title: Illumina Genome Analyzer II (Silene latifolia)

status: Public on Sep 29 2011

last: GEO

country: USA

organism: Silene latifolia

technology: high-throughput sequencing

distribution: virtual


title: Illumina Genome Analyzer II (Zostera marina)

organism: Zostera marina


title: Illumina Genome Analyzer II (Sorghum bicolor)

status: Public on Sep 28 2011

organism: Sorghum bicolor


title: Illumina Genome Analyzer II (Vitis vinifera)

organism: Vitis vinifera


title: NimbleGen Thermoplasma acidophilum DSM 1728 7K expression array

status: Public on Sep 27 2011

city: Martinsried (Planegg)

first: István

last: Nagy

address: Am Klopferspitz 18

department: Dept. of Structural Biology

country: Germany

institute: Max Planck Institute of Biochemistry

organism: Thermoplasma acidophilum DSM 1728

technology: in situ oligonucleotide

description:
NimbleGen design ID: 4453
NimbleGen design name: TI273075 60mer

Probes were selected for all protein sequences (1482). The median number of probes per sequence is 20, and each probe is replicated 5 times on the chip. The probes are randomly distributed over the surface of the array. Unused features are filled with randomly generated probes of comparable GC content.

The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  Probe sequences available in the ndf file.

NimbleGen array description files are linked below as supplementary files:
2006-07-27_TI273075_60mer.ndf
2006-07-27_TI273075_60mer.ngd

GenBank accession number of T. acidophilum DSM 1728 genome: NC_002578.1

distribution: custom-commercial

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


title: Illumina Genome Analyzer II (Setaria italica)

organism: Setaria italica


title: Agilent 45K CpG Island microarrays

city: Los Angeles

first: Reshmi

last: Chowdhury

state: CA

address: 635 Charles E. Young Drive South

department: Neuro-Oncology

institute: UCLA

organism: Homo sapiens

description: a subset of the GPL9767 - Agilent 244K CpG Island microarray

manufacture_protocol: Same as GEO platform GPL9767


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray Hs133P_Hs_ENTREZG version 10)

status: Public on Mar 01 2010

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

technology: spotted oligonucleotide

description: Custom CDF (Brainarray Entrez Gene v10.0.0)

manufacture_protocol: see manufacturer's web site


title: MYcroarray Mycobacterium tuberculosis H37Rv 3x20K-5rep

status: Public on Nov 28 2012

city: Amherst

first: Andrea

last: Cossu

state: MA

address: 102 Holdsworth way

department: Department of Food Science

institute: University of Massachusetts, Amherst

organism: Mycobacterium tuberculosis H37Rv

manufacture_protocol: In Situ Synthesis Technology: oligonucleotides are directly synthesize on low-background glass slides polished to atomic flatness (±20 angstroms). The synthesis is performed by using the robust phosphoramidite chemistry.  Catalog bacteria mycroarray: Mycobacterium tuberculosis H37Rv Microarrays 3X20K


title: MYcroarray Mycobacterium smegmatis str. MC2 155 3x20K

organism: Mycolicibacterium smegmatis MC2 155

manufacture_protocol: In Situ Synthesis Technology: oligonucleotides are directly synthesize on low-background glass slides polished to atomic flatness (±20 angstroms). The synthesis is performed by using the robust phosphoramidite chemistry.  Catalog bacteria mycroarray: Mycobacterium smegmatis str. MC2 155 Microarrays 3X20K


title: Agilent-026595 Whole Chr array_18 19 21 [Probe Name Version]

status: Public on Sep 26 2011

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Human whole chromosomal ChIP-on-CHIP microarray. Chr 18, 19, 21. Designed by Agilent eArray: Build Number: H. sapiens, UCSC hg18, NCBI;  Advanced HD Search by Genomic Intervals;  Tm Filter: Yes;  Hm Filter: Yes.

Arrays of this design have barcodes that begin with 16026595 or 2526595.

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.

This platform uses the Probe Name as the identifier, the Feature Number version is GPL14618.

distribution: commercial

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


title: Agilent-027811 SurePrint G3 Human Promoter Microarray 1x1M [Probe Name Version]

description:
SurePrint G3 Human Promoter Microarray 1x1M

Arrays of this design have barcodes that begin with 16027811 or 2527811.

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.

This platform uses the Probe Name as the identifier, the Feature Number version is GPL14619.


title: R. conorii chip V2

city: Marseille

first: Aurélie

last: Renvoisé

address: 27 bd Jean Moulin

country: France

institute: Urmite

organism: Rickettsia conorii str. Malish 7

first: Svetlana

last: Shabalina

first: Khalid

last: El Karkouri

first: Gregory

last: Gimenez

first: Eugene

last: Koonin

first: Didier

last: Raoult

manufacture_protocol:
For information, see:
http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/pages/gp43127.aspx


title: RayBio Human Cytokine Antibody Array G Series 2000; 6-8 array

status: Public on Nov 22 2011

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

technology: antibody

description: Human 6 - 8 arrays.gal

manufacture_protocol: see manufacturer's website


title: RayBio Human Cytokine Antibody Array G Series 2000; 8-8 array

description: Human 8 - 8 arrays.gal


title: RayBio Human Cytokine Antibody Array G Series 2000; 7-8 array

description: Human 7 - 8 arrays.gal


title: Multispecies Custom miRNA microarray

status: Public on Sep 24 2011

city: Nanjing

first: Yan

last: Zeng

state: Jiangsu

address: XuanWu District, No.1 WeiGang

country: China

institute: Nanjing Agricultural University

organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

description: NCode Multi-species miRNA Microarray Probe Set Version 2.0  (Cat. # MIRMPS2-01)

distribution: non-commercial

manufacturer: Biomedical Genomics Center Microarray Facility at the University of Minnesota

manufacture_protocol: A miRNA probe set was purchased from Invitrogen, which was designed based on the Sanger miRBase Sequence Database, Release 9.0.  The set contains approximately 1,140 oligonucleotides of 34 to 44 nt long as probes.  They are complementary to C. elegans, Drosophila, zebrafish, mouse, rat, and human miRNAs, and also include a number of internal and negative control probes.  The oligonucleotides were dissolved in 3 x SSC and quadruply printed on Corning GAPSTM II coated slides  using a BioRobotics Microgrid II spotter"


title: Genotypic Technology designed Custom Cavia porcellus 4x44k Gene Expression Array (Agilent-AMADID-19424)

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: Cavia porcellus

first: Mugasimangalam

middle: C

last: Raja


title: GNF1H

status: Public on Mar 19 2004

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description:
GNF1H
In 2002, we identified a non-redundant set of human target sequences using the following sources: RefSeq (15,491 sequences), Celera (49,859 sequences), and Ensembl (33,698 sequences). First, all sequences were RepeatMasked to remove repetitive elements. Next, sequence identity between individual sequences was established using pairwise BLAT or BLAST and sim4. The results from single-linkage clustering were further triaged to produce a final target set of 44,775 targets with the highest degree of confidence of computational prediction (biasing toward sequences containing Interpro domains and away from non-coding RNAs). Finally, the human sequence set was pruned of all targets already represented on Affymetrix's commercially available U133A array, leaving 22,645 target sequences for our custom array. The final target sets were submitted to the Affymetrix's chip design pipeline for fabrication of the GNF1H arrays.

Update: At the time of publication (2004, DOI: 10.1073/pnas.0400782101), by request from Celera, we have masked any and all sequences that were derived from Celera data. We have been able to re-annotate and associate 11,406 probe sets to public data, and for the rest (11,086 probe sets), we masked the sequences by poly-N and replaced their annotation if any with "predicted transcript (Celera)" and their target regions and individual probe sequences are all unavailable. For approximately 750 more probe sets, the annotation is based on the orthologous annotation data available in 2004 and the phrase "a predicted transcript (Celera), similar to :[insert the rest [e.g. M.musculus]]" should be implied. Caveat emptor: Even though all these sets are designed from human transcripts and computational predictions, it should not be expected that they are efficient to assay the modern version of any human transcript. All individual probe sequences for 11,406 sets are provided for the interested parties to do their own sequence analysis (suggested route: blast/blat or otherwise align individual probes to the most recent genome+transcriptome database and use a >8 out of 11 voting system to determine the most likely target(s)). Such analysis will be in most cases more precise than any precomputed annotation (however, in many cases this new, precise annotation will be "intergenic region", "intron", "antisense to :" - due to old age of the array probes may have been designed outside of the true UTR, the 2002 genomic sequence may have been misassembled, predictions were truncated or completely wrong etc).


title: SABiosciences Mouse Inflammatory Cytokines and Receptors PAMM-011

city: Madrid

first: Sonsoles

last: Hortelano

address: Carretera de Majadahonda-Pozuelo Km 2

country: Spain

institute: ISCIII

organism: Mus musculus

technology: RT-PCR


title: Nimblegen HD4 Yeast 12X ~270K array [110413_Scer_LI_ChIP]

status: Public on Mar 04 2012

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 408 Fordham Hal, CB#3280

department: Biology

institute: UNC-Chapel Hill

organism: Saccharomyces cerevisiae

description: Genome build information: R64 Build


title: [MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [custom CDF: MoEx10stv1_Mm_ENST]

status: Public on Mar 22 2012

city: Corvallis

first: Stephen

last: Ramsey

state: OR

address: Dryden Hall 208A

department: Biomedical Sciences

institute: Oregon State University

description: This is identical to GPL6096 but a custom cdf environment was used to extract data. Microarray analysis was performed using PGF file derived from the CDF file obtained from the University of Michigan CustomCDF probe-to-probeset mappings (Custom CDF, ENST, version 13). The PGF file, the Affymetrix CLF file describing the probe layout on the microarray, and the annotation file describing each probeset are linked below as supplementary files.

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

manufacture_protocol: Affymetrix


title: NanoString nCounter Mouse Gene Expression Custom CodeSet

status: Public on Aug 30 2012

city: Columbus

first: Madhu

last: Ouseph

state: Ohio

address: 460w 12th Ave

institute: The Ohio State University


title: Agilent-026687 Whole Mouse Genome Microarray 4x44K v2 (Probe Name version)

first: GEO

last: admin


title: Taqman qRT-PCR Homo sapiens 384

status: Public on Nov 16 2011

city: Namur

first: jean-pierre

last: gillet

address: 61 Rue de Bruxelles

department: URPhyM

country: Belgium

institute: University of Namur

description: TaqMan-based qRT-PCR assay


title: Agilent-025480 Candida albicans Custom Expression Array (Feature Number version)

status: Public on Oct 03 2011

city: Hsin-chu

first: Yan-Yu

last: Chen

address: No. 101, Section 2, Kuang-Fu Road

department: Chemical Engineering

country: Taiwan

institute: NTHU

organism: Candida albicans


title: MYcroarray Mycobacterium avium subsp. paratuberculosis K-10 3x20K-4rep

status: Public on May 31 2012

first: Andrea

last: Cossu

manufacture_protocol: In Situ Synthesis Technology: oligonucleotides are directly synthesize on low-background glass slides polished to atomic flatness (±20 angstroms). The synthesis is performed by using the robust phosphoramidite chemistry.  Catalog bacteria mycroarray: Mycobacterium avium subsp. paratuberculosis K-10 3X20K


title: Applied Biosystems Low Density Taquman Rat Inflammatory Array

status: Public on Sep 23 2011

city: Columbia

first: Jennifer

middle: L.

last: McLarty

state: SC

address: 6349 Garners Ferry Road

department: Cell Biology and Anatomy

institute: University of South Carolina-School of Medicine

organism: Rattus norvegicus

description: see manufacturer's website


title: Agilent-017777 Whole Human Genome (hg18) Custom 1×244k Array (Feature Number version)

city: Houston

first: Robert

middle: A

last: Waterland

state: TX

address: 1100 Bates St.,

institute: Baylor College of Medicine


title: Agilent_44k_021626

organism: Danio rerio

manufacture_protocol: Agilent Ink Jet manufactured


title: AB SOLiD 4 System (Macropus eugenii)

status: Public on Sep 21 2011

last: GEO

organism: Notamacropus eugenii


title: AB SOLiD 4 System (Drosophila melanogaster)

organism: Drosophila melanogaster


title: Affymetrix GeneChip Human Genome U133A 2.0 Array [CDF: Brainarray Version 10, Hs133Av2_Hs_ENTREZG]

status: Public on Dec 04 2012

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

description: This is identical to GPL571 but a custom Brain Array  CDF environment (hs133av2hsentrezgcdf version 10) was used to extract data.

relation: Alternative to: GPL571 (Alternative CDF[official])

manufacture_protocol: Standard Affymetrix Protocol


title: Illumina Genome Analyzer II (Aedes albopictus)

status: Public on Sep 20 2011

organism: Aedes albopictus


title: Agilent-014717 Mouse Promoter ChIP-on-Chip Set 244K, Microarray 2 of 2 (G4490A) (Probe Name version)

last: Agilent Technologies

description:
Mouse Promoter ChIP-on-Chip Set 244K 2 of 2

Arrays of this design have barcodes that begin with 16014717 or 2514717.

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

The ID column represents the Agilent Probe Name.

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

*****The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL4129

relation: Alternative to: GPL4129 (Feature Number version)


title: Vibrio vulnificus whole genome TwinChip

city: Seoul

first: Seung Min

last: Kim

address: 1 Gwanakro

country: South Korea

institute: Seoul National University

organism: Vibrio vulnificus

manufacture_protocol: The V. vulnificus whole genome TwinChip, which has two blocks, up (upper) and dn (lower), manufactured and kindly provided by the  21C Frontier Microbial Genomics and Applications Center (Daejeon, South Korea)


title: Illumina Sentrix Mouse-6 Array

status: Public on Sep 19 2011

city: Toledo

first: Hironori

last: Matsushima

state: OH

address: 3000 Arlington Avenue Mail Stop 1021

department: Medical Microbiology and Immunology

institute: University of Toledo College of Medicine

technology: oligonucleotide beads

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


title: NimbleGen Zebrafish Gene Expression 385K Array

status: Public on Sep 22 2011

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description:
Format: 385K
Source: Ensembl and UCSC
Build: Zv7


title: 454 GS FLX Titanium (Homo sapiens)


title: Z. Jeffrey Chen Laboratory Spotted Arabidopsis 70mer Oligo Microarray version 1.0

status: Public on Sep 16 2011

city: Austin

first: Z Jeffrey

middle: Jeffrey

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

organism: Arabidopsis thaliana

description:
This oligonucleotide array is produced from the Operon Version 1.0.
Spotted Arabidopsis 70-mer oligo-gene microarrays using 26,090 annotated genes were cooperatively developed with QIAGEN (Valencia, CA) and Operon (Alameda, CA) (LEE et al. 2004; TIAN et al. 2005; WANG et al. 2005). The 70-mer oligo was designed from the 3'-end of each annotated gene. Every feature was spotted once on each slide.

manufacturer: The Jeffrey Chen Laboratory, The University of Texas at Austin

first: Zenjian

middle: J

manufacture_protocol: GeneMachines Omnigrid Accent


title: Illumina Genome Analyzer II (Aedes aegypti)

organism: Aedes aegypti


title: Agilent_026345_Lotus japonicus_LjNov09

city: Fredriksberg

first: Dale

last: Shelton

address: Thorvaldsensvej 40

department: Dept. Plant Biology and Biotechnology

country: Denmark

institute: University of Copenhagen

organism: Lotus japonicus

description:
Arrays of this design have barcodes that begin with 16026345 or 2526345.

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: MGX_Coffee_microarray_15K

city: Montpellier

first: Laurent

last: Journot

address: 141 rue de la Cardonille

institute: MGX - Montpellier GenomiX

organism: Coffea arabica

description:
The Coffea Genome Oligo contains 15.580 70mers representing 15.580 genes.
The Coffea canephora long oligonucleotide set was designed and synthetized by Operon (Town, State) based on the SGN Coffee built II (15721 unigenes; http://solgenomics.net/ ). An amino linker was attached to the 5'-end of each oligonucleotide. The oligonucleotides, selected to limit secondary structure, have a melting temperature of 67 ± 3°C, length 65 ± 5 bases, GC content 43 ± 5 %. More than 98 % of the oligonucleotides were within 1000 bases from the 3'-end of the available gene sequence. For 195 unigenes, no adequate oligonucleotide could be designed and so correspond to "missing genes". BLAST alignments were performed to identify oligonucleotides that could cross-hybridize with other sequences of the SGN Coffee Built II. Three oligonucleotides (opCocaV10004674, opCocaV10014770, opCocaV10009077) cover more than one unigene. Finally out of 15522 oligonucleotides designed, there are 371 oligonucleotides which have > 70% of overall identity to another unigene and have a contiguous identical length of more than 20nt common to another unigene.
The set also includes 12 unique positive and 12 unique negative controls provided in 16 replicates in a 384-well plate.

manufacturer: design: Operon - Array : Montpellier GenomiX

first: Amélie

last: Bardil

first: Benoit

last: Bertrand

first: Christine

last: Combtes

first: Christelle

last: Dantec

first: Alexandre

last: De Kochko

first: Stéphane

last: Dussert

first: Séverine

last: Foucrier

first: Ivanna

last: Fuentes

first: Thierry

last: Joët

first: Philippe

last: Lashermes

last: Leroy

first: Lukas

last: Müller

first: Isabelle

last: Privat

first: David

last: Pot

first: Dany

last: Severac

manufacture_protocol:
Manufacturing microarrays
The Coffea Array were spotted using the Amersham Biosciences Lucidea Array spotter on epoxysilane-coated mirror glass slides (Genewave). Negative and positive control oligo were also printed into 24 different sectors of each slide. After printing, the slides were stored at room temperature in a dessicator.


title: Agilent-032957 Streptomyces bingchenggensis-1-1

city: Haerbin

first: zhang

last: bo

state: Heilongjiang

address: Mucai street 59#

department: Life Sciences

institute: Northeast Agricultural University

organism: Streptomyces bingchenggensis BCW-1

technology: spotted DNA/cDNA


title: Genome and Microarray laboratory University of Cincinnati Streptococcus pyogenes 2

status: Public on Sep 15 2011

city: Stockholm

first: Erika

last: Hertzén

address: Karolinska University Hospital, Huddinge, Center for Infectious Medicine, F59

country: Sweden

institute: Karolinska Institutet

organism: Streptococcus pyogenes

manufacturer: Oligonucleotides were spotted on glass microarrays at Microarrays Inc., Huntsville,USA, with oligo sets designed and provided by Drs. J. Scott and K. McIver at Emory University School of Medicine, Atlanta, Georgia USA.

manufacture_protocol: The arrays contain all 2,346 open reading frames of the M1T1, strain SF370 of S. pyogenes (GenBank accession #NC_002737) with additional open reading frames (mainly phage encoded) from strains MGAS8232 (GenBank accession# NC_003485) and and MGAS315 (GenBank accession # NC_004070). Each open reading frame was spotted in triplicate.


title: USC_F.merg_44K_v1

city: Sippy Downs

first: Nicole

last: Ertl

state: Queensland

address: 90 Sippy Downs Drive

department: FOSHE - GeneCology

country: Australia

institute: University of the Sunshine Coast

organism: Penaeus merguiensis

description: Accession strings in the GEO submission refer only to the EST names given to transcriptome sequences by the sequencing company. No annotation/sequence ID from a public database has been included, as sequence information for prawns is very limited and a large proportion of the sequencs were unable to be annotated.

manufacture_protocol: 4 probes per gene, chemical synthesis (in situ oligonucleotide), Agilent custom-commercial, 60 bp probe length, hybridisation according to Agilent protocol


title: Agilent-021540 LjFlavTF

first: Dale

last: Shelton

description:
Arrays of this design have barcodes that begin with 16021540 or 2521540.

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.
Most of the sequences are in the format 'CHI03_chr5.CM0260.370.nc' where the first part is a putative gene assignment and the next is a chromosome, contig and unique gene identifier on the web page associated with the genome sequence of this species http://www.kazusa.or.jp/lotus/index.html.


title: Exiqon custom Homo sapiens miRNA array [DesignedForVersion: miRBase ver.9.2, CurrentVersion: miRBase ver.10.0]

city: Shanghai

first: Wei-Wen

last: Jiang

address: Room 305, Building #1,639 Zhi Zao Ju Road

institute: Department of Oral Mucosal Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

organism: Homo sapiens

manufacture_protocol: See manufacturer's website: http://www.exiqon.com/array miRBase_Designed For Version=miRBase ver. 9.2 miRBase_CurrentVersion=miRBase ver. 10.0


title: Ambion mirVana miRNA bioarray 1566V2_Jun12

status: Public on Sep 14 2011

first: Woong Yang

last: Park

address: 28 Yongondong, Chongnogu

department: Biochemistry and Molecular Biology

organism:
Homo sapiens
Mus musculus
Rattus norvegicus


title: Custom Agilent translocation-CGH (tCGH) myeloid leukemia array

city: Seattle

first: Harvey

middle: Allan

last: Greisman

state: WA

address: 1959 NE Pacific Street

department: Laboratory Medicine

institute: University of Washington

first: Noah

middle: G

last: Hoffman

first: Hye

middle: S

last: Yi

manufacture_protocol: See manufacturer's website


title: Custom Agilent translocation-CGH (tCGH) lymphoma array


title: Photorhabdus luminescens subsp. laumondii TTO1 3x20k microarray

city: East Lansing

first: Todd

last: Ciche

state: MI

address: 2215 MMG, BPS Building, MSU

institute: Michigan State University

organism: Photorhabdus laumondii subsp. laumondii TTO1


title: Agilent-031735 Replication Timing 15.10 [Probe Name version]

status: Public on Sep 13 2011

city: Rehovot

first: Ariel

last: Gispan

address: P.O. Box 26

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

organism: Saccharomyces cerevisiae

description:
Arrays of this design have barcodes that begin with 16031735 or 2531735.

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 includes the Agilent Probe Names.


title: McIntyre D. simulans 2m v1.0

city: Gainesville

first: Yajie

last: Yang

state: FL

address: 2033 Mowry Road Room 118

institute: UF

organism: Drosophila simulans

first: Rita

middle: M

last: Graze

first: Brandon

last: Waltz

first: Sergey

last: Nuzhdin

first: Marta

middle: L

last: Wayne

first: Lauren

last: McIntyre

manufacture_protocol:
The chip has approximately 2.5 million features, covering 4 types of probe sets:  custom SNP probe sets,  3’ expression probe sets s from the Affymetrix Drosophila expression array 2.0 (all perfect-match probes), selected probes from the Affymetrix Drosophila tiling array version 2.0 (exonic perfect-match probes), and  standard Affymetrix negative control probe sets. Custom SNP probe sets were designed to for genotyping and ASE assays. Each SNP probe set includes 24 probes corresponding to four bases at the SNP site, both forward and reverse strands, and three positions of the SNP relative to the central base of the probe.
For SNP identification, alignment sets were created from multiple sequence sources, including FlyBase R5.4 exons (68,536), 6 DPGP D. simulans strain genomes (assembled against the R4.2 D. melanogaster genome), and all Genbank D. simulans sequences (343,420) that were not annotated as “whole genome”.  For each R5.4 exon the genome location in R4.2 was determined by BLAST alignment to the D. melanogaster R4.2 genome. The location was determined as where the longest alignment was found for multihit exons. Exons that mapped to more than one location or to chromosomes 4 or U were excluded. The remaining unique exons were BLAST (ref) aligned to the DPGP genomes and  Genbank sequences. All sequences were then aligned using ClustalW(cite), creating a multiple  sequence alignment for each exon at its genome position, from which SNPs were identified. SNPs were selected by quality criteria using the information from their supportive sequences. If there were fewer than 5 sequences supporting this SNP, or if more than 1 SNP occurred in the design window makeing the alignment suspected, the SNP was discarded. Genome position was not considered for SNP selection. The selected SNPs could be located at any position of an exon. There were 566 exons where SNP data was identified from Genbank alone, and 52,188 exons for which SNP data was identified from DPGP alone. Only 357 exons had no identified SNPs in either Genbank or DPGP.
At each nucleotide where a D. simulans SNP was present a 35 bp design window was created- 17 bases upstream and 17 bp downstream from the SNP.  There were 589,915 design windows created, corresponding to 13,637 genes.  Design windows were compared to the D. melanogaster genome (v 4.7 as this is the assembly used for the DPGP data) using BLAST.  There were 563,558 design windows found to be unique to the genome.  If there were multiple SNPs in the design window, or if the SNPs identified were not biallelic those SNPS were discarded. After this initial selection, there were 196,345 biallelic SNPs in unique design windows with no other SNPs. For each design window 24 probes were constructed. For each SNP, probes for all 4 bases were designed12 each for the forward and reverse strands, with the SNP at the 0, +4, and -4 position.  Probe sets were eliminated if any probe in the probe set contained a homopolymer run or could not be synthesized.  The remaining 189,946 probe sets were examined for hybridization quality predicted using an Affymetrix internal scoring algorithm that takes into account, Tm, secondary structure and previous empirical observations.  Probe sets were eliminated if 1/3 or more of the probes had poor predicted hybridization.  For all genes with 7 or fewer SNPs, all SNPs were selected.  Finally, if a gene had more than 7 SNPs with many of them being high coverage (more than 4 lines supporting the SNP), the probe sets with the best predicted hybridization were selected.  This led to a total of 61,142 probe sets selected.  To fill the chip an additional 610 were selected at random from the set of genes with more than 7 SNPs per gene for a total of 61,752 probe sets.  Overall, SNP probe sets were designed for 11,946 genes (R5.26, 12,385 genes of R5.4 at the time of chip design), covering 87% of the known transcriptome.
Also printed on the chip were all the positive match (PM) probes on the 3’ IVT Affymetrix Drosophila 2.0 array (n=262,766); all tiling probes in exons (FlyBase 5.11 n=699,856) from the Affymetrix Drosophila 2.0 tiling array; GC band controls (n=16,943); and hybridization and labeling controls (n=1,644).  Overall, a total of 2,463,630 probes are on the chip. The probes from the 3’ IVT array allow for clear gene level detection calls and will be referred as “3’ expression probes” in the following text. The tiling probes provide controls for measurement of signal fluctuation caused by 5’ bias in expression assays as well as measurement of alternative exon usage, and they will be referred as “exon probes” hereby.


title: Agilent-031735 Replication Timing 15.10 [Feature Number version]

description:
Arrays of this design have barcodes that begin with 16031735 or 2531735.

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: Jilin University Mycobacterium tuberculosis array (Probe Name version)

city: Changchun

first: Lu

last: Yu

address: Xi'an Road 5333

institute: Jilin university

organism: Mycobacterium tuberculosis H37Rv

last: Guo

relation: Alternative to: GPL11396 (Feature Number version)

manufacture_protocol: refer to www.agilent.com


title: Agilent-014716 Mouse Promoter ChIP-on-Chip Set 244K, Microarray 1 of 2 (G4490A) (Probe Name version)

city: Palo Alto

last: Agilent Technologies

state: CA

institute: Agilent Technologies

organism: Mus musculus

description:
Mouse Promoter ChIP-on-Chip Set 244K 1 of 2

Arrays of this design have barcodes that begin with 16014716 or 2514716.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

*****The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL4128

relation: Alternative to: GPL4128 (Feature Number version)


title: Illumina HiSeq 2000 (Cryptococcus neoformans)

last: GEO

organism: Cryptococcus neoformans


title: AAHRU_Channel catfish_65K array

status: Public on Sep 10 2011

city: AUBURN

first: julia

last: pridgeon

state: AL

address: 990 WIRE ROAD

department: AAHRU

institute: USDA, ARS

organism: Ictalurus punctatus

description: NimbleGen design name 080813_Yeh_Catfish_expr, NimbleGen design ID 8072.  Started with sequences from a previous design (design_id 1819), mysql db catfish_050412, from GenBank ESTs, and from catfish gene index at dana farber cancer inst, removed sequences from first two sources that were wholly contained in the CFGI sequences; sequences remaining 65,182; selected 3 probes per sequence, two copies on array.

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


title: Illumina Genome Analyzer IIx (Cryptococcus neoformans)


title: SMD Print_1600 (Saccharomyces cerevisiae and Saccharomyces bayanus)

city: Stanford

first: Barbara

last: Dunn

department: Genetics

institute: Stanford University

organism:
Saccharomyces bayanus
Saccharomyces cerevisiae

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: SMD Print_1181 (Saccharomyces bayanus and Saccharomyces cerevisiae)


title: Bead-based custom synovial antigen array_Stanford_Robinson Lab_v1.0

first: William

last: Robinson

address: 269 Campus Dr

technology: spotted peptide or protein

description:
Bead-based multiplex immunoassay

Fibrinogen A was purified from human blood, vimentin was purified from bovine lens, and histone 2B was purified from calf thymus.  All peptides represent human sequences. Anti-human IgG-PE secondary antibody was a goat monoclonal antibody.

A custom made panel of putative rheumatoid arthritis associated autoantigens consisting of native and/or citrullinated proteins and peptides were conjugated to Luminex beads (Bio-Plex, Bio-Rad Laboratories, Inc).

manufacture_protocol: Peptide antigens were synthesized (by Fmoc chemistry) with N-terminal biotin. Bio-Plex beads were coupled to streptavidin using imide chemistry. The biotinylated peptides were then conjugated to the streptavidin-coated beads. Protein antigens were directly coupled to Bio-Plex beads using imide chemistry.


title: Bio-Plex Pro Human Cytokine and Chemokine Assays_Stanford_Robinson Lab_v1.0

description:
Bead-based multiplex immunoassay

Capture and secondary anti-cytokine antibodies for sandwich immunoassay were commercially obtained and proprietary.

manufacture_protocol: The manufacturer's recommended protocol and fully detailed instructions are available at http://www.bio-rad.com.


title: MBPL human 30k P7

status: Public on Sep 09 2011

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

institute: nthu

description: There are 32448 spots within a array.7334 human clone were printing 4 duplicate in a array. Additionally, we printing 10 doping control genes (SpotReport™-10 Array Validation System , Stratagene) and one house-keeping gene , 5 negative control gene as quality control indicator. total 16 quality control indicator were printing 2 duplicate in each block.

first: Ian

last: Hsu

first: MinLung

last: Tsai

first: WeiChung

last: Cheng

first: ChingLung

last: Huang

first: ChaangRay

last: Chen

manufacture_protocol: Arrayer obtained from Dr. Patrick O. Brown MGuide II and ArrayMarker program version 2.3.2 (Dr. Joseph DeRisi, university of California, San Francisco) with 48 spotting pins (TeleChem).We control printing condition in temperature 25~27°C and Humidity about 49~51%, and printing on April 2005. cDNA clones were purchased from Incyte Genomics and 7334 sequence-verified clones were amplified by PCR.We purified these 7334 clones by isopropanol precipitation and used 3×saline-sodium citrate (SSC) as spotting solution. cDNA spotted on GAPS Ⅱ coated slides (Corning Incorporated)coating of pure gamma amino propylsilane.


title: NYUDM Human 40 antibodies v1.0

city: New York

first: Minal

last: Dalvi

state: NY

address: 345 East 24th Street, Rm 917

department: Department of Basic Science

institute: New York University

description: Circular feature type

last: Abrams

first: Cheryl

last: Barber

first: Robert

last: Norman

first: Daniel

last: Malamud

manufacture_protocol: The array is a glass slide based array. The arrays are manufactured using non-contact arrayer. Capture antibodies are spotted on the glass slide (4 spots per antibody). The array follows sandwich elisa format. The capture and detection antibody pairs were selected based on RayBiotech Inc. experimental data that identified cross-reactivity of antibodies.


title: NYUDM Human 507 antibodies v1.0

manufacture_protocol:
A. Dialysis of Sample
The saliva sample should be dialyzed with a Dialysis tube (Item A) before the biotin-labeling procedure. We recommend loading 200 μl saliva into a dialyzer and dialyzing with at least 500 ml 1X PBS buffer (pH= 8) at 4 0C. Change the 1X PBS buffer and dialyze again. Allow at least 3 h for each dialysis step, stir gently. The sample total volume may be changed after dialysis.
B. Biotin-labeling Sample
Avoid contamination with any solution containing amines
(i.e., Tris, glycine) as well as Azide during the biotinylation process.
1. Briefly spin down Internal Control tube (Item C) before use.
Add 100 μl 1X PBS, pH=8.0 into the Internal Control tube, pipette up and down to dissolve the powder. Add 40 μl prepared Internal Control into a new tube containing 35 μl dialyzed serum or plasma sample and 155 μl Serum Buffer (Item K).
2. Immediately before use, briefly spin down the Labeling
Reagent tube (Item B). Add 100 μl 1X PBS into the tube, pipette up and down or vortex slightly to dissolve the powder to prepare 1X Labeling Reagent Solution.
3. Add an appropriate amount* of prepared Labeling Reagent into above tube with sample in step 2, mix well immediately.
Incubate the reaction solution at room temperature with gentle shaking for 30 min. Gently tap the tube to mix the reaction solution every 5 min.
* For labeling saliva: 36 μl of 1X Labeling Reagent Solution for labeling 1 mg total protein.
4. Add 3 μl Stop Solution (Item D) into above reaction solution and immediately dialyze as directed in Step B.
5. Samples should be centrifuged at 10,000 g for 5 min (4°C) after Dialysis.
C. Dry the Glass Chip
Open the box containing glass chip, and take it out, and then let it air dry for 1 hour in a clean environment before use.
Note: Protect the chip from dust or others contaminants.
D. Blocking and Incubation of Antibody Array
1. Add 400 μl of Blocking Buffer (Item F) into each well (Glass Chip with Frame, Item E) and incubate at room temperature for 1h to block slides. Make sure there are no bubbles are in the well.
2. Decant Blocking Buffer from each well (make sure to remove all of buffer). Add 400 μl of each sample (diluted 1:10 in blocking buffer) into appropriate wells. Incubate arrays with sample at room temperature for 2 hours with gentle shaking or 4 °C for overnight.
3. Decant the samples from each well, and wash 3 times with 800 μl of 1X Wash Buffer I (Item G) at room temperature with gentle shaking for 5 min per wash.
4. Put the glass chip with frame into a box with 1X Wash Buffer I (cover the whole glass slide and frame with Wash Buffer I), and wash 2 times at room temperature with gentle shaking for 10 min per wash.
5. Decant the Wash Buffer I from each well, Put the glass chip with frame into the box with Wash Buffer II (cover the whole glass slide and frame with Wash Buffer II), and wash 2 times at room temperature with gentle shaking for 5 min.
6. Remove all of Wash Buffer II in the well. Add 400 μl of 1X Fluorescent dye-Conjugated Streptavidin (cy3 equivalent) to each subarray. Cover the incubation chamber with Adhesive film, and then cover the plate with aluminum foil to avoid exposure to light or incubate in dark room (avoid array slide exposure to light in the following steps 7, 8, 9, 10 and 11).
Note: briefly spin down the Fluorescent dye-Conjugated
Streptavidin (cy3 equivalent) (Item I) before use. Add 1000 μl of Blocking Buffer into the tube to prepare a Streptavidin
Concentrate. Pipette up and down to mix gently (don’t store the Concentrate for next day use). Add 200 μl of Streptavidin
Concentrate into a tube with 800 μl of Blocking Buffer. Mix gently to prepare 1 X Streptavidin solution.
7. Incubate at room temperature for 2 hours with gentle shaking
8. Decant the solution and disassemble the slide out of the incubation frame and chamber. Disassemble the device by pushing clips outward from the slide side. Carefully remove the slide from the gasket.
9. Gently put the glass chip into a 30 ml centrifuge tube provided with 30 ml of 1X Wash Buffer I (add enough Wash Buffer I to cover the whole slide). Gently shake for 10 min. Remove the wash buffer. Repeat 2 times for a total of 3 washes.
10. Wash the glass chip with 30 ml of 1X Wash Buffer II. Repeat one time for a total of two washes for 5 min per wash.
11. Finally wash the glass chip with 30 ml of deionized or distilled water for 5 min.
E. Fluorescence Detection
Put the glass chip into a 30 ml centrifuge tube provided, and dry the glass chip by centrifuge at 1,000 rpm for 3 minutes. You can also let the glass chip dry completely in a clean environment (protect from light). Make sure the slides are absolutely dry before the scanning procedure. The signals can be visualized with a laser scanner, such as the Axon GenePix, using the cy3 channel.


title: Illumina Genome Analyzer (Cimex lectularius)

status: Public on Sep 01 2011

organism: Cimex lectularius


title: PIQOR (TM) Immunology Microarray, human, antisense (681)

status: Public on Sep 07 2011

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

institute: Miltenyi Biotec GmbH

description: The PIQOR (TM) Immunology Microarray is composed of 1070 human specific cDNAs. These cDNAs include for each array six house-keeping genes as positive controls. In addition four E. coli DNA fragments and the corresponding in vitro transcribed RNAs (spiking controls) provide a control for the labeling and hybridisation efficiency. Two negative controls are given by spotted herring sperm DNA and buffer, respectively. All features are spotted in quadruplicate. The Platform data table reflects a condensed representation of the quadruplicate features.

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio

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


title: PIQOR (TM) Immunology  Microarray, mouse, antisense (672)

description: The PIQOR (TM) Immunology Microarray is composed of 1070 mouse specific cDNAs. These cDNAs include for each array six house-keeping genes as positive controls. In addition four E. coli DNA fragments and the corresponding in vitro transcribed RNAs (spiking controls) provide a control for the labeling and hybridisation efficiency. Two negative controls are given by spotted herring sperm DNA and buffer, respectively. All features are spotted in quadruplicate. The Platform data table reflects a condensed representation of the quadruplicate features.


title: Penaeus monodon 2.2k microarray

status: Public on Sep 02 2011

first: Abigail

last: Elizur

address: Sippy Downs Drive

department: Science and Education

organism: Penaeus monodon

description: Microarray construction. A total of 1152 sequences were selected from the cDNA libraries created for this study together with an additional 387 sequences obtained from P. monodon EST collections from publicly available databases (GenBank (http://www.ncbi.nlm.nih.gov)) for inclusion as probes on the microarrays. Oligonucleotide microarrays were produced by CombiMatrix corporation (Mukilteo, USA) using the CustomArray™ 4×2K platform which contains four identical, independent 2240-feature microarrays on each slide. Between two and five oligonucleotide probes were designed and incorporated on each microarray for each of the selected transcripts.


title: MZH_Zebrafish_16k_v1.0

city: Nagoya

first: Shin'ichi

last: Akiyama

state: Aichi

address: 65 Tsurumaicho

department: Department of Nephrology

country: Japan

institute: Nagoya University Graduate School of Medicine

organism: Danio rerio

first: Shin’ichi

first: Yutaka

last: Tamaru

manufacture_protocol: Zebrafish oligo nucleotide set “Zebra Fish Oligonucleotide Library XEBLIB96-library” was purchased from Sigma aldrich. This oligonucleotide library consists of 16,399 oligos, which represent 16,228 oligos plus 171 control oligos. This is a specially designed oligo set that was selected to best represent all of the genes associated with the public mRNA sequences. These 65-mers have a 5'-C6 amino modification for flexible and universal covalent binding of the oligo to a variety of substrates. The oligonucleotides were spotted on a aminosilane coated glass slide (Matsunami glass Co. Ltd.) by using GENE SHOT arrayer (Nippon Gaishi Co. Ltd.).


title: Illumina MouseWG-6 v2.0 expression beadchip (Gene version based on MouseWG6_V2_0_R0_11278593_A)

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

manufacture_protocol: see manufacturer's website


title: INRA GeneChip Rosa genome 5K Array version 1

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

organism: Rosa

first: Mohammed

last: Bendahmane

first: Fabrice

last: Foucher

first: Sandrine

last: Balzergue

manufacture_protocol:
The photolithographic process begins by coating a 5″ x 5″ quartz wafer with a light-sensitive chemical compound that prevents coupling between the wafer and the first nucleotide of the DNA probe being created. Lithographic masks are used to either block or transmit light onto specific locations of the wafer surface. The surface is then flooded with a solution containing either adenine, thymine, cytosine, or guanine, and coupling occurs only in those regions on the glass that have been deprotected through illumination.
The coupled nucleotide also bears a light-sensitive protecting group, so the cycle can be repeated. In this way, the microarray is built as the probes are synthesized through repeated cycles of deprotection and coupling. The process is repeated until the probes reach their full length, usually 25 nucleotides. Commercially available arrays are typically manufactured at a density of over 1.3 million unique features per array. Depending on the demands of the experiment and the number of probes required per array, each quartz wafer can be diced into tens or hundreds of individual arrays.


title: SWEGENE Human_v2.1.1 55K_condensed

status: Public on Sep 03 2011

city: Lund

first: Morten

last: Krogh

address: Skrivarevagen 9

institute: Amber Biosciences

manufacture_protocol: Arrays were produced by the Swegene DNA micro array resource center at Lund University by using probes from Operon. Probes were recovered in Corning Universal Spotting Solution and printed on amino-silane-coated glass slides (UltraGAPS from Corning) using a MicroGrid2 robot (BioRobotics).


title: Rice 44K (ORF version)

city: Tsukuba

first: Hiroshi

last: Takatsuji

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Plant Sciences

organism: Oryza sativa

first: Masaki

last: Shimono

first: Akira

last: Nakayama

manufacture_protocol:
Probe Length:   60 bases
Probe Orientation:   Sense
genes/microarray: 44000
Content Source: Japan - National Institute of Agrobiological Sciences, Dr. Shoshi Kikuchi
Feature size:  115 microns


title: Anti-viral Innate Immunity Pathway PCR assay Panel

status: Public on Sep 08 2011

city: Boston

first: Shitao

last: Li

state: MA

address: 77 Ave Louis Pasteur

department: MBIB

institute: Harvard Medical School

description: real time PCR assay


title: Children's Hospital Boston Danio rerio 385K Array [071105_Zv7 - gene level]

status: Public on Sep 06 2011

first: Xiaoying

last: Bai

address: 1 Blackfan Circle

institute: Children's Hospital Boston

manufacture_protocol: see manufacturer's web sitesee manufacturer's web site


title: NimbleGen Danio rerio [100718_Zv7_EXPR]

city: Durham

first: Michael

last: Czerwinski

state: North Carolina

address: 4034 GSRBII Research Drive

department: Cell Biology

institute: Duke University


title: BaSysBio Staphylococcus aureus T1 385K array

city: Greifswald

first: Ulrike

last: Mäder

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

department: Functional Genomics

institute: University Medicine Greifswald

organism: Staphylococcus aureus subsp. aureus NCTC 8325


title: Agilent-023443 Equine Central Nervous System and Splenic Transcriptome Microarray

first: Melissa

last: Bourgeois

address: 2015 SW 16th Ave

institute: University of Florida

organism: Equus caballus

description:
Arrays of this design have barcodes that begin with 16023443 or 2523443.

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: BCCRC whole genome tilling path array v2 (March 2006 build)

city: Vancouver

first: Raj

last: Chari

state: BC

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

country: Canada

institute: BC Cancer Research Centre

organism: Homo sapiens

first: William

middle: W

last: Lockwood

first: Wan

last: Lam

manufacture_protocol: ~27,000 bacterial artificial chromosomes (BACs) spotted in duplicate


title: Streptococcus gordonii Challis whole genome array SG-2

city: Buffalo

first: Anna

last: Nikitkova

address: 3435 Main St.

country: USA

institute: University at Buffalo

organism: Streptococcus gordonii str. Challis

manufacturer: Gill, Steven, R.; University of Rochester, Department of Microbiology and the Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY 14642. Steven_Gill@urmc.rochester.edu

middle: E

first: Elaine

last: Haase

first: Margaret

last: Vickerman

first: Steven

last: Gill

first: Frank

last: Scannapieco

manufacture_protocol:
Unique 70-mer oligonucleotides were identified for each of the 2,186 open reading
frames (ORFs) identified in the initial annotation of the Streptococcus gordonii CH1 Challis genome {Vickerman, 2007}. Oligonucleotides were resuspended at 25 uM final concentration in Nexterion Spot spotting solution (SCHOTT#1066029) and printed onto bar-coded Nexterion Epoxy coated slides (SCHOTT #1064016) using an QArray2 printer (Genetix USA Inc., Boston, MA) located in the genomics core at Roswell Park Cancer Institute (RPCI) in Buffalo. Print configuration is 48 blocks in a 4 X 12 arrangement. Spot diameters are approximately 90-100 microns. Control reporters included 10 Arabidopsis gene fragments. After printing, oligonucleotides were cross-linked to the slides by UV irradiation at 250 mJ/cm2 (Stratalinker UV Crosslinker, Stratagene) and subsequently stored at room temperature in a desiccated chamber until use. The oligonucleotides were spotted in four replicates each, which compensate for spot to spot variation within each slide and allows for greater overall precision of the data. Quality control consisted of self-self hybridizations and determination of total spot saturation using SYBR dyes (Molecular Probes, Eugene, OR) that intercalate between DNA strands and can be used to check spotting consistency. Quality control experiments were re-run on each new batch of printed microarray slides.


title: Agilent-025090 P.pacificus-version2

city: Ipswich

first: Amit

last: Sinha

address: 240 County Road

institute: New England Biolabs

organism: Pristionchus pacificus

description:
P.pacificus transcriptome version 2 : 2009-08-13

Arrays of this design have barcodes that begin with 16025090 or 2525090.

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: Illumina Genome Analyzer II (Tetranychus urticae)

status: Public on Aug 18 2011

last: GEO

organism: Tetranychus urticae


title: Macrogen Human BAC clone 4K array

city: Ube

first: Atsunori

last: Oga

state: Yamaguchi

address: Minami-Kogushi 1-1-1

department: Pathology

institute: Yamaguchi University

description:
BAC clone Chip
Platform table annotations based on NCBI build 36

manufacture_protocol: See manufacturer's website.


title: Plant Systems Biology Lab, Vitis vinifera 3.4K cDNA microarray

status: Public on Apr 07 2011

city: Lisboa

first: Andreia

last: Figueiredo

address: Campo Grande

department: UMBPB

country: Portugal

institute: ICAT/FCUL

organism: Vitis vinifera

description: Each clone was printed twice in the same sub-grid.

manufacture_protocol:
cDNAs were spotted.
Printing parameters are according to Figueiredo et al., 2008 (PMID 18648103).


title: Clostridium phytofermentans 3.8K 49-5241 expression array

city: Amherst

first: Jeffrey

last: Blanchard

address: 203 Morrill Science Center IVN

department: Biology

institute: University of Massachusetts Amherst

organism: Lachnoclostridium phytofermentans

manufacture_protocol:
Array format: Affymetrix 49-5421
Feature size:  11um


title: CAASICS-plant microRNA -miRBase 9.1

city: Beijing

first: Chuanxiao

last: Xie

address: Zhong-guan-cun South St. No12

department: Institute of Crop Science

institute: Chinese Academy of Agricultural Sciences

organism:
Physcomitrium patens
Populus trichocarpa
Arabidopsis thaliana
Glycine max
Medicago truncatula
Oryza sativa
Saccharum officinarum
Sorghum bicolor
Zea mays

manufacture_protocol:
The plant miRNA microarray V2.0 is based on 994 sequences in miRBase 9.1 (Feberary 2007) of Sanger Database. 348 unique miRNAs were retained after removing the redundant sequences. Coupled with 4 miRNAs predicted by Zhu Jian-Kang on Cell Journal, and 74 miRNAs predicted by Chen Fan (CAS), there are 426 miRNAs probes in all on the array. These probes were spotted on a piece of 75mm multiply 25mm, chemical modified glass using SmartArrayTM (CapitalBio Corp., Beijing, China ) machine. Eight manufactered RNA with 30nt in length were used as exogenous controls (Zip5, Zip13, Zip15, Zip21, Zip23, Zip25, Y2, Y3). Hex was used as positive control and 50% DMSO was negetive control.
The whole array was divided as 4 subarray. There are 18 rows and 21 columns in each subarray. The diameter of spots was 150 micrometer with 225 micrometer intervals between two spots. Each probe was spotted in three technical replicants.


title: Nimblegen Homo sapiens HG18 Expression Array 4x72k (All Probes)

status: Public on Feb 01 2011

city: Madison

first: Inc

last: Nimblegen Systems

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description:
This is a whole genome human expression array in 4-plex format provided by Nimblegen. See manufacturer's website at http://www.nimblegen.com/.

Format: 4x72K
Source: NCBI
Build: HG18
Probe Length: 60mer
Design Name: HG18 60mer expr 4plex
Genes: 24,000
Probes/ Target: 3
Replicates: 1

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


title: Jilin University Mycobacterium tuberculosis array (Feature Number version)

status: Public on Jan 08 2011

city: Changchun

first: Lu

last: Yu

address: Xi'an Road 5333

institute: Jilin university

organism: Mycobacterium tuberculosis H37Rv

last: Guo

relation: Alternative to: GPL14570 (Probe Name version)

manufacture_protocol: refer to www.agilent.com


title: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array [CDF: Hs133P_Hs_ENSG_8]

status: Public on Dec 31 2010

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

institute: University of Helsinki

description: Custom Brain Array CDF.


title: NimbleGen Human DNA Methylation 2.1M Deluxe Promoter Array [100205_HG18_Promoter_MeDIP_HX1]

status: Public on Mar 20 2011

city: Bethesda

first: Lai

last: Wei

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

description:
Design ID: 11333
Design name: 100205_HG18_Promoter_MeDIP_3
Genome build: HG18, NCBI36

HX1 - HG18 promoter design, mean probe spacing 99, median 100.  This design consists of:  1) Promoter regions, from 7250 bases upstream of each TSS to 3250 bases downstream;  2) miRNA genes, starting from 15kbp upstream of the mature gene product to its 3' end;  3) CpG islands;  4) ENCODE regions.  Probes were chosen from the hg18_tiling database.  Most probes were chosen at an int65win35max1.  Any region that resulted in no coverage from this selection was  re-selected at int10win90max10.

Native array description file: 100205_HG18_Promoter_MeDIP_HX1.ndf
Native array description file: 100205_HG18_Promoter_MeDIP_HX1.pos

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


title: Human Meth 2.1M WG-T 10-10 [0701_HG18_TILE_10_HX1]

status: Public on Jun 23 2010

city: New York

first: Andrew

last: Sharp

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

first: Eugenia

last: Migliavacca

first: Elisavet

last: Stathaki

first: Stylianos

last: Antonarakis

manufacture_protocol: see manufacturer's web site


title: Human Meth 2.1M WG-T 8-10 [0701_HG18_TILE_08_HX1]

status: Public on Jun 12 2010


title: Agilent-016002 Custom Gene Expression Array for Candida glabrata 4x44k G2519F

first: Ying-Lien

last: Chen

state: NC

address: Dept. of Molecular Genetics and Microbiology, Duke University Medical Center

department: Molecular Genetics and Microbiology

organism: Nakaseomyces glabratus

manufacture_protocol: Standard Agilent protocols for Agilent Custom Oligo Microarray 4x44k G2519F


title: [Glyco_v4_Mm] Affymetrix Glyco v4 GeneChip

status: Public on Oct 23 2010

city: La Jolla

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

organism: Mus musculus

description:
The Glyco v4 array was designed in 2008 and consists of probesets targeting genes coding for glycosyl transferases, carbohydrate binding proteins, glycan degradation enzymes, nucleotide sugar transporters, mucins, adhesion molecules, chemokines, cytokines, growth factors and their receptors, interleukins and their receptors and proteoglycans. In addition, a set of "housekeeping" and control genes are included on the array. The array contains probe set for both mouse and human gene sequences and can be use to analyze RNA from both species.

This array also includes "GC bin" probes (100 for each bin) for use in background correction. These probes are used as an alternative to the PM/MM-based background correction methods. Mismatch probes are not used on this array.

There are separate library files for human and mouse probesets. The human library file includes all probesets on the array except mouse probes and vis versa for the mouse library file.  The human CDF file is named: "GLYCOv4_Hs" and the mouse CDF file is named: "GLYCOv4_Mm".

Probeset design: The v4 array uses 25 probes to target the first 600 bases from 3' end of each transcript. This region is called Probe Set Region 1 indicated by a psr1 in the probe set name. Up to 4 additional sets of  5 probes are used to target the transcript in 280 base increments upstream (towards the 5' end of the transcript) from the first 600 base region. These are indicated as psr2, psr3 and psr4 in the probeset name. If no psr appears in the probe set name, this indicates that probes are targeting Probe Set Region 1 and that no additional probe sets were designed upstream (towards the 5' end of the transcript) for this transcript accession. Generally only data from Probe Set Region 1 are shown. Data from psr2-4 is generally ignored. All probes are for antisense target and may include a suffix of "_s", "_x" consistent with Affymetrix probe design algorithms used for all commercial Affymetrix 3' arrays.


title: Agilent-022520 Brassica napus 4x44K

status: Public on Jan 20 2011

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

institute: Genotypic Technology

organism: Brassica napus


title: NimbleGen Human Meth 385K Prom Plus CpG Array [2006-11-02_HG18_CpG_Promo]

status: Public on Jan 01 2010

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: 385K
Source: UCSC
Build: HG18
Probe Length: 50-75mer
Recommended Storage: Store arrays desiccated at room temperature.

manufacture_protocol: See www.nimblegen.com


title: Children's Hospital Boston Danio rerio 385K Array [071105_Zv7]

status: Public on Jul 13 2010

city: Boston

first: Xiaoying

last: Bai

address: 1 Blackfan Circle

institute: Children's Hospital Boston


title: UH-UGA Rice PM 15.5k cDNA Array

status: Public on Nov 12 2009

city: Hyderabad

first: Markandeya

last: Gorantla

state: Andhra Pradesh

address: University of Hyderabad

department: Department of Plant Science

institute: university of Hyderabad

first: V

middle: B

last: Reddy Lachagari

first: Ravindra

middle: P

last: Babu

first: Alex

middle: F

last: Feltus

first: Sivaram

last: Lekkala

first: Pamakrishna

last: Wusirijka

first: Jeffery

last: Bennetzen

first: M

middle: K

last: Reddy

middle: H

last: Paterson

first: Arjula

manufacture_protocol:
1. cDNA microarray chip consisting of 15552 features with 5664 ESTs from drought stress induced cDNA library of Oryza sativa cv Nagina22,  1152 ESTs from drought stressed Pennisetum glaucum,  24 yeast artificial genes  and  48 samples of λ (Lambda) DNA, (Takara, Japan).  cDNAs  were printed in duplicate on superamine coated glass substrate using Omnigrid (GeneMachines).  The machine was calibrated for 384 Nunc square well plates, CMP3 print head and stealth printing pins and 75mm x 25 mm microarray glass slides were used, we have used 16 pins altogether in 4 x 4 format, which will give us an option to print 4 subarrays along Y direction and 4 arrays in X direction. The origin offset values set were 3000 micron in X direction and 2000 microns in Y direction. We have used 225μ spot to spot spacing in a subarray. The No of spots printed in a subarray is 18 clones in X direction and 18 clones in Y direction, the number of clones printed in one su
barray is 18 x 18 = 324 stamps, in which 162 clones have been printed onto each subarray. The maximum number of arrays which would be printed were 4 in which we limited to 3 arrays, with a spacing of 500 microns each, in which a maximum number of 7776 clones in duplicate could be printed. The above format allowed us to print 7680 samples in duplicate including blanks. For printing the sample intake was for every 100 slides, the dip time being 1000 milliseconds, with each dip the sample is taken in by capillary action and is sufficient enough to print 200 stamps. The sample volume which is delivered in each stamping is around 0.5 to 0.7 ηl. After each printing the pins are sonicated for 2000 milliseconds, followed by washing in sterile water for 3000 milliseconds and drying under vacuum for 2000 milliseconds which is repeated thrice, the final cycle has an extended drying time of 3000 milliseconds. After each 384 well plate the pins are also sonicated thrice for 3000 millise
conds. During each dip, in order to avoid the possibility of sample sticking to the walls of the pins, which can cause excess sample being deposited on slides will result in run over of samples, the pins are initially blotted on a poly-L-Lysine coated blot pad 10 times with 150 micron spot to spot spacing such that no sample remains along the walls of the pins. The time taken by the robotic gridder to print 7680 samples in duplicate is 36 hours. The cDNAs were printed with a relative humidity between 45 to 50% RH, this is very critical in printing good and reproducible microarrays. And also before printing calibration of wash station, dry station, sonicator and slides across the platen of the slide holder is of utmost importance for uniform spot morphology in all the printed slides. Array printing:Microarraying was by robotic systems we used a microarray robot built by Gene Machines California (genomic solutions). We have used aminosilane coated slides from Telechem these Su
perAmine, aminosilane coated glass microscope slides have been the most consistent, when printed in 50% DMSO as a printing solution at 45% relative humidity and a constant temperature of 72oF (22oC). We have used quill pens (Arrayit ChipMaker3 microspotting pins from Telechem International Inc.) which were very durable and could reproduce high-quality spots with good precision, all arrays were printed with the same set of ChipMaker 3 pins for more than six months. Following printing, the slides were rehydrated on a steam coming from a 500ml conical flask containing MilliQ water, which was kept boiling on a hot plate. Care was taken such that all the slides were uniformly rehydrated, the slides were just passed over the steam with the array side down 2 to 3 times until a thin layer of mist was formed on the printed side, extreme care was taken not to rehydrate such that the spots run into each other following rehydration the slides were immediately snap dried for 5 sec on a h
ot glass plate. The slides were allowed to dry and spotted DNA was fixed to slide by UVcrosslinking at 320 mJ using a Stratalinker (Stratagene, Cat# 400071) and by baking at 80o C for 2 hrs. Printed slides were stored in a light-tight box in a bench-top dessicator, with desiccant and were kept at 4o C until they were used for hybridization.
2. Total RNA was isolated from leaf and panicle samples collected at different time intervals after stress treatment using Trizol (Chirgwin et al., 1979; Chomczynski and Sacchi, 1987) from Life Technologies with minor modifications. The harvested tissues were stored immediately in RNA later (Ambion) and stored at 4oC for 24 hours and after which the RNA latter was removed and the samples were quick frozen in liquid nitrogen and stored at –70oC. Five grams of freshly harvested or frozen tissues were ground in liquid nitrogen to a fine powder, transferred to 50ml tubes with 15ml of Trizol in it. The sample was resuspended well in Trizol and incubated at room temperature for 5 minutes. Cellular debris was removed by centrifugation at 4000 rpm (2700 g) for 15min at 4oC. The supernatant was transferred to a fresh RNAase free 50 ml oakridge tube. To it 3ml of chloroform (0.2 ml/1 ml Trizol) was added and shaken vigorously for 1 minute. After which the suspension was incubated at
room temperature for 5 minutes. The samples were centrifuged at 4000rpm (2700 g) for 15min at 4oC to remove proteins and high molecular weight DNA, following centrifugation three different layers are observed. The top supernatant layer contains RNA, the intermittent layer is a denatured protein layer, and the lower layer is high molecular weight DNA. The upper aqueous layer was carefully removed without disturbing the protein layer and was transferred to a fresh RNAase free oakridge tube. To this equal volume of isopropanol was added to precipitate the RNA and was incubated at RT for 15 minutes. Following which the precipitated sample was centrifuged at 15,000rpm (21,000g) for 15 minutes to pellet the RNA. The supernatant was discarded and the pellet resuspended in 70% ethanol. The RNA pellet was resuspended in diethylpyrocarbonate (DEPC) treated water. The quality of the total RNA was determined through 1.2% denatured agarose formaldehyde gel and concentration estimated sp
ectrophotometrically. For labeling  the samples were resuspended in 1/10th volume DEPC treated sodium acetate and 2.5 volumes ethanol. Prior to labeling the precipitated RNA was spun at 12000 RPM for 10 min and washed with 70% ethanol. The RNA was dried in a savant rotary vapor trap and resuspended in RNAase free milliQ water for labeling.
3. Probes for microarray analysis are prepared from RNA templates by first strand synthesis of cDNA containing amino-allyl-labeled nucleotide dCTP and amino-hexyl modified dATP for both control and stress samples, followed by a covalent coupling to the NHS-ester of the appropriate Cyanine fluor. This method has proven highly efficient for labeling all kinds of tissues from rice for expression analysis.  Superscript III RT (Life Technologies; Cat# L-1014-02) was used to  generates probes with significantly greater activity. Coupling of modified cDNA with fluorescent probes was done by photostable Alexafluor  fluorescent dyes (we have used Alexafluor 488, and 555 for control labeling and Alexafluor 594, and 647 NHS ester dyes for coupling stressed samples), The  photosensitivity of dyes was minimized by avoiding exposure to light during labeling, hybridization, washing, and scanning processes. Upon receipt, these NHS ester dyes were stored in light- proof tubes and stored at -
20oC until needed. All reactions were carried out in foil-wrapped tubes and all hybridizations and washes in foil-wrapped containers.Labeling procedure First strand amino modified cDNA synthesis recipe step 1:Prior to labeling the Quality of total RNA for both control and stressed experimental sample, were quantified and  40μg of total RNA was resuspended in not more than 10μl DEPC treated water. Anchored oligo DT prim 2.0μl. DEPC treated water was added to make-up a final volume of 30.0 μl.  The above RXN was Incubate for 2 hours at 42o C in a thermocycler.  Alkaline hydrolysis and neutralization step 2:To the reaction from step 1, 15 μl 1N NaoH was added to denature the RNA through hydrolysis from RNA-DNA hybrid and was incubated for 10 minutes at 70o C for complete RNA denaturation. To this 15μl of 1N HCL was added to neutralize the pH and mixed gently. To the above reaction 20μl Sod.Acetate, pH 5.2 was added and mixed gently. Once the  cDNA is generated with amino-m
odified nucleotides the cDNA was purified to remove unincorporated dNTPs and hydrolyzed RNA, using bind wash elute SNAP columns (Life Technologies) as per manufacturers instructions following which, the cDNA was O/N ethanol precipitated by adding 1/10th volume Sodium Acetate and 2.5 volumes ethanol. First strand cDNA dye coupling step 3:To the aminoallyl and aminohexyl modified cDNA precipitated in step2, was further   centrifuged at 12000 RPM for 10 min to pellet it down and the pellet was washed with 70% ethanol and dried down in speedvac (Savant). The pellet was dissolved in 6μl sterile water. For coupling of the dye, the dye vails (Alexa fluor dyes) were allowed to come down to room temperature in order to avoid condensation of water inside the vial. The dyes were dissolved in 4μl of DMSO. For coupling 10μl of 2x coupling buffer (sodium bicarbonate) was added to modified cDNA to bring the final concentration to 1x, to the above reaction 4μl of the dissolved dye was added and allowed to couple overnight in dark at room temperature. Further, the cDNA was purified by bind wash elute SNAP columns (Life Technologies) as per manufacturers instructions to remove any unreacted free dye molecules.
4. Hybridization:The dye labeled cDNA once quantified, equal amounts of cDNA from tester and reference samples were pooled and was precipitate by adding 1/10th of Sodium acetate and 2.5 volumes of ethanol, the cDNA populations are spun at  8000 RPM for 10 min, to pellet down the cDNA, extreme care was taken not to disturb the pellet while decanting. The pellet was washed with 70% ethanol and dried in speedvac, and the pellet was directly dissolved in 50μl of low temperature hybridization buffer from sigma. Preparation of slides for Pre-hybridization/ Hybridization:We have developed protocols that give reproducible, high-quality hybridization results while maximizing the measured fluorescence from the array. Aminosilane coated slides bind DNA with high efficiency. Prior to hybridization, the free amine groups on the slide were blocked or inactivated to avoid nonspecific binding of labeled cDNA to the slide which can deplete the probe and produce high background. The slides we
re blocked in Sodium Borate and Succinic anhydride, a solution of 0.5M Sodium Borate was prepared by dissolving Sodium Borate by heating until it got dissolved and ph was adjusted to 8.0. Simultaneously 900mg succinic anhydride was dissolved in 47ml of 1 methyl 2 pyrillidone (Sigma Aldrich), in a 50ml falcon tube and as soon as the last flake of succinic anhydride was dissolved 2.2ml, 0.5M Sodium Borate was added and was mixed well. Microarray slides stored at 4 deg C were allowed to come to room temperature, the required number of slides were dipped in the above solution and kept for shaking on an orbital shaker for 15 min, and care was taken that the printed side does not touch each other, the slides were placed in opposite direction such that the non printed side touches each other. This was Scaled up if more than 2 slides were processed using a Lipshaw slide holder and jar. After 15 min the slides were washed in 0.1% SDS for 2 min in a clean glass jar (Lipshaw dish stain
ing assembly) the SDS solution was removed and a brief 10sec wash was performed with milliQ water, and were transferred to a fresh dish jar containing  2XSSC,  the slides were washed twice with 2X SSC for 2 min each. Denaturing and fixing:Denaturation was performed by dipping the slides in boiling hot water at 95o C and incubating them for 2 min. The denatured DNA was fixed by transferring the slides in ice cold 200 pint 95% ethanol (Aldrich), care was taken to avoid shattering of slides due to sudden transfer of slides from boiling hot water to ice cold ethanol. Slides were retained in ice cold ethanol for 2 to 3 min before being transferred to a 50ml falcon tube with a tissue paper at the bottom and the slides. The slides were spun without cap at 1000RPM for 5 min at RT, there is every possibility that the slide coating could peel off but the substrate we selected withstood the pre-hybridization conditions and all the slides processed did not peel. After spinning the slide
s were immediately used for hybridization. Target hybridization:The labeled cDNA dissolved in low temperature hybridization buffer from sigma, two blocking agents yeast tRNA (Sigma) at a concentration of 20μg per hybridization, and 2μg poly DA (Sigma) per hybridization were used to block non-specific hybridization, these two were mixed with the labeled target and was denatured at 95o C for 5 minutes, during this period the pre-hybridized slides were heated to bring the slides to 45oC for hybridization. After denaturation the labeled probe was applied to a pre-hybridized microarray slide and covered with 22mm x 60mm plastic hybrid-slips (Sigma, Schleicher and Schuell Gmbh). Once the coverslip is properly placed without any air bubble trapped between the slide and the coverslip, the slides were inverted (array side down) and kept inside a 50ml falcon tube, which we used as an makeshift hybridization chamber, a small piece of tissue paper was soaked with 1ml of 3x SSC and was
kept inside the bottom of falcon tube to maintain humidity during hybridization and to avoid drying of the target, which will make the coverslip stick to the slide and result in failure of hybridization. We placed the 50ml falcon tube in hybridization bottle (Amersham Pharmacia) and with support on two sides with bottle holders these units were dipped in hot water bath set at 50oC. Weight rings were used between the bottles to avoid floating of the hybridization bottles. Hybridization was allowed to carry out for 16 hours in dark at 50oC. Washing:The slides from the water bath were taken out after 16 hours of hybridization and these slides were carefully dipped in wash buffer 1 (1x SSC , 0.03% SDS), the slides were shaken gently until the coverslip come off by itself, in any case care was taken not to take of the coverslips manually, but rather was allowed to soak in the buffer for some more time by shaking gently. Once the coverslips come off, the slides were transferred t
o wash buffer 2 (0.2x SSC)  and the slides were washed  for 2 min by gently shaking and then transferred to wash buffer 3 (0.05x SSC) these slides were further washed with gently agitation for 5 min. The slides were then transferred to a 50ml falcon tube and with its lid open were spun at 1000 RPM for 5 min in order to dry the slides for scanning. Extreme care was taken that the slides are not dried between transfers.
5. Scanning of the hybridized slide was done using ScanArray 3000 (Genomic solutions). Hybridized slides are scanned first in the high wave length channel (594nm and 647nm), and then the lower wavelength (488nm and 555nm), as high wave length channel dyes are more susceptible to photo-degradation than lower wavelength channels. Data from each fluorescence channel was collected and stored as a 16-bit TIFF image. To quantify the right intensities slides were scanned as soon as possible after washing. The slides were scanned at appropriate PMT gain and 100% laser power, the slides were scanned at various PMT gains from low to high at 30 microns scan resolution, then appropriate PMT settings for both the dye wavelength was standardized. Scanning was done at PMTs where we could observe 20 to 30 white spots as such the overall intensities are good. This was determined by observing the RI (Ratio Vs Intensity) plot of intensities. Once the right PMT gains for both the channels were
determined, the slides were scanned at 10micron resolution. During quantification we used the highest threshold limits for spot intensity calculation and ANOVA for performed for these low PMT and High PMT technical replicates. During quantification care was taken that the week spots and saturated spots are flagged off during intensity calculation. To minimize the background fluorescence, care was taken such that the background fluorescence is as low as possible, using appropriate blocking agents. Scanned images generated from microarray experiment were quantified with Quantarray (GSI Lumonics), software
6. Data from each fluorescence channel was collected and stored as a 16-bit TIFF image. The two images were loaded on to the two different channels of Quantarray and grids were generated taking printing style in to the consideration. Overlay of the two channel intensities revealed the hybridization was good and more or less similar intensities were observed in adjacent in-slide replicates. A total of 48 blocks with 324 features in each were generated with 12 rows and 4 columns in each covering all the ~15550 features including controls. A total of 15552 cells were generated with 5 - 23 pixel spot size adjusted as to cover all the features of the superimposed slide. In house custom perl scripts were written to facilitate the annotation to the features on the array. Annotation including gene function, chromosome Bac/Pac location, map positions, unigene cluster, functional classification, and redundancy were provided to facilitate further analysis with ease. All the grids were
processed and spots were quantified in the cells eliminating local background. The spots with poor quality in either of the slide were flagged off and were eliminated during the normalization. The intensities captured at the saturated level were excluded from further analysis and quantified spots from each analysis were stored for further analysis.
7. Rice seeds were surface sterilized, washed and germinated in a growth chamber. Fifteen day old seedlings were transplanted in the field for drought stress induction. The transplanted seedlings were grown in 100% field capacity with 2cm standing water until day 30. Field drought stress was initiated from day 31 at 100%, 60%, 40% and 15% field capacities designated as A1, A2, A3, and A4. It took 8 days for the onset of the actual drought for the experimental plots to reach to their designated field capacities from 100% FC. The irrigation Samples were collected at various stages and drought stress regimes based on the developmental stages of the plant. Rainout shelter was constructed to cover the plots during rainy days to keep the plants from rain during experiment. The rainout shelter was provided with free moving rail tracks to move forward and backward. Proper care was taken to avoid any shade of rainout shelter keep on plants. The drought stress induction was monitored
through high-precision digital irrigation controllers procured from Netafim Inc (Israel). Irrigation was given taking Plot A1 /AR1 as 100% field capacity, which is a control plot in this experiment, and irrigation was set up in the other plots as shown in the table below with moisture probes/Timer controllers using digital controllers.


title: Tdalmanni Agilent 44K Oligoarray Slide1

status: Public on Aug 21 2009

city: College Park

first: Gerald

last: Wilkinson

address: Bldg 144, 4094 Campus Dr

institute: University of Maryland

organism: Teleopsis dalmanni

description: Each 44K array contains 9 features for each of ~3600 genes that have been identified in an EST study of eye-antennal discs from late instar larvae or pupae of a diopsid stalk-eyed fly.  cDNA clusters were included that had 1) significant homology to known genes in Drosophila or Anopheles, 2) an ORF larger than 300 bp (labeled ORF-) or 3) more than four associated cDNA clones (labeled X-). Three 60 bp oligonucleotide probes were designed for each gene based on the consensus sequence with the highest Blast hit or largest ORF within each cluster.  Each probe occurs in triplicate.

first: Richard

last: Baker

manufacture_protocol: Custom designed using eArray, chemical synthesis


title: ChIP chip data for Ftz and Eve proteins during early embryogenesis

status: Public on Apr 02 2009

city: Chicago

first: Kevin

last: White

state: IL

address: 400 CLSC

institute: University of Chicago

organism: Drosophila melanogaster

first: Murad

last: Ghanim

first: Sujun

last: Hua

first: Christopher

last: Brown

manufacture_protocol: In situ oligonucleotide synthesis on glass substrate; high density


title: NimbleGen Saccharomyces cerevisiae 4x72k expression array [TI4932_60mer_expr]

status: Public on Apr 22 2009

city: Emeryville

first: Mario

last: Ouellet

address: 5885 Hollis St., 4th Floor

institute: Joint BioEnergy Institute

organism: Saccharomyces cerevisiae

description:
Genes: 5,747
Probes/ Target: 6
Replicates: 2

The Platform data table reflects a condensed representation of the array's replicate features.
Native NimbleGen files (ndf, ngd) are linked below as supplementary files.

first: Aindrila

last: Mukhopadhyay

first: Jay

middle: D

last: Keasling


title: 454 GS FLX (Mus musculus)

status: Public on Sep 23 2009

last: GEO


title: SWEGENE H_v2.1.1 55K

status: Public on Jul 14 2007

city: Lund

first: Johan

last: Staaf

address: Medicon Village

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

first: Ake

last: Borg

relation: Alternative to: GPL14374 (condensed on CloneID)

manufacture_protocol: Arrays were produced by the Swegene DNA micro array resource center at Lund University by using probes from Operon. Probes were recovered in Corning Universal Spotting Solution and printed on amino-silane-coated glass slides (UltraGAPS from Corning) using a MicroGrid2 robot (BioRobotics).


title: Beijing Institute of Microbiology and Epidemiology Streptococcus suis 05ZYH33 2.2K

status: Public on Dec 02 2009

first: Ruifu

last: Yang

address: No.20, DOngdajie, Fengtai

organism: Streptococcus suis 05ZYH33

manufacture_protocol:
Based on the whole-genome sequences of Streptococcus suis serotype 2 strain 05ZYH33, a total number of 2194 annotated open reading frames (ORFs) were selected after the exclusion of ORFs encoding IS protein, integrase, and transposase (The word “gene” will be used in the following part of this paper in reference to the ORF). Those highly homologous to each other at nucleotide level were also excluded. Gene specific primer pairs (16bp to 18bp in length) were designed to amplify nearly the full length of each gene. All primers were synthesized by Illumina Co. (San Diego, CA, U. S. A).
300µl of PCR product was obtained for each gene. PCR amplifications were performed in 96-well plates by using a DNA thermocycler (Biometra UNOII). 100 µl of PCR reaction mixture, containing 50 mM KCl, 10 mM Tris-HCl (pH8.0), 2.5 mM MgCl2, 0.001% gelatin, 0.1% BSA, 150 µM of each dATP, dCTP, dGTP and dTTP, 0.6 µM of each primer, 5 units of Taq DNA polymerase (MBI Fermentas), and 20 ng of template DNA, was predenatured at 95°C for 5 min. Then 30 cycles of 94°C for 1 min, 58°C for 1 min 30 sec and 72°C for 2 min were performed with a final extension at 72°C for 10 min. Each PCR product was verified by agarose gel electrophoresis and was scored as successful if a single band of the expected mobility was detected. DNA smear, multiple bands, or single band of unexpected size were characterized as unsuccessful reactions. Primer pairs from unsuccessful PCR reactions were re-amplified with altered annealing temperatures to get the desired single band of products. A few primers had to be redesigned to ensure successful amplification. In the end, 2156 genes were amplified successfully.
PCR products were purified by using 96-well Multiscreen PCR plates (Millipore) following the user manual’s instruction. The purified DNAs were air dried at 65°C, and were resuspended in 30 µl of 50% DMSO solution. 10 µl of the purified PCR product was transferred into Genetix 7020 384-well Polystyrene Plates for microarray printing. Each of the PCR products was spotted in duplicate on CSS-1000 silylated glass slides (CEL) by using a SpotArray72 Microarray Printing System (Perkin Elmer Life Sciences) with 16 Telechem SMP3 Stealth Pins (4×4 Layout). Genomic DNA of strain 05ZYH33(its genomic content is identical to that of epidemic strain 05ZYH33，CP000407.gbk), salmon sperm DNA and 50% DMSO solution were included in the microarray design as internal control elements. The spotted slides were stored in dry environment at room temperature for at least 12 hr, and then were crosslinked twice by using a UV Stratalinker (Hoefer) each at a total energy of 60 microjoules. The spotted CSS-1000 silylated slides need not any blocking procedure, such as the blocking of unreacted aldehyde groups and the prehybridization. The microarray slide to be hybridized was simply washed in water for 2 min to remove the unbounded DNA and then was blown to dry with hot air.


title: DJF Pig 55K v1

status: Public on Jan 11 2008

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

institute: Aarhus University, Faculty of Agricultural Sciences

organism: Sus scrofa

manufacturer: University of Aarhus, Faculty of Agricultural Sciences

first: Christian

last: Bendixen

first: Lene

middle: N

last: Conley

first: Frank

last: Panitz

first: Henrik

last: Hornshøj

manufacture_protocol:
DIAS_PIG_55K4_v1 consists of 55.548 features: 26.877 PCR products amplified from cDNA clones and 867 control features spotted as neighbor duplicates in a 4 x 12 array with sub-arrays each consisting of 34 x 34 spots.
The cDNA clones were selected from the cDNA libraries generated in the Sino-Danish Pig Genome Sequencing Consortium using BLASTN sequence similarity (P ≤ 10-8) such that the cDNAs covered the largest possible number of human gene transcripts in NCBI’s RefSeq database, release 15. To represent previously uncharacterized genes and candidate porcine specific genes we added cDNAs to the selection list, for which their EST clusters, of minimum depth 3, showed limited or no similarity to any known mammalian gene transcripts. The selected clones were rearrayed from the libraries using a QPixII (Genetix), amplified by PCR and purified using the 384 well Microarray PCR Purification Kit (Telechem International). The PCR products were evaluated by agarose gels and dried by speed vac and resuspended in spotting solution. The control features consists of positive spots (also known as “landing lights”), blanks (spotting buffer) and selected spots from the Lucidea Universal ScoreCard (GE Healthcare) which contains both intensity dilution series and different ratios. The positive spot was prepared by PCR amplification of a bovine EST fragment using a dNTP mix containing amino allyl-dUTP followed by labeling with Alexa-488, -555, -594 and -647. The arrays were spotted on UltraGAPS slides (Corning Incorporated) at 20 C/55 % RH using an SDDC-2 MicroArrayer (BioRad) with 48 x 946 MP2.5 pins (Telechem International) with DNA resuspended in Micro Spotting Solution Plus (Telechem International). Slides were dried and UV cross-linked (300 mJ) and stored in a vacuum desiccator until use.

The sequences of the cDNA clones can be found in the attached file "GPL6173_array_cDNA_28k_2005-07-13.cDNA.scr.zip". The attached .gal file contains the original annotation, but an updated version of the annotations have been obtained by blast against mammalian refseq (version 34, file: "GPL6173_p55k-vs-mam-refseq34-2009-04-17.txt") and against Human refseq (release 2009-03-09, file: "GPL6173_p55k-vs-hsa-refseq-2009-04-17.txt") (Rank = 1, Minimum alignment length = 50, Minimum percent alignment = 85 %). An annotation package (file: GPL6173_55k3Ver2HsRs20090309AL50PA85_1.0.zip") has furthermore been built in R (version 2.8.0) using AnnBuilder (version 1.20.0).


title: DIAS_PIG_55K3_v1

status: Public on May 23 2006

manufacturer: Danish Institute of Agricultural Sciences

first: Per

last: Horn

manufacture_protocol:
DIAS_PIG_55K3_v1 consists of 55.548 features: 26.877 PCR products from cDNA clones and 867 control features spotted as neighbor duplicates in a 4 x 12 array with sub-arrays each consisting of 34 x 34 spots.
The DNA fragments were amplified from cDNA clones selected from the cDNA libraries generated in the Sino-Danish Pig Genome Sequencing Consortium (Gorodkin et al.: Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 ESTs. Genome Biol 2007, 8:R45). The cDNA clones were selected to represent the largest possible number of human gene transcripts. EST clusters for human gene transcripts in NCBI’s RefSeq database release 17 were created using BLASTN sequence similarity program implemented to run on a DeCypher computer [http://www.timelogic.com] with P-value at or below 10-8. Within each cluster one cDNA with the minimum predicted distance to the 3’ end of the human gene transcript was selected. Microarray cDNAs were mapped to GO terms and KEGG pathways based on the human accession id, obtained from BLASTN, using the AnnBuilder package from Bioconductor. To represent uncharacterized genes on the microarray, a set of EST sequence clusters without BLASTN sequence similarity to any known human gene transcript was created and clustered using the “all-vs-all” TERACLU algorithm on a DeCypher computer from TimeLogic [http://www.timelogic.com]. We added one cDNA to the selection list for each of EST clusters with a minimum depth of 3 ESTs and minimum predicted distance to the 3’ end of the assembled EST contig. Of the 26.877 cDNAs, 21.417 map to 15.831 human gene transcript IDs corresponding to roughly 1.35 cDNAs per gene transcript. The remaining 5.460 cDNAs were thus estimated to cover around 4.036 gene transcripts yielding approximately 19.867 gene transcripts in total. The selected clones were rearrayed from the libraries using a QPixII (Genetix), amplified by PCR and purified using the 384 well Microarray PCR Purification Kit (Telechem International). The PCR products were evaluated by agarose gels and dried by speed vac and resuspended in spotting solution. The control features consists of positive spots (also known as “landing lights”), blanks (spotting buffer) and selected spots from the Lucidea Universal ScoreCard (GE Healthcare) which contains both intensity dilution series and different ratios. The positive spot was prepared by PCR amplification of a bovine EST fragment with a primer pair where one of the primers was labeled with Alexa-488 or Alexa-594. The arrays were spotted on UltraGAPS slides (Corning Incorporated) at 20 C/55 % RH using an SDDC-2 MicroArrayer (BioRad) with 48 x 946 MP2.5 pins (Telechem International) with DNA resuspended in Micro Spotting Solution Plus (Telechem International). Slides were dried and UV cross-linked (300 mJ) and stored in a vacuum desiccator until use.

The sequences of the cDNA clones can be found in the attached file "GPL3608_array_cDNA_28k_2005-07-13.cDNA.scr.zip". The attached .gal file contains the original annotation, but an updated version of the annotations have been obtained by blast against mammalian refseq (version 34, file: "GPL3608_p55k-vs-mam-refseq34-2009-04-17.txt") and against Human refseq (release 2009-03-09, file: "GPL3608_p55k-vs-hsa-refseq-2009-04-17.txt") (Rank = 1, Minimum alignment length = 50, Minimum percent alignment = 85 %). An annotation package (file: "GPL3608_p55k3Ver2HsRs20090309AL50PA85_1.0.zip") has furthermore been built in R (version 2.8.0) using AnnBuilder (version 1.20.0).


title: Affymetrix Rhodopseudomonas palustris GeneChip 2

status: Public on Jun 29 2007

city: Seattle

first: Yasuhiro

last: Oda

state: WA

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

department: Department of Microbiology

institute: University of Washington

organism: Rhodopseudomonas palustris

first: Caroline

last: Harwood

first: Everett

last: Greenberg

first: Amy

last: Schaefer

manufacture_protocol: A high-density oligonucleotide microarray was custom designed and manufactured by Affymetrix based on the sequences of ORFs and intergenic regions.


title: 3D-Gene Yeast Oligo chip S.cerevisiae 6k

status: Public on Oct 10 2006

city: Kamakura

first: Satoko

last: Takizawa

state: Kanagawa

address: 6-10-1 Tebiro

department: New Frontiers Research Laboratories

institute: TORAY Industries, Inc.

description: Ultra-sensitive DNA chip for S.cerevisiae genome wide gene expression analysis


title: Illumina Genome Analyzer IIx (Saccharomyces cerevisiae)

status: Public on Mar 11 2011