title: NanoString nCounter Human miRNA Expression Assay

status: Public on Jul 31 2014

city: Philadelphia

first: Paul

middle: F

last: Bray

state: PENNSYLVANIA

address: 1015 Chestnut Street

department: Hematology

country: USA

institute: Thomas Jefferson University

organism: Homo sapiens

technology: in situ oligonucleotide

distribution: custom-commercial

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


title: NanoString nCounter Human miRNA Expression Assay v.2


title: Agilent-040255  Lactococcus lactis subsp. cremoris GE214 array (Feature number version)

status: Public on Jul 08 2015

city: Villaviciosa

first: Victor

last: Ladero

state: Select if applicable

address: Paseo Rio Linares S/N

department: Technology and Biotechnology of dairy products

country: Spain

institute: IPLA-CSIC

organism: Lactococcus cremoris subsp. cremoris GE214

description:
GE214-Victor
Gene features of L lactis cremoris GE214 from IPLA spain

Arrays of this design have barcodes that begin with 16040255 or 2540255.

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: NanoString nCounter Human HCC classification assay

status: Public on Jun 17 2015

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

technology: other

manufacture_protocol: See manufacturer's website


title: Burkholderia cenocepacia - 100k - v2

city: East Lansing

first: erick

last: cardenas

state: Michigan

address: 540 Plant and Soil Sciences Building

institute: Michigan State University

organism: Burkholderia cenocepacia

technology: spotted DNA/cDNA


title: Agilent-046663 Trees_MS_expr_X4 [Probe Name Version]

status: Public on Jan 07 2015

city: Taipei

first: Ting-Fang

last: Wang

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

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

organism: Trichoderma reesei

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

relation: Alternative to: GPL18937 (Feature Number Version)


title: Nanostring nCounter ImmVar CD4+ T cell Custom CodeSet

status: Public on Aug 28 2014

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

distribution: virtual

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


title: Asterids-specific array

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Plenty Road

department: School of Science

country: Australia

institute: RMIT University

organism: asterids

description: specific for all species belonging to Asterids clade of plants

distribution: non-commercial

first: Edwin

last: Pang

manufacture_protocol:
Plant material and genomic DNA extraction : Leaf tissues of 67 species representing the Asterid clade (AC) and 104 species representing the non-asterid angiosperms and non-angiosperms (NA) were obtained from the herbarium at Southern Cross University Plant Science, NSW, Australia. High quality genomic DNA (gDNA) was extracted from these specimens using DNeasy® Plant Mini Kit (Qiagen Inc., Australia). The quantity of DNA was measured using Eppendorf spectrophotometer whilst the quality/integrity was assessed by 1.5% agarose gel electrophoresis.
Genomic DNA subtraction and library construction : The gDNA was pooled into two separate groups, AC and NA, by mixing equal quantities of DNA from individual species belonging to that group. Subsequently, 4 μg of pooled gDNA from each group was restriction digested in a 50 μL reaction using 5U of HaeIII and AluI (New England Biolabs). As previously described (Jayasinghe et al., 2007), the digested NA gDNA pool was subtracted from digested AC gDNA pool to isolate AC-specific DNA using the Clontech PCR-SelectTM cDNA Subtraction Kit (Clontech, Mountain View, CA).  The AC-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 283 clones with insert of 250-750 bp.
AC-specific clone amplification and SDA printing : The 283 AC-specific DNA clones were amplified in 100 μL PCR reactions using Clontech nested primers as described (Jayasinghe et al., 2007). PCR products were transferred into V-bottom polypropylene 96-well plates and purified by ethanol/sodium acetate precipitation before resuspending in 50% dimethyl sulfoxide (DMSO). The control spots on the SDA included printing control (Cy-3) and negative controls viz., printing buffer (50% DMSO), nested primer 1 and 2R (Clontech, Mountain View, CA), and pGEM-T® Easy Vector (Promega, Madison, WI) digested with HaeIII and AluI. The 283 AC-specific DNA fragments along with controls were spotted on a Corning GAPS II coated slides (Corning Incorporated Life Sciences, Acton, MA) using BioRobotics MicroGrid II Compact (Genomics Solutions, Ann Arbor, MI) microarray spotter at RMIT University, Australia.


title: Burkholderia cenocepacia - 91k - v2


title: Illumina HiSeq 2000 (Candida glabrata CBS 138)

status: Public on Jul 28 2014

last: GEO

organism: Nakaseomyces glabratus CBS 138

technology: high-throughput sequencing


title: NimbleGen Drosophila DM2 WG CGH Whole Genome tiling array

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Drosophila melanogaster

description:
Array was based on genome build: UCSC DM2 April 2004. Probe Length: 50-75 bp. Median probe Spacing: 308 bp.
design name = 080605_DM2_WG_CGH
design id = 7711
catalog number = B2440001-00-01

distribution: commercial

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


title: [PATA1w520385F] Affymetrix Pseudomonas aeruginosa PAO1 custom tiling array

status: Public on Jul 30 2014

city: Karlsruhe

first: Andreas

last: Doetsch

address: Haid-und-Neu-Str. 9

department: Physiology and Biochemistry of Nutrition

country: Germany

institute: Max Rubner-Institute

organism: Pseudomonas aeruginosa PAO1

last: Dötsch

first: Claudia

last: Pommerenke

first: Florian

last: Bredenbruch

first: Robert

last: Geffers

first: Susanne

last: Häussler

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


title: Agilent-038169 human miRNA novirus v18.0

city: shanghai

first: qian

last: jin

address: libing road

country: China

institute: MSP

description:
Arrays of this design have barcodes that begin with 16038169 or 2538169.

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: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [HuEx_1_0_st_v2.na29.hg18.RefSeq-core]

city: South San Francisco

first: Ru-Fang

last: Yeh

state: CA

address: 1 DNA Way

institute: Genentech

description:
Annotation is based on human genome build hg18.
HuEx_1_0_st_v2.na29.hg18.RefSeq_Core_transrcipt.csv

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

manufacture_protocol: See manufacturer's web site.


title: FungiANC (GeneChip FungiANCa520710F)

city: Lisboa

first: Cristina

middle: Silva

last: Pereira

address: Rua da Quinta Grande nº6

country: Portugal

institute: Instituto de Tecnologia Química e Biológica (ITQB)

organism:
Aspergillus nidulans FGSC A4
Neurospora crassa OR74A

manufacture_protocol: The parameters chosen for the custom array design were as follows: 11-micron feature size, 49-5241 array format, eukaryotic antisense target type, perfect-match probes only, probe selection region: 600 bases from 3' end and per instruction file, and eight as the minimum acceptable probes per sequence.


title: [ChiGene-1_0-st] Affymetrix Chicken Gene 1.0 ST Array [transcript (gene) version]

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Gallus gallus

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=ChiGene-1_0-st-v1
#%lib_set_name=ChiGene-1_0-st
#%lib_set_version=v1
#%genome-species=Gallus gallus
#%genome-version=galgal3
#%genome-version-ucsc=galgal3
#%genome-version-create_date=2006-05-00
#%genome-lifted-method=NONE
#%genome-lifted_from-species=Gallus gallus
#%genome-lifted_from-version-ucsc=galgal3
#%netaffx-annotation-date=2013-08-30

manufacture_protocol: See manufacturer's web site


title: Illumina HiSeq 2000 (Cricetulus griseus)

organism: Cricetulus griseus


title: Illumina Genome Analyzer (Mus musculus x Mus spretus)

status: Public on Jul 25 2014

organism: Mus musculus x Mus spretus


title: Illumina HiSeq 2000 (Oncorhynchus tshawytscha)

organism: Oncorhynchus tshawytscha


title: GenoToul/Biopuces Saccharomyces cerevisiae 15k array

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

country: France

institute: INRA

organism: Saccharomyces cerevisiae

technology: spotted oligonucleotide

manufacture_protocol: see manufacturer's website http://biopuce.insa-toulouse.fr


title: Nitrosomonas europaea Kangchen Custom Expression Microarray

city: 上海

first: pan

last: zhong

state: 上海

address: 上海市徐汇区虹漕路421号63栋2楼

institute: 上海康成生物工程有限公司

organism: Nitrosomonas europaea


title: [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array [HGU133A2_Hs_ENTREZG_16.0.0]

status: Public on Jul 24 2014

description: Brainarray: HGU133A2_Hs_ENTREZG_16.0.0


title: GeoChip 4.2

status: Public on Jul 22 2014

city: Krakow

first: Hamed

last: Azarbad

address: Gronostajowa 7

country: Poland

institute: Jagiellonian University

organism: Bacteria

description: Soil microbes


title: [Xcel] Affymetrix Human Almac Xcel Array

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=2013-10-23 GMT-08:00 15:51:33
#%chip_type=Xcel
#%genome-species=Homo sapiens
#%genome-version=hg19
#%genome-version-ucsc=hg19
#%genome-version-ncbi=GRCh37
#%genome-version-create_date=2009-02-00
#%ensembl-date=2013-06-10
#%ensembl-version=71
#%entrezgene-date=2013-05-07
#%genbank-date=2013-06-15
#%genbank-version=196
#%mirbase-date=2012-07-16
#%mirbase-version=18
#%refseq-date=2013-04-29
#%refseq-version=59
#%unigene-date=2012-07-18
#%netaffx-annotation-date=2013-10-15
#%netaffx-annotation-netaffx-build=34
#%netaffx-annotation-tabular-format-version=1.0
#%omim-date=2012-07-11
#%netaffx-annotation-docgen-method=com.affymetrix.database.docgen.DocGenDriver
#%netaffx-annotation-docgen-version=cluster_friendly_submission
##This database contains information from the Online Mendelian Inheritance in Man (OMIM (R)) database, which has been obtained under a license from the Johns Hopkins University.  This database/product does not represent the entire, unmodified OMIM(R) database, which is available in its entirety at www.ncbi.nlm.nih.gov/omim/.

July 24, 2014: annotation table created with netaffx build 34

manufacture_protocol: see manufacturer's web site


title: Moldovan Lab Custom RT-PCR Array S/PC

status: Public on Jul 21 2014

city: Indianapolis

first: Leni

last: Moldovan

state: IN

address: 980 W Walnut St., Rm. C422

department: Ophthalmology

institute: Indiana University

technology: RT-PCR

description: real-time PCR assay

manufacturer: The arrays were designed in the Moldovan Lab and commercial primers (Qiagen) were loaded in 384-well plates in the Plant-Microbe Genomics Facility (The Ohio State University).

manufacture_protocol: Primers (Qiagen) were diluted 1:20 with molecular-grade water, and 5 μL/well were added to 384-well plates using a Biomek® FX Laboratory Automation Workstation (Beckman Coulter, Inc., Brea, CA). The plates were left to dry overnight in a sterile hood and stored covered at -20ºC until use.


title: Exiqon, miRCURY LNA microRNA array, 7th gen (hsa, mirbase 21)

city: Vedbaek

first: Michael

last: Thorsen

address: Skelstedet 16

country: Denmark

institute: Exiqon

organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Saimiriine gammaherpesvirus 2
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

manufacturer: Exiqon A/S, Skelstedet 16, 2950 Vedbaek, Denmark

first: Jorg

last: Krummheuer

manufacture_protocol: See Exiqon website


title: Exiqon, miRCURY LNA microRNA array, 6th gen (hsa, mirbase 21)

description: Herpesvirus saimiri strain A11


title: Exiqon, miRCURY LNA microRNA array, 6th gen (hsa, mirbase 17)

status: Public on Jul 23 2014

description: Herpesvirus saimiri strain A11


title: Illumina HiSeq 2000 (Anopheles merus)

last: GEO

organism: Anopheles merus


title: Illumina HiSeq 1500 (Trichoderma reesei)

status: Public on Jul 18 2014


title: S. Cerevisiae Flocculation array

city: Hannover

first: Frank

last: Stahl

address: Callinstr. 3

department: Institut für Technische Chemie

institute: Universität Hannover

manufacture_protocol: Oligonucleotide design and synthesis: 50mer and 70mer oligonucleotides with a 5’ aminolink were designed and synthesised by Invitrogen (Darmstadt, Germany) respectively Operon (Cologne, Germany). Spotting protocol: To produce microarrays silylated slides were purchased from TeleChemTM International Inc. (Sunnyvale, CA, USA) and the printing of the oligonucleotides was performed by using an AffymetrixTM 417 arrayer. Oligonucleotide solutions were prepared in 96-well-plates containing each 30 µl. The concentration of the printed oligonucleotides was 50 µM in 1x ArrayItTM Microarray Spotting Solution Plus. After spotting, the slides were incubated at 80 °C for 2 h. Slides were blocked in SSC containing 1% BSA (Sigma) for 45 min and rinsed with water for 5 min.


title: OpArray Human 35K [oligo_ID version]

city: Frederick

first: Dennis

last: Klinman

state: Maryland

address: 1050 Boyles St

department: Cancer and Inflammation Program

institute: National Institutes of Health

organism: Homo sapiens

description: Based on the Ensembl human database build (NCBI-35c), with a full coverage on NCBI human Refseq dataset (04/04/2005), the Human MI ReadyArray also integrates a significant portion of unique full-length cDNA clone sequences from the H-Invitational Database (release 1.8). A variety of data sources were used to provide gene expression coverage for genes from the human mitochondrial genome, RNA genes, microRNA genes, the endogenous human viral genes and the exogenous reporter genes.

manufacture_protocol:
This long oligo microarray contains 35,035 oligonucleotide probes, representing approximately 25,100 unique genes and 39,600 transcripts. A subset of the total set (31,387 probes) are contained within the span of a single exon to provide the microarray detection precision at the transcript and gene levels. Of these 31,387 single exon probes, 26,283 of them are suitable for Comparative Genome Hybridization (CGH) studies.
Microarray Inc (MI) precisely prints these probes onto a single 1 inch x 3 inch standard-sized slide within HEPA filtered, environmentally controlled clean-rooms. Our manufacturing processes utilize MI proprietary technologies and intellectual property licensed through Oxford Gene Technology.


title: Illumina HiSeq 2000 (Anopheles coluzzii)

organism: Anopheles coluzzii


title: Agilent-048472 ferret_Ens60_all_RNAseq_180k 046983

city: Seattle

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

organism: Mustela putorius furo

description:
Arrays of this design have barcodes that begin with 16048472 or 2548472.
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.
Orientation:
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
The ID column represents the Agilent Feature Extraction feature number.
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.
copy of original design 046983


title: Illumina MiSeq (Chlamydomonas reinhardtii)

organism: Chlamydomonas reinhardtii


title: Agilent-014597 ISQ Chip Folsomia candida Collembola VU 2

status: Public on Jul 19 2014

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

country: Netherlands

institute: MicroLife Solutions

organism: Folsomia candida

description:
Folsomia candida microarray 2x11
second platform for this microarray, does not contain control spots
Arrays of this design have barcodes that begin with 251459710052

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 Ustilago maydis array [080805_UM_SG_EXP]

city: San Nicolas de los Garza

first: Elva

middle: Teresa

last: Aréchiga-Carvajal

state: Nuevo León

address: Av. Pedro de Alba

country: Mexico

organism: Mycosarcoma maydis

description:
Five different oligonucleotide probes per gene (60 nt in length) per duplicate represented each of the 6,883 genes of the U.maydis genome.
Nimblegene_8036 080805_UM_SG_EXP Design based on 080424_Gold_TI5270_60mer_expr, however, with several changes;
maize sequences have been added (probes = 220).
There is a special (hand selected) selection of 23 genes that is on the array a total of 4 times (5 probes per target).
Plus several genes have been replicated on the array.

DESIGN_ID: 8036
DESIGN_NAME: 080805_UM_SG_EXP

native array description file: 080805_UM_SG_EXP.ndf
native array description file: 080805_UM_SG_EXP.ngd

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


title: Agilent-027381 Oryzias latipes NIBB_medakav4

city: Okazaki

first: Toshiya

last: Nishimura

address: 5-1 Higashiyama Myodaiji-cho

country: Japan

institute: National Institute for Basic Biology

organism: Oryzias latipes

description:
Arrays of this design have barcodes that begin with 16027381 or 2527381.

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 (Rhodopseudomonas palustris)

status: Public on Jul 17 2014

organism: Rhodopseudomonas palustris


title: Agilent-048471 ferret_Ens69_plus_mRNAseq_60k 046935

description:
Arrays of this design have barcodes that begin with 16048471 or 2548471.
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.
Ferret design - copy of original design 046935
Orientation:
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
The ID column represents the Agilent Feature Extraction feature number.
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: LC Sciences LC_MRA-1001_miRHuman_17

city: Houston

first: Christoph

last: Eicken

address: 2575 W. Bellfort

institute: LC Sciences, LLC

description: The complete platform design is available under GEO accession number GPL13836

manufacture_protocol: human miRNA microarray with 100% coverage of mature human miRNAs listed in miRBase version 17.0. Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes are made by in situ synthesis using PGR (photogenerated reagent) chemistry.


title: LC_MRA-1002_miRMouse_20

organism: Mus musculus

manufacture_protocol: mouse miRNA microarray with 100% coverage of mature mouse miRNAs listed in miRBase version 20. Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes are made by in situ synthesis using PGR (photogenerated reagent) chemistry.


title: Illumina HiSeq 2500 (Brucella melitensis)

organism: Brucella melitensis


title: Agilent-020186 C.elegans v2 (Name as ID)

city: Montreal

first: Sylvie

last: Rocheleau

state: Quebec

address: 6100 Royalmount Avenue

country: Canada

institute: National Research Council Canada

organism: Caenorhabditis elegans

manufacture_protocol: Catalogue G2519F-020186


title: Illumina ratRef-12 v1.0 expression beadchip

status: Public on Dec 13 2007

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

organism: Rattus norvegicus

technology: oligonucleotide beads

description:
The RatRef-12 Expression BeadChip includes twelve genome-scale, gene expression microarrays built using Illumina’s multi-sample Array of Arrays format. BeadChip content (22,523 probes per array) was selected from theNational Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database.

Please use the GEO Data Submission Report Plug-in v1.0 for Gene Expression which may be downloaded from https://icom.illumina.com/icom/software.ilmn?id=234 to format the normalized and raw data.  These should be submitted as part of a GEOarchive.  Instructions for assembling a GEOarchive may be found at http://www.ncbi.nlm.nih.gov/projects/geo/info/spreadsheet.html

manufacture_protocol: see manufacturer's website


title: Rosetta/Merck Human RSTA Custom Affymetrix 2.0 microarray [HuRSTA-2a520709]

status: Public on May 05 2010

first: Amit

middle: V

last: Kulkarni

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

description: Contains probesets for each transcript. Probeset is made of 4 to 20 distinct probes.

first: John

last: Castle

manufacture_protocol: See manufacturer website.


title: Illumina Genome Analyzer IIx (Cricetulus griseus)

status: Public on Jul 16 2014

organism: Cricetulus griseus


title: Agilent-035742 Custom Sarcophaga crassipalpis Array (Ag-S.Crassipalpis)

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

organism: Sarcophaga crassipalpis

first: Ellen

last: Danneels

first: Dirk

last: De Graaf

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


title: Illumina HiSeq 2000 (Dinoponera quadriceps)

organism: Dinoponera quadriceps


title: AB 5500xl Genetic Analyzer (Malus domestica)

organism: Malus domestica


title: Illumina MiSeq (Volvox carteri)

organism: Volvox carteri


title: Illumina HiSeq 2500 (Escherichia coli CFT073)

organism: Escherichia coli CFT073


title: Illumina HiSeq 2000 (Polistes canadensis)

organism: Polistes canadensis


title: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)


title: Illumina HumanOmni2.5-8v1.1 beadchip

organism: Homo sapiens

manufacture_protocol: See manufacturer's website


title: Explorer Antibody array

city: Daejeon

first: Myung-Shin

last: Lee

address: Yongdu-dong, Jung-gu

department: Microbiology and Immunology

country: South Korea

institute: Eulji University School of Medicine

technology: spotted peptide or protein

description: The Explorer Antibody Array is a comprehensive array consisting of 656 highly specific and well-characterized antibodies covering more than nine pathways.

manufacture_protocol: The antibodies are printed on polymer coated glass slides and can be read on all microarray scanners that are compatible with 76 x 25 x 1 mm (3 in. x 1 in. x 1mm) slides.


title: NERCMDSNU Homo sapiens 15K  version 1.0

city: Xi'an

first: Xi

last: Wang

address: No.76 Yanta West Road

institute: Xi‘an Jiaotong University Health Science Center

manufacturer: National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, Shaanxi

manufacture_protocol:
1. Use the primer 5.0 to design probes and test them with oligo6.0 software. The principles of probe design as follows:(1) the length of probe is 59 bases, and annealing temperature is 78.0±5.°C, (2) tandem duplication bases was not more than 6,(3) the stem structure of stem loop in the internal of probes was not more than 6bases, (4) the most stable secondary structure base pairing of probe molecule was less than 6bp, (5) the Score value is less than 40, after comparing the probes with non-targeting gene sequence, which means the serial homology fragments were not more than 20 bases.
2. Dissolve the probes to 40 uM solution with sterilization, and inject into 169 pore plate after mixed with sample application buffer solution. Then put the probes on the surface of amination film base (home made) by using GeeDomSmartArrayer 48.


title: SMRT CGH v2

status: Public on Jul 15 2014

city: Vancouver

first: Christopher

middle: Trevor Daniel

last: Dickman

state: BC

address: 675 West 10th Ave

institute: BC Cancer Research Center

description: BAC Clones beginning with N0 or F0 belong to the Roswell park Cancer Institute libraries 11 and 13 (RP11 and RP13), respectively; those beginning with M belong to the Caltech-D (CTD) library


title: Illumina Genome Analyzer IIx (Escherichia coli)

status: Public on Jul 14 2014

last: GEO

organism: Escherichia coli


title: Agilent-063251 Clostridium difficile CD630_expression-02

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

organism: Clostridioides difficile

description:
Arrays of this design have barcodes that begin with 16063251 or 2563251.
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Feature Extraction feature number.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

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


title: Agilent-025748 Corynebacterium glutamicum CGRarray

city: Shinjuku-ku

first: Norihiko

last: Takemoto

state: Tokyo

institute: Research Institute of National Center for Global Health and Medicine

organism: Corynebacterium glutamicum R

description:
all_ORF_177bp_fragments

Arrays of this design have barcodes that begin with 16025748 or 2525748.

The ID column represents the Agilent Probe name.


title: Human Discover chips oligo array

city: Pune

first: Sanjay

last: Mukherjee

state: Maharashtra

address: Ganeshkhind

department: Department of Zoology

country: India

institute: University of Pune

description: oligonucleotide probe sequences are proprietary and were not available for submission.


title: TIGR NSF rice oligonucleotide microarray A and B

city: Fayetteville

first: Nilda

last: Burgos

address: 1366 W Altheimer Dr

country: USA

institute: University of Arkansas

organism: Oryza sativa Japonica Group

description:
NSF-45K array.
About 45,000 oligonucleotides corresponding to ORFs encoded by the Nipponbare genome were printed on two separate glass slides (A and B).

manufacturer: The Institute for Genomic Research (TIGR)

manufacture_protocol: Oligonucleotides (~60-mer) corresponding to ORFs in the Nipponbare genomic sequence were synthesized and printed on amine-coated glass slides by TIGR. Microarray slides were purchased through the NSF rice oligonucleotide microarray project (UC Davis).


title: Agilent-022122 MCAMYOSHI1

city: Kawasaki

first: Yoshiyuki

last: Watanabe

state: Kanagawa

address: 2-16-1 Sugao Miyamaeku

department: Department of Internal Medicine, Division of Gastroenterology and Hepatology

institute: St.Marianna University School of Medicine

description:
Arrays of this design have barcodes that begin with 16022122 or 2522122.

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: Candida dubliniensis V.2

status: Public on Jul 11 2014

city: Dublin

first: Gary

middle: P.

last: Moran

address: Lincoln Place

department: Dental Science

country: Ireland

institute: Trinity College Dublin

organism: Candida dubliniensis

description: Agilent Sure Print 4x44K Array


title: Anopheles stephensi 63K

city: Baltimore

first: George

last: Dimopoulos

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

organism: Anopheles stephensi

manufacture_protocol: Agilent


title: AmpeloArray 1.0 developed by University of Verona and Fondazione Edmund Mach

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

organism: Ampelomyces quisqualis

description:
Spots size: 25 microns
Total number of spots: 94928
Number of spots replicates per oligo: 1-2

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

first: Lorenzo

last: Tosi

first: Massimo

last: Delledonne

first: Alessandro

last: Ferrari

first: Antonio

last: Chimento

first: Paola

last: Tononi

first: Monika

last: Maurhofer

first: Cesare

last: Gessler

first: Ilaria

last: Pertot

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


title: TaqMan® OpenArray® Rodent MicroRNA Panel (4470188)

city: Minneapolis

first: emilyn

middle: U

last: alejandro

state: MN

department: Integrative Biology and Physiology

institute: University of Minnesota

organism: Mus musculus

description: The TaqMan® OpenArray® Rodent MicroRNA Panel, QuantStudio™ 12K Flex is a fixed-content panel containing validated rodent (mouse and rat) TaqMan® MicroRNA Assays derived from Sanger miRBase release v.15

manufacturer: Applied Biosystems by Life Technologies (Thermo Fisher)


title: NimbleGen Paramecium tetraurelia expression array SET01-02 [101018_Paramecium_LS_EXP]

city: Saarbrücken

first: Martin

last: Simon

address: Campus A2 4

department: Centre for Human and Molecular Biology

institute: Saarland University

organism: Paramecium tetraurelia

description:
NimbleGen-P.tetraurlia-SET01-02-50mer
SET01 contains three sense and three as-probes per annotated transcript (previoulsy described in Arnaiz et al. BMC Gemomics 2010); SET02 was redesigned by Nimblegen and contains 12 as-probes per annotated transcript

manufacture_protocol: In situ oligonucleotide synthesis as described in www.nimblegen.com


title: [Atdschip_tiling] Affymetrix AGRONOMICS Tiling Array [CDF: agronomics1_TAIR10_gene_antisense]

status: Public on Jul 10 2014

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Arabidopsis thaliana

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


title: AmpeloArray 2.0 developed by University of Verona and Fondazione Edmund Mach

description:
Spots size: 25 microns
Total number of spots: 94928
Number of spots replicates per oligo: 2-3


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [CDF: HuEx10stv2_Hs_ENSG_14]

description: Probe set data extracted from custom CDF [Brainarray Version 14.0]

manufacture_protocol: See manufacturer's web site


title: Agilent-012657 Agrobacterium tumefaciens 11K array

status: Public on Jul 26 2014

city: Bloomington

first: Aaron

last: Buechlein

address: 1001 E 3rd St

department: Center for Genomics and Bioinformatics

institute: Indiana University

organism: Agrobacterium tumefaciens

description: AMADID # 012657 (11K/features/array)(001,002), Single Customer


title: Illumina HiSeq 2000 (Acinetobacter baumannii 983759)

last: GEO

organism: Acinetobacter sp. 983759


title: Illumina HiSeq 2500 (Acinetobacter baumannii 983759)


title: Illumina HiSeq 2500 (Acinetobacter baumannii 1564232)

organism: Acinetobacter sp. 1564232


title: Illumina HiSeq 2500 (Acinetobacter baumannii 478810)

organism: Acinetobacter sp. 478810


title: Illumina HiSeq 2500 (Agrobacterium tumefaciens)

status: Public on Jul 07 2014


title: AB 5500xl Genetic Analyzer (Bos taurus)

status: Public on Jul 08 2014

organism: Bos taurus


title: Illumina HiSeq 2500 (Acinetobacter baumannii 1457504)

organism: Acinetobacter baumannii 1457504


title: AB SOLiD 4 System (Sus scrofa)

organism: Sus scrofa


title: CAT-3x15K-Deinococcus-radiodurans-R1 array

city: Jeongeup

first: Im

last: Seong Hun

address: Jeongeup 580-185, Republic of KoreaInstitute

institute: Korea Atomic Energy Research Institute

organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

manufacture_protocol: see manufacturer's website (MYcroarray.com)


title: Illumina HiSeq 2000 (Acinetobacter baumannii 478810)


title: Illumina HiSeq 2500 (Acinetobacter baumannii 1592897)

organism: Acinetobacter sp. 1592897


title: Illumina HiSeq 2000 (Acinetobacter baumannii 34654)

organism: Acinetobacter baumannii 34654


title: Illumina HiSeq 2500 (Acinetobacter baumannii 34654)


title: Illumina HiSeq 2000 (Acinetobacter baumannii 1457504)


title: Illumina HiSeq 2500 (Acinetobacter baumannii 1000160)

organism: Acinetobacter sp. 1000160


title: Illumina HiSeq 2000 (Acinetobacter baumannii 1592897)


title: Illumina HiSeq 2000 (Acinetobacter baumannii 1207552)

organism: Acinetobacter baumannii 1207552


title: CustomArray 4x2K Enterococcus microarray

city: Tromso

first: Christopher

last: Fenton

state: Norge

address: MH bygget

department: GSCT

country: Norway

institute: Universiry of Tromso

organism:
Enterococcus faecalis
Enterococcus faecium

description:
Theresa_custom_v1
All together 272 DNA targets representing mobile genetic elements and antimicrobial resistance determinants associated with enterococci were spotted on a CustomArray 4x2K microarray from CustomArray Inc. Each fourplex microarray slide contain four identical sectors  that were stripped and re-hybridized up to six times.  Each target was represented by 1-5 probes each. The total of 1250 probes were Tm balanced by altering their lenght between 35 and 40 nucleotides.


title: Illumina HiSeq 2000 (Echinococcus multilocularis)

organism: Echinococcus multilocularis


title: Illumina HiSeq 2500 (Acinetobacter baumannii 1428368)

organism: Acinetobacter baumannii 1428368


title: Illumina HiSeq 2000 (Acinetobacter baumannii 1428368)


title: Illumina HiSeq 2500 (Acinetobacter baumannii 1207552)


title: Illumina HiSeq 2000 (Echinococcus granulosus)

organism: Echinococcus granulosus


title: Illumina HiSeq 2000 (Acinetobacter baumannii 1000160)


title: Agilent-030218 salmonella enterica cerro 87 8X15K array [Probe Name Version]

city: shanghai

first: qian

last: jin

address: libing road

institute: MSP

organism: Salmonella enterica subsp. enterica serovar Cerro


title: Agilent-042421 Rabbit BDR version 2 [Probe Name Version]

city: JOUY EN JOSAS

first: Vincent

last: Jacquier

address: INRA CEA GABI GIS Domaine de Vilvert bat 320

department: GABI

institute: INRA

organism: Oryctolagus cuniculus

description: Arrays of this design have barcodes that begin with 16042421 or 2542421.


title: Agilent-025942 Mycobacterium tuberculosis H37rv_oligoDB 024084

first: Alexandre

last: Pawlik

address: 28 rue du Dr. Roux

organism: Mycobacterium tuberculosis


title: Aquagenomic Sparus aurata oligonucleotide-microarray (SAQ) (condensed version)

status: Public on Jul 09 2014

city: Castellón

first: Josep

middle: A

last: Calduch-Giner

address: Ribera de Cabanes

country: Spain

institute: Institute of Aquaculture Torre de la Sal (CSIC)

organism: Sparus aurata

description: A total of 43,398 oligonucleotide probes were used to construct a high-density seabream microarray based on the Agilent 4 x 44 K design format. 7,285 transcripts with annotated sequences were spotted in triplicate onto the slide (total probes 21,855), as well as 8,377 ESTs without annotation, 183 enriched sequences (GenBank) with 15 replicated probes (total probes 2,745), and finally 1,417 internal control probes of Agilent (N = 43,398). The platform developed used all available public ESTs stored and annotated in the Aquagenomic Consortium seabream library (10K).

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


title: Illumina HiSeq 2500 (Bifidobacterium bifidum)

status: Public on Jul 03 2014

organism: Bifidobacterium bifidum


title: Agilent-015241 Rice Gene Expression Microarray

city: Bellaterra (Cerdanyola del Vallés)

first: Sonia

last: Campo

state: Barcelona

address: Parc de Recerca UAB Edifici CRAG, Campus UAB

institute: Center for Research in Agricultural Genomics (CRAG)

organism: Oryza sativa

description:
NIAS_GreenTechnoProject_4x44K_FullName

Arrays of this design have barcodes that begin with 16015241 or 2515241.

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-028911 Oryza sativa eArray-N30 [condensed version]

organism: Oryza sativa Japonica Group

description: Each array has 3 different specific oligonucleotides recognizing the same locus. The 3 probes have been condensed in this Platform; the name of 1 of the probes is used to represent the 3 probes.

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


title: Illumina Genome Analyzer IIx (Streptomyces coelicolor)

status: Public on Jul 02 2014

organism: Streptomyces coelicolor


title: Agilent-027234 custom_Pseudomonas sp. M18_ 8*15K [Probe name version]

city: Shanghai

first: yaqian

last: Li

address: Dongchuan Road

country: China

institute: Shanghai Jiaotong University

organism: Pseudomonas sp. M18


title: Ion Torrent Proton (Ovis aries)

status: Public on Jul 01 2014

organism: Ovis aries


title: HumanOmniExpress-12v1 BeadChip

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

organism: Homo sapiens


title: Agilent-019494 Streptomyces clavuligerus DDTS_02 Microarray (Feature Number version)

city: León

first: Paloma

last: Liras

state: León, Spain

address: Facultad de Biología. Campus de Vegazana

department: Molecular Biology

institute: Universidad de León

organism: Streptomyces clavuligerus

description:
Arrays of this design have barcodes that begin with 16019494 or 2519494.
Features are 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: Custom Febit Aspergillus nidulans biA1 veA1 biochip

city: Sevilla

first: Gabriel

last: Gutierrez

address: PO BOX 1095

department: Genetics

institute: University of Seville

organism: Aspergillus nidulans

manufacture_protocol: The Geniom biochips used for this study were synthesized with the Geniom One instrument applying febit's standard shortmer kit for oligonucleotide synthesis. The Biochip was manufactured exactly to precise specifications and achieved the standard quality criteria. The light-activated in-situ oligonucleotide synthesis using a digital micromirror device was performed within the Geniom One instrument on an activated three-dimensional reaction carrier consisting of a glass-silicon-glass sandwich (Biochip). Using standard DNA synthesis reagents and 3'-phosphoramidites carrying a 5'-photolabile protective group, oligonucleotides were synthesized in parallel in eight individually accessible microchannels (referred to as arrays) of one biochip. Prior to synthesis, the glass surface was activated by coating with a spacer to facilitate probe-target interaction and to avoid probe-probe interference.


title: Agilent-025976 Mouse CpG Island ChIP-on-Chip Microarray 1x1M mm9 (Probe Name version)

city: Hannover

first: Michael

last: Heuser

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

organism: Mus musculus


title: WashU C. neoformans 24k Ver2

city: Madison

first: Christina

last: Hull

state: WI

address: 440 Henry Mall

department: Biomolecular Chemistry, Medical Microbiology and Immunology

institute: University of Wisconsin- Madison

organism: Cryptococcus neoformans

manufacturer: Washington University Genome Science Center

manufacture_protocol:
Arrays are printed on epoxy-silane slides. Common spot diameter is 90μM. The
distance between spots is 191μm. There are
23 Rows,
22 Columns, and
48 Subarrays. Number
of C. neoformans oligos: 11,343, printed in duplicate. Total number of control organism oligos: 27, printed in duplicate unless otherwise noted. A. thaliana (Stratagene): 10 (printed in quadruplicate) H. sapiens: 4 M. musculus: 3 R. norvegicus: 3 Dictyostelium: 3 D. melanogaster: 2 C. elegans: 2. C. neoformans, model organism, and control features printed at 20μM.


title: Agilent-014706 and Agilent-014707 Human Promoter ChIP-on-Chip Set 244K, Microarray combined G4489A (Probe name version)

city: Vienna

first: Manuela

last: Hofner

address: Muthgasse 11/2

department: Molecular Diagnostics

country: Austria

institute: Austrian Institute of Technology - AIT

description:
Human Promoter ChIP-on-Chip Set 244K 2 of 2

The ID column represents the Agilent probe names.

A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL4125.


title: NimbleGen Rhesus macaque Nimblegen Custom 12-plex array [090806_RheMac_exp]

city: Davis

first: Matt

middle: L

last: Settles

state: CA

address: 451 Health Sciences Sr

department: Genome Center

institute: University of California, Davis

organism: Macaca mulatta

description: 12-plex microarray

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


title: Chicken Gene 1.0 ST Array

status: Public on Mar 04 2014

city: Edinburgh

first: Katherine

last: Long

address: 5 Little France Drive

department: Centre for Regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

organism: Gallus gallus

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=Mon Oct  1 15:31:00 2012 PDT
#%chip_type=ChiGene-1_0-st-v1
#%lib_set_name=ChiGene-1_0-st
#%lib_set_version=v1
#%genome-species=Gallus gallus
#%genome-version=galgal3
#%genome-version-ucsc=galgal3
#%genome-version-create_date=2006-05-00
#%genome-lifted-method=NONE
#%genome-lifted_from-species=Gallus gallus
#%genome-lifted_from-version-ucsc=galgal3
#%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=transcript_cluster
#%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=


title: NimbleGen Plasmodium falciparum 385K tiling expression array [2007-05-16_Pfal_DS_Tiling; gene-level]

city: Seattle

first: Robert

middle: D

last: Morrison

address: 307 Westlake Ave N

institute: Center for Infectious Disease Research

organism: Plasmodium falciparum

description:
NimbleGen design name:  2007-05-16_Pfal_DS_Tiling
NimbleGen design ID: 5713

A high coverage expression design tiling the entire genome of P.falciparum (PlasmoDB v5.2),  with 386,222 perfect match probes (probe length 50-75bp, spaced every 60-85bp along genome).  The design includes random GC and other control probes.
The Platform data table reflects a complete remapping of the original probe sequences to the recent genomic resequencing and reannotation of P. falciparum by GeneDB (Mar 1, 2013,  PlasmoDB version 9.2).  The original .ndf and .pos files are linked below as supplementary files.

native array description file: 2007-05-16_Pfal_DS_Tiling.ndf
native array description file: 2007-05-16_Pfal_DS_Tiling.pos
native array description file: 2007-05-16_Pfal_DS_Tiling.ProbeMap.txt

2007-05-16_Pfal_DS_Tiling.ProbeMap.txt contains the following columns;

PROBE_ID: unique identifier for each probe on the array, identical to PROBE_ID in the original .ndf file
SEQ_ID: chromosome identifier of the remapped probe location, in new GeneDB/PlasmoDB notation
POSITION: starting coordinate (base 1) of remapped probe location on the chromosome's forward strand
END: ending coordinate (base 1) of remapped probe location on the chromosome's forward strand
MATCH: Blast match result from best alignment of original probe sequence to the new re-sequenced genome
E_VALUE: Blast E value from best alignment of original probe sequence to the new re-sequenced genome
GENE_ID: gene identifier of the annotation locus the probe falls inside of.  Intergenic spaces between genes are assinged a unique numbered identifier containing the flag '(ng)'
EXON_ID: gene identifier of the coding exon the probe falls inside of.  Probes landing outside of coding exons will have a blank ExonID.  All probes with the same ExonID are averaged to get a single gene expression value.

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


title: Agilent-042421 Rabbit BDR version 2 [Feature Number Version]

status: Public on Feb 22 2013

country: France

organism: Oryctolagus cuniculus

description:
Arrays of this design have barcodes that begin with 16042421 or 2542421.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

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


title: Agilent-035923 UniversityPadova_Ruditapes philippinarum_8x15K_v2.0

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

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

institute: University of Padova

organism: Ruditapes philippinarum

description: From the total of 1,438,665 R. philippinarum reads obtained through 454 sequencing (SRA020646 and SRA046855), the Newbler software package (GS De Novo Assembler v2.6, Roche) was able to assemble 88.24% of the raw sequences, with 11.76% of them (169,223) remaining as singletons. The assembly resulted in 26,708 isotigs grouped into 15,175 isogroups and 156 contigs. The longest isotig of each isogroup, the contigs, the singletons with more than 200 bp of continuous sequence with a Phred Q>20 (18,545) and the NCBI EST sequences (2,050) were then considered for the annotation. Putative identities of assembled sequences and singletons were obtained by running Blastx and Blastn similarity searches on several protein and nucleotide reference databases. Alignments with an E-value of at most 1 E-3 and 1 E-5 were considered significant for the protein and nucleotide databases, respectively. A total of 12,156 successfully annotated transcripts were considered for the R. philippinarum DNA microrrray design. All Isotigs are stored in the public Transcriptome Shotgun Assembly Sequence Database (TSA, http://www.ncbi.nlm.nih.gov/genbank/tsa/) under accession number GAEH00000000 (note: publicly available after paper publication). All singletons considered for the microarray design are stored in the public database Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra/) under accession numbers SRA020646 and SRA04685. As most sequence reads were obtained from a non-directional cDNA library, sense strand orientation was inferred putatively from that of homologous protein sequences of other species. One probe for annotated transcripts with known orientation was designed to construct a high-density oligo-DNA microarray, while two probes with both orientations were designed for contigs with ambiguous orientation. A total of 13, 671 probes representing 12,108 unique transcripts were designed using the Agilent eArray interface (https://earray.chem.agilent.com/earray/), which applies proprietary prediction algorithms to design 60-mer oligoprobes.

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


title: NimbleGen Human ChIP-CHIP 3 x 720k REFSEQ Promoter Array [090618_HG18_Refseq_Prom_ChIP and 100718_HG18_Refseq_Prom_ChIP]

status: Public on Nov 18 2012

city: Worcester

first: Glenn

middle: Arthur

last: Maston

state: MA

address: 364 Plantation Street

department: Program in Gene Function & Expression

institute: University of MA medical School

description:
The array is designed to tile across the promoter region, from -3200 bp to +800 bp relative to the transcriptional start site (TSS), of 22,542 REFSEQ promoters, based upon HG18.  The probes are 50-75 bp in size and tiled to have an average spacing of 100 bp between probes.

Build: Hg18, NCBI 36
There are two design names for the same platform since there was a redesign.  The probes are the same on both designs, but in the 100718_HG18_Refseq_Prom_ChIP design ~4K control probes are duplicated.
Catalog #: 05924405001

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


title: NanoString nCounter Human Cancer Reference Kit

city: Boston

first: Svitlana

last: Tyekucheva

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

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


title: Wistar/Shiekhattar-human-44k-1.0

status: Public on Apr 12 2011

city: Berlin

first: Ulf

middle: Andersson

last: Ørom

address: Ihnestrasse 63-73

department: OWL

institute: Max Planck Institute for Molecular Genetics

manufacture_protocol: Agilent Technologies custom array synthesis with probes for transcripts.


title: Affymetrix OncoScan™ FFPE Express V2 334K

status: Public on Jul 07 2013

first: Markus

last: Riester

address: 3 Blackfan Circle

department: Biostatistics & Computational Biology

description:
A platform that offers high-quality copy number, genotype, and somatic mutation data with whole-genome coverage and high resolution in cancer genes for FFPE samples. This array should be used together with the MIP (Molecular Inversion Probes) technology.

Annotations correspond to NCBI build 36.

manufacture_protocol: See manufacturer's web site.


title: MRA-1001_miRHuman_17

status: Public on Jul 12 2011

city: Houston

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

description: Human miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 17

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


title: Lactobacillus johnsonii LA-1 44K 60-mer array, Version 2

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

organism: Lactobacillus johnsonii


title: Illumina HiSeq 2000 (Xenopus laevis)

status: Public on Sep 04 2013

last: GEO

organism: Xenopus laevis


title: Mycobacterium smegmatis version 4

status: Public on Jun 15 2012

city: Dunedin

first: Jennifer

middle: R

last: Robson

address: 720 Cumberland Street

department: Microbiology and Immunology

country: New Zealand

institute: University of Otago

organism: Mycolicibacterium smegmatis MC2 155

description: 70mer Oligonucleotide, Aminosilane, 3x replicate oligo printings

manufacturer: Pathogen Functional Genomics Resource Center

manufacture_protocol: QMS, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Affymetrix AGRONOMICS Tiling Array [CDF: agronomics1_TAIR9_gene]

status: Public on Jan 17 2012

city: Zwijnaarde

first: Megan

last: Andriankaja

address: 927 Technologiepark

institute: VIB-PSB

organism: Arabidopsis thaliana

description: The TAIR9 CDF was used.  Reference Platform with TAIR7 mapping is contained in GEO as GPL13479.

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: AB 5500xl Genetic Analyzer (Homo sapiens)

status: Public on Nov 15 2012


title: Illumina Genome Analyzer II (Macaca mulatta)

status: Public on Sep 08 2009


title: LMB microarray 15K (Agilent format)

status: Public on Mar 24 2011

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

organism: Micropterus salmoides

first: Nancy

last: Denslow

manufacture_protocol: SurePrint G3 Gene Expression Microarrays


title: Agilent-046064 Unrestricted_Human_miRNA_V19.0_Microarray (miRNA ID version)

status: Public on Mar 11 2014

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

relation: Alternative to: GPL18044 (Feature number version)


title: ENS SGDB Trichoderma reesei Tr20_Tiling140_1 240k oligo array

status: Public on Mar 15 2010

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

institute: École normale supérieure

organism: Trichoderma reesei

description:
Trichoderma reesei Tiling array. One probe has been design every 140 base every other strand.
The probe design has been done according to T. reesei v2.0 genome assembly from the DOE JGI available here: http://genome.jgi-psf.org/Trire2/Trire2.home.html
The probe ID is a code to fing genome localisation of each probe: Scaffold_Start_Strand
The first number indicate the scaffold number
The second number is the start position of the probe
The third number is the strand FWD or REV

An alternative version of this platform is accessioned as GPL18867

last: Le Crom

first: Laurent

last: Jourdren

first: Aurélie

last: Duclos

manufacture_protocol: In situ oligonucleotide synthesis of 60mer custom oligos. See manufacturer's web site at http://www.agilent.com/.


title: Arabidopsis Yale 12K

status: Public on Jul 09 2005

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

description:
Arabidopsis Yale 12K
Platform_manufacture_protocol: as described in Yale Labs manual
Platform_manufacturer: Yale W.M. Keck Center Microarray Core Facility
Platform_technology: spotted cDNA


title: Agilent-016989 Synechocystis sp. PCC 6803 8x15K custom array

status: Public on Mar 15 2008

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

organism: Synechocystis sp. PCC 6803

first: Wolfgang

last: Hess

first: Annegret

last: Wilde

manufacture_protocol:
Agilent’s SurePrint technology
8x15K custom design


title: Arabidopsis Yale 9.2K

description:
Arabidopsis Yale 9.2K
Platform_manufacture_protocol: as described in Yale Labs manual
Platform_manufacturer: Yale W.M. Keck Center Microarray Core Facility
Platform_technology: spotted cDNA


title: ZB/SBS-NTU Plasmodium falciparum 3D7 11.4K v1.1

status: Public on Nov 27 2010

city: Singapore

first: Sachel

last: Mok

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

first: Guangan

last: Hu

first: Zbynek

last: Bozdech

first: Manuel

last: Llinás

first: Jingguang

last: Li

first: Peter

last: Preiser

first: Bernardo

middle: J

last: Foth

manufacture_protocol:
Long oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350.
The 70-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biology 2003, 4:R9.


title: ZB/SBS-NTU Plasmodium falciparum 3D7 11.4K v2

status: Public on Jul 04 2014

description:
Genome Build: GeneDB version 3
Plasmodium falciparum 3D7 homepage on GeneDB: http://www.genedb.org/Homepage/Pfalciparum

manufacture_protocol:
Long oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350.
The 70/50-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biology 2003, 4:R9.


title: Agilent-021876 Populus 4x44K v1.0 (Feature Number version)

status: Public on Sep 14 2012

city: Athens

first: Chung-Jui

last: Tsai

state: GA

address: 120 Green Street

department: School of Forestry and Natural Resources

institute: University of Georgia

organism: Populus trichocarpa

description:
Whole-genome expression array.
Arrays of this design have barcodes that begin with 16021876 or 2521876.
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 GPL17041


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [probe set (exon) version]

status: Public on May 21 2007

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Homo sapiens

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 Mar 11 17:51:22 2009 PDT
#%chip_type=HuEx-1_0-st-v2
#%lib_set_name=HuEx-1_0-st
#%lib_set_version=v2
#%genome-species=Homo sapiens
#%genome-version=hg18
#%genome-version-ucsc=hg18
#%genome-version-ncbi=36
#%genome-version-create_date=2006-03
#%netaffx-annotation-date=2009-03-16
#%netaffx-annotation-netaffx-build=28

relation: Alternative to: GPL9113 (Alternative CDF)

relation: Alternative to: GPL10585 (Alternative CDF [HuEx10stv2_Hs_VEGAE_v10])

manufacture_protocol: See manufacturer's web site


title: [OncoScan] Affymetrix OncoScan FFPE Assay

status: Public on Apr 23 2014

description:
#OncoScan.na33.r1.annot.csv
#%create_date=2013-09-24 GMT-08:00 18:05:59
#%chip_type=OncoScan
#%genome-species=Homo sapiens
#%genome-version=hg19
#%genome-version-ucsc=hg19
#%genome-version-ncbi=37
#%genome-version-create_date=2009-02-00
#%dbSNP-date=2011-03-11
#%dbSNP-version=135
#%hapmap-date=2008-01-08
#%hapmap-version=23
#%dgv-date=2010-10-00
#%dgv-version=10
#%netaffx-annotation-date=2012-11-05
#%netaffx-annotation-netaffx-build=33

manufacture_protocol: see manufacturer's web site