title: GenoExplorerTM microRNA array ver.2011

status: Public on Jan 15 2015

city: New York

first: Jia Min

last: Loo

state: NY

address: 1230 York Avenue #342

country: USA

institute: The Rockefeller University

organism: Homo sapiens

technology: spotted oligonucleotide

distribution: commercial

manufacture_protocol: Please see complete manufacturer information at http://www.genosensorcorp.com/info_about_service.html


title: Agilent-037639 Bacillus subtilis 168 (Probe Name version)

status: Public on Nov 19 2014

city: Groningen

first: Wout

last: Overkamp

address: Nijenborgh 7

country: Netherlands

institute: Rijksuniversiteit Groningen, Department of Molecular Genetics

organism: Bacillus subtilis subsp. subtilis str. 168

technology: in situ oligonucleotide

description:
Arrays of this design have barcodes that begin with 16037639 or 2537639.

The ID column represents the Agilent Probe name.

*** 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 GPL17104

distribution: custom-commercial

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


title: GenoExplorerTM microRNA array ver.2010


title: Agilent-047432 eco_k12_mg1655_23bp 047431

status: Public on Jul 22 2014

city: Seattle

first: Aaron

last: Brooks

state: WA

address: 401 Terry Avenue North

institute: Institute for Systems Biology

organism: Escherichia coli

description:
E coli K12 MG1655 tiling array, 23bp sliding window. Includes >10,000 probes surrounding predicted operon break sites, 6 bp resolution

Arrays of this design have barcodes that begin with 16047432 or 2547432.

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: PINARRAY2

status: Public on Feb 27 2015

city: Malaga

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

organism: Pinus pinaster

technology: spotted DNA/cDNA

distribution: non-commercial

manufacture_protocol:
1. Probes were PCR-amplified from four SSH libraries. SSH libraries were constructued with the PCR-select cDNA subtraction kit (Clontech, Palo Alto, CA, USA). Two SSH libraries were produced using cDNAs from compression and opposite differentiating xylem by performing the subtraction procedure in both directions. Two additional SSH libraries were produced using cDNA from juvenile and mature differentiating xylem by the same procedure. Nested PCR primers 1 and 2R included in the kit were used for PCR amplification.
2. PCR products were purified with 96-well multiscreen filter plates (Millipore Corp. Bedford, MA)
3. Purified-cDNA probes in 50% DMSO were prepared to a concentration between 100 and 200 ng/µl in 384-well plates (Genetix)
4. cDNA probe was printed in duplicate onto ULTRA gaps II coated slides (Corning, NY, USA) using a Qarray2 (Genetix Ltd, Queensway, UK) with a telechem printing head and 16 split pins (Biorobotics, Cambridge, UK) with a 4 x 4 configuration.
5. After printing, the slides were dried at room temperature and the spotted cDNA were cross-linked to the slide surface by UV irradiation at 300 mJ/cm²


title: Agilent-034429 holi_V01 034240

status: Public on Jun 24 2014

city: Zagreb

first: Tomislav

last: Domazet-Loso

address: Bijenicka cesta 54

department: Division of Molecluar Biology

country: Croatia

institute: Ruder Boskovic Institute

organism: Hydra oligactis

description:
Arrays of this design have barcodes that begin with 16034429 or 2534429.

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: CRIBI Tiling array for the identification of 5' end of pig miRNAs

status: Public on Mar 31 2014

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

organism: Sus scrofa

manufacturer: CRIBI biotechnology centre http://microcribi.cribi.unipd.it

manufacture_protocol: 12K Combimatrix microarray were synthesized using the Combimatrix synthesizer (Combimatrix) that allows in-situ synthesis of oligonucleotide probes through the phosphoramidites chemistry.


title: Ion Torrent PGM (Rhodococcus jostii)

last: GEO

organism: Rhodococcus jostii

technology: high-throughput sequencing

distribution: virtual


title: CRIBI pig mRNA expression array [Ensembl (Ver. 56) and UniGene (Ver. 38)] (averaged probe version)

manufacture_protocol: 90K Combimatrix microarray were synthesized using the Combimatrix synthesizer (Combimatrix) that allows in-situ synthesis of oligonucleotide probes through the phosphoramidites chemistry.


title: CRIBI Tiling array for the identification of 3' end of pig miRNAs (platform 2)


title: Illumina HiSeq 2000 (Mucor circinelloides f. lusitanicus)

organism: Mucor lusitanicus


title: CRIBI Tiling array for the identification of 3' end of pig miRNAs (platform 1)


title: CRIBI pig mRNA expression array [platform 2]

description: Concerning mRNAs Ensembl transcripts (Ver. 56) and UniGene (Ver. 38) sequences were used to produce a pig dedicated microarray platform to analyze mRNAs gene expression. Based on sequence similarity we rejected UniGene features that overlapped more than 40% with an Ensembl transcript. After this filter we obtained 40,267 UniGene clusters and 19,603 Ensembl transcripts (protein coding + pseudogenes + retrotransposed elements). Starting from these sequences, the microarray probes were computed using 6 different algorithms. We obtained probes with different specificity and different distances from the mRNA 3 -end. The two best probes for every sequence, basing on the reliability of the prediction algorithm and their vicinity to the 3 -end were experimentally tested for their specificity and performance (GEO: ..). For any transcript with a replicated probe, we selected the probe that was the most responsive and specific in a hybridization trial performed with a pool of mRNAs from 20tissues. The specificity was based on the intensity fluorescence, as suggested by Kronick (Kronick 2004). Replicated probes with higher intensity fluorescence were considered the most responsive for the specific gene. The resulting whole genome microarray, here used for the gene expression analysis, was composed by 17,048 replicated probes and 963 not replicated specific for the Ensembl transcripts, 11,363 replicated probes specific for the UniGene clusters of length comprised between 778 nt and 1,348 nt (Figure SM1), and 28,790 single probes specific for the remaining UniGene clusters. All probes mapped proximally to the 3 end of the target sequences (Figure SM2 A and SM2 B): 98.2% of the probes for the Ensembl transcripts mapped within 2,000 nt from their 3 end while the percentage for UniGene clusters reached 99.9%. 114 UniGene clusters and 1,592 Ensembl transcripts were not identified by specific probes.


title: CRIBI Pig 2K miRNA array

manufacture_protocol: 2K Combimatrix microarray were synthesized using the Combimatrix synthesizer (Combimatrix) that allows in-situ synthesis of oligonucleotide probes through the phosphoramidites chemistry.


title: Illumina HiSeq 2000 (Ehrlichia sp. HF)

status: Public on Mar 28 2014

organism: Ehrlichia japonica


title: [Fusariuma520094] Affymetrix Fusarium GeneChip 2006

city: Shanghai

first: Weihua

last: Tang

address: 300 Fenglin Rd

country: China

institute: Shanghai Inst. Plant Phys. & Eco.

organism: Fusarium graminearum

manufacture_protocol: see manufacturer's web site


title: Illumina HiSeq 2000 (Ixodes scapularis)

organism: Ixodes scapularis


title: Illumina HiSeq 2000 (Ehrlichia chaffeensis str. Wakulla)

organism: Ehrlichia chaffeensis str. Wakulla


title: Illumina MiSeq (Phaeodactylum tricornutum)

status: Public on Mar 29 2014

organism: Phaeodactylum tricornutum


title: Illumina HiSeq 2000 (Ehrlichia chaffeensis str. West Paces)

organism: Ehrlichia chaffeensis str. West Paces


title: Agilent-030094 Candida albicans 15k v2 Barcode microarray

city: Paris

first: Sadri

last: ZNAIDI

address: 25 rue du Docteur Roux

department: Mycology Department

country: France

institute: Institut Pasteur

organism: Candida albicans


title: Illumina HiSeq 2000 (Ehrlichia chaffeensis str. Osceola)

organism: Ehrlichia chaffeensis str. Osceola


title: Illumina HiSeq 2000 (Ehrlichia chaffeensis str. Liberty)

organism: Ehrlichia chaffeensis str. Liberty


title: Illumina HiSeq 2000 (Ehrlichia chaffeensis str. Jax)

organism: Ehrlichia chaffeensis str. Jax


title: Illumina HiSeq 2000 (Ehrlichia chaffeensis str. Heartland)

organism: Ehrlichia chaffeensis str. Heartland


title: Illumina HiSeq 2000 (Ehrlichia chaffeensis str. Arkansas)

organism: Ehrlichia chaffeensis str. Arkansas


title: Agilent-019492 Project-0160-002

status: Public on Mar 27 2014

city: Dublin

first: Heather

middle: J

last: Quinn

address: College green

department: Microbiology

country: Ireland

institute: Trinity College Dublin

organism: Escherichia coli K-12

description:
K12 composite design with RNA genes

Arrays of this design have barcodes that begin with 16019492 or 2519492.

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: NimbleGen Plasmodium falciparum 120525_Pfal_CJ_Reseq_CGH

city: Baltiomore

first: Christopher

last: Jacob

state: MD

address: 685 W. Baltimore St.

department: Center for Vaccine Development

institute: University of Maryland School of Medicine

organism: Plasmodium falciparum

description:
Genome build information - PlasmoDB v.5.5
resequencing array for 33,716 genomic loci
120525_Pfal_CJ_Reseq_CGH.ndf
120525_Pfal_CJ_Reseq_CGH.pos

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


title: [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [hugene20st_Hs_ENSG]

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Homo sapiens

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

November 15, 2012: HuGene-2_0-st-v1.na33.hg19.transcript.csv

manufacture_protocol: See manufacturer's web site


title: Illumina HiSeq 2000 (Acropora hyacinthus complex sp. E JTL-2012)

organism: Acropora aff. hyacinthus sp. E JTL-2012


title: Illumina HiSeq 2000 (Candida albicans; Mus musculus)

status: Public on Mar 21 2014

organism:
Candida albicans
Mus musculus


title: Agilent-029556 Prunus mume 3X60K microarray

status: Public on Mar 26 2014

city: Kyoto

first: Hisayo

last: Yamane

address: Sakyo-ku

department: Grad. Sch. of Agriculture

country: Japan

institute: Kyoto University

organism: Prunus mume

description:
The ORF sequences (Japanese apricot unigene sequences) corresponding to each probe are provided in the 'target_seq.txt' file.
We have obtained these sequences by 454-pyrosequencing and have not deposited our unigenes to GenBank but deposited short read sequences to DDBJ DRA (DRP000532).
Our obtained Prunus mume unigene sequences are purblicly open in our database http://bioinf.mind.meiji.ac.jp/JADB/index.html

EST ID corresponds to identifier used in Prunus mume unigenes
Several probes are not from Prunus mume unigenes but from peach gene ID (http://www.rosaceae.org/) and those probes do not have EST ID and only have gene ID.

manufacture_protocol: The 113629 unigenes obtained previously (Habu et al., 2012) were used for microarray probe selection using the Agilent eArray application tool (https://earray.chem.agilent.com/earray/) following the manufacture’s instruction manual.


title: AB SOLiD 4 System (Pseudo-nitzschia multiseries)

status: Public on Mar 24 2014

organism: Pseudo-nitzschia multiseries


title: Illumina HiSeq 2000 (Deinococcus deserti)

status: Public on Mar 20 2014

organism: Deinococcus deserti


title: Illumina HiSeq 2000 (Bordetella holmesii)

organism: Bordetella holmesii


title: Illumina HiSeq 2000 (Thermococcus kodakarensis KOD1)

organism: Thermococcus kodakarensis KOD1


title: Illumina Genome Analyzer II (Kluyveromyces lactis)

organism: Kluyveromyces lactis


title: Microarray for gene expression of Pseudozyma antarctica T-34 and Ustilago maydis UM521 [100617_RDKK270_PantUmay_expr]

city: Tsukuba

first: Hideaki

last: Koike

state: Ibaraki

address: Higashi 1-1-1

institute: National Institute of Advanced Industrial Science and Technology

organism:
Mycosarcoma maydis
Moesziomyces antarcticus T-34

description: NimbleGen design name 100617_RDKK270_PantUmay.  An expression design for 6,555 genes from Pseudozyma and 6,846 genes from Ustilago.  Each probe is replicated 5 times.  The design includes random GC and other control probes.

manufacture_protocol: 4x72K DNA array . See manufacturer's website at http://www.nimblegen.com/.


title: Illumina HiSeq 2000 (Candida albicans; Homo sapiens)

organism:
Candida albicans
Homo sapiens


title: Custom Staphylococcus aureus 8x15k Gene Expression Microarray (AMADID:27491)

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

organism: Staphylococcus aureus

description: designed by Genotypic Technology Private Limited


title: AB SOLiD 4 System (Thalassiosira pseudonana)

organism: Thalassiosira pseudonana


title: AB SOLiD 4 System (Fragilariopsis cylindrus)

organism: Fragilariopsis cylindrus


title: IMP Genomics Mouse 53MM

status: Public on Mar 22 2014

city: MADRID

first: Erwin

middle: F

last: Wagner

address: C/ Melchor Fernández Almagro, 3

department: F-BBVA CCBP

institute: CNIO

organism: Mus musculus

manufacture_protocol: Prepare in house spotted  DNA Microarrays      PCRs and Printing        Dilution plates:    Prepare 96 well pates and label them ( eg. 1130 Dil)  Aliquot 95 µl dd water into each well (roboter “95µl verteilen”)  Pipette 5µl from the copy plate into the Dilution plate (roboter “dilution plate”).  (If you do not perform immediately:  Heat for 10 min at 94°C ( PCR machine)  Spin down  Freeze away or perform PCR reaction)      PCRmix for a 96 well plate:    550µl 10x buffer (100mM Tris.HCl pH8.3, 500mM KCl)  11µl UNI-primer (1µg/µl CCCAGTCACGACGTTG)  11µl REV-primer (1µg/µl CACAGGAAACAGCTATG)  11µl 1M MgCl2 (has to be adjusted to Taq used)  44µl 25mM dNTPs  110µl Taq  1887µl dd water  2514µl 3M Betaine  5138µl total Volume (45µl per well)    PCR Reaction:    Transfer 5µl of the working dilution (see bacteria growth) to PCR-plate (MJResearch, skirted plate) containing 45µl PCRmix,     seal plate with sealing sheet (ABGene AB-0558)    Spin down    PCR program:  94°C 1min      35X 94°C 30sec    52°C 30sec    72°C 1min 30sec    72°C 5min      Load 5µl PCR product on a 1% agarose gel for quality control        Preparation for printing the PCR products:    Concentrate PCR products in a Speedvac (Determine time until no further reduction of volume is seen, in our case it is at least 4 hours when using 8 plates per batch, final volume is approximately 6-7 µl)    Add 6µl 6xSSC    Shake vigorously up to 3 hours at 4°C (we use a modified vortex,  probably mixing with pipetting robot before transfer into 384 well plates will do)    Transfer into 384 well plates    Store PCR-plates at –80°C    Spot onto Schott Nexterion A slides      Slide Blocking:  Fixation:  Put slides 30 min on 80°C heating plate and cross link with 600mJ(Schott) or 60mJ with Poly-lysine slides    Blocking:  Dissolve 1.37 g Succinic Anhydride in 90ml N-Methyl - Pyrrolidone   Add 2.5 ml N-methylimidazol (FLUKA)    Immediately pour it into a slide chamber and incubate slides for 1 hour with slight agitation    transfer slide into 0.1 % SDS for 20sec.    transfer into H2O for 20sec    Denature:  Slides are briefly washed in water (or DCE) and incubated for 4 min in a boiling water bath    After a brief rinse in 95% EtOH spin slides 4 min 1200rpm for drying     For 30 slides in a big chamber with 300 ml blocking solution:  (4,11 g SA in 270 ml NMP and 7,5 ml NMI)


title: Illumina HiSeq 2000 (Oryctolagus cuniculus)

organism: Oryctolagus cuniculus


title: Illumina HiSeq 2500 (Xenopus (Silurana) tropicalis)

organism: Xenopus tropicalis


title: Jilin University Illumina DGE system

status: Public on Mar 25 2014

city: jilin

first: liu

last: qianhong

state: jilin

address: No.77, Hanlin Road, Economic Development Districe

department: College of Animal Science and Veterinary Medicine

institute: Jilin Agricultural Science and Technology University

technology: other

manufacture_protocol: Solexa/Illumina's digital gene expression system, a tag-based transcriptome sequencing method.


title: MRA-1002_miRMouse_17

city: Los Angeles

first: Shiyu

last: Liu

address: 2250 Alcazar Street, CSA103

institute: CCMB


title: Illumina HiSeq 1000 (Rattus norvegicus)

organism: Rattus norvegicus


title: NimbleGen Estuarine Microbial Community Array [Berkeley Pier; Od_Ps_Bpier_V3C]

city: Livermore

first: Xavier

last: Mayali

state: CA

address: 7000 East Ave

department: Chemical Science

institute: Lawrence Livermore National Laboratory

organism: marine metagenome

description:
mixed community
B_pier

manufacture_protocol: on ITO glass slides functionalized with superepoxy2 by Arrayit


title: Agilent-041518 Sodalis glossinidius 8x15k array_v1

city: Montpellier

first: Anne

last: Geiger

address: Laboratoire de Recherches et de Coordination sur les Trypanosomoses TA,A-17 / G Campus international de Baillarguet

institute: UMR 177 IRD-CIRAD

organism: Sodalis glossinidius

description:
Sodalis glossinidius array v1

Arrays of this design have barcodes that begin with 16041518 or 2541518.

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 (Gasterosteus aculeatus)

organism: Gasterosteus aculeatus


title: Illumina HumanHT-12 V3.0 expression beadchip [HumanHT-12_V3_0_R2_11283641_A]

organism: Homo sapiens

technology: oligonucleotide beads

manufacture_protocol: See the manufacturer's website.


title: Agilent-020980 Acropora formosa coral 8x15K

city: Vicksburg

first: Kurt

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

organism: Acropora formosa

description:
Coral consortium including endosymbionts of the branched coral Acropora formosa.
Microarray Development Methods: An RNA library was assembled by sampling RNA from controls and all RDX exposure treatments performed in the 5d A. formosa bioassay. Full-length cDNAs were reverse transcribed from the coral RNA library using Clontech SMART-PCR (Clontech Laboratories Inc., Mountain View, CA). In order to generate sequence information for as many unique cDNAs as possible, the cDNA library was normalized using the Trimmer cDNA Normalization Kit (Evrogen JSC, Moscow, Russia) to insure sequencing of both high- and low-abundance transcripts. The normalized cDNA library was sequenced using massively-parallel Roche 454 GS-FLX pyrosequencing (Margulies et al. 2005) with several modifications that improved sequence reproducibility while reducing labor-intensive sample manipulations (Wiley, et al. 2009 and Roossinck, et al. 2010). The conceptual pipeline for sequence processing and annotation has been illustrated in supplemental Figure S1. Sequences were quality filtered and sequence assembly was conducted using CAP3 software. Contigs and singletons were searched against the NCBI GenBank protein database using blastx where E ≤ 10-5 was considered a significant match to an expressed sequence tag (EST). Gene targets were annotated where possible with identity, functionality using KEGG and KOG databases. In order to study the metabolic profile of coral symbionts, sequence reads were split into two different bins using the phylogenetic information provided by BLAST. Sequences associated with non-coral species were extracted at the Anthozoa class. Metabolic profiles of coral and non-coral sequences were then compared by calculating the ratio of the transcripts. The 7,500 sequences identified with the lowest E values (which represent the best homology to known genes) were uploaded to eArray (Agilent Technologies) in both forward and reverse sequence orientation (due to lack of reading-frame information to assess the sense strand). eArray was utilized to incorporate these 15,000, 60mer oligonucleotide probes into a custom microarray design (Agilent Technologies) for A. formosa. This design represents 7,500 sense-antisense probe-pairs providing quality control of the microarray analysis for cross hybridization. One probe in each probe pair represents a nonsense sequence and our expectation was that no target should have specific binding to it (see above for anti-sense strand exclusion methods).

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


title: Agilent-028889 Tursiops truncatus AM_v1

city: Ferrara

first: Annalaura

last: Mancia

address: via L.Borsari, 46

department: Life Sciences and Biotechnology

institute: University of Ferrara

organism: Tursiops truncatus

description:
Arrays of this design have barcodes that begin with 16028889 or 2528889.

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-021323 Zebra Finch AgilentSongbird2 Oligoarray

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Taeniopygia guttata

description:
Part #: G2514F and AMADID #: 021323
The Agilent songbird array contains over 43K unique transcripts, many of which can be used to distinguish between specific splice variants. The sequences used for generating features (probes) on the array are from sequencing projects performed at the Keck Center of the University of Illinois, at Rockefeller University by Xiao-Chieng Li, and at Duke University. All of these sequences are stored in the songbirdtranscriptome.net website. In addition to these sequences, over 450 features on the array were designed from clones found in genbank.


title: Agilent-040802 Eh-Expression-v2

city: Bayreuth

first: Alfons

middle: R

last: Weig

address: Universitaetsstrasse 30

department: Genomics and Bioinformatics

country: Germany

institute: University of Bayreuth

organism: Aspergillus ruber

description:
4 probes per CDS, best distribution

Arrays of this design have barcodes that begin with 16040802 or 2540802.

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


title: Agilent-033226 smed_v2

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

organism: Schmidtea mediterranea

description:
2nd generation of Schmidtea med. array, incporporating more recent view of transcriptome. Contains new probes and some probes from smed_v1.
Arrays of this design have barcodes that begin with 16033226 or 2533226.
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.

The array was designed in 2011 using ArrayOligoSelector (Bozdech et al. 2003) and any available sequence that might represent a flatworm transcript as a design target. The Accession String column contains legacy information about the source of each sequence. The "supported" and "unsupported? entries denote Maker gene predictions (Canterel et al., 2008; Robb et al.,2008) with or without EST support, respectively. The "blythe", "blythe_rajewski", and "rajewski" entries denote sequences from Martin Blythe (Blythe et al., 2010) or Nikolaus Rajewsky (Adamidi et al., 2011) obtained prior to publication. Entries marked "contigs", "smed_20110214", or "sanchez" denote sequences or assemblies curated in the Sanchez lab. For ids ending in 1 or 3 sets of digits separated by an underscore, the last set of digits represents the distance between the 3' end of design target and the 70-mer oligo probe.

Adamidi C, Wang Y, Gruen D, Mastrobuoni G, You X, Tolle D, Dodt M,Mackowiak SD, Gogol-Doering A, Oenal P, Rybak A, Ross E, Sanchez Alvarado A, Kempa S, Dieterich C, Rajewsky N, Chen W. (2011) De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. Genome Res. 2011 21(7):1193-200. PMID: 21536722

Bozdech Z, Zhu J, Joachimiak MP, Cohen FE, Pulliam B, DeRisi JL. (2003). Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol. 4(2):R9.PMID: 12620119

Blythe MJ, Kao D, Malla S, Rowsell J, Wilson R, Evans D, Jowett J, Hall A, Lemay V, Lam S, Aboobaker AA. (2010) A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology. PLoS One. 2010 5(12):e15617. PMID: 21179477

Cantarel BL, Korf I, Robb SM, Parra G, Ross E, et al. (2008) MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res 18: 188-196. PMID: 18025269

Robb SM, Ross E, Sanchez Alvarado A (2008) SmedGD: the Schmidtea mediterranea genome database. Nucleic Acids Res 36: D599-606. PMID: 17881371


title: Illumina Genome Analyzer IIx (Saccharum hybrid cultivar SP90-3414)

status: Public on Mar 19 2014

last: GEO

organism: Saccharum hybrid cultivar SP90-3414


title: NimbleGen Staphylococcus aureus IRN 4000005890 (NimbleGen Design Name)

city: Albuquerque

first: Brian

middle: Marshall

last: Gray

state: NM

address: 1 University of New Mexico

department: Pharmaceutical Sciences

institute: University of New Mexico

organism: Staphylococcus aureus

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.
120912_Saur_9_USA300_BG_exp.ndf
120911_Saur_9_USA300_BG_exp.ngd

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 IIx (Saccharum hybrid cultivar CTC6)

organism: Saccharum hybrid cultivar CTC6


title: Illumina MiSeq (Heligmosomoides polygyrus)

status: Public on Mar 18 2014

organism: Heligmosomoides polygyrus


title: Illumina HiSeq 2000 (Homo sapiens; Human respiratory syncytial virus)

status: Public on Mar 17 2014

organism:
Homo sapiens
human respiratory syncytial virus


title: miRCURY LNA microRNA array, product number: 208500, array version: 7th Gen, array batch number 35003

status: Public on Mar 14 2014

city: Bad Krozingen

first: Thomas

middle: G

last: Nuehrenberg

state: Baden-Württemberg

address: Südring 15

department: Klinik für Kardiologie II

institute: Universitäts-Herzzentrum Freiburg • Bad Krozingen

description: miRCURY LNA microRNA Array 7th Gen (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 18.0.

manufacture_protocol: Exiqons microRNA arrays feature Tm-normalized LNA-enhanced capture probes, designed for excellent specificity and sensitivity even for AT-rich microRNAs. They offer great reproducibility with 99 % correlation between arrays and a dynamic range greater than 5 orders of magnitude.


title: Exiqon miRCURY LNA microRNA array [miRBase v18.0 version]

city: Suzhou

first: Chun

last: Zhang

institute: Suzhou Institute of Biomedical Engineering and Technology, Chinise Academy of Sciences


title: Agilent-026986 Custom Whole Genome Mouse 8x60k designed by Genotypic Technology Pvt. Ltd. Feature Number

status: Public on Mar 12 2014

first: Vrushali

middle: Umakant

last: Deshpande

address: No. 258/A, Bommasandra Industrial Area,

department: Molecular Immunology

institute: Thrombosis Research Institute

organism: Mus musculus

first: Raja

middle: C

last: Mugasimangalam

manufacture_protocol: Agilent Technologies


title: NimbleGen Sheep CGH 3x1.4M Whole-Genome Tiling Array [121109_Sheep_oviAri1_WG_SW_CGH]

status: Public on Mar 13 2014

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Ovis aries

description:
Build: Oav1,NCBI83
Median Probe Spacing: 1325

manufacture_protocol: See www.nimblegen.com


title: AB 5500xl Genetic Analyzer (Desulfovibrio hydrothermalis AM13 = DSM 14728)

status: Public on Mar 10 2014

organism: Maridesulfovibrio hydrothermalis AM13 = DSM 14728


title: PacBio RS (Gemmatimonadetes bacterium KBS708)

status: Public on Mar 11 2014

organism: Gemmatirosa kalamazoonensis


title: Ehrlichia ruminantium IPMC june 2012 earray 8x60k

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

organism: Ehrlichia ruminantium

first: Bernard

last: Mari

first: Pascal

last: Barbry

manufacture_protocol: spotted oligonucleotide


title: Illumina Human 12k DASL assay

city: La Jolla

first: Maggie

last: Chow

address: 8110 La Jolla Shores Dr. Ste 201

department: Neuroscience

institute: NIH-UC San Diego Autism Center of Excellence

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


title: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [AltAnalyze probeset-to-Ensembl mapping]

city: San Francisco

last: Cao

address: 1650 Owens Street

department: Department of Pharmaceutical Chemistry

institute: gladstone institute of cardiovascular disease

description: Ensembl 65 database, Genome build Hg18. AltAnalyze constitutive annotated probesets

relation: Alternative to: GPL6244 (AltAnalyze [official])


title: SABiosciences Rat Stem Cell Transcription Factors - RT2 Profiler PCR Array

city: Montreal

first: Jennifer

last: Maselli

state: Quebec

address: 3655 Prom Sir William Osler

country: Canada

institute: McGill University

organism: Rattus norvegicus

technology: RT-PCR

description: SABiosciences RT² Profiler panel of PCR assays.

manufacture_protocol: See manufacturer's website.


title: Agilent-020181 Genotypic Technology Custom Mycobacterium tuberculosis h37Rv Whole Genome 8x15k GE (by gene)

city: Bangalore

first: Genotypic

last: technology

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

organism: Mycobacterium tuberculosis H37Rv

description: Official platform deposited under GPL13238


title: Illumina Genome Analyzer IIx (Heligmosomoides polygyrus)


title: Illumina HumanRef-8 v3.0 expression beadchip (controls added)

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Homo sapiens

description:
**This platform records include the probes in the original GPL6883 platform and 5 additional ILMN_Control probes.

The HumanRef-8 v3.0 Expression BeadChip features up-to-date content derived from the National Center for Biotechnology Information Reference Sequence (NCBI RefSeq) database (Build 36.2, Release 22).

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

manufacture_protocol: see manufacturer's website


title: Rodent A v2.0

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

description: PCR assay


title: Exiqon Mouse miRCURY 6th generation LNA microRNA array [Condensed ProbeID Version]

description: miRCURY 6th generation LNA™ microRNA array


title: Gossypium arboreum 9.4K

status: Public on Mar 08 2014

city: Lahore

first: Muhammad

middle: Younas

last: khan

state: Punjab

address: Thokar Niaz Baig

department: Molecular biology

country: Pakistan

institute: National centre of Excellence in Molecular biology

organism: Gossypium arboreum

description: super amine-2

manufacturer: National Centre of Excellence in Molecular Biology (CEMB), University of the Punjab Lahore Pakistan

last: Younas KhanBarozai

first: Tayyab

last: Hussnain

manufacture_protocol: cDNA library from wild cotton (Gossypium arboreum) plant leaves has been developed through Cloneminer Invitrogen cDNA library construction kit. The insert cDNAs were PCR amplified through M13 universal primers. The PCR products were spotted on a glass slide of ArrayIt® brand SuperAmine 2 using a microspotter (microGrid610) made by Genomic Solutions®.


title: Illumina HiSeq 2000 (Ficus obtusifolia)

status: Public on Mar 07 2014

last: GEO

organism: Ficus obtusifolia


title: SCAU_miRChicken_14

city: guang-zhou

first: HongMei

last: Li

state: Guang -dong

address: wu shan

institute: South China Agricultural University

organism: Gallus gallus

description:
Version number: miRChicken_14_SCAU_091022
Based on Sanger miRBase Release 14.

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


title: EmbryoGENE DNA Methylation Array Bovine 2x400K v2.0

city: Quebec

first: Eric

last: Fournier

address: 2325 Rue de l'Universite

department: Departement des sciences animales

institute: Universite Laval

organism: Bos taurus

description: Assembly Bos_taurus_UMD_3.1


title: Agilent-022595 Ostrinia nubilalis ECB Gut Expression

city: College Station

first: jianxiu

last: yao

state: Texas

address: 422 Minne heep center

department: Entomology

institute: Texas A&M university

organism: Ostrinia nubilalis

description:
Ostrinia nubilalis

Arrays of this design have barcodes that begin with 16022595 or 2522595.

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


title: Agilent-057949 Streptococcus_suis_SC84 8X15K Microarray (Probe Name version)

city: shanghai

first: qian

last: jin

address: libing road

institute: MSP

organism: Streptococcus suis SC84

description: Arrays of this design have barcodes that begin with 16057949 or 2557949.


title: [Mouse430_2_ENST_13.0.0] Affymetrix GeneChip Mouse Genome 430 2.0 Array [Brainarray Version 13]

description:
Based on Mouse430A2_Mm_ENST_13.0.0 CDF available from Brainarray:
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13.0.0/enst.asp


title: [Axiom_GW_Hu_SNP] Affymetrix Axiom Genome-Wide CEU 1 Array Plate

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

description:
##For information about the Annotation file content, please see the bundled README file.
#%create_date=2013-09-10 GMT-08:00 15:47:36
#%chip_type=Axiom_GW_Hu_SNP
#%genome-species=Homo sapiens
#%genome-version=hg19
#%genome-version-ucsc=hg19
#%genome-version-ncbi=37
#%genome-version-create_date=2009-02-00
#%mitochondrion-version=NC_001807
#%dbSNP-date=2012-06-26
#%dbSNP-version=137
#%hapmap-date=2008-01-08
#%hapmap-version=23
#%omim-date=2013-07-09
#%allele_frequency_data_reference=1KGp1_mar2012
#%netaffx-annotation-date=2013-07-01
#%netaffx-annotation-netaffx-build=34
#%netaffx-annotation-tabular-format-version=1.5

manufacture_protocol: see manufacturer's web site


title: Illumina HiSeq 2500 (Oxytricha trifallax)

organism: Oxytricha trifallax


title: Illumina HiSeq 2000 (Aspergillus fumigatus CEA10)

status: Public on Mar 06 2014

organism: Aspergillus fumigatus CEA10


title: [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array [CDF: Brainarray Mouse4302_Mm_ENTREZG_12.1.0]

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

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

manufacture_protocol: This is identical to GPL1261 but a custom cdf environmnet was used to extract data. The cdf can be found at the link below.


title: Agilent-037314 Teleopsis dalmanni CGH (CGH_II_PG1_037314_D_20111107.gal)

city: College Park

first: Gerald

middle: S

last: Wilkinson

address: Bldg 144, 4094 Campus Dr

department: Biology

institute: University of Maryland

organism: Teleopsis dalmanni

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


title: NimbleGen Leptosphaeria maculans whole genome 4*72K array v1

city: Thiverval-Grignon

first: Isabelle

last: Fudal

address: avenue Lucien Bretignieres

institute: INRA

organism: Plenodomus lingam

description: The Leptosphaeria maculans custom-exon array (4*72K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) contains 5 independent, non-identical, 60-mer probes per gene model. Included in the oligoarray are 12,457 predicted gene models, 467  genes encoding small secreted proteins not included in the predicted gene models, 1402 clustered EST that did not match with the gene models, 2008 random 60-mer control probes and labelling controls.


title: Illumina HiSeq 2000 (Crassostrea angulata)

status: Public on Mar 05 2014

organism: Magallana angulata


title: Jose's miRNA probes based on miRNArthropoda_15_UC_100610

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
Drosophila simulans
Drosophila yakuba

manufacture_protocol: see LC Sciences


title: [MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [CDF: Brainarray Ver. 14.1.0, MoEx10stv1_Mm_ENSG]

city: Helsinki

first: Miika

last: Mehine

address: P.O. Box 63 (Haartmaninkatu 8)

country: Finland

institute: University of Helsinki

organism: Mus musculus

relation: Alternative to: GPL6096 (Alternative CDF [official])

manufacture_protocol: This is identical to GPL6096 but a custom cdf environment was used to extract data. Microarray analysis was performed using customCDF from Brainarray (Brainarray Version 14.1.0, MoEx10stv1_Mm_ENSG). The custom cdf is linked below as a supplementary file.


title: Illumina HiSeq 2000 (Colletotrichum gloeosporioides; Solanum lycopersicum)

status: Public on Mar 04 2014

organism:
Solanum lycopersicum
Colletotrichum gloeosporioides


title: Luminex Multi-species miRNA array (miRBase 8.0)

city: Columbus

first: Chandan

middle: K

last: Sen

state: Ohio

address: 473W. 12th Avenue,

department: Surgery

institute: Ohio State University Wexner Medical Center

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description:
Bead based array
Sanger miRBase 8.0


title: Illumina HiSeq 2000 (Pseudomonas aeruginosa MPAO1/P1)

status: Public on Mar 03 2014

organism: Pseudomonas aeruginosa MPAO1/P1


title: nCounter Analysis System, nCounter® Mouse miRNA Expression Assays

city: Otsu

first: Masaki

last: Mori

state: Shiga

address: Tsukinowa-cho, Seta

department: Molecular Neuroscience Research Center

institute: Shiga University of Medical Science


title: [ChiGene-1_0-st] Affymetrix Chicken Gene 1.0 ST Array [probeset version]

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=Mon Apr 15 11:23:16 2013 PDT
#%chip_type=ChiGene-1_0-st-v1
#%lib_set_name=ChiGene-1_0-st
#%lib_set_version=v1
#%genome-species=Gallus gallus
#%genome-version=galgal3
#%genome-version-ucsc=galgal3
#%genome-version-create_date=2006-05-00
#%genome-lifted-method=NONE
#%genome-lifted_from-species=Gallus gallus
#%genome-lifted_from-version-ucsc=galgal3
#%netaffx-annotation-date=2012-09-15
#%netaffx-annotation-netaffx-build=33
#%netaffx-annotation-tabular-data-version=1.1
#%netaffx-annotation-tabular-format-version=1.1
#%netaffx-annotation-data-type=probe_set
#%netaffx-annotation-docgen-method=module:affy/annotation_update/builder; exec:create-download-file.pl
#%netaffx-annotation-docgen-version=8487
#%netaffx-annotation-url-transcript=www.affymetrix.com/analysis/netaffx/gene/transcript.affx?pk=
#%netaffx-annotation-url-mrna=www.affymetrix.com/analysis/netaffx/gene/rna.affx?pk=

manufacture_protocol: See manufacturer's web site


title: ABI Taqman 94 gene expression assays

status: Public on Mar 02 2014

city: La Jolla

first: John

last: Chang

address: 9500 Gilman Drive

department: Medicine

institute: UCSD


title: Illumina HiSeq 2000 (Staphylococcus aureus subsp. aureus str. Newman)


title: Sabiosciences RT2 Profiler DNA Damage Signaling Pathway PCR Array

city: Baltimore

first: Saniya

last: Fayzullina

state: MD

address: 720 Rutland Avenue Ross Bldg., Room 558

department: Pathology

institute: Johns Hopkins School of Medicine

description:
RT-PCR assay
SABiosciences RT² Profiler PCR Array System


title: OGT-PseudomonasPA01-0148_018645

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

organism: Pseudomonas aeruginosa PAO1

manufacture_protocol: Array designed and manufactured by OGT, 60 base oligos, three oligos per target gene.


title: Phytophthora parasitica array

status: Public on Mar 01 2014

city: Sophia Antipolis

first: Gourgues

last: Mathieu

address: 400 routes des Chappes, BP167

department: UMR Institut Sophia Agrobiotech

institute: University of Nice Sophia Antipolis

organism: Phytophthora nicotianae

description:
The platform was obtained using contig sequences derived from the Phytophthora parasitica EST sequences available in public databases. The EST were obtained from various developmental stages including cell types involved in plant infection. A total of 12632 ESTs was assembled in 1572 contigs and 3879 singletons giving a final 5451-unisequence set. We ascribed 4398 sequences (81 %) to Phytophthora parasitica and 729 sequences (13 %) to plant. The origin of 324 sequences (6 %) remained unknown.    DESIGN_ID DESIGN_NAME DESCRIPTION   7680 080529_Phytophthora_parasitica_expr expression design for Phytophthora parasitica; customer provided 5451 seqs + 11 control seqs; 11 probes/seq, used full transcript length,  pos_weight=50, removed grossly overlapping probes by hand (56,524 probes, 5438 exemplars for 5438 seqs, 1217 seqs had fewer than 11 probes, 24 seqs with no probes); 4 cy of each probe on array
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: Biogemma NimbleGen Maize Custom Expression Array [130114_Zea_Mays_45K_BGA]

city: Montpellier

first: Cecilio

middle: Frois

last: Caldeira

address: 2 place Viala

department: Herault

institute: INRA - Institut National de la Recherche Agronomique

organism: Zea mays


title: Agilent-029050 Glycine max array

city: New Delhi

first: rajiv

middle: kumar

last: yadav

address: Aruna Asaf Ali Marg

institute: National Institute of Plant Genome Research

organism: Glycine max


title: miRCURY LNA microRNA Array, 6th generation - hsa, mmu & rno (miRBase 17)

city: Maastricht

first: Wim

last: Van den Hof

address: Universiteitssingel 50

department: Toxicogenomics

institute: Maastricht University

manufacture_protocol: See manufacturers website


title: NFkB 96 StellArray qPCR array

city: Rome

first: Guido

last: Leoni

address: Via Pontina

department: Bioinformatics

institute: IRBM

organism: Homo sapiens


title: SMD Print_1564 hoaa Homo sapiens (condensed)

city: Stockholm

first: Cinzia

last: Bersani

address: Cancer Center Karolinska, R8:04

country: Sweden

institute: Karolinska Institutet

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: Lawrence Livermore Microbial Detection Array version 2f

city: Livermore

first: Kevin

last: McLoughlin

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

organism: synthetic construct

description: Described in 'Gardner et al. A Microbial Detection Array (MDA) for Viral and Bacterial Detection. BMC Genomics 2010 Nov 25;11:668'

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


title: [ZebGene-1_1-st] Affymetrix Genechip Zebrafish ST Genome Array 1.1, brainarray version 15 [zebgene11st_Dr_ENTREZG]

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Danio rerio

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


title: NimbleGen Zebrafish 12x135K Array based on Zv9 [090818_Zv7_EXPR]

status: Public on Feb 28 2014

city: Moscow

first: Maia

last: Benner

state: Idaho

address: 875 Perimeter Drive

department: Biological Sciences

institute: University of Idaho

description:
Each probe is replicated 3 times. The design includes random GC and other control probes.

The NimbleGen 12-plex zebrafish microarray 090818_Zv7_EXPR was designed based on the Sanger Zv7 zebrafish genome build. This Platform represents a custom NimbleGen Design File (NDF) that was based on zebrafish genome build (Sanger Zv9). Probe sequences from the NimbleGen microarray (113,549 probes) were aligned to Ensembl Zv9 transcripts (53,067) using the Sequence Search and Alignment by Hashing Algorithm (SSAHA2; parameters -kmer 13, -skip 2, -seeds 2, -score 12, -cmatch 9, -ckmer 6). Alignments were filtered based on the following conditions: (probe length – number of mismatches) ≤ 4, no gapped alignments, common strand per transcript (+/-), probes had only one matching gene, ≥ 3 probes per transcript, and only canonical transcripts (15,650 remaining transcripts).

The Platform data table reflects a condensed representation of the custom NDF's SEQ_ID features.


title: NimbleGen Mouse DNA Methylation 385K CpG Island Plus RefSeq Promoter Array [2007-02-27_MM8_CpG_Island_Pro]

city: London

first: Simone

last: Di Giovanni

address: DuCane Road W12 ONN UK

institute: Imperial College

description:
Build MM8
Design 5313


title: NVH_Escherichia coli_v1_array

city: Oslo

first: Hildegunn

last: Iversen

address: P.O.Box 8146 Dep

department: Department of Food Safety and Infection Biology

country: Norway

institute: Norwegian School of Veterinary Science

organism: Escherichia coli O103:H2 str. 12009

description: The ndf.txt is linked below as a supplementary file.


title: Illumina HiSeq 2000 (Aspergillus fumigatus)

status: Public on Feb 18 2014

last: GEO

country: USA

organism: Aspergillus fumigatus


title: NimbleGen Arabidopsis CGH 3 x 720 K whole genome custom tiling array [090325_Athal_EB_CGH_HX1]

status: Public on Feb 25 2014

city: Oxford

first: Eric

last: Belfield

state: England

address: South Parks Road

department: Plant Sciences

institute: Oxford University

organism: Arabidopsis thaliana

description:
Designname: 090325_Athal_EB_CGH_HX1
Designid: 9497
Genome build: TAIR8


title: [Mouse430_2] Affymetrix GeneChip Mouse Genome 430 2.0 Array [CDF: Brainarray Mouse4302_Mm_ENTREZG_12.1.0, Entrez ID version]

status: Public on Dec 05 2013

first: Linda

last: Rieswijk

country: Netherlands


title: [MoGene-2_0-st] Affymetrix Mouse Gene 2.0 ST Array [mogene20st_Mm_ENSG_17]

status: Public on Jul 05 2013

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

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

CDF available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/17.0.0/ensg.asp

relation: Alternative to: GPL16570 (Official CDF [MoGene-2_0-st])


title: NimbleGen Homo sapiens HG18 expression array (12x135k) [100718_HG18_opt_expr_HX12]

status: Public on Sep 01 2013

description:
designname: 100718_HG18_opt_expr_HX12
slide barcode 539051


title: Agilent-020912 Streptomyces coelicolor 15K

status: Public on Jan 05 2011

city: Shanghai

first: Yinhua

last: Lu

address: 300 Fenglin Road

department: Institute of Plant physiology and ecology

institute: Shanghai Institutes for Biological Sciences

organism: Streptomyces coelicolor

manufacture_protocol: Agilent Manufacture Protocol


title: Agilent-037639 Bacillus subtilis 168 Bsubt-nov2011

status: Public on May 02 2013

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

organism: Bacillus subtilis subsp. subtilis str. 168

description:
Arrays of this design have barcodes that begin with 16037639 or 2537639.

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.

*** The ID column includes the Agilent Feature numbers. A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL18393.

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


title: NimbleGen HG18_60mer_expr

status: Public on May 16 2008

city: Las Vegas

first: Yupo

last: Ma

state: NV

address: 1 Breakthrough Way

institute: Nevada Cancer Institute

first: Taylor

last: Fowles

manufacture_protocol: Please see manufacture's website


title: Nanostring nCounter ImmVar DC Custom CodeSet

city: Cambridge

first: Nir

last: Hacohen

state: MA

address: 7 Cambridge Center

institute: Broad Institute

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


title: Illumina Genome Analyzer IIx (Drosophila melanogaster)

status: Public on Nov 12 2010

organism: Drosophila melanogaster


title: nCounter Analysis System, nCounter® Human miRNA Expression Assays

city: Otsu

first: Masaki

last: Mori

address: Tsukinowa-cho, Seta

institute: Shiga University of Medical Science