title: [Mouse430_2_Mm_UG] Affymetrix GeneChip Mouse Genome 430 2.0 Array [Brainarray Version 9]

status: Public on May 15 2008

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

country: USA

institute: NCBI/NLM/NIH

organism: Mus musculus

technology: in situ oligonucleotide

description:
CDF file was created by Microarray Lab at the Molecular and Behavioral Neuroscience Institute at the University of Michigan.
After probe sequences are BLASTed against the latest UniGene Build and genome sequence, a series of filtering and grouping criteria are applied for different CDF files.
A probe must hit only one genomic location.
Probes that can be mapped to the same target sequence in the correct direction are grouped together in the same probe set;
Each probe set must contain at least three oligonucleotide probes and probes in a set are ordered according to their location in the corresponding exon;

distribution: custom-commercial

first: Stephanie

last: Hirner

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

manufacture_protocol: This is identical to GPL1261 but a custom cdf environment was used to extract data. The custom CDF (Mm_Unigene_9) can be found at the Web link below and also as a supplementary file at the foot of the record.


title: Rosetta/Merck Mouse 38.4K RSTA Custom Affymetrix 1.0 microarray Custom CDF

status: Public on Dec 08 2009

city: Seattle

first: Amit

middle: V

last: Kulkarni

state: WA

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

description: Oligonucleotide array

first: John

last: Castle

manufacture_protocol: ontains 25-mer probes grouped to form probesets. Standard Affy platform.


title: NimbleGen-human-430K-custom-tiling

status: Public on Jun 30 2012

city: St. Louis

first: Mack

last: Su

state: Missouri

address: 660 South Euclid Avenue

institute: Washington University in St. Louis School of Medicine

organism: Homo sapiens

manufacture_protocol: Custom arrays with twelve identical sections were manufactured by NimbleGen. Each section contained 60bp probes spanning the entire region of chromosome 4 from 1.642Mb to 2.072Mb including both forward and reverse strands. Ten housekeeping genes covered by ten probes each served as controls. Every experimental and housekeeping probe existed in quadruplicate as an additional control.


title: Hitachisoft AceGene Human Oligo Chip 30K Subset B

status: Public on Jun 18 2004

last: Hitachi Software Engineering Co.

country: Japan

institute: Hitachi Software Engineering Co., Ltd.

technology: spotted oligonucleotide

distribution: commercial

manufacture_protocol: see manufacturer's web site


title: [RN_U34] Affymetrix Rat Neurobiology U34 Array

status: Public on Mar 11 2002

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Rattus norvegicus

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

June 03, 2009: annotation table updated with netaffx build 28
June 21, 2012: annotation table updated with netaffx build 32

manufacture_protocol:
see manufacturer's web site

Has 1322 entries and was indexed 29-Jan-2002.
Sequences were selected based on their known relevance to the field of neurobiology.
Contains probes for >1,200 mRNA sequences selected from Build 34 of the UniGene database.


title: NimbleGen 3x1.4M Maize Methylation Array

status: Public on Aug 26 2012

city: St. Paul

first: Steve

middle: R

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

organism: Zea mays

description:
Design name: 110325_Zea_mays_NS_CGH
Design ID: 550571

Native array description file: 110325_Zea_mays_NS_CGH.ndf
Native array description file: 110325_Zea_mays_NS_CGH.pos

Coordinates based on the B73 reference genome v2 physical positions (assembly RefGen_v2).

Array was designed using probes initially found on the Maize 2.1M array platform (GPL13499). Probes were selected by being single-copy sequences within the maize RefGen_v2 masked genomic sequence.

PROBE_ID values from this platform are conserved from their selections from GPL13499, allowing easy cross-comparison between experimental platforms.


title: Illumina Genome Analyzer II (Rhodopseudomonas palustris CGA009)

status: Public on Jun 29 2012

last: GEO

organism: Rhodopseudomonas palustris CGA009

technology: high-throughput sequencing

distribution: virtual


title: Human Primates 1K miRNA array miRBase 13

city: Hsinchu

first: Sean

last: Chang

address: 6F, NO.6 Technology Road 5

department: R&D

country: Taiwan

institute: PhalanxBiotech Group

organism:
Primates
Homo sapiens

description: Human & Primates miRNA microarray designed and annotated based on Sanger's miRBase release 13.

manufacture_protocol: See http://www.phalanxbiotech.com/ for updated protocols


title: Illumina Genome Analyzer II (Rhodosporidium toruloides)

organism: Rhodotorula toruloides


title: Agilent-032958 Custom Candida glabrata 4x44K Gene Expression Microarray

status: Public on Aug 17 2012

city: Hyderabad

first: Rupinder

last: Kaur

state: AP

address: Building 7, Gruhakalpa,Nampally

department: Fungal Pathogenesis

country: India

institute: Centre for DNA Fingerprinting and Diagnostics

organism: Nakaseomyces glabratus CBS 138

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


title: NimbleGen E.coli_R.sphaeroides custom array_4X72K format [090611_Unk_SY_EXP]

city: Madison

first: Safak

last: Yilmaz

state: Wisconsin

address: 2 University Houses

institute: UW-Madison

organism:
Escherichia coli K-12
Cereibacter sphaeroides 2.4.1

description:
NimbleGen design name 090611_Unk_SY_EXP, NimbleGen design ID 10113.  A custom design in 4X72K format.  Each probe is replicated 3 times.  The design includes random GC and other control probes.
The .ndf file is provided as a supplementary file.

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


title: IGBMC-Mouse-10K-MM11E

city: Illkirch

first: Bernard

last: Jost

address: 1, rue  Laurent Fries

country: France

institute: IGBMC

technology: spotted DNA/cDNA

distribution: non-commercial

manufacture_protocol:
1. Microarrays contain 10,752 murine cDNA clones obtained from five different cDNA bank sources, corresponding to 2150 genes.
2. Plasmid templates for the 10,752 clones were isolated from bacterial clones and inserts were amplified by PCR.
3. PCR products were checked on agarose gels and purified by filtration on 96-well MAFB NOB50 multiscreen-FB filter plates (Millipore, Bedford, MA, USA)
4. Purified PCR products were dried by evaporation at room temperature in a speedvac® (SC210A, Savant Instruments, Holbrook, NY, USA)
5. Dried PCR products were resuspended in 75 % formamide/25% milliQ water at a final concentration of 0.5 µg/µl and were incubated for 48 h at 4C.
6. The products were transferred to a 1536 well plate (#3950, Corning, NY, USA).
7. A Microdgrid II arrayer (Genomics Solutions, Cambridge, UK) was used to print each product on ultraGAPS Coated Slides (# 40016, Corning Ltd) at 20-22C, in 45% relative humidity.
8. Arrays were dried 48 h in a dessicator, then DNA was cross-linked to the slide by UV irradiation (600 mJoules) in a UV2500 Stratalinker (Stratagene, La Jolla, CA, USA).


title: [HG_U95B] Affymetrix Human Genome U95B Array

manufacture_protocol:
see manufacturer's web site

The Human Genome U95 (HG-U95) Set, consisting of five GeneChip arrays, contains almost 63,000 probe sets interrogating approximately 54,000 clusters derived from the UniGene database (Build 95).
Based on this build and associated annotations, the HG-U95Av2 Array represents approximately 10,000 full-length genes, while arrays B through E represent approximately 50,000 EST clusters.


title: Agilent-030844 Lachancea kluyveri tiling array

city: San Francisco

first: Lauren

middle: N

last: Booth

address: 600 16th Street, N374

department: Micobiology and Immunology

institute: University of California, San Francisco

organism: Lachancea kluyveri

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


title: [HG_U95C] Affymetrix Human Genome U95C Array


title: Citrus root 8K v1.0

status: Public on Jun 02 2015

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

organism: Citrus

description: Spots size: 25 microns. Total number of spots: 94928 . 7,697 specific probes of 35-40 bp in length were designed using OligoArray 2.1 software. Oligos were synthesized in 11 replicates distributed at random, non-adjacent positions on the chip.

manufacturer: University of Verona - Scientific and Technological Department - Plant Functional Genomics Centre

manufacture_protocol: Probes are directly synthesized on a 90k Combimatrix array by an in situ oligo synthesis system developed by Combimatrix Corporation (Mukilteo, USA) using the Combimatrix CustomArray synthesizer. Standard synthesis protocol provided by Combimatrix was used.


title: Agilent-033668 Pig_1_Wound_repair_ensembl

city: Dolni Dobrouc

first: Rastislav

last: Slavkovský

address: Dolni Dobrouc 401

country: Czech Republic

institute: Contipro Biotech

organism: Sus scrofa


title: Human Encode 384K HG18 methylation array

status: Public on Jun 28 2012

first: Bing

last: Yang

state: WI

address: 1111 Highland Ave

department: Urology

description:
human Encode HG18 methylation array, 385,000 probes, Design Name:2007-10-25_HG18_ENCODE, Design ID: 6569.
2007-10-25_HG18_ENCODE.ndf
2007-10-25_HG18_ENCODE.pos


title: NimbleGen mouse DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Arrays

status: Public on Nov 28 2012

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
Format: 3X720K
Source: UCSC
Build: MM9
Probe Length: 50-75mer
Median Probe Spacing: 255
100718_MM9_CpG_Refseq_Prom_MeDIP.ndf
100718_MM9_CpG_Refseq_Prom_MeDIP.pos
100718_MM9_CpG_Refseq_Prom_MeDIP_FT.txt
100718_MM9_CpG_Refseq_Prom_MeDIP_FT_with_gpl_info.txt


title: Illumina Genome Analyzer II (Squalius pyrenaicus)

organism: Squalius pyrenaicus


title: Illumina Genome Analyzer II (Squalius alburnoides)

organism: Squalius alburnoides


title: febit Mus musculus miRNA Geniom Biochip miRBase V12.0

status: Public on Jun 23 2012

city: Bar Harbor

first: Timothy

middle: Michael

last: Stearns

state: ME

address: 600 Main Street

department: Computational Sciences

institute: The Jackson Laboratory

description: Each array contains 5 replicates of 609 miRNAs and miRNA star sequences as annotated in the Sanger miRBase 12.0.


title: HOMIM-V4a

status: Public on Jun 26 2012

city: Boston

first: Bruce

middle: J

last: Paster

state: MA

address: 140 Fenway

institute: The Forsyth Institute

organism: Bacteria

manufacturer: Michigan State University Research Technology Support Facility

manufacture_protocol: 16S rRNA-based oligonucleotide reverse capture probes were custom synthesized with a 5’-(C6)-amine modified base, eight spacer thymidines and 18 to 20-nucleotides of target sequence, and printed on 25 x 76 mm aldehyde-coated glass slides


title: Agilent-031148 Yarrowia lipolytica V2 [Probe Name version]

city: Thiverval-Grignon

first: Nicolas

last: Morin

address: Av. Lucien Bretignières

department: UMR 1319 Micalis

institute: INRA

organism: Yarrowia lipolytica

description:
Yarrowia lipolytica V2

Arrays of this design have barcodes that begin with 16031148 or 2531148.

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-019118 Human miRNA Microarray 2.0 (iG_Human-miRNA_15k_v2)

city: Valencia

first: Jose

middle: Antonio

last: Martinez-Conejero

address: C/ Guadassuar 1, bajo

country: Spain

institute: iGenomix

first: Signe

last: Altmäe

middle: A

first: Francisco

last: Esteban

first: Maria

last: Ruiz-Alonso

first: Anneli

last: Stavreus-Evers

last: Horcajadas

first: Andres

last: Salumets

manufacture_protocol: See manufacturer protocols


title: Illumina HiSeq 2000 (Campylobacter jejuni RM1221)

status: Public on Jun 22 2012

last: GEO

organism: Campylobacter jejuni RM1221


title: Illumina HiSeq 2000 (Campylobacter jejuni subsp. jejuni 81-176)


title: Illumina Genome Analyzer IIx (Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344)


title: Illumina HiSeq 2000 (Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819)


title: Illumina HiSeq 2000 (Campylobacter jejuni subsp. jejuni 81116)


title: Illumina Genome Analyzer IIx (Saccharomyces bayanus)

organism: Saccharomyces bayanus


title: Illumina Genome Analyzer IIx (Saccharomyces paradoxus)

organism: Saccharomyces paradoxus


title: Illumina Genome Analyzer IIx (Saccharomyces mikatae)

organism: Saccharomyces mikatae


title: Custom Agilent Mouse miRNA [BEL-ITRI_15K_v1]

status: Public on Jun 18 2012

first: Cheng-Tao

address: 195, Sec. 4, Chung Hsing Rd., Chutung

institute: Industrial Technology Research Institute

organism: Mus musculus

description: This platform represents the mouse miRNAs only

first: Chung-Ya

last: Liao

first: Yu-Yu

last: Lin

first: Yu-Ching

last: Chang

first: Yen-Ju


title: [HT_MG-430_PM] Affymetrix HT MG-430 PM Array Plate [CDF: mouse4302daiplusv6cdf]

status: Public on Jun 25 2012

city: Bilthoven

first: Mirjam

middle: M

last: Schaap

address: Antonie van Leeuwenhoeklaan 9

country: Netherlands

institute: RIVM

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


title: Illumina HiSeq 2000 (Nanoarchaeum equitans)

status: Public on Jun 19 2012

organism: Nanoarchaeum equitans


title: febit Homo sapiens miRBase 16.0

status: Public on Jun 20 2012

city: Bad Krozingen

first: Thomas

middle: G

last: Nuehrenberg

state: Baden-Württemberg

address: Südring 15

department: Klinik für Kardiologie II

country: Germany

institute: Universitäts-Herzzentrum Freiburg • Bad Krozingen

organism: Homo sapiens

description:
Geniom Biochip MPEA homo sapiens. The array is built on the miRNA base 16.0
in-situ oligonucleotides - additional nucleotides are bound on the 5'end of each capture oligonucleotide necessary for the enzymatic extention in the labeling procedure. The probes are synthesized with intra-array replicates to increase the statistical confidence and to compensate for potential positional effects. As a result the raw data files contain a total of 11 data points for each miRNA. The intensities of blank probes which consist only of one single T nucleotide are used for background corrections. Spike-in controls for the labeling effciency are also present. In order to have a grip on the hybridization process as well as positioning features, additional hybridization controls are added to the array template. Blank, labeling control and hybridization control probes are not included in the data analysis.

manufacture_protocol: MicroRNAs (miRNAs) are endogenous, non-coding RNAs that play a fundamental role in gene regulation and have critical functions across various biological processes. Pairing to mRNAs of protein-coding genes, they direct posttranscriptional repression by altering the stability or translational efficiency of their target mRNAs. Recent studies indicate that miRNAs are involved in the development of human malignancies, suggesting that they represent a promising new class of cancer biomarkers. Identifying miRNAs involved in specific cancers could provide useful diagnostic information, allow disease classification and reveal potential treatment targets. MPEA: On-Chip Labeling for Highest Sensitivity Enzymatic labeling assay requires minimal sample amount In addition to the standard hybridization of pre-labeled RNA, the microfluidic Geniom Biochip enables a highly sensitive enzymatic labeling protocol.The unique Microfluidic Primer Extension Assay (MPEA) uses unlabeled miRNAs for hybridization. In a second step, Klenow fragment of DNA polymerase I is added directly into the channels of the microfluidic chip, where the specific elongation of the bound miRNAs takes place. The method combines the specificity of a hybridization assay with the discriminatory power of an enzymatic extension and reduces the required sample amount to a minimum.


title: [Mouse430_2_Mm_ENSG_14.0.0] Affymetrix GeneChip Mouse Genome 430 2.0 Array [Brainarray Version 14]

status: Public on Jun 21 2012

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

manufacture_protocol: see manufacturer's website


title: LC sciences pig microRNA 236 V16.0

city: Nanjing

first: Runsheng

last: Li

state: Jiangsu

department: Nanjing Agricultural University

country: China

institute: Nanjing Agricultural University

manufacture_protocol: Microarrays designed for microRNA expression profiling and built on the flexible and powerful µParaflo® microfluidic on-chip synthesis platform. 236 miRNAs based on miRBase Release 16.0 and 100 custom miRNA sequences based on the solex deep sequencing results (li et al.,2010) are arrayed on the chip. Each probe is repeated 9 times. Layout File: miRPig16_layout.txt


title: NimbleGen Human CGH 4.2M Whole-Genome Tiling Array v1.0 array [100710_HG19_WG_CGH_v1.0_UX1]

status: Public on Jun 27 2012

first: Inc

last: Nimblegen Systems

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description:
Annotation in this record based on hg19.
Design name: 100710_HG19_WG_CGH_PERF_01
Design name: 100710_HG19_WG_CGH_PERF_02
Design name: 100710_HG19_WG_CGH_PERF_03
Design id: 538913

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


title: MRC Toxicology Unit Mus musculus 23k MEEBO probe set slide B

city: Leicester

first: Kate

middle: Marie

last: Dudek

address: Hodgkin Building, Lancaster Road

department: Genomics Group

country: United Kingdom

institute: MRC Toxicology Unit

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 and B) due to space constraints.


title: NimbleGen Borrelia burgdorferi B31 Expression array [080814_Bbur_B31_exp]

organism: Borreliella burgdorferi B31

description:
DESIGN_ID: 8078
DESIGN_NAME: 080814_Bbur_B31_exp
4-plex expression design for Borrelia burgdorferi B31 (TI 224326), selected probes from 1-plex design (TI224326) database, 1639 initial CDS seqs, selected 9 probes per target (1538 exemplars representing 1618 seqs), 45-60 base length; 5 copies on array.


title: [RG_U34C] Affymetrix Rat Genome U34 Array

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Rattus norvegicus

manufacture_protocol:
see manufacturer's web site

The RG-U34 set includes 3 arrays with a total of 26379 entries and was indexed 29-Jan-2002.
The set includes ~7,000 known genes and >17,000 EST clusters.
The A array contains probes derived from all full-length or annotated genes as well as thousands of EST clusters.
The B and C arrays contain only EST clusters.


title: [RG_U34B] Affymetrix Rat Genome U34 Array


title: MRC Toxicology Unit Mus musculus 23k MEEBO probe set slide A


title: miRNAChip_MS_V1

city: Aveiro

first: Patrícia

middle: Matos

last: Pereira

address: Campus Universitário de Santiago

department: Biology

country: Portugal

institute: University of Aveiro

organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus
Takifugu rubripes

manufacturer: National Facility for DNA Microarrays - University of Aveiro

manufacture_protocol: The spotted oligo library was the NCodeTM multi-species miRNA probe set V2 from Invitrogen. This library contains 1164 34-44mer unmodified DNA oligonucleotides targeting human, rat and mouse, Drosophila, C.elegans and zebrafish mature miRNA sequences from miRBase Sequence Database version 9.0. In addition, the mirVana miRNA Probe Set includes 24 probes targeting an exclusive set of newly identified zebrafish miRNAs, one positive control and several mismatch controls for screening 1- and 2-base sequence mismatches. The library is provided in 384-well plates in lyophilized form.  LIQUID HANDLING: The goal was 20 uM oligos in 150 mM phosfate buffer in 384-well plates (Genetix X-6004) ready for robotic spotting.  1. Lyophilized oligos (500 pmol in 384-well plates) were resuspended in 150 mM phosphate buffer to a concentration of 20 uM using a liquid handling station (Sciclone LH 3000, Caliper).  2. Shaking overnight at 4 ºC, at 100 rpm. The 384-well plate was stored at -80 ºC ready for spotting.  3. The remaining stock in 384-well plates was air dried at room temperature after spotting and stored at -80 ºC. When necessary, milliQ water was used to resuspend the oligos accounting for lost volume.  SPOTTING:  1. The 34-44mer probes were transfered in quadruplicate from the 384-well plates and printed on Nexterion E slides (SCHOTT) with a BioRobotics MicroGrid Compact II spotter (Genomic Solutions) in an environment controlled room. Humidity was 60% ± 2%. Temperature was 21 ºC in the spotter. Quill Pins type MicroSpot2500 (BioRobotics) were used for spotting.  2. For probe fixation, the printed slides were incubated in a humidity chamber at room temperature, overnight.  3. Slides were stored in a desiccator-cabinet (Nalgene, with blue Silica (Sigma)) ready to use (continue with our hybridization protocol).


title: JCVI PFGRC Streptococcus mutans 13K v3 array designed primarily based on strain UA159 [ORF version]

city: Rochester

first: Roberta

middle: C

last: Faustoferri

state: NY

address: 601 Elmwood Ave. Box 611

department: Center for Oral Biology

institute: University of Rochester Medical Center

organism: Streptococcus mutans

description:
condensed, ORF (primary locus primarily hit by the oligo) ID

The ID column includes the ORF ID. A different version of this platform with the unique oligo ID in the ID column is assigned accession number GPL9277

manufacture_protocol: 3QSM, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Agilent-022520 Brassica napus 4x44K (Probe Name version)

organism: Brassica napus

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 GPL14582.

relation: Alternative to: GPL14582 (Feature Number version)


title: SLRI_Yeast_Barcode_13k [condensed version]

status: Public on Jun 15 2012

city: marseille

first: bertrand

last: llorente

address: 31 chemin josephh aiguier

institute: cnrs

organism: Saccharomyces cerevisiae

description: restricted to non-profit research organization

manufacturer: Microarray lab. Samuel Lunenfeld research institute.

manufacture_protocol: Detailed available through EBI ArrayExpress accession number A-MEXP-714


title: Illumina Genome Analyzer IIx (Hordeum vulgare)

organism: Hordeum vulgare


title: NimbleGen_EcoliK12_72K_090224_Zmob_expr

city: Madison

first: Michael

middle: S

last: Schwalbach

address: 1550 Linden Dr

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin-Madison

organism: Escherichia coli str. K-12 substr. MG1655

description: 4plex array

manufacture_protocol: High-density DNA array. See manufacturer's website for details.


title: Agilent-018325 Human LK 15K CpG 2

status: Public on Jun 17 2012

city: Sapporo

first: Eiichiro

last: Yamamoto

address: South-1, West-16, Chuo-ku

institute: Sapporo medical university

description:
Arrays of this design have barcodes that begin with 16018325 or 2518325.

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: Arabidopsis thaliana 34K NARC serie 7

status: Public on Jun 16 2012

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

organism: Arabidopsis thaliana

description: Norwegian Arabidopsis Research Center (NARC)

manufacturer: Norwegian Microarray Consortium, Trondheim

first: Atle

last: Bones

first: Torfinn

last: Sparstad

first: Hallgeir

last: Bergum

manufacture_protocol:
1. Oligos used in the production of the microarrays are from the Qiagen-Operon Arabidopsis Genome Array Ready Oligo Set (AROS) Version 3.0, while the custom made oligos were produced by Operon (Alameda, CA, USA) or MWG (Ebersberg, Germany). Information about the AROS probes is available at: http://omad.operon.com/arabidopsis/
2. Oligos are arrayed in Genetix X6004 384 well plates with V-shaped bottom. Each well contain 600 pmol 70 mer oligo
3. Oligos were resuspended in 16 µl Milli-Q-filtered DNase free water and 8 µl from each well were transfered to new set of Genetix X6004 384 well plates using a Tecan Genesis RSP 200 liquid handling workstation.
4. 8 µl DMSO were added to each well giving a final oligo consentration of ~20 µM and 50% DMSO.
5. The plates were sealed with ABgene Adhesive PCR Foil seals and centrifuged at 1000 rpm in a Sorvall RT6000B centrifuge. The plates were stored at -20C.
6. The plates were thawed and placed on a rotary shaker for 12 hour before printing of oligos.
7. The oligos were printed on amino silane coated UltraGaps slides (Corning, NY, USA) using a BioRobotics MicroGrid II robot (Genomic Solutions, MI, USA).
8. After printing the micorarray slides were exposed for UV light in a Stratalinker 2400 UV crosslinker (Stratagene), at 800 milijoules/cm2.
9. Microarray slides were stored under low humidity conditions and not exposed to light.


title: Arraystar Mouse Stringent LncRNA microarray

city: Rockville

first: Panos

last: Pan

address: 9430 Key West Avenue

institute: Arraystar Inc.


title: Environment Canada PESC 207 gene rainbow trout

city: Burnaby

first: Heather

last: Osachoff

state: BC

address: 8888 University Way

department: Biological Sciences

country: Canada

institute: Simon Fraser University

organism: Oncorhynchus mykiss

manufacturer: The Microarray Facility of The Prostate Centre at Vancouver General Hospital (Vancouver, BC, Canada)

middle: L

first: Graham

last: van Aggelen

middle: P

last: Mommsen

first: Rachel

last: Skirrow

first: Chris

last: Kennedy

manufacture_protocol: Printed on EZ-rays™ aminosilane coated slides (Matrix Technologies Corp.) with a Biorobotics Microgrid II microarray printer (Genomic Solutions) equipped with Microspot 10K quill pins (Biorobotics) in a 48-pin tool that deposited ~ 0.1 ng cDNA pieces per spot.  Each gene printed in duplicate.  GFP was used to mark corners of grids.


title: Illumina Genome Analyzer IIx (Anopheles gambiae)

status: Public on Jun 13 2012

last: GEO

organism: Anopheles gambiae


title: Illumina MiSeq (Caenorhabditis elegans)

organism: Caenorhabditis elegans


title: Custom Chironomus riparius Expression Array

status: Public on Jun 08 2012

city: Amsterdam

first: Wim

last: de Leeuw

address: Science Park 904

department: Swammerdam Institute for Life Sciences

institute: University of Amsterdam

organism:
Chironomus tentans
Aedes aegypti
Anopheles gambiae
Culex quinquefasciatus
Anopheles darlingi
Anopheles funestus
Chironomus riparius

description: To select the most reliable and biological relevant probes from the previously designed probe-library, it is necessary to develop a probe-selection microarray containing the probe-library and ample negative-control probes that do not to recognize any sequence in GenBank. The aCGH experiment subsequently allows the identification of probes that hybridize with the gDNA of the non-model organism. Assuming a limited chance on random homology, an aCGH experiment should allow considerable clean-up of the NGS data, eliminating NGS reads that originate from contamination or technological errors, and simultaneously allow selection of the relevant probes for the final expression microarray.

first: Marino

last: Marinković

first: Mark

last: de Jong

first: Michiel

middle: H

last: Kraak

last: Admiraal

first: Timo

last: Breit

first: Martijs

last: Jonker


title: NimbleGen Desulfovibrio africanus array [080225_D_afric_SB_expr_X4]

status: Public on Jun 07 2012

city: Oak Ridge

first: James

last: Moberly

state: TN

address: 1 Bethel Valley Rd

department: Biosciences Division

institute: Oak Ridge National Laboratory

organism: Desulfocurvibacter africanus subsp. africanus str. Walvis Bay

description:
NimbleGen design name 080225_D_afric_SB_expr_X4.  The design includes Nimblegen standard control probes
Each chip measures the expression level of 4,585 genes and intergenic regions from Desulfovibrio africanus strain Walvis Bay on a custom Nimblegen format with 75-mer probes with tiled in 4-plex format.

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


title: Combimatrix C. botulinum A ATCC 3502 3.5K

city: Cremona

first: Daniela

last: Bassi

state: CR

address: via Milano 24

department: Istituto di Microbiologia

institute: Università Cattolica del Sacro Cuore

organism: Clostridium botulinum A str. ATCC 3502

description:
Spots size: 25 microns
Total number of spots: 94928
Number of spots replicates per oligo: 3  Probes corresponding to 3400 genomic CDSs of C. botulinum A  ATCC 3502 were synthesized in three replicates randomly distributed on the chip.

first: Fabrizio

last: Cappa

first: Pier

last: Cocconcelli

manufacture_protocol: Probes are directly synthesized on a 12k Combimatrix array by an in situ oligo synthesis system developed by Combimatrix Corporation (Mukilteo, USA) using the Combimatrix CustomArray synthesizer. Standard synthesis protocol provided by Combimatrix was used.


title: Illumina Genome Analyzer II (Aphis gossypii)

status: Public on Jun 11 2012

organism: Aphis gossypii


title: FSU-Schco1-Microarray v1.0

city: Jena

first: Erika

last: Kothe

address: Neugasse 25

department: Microbial Communication, Institute of Microbiology

institute: Friedrich-Schiller-University

organism: Schizophyllum commune

description: The microarray used in the present study contains probes for the 13,181 predicted gene models. It is based primarily upon the FilteredModels3 of Schizophyllum commune v1.0 genome project. Corresponds to S. commune strain H4-8 (A4,6; B3,2).

manufacture_protocol: The probe synthesis, sample labeling, hybridization and detection was performed by manufacturer. The oligonucleotides (probes, 50-mers) were synthesized in situ, using standard DNA synthesis reagents and 3`-phosphoramidites carrying a 5`-photolabile protective group, and spotted on a glass surface. The MassageAmpTM-Biotin Enhanced RNA Kit from Ambion was used for the labeling of RNA. Hybridization was done automatically over night (16 hours) at 45°C using RT-Analyzer from febit. The biotin labeling was detected with streptavidinphycoerythrin (SAPE), in combination with Consecutive Signal Enhancement (CSE) procedure from febit. The feature recognition, using Cy3 filter set, and signal calculation were done automatically within milliseconds.


title: CGEP TOM1 Tomato 13.4k cDNA microarray

city: Madrid

first: Gloria

middle: Garcia

last: Casado

state: Madrid

address: C/Darwin 3

department: Genomica

institute: CNB-CSIC

organism: Solanum lycopersicum

manufacturer: Center for Gene Expression Profiling (CGEP) at the Boyce Thompson Institute (BTI)


title: Nimblegen Rat DNA 385K CpG Island Plus RefSeq Promoter Array

status: Public on Jun 06 2012

city: Beaverton

first: Alejandro

last: Lomniczi

state: OR

address: 505 NW 185th Ave

department: Neuroscience

institute: Oregon National Primate Research Center - OHSU

organism: Rattus norvegicus

description:
Annotation in this record based on UCSC rat build 34.
080212_RN34_CpG_Island_Pro.ndf
080212_RN34_CpG_Island_Pro.pos


title: Salivary_qPCR_Fluidigm

city: Menlo Park

first: Denise

last: Nishita

address: 333 Ravenswood Ave.

department: Molecular Genetics

institute: SRI International

organism: Homo sapiens

technology: RT-PCR

first: Aditi

last: Mallack

first: Andrew

middle: W

last: Bergen

first: Martha

last: Michel

first: Xin

last: Wei

manufacture_protocol: See manufacturer's website


title: AB SOLiD System 3.0 (Equus caballus)

status: Public on Jun 14 2012

last: GEO

organism: Equus caballus


title: Illumina Genome Analyzer II (Oryza sativa Japonica Group x Oryza sativa Indica Group)

status: Public on Jun 05 2012


title: AB SOLiD 4 System (Prunus persica)

organism: Prunus persica


title: GeneSQUARE Mouse 5K multiple assay DNA microarray

city: Otsu

first: Shigeo

last: Shinohara

state: Shiga

address: 3-31-13 Saigawa

department: Nutraceuticals Division

institute: Otsuka Pharmaceutical Co., Ltd.

organism: Mus musculus

manufacture_protocol: GeneSQUARE multiple assay DNA microarray metabolic syndrome user manual version 1.52


title: Affymetrix GeneChip Human Genome HG-U133A Custom CDF [ncilpg_U133Agb]

city: Bethesda

first: Henry

last: Zhang

state: MD

address: 49 Convent Drive

department: NICHD Bioinformatics and Scientific Programming Core

institute: NICHD

description: Custom CDF environment was used to extract data [ncilpg_U133Agb]. The custom CDF files for Afffymetrix GeneChip are developed by Laboratory of Population Genetics, NCI, NIH to replace the commercial CDF file provided by Affymetrix company. The custom CDF files rearrange Affymetrix probes into gene-based probe sets. Each Affymetrix probe was mapped to an Entrez Gene ID via its match to mRNA sequences. Probesets are named after their Entrez Gene IDs. The custom CDF files can be imported to Bioconductor for expression analysis.

relation: Alternative to: GPL96 (Alternative CDF [official])

manufacture_protocol: see manufacturer's web site


title: AB SOLiD System 3.0 (Strongylocentrotus purpuratus)

organism: Strongylocentrotus purpuratus


title: Human 11k cDNA arrays

status: Public on Jun 01 2012

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

description: The cDNAs used for the slides were isolated from cDNA libraries of CP64-MEL melanoma cell line, normal melanocyte, leukocytes and fetal brain (Invitrogen Carlsbad, CA). Slides containing 25K spots with 11K identified cDNA by sequencing were printed.

first: Frédérick

first: Marie-Jeanne

last: Simons

manufacture_protocol: The cDNA inserts were amplified from replica plate cultures by PCR, purified and mechanically spotted onto Amino-silane coated slides (UltraGAPS, Corning) using a MicroGridII robotic spotter (BioRobotics).


title: Chr. Hansen A/S_Streptococcus thermophilus_2304_v2.0

status: Public on Jun 10 2012

city: Cadorago

first: Martin

middle: Bastian

last: Pedersen

state: CO

address: Via Manzoni 29

department: R&D

institute: Sacco Srl

organism: Streptococcus thermophilus

description: Array layout file, i.e. the *.gal file, is attached.

first: Ondrej

last: Valina

first: Thomas

middle: B

last: Rasmussen

manufacture_protocol: DNA oligos were purchased from Bioneer Corporation at 50nmol synthesis scale with BioRP purification and in lyophilized state (Daedeok-gu, Daejeon, South Korea). Oligos were dissolved at 10uM in 50% DMSO and printed in 2 replicates on UltraGAPS slides (Corning B.V., Schiphol-Rijk, The Netherlands) using a Genpak ARRAY 21 arrayer (Genetix Ltd., Hampshire, United Kingdom) with 16 SMP3 pins, (TeleChem International Inc., Sunnyvale, CA) giving a spot diameter of 100-120mm. Washing was performed between each print cycle for 20s in water followed by 20s in 70% ethanol. The relative humidity was kept at 48 ± 5% by placing a water bath at the appropriate temperature below the air inlet of the arrayer. The oligos were cross-linked to the surface using a Stratalinker 1800 UV Crosslinker set at 70mJ/cm2 (Stratagene). Printed arrays were stored in aluminium pouches with five arrays each and silica gel to remove humidity.


title: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_Hs_ENTREZG version 13.0.0]

status: Public on Jun 04 2012

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: Probe set data extracted from custom CDF (hugene10stv1hsentrezgcdf_13.0.0)

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

manufacture_protocol: See manufacturer's web site


title: Illumina Genome Analyzer II (Tigriopus californicus)

organism: Tigriopus californicus


title: Agilent-027139 Nofima Atlantic salmon microarray version 4

status: Public on Jun 09 2012

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

institute: Nofima AS

organism: Salmo salar

description: GE 4x44k oligo microarray that covers 21 k unique transcripts of Atlantic salmon. Oligonucleotides, 60-mer plus a linker, are synthesized directly on a glass slide using the Agilent's SurePrint Technology; oligo design was carried out by eArray.

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


title: Agilent-021412 nONCOchip_1.0 021253

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

institute: Fraunhofer Institute for Cell Therapy and Immunology

description:
Arrays of this design have barcodes that begin with 16021412 or 2521412.
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.

first: Jörg

last: Hackermüller

first: Friedemann

last: Horn


title: Illumina Genome Analyzer II (Oryza sativa Indica Group x Oryza sativa Japonica Group)


title: Applied Biological Materials human miRNA (AMB C201)

city: Vancouver

first: Seyed Mehdi

last: Jafarnejad

address: Room 436A, 2660 Oak St.

department: Dermatology and Skin Science

institute: The University of British Columbia

description: PCR-based  miRNA profiling assay

manufacture_protocol: see manufacturer's website


title: Illumina HiSeq 2000 (Dictyostelium discoideum)

organism: Dictyostelium discoideum


title: NimbleGen Mouse 2.1M tiling array [100718_MM8_Economy_01_HX1]

city: Madison

first: Inc

last: Nimblegen Systems

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description:
Annotation based on UCSC mouse genome assembly Feb 2006 (mm8)
DESIGN_ID: 536133
DESIGN_NAME: 100718_MM8_Economy_01
DESIGN_NAME: 100718_MM8_Economy_02
DESIGN_NAME: 100718_MM8_Economy_03

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


title: NimbleGen Human CGH 385K Chromosome 21 Tiling Array [2006-09-22_HG18_CHR21_FT]

city: Tallahassee

first: Benjamin

last: Pope

state: FL

address: 319 Stadium Dr

department: Biological Science

institute: Florida State University

description:
Build: Hg18, NCBI 36

native array description file: 2006-09-22_HG18_CHR21_FT.ndf
native array description file: 2006-09-22_HG18_CHR21_FT.pos

manufacture_protocol: See www.nimblegen.com


title: Systemic Analysis of Araboidopsis Promoters (SAP, Benhamed et al. 2008) [Membrane B]

city: Gatersleben

first: Gudrun

last: Moenke

address: Corrensstr. 3

institute: IPK

organism: Arabidopsis thaliana

manufacturer: Weisshaar lab (Bielefeld University, Chair of Genome Research); Altschmied lab (IPK Gatersleben)

manufacture_protocol: For large scale identification of precipitated and amplified chromatin fragments, a macroarray was spotted using 11,904 PCR products comprising upstream regions of Arabidopsis genes which were obtained from the European SAP-project (Systemic analysis of Arabidopsis promoters, (Benhamed et al., 2008). Amplicons were purified by reverse osmosis using MinElute plates (Qiagen, Hilden, Germany) and resuspended in 20µl TE buffer and analyzed on 1% agarose gels before spotting. Approximately 75% of the amplicons appeared as single bands. Amplicons were mixed 1:1 (v/v) with 1M NaOH, 5M NaCl and spotted in duplicate onto positively charged Biodyne B nylon membranes (Pall, Dreieich, Germany) at a density of 140 spots/cm2 using a Microgrid III robot (BioRobotics, Cambrigde, England). After spotting, membranes were washed with 0,5M NaOH, 1,5M NaCl for 5min, neutralized in 1,5M NaCl, 0,5M Tris-HCl, pH 7,4 for 5min, cross-linked in a UV-Stratlinker 2400 (Stratagene, Cedar Creek, United States) at 120mJ and baked for 30min at 80°C in a thermal oven. Amplicons were distributed on two membranes (membrane A and B).


title: Systemic Analysis of Araboidopsis Promoters (SAP, Benhamed et al. 2008) [Membrane A]


title: Agilent-024017 Custom Bacillus subtilis_15K [BSU number version]

city: Merritt Island

first: Wayne

last: Nicholson

address: 505 Odyssey Way, Rm. 201-B

department: Microbiology and Cell Science

institute: University of Florida

organism: Bacillus subtilis subsp. subtilis str. 168

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


title: Illumina HiSeq 2000 (Chenopodium amaranticolor)

last: GEO

organism: Chenopodium amaranticolor


title: ZB/SBS-NTU Plasmodium chabaudi chabaudi 4K v1.0

city: Singapore

first: Peter

last: Preiser

address: 60 Nanyang Drive, School of Biological Sciences

country: Singapore

institute: Nanyang Technological University, School of Biological Sciences

organism: Plasmodium chabaudi chabaudi

first: Kingsley

last: Liew

first: Guangan

last: Hu

first: Zbynek

last: Bozdech

middle: R

manufacture_protocol:
Modified protocol as described by Hu et al, 2007.
Since Plasmodium yoelii is the only RMP with a published draft genome, we first designed oligonucleotides against the predicted Plasmodium yoelii gene models. Next, all possible oligonucleotides of Plasmodium yoelii were used to query the homologous regions of the other two rodent malaria parasite species. Next, four parameters were used to select for the best oligonucleotide, namely: BLAST scores (first and second hit), GC content, sequence complexity and self-annealing scores. Each score is then transformed into a rank and a weighted rank-sum is calculated for each oligonucleotide with the final oligonucleotide being selected based on the smallest rank-sum value. These oligonucleotides were then selected to be optimal for all three species, followed by oligonucleotides for Plasmodium yoelii and Plasmodium berghei and then for Plasmodium yoelii and Plasmodium chabaudi. For the remaining predicted open reading frames oligonucleotides specific for each species were then designed.
References:
Hu G, Llinas M, Li J, Preiser PR, Bozdech Z: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350.


title: Agilent-017743 Physcomitrella custom 4x44K array

status: Public on Mar 06 2012

city: Lausanne

first: Andrija

last: Finka

address: Batiment Biophore

department: Department of Plant Molecular Biology

country: Switzerland

institute: University of Lausanne

organism: Physcomitrium patens


title: Agilent custom Arabidopsis thaliana 45K

city: Zurich

first: Samuel

middle: Elias

last: Wuest

address: Winterthurerstrasse 190

department: Institute of Evolutionary Biology and Environmental Studies

institute: University of Zurich


title: Agilent Gene Expression Array for Schizosaccharomyces japonicus 8x15K AMAMID=021535

city: Cambridge

first: Dawn

last: Thompson

address: 7 Cambridge Center

country: USA

institute: Broad Institute

organism: Schizosaccharomyces japonicus

description: Regev lab custom

manufacture_protocol: Standard Agilent protocols for Agilent 8x15K Oligo Microarrays


title: UWMadison/Donohue Streptomyces coelicolor A3(2) 385K_v1.0

status: Public on Jun 03 2012

first: Yann

last: Dufour

address: 1550 Linden Drive

department: Bacteriology

institute: University of Wisconsin - Madison

organism: Streptomyces coelicolor A3(2)

first: Min-Sik

last: Kim

first: Ji-Sun

last: Yoo

first: Yoobok

last: Cho

first: Joo-Hong

last: Park

first: Gi-Baeg

last: Nam

first: HaeMin

first: Timothy

last: Donohue

first: Jung-Hye

last: Roe

manufacture_protocol: 385K Custom Array manufactured according to Nimblegen standard protocol. The probes were designed using the ‘chipD’ software (Dufour et al., 2010). The parameters were set to obtain complete tilling of the genome with overlapping isothermal probes that ranged from 35 to 75 bases with an average spacing of 24 bases.


title: NimbleGen Mouse array [090901_MM9_EXP]

status: Public on Jun 02 2012

city: Shanghai

first: Huang

last: Jianhua

address: Wulumuqi Middle Road

institute: Institute of Integrated Chinese and Western Medicine, Huashan Hospital, Fudan University

description: Design Name: 090901_MM9_EXP

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


title: NimbleGen mouse expression array (2006-08-03_MM8_60mer_expr)

city: Rennes

first: Aurelien

last: Serandour

address: Bâtiment 13, Campus de Beaulieu

department: UMR CNRS 6290

institute: Université de Rennes 1

description:
Design_ID: 4543

Expression design for mouse (mm8; NCBI Build 36). 9 60mer probes per gene. 42586 exemplar genes representing a total of 53127 transcripts/variants. See manufacturer's website at http://www.nimblegen.com/.

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


title: [CINT06a520380F] Affymetrix Ciona intestinalis custom-designed array

city: Tucson

first: Bradley

middle: J

last: Davidson

state: AZ

department: Molecular Cardiovascular Research Program

institute: University of Arizona

organism: Ciona intestinalis

description:
Probe identifiers:

There are a few different types of probe identifiers, including:

* MKG.<number>.<number>_s<OptionalNumber>_at
* Fis_ciad<number>_at
* TGxxxxx_at
* Gastxxx_at
* Zellerxxx_at

A probe identifier in the format MKG.7.115_s_at indicates that this probe targets the gene model KYOTOGRAIL2005.7.115 described in the http://aniseed.cnrs.fr database. The suffixes s0, s1, s2, etc. signify different "supplemental" gene models for the same locus.

The Aniseed transcript model pages for these models are located at URLs such as: http://www.aniseed.cnrs.fr/molecule-gene.php?name=KYOTOGRAIL2005.7.115.1

The Fis and TG probe identifiers refer to additional gene models based on EST data that were not covered by the KyotoGrail predictions. A probe identifier like Fis_ciad008l03 is based on a full-insert sequence. These have been submitted to GenBank and can be found in the GenBank EST section, e.g., http://www.ncbi.nlm.nih.gov/nucest?term=ciad008l03 .

The GastmiR and ZellerMiR identifiers are probe sets against Ciona microRNAs models.  The models were generated by the labs of Terry Gaasterland (UCSD) and Robert Zeller (SDSU), respectively.

Gene identifiers:

The Platform table includes a "jgi1_GeneID" column with JGI1 gene model identifiers. JGI1 identifiers have the format ci0100<number>.

Further information on these JGI1 gene models can be found at URLs such as:
http://genome.jgi-psf.org/cgi-bin/dispGeneModel?db=ciona4&id=142570
http://ghost.zool.kyoto-u.ac.jp/cgi-bin/gb2/gbrowse/kh/?name=mRNA%3Aci0100142570;dbid=clone%3Adatabase
http://www.aniseed.cnrs.fr/molecule-gene.php?name=ci0100142570

This array is also described in ArrayExpress (http://www.ebi.ac.uk/arrayexpress/arrays/A-AFFY-106).

The oligonucleotide sequences are available in the supplementary file GPL15657_probe.fa.gz.

first: Takeshi

last: Kawashima

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


title: [HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [CDF: Brainarray Entrez gene CDF v14.1, hugene11stv1hsentrezg]

city: Bethesda

first: GEO

last: admin

organism: Homo sapiens

description: This identical to GPL11532 but a custom cdf environmnet was used to extract data. The cdf can be found at the link below.

relation: Alternative to: GPL11532 (Alternative CDF [official])

manufacture_protocol: see the Affymetrix website


title: [Mouse430_2_Mm_REFSEQ] Affymetrix GeneChip Mouse Genome 430 2.0 Array [Brainarray Version 14]

status: Public on May 19 2011


title: FDA / CBER Human 16K

city: Belgrade

first: Vladan

middle: Predrag

last: Cokic

address: Dr Subotica 4

country: Serbia

institute: Institute for Medical Research

manufacturer: Operon's Human Genome Array-Ready Oligo Set (Operon Inc. Valencia, CA)

manufacture_protocol:
The arrays were produced in house by spotting oligonucleotides on poly-L-lysine coated glass slides by Gene Machines robotics (Omnigrid, San Carlos, CA).
High quality oligonucleotide glass array containing a total of 16,659 seventy-mer oligonucleotides chosen from 750 bases of the 3' end of each ORF


title: NimbleGen Apis mellifera 4.0 Whole-genome CGH Tiling Array Set (4 of 4)

status: Public on Feb 01 2011

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

organism: Apis mellifera

description:
This is a Western honey bee or European honey bee (Apis mellifera) whole-genome tiling array set (4 of 4) in HD2 1-plex format with 2.1M probes, manufactured by Roche NimbleGen.
Custom array design.

first: John

middle: K

last: Colbourne

first: Jeong-Hyeon

last: Choi

first: Gene

last: Robinson


title: Nimblegen Drosophila melanogaster r5.25 Expression Array (12x135k)

status: Public on Mar 30 2011

organism: Drosophila melanogaster

description: This is a whole fruitfuly genome exon and transcript expression array in 12-plex format provided by Roche Nimblegen. See manufacturer's website at http://www.nimblegen.com/.


title: NimbleGen Apis mellifera 4.0 Whole-genome CGH Tiling Array Set (3 of 4)

description:
This is a Western honey bee or European honey bee (Apis mellifera) whole-genome tiling array set (3 of 4) in HD2 1-plex format with 2.1M probes, manufactured by Roche NimbleGen.
Custom array design.


title: NimbleGen Apis mellifera 4.0 Whole-genome CGH Tiling Array Set (1 of 4)

description:
This is a Western honey bee or European honey bee (Apis mellifera) whole-genome tiling array set (1 of 4) in HD2 1-plex format with 2.1M probes, manufactured by Roche NimbleGen.
Custom array design.


title: NimbleGen Daphnia pulex Whole-genome Tiling Array Set (2 of 2)

organism: Daphnia pulex

description:
This is a Daphnia pulex whole-genome tiling array set (2 of 2) in HD2 1-plex format with 2.1M probes, manufactured by Roche NimbleGen.
Daphnia pulex annotated draft genome assembly GenBank accession number: ACJG00000000.


title: Illumina HiSeq 2000 (Ovis aries)

last: GEO

organism: Ovis aries


title: [Mouse430_2_Mm_REFSEQ] Affymetrix GeneChip Mouse Genome 430 2.0 Array [Brainarray Version 13]

status: Public on Jun 24 2011

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Mus musculus

description: This identical to GPL1261 but a custom CDF environment [Mouse4302_Mm_REFSEQ_v13] was used to extract data.


title: [Mouse430_2_Mm_REFSEQ] Affymetrix GeneChip Mouse Genome 430 2.0 Array [Brainarray Version 12]

status: Public on Nov 15 2010

description:
This is identical to GPL1261 but a custom CDF environment was used to extract data [Brainarray Version 12, Mouse4302_Mm_REFSEQ].

CDF and other files can be downloaded at: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/12.1.0/refseq.asp


title: NimbleGen Drosophila melanogaster Whole Genome 2.1M tiling array [100718_DM_5_Catalog_tiling_HX1]

first: Inc

last: Nimblegen Systems

state: WI

description:
D. mel ChIP 2.1M WG-T Arr Del
Design Name: 100718_DM_5_HX1_Catalog_tiling1
Design Name: 100718_DM_5_HX1_Catalog_tiling2
Design Name: 100718_DM_5_HX1_Catalog_tiling3
Design_ID = 535483
Format: 2.1M
Build: UCSC DM3 [corresponds to BDGP/FlyBaseGenBank Release 5]
SLIDE_LAYOUT_NAME: NimbleChip_HX1

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


title: Agilent-022520 Brassica napus 4x44K

status: Public on Sep 15 2011

organism: Brassica napus

relation: Alternative to: GPL15739 (Probe Name version)


title: NimbleGen mouse (mm8) whole genome tiling array 1 of 4 [2007-08-17_MM8_Economy_01]

status: Public on Nov 05 2008

manufacture_protocol: Mouse whole genome tiling arrays


title: [hjay] Affymetrix GeneChip Human HJAY Array

status: Public on Jan 10 2012

manufacture_protocol: See manufacturers website


title: NimbleGen mouse (mm8) whole genome tiling array 3 of 4 [2007-08-17_MM8_Economy_03]


title: Print_500

status: Public on Jul 29 2008

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

organism: Caenorhabditis elegans

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: [Mouse430_2_Mm_EntrezG] Affymetrix GeneChip Mouse Genome 430 2.0 Array [Brainarray Version 13]

status: Public on Oct 05 2011

manufacture_protocol:
This is identical to GPL1261 but a custom CDF environment was used to extract data [Brainarray Version 13, Mouse4302_Mm_ENTREZG].
CDF and other files can be downloaded at: (see web link below).


title: NimbleGen Apis mellifera 4.0 Whole-genome CGH Tiling Array Set (2 of 4)

description:
This is a Western honey bee or European honey bee (Apis mellifera) whole-genome tiling array set (2 of 4) in HD2 1-plex format with 2.1M probes, manufactured by Roche NimbleGen.
Custom array design.


title: NimbleGen mouse (mm8) whole genome tiling array 2 of 4 [2007-08-17_MM8_Economy_02]


title: NimbleGen mouse (mm8) whole genome tiling array 4 of 4 [2007-08-17_MM8_Economy_04]


title: NimbleGen Daphnia pulex Whole-genome Tiling Array Set (1 of 2)

description:
This is a Daphnia pulex whole-genome tiling array set (1 of 2) in HD2 1-plex format with 2.1M probes, manufactured by Roche NimbleGen.
Daphnia pulex annotated draft genome assembly GenBank accession number: ACJG00000000.


title: Aedes aegypti Genome Array Annotation 1.0

status: Public on May 15 2007

city: Baltimore

first: George

last: Dimopoulos

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

organism: Aedes aegypti

first: Zhiyong

last: Xi

manufacture_protocol: In Situ Synthesis


title: Illumina Genome Analyzer II (Human herpesvirus 8)

status: Public on Jun 01 2012

organism: Human gammaherpesvirus 8


title: Indiana University/CGB-Daphnia-10K-Gen 3

status: Public on Mar 16 2011

manufacture_protocol:
1. Lyophilized oligos are arrayed in Genetix 384-well polypropylene microarray plate. Each well contains XXX pmol of 70-mer oligo.
2. Resuspend lyophilized oligos in 10ul of 150mM NaPO4, giving 30uM final concentration. 150mM NaPO4 is made from 150mM Na2HPO4 and 150mM NaH2PO4 in nuclease-free water and filtered with 0.45um Stericup Filter.
3. Seal plates with Co-Star Corning Thermowell Aluminum Sealing tape (cat # 07200684)
4. Centrifuge plate in Allegra 25R centrifuge at 2000 rcf for 1 minute.
5. Incubate at 4 degrees Celcius for 16 hours to aid resuspension of DNA.
6. Shake plates in flat bottom shaker at room temperature (15 -30 degrees Celcius) at 200 rpm for 60 mins.
7. Centrifuge plate in Allegra 25R centrifuge at 2000 rcf for 1 minute.
8. Store plates at 4 degrees Celcius until ready to print.
9. Print 6 plates at a time to minimize evaporation; remove plates from 4 degree storage.
10. Remove seal from plate. Place in appropriate plate cassette.
11. Initiate print run method.
12. After these 6 plates are printed, remove and reseal the plates. Store at 4 degrees Celcius. Repeat steps 9 and 10 until all desired plates are printed.
13. After print run is complete, plates are stored at 4 degrees.


title: CombiMatrix_custom design 7327

city: Beaverton

first: Maria

last: Smit

address: 20000 NW Walker Rd

department: Environmental and Biomolecular Systems

institute: Oregon Health and Science University

organism:
Bradyrhizobium
Rhizobium
Skeletonema
Thalassiosira
Pseudo-nitzschia
Mesorhizobium
Roseovarius
uncultured marine crenarchaeote
uncultured Pelagibacterales bacterium

manufacturer: CombiMatrix Corporation, CustomArray Inc.

manufacture_protocol:
The custom oligonucleotide microarray is synthesized on a semiconductor using an electrochemical synthesis process. Each oligonucleotide probe (spot) is synthesized on a platinum electrode that is independently controlled by the synthesizer’s computer. Synthesis is based on established phosphoramidite chemistry and occurs at thousands of sites simultaneously according to a computer algorithm that activates only specified electrodes. Since physical photolithographic masks, mechanical micromirrors, or inkjet technologies are not involved in the process, all probes can be easily changed without extra time or cost.
The oligonucleotides are synthesized in a proprietary porous reaction layer that coats the surface of the semiconductor, and acts to covalently attach the oligonucleotide to the surface of the chip.