title: Illumina Genome Analyzer II (Fusarium virguliforme Mont-1)

status: Public on Aug 29 2016

last: GEO

country: USA

organism: Fusarium virguliforme Mont-1

technology: high-throughput sequencing

distribution: virtual


title: Agilent-023297 Grape Oligo 4×44K Microarray (Feature Number version)

status: Public on Aug 30 2016

city: Chiayi City

first: Yung-fu

last: Yen

address: 300, University Road

department: Bioagricultural Science

country: Taiwan

institute: National Chiayi University

organism: Homo sapiens

technology: in situ oligonucleotide

description: Probe sequences are based on Vitis_vinifera_mRNA_v1.fa (http://www.genoscope.cns.fr/externe/Download/Projets/Projet_ML/data/8X/annotation/).

distribution: custom-commercial

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


title: Exiqon Human miRCURY LNA microRNA Array, 7th generation - (miRBase v18.0)

status: Public on Aug 31 2016

city: Cork

first: Anand

last: Gururajan

address: Western Road

department: Anatomy & Neuroscience

country: Ireland

institute: University College Cork

technology: spotted oligonucleotide

manufacture_protocol: See Exiqon website


title: Agilent-061991 HumiChip2 Nov 13th 061941

city: Norman

first: Qichao

last: Tu

state: OK

address: 101 David L Boren Blvd

institute: University of Oklahoma

organism: human metagenome


title: Agilent-040555 Human HG19 CGH array (Probe name version)

city: Oxford

first: Bass

last: Hassan

state: Oxfordshire

address: South Parks Road

department: Sir William Dunn School of Pathology, Oxford Molecular Pathology Institute

country: United Kingdom

institute: University of Oxford

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


title: Illumina HiSeq 2500 (Acrobeloides nanus)

organism: Acrobeloides nanus


title: Illumina Genome Analyzer II (Fusarium virguliforme Mont-1; Glycine max)

organism:
Glycine max
Fusarium virguliforme Mont-1


title: LC Sciences Branchiostoma belcheri Custom Array LCB_D140317

status: Public on Dec 08 2016

city: Beihai

first: Xin

last: Liao

state: Guangxi

address: 2# JinHaian Road

department: School of Life Sciences

country: China

institute: Nanjing University

organism: Branchiostoma belcheri

manufacture_protocol: Arrays are made based 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: NanoString nCounter customized human colorectal cancer gene expression platform

city: Nashville

first: Jing

last: Zhu

state: TN

institute: Vanderbilt University

technology: other

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


title: Illumina HiSeq 2500 (Pseudomonas cichorii JBC1)

status: Public on Aug 28 2016

organism: Pseudomonas cichorii JBC1


title: NAU-30K_Salmonella_Typhimurium_str_LT2 v1.0

city: Flagstaff

first: Andrew

last: Koppisch

state: AZ

address: PO Box 5698

department: Chemistry

institute: Northern Arizona University

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

technology: spotted DNA/cDNA

manufacture_protocol: Each slide has one array composed of 30,721 potential addresses for probes, of which 26,346 spots contain 45-47mer probes for Salmonella enterica (SE) genes, 3,654 features are “empty” (i.e., they contain no probe), 608 features contain MYcroarray in-house QC probes and 112 features contain positive control probes for assessing hybridization and washing stringency. Each SE gene is surveyed by one unique probe sequence. There are 6 identical replicates of each SE probe sequence such that a total of 4,391 SE genes are surveyed by each array.


title: Illumina HiSeq 2500 (Panagrellus redivivus)

organism: Panagrellus redivivus


title: SABiosciences RT² Profiler panel of PCR assays [PAMM-3803Z]

status: Public on Aug 27 2016

city: Albuquerque

first: Donna

middle: Frances

last: Kuseiwtt

state: NM

address: Reginald Heber Fitz Hall, Room 335;  915 Camino de Salud

department: Pathology

institute: University of New Mexico School of Medicine

organism: Mus musculus

technology: RT-PCR

description: Mouse Inflammatory Response & Autoimmunity PCR Array

manufacture_protocol: see manufacturer's website


title: Illumina HiSeq 4000 (Streptococcus pneumoniae TIGR4)

status: Public on Aug 26 2016

organism: Streptococcus pneumoniae TIGR4


title: 121211-allmis-ms-meth-ux1

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

organism: Alligator mississippiensis

description:
The array used for the differential methylation analysis was a DNA methylated custom array by Roche Nimblegen that consisted of a Whole Genome Tiling Array of the American Alligator (Alligator mississippiensis) made of two chip set arrays with a 200bp resolution (121211-allmis-ms-meth-ux1). Probe sizes were 50-75mer in length and median probe spacing was 200bp.

The December 2014 report of the Alligator mississippiensis genome produced by the Genome Sequencing Center was retrieved (http://crocgenome.hpc.msstate.edu/crocbase/gbrowsers.html, http://crocgenome.hpc.msstate.edu/gb2/gbrowse/gator/). A seed file was constructed and a BSgenome package was forged for using the Alligator DNA sequence in the R code (Herve Pages BSgenome: Infrastructure for Biostrings-based genome data packages. R package version 1.24.0). This sequence was used to design the custom tiling arrays and to perform the bioinformatics.


title: Agilent-069856 Medaka v19 miRNA

city: Rennes

first: Julien

last: Bobe

address: Campus de Beaulieu

country: France

institute: Institut National de la Recherche Agronomique

organism: Oryzias latipes

description:
Arrays of this design have barcodes that begin with 16069856 or 2569856.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

distribution: commercial


title: Illumina HiSeq 2000 (Pseudomonas phage PAK_P4)

status: Public on Aug 24 2016

organism: Pseudomonas phage PAK_P4


title: Illumina HiSeq 2500 (Ceratitis capitata)

organism: Ceratitis capitata


title: AB 5500xl Genetic Analyzer (Escherichia coli O157:H7 str. EDL933)

status: Public on Aug 23 2016

organism: Escherichia coli O157:H7 str. EDL933


title: ACRI Human2 oligo array

city: Moncton

first: Daniel

last: Leger

state: New Brunswick

address: 35 Providence Street

department: IARC

country: Canada

institute: Atlantic Cancer Research Institute

distribution: non-commercial

manufacturer: Atlantic Cancer Research Institute (New Brunswick, Canada)

manufacture_protocol:
50-mer oligos printed on Schott epoxy slides using 50 um silicon microarray pins (Parallell Synthesis Technologies) and OmniGrid OGR-04 microarrayer (Digilab Genomics Solutions).
Microarrays consist of 16871 oligos and blanks (buffer only) arrayed in duplicates as 34944 spots arranged in 48 (4 x 12) grids of 26 columns by 28 rows with side by side duplicates.


title: Illumina HumanHT-12 V4.0 expression beadchip (reannotation)

status: Public on Aug 25 2016

city: Clayton

first: Moshe

last: Olshansky

state: Vic

address: 19 Innovation Walk (Bldg 76)

department: Microbiology

country: Australia

institute: Monash University

technology: oligonucleotide beads


title: Agilent-045822 Corynebacterium glutamicum ATCC 13032 8X15K array [Probe Name Version]

city: shanghai

first: qian

last: jin

address: libing road

institute: MSP

organism: Corynebacterium glutamicum ATCC 13032


title: Illumina MiSeq (Canis lupus familiaris)

organism: Canis lupus familiaris


title: Agilent-025748 Corynebacterium glutamicum CGRarray (Feature ID)

status: Public on Aug 22 2016

city: Kyoto

first: Masayuki

last: Inui

address: 9-2 Kizugawadai, Kizugawa

country: Japan

institute: Research institute of Innovative Technology for the Earth (RITE)

organism: Corynebacterium glutamicum R


title: Illumina MiSeq (Aspergillus nidulans)

organism: Aspergillus nidulans


title: Illumina Genome Analyzer (Microtus ochrogaster)

status: Public on Aug 19 2016

organism: Microtus ochrogaster


title: Illumina MiSeq (Macaca)

organism: Macaca


title: Agilent-032510 Custom Aspergillus niger Gene Expression Microarray 4x44k

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: Aspergillus niger


title: Nimblegen Whole Genome Apple Array [120906_Malus_PT_expr]

city: San Michele all'Adige

first: Fabrizio

last: Costa

state: N/A = Not Applicable

address: Via Mach 1

department: Center Agriculture Food Environment

country: Italy

institute: University of Trento

organism: Malus domestica

description:
12-plex array with 135,000 features per subarray

designid=574211
designname=120906_Malus_PT_expr

native array description file: 120906_Malus_PT_expr.ndf
native array description file: 120906_Malus_PT_expr.ngd

This array was designed starting from a RNA-seq of the samples we hybridised on the array.
When the sequence alignment matched the genome, they were coded with MDP0000xxx as reported at https://www.rosaceae.org/gb/gbrowse/malus_x_domestica_v1.0-primary/.
However, with RNA-seq we discovered novel genes, thus they are coded as CUFF (derived by Cufflinks, the software used by the bionic to count the reads from the RNA-seq), and they are not currently available in any database.

manufacture_protocol: Standard NimbleGen manufacture protocol.


title: Illumina HiSeq 2500 (Seriola lalandei dorsalis)

status: Public on Aug 21 2016

last: GEO

organism: Seriola lalandi dorsalis


title: Illumina HiSeq 1500 (Oidium neolycopersici)

organism: Erysiphe neolycopersici


title: Illumina MiSeq (Mycobacterium smegmatis)

organism: Mycolicibacterium smegmatis


title: Illumina HiSeq 1500 (Golovinomyces cichoracearum)

organism: Golovinomyces cichoracearum


title: Illumina HiSeq 2000 (Aspergillus flavus; Zea mays)

organism:
Zea mays
Aspergillus flavus


title: Agilent-062918 Human lncRNA array V4.0 (Probe name version)

city: Nanjing

first: Ying

last: Wu

address: Baiziting 42

institute: Nanjing Medical University Affiliated Cancer Hospital Cancer Institute of Jiangsu Province

organism: Homo sapiens

description: 78,243 human lncRNAs and 30,215 coding transcripts.


title: Nimblegen Staphylococcus aureus Gene Expression 12x135K Arrays [120629_Saureus_JHJ_exp]

city: Cheongju

first: Jung Wook

last: Kim

address: Osong Health Technology Administration Complex, 187

department: Division of Antimicrobial resistance

country: South Korea

institute: Korea National Research Institute of Health

organism: Staphylococcus aureus subsp. aureus Mu50

description:
NimbleGen design name 120629_Saureus_JHJ_exp_HX12,  expression design for 967 genes from S. aureus N315, total probes 10,637,  Each probe is replicated 3 times.  The design includes random GC and other control probes.

Native array description files:
120629_Saureus_JHJ_exp.ndf
120629_Saureus_JHJ_exp.ngd

DESIGN_ID:572421

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


title: Illumina HiSeq 2500 (Dasypus novemcinctus)

status: Public on Aug 18 2016

organism: Dasypus novemcinctus


title: Illumina HiSeq 2000 (Dasypus novemcinctus)


title: Illumina HiSeq 3000 (Vitis vinifera)

organism: Vitis vinifera


title: Maize ologonucleotide array 2k version

city: Hamburg

first: Stefan

last: Scholten

state: Hamburg

address: Ohnhorststrasse 18

department: Biocenter Klein Flottbek

country: Germany

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 µL 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: Agilent-062312 Nicotiana attenuata 60K [Probe Name version]

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

organism: Nicotiana attenuata


title: NanoString nCounter human PanCancer Pathways Custom Codeset

city: Birmingham

first: Sunil

last: Sudarshan

state: Alabama

address: 510 20th Street South

department: Urology

institute: UAB


title: Illumina Genome Analyzer IIx (Thermococcus onnurineus)

status: Public on Aug 17 2016

organism: Thermococcus onnurineus


title: Agilent-069985 Mycoplasma gallisepticum array

city: Moscow

first: Tatiana

middle: A.

last: Semashko

address: Malaya Pirogovskaya

country: Russia

institute: RCPCM

organism: Mycoplasmoides gallisepticum

description:
Arrays of this design have barcodes that begin with 16069985 or 2569985.

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 MiSeq (Thermococcus onnurineus)


title: Illumina HiSeq 2500 (Nicotiana tabacum)

organism: Nicotiana tabacum


title: Illumina HiSeq 2500 (Cavia porcellus)

organism: Cavia porcellus


title: Illumina HiSeq 2500 (Methylobacter tundripaludum; Methylotenera mobilis)

organism:
Methylobacter tundripaludum
Methylotenera mobilis


title: Illumina HiSeq 2500 (Methylobacter tundripaludum)

organism: Methylobacter tundripaludum


title: Illumina HiSeq 2500 (Methylotenera mobilis)

organism: Methylotenera mobilis


title: Nimblegen OID24708_Human, Design: 091105_HG18_AS_ChIP_HX1

city: Guangzhou

first: Alexander

middle: V.

last: Strunnikov

state: Guangdong

address: 190 Kai Yuan Avenue

institute: GIBH

manufacture_protocol: Roche-Nimblegen proprietary. The design of the arary was custom tiling design for repeat regions in the hg18 genome using TRF database sequences.  Straight-tiling through the sequences using isothermal 50-75mers (target 76C) using an interval of 44 (2,137,330 probes).  No uniqueness checking was performed as it was a repeat array.  The sequence for any initial sequence that was smaller than 50 bases was extended with itself in tandem, so that it would be >=50. The design included two control sets composed of 29,161 random sequence tiles and 181 tiles from the rDNA locus of S. cerevisiae.


title: Illumina NextSeq 500 (Drosophila melanogaster; Homo sapiens)

organism:
Drosophila melanogaster
Homo sapiens


title: Agilent-072436 Schmidtea mediterranea expression array (Probe Name version)

status: Public on Aug 15 2016

first: Dasaradhi

last: Palakodeti

address: GKVK Campus, Bellary road

department: TAS

institute: inStem, NCBS

organism: Schmidtea mediterranea

description: This is an custom made array with distal poly adenylation sites.

manufacture_protocol: See manufacturer's website


title: Agilent Schmidtea mediterranea AMADID: 72579

description:
This is an custom made array with proximal poly adenylation sites.
Raw data files associated with Sample records contain sequences of the probes


title: Sealfon Lab Mouse Gonadotrope Quantitative Real Time PCR assay panel

status: Public on Apr 07 2017

city: New York

first: Frederique

last: Ruf-Zamojski

state: NY

address: 1468 Madison Avenue

department: Neurology

institute: Mount Sinai Medical Center

organism: Mus musculus


title: Illumina HiSeq 2500 (Salmonella enterica subsp. enterica serovar Typhimurium str. 14028s Wu)

status: Public on Aug 16 2016


title: Illumina Genome Analyzer (Crassostrea hongkongensis)

organism: Magallana hongkongensis


title: Illumina HiSeq 2500 (Methylobacter tundripaludum 21/22)

organism: Methylobacter tundripaludum 21/22


title: Illumina NextSeq 500 (Pseudomonas putida)

status: Public on Aug 14 2016

organism: Pseudomonas putida


title: Illumina NextSeq 500 (Cricetulus griseus)

organism: Cricetulus griseus


title: Illumina HiSeq 2000 (Thiomonas sp. CB2)

status: Public on Aug 10 2016

organism: Thiomonas sp. CB2


title: Illumina HiSeq 2000 (Methanosarcina mazei Go1)

organism: Methanosarcina mazei Go1


title: Illumina HiSeq 2000 (Coccidioides posadasii)

status: Public on Aug 09 2016

organism: Coccidioides posadasii


title: Illumina HiSeq 4000 (Fragaria x ananassa)

status: Public on Aug 12 2016

organism: Fragaria x ananassa


title: Illumina HiSeq 2500 (Mactra chinensis)

organism: Mactra chinensis


title: 021764 Agilent Human Genotypic Designed CGH 105k Microarray [Probe name version]

status: Public on Aug 11 2016

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Homo sapiens

relation: Alternative to: GPL10722 (Feature Number Version)

manufacture_protocol: Refer to www.chem.agilent.com


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray HGU133Plus2_Hs_ENTREZG_v20]

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

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


title: Illumina NextSeq 500 (Paracoccus denitrificans)

organism: Paracoccus denitrificans


title: OpArray Human 35K array [oligo_ID version; MI_OpHRA_20921_gal_corr.gal]

city: London

first: Paolo

last: Salomoni

address: 72 Huntley St

department: Cancer Institute

institute: University College London

manufacture_protocol: according to manufacturer


title: Illumina HiSeq 2000 (Clostridioides difficile)

organism: Clostridioides difficile


title: Illumina HiSeq 2500 (Steinernema carpocapsae)

status: Public on Aug 05 2016

organism: Steinernema carpocapsae


title: [HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [HuGene11st_Hs_ENTREZG_18.0.0]

city: Tel Aviv

first: Carmit

last: Levy

address: Ramat Aviv

department: Human Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

description: Brainarray: HuGene11st_Hs_ENTREZG_18.0.0

manufacture_protocol: See manufacturer's web site


title: Illumina HiSeq 2000 (Neisseria meningitidis 8013)

organism: Neisseria meningitidis 8013


title: [HuGene-2_1-st] Affymetrix Human Gene 2.1 ST Array [gene name version]

status: Public on Aug 08 2016

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

September 06, 2013: HuGene-2_1-st-v1.na33.2.hg19.transcript.csv


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

description:
SurePrint G3 Human GE 8x60K Microarray

*** The ID column includes the SystematicName. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL13607.

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


title: Qiagen Human miFinder miScript miRNA PCR panel (MIHS-001Z)

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

department: Medicine

institute: Rutgers NJ Medical School

description:
Human miFinder miRNA PCR Array
miScript SYBR Green PCR Kit


title: Illumina HiSeq 2500 (Drosophila virilis)

organism: Drosophila virilis


title: Illumina MiSeq (Neisseria meningitidis 8013)


title: Illumina HiSeq 1500 (Bos taurus)

organism: Bos taurus


title: Illumina HiSeq 2500 (Drosophila erecta)

organism: Drosophila erecta


title: Illumina HiSeq 2500 (Drosophila simulans)

organism: Drosophila simulans


title: Illumina HiSeq 2500 (Drosophila sechellia)

organism: Drosophila sechellia


title: MRC Toxicology Unit-Mus musculus-38k-MEEBO probe set [slide A and slide B]

status: Public on Aug 04 2016

city: Didcot

first: Emma

middle: Louise

last: Marczylo

address: Harwell Campus, Chilton

department: Toxicology

institute: Public Health England

organism: Mus musculus

manufacturer: MRC Toxicology Unit, Systems Toxicology Group

manufacture_protocol: This is a new version of platform number GPL9106. 70-mer oligos (Invitrogen MEEBO probe set-originally Illumina) are supplied dried down at 200 pmol concentration in Genetix 384 well plates. The full printing set consists of 101 plates. Prior to printing Oligos are resuspended in 3 x SSC, 1.5 M Betaine, 30% ethylene glycol. Plates are loaded onto an ArrayJet microarrayer 48 at a time; the slides used are Genetix aldehyde plus. Printing is performed using inkjet-style technology to deposit oligo on each slide. The software requests the addition of the next batch of plates once the first 48 have been printed. The layout of the print is 3 blocks, each one consisting of 32 columns and 216 rows. We also included a marker plate top and bottom to make aligning the features easier. The entire print run is split over 2 slides (A: GPL15713; and B: GPL15714) due to space constraints.


title: Illumina HiSeq 2500 (Drosophila ananassae)

organism: Drosophila ananassae


title: Illumina HiSeq 4000 (Streptococcus pneumoniae)

organism: Streptococcus pneumoniae


title: Illumina MiSeq (Enterobacteria phage phiX174)

status: Public on Aug 03 2016

organism: Sinsheimervirus phiX174


title: Illumina NextSeq 500 (Zea mays subsp. mays)

organism: Zea mays subsp. mays


title: Illumina HiSeq 2500 (Glycine soja)

organism: Glycine soja


title: Illumina HiSeq 2500 (Mus musculus musculus x M. m. castaneus)

status: Public on Aug 02 2016

organism: Mus musculus musculus x Mus musculus castaneus


title: SUCEST-FUN Sugarcane 44k v1.0 (probe name version)

organism: Saccharum officinarum

description:
CaneRegNet microarray (44k multiplex chip, agilent) was designed using an in-house developed method for empirical selection of best performing probes (60bp long oligomers) for each SAS (Sugarcane Assembled Sequence - Pre Selection Strategy based on gene function and categorization). Were designed two probes for each cluster SAS from SUCEST Project, one in the sense orientation and another one in the antisense orientation if available or one sense probe. The microarray contain 21902 oligo probes in sense and antisense orientation corresponding of a total of 14522 SAS.

The ID column includes the Probe Names. A different version of this platform with a unique numeral id (for each 'spot' on the array) in the ID column is assigned accession number GPL14862.

manufacture_protocol: We labeled, hybridized, and washed the arrays according to Agilent's Two-Color Microarray-Based Gene Expression Analysis(Quick Amp labeling) Protocol (version 5.7, March 2008)


title: Illumina Genome Analyzer IIx (Oncorhynchus masou masou)

organism: Oncorhynchus masou masou


title: Illumina MiSeq (Cannabis sativa)

organism: Cannabis sativa


title: Illumina HiSeq 2000 ([Enterobacter] aerogenes)

organism: Klebsiella aerogenes


title: Illumina NextSeq 500 (Alligator mississippiensis)

organism: Alligator mississippiensis


title: Agilent-065138 8x15k C. albicans assembly 21 [Probe name version]

organism: Candida albicans

description:
Changed microarray design to 8x15k

Arrays of this design have barcodes that begin with 16065138 or 2565138.

relation: Alternative to: GPL22236 (Feature Number Version)


title: Illumina HiSeq 3000 (Neofusicoccum parvum; Vitis vinifera)

status: Public on Aug 01 2016

organism:
Vitis vinifera
Neofusicoccum parvum


title: Illumina HiSeq 3000 (Neofusicoccum parvum)

organism: Neofusicoccum parvum


title: Illumina HiSeq 2000 (Serratia sp. BW106)

organism: Serratia sp. BW106


title: Geochip 5.0

city: Changsha

first: Shiqi

last: Jie

state: Hunan

address: Lushan South Road 932

institute: Central South University

organism:
Bacteria
Archaea
Eukaryota
Viruses

description: A original high throughput tool to provide significative information for the microbial community structure, composition and potential metabolic capacity, has been widely used to analyze microbial community from various habitats

first: Jizhong

last: Zhou

manufacture_protocol: see manufacturer's web site


title: Biomark 96.96 dynamic array for salivary extracellular vesicles real-time qRT-PCR

city: Koto

first: Kiyotaka

last: Shiba

state: Tokyo

address: Ariake 3-8-31

institute: Japanese Foundation for Cancer Research

organism: Homo sapiens

description: PCR assay


title: 3D-Gene Mouse miRNA V11_1.0.0

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

organism: Mus musculus

manufacture_protocol: See manufacture's web site


title: Candida albicans Microarray designed by Genotypic Technology Private Limited (AMADID-016356) [Gene name version]

city: New Delhi

first: Krishnamurthy

last: Natarajan

state: Delhi

address: 314/325, School of life sciences, JNU

department: School of life sciences

institute: Jawaharlal Nehru University

description: Gene Name version of platform GPL17211


title: Agilent-038224 Acinetobacter baumannii array v1 (Feature number version)

city: A Coruña

first: Margarita

last: Poza

address: As Xubias

country: Spain

institute: Fundacion Prof Novoa Santos-Insituto de Investigacion Biomedica

organism: Acinetobacter baumannii

description:
Agilent-038224 AcBa v1

Arrays of this design have barcodes that begin with 16038224 or 2538224.

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 (Mesocestoides corti)

last: GEO

organism: Mesocestoides corti


title: NimbleGen Brucella suis Expression Array [2006-07-27_TI204722_60mer]

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Brucella suis

manufacture_protocol: in situ oligonucleotide


title: Agilent-021113 Tobacco Gene Expression Microarray 4x44K (GeneName version)

city: Bangalore

first: Genotypic

last: technology

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

institute: Genotypic Technology

organism: Nicotiana tabacum

description:
Arrays of this design have barcodes that begin with 16021113 or 2521113.

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 GenBank ID.

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

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

relation: Alternative to: GPL10098 (Feature Number version)


title: Agilent-028916 Mouse 8x60k CGH [Feature number version]

status: Public on May 04 2016

city: Graz

first: Vendula

last: Svendova

address: Auenbruggerplatz 2

country: Austria

institute: Medical University Graz

description:
selected from 162k probe set extended by 1M chrY set

Arrays of this design have barcodes that begin with 16028916 or 2528916.

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.

relation: Alternative to: GPL17189 (Probe name version)


title: Agilent-065138 8x15k C. albicans assembly 21

status: Public on Jul 27 2016

city: Dublin

first: Geraldine

last: Butler

address: Belfield

department: School of Biomolecular and Biomedical Science

institute: University Colege Dublin Conway Institute

description:
Changed microarray design to 8x15k

Arrays of this design have barcodes that begin with 16065138 or 2565138.

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.

relation: Alternative to: GPL22275 (Probe Name Version)


title: [HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [HuGene11stv1_Hs_ENSG version 19.0.0]

country: USA

description:
Probe set data extracted from custom CDF (HuGene11stv1_Hs_ENSG.cdf v19.0.0).
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/19.0.0/ensg.asp


title: LCSciences Human miRNA Array miRBase release 19 [miRBase ID version]

city: Jinan

first: Peng

last: Gao

address: Wen Hua Xi Road 44

institute: Shandong University

description: catalog number MRA-1001B1

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


title: Agilent-050029 Trichophyton rubrum  v1 027344

city: RIBEIRAO PRETO

first: Tamires

middle: Aparecida

last: Bitencourt

state: SP

address: AV COSTABILE ROMANO 2221

department: BIOTECNOLOGY

country: Brazil

institute: UNAERP

organism: Trichophyton rubrum

description:
Lamina construida somente com as sequencias unicas cuja redundancia foi retirada pela comparacao dos probe groups total e aquele sem os BC_score 4

Arrays of this design have barcodes that begin with 16050029 or 2550029.

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 2.1M array, custom made

status: Public on Jul 31 2016

city: Kongens Lyngby

first: Henrik

middle: Bjørn

last: Nielsen

address: Kemitorvet, b. 208

department: Systems Biology

country: Denmark

institute: Technical University of Denmark

organism: human gut metagenome

description:
091111_Unk_LG_CGH_HX1.ndf
091111_Unk_LG_CGH_HX1.ndg


title: Nimblegen Plasmodium falciparum 100813_LC_Pfal_5833_expr

status: Public on Dec 01 2015

city: Notre Dame

first: Michael

middle: T

last: Ferdig

state: IN

address: 100 Galvin Life Sciences Center

department: Biological Sciences

institute: University of Notre Dame

organism: Plasmodium falciparum

manufacture_protocol: High-density gene expression array manufactured by NimbleGen Inc using Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.


title: 021764 Agilent Human Genotypic Designed CGH 105k Microarray

status: Public on Jul 28 2010

first: madavan

last: vasudevan

address: Kasturi Nagar

institute: Theomics International Private Limited

first: Raja

middle: C

last: Mugasimangalam

first: Rohit

middle: N

last: Shukla

first: Shruti

last: Sinha

relation: Alternative to: GPL22311 (Probe name version)


title: NimbleGen Mouse CGH 3x720K Whole-Genome Tiling Array [100718_MM9_WG_CGH]

status: Public on Apr 27 2012

city: Shanghai

first: Linyu

last: Shi

address: 320 Yueyang Road

institute: Institute of Biochemistry and Cell Biology,Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences

description: Build: MM9

manufacture_protocol: See www.nimblegen.com


title: Custom TaqMan: qPCR ViiA7 real-time PCR system

status: Public on Aug 31 2015

city: Prague 10

first: Pavel

last: Soucek

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

manufacturer: Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic

manufacture_protocol:
Custom made-to-order or pre-designed TaqMan assays were used with protocol recommended by the producer (Life Technologies Corp., Carlsbad, CA, USA)
qPCR was performed in ViiA7 real-time PCR system produced by Life Technologies (Carlsbad, CA)


title: [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [CDF: hugene20st_Hs_ENTREZG, Brainarray version 18.0.0]

status: Public on Feb 18 2015

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

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

relation: Alternative to: GPL16686 (Alternative CDF [official])

manufacture_protocol: See manufacturer's web site.


title: [AN10000a520725F]Affymetrix Aspergillus nidulans 10K custom array

status: Public on Aug 14 2010

city: tsukuba

first: masuo

last: shunsuke

address: 1-1-1 tennodai

institute: university of tsukuba

organism: Aspergillus nidulans


title: SUCEST-FUN Sugarcane 44k v1.0

status: Public on Jul 31 2012

city: São Paulo

first: Milton

middle: Yutaka

last: Nishiyama Jr

state: São Paulo

address: Av. Professor Lineu Prestes, 748

department: Biochemistry

institute: Universidade de São Paulo - USP

organism: Saccharum officinarum

description:
CaneRegNet microarray (44k multiplex chip, agilent) was designed using an in-house developed method for empirical selection of best performing probes (60bp long oligomers) for each SAS (Sugarcane Assembled Sequence - Pre Selection Strategy based on gene function and categorization). Were designed two probes for each cluster SAS from SUCEST Project, one in the sense orientation and another one in the antisense orientation if available or one sense probe. The microarray contain 21902 oligo probes in sense and antisense orientation corresponding of a total of 14522 SAS.

The ID column includes unique numeral id (for each 'spot' on the array). A different version of this platform with unique probe name in the ID column is assigned accession number GPL22278.

first: Carolina

middle: G

last: Lembke

middle: Y

last: Nishiyama-Jr

first: Paloma

middle: M

last: Sato

first: Rodrigo

middle: F

last: de Andrade

first: Glaucia

last: Souza


title: NimbleGen Drosophila melanogaster Whole Genome 2.1M tiling array [DM_5_Catalog_tiling_HX1; DesignID 6725]

status: Public on Dec 23 2011

first: Inc

last: Nimblegen Systems

organism: Drosophila melanogaster

description:
Platform annotations based on UCSC dm3 (BDGP Release 5).
NimbleGen ChIP 2.1M WG-T (2.1M Drosophila melanogaster - Whole Genome Tiling Set)
Design_ID = 6725
Native NimbleGen files linked below.

From NimbleGen's website:
* Format: 2.1M
* Source: UCSC
* Build: DM3
* Probe Length: 50-75mer
* Median Probe Spacing: 55bp
* Design Name: D. mel ChIP 2.1M WG-T Arr Del

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


title: Illumina Genome Analyzer (Arabidopsis thaliana)

status: Public on Aug 20 2009

last: GEO

organism: Arabidopsis thaliana


title: Illumina HiSeq 1500 (Saccharomyces cerevisiae)

status: Public on Dec 18 2013

organism: Saccharomyces cerevisiae


title: Agilent-070155 Mouse miRNA Microarray (miRBase Release 21.0, miRNA ID version)

status: Public on Dec 21 2015

description: Catalog miRNA expression microarray for mouse, 8x60K

relation: Alternative to: GPL22383 (Feature Extraction Number version)