version]

city: Odense C

first: Martin

middle: Jakob

last: Larsen

address: Sdr. Boulevard 29

department: Dept. of Clinical Genetics

institute: Odense University Hospital


title: Agilent-027310 Trichoderma virens WG GE Microarray

city: Haifa

first: Benjamin

last: Horwitz

state: Israel

address: Dept Biology Technion

institute: Technion

organism: Trichoderma virens

description:
Microarray designed for Trichoderma virens WG Gene Expression Microarray. The annotation mapped from JGI(Trichoderma virens Gv29-8) according to the protein id.

Arrays of this design have barcodes that begin with 16027310 or 2527310.

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-039385 porcine microarray

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

institute: INRA

organism: Sus scrofa

description:
Arrays of this design have barcodes that begin with 16039385 or 2539385.

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-024550] USP Schistosoma mansoni 4x44K oligo-array version 2.0

status: Public on Dec 16 2014

city: São Paulo

first: Katia

middle: Cristina Pereira

last: Oliveira

state: O

address: Av Prof lineu prestes 748

department: Centro de Parasitologia e Micologia

country: Brazil

institute: Instituto Adolfo Lutz

organism: Schistosoma mansoni

manufacture_protocol: This platform has the same oligos that GPL8606 just a diferent arranjment. All transcript information for S. mansoni available at both nr and dbEST databases at GenBank as of March, 2006 were filtered for contaminants and assembled with the CAP3 program. BLASTx were performed against the nr, with a cutoff of 1x10-10. The highest score alignment was used for annotation and assignment of the coding strand, in which the probe was designed. Those without significant hits against nr were annotated as no match, and probes for both strands were designed. In order to include possible new S. mansoni genes that have orthologous expressed sequences in S. japonicum but have not yet been cloned and sequenced in S. mansoni, we adopted the following strategy: S. japonicum RNA sequences from GenBank were assembled and submitted to a tBLASTx search against our assembled S. mansoni sequence set, and those with e-value lower than 1x10-20 were discarded. The remaining sequences were considered as S. japonicum transcripts without a clear corresponding S. mansoni transcript in the public database, thus being a candidate for a new S. mansoni gene. In order to obtain the S. mansoni sequence corresponding to these transcripts, the S. japonicum sequences were submitted to a BLASTn search against the S. manoni genome assembly (version 3), downloaded from the Wellcome Trust Sanger Institute. S. mansoni genomic loci that produced an alignment with at least 100 bases and had an identity higher than 70% were selected. Alternatively, tBLASTx was used, and S. mansoni genomic sequences were selected when they matched at least two high-scoring segment pairs (HSPs) each with e-value below 0.005. [NOTE added on October 2009: The criteria used for mapping S. japonicum evidence of transcription to the S. mansoni genome were poor; besides the set of bona fide probes, there were 521 spurious probes designed from japonicum information; all of these 521 probes were marked with a note *probe has no match to prediction=>abandon*, in the updated annotation table as of 28_October_2009. Expression data obtained with these 521 probes should be used with extreme caution.] These conserved regions in the S. mansoni genome were subsequently used in the probe design process. For each contig or singlet from the assembly, we selected all 60-mer sequences that satisfied a series of conditions that have been established by Agilent Technologies as follows: probes should not have 8 or more bases derived from low complexity regions; they should have a GC content of 35-55% and a melting temperature (Tm) of 68-76 Celsius degrees. In order to reduce cross-hybridization, each 60-mer sequence was searched by BLASTn against the S. mansoni genome sequence, downloaded from the Wellcome Trust Sanger Institute. In case that no hits were produced in this first search, the probes were used in a BLAST search against the CAP3 assembled mRNA/EST sequences. Probes were selected that had 100% match to the target sequence, which translates into a best-match alignment bit-score of 119. Those selected 60-mer sequences were checked for a low probability of cross-hybridization to non-specific targets by selecting probes for which the alignment bit-score of the second-best match was equal to or lower than 42.1. The selected probes were carried forward to the last step, which consisted of picking the probe closest to the 3-end for eachh target.


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

status: Public on Dec 17 2014

city: Santa Cruz

first: Yuan

last: Cao

address: 2161 Delaware Ave., Suite D

institute: Transderm Inc


title: [RCnGene-1_0-st] Affymetrix Rice (Chinese Build) Gene 1.0 ST Array [transcript (gene) version]

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

description:
Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

#%chip_type=RCnGene-1_0-st-v1
#%lib_set_name=RCnGene-1_0-st
#%lib_set_version=v1
#%genome-version=bgi102808
#%genome-version-ucsc=bgi102808
#%genome-lifted-method=psl-map.pl
#%genome-lifted_from-version-ucsc=bgi102808
#%netaffx-annotation-date=2014-02-11
#%netaffx-annotation-netaffx-build=34
#%netaffx-annotation-data-type=transcript_cluster

manufacture_protocol: See manufacturer's web site


title: Agilent-021963 NIFTS_Vvi_44K_01

city: Shizuoka

first: Hiroshi

last: Fujii

state: Shizuoka

address: 485-6 Okitsunakacho, Shimizu

department: Division of Citrus Research

institute: Institute of Fruit Tree Science, NARO

organism: Vitis vinifera

description:
H. Fujii and A. Azuma designed Vvi 44K microarray on 4, Nov, 2008 at NIFTS"

Arrays of this design have barcodes that begin with 16021963 or 2521963.

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: Rosetta/Merck Mouse 25k v1.1 microarray

city: Boston

first: Julja

last: Burchard

address: 33 Avenue Louis Pasteur

department: Computational & Systems Biology

institute: Merck & Co., Inc.

organism: Mus musculus

description:
Oligonucleotide array on glass.
Contains 60-mer probes (60-mer).

first: Amit

last: Kulkarni

first: John

last: Castle


title: Homo sapiens 20K v2 (Human breast cancer_ Julie V1)

state: CA


title: Illumina HiSeq 2500 (Haemophilus influenzae)

status: Public on Dec 15 2014

organism: Haemophilus influenzae


title: [Mouse4302_Mm_EntrezG] Affymetrix GeneChip Mouse Genome 430 2.0 Array [Mouse4302_Mm_ENTREZG_18.0.0]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

relation: Alternative to: GPL1261 (alternative CDF [official])

manufacture_protocol: This is identical to GPL1261 but a custom CDF environment was used to extract data [Brainarray Version 18, Mouse4302_Mm_ENTREZG_18.0.0].


title: NEIBank human eye tissues cDNA microarray

status: Public on Dec 13 2014

first: Katherine

middle: MacLean

last: Peterson

address: Building 6 Room 107B

institute: NEI, NIH

manufacture_protocol: see accompanying paper; custom produced from clones selected from NEIBank (http://neibank.nei.nih.gov)


title: Illumina HiSeq 2500 (Hydra vulgaris)

status: Public on Dec 12 2014

organism: Hydra vulgaris


title: MDACC miRNA V5.01 array

status: Public on Dec 11 2014

city: Washington

first: Yang

last: Liu

state: DC

address: 111 Michigan Ave NW

department: Center for Cancer and Immunology Research

institute: Childrens' National Medical Center

organism:
Homo sapiens
Mus musculus

manufacturer: Custom designed miRNA microarray chip by Dr. Chang-Gong Liu from MD Anderson Cancer Center, based on miRBASE V15

manufacture_protocol: Liu CG, Calin GA, Volinia S, Croce CM.MicroRNA expression profiling using microarrays. Nat Protoc. 2008;3(4):563-78. (PMID: 18388938)


title: Agilent-020791 Custom Mycobacterium smegmatis Gene Expression 8x15k Array

city: Bangalore

first: Nagasuma

last: Chandra

state: Karnataka

address: New Biological Science Building, IISc

department: Department of Biochemistry

institute: Indian Institute of Science

organism: Mycolicibacterium smegmatis

description:
AMADID:020791

Array designed by Genotypic Technology Private Limited.


title: Agilent-021827 Human miRNA Microarray [miRBase release 17.0 miRNA ID version]

organism: Homo sapiens

description: Grid_Date: 06-Jun-2011 [miRBase release 17.0 miRNA ID version]

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


title: Illumina HiSeq 2500 (Thermococcus onnurineus NA1)

status: Public on Dec 10 2014

organism: Thermococcus onnurineus NA1


title: Agilent-031863 Custom SurePrint G3 Gene Expression 4x180K [Probe Name Version]

city: Shirokanedai Minato-ku

first: Kana

last: Tominaga

state: Tokyo

department: Molecular therapy

institute: Insutitute of Medical Science, University of Tokyo

description: Design ID 031863

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


title: INDAC Drosophila melanogaster 13k

city: Paris

first: Capucine

last: TROLLET

address: GH Pitie Salpetriere Bat Babinski 47 bd de l'hopital

institute: Myology Research Center UMRS974 INSERM

organism: Drosophila melanogaster

description: custom array

manufacture_protocol: The INDAC oligo set (produced by Illumina) was printed in duplicate on poly-L-lysine coated slides by the Leiden Genome Technology Center (LGTC)


title: Homo sapiens 20K v1 (Human breast cancer_ Julie V1)

last: Punj


title: Illumina HiSeq 2000 (Suillus luteus)

status: Public on Dec 05 2014

last: GEO

organism: Suillus luteus


title: Agilent-021827 Human miRNA Microarray [miRBase release 15.0 miRNA ID version]

description: Grid_Date: 04-Jun-2010 [miRBase release 15.0 miRNA ID version]


title: MDACC miRNA V4.01 array

city: Chengdu

first: Chong

last: Chen

state: Sichuan

address: 17 Renmin S. Road-No. 3

department: State Key Laboratory of Biotherapy

institute: Sichuan University


title: Illumina HiSeq 2000 (Salmo salar)

organism: Salmo salar


title: Illumina HiSeq 2000 (Populus x canadensis)

organism: Populus x canadensis


title: Agilent-028728 SurePrint G3 Rat Exon 2x400K Microarray

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Rattus norvegicus

description:
Rat2x400KExon

Arrays of this design have barcodes that begin with 16028728 or 2528728.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Illumina Genome Analyzer II (Escherichia coli K-12)

status: Public on Dec 09 2014

organism: Escherichia coli K-12


title: LC Sciences CU Bull 3000 v1.0

city: Clemson

first: Scott

middle: L

last: Pratt

state: SC

address: 138 Poole Ag Center

institute: Clemson University

organism: synthetic construct

description:
µParaflo Microfluidic Biochip
all species for which data exists (as reported in databases such as miRBase, etc)

manufacture_protocol: Array was conducted by LC Sciences.


title: Illumina HiSeq 1500 (Amanita muscaria)

status: Public on Dec 04 2014

organism: Amanita muscaria


title: NimbleGen Rat 12x135K gene expression array [100718_Rat_HX12_expr]

city: Harbin

first: Xue

middle: dong

last: bo

state: Heilongjiang

address: 23 Youzheng Street

institute: The First Affiliated Hospital of Harbin Medical University

description: Format: 12x135k,Source: Ensembl,Build: RGSC 3.4,Probe Length: 60mer,Genes: 26,419,Probes/Target: 5,Replicates: 1

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


title: Illumina HiSeq 1500 (Staphylococcus aureus)

organism: Staphylococcus aureus


title: NimbleGen Oncorhynchus mykiss 12 x 135k Gene Expression Microarray

city: Göteborg

first: Bethanie

last: Carney Almroth

address: Medicinaregatan 38

department: Biological and Environmental Sciences

country: Sweden

institute: University of Gothenburg

organism: Oncorhynchus mykiss

description: NimbleGen design OID 32437

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


title: 454 GS Junior (Blattella germanica)

organism: Blattella germanica


title: Agilent-050530 IPGIM yeast 44K v1.0 [Feature Number Version]

status: Public on Dec 06 2014

city: Paris cedex 15

first: Alain

last: Jacquier

address: 25-28 rue du docteur roux

department: Génomes & génétique

institute: Institut Pasteur

organism: Saccharomyces cerevisiae S288C

description:
Yeast with probes for 3', 5', antisens, quiescent specific antisens, introns, cuts

Arrays of this design have barcodes that begin with 16050530 or 2550530.

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 (Haloxylon ammodendron)

status: Public on Dec 08 2014

organism: Haloxylon ammodendron


title: MI mouse exonic evidence-based oligonucleotide (MEEBO) microarray

city: Philadelphia

first: Konstantinos

last: Drosatos

state: PA

address: 3500 N. Broad st

department: Pharmacology

institute: Temple University

organism: Mus musculus

description: MI MEEBO fb OligoID Acc 2009-08-28 (Lot 20788).GAL

manufacture_protocol: Proprietary oligonucleotide deposition of the MEEBO (mouse exonic evidence-based oligonucleotide) probe set.


title: Illumina HiSeq 2000 (Escherichia coli K-12)


title: Agilent-031147 Multi 2010 MMKKK

city: Olsztyn

first: Monika

middle: M

last: Kaczmarek

address: Tuwima 10

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

organism:
Homo sapiens
Sus scrofa
Bos taurus
Mus musculus

description:
multispecies: ssc bta hsa mmu
Arrays of this design have barcodes that begin with 16031147 or 2531147.
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: MacAlpine Drosophila chr2L Agilent Array

city: Durham

first: Jason

middle: Alan

last: Belsky

state: NC

address: LSRC Room C333

department: Pharmacology and Cancer Biology

country: USA

institute: Duke University

manufacture_protocol: Agilent Technologies


title: Illumina HiSeq 2000 (Piloderma croceum)

organism: Piloderma croceum


title: Nimblegen Homo sapiens HG18 2.1M CNV Array [090518_HG18_CNV_v1_HX1]

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Homo sapiens

manufacture_protocol: see manufacturer's website


title: Illumina HiSeq 2000 (Scophthalmus maximus)

organism: Scophthalmus maximus


title: Illumina HiSeq 2000 (Amanita muscaria)


title: Illumina HiSeq 2000 (Paxillus involutus)

organism: Paxillus involutus


title: Illumina HiSeq 2000 (Oidiodendron maius)

organism: Oidiodendron maius


title: 454 GS FLX (Blattella germanica)


title: Illumina Genome Analyzer II (Ursus arctos)

organism: Ursus arctos


title: Illumina HiSeq 2000 (Tulasnella calospora)

organism: Tulasnella calospora


title: Illumina HiSeq 2000 (Ursus arctos)


title: Illumina HiSeq 2000 (Hebeloma cylindrosporum)

organism: Hebeloma cylindrosporum


title: 454 GS FLX Titanium (Ursus arctos)


title: Illumina HiSeq 2000 (Serendipita vermifera)

organism: Serendipita vermifera


title: Illumina MiSeq (Haemophilus parasuis str. Nagasaki)

organism: Glaesserella parasuis str. Nagasaki


title: Illumina MiSeq (Solanum pimpinellifolium)

organism: Solanum pimpinellifolium


title: Ion Torrent PGM (Haemophilus parasuis str. Nagasaki)


title: Illumina HiSeq 1500 (Hebeloma cylindrosporum)


title: Mycroarray Legionella pneumophila Philadelphia-1 genome array (including smallRNAs)

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:
CUST-3x20K-110928-Faucher
Legionella pneumophila Philadelphia-1 genome, including predicted 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: Illumina HiSeq 2000 (Helicobacter pylori)

status: Public on Dec 03 2014

organism: Helicobacter pylori


title: NimbleGen Onthophagus taurus Expression Array 12x135k (All Probes)

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

organism: Onthophagus taurus

description:
This is a horned beetle (Onthophagus taurus) whole-genome expression array in HD2 12x135K format manufactured by Roche NimbleGen.
090921_OT_JC_EXP.noColon.ndf
090921_OT_JC_EXP.noColon.txt


title: [MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [custom CDF: MoEx10stv1_Mm_ENST ver. 15]

city: Corvallis

first: Stephen

last: Ramsey

state: OR

address: Dryden Hall 208A

department: Biomedical Sciences

institute: Oregon State University

description: This is identical to GPL6096 but a custom cdf environment was used to extract data. Microarray analysis was performed using PGF file derived from the CDF file obtained from the University of Michigan CustomCDF probe-to-probeset mappings (Custom CDF, ENST, version 15). The PGF file, the Affymetrix CLF file describing the probe layout on the microarray, and the annotation file describing each probeset are linked below as supplementary files.

manufacture_protocol: Affymetrix


title: Illumina Genome Analyzer (Methyloversatilis universalis FAM5)

organism: Methyloversatilis universalis FAM5


title: Ion Torrent Proton (Exophiala dermatitidis)

status: Public on Dec 02 2014

organism: Exophiala dermatitidis


title: Illumina MiSeq (Peptoclostridium difficile 630)

organism: Clostridioides difficile 630


title: Illumina HiSeq 2500 (Helicobacter pylori)


title: Ion Torrent Proton (Rattus norvegicus)

organism: Rattus norvegicus


title: Exiqon miRCURY LNA Universal RT miRNA PCR (panel I+II)

city: Houston

first: Amin

last: mOMIN

state: TX

address: 6767 Bertner Ave

department: Clinical cancer prevention

institute: MD anderson cancer center

organism: Homo sapiens

manufacture_protocol: see Exiqon site


title: Illumina Genome Analyzer (Camellia sinensis)

organism: Camellia sinensis


title: [OviGene-1_1-st] Ovine Gene 1.1 ST Array [transcript (gene) version]

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Ovis aries

description:
Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

#%create_date=Wed Apr  2 21:43:34 2014 PDT
#%chip_type=OviGene-1_1-st-v1
#%lib_set_name=OviGene-1_1-st
#%lib_set_version=v1
#%genome-version=oar2
#%genome-version-ucsc=oar2
#%genome-lifted-method=NONE
#%genome-lifted_from-version-ucsc=oar2.0
#%netaffx-annotation-date=2013-08-30
#%netaffx-annotation-netaffx-build=34

Dec 02, 2014: annotation table based on netaffx build 34


title: Illumina MiSeq (Tribolium castaneum)

organism: Tribolium castaneum


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: MoGene10stv1_Mm_ENTREZG_16.0.0]

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Mus musculus

description: CDF: MoGene10stv1_Mm_ENTREZG_16.0.0

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: Illumina Genome Analyzer II (Oreochromis niloticus)

status: Public on Dec 01 2014

last: GEO

organism: Oreochromis niloticus


title: Gene Expression Plasmodium falciparum 8x15k

city: Bangalore

first: Genotypic

last: technology

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

country: India

institute: Genotypic Technology

organism: Plasmodium falciparum

description: designed by Genotypic Technology Private Limited (AMADID: 022127)


title: NCode Homo sapiens Non-coding arrays

city: Randwick, Sydney

first: Tao

last: Liu

state: NSW

address: Lowy Cancer Research Centre UNSW

country: Australia

institute: Children's Cancer Institute Australia

manufacture_protocol:
Array manufacturer: Agilent
Printing method: Agilent SurePrint technology
Layout: Two duplex subarrays, printed on the side of the slide with the “Agilent” label
Subarrays: Contain coding and non-coding probes and control probes
Replicates: 2 per feature, except controls
Probes: 60 bases each, sense strand
Spot size: 65 μm
Controls: Positive and negative, 1375 features per array, designed for use with RNA Spike-in Kits from Agilent
Unique probes per subarray: 22,074 coding RNA probes and 17,112 noncoding RNA probes


title: Human miRNA Microarray Release 14.0, 8x15K  (AMADID-G4471A-029297 )

manufacture_protocol: see www.chem.agilent.com


title: Mus musculus miRNA PCR assay panel

first: Regina

last: Lin

address: 207 Research Drive, #305

department: Immunology

description: PCR assay


title: Agilent-045769 Mycobacterium tuberculosis Custom Microarray (Feature number version)

city: Chennai

first: Alamelu

last: Raja

state: Tamil Nadu

address: No,1 Mayor sathyamoorthy Road, Chetpet

department: Department of Immunology

institute: National Institute for Research in Tuberculosis

organism: Mycobacterium tuberculosis

description: The ID column includes the Agilent Feature extraction numbers. A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL18248.

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


title: Arthrospira HX12

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

institute: SCK-CEN

organism: Limnospira indica PCC 8005

description:
Custom tiling array design (used for expression studies) with probes ranging from 50 up to 72 nucleotides, and an average length of 53 nucleotides, and an average spacing of 34 nucleotides between 2 different probes. Since the initial design is a tiling array - based on the complete genome sequence - no annotation was used for designing the array and the probes. Remapping of the probes to annotated genes is performed using a post-processing perl-script thereby adapting the .ndf-file
111123_Arthrospira_PM_expr_mage_v5.ndf


title: Ion Torrent PGM (Staphylococcus aureus)

organism: Staphylococcus aureus


title: Agilent-039731 SurePrint G3 Custom Human 8x60K Microarray

city: Groningen

first: Melanie

last: Winkle

state: Groningen

address: Hanzeplein 1

department: Pathology & Medical Biology

institute: UMC Groningen

description:
mRNA probes and a fraction of lncRNA probes are based on AMADID #028004 (Agilent). The remainder (i.e. custom probes) was designed based on a recently published lncRNA catalogue (Cabili et al. 2011 Genes Dev) using eArray software (Agilent).

Agilent SurePrint G3 platform in 8x60K format


title: UHN Microarray Centre Drosophila melanogaster D14k3 (alternative version)

status: Public on Nov 13 2014

city: Cologne

first: Julia

last: Hoffmann

address: Joseph-Stelzmann-Str. 9b

department: Partridge

country: Germany

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: Nimblegen HG18 CGX-6 PKI Array [091216_HG18_CGX6_v1]

status: Public on Nov 06 2014

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

institute: CHU Nice

description:
DESIGN_ID: 11106
DESIGN: 091216_HG18_CGX6_v1

manufacture_protocol: 091216_HG18_CGX6_v1 designed by Nimblegen. This array was provided by Perkin Elmer (réf. 06 510 825 001)


title: Agilent-031241 D. rerio 8x60k V3 Zebrafish 026437

status: Public on Sep 30 2014

city: Leipzig

first: Eva

last: Fetter

address: Permoserstraße 15

department: Bioanalytical Ecotoxicology

institute: UFZ-Helmholtz Centre for Environmental Research

organism: Danio rerio

description:
D. rerio (Zebrafish) Oligo Microarray V3

This Platform data table contains zebrafish genome version 3 annotation. The supplementary file 'GPL18967_031241_D_GEO_annotation_V9.txt' file contains annotation information updated to zebrafish genome annotation version 9.

Arrays of this design have barcodes that begin with 16031241 or 2531241.

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: BlueGnome/Illumina 24sure v3.0

status: Public on Jun 23 2014

city: Brussels

first: Kurt

last: Jacobs

address: Laarbeeklaan 103

department: Faculty of Medicine and Pharmacy

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

description: BAC array-based comparative genomic hybridization


title: 3D-Gene Mouse miRNA V19_1.0.0

status: Public on Mar 26 2014

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

manufacture_protocol: See manufacture's web site


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: MoGene10stv1_Mm_ENTREZG_15.1.0]

status: Public on Apr 07 2014

state: MD


title: CIT-MMJGGL Arabidopsis Small RNA 2k v1.0

city: Bellaterra

first: Jose Luis

last: Riechmann

state: Barcelona

address: Campus UAB - Edifici CRAG

institute: Center for Research in Agricultural Genomics

organism:
Arabidopsis thaliana
Caenorhabditis elegans
Drosophila melanogaster

description: Please note that the PRED* and MPSS* identifiers represent small RNA sequences from Arabidopsis that were either predicted (PRED) or identified through MPSS (massively parallel signature sequencing).

manufacturer: Caltech - MMJ Genetics and Genomics Laboratory

manufacture_protocol:
1. Oligos were synthesized with a 3' Amine C7 modification and arrayed in Genetix X7020 384-well plates. Each well contains 15 microliters of oligonucleotide at 50 micromolar in water.
2.Plates are dried in speed vac and then resuspended in 18 microliters per well of 150 mM Phophate buffer, pH 8.5, for a final probe concentration of 40 micromolar in 150 mM of Phosphate buffer. Seal plates.
3. Resuspend oligonucleotides overnight with shaking, near maximum rotational speed on flat-bed shaker.
4. Centrifuge plates at 1000 rpm for 3 minutes.
5. Remove seals and cover with plate lids. Place in appropriate location of plate holder.
6. Print arrays on Code Link slides using a BioRobotics MicrogridII arrayer, Biorobotcs TAS software, and a 16-pin configuration.
7. After print run is completed, block CodeLink slides using the standard CodeLink protocol, and pack slides under vacuum.
8. After print run is completed, dry plates on speed vac. For each subsequent preparation of these plates for a print run, add water to the wells instead of sodium phosphate buffer.


title: AIST Human EstrArray 2

status: Public on Jan 01 2014

city: Tokyo

first: zhu

last: yun

address: takanawa 4-21-12

institute: scinet company

manufacture_protocol: unknown


title: Agilent-023448 X. laevis (Frog) Oligo Microarray v2 [Probe name version]

status: Public on May 30 2013

city: Palo Alto

last: Agilent Technologies

state: CA

institute: Agilent Technologies

organism: Xenopus laevis


title: WT Btau 4.0 Array

status: Public on Jun 01 2013

city: Lexington

first: Jennifer

middle: Denyse

last: Patterson

state: KY

address: 215 WP Garrigus

department: Animal and Food Sciences

institute: University of Kentucky

organism: Bos taurus

description: WT Btau 4.0 Array is an early (non-commercial) version of the BovGene-1_0 commercial array.

manufacture_protocol: See manufacturer's web site


title: Illumina HiSeq 2000 (Prunus persica)

status: Public on Jun 06 2012

organism: Prunus persica


title: Agilent-028517 Rice Gene Expression 4x44K Microarray (Feature Number version)

status: Public on Feb 14 2012

city: Nagoya

first: Koichiro

last: Aya

state: Aichi

address: Furo-cho, Chikusa-ku

department: Bioscience and Biotechnology Center

institute: Nagoya University

organism: Oryza sativa

first: Makoto

last: Matsuoka


title: American and European eel microarray

city: Arcachon

first: lucie

last: baillon

address: place du docteur Peyneau

institute: université de Bordeaux UMR ePOC

organism:
Anguilla anguilla
Anguilla rostrata

manufacturer: Institut of GenopoleToulouse Midi-pyrénées , "Génome et transcriptome" (GeT) platform, Toulouse, France

manufacture_protocol:
One thousand oligonucleotide probes (60mers) were designed from a set of transcripts comprising both a American and European eels transcriptome assembled from a previous  RNA-seq study from hepatic transcriptome of 48 wild eels, collected in 8 sites (4 Canadian and 4 French sites; 6 fish per site) presenting a contamination gradient and a wide range of physicochemical conditions, was determined by high throughput RNA sequencing using Illumina Hiseq2000 technology. A total of 11,547 unique genes of known function were identified (evalue<10-3; size > 200 bp). In parallel, the contamination level of fish in 8 metals and 25 organic pollutants was determined and the temperature, salinity and dissolved oxygen concentration of each sampling sites were measured. Then, we carried out correlation analyses between the transcriptional level of a given gene and (i) contaminant concentrations in each individual fish, (ii) condition indices, (iii) physic-chemical characteristics of sampling sites by means of the factor analysis for multiple testing (FAMT) method (Friguet et al., 2009). The FAMT model was used with a unique threshold of 0.003 in order to identify genes for which their expression levels were more likely correlated with a single natural or anthropogenic factor. In total, 61 genes were significantly correlated with Ag, 64 with As, 60 with Cd, 64 with DDT, 49 with HCB, 55 with Hg, 35 with PBDE-47, 51 with PCB-sum, 68 with trans-nonachlor, 115 with lindane, 51 with hepatosomatic index (HSI), 18 with the Fulton condition factor (K), 68 with spleen-somatic index (SSI), 91 with salinity and 84 with sampling site temperature. To reach a total of 1000 candidate genes 66 genes for which their transcription level was significantly correlated with two factors were retained.  The probes were re-suspended in 3X SSC buffer  and printed on Corning® UltraGAPS TM Coated Slides with the Q-array Mini (Genetix) at the "Génome et transcriptome" (GeT) microarray platform (Toulouse, France). SPM3 (Telechem) Microarray Printing Pins were used to deposit 2nl per spot (100µm/spot) onto the slide.
The probes were then crosslinked with UV irradiation. The microarray layout consists of a 4-by-4 metagrid with 11 x 18 spots in the subgrids. Each line of 4 subgrids is separated by a line labeled spots in Cy3 and themselves separated by 5 lines of non-labeled spots. Each probe was triplicated on the microarray improving the robustness and repeatability of the measurements. The 1000 probes were deposited in a 4 x 4 metagrid.


title: Agilent-028005 Mouse Gene Expression 8x60K Microarray (G4852A)

status: Public on Aug 31 2011

city: Seattle

first: Daniel

middle: Edward

last: Zak

state: WA

address: 307 Westlake Ave N, Suite 5

institute: Seattle Biomedical Research Institute

manufacture_protocol: see Agilents site


title: Genotypic Custom Designed M. smegmatis Gene Expression 15K Profiling Microarray (Agilent-016421)

status: Public on Dec 23 2009

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

institute: Theomics International Private Limited

organism: Mycolicibacterium smegmatis MC2 155

first: Raja

middle: C

last: Mugasimangalam

first: Rohit

middle: N

last: Shukla

first: Shruti

last: Sinha

manufacture_protocol: Refer to www.chem.agilent.com


title: Valencia yeast v8

status: Public on Aug 23 2009

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

organism: Saccharomyces cerevisiae

description: Nylon macroarray (7 x 11 cm) with 6019 single spotted yeast ORF probes. Probes are PCR fragments comprising the whole ORF (5568 cases) or a 1000 bp-fragment from the ORF 3' end (451 cases).

manufacturer: Seccion de Chips de DNA-SCSIE (University of Valencia)

last: Garcia-Martinez

middle: E

manufacture_protocol: See Alberola et al. (2004), International Microbiology 7:199-206


title: SFBR_CrossSpecies_HyperArray

status: Public on Apr 08 2009

city: San Antonio

first: Laura

last: Cox

state: Texas

department: Genetics

institute: Texas Biomedical Research Institute

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

first: Carrie

last: Northcott

first: Jeremy

middle: P

last: Glenn

first: Robert

last: Shade

first: Candace

last: Kammerer

first: Carmen

last: Hinojosa-Laborde

first: Gregory

last: Fink

first: Joseph

middle: R

last: Haywood

manufacture_protocol: oligonucleotides were synthesized and nylon based arrays printed


title: Valencia yeast v10

status: Public on May 22 2011

description: Nylon macroarray (7 x 11 cm) with 6144 positions: 6035 single spotted yeast ORF/non-ORF gene probes; 45 probes for rRNA controls and 15 probes for B. subtilis genes as spiked controls. Probes are PCR fragments comprising the whole ORF (5558 cases) or a 1000 bp-fragment from the ORF 3' end (451 cases).

first: José

last: Pérez-Ortín

last: García-Martínez

manufacture_protocol: See Alberola et al. (2004), International Microbiology 7:199-206 (PMID 15492934).


title: JCVI PFGRC Streptococcus mutans 10K v1 array designed primarily based on strain UA159

status: Public on Sep 19 2006

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Streptococcus mutans

description: This set includes 1948 oligonucleotides, has 10752 spots distributed in 96 blocks.

manufacture_protocol: QSM, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 919043, pen id 10113, pen cycles -1, operator Kathy, humidity control On, humidity set point65


title: Valencia yeast v4

status: Public on Nov 18 2006


title: Valencia yeast v6

status: Public on May 21 2008