title: Agilent-028889 Tursiops truncatus AM_v1 [Probe name version]

status: Public on Nov 29 2016

city: Charleston

first: Marion

last: Neely

state: SC

address: 331 Ft. Johnson Rd

department: NCCOS

country: USA

institute: National Ocean Services

organism: Tursiops truncatus

technology: in situ oligonucleotide

description:
Arrays of this design have barcodes that begin with 16028889 or 2528889.

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.

distribution: custom-commercial

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


title: NIA Drosophila microarray

status: Public on Oct 02 2014

city: Baltiimore

first: Sige

last: Zou

state: MD

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

organism: Drosophila melanogaster

technology: spotted DNA/cDNA

distribution: non-commercial

manufacturer: Laboratory of Experimantal Gerontology, National Institute on Aging

manufacture_protocol: PCR products of 14,151 predicted or known genes in D. melanogaster were used to generate DNA microarray. The length of each PCR amplicon was 100-600 bp. cDNA was amplified with universal primers (AATGCAGGTTAACCTGGCTTATCG and AACGCGGCTACAATTAATACATAACC). PCR products were printed on 3-D slides (Full Moon Biosystems Inc.).


title: AB SOLiD 4 System (Drosophila virilis)

status: Public on Jun 30 2014

last: GEO

organism: Drosophila virilis

technology: high-throughput sequencing

distribution: virtual


title: AB 5500xl Genetic Analyzer (Drosophila montana)

organism: Drosophila montana


title: Affymetrix GeneChip Human Genome U133A 2.0 Array [CDF: HGU133A2_Hs_ENSG_17.1]

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Homo sapiens

description: This is identical to GPL571 but a custom CDF environment was used to extract data (CDF: HGU133A2_Hs_ENSG_17.1).

manufacture_protocol: Affymetrix standard protocol


title: CelluSpots™ - Custom Peptide Arrays

city: Homburg/Saar

first: Christian

middle: Clemens

last: Harz

state: Saarland

address: Kirrberger Strasse 100

department: Department of Human Genetics

country: Germany

institute: Saarland University

technology: spotted peptide or protein


title: GE Healthcare/Amersham Biosciences CodeLink™   Rat Whole Genome Bioarray

status: Public on Sep 29 2005

city: Tempe

first: Randall

last: Lockner

state: AZ

address: 7700 S River Parkway

department: Bioinformatics

institute: GE Healthcare Life Sciences

organism: Rattus norvegicus

technology: spotted oligonucleotide

description:
Well-annotated mRNA or coding sequences were chosen to ensure usefulness for a large range of applications in basic research, biotechnology, and drug development. Each sequence was carefully screened to ensure high-quality, specific probe design, and to reduce redundancy of gene targets. All of the probes designed to these sequences were functionally tested, and over 95% were functionally validated against 10 rat tissues to ensure best representation of the gene and biologically relevant results.

For flexibility and data preservation, CodeLink Rat Whole Genome Bioarrays are compatible with lower density CodeLink rat bioarrays. This means that existing data from CodeLink UniSet™ Rat 10K Bioarrays can be continuously used in future studies along with newly generated data from CodeLink Rat Whole Genome Bioarrays.

CodeLink users can submit data to GEO by exporting tab-delimited text files from the CodeLink software. The "Feature_id" header will need to be renamed to "ID_REF", and the "Normalized_intensity" header to "VALUE" before uploading the exported tables.

In addition, users are encouraged to include additional raw data columns in their data uploads. These additional columns do not need to be renamed.

distribution: commercial

manufacture_protocol: CodeLink Rat Whole Genome Bioarray is designed to interrogate approximately 34,000 transcripts representing most of the known and predictive genes of the rat genome, as it is described today in the public domain. Each transcript is represented by a 30-mer probe which is designed to conserved exons across the transcripts of targeted genes. The probe sequences, representing well annotated, full length and partial rat gene sequences, were designed based on sequences selected from the NCBI UniGene build #129, RefSeq database (April 1, 2004 release) and dbEST database (March 20, 2004 release).


title: SABiosciences Mouse PPAR Activation and Response PCR Array (Cat. No. PAMM-149Z)

city: Vicksburg

first: Mitchell

last: Wilbanks

state: MS

address: 3909 Halls Ferry Road

department: Environmental Laboratory

institute: US Army Engineer Research and Development Center

organism: Mus musculus

technology: RT-PCR

description: PCR assay

manufacture_protocol: see manufacturer's website


title: SABiosciences Mouse Glucose PCR Array (Cat. No. PAMM-006)

description: PCR assay


title: SABiosciences Mouse Fatty Acid Metabolism PCR Array (Cat. No. PAMM-007Z)

description: PCR assay


title: M. huakuii 7653R custom NimbleGen array_4X72K format [120703_Mesorhizo_CapBio_exp]

city: Wuhan

first: Youguo

last: Li

state: Hebei

address: No.1,Shizishan Street · Hongshan District

department: College of Life Science and Technology

country: China

institute: Huazhong Agricultural University

organism: Mesorhizobium huakuii 7653R

description:
NimbleGen design name 120703_Mesorhizo_CapBio_exp, NimbleGen design ID 39200. A custom design in 4X72K format. Each probe is replicated 3 times. The design includes random GC and other control probes.
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are linked below as supplementary files.

manufacture_protocol: High-density DNA array. See manufacturer's website at http://www.nimblegen.com/


title: AB SOLiD 4 System (Naumovozyma castellii)

status: Public on Jun 27 2014

organism: Naumovozyma castellii


title: NimbleGen T. cacao 17k array

city: Panama

first: Luis

last: Mejia

address: Roosvelt Ave. Tupper Building – 401

department: Smithsonian Tropical Research Institute

country: Panama

institute: Smithsonian Institution

organism: Theobroma cacao

description:
NimbleGen oligonucleotide glass custom T. cacao gene expression 4X72k (four arrays of 72000 probes) array, containing four probes of 50-60 mers in length for each of 17,247 Unigenes  (design ID 7114 manufactured by Roche).
080212_T_cacao_Praul_PennSU_expr.ndf
080212_T_cacao_Praul_PennSU_expr_X4.ncd
080212_T_cacao_17Karray.ngd

manufacture_protocol: This is a high-density DNA microarray made using Maskless Array Synthesizer (MAS) technology.


title: IMB E.coli 4.6K array [IMB_4.6K_E.coli_S]

city: Taipei

first: Sue

last: Lin-Chao

address: 128 Academia Road, Section 2, Nankang,

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

organism: Escherichia coli

manufacturer: Microarray Core Facility of the Institute of Molecular Biology, Academia Sinica, TW

manufacture_protocol:
Arrays were printed by standard protocols on corning GapsII aminosilane coated slides (Corning) using a Gene Machine(San Carlos, CA) OmniGrid 100 Instrument.
PCR products (0.5-1.5Kb) generated from cDNA library are printed on the array


title: Illumina HiSeq 2000 (Haemophilus influenzae)

organism: Haemophilus influenzae


title: AB SOLiD 4 System (Saccharomyces uvarum)

organism: Saccharomyces uvarum


title: AB SOLiD 4 System (Saccharomyces kudriavzevii)

organism: Saccharomyces kudriavzevii


title: T. cacao 3k 50-mer

manufacture_protocol: DNA printing onto “ArrayIt” epoxy coated slide, at 22C, 55% humidity using a GeneMachines Omnigrid robotic printer and Telechem Stealth SMP3B pins. Each oligo printed twice per slide. 3347 unigenes and a set of non-hybridizing oligos as negative and probe spike-in controls (Alien, Spot Validation System, Stratagene).


title: (OID28929)100603_Sus_scrofa_CB_expr_HX12

status: Public on Jun 28 2014

city: Hangzhou

first: Xi

last: Xia

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Feed Science

institute: Zhejiang University

organism: Sus scrofa

description: The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are linked below as supplementary files.

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


title: Human Neurological Development & Disease miRNA PCR array - MIHS-107Z

city: Hamamatsu

first: Mahesh

last: Mundalil Vasu

state: Shizuoka

address: 1-20-1 Handayama, Higashi Ward

department: Department of Psychiatry

country: Japan

institute: Hamamatsu University School of Medicine

description: miRNA PCR  Array; 84 miRNA assays


title: Serum miRNA profiling by quantitative RT PCR

description: miRNA expression by RT PCR


title: Agilent-039547 Streptomyces chattanoogensis L10 8X15K (Probe Name Version)

city: shanghai

first: qian

last: jin

address: libing road

institute: MSP

organism: Streptomyces chattanoogensis

description: Streptomyces chattanoogensis strain L10


title: Custom miScript miRNA PCR Array (CMIHS02055E)

description: miRNA PCR  custom Array; 41 miRNA assays


title: Agilent-040871 Drosophila melanogaster 8X60K with Spike (Probe Name version)

status: Public on Jun 26 2014

city: Bunkyo-ku

first: Masayuki

last: Miura

state: Tokyo

department: Genetics

institute: the University of Tokyo, Grad. Sch. Pharm. Sci

description: Arrays of this design have barcodes that begin with 16040871 or 2540871.

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


title: AB 5500 Genetic Analyzer (Coprinopsis cinerea)

organism: Coprinopsis cinerea


title: Affymetrix/Steinmetz Saccharomyces cerevisiae custom tiling array

organism: Saccharomyces cerevisiae

description:
Affymetrix 1lq file S.cerevisiae_tiling_Steinmetz.1lq

The MGED Ontology (http://mged.sourceforge.net/ontologies/MGEDontology.php)

first: Charles

last: Girardot

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


title: Illumina HiSeq 2500 (Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088)

status: Public on Jun 24 2014


title: Illumina HiSeq 2000 (Culex pipiens molestus)

status: Public on Jun 25 2014

organism: Culex pipiens molestus


title: Agilent-035370 Salmonid_60k_Array_V1_060711 035285

city: Oslo

first: You

last: Song

address: Økernveien 94

department: Ecotoxicology and Risk Assessment

country: Norway

institute: Norwegian Institute for Water Research (NIVA)

organism: salmonid fish


title: Agilent-040871 Drosophila melanogaster 8X60K with Spike (Feature Number version)

organism: Drosophila melanogaster

description:
Arrays of this design have barcodes that begin with 16040871 or 2540871.
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: AB 5500xl Genetic Analyzer (Drosophila simulans)

organism: Drosophila simulans


title: Agilent-037366 NextGenPoplar

city: Gainesville

first: Cintia

middle: Leite

last: Ribeiro

state: FL

address: 2033 Mowry Road room 320F

institute: University of Florida

organism: Populus trichocarpa

description:
Arrays of this design have barcodes that begin with 16037366 or 2537366.

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: FZ_IBG1_4plex_039120

status: Public on Jun 23 2014

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

organism:
Gluconobacter oxydans
Escherichia coli
Corynebacterium glutamicum
Bacillus subtilis subsp. subtilis str. 168

description: Agilent Technologies (Waldbronn, Germany)

manufacture_protocol: see Agilent Technologies


title: Agilent-39880 Unilever-Durham University Sorghum 28K array (Probe Name version)

status: Public on Jun 20 2014

city: Sharnbrook

first: Fei Ling

last: Lim

state: Bedfordshire

address: Colworth Science Park

country: United Kingdom

institute: Unilever

organism: Sorghum bicolor

description: Unilever-Durham University Sorghum 28K v39880


title: Affymetrix GeneChip Mouse Genome 430 2.0 Array [CDF: Mouse4302_Mm_REFSEQ v 16.0.0]

organism: Mus musculus

description: This identical to GPL1261 but a custom CDF environment was used to extract data.  The .cdf and mapping files are provided as supplementary files.

manufacture_protocol: see manufacturer's web site


title: NimbleGen C. elegans 72K Expression Array [080128_worm170_modENCODE_expr; SEQ_ID version]

city: Santa Cruz

first: Susan

last: Strome

state: CA

address: 1156 High St.

department: Molecular, Cell, and Developmental Biology

institute: UC Santa Cruz

organism: Caenorhabditis elegans

description:
NimbleGen 4 plex expression array. Array contains three probes per gene and is based on WS170.
***A different  version of this platform the probe ID or ORF in the ID column is assigned accession number GPL8673 and GPL18855, respectively.

manufacture_protocol: Details on the manufacture protocol can be found on http://www.nimblegen.com/technology/index.html


title: Ion Torrent PGM (Neisseria gonorrhoeae)

status: Public on Jun 19 2014

last: GEO

organism: Neisseria gonorrhoeae


title: Illumina HiSeq 2500 (Rhodobacter sphaeroides)

organism: Cereibacter sphaeroides


title: Custom Human HIV-specific B Cell RT-PCR array

last: Moir

state: Maryland

department: NIAID

institute: NIH

organism: Homo sapiens

manufacture_protocol: The custom format for TaqMan Array 96-well plate is 3x32. The cDNA was made using High capacity cDNA kit. The preamplification was  run based on Custom Taqman PreAmp protocol. The PCR was run by following Taqman Array plate protocol. ABI 7500 software v2.0.1. was used for data analysis.


title: Illumina HiSeq 2500 (Rhodobacter sphaeroides 2.4.1)

organism: Cereibacter sphaeroides 2.4.1


title: Illumina HiSeq 2000 (Rhodobacter sphaeroides)


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array (mogene10st_annotation.csv)

city: Mannheim

first: Johanna

middle: Daniela

last: Schott

address: Franz-Volhard-Straße 6

department: Mannheim Institute for Innate Immunoscience

institute: Heidelberg University

description: Probe sequences of pm probes were retrieved using the Bioconductor packages oligo (version 1.22.0) and pd.mogene.1.0.st.v1. Probes were mapped to the mouse RefSeq transcriptome as downloaded from the UCSC Genome Browser mm10 refGene table on February 5, 2013. Probes that match transcripts of more than one gene (as defined by a common gene symbol) were excluded. For mapping and further processing of probe information, the Bioconductor packages seqinr and Biostrings and in-house developed Perl scripts were used.

manufacture_protocol: See manufacturer's web site


title: Agilent-031786 M_edulis_12_17_10 031713

city: Boston

first: Helen

middle: C

last: Poynton

state: MA

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

organism: Mytilus edulis

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


title: Agilent-025836 Bacillus sp. N16-5 15K

status: Public on Jun 17 2014

city: Beijing

first: song

last: yajian

address: N0.1 Beichen Road

institute: institute of microbiology, chinese acadmy of science

organism: Bacillus sp. N16-5

description:
Arrays of this design have barcodes that begin with 16025836 or 2525836.

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 (Volvox carteri)

organism: Volvox carteri


title: Illumina HiSeq 2500 (Beauveria bassiana)

organism: Beauveria bassiana


title: Agilent-036527 Channel Catfish 8X60K Array

city: AUBURN

first: chao

last: li

address: 203 swingle hall

institute: auburn university

organism: Ictalurus punctatus

description:
Channel catfish/Blue catfish Array

Arrays of this design have barcodes that begin with 16036527 or 2536527.

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-039825 SEQCboku1Mv1

city: Vienna

first: Pawel

middle: P.

last: Labaj

address: Muthgasse 18

department: Department of Biotechnology

country: Austria

institute: Boku University Vienna

description:
Experimental high density gene expression tiling array for testing spliceform discrimination and quantification performance in collaboration with the FDA and Agilent as part of the SEQC/MAQC3 benchmark study.

The array probes 776 complex genes representative of the AceView gene model annotation (http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/), as well as 92 ERCC spike-in controls.


title: MIQE validated qPCR assays

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

institute: Fudan University

description:
PCR assay; total volume: 5 μl; instrument: CFX384 (with automation); mastermix: SsoAdvanced SYBR; primer concentration: 250 nM each
Samples: cDNA: 25 ng (total RNA equivalents); gDNA: 2.5 ng (Roche); NTC: water + carrier (5 ng/μl yeast transfer RNA); synthetic template (pooled 60-mers in concentration range: 2E7 – 2E1 copies)
PCR program: default cycling protocol for SsoAdvanced SYBR (Ta=60°C)


title: Illumina HiSeq 2000 (Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344)


title: AB 5500 Genetic Analyzer (Plasmodium berghei)

organism: Plasmodium berghei


title: Illumina Genome Analyzer IIx (Schistosoma japonicum)

organism: Schistosoma japonicum


title: Illumina HiSeq 2000 (Escherichia coli BW38028)

status: Public on Jun 16 2014

organism: Escherichia coli BW38028


title: Illumina Genome Analyzer II (Plasmodium berghei)


title: Agilent-063674 Lotus-nodule-ver2

city: Kita-gun

first: Mika

last: Nomura

state: Kagawa

address: 2393 Ikenobe Miki-cho

institute: Kagawa University

organism: Lotus japonicus

description:
Arrays of this design have barcodes that begin with 16063674 or 2563674.

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 (Pseudomonas syringae pv. phaseolicola)

organism: Pseudomonas savastanoi pv. phaseolicola


title: Agilent-025309 Synechocystis sp. PCC 6803 syn6803_expression_5probes

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

institute: University of Freiburg

organism: Synechocystis sp. PCC 6803

description:
Synechocystis6803  expression array with new annotation, 5probes/

Arrays of this design have barcodes that begin with 16025309 or 2525309.

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: 24sure Homo sapiens 3K BAC v3

first: Tian

last: Wang

address: 138 Yi Xue Yuan Road


title: Illumina HiSeq 2000 (Papio anubis)

organism: Papio anubis


title: INSA Lactococcus lactis 2K

city: Toulouse

first: Muriel

last: Cocaign-Bousquet

address: 135 avenue de Rangueil

department: UMR5504 INSA/CNRS - UMR792 INSA/INRA

country: France

institute: Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés

organism: Lactococcus lactis

description: nylon membrane positively charged (Roche) 8*12 cm

manufacturer: Eurogentec/Biochips Platform INSA Toulouse France

manufacture_protocol: Amplicons (PCR) were designed and amplified by Eurogentec. A mean length of 535 bp and final concentrations between 40 and 380 µg/l were obtained. PCR were diluted in DMSO 50 % in 384 wells spot plates and spotted (4 deposits/ spot) in duplicate on positively charged nylon membranes (Roche) with a Biogrid spotter (Biorobotics) with a 4*4 pattern.


title: Illumina HiSeq 2500 (Triticum aestivum)

organism: Triticum aestivum


title: Illumina HiSeq 2000 (Pseudomonas phage phiKZ)

status: Public on Jun 13 2014

organism: Phikzvirus phiKZ


title: Illumina HiSeq 2000 (Enterococcus faecalis)

organism: Enterococcus faecalis


title: Agilent-029624 Toxoplasma gondii Me49 genome-wide tiling microarray

city: Lille

first: Mathieu

last: Gissot

address: 1, rue du Pr. calmette

institute: CNRS

organism: Toxoplasma gondii ME49

description: Based on genome build ToxoDB 6.4 (http://toxodb.org/toxo/).


title: [Rat230_2] Affymetrix Rat Genome 230 2.0 Array [CDF: Version 15.1, ENTREZG]

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Rattus norvegicus

manufacture_protocol: See manufacturer's webiste


title: miRCURY LNA microRNA Array, 7th generation - hsa, mmu & rno (lot#35015, rno miRBase 19.0)

city: Vedbaek

first: Michael

last: Thorsen

address: Skelstedet 16

country: Denmark

institute: Exiqon

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

first: Jorg

last: Krummheuer

manufacture_protocol: See Exiqon website


title: Agilent-036226 AKAW110826

status: Public on Jun 14 2014

city: Kagoshima

first: Taiki

last: Futagami

address: Korimoto 1-21-24

department: Department of Agriculture

institute: Kagoshima University

organism: Aspergillus luchuensis IFO 4308

description:
Arrays of this design have barcodes that begin with 16036226 or 2536226.

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: LC_MRA-1001_miRHuman_15-miRNA-ID-version

city: Houston

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

organism: Homo sapiens

manufacture_protocol: human miRNA microarray with 100% coverage of mature human miRNAs listed in miRBase version 15.0. 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: GeoChip 4.2

first: Junjun

last: Ding

address: Haidian

institute: Tsinghua University

organism:
Bacteria
Archaea
Eukaryota
Viruses


title: NimbleGen_Zebra Finch_720k_v5.0 tiling array [100713_Tguttata_MS_CGH]

status: Public on Jun 12 2014

city: Pullman

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

organism: Taeniopygia guttata

description:
Whole Genome Tiling of ZebraFinch, n=719,596, mean probe interval 1393, median 1395bps
CGH custom design that consisted of a whole genome tiling array of Zebra Finch (Taeniopygia guttata) with 720,000 probes per array. The probe size ranged from 50-75mer in length with median probe spacing of 1395bp.

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


title: miRCURY LNA microRNA Array, v.11.0 - hsa, mmu & rno (lot#31089, hsa miRBase 14.0)

organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Herpesvirus saimiri (strain 11)
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae


title: Agilent_033054 Genome-wide Atlantic cod microarray, second version_ACIQ1

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

institute: Nofima AS

organism: Gadus morhua


title: LC Sciences MRA-1006_miRDrosophilaM_17

city: Manchester

first: Suzanne

last: Hunt

address: Dover Street

department: Life Sciences

institute: University of Manchester

organism: Drosophila melanogaster

description: miRNA annotations are from miRBase Release 17.0

manufacture_protocol: see LC Sciences


title: Illumina Genome Analyzer IIx (Veillonella parvula DSM 2008)

status: Public on Jun 11 2014

last: GEO

organism: Veillonella parvula DSM 2008


title: Illumina Genome Analyzer IIx (Pseudomonas aeruginosa PA14)

organism: Pseudomonas aeruginosa PA14


title: Illumina HiSeq 2000 (Eucalyptus grandis)

status: Public on Jun 10 2014

organism: Eucalyptus grandis


title: Illumina HiSeq 2000 (Chlorocebus sabaeus)

status: Public on Jun 09 2014

organism: Chlorocebus sabaeus


title: Illumina Genome Analyzer IIx (Pseudomonas aeruginosa PA14; Veillonella parvula DSM 2008)

organism:
Veillonella parvula DSM 2008
Pseudomonas aeruginosa PA14


title: NimbleGen_Zebra Finch_4.2M array_v3.1

description: DNA methylated custom array


title: AB 5500xl Genetic Analyzer (Desulfovibrio piezophilus C1TLV30)

status: Public on Jun 06 2014

organism: Pseudodesulfovibrio piezophilus C1TLV30


title: Illumina MiSeq (Shewanella oneidensis MR-1)

organism: Shewanella oneidensis MR-1


title: Agilent-048047 Genome-wide Atlantic cod microarray, second version_ACIQ2


title: AB SOLiD System (Solea senegalensis)

status: Public on Jun 08 2014

organism: Solea senegalensis


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [HuEx-1_0-st-v2.hg18.custom ENTREZG]

city: Salt Lake City

first: Andrea

last: Bild

state: UT

address: 112 Skaggs Hall

department: Pharmacology and Toxicology

institute: University of Utah

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


title: Illumina HiSeq 2500 (Pseudomonas aeruginosa PAO1)

organism: Pseudomonas aeruginosa PAO1


title: Illumina HiSeq 2000 (Mycobacterium tuberculosis)

organism: Mycobacterium tuberculosis


title: Agilent-017662 Danio rerio Zv7_USACEHR [Probe name version]

city: Ft. Detrick

first: Christine

last: Baer

state: MD

address: 568 Doughten Drive

department: Environmental Health Program

institute: Excet, Inc. / USACEHR

organism: Danio rerio

description:
Expression array with 2 probes per gene. Designed against Zv7 build.

Arrays of this design have barcodes that begin with 16017662 or 2517662.

The ID column represents the Agilent Probe name.


title: Sea Cucumber miRNA Array Release

city: QINGDAO

first: Muyan

last: Chen

address: 5 YUSHAN ROAD

institute: Ocean University of China

organism: Apostichopus japonicus

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 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: [PhyloChip] Affymetrix G3 PhyloChip [custom version]

city: Berkeley

first: Yvette

middle: M

last: Piceno

address: 1 Cyclotron Rd., MS 70A-3317

department: Ecology

institute: LBNL

organism: Bacteria

description: Second Genome G3 PhyloChip Assay: PN49-0002A


title: Illumina HiSeq 2500 (Chlorocebus sabaeus)


title: Nimblegen aCGH chip to genotype 1,611 dog CNVs

status: Public on Jun 05 2014

city: Barcelona

first: Oscar

last: Ramirez

state: APO/FPO EUROPE / ATLANTIC

address: Dr. Aiguader, 88

country: Spain

institute: Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra)

organism: Canis lupus familiaris

description:
High density custom 720K probe aCGH chip to systematically genotype 1,611 CNVs derived mainly from modern dog breeds
genome build: Canfam2


title: 100910_CW_P_ging_W83_expr_HX12

status: Public on Jun 04 2014

city: Los Angeles

first: Paul

last: Webster

address: 804 Bloom Walk

department: CEMMA

institute: University of Southern California

organism: Haemophilus influenzae

description: The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are linked below as supplementary files.


title: Illumina MouseWG-6 v2.0 expression beadchip [gene symbol version]

status: Public on Jun 03 2014

organism: Mus musculus

technology: oligonucleotide beads

description:
The MouseWG-6 v2.0 Expression BeadChip offer the most up-to-date content for whole-genome expression profiling in the mouse. Featuring content derived from the National Center for Biotechnology Information Reference Sequence (NCBI RefSeq) database (Build 36, Release 22).

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: Illumina MiSeq (Bombyx mori)

organism: Bombyx mori


title: Galbraith Laboratory Operon Long Oligonucleotide Microarray version 3.0 (ATv3.6.1.Z)

city: Lubbock

first: Christopher

middle: Dale

last: Rock

address: Flint and Main Sts.

department: Biological Sciences

institute: Texas Tech University

organism: Arabidopsis thaliana

description: genome release TAIR6

manufacturer: The Galbraith Laboratory, University of Arizona

manufacture_protocol: GeneMachines Omnigrid 300


title: 9K Echinococcus granulosus Genome Array

city: Urumqi

first: Guodong

last: Lü

state: Xinjiang

address: Liyushan north road

department: State Key Lab Cultivation Base for Xinjiang Major Diseases Research and Xinjiang Key Laboratory of Echinococcosis

institute: First Affiliated Hospital of Xinjiang Medical University

organism: Echinococcus granulosus

manufacture_protocol: as described in CapitalBio Corporation Manual


title: UniversityPadova_Ruditapes philippinarum_8x60K

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

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

country: Italy

institute: University of Padova

organism: Ruditapes decussatus

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


title: CytoSure Human Custom Oligonucleotide 4x180k Array v.025990

status: Public on Jun 01 2014

city: Stockholm

first: Johanna

last: Winberg

address: CMM L8:02, Karolinska University Hospital

department: Molecular Medicine and Surgery

country: Sweden

institute: Karolinska Institutet

organism: Homo sapiens

manufacture_protocol:
1. Substrate applied to glass wafers
2. Nucleic acids and reagents prepared for printing
3. Microarray surface deprotection
4. First layer of oligo monomers deposited onto the wafer
5. Steps 3 and 4 are repeated until a chain of 60 bases has been built up
6. Microarray wafers cut into 1 x 3 inch slides
7. QC of microarrays
8. Microarrays packaged and shipped


title: [Axiom_Exome319] Affymetrix Human Axiom Exome 319 Genotyping Array

city: Gyeonggi-do

first: Boyoung

last: Park

address: 323 Ilsan-ro, Ilsandong-gu, Goyang-si

country: South Korea

institute: National Cancer Centerm Korea

description:
#%create_date=2013-09-13 GMT-08:00 09:18:59
#%chip_type=Axiom_Exome319
#%genome-species=Homo sapiens
#%genome-version=hg19
#%genome-version-ucsc=hg19
#%genome-version-ncbi=37
#%genome-version-create_date=2009-02-00
#%mitochondrion-version=NC_001807
#%dbSNP-date=2012-06-26
#%dbSNP-version=137
#%hapmap-date=2008-01-08
#%hapmap-version=23
#%omim-date=2013-07-09
#%allele_frequency_data_reference=Affymetrix_internal_screen
#%netaffx-annotation-date=2013-07-01
#%netaffx-annotation-netaffx-build=34
#%netaffx-annotation-tabular-format-version=1.5

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


title: RT2 Profiler PCR Arrays PAHS-30C

city: BERN

first: Brigitte M.

last: FREY

state: BERN

address: Freiburgstrasse 15

department: Nephrology hypertension

country: Switzerland

institute: DKF

manufacture_protocol: see manufacturer's website. PCR assay


title: CodeLink Human 20K ver4.1 (Nov2013v)

city: Hiroshima

first: Keiji

last: Tanimoto

address: Kasumi 1-2-3, Minami-ku

institute: Research Institute for Radiation Biology and Medicine, Hiroshima University

description:
Commercially available CodeLink UniSet Human 20K I Bioarray with 19981 human probes, 108 positive bacterial controls, and 300 negative bacterial controls. Annotation: Nov/2013
NCBI annotation in these data was updated from GPL1928 by CodeLink.
Keywords = CodeLink Human 20K


title: miRCURY LNA microRNA Array, 5th generation - hsa, mmu & rno [miRBASE v.15.0]

city: Chicago

first: Miao

last: Sun

institute: University of Chicago

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description:
Array covering Sanger miRBase 15.0 and Exiqon miRPlus mature miRNAs.

Names, accession numbers and sequences are listed for mature miRNAs in miRBase 15.0. Some probes may target multiple miRNAs, in which case multiple miRNA names, accession numbers and sequences are listed separated by '/'

manufacture_protocol: See manufacturers website


title: Affymetrix GeneChip Mouse Genome 430 2.0 Array [CDF: Mouse430_2_custom]

status: Public on Apr 29 2014

city: East Lansing

first: Uros

last: Midic

state: MI

address: 474 S. Shaw Lane

department: Animal Sciences

institute: Michigan State University

description:
Custom CDF is comprised of the same probesets as the original CDF (platform GPL1261), but some probes were removed from their probesets.
The custom CDF was developed from the original Affymetrix CDF by removing probes that do not align to intended targets or cross-hybridize with non-homologous transcripts were removed from the respective probesets. Custom annotation were compiled by aligning remaining probe sequences to RefSeq mRNA sequences (downloaded 7/01/2013) for genes in GRC38 genome assembly.
Annotations provided in "Gene Symbol" and "Gene Description" columns only where we have sufficient evidence of hybridization.
Probesets lacking "Gene Symbol" and "Gene Description" annotations may be updated in the near future as our custom annotation develops further.
We did not use annotation provided by Affymetrix at all, but we added Gene Symbol, Gene Title and Entrez Gene from Affymetrix annotation table (Release 32) pending custom-annotation of probesets in the near future.

manufacture_protocol: see manufacturer's web site


title: USACH_E_coli_9K_v1.0

status: Public on Sep 01 2013

city: Santiago

first: David

middle: Enrique

last: Loyola

state: Santiago

address: Avenida Libertador Bernardo O'Higgins 340

country: Chile

institute: OMICS Solutions, Centro Nacional de Genómica y Bioinformática

organism: Escherichia coli

manufacture_protocol:
Escherichia coli - Our E. coli probe set for microarrays contains 9308 long oligos to investigate four strains of Escherichia coli and three E. coli-associated plasmids. Within the probe set there are:
4,269 ORF probes from K12,
5,306 ORF probes from O157:H7 (EDL933),
5,251 ORF probes from O157:H7 (Sakai)
5,366 ORF probes in CFT073
Among these gene expression probes for the E. coli-associated plasmids, 3 plasmid genes in OSAK1, 10 genes in pO157_Sakai and 97 genes in pO157_EDL933 are present in the probe set.


title: Agilent-019961 SmaI-CGI array (Probe Name version)

status: Public on Jun 02 2014

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

country: USA

institute: Augusta University

description:
Array feature coordinates based on genome build hg18.

Arrays of this design have barcodes that begin with 16019961 or 2519961.

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: Applied Biosystems Human MicroRNA Array A v2.0

status: Public on Jun 29 2013

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description:
PCR assay
Applied Biosystems Human MicroRNA Array v2. 0  Human Array A. Pre-designed TaqMan probe and primer sets for quantitative expression studies of human miRNAs.


title: Illumina MiSeq (Coprinopsis cinerea)

status: Public on May 15 2013

last: GEO

organism: Coprinopsis cinerea


title: Affymetrix Mouse Gene 1.0 ST Array with ERCC probe sets [transcript (gene) version]

status: Public on May 29 2014

city: Saint Louis

first: Takeshi

last: Egawa

state: MO

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

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

manufacture_protocol: See manufacturer's web site


title: [HG_U133A 2.0_Hs_ENTREZG_V13] Affymetrix GeneChip  HG_U133 V2.0 Array [Brainarray Entrez Version 13]

status: Public on Mar 27 2014

relation: Alternative to: GPL570 (Alternative CDF [official])

manufacture_protocol: This is identical to GPL571 but a custom CDF environment was used to extract data [Brainarray Version 13, HG_U133A2_Hs_ENTREZG]. CDF and other files can be downloaded at: (see web link below).


title: [Mouse430_2_Mm_REFSEQ] Affymetrix GeneChip Mouse Genome 430 2.0 Array [Brainarray Version 16]

status: Public on May 03 2013

city: San Francisco

first: Courtney

last: Onodera

address: 1450 Third St, HD374

institute: University of California, San Francisco

description: custom CDF of GPL1261


title: Agilent-027114 Genotypic Technology designed Custom Human Whole Genome 8x60k Microarray

status: Public on Mar 10 2011

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

first: Raja

last: Mugasimangalam


title: CytoSure Human Custom Oligonucleotide 4x180k Array v.031035


title: Soybean 1.4 Million CGH microarray

status: Public on Mar 30 2014

city: Saint Paul

first: Robert

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

organism: Glycine max

description:
Tiling array designed from the Glycine max genome (assembly version 1.01).  This genome version is deposited at DDBJ/EMBL/GenBank under the accession number ACUP01000000.
Whole-genome tiling array with a median length of approximately 500 bp between adjacent probes
110921_Gmax_RS_CGH.ndf
110921_Gmax_RS_CGH.pos


title: Illumina Genome Analyzer IIx (Saccharomyces cerevisiae BY4741)

status: Public on Jun 05 2013

organism: Saccharomyces cerevisiae BY4741


title: Illumina HiSeq 2000 (Aspergillus fumigatus Af293)

status: Public on May 01 2013

organism: Aspergillus fumigatus Af293


title: Affymetrix GeneChip Human Genome U133A 2.0 Array [CDF: HGU133A2_Hs_ENSG_16.0.0]

status: Public on Jul 24 2013

description: This is identical to GPL571 but a custom CDF environment was used to extract data (CDF: HGU133A2_Hs_ENSG_16.0.0).

manufacture_protocol: Affymetrix standard protocol


title: [HG-U219] Affymetrix Human Genome U219 Array (ENSG Brainarray CDF Version 14.1.0)

status: Public on Jul 12 2012


title: NimbleGen Mouse gene expression array [100718_MM9_EXP] (gene-level version)

status: Public on Aug 03 2012

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description:
DESIGN_ID: 534493
DESIGN_NAME:100718_MM9_EXP
SLIDE_LAYOUT_NAME: NimbleChip_HX12

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


title: Affymetrix HT HG-U133+ PM Array Plate [CDF: HTHGU133PlusPM_Hs_ENTREZG_v14]

description: This identical to GPL13158 but a custom cdf environmnet was used to extract data.

relation: Alternative to: GPL13158 (Alternative CDF [official])

manufacture_protocol: see the Affymetrix website


title: NimbleGen Clostridium thermocellum 3189 CDS array design id 8592

status: Public on Dec 15 2010

first: Brian

middle: G

last: Fox

address: 141b Biochemistry

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

organism: Acetivibrio thermocellus ATCC 27405

description:
NimbleGen design name: 081203_C_therm_27405_expr
Expression design for Clostridium thermocellum ATCC: 27405
3189 CDS.
Selected 15 60mer probes per target. For those with fewer than 15, selected 50-60mer. No exemplars--all targets have 15 probes. 8 copies on array.

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


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

status: Public on Sep 21 2010

manufacture_protocol: see manufacturer's website


title: Agilent Candida dubliniensis 12K V.2

status: Public on Feb 27 2010

city: Dublin

first: Gary

last: Moran

address: Lincoln Place

department: Dental Science

country: Ireland

institute: Trinity College Dublin

organism: Candida dubliniensis

description: All sequences were derived from the C. dubliniensis genome hosted by the Sanger Institute at http://old.genedb.org/genedb/cdubliniensis/ . You can use the locus tags provided below to search GeneDB at this link. Multiple sequences may be downloaded using the 'List Download' tool. The 'Browse Catalogues' tool will allow you to visualise individual chromosomes.

manufacture_protocol:
Agilent Sure Print 4x44K Array
See http://www.chem.agilent.com/en-US/Products/Instruments/dnamicroarrays/Pages/gp557.aspx


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

status: Public on Dec 16 2013

city: suzhou

first: shouli

last: wang

address: renai road 199, suzhou industrial park

department: pathology

country: China

institute: soochow university school of medicine

description: This platform represents the condensed Probe_ID view of GPL17292


title: ENS Phaeodactylum tricornutum 44k_v1.0

status: Public on Jun 01 2009

city: Paris

first: Laurent

last: Jourdren

address: 46 rue d'Ulm

department: Biologie

institute: École Normale Supérieure

organism: Phaeodactylum tricornutum

description:
Diatom expression arrays.
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: Pascal

last: Lopez

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


title: NimbleGen C. elegans 72K Expression Array 080128_worm170_modENCODE_expr

status: Public on Jun 10 2009

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 408 Fordham Hall, CB# 3280

department: Biology

institute: University of North Carolina at Chapel Hill

organism: Caenorhabditis elegans

description:
NimbleGen 4 plex expression array. Array contains three probes per gene and is based on WS170.

***A different version of this platform with the ORF or SEQ_ID in the ID column is assigned accession number GPL18855 and GPL18856, respectively.

first: Leo

last: Iniguez

manufacture_protocol: Details on the manufacture protocol can be found on http://www.nimblegen.com/technology/index.html


title: UW-Escherichia_coli_K12-4x72k-v1.0 [090224_EcoK12_Zmob_expr]

status: Public on May 24 2011

first: Rebecca

last: Lennen

address: 1415 Engineering Drive

department: Chemical and Biological Engineering

institute: University of Wisconsin-Madison

organism: Escherichia coli K-12

description: NimbleGen accession number NC_000913, 4x72000 probes per array covering 4254 genes, with 8 probes per target and 2 replicate blocks


title: Agilent custom ME and HK design array [8mer]

status: Public on Dec 02 2010

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

organism: synthetic construct

description: 8mer sequence depicted below is not the sequence represented on the array, but the targeted sequence. Please see the two array design files attached below for array probe sequences.

manufacture_protocol: This protein binding microarray (PBM) involved binding GST-tagged proteins to custom-designed, double-stranded 44K Agilent microarrays in order to determine their sequence preferences. The method is described in Berger et al., Nature Biotechnology 2006.