title: Agilent Human 1A Oligo UNC_custom array

status: Public on May 24 2004

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

country: USA

organism: Homo sapiens

technology: in situ oligonucleotide

description:
Represents about 21495 60-mer oligonucleotide probes which span conserved exons across the transcripts of the targeted full length genes in the home genome. About 17,000 probes are from Human 1A Oligo Microarray Kit. The other 4000 probes are specifically designed for Dr. Perou Lab at University of North Carolina at Chapel Hill.
Keywords = Human Breast Cancer
Keywords = Agilent Microarray Gene Expression
Keywords = GATA3 Mutation

distribution: custom-commercial

first: Jerry

last: Usary

middle: M


title: Rosetta/Merck Human 25k v2.2.1 microarray

status: Public on May 09 2005

city: Seattle

first: Amit

middle: V

last: Kulkarni

state: WA

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

description:
Oligonucleotide array on glass.
Contains 60-mer probes (60-mer).
Keywords = Human 25k microarray Merck

distribution: commercial

first: John

last: Castle

manufacture_protocol: see manufacturer's web site


title: Agilent Human 1A Oligo V2+UNC_custom array

status: Public on Oct 15 2004

description:
Represents about 21495 60-mer oligonucleotide probes which span conserved exons across the transcripts of the targeted full length genes in the home genome. About 17,000 probes are from Human 1A Oligo Microarray Kit. The other 4000 probes are specifically designed for Dr. Perou Lab at University of North Carolina at Chapel Hill.

Keywords = Agilent Microarray
Keywords = EGFR
Keywords = keratin

first: Torsten

middle: O

last: Nielsen

first: Forrest

middle: D

last: Hsu

first: Kristin

last: Jensen

first: Maggie

last: Cheang

first: Gamze

last: Karaca

first: Zhiyuan

last: Hu

first: Tina

last: Hernandez-Boussard

first: Chad

last: Livasy

first: Dave

last: Cowan

first: Lynn

last: Dressler

first: Lars

middle: A

last: Akslen

first: Joseph

last: Ragaz

first: Allen

last: Gown

first: Blake

last: Gilks

first: Matt

last: Van de Rijn


title: Agilent Human 1 cDNA Microarray

status: Public on Mar 24 2004

first: Charles

last: Perou

institute: University of North Carolina at Chapel Hill

technology: spotted DNA/cDNA

description:
12,814 unique clones, 97% map to named human genes;Sourced from Incyte's UniGene 1 and Human Drug Target DNA clone sets
Keywords = Agilent
Keywords = Human cDNA
Keywords = Microarray

first: Christine

last: Chung


title: Illumina Genome Analyzer (Fusarium graminearum)

status: Public on Jul 31 2015

last: GEO

organism: Fusarium graminearum

technology: high-throughput sequencing

distribution: virtual


title: UNC compugen oligo array for toxgenomics study

status: Public on Apr 18 2004

technology: spotted oligonucleotide

description:
Compugen oligo Catalog# HUMLIB96: Human OligoLibrary Release 1.0: 96 well format, 197 plates (18,861 oligos), plus about 1000 custom-designed oligos for Dr. Charles Perou's lab at University of North Carolina at Chapel Hill.
Keywords = Breast Cancer
Keywords = Chemotherapeutics
Keywords = Gene expression
Keywords = Microarray
Keywords = Compugen

distribution: non-commercial

first: Melissa

last: Troester

first: Katherine

last: Hoadley

first: Theresa

last: Sorlie

first: Brittney-Shea

last: Herbert

first: Jerry

last: Shay


title: TaqMan Human MicroRNA A Cards v2.1 + B Cards v3.0

status: Public on Dec 23 2015

city: Ghent

first: Hetty

middle: Hilde

last: Helsmoortel

address: De Pintelaan 185

department: Department of Pediatric Hematology-Oncology and Stem Cell Transplantation

country: Belgium

institute: Ghent University

technology: RT-PCR

description:
Designed to streamline experimental workflows, Megaplex? RT Primers provide a single reaction solution when preparing cDNA for real-time PCR analysis on a TaqMan® MicroRNA Array. Human Pool A v2.1 contains RT primers for 377 unique microRNAs and 4 controls. The microRNA targets represented in this pool tend be better characterized, more broadly expressed and?or expressed at a higher level compared to Human Pool B. Human Pool A v2.1 is intended for use with the TaqMan® Array, Human MicroRNA A Card v2.0, however, it can also be used to prepare cDNA for real-time analysis using the individual TaqMan® MicroRNA Assays.
Designed to streamline experimental workflows, Megaplex? RT Primers provide a single reaction solution when preparing cDNA for real-time PCR analysis on a TaqMan® MicroRNA Array. Human Pool B v3.0 contains RT primers for 377 unique microRNAs and 4 controls. The microRNA targets represented in this pool tend be less well characterized, more narrowly expressed and?or expressed at a lower level compared to Human Pool A. Human Pool B v3.0 is intended for use with the TaqMan® Array Human MicroRNA B Card v3.0, however, it can also be used to prepare cDNA for real-time analysis using the individual TaqMan® MicroRNA Assays.

Assay ID: Assay number (eg 358)
Assay Type: Assay type (eg mature miRNA)
Availability: Availability (eg inventoried)
Assay Name: Assay name (eg ath-miR159a)
Mature microRNA Sequence: Sequence
mirBase Names: Names in mirBase (www.mirbase.org)
mirBase Accession: Accession number in mirBase (www.mirbase.org)
mirBase Alias: Alias in mirBase (www.mirbase.org)
Target Species: Species
View Additional Species: Species
Pool Association: TaqMan microRNA Cards

manufacture_protocol: see manufacturer's website


title: Agilent-046004 Homo sapiens PD genes dec12 array

status: Public on Feb 01 2016

city: London

first: Christos

last: Proukakis

address: Rowland Hill Street

department: Clinical Neuroscience

country: United Kingdom

institute: UCL Institute of Neurology

description:
16 PD relevant genes, filter quality >0.5, 20 kb aroud each gene (30 for NCA and park2, 50 for GBA), and 1 Mb at 10kb probe density around SNCA, park2, GBA

Arrays of this design have barcodes that begin with 16046004 or 2546004.

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 (Mycoplasma pneumoniae)

status: Public on Jul 28 2015

organism: Mycoplasmoides pneumoniae


title: Illumina HiSeq 2000 (Staphylococcus aureus subsp. aureus ST398)

status: Public on Jul 29 2015


title: Illumina HiSeq 2000 (Staphylococcus aureus CN79)

organism: Staphylococcus aureus CN79


title: Illumina Genome Analyzer (Pseudomonas aeruginosa PA14)

organism: Pseudomonas aeruginosa PA14


title: TaqMan microRNA Low-Density Array pools A an B version 2.0

status: Public on Jan 16 2016

city: Munich

first: Katrin

middle: K

last: Fleischmann

address: Lindwurmstrasse 2a

department: Children’s Research Center

country: Germany

institute: Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-Univeristät München

description: TaqMan PCR assay for miRNAs


title: Clostridium thermocellum ATCC 27405 HX12 array (3 x 720k array)

city: Oak Ridge

first: Kyle

last: Sander

state: TN

address: 1 Bethel Valley Road, MS 6038

department: Biosciences

institute: University of Tennessee/Oak Ridge National Laboratory

organism: Acetivibrio thermocellus ATCC 27405

description: Custom array

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


title: 018538_Agilent Agaricus bisporus array

status: Public on Sep 14 2015

city: MAIDSTONE

first: KERRY

middle: STEVEN

last: BURTON

address: NEW ROAD, EAST MALLING

institute: EAST MALLING RESEARCH

organism: Agaricus bisporus

manufacture_protocol: Agilent


title: Illumina HiSeq 2500 (Marmota monax)

organism: Marmota monax


title: Illumina HiSeq 2500 (Arachis ipaensis)

status: Public on Jul 27 2015

organism: Arachis ipaensis


title: Illumina Mouse Ref8 v2.0 expression beadchip

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

organism: Mus musculus

technology: oligonucleotide beads


title: NimbleGen Theileria annulata and Bos taurus expression array [2006-10-17_AT_T_annulata]

city: Glasgow

first: William

last: Weir

address: Room 220, Henry Wellcome Building, Garscube Campus, Bearsden Road

department: Institute of Infection, Immunity and Inflammation

institute: University of Glasgow

organism:
Theileria annulata
Bos taurus

description: 1plex 385k expression array representing all available RefSeq RNA sequences plus additional EST sequences for Bos taurus and including all predicted coding sequences of the bovine intracellular parasite Theileria annulata. 60 mer probe array, five probes per gene, replicated in 2 blocks.


title: Illumina HiSeq 2500 (Arachis duranensis)

organism: Arachis duranensis


title: Agilent-036117 SurePrint G3 Arabidopsis splice-junction and alternative splicing 4x180K Microarray (Probe Name version)

status: Public on Jul 26 2015

city: Taipei

first: Chiung-Swey

middle: Joanne

last: Chang

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

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

organism: Arabidopsis thaliana

description:
Arabidopsis 4x180K splice-junction and alternative splicing

Arrays of this design have barcodes that begin with 16036117 or 2536117.

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 (Euphorbia esula)

status: Public on Jul 24 2015

organism: Euphorbia esula


title: LC sciences MRA-1003_miRRat_17

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Rattus norvegicus

manufacture_protocol: LCscience


title: Illumina HiSeq 2000 (Botryococcus braunii)

organism: Botryococcus braunii


title: Agilent-043287 Hsa miRNA microarray v18  [Probe Name version]

status: Public on Jul 22 2015

first: Karin

last: Weber

address: Veterinärstr. 13

department: Medizinische Kleintierklinik

institute: Zentrum für klinische Tiermedizin

description:
Human miRNAs miRBase v18 and viral miRNAs
Arrays of this design have barcodes that begin with 16043287 or 2543287.
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.


title: NimbleGen marine metagenome array [XM_Nov2012_RMB]

status: Public on Jul 23 2015

city: Livermore

first: Xavier

last: Mayali

state: CA

address: 7000 East Ave

department: Chemical Science

institute: Lawrence Livermore National Laboratory

organism: marine metagenome

description: 25 bp probes targeting the 16S rRNA of uncultivated microbes of mixed microbial communities

manufacture_protocol: ITO coated glass slides


title: 29K Cotton Genome Array

city: Anyang

first: Lu

middle: You

last: Yuan

state: Henan

address: Huanghe Road 38#

department: Molecular Breeding

country: China

institute: Cotton Research Institute, Chinese Academy of Agricultyral Science

organism: Gossypium hirsutum

manufacturer: CapitalBio Corporation,National Engineering Research Center for Beijing Biochip Technology,18 Life Science Parkway, Beijing 102206, China

manufacture_protocol:
1.29K Cotton Genome cDNA microarray constructed by Peking University and CapitalBio Corp. The Peking University construct cDNA library and provide PCR products (Shi et al., 2006). And PCR products were printed in SmartArrayTM (CapitalBio Corp., Beijing, China).
2. Hex was used as positive control.
3. 50% DMSO was used as negative control.
4.Several housekeeping genes were used as hybridization positive control.
5.Eight sequence derived from intergenic regions of the yeast genome showing no significant homology with any existing cotton sequences in GenBank were used as external controls.


title: Illumina HiSeq 2000 (Bacillus thuringiensis)

status: Public on Jul 21 2015

last: GEO

organism: Bacillus thuringiensis


title: mirVana miRNA Probe Set and customized panel

city: Boston

first: Yu-Hua

last: Tseng

state: MA

address: 1 Joslin Place

institute: Joslin Diabetes Center Harvard Medical School

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: Ambion miRNA 1564V1


title: KRIBB Hansenula 17K v1.0

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: Ogataea angusta

manufacture_protocol: DNA spotted onto aldehyde-coated glass microscope slides.


title: Agilent-030493 SurePrint G3 Mouse Exon 4x180K Microarray (Probe Name version)

description:
Mouse4x180KExon

Arrays of this design have barcodes that begin with 16030493 or 2530493.

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

The ID column represents the Agilent Probe Name.

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

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

*** The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL18140.


title: Illumina MiSeq (Nesterenkonia sp. AN1)

organism: Nesterenkonia sp. AN1


title: Illumina Genome Analyzer IIx (Neisseria gonorrhoeae)

organism: Neisseria gonorrhoeae


title: Illumina HiSeq 2000 (Phoenix dactylifera)

organism: Phoenix dactylifera


title: Illumina HiSeq 2000 (Bos indicus)

organism: Bos indicus


title: Illumina HiSeq 2500 (Carollia perspicillata)

organism: Carollia perspicillata


title: Agilent-033677 Biomphalaria glabrata Transcriptome v2_13Apr11 030447

city: Albuquerque

first: Si-Ming

last: Zhang

state: NM

address: Castetter Hall

department: Biology

institute: University of New Mexico

organism: Biomphalaria glabrata

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

first: Coen

last: Adema

first: George

middle: H

last: Rosenberg

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

Publicly available cDNA sequences (Genbank, dbEST, SRA; 2010) for Biomphalaria glabrata were assembled using Mira. Transcripts were analyzed and as needed reverse complemented for longest continuous ORF. A total  of 30593 predicted transcripts, supplemented with 15 mitochondrial gene sequences from Biomphalaria glabrata, 26 (12 nuclear + 14 mitochondrial) gene sequences from Schistosoma mansoni and  12 (9 nuclear + 3 mitochondrial) gene sequences from Echinostoma paraensei) were used as targets for e-array (Agilent) design of unique 60-mer probe sequences. Duplicate probes were arranged in 8 x 60k custom microarray format with Agilent 60-mer SurePrint technology.  Design name Biomphalaria glabrata Transcriptome v2_13Apr11. Created date 13 Apr 2011. Control Grid: IS-62976-8-V2_60kby8_GX_EQC_201000210 . Feature layout: randomized. Design ID: 033677


title: NimbleGen CGH 12x135K Microarray

city: Albany

first: Yi

last: Wang

address: 800 Buchanan Street

institute: USDA, ARS, WRRC

organism: Triticum aestivum


title: Illumina HiSeq 2500 (Neisseria gonorrhoeae)


title: Illumina Genome Analyzer II (Penicillium oxalicum)

organism: Penicillium oxalicum


title: Illumina HiSeq 2000 (Capsaspora owczarzaki)

organism: Capsaspora owczarzaki


title: LC Sciences MRA-1001-UNT_042313_miRHuman_19 (miRNA_ID version)

status: Public on Jul 30 2015

city: Detroit

first: Fazlul

middle: H.

last: Sarkar

state: MI

address: 4100 John R

department: Pathology

institute: Wayne State University School of Medicine

organism: Homo sapiens

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


title: Agilent-034627 AE2011SS Aedes aegypti array

city: Baltimore

last: Dimopoulos

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

organism: Aedes aegypti

description:
Arrays of this design have barcodes that begin with 16034627 or 2534627.

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 (Drosophila mettleri)

status: Public on Jul 20 2015

organism: Drosophila mettleri


title: Illumina HiSeq 2000 (Astragalus chrysochlorus)

organism: Astragalus chrysochlorus


title: Schistosoma japonicum 12 x 135k microarray

status: Public on Jul 19 2015

city: Beijing

first: Shuai

last: Liu

address: Dong Dan San Tiao 9, Beijing, China

institute: Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College

organism: Schistosoma japonicum

description:
The platform was designed using the sequences obtained from schistosome genome and UniGene database  on NCBI by NimbleGen. A total of 21,861 target sequences (20,194 sequences derived from S. japonicum and 1,667 sequences derived from S. mansoni) were provided for array design, for each of the sequences, 3 or 4 unique 60-mer oligonucleotide probes were designed. There were 131,092 experimental probes corresponding to both strands of the genomic DNA on the microarray. Besides the experimental probes, control probes were printed on the array. Probes with random sequences were printed as negative control and eight spike-RNA probes which from the intergenic sequence of yeast as positive controls. The microarray was manufactured by NimbleGen.
The native array description file  and  schistosome sequence file used for arrray design are linked below as supplementary files.
110218_Sjaponicum_YR_exp_2.ndf

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


title: Agilent-22020 Dictyostelium discoideum AX2 16K array

status: Public on Jul 18 2015

city: Pune

first: Bharat

middle: Ravi

last: Iyengar

address: Dr Homi Bhabha Road

department: Chemical Engineering and Process Development

country: India

institute: CSIR-National Chemical Laboratory

organism: Dictyostelium discoideum AX2


title: miRCURY LNA Universal RT microRNA V2.M and V2.R (panel I+II)

status: Public on Jul 17 2015

city: Shanghai

first: Xiaoping

last: Su

address: 800 Xiangyin Road

institute: National Key Laboratory of Medical Immunology & Institute of Immunology

description:
miRCURY LNA Universal RT microRNA PCR, Ready-to-Use PCR Panels Plate layout files for V2.M and V2.R
PCR assay


title: Illumina HiSeq 2000 (Nitrosomonas europaea)

status: Public on Jul 16 2015

organism: Nitrosomonas europaea


title: Agilent-066044 OE Custom Bacillus subtilis GE Microarray [Probe Name version]

city: Nanjing

first: weiying

last: wang

address: 1 Wenyuan Road

department: College of Life Sciences

institute: Nanjing Normal University

organism: Bacillus subtilis

description: Arrays of this design have barcodes that begin with 16066044 or 2566044.


title: Illumina HumanHap650Yv3 Genotyping BeadChip (HumanHap650Yv3_A; Name version)

last: admin

description: over 655,000 tag SNP markers derived from the International HapMap Project

relation: Alternative to: GPL6987 (IlmnID version)

manufacture_protocol: See manufacturer's website


title: nCounter® Human miRNA Assay (v1.0, Nanostring)

city: Toronto

first: Jeff

last: Bruce

state: Ontario

address: 101 College St.

country: Canada

institute: Princess Margaret Cancer Centre

technology: other


title: Applied Biosystems Taqman Array Rodent MicroRNA CardB v3.0

organism: Mus musculus

description: Catalog number: 4444909


title: Mouse siRNA screening array

status: Public on Jul 15 2015

city: New York

first: Alessia

last: Deglincerti

state: NY

address: 1230 York Ave

institute: The Rockefeller University

manufacture_protocol: Pools of 3 siRNAs per well


title: AB SOLiD System 3.0 (Fundulus heteroclitus)

organism: Fundulus heteroclitus


title: Applied Biosystems Rodent MicroRNA Cards (A+B Cards)

city: Fukushima

first: Hayato

last: Go

state: Fukushima

address: Hikarigaoka 1

department: Pediatrics

country: Japan

institute: Fukushima Medical University

description:
PCR assay
Two array card set (Array Card Rodent A v2.1 and Array Card Rodent B)


title: Illumina HiSeq 2000 (Polistes fuscatus)

last: GEO

organism: Polistes fuscatus


title: [MoGene-2_0-st] Affymetrix Mouse Gene 2.0 ST Array (mogene20st_Mm_ENTREZG_19)

first: GEO

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: This array is identical to GPL16570 but the data were analyzed with custom CDF environment Brainarray mogene20st_Mm_ENTREZG_19 available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/19.0.0/entrezg.asp.

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

manufacture_protocol: See manufacturer's web site.


title: Illumina HiSeq 2000 (Petunia x hybrida)

organism: Petunia x hybrida


title: Ion Torrent Proton (Arabidopsis thaliana)

organism: Arabidopsis thaliana


title: Illumina NextSeq 500 (Sorghum bicolor)

status: Public on Jul 14 2015

organism: Sorghum bicolor


title: Illumina MiSeq (Dunaliella tertiolecta)

organism: Dunaliella tertiolecta


title: Biomark 96.96 dynamic array single-cell real-time qRT-PCR

city: San Francisco

first: Devon

last: Lawson

state: California

address: 513 Parnassus Ave Hsw 1301

department: Anatomy

institute: UCSF

description:
PCR assay
n/a


title: Agilent-021828 Unrestricted Mouse miRNA Microarray (V2) (Probe name version)

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Mouse miRNA Microarray 2.0

Arrays of this design have barcodes that begin with 16021828 or 2521828.


title: Fluidigm 96×96 nanofluidic arrays for  96 genes: blood informative transcripts

city: Atlanta

first: Monica

middle: L.

last: Rojas-Peña

state: GA

address: 310 Ferst Dr.

department: School of Biology

institute: Georgia Institute of Technology

description: Fluidigm 96×96 nanofluidic arrays targeting a set of 96 transcripts that are broadly informative of the major axes of variation for peripheral blood gene expression from Preininger et al. (2013)


title: Custom Agilent S. cerevisiae 8x15k Gene expresssion (AMADID: 016333) designed by Genotypic Technology Private LTD

status: Public on Jul 13 2015

city: Bangalore

first: Malathi

last: Srinivasan

state: Karnataka

address: Allalasandra, GKVK Post, Bellary Road

department: Lipidomic Center

institute: Central Food Technological Research Institute

organism: Saccharomyces cerevisiae


title: [RheGene-1_1-st] Rhesus Gene 1.1 ST Array [transcript (gene) version]

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Macaca mulatta

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

Annotations from RheGene-1_1-st-v1.na34.rhemac2.transcript.csv:
#%create_date=Wed Apr  2 23:55:22 2014 PDT
#%chip_type=RheGene-1_1-st-v1
#%lib_set_name=RheGene-1_1-st
#%lib_set_version=v1
#%genome-species=Macaca mulatta
#%genome-version=rhemac2
#%genome-version-ucsc=rhemac2
#%genome-version-create_date=2006-01-00
#%genome-lifted-method=psl-map.pl
#%genome-lifted_from-species=Macaca mulatta
#%genome-lifted_from-version-ucsc=rhemac2
#%netaffx-annotation-date=2013-08-30
#%netaffx-annotation-netaffx-build=34
#%netaffx-annotation-data-type=transcript_cluster

manufacture_protocol: See manufacturer's web site


title: Agilent-069507 ArrayXS_Danio_rerio_V1 (Probe Name version)

city: Bad Nauheim

first: Michael

middle: Patrick

last: Housley

state: Hessen

address: Ludwigstr. 43

department: Developmental Genetics

institute: Max Planck Institute

organism: Danio rerio

description:
OakLabs MyArray strategy, ArrayXS Zebrafish, September 2014, Zv9 release 75

The provided SEQUENCE is only a subset of at least 30 nucleotides of the sequence in the design (this is a kind of copy protection).

*** A different version of this platform with the Agilent feature numbers in the ID column is assigned accession number GPL19785.


title: Exiqon Human miRCURY LNA  RT miRNA PCR

city: Madrid

first: José Ramón

middle: Lamas

last: Lamas

state: MADRID

address: Calle Profesor Martín Lagos s/n. Hospital Clínico san Carlos

department: Rheumatology

country: Spain

institute: Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC)

organism: Homo sapiens

description:
Custom miRNA PCR assay panel
PCR assay


title: Agilent-053929 Tetranychus cinnabarinus [Probe name version]

city: Beibei

first: Zhifeng

last: Xu

state: Chongqing

address: Tiansheng street 2#

institute: Southwest University

organism: Tetranychus cinnabarinus

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


title: Illumina MiSeq (Bacillus subtilis PY79)

organism: Bacillus subtilis PY79


title: Agilent-037880/INRA Sus scrofa 60K v1 (enriched with immune system muscle and adipose tissue genes) [Probe names]

city: Toulouse

first: Alix

last: Pierron

address: 180 chemin de Tournefeuille

country: France

institute: INRA

organism: Sus scrofa

description:
Arrays of this design have barcodes that begin with 16037880 or 2537880
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Feature Extraction feature number.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

first: A

last: Vincent

first: M

last: Jegou

first: F

last: Moreews

first: I

last: Louveau

last: Damon

first: C

last: Rogel-Gaillard

first: L

last: Liaubet

last: Le Huerou-Luron

manufacture_protocol: see manufacturer's web site at http://www.genomics.agilent.com/GenericB.aspx?PageType=Custom&SubPageType=Custom&PageID=2011


title: Mycroarray.com Escherichia coli K-12 3X15

status: Public on Jul 10 2015

city: chongup

first: sun

middle: wook

last: Jeong

state: Chonbuk

address: Sinjeongdong 1266

department: Radiation biotechnology

institute: Korea atomic energy research institute

organism: Escherichia coli K-12

manufacture_protocol: ss-DNA is synthesized in situ on glass substrates functionalized with amines. The systhesis process is properietary but uses digital micromirror mediated photolithography to generate sufficient acid locally to remove acid labile protecting groups on 5'-terminal phosphoramidite monomers where the next phosphoramidite base will be coupled. The arrays can be used to hybridize cRNA or cDNA.


title: 29K Arabidopsis Array

city: shijiazhuang

first: hongtao

last: Ji

state: hebei

address: 286 huaizhong rode

department: Centor for agricultural resources Research

institute: Institute of genetics and developmental biology,Chinese academy of sciences

manufacture_protocol: as described in CapitalBio Corporation Manual


title: Agilent-062168 Bovine-miRNA-v19_60K

status: Public on Jul 09 2015

city: Tsukuba

first: Susumu

last: Muroya

state: Ibaraki

address: Ikenodai 2

department: Animal Products Research Division

institute: NARO Institute of Livestock and Grassland Science

organism: Bos taurus

description:
Arrays of this design have barcodes that begin with 16062168 or 2562168.
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: Ion Torrent Proton (Staphylococcus aureus)

status: Public on Jul 08 2015

last: GEO

organism: Staphylococcus aureus


title: Illumina HiSeq 2500 (Mycobacterium tuberculosis H37Rv)

organism: Mycobacterium tuberculosis H37Rv


title: miRCURY LNA microRNA Array, v.11.0 - hsa, mmu & rno, miRBase 13.0

status: Public on Jul 07 2015

city: Vedbaek

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
Herpesvirus saimiri (strain 11)
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

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

first: Jorg

last: Krummheuer

manufacture_protocol: See Exiqon website


title: miRCURY LNA microRNA Array, 5th generation - hsa, mmu & rno, miRBase 15.0


title: Illumina Genome Analyzer II (Burkholderia glumae BGR1)

organism: Burkholderia glumae BGR1


title: Agilent Custom P. falciparum 8x15k Array designed by Ashis Das, Raja CM & Genotypic Technology Pvt. Ltd. (AMADID:24956)

city: Pilani

first: Ashis

middle: Kumar

last: Das

state: Rajasthan

address: Vidya Vihar

department: Biological Sciences

institute: Birla Institute of Technology & Science,Pilani (Pilani Campus)

organism: Plasmodium falciparum


title: NimbleGen Rat RefSeq Promoter 730k array [100718_RN34_Refseq_Prom_ChIP]

city: Newark

first: Daniel

middle: J

last: Cook

state: DE

address: 104 Academy St.

department: Chemical and Biomolecular Engineering

institute: University of Delaware

organism: Rattus norvegicus

description: DESIGN_NAME: 100718_RN34_Refseq_Prom_ChIP

manufacture_protocol: see NimbleGen website


title: Haloferax mediterranei_CGH

city: Beijing

first: Haibo

last: Yang

address: No.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

organism: Haloferax mediterranei

description: the array was designed according to the former version genome of Haloferax mediterranei (CP001868.1-CP001871.1)

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


title: Autoantigen and Cytokine Protein Microarray II

city: Stanford

first: Jacob

last: Rosenberg

state: CA

address: 269 Campus Drive, CCSR 2240

institute: Stanford

technology: spotted peptide or protein

description:
Custom designed and printed in the Utz Laboratory.
Known autoantigens, cytokines, chemokines, growth factors and receptors were printed onto microarrays. All targets were printed in triplicate.

manufacture_protocol: Custom


title: GeoChip

city: Bogota

first: Carlos

middle: Alexander

last: Ruiz Perez

state: CUNDINAMARCA

country: Colombia

institute: Corporacion CorpoGen

organism:
Bacteria
Archaea
Eukaryota
Viruses

manufacture_protocol: see Nimblegen


title: Ion Torrent PGM (Rattus norvegicus)


title: Agilent-scanner-UNC-custom-4X44K-without-Virus (probe name version)

status: Public on Jun 11 2015

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: Same as GPL10481 but with UNC microarray database probe names instead of Agilent Feature numbers in the ID column.

relation: Alternative to: GPL10481 ([feature numbers version])

manufacture_protocol: Agilent printing protocol


title: Illumina HiSeq 2500 (Rapana venosa)

status: Public on Jul 06 2015

organism: Rapana venosa


title: NanoString nCounter Gene Expression Human UNC  124 list

status: Public on Jun 23 2014


title: Agilent-030493 SurePrint G3 Mouse Exon 4x180K Microarray

status: Public on Jan 08 2014

city: Matsumoto

first: Shin-ya

last: Nishio

state: Nagano

address: 3-1-1 Asahi

department: Department of Otorhinolaryngology

institute: Shinshu University School of Medicine

organism: Mus musculus

description:
Mouse4x180KExon

Arrays of this design have barcodes that begin with 16030493 or 2530493.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL20726.


title: Illumina HiSeq 2500 (Clostridium perfringens)

organism: Clostridium perfringens


title: NanoString nCounter Gene Expression Human UNC  142 list

status: Public on Aug 31 2013

organism: Homo sapiens


title: Ncode Mus musculus Non-coding array

city: Carlsbad

first: Sagar

middle: S

last: Damle

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

manufacture_protocol: This array targets 10,802 putative long noncoding RNAs and 25,179 coding RNA transcripts.


title: NanoString nCounter human DNA damage response and repair pathways platform

status: Public on Jul 01 2015

city: Toronto

first: Kenneth

middle: Chung-kan

last: Chu

state: Ontario

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

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


title: Illumina HiSeq 2500 (Haloferax mediterranei)


title: Illumina HiSeq 2000 (Talinum fruticosum)

organism: Talinum fruticosum


title: Illumina Genome Analyzer IIx (Acropora millepora)

status: Public on Oct 17 2011

organism: Acropora millepora


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

city: Los Angeles

first: Sylvie

last: Bradesi

address: 10833 Le Conte Avenue

department: Digestive Diseases

institute: UCLA

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

manufacture_protocol: see manufacturer's website


title: Agilent-scanner-UNC-custom-4X44K-V2-Barcode26652

status: Public on Nov 16 2012


title: NanoString nCounter Human miRNA Expression Assay v2 [mRNA ID]

city: Bethesda

first: Eric

middle: C

last: Polley

state: MD

address: 9609 Medical Center Drive, Rm 5W118

department: Biometric Research Branch

institute: National Cancer Institute

manufacture_protocol: See manufacturer's website (http://www.nanostring.com/products/miRNA)


title: Agilent Scanner Human 1x44K V7 Barcode12391

status: Public on Mar 11 2011

manufacture_protocol: agilent technology


title: Agilent-069507 ArrayXS_Danio_rerio_V1 (Feature number version)

status: Public on Feb 13 2015

city: Hennigsdorf

first: Martina

last: Schad

address: Neuendorfstrasse 16b

institute: OakLabs GmbH

organism: Danio rerio

description:
The provided SEQUENCE is only a subset of at least 30 nucleotides of the sequence in the design (this is a kind of copy protection).

*** A different version of this platform with the Agilent Probe Names in the ID column is assigned accession number GPL20686.


title: Agilent-PEROU-LAB-CUSTOM-HS-244K-CGH-BARCODE20421

status: Public on Mar 20 2012

first: George

last: Chao

middle: M

manufacture_protocol: Agilent protocol. Design based on hg18 genome assembly.


title: UNC PerouLab 44K Custom Human1 Array

status: Public on Apr 16 2009


title: Oyster Crassostrea gigas microarray v1

status: Public on Oct 16 2011

city: Caen

first: Nolwenn

middle: Marie

last: Dheilly

address: Esplanade de la Paix

department: Biological sciences

institute: Universite de caen

organism: Magallana gigas

description:
design id 025380
4 x 44K
control grid IS-45220-4-V1_4x44K_GX_EQC_V20060608


title: Agilent-scanner-UNC-custom-4X44K-without-Virus

status: Public on Jun 03 2010

relation: Alternative to: GPL20311 ([probe name version])


title: Agilent-015210 Benfey/Cui Arabidopsis custom whole genome promoter array 244k v1.0

status: Public on May 03 2010

city: Tallahassee

first: Hongchang

last: Cui

state: FL

address: 319 Stadium Dr.

department: Biological Science

institute: Florida State University

organism: Arabidopsis thaliana


title: Agilent-019569 ECUST Subtilis 8*15K v1.0

status: Public on Sep 09 2009

city: Shanghai

first: Hui

last: Yu

address: No.100, Rd. Qinzhou

institute: Shanghai Center for Bioinformation Technology

organism: Bacillus subtilis subsp. subtilis str. 168

manufacture_protocol:
A total of 4104 B.subtilis genes were selected from the SubtiList database, of which 2230 were known.
Three probes of a length of 60mer were designed for each of the 4104 genes using Agilent eArray 5.0 program according to the manufacturer's recommendations (https://earray.chem.agilent.com/earray/). These lead to 12312 probes with prefix 'CUST_'.
Another 108 probes (of a 45mer or 46mer length) were designed for 108 B.subtilis genes with other methods and they were spotted on the array in varied replicate numbers, resulting a total of 2896 spots for such 'Bsu####' probes.
A total of 15,744 features (15,208 non-controls and 536 controls) were spotted on each grid of the microarray.
One microarray contains 8 grids of identical components.

*** A different version of this platform with the Agilent probe names in the ID column is assigned accession number GPL20761.


title: Agi-perou-lab-custom-MM-144K-arrays-BARCODE25503

status: Public on Apr 22 2011


title: Whole Human Genome Oligo Microarray (GenePix version)

status: Public on Apr 14 2009


title: Illumina HiSeq 2500 (Streptococcus pyogenes)

status: Public on Jul 02 2015

last: GEO

organism: Streptococcus pyogenes


title: Agilent-021828 Unrestricted Mouse miRNA Microarray (V2) (Feature Number version)

status: Public on May 06 2010

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Mouse miRNA Microarray 2.0

Arrays of this design have barcodes that begin with 16021828 or 2521828.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL13493.

relation:
Alternative to: GPL13493
Alternative to: GPL20689


title: UNC PerouLab 244K Custom Human Array version 4

description: agilent catalog probes plus custom probes designed at Dr. Charles Perou Lab at UNC

manufacture_protocol: Agilent Technology (see manufacturer's website)


title: UNC PerouLab 244K Custom Human Array version 3

description: Agilent catalog probes plus custom probes designed at Dr. Charles Perou lab at UNC chapel hill


title: Illumina HiSeq 2000 (Pan troglodytes)

status: Public on Mar 18 2013

organism: Pan troglodytes


title: UNC PerouLab 244K Custom Human Array version 3 with barcode-15847


title: Agilent-046856 1kG-SV-1M-updated-2

city: Farmington

last: Lee

state: CT

address: 10 Discovery Dr.

institute: Jackson Laboratory for Genomic Medicine

description:
Arrays of this design have barcodes that begin with 16046856 or 2546856.

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 Axon scanner UNC custom 4X44K without Virus

status: Public on Oct 28 2008

manufacture_protocol: agilent printing protocol


title: Illumina HumanHap650Yv3 Genotyping BeadChip (HumanHap650Yv3_A)

status: Public on Jun 23 2008

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

description: over 655,000 tag SNP markers derived from the International HapMap Project

manufacture_protocol: See manufacturer's website


title: UNC PerouLab 244K Custom Human Array version 5


title: Mouse-Agilent-22K-D20030711

status: Public on Jul 30 2010


title: Kyoto University Custom Agilent Ciona intestinalis 1M Tiling Array

status: Public on Mar 09 2010

city: Kyoto

first: Atsushi

last: Kubo

state: Kyoto

address: Sakyo-ku

department: Department of zoology, Graduate School of Science

institute: Kyoto University

organism: Ciona intestinalis

first: Yutaka

last: Satou

manufacture_protocol:
The microarray was manufactured by Agilent Technologies.
The details can be found in their web site http://www.chem.agilent.com/Scripts/PCol.asp?lPage=494


title: Agilent UNC Perou Lab Homo sapiens 1X44k custom with virus probes

status: Public on Apr 19 2008

last: Perou

first: Junyuan

last: Wu

manufacture_protocol: Agilent Printing Technology


title: [DM_tiling2_MR] Affymetrix Drosophila Tiling 2.0R Array

status: Public on Mar 19 2008

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Drosophila melanogaster

description:
Tiling array 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 Drosophila Tiling 2.0R Array builds on the content of its predecessor and includes additional sequences that have since become available through the Berkeley Drosophila Genome Project (BDGP). The majority of the new sequences are located in the heterochromatin regions of the Drosophila genome.

Based on BDGP genome release 5

25-mer oligonucleotide probes interrogate the entire genome with an average 38-base-pair spacing

BPMAP and other files can be downloaded from the Affymetrix Web site below.

manufacture_protocol: see manufacturer's web site


title: Agilent UNC Perou Lab Homo sapiens 1X44K Custom Array

status: Public on Aug 03 2007

first: Zhiyuan

last: Hu


title: Rattus norvegicus CNS Array

status: Public on Jul 11 2015

city: Hannover

first: Frank

last: Stahl

address: Callinstr. 3

department: Institut für Technische Chemie

institute: Universität Hannover

organism: Rattus norvegicus

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