title: Agilent TALE_v2a_2

status: Public on Jun 10 2015

city: Boston

first: Julia

middle: M

last: Rogers

state: Massachusetts

address: 45 Shattuck Street

department: BCMP

country: USA

institute: Harvard Medical School

organism: synthetic construct

technology: in situ oligonucleotide

distribution: custom-commercial

manufacture_protocol: In situ oligosynthesized array with synthetic sequences containing the following classes of probes: (1) TALE binding sites for 24 TALE proteins with mono- or di- nucleotide substitutions in constant flanking sequence, in both orientations (2) TALE binding sites for 24 TALE proteins in flanking sequences with differing G/C content (3) TALE binding sites for 24 TALE proteins in constant flanking sequence, located at different positions within the probe sequence, in both orientations (4) 200 randomly generated negative control probes with at least four mismatches from any TALE target site. AMADID 043197.


title: Agilent TALE_v2a_1


title: Agilent TALE_v1


title: [uwyRhodo1a] Rhodobacter sphaeroides 2.4.1 GeneChip

status: Public on Mar 11 2003

city: Laramie

first: Mark

last: Gomelsky

state: WY

department: Molecular Biology

institute: University of Wyoming

organism: Cereibacter sphaeroides 2.4.1

description:
4242 candidate protein-encoding gene models
Keywords = genechip
Keywords = microarray
Keywords = expression profile
Keywords = transcription


title: Agilent HD CGH Microarray (2X105K) Oxford design AMADID#019015 (Probe name version)

status: Public on Apr 30 2014

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

organism: Homo sapiens

distribution: commercial

first: B

last: Ylstra

first: PP

last: Eijk

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


title: Agilent-045769 Mycobacterium tuberculosis Custom Microarray (Probe Name version)

city: Chennai

first: Alamelu

last: Raja

state: Tamil Nadu

address: No,1 Mayor sathyamoorthy Road, Chetpet

department: Department of Immunology

country: India

institute: National Institute for Research in Tuberculosis

organism: Mycobacterium tuberculosis

description: **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 GPL18388.


title: miRCURY LNA microRNA Array, 5th and 7th generation combined - hsa, mmu & rno (miRBase 19.0)

status: Public on May 18 2015

city: Maastricht

first: Linda

last: Rieswijk

address: Universiteitssingel 50

department: Toxicogenomics

institute: Maastricht University

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

technology: spotted oligonucleotide


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [AltAnalyze 2.0.6 beta probeset-to-Ensembl mapping]

city: Belfast

first: Simon

middle: S

last: McDade

address: 97 Lisburn Road

department: CCRCB

country: United Kingdom

institute: Queen's University Belfast

description: AltAnalyze version 2.0.6 beta summarized at an individual gene level for Constitutive exons

manufacture_protocol: see manufacturer's web site


title: Mycobacterium smegmatis version 4

city: Dunedin

first: Htin Lin

last: Aung

state: Otago

address: 720 Cumberland Street

department: Microbiology and Immunology

country: New Zealand

institute: University of Otago

organism: Mycolicibacterium smegmatis MC2 155

distribution: non-commercial

manufacturer: Pathogen Functional Genomics Resource Center

manufacture_protocol: QMS, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Agilent-040032 Mytilus edulis 60K Ontogenesis_Medulis_Larvae

city: Rimouski

first: Sleiman

last: Bassim

state: Quebec

address: 310, Allée des Ursulines

department: Oceanography

country: Canada

institute: UQAR

organism: Mytilus edulis

description:
Arrays of this design have barcodes that begin with 16040032 or 2540032.

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 (Staphylococcus aureus subsp. aureus NCTC 8325)

status: Public on Apr 29 2014

last: GEO

technology: high-throughput sequencing

distribution: virtual


title: Illumina HiSeq 2000 (Chlorostoma funebralis)

status: Public on Apr 28 2014

organism: Tegula funebralis


title: [TrueTag_10K_A] Rat Mapping 10K SNP

status: Public on Apr 26 2014

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Rattus norvegicus

manufacture_protocol: see manufacturer's website


title: [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array [CDF: Mouse4302_Mm_ENTREZG.cdf Brainarray version 17.0.0]

organism: Mus musculus

relation: Alternative to: GPL1261 (Alternative CDF)

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


title: NimbleGen Human 3 x 720k RefSeq Promoter Array [100205_HG18_Refseq_Prom_ChIP]

status: Public on Apr 25 2014

first: Kienan

last: Savage

address: 97 Lisburn Rd

department: Centre for Cancer Research and Cell Biology

description:
Tiling of promoter regions based on refFlat file downloaded from UCSC on May 7th  2009. Each TSS was tiled 3200bps upstream and 800bps downstream. n=717949, median probe spacing 104bps.
design id: 11400


title: TaqMan MicroRNA A+B Cards Set v3.0

city: Hong Kong

first: Chor Sang

last: Chim

address: Queen Mary Hospital

department: Medicine

country: Hong Kong

institute: The University of Hong Kong

technology: RT-PCR

description: PCR assay


title: NimbleGen Rat CpG Island Plus RefSeq Promoter 720k array [090618_RN34_CpG_Refseq_Prom_MeDIP]

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description:
Design_Name: 090618_RN34_CpG_Refseq_Prom_MeDIP
Design_ID: 10184

manufacture_protocol: see NimbleGen website


title: Arraystar Custom Cavia Porcellus Expression Microarray

city: Rockville

first: Panos

last: Pan

state: MD

address: 9430 Key West Avenue

institute: Arraystar Inc.

organism: Cavia porcellus


title: Arraystar Custom Capra Hircus Expression Microarray

organism: Capra hircus


title: TaqMan® OpenArray® Rodent MicroRNA Panel (4461105)

city: Baltimore

first: Kenneth

middle: W

last: Witwer

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

manufacturer: Applied Biosystems by Life Technologies (Thermo Fisher)

manufacture_protocol: see manufacturer's website: http://www.lifetechnologies.com/


title: Illumina Hiseq 1000 (Mus musculus)

status: Public on Apr 23 2014


title: Illumina HiSeq 2000 (Pseudozyma aphidis)

organism: Moesziomyces aphidis


title: NimbleGen Danio rerio array [Zebrafish_Zv9-e70-2]

status: Public on Apr 24 2014

city: Singapore

first: Woei Chang

last: Liew

address: 1 Research Link, NUS

country: Singapore

institute: Temasek Life Sciences Laboratory

organism: Danio rerio

description: Design based on Zv9 (version e70) of zebrafish genome assembly, with 31,477 target transcripts. The design includes random GC and other control probes. This platform has 12 arrays per slide.

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


title: NimbleGen Ignicoccus hospitalis 385k array

city: Knoxville

first: Louie

last: Wurch

state: TN

address: M313 Walters Life Sciences

institute: University of Tennessee

organism: Ignicoccus hospitalis

description:
www.nimblegen.com
NimbleGen_Ignicoccus.ndf
Nimblegen_Ignicoccus.ngd

manufacture_protocol: A high density gene expression microarray (1plex, 385k) containing 60mer oligonucleotide probes (up to 20 different probes per gene) for the 1442 protein encoding genes of I. hospitalis was designed and manufactured by Nimblegen (Roche NimbleGen, IN).


title: Illumina HiSeq 2000 (Burkholderia glumae BGR1)

status: Public on Apr 22 2014

organism: Burkholderia glumae BGR1


title: Illumina HiSeq 2000 (Ictalurus punctatus x Ictalurus furcatus)


title: Illumina HiSeq 2000 (Ictalurus punctatus)

organism: Ictalurus punctatus


title: Illumina HiSeq 2000 (Cannabis sativa)

organism: Cannabis sativa


title: Human 1 Mb - resolution CGH array

status: Public on Apr 18 2014

city: Stockholm

first: Anna

last: Kwiecinska

address: CCK R8:00

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institute

technology: spotted DNA/cDNA

description: The 1Mb clone set has been assembled by the Mapping Core, Map Finishing and Microarray Facility groups of the Wellcome Trust Sanger Institute, Hinxton, UK. The array has 24 subarrays (6 rows by 4 columns), each subarray consisted of 18 rows by 18 columns.

manufacturer: Department of Pathology, Univeristy of Cambridge

first: A

first: K

last: Ichimura

first: M

last: Berglund

last: Dinets

first: L

last: Sulaiman

first: V

middle: P

last: Collins

first: C

last: Larrson

last: Porwit

first: S

last: Bajalica Lagercrantz

manufacture_protocol:
1. BAC/PAC clones were grown in 2 x TY medium in a deep-well titrate plate at 37° overnight with chloramphenicol 25 µg/ml (BAC) or kanamycin 205 µg/ml (PAC).
2. DNA was extracted from BAC or PAC clone using modified alkali-lysis method (microprepping)
3. Approximately 5ng of BAC/PAC DNA was PCR amplified using three DOP-primers (Fiegler H., Genes Chromosomes Cancer 36_361-374,2003).
4. Two microlitre of the DOP-PCR products was futher amplified using 5'-Aminolink universal primer (Fiegler H., Genes Chromosomes Cancer 36_361-374,2003).
5. Three volumes of the Amino-PCR products were mixed with one volume of 4 x Spotting buffer (1 M Sodium phosphate buffer, pH8.5, 0,001% Sarkosyl) to make a spotting mix.
6. The spotting mix was filtered through Corning 96 Well white polystyrene filter plate with modified styrene insert (0.2 µm PVDF) by centrifugation.
7. The filtered spotting mix was transferred to a 384-well plate.
8. The spotting mix was printed in duplicate onto a CodeLink slide (GE Healthcare) using MicroGrid II robot (Genomic Solutions, Huntingdon, UK) in 4 x 4 subarrays.
9. The printed slides were incubated at room temperature for 24-72 hours in a humidified chamber.
10. The slides were treated with 1% ammonium hydroxide at room temperature for 5 min, then with 0,1% SDS at room temperature for 5 min.
11. The slides were heat-denaturated in a boiling water for 2 min, cooled, rinsed with water and dried.


title: Illumina HiSeq 2000 (Populus tremula x Populus alba)

status: Public on Apr 17 2014

last: GEO

organism: Populus tremula x Populus alba


title: Stanford – Robinson Lab - Cytokine and Acute Phase Assays - 65 - v1.0

city: Stanford

first: William

last: Robinson

address: 269 Campus Dr

institute: Stanford University

organism: synthetic construct

technology: other

description:
Bead-based multiplex immunoassay
Capture and secondary antibodies for sandwich immunoassay were commercially obtained and proprietary

manufacturer: Bio-Rad Laboratories, Inc. (M50-0KCAF0Y, MF0-005KMII, 171-AA001M, and 171-A4S07M) and EMD Millipore (HCYP2MAG-62K and HCYP3MAG-63K)

manufacture_protocol: The manufacturers’ recommended protocols and fully detailed instructions are available at http://www.bio-rad.com and http://www.millipore.com.


title: Affymetrix GeneChip Human Genome HTA_2_0 Array [CDF: Brainarray Version 18, hta20hsentrezgcdf v18.0.0]

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Homo sapiens

description: Data were extracted using hta20_Hs_ENTREZG.cdf

manufacture_protocol: Standard Affymetrix Protocol


title: Nimblegen Listeria monocytogenes EGD-e 090619_L_mono_EGD_e_expr

status: Public on Apr 19 2014

city: Dijon

first: Pascal

last: Piveteau

address: 17 rue Sully

country: France

institute: Université de Bourgogne INRA

organism: Listeria monocytogenes EGD-e

description:
NimbleGen design name 090619_L_mono_EGD_e_expr, NimbleGen design ID 10198. X4 expression design for Listeria monocytogenes EGD-e (2857 genes from genolist.pasteur.fr/ListiList/ 109sp sequence data) plus 15 additional genes; 45-60mer probes, 5 probes per target (2870 exemplars for 2872 sequences), 5 copies on array.   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: Agilent-031372 Pichia pastoris p/n G2565BA

city: Changchun

first: chongyang

last: Liang

state: Jilin

address: No.1266, Fujin Road

department: Pharmaceutical Sciences

country: China

institute: JiLin University

organism: Komagataella pastoris


title: Illumina HiSeq 2500 (Vitis vinifera subsp. silvestris)

status: Public on Apr 16 2014

organism: Vitis vinifera subsp. sylvestris


title: Illumina HiSeq 2500 (Salmo trutta)

organism: Salmo trutta


title: Illumina HiSeq 2000 (Acyrthosiphon pisum)

organism: Acyrthosiphon pisum


title: Genosensor human miRNA array

city: Daegu

first: You Mie

last: Lee

address: 80, Daehak-ro

country: South Korea

institute: Kyungpook National University


title: Agilent SurePrint G3 CBC lncRNA+mRNA microarray V2.0

city: Nanjing

first: Wen

last: Zhu

state: Jiangsu

address: 300 Guangzhou Road

department: Respiratory Medicine

institute: The First Affiliated Hospital, Nanjing Medical University


title: Agilent-024664 chlamydomonas full genome [condensed probe ID version]

city: Potsdam

first: Samuel

last: Arvidsson

state: Brandenburg

address: Am Muehlenberg 1

country: Germany

institute: Max Planck Institute of Molecular Plant Physiology

organism: Chlamydomonas reinhardtii

description:
Arrays of this design have barcodes that begin with 16024664 or 2524664.

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

The ID column represents the Agilent Probe Name.

This platform uses the Probe Name as the identifier, the Feature Number version is GPL14721.
The 3 probes have been condensed in this Platform;
the name of 1 of the probes (e.g. >190829) is used to represent the 3 probes (e.g.>190829/1, >190829/2, and >190829/3).


title: Illumina HiSeq 2500 (Vitis vinifera)

organism: Vitis vinifera


title: [FDA-LMON_expr] Affymetrix  Listeria GeneChip

city: Laurel

first: Atin

last: Datta

address: 8301 Muirkirk Rd

department: CFSAN/DVA

institute: FDA

organism: Listeria monocytogenes

description:
PMID 22457724
As this microarray includes sequences are from 24 different genomes, each design location refers a genome location.
For example, "Lm FSL F2-515" is sequence from L. monocytogenes strain FSL F2-515 and ID indicates the name of the probe set for the corresponding locus/ORF. Description is the basic annotation, though some may have been updated since the array was designed.
The SPOT_ID refers to the ORF/locus_ID or intergenic region (denoted by an IG at the start) examined.
All of the 24 genome sequences were pulled from NCBI. The locus tags for sequences from 15 genomes {CLIP81459 (eg. Lm4b_00380), HCC23, EGD-e (eg. LMHCC_0003), F2365 (eg. LMOf2365_0022), FSL J1-194 (eg. LMBG_01616), FSL J2-071 (eg. LMFG_01366), FSL N3-165 (eg. LMIG_00640), FSL R2-503 (eg. LMJG_02388), FSL R2-561 (eg. LMKG_00998), F6900 (eg. LMMG_03051), F6854 (eg. LMOf6854_0326), H7858 (eg. LMOh7858_0217), J2818 (LMPG_02290), 10403S (LMRG_00152), and HPB2262 (eg. LMSG_00007)} work readily in the GenBank system.
The remaining genomes were sequenced at the Broad Institute and the data can be found at http://www.broadinstitute.org/annotation/genome/listeria_group/MultiHome.html. For three of them, the annotation is searchable best at the Broad using the locus tags. They are FSL N1-017 (eg. LMHG_00112 which is now LMHG_10112), Finland 1988 (eg. LML_00218) and J0161 (eg. LMOG_00878). These annotations have been changed in some cases as the Broad Institute has updated some of their data.
Indeed, for these 18 genomes some of the annotations may have changed as sequencing was completed or otherwise modified by the sequencing facility since the microarray was originally designed. For this reason, we've provided GenBank accession numbers along with the corresponding nucleotide base locations, formatted as described below.
However, six of the genomes (FSL F2-515, FSL J1-175, FSL J1-208, FSL J2-003, FSL J2-064 and LO28) haven't been annotated by the Broad Institute. We performed an auto-annotation on those sequences and assigned locus tags based on the first four letters of their accession numbers.
The sequences for these targets can be identified as follows. For example, AARI_0004, we've provided the GenBank accession number for the strain AARI02000001 followed by ':4318-5304' (eg. AARI02000001:4318-5304). These latter numbers indicate the nucleotide sequence location corresponding to the ORF for which the probe sets were designed.
Finally, some of the strains had closed genome sequences which were used to identify intergenic regions. These loci are indicated by an "IG" in front of the strain's standard call letters. For example, an intergenic region from L. monocytogenes F2365 is IGLMOf2365_0003. The sequences for these loci can be identified as with the previous group. In the example IGLMOf2365_0003 can be found using AE017262:3014-3120 to look up the AE017262 accession and nucleotides 3014-3120.

manufacture_protocol: Affymetrix builds the oligonucleotides in situ via photolithography. The Listeria expression/genotyping microarray was designed to represent 64,539 annotated gene sequences from 24 sequenced strains of L. monocytogenes. The expression array consists of 253,361 25-mer oligonucleotides that represent a total of 18,630 probe sets including 45 AFFY controls, 4,481 intergenic regions and 14,104 genes. Each probe set contains approximately 28 oligonucleotide probes; up to 14 perfect match (PM) probes and 14 mismatch probes (MM). Mismatch probes are identical to the perfect match probe with the exception of a one nucleotide (nt) mismatch located at the 13th (middle) position of the oligo nucleotide sequence.


title: Illumina HiSeq 2000 (Peptoclostridium difficile)

status: Public on Apr 15 2014

organism: Clostridioides difficile


title: AB 5500xl Genetic Analyzer (Schizosaccharomyces pombe)

status: Public on Apr 13 2014

organism: Schizosaccharomyces pombe


title: Illumina Genome Analyzer II (Ixodes ricinus)

status: Public on Apr 11 2014

organism: Ixodes ricinus


title: 454 GS FLX (Ixodes ricinus)


title: Illumina HiSeq 2000 (Pseudomonas putida DOT-T1E)

organism: Pseudomonas putida DOT-T1E


title: Illumina HiSeq 2500 (Paragordius varius)

status: Public on Apr 09 2014

organism: Paragordius varius


title: RT2 miRNA PCR array

city: Salt Lake City

first: Jesse

middle: Worth

last: Rowley

state: Ut

institute: University of Utah

organism: Mus musculus

description: RT2 miRNA PCR array


title: Illumina HiSeq 2000 (Esox lucius)

status: Public on Apr 10 2014

organism: Esox lucius


title: [RaGene-2_0-st] Affymetrix Rat Gene 2.0 ST Array [ragene20st_Rn_ENTREZG ENTREZG_17.0.0]

city: Valencia

first: Roque

last: Bort

address: Campanar 21

department: Unidad Hepatologia Experimental

country: Spain

institute: IIS La Fe

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
This is identical to GPL17117 but a custom CDF environment was used to extract data [Brainarray Version 17, ragene20st_Rn_ENTREZG ENTREZG_17.0.0]. CDF and other files can be downloaded at: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp

relation: Alternative to: GPL17117 (Alternative CDF [official])

manufacture_protocol: See manufacturer's web site


title: BaSysBio Bacillus subtilis T2 385K array [110831_BaSysBio_expr]

city: Jouy-en-Josas

first: Olivier

last: Delumeau

address: Domaine de Vilvert

institute: INRA

organism: Bacillus subtilis subsp. subtilis str. 168


title: Illumina MiSeq (Nippostrongylus brasiliensis)

organism: Nippostrongylus brasiliensis


title: Illumina MiSeq (Hypsibius dujardini)

organism: Hypsibius dujardini


title: Illumina HiSeq 2000 (Caligus rogercresseyi)

organism: Caligus rogercresseyi


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array (custom CDF: HGU133Plus2_Hs_ENTREZG.cdf version 15.1.0)

organism: Homo sapiens

description: This array is identical to GPL570 but the data were analyzed with a custom CDF environment.

relation: Alternative to: GPL570 (Alternative CDF [official])

manufacture_protocol: Refer to Affymetrix manufacture protocol for HG-U133 Plus 2.0 array


title: Illumina MiSeq (Romanomermis culicivorax)

organism: Romanomermis culicivorax


title: Illumina HiSeq 2000 (Bacillus subtilis)

organism: Bacillus subtilis


title: Illumina MiSeq (Odontophora rectangula)

organism: Odontophora rectangula


title: Illumina MiSeq (Trichinella spiralis)

organism: Trichinella spiralis


title: Illumina MiSeq (Enoplus brevis)

organism: Enoplus brevis


title: Illumina MiSeq (Globodera pallida)

organism: Globodera pallida


title: Illumina MiSeq (Brugia malayi)

organism: Brugia malayi


title: UIUC Honey bee oligo 13K microarray v1

status: Public on Apr 08 2014

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

organism: Apis mellifera

manufacture_protocol: See manufacturer's webpage


title: [Bovine] Affymetrix Bovine Genome Array [CDF: Affyprobeminer, bovineccdscdf]

city: Athenry

first: Dermot

middle: G

last: Morris

state: Co. Galway

address: Animal & Grassland Research and Innovation Centre, Mellows Campus

department: Animal Bioscience Research Department

country: Ireland

institute: Teagasc

organism: Bos taurus

description:
This identical to GPL2112 but custom annotation were determined using the 'bovineccdscdf' cdf annotation file downloaded from the Affyprobeminer website which returned Entrez Gene gene name identifiers.
The cdf library is the same as the default 'bovinecdf' library for the Affymetrix array.

It is called in R using the following line -

arraydata@cdfName<-"bovinegeneccdscdf"


title: NimbleGen Listeria monocytogenes 3K

city: Edmonton

first: Lynn

last: McMullen

state: Alberta

address: 410 Ag/For

institute: University of Alberta

organism: Listeria monocytogenes


title: NanoString nCounter Mouse Analysis System [vomeronasal sensory neurons]

city: Frankfurt

first: Peter

last: Mombaerts

address: Max-von-Laue-Str. 3

institute: Max Planck Research Unit for Neurogenetics

organism: Mus musculus

description:
NanoString probes were designed for one third of the mouse Vmn2r gene repertoire, based on the reference C57BL/6 genome sequence.
CodeSet Chanel includes probes for 46 Vmn2r genes and nine non-classical class I MHC H2-Mv genes that are expressed specifically in mouse vomeronasal sensory neurons.

The platform data table represents full layout (including control probes).

manufacture_protocol:
http://www.nanostring.com/lifesciences/
Digital molecular barcoding technology
Custom CodeSets: Chanel


title: Illumina HiSeq 2000 (Eucalyptus nitens)

organism: Eucalyptus nitens


title: Functional gene array for anaerobic Hanford 100H aquifer community

city: Berkeley

first: Ulas

last: Karaoz

address: 1 Cyclotron Rd.

institute: LBNL

organism: mixed sample

description:
design name: 130110_Hanford_aquifer_UK_CGH
Custom 6x630k CGH design for Hanford aquifer community sequences. 313708 60mer probes were selected for the 44964 sequences provided by the customer. 7 probes were selected for 44618 sequences, 6 probes were selected for 95 sequences, 5 probes for 69 sequences, 4 probes for 58 sequences, 3 probes for 44 sequences, 2 probes for 36 sequences and 1 probe for 31 sequences. Probes were laid out in 2 replicates in containers BLOCK1 and BLOCK2. The remaining space on the array was filled with randomly-generated negative control probes of comparable length and composition.
native array description file: 130110_Hanford_aquifer_UK_CGH.ndf
native array description file: 130110_Hanford_aquifer_UK_CGH.pos
native array description file: 130110_Hanford_aquifer_UK_CGH_UX6.ncd


title: Illumina HiSeq 1000 (Peptoclostridium difficile 630)

status: Public on Apr 07 2014

last: GEO

organism: Clostridioides difficile 630


title: Illumina HumanExome-12 v1.0 BeadChip

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

technology: oligonucleotide beads

description:
HumanExome-12v1_A
coverage of putative functional exonic variants selected from over 12,000 individual exome and whole-genome sequences

The exonic content consists of > 250,000 markers representing diverse populations—including European, African, Chinese, and Hispanic individuals—and a range of common conditions, such as type 2 diabetes, cancer, metabolic, and psychiatric disorders.

HumanExome BeadChips deliver focused coverage of exonic regions, but do not include coverage outside of coding regions. Researchers can use these arrays to obtain new insights from previously genotyped cohorts, or run new studies focused on identifying functionally relevant associations.


title: Illumina HiSeq 2000 (Aegilops tauschii)

organism: Aegilops tauschii


title: Illumina HiSeq 2000 (Triticum turgidum)

organism: Triticum turgidum


title: Helicos HeliScope (Drosophila melanogaster)

status: Public on Apr 04 2014

organism: Drosophila melanogaster


title: Nimblegen custom Boechera CGH array 100811_Boechera_TS_CGH

city: Gatersleben

first: Timothy

last: Sharbel

address: Corrensstrasse 4

institute: IPK Gatersleben

organism:
Boechera stricta
Boechera holboellii
Boechera divaricarpa

description:
native array description file : 100811_Boechera_TS_CGH.ndf
native array description file : 100811_Boechera_TS_CGH.pos

manufacture_protocol: See manufacturer's website


title: AB 5500xl Genetic Analyzer (Rhodococcus erythropolis PR4)

status: Public on Apr 02 2014

organism: Rhodococcus erythropolis PR4


title: NimbleGen Aedes aegypti 12plex array [090305_Aedes_aegypti_TEfam_expr]

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

organism: Aedes aegypti

description:
design name: 090305_Aedes_aegypti_TEfam_expr
DESIGN_ID: 9290

An expression design for 17,494 genes/transposable_ORFs from Aedes aegypti with fourteen 60-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.

The SEQ_IDs are VectorBase GeneID number for the ORF to which the indicated probe is directed. Transposable element ORF to which the indicated probe is directed. These ORFs were predicted from the genome sequences of Aedes aegypti [PMID 17510324].

native array description file: 090305_Aedes_aegypti_TEfam_expr.ndf
native array description file: 090305_Aedes_aegypti_TEfam_expr.ngd


city: Singapore

first: Shugui

last: Wang

address: Biopolis Way, Matrix

institute: Danone Nutricia research

organism: Homo sapiens

manufacture_protocol: GEArray S Series Human Immunology Signaling Pathways Gene Array (discontinued)


title: Illumina Genome Analyzer (Kandelia candel)

organism: Kandelia candel


title: [thaiLANLa520655F] Custom Affymetrix  Burkholderia thailandensis E264 8k chip

status: Public on Apr 05 2014

city: Los Alamos

first: Chris

middle: J

last: Stubben

state: NM

address: MS M888

department: Bioscience Division

institute: Los Alamos National Lab

organism: Burkholderia thailandensis E264

description: A custom Affymetrix microarray was designed using Burkholderia thailandensis E264 gene annotations from Pathema and included 8711 probe sets targeting 5557 protein-coding genes and 2908 intergenic regions (IGRs) longer than 90 bases on the plus strand

manufacture_protocol: in situ oligonucleotide synthesis (see manufacturer's web site)


title: Illumina HiSeq 2500 (Euphorbia esula)

organism: Euphorbia esula


title: Illumina Genome Analyzer (Bruguiera gymnorhiza)

organism: Bruguiera gymnorhiza


title: Maize oligonucleotide array 1.5K version

status: Public on Apr 03 2014

city: Hamburg

first: Stefan

last: Scholten

state: Hamburg

address: Ohnhorststrasse 18

department: Biocenter Klein Flottbek

institute: University of Hamburg

organism: Zea mays

manufacture_protocol:
PRINTING OF THE OLIGONUCLEOTIDE MICROARRAYS
The oligonucleotides were synthesized by Ocimum Biosolutions (Ijsselstein, Netherlands) and printed on poly-L-lysine coated glass slides with a Microgrid II printer (BioRobotics, Boston, USA).
1. Add 15 uL of 3x SSC to each well of the 300 µM oligonucleotide set to make a 20 μM oligonucleotide solution.
2. Transfer onto an orbital shaker for 1 h at RT at 100 rpm. The oligonucleotides are now ready for printing.
3. The maize oligonucleotide microarrays are printed on poly-L-lysine coated glass slides (Menzel, Thermo Fisher Scientific) using microspot 2500 pins.
4. Printing conditions:
Microarray printer (Microgrid II printer, BioRobotics, Boston, USA). 55% relative humidity. We used microspot 2500 pins and spotted all oligos and controls (used negative controls: H300010599, H300013976, H300014151, H300016837; positive controls: Control_oligo-7, Control_oligo-12, MZ00023408, MZ00023618, MZ00023663 in two replicates.
IMMOBILIZATION OF THE OLIGONUCLEOTIDE ARRAY ELEMENTS
1. Rehydrate the microarray slide over 56 °C water for 2-3 seconds; snap-dry on a 65 °C heating block for 5 seconds. Repeat this step 3 times, examining the slides under a dissection microscope to verify complete re-hydration of all the spots. Crosslink the oligonucleotides to the slide surface by exposing the DNA-side of the microarray to UV irradiation. We employ a Stratalinker set at an energy level of 60 mJ. After crosslinking slides were once again dried on a 100 °C heating block.
2. Blocking of the slides was performed according to Diehl et al. (Nucleic Acids Research 2001, 29(7): e38). Therefore slides were incubated for 1 h in blocking solution (1 g succinic anhydride, 200 ml 1,2-Dichlorethane, 2.5 ml 1-Methylimidazole), then dipped twice in 1,2-Dichlorethane. At the end slides were placed for 2 min in boiling water and then briefly transferred to 98 % ethanol.
3. Air dry slides under a clean bench.
4. Store the slides in a light-proof box in a vacuum.


title: Illumina Genome Analyzer (Trypanosoma brucei)

organism: Trypanosoma brucei


title: Illumina HiSeq 2000 (Arachis hypogaea)

organism: Arachis hypogaea


title: microRNA Ready-to-use PCR, Human panel I+II, V2.R

city: Odence

first: Henrik

last: Ditzel

address: J.B. Winsløws Vej 25

country: Denmark

institute: University of Southern Denmark

description: PCR assay

manufacture_protocol: see manufacturer's website


title: [Mouse430_2] Affymetrix GeneChip Mouse Genome 430 2.0 Array [CDF: mouse4302daiplusv6cdf]

status: Public on Apr 01 2014

city: Leiden

first: Joost

last: Melis

address: Postbus 9600

department: Toxicogenetics

institute: Leiden University Medical Center

organism: Mus musculus

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

manufacture_protocol: Dai et al., NAR (2005), 33(20):e175 and de Leeuw et al.,BMC Res Notes. 2008; 1: 66


title: Agilent-15513 Barley full length cDNA Microarray

city: Tsukuba

first: Shingo

last: Nakamura

state: Ibaraki

address: Kannondai 2-1-18

country: Japan

institute: National Institute of Crop Science

organism: Hordeum vulgare

first: Takashi

last: Matsumoto

manufacture_protocol: Custom Oligo Microarray 4x44 (Design ID: 15513)


title: Exiqon LNA probes version 10 microRNA array

city: Maastricht

first: Kasper

last: Derks

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

institute: Maastricht University Medical Center

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description:
Exiqon LNA probes version 10
In house printed microRNA Custom Exiqon spotted locked nucleic acid (LNA) probes microarray

manufacturer: Center for Biomics, Erasmus MC, CA Rotterdam

manufacture_protocol: The LNA-based capture probeset (Exiqon version 10,) was spotted on Nexterion E slides using a Virtek Chipwriter Pro


title: Agilent-044504 lincRNA_hs_SBC 028279 [Probe Name Version]

city: Xi'an

first: Wei-Hua

last: Xu

state: Shaanxi

address: No. 127 West Changle Road

department: Hepatobiliary Surgery

institute: Xijing Hospital, Fourth Military Medical University

description: Arrays of this design have barcodes that begin with 16044504 or 2544504.

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


title: LC Sciences Chicken miRNA Array

city: Harbin

first: Zhijie

last: Li

address: No. 427 Maduan St.

institute: Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences

organism: Gallus gallus

description: 789 unique probes


title: mirVANA miRNA Bioarray V1

city: Taichung

first: Wei-Chien

last: Huang

address: 9F, No.6, Hsueh-Shih Road

department: Graduate Institute of Cancer Biology

country: Taiwan

institute: China Medical University

manufacture_protocol: The mirVana miRNA Bioarrays are an Ambion product that is manufactured by GE Healthcare and incorporates the CodeLink™ 3-D Gel Matrix slide surface. This aqueous environment elevates the probes away from the surface of the slide, allowing for maximum interaction between the probes and targets.


title: Agilent-044516 S.Scrofa 1M regional Tiling Array 042564

city: Dummerstorf

first: Klaus

last: Wimmers

state: Mecklenburg-Vorpommern

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology

organism: Sus scrofa

description:
Including 37 Pig genomic regions (SS10) and 4 gene regions (SS10.2),

Arrays of this design have barcodes that begin with 16044516 or 2544516.

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: Human 37K long oligo array version 4.0.3

city: Silver Spring

first: Raj

middle: K

last: Puri

state: Maryland

address: 10903 New Hampshire Ave

country: USA

institute: FDA


title: Nimblegen 090128 Vibrio cholerae Gene Expression Array

city: Corvallis

first: Claudia

last: Hase

address: 105 Magruder Hall

institute: Oregon State University

organism: Vibrio cholerae O1 biovar El Tor str. N16961

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.
native array description file: 090128_Vcho_exp.ndf
native array description file: 090128_Vcho_exp.ngd


title: ACC human 2K ver6.0.

city: Nagoya

first: Miyuki

middle: Suguro

last: Katayama

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

department: Division of Molecular Medicine

institute: Aichi Cancer Center Research Institute

manufacturer: Division of Molecular Medicine, Aichi Cancer Center Research Institute

manufacture_protocol: The array consisted of 2,400 bacterial artificial chromosome (BAC) and P-1 derived artificial chromosome (PAC) clones, covering the human genome at roughly a 1.5-Mb resolution, from library RP11 and 13 for BAC clones and RP1, 3, 4, and 5 for PAC clones. These clones were obtained from the BACPAC Resource Center at the Children’s Hospital Oakland Research Institute (Oakland, CA). 4 Each clone was cultured in Terrific Broth medium with the chloramphenicol (25 μg/ml), and BAC and PAC DNA was extracted with a plasmid Mini-kit (Qiagen). The location of each clone was also confirmed by FISH analysis. Roughly 10% of these clones could not be assigned to their expected region and excluded from this study, whereas the confirmed clones were used for array CGH. We used 10 ng of BAC and PAC DNA as the template for degenerate oligonucleotide primed PCR with the primer 5′-CCGACTCGAGNNNNNNATGTGG-3′, where n = A, C, G, or T (24) . Amplifications were performed on a TaKaRa PCR Thermal Cycler MP (TaKaRa) using ExTaq polymerase (TaKaRa). Degenerate oligonucleotide primed-PCR products were enriched by ethanol precipitation and dissolved in distilled water, and then equal volume of DNA spotting solution DSP0050 (MATSUNAMI, Osaka, Japan) was added (∼1 μg/μl). DNA was robotically spotted (NGK Insulators, Ltd.) in duplicate onto CodeLink activated slides (GE Healthcare Life Sciences).


title: Agilent-021827 Human miRNA Microarray G4470C (miRNA ID version)

city: Palo Alto

last: Agilent Technologies

state: CA

institute: Agilent Technologies

description:
Arrays of this design have barcodes that begin with 16021827 or 2521827.
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.
Human miRNA Microarray 3.0
Orientation:
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
The ID column represents the Agilent Feature Extraction feature number.
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: [HT_HG-U133A] Affymetrix Human Genome U133A Array (custom CDF: HTHGU133A_Hs_ENTREZG.cdf version 17.0.0)

status: Public on Nov 07 2013

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: Identical to GPL3921 but used a custom CDF

relation: Alternative to: GPL3921 (official platform)

manufacture_protocol: see manufacturer's web site


title: Ion Torrent PGM (Haemophilus parasuis)

last: GEO

organism: Glaesserella parasuis


title: miRCURY LNA microRNA Array (miRBASE 14.0, lot numbers 31015 and 31078)

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

institute: Juntendo University

manufacture_protocol: See manufacturers website


title: BaSysBio Bacillus subtilis T2 385K array [090325_CBS_DTU_Bsub_T2]

status: Public on Jan 15 2013

city: Paris

first: Harald

last: Putzer

address: 13, rue P. et M. Curie

department: UPR9073, IBPC

institute: CNRS

organism: Bacillus subtilis subsp. subtilis str. 168

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


title: PHRI-UMNDJ Human cytomegalovirus 1.5K CAG_HCMV [gene-level]

status: Public on Jul 21 2012

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

organism: Human betaherpesvirus 5

manufacturer: The Center for Applied Genomics at the Public Health Research Insitute of UMDNJ

manufacture_protocol: The HCMV arrays were printed and processed as described previously (Yang et al 2005).  Briefly, the array contains 65-mer oligonucleotides representing 197 predicted open reading frames of the HCMV strain AD169, 20 oligonucleotides for ORFs in the Toledo strain that are not found in AD169 and 42 human genes as controls.


title: IMB yeast 7K operon oligo array for gene expression

status: Public on Mar 28 2014

city: Taipei

first: Jun-Yi

last: Leu

address: No. 128, Sec. 2, Academia Rd., Nangang Dist.

institute: Institute of Molecular Biology

organism: Saccharomyces cerevisiae

manufacturer: Microarray Core Facility of the Institute of Molecular Biology, Academia Sinica, TW.

manufacture_protocol: Arrays were printed by standard protocols on CodeLink Activated slides (GE Healthcare) using a Gene Machine (San Carlos, CA) OmniGrid 100 Instrument.


title: Mmca_MOUSE_NIAID

status: Public on Mar 31 2010

city: Seoul

first: Dong-Mi

last: Shin

address: 1 gwanak-ro

institute: seoul national university

manufacture_protocol:
The specifications include:
Length: 70 bases
Modification: 5'-C6 amino modifier
Oligo synthesis efficiency: < 99%
Reduced propensity to form secondary structure
Minimized cross-hybridization potential to non-target mouse or human genes
Consistent theoretical melting temperature with all other oligonucleotides
Bias to the 3' end of the gene for enhanced cDNA labeling
Targeted sequence region of high sequence fidelity and accuracy
Positive and negative controls provided
Oligonucleotides are purified for enriched full-length product and desalted


title: BaSysBio Bacillus subtilis T1 385K array [070910_BaSysBio_expr]

status: Public on Mar 06 2012

city: Greifswald

first: Ulrike

last: Mäder

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

department: Functional Genomics

institute: University Medicine Greifswald

description:
AL009126.3
native array description file: 070910_BaSysBio_expr.ndf
native array description file: 070910_BaSysBio_expr.pos


title: Mmbe-Mouse-NIAID

status: Public on Feb 01 2010


title: Agilent-016322 Yeast Gene Expression 8x15K Microarray (Systematic Name version)

status: Public on Mar 28 2011

description:
15,208 S. cerevisiae (S288C strain) ORFs represented.
Contents sourced from Saccharomyces Genome Database (SGD), January, 2004.

This oligonucleotide microarray will enable researchers to simultaneously characterize expression of many thousands of yeast genes and identify gene activity during important biological processes, such as yeast growth, adaptation, and response to drug candidates.

Arrays of this design have barcodes that begin with 16016322 or 2516322.
Agilent part number (V2): G4813A

Orientation:
Features are 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 SystematicName.

manufacture_protocol:
Agilent 60-mer SurePrint technology.
See manufacturer's web site at http://www.agilent.com/.


title: Agilent-022522 SurePrint G3 CGH array 4X180K (Probe Name version)

status: Public on Feb 19 2013

organism: Homo sapiens

description:
170k BaBo UMCG plus Cancer Census.
Arrays of this design have barcodes that begin with 16022522 or 2522522.
design AMADID#022522


title: Agilent-031184 Unrestricted_Mouse_miRNA_V16.0_Microarray (Feature Number version)

status: Public on Dec 15 2011

description:
all mouse and mouse viral miRNAs

Arrays of this design have barcodes that begin with 16031184 or 2531184.

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.


status: Public on Mar 03 2011

description:
AL009126.3
090325_CBS_DTU_Bsub_T2.ndf
090325_CBS_DTU_Bsub_T2.pos


title: BaSysBio Bacillus subtilis T1 385K array version 1 [070910_basysbio_expr]

status: Public on Jun 10 2009

city: Kongens Lyngby

first: Simon

last: Rasmussen

address: Kemitorvet, Building 208

department: Department of Systems Biology

institute: Technical University of Denmark

description: This array is designed for Bacillus subtilis #168 (pre 2009 sequence) under the BaSysBio consortium (EU-FP6). The probes are tiled along the genome in 22 nt intervals and covers both strands and strand-specific labeling enables measurements from both strands in one experiment.

first: Hanne

last: Jarmer

first: Henrik

middle: B

last: Nielsen

manufacture_protocol: 385K feature NimbleGen arrays designed using OligoWiz 2.0 with long iso-thermal probes (45-65 nt) covering the entire genome of Bacillus subtilis #168 Trp+ in 22 nt intervals on each strand with an 11 nt offset between strands.


title: OpArray Human 35K

status: Public on Oct 14 2009

city: Gwangju

first: Da-Woon

last: jung

address: 1 Oryong-Dong

department: Life Science

institute: Gwangju Institute of Science and Technology

manufacture_protocol: 70mer oligonucleotide, Contains 35,035 oligos (Genome oligos, Positive control oligos, Randomized negative control oligos, Spiking negative control oligos and  Alien control oligos), 35,035 genome oligos represents 25,100 predicted genes  or 39,600 gene transcripts, Spotted on Epoxy coated slides (Schott Nexterion) in collaboration with Microarray Inc. to provide best hybridization  kinetics with very low background, Supplied as DNA immobilized  ready to use


title: NIAID/NIH Mus musculus 18K array version 1

status: Public on Sep 30 2008


title: Illumina HiSeq 2000 (Ehrlichia chaffeensis str. Saint Vincent)


title: Illumina HumanExome-12 v1.1 BeadChip

status: Public on Apr 08 2014

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

description:
HumanExome-12v1-1_A.bpm
coverage of putative functional exonic variants selected from over 12,000 individual exome and whole-genome sequences

The exonic content consists of > 250,000 markers representing diverse populations—including European, African, Chinese, and Hispanic individuals—and a range of common conditions, such as type 2 diabetes, cancer, metabolic, and psychiatric disorders.

HumanExome BeadChips deliver focused coverage of exonic regions, but do not include coverage outside of coding regions. Researchers can use these arrays to obtain new insights from previously genotyped cohorts, or run new studies focused on identifying functionally relevant associations.


title: NIAID/NIH Mouse Mmbe-33 Array

status: Public on Oct 15 2011

manufacture_protocol: Length: 70 bases; Modification: 5'-C6 amino modifier; Oligo synthesis efficiency: < 99%