title: Qiagen/SA Biosciences Mouse inflammatory cytokine and receptors gene expression array panel (PAMM-011A)

status: Public on Aug 08 2014

city: Gary

first: Roman

last: Dziarski

state: IN

address: 3400 Broadway

country: USA

institute: Indiana University School of Medicine-Northwest

organism: Mus musculus

technology: RT-PCR

description: Quantitative reverse transcription real-time PCR (qRT-PCR)

distribution: virtual

manufacture_protocol: see manufacturer's website


title: 3D-Gene Mouse miRNA Oligo chip 16v1.0.0

status: Public on May 31 2014

city: Palo Altp

first: Mollie

middle: Elizabeth

last: Jacobs

state: CA

address: 3801 Miranda AVE

department: Medicine

institute: Stanford University

technology: spotted oligonucleotide

distribution: custom-commercial

manufacture_protocol: See manufacture's web site


title: Human miRNA PCR arrays

status: Public on May 30 2014

city: Buffalo

first: AC

last: CHANG

address: Elm and Carlton

institute: RPCI

organism: Homo sapiens

description: PCR assay

manufacture_protocol: Please see manufacturer's website


title: Agilent-036223 Vitis_vinifera.IGGP_12x.2_vs20110825

status: Public on Sep 29 2014

city: Urrbrae

first: Sam

last: Henderson

state: South Australia

address: Hartley Grove

country: Australia

institute: University of Adeladie

organism: Vitis vinifera

technology: in situ oligonucleotide

description:
Arrays of this design have barcodes that begin with 16036223 or 2536223.

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.

distribution: commercial

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


title: Illumina Genome Analyzer IIx (Pyrococcus abyssi)

last: GEO

organism: Pyrococcus abyssi

technology: high-throughput sequencing


title: Illumina HiSeq 2000 (Streptomyces hygroscopicus subsp. jinggangensis 5008)


title: Nanosphere Verigene Gram-Positive Blood Culture Nucleic Acid Assay Microarray

city: Seoul

first: Seon Young

last: Kim

address: 101 Daehak-ro, Jongno-gu,

country: South Korea

institute: Seoul National University College of Medicine

organism:
Micrococcus
Staphylococcus
Staphylococcus aureus
Staphylococcus epidermidis
Streptococcus
Streptococcus agalactiae
Streptococcus pneumoniae
Streptococcus pyogenes
Enterococcus faecalis
Enterococcus faecium
Listeria
Staphylococcus lugdunensis
Streptococcus anginosus group

description:
Gold nanoparticle microarray
Array includes hexaplicated spots for targets and Positive control spots, PC1, PC2, and negative control spots, background controls, and imaging contorls


title: Agilent-021827 Human miRNA Microarray [miRNA_107_Sep09]

city: Vancouver

first: Paul

last: Pavlidis

state: British Columbia

address: 177 Michael Smith Laboratories 2185 East Mall

department: Centre for High-Throughput Biology / Psychiatry

country: Canada

institute: University of British Columbia

description: Table corresponds to miRNA_107_Sep09 Agilent Feature Extraction file.

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


title: AB 5500 Genetic Analyzer (Saccharomyces cerevisiae BY4741)

status: Public on May 29 2014

organism: Saccharomyces cerevisiae BY4741


title: NimbleGen Pig Array

city: Nanjing

first: li

last: bin

state: Jiangsu

address: Zhong-ling street 50

country: China

institute: Jiangsu Academy of Agricultural Sciences

organism: Sus scrofa

description: description of gene name

manufacture_protocol: see manufacture's web site www.nimbleGen.com


title: Agilent-044345 UniversityPadova_Mytilus galloprovincialis_8x60K

status: Public on Dec 27 2014

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: Mytilus galloprovincialis

description: Roche 454 sequencing of hemocytes, oocytes, larval stages (trochophores, veliger, pediveliger, settled larvae, one moth seed) and adult tissues (gills, foot, mantle, muscle, digestive gland, gonads) have been performed. A total of 1,325,571 reads have been obtained and assembled through MIRA3 (default parameters). Assembly produced a total of 103,995 transcripts. A preliminary annotation was obtained for 43,218 contigs (41.5%) through Blast similarity searches conducted against several protein databases (e-value 1 E-5). 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 probes. A total of 59,971 out of 59,997 probes were successfully obtained, representing 50,680 different M. galloprovincialis contigs.

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


title: Illumina HiSeq 2000 (Nitrobacter winogradskyi)

status: Public on May 28 2014

organism: Nitrobacter winogradskyi


title: Lactococcus lactis KCTC 3769T whole genome expression array

first: Maytiya

last: Konkit

address: 84, Heukseok-ro, Dongjak-ku

department: Microbiology

institute: Chung-Ang University

organism: Lactococcus lactis

description:
Catalog Number: A4437-00-01, Design Name: 130108_T1272623_60mer_exp, Description: L. lactis KCTC 3769T, Accession Numbers: NC_002662, Genes: 2321, Probes/Transcript: 17, Probes: 4 x 72,000, Replicates: 5
Nimblegen Expression L. lactis KCTC 3769T 4X72K, Probe Length: 60mer, Number of Probes per, Target:6-17, Number of Replicate probe Sets per Array: 2-3, Feature Size: 16x16um, Array Size: 7.8x5.7mm, Slide size: 1x3 in.(25x76mm)
130108_T1272623_60mer_exp.ndf
130108_T1272623_60mer_exp.ndg

manufacture_protocol: NimbleGen Systems Inc.


title: Illumina MiSeq (Nitrobacter winogradskyi; Nitrosomonas europaea)

organism:
Nitrobacter winogradskyi
Nitrosomonas europaea


title: Illumina MiSeq (Nitrobacter winogradskyi)


title: Agilent-033151 NF1_array_complete

city: Ulm

first: Julia

last: Vogt

address: Albert-Einstein Allee 11

department: Institute of Human Genetics

country: Germany

institute: Ulm University

description:
NF1-Array_complete
Arrays of this design have barcodes that begin with 16033151 or 2533151.
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: Ion Torrent Proton (Macaca fascicularis)

status: Public on May 27 2014

organism: Macaca fascicularis


title: Illumina MiSeq (Nitrosomonas europaea)

organism: Nitrosomonas europaea


title: Illumina Genome Analyzer II (Fragilariopsis cylindrus CCMP1102)

organism: Fragilariopsis cylindrus CCMP1102


title: 454 GS (Arabidopsis arenosa; Arabidopsis thaliana)

organism:
Arabidopsis thaliana
Arabidopsis arenosa


title: NimbleGen Homo sapiens Expression Array [PROBE_ID version; 100718_HG18_opt_expr]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description:
FORMAT: 12x135K.
DESIGN_NAME: 100718_HG18_opt_expr
DESIGN_ID: 535523

relation: Alternative to: GPL16025 (SEQ_ID version)

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


title: Illumina Genome Analyzer II (Thalassiosira pseudonana CCMP1335)

organism: Thalassiosira pseudonana CCMP1335


title: 6K Yeast Genome Array

status: Public on May 26 2014

city: Jinan

first: Xiaoming

last: Bao

state: Shandong

address: Shanda Nan Road 27

department: State Key Laboratory of Microbial Technology

institute: Shandong University

organism: Saccharomyces cerevisiae

manufacture_protocol: The 6K Yeast Genome Array  contains 6389 70mer probes representing 6389 Saccharomyces cerevisiae open reading frames (ORFs). All 6389 probes are designed from the set of open reading frames (ORFs) obtained from the Saccharomyces Genome Database (SGD) at Stanford University (http://genome-www.stanford.edu/Saccharomyces/). The cDNA library is arrayed in 75×25 mm、chemically modified glass slide using SmartArrayTM (CapitalBio Corp., Beijing, China ). The yeast housekeeping gne Actin、RPS4B and yeast genomic DNA (used as positive control) were also arrayed in the same glass slide.  Hex was used as positive control in the pointting step, while salmon sperm DNA and 50% DMSO buffer was used as negative control in the pointting step. All the dot matrix divided into 48 sub-matrixes. The dot spacing is 200 um and the dot diameter is 160 um. Each gene repeat three times.


title: EXIQON miRCURY V10.1 LNA array

status: Public on May 23 2014

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

country: United Kingdom

institute: University of Stirling

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

description: Spotted Locked Nucleic Acid (LNA) on glass slides.


title: Illumina HiSeq 2000 (Vitis vinifera)


title: AB SOLiD System 3.0 (Panicum virgatum)

status: Public on May 22 2014

organism: Panicum virgatum


title: Qiagen/SABiosciences Human Cancer PathwayFinder PCR Array [PAHS-033A]

city: Rio de Janeiro

first: Tatiana

middle: Martins

last: Tilli

address: Andre Cavalcanti, 37 - Centro

country: Brazil

institute: Instituto Nacional de Câncer

organism: Homo sapiens

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


title: Agilent-034027 hscircexp_a [Probe Name Version]

city: Heidelberg

first: Anton

last: Shostak

address: Im Neuenheimer Feld 328

department: Circadian Rhythms and Molecular Clocks

institute: Heidelberg University Biochemistry Center (BZH)

description:
Arrays of this design have barcodes that begin with 16034027 or 2534027.

Supplementary file includes Feature Numbers and probe sequences.


title: Illumina HiSeq 2000 (Mycobacterium tuberculosis CDC1551)

status: Public on May 21 2014

organism: Mycobacterium tuberculosis CDC1551


title: Illumina Genome Analyzer (Myotis ricketti)

organism: Myotis pilosus


title: Illumina HiSeq 2000 (Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821)

status: Public on May 19 2014


title: Illumina HiSeq 2500 (Candidatus Liberibacter solanacearum)

organism: Candidatus Liberibacter solanacearum


title: Agilent-031723 Sparus aurata SAPD_v.3 (Feature Number version)

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

organism: Sparus aurata

description: GE 8x15k oligo microarray that covers 12,879 annotated transcripts of the gilthead sea bream (Sparus aurata). Oligonucleotides, 60-mer plus a linker, are synthesized directly on a glass slide using Agilent's SurePrint Technology. A total of 8,143 probes were already employed on a previous version of the microarray (GPL6467) and maintained the same ProbeName (ContigName plus suffix _1 or _2). To them, one probe (ContigName without any suffix) for 4,002 transcripts with known orientation was added. In addition, 2 probes with different orientation (sense and antisense) were designed for transcripts with unknown orientation. Both independent probes designed for the same transcript are named with an univocal ID; the sense probes are distinguished by suffix_S, while the anti-sense probes are distinguished by suffix _AS. For probes employed on GPL6467, the sequence and description of each gene (contig) are available in the SAPD (Sparus aurata PaDova) database (http://enne.cribi.unipd.it:5555/biomart/martview ; described in Ferraresso et al. 2008 (PMID 19055773)), where contig ID corresponds to probe ID on the array.

manufacture_protocol: See SurePrint Technology at manufacturer's web site (www.agilent.com).


title: Illumina Human660W-Quad v1.0 BeadChip (hg19)

city: Shanghai

first: Zhaohui

last: Gu

state: Shanghai

address: 197 Rui Jin Road II

department: School of Medicine

institute: Shanghai Jiao Tong University

technology: oligonucleotide beads

description: Reference file version: Human660W-Quad_v1_H (hg19)

manufacture_protocol: See manufacturer's website


title: ICDC Streptoccus suis 89/1591 120K tilling array map1

status: Public on May 20 2014

city: Beijing

first: Xiao

last: Zheng

address: Liuzi five hao

institute: China CDC

organism: Streptococcus suis

description:
Annotation in this record based on Streptococcus suis 89/1591 (GenBank accession number AAFA00000000.3).
Customized tilling arrays were generated by using 32-mer oligonucleotide probes spaced every eight bases across the reference genome on both strands.

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


title: NimbleGen Danio rerio expression array [090821_Danio_MAD_Dr_135K_EXP001]

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

organism: Danio rerio

description:
Design Name = 090821_Danio_MAD_Dr_135K_EXP001
Design ID = 10504

Details for the D. rerio microarray can be found in Rauwerda et al. BMC Research Notes 2010. It is a three prime biased expression microarray with 63,751 target probes and 7,742 probes with random sequences not targeting to the D. rerio genome.

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


title: ICDC Streptoccus suis 89/1591 120K tilling array map2


title: NimbleGen Staphylococcus aureus multistrain array [091208_NIM_SA_TIMECOURSE_FW_EXP]

organism: Staphylococcus aureus

description:
Design Name = 091208_NIM_SA_TIMECOURSE_FW_EXP
Design ID = 11052

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


title: Agilent-033305 Chironomus riparius 1M CGH array

organism: Chironomus riparius

description: The microarray was designed against C. riparius mRNA sequencing reads, and has been used to identify trustworthy sequencing reads to design an expression array. This 1M array is therefore not functionally annotated.


title: NimbleGen Zea mays 135K microarray [110902_Zmay_5B_PT_exp_HX12]

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

institute: University of Verona

organism: Zea mays

description:
12-plex array with 135,000 features per subarray. Feature size 12 um. Array is based on the ZmB73_5b_FGS_cdna.fasta.gz (): http://ftp.maizesequence.org/current/filtered-set/ZmB73_5b_FGS_cdna.fasta.gz. Number of probes per transcript: 3.

DESIGN_ID: 558281
native array description file: 110902_Zmay_5B_PT_exp_HX12.ndf
native array description file: 110902_Zmay_5B_PT_exp_HX12.ngd

The following annotation files are generated using the sequence identifier information deposited at http://ftp.maizesequence.org/current/functional-annotations/
ZmB73_5a_xref.txt
platform_upgrade.txt

manufacture_protocol: Standard NimbleGen manufacture protocol http://www.nimblegen.com/products/chip/index.html


title: NimbleGen_Petunia hybrida _array

status: Public on May 17 2014

city: Grossbeeren

first: Philipp

last: Franken

address: Theodor-Echtermeyer-Weg 1

institute: Leibniz Institute of Vegetable and Ornamental Crops - IGZ EV

organism: Petunia x hybrida

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

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


title: Illumina Genome Analyzer II (Ornithorhynchus anatinus)

status: Public on May 15 2014

last: GEO

organism: Ornithorhynchus anatinus


title: Agilent-038542 Bacillus pumilus array [B.pumilusJo2-Jan12]

city: Greifswald

first: Birgit

last: Voigt

address: F.-L.-Jahnstr. 15

department: Institute for Microbiology

organism: Bacillus pumilus

description:
Arrays of this design have barcodes that begin with 16038542 or 2538542.

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 (Oryza sativa; Xanthomonas oryzae pv. oryzae)

status: Public on May 14 2014

organism:
Oryza sativa
Xanthomonas oryzae pv. oryzae


title: Illumina Genome Analyzer II (Canis lupus familiaris)

organism: Canis lupus familiaris


title: Exiqon miRCURY LNA™ Universal RT miRNA PCR Human Serum/Plasma focus panel

manufacture_protocol: miRCURY LNA™ Universal RT microRNA PCR, 4x Ready-to-Use Serum/Plasma Focus microRNA PCR Panels supplied in two 384-well PCR plates. Each panel comprises 179 LNA™ microRNA primer sets focusing on serum/plasma relevant human microRNAs, including candidate reference microRNAs and 5 Spike-in control primer sets. For use with Roche LightCycler 480 instruments


title: Agilent-019727 CBF Synechocystis OW_AT 15K Expression array (Probe name version)

status: Public on May 13 2014

city: Sevilla

first: Luis

last: Lopez Maury

address: Av Americo Vespucio 49

country: Spain

institute: IBVF

organism: Synechocystis sp. PCC 6803

description:
8x15K expression
Oligos by OligoWiz and eArray
trimmed Oligos
Tm matching

Arrays of this design have barcodes that begin with 16019727 or 2519727.

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

The ID column represents the Agilent Probe Names.

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: CodeLink™ Rat Whole Genome Array - reannotated

city: Giessen

first: Melanie

last: Markmann

state: Hessen

address: Rudolf-Buchheim-Str. 7

department: Anaesthesiology

institute: University of Giessen

organism: Rattus norvegicus

description:
CodeLink™ Rat Whole Genome Bioarray is designed to interrogate approximately 34,000 transcripts representing most of the known and predictive genes of the rat genome, as it is described today in the public domain. Each transcript is represented by a 30-mer probe which is designed to conserved exons across the transcripts of targeted genes.
The probe sequences, representing well-annotated, full-length and partial rat gene sequences, were designed based on sequences selected from the NCBI UniGene build #129, RefSeq database (April 1, 2004 release) and dbEST database (March 20, 2004 release). Well-annotated mRNA or coding sequences were chosen to ensure usefulness for a large range of applications in basic research, biotechnology, and drug development. Each sequence was carefully screened to ensure high-quality, specific probe design, and to reduce redundancy of gene targets. All of the probes designed to these sequences were functionally tested, and over 95% were functionally validated against 10 rat tissues to ensure best representation of the gene and biologically relevant results.

The genes represented by CODELINK probe sets were annotated using the biocLite package (BioConductor) with the library "rwgcod.db" for CodeLink Rat Whole Genome arrays.


title: OSU-CCC MicroRNA Microarray Version 2.0 [condensed version]

city: Milan

first: Elisabetta

last: Crippa

address: Via Adamello 16

institute: IFOM-FIRC Institute of Molecular Oncology

organism: Homo sapiens

manufacturer: Microarray Shared Resource, Comprehensive Cancer Center, The Ohio State University (OSU-CCC)

manufacture_protocol: Manufacured using GE Healthcare's CodeLink (TM) 3-D Gel Matrix Technology. CodeLink(tm) Activated Slides are designed to covalently immoblize amine-modified DNA for microarrays. The slides are coated with a 3-D surface chemistry comprised of a long-chain, hydrophilic polymer containing amine-reactive groups. This polymer is covalently crosslinked to itself and to the surface of the slide. The crosslinked polymer, combined with end-point attachment, orients the immobilized DNA, and holds it away from the surface of the slide. The 1x printing buffer consists of 50 mM sodium phosphate at pH 8.5. Codelink slides are manufactured by SurModics and were formally sold as 3D-Link(tm) Activated Slides. ¹ Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions that is fitted with a printhead and 16 SMP3 print tips from Telechem. The microRNA microarray probe set is based on 40mer oligonucleotides from Sigma-Genosys. ¹ Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl) to a normalized 25 micromolar concentration. The miRNA microarray spot densities are 200 microns (center-to-center). The microarrays are printed on Codelink Activated Slide (PN300011)) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [Hugene10st_Hs_ENST_16.0.0]

description: custom CDF: HuGene10stv1_Hs_ENST.cdf (version 13, defining probe sets for transcripts from Ensembl core database version 58)

relation: Alternative to: GPL6244 (alternative CDF[official])

manufacture_protocol: See manufacturer's web site


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

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 based on netaffx build 34


title: Rodent TaqMan® Low Density miRNA Arrays A+B v2.0

city: Camperdown

first: Justin

last: Wong

state: NSW

address: Building 93 Royal Prince Alfred Hospital

institute: Centenary Institute

organism: Mus musculus

description: RT-PCR quantification of mature microRNAs

manufacture_protocol: see manufacturer's website


title: Illumina HiSeq 2000 (Clostridium cellulolyticum)

organism: Ruminiclostridium cellulolyticum


title: [Celegans] Affymetrix C. elegans Genome Array [CDF: Celegans_Ce_ENTREZG version 16]

city: Bethesda

last: admin

organism: Caenorhabditis elegans

description:
This is identical to GPL200 but a custom CDF environment was used to extract data [Brainarray Version 16, Celegans_Ce_REFSEQ].

CDF can be downloaded from the Brainarray site:
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/16.0.0/entrezg.asp

manufacture_protocol: see manufacturer's web site


title: Illumina HiSeq 2000 (Rhizopus microsporus)

organism: Rhizopus microsporus


title: Illumina HiSeq 2000 (Larimichthys crocea)

organism: Larimichthys crocea


title: Agilent-014868 Rabbit Custom Microarray GE 8x15K (Probe name version)

city: Gainesville

first: Richard

middle: W

last: Moyer

state: FL

address: 1600 SW Archer Rd

institute: University of Florida

organism: Oryctolagus cuniculus

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


title: 454 GS FLX (Nelumbo nucifera)

organism: Nelumbo nucifera


title: Illumina Genome Analyzer IIx (Pantoea stewartii)

organism: Pantoea stewartii


title: Illumina HiSeq 2000 (Botrytis cinerea B05.10)

status: Public on May 12 2014

organism: Botrytis cinerea B05.10


title: Illumina HiSeq 2000 (Cucumis melo)

organism: Cucumis melo


title: Illumina HiSeq 2000 (Papio cynocephalus)

status: Public on May 08 2014

organism: Papio cynocephalus


title: Illumina HiSeq 2000 (Locusta migratoria)

organism: Locusta migratoria


title: NanoString nCounter GX Human Immunology v1

status: Public on May 09 2014

city: Seattle

first: Gregory

last: Gonye

state: WA

address: 530 Fairview Ave North

institute: NanoString Technologies

technology: other

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


title: LC_MRA-1001_miRHuman_11.0_080411 Sanger_miRBase 10.1 (miRNA ID version)

city: Wuhan

first: Wenxin

last: Li

address: Luojia Hill, Wuchang

institute: Wuhan University

description:
Human miRNA microarray with 100% coverage of mature miRNAs listed in Sanger miRBase version 10.1.
μParaflo™ microfluidic chip (human microRNAs, Sanger miRBase 10.1)
A μParaflo™ microfluidic chip using a microcirculation pump

manufacture_protocol: see manufacturere's website http://www.lc-bio.com, http://www.lcsciences.com


title: NimbleGen Triticum aestivum CGH 270K array [120227_Taest_SRS_CGH]

city: Aas

last: Belova

address: arboretveien 6

department: department of plant science

country: Norway

institute: cigene

organism: Triticum aestivum

description:
Custom 12x270k CGH probe layout for Triticum aestivum (wheat) chromosome 7B probes provided by the customer. 67,500 experimental probes were added to the array in four replicate probe sets (BLOCK1-BLOCK4). No chromosome positions were provided so no POS, GFF or GCSTATS files could be created. Empty features on the array were filled with randomly generated probes of comparable length and composition.

DESIGN_ID: 566481
design name: 120227_Taest_SRS_CGH

native array description file: 120227_Taest_SRS_CGH.ndf
native array description file: 120227_Taest_SRS_CGH_UX12.ncd

Platform Columns file:DesignFile.pdf


title: Illumina HiSeq 2000 (Phaseolus coccineus)

organism: Phaseolus coccineus


title: Illumina HiSeq 2000 (Candida parapsilosis)

organism: Candida parapsilosis


title: Zymomonas mobilis ZM4 6.7K (expr_HX4)

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

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


title: Ion Torrent Proton (Jatropha curcas)

organism: Jatropha curcas


title: Illumina Genome Analyzer IIx (Solanum habrochaites)

status: Public on May 06 2014

organism: Solanum habrochaites


title: Agilent-049384 Aplysia Tellabs Array - 60k - v1.0 (Feature Number version)

city: River Forest

first: Robert

middle: J

last: Calin-Jageman

state: IL

address: 7900 West Division

department: Psychology

institute: Dominican University

organism: Aplysia californica


title: Rat microRNA array

status: Public on May 07 2014

city: Stillwater

first: CHAOQUN

last: HUANG

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

institute: Oklahoma State University

organism: Rattus norvegicus

distribution: non-commercial

manufacture_protocol: Probe sets, which contained 5' amino modified C6 oligos were synthesized by Sigma-Genosys (Woodlands, TX) at 100 µM concentration and suspended in 3 × SSC buffer. The oligos were diluted to 25 µM with 3 × SSC prior to use. The probes were then printed onto epoxy-coated slides (CEL Associates, Pearland, TX) with an OmniGrid 100 array (GeneMachine, San Carlos, CA) at 65% humidity and then incubated for 48 hours at the same humidity. Each slide contained three identical blocks in a landscape orientation. Within each block every probe was printed 6 times in 3 separate pairs. The oligo set also contained one probe for U6 and 3 probes for tRNAs as positive controls as well as one probe for a plant miRNA as a negative control.


title: Gallus gallus 14K A-MEXP-831

city: Cambridge

first: Antony

last: Jackson

state: Cambridgeshire

address: Tennis Court Road, Cambridge

department: Department of Biochemistry

institute: University of Cambridge

organism: Gallus gallus

technology: spotted DNA/cDNA

manufacture_protocol:
Clones for the target sequences were arrayed and grown overnight in Ampicillin Lbroth in 1 ml deep 96 well plates
Plasmids were prepared from the clones using the Qiagen plasmid prep kit on a Bio8000 Robot
The purified plasmids were used as PCR templates using T7 and T3 primer sequences to amplify the multiple cloning blocks with the inserts.
The amplified DNA was purified on Millipore Multiscreen plates.
The DNA was quantified by picogren and diluted to a concentrtaion of 250ng/ul DNA in 1 x spotting buffer
The DNA was printed on to Corning CMT-GAPS slides using the BioRobot MicroGrid II
Slides were allowed to Air dry prior to processing according to manufacturers protcol for blocking any unused binding sites.
Slides were then stored desicated until used


title: Illumina HiSeq 2000 (Catharanthus roseus)

organism: Catharanthus roseus


title: NimbleGen Erynnis Propertius 385K 1.0

status: Public on May 05 2014

city: Notre Dame

first: Jessica

last: Hellmann

state: IN

address: 100 Galvin Life Science Center

department: Biological Sciences

institute: University of Notre Dame

organism: Gesta propertius

description: NimbleGen Design ID OID22213, design for 25734 assembled unigenes of Erynnis Propertius transcriptome, attempted 5 probes per transcript, each probe replicated 3 times. The design also included control probes.

manufacture_protocol: Proprietary NimbleGen design software was used on 25734 assembled transcripts/unigenes.


title: NimbleGen Papilio zelicaon 385K 1.0

organism: Papilio zelicaon

description:
NimbleGen Design ID OID22214, design for 34609 assembled unigenes of Papilio zelicaon transcriptome, attempted 4 probes per transcript, each probe replicated 3 times. The design also included control probes.
090930_PZ_JH_EXP.ndf

manufacture_protocol: Proprietary NimbleGen design software was used on 34609 assembled transcripts/unigenes.


title: NimbleGen Haemophilus influenzae supragenome 144K array v1.0 [121023_H_influenza_ASRI_RE_expr]

city: Philadelphia

first: Benjamin

last: Janto

state: PA

department: Microbiology & Immunology

institute: Drexel University College of Medicine

organism: Haemophilus influenzae

description:
NimbleGen design name: 121023_H_influenza_ASRI_RE_expr
NimbleGen Design ID: 576211
Native array description file: 121023_H_influenza_ASRI_RE_expr
Since there is no annotation, there is no NGD file.

NimbleGen design name 121023_H_influenza_ASRI_RE_expr. An expression design for 2,890 clusters / 4,536 subclusters from all genes identified in 24 strains of Haemophilus influenzae. ~3 60-mer probe pairs (PM/MM) per core subcluster and ~13 60-mer probe pairs (PM/MM) per distributed subcluster.  Each probe is replicated four times.  The design includes random GC and other non-Haemophilus influenzae (Streptococcus pneumoniae) negative control probes.

The Platform table includes only subclusters that are represented in Haemophilus influenzae CZ4126/02.


title: AB SOLiD 4 System (Arabidopsis halleri)

status: Public on May 04 2014

last: GEO

organism: Arabidopsis halleri


title: Illumina HiSeq 2000 (Phaseolus vulgaris)

organism: Phaseolus vulgaris


title: Homo sapiens 385K estrogen responsive regions of HG18 091202_RM_HG18_est_resp_ChIP

city: Rennes

first: Raphaël

last: Métivier

address: Campus de Beaulieu

country: France

institute: CNRS UMR 6290

organism: Homo sapiens

description:
HG18
This ChIP-chip design consists of 385K probes, covering 23 estrogen-responsive regions of HG18; 50-75mer probes, 110-base probe spacing.
091202_RM_HG18_est_resp_ChIP.ndf
091202_RM_HG18_est_resp_ChIP.pos


title: Agilent R.palustris Custom Microarray GE 8x15k

city: Taipei

first: Chia-Wei

last: Hu

address: No. 1, Sec. 4, Roosevelt Road

department: Institute of molecular and cellular biology

country: Taiwan

institute: National Taiwan university

organism: Rhodopseudomonas palustris CGA009


title: NanoString nCounter GX Human Immunology v2

first: GEO

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: GO annotations courtesy of the Gene Ontology Consortium (08-Sep-2009 release date)

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


title: Affymetrix AGRONOMICS Tiling Array [CDF: agronomics1_TAIRG_15.0.0]

organism: Arabidopsis thaliana

manufacture_protocol: In collaboration with Affymetrix, the European AGRON-OMICS project has developed a new array including probes representing both strands of the entire Arabidopsis genome. Performance comparison with the ATH1 array indicates that both microarrays yield data of comparable quality, but that the new tiling array yields expression information for significantly more genes, since the ATH1 array profiles only about 65% of >33.000 TAIR9 annotated genes. The AGRONOMICS1 arrays also carry all of the original ATH1 sense probes, thereby streamlining the integration with ATH1-based results.


title: Illumina HiSeq 2000 (Mesorhizobium alhagi CCNWXJ12-2)

organism: Mesorhizobium alhagi CCNWXJ12-2


title: Illumina HiSeq 2000 (Culex pipiens pallens)

organism: Culex pipiens pallens


title: MDACC miRNA V5.0 array

status: Public on May 01 2014

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

manufacturer: custom designed miRNA microarray chip by Dr. Chang-Gong Liu from MD Anderson Cancer Center, based on miRBASE V15


title: Ion Torrent PGM (Arabidopsis halleri)


title: AB SOLiD 4 System (Arabidopsis lyrata)

organism: Arabidopsis lyrata


title: Exiqon Human miRCURY LNA Array (version 11.0) [miRBase 17]

city: Jinan

first: Xi

address: 44 Wen Hua West Road

institute: Shandong University

description:
Spotted miRNAs representing human and related viruses
Annotations based on miRBase version 17.

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


title: Illumina HiSeq 2000 (Pseudomonas aeruginosa)

organism: Pseudomonas aeruginosa


title: Illumina HiSeq 2000 (Macaca fascicularis)

organism: Macaca fascicularis


title: Agilent-018658

city: Thiverval Grignon

first: Reine

last: Malek

address: Avenue Lucien Brétignières

institute: INRA, UMR 1319 MICALIS

organism: Debaryomyces hansenii

manufacture_protocol: Standard Agilent protocols for Agilent Custom Oligo Microarray 8x15K


title: Agilent-037118 SN_single1_chr1 Custom Human 60k array (Feature Number version)

city: Atlanta

first: Scott

last: Newman

state: GA

address: 615 Michael Street

department: Human Genetics

institute: Emory University

description:
Agilent-037118 SN_single1_chr1

Arrays of this design have barcodes that begin with 16037118 or 2537118.

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-038641 OncoNIM CD3.0 Human CGH Microarray 8x60K (Feature Number version)

city: Madrid

first: Javier

last: Suela

state: M

address: Faraday 7

institute: NIMGenetics

description:
Agilent-038641 OncoNIM CD 3.0 036741

Arrays of this design have barcodes that begin with 16038641 or 2538641.

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-035750 Tilapia_chip

city: Bet Dagan

first: Orly

last: Eshel

address: The Volcani Center POB 6

department: Institute of Animal Science

country: Israel

institute: ARO

organism: Oreochromis niloticus


title: Agilent-038072 Gallus gallus array

city: Jouy en Josas

first: pierre

last: Sibille

address: domaine de Vilvert, bât 440

department: Virologie et Immunologie Moléculaires

institute: INRA

organism: Gallus gallus

description:
Agilent-038072 phylogenDC-galgal_1325503001035complet

Arrays of this design have barcodes that begin with 16038072 or 2538072.

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: 060783 Agilent Pinctada fucata array

status: Public on May 02 2014

city: Beijing

first: Shiguo

last: Li

state: Beijing

address: Tsinghua University

department: School of Life Sciences

institute: Tsinghua University

organism: Pinctada fucata

manufacture_protocol: see Agilent


title: NimbleGen S. cerevisiae ChIP-chip 385K Whole-Genome Tiling Array [2006-07-18_Scerevisiae_ChIP]

status: Public on Apr 19 2012

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Saccharomyces cerevisiae

description:
Design name  2006-07-18_Scerevisiae_ChIP
Format: 385K
Source: RefSeq
Build: sacCer1
Probe Length: 50mer
Median Probe Spacing: 32bp
http://www.nimblegen.com/products/chip/wgt/scerevisiae/385k/index.html

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


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

status: Public on Jan 29 2014

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Mus musculus

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

#%create_date=Thu Mar 28 11:12:16 2013 PDT
#%chip_type=MoGene-2_0-st-v1
#%lib_set_name=MoGene-2_0-st
#%lib_set_version=v1
#%genome-species=Mus musculus
#%genome-version=mm10
#%genome-version-ucsc=mm10
#%genome-version-ncbi=38
#%genome-version-create_date=2011-12-00
#%genome-lifted-method=liftOver
#%genome-lifted_from-species=Mus musculus
#%genome-lifted_from-version-ucsc=mm10
#%genome-lifted_from-version-ncbi=38
#%netaffx-annotation-date=2012-09-30
#%netaffx-annotation-netaffx-build=33

manufacture_protocol: See manufacturer's web site


title: OSU-CCC hsa-miRNA-chip version 3 [condensed human miRNA version]

city: Columbus

first: Ramiro

last: Garzon

address: 460 12th street

institute: Ohio State University

manufacture_protocol: Manufacured using GE Healthcare's CodeLink (TM) 3-D Gel Matrix Technology. CodeLink(tm) Activated Slides are designed to covalently immoblize amine-modified DNA for microarrays. The slides are coated with a 3-D surface chemistry comprised of a long-chain, hydrophilic polymer containing amine-reactive groups. This polymer is covalently crosslinked to itself and to the surface of the slide. The crosslinked polymer, combined with end-point attachment, orients the immobilized DNA, and holds it away from the surface of the slide. The 1x printing buffer consists of 50 mM sodium phosphate at pH 8.5. Codelink slides are manufactured by SurModics and were formally sold as 3D-Link(tm) Activated Slides.   Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions (http://www.genomicsolutions.com ) that is fitted with a printhead and 16 SMP3 print tips from Telechem (http://www.arrayit.com). The microRNA microarray probe set is based on 40mer oligonucleotides from Sigma-Genosys.   Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl) to a normalized 25 micromolar concentration. The miRNA microarray spot densities are 200 microns (center-to-center). The microarrays are printed on Codelink Activated Slide (PN300011)) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: Agilent-045271 Smed_v5_array_111412

city: Evanston

first: Christian

middle: Paul

last: Petersen

address: 2205 Tech Drive, Hogan 2-100

department: Molecular Biosciences

institute: Northwestern University

organism: Schmidtea mediterranea

description:
Arrays of this design have barcodes that begin with 16045271 or 2545271.

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

The ID column represents the Agilent Feature Extraction feature number.


title: Agilent-032431 DictyEX1

city: New York

first: Si

state: New York

address: 12 Waverly Place

department: Biology

institute: New York University

organism: Dictyostelium discoideum

description:
Arrays of this design have barcodes that begin with 16032431 or 2532431.

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: AB 5500xl Genetic Analyzer (Salmonella enterica subsp. enterica serovar Typhimurium)


title: Agilent-045343 Saccharomyces cerevisiae VinVoile 8x15K

status: Public on Apr 30 2014

city: Montpellier cedex1

first: Jean-Luc

last: Legras

address: 2, place Viala

department: UMR1083, Science pour l'Oenologie

description:
This isothermal melting probes array has been designed from the comparison of genome sequence P3 and RM11.1a according to PMID 22065438.

RM11.1a genome sequence can be obtained at: http://www.broadinstitute.org/annotation/genome/saccharomyces_cerevisiae.3/Home.html

Briefly, the array is built on pairs of probes, with each probe specific to one parent to calculate the hybridization differences between each probes in a pair which is proportional to the allele frequencies. The manner the probes used for the analysis are coded such as:
SACE-rm11-Chr03_1000412_1000394_1000422_r_P3
SACE-rm11-Chr03_1000412_1000395_1000422_f_RM11
where SACE-rm11 is the reference genome, Chr03_1000412 the SNP location, 1000394_1000422 the coordinates of the probe, and P3 or RM11 the name of the ancestral allele.

the array contains 6317 position for which a pair of probes has been designed, 1000 control non allele specific probes, and 300 probes that are deposited 5 times as repeat controls; The minimum distance between SNP is 441. The maximum distance is 54501 between position Chr05 9902429 to 956930, and then 20108 between position Chr07 585434 to 605541

Arrays of this design have barcodes that begin with 16045343 or 2545343.

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

The ID column represents the Agilent probe name.

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

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


title: Agilent-035590 UNBSJ rainbow darter 180K v1.0

status: Public on Dec 09 2013

city: Saint John

first: Paulina

middle: Andrea

last: Bahamonde

state: New Brunswick

address: 100 Tucker Park Road

department: Biology Department

institute: University of New Brunswick

organism: Etheostoma caeruleum

description: Please note that the platform annotations are based on top blast hits, not probe design. There is no gene annotation for rainbow darter on the database so far.

manufacture_protocol: RNA extraction normalized in Evrogen (moscow, Russia) - 454 sequencing Roche (Quebec, Canada) - annotation at Genotypic Technology (Bangalore, India) - Microarray print by invitrogen


title: Agilent-042279 Enchytraeus crypticus_v1

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

institute: MicroLife Solutions

organism: Enchytraeus crypticus

description:
Enchytraeus crypticus' microarray 4x180K_v1_20120720

Arrays of this design have barcodes that begin with 16042279 or 2542279.

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: OSU_CCC v4.0 [condensed version]

status: Public on Jul 22 2009

city: Padova

first: Matteo

last: Fassan

state: PD

address: via Gabelli 61

department: Department of Diagnostic Sciences & Special Therapies

institute: University of Padova

organism:
Homo sapiens
Mus musculus


title: SMD Print_1484 hoz

status: Public on Nov 15 2010

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

organism: Homo sapiens

manufacturer: Stanford Functional Genomics Facility, Stanford School of Medicine

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


title: JCVI PFGRC Bacillus anthracis 13K v4 array designed primarily based on strain Ames

status: Public on Mar 18 2010

city: Rockville

first: PFGRC

last: JCVI

state: MD

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Bacillus anthracis

description: This set includes 5821 oligonucleotides, has 13056 spots distributed in 48 blocks.

manufacture_protocol: 4QBA, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: mogene10st_Mm_ENTREZG_17.1.0]

status: Public on Sep 27 2013

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

relation: Alternative to: GPL6246 (Alternative CDF [official])

manufacture_protocol: This is identical to GPL6246 but a custom cdf environment was used to extract data. The cdf can be found at the link below.


title: [Sp20b_M] Affymetrix S. pombe Tiling 1.0FR Array

status: Public on Dec 01 2008

organism: Schizosaccharomyces pombe

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

The GeneChip® S. pombe Tiling 1.0FR Array is designed for identifying novel transcripts, mapping sites of protein/DNA interaction in chromatin immunoprecipitation (ChIP) experiments, and other whole-genome experiments.

The S. pombe 1.0FR Array is a single array comprised of over 1.2 million perfect match/mismatch probe pairs tiled through the complete Schizosaccharomyces pombe genome. Sequence information for chromosomes 1 to 3 and telomere clones was drawn from the Wellcome Trust Sanger Institute (September 2004). Probes are tiled for both strands of the genome at an average of 20 base pair resolution, as measured from the central position of adjacent 25-mer oligos, creating an overlap of approximately 5 base pairs on adjacent probes.

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

relation: Alternative to: GPL9672 (Alternative CDF)

relation: Alternative to: GPL10187 (Alternative CDF)

manufacture_protocol: see manufacturer's web site


title: USP Schistosoma mansoni 4x44K oligo-array version 1.0

status: Public on Oct 29 2009

city: São Paulo

first: Katia

middle: Cristina Pereira

last: Oliveira

state: O

address: Av Prof lineu prestes 748

department: Centro de Parasitologia e Micologia

institute: Instituto Adolfo Lutz

organism: Schistosoma mansoni

first: Sergio

last: Verjovski-Almeida

first: Thiago

middle: M

last: Venancio

middle: C

first: Giulliana

middle: T

last: Almeida

first: Ricardo

last: DeMarco

manufacture_protocol: All transcript information for S. mansoni available at both nr and dbEST databases at GenBank as of March, 2006 were filtered for contaminants and assembled with the CAP3 program. BLASTx were performed against the nr, with a cutoff of 1x10-10. The highest score alignment was used for annotation and assignment of the coding strand, in which the probe was designed. Those without significant hits against nr were annotated as no match, and probes for both strands were designed. In order to include possible new S. mansoni genes that have orthologous expressed sequences in S. japonicum but have not yet been cloned and sequenced in S. mansoni, we adopted the following strategy: S. japonicum RNA sequences from GenBank were assembled and submitted to a tBLASTx search against our assembled S. mansoni sequence set, and those with e-value lower than 1x10-20 were discarded. The remaining sequences were considered as S. japonicum transcripts without a clear corresponding S. mansoni transcript in the public database, thus being a candidate for a new S. mansoni gene. In order to obtain the S. mansoni sequence corresponding to these transcripts, the S. japonicum sequences were submitted to a BLASTn search against the S. manoni genome assembly (version 3), downloaded from the Wellcome Trust Sanger Institute. S. mansoni genomic loci that produced an alignment with at least 100 bases and had an identity higher than 70% were selected. Alternatively, tBLASTx was used, and S. mansoni genomic sequences were selected when they matched at least two high-scoring segment pairs (HSPs) each with e-value below 0.005. [NOTE added on October 2009: The criteria used for mapping S. japonicum evidence of transcription to the S. mansoni genome were poor; besides the set of bona fide probes, there were 521 spurious probes designed from japonicum information; all of these 521 probes were marked with a note *probe has no match to prediction=>abandon*, in the updated annotation table as of 28_October_2009. Expression data obtained with these 521 probes should be used with extreme caution.] These conserved regions in the S. mansoni genome were subsequently used in the probe design process. For each contig or singlet from the assembly, we selected all 60-mer sequences that satisfied a series of conditions that have been established by Agilent Technologies as follows: probes should not have 8 or more bases derived from low complexity regions; they should have a GC content of 35-55% and a melting temperature (Tm) of 68-76 Celsius degrees. In order to reduce cross-hybridization, each 60-mer sequence was searched by BLASTn against the S. mansoni genome sequence, downloaded from the Wellcome Trust Sanger Institute. In case that no hits were produced in this first search, the probes were used in a BLAST search against the CAP3 assembled mRNA/EST sequences. Probes were selected that had 100% match to the target sequence, which translates into a best-match alignment bit-score of 119. Those selected 60-mer sequences were checked for a low probability of cross-hybridization to non-specific targets by selecting probes for which the alignment bit-score of the second-best match was equal to or lower than 42.1. The selected probes were carried forward to the last step, which consisted of picking the probe closest to the 3-end for eachh target.


title: Agilent-042064 UNBSJ rainbow darter 15k v2.0


title: Agilent-019667 WEHI_Citrobacterrodentium_15k_V1.0

status: Public on Sep 22 2008

city: Parkville

first: Matthew

last: Wakefield

state: VIC

address: 1G Royal Parade

department: Bioinformatics

institute: Walter and Eliza Hall Institute

organism: Citrobacter rodentium

first: Marija

last: Tauschek

first: Gad

last: Frankel

manufacture_protocol: In Situ synthesis


title: Illumina HiSeq 2000 (Escherichia coli BW25113)

status: Public on Feb 08 2012

last: GEO

organism: Escherichia coli BW25113


title: NimbleGen Homo sapiens Expression Array [100718_HG18_opt_expr]

status: Public on Sep 07 2012

first: Inc

last: Nimblegen Systems

description:
FORMAT: 12x135K.
DESIGN_NAME: 100718_HG18_opt_expr
DESIGN_ID: 535523

relation: Alternative to: GPL18734 (PROBE_ID version)

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


title: NanoString nCounter Nano105 Gene Expression Custom CodeSet

status: Public on Oct 25 2013

city: Barcelona

first: Aleix

last: Prat

address: Passeig Vall d´Hebron 119

department: Translational Genomics

institute: VHIO

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


title: 454 GS FLX (Homo sapiens)

status: Public on Sep 11 2009


title: Illumina MiSeq (Schizosaccharomyces pombe)

status: Public on Oct 16 2012


title: Agilent-019118 Human miRNA Microarray 2.0 G4470B (miRNA ID version)

status: Public on Feb 26 2009

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description: The Human miRNA Microarray contains probes for 723 human and 76 human viral microRNAs from the Sanger database v.10.1. Integrating Agilent's probe design and unique labeling methods, this microarray delivers robust data with a simple, streamlined protocol. The generation of complete miRNA expression profiles using robust and highly sensitive microarrays allows broad insight into human miRNA expression and regulation.    This platform is based on the GeneView file produced by Agilent's feature extraction software.