title: Qiagen Human Custom RT² Profiler PCR Array CAPH10410

status: Public on Jan 23 2017

city: Leuven

first: Joost

middle: J

last: van den Oord

address: Minderbroedersstraat 12, block q, box 1032

department: Department of Imaging & Pathology

country: Belgium

institute: KU Leuven

organism: Homo sapiens

technology: RT-PCR

description:
PCR assay
Qiagen Custom RT² Profiler PCR Array

distribution: virtual

manufacture_protocol: see manufacturer's website


title: HG18 WG CGH Nimblegen array

status: Public on Nov 14 2017

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

technology: in situ oligonucleotide

distribution: custom-commercial

manufacture_protocol: see manufacturer's web site


title: ICR_human_sar_v1

status: Public on Dec 31 2016

city: London

first: YF

last: Lee

address: 15 Cotswold Rd

country: United Kingdom

institute: Institute of Cancer Research

technology: spotted oligonucleotide

distribution: non-commercial

manufacture_protocol: as in Clark J, Edwards S, John M, Flohr P, Gordon T, Maillard K, et al. Identification of amplified and expressed genes in breast cancer by comparative hybridization onto microarrays of randomly selected cDNA clones. Genes Chromosomes Cancer 2002;34(1):104-14, except that the BioRobotics Microgrid II was used for gridding in this study.


title: NanoString nCounter Human miRNA Expression Assay

city: Taipei

first: Chung-Wu

last: Lin

state: Taiwan

address: 7 South Chung-Shan Road

department: Pathology

country: Taiwan

institute: National Taiwan University

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


title: RIKEN Cassava 60k v2.0 (probe name version)

city: Yokohama

first: Tetsuya

last: Sakurai

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

organism: Manihot esculenta

description: A total of 59,079 60-mer oligonucleotide probes were designed on the microarray.

first: Motoaki

last: Seki

first: Manabu

last: Ishitani

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


title: RIKEN Cassava 60k v2.0


title: Nanostring nCounter assay, mRNA signature for ANAC family of A.thaliana

status: Public on Apr 28 2018

city: Daejeon

first: Ji-Hwan

last: Park

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

organism: Arabidopsis thaliana

technology: other

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


title: Agilent  Zebrafish Gene Expression  8x60k Array AMADID: 064074 designed by Genotypic Technology Private Limited.

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: Danio rerio


title: TaqMan® Array Rodent MicroRNA A+B Cards Set v3.0 [4444909]

city: Beijing

first: xueming

last: zhao

address: No.2 Yuanmingyuanwestern road

country: China

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

organism: Mus musculus

description: PCR assay


title: Agilent-041913 Nicotiana attenuata 60K [Probe Name version]

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

country: Germany

institute: Max-Planck-Institute for Chemical Ecology

organism: Nicotiana attenuata

description: N. attenuata transcriptome microarray. The probe design for this microarray was done based on whole transcriptome data.


title: Exiqon miRCURY™ LNA miRNA v.11 (miRBASE version 16.0 )

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

country: USA

institute: Childrens National Hospital

organism: Drosophila melanogaster

manufacture_protocol: See manufacturer's website


title: Qiagen Human Custom RT² Profiler PCR Array CAPH10409


title: Agilent-034798 Streptococcus dysgalactiae subsp. Equisimilis 15K J11420

city: Tokyo

first: Shinya

last: Watanabe

address: 1-21-1 Toyama

department: Department of Infectious Diseases

institute: National Center for Global Health and Medicine

organism: Streptococcus dysgalactiae subsp. equisimilis

description:
Arrays of this design have barcodes that begin with 16034798 or 2534798.
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. uberis-specific array

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Plenty Road

department: School of Science

country: Australia

institute: RMIT University

organism: Streptococcus uberis

technology: spotted DNA/cDNA

manufacturer: Salem Abureema/Nitin Mantri/Margaret Deighton, RMIT University

manufacture_protocol: Streptococcus uberis isolates from cows with clinical mastitis and belonging to MLST types associated with virulence were selected as the source of genomic tester DNA. Isolates from cows with low cell counts and thought to represent possible non-virulent isolates were selected as the source of genomic driver DNA for suppression subtractive hybridization. All the isolates were collected during a previous study conducted at RMIT laboratory by Tomita et al. (2008). The tester pool consisted of six isolates belonging to GCC ST5 and GCC ST143, while the driver pool consisted of six isolates belonging to GCC ST86s.   The gDNA subtraction, library and microarray construction were performed according to the procedure described by Jayasinghe et al. (2007). Subtraction was conducted on the basis of manufacturer’s instructions (Clontech, 2008) described in the PCR-Select™ cDNA Subtraction Kit. Equal amounts of DNA extracted from six clinical mastitis isolates represented the tester pool while the driver pool was represented by equal amounts of DNA extracted from six low cell counts isolates.Subsequently, 4 μg of pooled gDNA from each group was restriction digested in a 50 μL reaction using 5U of Rsa I. As previously described (Jayasinghe et al., 2007), the digested driver gDNA pool was subtracted from digested tester gDNA pool to isolate tester-specific DNA using the Clontech PCR-SelectTM cDNA Subtraction Kit (Clontech, Mountain View, CA).The tester-specific DNA fragments were cloned into pGEM-T® Easy Vector (Promega, Madison, WI) and transformed into Escherichia coli JM109 competent cells (Promega, Madison, WI), resulting into 280 clones with insert of 250-750 bp.                                              Tester-specific clone amplification and SDA printing  Following the PCR amplification, approximately 80 µL of PCR products were transferred to V-bottom polypropylene 96-well plates. Using a multichannel pipette 96% of ethanol was added to a final concentration of 59% and 3M sodium acetate (pH 5.2) to a final concentration of 90 mM and the plasmid DNA was precipitated overnight at – 20oC. The plates were then centrifuged at 3000 rpm for 1.5 hr at 4oC. The supernatant was decanted using a pipette and the plates were inverted briefly to drain. The plasmid DNA pellet was washed with 70% ethanol prior of centrifugation and draining with the same conditions, the pellets air dried at room temperature for ≈2 hr. The plasmid DNAs were then resuspended in 50% dimethyl sulfoxide (DMSO) and stored at 4oC until use.   A total of 280 clones with inserts ranging from 250 bp to 750 bp, were transferred into a 384-well plate including the positive and negative controls. The control spots on the SDA included printing control (Cy-3) and negative controls; printing buffer (50% DMSO), nested PCR primers 1 and 2R, and pGEM®-T Easy vector. The positive controls consisted of three housekeeping genes; hasA, hasC, and pauA. The 280 clones together with the controls were printed on aminosilane-coated slides using a BioRobotics® MicroGrid II Compact arrayer (Genomics Solutions, Ann Arbor, MI) microarray spotter at RMIT University, Australia.


title: Custom LNA™ Universal RT microRNA PCR panels

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

description:
PCR assay
miRBase version 20

manufacture_protocol: microRNA PCR panel handbook for Cat# 203842


title: Agilent-031492 Listeria monocytogenes LMv2_0_0

status: Public on Dec 30 2016

city: Northampton

first: Stuart

middle: C

last: Allen

state: Northamptonshire

address: Boughton Green Road

department: Faculty of Health and Society

institute: University of Northampton

organism: Listeria monocytogenes

description:
BuG@S LMv2.0.0 - LMv2_0_0_genome

Arrays of this design have barcodes that begin with 16031492 or 2531492.

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-046663 Trees_MS_expr_X4 [Feature Number Version]

first: Ting-Fang

last: Wang

address: Academia Sinica. 128 Sec. 2, Academia Rd

department: Institute of Molecular Biology

institute: Academia Sinica

organism: Trichoderma reesei

description:
Arrays of this design have barcodes that begin with 16046663 or 2546663.
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.

relation: Alternative to: GPL18939 (Probe Name Version)


title: DKFZ_BreastSys_RPPA

city: Heidelberg

first: Ulrike

last: Korf

address: Im Neuenheimer Feld 580

department: Molecular Genome Analysis

institute: German Cancer Research Center

technology: spotted peptide or protein

description:
Spotted total protein from cell lysates (reverse phase protein array).
Each sample was printed as technical triplicate on the slide.

manufacturer: Division of Molecular Genome Analysis, B050, German Cancer Research Center

manufacture_protocol: Samples were printed on nitrocellulose-coated glass slides (Grace-Biolabs) using a solid-pin printer (Aushon 2470) equipped with 185 µm pins.


title: Illumina HiSeq 2000 (Mus musculus; Mycobacterium tuberculosis)

last: GEO

organism:
Mycobacterium tuberculosis
Mus musculus

technology: high-throughput sequencing


title: NimbleGen Petunia hybrida chip [111012_PAX_PT_expr_HX12]

city: VR

first: Alessandra

last: Amato

address: strada le grazie 15

country: Italy

institute: University of Verona

organism: Petunia x hybrida

description: Hybridization was carried out on a NImbleGen microarray 111012_PAX_PT_expr_HX12 chip (Roche, NimbleGen Inc.), representing 27,627 predicted genes on the basis of the Petunia axillaris genome.

manufacture_protocol: NimbleGen Arrays User’s Guide (V 3.2)


title: Illumina MiSeq (Hafnia alvei)

status: Public on Dec 29 2016

organism: Hafnia alvei


title: Illumina HiSeq 2500 (Odontobutis potamophila)

organism: Odontobutis potamophilus


title: Illumina HiSeq 2000 (Physalis pubescens)

organism: Physalis pubescens


title: [RheGene-1_0-st] Rhesus Gene 1.0 ST Array [probe set (exon) version]

city: Boston

first: MALIKA

last: AID

state: MA

address: 3 blackfan street

institute: BIDMC

organism: Macaca mulatta

description:
create_date=Fri Apr 12 15:07:05 2013 PDT
chip_type=RheGene-1_0-st-v1
lib_set_name=RheGene-1_0-st
lib_set_version=v1
genome-species=Macaca mulatta
genome-version=rhemac2
genome-version-ucsc=rhemac2
genome-version-create_date=2006-01-00
genome-lifted-method=psl-map.pl
genome-lifted_from-species=Macaca mulatta
genome-lifted_from-version-ucsc=rhemac2
netaffx-annotation-date=2012-09-15
netaffx-annotation-netaffx-build=33
netaffx-annotation-tabular-data-version=1.1
netaffx-annotation-tabular-format-version=1.1
netaffx-annotation-data-type=probe_set
netaffx-annotation-docgen-method=module:affy/annotation_update/builder; exec:create-download-file.pl
netaffx-annotation-docgen-version=8487
netaffx-annotation-url-transcript=www.affymetrix.com/analysis/netaffx/gene/transcript.affx?pk=
netaffx-annotation-url-mrna=www.affymetrix.com/analysis/netaffx/gene/rna.affx?pk=

manufacture_protocol: See manufacturer's web site


title: Illumina HiSeq 2500 (Mauremys reevesii)

status: Public on Dec 28 2016

organism: Mauremys reevesii


title: MRA-1001B1 Human miRNA Array miRbase release 19

city: Jinan

first: Peng

last: Gao

address: Wen Hua Xi Road 44

institute: Shandong University

organism: Homo sapiens

manufacture_protocol: Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579-596; (b) Zhu, Q., Hong, A., Sheng, N., Zhang, X., Jun, K.-Y., Srivannavit, O., Gulari, E., Gao, X., and Zhou, X. (2007) Microfluidic biochip for nucleic acid and protein analysis. in Methods Mol. Biol. Ed. Rampal, J. B. 382:287-312.;Bolstad, B. M., Irizarry, R. A., Astrandand, M., Speed, T. P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinfo. 19, 185-193.


title: Miltenyi Biotec miRXplore miRNA Microarray

city: Singapore

first: Yu

address: 11 Hospital Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

manufacture_protocol: protocol according to Miltenyi Biotec


title: Exiqon miRCURY LNA microRNA array, 7th generation [miRBase v18]

city: Chengdu

first: Xiaorong

last: Zhong

state: Sichuan

address: 5 Gongxing Lane, Wuhou District

institute: West China Hospital, Sichuan University


title: Illumina HiSeq 2500 (Nothobranchius rachovii)

status: Public on Dec 22 2016

organism: Nothobranchius rachovii


title: Illumina HiSeq 4000 (Agrobacterium sp. ATCC 31749)

status: Public on Dec 27 2016

organism: Agrobacterium sp. ATCC 31749


title: Illumina HiSeq 4000 (Komagataella pastoris)

organism: Komagataella pastoris


title: Illumina HiSeq 2500 (Nothobranchius kadleci)

organism: Nothobranchius kadleci


title: Human Tumor Metastasis PCR Array

city: Oxford

first: Zhichao

last: Ai

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

institute: University of Oxford

description:
Quantitative reverse transcription real-time PCR (qRT-PCR) on genes encoding several classes of protein factors including cell adhesion, ECM components, cell cycle, cell growth and proliferation, apoptosis, transcription factors and regulators and other genes related to tumor metastasis
SABiosciences RT² Profiler panel of PCR assays.


title: PacBio RS II (Ralstonia solanacearum)

organism: Ralstonia solanacearum


title: Agilent-046065 Mouse miRNA [Feature Number]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Mus musculus

distribution: commercial


title: MDACC Dr. Calin custom ncRNA array

city: Houston

first: Simone

last: Anfossi

state: Texas

address: 1515 Holcombe Blvd

department: Experimental Therapeutics

institute: UT MD Anderson Cancer Center

organism:
Homo sapiens
Mus musculus


title: Illumina HiSeq 2000 (Callosobruchus maculatus)

organism: Callosobruchus maculatus


title: Qiagen Human Inflammatory Cytokines & Receptors PCR Array(PAHS-011Z)

description:
Quantitative reverse transcription real-time PCR (qRT-PCR)
SABiosciences RT² Profiler panel of PCR assays.


title: Illumina HiSeq 2500 (Nothobranchius kuhntae)

organism: Nothobranchius kuhntae


title: Illumina HiSeq 2500 (Nothobranchius pienaari)

organism: Nothobranchius pienaari


title: Agilent-048771 4x44K Grape all [Probe Name version]

organism: Vitis vinifera

description:
Arrays of this design have barcodes that begin with 16048771 or 2548771.

Gene IDs and Grape genome information is available at: http://genomes.cribi.unipd.it/grape/


title: Illumina miseq (Saccharomyces cerevisiae)

organism: Saccharomyces cerevisiae


title: Illumina HiSeq 4000 (Lactobacillus acetotolerans)

organism: Lactobacillus acetotolerans


title: OSUrbt Oncorhynchus mykiss 1.6K v2.1

status: Public on Dec 20 2016

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

organism: Oncorhynchus mykiss

manufacture_protocol: Oligonucleotides were resuspended in spotting buffer (3X SSC and 1.5 M betaine) at 25 uM final concentration and were printed onto Corning UltraGap slides (Acton, MA) using a Biorobotics Microgrid II arrayer (Genomic Solutions, Ann Arbor, MI) with 16 pins. The trout 70-mers were each printed in duplicate and a set of ten SpotReport Alien Oligos (Stratagene, La Jolla, CA) were printed 16 times (once per block) on the array. After printing, slides were desiccated for 24-48 hrs and cross-linked with UV Stratalinker (Stratagene) at 600 mJ.


title: Illumina HiSeq 2000 (Sesbania cannabina)

status: Public on Dec 21 2016

organism: Sesbania cannabina


title: Illumina HiSeq 2500 (Nothobranchius korthausae)

organism: Nothobranchius korthausae


title: Agilent-073748 PPCD1 CNV 17.3-34.0 (Feature Number version)

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

state: CA

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

institute: Stein Eye Institute, UCLA

organism: Homo sapiens

description:
Array design is based on genome build hg19/GRCh37.
G4126A
Arrays of this design have barcodes that begin with 16073748 or 2573748.
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.

first: Derek

last: Le

first: Ricardo

middle: F

last: Frausto

first: Doug

last: Chung

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


title: Illumina Sentrix BeadChip Mouse WG-6 v2 array [Probe ID version]

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

technology: oligonucleotide beads

manufacture_protocol: See manufacturer's website.


title: Agilent-047308 Cricetulus griseus CHO2agl44v1

status: Public on Dec 23 2016

first: Gerald

last: Klanert

address: Muthgasse 18

department: Department of Biotechnology

institute: University of Natural Resources and Biotechnology

organism: Cricetulus griseus

description:
Chinese Hamster Ovary gene transcript expression v2 (Kreil Lab).

Arrays of this design have barcodes that begin with 16047308 or 2547308.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

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


title: Illumina HiSeq 2000 (Vibrio parahaemolyticus)

organism: Vibrio parahaemolyticus


title: Agilent-065185 Human Genome CGH 4X180K array [Probe Name Version]

city: Shanghai

first: shi

last: jie

institute: SHANGHAI BIOTECHNOLOGY CORPORATION

description: genome assembly: GRCh37/hg19


title: Exiqon miRCURY LNA microRNA Array, 7th generation - hsa (miRBase v18.0)

status: Public on Dec 24 2016

city: Berlin

first: Nathanael

last: Raschzok

address: Augustenburger Platz 1

department: Department of Surgery; Campus Charite Mitte / Campus Virchow Klinikum

institute: Charité - Universitätsmedizin Berlin

manufacture_protocol: see manufacturer's website


title: Illumina MiSeq (Actinobacillus succinogenes 130Z)

last: GEO

organism: Actinobacillus succinogenes 130Z


title: Illumina MiSeq (Zika virus)

status: Public on Dec 19 2016

organism: Zika virus


title: [FelGene-1_0] Feline Gene 1.0 ST Array [transcript (gene) version]

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Felis catus

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

FelGene-1_0-st-v1.na36.felcat8.transcript.csv
#%create_date=Wed Jun  1 21:09:02 2016 PDT
#%chip_type=FelGene-1_0-st-v1
#%lib_set_name=FelGene-1_0-st
#%lib_set_version=v1
#%genome-species=Felis catus
#%genome-version=felcat8
#%genome-version-ucsc=felcat8
#%genome-version-create_date=2014-11-01
#%genome-lifted-method=liftOver
#%genome-lifted_from-species=Felis catus
#%genome-lifted_from-version-ucsc=felcat3
#%netaffx-annotation-date=2016-03-15
#%netaffx-annotation-netaffx-build=36


title: Illumina MiSeq (Campylobacter jejuni)

organism: Campylobacter jejuni


title: NimbleGen Bovine 720K array v1.0 [101028_HK_btau_UMD3_meth.ndf]

city: Jouy en Josas Cedex

first: Helene

last: Kiefer

address: Domaine de Vilvert, Bat 230

country: France

institute: INRA

organism: Bos taurus

description:
UMD3.1 assembly, February 2010 release (ftp://ftp.ccb.jhu.edu/pub/data/assembly/Bos_taurus/Bos_taurus_UMD_3.0/annotation/)
Pseudogenes were filtered out from the file downloaded from the FTP site indicated above, resulting in a total of 21,296 genes, which were tiled from -2000 to +1360bp relative to the gene start. In addition, 22,387 probes covering potentially imprinted loci and surrounding regions, as well as one region devoid of CpGs, were added to the microarray

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


title: Agilent-066138 Dicentrarchus labrax 60K array (Probe Name version)

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

organism: Dicentrarchus labrax

description:
Arrays of this design have barcodes that begin with 16066138 or 2566138.

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

The ID column represents the Agilent Probe name.

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

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


title: Illumina HiSeq 2500 (Chromochloris zofingiensis)

status: Public on Dec 16 2016

organism: Chromochloris zofingiensis


title: Agilent-075257 Bovine Microarray FECUND INRA v2 022520 [PROBE NAME]

status: Public on Dec 15 2016

city: Jouy-en-Josas

first: Anaïs

last: Vitorino Carvalho

address: Domaine de Vilvert

department: BDR

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

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-022046 Citrus 44K long oligo array

status: Public on Dec 18 2016

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

institute: IBMCP

organism: Citrus

description: Design ID 022046


title: Illumina Genome Analyzer (Sedum alfredii)

status: Public on Dec 17 2016

organism: Sedum alfredii


title: 454 GS FLX (Sedum plumbizincicola)

organism: Sedum plumbizincicola


title: Geochip 5.0

city: Beijing

first: Tengxu

last: Wang

address: Tsinghua Yuan Street, No.1

department: School of Environment

institute: Tsinghua University

organism:
Bacteria
Archaea
Eukaryota
Viruses

manufacture_protocol: see manufacturer's web site


title: Agilent-066279 Bovine_Microarray_FECUND_INRA_v1 [PROBE NAME]

description:
Microarray pour expression génique chez la vache

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

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

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


title: Streptococcus pneumoniae D39 6x 7k

status: Public on Dec 12 2016

city: Seoul

first: Mukesh

middle: Kumar

last: Yadav

state: Seoul

department: Institute for Medical Device Clinical Trials

institute: Korea University

organism: Streptococcus pneumoniae D39


title: Illumina Genome Analyzer (Sedum plumbizincicola)


title: Affymetrix AGRONOMICS Tiling Array [remapping to TAIR10]

city: Warsaw

first: Rafal

last: Archacki

address: Pawinskiego 5A

country: Poland

institute: University of Warsaw

organism: Arabidopsis thaliana

description: This platform represents an independent mapping of the probe sequences to TAIR10. The supplementary file contains the probe id (probeset_x_y), chromosome, start position and strand.

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


title: Illumina HiSeq 2500 (Phormium tenax)

organism: Phormium tenax


title: Applied Biosystems TaqMan Rodent MicroRNA A Array v2.0 [4398967]

first: GEO

last: admin

organism:
Mus musculus
Rattus norvegicus

description: catalog number 4398967


title: Illumina Genome Analyzer II (Gallus)

organism: Gallus


title: Illumina Genome Analyzer IIx (Gallus)


title: Illumina NextSeq 500 (Streptomyces tsukubensis NRRL18488)

organism: Streptomyces tsukubensis NRRL18488


title: Illumina HiSeq 2500 (Polyodon spathula)

organism: Polyodon spathula


title: Illumina HiSeq 2000 (Moniezia expansa)

status: Public on Dec 13 2016

organism: Moniezia expansa


title: Illumina NextSeq 500 ([Candida] glabrata)

status: Public on Dec 09 2016

organism: Nakaseomyces glabratus


title: Illumina NextSeq 500 (unidentified)

organism: unidentified


title: Illumina HiSeq 2500 (Streptomyces hygroscopicus)

organism: Streptomyces hygroscopicus


title: Illumina HiSeq 2500 (Sordaria macrospora)

organism: Sordaria macrospora


title: Illumina MiSeq (uncultivated soil bacterium)

organism: uncultivated soil bacterium


title: Illumina HiSeq 2000 (Aspergillus luchuensis)

status: Public on Dec 11 2016

organism: Aspergillus luchuensis


title: Illumina MiniSeq (Drosophila melanogaster; Homo sapiens)

organism:
Drosophila melanogaster
Homo sapiens


title: Illumina HiSeq 2500 (Ascodesmis nigricans)

organism: Ascodesmis nigricans


title: Agilent-052809 Genotypic_Custom_WhiteSpruce_4x180K_CGH_Array [Probe name version]

status: Public on Dec 14 2016

city: Quebec

first: Julien

last: Prunier

state: QC

address: 1030 av. de la medecine

department: Forestry

country: Canada

institute: Université Laval

organism: Picea glauca

description:
Genotypic custom CGH probesprobes filetered from 1x1M array

Arrays of this design have barcodes that begin with 16052809 or 2552809.


title: Illumina HiSeq 2000 (Procambarus fallax)

organism: Procambarus fallax


title: Illumina HiSeq 2500 (Antirrhinum majus)

organism: Antirrhinum majus


title: Illumina HiSeq 2000 (Xenopus tropicalis x Xenopus laevis)

organism: Xenopus tropicalis x Xenopus laevis


title: Illumina HiSeq 2500 (Dictyostelium discoideum)

organism: Dictyostelium discoideum


title: Illumina HiSeq 1000 (Mesocricetus auratus)

organism: Mesocricetus auratus


title: Illumina Genome Analyzer IIx (Cucumis sativus)

organism: Cucumis sativus


title: Illumina MiSeq (Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344)


title: HumanV2 GE 8x60K Microarrays, Agilent design ID: 039494 (original references: GPL19775 and GPL19773)

status: Public on Dec 07 2016

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

organism: Homo sapiens

description: HumanV2 GE 8x60K Microarrays, Agilent microarray design ID: 039494 (original commercial platform references are GPL19775 and GPL19773)

manufacture_protocol: See manufacturer's web page


title: Lymphochip DNA microarray

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

manufacture_protocol: Composed of genes whose products are preferentially expressed in lymphoid cells and genes thought or confirmed to play a part in cancer or immune function. These microarrays were constructed from 12,196 clones of complementary DNA (i.e., microarray features) and were used to quantitate the expression of messenger RNA in the tumors.


title: Illumina HiSeq 2500 (Homo sapiens; Human papillomavirus type 16)

status: Public on Dec 08 2016

organism:
Homo sapiens
Human papillomavirus 16


title: Agilent-074512 CBCmouselncRNAmRNA180k

city: Tianjin

first: Ming

last: Cui

address: 238 Baidi Road

department: Institute of Radiation Medicine,

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

organism: Mus musculus

description:
Arrays of this design have barcodes that begin with 16074512 or 2574512.

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 4000 (Caenorhabditis elegans)

organism: Caenorhabditis elegans


title: Illumina NextSeq 500 (Taeniopygia guttata)

status: Public on Dec 10 2016

organism: Taeniopygia guttata


title: Illumina HiSeq 2500 (Homo sapiens; Human papillomavirus type 18)

organism:
Homo sapiens
human papillomavirus 18


title: Agilent-014879 Whole Rat Genome Microarray 4x44K G4131F (Feature Number version)

status: Public on Aug 17 2006

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Rattus norvegicus

description:
With a focus on well known rat genes and homologues to human and mouse genes with useful annotation, Agilent's Whole Rat Genome Oligo – 4X44K microarray provides researchers with a new tool for modeling human biology in the rat model organism. For researchers, this means they now have access to a microarray made up of relevant content that has been empirically validated by Agilent.

Arrays of this design have barcodes that begin with 16014879 or 2514879.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7294.


title: Exiqon Human PCR panels I+II, V2

status: Public on Dec 03 2016

city: Obu

first: SAYURI

last: HIGAKI

state: Aichi

address: 7-430 Morioka-cho

department: Medical Genome Center

institute: National Center for Geriatrics and Gerotology


title: Illumina HiSeq 4000 ((Citrus unshiu x Citrus sinensis) x Citrus reticulata)

status: Public on Dec 06 2016


title: Illumina HiSeq 4000 (Osmanthus fragrans)

status: Public on Dec 05 2016

organism: Osmanthus fragrans


title: Illumina MiSeq (Aedes aegypti)

organism: Aedes aegypti


title: UHNMAC Yeast 6.4 K array (Y6.4K) version 7 [Gene-level version]

city: Paterna

first: Jordi

last: Tronchoni

address: Avda. Agustín Escardino, 7

institute: CSIC

organism: Saccharomyces cerevisiae

description:
spotted DNA/cDNA (double-spotted array containing 6240 yeast ESTs derived from PCR amplification of synthetic EST clones, plus 320 control spots of Arabidopsis totalling 6.4K).
Grid rows: 12; grid columns: 4; rows: 17; columns: 16, grid to grid distance: 4500 um; spot to spot distance: 200 um; spot size: 100 um.

manufacturer: Microarray Centre - University Health Network - Toronto - Canada

manufacture_protocol:
Microarrays are printed on UltraGAPS slides (Corning Inc.) using hihg-precision robotics. Printed arrays are processed following Corning's protocol and are ready-to-use.
1. Acquisition of bacterial clone set — our Yeast 6.4k clone set is derived from Research Genetics Genepairs. Detailed information about the ORFs and sequences can be found at http://www.yeastgenome.org/
2. Clone set is PCR amplified and DNA purified in working 96 well plates.
3. The purified DNA is then transferred to 384 well source plates with DNA concentration ranging from 0.10ug/ul to 0.25ug/ul.  These are used for spotting.
4. Microarrays are printed on UltraGAPS ™  slides (Corning Inc.) using hihg-precision robotics (up to 48 pins or print heads). Printed arrays are processed following Corning's protocol and are ready-to-use.
Up to 120 slides are printed in each batch and batches that result in greater than 95% printing fidelity are selected for post printing quality control tests
(measuring spot morphology, quality of background and signal intensity in a real hybridization using yeast total RNA, vector probe labeling method and terminal transferase tailing method).


title: Illumina HiSeq 2500 (mouse gut metagenome)

status: Public on Dec 02 2016

last: GEO

organism: mouse gut metagenome


title: Illumina HiSeq 1000 (mouse gut metagenome)


title: Illumina NextSeq 500 (Vibrio harveyi)

status: Public on Dec 04 2016

organism: Vibrio harveyi


title: NanoString Expression Assay, nCounter Prognostic LSC mRNA signature for AML

city: Toronto

first: Stanley

last: Ng

state: Ontario

address: 160 College Street

institute: Univerity of Toronto

description: Technologies custom codeset

manufacture_protocol: See manufacturer's website


title: Agilent-039714 LincRNA SurePrint G3 Human GE 8x60K Microarray PVD 028004 [Probe Name version]

city: Gainesville

first: Thomas

last: Schmittgen

state: FL - FLORIDA

address: 2033 Mowry Road

department: Pharmacy

institute: Univ of Florida

description:
The good old SurePrint G3 Human gene expression array but with more lincRNA probes

Arrays of this design have barcodes that begin with 16039714 or 2539714.

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.


title: Human Operon V1.1 printed oligonucleotide array

status: Public on Dec 01 2016

city: Baltimore

first: Nariman

last: Balenga

address: 655 W. Baltimore St, Room 10-010B

department: Surgery

institute: University of Maryland School of Medicine

manufacture_protocol: Duke Microarray Facility printed the oligonucleotide slides manufacture protocol: Gene Machines Omni Grid 100 arrayer was used to print the Human Operon V2.0 oligonucleotides onto Corning UltraGap glass slides.


title: Illumina HiSeq 4000 (Methylosinus trichosporium)

organism: Methylosinus trichosporium


title: Agilent-075002 Mycobacterium tuberculosis array

first: Liyan

last: Yu

address: 1# Tian Tan Xi Li, Chongwen district

department: Institute of Medicinal Biotechnology

organism: Mycobacterium tuberculosis

description:
NC 000962 GE; TB_NC962_TM80_TRIM_2015 04749

Arrays of this design have barcodes that begin with 16075002 or 2575002.

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-045110 AGP Porcine 44K oligo array v4.1 AGPOA4.1 (Probe name version)

city: Tsukuba

first: Hirohide

last: Uenishi

state: Ibaraki

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

organism: Sus scrofa


title: Illumina HiSeq 4000 (Citrus reticulata x Citrus sinensis)

organism: Citrus reticulata x Citrus sinensis


title: Illumina MiSeq (Pinellia ternata)

organism: Pinellia ternata


title: Illumina HiSeq 1500 (Xenopus tropicalis x Xenopus laevis)

organism: Xenopus tropicalis x Xenopus laevis


title: NimbleGen_Azotobacter vinelandii_5k array v1.0 [080201_HE_NTNU_Azo_vinelandii_expr]

city: Trondheim

first: Helga

last: Ertesvåg

address: Sem Sælands vg 6-8

country: Norway

institute: Norwegian University of Science and Technology

organism: Azotobacter vinelandii DJ

description: NimbleGen Serial No: 080201_HE_NTNU_Azo_vinelandii_expr_x4. A 4x72k array covering 5012 genes from Azotobacter vinelandii DJ. SEQ_IDs are based on the geneIDs from the A. vinelandii DJ genome annotation. The geneIDs of certain ORFs in the DJ genome were however reassigned after manufacture of the array, causing a discrepancy between the SEQ_ID and GENE_ID columns in the matrix worksheet.

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


title: Illumina HiSeq 2000 (Clostridium autoethanogenum)

organism: Clostridium autoethanogenum


title: Nimblegen Human CGH 3x720K Whole-Genome Exon-Focused Array [090826_HG18_CGH_CCDS]

first: Rose

last: Yang

address: 9609 Medical Center Dr

department: Division of Cancer Epidemiology and Genetics

institute: National Cancer Institute

organism: Homo sapiens

manufacture_protocol: see web site


title: Illumina Genome Analyzer IIx (Macropus eugenii)

organism: Notamacropus eugenii


title: sciTracer_Staphylococcus_aureus_N315_Scienion2003

city: Bonn

first: Peter

last: Sass

state: NRW

address: Sigmund-Freud-Straße 25

department: Institute for Microbiology (IMMIP)

institute: University of Bonn

organism: Staphylococcus aureus subsp. aureus N315

manufacture_protocol: The sciTRACER S. aureus contains 2338 PCR products from all 2593 ORFs in the annotated genome (Ref ID: NC_002745), arranged in unique and second sequences: since the ORFs sizes range from 51 bp (e.g.: 13700427) up to 2kb (e.g.: 13701232), additional second PCR products have been developed. As unique sequences, 2333 PCR products and as second sequences, 333 PCR products are immobilized from which 5 are not in the group of unique gene fragments. All unique products cover 90 % of all ORFs. All PCR fragments are purified, concentration normalized, dissolved in spotting solution and spotted robotically onto modified glass slides. They are represented twice (duplicates) on each array. Controls are usually spotted in the last row of each subarray block forming the control area and comprising controls for spiking and endogenous controls. The SCIENION control set consists of positive, negative and multifunctional elements. All references/controls are spotted in a special pattern enabling functional monitoring of the entire experimental process. The glass slides are processed and ready for hybridization reaction. For easy correlation of gene names to their spot position on the slide the “Spot Identification Pattern-Table” (gal-file) is available. Information source: The genes represented on sciTRACER S. aureus are selected from order requests derived from the University of Würzburg, Infectious Biology Group (Head: Prof. Dr. Jörg Hacker) at the Institut für Molekulare Infektionsbiologie. Generation of sequences: 1. The PCR fragments derive mostly from regions at the last 500 nt from the 3’ end and have an average size of 355 bps. In case that the predicted ORF displayed a size unsuitable for appropriate amplicon generation, the primer design was extended towards flanking regions in order to cover the desired ORF. 2. All selected sequences are designed to provide the highest specificity and display minimal similarity to other mRNA and DNA sequences within the specified host genome. 3. In order to obtain strong and comparable sensitivity and signal specificity, all fragments are designed to feature similar lengths, comparable G/C-contents and optimized melting temperatures. 4. Based on algorithmic and manual revisions of the predicted sequences, the designed PCR fragments are well suited for the generation of highly reliable gene expression data. Quality controls: All sequences are validated in silico and approved by size control and sequence verification. The spot morphology is checked by automated optical control and hybridization of labeled RNA or SyBRGreenI® assay. Functional tests are performed by complex hybridization with labeled reference RNA for each batch. Source Organism: Staphylococcus aureus N 315 (NC_002745, contig BA000018) Microarray mapping: Each SCIENION microarray consists of two regions: the hybridizing region and the identifier region. The identifier region carries a sticker showing the name of the product, the date of production, batch number and the ID of the array. This region also serves to grasp the slide. The DNA microarray is in the center of the hybridizing region. Spot distance and feature size: The spot distance (center to center) is 375 µm. The array size is approximately 54 mm x 18 mm (height x broadness). Each array consists of 48 blocks and each block comprises 12 x 11 spots. These blocks are separated by a blank line and display a defined order. to Product description: The sciTRACER S. aureus contains 2338 PCR products from all 2593 ORFs in the annotated genome (Ref ID: NC_002745), arranged in unique and second sequences: since the ORFs sizes range from 51 bp (e.g.: 13700427) up to 2kb (e.g.: 13701232), additional second PCR products have been developed. As unique sequences, 2333 PCR products and as second sequences, 333 PCR products are immobilized from which 5 are not in the group of unique gene fragments. All unique products cover 90 % of all ORFs. All PCR fragments are purified, concentration normalized, dissolved in spotting solution and spotted robotically onto modified glass slides. They are represented twice (duplicates) on each array. Controls are usually spotted in the last row of each subarray block forming the control area and comprising controls for spiking and endogenous controls. The SCIENION control set consists of positive, negative and multifunctional elements. All references/controls are spotted in a special pattern enabling functional monitoring of the entire experimental process. The glass slides are processed and ready for hybridization reaction. For easy correlation of gene names to their spot position on the slide the “Spot Identification Pattern-Table” (gal-file) is available. Information source: The genes represented on sciTRACER S. aureus are selected from order requests derived from the University of Würzburg, Infectious Biology Group (Head: Prof. Dr. Jörg Hacker) at the Institut für Molekulare Infektionsbiologie. Generation of sequences: 1. The PCR fragments derive mostly from regions at the last 500 nt from the 3’ end and have an average size of 355 bps. In case that the predicted ORF displayed a size unsuitable for appropriate amplicon generation, the primer design was extended towards flanking regions in order to cover the desired ORF. 2. All selected sequences are designed to provide the highest specificity and display minimal similarity to other mRNA and DNA sequences within the specified host genome. 3. In order to obtain strong and comparable sensitivity and signal specificity, all fragments are designed to feature similar lengths, comparable G/C-contents and optimized melting temperatures. 4. Based on algorithmic and manual revisions of the predicted sequences, the designed PCR fragments are well suited for the generation of highly reliable gene expression data. Quality controls: All sequences are validated in silico and approved by size control and sequence verification. The spot morphology is checked by automated optical control and hybridization of labeled RNA or SyBRGreenI® assay. Functional tests are performed by complex hybridization with labeled reference RNA for each batch. Source Organism: Staphylococcus aureus N 315 (NC_002745, contig BA000018) Microarray mapping: Each SCIENION microarray consists of two regions: the hybridizing region and the identifier region. The identifier region carries a sticker showing the name of the product, the date of production, batch number and the ID of the array. This region also serves to grasp the slide. The DNA microarray is in the center of the hybridizing region. Spot distance and feature size: The spot distance (center to center) is 375 µm. The array size is approximately 54 mm x 18 mm (height x broadness). Each array consists of 48 blocks and each block comprises 12 x 11 spots. These blocks are separated by a blank line and display a defined order.


title: Illumina HiSeq 2500 (Bombus terrestris audax)

organism: Bombus terrestris audax


title: [hGlue_3_0] Custom Affymetrix Human Transcriptome Array

status: Public on Jul 05 2015

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description: This is a propietary array.

manufacture_protocol: See manufacturer's web site


title: Agilent-068681 CAZyChip prototype 2 [Probe Name version]

city: Toulouse

first: Anne

last: Abot

address: 135 route de Narbone

department: LISBP

institute: INSA/INRA/CNRS

organism: Bacteria

description:
Arrays of this design have barcodes that begin with 16068681 or 2568681.

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 NextSeq 500 (mixed sample)

organism: mixed sample


title: Exiqon microRNA Ready-to-Use PCR, Human panel I+II, V3.R

status: Public on Aug 07 2015

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

description:
PCR assay
miRCURY LNA™ Universal RT microRNA PCR, 4x Human panel I+II in 384well PCR plates (type R), one reaction each of 752 human microRNAs plus control assays. For use with Roche LightCycler 480 instruments.

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


title: AB SOLiD 3 Plus System (Homo sapiens)

status: Public on May 22 2014


title: Illumina HiSeq 2000 (Kluyveromyces lactis)

status: Public on Jul 14 2016

organism: Kluyveromyces lactis


title: [MoGene-2_0-st] Affymetrix Mouse Gene 2.0 ST Array (mogene20st_Mm_ENTREZG_20.0.0)

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Mus musculus

description: This Platform is identical to GPL16570 but a custom CDF environment was used to extract data [Brainarray Version 20, mogene20st]. The CDF file can be downloaded using the supplementary file link at the bottom of this record; the CDF and other files can be downloaded at: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/20.0.0/entrezg.asp

relation: Alternative to: GPL16570 (Alternative CDF [official])

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


title: Illumina HiSeq 2500 (Plasmodium berghei)

status: Public on Jun 06 2015

organism: Plasmodium berghei


title: Agilent SSU 8 x 15K (Feature Number version)

status: Public on Mar 18 2014

city: Wageningen

last: van Baarlen

address: De Elst 1

department: Animal Sciences

country: Netherlands

institute: Wageningen University

organism: Streptococcus suis

description:
platform ID EBI (ArrayExpress): A-MEXP-1671
platform description EBI (ArrayExpress): http://www.ebi.ac.uk/arrayexpress/arrays/A-MEXP-1671

manufacture_protocol: SSU 8 x 15K is produced by Agilent Technologies, according to their standard protocols: Both catalog and custom microarrays are manufactured using a proprietary non-contact industrial inkjet printing process, in which oligo monomers are deposited uniformly onto specially-prepared glass slides. This in situ synthesis process prints 60-mer length oligonucleotide probes, base-by-base, from digital sequence files. The precise inkjet process enables the delivery of extremely small, accurate volumes (picoliters) of the chemicals to be spotted. Standard phosphoramidite chemistry used in the reactions allows for very high coupling efficiencies to be maintained at each step in the synthesis of the full-length oligonucleotide. Precise quantities are reproducibly deposited on the fly. This engineering feat is achieved without stopping, to make contact with the slide surface and without introducing surface-contact feature anomalies, resulting in consistent spot uniformity and traceability. In addition, multiple microarrays can be printed simultaneously in a single manufacturing run.


title: Illumina HiSeq 2000 (Heterocephalus glaber)

status: Public on Jun 30 2011

organism: Heterocephalus glaber


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

status: Public on Dec 07 2012

city: Philadelphia

first: Bassel

middle: E

last: Sawaya

state: PA

address: 3307 N. Broad Street

department: Neurology

institute: Temple University

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


title: NimbleGen Drosophila serrata Custom 12.135K array [110608_Dser_SC_expr_HX12]

status: Public on Nov 05 2013

city: St Lucia

first: Stephen

last: Chenoweth

state: QLD

address: The School of Biological Sciences, The University of Queensland

department: Biological Sciences

institute: The University of Queensland, Australia

organism: Drosophila serrata

description:
NimbleGen design name: 110608_Dser_SC_expr
NimbleGen design ID: 554281
Native array description file: 110608_Dser_SC_expr.ndf
Five 60-mer probes for 11,631 unique Expressed Sequence Tags (ESTs) from Drosophila serrata. Each probe is replicated 2 times. The design includes random and other control probes.
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features. The .ndf file is linked below as a supplementary file.
The sequences of the ESTs are in the 'GPL16969_110608_Dser_SC_expr.ndf' file.


title: Agilent-076500 Human lncRNA+mRNA array (Probe name version)

status: Public on Dec 07 2016

city: Nanjing

first: Yue

state: Jiangsu

address: No. 300, Guangzhou Road

department: Department of Thoracic Surgery

institute: the First Affiliated Hospital of Nanjing Medical University


title: Illumina HiSeq 2000 (Cellvibrio japonicus)

organism: Cellvibrio japonicus


title: Illumina HiSeq 2500 (Anas platyrhynchos)

status: Public on Oct 20 2016

organism: Anas platyrhynchos


title: Agilent-074036 SurePrint G3 Rat GE v2 8x60K Microarray G4858A (Feature Number version)

status: Public on Jul 19 2016

state: MD

organism: Rattus norvegicus

description:
Catalog gene expression microarray for Rat, v2 8x60K

Design based on RefSeq Build 66, Ensemble Release 76, Unigene Build 236, GenBank (Aug 2014).

Arrays of this design have barcodes that begin with 16074036 or 2574036.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: NimbleGen Daphnia pulex Expression Array 12x135k (All Probes) [080925_Daphnia_UI_JC_expr]

status: Public on Feb 01 2011

city: Notre Dame

first: Jacqueline

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

organism: Daphnia pulex

description: This is a custom design whole Daphnia genome expression array in 12-plex format manufactured by Roche Nimblegen. Genes based on Daphnia pulex annotated draft genome assembly GenBank accession number: ACJG00000000.


title: Agilent-074036 SurePrint G3 Rat GE v2 8x60K Microarray G4858A (Probe Name version)

description:
Catalog gene expression microarray for Rat, v2 8x60K.

Design based on RefSeq Build 66, Ensembl Release 76, UniGene Build 236, GenBank (Aug 2014).

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


title: Illumina HiScanSQ (Mus musculus)

status: Public on Oct 12 2012


title: Illumina HiSeq 2000 (Glycine max)

status: Public on Dec 14 2011

organism: Glycine max


title: Agilent-028282 Whole Rat Genome Microarray 4x44K v3 (Probe Name version)

status: Public on Oct 14 2011

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Whole Rat Genome Microarray 4x44K v3

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

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

The ID column represents the Agilent 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.