title: Agilent-028863 Human CpG island microarray Agilent SurePrint G3 2x400K (Probe name version)

status: Public on Nov 15 2015

city: Jena

first: Norman

last: Häfner

address: Bachstrasse 18

department: Gynecology

country: Germany

institute: Jena University Hospital

organism: Homo sapiens

technology: in situ oligonucleotide

description: Probe mapping based on genome build hg19.

distribution: custom-commercial

manufacture_protocol: Agilent SurePrint Technology, see www.agilent.com


title: ZB/SBS-NTU Plasmodium knowlesi 11.6K v1

status: Public on Jun 08 2015

city: Singapore

first: Zbynek

last: Bozdech

state: Select if applicable

department: Molecular Genetics&Cell Biology

country: Singapore

institute: Nanyang Technological University

organism: Plasmodium knowlesi

technology: spotted oligonucleotide

distribution: non-commercial

manufacture_protocol: Long oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350.  The 60-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biology 2003, 4:R9.


title: SMD Print_1484 hoz [condensed]

status: Public on Oct 31 2014

city: San Francisco

first: Nikoleta

last: Tsvetanova

state: CA

address: 600 16th street

country: USA

institute: University of California, San Francisco

technology: spotted DNA/cDNA

manufacturer: Stanford Functional Genomics Facility, Stanford School of Medicine

manufacture_protocol: Material is transferred from microtiter plate wells to the slide surface by an automated print head


title: Genotypic Technology designed Custom Mouse Promoter 244k ChIP-on-chip Array (AMADID-019046)

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: Mus musculus

description:
designed  by Genotypic Technology Private Limited

Arrays for two-color ChIP-on-Chip experiment, Organism: Mus musculus

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


title: Illumina HiSeq 2000 (Homo sapiens; Human herpesvirus 8)

status: Public on Oct 29 2014

last: GEO

organism:
Homo sapiens
Human gammaherpesvirus 8

technology: high-throughput sequencing

distribution: virtual


title: Illumina MiSeq (Acinetobacter baumannii ATCC 19606 = CIP 70.34)

organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841


title: Illumina MiSeq (Oreochromis niloticus)

status: Public on Oct 28 2014

organism: Oreochromis niloticus


title: Affymetrix C. elegans Gene 1.1 ST Array

status: Public on May 20 2015

city: Ann Arbor

first: X.Z Shawn

last: Xu

state: Michigan

address: 210 Washtenaw Ave, Room 6115A

institute: Life Sciences Institute, University of Michigan

organism: Caenorhabditis elegans

description:
#%create_date=Tue May 14 12:58:05 2013 PDT
#%chip_type=EleGene-1_1-st-v1
#%lib_set_name=EleGene-1_1-st
#%lib_set_version=v1
#%genome-species=Caenorhabditis elegans
#%genome-version=ce6
#%genome-version-ucsc=ce6
#%genome-version-create_date=2008-05-00
#%genome-lifted-method=NONE
#%genome-lifted_from-species=Caenorhabditis elegans
#%genome-lifted_from-version-ucsc=ce6
#%netaffx-annotation-date=2013-05-05
#%netaffx-annotation-netaffx-build=33
#%netaffx-annotation-tabular-data-version=1.1
#%netaffx-annotation-tabular-format-version=1.1
#%netaffx-annotation-data-type=transcript_cluster
#%netaffx-annotation-docgen-method=module:affy/annotation_update/builder; exec:create-download-file.pl
#%netaffx-annotation-docgen-version=8487
#%netaffx-annotation-url-transcript=www.affymetrix.com/analysis/netaffx/gene/transcript.affx?pk=
#%netaffx-annotation-url-mrna=www.affymetrix.com/analysis/netaffx/gene/rna.affx?pk=
# probeset_id refers to the transcript cluster id

manufacture_protocol: See manufacturer's web site


title: KCC 23K Mouse Microarray

status: Public on Oct 30 2014

city: Philadelphia

first: My

last: Mahoney

state: PA

address: 233 South 10th Street, Suite 428  BLSB

department: Dermatology & Cutaneous Biology

institute: Thomas Jefferson University

manufacture_protocol: The oligos were resuspended in 50 mM phosphate buffer pH 8.0 at 20 mM concentration.  The individual oligo-probe was printed on CodeLink activated slides  under 45% humidity by GeneMachine OmniGrid 100 Microarrayer in 4 x 12 pin configuration and 20 x 20 spot configuration of each subarray.  The spot diameter was 100 µm and distance from center to center was 200µm. The microarrays were ready for sample hybridization after additional 100 mM Taurine/Bicine blocking and 4X SSC/0.1% SDS washing steps.


title: Illumina Genome Analyzer IIx (Acinetobacter baumannii ATCC 19606 = CIP 70.34)


title: [AraGene-1_1-st] Arabidopsis Gene 1.1 ST Array [CDF: aragene11st_At_TAIRT.cdf version 17]

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Arabidopsis thaliana

manufacture_protocol: This is identical to GPL17133 but a custom cdf environment was used to extract data.  (from http://brainarray.mbni.med.umich.edu version 17). The custom cdf is linked below as a supplementary file.


title: [HT_MG-430_PM] Affymetrix Mouse HT MG-430 PM Array Plate [CDF: mouse4302daiplusv6cdf]

status: Public on Oct 27 2014

city: Bilthoven

first: Mirjam

middle: M

last: Schaap

address: Antonie van Leeuwenhoeklaan 9

country: Netherlands

institute: RIVM

manufacture_protocol: Dai et al., NAR (2005), 33(20):e175 and de Leeuw et al.,BMC Res Notes. 2008; 1: 66


title: miRXplore TM Microarray (808)

city: Sapporo

first: Naoki

last: Tanimizu

address: S1, W17, Chuou-ku

country: Japan

institute: Sapporo Medical University

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

distribution: commercial

manufacture_protocol: Miltenyi Biotec


title: Illumina HiSeq 1000 (Vitis vinifera)

organism: Vitis vinifera


title: Agilent-034174 Clostridium thermocellum mgcb1

status: Public on Oct 26 2014

city: Winnipeg

first: Richard

last: Sparling

state: MB

address: 418 Buller Building

department: Microbiology

country: Canada

institute: University of Manitoba

organism: Acetivibrio thermocellus

description:
Arrays of this design have barcodes that begin with 16034174 or 2534174.

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 10k cDNA Array

city: Fort Detrick

first: seid

last: muhie

state: MD

address: 568 Doughten Dr

department: Systems Biology Enterprise

institute: USACEHR

manufacturer: In house manufactured using sequence-verified PCR elements produced from ~10,000 well-characterized human genes of The Easy to Spot Human UniGEM™ V2.0 cDNA Library (Incyte Genomics Inc., Wilmington, DE).

manufacture_protocol: The PCR products, ranging between 500 to 700 base pairs, were deposited in 3x saline sodium citrate (SSC) at an average concentration of 165 ug/ml on CMT-GAPSTM II (γ-aminopropylsilane) coated slides (Corning Inc., Corning, NY), using VersArray™ MicroArrayer (Bio-Rad, Hercules, CA).  The cDNAs were UV-cross-linked at 120 mJ/cm2 using UV Stratalinker 2400 (Stratagene, La Jolla, CA).  The microarrays were baked at 80C for four hours.  The slides were treated with succinic anhydride and N-methyl-2-pyrrolidinone to remove excess amines.


title: Agilent-037124 SN_single7_chr8.9  [Probe Name Version]

status: Public on Oct 25 2014

city: Atlanta

first: Karen

middle: E

last: Hermetz

state: GA

address: 1518 Clifton Rd

department: Human Genetics

institute: Emory University School of Medicine

description:
Probe coordinates are based on genome build hg19

Arrays of this design have barcodes that begin with 16036676 or 2536676.

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.

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: TUGRAZ miRNA array TUGRAZ-HSA_MMU_RNO-MRC23 [Exiqon Probe ID version]

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

description:
This platform is related to GPL18028 but contains all probes on the array. The Exiqon ID is used as the "ID".

Probes for "Cy3_Anchor", "Empty", and "unknown" were all given Exiqon IDs of '0'. In this platform, "Empty" has ID = 0, while "Cy3_Anchor" has an ID = "Cy3_Anchor" and "unknown" has an ID = "unknown".

manufacturer: RNA Biology Group, Institute for Genomics and Bioinformatics, Graz University of Technology, 8010 Graz, Austria

manufacture_protocol: Epoxy-coated Nexterion glass slides were spotted using the miRBase version 16.0 locked nucleic acid (LNA) probe set consisting of 2367 probes against human, mouse and rate miRNAs in 8 replicates.


title: Agilent-037123 SN_single6_chr7.8 [Probe Name Version]


title: [AraGene-1_1-st] Arabidopsis Gene 1.1 ST Array [CDF: aragene11st_At_TAIRG version 17]

manufacture_protocol: This is identical to GPL17133 but a custom cdf environment was used to extract data. The custom CDF file is based on Ensembl genes (from http://brainarray.mbni.med.umich.edu version 17). The custom cdf is linked below as a supplementary file.


title: Agilent-037121 SN_single4_chr3.4.5  [Probe Name Version]


title: Agilent-037120 SN_single3_chr2.3  [Probe Name Version]


title: Agilent-037122 SN_single5_chr5.6  [Probe Name Version]


title: Agilent-037119 SN_single2_chr1.2 [Probe Name Version]


title: Agilent-037118 SN_single1_chr1 [Probe Name Version]


title: Agilent-036678 Copy_of_SN_multipleA_55k_1316617017659 [Probe Name Version]


title: Agilent-036677 Copy_of_SN_multipleB_55k_1316616996710 [Probe Name Version]


title: Agilent-036676 Copy_of_SN_multipleC_55k_1316616790670 [Probe Name Version]


title: Agilent-037132 SN_single15_chrXp [Probe Name Version]


title: Agilent-037133 SN_single16_chrXq  [Probe Name Version]


title: Agilent-037131 SN_single14_chr22.X  [Probe Name Version]


title: Agilent-037130 SN_single13_chr18.19.20.21 [Probe Name Version]


title: Agilent-037128 SN_single11_chr15.16  [Probe Name Version]


title: Agilent-037129 SN_single12_chr17.18  [Probe Name Version]


title: Illumina HiSeq 2000 (Colletotrichum higginsianum IMI 349063)

status: Public on Oct 24 2014

organism: Colletotrichum higginsianum IMI 349063


title: Illumina HiSeq 2000 (Tigriopus californicus)

organism: Tigriopus californicus


title: AB SOLiD System 2.0 (Phytophthora infestans)

organism: Phytophthora infestans


title: Agilent-037127 SN_single10_chr12.13.14  [Probe Name Version]


title: Agilent-037126 SN_single9_chr11.12  [Probe Name Version]


title: Agilent-037125 SN_single8_chr9.10 [Probe Name Version]


title: Phytophthora ramorum 4x72K v2.0 [100526_Pram_UCDavis_TK_exp]

city: Davis

first: Takao

last: Kasuga

address: 382 Huchison Hall

institute: USDA-ARS

organism: Phytophthora ramorum

manufacture_protocol: Roche NimbleGen’s proprietary Maskless Array Synthesis technology was to synthesize long oligo, high-density DNA microarrays.  Approximately four 60mer oligo probes were designed for each target on the array. Targets include 15,495 Phytophthora ramorum genome according to Gene models Phytophthora ramorum v1.0 as well as new 2,506 transcript sequences according to Illumina sequencing.  (http://genome.jgi-psf.org/ramorum1/ramorum1.home.html).  Also,


title: Illumina MiSeq (Paeonia ostii)

status: Public on Oct 23 2014

organism: Paeonia ostii


title: SABiosciences Human chemokines & cytokines PCR Array Catalog #:PAHS-150

city: Leiden

first: Rob

last: Mariman

address: Zernikedreef 9

institute: TNO

technology: RT-PCR

description:
PCR assay
Human chemokines & cytokines

manufacture_protocol: see manufacturer's website


title: Illumina HiSeq 2000 (Yersinia enterocolitica subsp. palearctica Y11)

status: Public on Oct 22 2014


title: GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray

status: Public on Sep 29 2005

city: Tempe

first: Randall

last: Lockner

state: AZ

address: 7700 S River Parkway

department: Bioinformatics

institute: GE Healthcare Life Sciences

description:
CodeLink Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55 000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55 000 probes represent well annotated, full length, and partial human gene sequences from major public databases. CodeLink Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release). Some sequences for design were derived from Incyte LifeSeq™ Gold and Foundation databases.

Well-annotated mRNA or coding sequences were chosen to ensure usefulness for a large range of applications in basic research, biotechnology, and drug development. Each sequence was carefully screened to ensure high-quality, specific probe design, and to reduce redundancy of gene targets. All of the probes designed to these sequences were functionally tested, and over 80% were functionally validated against 25 human tissues to ensure best representation of the gene and biologically relevant results.

As a result of their high-quality probe content and design, CodeLink Human Whole Genome Bioarrays are useful for performing differential expression studies of many important biological processes in a single experiment. For instance, CodeLink Human Whole Genome Bioarray can be used to study unique gene expression profiles at different stages of oncogenesis. These studies help to characterize and understand tumor types and tumor progression for use in drug target identification and personalized medicine. In addition, this bioarray enables the investigation of cell and tissue reactions to their environment from stimulus reception to signal transduction processing and response. This bioarray comprehensively covers cell differentiation, development, apoptosis, and metabolism for drugs and other cellular biomolecules.

Expression profiling of the genes involved in these types of biological processes can be directly applied to target identification, pathway characterization, and drug effect prediction in basic research and drug development.

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

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

relation: Alternative to: GPL18134 ([DISCOVERY PROBE_TYPE])


title: Agilent-038112 mouse miRNA microarray, Release 18.0 (miRNA ID version)

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies


title: miRCURY LNA microRNA Array, 7th gen - hsa, mmu & rno v2

city: Dallas

first: Xiaoyu

last: Wang

state: Texas

address: ND3 200, 6001 Forest Park Rd

department: Cancer Center

institute: Ut Southwestern Medical Center

description: LNA™-enhanced   Tm-normalized capture probes


title: miRCURY LNA microRNA Array, 7th gen - hsa, mmu & rno v1


title: Illumina HiSeq 2000 (Salicornia europaea)

status: Public on Oct 20 2014

organism: Salicornia europaea


title: CUST-6x5K-RumenBactArray

city: Columbus

first: Amlan

middle: Kumar

last: Patra

state: OHIO

address: 2029 Fyffe Road

department: Animal Science

institute: The Ohio State University

organism: bovine gut metagenome

description: The RumenBactArray probes were designed from the 16S rRNA sequences of cultured and uncultured rumen bacteria

manufacture_protocol: Probes were synthesized onto a 6 × 5K custom oligonucleotide microarray by MYcroarray (Ann Arbor, MI), with each probe epresented in triplicates. For more information, refer to manufacturer's web site


title: Illumina HiSeq 2000 (Hippophae rhamnoides)

organism: Hippophae rhamnoides


title: Human Apoptosis miScript miRNA PCR Array

status: Public on Oct 21 2014

city: Houston

first: Peijing

last: zhang

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

organism: Homo sapiens

description:
PCR assay
SABiosciences RT² Profiler panel of PCR assays.


title: Microarrays Inc. Human MI ReadyArray – 49K Genomic Array (HS1100) [HEEBO]

city: Göttingen

first: Silvia

last: von der Heyde

address: Humboldtalle 32

department: Medical Statistics

institute: University Medical Center Göttingen

manufacture_protocol: see manufacturer's web site


title: Illumina HiSeq 2000 (Drosophila erecta)

last: GEO

organism: Drosophila erecta


title: Custom-made human 18K cDNA microarrays (Operon v2.0)

city: Groningen

first: Jourik

middle: A

last: Gietema

address: Hanzeplein 1

department: Medical Oncology

institute: UMCG

manufacture_protocol: Operon v2.0 (Human Genome Oligo Set V2)


title: [hGlue_3_0_v1] Affymetrix Human hGlue_3_0_v1 Array

city: TaiYuan

first: Zhifen

last: Liu

state: Shanxi

address: 85 Jiefang South Road

department: Psychiatry

country: China

institute: 1st hospital of Shanxi Medical University

description: 34834 mRNAs and 39224 lncRNAs


title: Illumina HiSeq 2000 (Diabrotica virgifera virgifera)

status: Public on Oct 18 2014

organism: Diabrotica virgifera virgifera


title: Qiagen Mouse Cytokines and Chemokines RT2 profiler PCR array  (PAMM-150A)

city: Lexington

first: Phillip

middle: J

last: Bridges

state: KY

address: 206 WP Garrigus Building

department: Animal and Food Sciences

institute: University of Kentucky

organism: Mus musculus

description: PCR array


title: [HuGene10stv1_Hs_ENSG] Affymetrix GeneChip Human Gene 1.0 ST Array [Brainarray Version 12 CDF]

status: Public on Oct 17 2014

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH


title: Agilent-042675 Gallus gallus 8X60K gene expression array

city: Hyderabad

first: Tarun

middle: K

last: Bhattacharya

address: Rajendranagar

institute: Directorate of Poultry Research

organism: Gallus gallus

description: Custom Gene Expression Gallus gallus 8X60K (AMADID: 042675) designed by Genotypic Technology Private Limited.


title: Agilent-035925 microSOPHIA3.0 (4X44K)

city: Valencia

first: Francisco

last: Martinez

state: Valencia

address: Avenida Campanar 21

department: Unidad de Genetica

country: Spain

institute: Hospital Universitari i Politecnic La Fe

description: Probe Name Version


title: Autoantigen Microarray

first: yun

last: lian

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

technology: spotted peptide or protein

manufacturer: University of Texas Southwestern Medical Center

manufacture_protocol: see attached


title: NimbleGen Ashbya gossypii ATCC 10895 12x135K array [110216_Egossypii_TA_exp]

status: Public on Oct 16 2014

city: Braga

first: Tatiana

middle: Quinta

last: Aguiar

address: Campus de Gualtar

country: Portugal

institute: Centre of Biological Engineering of the Universisty of Minho

organism: Eremothecium gossypii ATCC 10895

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

Designname: 110216_Egossypii_TA_exp
DESIGN_ID: 548771

native array description file: 110216_Egossypii_TA_exp.ndf
native array description file: 110216_Egossypii_TA_exp.ngd

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


title: 12x135K Coprinopsis cinerea whole genome expression array

city: Shatin

first: Xuanjin

last: Cheng

address: Rm 386, Science Center South Block

department: School of Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

organism: Coprinopsis cinerea

description: Expression profiling by DNA microarray.

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


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

status: Public on Oct 15 2014

city: Cambridge

first: Kendell

last: Clement

state: MA

address: 7 Divinity Ave.

institute: Harvard University

technology: oligonucleotide beads

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_SYMBOL values in the ID column.


title: Phalanx Human OneArray (version 4.3)

city: Pomona

first: Maria

middle: P

last: Lambros

address: 309 E Second Street

department: Pharmaceutical Sciences

institute: Western Univ of Health Sci


title: NimblenGen ZM4 12*135K

status: Public on Oct 14 2014

city: chengdu

first: kun

state: sichuan

address: section 29，Wangjiang Rd.

department: College of Life Sciences

institute: Sichuan University

organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

description: The .ndf and .ngd files are linked below as supplementary files.

manufacture_protocol: CapitalBio Corporation (Beijing, China)


title: Agilent-021332 Rat_CpG_Island 2x105K Array [Feature Number Version]

city: Hachioji

first: Chiho

last: Yoshida

address: Takakura 9-1

institute: Agilent Technologies

organism: Rattus norvegicus

description:
Rat CpG Microarray. probes are collected from agilent hd-chip data base

Arrays of this design have barcodes that begin with 16021332 or 2521332.

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.

relation: Alternative to: GPL19297 (Probe Name Version)

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


title: LC Sciences MRA-1001-UNT_090814_miRHuman_20 (miRNA_ID version)

status: Public on Oct 10 2014

first: Christoph

last: Eicken

address: 2575 W. Bellfort

institute: LC Sciences, LLC

description:
Human miRNA microarray with 100% coverage of mature human miRNAs listed in miRBase version 13 plus additional custom sequences provided by the customer.
LC_MRA-1001-UNT_090814_miRHuman_20

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: Illumina Genome Analyzer II (Bursaphelenchus xylophilus)

organism: Bursaphelenchus xylophilus


title: Illumina HiSeq 2000 (Alternanthera philoxeroides)

organism: Alternanthera philoxeroides


title: NimbleGen C. elegans 72K Expression Array [080128_worm170_modENCODE_expr; gene-level]

status: Public on Oct 11 2014

city: Santa Cruz

first: Susan

last: Strome

state: CA

address: 1156 High St.

department: Molecular, Cell, and Developmental Biology

institute: UC Santa Cruz

organism: Caenorhabditis elegans

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

***A different  version of this platform the probe ID or SEQ_ID in the ID column is assigned accession number GPL8673 and GPL18856,respectively.

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


title: Illumina Genome Analyzer II (Nelumbo nucifera)

status: Public on Oct 09 2014

organism: Nelumbo nucifera


title: Illumina Genome Analyzer II (Cicer arietinum)

organism: Cicer arietinum


title: Illumina HiSeq 1500 (Eucalyptus grandis)

organism: Eucalyptus grandis


title: Illumina HiSeq 1500 (Eucalyptus grandis; Pisolithus microcarpus)

organism:
Eucalyptus grandis
Pisolithus microcarpus


title: Illumina HiSeq 2000 (Solanum lycopersicum x Solanum pimpinellifolium)


title: Illumina HiSeq 2000 (Alhagi sparsifolia)

status: Public on Oct 08 2014

organism: Alhagi sparsifolia


title: Illumina HiSeq 2000 (Anisodus acutangulus)

organism: Anisodus acutangulus


title: Illumina HiSeq 2000 (Oncorhynchus mykiss)

organism: Oncorhynchus mykiss


title: Illumina MiSeq (Mycobacterium tuberculosis)

status: Public on Oct 07 2014

organism: Mycobacterium tuberculosis


title: Cellvibrio japonicus custom NimbleGen Array

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

organism: Cellvibrio japonicus

description:
NimbleGen design name: Cellvibrio_japonicus_custom_NimbleGen_Array.  An expression design for 3710 genes from Cellvibrio japonicus with 24-mer probe pairs (PM/MM) per gene. Each probe is replicated 3 times. The design includes random GC and other control probes. The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features. The .ndf and .ngd files are linked below as supplementary files:
Cellvibrio_japonicus_Array.ndf
Cellvibrio_japonicus_Array.ngd

manufacture_protocol: High-density DNA array with custom probes for Cellvibrio japonicus


title: Illumina HiSeq 2000 (Vibrio cholerae)

status: Public on Oct 06 2014

organism: Vibrio cholerae


title: [HuGene-2_1-st] Affymetrix Human Gene 2.1 ST Array [HuGene21st_Hs_ENTREZG_16.0.0]

organism: Homo sapiens

manufacture_protocol: See manufacturer's web site


title: Agilent-045004 Sea Bass v3 with 300Techreps_3

status: Public on Oct 01 2014

city: Singapore

first: Junhui

last: Jiang

address: 1 Research Link National University of Singapore

institute: Temasek Life Sciences Laboratory

organism: Lates calcarifer

description:
Seabass_v3_with300Techreps_3
300 tech reps chosen from the 60K probe design and added in as a probe group (i.e. all probes for a sequence have the SAME probe ID)

Arrays of this design have barcodes that begin with 16045004 or 2545004.

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: Duke/RG_nonconsensus_v1

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

organism: synthetic construct

manufacture_protocol: In situ oligosynthesized array with proprietary synthetic sequences that target c-Myc/Max/Mad1 binding sites flanked by repetitive DNA elements


title: Illumina MiSeq (Zea mays)

last: GEO

organism: Zea mays


title: Illumina MiSeq (Plasmodium berghei)

organism: Plasmodium berghei


title: TUGRAZ miRNA array TUGRAZ-HSA_MMU_RNO-MRC23

status: Public on Jan 07 2014

city: Vienna

first: Matthias

last: Hackl

address: Leberstrasse 20

institute: TAmiRNA GmbH

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

manufacture_protocol: Epoxy-coated Nexterion glass slides were spotted using the miRBase version 16.0 locked nucleic acid (LNA) probe set consisting of 2367 probes against human, mouse and rate miRNAs in 8 replicates.


title: Illumina HiSeq 2500 (Oryza sativa)

organism: Oryza sativa


title: Bordetella pertussis Whole genome array

city: Lille

first: David

last: Hot

address: 1 rue du professeur Calmette

department: Center for Infection and Immunity of Lille

country: France

institute: Institut Pasteur de Lille

organism: Bordetella pertussis

manufacture_protocol: Long oligonucleotide probes were designed on the sequences of the 3554 open reading frames (all coding CDS except transposases of IS elements) of B. pertussis Tohama I genome using OligoArray v2.1 [1]. Oligonucleotides were synthesized by Sigma-Aldrich and spotted on duplicat on Nexterion AL slides (Schott Nexterion) in 1x SciSpot-AM buffer (Scienion) using a Q-Array II spotter (Genetix).


title: Illumina HiSeq 2000 (Botryllus schlosseri)

organism: Botryllus schlosseri


title: Illumina HiSeq 2000 (Klebsiella pneumoniae)

status: Public on Oct 03 2014

organism: Klebsiella pneumoniae


title: Agilent-036466 Bovine miRNA microarray (Release 17.0)

status: Public on Oct 02 2014

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Bos taurus


title: NimbleGen Pfalciparum 385k array v1.0 [2005-05-10_Plasmodium_3D7_WG_CGH]

city: Notre Dame

first: Michael

last: Ferdig

state: IN

address: 280 Galvin Life Science

department: Biological Sciences

institute: University of Notre Dame

organism: Plasmodium falciparum 3D7

description: Plasmodium falciparum 3D7 genome (Genome Build from 2005)

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


title: Legionella ITS oligonucleotide microarray

status: Public on Oct 04 2014

city: Tianjin

first: Boyang

last: Cao

address: #23 HongDa Street

institute: Nankai Univ

organism: Legionella

manufacture_protocol: The probes were dissolved in 50% dimethyl sulfoxide (DMSO) to a final concentration of 1 µg/µL and coated onto aldehyde group-modified glass slides (CapitalBio Corporation, Beijing, China) using SpotArray 72 (Perkin-Elmer Corporation, CA, USA). Each probe was spotted in triplicate. Coated slides were dried and stored at room temperature in the dark. Each glass slide contained eight individual arrays framed with an 8-sample cover slip containing individual reaction chambers.


title: Streptococcus mutans UA159 Agilent single-channel 15K genechip

city: Köln

first: Yulong

last: Niu

state: Nordrhein-Westfalen

address: Carl-von-Linne-Weg 10

department: Plant Microbe Interactions

institute: Max Planck Institute for Plant Breeding Research

organism: Streptococcus mutans UA159

description: The custom-commercial Agilent microarray covers 1998 S.mutans genes, and each genes are replicated by using 7 probes. This desigh also includes control probes.

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


title: MRA-1001B1 miR Human v18

city: Murcia

first: Salam

last: Salloum-Asfar

state: Murcia

address: Ronda Garay, s/n

institute: Centro Regional de Hemodonación, Universidad de Murcia

manufacture_protocol: see manufacturer's webiste


title: MRA-1001B1 miR Human v19


title: Illumina MiSeq (Plasmodium falciparum)

organism: Plasmodium falciparum


title: Agilent-041846 Streptococcus gordonii

city: Newcastle

first: Matthew

last: Bashton

address: Newcastle

country: United Kingdom

institute: Newcastle Univerity

organism: Streptococcus gordonii

description:
Streptococcus gordonii gene expression array.

Arrays of this design have barcodes that begin with 16041846 or 2541846.

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: Applied Biosystems Human Taqman MicroRNA Array v3.0

city: Rotterdam

first: Martin

middle: Anne

last: Rijlaarsdam

address: Wytemaweg 80

department: Pathology

institute: Erasmus MC

description: qRT-PCR TaqMan Low-Density Array (2 pools / plates: A and B). Each Pool targets 377 unique miRNAs and additional control targets and allows for profiling up to of 754  unique miRNAs across the two pools.

manufacturer: Thermo Fisher / Applied Biosystems / Life Technologies

manufacture_protocol: see manufacturer's website: http://www.lifetechnologies.com/order/catalog/product/4444913


title: NimbleGen Ferroglobus placidus strain DSM 10642 v1.0 (07/16/2014)

city: Amherst

first: Dawn

last: Holmes

state: Massachusetts

address: 639 N Pleasant St Morrill IVN 422C

department: Microbiology

institute: University of Massachusetts Amherst

organism: Ferroglobus placidus DSM 10642

description:
4-plex expression for Ferroglobus placidus strain DSM 10642; from http://genome.ornl.gov/microbiol/fpla, 15jan09 gene models; 2613 starting genes; 9 probes per target, 45-60mer probes, 2613 exemplars for 2613 genes, 3 copies of each probe on the array
091030_ZS_Fplacidus_expr.ndf
091030_ZS_Fplacidus_expr.ngd
091030_ZS_Fplacidus_expr_X4.ncd


title: Illumina MouseWG-6 v2.0 expression beadchip (unofficial custom annotation)

city: Natanya

first: Tal

middle: Haim

last: Hasson

address: Hatrufa 12

department: Analytical R&D

country: Israel

institute: Teva Pharmaceuticals

organism: Mus musculus

description: This is an alternate annotation for the GPL6887 array that includes all probesets including those that are unmapped. Unmapped probesets (probesets that do not start with ILMN_) are annotated with their array address ID where noted (SPOTID column)

manufacture_protocol: see manufacturer's website


title: Applied Biosystems Taqman Low Density Array Human microRNA Card A+B Set v3.0

status: Public on Aug 01 2014

city: Bethesda

state: MD

organism: Homo sapiens

description: PCR assay: Human Array MicroRNA Cards A+B v3.0


title: [Axiom_Maize600] Affymetrix Axiom® Maize Genotyping Array

status: Public on Jun 11 2014

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

description:
The Axiom® Maize Genotyping Array interrogates 616,201 polymorphic variants (609,442 SNPs and 6,759 indels) to represent the global diversity in the maize genome. Development of the array is described in the following publication:
Unterseer S, Bauer E, Haberer G, Seidel M, Knaak C, Ouzunova M, Meitinger T, Strom TM, Fries R, Pausch H, Bertani C, Davassi A, Mayer KFX, Schön C-C (2014) A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array. BMC Genomics 15:823, PMID: 25266061
The array was designed by the AgroClustER Synbreed (funded by the German Ministry of Education and Research, BMBF) through a collaboration led by Prof. Dr. Chris-Carolin Schön, Dr. Eva Bauer, and Sandra Unterseer (Technische Universität München, Germany), and Dr. Georg Haberer and Michael Seidel (Helmholtz Zentrum München, Germany) through Affymetrix® Expert Design Program.

first: Eva

last: Bauer

first: Sandra

last: Unterseer

first: Georg

last: Haberer

last: Seidel

first: Carsten

last: Knaak

first: Milena

last: Ouzunova

first: Thomas

last: Meitinger

first: Tim

last: Strom

first: Ruedi

last: Fries

first: Hubert

last: Pausch

first: Christofer

last: Bertani

first: Alessandro

last: Davassi

first: Klaus

middle: F

last: Mayer

first: Chris-Carolin

last: Schön

manufacture_protocol: see manufacturer's web site


title: [RaGene-2_0-st] Affymetrix Rat Gene 2.0 ST Array [probe set (exon) version]

status: Public on May 12 2014

organism: Rattus norvegicus

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

#%create_date=Thu Mar 28 15:51:14 2013 PDT
#%chip_type=RaGene-2_0-st-v1
#%lib_set_name=RaGene-2_0-st
#%lib_set_version=v1
#%genome-species=Rattus norvegicus
#%genome-version=rn4
#%genome-version-ucsc=rn4
#%genome-version-ncbi=Rnor3.4
#%genome-version-create_date=2004-11-00
#%genome-lifted_from-species=Rattus norvegicus
#%genome-lifted_from-version-ucsc=rn4
#%genome-lifted_from-version-ncbi=Rnor3.4
#%netaffx-annotation-date=2012-09-30
#%netaffx-annotation-netaffx-build=33


title: Illumina HiSeq 2000 (Polistes metricus)

last: GEO

organism: Polistes metricus


title: Leishmania donovani Gene Expression 8x15k Microarray - Genotypic Technology Private Limited (AMADID: 035638)

status: Public on Aug 05 2013

city: Guwahati

first: Vikash

last: Dubey

state: Assam

address: Room No. 102

department: Department of Biotechnology

institute: Indian Institute of Technology Guwahati

organism: Leishmania donovani

description: Organism: Leishmania donovani, Microarray GeneExpression 8x15k designed by Genotypic Technology Private Limited. (AMADID: 035638)

relation: Alternative to: GPL19308 (Probe Name Version)


title: Nimblegen Mouse HD2 whole genome

status: Public on Feb 04 2010

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

description:
NCBI 37
#native array description file = 080429_MM9_LP_Tiling_HX1.ndf

manufacture_protocol: see Nimblegen website


title: Agilent-038112 mouse miRNA microarray, Release 18.0 (Feature Number version)

status: Public on Mar 03 2013

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Arrays of this design have barcodes that begin with 16038112 or 2538112.

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: STv7bE_MMCC

status: Public on Aug 04 2007

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

organism: Salmonella enterica

first: Steffen

last: Porwollik

first: Pui

last: Cheng

manufacture_protocol: custom made Salmonella PCR product array


title: [Mm_PromPR] Affymetrix Mouse Promoter 1.0R Array

status: Public on Sep 06 2007

last: Affymetrix

description:
The GeneChip® Mouse Promoter 1.0R Array is designed for chromatin immunoprecipitation (ChIP) experiments. The Mouse Promoter 1.0R Array is a single array comprised of over 4.6 million probes tiled to interrogate over 28,000 mouse promoter regions. Sequences used in the design of the Mouse Promoter 1.0R Array were selected from NCBI mouse genome assembly (version 33). Repetitive elements were removed by RepeatMasker. Promoter regions were selected using sequence information from:

33,559 ENSEMBL genes (version 30_33f March 23, 2005)
18,167 RefSeq mRNAs (NCBI GenBank® April 7, 2005)
27,707 complete-CDS mRNAs (NCBI GenBank® April 7, 2005)

The sequences selected for the Mouse Promoter 1.0R Array are a subset of the content used in the whole-genome ChIP array set, the Mouse Tiling 2.0R Array Set.

Probes are tiled at an average resolution of 35 base pairs, as measured from the central position of adjacent 25-mer oligos, leaving a gap of approximately 10 base pairs between probes. Each promoter region covers approximately 6 kb upstream through 2.5 kb downstream of 5' transcription start sites.

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


title: Agilent-029297 Human miRNA Microarray (Feature Number version)

status: Public on Nov 30 2011

relation:
Alternative to: GPL10656
Alternative to: GPL16298
Alternative to: GPL19263

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


title: Illumina HumanOmniExpressFFPE-12 BeadChip

city: East Melbourne

first: Dariush

last: Etemadmoghadam

address: St Andrew's Place

country: Australia

institute: Peter MacCallum Cancer Centre

description: Annotations based on hg19.

manufacture_protocol: See manufacturer's website


title: Agilent-031189 Unrestricted_Rat_miRNA_v16.0_Microarray (miRNA ID version)

status: Public on Nov 08 2011

description: Rat miRNAs miRBase Release 16.0.

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


title: [Flavus_22683_AFLAVUSa520391F] NCSU Payne_Aspergillus Array

status: Public on Mar 11 2010

city: Raleigh

first: David

middle: Ryan

last: Georgianna

address: 851 Main Campus Dr

department: Plant Pathology

institute: North Carolina State University

organism:
Zea mays
Aspergillus flavus
Aspergillus oryzae

first: Gary

last: Payne

first: Charles

last: Woloshuk

first: Nancy

last: Keller

first: Juijang

last: Yu

manufacture_protocol: Standard Affymetrix protocols were followed and can be found at http://www.affymetrix.com/support/technical/manual/technical_manual.afx


title: Illumina HiSeq 2000 (Oryza sativa)

status: Public on Feb 11 2011

organism: Oryza sativa