title: Applied Biosystems, TaqMan® Low Density Array (TLDA) Human MicroRNA Cards v3.0

status: Public on Feb 19 2017

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

department: Medical Oncology

country: Netherlands

institute: Erasmus University Medical Center

organism: Homo sapiens

technology: RT-PCR

description: PCR assay

distribution: virtual

manufacture_protocol: see manufacturer's website


title: BaSysBio Bacillus subtilis T3 400K array

status: Public on Nov 29 2016

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

organism: Bacillus subtilis subsp. subtilis str. 168

technology: in situ oligonucleotide

distribution: custom-commercial

manufacture_protocol: The arrays are produced by Agilent Technologies SurePrint technology (for details, see manufacturer's web site).


title: Custom Fluidigm array with human genes related to celiac disease

status: Public on Oct 31 2016

city: Leioa

first: Jose Ramon

last: Bilbao

state: Outside the US or Canada

address: Bº Sarriena

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

description:
RT-PCR assay.
Taqman Gene Expression assay.

manufacture_protocol: Fluidigm 96.96 Fast Real-Time PCR Workflow Quick Reference (PN 100-2637).


title: Illumina HiSeq 4000 (Tetrapisispora blattae)

last: GEO

country: USA

organism: Henningerozyma blattae

technology: high-throughput sequencing


title: Illumina HiSeq 2000 (Zygosaccharomyces rouxii)

organism: Zygosaccharomyces rouxii


title: Illumina HiSeq 3000 (Gallus gallus)

organism: Gallus gallus


title: Agilent-030000 Folsomia candida 44K F_candida 029999

status: Public on Oct 30 2016

city: Beijing

first: Min

last: Qiao

address: Shuangqing Road 18

country: China

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

organism: Folsomia candida

description:
F.candida

Arrays of this design have barcodes that begin with 16030000 or 2530000.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

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


title: Illumina HiSeq 2000 (Raphanus sativus)

organism: Raphanus sativus


title: Agilent-030524 Synechococcus sp. CC9902_CC9311_Oct2010

status: Public on Oct 28 2016

city: Livermore

first: Rhona

last: Stuart

state: CA

address: 7000 East Ave.

institute: Lawrence Livermore National Laboratory

organism:
Synechococcus sp. CC9311
Synechococcus sp. CC9902

description: CC9902 complete, CC9311 some hypos removed


title: Agilent-073189 Cplex_2 G4125A array (Feature number version)

city: Houston

first: Shen

last: Gu

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description:
Arrays of this design have barcodes that begin with 16073189 or 2573189

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-073188 Cplex_1 G4125A array (Feature number version)

description:
Arrays of this design have barcodes that begin with 16073188 or 2573188

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Illumina HiSeq 2500 (Drosophila yakuba)

status: Public on Oct 27 2016

organism: Drosophila yakuba


title: Illumina HiSeq 2000 ([Candida] glabrata)

organism: Nakaseomyces glabratus


title: Agilent-024241 Xq22_44K  array (Feature number version)

description:
Arrays of this design have barcodes that begin with 16024241 or 2524241.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-071585 19q G4125A array (Feature number version)

description:
Arrays of this design have barcodes that begin with 16071585 or 2571585

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-029411 B.taurus Gene Expression  8x60k Array AMADID: 029411

status: Public on Oct 26 2016

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: Bos taurus


title: Illumina HiSeq 2000 (Lachancea kluyveri)

organism: Lachancea kluyveri


title: Illumina HiSeq 2500 (Ipomoea batatas)

organism: Ipomoea batatas


title: Illumina HiSeq 2500 (Rhizopus microsporus)

organism: Rhizopus microsporus


title: Illumina MiSeq (Streptococcus pneumoniae)

organism: Streptococcus pneumoniae


title: [AraGene-1_0-st] Arabidopsis Gene 1.0 ST Array [CDF: aragene10st_At_TAIRG version 19]

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 19, aragene10st ]. CDF and other files can be downloaded at: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/19.0.0/tairg.asp


title: Illumina HiSeq 2000 (Leptobrachium boringii)

status: Public on Oct 21 2016

organism: Leptobrachium boringii


title: [AraGene-1_1-st] Arabidopsis Gene 1.1 ST Array [CDF: aragene11st_At_TAIRG version 19]

status: Public on Oct 25 2016

description:
This is identical to GPL17133 but a custom cdf environment was used to extract data.
The custom CDF file is aragene11st_At_TAIRG_19.0.0 at:
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp
and is linked below as a supplementary file.

relation: Alternative to: GPL17133 (alternative CDF [official])

manufacture_protocol: Affymetrix protocol


title: Illumina HiSeq 2000 (Galdieria sulphuraria)

organism: Galdieria sulphuraria


title: Nanostring Petromyzon marinus nCounter Gene Expression Assay

city: Lexington

first: Mark

last: Evers

state: Kentucky

address: 800 Rose Street

department: College of Medicine

institute: University of Kentucky

organism: Petromyzon marinus

technology: other


title: Ion Torrent PGM (Xenopus tropicalis)

organism: Xenopus tropicalis


title: Northwest A&F University Goat S-Poly(T) miRNA assay

city: Xi'an

first: Zhi

last: Chen

state: Select a State or Province

address: 22 Xinong Road, Yangling

department: Shaanxi Key Laboratory of Molecular Biology for Agriculture

institute: College of Animal Science and Technology, Northwest A&F University,  China

organism: Capra hircus

description: S-Poly(T) RT-PCR assay.


title: Illumina HiSeq 2000 (Dromaius novaehollandiae)

organism: Dromaius novaehollandiae


title: Illumina NextSeq 500 (Saccharomyces uvarum)

status: Public on Oct 19 2016

organism: Saccharomyces uvarum


title: Illumina NextSeq 500 (Saccharomyces paradoxus)

organism: Saccharomyces paradoxus


title: Illumina NextSeq 500 (Saccharomyces cerevisiae x Saccharomyces paradoxus)


title: LC Sciences_MRA-1041_miRHumanViruses_21b (miRNA ID version)

status: Public on Oct 23 2016

city: Jinan

first: Wei

last: Wang

state: Shandong

address: West Wenhua Road

department: Department of Neurology

institute: Qilu Hospital, Shandong University

organism: Homo sapiens

description:
Part number: MRA-1041
Based on miRBase version 21.

manufacture_protocol: Arrays are made based on 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://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes are made by in situ synthesis using PGR (photogenerated reagent) chemistry.


title: NimbleGen Ustilago maydis array [080805_UM_SG_EXP]

status: Public on Oct 22 2016

city: Irapuato

first: Claudia

middle: Geraldine

last: Leon-Ramirez

state: Guanajuato

address: Km. 9.6 Lib. Nte Carretera Irapuato-León

department: Ingeniería Genética

country: Mexico

institute: Cinvestav Unidad Irapuato

organism: Mycosarcoma maydis

description:
DESIGN_ID: 8036
DESIGN_NAME: 080805_UM_SG_EXP

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


title: Illumina NextSeq 500 (Saccharomyces paradoxus x Saccharomyces uvarum)


title: Illumina HiSeq 2500 (Pseudomonas protegens)

status: Public on Oct 20 2016

organism: Pseudomonas protegens


title: Fluidigm mouse gene panel for CLP analysis

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

organism: Mus musculus

description: PCR assay


title: NanoString nCounter Human miRGE Expression Assay Custom CodeSet

status: Public on Oct 24 2016

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

description: NanoString nCounter Analysis System: Hybridization-based target capture, imaging, and counting technology utilizing digital color-coded barcodes.

manufacture_protocol: A NanoString nCounter miRGE CodeSet (miX_H_TP53) was custom-designed to enable the expression profiling of 105 TP53-associated transcripts (96 mRNAs, 10 miRNAs) plus 5 normalization control transcripts. Complete details of the gene targets and probe sequences are presented. The technology employs gene-specific CodeSets consisting of target-specific capture and reporter probes 35-50 bases in length. The reporter probes contain molecular, color-coded barcodes that afford high sensitivity and capability for high multiplexing. Targets were selected on the basis of their involvement in the canonical p53 signaling network as being either direct transcriptional targets of p53, known modulators of p53 function, and/or genes altered in response to TP53 mutation and loss/gain-of function.


title: Illumina NextSeq 500 (Saccharomyces cerevisiae x Saccharomyces uvarum)


title: Illumina NextSeq 500 (Musca domestica)

organism: Musca domestica


title: Agilent-021529 SurePrint G3 Human CGH Microarray Kit, 1x1M, design ID 21529 [hg19:GRCh37:Feb2009]

city: Saarbruecken

first: Valentina

last: Galata

state: Saarland

address: Campus, E2.1

department: Chair for Clinical Bioinformatics

institute: Saarland University

description:
Human CGH Whole Genome Microarray, 1x1M
genome build: hg19:GRCh37:Feb2009
File: SurePrint\ G3\ Human\ CGH\ Microarray\ 1x1M_021529_D_GEO_20111015.txt
The GEO file for SurePrint G3 Human CGH Microarray 1x1M was downloaded from Agilent SureDesign webpage.
File: platform_data.tsv
The GEO file from Agilent SureDesign was processed as follows:
The row and column values were set to the row and column values of the corresponding feature (column FEATURE_NUM) in the raw files; the unique probe ID (column ID) was derived from the raw files.
File: platform_data_condensed.tsv
The processed platform table was aggregated by the unqiue probe ID. Control probes, probes without a chromosomal position (column CHROMOSOMAL_LOCATION), and probes lying on chromosome X, Y, or M were removed.


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [CDF: genemapperhumanexon1.0cdf_3.0]

city: Salamanca

first: Beatriz

middle: Roson

last: Burgo

address: Campus Miguel de Unamuno

department: Cancer Research Centre

institute: Consejo Superior de Investigaciones Científicas & Universidad de Salamanca


title: Illumina HiSeq 2000 (Mactra quadrangularis)

organism: Mactra quadrangularis


title: Illumina HiSeq 2000 (Meloidogyne incognita; Solanum lycopersicum)

status: Public on Oct 14 2016

organism:
Solanum lycopersicum
Meloidogyne incognita


title: Agilent-044459 mCNV2_design1

first: Pengfei

last: Liu

address: 2450 Holcombe Blvd, O270F

description:
Arrays of this design have barcodes that begin with 16044459 or 2544459.

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: SABiosciences Cytokines & Chemokines RT² profiler PCR array

status: Public on Oct 12 2016

city: Tokyo

first: Sabine

last: Gouraud

address: 3-10-2  Osawa, Mitaka

country: Japan

institute: International Christian University

organism: Rattus norvegicus

description:
Cytokines & Chemokines
SABiosciences RT² Profiler panel of PCR assays.

manufacture_protocol: See manufacturer's website.


title: Agilent-069325 mcnv4_7_3 G4125A

description:
Arrays of this design have barcodes that begin with 16069325 or 2569325

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-044360 mCNV1_design1

description:
Arrays of this design have barcodes that begin with 16044360 or 2544360.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent Custom P. vivax 8x15k Array designed by Ashis Das, Raja CM & Genotypic Technology Pvt. Ltd. (AMADID:022126)

status: Public on Oct 18 2016

city: Pilani

first: Ashis

middle: Kumar

last: Das

state: Rajasthan

address: Vidya Vihar

department: Biological Sciences

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

organism: Plasmodium vivax

first: Raja

middle: C

last: Mugasimangalam


title: Illumina HiSeq 2500 (Geospiza fuliginosa)

status: Public on Oct 11 2016

last: GEO

organism: Geospiza fuliginosa


title: Illumina HiSeq 2000 (Mus musculus; Xenopus laevis)

organism:
Xenopus laevis
Mus musculus


title: Applied Biosystems (Thermo Fisher) Human TaqMan Custom Array

city: Baltimore

first: Kenneth

middle: W

last: Witwer

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine


title: Agilent-029954 Stickleback_UIUC2

city: Cleveland

first: Yibayiri

middle: Osee

last: Sanogo

state: OH

address: 9500 S Euclid Ave

department: Genomics Core

institute: Cleveland Clinic Foundation

organism: Gasterosteus aculeatus

description:
Arrays of this design have barcodes that begin with 16029954 or 2529954.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [CDF: hugene20st_Hs_ENTREZG.cdf, Brainarray version 20.0.0]

status: Public on Oct 16 2016

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: This array is identical to GPL16686 but the data were analyzed with a custom CDF environment.

manufacture_protocol: See manufacturer's web site.


title: Agilent-024347 Arraystar Custom Mouse MM9 piRNA Microarray

city: Rockville

first: Panos

last: Pan

address: 9430 Key West Avenue

institute: Arraystar Inc.

description:
Agilent-024347
The ArrayStar MM9 piRNA array is designed for profiling of piRNAs in mouse germ cells.
Mouse piRNAs are downloaded from NCBI database, and mapped to the MM9 genome sequence using UCSC Blat.
piRNAs with good match are selected and on this array probes of more than 41000 piRNAs are designed successfully using a duplex method.
All the probes are spotted once.

ALL of the represented probes are Designed by Agilent's eArray
Sequence orientation, accuracy, and clustering assembly classification validated with Mouse MM9
4 X 44K slide formats printed using Agilent's 60-mer SurePrint technology


title: Illumina HiSeq 2500 (Geospiza fortis)

organism: Geospiza fortis


title: Illumina NextSeq 500 (Onthophagus taurus)

organism: Onthophagus taurus


title: Illumina HiSeq 2000 (Ustilago bromivora)

status: Public on Oct 07 2016

organism: Ustilago bromivora


title: Illumina HiSeq 2000 (Colocasia esculenta)

status: Public on Oct 10 2016

organism: Colocasia esculenta


title: Ion Torrent PGM (Shigella dysenteriae)

status: Public on Oct 06 2016

organism: Shigella dysenteriae


title: Illumina HiSeq 2000 (Streptococcus suis)

organism: Streptococcus suis


title: Illumina NextSeq 500 (Debaryomyces hansenii)

organism: Debaryomyces hansenii


title: Agilent-021332 Rat_CpG_Island 2x105K Array [Probe Name Version]

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

institute: National Institutes for Quantum and Radiological Science and Technology

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 Probe Name.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

relation: Alternative to: GPL19288 (Feature Number Version)


title: [Mm_PromPF_v02] Affymetrix Mouse Promoter 1.0F Array

city: Peoria

first: Kewei

state: IL

address: One Illini Dr.

institute: Univ. of Illinois College of Medicine at Peoria

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


title: Agilent-028827 Hordeum vulgare Harvest Assembly IPK (Feature Number version)

city: Los Banos

last: Sreenivasulu

address: Metro Manila

country: Philippines

institute: IRRI

organism: Hordeum vulgare

description:
This array is an assembly of best probes from sequence data provided by Dr. Neese Sreenivasulu (srinivas@ipk-gatersleben.de) from the IPK in Gatersleben in Germany.

Arrays of this design have barcodes that begin with 16028827 or 2528827.

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 (Bifidobacterium longum)

organism: Bifidobacterium longum


title: NanoString nCounter Human GX PanCancer Pathway Panel and Custom Probe Set

status: Public on Oct 09 2016

city: Berlin

first: Daniel

last: Noerenberg

address: Augustenburger Platz 1

department: Hematooncology

institute: Charité University Medicine

organism: Homo sapiens

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


title: Illumina NextSeq 500 (Kluyveromyces lactis)

organism: Kluyveromyces lactis


title: Agilent-028827 Hordeum vulgare Harvest Assembly IPK (Probe Name version)

description: This array is an assembly of best probes from sequence data provided by Dr. Neese Sreenivasulu (srinivas@ipk-gatersleben.de) from the IPK in Gatersleben in Germany.


title: LCS miRHuman 16

status: Public on Oct 04 2016

city: Hangzhou

first: Wengong

last: Si

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Zhejiang university

manufacture_protocol: Arrays are made based μParaflo microfluidic chip using a micro-circulation pump (AtacticTechnologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.


title: Illumina HiSeq 2000 (Bacillus phage AR9; Bacillus subtilis)

status: Public on Oct 03 2016

organism:
Bacillus subtilis
Bacillus phage AR9


title: Illumina HiSeq 2000 (Catharus ustulatus)

organism: Catharus ustulatus


title: Danio rerio 090701_Zv8_GB_EXP_HX12

city: Houston

first: Ghislain

last: Breton

address: 6431 Fannin St MSB 4.216

department: Integrative Biology & Pharmacology

institute: McGovern Medical School

organism: Danio rerio

description:
NimbleGen design name 090701_Zv8_GB_EXP_HX12, NimbleGen design ID 22743. Four probes were designed for 27,082 out of the 28,717 annotated transcripts in Zv8.  The design includes 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.
090701_Zv8_GB_EXP_HX12.ncd
090701_Zv8_GB_EXP.ndf
090701_Zv8_GB_EXP.ngd


title: [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array [CDF: Mouse4302_Mm_ENSG v19.0.0]

organism: Mus musculus

technology: spotted oligonucleotide

relation: Alternative to: GPL1261 (Alternative CDF)

manufacture_protocol: This is identical to GPL1261 but a custom cdf environment was used to extract data. We used custom chip definition files (CDF) based on Ensembl gene annotation v19.


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

status: Public on Jul 16 2015

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description:
Catalog number: 4444909
https://www.lifetechnologies.com/order/catalog/product/4444909

distribution: commercial

manufacture_protocol: see manufacturer's web site


title: NimbleGen Alicyclobacillus acidocaldarius 4X72K array [090625_Aaci_JL_exp; MATCH_INDEX version]

status: Public on Aug 31 2016

city: Richland

first: Brady

last: Lee

state: Washington

address: 902 Battelle Boulevard

institute: Pacific Northwest National Laboratory

organism: Alicyclobacillus acidocaldarius

description: NimbleGen design name 090625_Aaci_JL_exp, NimbleGen design ID 10234.  A 1:2 expression design for 3,554 genes from Alicyclobacillus acidocaldaruis ATCC27009/DSM 446 with 7 60-mer probe pairs (PM/MM) per gene.  Each probe is replicated 3 times.  The design includes random GC and other control probes.  The .ndf and .ngd files are linked below as supplementary files.


title: RIBOBIO Pseudomonas aeruginosa 12K Custom Array

status: Public on Oct 01 2016

city: ChongQing

first: Xia

last: Zhao

address: Shapingba

institute: Third military medical school

organism: Pseudomonas aeruginosa

technology: spotted DNA/cDNA

manufacture_protocol: The standard process of microarray


title: Agilent-045560 Arabidopsis thaliana 8x60k v1_complete

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

institute: Centro Nacinal de Biotecnologia-CSIC

organism: Arabidopsis thaliana

description:
Microarray based on catalog V4 and includes custom-designed probes to cover 2 probes for most of the genes in TAIR10. Also includes probes for "otherRNA" and lincRNA as in Liu et al. (Plant Cell, 2012) and probes for miRNA precursors in miRBase not included in other probe groups

Arrays of this design have barcodes that begin with 16045560 or 2545560.

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: 4PLEX_MAIZE_064491

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

organism: Zea mays

description:
number of probes: 39210 Forward for cDNA in duplicate + 152 probes for ncRNA + 18 controles in triplicate + 10 spikes.
contributor: Stephanie Pateyron

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


city: Taipei

first: Chien-Wei

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang-Ming University

technology: antibody

manufacture_protocol: Protocol is following the manufacturer’s directions (Ray biotech Mouse L308 Array, Glass Slide Cat# AAM-BLG-1-4). See http://www.raybiotech.com/files/manual/Antibody-Array/AAM-BLG-1.pdf


title: CHB Illumina MouseRef-8 v2.0 expression beadchip

status: Public on Apr 07 2010

city: Boston

first: Hao

last: Zhu

state: MA

address: 7th Floor Karp, 300 Longwood Ave.

department: Hematology/Oncology

institute: Children's Hospital of Boston

technology: oligonucleotide beads

manufacture_protocol:
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).

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: Applied Biosystems TaqMan OpenArray Rodent MicroRNA Panel

organism:
Mus musculus
Rattus norvegicus


title: Agilent-044559 Bacillus subtilis Custom Agilent 44k AllFeat_v1 [Probe Name version]

status: Public on May 24 2016

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

institute: University Medicine Greifswald

organism: Bacillus subtilis subsp. subtilis str. 168

manufacture_protocol: The arrays are produced by Agilent Technologies SurePrint technology (for details, see manufacturer's web site). Each protein coding gene of Bacillus subtilis str. 168 (GenBank record AL009126.2) is represented by 1 to 5 long oligonucleotides.


title: Agilent-050524 CMGG Human V2.0 60k

status: Public on Jun 08 2015

city: Gent

first: Pieter

last: mestdagh

address: De Pintelaan 185

country: Belgium

institute: Center for Medical Genetics

manufacture_protocol: SurePrint


title: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [hugene10st_Hs_ENTREZG, Brainarray v18]

status: Public on Feb 25 2015

description: Brainarray: hugene10st_Hs_ENTREZG_18

manufacture_protocol: See manufacturer's web site


title: Illumina NextSeq 500 (Macaca fascicularis)

last: GEO

organism: Macaca fascicularis


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

status: Public on Jan 11 2013

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Sus scrofa

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

Jan 11, 2013: annotation table updated with netaffx build 33

relation: Alternative to: GPL22530 ([porgene10st_Ss_ENTREZG_17.0.0])


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

status: Public on May 07 2013

description:
Annotations are from AraGene-1_1-st-v1.na34.tair10.transcript.csv:
#%create_date=Mon May  5 14:18:10 2014 PDT
#%chip_type=AraGene-1_1-st-v1
#%lib_set_name=AraGene-1_1-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=2013-08-30
#%netaffx-annotation-netaffx-build=34

relation: Alternative to: GPL17134 (alternative CDF)

relation: Alternative to: GPL19358 (alternative cdf)

relation: Alternative to: GPL22599 (alternative CDF [aragene11st_At_TAIRG version 19])


title: AB 5500xl Genetic Analyzer (Mus musculus)

status: Public on Aug 08 2012


title: Agilent-014693 Human Genome CGH Microarray 244A (Feature number version)

status: Public on Aug 15 2006

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
This microarray is Agilent’s premium product for human DNA copy-number profiling. Over 236,000 60-mer oligonucleotide probes, specifically optimized for copy-number measurement, span coding and non-coding genomic sequences with median spacing of 7.4 kb and 16.5 kb respectively. This microarray is designed for use with Agilent’s optimized assay protocols, enabling researchers to use nanogram levels of total genomic DNA without complexity reduction.

Arrays of this design have barcodes that begin with 16014693 or 2514693.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL9128.

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


title: Agilent-028004 SurePrint G3 Human GE 8x60K Microarray (Probe Name Version)

status: Public on Sep 08 2011

description:
SurePrint G3 Human GE 8x60K Microarray

*** 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 GPL13607.