title: Toray Homo sapiens 1.1K esophageal cancer array

status: Public on Aug 31 2013

city: Kyoto

first: Akira

last: Myomoto

address: Yoshida-Shimoadachi

country: Japan

institute: Kyoto Univ.

organism: Homo sapiens

technology: spotted oligonucleotide

distribution: custom-commercial

manufacture_protocol:
See Toray web-site.
http://www.3d-gene.com/en/products/pro_009.html


title: GSK-3 Knockdown in MDA-MB-231 Reverse Phase Protein Array

city: Houston

first: Debra

last: Smith

state: TX

address: 7435 Fannin St

department: Systems Biology

country: USA

institute: UT MDACC

technology: spotted peptide or protein

distribution: non-commercial

manufacturer: Functional Proteomics Reverse Phase Protein Array Core Facility at The University of Texas M.D. Anderson Cancer Center

middle: L

first: Yiling

last: Lu

first: Shuying

last: Liu

first: Gordon

last: Mills

manufacture_protocol:
1) Cell lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11 x11 format.
2) Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
3) Slides were scanned on a flatbed scanner to produce 16-bit tiff image.
4) Spots from tiff images were identified and the density was quantified by MicroVigene.
5) Relative protein levels for each sample were determined by interpolation of each dilution curves from the "standard curve" (supercurve) of the slide (antibody).  Supercurve is constructed by a script in R written by Bioinformatics.  These values (given as log2 values) are defined as "raw data".
6) All the data points were normalized for protein loading and transformed to linear value designated as "Normalized Linear".
7) "Normalized Linear" value was transformed to Log (natural) value and median-centered for Hierarchical Cluster analysis.


title: Streptococcus mutans UA159 NimbleGen Genechip 72k [gene-level version]

city: Köln

first: Yulong

last: Niu

state: Nordrhein-Westfalen

address: Carl-von-Linne-Weg 10

department: Plant Microbe Interactions

country: Germany

institute: Max Planck Institute for Plant Breeding Research

organism: Streptococcus mutans UA159

technology: in situ oligonucleotide

description:
NimbleGen oligoarrays include 1949 Streptococcus mutans UA159 open reading frames with twelve 24-mer probe pairs (PM/MM) per gene, and each probe is replicated 3 times. This design also 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 prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.


title: Lactococcus lactis IL1403 and lactococcal plasmids 2.5K

city: Tsukuba

first: Miho

last: Kobayashi

address: 2 Ikenodai

department: Animal Products Research

institute: National Institute of Livestock and Grassland Science

organism: Lactococcus lactis

description: The genome sequences and ORF predictions for the chromosome of L. lactis IL1403 and several lactococcal plasmids were obtained from GenBank (accession numbers J05748, AF247159, X99798, AF409136, AF242367, AF036485, AF243383, AF207855, J04962, and AE005176). The genome sequences encoded a total of 2533 predicted ORFs (2425 genes from IL1403 and 108 genes from plasmids). The custom oligonucleotide microarrays contained 111,452 probe pairs, with each pair containing a perfect-match 24-mer oligonucleotide probe. Microarray hybridization experiments were performed at the GeneFrontier Corporation (Tokyo, Japan).


title: Illumina HiSeq 2000 (mixed libraries)

status: Public on Aug 29 2013

last: GEO

organism: mixed libraries

technology: high-throughput sequencing

distribution: virtual


title: Illumina Genome Analyzer (Bactrocera dorsalis)

organism: Bactrocera dorsalis


title: Illumina Genome Analyzer II (Neurospora crassa OR74A)

organism: Neurospora crassa OR74A


title: Luminex Homo sapiens bead-based microRNA profiling platform

status: Public on Dec 21 2013

city: Heidelberg

first: Sven

last: Diederichs

address: Im Neuenheimer Feld 280

department: RNA Biology & Cancer

institute: German Cancer Research Center (DKFZ)

technology: oligonucleotide beads

manufacture_protocol: Jun Lu et al., Nature 2005, PMID: 15944708


title: JCVI PFGRC Mycobacterium tuberculosis 16K v5 array designed primarily based on strain H37Rv (ORF version)

status: Public on Nov 15 2013

city: Berkeley, CA

first: Stavroula

last: Hatzios

address: B84 Hildebrand Hall #1460

institute: UC Berkeley

organism: Mycobacterium tuberculosis

description: This set includes 4735 oligonucleotides, has 16416 spots distributed in 48 blocks.

manufacture_protocol: 5QMT, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Mycobacterium tuberculosis 22K v4 array designed primarily based on strain H37Rv (orf version)

description: This set includes 4742 oligonucleotides, has 22176 spots distributed in 48 blocks.

manufacture_protocol: 4QMT, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Illumina MiSeq (Homo sapiens; Saccharomyces cerevisiae)

organism:
Saccharomyces cerevisiae
Homo sapiens


title: Illumina HiSeq 2000 ([Clostridium] difficile)

status: Public on Aug 30 2013

organism: Clostridioides difficile


title: Illumina HiSeq 2000 (Anopheles gambiae)

status: Public on Aug 28 2013

organism: Anopheles gambiae


title: Agilent-028432 Human Bladder_4x180K_CGH_array (Probe Name version)

city: Lund

first: Mattias

last: Aine

address: Klinikgatan 28

department: Oncology

country: Sweden

institute: Lund University

description:
Bladder zoom in 4x180K containing all probes in 4x44K design

Arrays of this design have barcodes that begin with 16028432 or 2528432.

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.

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


title: SDB_Welch_P_atrosepticum_4.4k array

city: Cambridge

first: Steven

middle: Douglas

last: Bowden

address: Building O, Downing Site

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

organism: Pectobacterium atrosepticum SCRI1043

description:
NimbleGen design name 110829_Ecar_expr.  A 1:2 expression design for 4,472 genes from Pectobacterium atrosepticum SCRI1043 with eight 60-mer probe pairs (PM/MM) per gene.  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.


title: Illumina HiSeq 2000 (Medicago sativa)

organism: Medicago sativa


title: LC Sciences Soybean miRNA Array

city: Guangzhou

first: Xiaolong

last: Fang

address: NO. 483 Wushan Road Tianhe District

country: China

institute: College of Agriculture, South China Agricultural University

organism: Glycine max

description:
version: miRSoybean_SCAU_120308 array
part no. MRA-2001
The array design was based on 694 conserved miRNA mature sequences of legumes downloaded in miRBase Release 18.0 (http://www.mirbase.org/) and 259 well characterized miRNAs published in papers (Barrera-Figueroa et al., 2011; Chen et al., 2012; Li et al., 2011; Zeng et al., 2012; Zhang et al., 2008; Zhou et al., 2012b).

manufacture_protocol: On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.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 were made by in situ synthesis using PGR (photogenerated reagent) chemistry.


title: Oryza sativa Whole Genome 8x60k Gene Expression Microarray (AMADID: 031380)

status: Public on Aug 27 2013

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

organism: Oryza sativa

description: designed  by Genotypic Technology Private Limited


title: Illumina Genome Analyzer II (Neisseria gonorrhoeae)

status: Public on Aug 26 2013

organism: Neisseria gonorrhoeae


title: BC013

city: Boston

first: Jennifer

last: Bowen

state: MA

address: 100 Morrissey Blvd

department: Biology

institute: University of Massachusetts Boston

organism: synthetic construct

manufacture_protocol:
1.The probe oligonucleotides are printed onto Corning Ultragaps or Erie Scientific Epoxy Silane slides using a DeRisi style arrayer (DiRisi et al., 1997) and pins from Parallel Synthesis.
2.The 70-mer oligo probes (Operon Technologies) were adjusted to a concentration of 0.05 mg ml-1 in 50%  DMSO and were spotted on CMT-GAPS amino silane-coated  glass slides (Corning, Corning, NY).
3. After printing, the slides were baked at 80°C for 3 h and stored in the dark at room temperature under slight vacuum in a dessicator.


title: Illumina HiSeq 2000 (Plasmodium falciparum 3D7)

organism: Plasmodium falciparum 3D7


title: BC010


title: Illumina HiSeq 2000 (Mus musculus domesticus)

organism: Mus musculus domesticus


title: BC012

status: Public on Aug 24 2013

city: Princeton

first: Bess

middle: B

last: Ward

state: NJ

address: Washington Road

department: Geosciences

institute: Princeton University

organism: artificial sequences


title: BC009


title: Affymetrix GeneChip Mouse Genome 430 2.0 Array [CDF: Mm_ENTREZG_10]

status: Public on Nov 05 2008

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

organism: Mus musculus

description:
CDF file was created by Microarray Lab at the Molecular and Behavioral Neuroscience Institute at the University of Michigan.
Oligonucleotide probes on GeneChips were reorganized based on the latest genome and transcriptome information. In this particular case the Entrez Gene database (build: Jun 28, 2007) was used as source.
For the CDF file based on Entrez Gene:
A probe must hit only one genomic location;
Probes that can be mapped to the same target sequence in the correct direction are grouped together in the same probe set;
Each probe set must contain at least three oligonucleotide probes and probes in a set are ordered according to their location in the corresponding exon.
For detailed description please see the paper and website.

manufacture_protocol: This array is identical to GPL1261 but a custom, remapped CDF environment is used to extract data. This is version 10 of the remapped CDF. The CDF for various platforms can be found at the link below.


title: Mycroarray-Saccharomyces_cerevisiae-30K

status: Public on Aug 23 2013

city: Seoul

first: Hye Yun

last: Moon

state: Seoul

address: , 221 Heukseok-dong, Dongjak-gu

department: Department of Life Science

country: South Korea

institute: Chung-Ang university

organism: Saccharomyces cerevisiae

description: Saccharomyces Cerevisiae Oligonucleotide 30K Microarrays

distribution: commercial

first: HyeYun

first: HyunAh

last: Kang

manufacture_protocol:
We directly synthesize them on a microscope slide. Our synthesis is using the robust phosphoramidite chemistry refined since the 1970's for commercial oligonucleotide synthesis. In standard oligonucleotide synthesis, the terminal acid-labile protective group of a growing oligomer is removed by a treatment with a strong acid.
The only modification we have introduced in our process is the usage of a photo-generated acid. At a given synthesis cycle, each spot that needs to be deprotected is exposed to light in the presence of a photogenerated acid precursor, leading to local acid production and cleavage of the terminal protective group. Only the deprotected spots will be able to react with a new monomer. By so doing, we can synthesize tens of thousands oligonucleotides in parallel on the same microarray substrate.
The advantage of using the phosphoramidite chemistry is that we can synthesize oligonucleotides at a reduced cost compared to other chemistries while maintaining our stepwise yield well above 99%.
To expose the oligonucleotide spots to light during the deprotection step of the synthesis cycle, we do not use any physical mask but instead we use a digital micromirror device (DMD) made of several hundred of thousands individually addressable mirrors. At each deprotection step, a computer simply generates an image to be projected on the microarray surface. Using this digital photolithography approach, we can synthesize any custom microarray with no upfront design cost or minimal order size.
We synthesize our microarrays on high quality microscope slides. For uniform synthesis and hybridization and enhanced scanner image quality, we use only low-background glass slides polished to atomic flatness (±20 angstroms). Their precise physical dimension (25 ± 0.2 mm x 76 ± 0.3 mm x 0.940 mm ± 0.025 mm) is compatible with all major brands of slide microarray scanners.


title: Agilent-035137 Catostomus snyderi array

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: UNIVERSITY OF FLORIDA

organism: Catostomus snyderi

description:
Arrays of this design have barcodes that begin with 16035137 or 2535137.

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 Staphylococcus aureus 3.8K oligo array [2009_08_03_RDKK206_Saur_60mer_expr]

city: Bunkyo-Ku

first: tomomi

last: hishinuma

state: Tokyo

institute: juntendo university

organism: Staphylococcus aureus

description:
Native array description files:
2009_08_03_RDKK206_Saur_60mer_expr.ndf
2009_08_03_RDKK206_Saur_60mer_expr.ngd

first: Keiichi

last: Hiramatsu

first: Longzhu

last: Cui

first: Tomomi

last: Hishinuma

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


title: NimbleGen Custom Mouse Neuronal Tiling Array [120509_MM9_BHB_ChIP]

city: Edinburgh

first: Gillian

last: Taylor

address: MRC HGU Crewe Road South

institute: IGMM

description: Custom NimbleGen tiling microarrays were designed using http://genome.ucsc.edu/MM9 NCBI37.  Co-ordinates and genes covered are described below.  Exact probe positions are detailed in file 120509_MM9_BHB_ChIP.pos

manufacture_protocol: Nimblegen manufacture protocol


title: PacBio RS (Pseudomonas phage PaP1)

status: Public on Aug 22 2013

last: GEO

organism: Pseudomonas phage PaP1


title: Agilent-032180 S. cerevisiae DalChipJan11

city: Rehovot

first: Zvi

last: Tamari

address: 234 Herzl St.

country: Israel

institute: Weizmann Institute of Science

description:
Arrays of this design have barcodes that begin with 16032180 or 2532180.

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.


city: Ann Arbor

first: Ilona

last: Kryczek

address: 1150 W. Medical Center Dr.

institute: University of Michigan

organism: Homo sapiens

technology: RT-PCR

description:
PCR assay
Each TaqMan® OpenArray® Human MicroRNA Panel, QuantStudio™ 12K Flex contains 754 well-characterized human miRNA sequences from the Sanger miRBase v14. All 754 assays have been functionally validated with miRNA artificial templates.

manufacture_protocol: see manufacturer's website (http://www.appliedbiosystems.com/).


title: Agilent-037300 S. paradoxus YParNov11

organism: Saccharomyces paradoxus

description:
Arrays of this design have barcodes that begin with 16037300 or 2537300.

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 HumanOmni1-Quad BeadChip  (4v1MultiUse_15014141_B)

status: Public on Aug 21 2013

city: Chieti Scalo

first: Renato

last: Mariani-Costantini

state: CH

address: Via Colle dell'Ara

department: Ageing Research Center (CeSI)

country: Italy

institute: "G. d'Annunzio" University Foundation

manufacture_protocol: See manufacturer's website


title: Arabidopsis thaliana MPSS

city: Irapuato

first: Alma

last: Armenta

address: Km 9.6 Libramiento Norte Carretera León

country: Mexico

institute: CINVESTAV

organism: Arabidopsis thaliana

technology: MPSS


title: Affymetrix Gilmorea520187F Enterococcus faecalis V583 array

status: Public on Aug 20 2013

city: Miami

first: Vijayalakshmi

middle: S

last: Iyer

state: Florida

address: 1600 NW 10th Avenue, RMSB 2048

institute: University of Miami, Miller School of Medicine

organism: Enterococcus faecalis V583

manufacture_protocol: see manufacturer's web site


title: Illumina HiSeq 2000 (Saccharomyces cerevisiae x Saccharomyces paradoxus)


title: Illumina HiSeq 2000 (Saccharomyces paradoxus)


title: Yersinia intermedia ATCC 29909 384k array

city: Madison

first: Lavanya

last: Babujee

state: WI

address: 425 Henry Mall

department: Genetics

institute: UW-Madison

organism: Yersinia intermedia ATCC 29909

description:
NimbleGen design name Yersinia intermedia ATCC 29909, NimbleGen design ID OID 30956.  A whole-genome-tiled array design with ~320,000 probes representing 3953 genes that included 3887 protein coding genes (and 18 likely pseudogenes), 12 non-coding RNAs and 36 tRNAs. The design includes random GC and other control probes.
Yin29909_overlap_DF


title: 454 GS 20 (Phytophthora sojae)

organism: Phytophthora sojae


title: Illumina Genome Analyzer IIx (Rhizobium etli)

organism: Rhizobium etli


title: miRXplore TM Microarray (968)

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

institute: Miltenyi Biotec GmbH

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

technology: spotted DNA/cDNA

description: The miRXplore TM Microarray is composed of 6428 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 1510 miRNA sequences and 97 controls with all probes spotted in quadruplicates. The 1510 miRNA sequences covered sequence verified miRNAs of the species human (898) mouse (742) and rat (505) as well as viral miRNAs (148) as deposited in the miRBase sequence database version 17.0. The 97 positive and negative control probes were chosen as follows. Three sets of controls, miRControl 1 (four sequences used to assess efficiency and sensitivity of labelling), miRControl 2 (single sequence used to assess efficiency of small RNA enrichment) and miRControl 3 (43 sequences used to normalize signal intensities across different samples and arrays) were artificial sequences chosen not be present in any of the human, mouse, rat or viral genome. A fourth set of positive controls presented 36 positive small but non-miRNA sequences including probes e.g. for 5.1 sRNA, tRNAs, and U6 RNAs. A fifth set of oligonucleotides included 13 negative controls like different single or double mismatch, antisense, or scrambled miRNA sequences. Microarrays were manufactured by Miltenyi Biotec. Briefly, 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides in quadruplicates using a customized piezoelectric spotter.

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio


title: 454 GS 20 (Phytophthora ramorum)

organism: Phytophthora ramorum


title: Illumina Genome Analyzer (Phytophthora infestans)

organism: Phytophthora infestans


title: SuperArray GEArray Series Human Wnt Signaling Pathway Gene Array

city: Pittsburgh

first: David

middle: A.

last: Geller

state: Pennsylvania

address: 200 Lothrop St. BST W1507

department: Surgery

institute: University of Pittsburgh

description: Oligo GEArray expression array consists of spotted cDNA fragments encoding 114 genes involved in and downstream of Wnt signaling. Control sequences: PUC18, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and β-actin.

manufacture_protocol: see manufacturer's web site (www.sabiosciences.com)


title: Agilent-029412 E. coli K-12 MG1655 Summer 2010_Updated annotation

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

institute: University of Sheffield

organism: Escherichia coli

description:
Expression microarray for Escherichia coli K-12 substrain MG1655

Arrays of this design have barcodes that begin with 16029412 or 2529412.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Illumina Genome Analyzer IIx (Populus trichocarpa)

status: Public on Aug 15 2013

organism: Populus trichocarpa


title: 454 GS FLX (Schizosaccharomyces pombe)

status: Public on Aug 19 2013

organism: Schizosaccharomyces pombe


title: Nimblegen Clemson E. coli MG1655 Custom 135K

status: Public on Aug 16 2013

city: Clemson

first: Faraz

last: Baig

state: SC

address: 208 Biosystems Research Complex

department: Bioengineering

institute: Clemson University

organism: Escherichia coli str. K-12 substr. MG1655

description:
091117_SH_Ecoli_K12_expr.ngd
091117_SH_Ecoli_K12_expr.ndf
091117_SH_Ecoli_K12_expr_HX12.ncd

manufacture_protocol: see manufacturer's website


title: [MPIO-ZF1s520811] Affymetrix Zebra finch Custom Array [transcript version]

city: Seewiesen-Starnberg

first: Carolina

last: Frankl-Vilches

state: Bavaria

address: Eberhard-Gwinner-Str. 6a

department: Behavioural Neurobiology

institute: Max Planck Institute for Ornithology

organism: Taeniopygia guttata

description: MYGENECHIP2 RNA HD 1M, 5 micron feature size, 49 Array format. The arrays contain a total of 232,620 probes sets and 5,730,824 probes. Whole transcript Sense cDNA target type.

manufacture_protocol: Affymetrix prokaryotic array protocol (see Affymetrix website)


title: Nimblegen Mouse MM9_KF_Meth array [100520_MM9_KF_Meth]

first: Maria

middle: Eugenia

last: Figueroa

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

organism: Mus musculus

description:
designname=100520_MM9_KF_Meth
Array based on the mouse genome (mm9) release.
Condensed on SEQ_ID of .pos file.

manufacture_protocol: See manufacturer's website.


title: Camellia sinensis 4x44k Microarray  designed by Genotypic Technology Private  Limited. (AMADID:043117)

city: Bangalore

first: Genotypic

last: technology

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

institute: Genotypic Technology

organism: Camellia sinensis

first: K

middle: N

last: Chandrashekara


title: Exiqon microRNA Ready-to-Use PCR, Human panel I+II, V2.M

city: Richmond

first: William

middle: Thomas

last: Budd

state: VA

address: 401 College Street Room 1-112

department: Department of Biochemistry and Molecular Biology

institute: Virginia Commonwealth University

organism: Homo sapiens

description: PCR assay


title: Nimblegen Human HG19_HELP array [100128_HG19_MKF_HELP_ChIP]

description:
designname=100128_HG19_MKF_HELP_ChIP
Array based on the human genome (hg19) release.
Condensed on SEQ_ID of .pos file.


title: Albert Einstein College of Medicine Mouse array

city: Queens

first: Sandra

middle: Eve

last: Reznik

state: NY

address: 8000 Utopia Parkway

department: Pharmaceutical Sciences

institute: St. John's University

description: three axis robot

manufacturer: Albert Einstein College of Medicine, Bronx, NY

manufacture_protocol:
Newport Vibration Isolation Workstation
table with a research-grade laser tabletop measuring three feet by five feet by two inches.
The X-axis slide ( GL20) runs the full length of the table and is bolted to one edge of the tabletop.
The Y-axis mechanical slide ( KR46) is mounted perpendicular to and on top of the two X-axis slides.
The Z-axis mechanical slide consists of a high precision miniature slide ( KR20) mounted perpendicular to both the X-axis and Y-axis using a third mounting block resting on the Y-axis slide.
The Pen Tip Assembly consists of a proprietary design having 12 pen tips contained within a precision-machined housing that is supported by the moving block on the Z-axis slide.
The mechanical slides are positioned with motors and servo amplifiers from Yaskawa.
The amplifiers are matched to the motor sizes and include built-in microprocessor control, solid state high voltage power circuits and a plug-in controller for monitoring and tuning each amplifier.
The PC based servo controller is a four axes controller card supplied by Delta Tau.
The computer is a Gateway 2000 model P5-166, a 166Mhz Pentium PC with 32Mbyte RAM, 3.2GB hard drive and 17 inch monitor.
The Servo Controller card runs its own program language and was programmed separately for the appropriate motion routines.
The titer plate holder consists of a modular assembly that simply snaps into position with spring loaded keying pins designed to fit into the 1 inch holes on the laser table.


title: NimbleGen human oral metagenome array [HuMiChip V1.0]

city: Norman

first: Qichao

last: Tu

state: OK

address: 101 David L Boren Blvd

institute: University of Oklahoma

organism: human metagenome

description:
Microbial ecological functional gene array targeting 139 gene families that play important roles in various pathways

The array originally targeted microbial sequences from several different human body, however, the current platform data table represents the oral microbial portion.

Since this is a functional gene array designed from some draft bacterial genomes and metagenomes, standard sequence identifier numbers for most of them are not available at the time the probes were designed. Thus only the gene name for the probes are provided.

DESIGN_ID: 11639
native array description file: HuMiChip.ndf

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


title: Thermo Scientific Dharmacon microRNA human array

city: PHILADELPHIA

first: Chirayu

middle: Pankaj

last: Goswami

state: PA

address: 110 S 11TH STREET

department: MOLECULAR DIAGNOSTIC LABORATORY

institute: THOMAS JEFFERSON UNIVERSITY HOSPITAL


title: SABiosciences Mouse Type I Interferon Response PCR Array

city: La Jolla

first: Hui-Wen

last: Chen

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

description:
PCR assay
SABiosciences RT² Profiler panel of PCR assays


title: Agilent-030593 Tribolium castaneum array

city: Princeton

first: Ann

last: Tate

address: 106A Guyot Hall

department: Ecology and Evolutionary Biology

institute: Princeton University

organism: Tribolium castaneum

description:
trib inf. Oct 2010
Arrays of this design have barcodes that begin with 16030593 or 2530593.
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 1000 (Saccharomyces cerevisiae)

last: GEO

organism: Saccharomyces cerevisiae


title: NIA MGC, Mammalian Genome Collection

status: Public on Aug 14 2013

city: Montreal

first: Imed

last: Gallouzi

state: QC

address: 3655 Promenade Sir William Osler

department: Biochemistry

country: Canada

institute: McGill University

manufacture_protocol: spotted DNA/cDNA


title: miRCURY™ LNA microRNA array v11.0 hmr, miRBase 13.0 + miRPlus

manufacture_protocol: see Exiqon website


title: Illumina HiSeq 2000 (Rhodobacter sphaeroides ATCC 17029)

organism: Cereibacter sphaeroides ATCC 17029


title: JCVI PFGRC Vibrio cholerae 13K v3 array designed primarily based on strain N16961 [Full array version]

status: Public on Aug 13 2013

first: James

last: Bina

address: 450 Technology Dr

department: Microbiology and Molecular Genetics

organism: Vibrio cholerae

description:
This set includes 3754 oligonucleotides, has 13872 spots distributed in 48 blocks.
# revision: 082509
# organism: Vibrio cholerae
# slide version: 3
# strain: N16961
# sequence data repository: N16961 - JCVI CMR

manufacture_protocol: 3QVC, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Exiqon miRCURY LNA microRNA array; 7th generation; batch 208500-2, 208510; lot 35009 –  hsa, mmu & rno (miRBase 19.0)

city: Warsaw

first: Katarzyna

last: Lukasiuk

address: 3 Pasteur Street

department: Department of Molecular and Cellular Neurobiology

country: Poland

institute: Nencki Institute of Experimental Biology Polish Academy of Sciences

organism: Rattus norvegicus

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


title: Illumina HiSeq 2000 (Escherichia coli BL21(DE3))

organism: Escherichia coli BL21(DE3)


title: Illumina Genome Analyzer IIx (mixed culture KAZ_0815)

organism: mixed culture KAZ_0815


title: Illumina MiSeq (mixed culture KAZ_0815)


title: Illumina Genome Analyzer IIx (Enterobacterio phage MS2)

status: Public on Aug 12 2013

organism: Escherichia phage MS2


title: Agilent-035980 ponAbe2_HD_1M_3

status: Public on Aug 10 2013

city: Boston

first: Charles

last: Lee

state: MA

address: 221 Longwood Ave., EBRC-422

department: Pathology

institute: Brigham and Women's Hospital/Harvard Medical School

organism: Pongo pygmaeus

description:
Arrays of this design have barcodes that begin with 16035980 or 2535980.

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: NimbleGen 12x270K Custom Maize Methylation Array

city: St. Paul

first: Steve

middle: R

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

organism: Zea mays

description: B73 RefGen_v2 (order ID#: OID40141)


title: Agilent-035979 ponAbe2_HD_1M_2

description:
Arrays of this design have barcodes that begin with 16035979 or 2535979.

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-035955 ponAbe2_HD_1M_7

description:
Arrays of this design have barcodes that begin with 16035955 or 2535955.

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-035950 ponAbe2_HD_400K_10

description:
Arrays of this design have barcodes that begin with 16035950 or 2535950.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Illumina Genome Analyzer IIx (Rhodobacter sphaeroides ATCC 17025)

organism: Cereibacter sphaeroides ATCC 17025


title: Illumina HiSeq 2000 (Rhodobacter sphaeroides ATCC 17025)


title: Illumina HiSeq 2000 (Fusarium graminearum)

organism: Fusarium graminearum


title: Sequence Validated Human cDNA library by ResGen (Invitrogen) [print version 1]

city: Grand Rapids

first: Sok Kean

last: Khoo

state: MI

address: 333 Bostwick NE

institute: Van Andel Institute

manufacturer: Microarray Core Facility at the Van Andel Institute

manufacture_protocol:
1.cDNA probes are stored in Corning 96-well microtiter plates. Each well contains 1,000 pmol of cDNA clone.
2. Resuspend cDNA probes in PBS to 100 uM and rearray 100 µL into 384-well (Genetix microarray plate cat# 7022).
3. Seal plates with Corning seals and store at -80 °C until print.
4. For printing process, remove seals and cover with plate lids. Place in appropriate location of plate cassette. Plate lids are removed just before print run is started to minimize evaporation time before printing.  All arrays are printed on Corning CmT-Gaps2 amino-silane coated slides.
5. After the print run is completed, allow slides to dry at room temp before vacuum sealed and store at 4 °C.
6. For each subsequent preparation of a print run, wash microarray quill pins with PBS to remove residues.


title: Sequence Validated Human cDNA library by ResGen (Invitrogen) [print version 2]


title: Illumina HiSeq 2000 (Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74)


title: Agilent-035978 ponAbe2_HD_1M_1

description:
Arrays of this design have barcodes that begin with 16035978 or 2535978.

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: Human Oxidative Stress and Antioxidant Defense

status: Public on Aug 11 2013

city: Urbana

first: Michael

middle: J

last: Plewa

state: IL

address: 1101 W Peabody Dr

department: Crop Sciences

institute: University of Illinois at Urbana-Champaign

description:
SABiosciences RT2 Profiler™ PCR Array
Human genes involved in the generation or detoxification of ROS or genes whose transcription is responsive to oxidative stress.


title: Agilent-035957 ponAbe2_HD_1M_9

description:
Arrays of this design have barcodes that begin with 16035957 or 2535957.

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: [HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [HuGene11stv1_Hs_ENTREZG_17.0.0]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: Brainarray: HuGene11stv1_Hs_ENTREZG_17.0.0

manufacture_protocol: See manufacturer's web site


title: Agilent-035956 ponAbe2_HD_1M_8

description:
Arrays of this design have barcodes that begin with 16035956 or 2535956.

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-035952 ponAbe2_HD_1M_4

description:
Arrays of this design have barcodes that begin with 16035952 or 2535952.

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-035954 ponAbe2_HD_1M_6

description:
Arrays of this design have barcodes that begin with 16035954 or 2535954.

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-034037 PanTro2_HD_1M_9

organism: Pan troglodytes

description:
Arrays of this design have barcodes that begin with 16034037 or 2534037.

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-035944 ponAbe2_HD_1M_5

description:
Arrays of this design have barcodes that begin with 16035944 or 2535944.

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-034048 RheMac2_HD_1M_8

organism: Macaca mulatta

description:
Arrays of this design have barcodes that begin with 16034048 or 2534048.

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-034047 RheMac2_HD_400K_10

description:
Arrays of this design have barcodes that begin with 16034047 or 2534047.

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-034033 PanTro2_HD_1M_5

description:
Arrays of this design have barcodes that begin with 16034033 or 2534033.

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-034045 RheMac2_HD_1M_7

description:
Arrays of this design have barcodes that begin with 16034045 or 2534045.

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-034046 RheMac2_HD_1M_9

description:
Arrays of this design have barcodes that begin with 16034046 or 2534046.

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-034032 PanTro2_HD_1M_4

description:
Arrays of this design have barcodes that begin with 16034032 or 2534032.

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: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_Hs_ENTREZG_17.0.0]

description: Brainarray: HuGene10stv1_Hs_ENTREZG_17.0.0


title: Agilent-034043 RheMac2_HD_1M_5

description:
Arrays of this design have barcodes that begin with 16034043 or 2534043.

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-034042 RheMac2_HD_1M_4

description:
Arrays of this design have barcodes that begin with 16034042 or 2534042.

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-034044 RheMac2_HD_1M_6

description:
Arrays of this design have barcodes that begin with 16034044 or 2534044.

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-034041 RheMac2_HD_1M_3

description:
Arrays of this design have barcodes that begin with 16034041 or 2534041.

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-034029 PanTro_HD_1M_1

description:
Arrays of this design have barcodes that begin with 16034029 or 2534029.

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-034030 PanTro2_HD_1M_2

description:
Arrays of this design have barcodes that begin with 16034030 or 2534030.

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-034038 RheMac2_HD_1M_1

description:
Arrays of this design have barcodes that begin with 16034038 or 2534038.

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-034040 PanTro2_HD_1M_10

description:
Arrays of this design have barcodes that begin with 16034040 or 2534040.

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-034035 PanTro2_HD_1M_7

description:
Arrays of this design have barcodes that begin with 16034035 or 2534035.

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-026185 AGTRAN2009 array

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 gambiae

description:
function Group   databaseFG
I/A P/A: putative immunity and apoptosis APO: apoptosis I, I(FBN), I(LRR)
R/S/M RE/ST:oxidoreductive, stress-related MIT: mitochondrial Redox/Stress/MIT
P/D PR/DI: proteolysis, digestion  DIG, PROT
C/S CY/ST: cytoskeletal,structural  CS, CSR
TRP TRP: transporter  TRP
MET MET: metabolism  M
R/T/T R/T/T: replication, transcription,translation  RTT
DIV DIV: diverse  D
UKN unknown  U

manufacture_protocol: Agilent


title: Agilent-034036 PanTro2_HD_1M_8

description:
Arrays of this design have barcodes that begin with 16034036 or 2534036.

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-034039 RheMac2_HD_1M_2

description:
Arrays of this design have barcodes that begin with 16034039 or 2534039.

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 pig CGH array

status: Public on Aug 09 2013

city: Wuhan

first: Fenge

last: Li

state: Hubei

address: Shizishan Street

institute: Huazhong Agricultural University

organism: Sus scrofa

description:
Platform is based on Sus scrofa genome version 9.0.
NimbleGen design ID 549111
native array description file: 110221_SusScr2_YR_CGH.ndf
native array description file: 110221_SusScr2_YR_CGH.pos

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


title: TU Graz miRNA array

city: Vienna

first: Rotraud

last: Wieser

address: Waehringer Guertel 18-20

department: Clinic of Medicine I

country: Austria

institute: Medical University of Vienna

organism: Homo sapiens

manufacture_protocol: LNA modified oligonucleotide probes specific for the 559 human miRNAs contained in miRBase version 9.2 (http://www.mirbase.org/) as well as probes for 77 proprietary miRPlus sequences (Exiqon) were spotted onto Hisens epoxy-coated glass slides (Schott Nexterion) in eight replicates.


title: Agilent-034034 PanTro2_HD_1M_6

description:
Arrays of this design have barcodes that begin with 16034034 or 2534034.

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: Affymetrix custom miRNA array [hsMiR-v1s520779F]

city: Basel

first: Lukas

last: Baeriswyl

address: Fabrikstrasse 10

department: Human Genetics and Genomics

country: Switzerland

institute: Novartis Pharma AG

description: The HsMir v1s520779F custom array is primarly based on the commercially available Affymetrix microRNA microarray version 2.0 (Affymetrix GeneChip miRNA 2.0 Array datasheet P/N EXP00180 Rev 1) with i) microRNA probe sequences updated using miRBase version 17 ii) all human pre-microRNAs removed iii) all non-human sequences removed iv) all viral target sequences removed. In summary, the array contains 1738 mature microRNAs and 2333 other small RNAs (such as small nucleolar RNAs or small cajal body-specific RNAs) probe sequences plus the Affymetrix hybridization and normalization control probesets.

manufacture_protocol: as described in manufacturers website


title: Tongji University School of Medicine TaqMan MicroRNA Array v2.0 B

status: Public on Aug 08 2013

city: Shanghai

first: junjie

last: xiao

address: 150 Ji Mo Road

institute: Key Laboratory of Arrhythmias, Ministry of Education, China (Tongji University School of Medicine)

manufacture_protocol: The TaqMan® Human MicroRNA Array Set v2.0 is a two card set containing a total of 364 TaqMan® MicroRNA Assays per card. The set enables accurate quantitation of 667 human microRNAs. The content is derived from miRBase v10, and provides close to full coverage of Sanger.


title: 454 GS FLX (Campylobacter jejuni)

organism: Campylobacter jejuni


title: Illumina HiSeq 2000 (Tuber melanosporum)

organism: Tuber melanosporum


title: Tongji University School of Medicine TaqMan MicroRNA Array v2.0 A


title: Duke/Schmid Halobacterium 100

status: Public on Aug 07 2013

city: Durham

first: Horia

last: Todor

state: North Carolina

address: 125 Science Drive

department: Biology

institute: Duke University

organism: Halobacterium salinarum NRC-1

technology: other

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


title: Illumina Genome Analyzer IIx (Prunus persica)

status: Public on Aug 06 2013

organism: Prunus persica


title: Illumina HiSeq 2000 (Staphylococcus aureus subsp. aureus USA300)


title: Chironomus_riparius_Gene_Expression_microarray

city: Amsterdam

first: Floyd

last: Wittink

address: Kruislaan 318

department: MAD

institute: Universiteit van Amsterdam

organism: Chironomus riparius

description:
1201127_Crip_OGB_exp.ndf
120127_Crip_OGB_exp_HX12.ncd

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


title: Agilent-034031 PanTro_HD_1M_3

description:
Arrays of this design have barcodes that begin with 16034031 or 2534031.

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-034067 Oncorhynchus mykiss RTG_Array_Ver.1 032182 (Feature Number version)

city: Minato-ku

first: Makoto

last: Hayashi

state: Tokyo

address: Konan 4-5-7

department: Department of Marine Biosciences

institute: Tokyo University of Marine Science and Technology

organism: Oncorhynchus mykiss

description:
Arrays of this design have barcodes that begin with 16034067 or 2534067.

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 (Prochlorococcus marinus subsp. pastoris str. CCMP1986)

status: Public on Aug 02 2013

last: GEO


title: Illumina HiSeq 2000 (Enterobacteria phage lambda)

organism: Lambdavirus lambda


title: Agilent-026851 Helicobacter pylori [Entrez Gene ID version]

status: Public on Aug 05 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 Entrez Gene ID number.


title: Nimblegen Human HG19_HELP array [100128_HG19_MKF_HELP_ChIP]

city: New York

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description:
designname=100128_HG19_MKF_HELP_ChIP
designid=11291
Array based on the human genome (hg19) release.
Condensed on SEQ_ID of .pos file.

manufacture_protocol: See manufacturer's website.


title: NimbleGen Desulfovibrio alaskensis str. G20 12-plex [110215_Ddesul_strG20_JK_exp]

status: Public on Aug 03 2013

city: Berkeley

first: Jennifer

middle: V

last: Kuehl

state: California

address: 1 Cyclotron Road

department: Physical Biosciences

institute: Lawrence Berkeley National Laboratory

organism: Oleidesulfovibrio alaskensis G20

description:
127,979 60-mer probes with different genic sequences in a 12-plex format.

Native array description file: 110215_Ddesul_strG20_JK_exp.ndf


title: Illumina HiSeq 2000 (Nannospalax galili)

organism: Nannospalax galili


title: ORB Sanger 15 miRNA microarray

status: Public on Aug 04 2013

city: Morgantown

first: Dajie

last: Luo

state: West Virginia

address: P.O. Box 9300 Room 2816 HSS

institute: West Virginia University

organism: synthetic construct

description: 34-46 bp oligonucleotide microarray - single color

manufacture_protocol: Proprietary spotting of DNA oligonucleotides containing dimer or trimer repeat of reverse complement of target sequence.


title: Escherichia coli SE15 30K Microarray

city: Suwon

first: Sang Rim

last: Kang

address: San 94-6,Iui-dong

department: Department of biological engineering

institute: Kyonggi University

organism: Escherichia coli SE15

manufacture_protocol: see mabufacturer's website


title: Illumina Genome Analyzer II (Desulfovibrio alaskensis G20)


title: Agilent-021569 Physcomitrella patens 4 x 35 K array

status: Public on Aug 01 2013

city: Setagaya-ku

first: Kenji

last: KOMATSU

address: 1-1-1 Sakuragaoka

department: Department of Bioproduction Technology

institute: Tokyo University of Agriculture

organism: Physcomitrium patens

last: Komatsu

first: Norihiro

last: Suzuki

first: Mayuri

last: Kuwamura

first: Yuri

last: Nishikawa

first: Mao

last: Nakatani

first: Hitomi

last: Ohtawa

first: Daisuke

last: Takezawa

first: Motoaki

last: Seki

first: Maho

last: Tanaka

first: Teruaki

last: Taji

first: Takahisa

first: Yoichi

last: Sakata

manufacture_protocol: The microarray is manufactured by Agilent Technologies. For detailed information see manufacturer's website at http://www.agilent.com/


title: Tmar_Design_v2

city: La Jolla

first: Haythem

last: Latif

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Drive

institute: University of California San Diego

organism: Thermotoga maritima MSB8

description:
NimbleGen tiling array for Thermotoga maritima.
#native array description file = Tmar_Design_v2.ndf
#native array description file = Tmar_Design_v2.ngd


title: Agilent-035981 spod array

city: Harpenden

first: Chris

last: Bass

state: Hertfordshire

address: West Common

department: Biological Chemistry

institute: Rothamsted Research

organism: Spodoptera frugiperda

description:
Arrays of this design have barcodes that begin with 16035981 or 2535981.

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 2500 (Drosophila melanogaster; Saccharomyces cerevisiae)

last: GEO

organism:
Saccharomyces cerevisiae
Drosophila melanogaster


title: Agilent-015482 Homo sapiens Claudia ChX zoom

city: Houston

first: James

last: Lupski

address: One Baylor Plaza, 604B

institute: Baylor College of Medicine

organism: Homo sapiens

description:
chX150-154; chrX:97-107; chrX:6.2-8.6; 1000 Y; 1000 autosomal controls

Arrays of this design have barcodes that begin with 16015482 or 2515482.

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-028035 hsa_miRNA14_Virus

city: GuangZhou

first: jinze

last: zheng

address: Dongfeng east road 651#

institute: Sun Yat-Sen University Cancer Center

description:
Arrays of this design have barcodes that begin with 16028035 or 2528035.
The version of miRBase in our microarray was v12.


title: Exiqon miRCURY LNA microRNA array [version 12 and 16 merged]

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

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


title: Agilent-025384 Homo sapiens Xq28_2009

description:
Arrays of this design have barcodes that begin with 16025384 or 2525384.

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: [STYLMONOa520430F] Affymetrix S. enterica subsp. enterica serovar Typhimurium str. LT2  and L.monocytogenes EGD-e array

status: Public on Jul 23 2013

city: Stanford

first: Justin

last: Sonnenburg

address: 299 Campus Drive

department: Microbiology and Immunology

institute: Stanford University

organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Listeria monocytogenes EGD-e

first: Bart

middle: C

last: Weimer

manufacture_protocol: see manufacturer's website


title: Illumina HiSeq 2000 (Campylobacter jejuni)

organism: Campylobacter jejuni


title: Ion Torrent PGM (Drosophila melanogaster)

organism: Drosophila melanogaster


title: PHRI-UMNDJ-CAG Bacillis subtilis 4.1K V1.0

status: Public on Feb 20 2013

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

organism: Bacillus subtilis

manufacturer: The Center for Applied Genomics at the Public Health Research Insitute of UMDNJ

manufacture_protocol: Oligonucleotides 65mer long from the B. Subtilis OligoLibrary by Compugen and Sigma-Genosys set were spotted using a Genemachines omnigrid arrayer at a concentration of 25uM in 3x SSC onto glass slides coated with Poly-L-Lysine.


title: Agilent-034067 Oncorhynchus mykiss RTG_Array_Ver.1 032182 (Probe Name version)

status: Public on Jun 12 2012

first: Makoto

last: Hayashi

country: Japan

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


title: miRXplore TM Microarray (958)

status: Public on Feb 16 2012

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

institute: Miltenyi Biotec GmbH

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: The miRXplore TM Microarray is composed of 6428 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 1510 miRNA sequences and 97 controls with all probes spotted in quadruplicates. The 1510 miRNA sequences covered sequence verified miRNAs of the species human (898) mouse (742) and rat (505) as well as viral miRNAs (148) as deposited in the miRBase sequence database version 17.0. The 97 positive and negative control probes were chosen as follows. Three sets of controls, miRControl 1 (four sequences used to assess efficiency and sensitivity of labelling), miRControl 2 (single sequence used to assess efficiency of small RNA enrichment) and miRControl 3 (43 sequences used to normalize signal intensities across different samples and arrays) were artificial sequences chosen not be present in any of the human, mouse, rat or viral genome. A fourth set of positive controls presented 36 positive small but non-miRNA sequences including probes e.g. for 5.1 sRNA, tRNAs, and U6 RNAs. A fifth set of oligonucleotides included 13 negative controls like different single or double mismatch, antisense, or scrambled miRNA sequences. Microarrays were manufactured by Miltenyi Biotec. Briefly, 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides in quadruplicates using a customized piezoelectric spotter.

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio

manufacture_protocol: 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted four times on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides using a customized piezoelectric spotter.


title: NimbleGen custom mouse imprinted array [110228_MM9_PS_ChIP]

status: Public on Jul 31 2013

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

country: USA

institute: City of Hope National Medical Center

organism: Mus musculus

description:
Design name: 110228_MM9_PS_ChIP
Design ID: 549521
Native array description file: 110228_MM9_PS_ChIP.ndf
Native array description file: 110228_MM9_PS_ChIP.pos

Annotation in this Platform is based on NCBI mouse build 37 (mm9).
Genomic regions along imprinted domains, IAPs and control regions, isothermal tiling oligos at 100bp.

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


title: Targeted array-based proteomics [RPPA-HCC1954]

status: Public on Oct 22 2012

city: Heidelberg

first: Ulrike

last: Korf

address: Im Neuenheimer Feld 580

department: Molecular Genome Analysis

country: Germany

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: Agilent-031235 Oryza sativa hokudai_ikushu-3

status: Public on Jul 30 2013

city: Sapporo

first: Yuji

last: Kishima

address: Kita-ku Kita 9 Nishi 9 W105

institute: Hokkaido University

organism: Oryza sativa

description:
Database for ORS:
http://rice.plantbiology.msu.edu/annotation_oryza.shtml

Arrays of this design have barcodes that begin with 16031235 or 2531235.

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: Targeted array-based proteomics [RPPA-Longterm]


title: Agilent-021781 1X1M Drosophila Tiling Array

status: Public on Dec 09 2010

city: Chicago

first: Kevin

middle: P.

last: White

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

description:
resolution: 160bp
genome version: dm2


title: Agilent-027389 Mycobacterium bovis BCG Pasteur

status: Public on Jun 21 2011

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

organism: Mycobacterium tuberculosis variant bovis BCG

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

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: Affymetrix Human Exon 1.0 ST Array [probeset (exon) custom CDF based on Ensembl v.49]

status: Public on Aug 20 2010

city: Turku

first: Henna

last: Kallionpää

address: P.O. Box 123

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

description: Chip description file based on Ensembl v.49

relation: Alternative to: GPL5188 (Alternative CDF [official])

manufacture_protocol: See manufacturer's web site


title: Illumina Hiseq 2000 (Homo sapiens)

status: Public on Aug 09 2013

last: GEO


title: Agilent-019183 Drosophila melanogaster Whole Genome ChIP-on-Chip Set 244K, Microarray 2 of 3

status: Public on Mar 18 2009

middle: P

first: Nicolas

last: Negre

first: Parantu

middle: K

last: Shah


title: Agilent-019184 Drosophila melanogaster Whole Genome ChIP-on-Chip Set 244K, Microarray 3 of 3


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

status: Public on Jan 07 2012

city: St. Louis

first: Amy

middle: M.

last: Becker

state: MO

address: 660 S. Euclide Ave.

department: Pathology and Immunology

institute: Washington University School of Medicine

description:
The MouseRef-8 v2.0 Expression BeadChip offer the most up-to-date content for whole-genome expression profiling in the mouse. Featuring content derived from the National Center for Biotechnology Information Reference Sequence (NCBI RefSeq) database (Build 36, Release 22).

The official version of this platform is accession number GPL6885. This version includes ILMN_GENE values in the ID column.


title: Agilent-019182 Drosophila melanogaster Whole Genome ChIP-on-Chip Set 244K, Microarray 1 of 3


title: Illumina Genome Analyzer IIx (Rattus norvegicus)

status: Public on Jul 12 2010

organism: Rattus norvegicus


title: [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array

status: Public on May 13 2006

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

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

The GeneChip® Human Mapping 500K Array Set provides consistently high coverage across different populations. It is comprised of two arrays, each capable of genotyping on average 250,000 SNPs (approximately 262,000 for Nsp arrays and 238,000 for Sty arrays).

manufacture_protocol: see manufacturer's web site