title: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [custom CDF: hugene10stv1_75_030.cdf]

status: Public on Feb 28 2017

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

organism: Homo sapiens

technology: in situ oligonucleotide

description:
Probe set data extracted from custom CDF:
hugene10stv1_75_030.cdf

For transcript probe set definition a custom CDF package was used, that was based on a complete re-alignment of the Exon microarray oligo-probes and annotation to Ensembl version 75.

distribution: custom-commercial

manufacture_protocol: see manufacturer's web site


title: Illumina NextSeq 500 (Anaeromyces sp. KS-2015)

last: GEO

country: USA

organism: Anaeromyces robustus

technology: high-throughput sequencing

distribution: virtual


title: Qiagen apoptosus RT-PCR array - mouse antigen specific T cells

city: San Frnacisco

first: Chien-Chun

middle: Steven

last: Pai

state: CA

address: 513 Parnassus Ave

department: Hematology Oncology

institute: UCSF

organism: Mus musculus

technology: RT-PCR

description: RT2 Profiler PCR Arrays

manufacture_protocol: see manufacturer's website


title: Illumina NextSeq 500 (Neocallimastix sp. KS-2015)

organism: Neocallimastix californiae


title: Illumina HiSeq 2500 (Bombyx mori)

organism: Bombyx mori


title: Illumina HiSeq 2500 (Duddingtonia flagrans)

organism: Arthrobotrys flagrans


title: Illumina Genome Analyzer II (Steatoda grossa)

status: Public on Feb 24 2017

organism: Steatoda grossa


title: Illumina HiScanSQ (Vitis riparia)

status: Public on Feb 27 2017

organism: Vitis riparia


title: Illumina Illumina HumanCore-12v1-0-B BeadChip

city: Barcelona

first: Luis Alberto

middle: Perez

last: Jurado

state: Barcelona

address: Doctor Aiguader, 88 (PRBB)

department: Department of Experimental and Health Sciences

country: Spain

institute: Universitat Pompeu Fabra

technology: oligonucleotide beads

manufacture_protocol: See manufacturer's website


title: Agilent-033229 Streptococcus mutans whole-genome 15k array (Probe name version)

city: Guangzhou

first: Jia

last: Liu

state: Guangzhou

address: 74 Zhong Shan Er Road,

country: China

institute: Sun Yat Sen University

organism: Streptococcus mutans

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


title: Illumina Genome Analyzer (Latrodectus hesperus)

organism: Latrodectus hesperus


title: Illumina HiSeq 2000 (Steatoda grossa)


title: Bluegnome Human CytoChip ArrayCGH v2

status: Public on Feb 25 2017

city: Aarhus

first: Jian

last: Li

address: The Bartholin Building

department: Institute of Biomedicine

country: Denmark

institute: Aarhus University

technology: spotted DNA/cDNA


title: Illumina Genome Analyzer II (Latrodectus hesperus)


title: Illumina Hiseq 1500 (Homo sapiens)


title: Illumina Hiseq 1500 (Homo sapiens; Leishmania donovani)

organism:
Leishmania donovani
Homo sapiens


title: Illumina HiSeq 2000 (Latrodectus geometricus)

organism: Latrodectus geometricus


title: Illumina Genome Analyzer II (Latrodectus geometricus)


title: Illumina HiSeq 2000 (Latrodectus hesperus)


title: Illumina Hiseq 1500 (Leishmania donovani)

organism: Leishmania donovani


title: [MoGene-2_1-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: MoGene21stv1_Mm_ENTREZG_17.0.0]

status: Public on Feb 22 2017

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

manufacture_protocol: This is identical to GPL17400 but a custom cdf environment was used to extract data. The cdf can be found at the link below.


title: Illumina HiSeq 2000 (Frankia sp. CcI6)

organism: Frankia sp. CcI6


title: nCounter Mouse Inflammation gene expression assay

city: Tianjin

first: Fu-Dong

last: Shi

address: 154 Anshan Rd.

institute: Tianjin Medical University General Hospital

technology: other

distribution: commercial

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


title: Agilent-062763 Swine microarray 026440

status: Public on Feb 23 2017

city: Pulawy

first: Magdalena

last: Materniak-Kornas

address: Partyzantow 57

department: Biochemistry

country: Poland

institute: National Veterinary Research Institute

organism: Sus scrofa

description:
4x44K 026440

Arrays of this design have barcodes that begin with 16062763 or 2562763.

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 (Escherichia coli; Pseudomonas putida)

organism:
Pseudomonas putida
Escherichia coli


title: Illumina HiSeq 2000 (Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759)


title: [Mouse4302_Mm_EntrezG] Affymetrix GeneChip Mouse Genome 430 2.0 Array [Mouse4302_Mm_ENTREZG_21.0.0]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

relation: Alternative to: GPL1261 (alternative CDF [official])

manufacture_protocol: This is identical to GPL1261 but a custom CDF environment was used to extract data. [Brainarray Version 21, Mouse4302_Mm_ENTREZG_21.0.0].


title: SOMAscan human proteomic assay [SOMAscan Assay 1.3k]

status: Public on Aug 03 2017

city: Worcester

first: Dr Yvonne

last: Edwards

state: MA

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

technology: spotted peptide or protein


title: Illumina HiSeq 2000 (Cryptococcus amylolentus)

status: Public on Feb 21 2017

organism: Cryptococcus amylolentus


title: Illumina HiSeq 2500 (Ciona intestinalis)

organism: Ciona intestinalis


title: Illumina NextSeq 500 (Drosophila melanogaster; Drosophila virilis)

status: Public on Feb 17 2017

organism:
Drosophila melanogaster
Drosophila virilis


title: AB 5500xl Genetic Analyzer (Helicobacter pylori J99)

status: Public on Feb 16 2017

organism: Helicobacter pylori J99


title: Illumina NextSeq 500 (Bacillus subtilis PY79)

organism: Bacillus subtilis PY79


title: Illumina HiSeq 2500 (Ganoderma lucidum G.260125-1)

organism: Ganoderma lucidum G.260125-1


title: Illumina NextSeq 500 (Plasmodium berghei)

organism: Plasmodium berghei


title: 20060419MD_PMC

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

organism:
Saccharomyces bayanus
Saccharomyces cerevisiae

technology: spotted oligonucleotide

description: Dunham project-SCSB-1-print 3, a multi-organism print.   Printed in orange packing mode #3. Gal file must be ammended post download. Slides need to be crosslinked at ~70 mJ before use.

distribution: non-commercial

manufacturer: Lewis-Sigler Institute Microarray Facility

manufacture_protocol:
The following parameters were used to manufacture the printed array named "20060419MD_PMC"
Printer: Arrayer 250A
Array Configuration: (columns X rows) 48 sectors ( 4 X 12 spotted) Standard 48 tip
Spot Columns per Sector: 24
Spot Rows per Sector: 22
Column Spacing: 184
Row Spacing: 155
Plate Orientation: rotated 90 degrees clockwise (P1 top-left, A1 top-right)
Printhead Dip Dynamics: top to bottom, right to left
Sector Spotting Dynamics: left to right, top to bottom
Number of Slides: 240
Plates used in this print, in order.
PLATEID PLATENAME PLATE_VISITS IS_FLIPPED
100514 HYBRIDSC_2
100517 HYBRIDSC_5
100525 HYBRIDSC_13
100515 HYBRIDSC_3
100528 HYBRIDSC_16
100523 HYBRIDSC_11
100521 HYBRIDSC_9
100519 HYBRIDSC_7
100524 HYBRIDSC_12
100527 HYBRIDSC_15
100520 HYBRIDSC_8
100516 HYBRIDSC_4
100522 HYBRIDSC_10
100513 HYBRIDSC_1
100526 HYBRIDSC_14
100518 HYBRIDSC_6
100529 HYBRIDSC_17
100504 HYBRIDSB_5
100512 HYBRIDSB_13
100506 HYBRIDSB_7
100510 HYBRIDSB_11
100502 HYBRIDSB_3
100509 HYBRIDSB_10
100501 HYBRIDSB_2
100503 HYBRIDSB_4
100507 HYBRIDSB_8
100511 HYBRIDSB_12
100500 HYBRIDSB_1
100508 HYBRIDSB_9
100505 HYBRIDSB_6
37369 EMPTY_SC_1
37369 EMPTY_SC_1
37369 EMPTY_SC_1
37369 EMPTY_SC_1
37369 EMPTY_SC_1
37369 EMPTY_SC_1
100520 HYBRIDSC_8  1
100527 HYBRIDSC_15  1
100524 HYBRIDSC_12  1
100521 HYBRIDSC_9  1
100519 HYBRIDSC_7  1
100523 HYBRIDSC_11  1
100517 HYBRIDSC_5  1
100528 HYBRIDSC_16  1
100525 HYBRIDSC_13  1
100515 HYBRIDSC_3  1
100514 HYBRIDSC_2  1
100529 HYBRIDSC_17  1
100518 HYBRIDSC_6  1
100526 HYBRIDSC_14  1
100522 HYBRIDSC_10  1
100513 HYBRIDSC_1  1
100516 HYBRIDSC_4  1
100508 HYBRIDSB_9  1
100500 HYBRIDSB_1  1
100501 HYBRIDSB_2  1
100505 HYBRIDSB_6  1
100507 HYBRIDSB_8  1
100511 HYBRIDSB_12  1
100509 HYBRIDSB_10  1
100502 HYBRIDSB_3  1
100510 HYBRIDSB_11  1
100503 HYBRIDSB_4  1
100506 HYBRIDSB_7  1
100504 HYBRIDSB_5  1
100512 HYBRIDSB_13  1


title: Brachypodium distachyon BdPP2C genes using Bio-Rad CFX 96 M02 assay panel

status: Public on Feb 14 2017

city: Shanghai

first: Zhaoqing

last: Chu

address: 3888 Chenhua Road, Songjiang

institute: Shanghai Chenshan Plant Science Research Center, CAS

organism: Brachypodium distachyon

description: PCR assay


title: Enterococcus feacalis V583 genomic DNA array

city: Houston

first: Peng

last: Gao

state: Texas

address: SRB 301V, 1825 Pressler Street

department: IMM

institute: UTHealth

organism: Enterococcus faecalis

manufacture_protocol: in house


title: Illumina HiSeq 2000 (Apalone spinifera)

organism: Apalone spinifera


title: Agilent-026619 Human ncRNA + mRNA array (Probe name version)

status: Public on Feb 15 2017

city: Changsha

first: Zheng

last: Zhou

address: Lushan Road (S), Yuelu District

institute: Hunan University

organism: Homo sapiens

description: Grid_GenomicBuild = hg19:GRCh37:Feb2009


title: Illumina HiSeq 2000 (Chrysemys picta)

organism: Chrysemys picta


title: CapitalBioMiamiOtoArray Human Microarray

city: Miami

first: Denise

last: Yan

state: FL

address: 1601 NW 12th Ave

department: Otolaryngology

institute: University of Miami

description: The microarray is composed of a fluidic manifold made of polycarbonate glued on the glass slide to introduce a dynamic hybridization for signal enhancement and acceleration of reaction kinetics. The tag probes contain a poly (dT) spacer and a 5' amino group, are diluted in 50% dimethyl sulfoxide (DMSO) to a final concentration of 15 micromole and are spotted with a SmartArrayer 136 spotter (CapitalBio) on the aldehyde-functionalized glass slides. Each tag probe is spotted in triplicate. The diameter of each spot is approximately 150 micrometers.


title: Illumina NextSeq 500 (Homo sapiens; synthetic construct)

status: Public on Feb 10 2017

organism:
Homo sapiens
synthetic construct


title: Source Precision Medicine RT-PCR assay

city: Cambridge

first: Karl

middle: George

last: Wassmann

address: 245 First Street Suite 1800-109

institute: CheckPoint Sciences Inc.

description:
PCR assay
Panel of 169 genes associated with inflammation, immunity, the CTLA4 pathway, oncogenes, and melanoma-specific genes used for exploratory purposes

manufacture_protocol:
see published patent application US20110070582 A1 titled Gene Expression Profiling for Predicting the Response to Immunotherapy and/or the Survivability of Melanoma Subjects
exploratory PCR Assay not commercially available


title: Illumina MiSeq (Escherichia coli O157:H7 str. EDL933)

organism: Escherichia coli O157:H7 str. EDL933


title: USaar_Human_1827_v1 protein macroarray

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

country: Germany

institute: Saarland University

description: spotted bacterial expression clone of human cDNA library

manufacturer: RZPD Deutsches Resourcenzentrum (now Source Bioscience)

manufacture_protocol: Customized subarray of 1827 selected E.coli cDNA clones of hex1 library were manufactured as described in Buessow et al., 1998 (PMID:9776767). Clones were spotted in duplicates.


title: Illumina Genome Analyzer IIx (Aspergillus nidulans)

status: Public on Feb 09 2017

last: GEO

organism: Aspergillus nidulans


title: Agilent-27061/Klug lab - Rhodobacter sphaeroides - 15k array Version 2 (144 sRNA) (condensed Probe Identifier version)

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

organism: Cereibacter sphaeroides 2.4.1

description:
Spotted 60 nt oligonucleotide

The microarray contains probes against 4,304 protein-coding genes, 79 rRNA and tRNA genes, and 144 intergenic regions. Three antisense probes with a length of 60 nt were designed for each gene or intergenic region, when possible.

manufacture_protocol: Microarray construction was performed following the instructions of Agilent (www.chem.agilent.com).


title: NimbleGen Daphnia pulex Expression Array 12x135k (PROBE DESIGN ID)

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

organism: Daphnia pulex

description: This is a custom design whole Daphnia genome expression array in 12-plex format manufactured by Roche Nimblegen. Genes based on Daphnia pulex annotated draft genome assembly GenBank accession number: ACJG00000000.

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


title: Illumina HiSeq 2000 (Pycnoporus coccineus)

organism: Trametes coccinea


title: Illumina HiScanSQ (Aspergillus fumigatus)

status: Public on Feb 13 2017

organism: Aspergillus fumigatus


title: University of Arizona Sus scrofa 27.5 K oligo array

city: Berlin

first: Soroush

last: Sharbati

address: Oertzenweg 19b

department: Institute of Veterinary Biochemistry

institute: Freie Universitaet Berlin

organism: Sus scrofa

manufacture_protocol: Information available at http://www.pigoligoarray.org


title: Agilent-059631 BJR_2013_Pa_Pc [Feature Number version]

city: Pretoria

first: Bianca

last: Reeksting

address: 117 Lunnon Road

department: Department of Genetics

country: South Africa

institute: University of Pretoria

organism: Persea americana

description:
Arrays of this design have barcodes that begin with 16059631 or 2559631.

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: Brachypodium distachyon BdbZIP genes using Bio-Rad CFX 96 M02 assay panel

description: PCR assay


title: HiSeq X Ten (Macaca fascicularis)

organism: Macaca fascicularis


title: Illumina HiSeq 2500 (Oreochromis niloticus)

organism: Oreochromis niloticus


title: Illumina HiSeq 1500 (Homo sapiens; Mus musculus)

organism:
Homo sapiens
Mus musculus


title: Breast cancer tissue array

city: Chongqing

first: jianjun

last: li

address: No. 29, Gaotanyan Street, Shapingba District

institute: Department of Oncology, Southwest Hospital

technology: tissue

description:
Tumor specimens from patients diagnosed with primary  breast carcinoma were collected at the time of surgery between 2004 and 2010 from the Southwest hospital in Chongqing, China. None of the patients had received neoadjuvant therapy. The non clinical stage cases and lost cases were removed. Tumor specimens were processed within 30 min after surgery. On average, 5um-thick sections were prepared. All samples from patients were reviewed histologically by hematoxylin and eosin staining, and used to construct the tissue microarray (TMA) slides.
Collaboration with Shanghai Biochip Company Ltd, Shanghai, China


title: Agilent-062716 OE Rat lncRNA Microarray v2.0 028279 (Probe Name version)

city: SuZhou

first: Yanhong

last: Li

address: Jingde road 303

department: Department of nephrology, Institute of pediatric research

institute: Children’s Hospital affiliated to Soochow University

organism: Rattus norvegicus

description: Arrays of this design have barcodes that begin with 16062716 or 2562716.

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


title: NimbleGen Human 2.1M array v1.0 [110201_HG19_KB_ChIP_HX1]

city: Baltimore

first: John

middle: G

last: Zampella

address: 733 N Broadway

department: Dermatology

institute: Johns Hopkins University School of Medicine

description:
Annotations are based on the Hg19 build of the human genome
genomic tiled micro-array was tiled with known cancer genes +10kb of the flanking regions
DESIGN_ID: 548081
Design name:110201_HG19_KB_ChIP_HX1
native array description file: 110201_HG19_KB_ChIP_HX1.ndf
native array description file: 110201_HG19_KB_ChIP_HX1.pos

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


title: Strawberry 3264 cDNA microarray

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

institute: IBMCP

organism: Fragaria x ananassa

manufacture_protocol:
1. purified PCR products are arranged in 384-well falt-bottom plates at 400 ng/uL on 50% DMSO spotting buffer
2. Slides are printed using a Microgid II arrayer from Molecular Devices. AminoSilane Coated Slides from Corning are used.
3. Slides are crosslinked at 300 mJ and kept dry until use in a dessicator.


title: AB SOLiD 4 System (Trypanosoma cruzi)

organism: Trypanosoma cruzi


title: Illumina HiSeq 4000 (Felis catus)

organism: Felis catus


title: illumina Genome Analyzer IIx (Homo sapiens)

organism: Homo sapiens


title: NanoString nCounter Mouse miRNA Expression Assay

status: Public on Feb 11 2017

city: New York

first: Stefanie

last: Wohl

state: NY

address: 33w 42nd Street

department: Biological and Vision Sciences

institute: SUNY Optometry

organism: Mus musculus

description:
Mm v1.5 miRNA Assay Kit 12 rxn GXA-MMIR15-12
The miRBase version represented in NanoString panel v1.5 is miRBase 21.
digital color-coded barcode technology, insitu-nucleotide


title: Illumina HiSeq 2500 (Sulfolobus acidocaldarius)

organism: Sulfolobus acidocaldarius


title: Brachypodium distachyon MAPK genes using Bio-Rad CFX 96 M02 assay panel

organism: Brachypodium distachyon

description: PCR assay


title: RMIT University Strawberry-specific Array

city: Bundoora

first: Mian-Chee

last: Gor

state: Victoria

address: Plenty Road

department: School of Applied Sciences

country: Australia

institute: RMIT University

manufacturer: Mian Chee Gor/Nitin Mantri/Edwin Pang, RMIT University

manufacture_protocol: In order to develop genomic DNA representation for the subtraction, DNA from five strawberry genotypes (Albion, Juliette, 07-102-41, 07-095-35, 04-069-91) and nine non-angiosperm species (Dryopteris kuratae, Dicksonia antarctica, Asplenium australasicum, Blechnum tabulare, Wollemia nobilis, Cupressus macrocarpa, Juniperus communis, Cycas revoluta and Ginkgo biloba) were sourced. gDNA was extracted using Qiagen DNeasy Plant Mini Kit (Qiagen, Valencia, CA). Prior to subtraction, genomic representations were prepared by pooling equal amount of DNA extracted from five strawberry genotypes and nine non-angiosperm species into tester and driver pools, respectively to a final amount of 4 µg. The pooled DNA samples were then fragmented overnight with 15 units of AluI and HaeIII restriction enzymes (NEB, Ipswich, MA) in 100 µL of digestion mixture. The subsequent gDNA subtraction was performed using the PCR-SelectTM cDNA Subtraction kit (Clontech, Mountain View, CA) based on Suppression Subtractive Hybridization (SSH) method with a few modifications as described in Olarte et al. (2013). Briefly, the digested tester pool was purified with phenol/chloroform extraction, divided into two portions and ligated with Adaptor 1 and Adaptor 2R, respectively. The ligated products were then subjected to two rounds of tester-driver hybridisation. To perform the hybridisation step, excess driver was added to obtain a tester to driver ratio of 1:60. In addition, the spike-in control was removed by adding approximately 20.4 ng of human skeletal muscle cDNA into the driver pool. Finally, subtracted DNA fragments (specific to strawberry) present in the tester but absent in the driver were selectively amplified by Suppression PCR and further enriched with nested PCR as described in the user manual. The nested PCR products were cloned into pGEM®-T Easy vector and transformed into E. coli JM109 competent cells (Promega, San Luis Obispo, CA) according to the manufacturer’s instructions. For microarray construction, 331 white colonies were randomly amplified using Nested Primer 1 and Nested Primer 2R provided in the PCR-SelectTM cDNA Subtraction kit. The PCR products of 290 strawberry-specific clones ranging from 200 - 1,000 bp were precipitated overnight by adding 0.1 volume of 3M sodium acetate (pH 5.2) and 2 volumes of absolute ethanol. The resulting pellets after centrifugation were washed in 70 % ethanol, air dried and resuspended in 15 µL of 50 % DMSO printing buffer. DNA concentration of each PCR product was normalised to 250 ng/µL. Together with nine negative controls (50% DMSO, Nested Primer 1, Nested Primer 2R, and AluI and HaeIII digested pGEMT-Easy vector), six positive controls (beta-actin, pectate lyase B, alcohol acyltransferase, alcohol dehydrogenase, sesquiterpene synthase and the subtracted PCR product), two printing controls (Cy-3 and Cy-5) and one spike-in controls (aromatase gene derived from the ovary tissue of Murray River Rainbowfish), 10 µL of each strawberry-specific clone was arrayed onto Corning® GAPSTM II coated slides (Corning Incorporated, NY, USA) using a BioRobotics® MicroGrid II Compact array printing robot (Genomics Solutions, Ann Arbor, MI) at RMIT University, resulting in a 308-feature strawberry-specific SDA. Each slide contained two subarrays comprising of six technical replicates, where each technical replicate consisted of 308 samples.


title: Illumina HiSeq 2000 (Chlamydia pneumoniae)

status: Public on Feb 08 2017

organism: Chlamydia pneumoniae


title: Agilent-077173 Bovine miRNA ver.21 60k [Gene name version]

city: Tsukuba

first: Susumu

last: Muroya

state: Ibaraki

address: Ikenodai 2

department: Animal Products Research Division

country: Japan

institute: NARO Institute of Livestock and Grassland Science

organism: Bos taurus

description:
Arrays of this design have barcodes that begin with 16077173 or 2577173.

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.


title: [RG_U34A] Affymetrix Rat Genome U34 Array

status: Public on Mar 11 2002

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

June 03, 2009: annotation table updated with netaffx build 28
June 08, 2012: annotation table updated with netaffx build 32
June 27, 2016: annotation table updated with netaffx build 35

relation: Alternative to: GPL13653 (Alternative CDF)

manufacture_protocol:
see manufacturer's web site

The RG-U34 set includes 3 arrays with a total of 26379 entries and was indexed 29-Jan-2002.
The set includes ~7,000 known genes and >17,000 EST clusters.
The A array contains probes derived from all full-length or annotated genes as well as thousands of EST clusters.
The B and C arrays contain only EST clusters.


title: Oyster Mushroom Custom Microarray

city: Kami-ina

first: Masanobu

last: Kojima

state: Nagano

address: 8304 Minami-minowa

department: Bioscience and Biotechnology

institute: Shinshu University

organism: Pleurotus ostreatus


title: Agilent-034141 Neisseria gonorrhoeae Genotypic_EA500_N_gonorrhoeae_8x15k_GE 023571

city: Warsaw

first: Monika

middle: Julita

last: Adamczyk-Poplawska

address: Miecznikowa 1

institute: University of Warsaw

organism: Neisseria gonorrhoeae

description:
neisseria gonorrhoeae genome

Arrays of this design have barcodes that begin with 16034141 or 2534141.

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: Exiqon miRCURY LNA microRNA array, 6th generation [miRBase v17, condensed Probe_ID version]

city: Hangzhou

first: Ting

middle: ting

last: Sun

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Neuroscience and Anatomy

institute: Zhejiang University School of Medicine

description:
Supplier=Exiqon A/S
ProductDate=November 2010
ProductNumber=208400,208401,208402
LotNumberRange=34101-34101
URL=http://www.exiqon.com/SEEEMS/26.asp
Organism(s)=Mus musculus, Mouse cytomegalovirus, Mouse gammaherpesvirus
GalFileCreationDate=2011-07-29 16:34
ArrayContents_DesignedFor=miRBase 16.0
ArrayContents_CurrentNameColumn=miRBase 17.0
ArrayContents_CurrentNameColumnCoverage=Mus musculus and related vira:94.26%


title: miRCURY LNA microRNA Array,6th generation -hsa,mmu & rno [miRbase Release 16.0]

city: Tangshan

first: Yuntao

last: Zhou

state: Hebei

address: Wenhua Road, No.27

department: Clinical Laboratory Center

institute: Tangshan Gongren Hospital

manufacture_protocol: See manufacturers website (www.exiqon.com)


title: Illumina HiSeq 2500 (Enterococcus faecium Aus0004)

status: Public on Feb 03 2017

last: GEO

organism: Enterococcus faecium Aus0004


title: Illumina HiSeq 1000 (Lobosphaera incisa)

organism: Lobosphaera incisa


title: [TomGene-1_1-st] Affymetrix Tomato Genome Array

city: Chania

first: Panagiotis

last: Kalaitzis

address: Alsyllio Agrokepio, 1 Makedonias str

department: Horticultural Genetics and Biotechnology

country: Greece

institute: Mediterranean Agronomic Institute of Chania (MAICh)

organism: Solanum lycopersicum

description:
#%create_date=Mon Aug  5 12:39:13 PDT 2013
#%chip_type=TomGene-1_1-st
#%lib_set_name=TomGene-1_1-st
#%lib_set_version=r4
#%genome-species=Solanum lycopersicum
#%genome-version=SL2_40
#%genome-version-create_date=2011_04_06
#%annotation-version=design-time
## probeset_id refers to the transcript cluster id

manufacture_protocol: see manufacturer's web site


title: Illumina MiSeq (Paulownia elongata)

organism: Paulownia elongata


title: Illumina MiSeq (Candida albicans)

status: Public on Feb 07 2017

organism: Candida albicans


title: Illumina NextSeq 500 (Oryzias latipes)

organism: Oryzias latipes


title: [MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [AltAnalyze probeset-to-Ensembl mapping]

status: Public on Feb 02 2017

city: Glasgow

first: Torsten

last: Stein

address: College of MVLS

department: School of Medicine

country: United Kingdom

institute: University of Glasgow

description: Ensembl build: EnsMart72


title: Nitric Oxide Signaling Pathway PCR Array

status: Public on Feb 01 2017

city: san diego

first: mario

last: chojkier

state: ca

address: 3350 la jolla village drive

department: Medicine

institute: UCSD

description: SABiosciences RT² Profiler panel of PCR assays.

manufacture_protocol: see manufacturer's website


title: PacBio RS II (Tetrahymena thermophila)

organism: Tetrahymena thermophila


title: Pitt BC1 C1343 Five Gene Expression Panel Custom Codeset

city: Pittsburgh

first: Rekha

last: Gyanchandani

state: PA

address: 204 Craft Avenue

department: Pharmacology & Chemical Biology

institute: University of Pittsburgh

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


title: Illumina HiSeq 2000 (Cercospora zeina; Zea mays)

organism:
Zea mays
Cercospora zeina


title: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110)

status: Public on Feb 06 2017


title: Illumina NextSeq 500 (Didelphis virginiana)

organism: Didelphis virginiana


title: Agilent-084536 0GyLa G4125A CGH array [Feature Number version]

status: Public on Jul 27 2016

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

institute: Institute for Environmental Science

description:
Agilent-084536 0GyLa  G4125A

Arrays of this design have barcodes that begin with 16084536 or 2584536

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 2500 (Meriones unguiculatus)

organism: Meriones unguiculatus


title: Roche-NimbleGen-Slide-512049-A02

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University

organism: Haloferax volcanii

description:
NimbleGen design name Slide-5120049-A02. NimbleGen design ID 512049, 12 x 135k arrays per slide. Gene expression design for 3,982 genes from Haloferax volcanii DS2 with 8 unique 60-mer probes per gene.  Each probe is replicated 4 times per array.  The design includes several types of control probes, including crosshybridization, random GC, synthesis, grid alignment, etc.
native array description file: 100916_Hvol_TP_exp.ndf
native array description file: 100916_Hvol_TP_exp.ngd


title: Illumina HiSeq 2000 (Sclerotinia sclerotiorum)

organism: Sclerotinia sclerotiorum


title: 3D-Gene Rat miRNA V21_1.0.0

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

organism: Rattus norvegicus

description: Based on miRBase release 21.

manufacture_protocol: See manufacturer's web site.


title: Illumina HiSeq 3000 (Margaritifera margaritifera)

organism: Pinctada margaritifera


title: Exiqon miRCURY LNA microRNA Array, 7th generation REV  - hsa, mmu & rno (miRBase v18.0)

status: Public on Jun 30 2016

city: Xi'an

first: Hai-Qiang

last: Wang

email: hqwang@sntcm.edu.cn, drwanghq@163.com

address: Xixian Avenue, Xixian District

department: Insititute of Integrative Medicine

institute: Shaanxi University of Chinese Medicine

organism: Homo sapiens

description:
Product=miRCURY LNA microRNA Array, 7th generation REV - hsa, mmu & rno
ProductDate=March 2012
ProductNumber=208520,208521,208522
LotNumberRange=35106-35106
ArrayContents_DesignedFor=miRBase 18.0


title: [AraGene-1_0-st] Arabidopsis Gene 1.0 ST Array [CDF: aragene10st_At_TAIRG version 20]

status: Public on Jan 31 2017

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Arabidopsis thaliana

relation: Alternative to: GPL17416 (alternative CDF [official])

manufacture_protocol: This is identical to GPL17416  but a custom CDF environment was used to extract data [Brainarray Version 20, aragene10st ]. CDF and other files can be downloaded at: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/20.0.0/tairg.asp


title: Illumina MiSeq (Drosophila melanogaster; Homo sapiens)

status: Public on May 08 2015

organism:
Drosophila melanogaster
Homo sapiens


title: UCBL-CNRS_MAP_UMR5240_Dickeya_dadantii_4.3k array [080627_Erwinia _chrysanthemi_expr]

status: Public on Dec 01 2012

city: Villeurbanne

first: Yvan

last: Rahbé

address: INSA-Lyon, 20 ave. A.-Einstein

department: SPE

country: France

institute: INRA

organism: Dickeya dadantii 3937

description: NimbleGen design name 080627_Erwinia _chrysanthemi_expr, NimbleGen design ID 7805 A 1:2 expression design for 4597 genes from Dickeya dadantii 3937  with 5 70-mer probe pairs (PM/MM) per gene.  Each probe is replicated 3 times.  The design includes random GC and other control probes.


title: Agilent-070119 Sheep Whole Transcriptome 4x44k.1 070000

status: Public on Apr 25 2016

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

organism: Ovis aries

description:
Sheep (ovis aries) whole genome microarray platform

Arrays of this design have barcodes that begin with 16070119 or 2570119.

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 (Neobellieria bullata)

organism: Sarcophaga bullata


title: Agilent-060509 Zebrafish Expression Zv9 2013 (Probe name version)

status: Public on Jan 01 2016

city: West Lafayette

first: Jennifer

last: Freeman

address: 915 West State Street

institute: Purdue University

organism: Danio rerio

description:
Includes all 128,291 probes + 44K design and others
Arrays of this design have barcodes that begin with 16060509 or 2560509.

relation: Alternative to: GPL23074 (Feature number version)


title: Agilent Human 1A Oligo UNC custom Microarrays

status: Public on Feb 23 2005

city: Chapel Hill

first: Charles

middle: M.

last: Perou

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

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

description: Represents about 22K 60-mer oligonucleotide probes which span conserved exons across the transcripts of the targeted full length genes (Incyte Foundation) in the home genome. About 17,000 probes are from Human 1A Oligo Microarray Kit. The other 4000 probes are specifically designed for Dr. Charles Perou Lab at University of North Carolina at Chapel Hill.

middle: M

first: George

last: Wu


title: Illumina HiSeq 1500 (Caenorhabditis elegans)

status: Public on May 27 2014

organism: Caenorhabditis elegans


title: AB SOLiD 4 System (Mus musculus)

status: Public on Sep 21 2011

organism: Mus musculus


title: Illumina HiSeq 2000 (Macaca mulatta)

status: Public on Dec 03 2011

organism: Macaca mulatta


title: [RTA-1_0] Affymetrix Rat Transcriptome Array 1.0 [transcript (gene) CSV version]

status: Public on Aug 30 2016

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

description:
Annotation was derived from the Affymetrix annotation file RTA-1_0.na36.rn6.transcript.csv:

#%create_date=Wed Jun  8 16:48:57 2016 PDT
#%chip_type=RTA-1_0
#%lib_set_name=RTA-1_0
#%lib_set_version=r1
#%genome-species=Rattus norvegicus
#%genome-version=rn6
#%genome-version-ucsc=rn6
#%genome-version-ncbi=Rnor_6.0
#%genome-version-create_date=2014-07-30
#%genome-lifted-method=psl-map.pl
#%genome-lifted_from-species=Rattus norvegicus
#%genome-lifted_from-version-ucsc=rn6
#%genome-lifted_from-version-ncbi=Rnor_6.0
#%netaffx-annotation-date=2016-03-15
#%netaffx-annotation-netaffx-build=36
#%netaffx-annotation-data-type=transcript_cluster

manufacture_protocol: See manufacturers website


title: Illumina NextSeq 500 (Bos taurus)

status: Public on Feb 10 2017

organism: Bos taurus


title: [AraGene-1_0-st] Arabidopsis Gene 1.0 ST Array [transcript (gene) version]

status: Public on Jul 08 2013

description:
#%create_date=Wed May  1 12:43:31 2013 PDT
#%chip_type=AraGene-1_0-st-v1
#%lib_set_name=AraGene-1_0-st
#%lib_set_version=v1
#%genome-version=tair10
#%genome-version-ucsc=tair10
#%genome-lifted-method=NONE
#%genome-lifted_from-version-ucsc=tair10
#%netaffx-annotation-date=2012-09-15
#%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=

relation: Alternative to: GPL17417 (alternative CDF)

relation: Alternative to: GPL21430 (alternative CDF (aragene10st_At_TAIRG version 18))

relation: Alternative to: GPL22603 (alternative CDF [aragene10st_At_TAIRG version 19])

relation: Alternative to: GPL23011 (alternative CDF [aragene10st_At_TAIRG version 20])

manufacture_protocol: See manufacturer's web site


title: [Yeast_2] Affymetrix Yeast Genome 2.0 Array

status: Public on Jun 13 2005

organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

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® Yeast Genome 2.0 Array contains probe sets to detect transcripts from both Saccharomyces cerevisiae and Schizosaccharomyces pombe, which are the two most commonly studied species of yeast. Providing comprehensive coverage of both species, the GeneChip Yeast Genome 2.0 Array includes approximately 5,744 probe sets for 5,841 of the 5,845 genes present in S. cerevisiae and 5,021 probe sets for all 5,031 genes present in S. pombe

relation: Alternative to: GPL9671 (Alternative CDF)

relation: Alternative to: GPL13150 (Alternative CDF)

manufacture_protocol: The sequence information for this array was selected from public data sources GenBank® (May 2004) and Sanger Center (June 2004) for the S. cerevisiae and S. pombe genomes, respectively. Probe sets on the array include 11 oligonucleotide pairs to detect each transcript.