title: AB SOLiD System (Rhizomucor miehei)

status: Public on Aug 22 2011

last: GEO

country: USA

organism: Rhizomucor miehei

technology: high-throughput sequencing

distribution: virtual


title: Illumina Genome Analyzer IIx (Bacillus subtilis)

organism: Bacillus subtilis


title: Illumina Genome Analyzer II (Drosophila willistoni)

status: Public on Aug 29 2011

organism: Drosophila willistoni


title: Illumina HiSeq 2000 (Drosophila willistoni)


title: Illumina Genome Analyzer IIx (Bifidobacterium animalis subsp. lactis CNCM I-2494; Lactobacillus delbrueckii subsp. bulgaricus; Lactococcus lactis subsp. cremoris CNCM I-1631; Streptococcus thermophilus CNCM I-1630)

status: Public on Aug 25 2011

organism:
Lactobacillus delbrueckii subsp. bulgaricus
Lactococcus lactis subsp. lactis CNCM I-1631
Bifidobacterium animalis subsp. lactis CNCM I-2494
Streptococcus thermophilus CNCM I-1630


title: Illumina Genome Analyzer IIx (Bacteroides; Bifidobacterium animalis subsp. lactis CNCM I-2494; Clostridia; Collinsella; Lactobacillus; Parabacteroides; Ruminococcus; Streptococcus thermophilus)

organism:
Bacteroides
Ruminococcus
Streptococcus thermophilus
Lactobacillus
Collinsella
Clostridia
Parabacteroides
Bifidobacterium animalis subsp. lactis CNCM I-2494


title: mirVana 1.3K v1.4 201205

status: Public on Aug 23 2011

city: Oslo

first: Heidi

middle: Maria

last: Namløs

address: PO Box 4953 Nydalen

department: Institute for cancer research, The Norwegian Radium Hospital

country: Norway

institute: Oslo University Hospital

organism: Homo sapiens

technology: spotted oligonucleotide

distribution: non-commercial

manufacturer: Norwegian Microarray Consortium (www.microarray.no), University of Oslo

manufacture_protocol:
The miRNA microarray experiments were performed using in-house spotted amino silane coated CMT UltraGAPS slides (Corning Life Sciences, Corning, NY, USA)
Each slide contained two independent arrays printed using the mirVana Probe Set v1, consisting of probes corresponding to 384 human, rat and mouse miRNAs (Life Technologies).
Each probe was printed in triplicate and the slides were UV-crosslinked to immobilize the double stranded probes


title: Agilent-026893 CTCFpedigreeArray3

status: Public on Aug 31 2011

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

technology: in situ oligonucleotide

description:
This is an array for targeted resequencing of the 134 bp interval surrounding 46,568 CTCF binding sites in CEPH pedigree 1459. Coordinates are hg18.

Tm-optimized

Arrays of this design have barcodes that begin with 16026893 or 2526893.

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: custom-commercial

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


title: Illumina Genome Analyzer IIx (Bifidobacterium animalis subsp. lactis CNCM I-2494)


title: Illumina Genome Analyzer IIx (human gut metagenome)

organism: human gut metagenome


title: Custom NimbleGen Nucleosome Position Analysis Array [080108_HG18_GS_ChIP]

status: Public on Aug 21 2011

city: Boston

first: Gavin

middle: R.

last: Schnitzler

state: MA

address: 800 Washington St. Box 80

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

description:
Custom array for mapping nucleosome positions on glucocorticoid receptor and cell-cycle regulated genes. Oligos on the array all map to a single location in the human hg18 genome build (also called 36.1).  Closely tiled genomic microarray for Chip2 and nucleosome position analysis, covering ~50kb regions of select human genes that are regulated by human SWI/SNF and/or GR.  Probes selected from OID12189_redo, int2, length 50 of various HG18 regions and customer supplied sequences, mean 9bp, median 10.
DESIGN_ID: 6938
DESIGN_NAME: 080108_HG18_GS_ChIP

manufacture_protocol: NimbleGen custom array spotting technology (circa 2008)


title: 3D-Gene Human miRNA V15_1.0.1

status: Public on Aug 17 2011

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

distribution: commercial

manufacture_protocol: See manufacture's web site


title: Illumina Genome Analyzer II (human oral metagenome)

organism: human oral metagenome


title: Histoplasma_capsulatum_G217B_WGTA_027820

status: Public on Aug 12 2011

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

organism: Histoplasma capsulatum

first: Catherine

middle: K

last: Foo

first: Anita

last: Sil

manufacture_protocol: Arrays were designed based on the Washington University Genome Sequencing Center (GSC) Histoplasma capsulatum strain G217B genome assembly as of 11/30/2004. Degenerate sequence and transposable elements were removed from the assembly using RepeatMasker with default parameters and the repeat families determined by the GSC. The remaining sequence was tiled with 50mer probes at an average frequency of one probe every 60 base pairs. Probe spacing was adjusted to minimize variation in melting temperature, and a subset of probes were truncated to optimize synthesis, in collaboration with CombiMatrix. The number of arrays used to tile a given contig was minimized, and the location of tiling probes was randomized within a given array. In addition, each array contained a common set of control probes, viz.: quality control (QC) and negative control (NC) probes designed by CombiMatrix; positive control probes tiling the genomic loci and non-genic flanking sequence of TEF1(P40911), TYR1, and CBP1(AF006209); and probes specific to a spike-in control sequence. Arrays were synthesized by CombiMatrix.


title: Histoplasma_capsulatum_G217B_WGTA_2052


title: [HT_Rat-Focus] Affymetrix HT Rat Focus Array

status: Public on Aug 24 2011

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Rattus norvegicus

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

#%create_date=2011-06-09 GMT-08:00 19:04:45
#%chip_type=HT_Rat-Focus
#%genome-species=Rattus norvegicus
#%genome-version=rn4
#%genome-version-ucsc=rn4
#%genome-version-create_date=2004-11-00
#%ensembl-date=2010-10-00
#%ensembl-version=60
#%entrezgene-date=2010-11-30
#%genbank-date=2010-10-15
#%genbank-version=180
#%ipi-date=2010-11-12
#%refseq-date=2010-11-7
#%refseq-version=41
#%netaffx-annotation-date=2011-06-22
#%netaffx-annotation-netaffx-build=32

manufacture_protocol: see manufacturer's web site


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray ENSG Version 14.1]

status: Public on Aug 26 2011

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

manufacture_protocol: see manufacturer's protocol


title: CapitalBio custom Human microRNA array

status: Public on Aug 13 2011

city: Guangzhou

first: Rongrong

last: Wei

address: 651 Dongfeng East Road

country: China

institute: Sun Yat-sen University

manufacturer: State Key Laboratory of Oncology in South China,Sun Yat-sen University

first: Guoliang

last: Huang

first: Huiyun

last: wang

manufacture_protocol:
Probe: synthesized by Invitrogen (Shanghai, China).
Microarray process: The microarray fabrication process in house was described in our previous study (Wang HY, Luo M, et.ct, Genome Res 2005;15:276-283) except for the printing by a SmartArrayTM -136 printer (CapitalBio Inc., Beijing, China).
Spotting protocol: Every probe was printed twice on the glass.
1456 spots were printed in 4 blocks. There were  364 spots  in every block.


title: NimbleGen Streptococcus mutans UA159 385K expression array [2004-07-14_SmutansUA159_24mer]

status: Public on Aug 18 2011

city: Chiyoda-ku

first: Hiromasa

last: Tsuda

state: Tokyo

address: 1-8-13 Kanda-surugadai

department: Biochemistry

institute: Nihon University School of Dentistry

organism: Streptococcus mutans UA159

description:
NimbleGen design name: 2004-07-14_SmutansUA159_24mer, NimbleGen design ID: 1201.  1:4 design for 1960  Streptococcus mutans UA159 (tax id: 210007) genes with sixteen 24-mer probe pairs (PM/MM) per gene.  Each probe is replicated 3 times.  The design includes random GC and other control probes.
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are linked below as supplementary files.

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


title: Histoplasma_capsulatum_G217B_WGTA_2045


title: Agilent custom array Minitrout 12.8K ID:032303

status: Public on Jul 18 2012

city: Madrid

first: Julio

middle: M

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

country: Spain

institute: INIA

organism: Oncorhynchus mykiss

manufacture_protocol:
Manufacturing:Agilent 60-mer SurePrint technology. Custom
8x15K Format:15K Array/Slide:8 Available Features/Array:15,208


title: PIQOR (TM) Skin  Microarray, human, antisense (914)

status: Public on Aug 30 2011

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

country: Germany

institute: Miltenyi Biotec GmbH

technology: spotted DNA/cDNA

description: The PIQOR (TM) Skin Microarray is composed of 1302 human specific cDNAs. These cDNAs include for each array six house-keeping genes as positive controls. In addition four E. coli DNA fragments and the corresponding in vitro transcribed RNAs (spiking controls) provide a control for the labeling and hybridisation efficiency. Two negative controls are given by spotted herring sperm DNA and buffer, respectively. All features are spotted in quadruplicate. The Platform data table reflects a condensed representation of the quadruplicate features.

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio

manufacture_protocol: Defined 200-400 bp fragments of selected cDNAs were generated by RT-PCR, cloned and sequence-verified. Amplified and purified cDNA inserts were spotted in quadruplicate on PIQOR slides using a proprietary piezoelectric spotter. The PIQOR slides were coated in a 2 step process generating a surface which covalently binds DNA molecules.


title: Histoplasma_capsulatum_G217B_WGTA_2048


title: Histoplasma_capsulatum_G217B_WGTA_2050


title: [HTMG430PM_Mm_ENTREZG] Affymetrix HT MG-430 PM Array Plate [Brainarray version 13]

status: Public on Aug 19 2011

organism: Mus musculus

relation: Alternative to: GPL11180 (Alternative CDF [official])


title: Histoplasma_capsulatum_G217B_WGTA_2051


title: PIQOR (TM) Skin  Microarray, human, antisense (925)


title: The Huck Institutes cocoa_ingenic_1

city: Reading

first: Nicholas

last: Cryer

state: Berkshire

address: Whiteknights Campus

department: School of Biological Sciences

country: United Kingdom

institute: University of Reading

organism: Theobroma cacao

manufacturer: DNA Microarray Facility at the The Huck Institutes of Life Sciences of the Pennsylvania State University (USA)

first: Craig

last: Praul

first: Siela

last: Maximova

manufacture_protocol: Probes were printed onto aminosilane coated slides using a GeneMachines OmniGrid microarrayer. Printing was performed at at 22°C and 55% humidity using Telechem Stealth SMP3B pins. Oligos were spotted in 2 replicate sets on each slide. As negative and probe spiking controls for normalization, a set of non-hybridizing oligos was also printed throughout the array (Alien, Spot Validation System, Stratagene).


title: NimbleGen_071112_Shewanella oneidensis MR-1 4x72K array

status: Public on Aug 20 2011

city: corvallis

first: Shoutao

last: Xu

state: OR

address: 116 gilmore hall, OSU

department: Department of biological and ecological engineering

institute: oregon State University

organism: Shewanella oneidensis MR-1

description:
NimbleGen design name 071112 Sone MR1 EXP X4, NimbleGen design multiplex (4x72K) array formats .  expression design for 4,295 genes.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.

designID : 6669
native array description file : 071112_Sone_MR1_EXP.ndf
native array description file : 071112_Sone_MR1_EXP.ngd

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


title: Histoplasma_capsulatum_G217B_WGTA_028428

last: Voorhies


title: Histoplasma_capsulatum_G217B_WGTA_028416

last: Foo


title: Histoplasma_capsulatum_G217B_WGTA_027874

last: Sil


title: Histoplasma_capsulatum_G217B_WGTA_028401


title: Histoplasma_capsulatum_G217B_WGTA_027873


title: Histoplasma_capsulatum_G217B_WGTA_027851


title: Histoplasma_capsulatum_G217B_WGTA_027848


title: Histoplasma_capsulatum_G217B_WGTA_027817


title: Histoplasma_capsulatum_G217B_WGTA_027598


title: Histoplasma_capsulatum_G217B_WGTA_027815


title: Histoplasma_capsulatum_G217B_WGTA_027596


title: Histoplasma_capsulatum_G217B_WGTA_027847


title: Histoplasma_capsulatum_G217B_WGTA_027840


title: Histoplasma_capsulatum_G217B_WGTA_027845


title: Histoplasma_capsulatum_G217B_WGTA_027593


title: Histoplasma_capsulatum_G217B_WGTA_027831


title: Histoplasma_capsulatum_G217B_WGTA_027844


title: Histoplasma_capsulatum_G217B_WGTA_027834


title: Histoplasma_capsulatum_G217B_WGTA_027592


title: Histoplasma_capsulatum_G217B_WGTA_027837


title: Histoplasma_capsulatum_G217B_WGTA_027819


title: Histoplasma_capsulatum_G217B_WGTA_027821


title: Histoplasma_capsulatum_G217B_WGTA_027562


title: Histoplasma_capsulatum_G217B_WGTA_027732


title: Histoplasma_capsulatum_G217B_WGTA_027600


title: Histoplasma_capsulatum_G217B_WGTA_027558


title: Histoplasma_capsulatum_G217B_WGTA_027553


title: Histoplasma_capsulatum_G217B_WGTA_027554


title: Histoplasma_capsulatum_G217B_WGTA_027557


title: Histoplasma_capsulatum_G217B_WGTA_027597


title: Histoplasma_capsulatum_G217B_WGTA_027565


title: Histoplasma_capsulatum_G217B_WGTA_027584


title: Histoplasma_capsulatum_G217B_WGTA_027556


title: Histoplasma_capsulatum_G217B_WGTA_027589


title: Histoplasma_capsulatum_G217B_WGTA_027547


title: Histoplasma_capsulatum_G217B_WGTA_027540


title: Histoplasma_capsulatum_G217B_WGTA_027545


title: Histoplasma_capsulatum_G217B_WGTA_027532


title: Histoplasma_capsulatum_G217B_WGTA_027531


title: Histoplasma_capsulatum_G217B_WGTA_027524


title: Histoplasma_capsulatum_G217B_WGTA_027527


title: Histoplasma_capsulatum_G217B_WGTA_027521


title: Histoplasma_capsulatum_G217B_WGTA_027528


title: Histoplasma_capsulatum_G217B_WGTA_027519


title: Histoplasma_capsulatum_G217B_WGTA_027163


title: Histoplasma_capsulatum_G217B_WGTA_027518


title: Histoplasma_capsulatum_G217B_WGTA_027522


title: Histoplasma_capsulatum_G217B_WGTA_027520


title: Histoplasma_capsulatum_G217B_WGTA_027161


title: NimbleGen 12-plex Gene Expression Array for Cynomolgus monkey (135K)

city: Basel

first: Tobias

last: Heckel

address: Grenzacherstr. 124

country: Switzerland

institute: F.Hoffmann-La Roche AG

organism: Macaca fascicularis

description:
The NimbleGen design is based on the Cynomolgus monkey genome/transcriptome version: v3 transcriptome.  An expression design with 20,047 probe sets for 25,798 transcripts including transcript variants covering 16,896 genes with six 60-mer probes (PM) per probe set. The number of replicates is 1 - i.e., only one set of probes on the array. The design includes random GC and other control probes.

NimbleGen design name: 091006_Cynomolgus_ERCC_expr_HX12

Native array description files:
091006_Cynomolgus_ERCC_expr.ndf
091006_Cynomolgus_ERCC_expr.ngd

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.

Transcript identifiers are composed as follows:

The Macaca fascicularis ID_REF is composed of a human NCBI GeneID and a human NCBI RefSeq transcript ID orthologous to the Macaca fascicularis transcript (note that the category NM is omitted for the predicted Cynomolgus transcripts).

Example: ID_REF = 10000_005465_cyno_0m0 = Cynomolgus transcript orthologous to human NCBI GeneID 10000 and human NCBI RefSeq ID NM_005465.


title: Histoplasma_capsulatum_G217B_WGTA_027516

first: Mark


title: Histoplasma_capsulatum_G217B_WGTA_027533

first: Catherine


title: Histoplasma_capsulatum_G217B_WGTA_027162

first: Anita


title: Histoplasma_capsulatum_G217B_WGTA_027159


title: Histoplasma_capsulatum_G217B_WGTA_027147


title: Histoplasma_capsulatum_G217B_WGTA_027157


title: Histoplasma_capsulatum_G217B_WGTA_027169


title: Histoplasma_capsulatum_G217B_WGTA_027153


title: Histoplasma_capsulatum_G217B_WGTA_027168


title: Histoplasma_capsulatum_G217B_WGTA_027146


title: Histoplasma_capsulatum_G217B_WGTA_027143


title: Histoplasma_capsulatum_G217B_WGTA_027145


title: Histoplasma_capsulatum_G217B_WGTA_027139


title: Histoplasma_capsulatum_G217B_WGTA_027141


title: Histoplasma_capsulatum_G217B_WGTA_027142


title: Histoplasma_capsulatum_G217B_WGTA_027137


title: Histoplasma_capsulatum_G217B_WGTA_027127


title: Histoplasma_capsulatum_G217B_WGTA_027116


title: Histoplasma_capsulatum_G217B_WGTA_027122


title: Histoplasma_capsulatum_G217B_WGTA_026611


title: Histoplasma_capsulatum_G217B_WGTA_027136


title: Histoplasma_capsulatum_G217B_WGTA_026602


title: Histoplasma_capsulatum_G217B_WGTA_026597


title: Histoplasma_capsulatum_G217B_WGTA_026592


title: Histoplasma_capsulatum_G217B_WGTA_026588


title: Histoplasma_capsulatum_G217B_WGTA_027134


title: Histoplasma_capsulatum_G217B_WGTA_026581


title: Histoplasma_capsulatum_G217B_WGTA_026580


title: Histoplasma_capsulatum_G217B_WGTA_026587


title: Histoplasma_capsulatum_G217B_WGTA_026589


title: Histoplasma_capsulatum_G217B_WGTA_026578


title: Histoplasma_capsulatum_G217B_WGTA_027140


title: Histoplasma_capsulatum_G217B_WGTA_026573


title: Histoplasma_capsulatum_G217B_WGTA_026585


title: Histoplasma_capsulatum_G217B_WGTA_026217


title: Histoplasma_capsulatum_G217B_WGTA_026222


title: Agilent E. coli Gene Expression Microarray G4813A (GenePix version)

status: Public on Aug 11 2011

city: Princeton

first: Alison

last: Hottes

state: NJ

address: 220 Carl Icahn Lab Washington Road

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

organism:
Escherichia coli O157:H7 str. EDL933
Escherichia coli CFT073
Escherichia coli O157:H7 str. Sakai
Escherichia coli str. K-12 substr. MG1655

description:
Agilent-020097 (GenePix scanner)
Content sourced from TIGR Comprehensive Microbial Resources database
K12-MG1655 (Version 1), Dec 2000
O157:H7 VT2-Sakai (Version 3), Apr 2001
CFT073 (Version 11), Aug 2003
EDL933 (Version 2), Apr 2001


title: Histoplasma_capsulatum_G217B_WGTA_026575


title: Illumina HiSeq 2000 (Camponotus floridanus)

last: GEO

organism: Camponotus floridanus


title: Agilent-028686 Tvap454 8x60 K oligo expression array (Probe Name version)

city: Harpenden

first: Nikos

last: Karatolos

state: Herts

address: West Common

institute: Rothamsted Research

organism: Trialeurodes vaporariorum

manufacture_protocol:
1.Oligos are arrayed in Greiner 384-well flat-bottom plates. Each well contains 600 pmol of 70-mer oligo.
Arrays were designed using Agilent eArray software. Custom gene expression arrays were generated by Agilent Technologies in their 8X60K format.   See manufacturer's web site at http://www.agilent.com/.


title: LC Sciences Human 470 miRHuman v9.1

city: Dijon

first: Laurent

last: Delva

address: 7 boulevard Jeanne d'Arc

country: France

institute: Inserm U866

description:
This platform contain probes for the human 470 miRNA described in miRBase v9.1.
Layout File: miRHuman_9.1_070207

manufacture_protocol: Microarrays designed for genome-wide microRNA expression profiling and built on the flexible and powerful µParaflo® microfluidic on-chip synthesis platform. The current probe content comes from version 9.1 of the miRBase sequence database.


title: Affymetrix Rat Expression 230A Array (CDF: rae230arnentrezgcdf_13.0.0)

status: Public on Aug 10 2011

city: Toronto

first: Cindy

middle: Q.

last: Yao

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: Custom CDF (Brainarray Entrez Gene v13.0.0)

relation: Alternative to: GPL341 (Alternative CDF [official])

manufacture_protocol: See manufacturer's web site


title: Illumina Genome Analyzer IIx (Entamoeba histolytica)

status: Public on Aug 09 2011

organism: Entamoeba histolytica


title: Affymetrix GeneChip Rat Genome 230 2.0 Array (CDF: rat2302rnentrezgcdf_13.0.0)

relation: Alternative to: GPL1355 (Alternative CDF [official])


title: Illumina HiSeq 2000 (Harpegnathos saltator)

organism: Harpegnathos saltator


title: Thermoanaerobacter pseudethanolicus 39E 2.3K oligo array version 1.0

city: Norman

first: Christopher

middle: L

last: Hemme

state: OK

address: 101 David L. Boren Blvd.

department: Botany and Microbiology

institute: University of Oklahoma

organism: Thermoanaerobacter pseudethanolicus ATCC 33223

description: The microarray contains genes for both Thermoanaerobacter species X514 and Thermoanaerobacter pseudethanolicus 39E.  The X514 probes are identical to GPL11001.  X514 was used as the reference and all X514 probes were included on the array.  Unique 39E genes (i.e. probes that do not cross-hybridize with X514) were included as unique spots on the array.  39E genes common between the two species were not included on the array and 39E probes that hybridized to X514 counterparts were mapped back to the 39E gene.  The genes (both common and unique) on the array are named according to the 39E annotation in Genbank.  A conversion file between the 39E and X514 gene names is attached for reference.

manufacturer: Institute for Environmental Genomics, University of Oklahoma, USA

first: Lu

last: Lin

first: Zhili

last: He

first: Aifen

last: Zhou

first: Liyou

last: Wu

first: Joy

last: Van Nostrand

manufacture_protocol: All designed oligonucleotides were commercially synthesized without modification by Invitrogen.  Oligonucleotide probes were prepared in 50% dimethyl sulfoxide (Sigma Chemical Co., MO).  (http://ieg.ou.edu/protocol/Protocols/DMSO_Printing_8.pdf)  The concentration of oligonucleotide probes was adjusted to 100pmol/L. were spotted onto SuperAmine glass slides (Telechem International, CA) using a PixSys 5500 robotic printer (CartesianTechnologies Inc., CA).  Each probe had two replicates on a single slide.  After printing, the oligonucleotide probes were fixed onto the slides by UV cross-linking (600 mJ of energy) according to the protocol of the manufacturer (Telechem International, CA). (http://aem.asm.org/cgi/reprint/71/7/3753)


title: NOAA Karenia brevis v3 (11K on 8x15K array format)

city: Charleston

first: Frances

last: Van Dolah

state: SC

address: 219 Fort Johnson Rd

institute: Marine Biotoxins Program, NOAA Center for Coastal Environmental Health and Biomolecular Research

organism: Karenia brevis

manufacture_protocol: 60-mer oligonucleotide probes were designed from EST contigs derived from Karenia brevis cDNA libraries using Array Designer v 4.0 following Agilent's recommendations for Tm, GC content, and position. Probes were submitted to Agilent's eArray website for randomization and addition of control probes. For details on printing see Agilent's website www.agilent.com.  60-mer oligonucleotide probes were designed from EST contigs derived from Karenia brevis cDNA libraries using Array Designer v 4.0 following Agilent's recommendations for Tm, GC content, and position. Probes were submitted to Agilent's eArray website for randomization and addition of control probes. For details on printing see Agilent's website www.agilent.com.  60-mer oligonucleotide probes were designed from EST contigs derived from Karenia brevis cDNA libraries using Array Designer v 4.0 following Agilent's recommendations for Tm, GC content, and position.  Probes were submitted to Agilent's eArray website for randomization and addition of control probes.  For details on printing see Agilent's website www.agilent.com.


title: Illumina Genome Analyzer II (Limanda limanda)

status: Public on Aug 02 2011

organism: Limanda limanda


title: Illumina Genome Analyzer IIx (Lupinus albus)

organism: Lupinus albus


title: Illumina Genome Analyzer IIx (Acinetobacter baumannii)

status: Public on Aug 04 2011

organism: Acinetobacter baumannii


title: Nimblegen T. cruzi 290K version 1.0

status: Public on Aug 06 2011

city: Athens

first: Todd

last: Minning

state: GA

address: Rm 310 Coverdell

department: CTEGD

institute: University of Georgia

organism: Trypanosoma cruzi

description: Trypanosoma cruzi CL-Brener strain

manufacture_protocol: See manufacturer's website


title: NimbleGen Human CGH 385K Whole-Genome Tiling Array [80101_HG18_WG_CGH_v2_X1]

status: Public on Aug 08 2011

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Homo sapiens

description:
native array description file : 080101_HG18_WG_CGH_v2_X1.ndf
native array description file : 080101_HG18_WG_CGH_v2_X1.pos
design ID : 6918

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


title: HG18_HELP

city: Bronx

first: John

last: Greally

state: NY

address: 1301 Morris Park Avenue

department: Genetics

institute: Albert Einstein College of Medicine

description:
Annotation in this record based on NCBI human build 36.1
Genomic regions representing >1.32 million loci genome-wide, representing each HpaII-amplifiable fragment from 50 – 2,000 bp with 1-2 oligonucleotides encoding unique sequence at each locus


title: ATH long intergenic non-coding RNA array v1 (Probe version)

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

organism: Arabidopsis thaliana

description: ATH long intergenic non-codingRNA (lincRNA) v1 array  are designed based on Agilent 8x15K formatted microarray platform. Arabidopsis lincRNAs are identified by analysis of 200 tiling-array datasets using Reproducibility-based Tiling-array Analysis Strategy(RepTAS). Based on the reproducibility of detection, transcript size, probe capacity, base composition, GC content and EST evidence, we finally selected 4,652 lincRNAs with high confidence to design expression array. The final array consisted of probes for these 4,652 lincRNAs, 173 pri-miRNAs, 248 nature antiscence RNA and 90 well-characterized protein-coding mRNAs. We desiged 3 probes for each transcript. Current annotation of ATH lincRNA v1 array is based on Arabidpisis genome annotation version TAIR9.

manufacturer: Laboratory of Plant Molecular Biology, Rockefeller University; Agilent Technologies"

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


title: Febit_IMIKRO_Streptococcus_pyogenes_16K_v1

city: Rostock

first: Nadja

last: Patenge

address: Schillingallee 70

department: Institute of Medical Microbiology, Virology and Hygiene

institute: University of Rostock

organism: Streptococcus pyogenes NZ131

manufacturer: Febit biomed GmbH Company (Heidelberg, Germany)

manufacture_protocol: in situ oligonucleotides,  custom-made tiling array of the intergenic regions (50 nucleotides probes length with a 15 nucleotides overlap) for both strands. Synthesis performed by Geniom Microarray Facility (Febit biomed GmbH, Heidelberg, Germany)


title: ATH long intergenic non-coding RNA array v1 (Feature Number version)

description: ATH long intergenic non-coding RNA (lincRNA) v1 array  are designed based on Agilent 8x15K formatted microarray platform. Arabidopsis lincRNAs are identified by analysis of 200 tiling-array datasets using Reproducibility-based Tiling-array Analysis Strategy(RepTAS). Based on the reproducibility of detection, transcript size, probe capacity, base composition, GC content and EST evidence, we finally selected 4,652 lincRNAs with high confidence to design expression array. The final array consisted of probes for these 4,652 lincRNAs, 173 pri-miRNAs, 248 nature anti-sense RNA and 90 well-characterized protein-coding mRNAs. We desiged 3 probes for each transcript. Current annotation of ATH lincRNA v1 array is based on Arabidpisis genome annotation version TAIR9.


title: 027169-Agilent Yeast Aarray for S.cerevisiae and S.paradoxus (4 X 44K)

status: Public on Aug 01 2011

city: Rehovot

first: Itay

last: Tirosh

address: herzl

department: Molecular genetics

country: Israel

institute: Weizmann Institute of Science

organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus

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


title: Murine 0.6K,cDNA array Version 8.0

city: Porto

first: Maria

middle: Salome

last: Gomes

address: Rua do Campo Alegre 823

department: IBMC/ICBAS

country: Portugal

institute: Universidad do Porto

organism: Mus musculus

manufacture_protocol: Preparation of the  iron chip microarray platform Clone amplification and purification: 894 murine 'expressed sequence tag' (EST) clones,that were sequence verified from both ends were chosen for the iron chip. The ESTs were selected to contain the 3'end of a cDNA (i.e. the polyadenylation signal) and to extend for at least 300bp towards the 5'end. In addition,15 positive and negative controls were chosen,that are derived from bacterial and arabidopsis genomes (see below). All clones were PCR amplified with 5´amino-alkyl modified vector primers using the Roche Diagnostics Expand High Fidelity PCR System. The PCR products were purified on a BIOMEK 2000 robot (Beckman),using the Macherey-Nagel NucleoSpin Multi-96 Extract PCR purification system. After purification,5 µl of the purified PCR reaction were subjected to quality control on 1% agarose gels. Size,quality (single vs. multiple bands) and concentration of the PCR fragments were determined. SSC buffer was added,resulting in a final concentration of 2xSSC. 9 µl of the diluted PCR products were transferred to a 384-well plate for spotting. Spotting and attachment: Silanised glass slides were used as a platform for spotting on the Omnigrid (GeneMachines) spotting robot. Split pins from Telechem (spot size 120 µm) were used. All clones were spotted in triplicates next to each other. External controls and selected house keeping genes were spotted in dilutions 1:1,1:2 and 1:4. Cy3 labelled oligonucleotides were spotted to control the performance of the spotting needles and DNA attachment quality in four of the eight resulting subgrids. Spotting was performed at 24°C,60% relative humidity. After spotting,the slides were immediately placed in a 50°C humid oven for 3 hours and additionally baked at 100°C for 10 min,to stabilise DNA binding to the silanised glass surface


title: Potato 10k cDNA array version 4 (CLONE_ID version)

city: Waipahu

first: Ratnesh

last: Singh

state: HI

address: 94-340 Kunia Rd

institute: Hawaii Agriculture Research Center

organism: Solanum tuberosum

description:
Spotted PCR amplified cDNA array on glass.
This version 4 set includes PCR products amplified from 15264 potato EST clones.
Each PCR product is duplicated on the slide. The number of total spots including empty and controls is 32448.


title: SFGF Human 41K cDNA array (print batches: SHGO and SHEB)

city: Palo Alto

first: Bing

last: Zhang

address: 3373 Hillview Ave

institute: Stanford University


title: SBO_LAB_2k_version2

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

organism:
Leuconostoc mesenteroides
Oenococcus oeni
Pediococcus acidilactici
Pediococcus pentosaceus
Staphylococcus aureus
Streptococcus thermophilus
Enterococcus faecalis
Enterococcus faecium
Enterococcus hirae
Lactococcus lactis
Lactobacillus acidophilus
Levilactobacillus brevis
Lentilactobacillus buchneri
Lacticaseibacillus casei
Weissella confusa
Lactobacillus delbrueckii
Lactobacillus helveticus
Lentilactobacillus hilgardii
Lactiplantibacillus pentosus
Lactiplantibacillus plantarum
Lactobacillus gasseri
Lacticaseibacillus paracasei
Limosilactobacillus reuteri
Latilactobacillus sakei
Companilactobacillus alimentarius
Lactobacillus amylovorus
Companilactobacillus farciminis
Limosilactobacillus fermentum
Fructilactobacillus fructivorans
Fructilactobacillus sanfranciscensis
Bifidobacterium
Brevibacterium linens
Latilactobacillus curvatus
Lactobacillus johnsonii
Leuconostoc citreum
Leuconostoc pseudomesenteroides
Limosilactobacillus pontis
Enterococcus casseliflavus
Mammaliicoccus lentus
Limosilactobacillus panis
Lacticaseibacillus rhamnosus
Lactobacillus crispatus
Enterococcus mundtii
Lactiplantibacillus paraplantarum
Companilactobacillus paralimentarius
Limosilactobacillus frumenti
Lentilactobacillus parabuchneri
Companilactobacillus mindensis
Furfurilactobacillus rossiae

description: This species-independent microarray for Lactic Acid Bacteria (LAB) enables to assess the expression of genes that play a key role in the production of sugar carbolites, bacteriocins, exopolysaccharides, and aromas, in probiotic and biosafety characteristics, and in stress response.  The array design contains 20,160 features (30-mer oligonucleotides) printed in a layout of 12 meta rows and 4 meta columns; consisting out of 20 rows and 21 columns per block. The array measures the expression of 6,209 functional genes. All oligonucleotides were spotted with three duplicates, except for 16 oligonucleotides which had 6 replicates. The Lucidea Universal ScoreCard Controls (Amersham Biosciences Buckinghamshire, UK) are added (864 spots). A set of 621 spots remained empty.

first: Stefan

last: Weckx

first: Joke

last: Allemeersch

first: Roel

last: Van der Meulen

first: Gino

last: Vrancken

first: Luc

last: De Vuyst

first: Paul

last: Van Hummelen

manufacture_protocol: The oligos were obtained from Isogen Life Science BV and Sigma Genosys and diluted to 25 µM in 100 mM Na-Phosphate buffer plus 0.000675% sarcosyl (Sigma-Aldrich). A MicroGrid II spotter (Genomic Solutions, Huntingdon, United Kingdom) was used to spot the oligos using 10K pins on CodeLink™ Activated Slides (GE Healthcare, Bucks, United Kingdom). After spotting, the CodeLink™ Activated Slides were placed in a humid chamber containing saturated NaCl for minimal 24 h. Unused active groups were blocked with preheated blocking solution (50 mM ethanolamine, 0.1M Tris pH=9.0) at 50 °C for 30 min. Slides were rinsed twice with MilliQ water and washed with preheated 4xSSC, 0.1% SDS at 50 °C for 30 min in a shaking water bath. Slides were rinsed with MilliQ water and dried by centrifugation at 800 rpm for 3 min.


title: NimbleGen Drosophila melanogaster array [090828_Dmel_exp]

status: Public on Aug 03 2011

city: Wuhan

first: Xiao-Qin

last: Xia

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

department: Center for Molelcular and Cellular Biology of Aquatic Organisms

institute: Institute of Hydrobiology, the Chinese Academy of Sciences

organism: Drosophila melanogaster

description:
12-plex expression design for Drosophila melanogaster, Flybase release 5.7, 21,051 initial CDS seqs; 8 probes per target, 1 copy of probes on array; 16,637 exemplars representing 21,039 CDS sequences
DESIGN_ID: 10545
DESIGN_NAME: 090828_Dmel_exp

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


title: NimbleGen Homo sapiens CGH HX3 array [090130_HG18_Decipher_opt]

status: Public on Jun 30 2011

first: Stephen

middle: W

last: Scherer

address: 686 Bay Street

department: Genetics and Genomic Biology

institute: The Hospital for Sick Children

description:
Genome build: hg18
NimbleGen Homo Sapiens 9105 HG18 WG CGH HX3


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

status: Public on Jul 01 2011

city: Toledo

first: Rodrigo

last: Maza

state: Toledo

address: Finca La Peraleda s/n

department: Unidad de Neurología Experimental

institute: Hospital Nacional de Parapléjicos (SESCAM)

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

description: Array covering Sanger miRBase 12.0 and Exiqon miRPlus mature miRNAs.

manufacture_protocol: See manufacturers website


title: WUSTL Yersinia pestis 14K array

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

organism: Yersinia pestis

manufacturer: Washington University School of Medicine

manufacture_protocol: Oligos were synthesized using standard methods by Illumina (San Diego, CA). The oligonucleotides were dissolved at a concentration of 50 μM in 3X SSC with 0.75M betaine and were printed in triplicate on Corning Epoxy slides by a locally constructed linear servo arrayer.


title: Grape Custom Array 4x2K developed by Malacarne et al. for grapevine-P.viticola interaction analysis

status: Public on Apr 27 2011

city: S. Michele a/Adige

first: Giulia

last: Malacarne

state: Trento

address: Via Edmund Mach,1

department: Genomics and Biology of Fruit Crops Department

country: Italy

institute: Edmund Mach Foundation

organism: Vitis vinifera

manufacture_protocol: Probes were directly synthesized on a 4x2K Combimatrix array by an in situ oligo synthesis system developed by Combimatrix Corporation (Mukilteo, USA) using the Combimatrix CustomArray synthesizer. Standard synthesis protocol provided by Combimatrix  was used.


title: Taqman Array Human MicroRNA A Card v2.0

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

technology: RT-PCR

description:
Format: 384-well plate
Manufacturer: Applied Biosystems
See manufacturer's website (http://www.appliedbiosystems.com/).


title: Agilent-017903 Staphylococcus aureus V5 Bis 15K (basic)

status: Public on Nov 07 2008

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

institute: Genomic Research Laboratory

organism:
Staphylococcus aureus
Staphylococcus aureus subsp. aureus NCTC 8325
Staphylococcus aureus subsp. aureus COL
Staphylococcus aureus subsp. aureus Mu50
Staphylococcus aureus subsp. aureus N315
Staphylococcus aureus subsp. aureus MW2
Staphylococcus aureus subsp. aureus MRSA252
Staphylococcus aureus subsp. aureus MSSA476
Staphylococcus aureus subsp. aureus USA300

description: 60-mers oligonucleotide probes, in-situ synthesis

first: Patrice

last: Francois

first: Antoine

last: Huyghe

first: Jacques

last: Schrenzel

manufacture_protocol: Sure Print Technology-In situ synthesis


title: LMEUC_Efae_26K_v1

status: Public on Apr 21 2011

city: Caen

first: jean-christophe

last: giard

address: esplanade de la paix

institute: Université de Caen

organism: Enterococcus faecalis V583

manufacture_protocol: in situ oligonucleotides, E. faecalis V583 custom-made tiling array of the intergenic regions (50 nucleotides probes length with an15 nucleotides overlap) for both strands. Synthesis performed by Geniom Microarray Facility (Febit biomed GmbH, Heidelberg, Germany)


title: Agilent-030521 Halobacterium sp. NRC-1 Tiling V1 013324

status: Public on Apr 22 2011

city: Seattle

first: Serdar

last: Turkarslan

state: WA

address: 401 Terry Ave

institute: Institute for Systems Biology

organism: Halobacterium salinarum NRC-1

description:
Halobacterium sp. NRC-1 Whole genome tiling Array. 60 bp tiles with 24 bp spacing.  Includes 237 probes for 150 ncRNA selected from Next-Gen sequencing

Arrays of this design have barcodes that begin with 16030521 or 2530521.

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: Cotton cDNA array (28,178 features)

status: Public on Jun 01 2010

city: Beijing

first: Yu-Xian

last: Zhu

address: 5# Summer Palace Road

institute: College of life sciences, Peking University

organism: Gossypium hirsutum

manufacturer: CapitalBio Corporation, National Engineering Research Center for Beijing Biochip Technology, 18 Life Science Parkway, Beijing 102206, China

first: Xiang

last: Jin

first: Liang

last: Zhang

first: Jing

last: Cheng

first: Yuxian

manufacture_protocol:
To establish upland cotton fiber-specific cDNA array, we constructed cDNA library from 5-10 day post anthesis cotton fibers when fiber cells elongate most quickly. Secondly, we randomly sequenced over 100,000 ESTs from this library and acquired a gene pool of more than 28,000 UniESTs. The cotton UniESTs were then PCR-amplified and printed onto microarray. This array is comprised of 28,178 high-quality cotton cDNAs (with average length = 768bp) representing over 24,000 cotton genes.
Individual bacterial clones were selected and distributed into 96-well plates. PCR amplification of DNA using primers specific to the plasmid vector sequences flanking the insert cDNA (T3 forward and T7 reverse primers) were performed in 96-well PCR plate in a Perkin-Elmer 9600 thermocycler in 50-μL reactions containing 1× PCR buffer (TaKaRa, Dalian, China), 2.0 mM MgCl2, 0.2mM dNTPs, 10 pmol of each primer, 5 units of Taq polymerase, and 10 ng plasmid template. The PCR cycle consisted of one round at 95℃ for 3 min, then 35 cycles including 95℃ for 1 min, 55℃ for 20s and 72℃ for 90s, with a final extension at 72℃ for 5 min. 1 μL of the PCR reactions was analyzed in a 1% agarose gel to verify the success of the amplification. The remaining PCR products were precipitated with addition of 100 μL of anhydrous ethanol and resuspended in 15 μL of 50% DMSO for arraying. As a result, 28,323 cDNA were amplified and printed on the cDNA microarrays.
cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine's linear RNA amplification method and subsequent enzymatic reaction. Double-stranded (ds) cDNA containing T7 RNA polymerase promoter sequence was synthesized from 10 μg of total RNA using a cDNA synthesis kit following the manufacturer’s instructions (TaKaRa). A T7-OligodT primer (5’-AAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGCGCTT TTTTTTTTTTTTTTTV -3’) was used to replace the poly T primer provided in the kit. Synthesized ds cDNA was purified using the PCR Purification kit (Qiagen) and purified products were eluted using 60-μL elution buffer. A half of the eluted ds cDNA was reduced to 8 μL before subjecting to in vitro transcription in 20 μL of reaction mixture using the T7 RiboMAX Express Large Scale RNA Production System (Promega) for 3 h at 37℃. Amplified RNA (aRNA) was purified using the RNeasy Mini kit (Qiagen). For labeling of the probes, 2 μg of aRNA was mixed with 2 μg of random hexamers, denatured at 70℃ for 5 min, cooled on ice before adding 4 μL of first strand synthesis buffer, 2 μL of 0.1M DTT, 1 μL 10 mM mixed dNTPs, and 1.5 μL SuperScript II (Invitrogen) to the system. The reaction mixture was first incubated at 25℃ for 10 min before transferring to 42℃ for 60 min. The labeled cDNA was purified using a PCR Purification kit (Qiagen), reduced to 10 μL volume and mixed with 2 μg of random nonamers, heated to 95°C for 3 min and cooled on ice immediately. 10×buffer, dNTP and Cy5- or Cy3-dCTP (Amersham Pharmacia Biotech) was added to a final concentration of 120 μM each for dATP, dGTP and dTTP, 60 μM for dCTP and 40 μM for Cy5 or Cy3 dyes respectively. One μL Klenow (Takara) was added to the mixture and the reaction progressed for 60 min at 37℃. The labeled cDNA was again purified with a PCR Purification kit (Qiagen), resuspended in elution buffer and quantitatively adjusted based on the efficiency of dye incorporation. Appropriate amount of the labeled cDNA was mixed in a final volume of 30 μL of hybridization solution that contains 50% formamide and 1×hybridization buffer (Amersham Bioscience), and was denatured at 95℃ for 3 min prior to loading onto a microarray. The array was hybridized at 42℃ overnight and was first washed for 5 min at 42°C with washing solutions that contain 0.2% SDS and 2×SSC followed by a second wash using washing solutions that contain 0.2% SSC for 5 min at room temperature.


title: CSHL Homo Sapiens 85k oligo array 4.0

status: Public on Oct 01 2008

city: Cold Spring Harbor

first: Vladimir

last: Grubor

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: Custom-designed NimbleGen manufactured oligonucleotide microarray 85k probes

first: Robert

last: Lucito

first: Michael

middle: H

last: Wigler

first: Joan

last: Alexander

first: Diane

last: Esposito

first: Jen

last: Troge

first: Lakshmi

last: Muthuswami

manufacture_protocol: photolithography


title: Potato 10k cDNA array version 4

status: Public on Jun 08 2006

city: Rockville

first: Jia

last: Liu

state: MD

address: 9712 Medical Center Drive

institute: Plant Genomics

first: C

middle: R

last: Buell

relation:
Alternative to: GPL10564
Alternative to: GPL14110

manufacture_protocol:
Spotted PCR amplified cDNA array on glass.
This version 4 set includes PCR products amplified from 15264 potato EST clones.
Each PCR product is duplicated on the slide. The number of total spots including empty and controls is 32448.


title: Agilent-020097 E. coli Gene Expression Microarray (Probe Name version)

status: Public on Apr 01 2011

last: Agilent Technologies

state: CA

institute: Agilent Technologies

organism:
Escherichia coli O157:H7 str. EDL933
Escherichia coli CFT073
Escherichia coli O157:H7 str. Sakai
Escherichia coli str. K-12 substr. MG1655

description:
E. coli (K12-MG1655, CFT073, O157-H7 EDL933, O157-H7 VT2-Sakai) Oligo 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 GPL13360.


title: Histoplasma_capsulatum_G217B_WGTA_026583

status: Public on Aug 12 2011

city: San Francisco

first: Mark

last: Voorhies

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

organism: Histoplasma capsulatum

first: Catherine

last: Foo

first: Anita

last: Sil

manufacture_protocol: Arrays were designed based on the Washington University Genome Sequencing Center (GSC) Histoplasma capsulatum strain G217B genome assembly as of 11/30/2004. Degenerate sequence and transposable elements were removed from the assembly using RepeatMasker with default parameters and the repeat families determined by the GSC. The remaining sequence was tiled with 50mer probes at an average frequency of one probe every 60 base pairs. Probe spacing was adjusted to minimize variation in melting temperature, and a subset of probes were truncated to optimize synthesis, in collaboration with CombiMatrix. The number of arrays used to tile a given contig was minimized, and the location of tiling probes was randomized within a given array. In addition, each array contained a common set of control probes, viz.: quality control (QC) and negative control (NC) probes designed by CombiMatrix; positive control probes tiling the genomic loci and non-genic flanking sequence of TEF1(P40911), TYR1, and CBP1(AF006209); and probes specific to a spike-in control sequence. Arrays were synthesized by CombiMatrix.