title: Illumina HiSeq 2000 (Bos indicus x Bos taurus)

status: Public on Jan 29 2016

last: GEO

country: USA

organism: Bos indicus x Bos taurus

technology: high-throughput sequencing

distribution: virtual


title: NimbleGen Mouse ChIP-chip Array [090826_MM9_JD_ChIP_HX1]

status: Public on Jan 31 2016

city: Boston

first: Guray

last: Kuzu

address: 185 Cambridge Street

institute: Massachusetts General Hospital

organism: Mus musculus

technology: in situ oligonucleotide

description:
Annotation based on the UCSC mm9 assembly genome.
The 50-mer probes were selected every 20 bases with no repeat masking, for both forward and reverse.

distribution: custom-commercial

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


title: Mouse 32K Genome Array

city: Beijing

first: Zhe

last: Wang

address: 18 Shuangqing Road

country: China

institute: Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences

technology: spotted oligonucleotide

manufacture_protocol: see manufcturer's websiet


title: AB 5500xl Genetic Analyzer (Xenopus laevis)

status: Public on Jan 27 2016

organism: Xenopus laevis


title: Invitrogen Ncode Human Noncoding RNA Array

status: Public on Jan 28 2016

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

organism: Homo sapiens

manufacture_protocol: See manufacturer's website.


title: Illumina HiSeq 2500 (Synechococcus sp. PCC 7002)

organism: Picosynechococcus sp. PCC 7002


title: Agilent-048532 MALARIAARRAY_JM [Feature Number version]

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

institute: University of South Florida

organism: Plasmodium falciparum

description:
Arrays of this design have barcodes that begin with 16048532 or 2548532.

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: Agilent-034592 Arabidopsis thaliana PSC_Custom

city: Yokohama

first: Akihiro

last: Matsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

organism: Arabidopsis thaliana

description: the probes were designed based on expressed genes and transcripts of TAIR 10 genome using previous tiling-array and RNA-seq analyses (Kawaguchi et al. 2012; Matsui et al. 2008; Okamoto et al. 2010).


title: Agilent-061413 P. pseudoalcaligenes Psepse v1

city: Córdoba

first: Victor M.

last: Luque

address: Edificio Severo Ochoa 1ª planta, Campus de Rabanales

department: Departamento de Bioquímica y Biología Molecular

country: Spain

institute: Universidad de Córdoba

organism: Ectopseudomonas oleovorans CECT 5344

description:
Pseudomonas pseudoalcaligenes CECT 5344
Based on HG916826.1 complete genome
Arrays of this design have barcodes that begin with 16061413 or 2561413.
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.

first: Victor

middle: M

last: Luque-Almagro

first: Maria

middle: P

last: Escribano

first: Isabel

last: Manso

first: Lara

last: Sáez

first: Purificación

last: Cabello

first: Conrado

last: Moreno-Vivirán

first: María

middle: D

last: Roldán


title: Illumina MiSeq (unidentified plasmid)

status: Public on Jan 26 2016

organism: unidentified plasmid


title: [hGlue_3_0_v1] Custom Affymetrix Human Transcriptome Array

city: Guangzhou

first: Wen-Tao

state: Guangdong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: sun yat sen university

manufacture_protocol: See manufacturer's web site


title: Illumina MiSeq (Saccharomyces cerevisiae BY4741)

status: Public on Jan 25 2016

organism: Saccharomyces cerevisiae BY4741


title: Illumina HiSeq 2500 (Mamestra configurata nucleopolyhedrovirus A)

status: Public on Jan 22 2016


title: Agilent-032353 PigExp8x60_epi [ENSEMBL_ID]

status: Public on Jan 23 2016

city: Dummerstorf

first: Constance

last: Nebendahl

address: Wilhelm-Stahl Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology

organism: Sus scrofa

description:
PigExpression8x60 for Epifood

Arrays of this design have barcodes that begin with 16032353 or 2532353.

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 Ensembl IDs. The files linked below have the PigEx numbers and the associations to sequence and the Ensembl IDs.

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.


title: Illumina Genome Analyzer IIx (Cucumis melo)

organism: Cucumis melo


title: Illumina HiScanSQ (Nicotiana benthamiana)

status: Public on Jan 21 2016

organism: Nicotiana benthamiana


title: Illumina HiSeq 2000 (Yersinia enterocolitica; Yersinia phage phiR1-37)

organism:
Yersinia enterocolitica
Yersinia phage phiR1-37


title: Illumina HiSeq 1000 (Zonotrichia albicollis)

organism: Zonotrichia albicollis


title: Illumina HiSeq 2500 (Streptococcus pneumoniae TIGR4)

status: Public on Jan 19 2016

organism: Streptococcus pneumoniae TIGR4


title: [RCnGene-1_1-st] Affymetrix Rice Gene 1.1 ST Array [transcript (gene) version]

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Oryza sativa

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

#%chip_type=RCnGene-1_1-st-v1
#%lib_set_name=RCnGene-1_1-st
#%lib_set_version=v1
#%genome-version=bgi102808
#%genome-version-ucsc=bgi102808
#%genome-lifted-method=psl-map.pl
#%genome-lifted_from-version-ucsc=bgi102808
#%netaffx-annotation-date=2014-02-11
#%netaffx-annotation-netaffx-build=34
#%netaffx-annotation-data-type=transcript_cluster

distribution: commercial


title: Agilent-044572 Leptospira interrogans serovar Copenhageni L_copenhageni_Butanta

city: Sao Paulo

first: Paulo

last: Lee Ho

state: SP

address: 1500 Vital Brazil

department: Centro de Biotecnologia

country: Brazil

institute: Instituto Butantan

description:
Leptospira copenhageni gene expression microarray

Arrays of this design have barcodes that begin with 16044572 or 2544572.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: miRCURY LNA microRNA Array, v.11.0 - hsa, mmu & rno [miRBase 14.0]

city: guangzhou

first: li

last: jun

state: guangdong

address: Tianhe District Tianhe Road, No. 600

institute: The third affiliated hospital of sun YAT-SEN University

organism: Rattus norvegicus

description:
ProductNumber=208200-A,208201-A,208202-A
LotNumberRange=31087-31087

GalFileCreationDate=2010-01-04 15:07
ArrayContents_DesignedFor=miRBase 11.0
ArrayContents_CurrentNameColumn=miRBase 14.0
ArrayContents_CurrentNameColumnCoverage=Rattus norvegicus:95.88%

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


title: Illumina HiSeq 2500 (Zea mays subsp. mexicana)

status: Public on Jan 18 2016

last: GEO

organism: Zea mays subsp. mexicana


title: Illumina HiSeq 2500 (Bacillus subtilis subsp. subtilis str. 168)


title: Illumina Genome Analyzer IIx (Rhodococcus jostii)

status: Public on Jan 24 2016

organism: Rhodococcus jostii


title: Illumina NextSeq 500 (Cucumis melo)


title: Qiagen Custom Human Cardiovascular Disease PCR Array (PAHS-174Z with 4 genes added)

status: Public on Jan 20 2016

city: Ann Arbor

first: Guihua

last: Jiang

state: MI

address: 109 Zina Pitcher PL

department: Surgery

institute: University of Michigan

organism: Homo sapiens

technology: RT-PCR

description: PCR assay for the 7900HT. The RTC and PPC wells H08-H11 were removed and replaced with NOTCH1, GATA4, HAND1, MYL2)

manufacture_protocol: see manufacturer's website


title: Kluyveromyces lactis NRRL Y-1140 Microarray, 20K

status: Public on Jan 17 2016

city: Bratislava

first: Nora

last: Toth Hervay

address: Ilkovicova 6

country: Slovakia

institute: Deparment of Microbiology and Virology,Faculty of Natural Sciences, Comenius University in Bratislava

organism: Kluyveromyces lactis NRRL Y-1140

manufacturer: MYcroarray (5692 Plymouth Road, Ann Arbor, MI 48105, USA)

manufacture_protocol: Kluyveromyces lactis NRRL Y-1140 has 5327 genes. The manufacturer used 15437 probes designed to survey 5260 genes (or 98.7% of all genes) for this organism. The Kluyveromyces lactis NRRL Y-1140 genome used for the probe design was provided in 6 pieces of sequence ( NC_006037, NC_006038, NC_006039, NC_006040, NC_006041, NC_006042 ) representing a total of 5327 transcripts. The the sequences were analyzed for their GC content as this is an important parameter for probe design. The average GC content of the coding sequences was 40%, with a minimum and a maximum of 0% and 58% respectively. Ninety percent of the sequences had a GC content comprised between 36% and 45%. The values have been used to set OligoArray options during design. The parameter set used for this particular design is available here <http://berry.engin.umich.edu/oligoarraydb/parameter.php?org_id=644>.


title: Illumina MiSeq (Bacillus subtilis)

organism: Bacillus subtilis


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

status: Public on Jan 15 2016

city: Kunming

first: Kunhua

last: Wang

state: Yunnan

address: #295 Xichang Road

department: Department of Gastrointestinal and Hernia Surgery

institute: First affiliated Hospital of Kunming Medical University

description:
Product=miRCURY LNA microRNA Array, 7th generation REV - hsa, mmu & rno
ArrayContents_DesignedFor=miRBase 18.0


title: Illumina HiSeq 2500 (Entamoeba histolytica HM-1:IMSS)

organism: Entamoeba histolytica HM-1:IMSS


city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

description:
catalog number: 4444909

The TaqMan® Array Rodent MicroRNA A+B Cards Set v3.0 is a two card set containing a total of 384 TaqMan® MicroRNA Assays per card. The set enables accurate quantitation of 641 and 373 unique microRNAs for mouse and rat respectively in as little as 5 hours. Included on each array is three TaqMan® MicroRNA Assay endogenous controls for each species to aid in data normalization and one TaqMan® MicroRNA Assay not related to rodent as a negative control. Detail on the included assays is available in the Target List file. Purchase of the MegaplexTM RT Primers, Rodent Pool Set v3.0 is required to run this array set. An additional preamplification step is enabled by MegaplexTM PreAmp Primers, Rodent Pool Set v3.0 for situations where sensitivity is of the utmost importance and/or sample is limiting.


title: Illumina Genome Analyzer IIx (Ixodes ricinus)

organism: Ixodes ricinus


title: Agilent-060200 Clostridium beijerinckii NCIMB8052 8×15K array

city: Wooster

first: Yan

last: Zhang

state: OH

address: 1680 Madison Avenue

department: Animal Sciences

institute: The Ohio State University

organism: Clostridium beijerinckii NCIMB 8052


title: 3D-Gene Mouse miRNA V21_1.0.0

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

organism: Mus musculus

manufacture_protocol: See manufacture's web site


title: Illumina Genome Analyzer II (Bat gammaherpesvirus 8; Myotis velifer)

status: Public on Jan 13 2016

organism:
Myotis velifer
Bat gammaherpesvirus 8


title: Ion Torrent Proton (Sus scrofa)

organism: Sus scrofa


title: ABI Human Genome Survey Microarray Version 2

status: Public on Jan 13 2006

city: Rockville

first: chunlin

last: xiao

state: MD

address: 45 West Gude Drive

institute: Applied Biosystem

description: See manufacturer's web site


title: Agilent-041648 LincRNA 60K Microarray PVD version 2 (probe name version)

city: Gent

first: Pieter

last: mestdagh

address: De Pintelaan 185

country: Belgium

institute: Center for Medical Genetics

description:
New version of the custom lincRNA expression array. The missing probe group 028004_028004_D_20100409_10 is included
eatures 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 probe names


title: Illumina HiSeq 2500 (Petunia x hybrida)

status: Public on Jan 14 2016

organism: Petunia x hybrida


title: [MTA-1_0] Affymetrix Mouse Transcriptome Array 1.0 [probeset (exon) CDF version]

description:
This platfrom configures to MTA-1_0.r1.exon.cdf. Annotation was derived from the Affymetrix annotation file MTA-1_0.na35.mm10.probeset.csv:

#%create_date=Wed Jan 14 11:30:18 2015 PST
#%chip_type=MTA-1_0
#%lib_set_name=MTA-1_0
#%lib_set_version=r1
#%genome-species=Mus musculus
#%genome-version=mm10
#%genome-version-ucsc=mm10
#%genome-version-ncbi=38
#%genome-version-create_date=2011-12-00
#%netaffx-annotation-date=2014-10-15
#%netaffx-annotation-netaffx-build=35

manufacture_protocol: See manufacturers website


title: Illumina HiSeq 2000 (Mrakia psychrophila)

status: Public on Jan 12 2016

organism: Mrakia psychrophila


title: Illumina MiSeq (Hoolock leuconedys)

organism: Hoolock leuconedys


title: Illumina MiSeq (Pan troglodytes)

organism: Pan troglodytes


title: Ion Torrent PGM (Olea europaea)

status: Public on Jan 11 2016

organism: Olea europaea


title: Illumina HiSeq 2500 (Listeria monocytogenes)

organism: Listeria monocytogenes


title: Agilent-066433 Leucaena leucocephala Expression array (Systematic Name version)

city: Honolulu

first: Kazue

last: Ishihara

state: HI

address: 1955 East-West Rd AgSci 218

department: Molecular Biosciences and Bioengineering

institute: University of Hawaii at Manoa

organism: Leucaena leucocephala


title: Illumina HiSeq 2500 (Caulobacter crescentus NA1000)

organism: Caulobacter vibrioides NA1000


title: Illumina HiSeq 2000 (Eurytemora affinis)

status: Public on Jan 08 2016

organism: Eurytemora affinis


title: Illumina Genome Analyzer II (Citrus maxima)

organism: Citrus maxima


title: Agilent-025581 UBT-ZBv1

city: Bayreuth

first: Alfons

middle: R

last: Weig

address: Universitaetsstrasse 30

department: Genomics and Bioinformatics

institute: University of Bayreuth

organism: Saccharomyces cerevisiae


title: LC Sciences Mouse miRNA Array MRA-1002_miRMouse_19 (miRNA_ID version)

city: Cincinnati

first: JIALIANG

last: LIANG

address: 231 Albert Sabin Way

department: Department of Pathology and Laboratory Medicine

institute: University of Cincinnati

description: Based on Sanger miRBase Release 19

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: University Padova Chamelea gallina 8x15K

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

organism: Chamelea gallina

description: To design  the first C. gallina-specific oligo-array, the transcriptome obtained by Coppe and colleagues (2012) representing 36,422 contigs of high quality has been considered.  These contigs have been re-annotated  through blastx similarity searches conducted against SwissProt database and few protein databases available on Ensembl Genome Browser: Crassostrea gigas, Strongylocentrus purpuratus, Homo sapiens, Danio rerio, and Drosophila melanogaster. Alignments with an E-value of at most 1 E-5 were considered significant and only the best hit per contig was taken into account.   Probe design started with the selection of target sequences to be represented onto the C. gallina microarray. All annotated entries (9,939) were included. In addition, to fill the DNA microarray platform, a total of   2,167 non annotated transcripts with highest sequence quality have been considered. As most sequence reads were obtained from a non-directional cDNA library, sense strand orientation was inferred putatively from that of homologuous protein sequences of other species. One probe for annotated transcripts with known orientation was designed, while two probes with both orientations were designed for non annotated contigs and for contigs with ambiguous orientation. Probe design was carried out using the Agilent eArray interface [https://earray.chem.agilent.com/earray/], which applies proprietary prediction algorithms to design 60 mer oligoprobes. A total of 14,719, representing 12,064 C: gallina transcripts were successfully obtained. Of these, 300 probes designed on known-orientation transcripts, were synthesized in duplicate on the array in order to test for “reproducibility-within-array”. New microarrays were synthesized in situ using the Agilent ink-jet technology with a 8 × 15 K format. Each array included default positive and negative controls.

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


title: Illumina MiSeq (Glycine max)

status: Public on Jan 07 2016

organism: Glycine max


title: Illumina HiSeq 2000 (Coccomyxa subellipsoidea C-169)

organism: Coccomyxa subellipsoidea C-169


title: Illumina HiSeq 2000 (Photorhabdus luminescens subsp. laumondii TTO1)

status: Public on Jan 05 2016

organism: Photorhabdus laumondii subsp. laumondii TTO1


title: Escherichia coli CFT073 30K Microarrays

city: Jeonju

first: Younghoon

last: Kim

address: 567 Baekje-Daero, Deokjin-Gu

department: Department of Animal Science

country: South Korea

institute: Chonbuk National University

organism: Escherichia coli CFT073

description: 14425 probes surveying 5276 genes


title: Illumina HiSeq 2000 (Tetranychus cinnabarinus)

status: Public on Jan 06 2016

organism: Tetranychus cinnabarinus


title: Agilent-045142 Human LncRNA v4 4X180K [Probe Name Version]

city: shanghai

first: qian

last: jin

address: libing road

institute: MSP

organism: Homo sapiens

description:
Arrays of this design have barcodes that begin with 16045142 or 2545142.

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 MiSeq (Macaca mulatta)

organism: Macaca mulatta


title: Illumina HiSeq 2000 (Vulpes vulpes)

status: Public on Jan 04 2016

organism: Vulpes vulpes


title: Illumina HiSeq 2000 (Pseudomonas phage PAK_P3)

organism: Pseudomonas phage PAK_P3


title: Agilent-059389 Custom Chicken Gene Expression 8X60k (AMADID: G4102A_059389)

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: Gallus gallus

description: designed by Genotypic Technology Private Limited


title: Illumina NextSeq 500 (Capra hircus)

organism: Capra hircus


title: Oryzon Murine 90K v1

status: Public on Jan 03 2016

city: Pamplona

first: Daniel

last: Ajona

address: Pio XII, 55

institute: CIMA

organism: Mus musculus

distribution: non-commercial

manufacture_protocol: Oryzon Genomics Propietary


title: Agilent-059612 Custom Duck Gene Expression 8X60k (AMADID: G4102A_059612)

organism: Anas platyrhynchos

description: designed by Genotypic Technology Private Limited , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)


title: Agilent Custom Human Promoter Microarray, 2X400K  designed by Genotypic Technology Private  Limited. (AMADID:031385)

status: Public on Jan 02 2016


title: Homo sapiens 380 apoptosis gene array

status: Public on Jan 01 2016

city: Lucknow

first: Ajit

middle: K.

last: Shasany

state: Uttar Pradesh

address: P.O. CIMAP

department: Biotechnology Division

institute: CSIR-Central Institute of Medicinal and Aromatic Plants

description:
Customized from commercially available oligos AROSTM (Array Ready Oligo Sets) from Operon Inc.
Customized from commercially available oligos AROSTM (Array Ready Oligo Sets) from Operon Inc.

first: Sunita

middle: S

last: Dhawan

first: Uzma

last: Faridi

middle: K

first: Mahendra

last: Darokar

manufacture_protocol: A total of 380 genes related with apoptosis  were arrayed. These included controls for detection of differences at gene expression levels in some of the very important apoptotic biomarkers. For arraying AROSTM apoptosis gene set was utilized for customized arraying essentially utilizing the MICROARRAY PROCEDURES USED AT OPERON* on Ultragap slides (Corning). Spotted microarray slides were stored at room temperature in a dry, dust free environment protected from light.


title: Leishmania donovani - Genotypic Technology Private Limited (AMADID: 035638) Array [Probe Name Version]

city: Kolkata

first: Syamal

last: Roy

state: West Bengal

address: 4, Raja SC Mullick Road

department: Infectious Disease and Immunology

institute: Indian Institute of Chemical Biology

organism: Leishmania donovani

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

Probe name version


title: TaqMan® Array Rodent MicroRNA A Card v2.0

city: Yonago-city

first: Kinya

last: Okamoto

state: Tottori

address: 36-1, Nishi-cho

department: Second Dept. Internal Medicine

institute: Tottori University

organism:
Mus musculus
Rattus norvegicus

description: PCR assay


title: Agilent-016332 Human Gene Expression 8X15k (AMADID: 16332)

description: Agilent Custom Human Gene Expression 8X15k (AMADID: 16332) designed by Genotypic Technology Private Limited

first: Raja

last: Mugasimangalam


title: Agilent-045291 Porcinet_60k_Nov2012 array (Probe name version)

city: Castanet-Tolosan

first: Herve

last: Acloque

address: 24 chemin de Borde Rouge

department: Animal Genetics

country: France

institute: INRA

organism: Sus scrofa

description:
enriched with pluripotency, germ fate, spermatogenesis, oocyte and testis probes

Arrays of this design have barcodes that begin with 16045291 or 2545291.

The ID column represents the Agilent Feature Extraction ProbeNames.


title: Custom Agilent  Eucalyptus 8x60k Microarray Gene expression  (AMADID: 59849 ) designed by Genotypic Technology Pvt.Ltd.

organism: Eucalyptus


title: Agilent-062918 Human lncRNA array V4.0 (Probe name version)

city: Shanghai

first: Yingjia

last: Xu

address: No.241, Huaihai west Road,

institute: Shanghai Chest Hospital

description: 78,243 human lncRNAs and 30,215 coding transcripts.


title: BWH-TYP-C1976 human custom Nanostring codesets

city: Boston

first: Tracy

last: Young-Pearse

state: MA

address: HIM 760, 77 Avenue Louis Pasteur

department: Ann Romney Center For Neurologic Disease

institute: Brigham and Women"s Hospital

technology: other


title: BWH-TYP-C2779 human custom Nanostring codesets


title: Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F (Gene-level version)

city: Minato-ku

first: Yukihiro

last: Kobayashi

state: Tokyo

department: Department of Marine Biosciences

institute: Tokyo University of Marine Science and Technology


title: CSU A. ferrooxidans ATCC 23270 10k v1.0

city: Changsha

first: Liyuan

last: Ma

address: 932 S. Lushan Rd.

institute: Central South University

organism: Acidithiobacillus ferrooxidans

technology: spotted DNA/cDNA

description: Acidithiobacillus ferrooxidans ATCC 23270


title: Agilent-034004 IITR_EBD_Multibacterium Custom 8X15K Array (Probe Name version)

organism: Bacteria

description: IITR_EBD_Multibacterium Custom 8X15K Array designed by Genotypic Technology Private Limited  (AMADID:034004)

first: Abhay

last: Bajaj

first: Natesan

last: Manickam


title: SWEGENE_BAC_32K_Full (clone version)

city: Lund

first: Ida

last: Johansson

address: Department of Oncology Clinical Sciences Lund University BMC C13

country: Sweden

institute: Lund University

description: The 32k BAC Re-Array set Ver. 1.0 (32,433 BAC clones) was obtained from the BACPAC Resource Center at Children's Hospital Oakland Research Institute, Oakland (CA, US). The average resolution of the whole genome tiling clone set is 46kb. Clones were mapped to human genome build 17 (UCSC Human Genome Browser)

first: Ake

last: Borg

manufacture_protocol: Arrays were produced using amplified genomic DNA from BAC clones. Amplification was performed using degenerate oligonucleotide primed PCR and products were purified by size-exclusion filtration and verified by agarose gel electrophoresis. After purification, products were dried down, recovered in 50% DMSO to a concentration of 500-1000ng/µl, and printed on amino-silane-coated glass slides (UltraGAPS from Corning) using a MicroGrid2 robot (BioRobotics) equipped with MicroSpot2500 pins (BioRobotics).


title: Illumina HiSeq 1500 (Thalassiosira weissflogii)

status: Public on Jun 03 2015

last: GEO

organism: Conticribra weissflogii


title: Bifidobacterium array

city: Parma

first: Marco

last: Ventura

address: Viale delle Scienze 11/A

department: Dept. Life Sciences

institute: University of Parma

organism: Bifidobacterium

description:
Array contains 4 Bifidobacterium species;

BBPR corresponds to B.bifidum PRL2010 (NC_014638.1)
Blon corresponds to B.longum subsp. infantis ATCC15697 (NC_017219.1)
BrMilk corresponds to B.breve 12L (project ID PRJNA214949, pending)
22L corresponds to B. adolescentis 22L (not in public database)


title: PacBio RS II (Homo sapiens)


title: Phalanx Mouse & Rat miRNA OneArray (miRBase13)

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description:
The Phalanx Mouse & Rat miRNA OneArray includes mouse and rat probes. This Platform represents only the mouse probes, annotated with miRBase 13.

616 unique sequence (probe) in this array (MRmiOA 1.0) was spotted in triplicate.

The Platform data table reflects the arrays replicate features. A condensed representation of the array's replicate features (based on miRBase13 ID) is GPL11415

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


title: [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array [Custom CDF: (Ath1121501_At_TAIRG.cdf v18.0.0]

status: Public on Oct 23 2015

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Arabidopsis thaliana

relation: Alternative to: GPL198 (Alternative CDF [official])

manufacture_protocol:
see manufacturer's web site
v18.0.0 Arabidopsis Custom CDF from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF


title: Agilent RISET 1.0 8x15K 60mer oligonucleotide microarray

status: Public on Dec 30 2012

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyi Biotec GmbH

organism: Homo sapiens

description:
Agilent-017772
Custom Agilent 8x15K 60mer oligonucleotide microarray comprising 4,610 probes in triplicates. The microarray is dedicated to transplantation research and was designed based on current literature and published and unpublished data provided by the RISET consortium. For the probe selection procedure, we specially focused on the detection of multiple transcript variants of a gene, on optimized hybridization properties of the probes, and on the avoidance of crosshybridization. The RISET 1.0 platform is a precursor of the RISET 2.0 microarray (GPL8136).

manufacture_protocol: See www.agilent.com


title: Agilent-021791 D. melanogaster (FruitFly) Oligo Microarray 4x44K v. 2 (Probe Name version)

status: Public on Mar 19 2013

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Drosophila melanogaster

description:
Agilent has developed a genome-wide fruit fly microarray to enable scientists to study gene expression profiling at the global level and enhance our understanding of fruit fly biology and gene functions.

*** 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 GPL6385.


title: GMAP-UTS520601 array

city: Toronto

first: Pamela

last: Ohashi

state: Ontario

address: 610 University Ave

country: Canada

institute: Princess Margaret Cancer Centre

manufacture_protocol: GMAP-UTS520601 array


title: Phalanx Human OneArray® v5

status: Public on Jun 14 2011

city: Hsinchu Science Park

first: Phalanx

last: Biotech

state: Hsinchu

address: 6 Technology Road 5, 6th Floor

institute: Phalanx Biotech

description:
Annotation is based on two databases:
. NCBI RefSeq release 45
. Ensembl release 61 cDNA sequences and
homo_sapiens_core_61_37f annotations


title: Illumina Genome Analyzer II (Arabidopsis thaliana)

status: Public on Sep 28 2009


title: Illumina HumanHT-12 V4.0 expression beadchip (gene symbol)

status: Public on Sep 10 2010

technology: oligonucleotide beads

description:
The HumanHT-12 v4 Expression BeadChip provides high throughput processing of 12 samples per BeadChip without the need for expensive, specialized automation. The BeadChip is designed to support flexible usage across a wide-spectrum of experiments.

The updated content on the HumanHT-12 v4 Expression BeadChips provides more biologically meaningful results through genome-wide transcriptional coverage of well-characterized genes, gene candidates, and splice variants.

Each array on the HumanHT-12 v4 Expression BeadChip targets more than 31,000 annotated genes with more than 47,000 probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq Release 38 (November 7, 2009) and other sources.

Please use the GEO Data Submission Report Plug-in v1.0 for Gene Expression which may be downloaded from https://icom.illumina.com/icom/software.ilmn?id=234 to format the normalized and raw data.  These should be submitted as part of a GEOarchive.  Instructions for assembling a GEOarchive may be found at http://www.ncbi.nlm.nih.gov/projects/geo/info/spreadsheet.html


title: Potato 10k cDNA array version 3

status: Public on Mar 16 2005

city: Rockville

first: Li

last: Zheng

address: 9712 Medical Center Dr.

institute: The Institute for Genomic Research

organism: Solanum tuberosum

description:
Spotted PCR amplified cDNA array on glass.
This version 3 set includes PCR products amplified from 15264 potato EST clones.
Each PCR product is duplicated on the slide. The number of total spots including empty and controls is 32448.

first: Carol

middle: Robin

last: Buell


title: Illumina NextSeq 500 (Xenopus laevis)

status: Public on Dec 16 2015

organism: Xenopus laevis


title: miRCURY LNA microRNA Array, v.10.0 - hsa, mmu & rno

status: Public on Dec 19 2008

city: Vedbaek

first: Exiqon

last: A/S

address: Bygstubben 9

country: Denmark

institute: Exiqon A/S

organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

description:
Array covering Sanger miRBase 12.0 and Exiqon miRPlus mature miRNAs.
The platform information provided is from the time of the design.
Names, accession numbers and sequences are listed for mature miRNAs in miRBase 12.0. Some probes may target multiple miRNAs, in which case multiple miRNA names, accession numbers and sequences are listed separated by '/'


title: Illumina NextSeq 500 (Pseudomonas aeruginosa)

organism: Pseudomonas aeruginosa


title: [Sc03b_MR] Affymetrix GeneChip S. cerevisiae Tiling 1.0R Array

status: Public on Sep 04 2008

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Saccharomyces cerevisiae

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

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

relation: Alternative to: GPL9286 (Alternative CDF)

manufacture_protocol:
Designed for identifying novel transcripts, mapping sites of protein/DNA interaction in chromatin immunoprecipitation (ChIP) experiments, and other whole-genome experiments

Single array comprised of over 3.2 million perfect match/mismatch probe pairs tiled through the complete Saccharomyces cerevisiae genome.

The array also contains probes to interrogate a 2-µm circle plasmid (NCBI Accession J01347).

Probes are tiled at an average of 5 base pair resolution, as measured from the central position of adjacent 25-mer oligos, creating an overlap of approximately 20 base pairs on adjacent probes.