title: Stonybrook_Redgreengene.com-S.cerevisiae-9.2k-A11

status: Public on Oct 31 2013

city: Stony Brook

first: Ying

last: Cai

state: New York

address: Life Sciences Building Rm 363

department: Molecular Genetics and Microbiology

country: USA

institute: Stony Brook University

organism: Saccharomyces cerevisiae

technology: spotted oligonucleotide

distribution: non-commercial

manufacture_protocol: dsDNA PCR products were generateed against 3'biased protion of (SGC predicted) genes and printed on aminosylane (Erie Scientific)-coated slides. Spotting was done using a robot with of the DeRisi design and ArrayMaker2 software.  Parallel synthesis silicon pins (50µm) were used.


title: RayBio C-Series Human Cytokine Antibody Array 5

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Homo sapiens

technology: antibody

distribution: commercial

manufacture_protocol: See manufacturer's website (http://www.raybiotech.com/c-series-membrane-based-antibody-arrays.html)


title: NimbleGen Human Whole-Genome Tiling Array Set (5of10) [100718_HG18_TILE_05_HX1]

city: Research Triangle Park

first: Deepak

last: Mav

state: NC

address: 2 Davis Drive

institute: Sciome LLC

technology: in situ oligonucleotide

description:
Whole human genome tiling array
Array 5 of 10
Designname:
100718_HG18_TILE_05_HX1
Build: HG18

distribution: custom-commercial

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


title: 091006_AD_ZM4_2_1M_exp_HX1

city: Berkeley

first: Morgan

middle: N

last: Price

state: CA

address: 1 Cyclotron Road Mailstop 977-152

department: Physical Biosciences Division

institute: Lawrence Berkeley Lab

organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

description:
Genome sequence from refseq (main chromosome and 5 plasmids)
Analysis was not based on gene annotation except that only coding probes were used to build the model of how genomic control intensity affects tiling intensity
native array description file = 091006_AD_ZM4_2_1M_exp_HX1.ndf

manufacture_protocol: NimbleGen


title: [Hu03Plusa520637F] Affymetrix Human Eos Hu03plus Array

city: Redwood City

first: Josue

last: Samayoa

address: 1500 Seaport BLVD

institute: AbbVie Biotherapeutics Inc.

manufacture_protocol: see manufacturer's web site


title: Illumina HiSeq 1000 (Nostoc sp. PCC 7120)

status: Public on Oct 30 2013

last: GEO

organism: Nostoc sp. PCC 7120 = FACHB-418

technology: high-throughput sequencing

distribution: virtual


title: NimbleGen Arabidopsis thaliana Gene Expression 12x135K Array [080924_AT6_expr_HX12]

city: Singapore

first: Toshiro

last: Ito

address: 1 Research Link, National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

organism: Arabidopsis thaliana

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


title: Illumina Genome Analyzer II (Mycobacterium marinum)

organism: Mycobacterium marinum


title: Illumina HiSeq 2000 (Saccharomyces cerevisiae SK1)

organism: Saccharomyces cerevisiae SK1


title: Illumina HiScanSQ (Bos taurus)

organism: Bos taurus


title: Illumina Genome Analyzer II (Mycobacterium bovis)

organism: Mycobacterium tuberculosis variant bovis


title: Exiqon microRNA array G6 hmr, lot #34004, miRBase 16

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

description: Herpesvirus saimiri strain A11

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

first: Jorg

last: Krummheuer

manufacture_protocol: See Exiqon website


title: Exiqon microRNA array 11.0 hmr, lot#31079, miRBase 14

description: Herpesvirus saimiri strain A11


title: Illumina Genome Analyzer II (Anabaena)

status: Public on Oct 29 2013

organism: Anabaena


title: Exiqon microRNA array 11.0 hmr, lot #31076, miRBase 14

description: Herpesvirus saimiri strain A11


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

status: Public on Oct 28 2013

city: Dallas

first: Nicolai S.C.

last: van Oers

state: Texas

address: 6000 Harry Hines Blvd

department: Immunology

institute: University of Texas Southwestern Medical Center

organism: Mus musculus

technology: oligonucleotide beads

manufacture_protocol: see manufacturer's website


title: Illumina HiSeq 2000 (Exophiala dermatitidis)

status: Public on Oct 24 2013

organism: Exophiala dermatitidis


title: CapitalBio Mammalian miRNA Array V4.0 (miRBase 12.0)

city: Beijing

first: Ling-fei

last: Jia

address: 22 Zhongguancun Avenue South, Haidian District

country: China

institute: Peking University School and Hospital of Stomatology

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: Mammalian miRNA Array V4.0 (miRBase 12.0. CapitalBio, Beijing, China)

manufacture_protocol: as described in CapitalBio Corporation Manual


title: Illumina HiSeq 2000 (Clostridium thermocellum)

status: Public on Oct 26 2013

organism: Acetivibrio thermocellus


title: SBC human lncRNA 8*60K

city: shanghai

first: qian

last: jin

address: libing road

institute: MSP

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


title: Illumina HiSeq 2000 (Rhodopseudomonas palustris CGA009)

organism: Rhodopseudomonas palustris CGA009


title: NimbleGen Rat Promoter Array [2006-10-31_RN34_promoter_2of2]

city: Saskatoon

first: Deborah

last: Anderson

state: Saskatchewan

address: 107 Wiggins Road

country: Canada

institute: University of Saskatchewan

organism: Rattus norvegicus

description:
Design ID: 4809
Design name: 2006-10-31_RN34_promoter_2of2
Genome build: RN34

Second of two arrays in the consolidated promoter region design for the rat genome (rn34). Array two contains promoter regions from chromosomes 7 (through position 138512442) through chr20, chrX and the "random" chromosomes.
Includes 4500 bp upstream of transcriptional start and 1125 bp downstream. Isothermal probes using dual tm/cycle restriction:, 50-75 bp, tm 76, 148 cycles, 15-mer frequency of 100. Probes selected from rn34_tiling database using interval of 75 bp and window size of 25 bp. Interval spacing: 104 bp (mean); 105 bp (median).

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


title: Illumina HiSeq 2000 (Megalobrama amblycephala)

organism: Megalobrama amblycephala


title: Exiqon miRCURY LNA microRNA array

status: Public on Oct 25 2013

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

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


title: [Blactisa520677F] Affymetrix Bifidobacterium animalis array

status: Public on Oct 23 2013

city: Raleigh

first: Todd

middle: Robert

last: Klaenhammer

department: Department of Food, Bioprocessing, and Nutrition Sciences

institute: North Carolina State University

organism: Bifidobacterium animalis subsp. lactis Bl-04

first: Joakim

middle: M

last: Andersen

first: Yong

middle: J

last: Goh

middle: R

manufacture_protocol: see Affymetrix site


title: UWAPG Yeast 6K v1.0

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425-G Henry Mall

department: Genetics

institute: University of Wisconsin - Madison

organism: Saccharomyces cerevisiae

manufacturer: University of Wisconsin Genome Expression Center

manufacture_protocol: Spotted DNA arrays were made in house using an OmniGrid spotting microarrayer to deposit 70mer oligos representing each yeast open reading frame (Qiagen Yeast Oligos V1.1.1) onto custom made poly-lysine coated glass microscope slides.


title: NimbleGen Rat Promoter Array [2006-10-31_RN34_promoter_1of2]

description:
Design ID: 4808
Design name: 2006-10-31_RN34_promoter_1of2
Genome build: RN34

First of two arrays in the consolidated promoter region design for the rat genome (rn34). Array one contains promoter regions from chromosomes 1 through 7 (through position 138518067).
Includes 4500 bp upstream of transcriptional start and 1125 bp downstream. Isothermal probes using dual tm/cycle restriction:, 50-75 bp, tm 76, 148 cycles, 15-mer frequency of 100. Probes selected from rn34_tiling database using interval of 75 bp and window size of 25 bp. Interval spacing: 104 bp (mean); 105 bp (median).


title: Saccharomyces cerevisiae 12x135K Array

city: Copenhagen V.

first: Richard

last: Baerends

state: Sealland

address: Gamle Carlsberg Vej 10

department: Yeast Biology

institute: Carlsberg Laboratory

organism: Saccharomyces cerevisiae S288C

description:
NimbleGen design name 090828 Scer EXP HX12, NimbleGen catalog no. 05543835001.  A expression design with 12 arrays which each measures 5,777 genes from Saccharomyces cerevisiae S288C with eight 60-mer probes per gene, with three-fold technical redundancy. 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, .ngd and .ncd files are linked below as supplementary files.

manufacture_protocol: High-density 12-plex DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.


title: UNIL_fireant_25K_vE_and_vI

city: Lausanne

first: Yannick

last: Wurm

address: Biophore

department: Ecology and Evolution

country: Switzerland

institute: University of Lausanne

organism: Solenopsis invicta

technology: spotted DNA/cDNA

description: This platform represents two prints ("E" and "I") of the "same" microarray.

manufacturer: UNIL: Laurent Keller Laboratory and DNA Array Facility Lausanne

manufacture_protocol: Bacteria clones were inoculated into PCR plates containing 5 µl modified LB-ampicillin broth (20% concentration LB and without NaCl) and grown overnight. Plasmid inserts were amplified by PCR after adding 95 µl of PCR mix. A single primer, SMART PCR primer 5’-AAGCAGTGGTATCAACGCAGAGT-3’, which matches both the 3’ and 5’ SMART adapter of the inserts was used. PCR mixes contained 0.4 µl 5U/µl TAQ (Qiagen), 10 µL 10x Qiagen buffer, 20 µl Q solution, 4 µl 25 mM MgCl2, 1.5 µl 25 mM dNTPs, and 1 µl 100 µM SMART PCR primer. An initial 9-min denaturation at 94 °C was followed by 40 cycles of 30 sec at 94°C, 30 sec at 59°C, and 3 min at 72°C. The reaction ended with an additional incubation of 7 min at 72°C. Two microliters of each PCR product were analyzed on a 1% agarose gel. Gel pictures were visually examined to classify all PCR products as follows: “strong single band” (78.4 %), “no band” (3.9 %), or “weak or multiple bands” (17.5 %). This data is in Wang et al 2007  Supplemental Table F. PCR products were purified by a standard NaOAc/ethanol precipitation, resuspended in 30 µl water and transferred into duplicate 384-well plates using a Biomek FX liquid-handling robot (Beckman Coulter). Then PCR products were dried and resuspended in 20 µL 3x SSC, 1.5 M betaine. We also resuspended 48 times 10 commercial exogenous controls (SpotReport Alien cDNA Array Validation System, Stratagene) in 3x SSC, 1.5 M betaine, one set for each subgrid of the microarray. Microarrays were printed on aldehydesilane-coated slides (NexterionTM Slide AL, Schott Nexterion), using an OmniGrid 300 spotting robot (GeneMachines). Spot and printing quality were assessed visually under a dissecting microscope after printing. While a few slides had minor defects (e.g., a few spots missing or damaged by dust particles), the majority of slides exhibited no defects. DNA was crosslinked to slides by baking at 80°C for 1 h. Afterwards, the slides were post-processed with NaBH4 using the manufacturers recommended protocol.


title: Illumina HiSeq 1000 (Chlamydomonas reinhardtii)

organism: Chlamydomonas reinhardtii


title: NimbleGen Human 2.1M Deluxe Promoter Array [080814_HG18_Deluxe_Promoter_HX1]

organism: Homo sapiens

description:
Design ID: 8076
Design name: 080814_HG18_Deluxe_Promoter_HX1
Genome build: HG18

HG18 promoter design,  mean probe spacing 99, median 100.  This design consists of (from Jacob):
1) Promoter regions, from 7250 bases upstream of each TSS to 3250 bases downstream.
2) miRNA genes, starting from 15kbp upstream of the mature gene product to its 3' end.
3) CpG islands.
4) ENCODE regions.
Probes were chosen from the hg18_tiling database. Most probes were chosen at an int65win35max1. Any region that resulted in no coverage from this selection was  re-selected at int10win90max10.
Slide 1 of 3. August 2008 - update to some regions. Probes are completely randomized across DMD's.


title: E. coli April-07_v2

city: Stanford

first: Jasmine

middle: L.

last: Loveland

state: California

address: 371 Serra Mall Rm 320

department: Biology

institute: Stanford University

organism: Escherichia coli

manufacture_protocol: Array consists of 48 blocks; each block is a grid of 21 rows x 21 columns, totalling 441 spots in each block. Each spot is comprised of 70-mer oligos representing a single gene. The 48 blocks on the array are divided into 3 identical sets of 18 blocks each, such that each gene is spotted onto the array in triplicate.


title: Agilent-036930 Pine_oak1

city: Gainesville

first: John

last: Davis

state: FL

address: 365 Newins-Ziegler Hall

department: School of Forest Resources and Conservation

institute: University of Florida

organism: Cronartium quercuum

description:
Arrays of this design have barcodes that begin with 16036930 or 2536930.

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: miRCURY LNA microRNA Array, 5th generation - hsa, mmu & rno

city: Hobart

first: Minghui Jessica

last: Chen

state: Tasmania

address: Menzies Research Institute, University of Tasmania, Private Bag 24

department: Neuroscience group

country: Australia

institute: Menzies Research Institute

description:
Product no: 208300-A
miRBase version 15.0
Platform data table based on file:
gal_208300-A,208301-A,208302-A_lot33013-33013_hsa,mmu,rno-and-related-vira_from_mb150,miRPlus.gal


title: HRneg prognostic signatures PCR assay panel

city: Novato

first: Christina

last: Yau

address: 8001 Redwood Blvd

institute: Buck Institute of Age Research

technology: RT-PCR

description: Multiplex RT-PCR TaqMan assays.

manufacture_protocol: Primers ranging from 15-29 bp in length are designed to assay the expression of target genes at sequence locations corresponding to their Affymetrix U133A probe sets identified as prognostic in previous expression microarray data analyses.


title: Illumina HiSeq 2000 (Acromyrmex echinatior)

last: GEO

organism: Acromyrmex echinatior


title: Mouse MM1200 OpArray [MM1200_Mouse_OpArray_GAL]

status: Public on Oct 22 2013

city: Houston

first: Anne

middle: Chinenye

last: Katchy

address: 3605 Cullen Blvd, Room 3021

department: CNRCS, Biology and Biochemistry

institute: University of Houston

manufacture_protocol:
See http://www.microarrays.com/dna-arrays.php.
Mouse OpArray contains 35,852 long oligo probes representing approximately 25,000 genes and about 38,000 gene transcripts based on the Ensembl Mouse Database release 26.33b.1, Mouse Genome Sequencing Project, NCBI RefSeq, Riken full-length cDNA clone sequences, and other GenBank sequences. On this gene expression microarray for the mouse genome, 21,335 mouse NCBI RefSeq gene transcript sequences are represented. These gene expression probes allow detection of alternative splicing variants using common, partial common and individual transcript oligos.


title: Agilent-040537 Aspergillus flavus 15K hqm_4.27

city: Qingdao

first: Qing

last: Kong

state: Shandong

address: Yushan Road 5

department: Food Science and Engineering

institute: Ocean University of China

organism: Aspergillus flavus

description:
Arrays of this design have barcodes that begin with 16040537 or 2540537.

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 Human LncRNA 12x135K Array V1.0 [110505_CB_Seq50more_human_expr]

last: Jia

description:
NimbleGen Human LncRNA Array V1.0 (12×135K, Roche Nimblegen, Mannheim, Germany). The array contains probes interrogating 30,618 lncRNAs collected from multiple authoritative databases, such as RefSeq, ENSEMBL, Chen Runsheng’s Lab (Institute of Biophysics, Chinese Academy of Science) and other related literature.
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: As described in CapitalBio Corporation Manual


title: TaqMan® Array Human MicroRNA Cards Set v2.0 A/B

city: Tokyo

first: Kazuhiro

last: Kitamura

address: 1-1-5, Sendagi, Bunkyo-ku

department: Department of Pulmonary Medicine and Oncology, Graduate School of Medicine

country: Japan

institute: Nippon Medical School

description: PCR assay


title: Nimblegen Mouse 2M Tiled Array_2o4 [100205_MM9_Economy_MeDIP_02_HX]

city: Edinburgh

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

organism: Mus musculus

description: Design Name: 100205_MM9_Economy_MeDIP_02_HX

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


title: Agilent-021827 Human miRNA Microarray 8x15k_miRBase release 12.0 (miRNA ID version)

first: Genotypic

last: technology

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

institute: Genotypic Technology

description: Agilent one-color experiment,Organism: Homo sapiens ,Agilent-021827 Human miRNA Microarray 8x15k  (miRBase release 12.0 miRNA ID version)


title: Life Technologies Human TaqMan MicroRNA Assays

city: Toronto

first: Shirley

last: Tam

state: Ontario

address: 661 University Avenue, Suite 510, MaRS Building, West Tower

department: Genome Technologies

institute: Ontario Institute for Cancer Research

description: PCR assay


title: Illumina HiSeq 2000 (Babesia bovis)

organism: Babesia bovis


title: NanoString nCounter Human v1 miRNA Expression Assay

technology: other

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


title: Illumina Genome Analyzer (Cryptococcus neoformans var. grubii)

organism: Cryptococcus neoformans


title: LC_MRA-1038_miRPlants_15

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

organism:
Physcomitrium patens
Picea glauca
Picea sitchensis
Pinus taeda
Liriodendron tulipifera
Persea americana
Populus tremuloides
Populus trichocarpa
Populus trichocarpa x Populus deltoides
Malus domestica
Prunus persica
Lupinus luteus
Medicago truncatula
Phaseolus vulgaris
Phaseolus coccineus
Manihot esculenta
Ricinus communis
Nicotiana sylvestris
Nicotiana tabacum
Nicotiana benthamiana
Petunia x hybrida
Ipomoea batatas
Lactuca sativa
Hordeum vulgare
Oryza rufipogon
Oryza sativa
Oryza brachyantha
Oryza nivara
Cenchrus americanus
Sorghum bicolor
Lolium arundinaceum
Phleum pratense
Lotus japonicus
Cenchrus ciliaris
Ipomoea nil
Prunus armeniaca
Peridictyon sanctum
Panicum virgatum
Populus tremula x Populus tremuloides
Rorippa indica
Oryza barthii
Nasturtium officinale
Nuphar advena
Prunus salicina
Hordeum vulgare subsp. vulgare
Populus tremula
Oenocarpus bataua
Malcolmia maritima

manufacture_protocol: plant miRNA microarray with 100% coverage of mature plant 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: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray HGU133Plus2_Hs_ENTREZG_v17]

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: This array is identical to GPL570 but the data were analyzed with a custom CDF environment.

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

manufacture_protocol: Refer to Affymetrix manufacture protocol for HG-U133 Plus 2.0 array


title: Brassica rapa 300k Microarray v2.0 [2007-10-15_GGB_B_rapa_082207]

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

organism: Brassica rapa

description:
Probes are designed from 47,548 UniGenes, 31,057 of which are cDNA/EST-supported genes. 47,548 clones are deposited on a Br300K microarray with seven probes of 60 nt length within the 3' 150 bp region.
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features. The .ndf file is linked below as a supplementary file.
Native array description file: 2007-10-15_GGB_B_rapa_082207.ndf
Native array description file: 2007-10-15_GGB_B_rapa_082207.ncd

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


title: Illumina HumanOmni2.5S-8v1_B

status: Public on Oct 18 2013

city: Montreal

first: Tomi

last: Pastinen

state: QC

address: 740 Dr Penfield

department: Human & Medical Genetics

institute: McGill University

manufacture_protocol: See manufacturer's website


title: Illumina HiSeq 2000 (Listeria monocytogenes EGD)

status: Public on Oct 21 2013

organism: Listeria monocytogenes EGD


title: TaqMan® OpenArray® Human MicroRNA Panel (miRBase v14)

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

institute: Washington University in St.Louis

manufacture_protocol: see manufacturer's website - PCR asay


title: Agilent-026851 Helicobacter pylori [Feature number version]

status: Public on Oct 10 2013

city: Cambridge

first: Alexander

last: Sheh

state: ma

address: 77 Massachusetts ave 16-828

department: Biological Engineering

institute: MIT

organism:
Helicobacter pylori 26695
Helicobacter pylori J99
Helicobacter pylori HPAG1
Helicobacter pylori Shi470
Helicobacter pylori G27
Helicobacter pylori P12
Helicobacter pylori B38

description:
26695, J99, P12, G27, HPAG1, Shi470, B38

Arrays of this design have barcodes that begin with 16026851 or 2526851.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

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


title: Illumina HiSeq 2000 (Methylocystis sp. SB2)

status: Public on Oct 17 2013

organism: Methylocystis sp. SB2


title: 022125-Agilent Mycobacterium tuberculosis H37Ra 8x15K (Probe Name version)

status: Public on Oct 09 2013

city: Hefei

first: Yuzhi

last: Hong

state: Anhui Province

address: 3 Feixi Road

department: Modern Experiment Technology Center

institute: Anhui University

organism: Mycobacterium tuberculosis H37Ra

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


title: IPK Hordeum vulgare 12k SEED2

status: Public on Oct 15 2013

city: Gatersleben

first: Athmer

last: Benedikt

address: Correnstrasse 3

country: Germany

institute: IPK Gatersleben

organism: Hordeum vulgare


title: Vibrio vulnificus CMCP6 whole genome TwinChip

city: Seoul

first: Jin Hwan

last: Park

address: Gwanak-ro 599

institute: Seoul National University

organism: Vibrio vulnificus CMCP6

manufacture_protocol: The V. vulnificus whole genome TwinChip, which has two blocks, up (upper) and dn (lower), manufactured and kindly provided by the  21C Frontier Microbial Genomics and Applications Center (Daejeon, South Korea)


title: Illumina MiSeq (Vibrio parahaemolyticus)

last: GEO

organism: Vibrio parahaemolyticus


title: UNIL_fireant_25K_vG_and_vI

status: Public on Oct 20 2013

city: Lausanne

first: Yannick

last: Wurm

address: Biophore

institute: University of Lausanne

organism: Solenopsis invicta

description: This platform represents two prints ("G" and "I") of the "same" microarray.


title: Fusarium fujikuroi annotation version 1 gene expression array [110407_UG_Ffujikuroi_expr_HX12]

status: Public on Oct 05 2013

city: Neuherberg, Germany

first: Christian

last: Sieber

address: Ingolstädter Landstraße 1

department: Institute of Bioinformatics and Systems Biology

institute: Helmholtz Zentrum München

organism: Fusarium fujikuroi

description: NimbleGen design name 110407_UG_Ffujikuroi_expr_HX12


title: Agilent-036974 S. solea array (Feature Number version)

status: Public on Oct 07 2013

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

organism: Solea solea

description: GE 8x15k oligo microarray that covers 14,531 annotated transcripts (Isotigs and Singletons) of the common sole (Solea solea). Roche 454 sequence reads were produced from a normalized cDNA library constructed using a mixture of RNAs from whole larvae (1-4-6-11-13-18-20-33 days posth hatching) and adult tissues (liver and intestine). All 454 sequences were then assembled into Isotigs, representing putative transcripts, by using Newbler 2.6 software with default settings. All assembled Isotigs are stored in the public database Transcriptome Shotgun Assembly Sequence Database (TSA, http://www.ncbi.nlm.nih.gov/genbank/tsa) under accession number GAAQ00000000, while Singletons can be directly retrieved from the NCBI Sequence Read Archive (SRA) under accession number SRA058691. Microarray design has been carried out on the basis of 25,252 contigs (Isotigs) and 66,026 singletons (with a minimal length of 200 nt) obtained from the Roche 454 sequencing of a normalized cDNA library of sole larval stages (from 1 to 33 days post hatching) and adult tissues. Only annotated sequences were used for microarray design. One probe for annotated sequences with known orientation (14,357) was designed while, whenever possible, two probes with both orientations were designed for sequences with unknown/ambiguous orientation (174 indicated by Isotig/Singleton ID plus prefix S_ or AS_ ). A total of 14,701 oligonucleotide probes (60 nt) were in situ synthesized onto the array, using Agilent non-contact ink-jet technology (8 x 15K format, including default positive and negative controls).  Probe ID on the array corresponds to transcript name (either Isotig or Singleton).

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


title: Agilent-034134 human gut microbiota CAZyme Microarray

city: Marseille

first: Abdessamad

last: EL KAOUTARI

state: France

address: 27 boulevard Lei Roure

country: France

institute: INSERM

organism: human gut metagenome

description:
Microarray design of CAZyme genes in human gut microbiota

Arrays of this design have barcodes that begin with 16034134 or 2534134.

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-028789 ATTA-V1 [Probe name version]

status: Public on Oct 01 2013

city: Jena

first: Heiko

last: Vogel

address: Hans-Knoell-Strasse 8

department: Dpt. of Entomology

institute: Max Planck Institute for Chemical Ecology

organism: Atta vollenweideri

description:
Atta vollenweideri_Antennae

Arrays of this design have barcodes that begin with 16028789 or 2528789.

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.


title: Agilent-018519 Human Chromosome 17 Custom Tiling Array

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

organism: Homo sapiens

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

DesignID : 018519

manufacture_protocol: Agilent uses jet-directed in-situ synthesis. see manufacturer's web site at http://www.agilent.com/


title: IBMT Salmonella Enteritidis library screening

city: Potsdam

first: Sebastian

last: Hoppe

address: Am Mühlenberg 13

department: Bioanalytics and Biosensorics

institute: Fraunhofer Institute for Cell Therapy and Immunology

organism: Escherichia coli

technology: spotted peptide or protein

manufacturer: platform Halolink Arrays (Promega), spotting performed at IBMT

manufacture_protocol: Spotting was performed with a Qarray2 (Genetix)


title: Hessian Fly 1.3 K miRNA

city: Lincoln

first: Chitvan

last: Khajuria

state: NE

address: 103 Entomology Hall

institute: University of Nebraska-Lincoln

organism: synthetic construct

manufacture_protocol: see  manufacturer's website


title: TaqMan OpenArray Human MicroRNA Panel (4461104)

city: Baltimore

first: Kenneth

middle: W

last: Witwer

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

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


title: Agilent-033170 Manila clam 8x15k oligo microarray

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

organism: Ruditapes philippinarum

description: GE 8x15k oligo microarray that covers 11,906 transcripts of the Manila clam (Ruditapes philippinarum). Oligonucleotides, 60-mer plus a “linker”, are synthesized directly on glass slide using the Agilent’s SurePrint Tecnology. A total of 11,197 probes were already employed on a previous version of the microarray (GPL10900) and maintained the same Probe ID (contig ID plus suffix _1, _2, _AS or _S). To them, one  probe (contig ID without any suffix) for  transcripts with known orientation was added. In addition, 2 probes with different orientation (sense and antisense) were designed for transcripts with unknown orientation. Manila clam 18X5 microarray represent a total of 14,156 probes representing 11,906 transcripts.Both independent probes designed for the same transcript are named with an univocal ID; the sense probes are distinguished by suffix_S while the anti-sense probes are distinguished by suffix _AS. As for probes employed on GPL10900, sequence and description of each gene (contig) are available in the Ruphidatabase (Milan et. al 2011),  where contig ID corresponds to probe ID  on the array.


title: NimbleGen Nicotiana tabacum V2 microarray [111027_Ntab_GSK_exp]

first: Yeon-Ki

last: Kim

address: 38-2 Namdong

organism: Nicotiana tabacum

description:
Probes are designed from 34,052 genes deposited at the The National Center for Biotechnology Information (NCBI; http://www.ncbi.nlm.nih.gov/). Further information on this microarray, including statistical analysis, can be found at GreenGene Biotech (http://www.ggbio.com). Among the genes on the microarray, 29,413 are from representative Nicotiana tobaccum with cDNA/EST supports, and 4,641 genes have been predicted without cDNA/EST supports.
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features. The .ndf file is linked below as a supplementary file.
Native array description file: 111027_Ntab_GSK_exp.ndf
Native array description file: 111027_Ntab_GSK_exp_HX12.ncd


title: AB SOLiD System 3.0 (Nicotiana tabacum)

status: Public on Feb 02 2013


title: Agilent-017202 whole mouse genome (mm8) custom 2x105k array

city: Houston

first: Ge

last: Li

address: 1100 Bates St.

department: Pediatrics

institute: Baylor College of Medicine

organism: Mus musculus

manufacture_protocol: Agilent


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray HGU133Plus2_Hs_ENTREZG_v16]

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH


title: Targeted array-based proteomics [RPPA-SKBR3]

status: Public on Oct 22 2012

city: Heidelberg

first: Ulrike

last: Korf

address: Im Neuenheimer Feld 580

department: Molecular Genome Analysis

institute: German Cancer Research Center

description: reverse phase protein array (RPPA/RPA), lysate array

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

manufacture_protocol: Arrays were prepared on nitrocellulose-coated glass (Grace Biolabs) slides by using a solid-pin arrayer (Aushon 2470) with 180 µm pins.


title: Phalanx Human OneArray Ver. 5 Release 4

status: Public on Apr 28 2012

city: Hsinchu

last: Chang

address: 6F, NO.6 Technology Road 5

department: R&D

country: Taiwan

institute: PhalanxBiotech Group

description:
Annotation is based on two databases:
. NCBI RefSeq release 52
. Ensembl release 66 cDNA sequences and
homo_sapiens_core_66_37f annotations

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


title: NanoString nCounter Gama2 Gene Expression Custom CodeSet

status: Public on Jul 01 2011

first: Lucio

last: Gama

state: MD - EUA

address: 733 N Broadway St - BRB 831

institute: Johns Hopkins School of Medicine

organism: Macaca nemestrina

description:
Gama2 CodeSet is specific for inflammatory genes.
Gama2 CodeSet Probe count: 92

In brief, a multiplexed probe library is made with two sequence-specific probes (Capture and Reporter) for each gene of interest.  The first probe, a Capture probe, contains a 35- to 50-base sequence complementary to a particular target mRNA plus a short common sequence coupled to an affinity tag such as biotin. The second probe, the Reporter probe, contains a second 35- to 50-base sequence complementary to the target mRNA, which is coupled to a color-coded tag that provides the detection signal. The tag consists of a single-stranded DNA molecule, the backbone, annealed to a series of complementary in vitro transcribed RNA segments each labeled with a specific fluorophore. The linear order of these differently colored RNA segments creates a unique code for each gene of interest.

Capture and Reporter probes are synthesized in 96-well plates using a semi-automated process.

A different version of this platform with Gene Symbol in the ID column is assigned accession number GPL17804.

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


title: Agilent-015508 Human miRNA Microarray, pre-commercial version 6.0 (Unique miRNA version)

status: Public on Sep 22 2008

city: Oslo

first: Hilde

last: Johnsen

address: Montebello

department: Genetics

country: Norway

institute: Norwegian Radium Hospital

description:
Agilent Human miRNA Microarray, Beta-Version 1
Beta version of protocol G4470A (Agilent). The array contains no viral miRNA and the control probes are different. Based on Sanger database v 9.1.

*** The ID column represents ascending integers (i.e., 1 to 470) arbitrarily assigned to the unique miRNAs.  A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column, representing all of the replicate probes per miRNA, is assigned accession number GPL6968.


title: [MoGene-2_0-st] Affymetrix Mouse Gene 2.0 ST Array [mogene20st_Mm_ENTREZG_17.1.0]

description: Brainarray mogene20st_Mm_ENTREZG_17.1.0

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

manufacture_protocol: See manufacturer's web site


title: JCVI PFGRC Streptococcus mutans 10K v2.1 array designed primarily based on strain UA159 [FULL_FEATURE_LAYOUT]

status: Public on Sep 19 2006

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Streptococcus mutans

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

manufacture_protocol: 2QSM, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 6075497, pen id 10185, pen cycles -1, operator cs, humidity control On, humidity set point65


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray HGU133Plus2_Hs_ENTREZG_v15]

status: Public on Dec 05 2012

manufacture_protocol: Refer to Affymetrix manufacture protocol for HG-U133 Plus 2.0 array