title: MIT S.cerevisiae ORF 15K version 4.2

status: Public on Mar 18 2008

city: Cambridge

first: Joel

last: Moxley

state: MA

address: 77 Massachusettes Ave

country: USA

institute: MIT

organism: Saccharomyces cerevisiae

technology: spotted oligonucleotide

description: Array with 15488 features, in 32 zones, with 12558 biosequences representing 14966 reporters and 0 composite sequences, with surface type polylysine

distribution: non-commercial

manufacture_protocol: Microarrays were spotted on UltraGAPS II slides (Corning) using an OmniGrid 100 microarrayer (GeneMachines). After spotting, arrays were baked at 80°C for 2 hours, cross-linked at 300 mJ in a UV Stratalinker 2400 (Stratagene), and stored under vacuum. Hybridizations were conducted at 42°C for 15 hours using the Lucidea SlidePro automated hybridization machine (Amersham Biosciences).  Described in A-MEXP-217.mageml.tgz


title: Bacillus cereus ATCC 14579 amplicon-based 12k microarray

status: Public on Mar 27 2008

city: Wageningen

first: Menno

middle: van der

last: Voort

address: Bomenweg 2

department: Agrotechnology and Food Sciences Group

country: Netherlands

institute: Wageningen UR

organism: Bacillus cereus ATCC 14579

technology: spotted DNA/cDNA

last: van der Voort

first: Tjakko

last: Abee

first: Oscar

middle: P

last: Kuipers

first: Anne

last: de Jong

manufacture_protocol: Amplicon based DNA-microarrays were constructed for B. cereus ATCC 14579 as described for Lactococcus lactis IL1403 (Kuipers et al., 2002; van Hijum et al., 2005) with modifications as detailed below. Amplicons were designed on 5199 genes selected from the 5311 annotated genes (ORFs smaller than 80 bp were omitted) on the genome of B. cereus ATCC 14579 (Ivanova et al., 2003). To reduce cross-hybridization between probe and target DNA sequences the amplicons had sizes of 70 – 700 bp (depending on gene sizes) and comprised the most unique part of a gene. The amplicons were synthesized by EuroGentec (Seraing, Belgium) in two amplification steps. In the first amplification step, primers were used with a unique tag-sequence for B. cereus ATCC 14579 (forward primers were extended with the sequence: 5’-TCGGGCAGCTGCTCC-3’; and reverse primers with the sequence: 5’-TGGCGCCCCTAGATG -3’). Two copies of each amplicon were present per array, resulting in microarrays comprising 10398 spots.


title: NimbleGen Mouse 2.1M NCBI36

status: Public on Mar 12 2008

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

organism: Mus musculus

technology: in situ oligonucleotide

distribution: custom-commercial

manufacture_protocol: Maskless array synthesis was used to construct isothermal arrays. Probes had a median probe spacing of 1.015 kb. Probes were synthesized using an isothermal format (Tm = 76°C) and varied in length from 45 to 75 bp.


title: NimbleGen Mouse 3.1M NCBI36

manufacture_protocol: Maskless array synthesis was used to construct isothermal arrays. Probes had a median probe spacing of 0.49 kb. Probes were synthesized using an isothermal format (Tm = 76°C) and varied in length from 45 to 75 bp.


title: University of Wuerzburg Listeria monocytogenes PTS 1K microarray version1

status: Public on Mar 08 2008

city: Würzburg

first: Regina

last: Stoll

address: Biozentrum, Am Hubland

country: Germany

institute: Lehrstuhl für Mikrobiologie

organism: Listeria monocytogenes

manufacture_protocol:
BF-Biolabs designs and produces custom-made microarrays for gene-identification, SNP- and gene-expression analysis. With respect to certain scientific or diagnostic tasks, BF-Biolabs uses specialized microarray production processes to achieve optimal specificity and sensitivity.
size of slide: 27 x 8 mm
Origin (x,y): 24,3mm ; 8,5 mm
Spot distance: 500 µm
replica: 3
subarrays: 12
size of on subarray: 8 x 8 spots


title: NimbleGen Homo sapiens HG18 RefSeq promoter array_386K

status: Public on Mar 31 2008

city: Seattle

first: Vitalina

last: Komashko

state: WA

address: 1100 Fairview Ave N

institute: Sage Bionetworks

organism: Homo sapiens


title: University of Adelaide microarray facility Exiqon LNA miRNA microarray_version8.1

status: Public on Mar 30 2008

city: St Lucia

first: Chung Fai

last: Wong

state: Q

address: 306 Carmody Rd

department: Livestock Industries

country: Australia

institute: CSIRO

organism:
Arabidopsis thaliana
Caenorhabditis elegans
Drosophila melanogaster
Gallus gallus
Macaca mulatta
Homo sapiens
Bos taurus
Mus musculus
Rattus norvegicus

first: ChungFai

first: Ross

middle: L

last: Tellam

manufacture_protocol: Arrays were spotted according to manufacturer's instructions by the University of Adelaide microarray facility.


title: AppChip2 (NRC-IBS Actinobacillus pleuropneumoniae L20)

status: Public on Mar 29 2008

city: Ottawa

first: John

middle: H

last: Nash

state: Ontario

address: 100 Sussex Drive

department: Institute for Biological Sciences

country: Canada

institute: National Research Council

organism: Actinobacillus pleuropneumoniae serovar 5b str. L20

description: PCR primers were designed for 1954 ORFs from the completed genomic sequence of Actinobacillus pleuropneumoniae L20 which comprised 2012 ORFs. Good amplicons of length greater than 160 nt were obtained for 1846 ORFs representing 92% coverage of ORFs. All amplicons are spotted in duplicate on the microarray and sheared total genomic DNA from A. pleuropneumoniae L20 and porcine DNA were spotted in the bottom row of each subarray as controls.

first: Wendy

middle: A

last: Findlay

first: Brian

last: Agnew

first: Simon

last: Foote

manufacture_protocol: DNA microarrayer (Bio-Rad) equipped with a 48-pin print-heads that uses "quill" pin technology (TeleChem / ArrayIt).


title: Novachip human 34.5k

city: Basel

first: Florent

last: Baty

address: Petersgraben 4

department: Pneumology

country: Switzerland

institute: Universitätsspital Basel

description:
Novachip is an evanescent resonator microarray platform. The approach takes advantage of a phenomenon that has been attributed as abnormal reflection. Excitation photons incident on the chip under resonance conditions couple into a thin corrugated metal oxide surface at the site of incidence. As a result of the transducer geometry, the energy is locally confined into the thin corrugated layer of high refractive index material. Consequently, strong electromagnetic fields are generated at the surface of the chip. The effect has been attributed as evanescent resonance and leads to increased fluorescence intensity of chromophores close to the surface. The effective field strength can be increased up to 100-fold by the confinement of the available excitation energy, depending on the optical properties of the used optical detection system. The Novachips used for the experiments described in the present paper have a resonance angle of 2° with respect to normal for TE polarized light of 633 nm wavelength. The observed increase of fluorescence intensity with the used Agilent microarray laser scanner was about 5-fold compared to glass slides processed under identical conditions.
The slides were cleaned and the AROS human v3 oligonucleotide set from Operon Inc. was arrayed with a Microgrid printer at 23°C and 55-60% relative humidity (total approx. 37K features, print buffer 4x SSC / 0.001% Sarcosyl). Scatter light scans (Tecan Laser Scanner) were used to assess the quality of the printed slides ("salt images"). Slides were stored sealed until use.

first: Wolfgang

last: Budach

first: Dieter

last: Neuschäfer

manufacture_protocol:
Isolation and quality control of RNA
Lysis and homogeneization is performed with 1 mL pre-warmed (60°C) TRIzol Reagent (Invitrogen Cat. No. 15596-026) and 5 mm stainless steel beads (Qiagen Cat. No. 69989, 2 times 2 min at 25 Hz in tissue lyser Mixer Mill 300 for 2-3 mm Ø biopsies). The extraction is completed by adding Phase Lock Gel (Eppendorf Cat. No. 0032007.970) during the phase extraction. Molecular biology grade glycogen (Roche Diagnostics GmbH, Cat. N. 901393) is added to the aqueous phase during the precipitation step. After purification step on RNeasy Microkit columns (Qiagen, Cat. No. 74004), the final cleaned total RNA is eluted in 14 µL of RNase free water and stored at -80°C. RNA levels, quality and purity are assessed with the use of RNA 6000 Nano and Pico assay on the Agilent 2100 Bioanalyzer.
Hybridization
A Tecan HS 4800 Hybridization station from Tecan, Inc. is used for prewash/hybridization/postwash of the microarrays. Prewash consists of 3 cycles with wash buffer at RT/75°C/50°C (each 20 s) followed by an additional 10 s wash with hybridization buffer at 50°C. One hundred L sample (100 ng labeled RNA) in hybridization buffer is then injected into the flow chambers at 50°C and agitated for 1 min. Subsequently, after 10 min at 75°C, the temperature is adjusted to 42°C for 16 h (agitation). The postwash consists in 4 cycles wash buffer at 42°C followed by an additional wash at 23°C (each 20 s). Finally, the slides are washed 3 times with diluted wash buffer at RT, dried in N2 stream, and scanned immediately with an Agilent LS fluorescence scanner (gain 80%).
Analysis of fluorescence images
The fluorescence images is analyzed by means of Array Pro (Mediacybernetics, Inc. US). Net signals is calculated by subtracting the 75 percentile of local corner background from trimmed mean of each spot (20% trimming on both sides of the intensity histogram). Individual samples are processed on separate slides in single color mode (Cy5). The 75 percentile of intensity histogram is adjusted to 200 counts (a.u.) for normalization of the microarrays. The image analysis is configured in a way that allowed an automated assessment of the quality of individual fluorescence spots (criteria: local fluorescence background, spots symmetry, presence in "salt image"/Print QC). Only microarrays with >98% qualified spots are used for further analysis.


title: CGH-SANGER 3K 8

status: Public on Mar 21 2008

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description:
The array contains 3657 distinct BAC and PAC sequences. The bacs were printed in 2 replicates. 3599 BACS are from the Sanger institute. 58 BACS were provided by K.U.Leuven Department CME (Belgium).
The bacs were amplified by DOP - PCR. In total the array design contains 7744 features printed in a layout of
4 meta rows, 4 meta columns, 22 rows per block and 22 columns per block.
This grid is printed twice on the glass slides allowing for two microarray assays per slide.

first: P

last: Van Hummelen

first: J

last: Vermeesch

manufacture_protocol:
MicroGrid Printing Protocol
Equipment:
1. Microgrid (Genomics Solutions, UK).
2. 384 microtiter plates (X7022, Genetix)
3. 16 MicroSpot quill pins - 10K (cat# BR001489, Genomics Solutions, UK)
4. Codelink slides (cat#: 30001100, GE Healthcare).
Printing 2 arrays of 4x4 blocks on 1 microscope slide:
1. Dissolve PCR products in 125mM Phosphate buffer, 0.000125% sarcosyl at concentrations ranging between 300 ng/ul and array in 384 microtiter plates.
2. Set spotter settings for 2 arrays of 4x4 blocks printed with 16 pins: column pitch = 185 um, row pitch = 185 um; Humidity 55%; 61 spots per source visit.
3. Make sure room temperature is between 20-24 degrees Celsius.
4. Place microtiter plates in the plate hotel with A1 in front left corner.
5. Place 60 to 120 slides on the slide-deck.
6. Start spotting early in the morning and stop spotting procedure at end of the day and remove pin set. Leave spotter overnight with vacuum and humidity settings on. Continue spotting the next morning until all plates are printed.
7. After spotting, incubate the slides in humid chamber with saturated NaCl for 24 to 72 hours.
8. Block 1%NH4OH.
9. Slides can be stored for at least 6 months in a dry-cabinet.


title: University of Alberta MAF Operon E. coli Genome Oligo Set Version 1.0 21k

status: Public on Mar 14 2008

city: Jefferson

first: Christopher

last: Elkins

state: AR

address: 3900 NCTR Drive

department: Microbiology

institute: FDA National Center for Toxicological Research

organism: Escherichia coli

manufacturer: University of Alberta (Canada) Department of Biological Sciences Microarray and Proteomics Facility

manufacture_protocol:
3x6K E. coli microarray on Corning epoxide slides.
Each E. coli slide contains 5,978 oligos and a control set of 12 positive and 12 negative controls in a 4 by 4 block of sub-arrays which are printed in triplicate filling the slide surface with a total of 19086 spots printed at 200 um spacing in both the horizontal and vertical direction.
The oligos are dissolved to a final concentration of 18.75 uM in 150 mM NaPO4 buffer (pH 8.7) prior to printing.
The Operon E. coli Genome Oligo Set Version 1.0 consists of 5,978 70mer probes representing three strains of E. coli. The respective numbers of open reading frames represented in the array are as follows: 4,289 ORFs in K12, 5,029 ORFs in O157:H7 (EDL933), and 4,836 ORFs in O157:H7 (Sakai). All 5,978 probes are designed within known and predicted ORFs. For this probe set design, Operon employed state-of-the-art methods and proprietary software.
All probes are Tm normalized to 75oC (+/- 5oC) and have a 5' amino linker.


title: Zebrafish (Danio rerio) Compugen 16K spotted array

first: Darrin

middle: F

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

institute: Institute for Molecular Bioscience, Uni of Qld

organism: Danio rerio

description: The Compugen 16K Danio rerio was used in the manufacture of this set.  The genes were annotated manually to update the descriptions to a more in depth and comprehensive level.


title: Rosetta/Merck Mouse JAX array 1.0 microarray

first: Amit

middle: V

last: Kulkarni

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

description:
Oligonucleotide array on glass.
Contains junction probes

distribution: commercial

last: Castle

manufacture_protocol: See manufacturer's website


title: UT Austin Iyer yeast whole genome platform

status: Public on Mar 17 2008

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

manufacture_protocol: Please refer to the Stanford Functional Genomics Facility website for all manufacture details.


title: Nevada Cancer Institute HG18 RefSeq Promoter tiling array 386K

status: Public on Mar 07 2008

city: Las Vegas

first: Yupo

last: Ma

state: NV

address: 1 Breakthrough Way

institute: Nevada Cancer Institute

description:
Source: UCSC
Build: HG18
Probe Length: 50-75mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
Recommended Storage: Store arrays desiccated at room temperature.

manufacture_protocol: Please see NimbleGen website


title: Hannon/CSHL-mouse-Illumina 1G sequencing-oocyte small RNAs

status: Public on Mar 28 2008

city: Cold spring Harbor

first: ravi

last: Sachidanandam

state: NY

address: 1 bungtown road

institute: Cold Spring Harbor Laboratory

technology: other

description: Solexa/Illumina 1G sequencing platform. Illumina Inc. San Diego, CA

distribution: virtual

manufacture_protocol: not applicable


title: Candida albicans ChIP-CHIP array

city: Montreal

first: Hugo

last: Lavoie

state: Quebec

address: 6100 Royalmount

department: Genetics

institute: CNRC-IRB

organism: Candida albicans

manufacturer: National Research Council Canada - Biotechnology Research Institute

first: Andre

last: Nantel

first: Jean-Sébastien

last: Deneault

first: Mélanie

last: Arbour

first: Herve

last: Hogues

first: Malcolm

last: Whiteway

manufacture_protocol:
Probe design was done using a sliding window of 70 bp moved from the 3' -> 5' end of the target sequence. Self-annealing was calculated at each position as well as the GC count. A pre-computed cumulative mask of all the significant alignments found in the genome was made to favour regions that are unique for each genomic region.
Oligos were resuspended at 22 µM concentration in 50% DMSO and spotted on Corning Ultragaps slides with a BioRad ChipWriter Pro microarray spotter equipped with 48 SMP3 pins (Telechem ArrayIt). UV crosslinking (600 mJ) was performed in a Stratagene UV Stratalinker.


title: Agilent-013910 Mouse Proximal Promoter ChIP-on-Chip Set, Microarray 1 of 2 (G4482A)

status: Public on Mar 19 2008

city: Palo Alto

last: Agilent Technologies

state: CA

institute: Agilent Technologies

description:
The Mouse Proximal Promoter ChIP-on-chip microarray set contains high-resolution, high performance 60-mer oligonucleotide microarrays that allow the location analysis of DNA binding proteins to promoter regions spanning    -1.0KB upstream to +0.3KB downstream of the transcriptional start sites. The two slide set provides coverage for ~17,000 of the best defined mouse transcripts.

Arrays of this design have barcodes that begin with 16013910 or 2513910.

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: FGRc UPR-RRP/RUM D. Hansenii Array

status: Public on Mar 15 2008

city: San Juan

first: Sandra

last: Pena de Ortiz

state: PR

address: Gandara Ave., JGD Bldg. Rooms 108, 204

department: Department of Biology

country: Puerto Rico

institute: University of Puerto Rico

organism: Debaryomyces hansenii

last: Peña de Ortiz

first: Michelle

middle: M

last: Martinez Montemayor

first: Govind

last: Nadathur

manufacture_protocol: Whole genome mRNA sequences from D. hansenii were downloaded in FASTA format from GenBank (http://www.ncbi.nih.gov) and saved into a text file. Sequences in text format were downloaded to the eArray web design application from Agilent Technologies (Santa Clara, CA) for probe design.  Two probes per target were designed in the sense orientation with a 3’ bias using base composition methodology as recommended by the manufacturer for gene expression arrays.  Using comparative genomics, probes were aligned to other yeast sequences and were classified according to their similarities: highly similar, similar, some similarities, weakly similar, and no similarities, all based on sequence homologies.  Probes were tested for self-complementarities, specificity, and cross reactivity. The best probes were used for generating a custom microarray arranged in an 8 X 15K format using a randomized lay out.  Each array included 12,640 probes, 60 bp of length, 459 positive (spike-in) controls, and 77 negative control probes distributed across the array.  Positive controls were used as a quality control of the cRNA synthesis, labeling, and hybridization steps, whereas negative controls were included to estimate fluorescence background and background variance.


title: L.interrogans PCR-based array version 1

city: shanghai

first: xiaokui

last: guo

state: shanghai

address: ChongQing nan Road 280

department: Department of Microbiology and Parasitology

country: China

institute: Shanghai Jiao Tong University

organism: Leptospira interrogans

description: The genechip is a glass-based DNA chip. The chip has 11664 spots, including 3290 L.interrogans genes, 19 positive  and 10 negative controls. The chip is divided into 36 sub-matrix. There is 18*18 spots in every sub-matrix.

first: Yue-Ying

last: Sheng

first: Jin-Hong

last: Qin

manufacture_protocol:
1.PCR-amplified 3290 CDSs (accession number GB: AE010300 for CI and GB: AE010301 for CII) of L.interrogans 56601 and purified in 96-wells plates.
2.PCR products are arrayed in 384-well flat-bottom plates. Each well contains 10 μl(about 2μg)  PCR products  finally purified and dissolved in 50% DMSO in TE at concentrations of 200ng/ul.
3.Centrifuge plates at 2000 rpm for 3 minutes.
4.Spotting the genechip using OmniGrid Arraying System robotically. Each products were arrayed in triplicate.
5.Hydrate the chip for 30 min in Arraying System, dry the chip for 2 hour at room temperature
Block the chio for 15min with blocking buffer, wash it with water, dry it at room temperature.


title: GE Healthcare/Amersham Biosciences CodeLink™ UniSet Mouse I Bioarray

city: Pittsburgh

first: Prabir

last: Ray

state: PA

address: 3459 Fifth Avenue

department: Medicine/Pulmonary

institute: University of Pittsburgh

description: CodeLink UniSet Mouse I Bioarray contains single-stranded oligonucleotide probes derived from a large majority of publicly available, well-annotated mRNA sequences found in the Mouse UniGene set of unique clusters. Each bioarray contains probes for an independent assay of all 10,000 genes in the set.

manufacture_protocol: see the manufacturer's wesite


title: Pork Quality Operon 70-mer oligo array

city: Ya'an

first: Mingzhou

last: Li

state: Sichuan

address: No.46  Xinkang Road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

organism: Sus scrofa

manufacturer: Oligos:Qiagen-Operon, Printed by: National Engineering Center for Biochip(Shanghai,China)

first: Xuewei

first: Li

last: Zhu

first: Yujiao

last: Guo

first: Lei

last: Chen

first: Qiang

first: Surong

last: Shuai

first: Anan

last: Jiang

first: Guangxi

last: Yang

first: Guoqing

last: Tang

first: Yanzhi

manufacture_protocol: The 152 probes from the Pig Genome Oligo Set and Extension V1.0 (OMAD Release: 04/13/04) representing 140 key genes involved in porcine muscle growth and adipose metabolism. The Qiagen 70-mer oligos designed from TIGR Tentative Consensus cDNA sequences and minimized cross-hybridization. The probes are Tm normalized to 78ºC (±5ºC) and have a 5' amino linker. The probes were printed on GAPS II Slides（Corning）coated with amino-silane by OmniGrid 100（GeneMachine）,and post-processed according to the manufacturer's protocol.


title: SHFO

status: Public on Mar 26 2008

city: Paris

first: Karine

last: Clement

address: place du parvis Notre-Dame

department: Service de Medecine et Nutrition

country: France

institute: Hotel-Dieu

manufacturer: Joan,,Hebert; SFGF, 2255, CCSR, Stanford, Ca, USA, 94025; 650-736-0075; jhebert@genome.Stanford.edu

manufacture_protocol: Material is transferred from microtiter plate wells to the slide surface by an automated print head


title: Human 19K v1.0

city: Sydney

first: Paromita (Romi)

last: Das Gupta

state: NSW

address: High St, Randwick

department: Dept Surgery

institute: Prince of Wales Hospital

description: Please the Adelaide Microarray Facility website

manufacture_protocol:
CompuGen Human OligoLibrary V1.0 (cat# HUMLIB384) comprising 18,861 60-mers representing 18,664 unique genes + 197 controls. Each oligo has a 5' C6-amino linker enabling covalent attachment to the substrate. An additional locally made control plate was also spotted. Probes were arrayed onto Corning Epoxide slides using 32 (8x4) tungsten pins in a Versarray Chipwriter Pro robot. Each pin printed an array of 625 spots arranged in 25 rows by 25 columns (20000 features per array).
Support Coated-glass
Coating Epoxide


title: Intestinal epithelial crypt and villi in conventional relative to germfree pig

status: Public on Mar 04 2008

city: Urbana

first: H

middle: Rex

last: Gaskins

state: IL

address: 1207 W Gregory Dr

department: Animal Sciences

institute: UIUC

manufacturer: University of Illinois at Urbana-Champaign, Urbana IL

first: Shankar

middle: R

last: Chowdhury

first: Dale

middle: K

last: King

first: B

last: Willing

first: Mark

last: Band

first: Adrienne

middle: B

last: Lane

first: Juan

middle: C

last: Marini

first: Laurie

last: Rund

first: John

middle: E

last: Beever

first: Larry

last: Schook

middle: J

last: Loor

first: Andrew

middle: G

last: Van Kessel

manufacture_protocol: Eight cesarean-derived piglets from two litters were randomly assigned to two GF isolators. Four piglets from one isolator were conventionalized with fecal slurry. On d 14, two cm long segments starting at the 85% of SI length measured distally of the pyloric sphincter were identified and embedded in Shandon Cryomatrix™ (Thermo Electron Corporation, Pittsburgh, PA). Microdissection and capture of villus and crypt cell populations were performed immediately on a Pixcell II ® LCM System (Arcturus) according to the manufacturer instructions. Two hundred to five hundred cells were collected onto a CapSure H LCM Cap (Arcturus) using the following parameters: spot size, 7.5 μm; power, 50 mW; pulse duration 2.00 s. Total RNA was isolated from laser captured villus and crypt cells using the PicoPureTM RNA isolation Kit (Arcturus) according to manufacturer’s recommendations. RNA from each sample was subjected to 2 rounds of amplification using the RiboAmpTM RNA linear amplification kit (Arcturus). Subsequently, RNA was reverse-transcribed into cDNA incorporating a T7 promoter. The cDNA was eluted with 16 μl of elution buffer and in vitro transcribed into amplified anti-sense RNA with a T7 RNA polymerase incorporating amino-allyl-UTP (Ambion, Austin, TX). The amplified anti-sense (aRNA) was labeled with Cy3 or Cy5 dyes. Each of the 16 cell populations was reversed labeled with Cy3 and Cy5 to account for dye labeling bias, resulting in 32 target samples for microarray hybridization. Porcine oligonucleotide set represents 13,297 porcine cDNAs and ESTs. A reference design was used in which each of the experimental samples was cohybridized with the reference sample that contained equal amounts of all the RNA samples used in the experiment. Single-spotted oligos were printed on GAPS II slides (Corning, Corning, NY) at the W. M. Keck Center for Comparative and Functional Genomics, University of Illinois. Following hybridization and washing, slides were scanned immediately for both dye channels with an Axon 4000B (Molecular Devices, Union City, CA) dual-laser confocal scanner and images were processed using GenePix v6.0 software (Molecular Devices).


title: Affymetrix GeneChip Mouse Genome 430 2.0 Array [CDF: Mm_UNIGENEG_8]

city: Heidelberg

first: Inka

last: Zschiedrich

address: Im NeuenheimerFeld 280

department: Molecular Metabolic Control

institute: German Cancer Research Center Heidelberg

description: CDF file was created by Microarray Lab at the Molecular and Behavioral Neuroscience Institute at the University of Michigan.  For the CDF file based on Unigene: A probe must hit only one genomic location; Probes that can be mapped to the same target sequence in the correct direction are grouped together in the same probe set;Each probe set must contain at least three oligonucleotide probes and probes in a set are ordered according to their location in the corresponding exon.

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

manufacture_protocol: This array is identical to GPL1261 but a custom, remapped CDF environment is used to extract data. This is version 8 of the remapped CDF. The CDF for various platforms can be found at the link below.


title: UCD AMDandekar CitrusClusteredComplimentHKfinal_1647_12k oligo array

status: Public on Mar 05 2008

city: Davis

first: Abhaya

last: Dandekar

address: One Shields Ave

department: Plant Sciences

institute: University of California, Davis

organism: Citrus sinensis

description:
Probe sequences are included in the raw data files linked to the related Sample records.  Gene targets without NCBI accessions in the Platform data table were not submitted to a public sequence database. They were derived from assembly citrus04122004 of the citrus EST database at the Core Genomics Facility (CGF), College of Agricultural and Environmental Sciences at UC Davis (http://cgf.ucdavis.edu/). However, the gene targets of this study are not found in the current assembly curated by CGF. In all but a few cases, targets were contigs assembled from one or more ESTs. In these cases, the sequence identifier given in the Platform data table consists of seven digits, beginning with '104' or '105'. (In the CGF database, these identifiers also contained 'CTG' preceding the seven digits.) Target identifiers that are not seven-digit numbers beginning with '104' or '105' were singletons in the assembly. In the Sample raw data files, the sequence identifier given in the Platform data table, the one associated with the probe, appears in the 'Name' column. In the latter, the beginning and ending positions of the oligo are appended with underscores to the identifier. Expression of 28 target sequences on the array were reported in detail in Goudeau et al. 2008 (doi:10.1016/j.plantsci.2007.11.017). References to contigs in the published article use identifiers with 'S' in place of '104' in the seven-digit identifiers used here.

The Platform data table reflects a condensed representation of the array's replicate features.  The full array layout representing all of the individual features (and identifier annotations eg, oligo sequence, positional information, etc.) is linked as a supplementary file at the foot of this record.

manufacture_protocol:
The array had four elements: genes of interest, spike-ins, negative controls, and housekeeping genes. All sequences were designed to eliminate cross-hybridization potential. In addition, probes for a given sequence were distributed across the array to minimize effects of local binding conditions. Included were housekeeping sequences for GAPDH (glyceraldehyde-3-phosphate dehydrogenase), β-tubulin, and an 18S ribosomal subunit. These were identical to those validated with real time quantitative PCR (RTQPCR). Also included were 16 negative controls, each represented by two probes for a total 32 features. These were chosen by Combimatrix based on the absence of sequence homologs in plants. 18 additional non-plant genes were selected by Combimatrix as positive “spike-in” controls. Spiked RNA was included in the hybridization reaction, with three genes each at six distinct concentrations. Each positive control was represented by ~80 probes for a total 1406 spike-in features. This large pool of spike-ins provided a strong normalization tool and identified featureless regions on the chip (given the relatively low number of genes of interest) which interfere with hybridization.
The experimental portion of the array contained 366 genes of interest, each represented by 15 sense and 15 antisense probes, for a total of 10,567 features.
Using CustomArray 12k (oligonucleotide), probes were synthesized directly on the chip surface, composed of a proprietary porous reaction layer. 12k arrays consist of 12,000 user definable oligonucleotide features, 35-40 nt optimum. Under each probe, a semiconductor electrode used electrochemical detritylation to control sequence synthesis at that spot without a physical mask as in lithographic synthesis. The process yields a 44 micron feature with 1.5 picomole sensitivity. The arrays were designed for one-color biotinilated hybridization experiments.


title: CGH-SANGER 3K 6 & 7

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

institute: VIB

description:
The array contains 3587 distinct BAC and PAC sequences.  The bacs were printed in 2 replicates. 3529 BACS are from the Sanger institute.  58 BACS were provided by K.U.Leuven Department CME (Belgium).
The bacs were amplified by DOP - PCR. In total the array design contains 7744 features printed in a layout of
4 meta rows, 4 meta columns, 22 rows per block and 22 columns per block.
This grid is printed twice on the glass slides allowing for two microarray assays per slide.

first: P

last: Van Hummelen

first: J

last: Vermeesch

manufacture_protocol:
MicroGrid Printing Protocol
Equipment:
1. Microgrid (Genomics Solutions, UK).
2. 384 microtiter plates (X7022, Genetix)
3. 16 MicroSpot quill pins - 10K (cat# BR001489, Genomics Solutions, UK)
4. Codelink slides (cat#: 30001100, GE Healthcare).
Printing 2 arrays of 4x4 blocks on 1 microscope slide:
1. Dissolve PCR products in 125mM Phosphate buffer, 0.000125% sarcosyl at concentrations ranging between 300 ng/ul and array in 384 microtiter plates.
2. Set spotter settings for 2 arrays of 4x4 blocks printed with 16 pins: column pitch = 185 um, row pitch = 185 um; Humidity 55%; 61 spots per source visit.
3. Make sure room temperature is between 20-24 degrees Celsius.
4. Place microtiter plates in the plate hotel with A1 in front left corner.
5. Place 60 to 120 slides on the slide-deck.
6. Start spotting early in the morning and stop spotting procedure at end of the day and remove pin set. Leave spotter overnight with vacuum and humidity settings on. Continue spotting the next morning until all plates are printed.
7. After spotting, incubate the slides in humid chamber with saturated NaCl for 24 to 72 hours.
8. Block 1%NH4OH.
9. Slides can be stored for at least 6 months in a dry-cabinet.


title: HPCGG_human_19k_Compugen_v1.0

status: Public on Mar 02 2008

city: Boston

first: Jason

middle: Blair

last: Warner

state: MA

address: 12 Carriage DrHarvard Medical School New Research Building, Room 466D

institute: Brigham & Women's Hospital / Harvard Medical School

first: Anthony

last: Philippakis

first: Savina

last: Jaeger

first: Fangxue

middle: S

last: He

first: Jolinta

last: Lin

first: Martha

last: Bulyk

manufacture_protocol: Compugen's human OligoLibrary Release 1.0 was printed by Harvard Medical School - Partners Healthcare Center for Genetics and Genomics (HPCGG).


title: GPC Biotech Bacillus subtilis 4K

status: Public on Mar 01 2008

city: Martinsried

first: Christoph

last: Schaab

address: Fraunhoferstrasse 20

institute: GPC Biotech AG

organism: Bacillus subtilis

description: The array contains 4205 oligonucleotide probes representing the complete Bacillus subtilis genome. The probes were spotted in duplicates onto nylon membranes.

first: Matthias

last: Borgmann

first: Bernd

last: Hutter

first: Igor

last: Ivanov

first: Hannes

last: Loferer

manufacture_protocol:
DNA fragments for open reading frames (ORFs) were computationally selected within the first third (proximal to the 5' end) of the coding region. Each fragment was checked for its uniqueness; up to 80% similarity with any other sequence on the genome was the maximum allowed. No DNA stretch greater than 24 nucleotides was identical to any other such stretch (with the exception of ORFs shorter than 140 bp, which were used in their entirety). Two or three fragments were generated for ORFs longer than 3,000 bp. Each fragment was prepared by annealing two 80-base oligonucleotides designed to overlap at their 3' ends to form a 20-bp duplex. An extension reaction was then performed to yield a full-length product of 140 bp. Briefly, each pair of
oligonucleotides was annealed in 20 mM Tris (pH 8.8)–10 mM KCl–10 mM
(NH4)2SO4 and extended overnight at 65°C in the presence of 1.5 mM (each) deoxynucleoside triphosphate, 10 mM MgSO4, 5x Q solution (Qiagen), and 8 U of Bst DNA polymerase (New England Biolabs, Beverly, Mass.).
Arrays were spotted using a robotic system from KAYBEE (UK) on a nylon membrane Biodyne B (Pall, UK). The spotting head contained 384 solid flat-bottom pins of 250 µm in diameter constructed in a format complementary to the polystyrene 384-well plates. The size of each spot, estimated by spotting ink and fluorescently labelled DNA, was ~350 µm and the distance between each spot was 833 µm.


title: Plymouth Marine Laboratory 454 sequences, 439K

status: Public on Feb 08 2008

city: Plymouth

first: Jack

middle: Anthony

last: Gilbert

state: Devon

address: Prospect Place

country: United Kingdom

institute: Plymouth Marine Laboratory

organism: marine metagenome


title: Hofmann_UCSB_Mytilus_2.5K_v1.0

city: Columbia

first: Sean

middle: P

last: Place

state: SC

address: 715 Sumter St.

department: Biological Sciences

institute: University of South Carolina

organism: Mytilus californianus

manufacturer: Oregon State University - Center for Genome Research and Biocomputing

first: Gretchen

last: Hofmann

first: Michael

last: O'Donnell

manufacture_protocol:
1. Samples are provided in 384-well plates with matching lids (Genetix part # X7022) at a concentration of 0.15 µg/µl for PCR products.
2. Samples must be in a starting volume of 15 µl of spotting buffer (1.5M Betaine, 3xSSC for Corning UltraGaps slides).
3. cDNAs are spotted on Corning ULTRAGaps (25 mm x 75 mm) using the Biorobotics Microgrid II.
4. printed slides are held in a desiccator for 24-48 hours after printing and X-linked at 225 mJ for cDNA/PCR products.


title: Agilent-013911 Mouse Proximal Promoter ChIP-on-Chip Set, Microarray 2 of 2 (G4482A)

last: Agilent Technologies

description:
The Mouse Proximal Promoter ChIP-on-chip microarray set contains high-resolution, high performance 60-mer oligonucleotide microarrays that allow the location analysis of DNA binding proteins to promoter regions spanning    -1.0KB upstream to +0.3KB downstream of the transcriptional start sites. The two slide set provides coverage for ~17,000 of the best defined mouse transcripts.

Arrays of this design have barcodes that begin with 16013911 or 2513911.

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: Candida albicans expression array

first: Hugo

last: Lavoie

first: Andre

last: Nantel

first: Jean-Sébastien

last: Deneault

first: Mélanie

last: Arbour

first: Herve

last: Hogues

first: Malcolm

last: Whiteway


title: Soybean 18k-A array

city: London

first: Mohan

last: babu

state: Ontario

address: 1391 Sandford

department: Virology

institute: AAFC

organism: Glycine max

manufacturer: Custom made array from University Illinois

manufacture_protocol: Soybean 18K-A array is manufactured by Lila Vodkin's lab, University of Illinois


title: TIGR_RAT_target_oligoarray_1

city: Washington, DC

first: Norman

middle: H

last: Lee

state: DC

address: 2300  I Street, N.W.

department: Pharmacology & Physiology

institute: The George Washington University Medical Center

organism: Rattus norvegicus

description: The arrays are printed on the barcoded side of the slide with approximate distance from the top, left side and right side of 3 mm. The array consists of 48 grids with each grid representing 576 spots in a 24 x 24 arrangement.

first: Bina

last: Joe

first: Bryan

last: Frank

manufacture_protocol:
TIGR Department of Mammalian Genomics protocol.
Synthesized oligos were resuspended at 50 uM in water. They were then combined with the printing buffer to a final concentration of 25 uM and final buffer percentage of 50% DMSO. The printing plates were arrayed onto aminosilane glass slides on a custom-built microarray robot from Brooks Automation (Cambridge, MA). Printed arrays were UV cross-linked to ensure binding.


title: GeneChip Human Tiling 1.0R Array set (14) - NCBI build 36

status: Public on Dec 31 2007

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

country: Japan

institute: The University of Tokyo

description:
For data analysis of the associated Samples, we calculated MAT scores based on the hyridization intensity data of the probes within 500bp windows. The coordinate column in the Platform data table represents the chromosome coordinates for the 500bp window center positions.

The supplementary files (linked below) also report the 500bp window start and end positions (and also sequence of 500bp unit region for used for analysis).

first: Kerstin

last: Wendt

first: Keisuke

last: Yoshida

first: Takehiko

last: Itoh

first: Masashige

last: Bando

first: Birgit

last: Koch

first: Erika

last: Schirghuber

first: Hiroyuki

last: Aburatani

first: Jan-Michael

last: Peters

manufacture_protocol: Oligonucleotide probes are synthesized in situ complementary to each corresponding sequences. 35 base pair resolution array.


title: GeneChip Human Tiling 1.0R Array set (12) - NCBI build 36


title: GeneChip Human Tiling 1.0R Array set (10) - NCBI build 36


title: Utz Lab human high-throughput immunophenotyping using transcription (HIT) array

status: Public on Mar 03 2008

city: Stanford

first: Michael

middle: George

last: Kattah

address: 269 Campus Dr., CCSR 2250

department: Medicine

institute: Stanford University

description:
This method employs a panel of monoclonal antibodies, each tagged with a unique oligonucleotide sequence that serves as a molecular barcode.  After staining a sample, T7 polymerase amplifies the tags which are then hybridized to a DNA microarray (see data table below) for indirect measurement of each analyte.
The Platform data table reflects a condensed representation of the array's replicate features.  The full array layout representing all of the individual features is linked as a supplementary file at the foot of this record.

first: John

last: Coller

first: Neekaan

last: Oshidary

first: Regina

last: Cheung

first: Paul

last: Utz

manufacture_protocol: For the microarrays, we spotted amine-modified 30mer oligonucleotides onto NHS-ester coated Codelink slides (GE Healthcare) at a concentration of 50 μM in 50 mM sodium phosphate buffer pH 8.5 (Sigma-Aldrich) using a BioRad VersArray Compact Microarrayer (BioRad) and processed the slides according to the manufacturer’s instructions.


title: GeneChip Human Tiling 1.0R Array set (7) - NCBI build 36


title: GBC_ FOAR03-S1-0002

city: Vancouver

first: Juergen

last: Ehlting

state: BC

address: 321 - 2185 East Mall

department: Michael Smith Laboratories

institute: University of British Columbia

organism: Arabidopsis thaliana

manufacturer: Opern Array-Ready Oligo Set v1, printed at the GenomeBC Gene Array Facility at The Prostate Centre, Vancouver BC, Canada

first: Jeff

last: Zeznik

first: Brian

last: Ellis

first: Carl

last: Douglas

first: Joerg

last: Bohlmann

manufacture_protocol: The Arabidopsis Genome Oligo Set Version 1.0 (Operon Biotechnologies, Huntsville, AL, USA) consists of 26090 70mer oligonucleotides (http://operon.com/arrays/oligosets_arabidopsis.php).  As positive controls, we included oligos for twelve housekeeping genes (Operon). As negative controls, we synthesized four oligonucleotides specific for human genes with no similarity to any Arabidopsis gene and included twelve oligonucleotides with no similarity to any Arabidopsis gene (Operon). We used a PCR amplified green fluorescent protein (GFP) cDNA (Invitrogen, Carlsbad, CA, USA) as an orientation marker. Oligonucleotides were resuspended in 384 well flat bottom plates (Nunc, Rochester, NY, USA) to a concentration of 100 mM in 3 x SSC. Oligos were printed on MicroGrid II robots using Microspot 10k pins (Biorobotics, Huntington, UK) depositing approximately 0.5 nl (0.0075 pmole) of each oligo onto EZ rays aminosilane slides (Apogent Discoveries, Hudson, NH, USA). The pitch of the grid used for this library was 0.2 mm. Oligos were UV cross linked at 3000 x 100 μJ using a UV Stratalinker 2400 (Stratagene, La Jolla, CA, USA).  We spotted single spots for the 26090 target oligonucleotides; in addition, each subgrid contained six replicate spots of each of the four human negative controls, three spots of equally distributed Operon negative controls, a single spot of each of the twelve house keeping controls, and GFP marker on each corner of the subgrid. The location of each oligo is given in this platform file.


title: GeneChip Human Tiling 1.0R Array set (5) - NCBI build 36

first: Katsuhiko

last: Shirahige

first: Kerstin

last: Wendt

first: Keisuke

last: Yoshida


title: HG18 promoter 2 array set (2 of 2)

city: Atlanta

first: Colleen

middle: D

last: McCabe

state: GA

address: 615 Michael St

institute: Emory University

manufacture_protocol: see Nimblegen website


title: University of Alberta MAF Operon E. coli Genome Oligo Set Version 1.0

city: Jefferson

first: Christopher

middle: A

last: Elkins

state: AR

address: 3900 NCTR Drive

department: Microbiology

institute: FDA National Center for Toxicological Research

manufacture_protocol:
3x6K E. coli microarray on Corning epoxide slides.
Each E. coli slide contains 5,978 oligos and a control set of 12 positive and 12 negative controls in a 4 by 4 block of sub-arrays which are printed in triplicate filling the slide surface with a total of 19086 spots printed at 200 um spacing in both the horizontal and vertical direction.
The oligos are dissolved to a final concentration of 18.75 uM in 150 mM NaPO4 buffer (pH 8.7) prior to printing.
The Operon E. coli Genome Oligo Set Version 1.0 consists of 5,978 70mer probes representing three strains of E. coli. The respective numbers of open reading frames represented in the array are as follows: 4,289 ORFs in K12, 5,029 ORFs in O157:H7 (EDL933), and 4,836 ORFs in O157:H7 (Sakai). All 5,978 probes are designed within known and predicted ORFs. For this probe set design, Operon employed state-of-the-art methods and proprietary software.
All probes are Tm normalized to 75oC (+/- 5oC) and have a 5' amino linker.


title: HG18 promoter 2 array set (1 of 2)


title: SFGF HEEBO Human Set v1.00

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

institute: ULB

description:
Probes:
Constitutive Exonic Probes (30,718): that will recognize all known transcripts of a gene.
Alternatively Spliced / Skipped Exonic Probes (8,441): will recognize exons that are present in some, but not all transcripts of a gene.
Non Coding RNA Probes (196): recogning non-protein coding transcripts (ribosomal RNAs, miRNAs).
BCR / TCR Genic / Regional Probes (372): recognizing transcripts from genes that undergo somatic rearrangement.
Other Probes (843): recognizing human mitochondrion derived DNA sequences.

Controls:
A total of 4,189 controls are included in the set, including
Negative Controls (398 and 194 buffer only): Buffer only and 410 random sequences are positioned throughout the set to assist in determining background.
Positive Controls (864): recognizing a small subset of human transcripts.
Doped Controls (1,384): recognizing non-human sequences that can be spiked into RNA samples

last: Fero

manufacture_protocol:
The Human Exonic Evidence Based Oligonucleotide (HEEBO) array was developed by a group of researchers from Stanford University with collaborators from UCSF, Rockefeller, Basel, and the Stowers Institute. The oligonucleotide set consists of 44,544 70mer probes that were designed using a transcriptome-based annotation of exonic structure for genomic loci.
Tip configuration : 48 tip


title: GeneChip Human Tiling 1.0R Array set (13) - NCBI build 36

first: Takehiko

last: Itoh

first: Masashige

last: Bando

first: Birgit

last: Koch

first: Erika

last: Schirghuber

first: Hiroyuki

last: Aburatani

first: Jan-Michael

last: Peters


title: Nimblegen Human 5K promoter array 1

status: Public on Jan 25 2007

city: Columbus

first: Victor

middle: X

last: Jin

state: OH

address: 333 West 10th Ave

department: Biomedical Informatics

institute: OSU Medical Center

manufacture_protocol: described at Nimblegen http://www.nimblegen.com


title: 2005-04-04_Human_Promo_ChIP

status: Public on Jul 25 2006

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

first: Peter

last: Scacheri

manufacture_protocol: Nimblegen


title: GeneChip Human Tiling 1.0R Array set (11) - NCBI build 36


title: GeneChip ENCODEver2.0R Array - NCBI build 36

first: Jan-Micahel

manufacture_protocol: Oligonucleotide probes are synthesized in situ complementary to each corresponding sequences. 7 base pair resolution array.


title: GeneChip Human Tiling 1.0R Array set (8) - NCBI build 36


title: GeneChip Human Tiling 1.0R Array set (9) - NCBI build 36


title: GeneChip Human Tiling 1.0R Array set (6) - NCBI build 36


title: GeneChip Human Tiling 1.0R Array set (2) - NCBI build 36


title: GeneChip Human Tiling 1.0R Array set (4) - NCBI build 36


title: GeneChip Human Tiling 1.0R Array set (1) - NCBI build 36


title: Ambion Human_Mouse_Rat mirVANA miRNA Bioarray_1566V1

status: Public on Oct 12 2006

first: Carmen

last: Marsit

address: 665 Huntington Avenue

department: Genetics and Complex Diseases

institute: Harvard School of Public Health

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description:
Manufactured using GE Healthcare’s CodeLink (TM) 3-D Gel Matrix Technology
Surface type: non-adsorptive
Attachment: covalent
The mirVana miRNA Bioarrays are an Ambion product that is manufactured by GE Healthcare and incorporates the CodeLink™ 3-D Gel Matrix slide surface. This aqueous environment elevates the probes away from the surface of the slide, allowing for maximum interaction between the probes and targets.

first: Karl

middle: T

last: Kelsey

first: Karen

last: Eddy

manufacture_protocol:
CodeLink(tm) Activated Slides are designed to covalently immobilize amine-modified DNA for microarrays. They are easy to use and are compatible with most available arraying and scanning instruments. CodeLink Activated Slides are coated with a novel 3-D surface chemistry comprised of a long-chain, hydrophilic polymer containing amine-reactive groups. This polymer is covalently crosslinked to itself and to the surface of the slide. The crosslinked polymer, combined with end-point attachment, orients the immobilized DNA, and holds it away from the surface of the slide.
Technical specifications:
Slide dimensions: 25 × 75 × 1 mm
1× Printing buffer: 50 mM sodium phosphate at pH 8.5
Codelink slides are manufacured by SurModics and were formally sold as 3D-Link(tm) Activated Slides.


title: NKI-CMF Homo sapiens 35k oligo array

status: Public on Apr 20 2006

city: Amsterdam

first: Daoud

last: Sie

address: Plesmanlaan 161

institute: Dutch Cancer Institute

organism: Homo sapiens

manufacturer: Central Microarray Facility, NKI Amsterdam

first: W

last: Brugman

first: M

last: Heimerikx

first: D

first: A

last: Velds

last: Nieuwland

first: R

last: Kerkhoven

manufacture_protocol: The Human Genome Oligo Set Version 3.0 arrays contain 34,580 probes representing 24,650 genes and 37,123 gene transcripts. All oligos are 70-mer sequences. The arrays consist of 37632 features (oligos and controls) and are printed in a 28x28 subarray layout using 48 Biorobotic 10K-microspot pins. We use 14 different Bacillus subtilus sequences as spike-controls printed in triplo in every subarray.


title: GeneChip Human Tiling 1.0R Array set (3) - NCBI build 36

first: Katsuhiko

last: Shirahige

first: Kerstin

last: Wendt

first: Keisuke

last: Yoshida

first: Takehiko

last: Itoh

first: Masashige

last: Bando

first: Birgit