title: platform_2005-04-20_Human_60mer_1in2

status: Public on Aug 31 2007

city: Notre Dame

first: Randy

last: Jeffrey

state: IN

address: Rm 232, Galvin Life Sciences Bldg

department: Biological Sciences

country: USA

institute: University of Notre Dame

organism: Homo sapiens

technology: in situ oligonucleotide

distribution: custom-commercial

first: Winnie

last: Wang

first: Martin

last: Tenniswood

manufacture_protocol: 1.  Please Refer to Nimblegen Systems


title: TIGR PFGRC Salmonella condensed 2

city: Dallas

first: Palmy

middle: R

last: Jesudhasan

state: TX

department: Microbiology

institute: University of Texas Southwestern Medical Center

organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Salmonella enterica subsp. enterica serovar Typhi str. CT18

technology: spotted DNA/cDNA

distribution: non-commercial

first: James

last: Zhu

first: Suresh

middle: D

last: Pillai

manufacture_protocol:
PFGRC_SALM, with arrayer LUCIDEA, mode
Normal, replicates 2, repeats 1, slide_dips -1, machine cycles 552382,
pen id 10113, pen cycles -1, operator Robin, humidity control On,
humidity set point 65


title: DKFZ Homo sapiens 8k BAC-array

status: Public on Aug 30 2007

city: Heidelberg

first: Christof

middle: Simon

last: Schlaeger

state: BW

address: INF 580

department: Molecular Genetics (B060)

country: Germany

institute: DKFZ

first: Radlwimmer

last: Bernhard

first: Lichter

last: Peter

manufacture_protocol: Whole-genome BAC-array. Isolated BAC-DNA was amplified by two-step DOP-PCR. PCR products were dissolved in 3xSSC, 1.5M betaine and spotted as triplicates on epoxysilane-coated slides.


title: Spectral Genomics 2600 Human BAC array v. 1

status: Public on Aug 18 2007

city: Houston

first: Ralf

last: Krahe

address: 1515 Holcombe Blvd., Unit #1010

department: Cancer Genetics

institute: University of Texas M.D. Anderson Cancer Center

manufacture_protocol: Taken directly from the manufacture website:The 2600 Human BAC contains 2,632 nonoverlapping BAC clones from the RPCI BAC library. Approximately 60 picogram of each BAC is spotted in duplicate. The Bac span the genome at approxiamtely 1 Mb intervals. Genomic loci of all the BACs have been verified by Spectral Genomics by doing end sequencing from both ends, FISH verifying by at least a third party and by using the latest genomic build available. Spots are 250 microns across. Center to center spacing of spots is 300 microns. BAC arrays have been pre-treated and are ready for direct hybridization.


title: KRIBB Hansenula 11K v1.1

city: Daejeon

first: Min Jeong

last: Sohn

address: 52 Eoeun-dong, Yuseong-gu

department: Protein therapeutics research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

organism: Ogataea angusta

description: duplicate of 5760 genes

first: MinJeong

first: HyunAh

last: Kang

first: Ohsuk

last: Kwon

first: Doo-Byoung

last: Oh

first: YunWi

first: YongKyung

last: Kim

first: Min-Gon

first: KwanSeok

first: SangKi

last: Rhee

first: Gerd

last: Gellissen

manufacture_protocol: DNA spotted onto aldehyde-coated glass slide


title: GE Healthcare/Amersham Biosciences CodeLink UniSet Mouse I Bioarray 10K (2004)

status: Public on Aug 02 2007

city: Giessen

first: Hamid

last: Hossain

address: Gaffky Str. 20

department: University of Giessen

institute: Institute for Medical Microbiology

organism: Mus musculus

technology: spotted oligonucleotide

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.
CodeLink users can submit data to GEO by exporting tab-delimited text files from the CodeLink software. The

first: Irina

last: Fenic

first: Felix

last: Thierer


title: KRIBB Hansenula 17K v1.0

description: Triplicate of 5760 spots

manufacture_protocol: DNA spotted onto aldehyde-coated glass microscope slides


title: Agilent Homo sapiens 44k custom array

status: Public on Aug 28 2007

city: boston

first: kwok-kin

last: wong

state: MA

address: 44 binney street

department: medical oncology

institute: dana farber cancer institute

description: Good array

first: Cheng

last: FAN

manufacture_protocol: Agilent


title: Spectral Genomics 2600 Human BAC array v. 2

first: Ralf


title: ARCS_human_1040_BCv5

status: Public on Aug 21 2007

city: Seibersdorf

first: Martin

last: Lauss

state: Lower Austria

address: Mendelstrasse 1

department: Life Sciences

country: Austria

institute: ARC Seibersdorf research

manufacturer: ARC Research Centers__Molecular Diagnostics

first: Klemens

last: Vierlinger

first: Sandra

last: Szameit

first: Andreas

last: Weinhaeusel

first: Christa

last: Noehammer

manufacture_protocol: 65-mer sense-strand oligonucleotides (VBC-genomics and Illumina) plus Lucidea Scorecard controls were spotted onto an ARCS-Epoxy coated glass slide using the Omnigrid Arrayer (Gene Machines). Olignucleotides are 10 microMolar and are buffered in 0.1M NaPhosphate containing 0.01% SDS. Probes are replicated 4 times on the array


title: Murine 22K cDNA array version 33.1

status: Public on Aug 29 2007

city: Vienna

first: J. Andrew

last: Pospisilik

address: Dr. Bohr-gasse 3

institute: IMBA

manufacture_protocol:
Arraying
1. Transfer PCR reactions to 96-well V-bottom tissue culture plates (Costar).Add 1/10 vol. 3M sodium acetate (pH 5.2) and equal volume isopropanol. Store at -20 C for a 2 hours.
2. Centrifuge in Sorvall at 3500 RPM for 45 min. Rinse with 70% EtOH, centrifuge again and dry.
2. Resuspend DNA in 12ul 3X SSC for a 4 hours and transfer to flexible U-bottom printing plates.
4. Spot DNA onto poly-l-lysine slides with an arrayer.
Post processing.
1. Rehydrate arrays by suspending slides over a dish of warm ddH2O. (~1 minute)
2. Snap-dry each array (DNA side up) on a 100°C hot plate for 3 seconds.
3. UV X-link DNA to the glass by using a Stratalinker set for 60 milliJoules
4. Dissolve 5g of succinic anhydride (Aldrich) in 315mL of n-methyl-pyrrolidinone.
5. To this, add 35mL of 0.2M NaBorate pH 8.0 (made by dissolving boric acid in water and adjusting the pH with NaOH), and stir until dissolved.
6. Soak arrays in this solution for 15 minutes with shaking.
7. Transfer arrays to 95°C water bath for 2 minutes
8. Quickly transfer arrays to 95% EtOH for 1 minute.
9. Remove excess liquid from slides by spinning the rack of slides on microtiter plate carriers at 500rpm.


title: ARCS_human_1040_tc2

status: Public on Aug 24 2007

manufacture_protocol: 65-mer sense-strand oligonucleotides (VBC-genomics and Illumina) plus Lucidea Scorecard controlswere spotted onto an ARCS-Epoxy coated glass slide using the Omnigrid Arrayer (Gene Machines). Olignucleotides are 10 microMolar and are buffered in 0.1M NaPhosphate containing 0.01% SDS. Probes are replicated 4 times on the array


title: Murine 22K cDNA array version 30.1


title: Geobacter sulfurreducens PCA cDNA array (IAS_GGS3)

city: Rockville

first: Chun-Hua

last: Wan

state: MD

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

organism: Geobacter sulfurreducens PCA

description:
In the platform data table, the following FEAT_Name values are of controls with additional description:
FEAT_NAME	Description
RCP1_AF168390	A. thaliana root cap 1 protein (RCP1)-Control
rbcL_U91966	A. thaliana ribulose-1,5-bisphosphate (rbcL)-control
Cab_X56062	A. thaliana chlorophyll a/b-binding protein (Cab)-control
rca_M86720	A. thaliana RUBISCO activase (RCA)-control
TIM_AF247559	A. thaliana triosephosphate isomerase (TIM)-Control
NAC1_AF198054	A. thaliana NAC1 (NAC1)-control
LTP6_AF159803	A. thaliana lipid transfer protein 6 (LTP6)-control
LTP4_AF159801	A. thaliana lipid transfer protein 4 (LTP4)-Control
RPK_X58149	A. thaliana ribulose-5-phosphate kinase (PRK)-control
XCP2_AF191028	A. thaliana papain-type cysteine endopeptidase (XCP2)-Control
POSITIVE	Positive Control-mixture of PCR templates
NEG1_Baculovirus_Vector	Control
NEG2_Human_Dynein	Control

The Platform data table reflects the condensed array layout. The full array layout representing the individual 6x-spotted features is linked below as a Supplementary file (ie, GPL5768_full_array_layout.txt).

manufacturer: The Barbara Methé Laboratory of The Institute for Genomic Research (now the J Craig Venter Institute)

first: Barbara

last: Methe

manufacture_protocol: Following amplification and cleanup, amplicons were resuspended to a concentration of 100-200nM in 50% DMSO and printed onto slides using a Brooks Automation Systems (Cambridge, MA) array spotter. All amplicons were spotted six times per slide. Postprinting, all slides were cross-linked using a Stralinker UV cross-linker (Stragene) and stored under vacuum until use.


title: platform_2003-11-10_Human_60mer_1in4

first: Randy

last: Jeffrey

first: Winnie

last: Wang

last: Tenniswood

manufacture_protocol: 1.  Please refer to Nimblegen Systems


title: Human 30K 60-mer oligo array

status: Public on Aug 16 2007

city: London

first: Andrew

middle: E

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

country: United Kingdom

institute: University College London

description: hydrophilic polymer containing N-hydroxysuccinimide (NHS) ester reactive groups

first: Bauke

last: Ylstra

manufacture_protocol: The Human Release 2.0 oligonucleotide library, containing 60mer oligonucleotides representing 28830 unique genes as designed by Compugen (San Jose, CA, USA), was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). The oligonucleotides were dissolved at 10 microM concentration in 50 mM sodium phosphate buffer pH 8.5 and single spotted onto CodeLink slides (Amersham Biosciences), using an OmniGrid 100 microarrayer (Genomic Solutions, Ann Arbor, MI, USA) equipped with SMP3 pins (TeleChem International, Sunnyvale, CA, USA). After printing slides were processed and blocked prior to use according to the manufacturer's protocol.


title: YUSM (K. White) D. melanogaster cDNA array (II)

status: Public on Aug 15 2007

city: La Jolla

first: Dan

last: Zhou

state: CA

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

institute: University of California, San Diego, School of Medicine

organism: Drosophila melanogaster

description: PCR fragment array for Drosophila melanogaster

first: Jin

last: Xue

first: Kevin

middle: P

last: White

first: Gabriel

middle: G

last: Haddad

manufacture_protocol: PCR fragments of ~95% of the genes in D. melanogaster BDGP release 4.0 were spotted. Array has 8 rows of 4 blocks each, numbered 1-32 starting in the upper left and ending in the lower right. 16 pins used to print.


title: Baylor/AZ_Mouse_Cytokine_Array

status: Public on Aug 23 2007

city: Macclesfield

first: stephanie

middle: ann

last: roberts

state: Cheshire

address: Alderley Park

department: RIRA

institute: astrazeneca

description: R & D Systems mouse cytokine array represents a comprehensive collection of cytokines, chemokines and other immunomodulatory factors as well as the receptors for these categories of molecules. The array consists of 514 different cloned cDNAs, printed as PCR products, on a positively charged nylon membrane. The amplified cDNA sequences contain coding sequence, avoiding repetitive sequence elements that are often associated with untranslated regions. All the cDNA sequences are verified prior to PCR. Each cDNA is printed in duplicate with 10ng of DNA per spot. In addition, eight positive control "housekeeping" genes, six negative controls and mouse genomic DNA are included on the array.

distribution: commercial

first: Shuhua

last: Han

first: George

last: Booth

first: Peter

last: Newham

first: Rachel

last: Barlow

first: Stephanie

last: Raines

first: Biao

last: Zheng

manufacture_protocol:
The manufacturers recommend the purification of total RNA using Qiagen RNeasy Maxi Kit. If the mouse Cytokine-specific Primers are being used then isolation of poly (A)+ RNA is not necessary.
The protocol recommends that the quality of RNA is checked using a spectrophotometer and agarose gel electrophoresis, the RNA sample should only be used if it is not degraded and there is no evidence of genomic contamination. In this experiment total RNA was isolated from the mouse joint samples and quantified and quality checked pre and post DNAse treatment using Agilent Technologies 2100 Bioanalyzer.
Radiolabelled cDNA is generated using Mouse Cytokine-specific primers. The cDNA labelling reaction involves two steps. First, the gene-specific primers are annealed to the RNA sample. Second, a radiolabelled nucleotide, dNTPs, buffer, RNase inhibitor and reverse transcriptase are added to promote cDNA synthesis. For radiolabelling R&D Systems recommends the use of 33P rather than 32P. The protocol recommends the use of 2ug of total RNA or 0.5ug of poly (A)+ RNA for the reaction. In this experiment it was found that 5ug Total RNA was optimal for the reaction.
The annealing reaction is assembled in a 0.5ml tube with; 4ul Mouse Cytokine specific primers + Total RNA, the volume is adjusted to 15ul using RNAse-free water. The annealing reaction is carried out by placing the reaction in a thermal cycler. The cycle used is 90oC for 2 mins, then ramp to 42oC over a period of 20 mins. Once 42oC is reached the reaction is centrifuged and the following components were added; reverse transcriptase buffer, dNTPs, alpha33P dCTP, RNAse inhibitor, AMV reverse transcriptase, RNAse free water. The final reaction volume is 30ul. The reaction is mixed and returned to the thermal cycler and incubated at 42oC for 2-3 hrs.
The labelled cDNA is then purified. Unincorporated nucletides need to be removed to minimize non-specific background hybridizaton to the arrays. A Sephadex G-25 spin column is used to do this. The sample is placed down the column and centrifuged at 110 x g for 4 mins. the eluate is saved as it contains the purified cDNA sample.
The labelling is assessed before and after column purification. The % incorporation is monitored using a scintillation counter. Typically incorporation shoudl be between 20-50%.
Hybridization:
1.Arrays are rinsed in 50ml 2X SSPE at room temp for 5 mins.the arrays are drained.
2. Denature Salmon Testes DNA in boiling water bath for 5 mins. Place on ice. Add to the hybridization solution before use to a final concentration of 100ug/ml.
3.pre-warm teh hybridization oven and the hybridization solution from step 2 to 65oC. Pre-Hybridize the cDNA array in 5ml hybridization solution for at least 1 hr at 65oC, in a roller bottle rotating at 6 rpm.
4. add all the labelled cDNA t 2-3 ml hybridization solution in a 15ml screw-top conical tube. Denature the cDNA at 90-95OC for 10 mins in a water bath.
5. Decant and discard the Hyb solution from the pre-hybridized array. Add the denatured labeled cDNA in teh Hyb solution to the array in the roller bottle
6. Hybridized overnight (12-18hrs) at 65oC
7. Decant the Hyb solution
8. Add 40-50ml of wash solution1 to the roller bottle (0.5 x SSPE, 1% SDS). Wash the array at room temp for 3 mins. Discard the wash solution.
9. Repeat step 8 twice.
10. Pre-warm the wash solution to 65oC. Add 80-100ml Wash solution 1. Wash arrays in the hybdridization oven at 65oC for 20 mins (6rpm). Discard wash solution.
11.Repeat step 10 once.
12. Pre-Warm the wash solution II to 65oC (0.1 x SSPE, 1% SDS). Add 80-100ml wash solution II to the roller bottle. Wash arrays at 65oC for 20 mins (6rpm). Discard the wash solution.
13. Remove the array from the roller bottle. Lay the array on a sheet of blotting paper.
14. Air-Dry the array for 5 mins.
15. Wrap the array in clear plastic wrap and subject it to autoradiography. In this experiment arays were scanned using a phosphoimager. The protocol recommends scanning images at 50um. Typically an overnight exposure to a phosphoimager screen should be sufficient.
Quantitation of gene expression signals is best determined from phosphoimager generated image files. The image files may be analysed using the phophoimager manufacturers software eg in this experiment ArrayVision software from Imaging Research, Inc. was used.


title: Murine 22K cDNA array version 38.1

first: J. Andrew

last: Pospisilik


title: TIGR PFGRC Salmonella condensed 1

first: Palmy

last: Jesudhasan

organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Salmonella enterica subsp. enterica serovar Typhi str. CT18

description: Epoxy

first: James

last: Zhu

first: Suresh

last: Pillai

manufacture_protocol: 4QST, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Affymetrix GeneChip Mouse Genome 430 2.0 Array [CDF: Mm430_Mm_REFSEQ_8]

city: Cincinnati

first: Huan

last: Xu

state: OH

address: 3333 Burnet Ave.

department: Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

description: This identical to GPL1261 but a custom CDF environment was used to extract data. The custom CDF(Mm430_Mm_REFSEQ_8) was described by Dai et al., NAR 2005 33(20), PMID: 16284200. The cdf can be found at the link below.

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

manufacture_protocol: see manufacturer's web site


title: Galbraith Laboratory Operon Long Oligonucleotide Microarray version 3.0 (ATq306.02.Z)

city: Tucson

first: David

middle: William

last: Galbraith

state: AZ

address: 303 Forbes Building

department: Plant Sciences and Bio5 Institute

institute: University of Arizona

organism: Arabidopsis thaliana

description: This oligonucleotide array is produced from the Operon Version 3.0 Array-Ready Oligo set (AROS), which comprises 29,110 70-mer oligonucleotides representing 26,173 protein-coding genes, and 28,964 protein-encoding gene transcripts, and 87 microRNA gene precursors.  AROS design is based on ATH1 release 5.0 of the TIGR Arabidopsis genome annotation database, and Release 4.0 of the miRNA Registry at the Sanger Institute.  Various additional elements are printed as controls.  Microarrays can be ordered from the Galbraith laboratory. This platform represents slides ATq3.06.02.001-ATq3.06.02.400 (http://www.ag.arizona.edu/microarray).

manufacturer: The Galbraith Laboratory, University of Arizona


title: Murine 22K cDNA array version 37.1


title: Bacterial Microarray Group, St George’s Hospital Medical Tv_0_0 array

city: Stanford

first: SMD

last: Staff

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

organism: Mycobacterium tuberculosis

description: Array with 4624 features, in 16 zones, with 15655 biosequences representing 4592 reporters and 3924 composite sequences, with surface type unknown

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


title: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array [CDF: Hs133P_Hs_REFSEQ_8]

description: This is identical to GPL570 but a custom CDF environment was used to extract data. The custom CDF (Hs133P_Hs_REFSEQ_8) was described by Dai et al., NAR 2005 33(20), PMID: 16284200. The cdf can be found at the link below.

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


title: rat angiogenesis oligo array

city: Indianapolis

last: Basile

address: 635 Barnhill Drive

department: Cellular & Integrative Physiology

institute: Indiana University

organism: Rattus norvegicus

manufacturer: Medical College of Wisconsin/Department of Physiology

first: Katherine

last: Fredrich

manufacture_protocol: The custom microarrays were manufactured at the Department of Physiology at the Medical College of wisconsin.  The microarrays were printed witha  GMS 417 robotic arrayer from Affymetrix (made by Genetic Microsystesm that has a printhead with 4 pin and ring print tips.  Arrays were prepared from 70 mer oligonucleotides that correlated to approximately 128 genes related to angiogenesis and approximately 12 genes considered to be positive controls;positive control genes were either genes considered to be generally highly expressed genes in the kidney, and/or genes known to be influenced by ischemia reperfusion injury in the rat kidney.   In addition, 10 cDNA derived from Research genetics clone sets were included for comparison but were not included in the final analysis.  All oligonucleotides and cDNA were resuspended in 50% DMSO and printed onto poly-L-lysine coated glass slides.Negeative control spots were included thatconsisted of 50% water/50% DMSO. Each gene was printed on each slide between 6-12 times.  Blank spots, included for background determination were printed 96 times. Spots were printed with 300 microns center to center, with a spot diameter of approximately 120-150 mucrons.    Print configuration is in 12 blocks in a 2 X 6 arrangement and a total of 1152 spots per slide.  Positive controls were included in each block. After printing, spoted nucleotides were cross linked to the slides by UV irradiation at 65 mJ (Stratalinker UV cross-linker, Stratagene) Thge microarrays were post processed according to the procedures on the Stanform website (http;// cmgm.stanford.edu/pbrown/protocols/index.html) and subsequently stored at room temperatures in a dessicated chamer until use.


title: Streptomyces griseus IFO13350 13K KG

city: Bunkyo-ku

first: Yasuo

last: Ohnishi

state: Tokyo

address: 1-1-1 Yayoi

department: Biotechnology

country: Japan

institute: University of Tokyo

organism: Streptomyces griseus

first: Hirofumi

last: Hara

first: Jun

last: Ishikawa

first: Sueharu

last: Horinouchi

manufacture_protocol: Oligonucleotides are consolidated into 384-well plates, lyophilized by speed-Vac, and resuspended in 3x SSC to a printing concentration of 30uM. Oligos are printed on aminosilane slides. Microspot 10K quill pins (Biorobotics) in a 48-pin tool were used to deposit <0.5 nL per spot onto the slide. The resulting microarrays have a 8 x 4 subgrid layout with 420 spots per subgrid, each spot having approximate diameter and pitch of 90 µm and 190µm, respectively. All of oligo mixture as a positive control was printed in subgrid corners to assist in placing on the grid. The slides were crosslinked in a UV Stratalinker 2400 (Stratagene) at 300mJ. Array quality was assessed by visual inspection and hybridization of representative slides from a print run by dye-labelled random 9-mer oligonucleotides. The quality control images were aquired via the ScanArray Express from Perkin Elmer at a 10 micron resolution and quantified with the Imagene 6.0 software suite.


title: E. coli O157 Sakai oligonucleotide DNA microarray

city: Kiyotake

first: Yoshitoshi

last: Ogura

state: Miyazaki

address: Kihara 5200

department: Frontier science reserch center

institute: University of Miyazaki

organism: Escherichia coli

manufacturer: Molecular Gene Technics, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.

first: Kousuke

last: Tashiro

first: Satoru

last: Kuhara

first: Tetsuya

last: Hayashi

manufacture_protocol: Oligonucleotide probes were prepared for all the protein-coding genes on the O157 Sakai genome (5,447 genes in total).  Principles for the probe design were 60-mer in length and two probes for each gene.  As for 542 repeated genes, we prepared a single probe for each repeated gene family.  Such probes totaled to 151 probes, each having two or more targets of more than 90% sequence identity on the O157 Sakai genome .  As for the singleton genes (4905 genes), we were able to design two different 60-mer probes for 4173 genes, but only one 60-mer probe for 725 genes and one 44 or 45-mer probes for 7 genes.  In total, 9,620 probes were synthesized (Sigma-Aldrich Japan, Tokyo, Japan), and each probe was spotted onto poly-L-Lysine coated glass slides (SD10011; Matsunami Glass Ind., Osaka, Japan) using SPBIO (Hitachi Software Engineering, Tokyo, Japan).


title: ARCS_human_1040_BCv3

first: Martin

last: Lauss

first: Klemens

last: Vierlinger

first: Sandra

last: Szameit

first: Andreas

last: Weinhaeusel

first: Christa

last: Noehammer


title: Zebrafish Oligonucleotide Library (Compugen)

status: Public on Aug 09 2007

city: Chapel Hill

first: John

middle: F

last: Rawls

state: NC

address: 111 Mason Farm Rd.

department: Department of Cell and Molecular Physiology

institute: University of North Carolina at Chapel Hill

organism: Danio rerio

description: This set of zebrafish oligonucleotides was designed by Compugen and synthesized by Sigma-Genosys. The set consists of 16,399 65-mer oligonucleotides representing 16,228 gene clusters and 171 control elements. Compugen and Sigma-Genosys no longer sell or support this product. Sequences are not for commercial use, copyright reserved to Compugen 2002.

manufacture_protocol: For each gene, one 65-mer oligonucleotide probe was designed from the 3' region of the sequence. Each probe was selected from a sequence segment that is common to a maximum number of splice-variants predicted for each gene.


title: Human Digestive Cancer 9k

status: Public on Aug 11 2007

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 human gene expression analysis especially in the digestive cancer studies

manufacture_protocol: See manufacturer's web site


title: IMI S.epidermidis RP62A v1.2

status: Public on Aug 14 2007

city: Würzburg

first: Hans

last: Kränzler

address: Röntgenring 11

department: Institut fuer Molekulare Infektionsbiologie

institute: University of Würzburg

organism: Staphylococcus epidermidis RP62A

first: Wilma

last: Ziebuhr

manufacture_protocol: unknown


title: USDA-ARS PSMRU Arcobacter butzleri V1

status: Public on Aug 10 2007

city: Albany

first: Craig

middle: T

last: Parker

address: 800 Buchanan St

department: PSM

institute: USDA ARS

organism: Aliarcobacter butzleri

description:
A microarray with 4488 features corresponding to almost all ORFs in the Arcobacter butzleri RM4018 genome (spots in duplicate).
Blocks per array:16
Columns per block:18
Rows per block:18
Corning barcoded UltraGAPS slides

manufacturer: Produce Safety and Microbiology, USDA-ARS, Albany CA

manufacture_protocol: PCR product array of ORF's from Arcobacter butzleri RM4018. PCR products resuspended in resuspended to an average concentration of 0.1-0.2 µg µl-1 in 20 µl of 50% dimethyl sulfoxide (DMSO) containing 0.3× Saline-Sodium Citrate (SSC). Spotted on Corning barcoded UltraGAPS slides using a GeneMachine Accent printer with ChipMaker pins.


title: Human Versarray 4.0

city: Heidelberg

first: Cordula

last: Tschuch

address: Neuenheimer Feld 580

institute: DKFZ

manufacturer: German Cancer Research Center; Division: Molecular Genetics

manufacture_protocol:
Synthetic 70mer oligonucleotides were dissolved in 15ml 3x SSC, 1.5M Betaine spotting buffer to a final concentration of 20 pmol/ml.
DANN spotting was performed on QMT epoxysilane coated slides in an air-conditioned room at 21°C and 42% relative humidity using a VersArray Chip Writer Pro System equipped with Stealth SMP3 Micro Spotting Pins.
Spot centers were 155 mm apart with a diameter of around 100mm per spot. The dipping time of the spotting pins was 2s for loading, spotting pins hit the arrays with 5mm/s.
Spots were printed in parallel using a print head containing 48 print tips. Printing proceeds from top to bottom and left to right in each print tip group.
The print head takes up template from standard 384-well plates, each individual plate supplying template for 8 consecutive spots in each tip group.
DNA adhesion to the glass surface was accomplised by 2h incubation at 60°C.


title: IMP Vienna microarray facility Murine 23K cDNA array version 20.1 layout 2

status: Public on Aug 08 2007

first: Meinrad

last: Busslinger

address: Dr. Bohr-Gasse 7

institute: Research Institute of Molecular Pathology

manufacture_protocol:
Arraying
1. Transfer PCR reactions to 96-well V-bottom tissue culture plates (Costar).Add 1/10 vol. 3M sodium acetate (pH 5.2) and equal volume isopropanol. Store at -20 C for a 2 hours.
2. Centrifuge in Sorvall at 3500 RPM for 45 min. Rinse with 70% EtOH, centrifuge again and dry.
2. Resuspend DNA in 12ul 3X SSC for a 4 hours and transfer to flexible U-bottom printing plates.
4. Spot DNA onto poly-l-lysine slides with an arrayer.
Post processing.
1. Rehydrate arrays by suspending slides over a dish of warm ddH2O. (~1 minute)
2. Snap-dry each array (DNA side up) on a 100°C hot plate for 3 seconds.
3. UV X-link DNA to the glass by using a Stratalinker set for 60 milliJoules
4. Dissolve 5g of succinic anhydride (Aldrich) in 315mL of n-methyl-pyrrolidinone.
5. To this, add 35mL of 0.2M NaBorate pH 8.0 (made by dissolving boric acid in water and adjusting the pH with NaOH), and stir until dissolved.
6. Soak arrays in this solution for 15 minutes with shaking.
7. Transfer arrays to 95°C water bath for 2 minutes
8. Quickly transfer arrays to 95% EtOH for 1 minute.
9. Remove excess liquid from slides by spinning the rack of slides on microtiter plate carriers at 500rpm.


title: University of Pennsylvania/Nathanson Lab_HomoSapiens_ChromosomeRegion_Virtual

status: Public on Aug 01 2007

city: Philadelphia

first: Carmen

middle: Elisa

last: Oquendo

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

technology: other

description:
This virtual platform comprises the chromosomal regions covered by the following three BAC arrays:
GPL5108: HomoSapiens_5215 unique BACS_FGA011806
GPL5109: HomoSapiens_5217 unique BACS_FGA061005
GPL5110: HomoSapiens_4798 unique BACS_FGA72904

Nucleotide coordinates correspond to the hg18 assembly (NCBI Build 36.1)

distribution: virtual

manufacturer: Weber Laboratory/School of Medicine/University of Pennsylvania

manufacture_protocol: This is a virtual platform representing three BAC arrays.


title: Ancylostoma caninum microarray - public and SSH ESTs

city: Herston

first: Alex

middle: C

last: Loukas

state: Queensland

address: 300 Herston Rd

department: Division of Infectious Diseases and Immunology

country: Australia

institute: the Queensland Institute of Medical Research

organism: Ancylostoma caninum

description: 2x11k arrays in 2x105k backings

first: Bennett

middle: J

last: Datu

first: Robin

middle: B

last: Gasser

first: Shivashankar

middle: H

last: Nagaraj

first: Eng

middle: K

last: Ong

first: Peter

last: O'Donoghue

first: Russell

last: McInnes

first: Shoba

last: Ranganathan

manufacture_protocol: Probe sequences were electronically submitted using eArray for ink-jet in-situ synthesis onto glass slides by Agilent Technologies (Santa Clara, California)


title: Geobacter sulfurreducens antisense-detecting 12K oligo array

city: Amherst

first: Derek

last: Lovley

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

department: Microbiology

institute: University of Massachusetts Amherst

organism: Geobacter sulfurreducens

description: each oligonucleotide is synthesized on an array of gold electrodes embedded in a silicon chip.

first: Bradley

middle: L

last: Postier

first: Raymond

last: DiDonato Jr.

manufacture_protocol: In-situ electrochemically synthesized oligonucleotide array.  For reference see: Mauer et al., Electrochemically generated acid and its containment to 100 micron reaction areas for the production of DNA microarrays.  PLoS ONE. 2006, Dec 20;1:e34.


title: Agilent-015366 Custom Human 244K CGH Microarray

city: Santa Clara

first: Alicia

last: Scheffer

address: 5301 Stevens Creek Blvd.

institute: Agilent Technologies

organism: Homo sapiens

description: Agilent Custom Human 244K CGH Microarray consisting of 60-mer oligonucleotides mapped to human genome build 35. Reference: de Smith et al, Human Molecular Genetics, 2007

first: Adam

last: de Smith

first: Anya

last: Tsalenko

first: Nick

last: Sampas

first: Alice

last: Yamada

last: Tsang

first: Amir

last: Ben-Dor

first: Zohar

last: Yakhini

first: Richard

last: Ellis

first: Laurakay

last: Bruhn

first: Stephen

last: Laderman

first: Philippe

last: Froguel

first: Alexandra

last: Blakemore

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


title: Exiqon-Rat/Mouse/Human-540-v8.0

city: Toronto

first: Ivy

last: Moffat

state: Ontario

address: 1 King's College Circle, Medical Science Building Rm.4302

department: Pharmacology

country: Canada

institute: University of Toronto

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

manufacture_protocol: The capture probes are melting-temperature-normalized Locked Nucleic Acid (LNA) enhanced oligonucleotides


title: CUFSL Listeria 6K oligonuclotide array v1.0

city: Ithaca

first: Sarita

last: Raengpradub

state: NY

address: 412 Stocking Hall

department: Food Science

institute: Cornell University

organism:
Listeria monocytogenes
Listeria innocua

manufacturer: Cornell University Microarray Core Facility, T2 002B Vet Research Tower, Cornell University, Ithaca, NY 14853 USA

first: Martin

last: Wiedmann

first: Kathryn

last: Boor

manufacture_protocol: 2,857 70mer oligonucleotides were designed by and purchased from Operon Biotechnologies, Inc. (Huntsville, AL, USA) to represent 2,857 ORFs from Listeria monocytogenes EGD. 70mer oligonucleotides were designed for 61 Listeria innocua ORFs (based on L. innocua Clip 11262) and five Saccharomyces cerevisiae ORFs (to serve as negative controls) using ArrayOligoSelector (http://arrayoligosel.sourceforge.net). Oligonucleotides were resuspended in 1X SSC + 0.0025% Sarkosyl to a final concentration of 25uM. All oligonucleotides and controls were spotted in duplicate on Corning UltraGAPS slides (Corning, NY, USA) using a custom built XYZ microarrayer (based on the original design of Pat Brown from Stanford University). Oligonucleotides were UV-crosslinked at 300mJ for 1 minute. Printing quality was checked using Cy3-labeled random sequence nonamers.


title: SHFQ

last: Stanford Microarray Database

manufacturer: Stanford Functional Genomics Facility,  Stanford School of Medicine


title: Gossypium hirsutum agilent array version 1.0

status: Public on Jun 26 2007

city: Raleigh

first: Earl

last: Taliercio

address: 3127 Ligon St

institute: USDA/ARS

organism: Gossypium hirsutum

description: Supplementary file GPL4739_sequence_update.txt containing the complete sequence of the genes represented on the array may be found at the foot of this record.

manufacture_protocol:
customer designed
oligos designed by "picky" program
oligos 40-60 nt
genes represented on array are likely overrepresented in fiber initials or stems
Assembly was done "in house"
each putative gene represented by 3 or four oligos
most putative genes represented by 4 different oligos
when only one unique oligo could be identified, gene was represented in triplicate


title: IAH/VLA Virus Detection Array VA1

city: Roslin

first: Michael

middle: Bryan

last: Watson

state: Midlothian, EH25 9PS

address: Roslin Biocentre

department: ARK-Genomics

institute: The Roslin Institute

organism: Viruses

first: Paul

last: Britton

first: Donald

last: King

first: Abu-Bakr

last: Abu-Median

first: Juliet

last: Dukes

first: Malcolm

last: Banks

first: Rod

last: Card

manufacture_protocol:
Oligos were synthesised commercially and spotted to Epoxy-coated glass slides using a Migrogrid II robot (Biorobotics) using previously published protocol [1]
1. Burton, J.E., et al., Development of a multi-pathogen oligonucleotide microarray for detection of Bacillus anthracis. Mol Cell Probes, 2005. 19(5): p. 349-57.


title: Geary Mycoplasma gallisepticum oligo array

status: Public on May 20 2007

city: Storrs

first: Steven

last: Geary

state: CT

address: 61 North Eagleville Rd

department: Pathobiology

institute: University of Connecticut

organism: Mycoplasmoides gallisepticum str. R

description: This array includes spotted 50-mer oligonucleotides, designed to represent nearly every open reading frame in the annotated M. gallisepticum genome.

first: Timothy

middle: S

last: Gorton

manufacture_protocol: Standard company protocol


title: IMI S.epidermidis RP62A v1.3

first: Hans

last: Kränzler

first: Wilma

last: Ziebuhr


title: UNMC_Homo Sapiens_10K_chipA

city: omaha

first: Javeed

last: Iqbal

state: NE

address: 40th street

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

manufacturer: Compugen oligonucleotide library spottet at Eppley Cancer Center Molecular Biology DNA Microarray Core

first: Karen

last: Dybkaer

first: Guimei

last: Zhou

first: Huimin

last: Geng

first: Li

last: Xiao

first: Alexander

last: Schmitz

first: Wing

last: Chan

manufacture_protocol:
Microarrays with 60-mer oligonucleotides (Compugen, Jamesburg, NJ) printed on lysine-coated glass slides representing 17,260 genes, including reference (control) genes were utilized for hybridization. Compugen oligo Catalog# HUMLIB96: Human OligoLibrary Release 1.0: 96 well format, 197 plates (18,861 oligos).
Oligonucleotide probes (60mers) were designed for each target gene (Compugen, Inc., Rockville, MD) and manufactured by Sigma-Genosys, Inc. (The Woodlands, TX).  Oligonucleotides (ONs) were resuspended (30µM) in 3X SSC and spotted by the DNA Microarray Facility at the Eppley Cancer Center/Unviersity of Nebraska Medical Center onto poly-L-lysine coated slides using a MagnaSpotter robot (BioAutomation Corp., Dallas, TX) with a 12-pin print head (Telechem, Sunnyvale, CA) configuration in a humidified, HEPA-filtered hood. After spotting, the DNA was cross-linked to the slides by UV irradiation (350mJ/cm2) with a Stratalinker UV Crosslinker (Stratagene, Inc., La Jolla, CA), blocked by succinic anhydride treatment, and rinsed in ethanol.  A total of 18,705 oligonucleotides were spotted representing 17,260 different genes.
GPL5376 (UNMC_Homo sapiens_10K_chipB) and GPL5377 (UNMC_Homo Sapiens_10K_chipA) together represent the 18,861 oligos in the Compugen oligonucleotide library.


title: Genotypic/UHN Human ss-H19K8 cDNA Array

status: Public on May 18 2007

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

manufacturer: Microarray Center - University Health Network (UHN) - The Toronto Medical Discovery Tower - 101 College Street - Rm 9-301 - Toronto, Ontario - M5G 1L7 - Canada

first: Tapas

last: Kundu

first: Parag

last: Sadhale

first: Ashok

last: Reddy

manufacture_protocol:
Human ss-H19K8, Arrayer used - SDD26, Slide type - Corning ultraGAP
Microarrays are printed on UltraGAPS™ slides (Corning Inc.) using high-precision robotics. Printed arrays are processed following Corning's protocol and are ready-to-use. Most of the quantification packages available for microarray analysis require certain parameters in order to provide grids to mark off spots. Below are the required specifications for all our arrays. Specifications of array layouts are defined based on the slide barcode located on the bottom of the scanned image.
This set includes 19200 cDNA clones from the IMAGE consortium, single spotted array containing 19,008 characterized and unknown human ESTs. The clone set has been sequence-verified at the Microarray Centre and the sequences can be downloaded for validation.  Negative control features include Arabidopsis, blank, and 3XSSC buffer.


title: IMI S.epidermidis RP62A v1.0


title: Chlamydomonas reinhardtii small RNA sequences

status: Public on May 15 2007

city: Beijing

first: Yijun

last: Qi

address: No.7 Science Park Road,Zhongguancun Life Science Park

country: China

institute: National Institute of Biological Sciences, Beijing

organism: Chlamydomonas reinhardtii

description: This dataset contains Chlamydomonas reinhardtii endogenous small RNA sequences from total extraxts. The sequences were obtained using high-throughput sequencing technology provided by 454. For technical details, see Tao Zhao, Guanglin Li, Shijun Mi, Shan Li, Gregory J. Hannon, Xiu-Jie Wang, and Yijun Qi. 2007. A Complex System of Small RNAs in the Unicellular Green Alga Chlamydomonas reinhardtii. Genes & Development

manufacture_protocol: please see the 454 website


title: Cotton_oligonucleotide_array_v1.0

status: Public on Sep 14 2006

city: Athens

first: Alan

middle: R

last: Gingle

state: GA

address: 111 Riverbend Rd.

department: Center for Applied Genetics Technologies

institute: University of Georgia

organism:
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

description:
Comment:  On this platform, we have not distinguished which features were specifically designed from each of the three different Gossypium species because all probes were designed from a single assembly of Gossypium ESTs.  An effort to do so, may have been misleading since all probes are expected to hybridize equally well to homologs in all three species due to their limited coding sequence divergence.
Supplementary information about this platform can be obtained at http://cottonevolution.info/microarray.
The oligo probes have been annotated with GenBank accession identifiers based on any one of the following criteria.
1) GB_ACC: A probe was specifically designed to target a particular mRNA with associated GenBank accession identifier.
2) GB_LIST1: A high quality alignment (length >= 60 and percent identities >= 92%) to a member of either the ESTother or nt databases.
3) GB_LIST2: A high quality alignment (length >= 60 and percent identities >= 92%) to a contig member of the estinformatics (http://www.estinformatics.org/) assembly for Gossypium (assembly date: 12/31/2006).  These annotations are based on EST membership in the aligned contig and not on direct high quality alignment to any member EST.  Therefore, the number of associated accessions can be quite large.
A number of the probes failed to meet any of these criteria and, therefore, have not been annotated with GenBank accession identifiers.  However, their available information can be accessed at http://cottonevolution.info/microarray.

manufacturer: Washington University microarray core facility

first: Joshua

middle: A

last: Udall

first: Jordan

last: Swanson

first: Lex

last: Flagel

first: Ran

last: Hovav

first: Ryan

last: Rapp

first: Dan

last: Nettleton

first: Jeffrey

middle: Z

last: Chen

first: Rod

last: Wing

first: Cari

last: Soderlund

first: Andrew

last: Paterson

first: Jonathan

last: Wendel

manufacture_protocol: After oligo design at Iowa State University, one set of oligonucleotides (12,006) were synthesized and aliquoted into 3 replicate plates of 1000 pmoles by IDT Technologies (Coralville, IA, USA).  An earlier set of oligonucleotides was synthesized for microarray development in the Chen lab at Texas A&M University.  An aliquot of 384-well plates from both sets of oligonucleotides was hydrated in water and diluted to the printing concentration with 3X SSC.  Two spots of each oligo from the same pin-dip were printed in separate slide sections on Corning epoxy slides at the Washington University Microarray Core facility using a locally constructed linear servo arrayer (after the DeRisi model, http://derisilabs.ucsf.edu/).  After printing, slides were allowed to dry in 50-70% humidity for 12-16 hrs at room temperature and subsequently cross-linked at 150 mJoules in a Strata-linker (Stratagene, Inc., La Jolla, CA, USA).  Two slides from the print batch were checked using SpotCheck (Genetix).  Printed cotton microarrays are publicly available at http://cottonevolution.info.


title: 3D-Gene Human miRNA Oligo chip

city: Kamakura

first: Satoko

last: Takizawa

address: 6-10-1 Tebiro

institute: TORAY Industries, Inc.

description: Ultra-sensitive DNA chip for human microRNA expression analysis

manufacture_protocol: See manufacturer's web site


title: Affymetrix Mus musculus 4K chromosome 11 and 16 CustomExpress Array

city: Columbus

first: Kirk

middle: M

last: McHugh

address: 700 Children's Drive

department: Cell & Developmental Biology

institute: Columbus Children's Hospital

organism: Mus musculus

manufacture_protocol: We designed a GeneChip CustomExpress array that contained all of the 4019 chromosome 11 and 16 mouse probe sets currently arrayed by Affymetrix (Santa Clara, CA) as well as an additional 70 sequences for which unique probe sets were designed. These 70 unique probe sets covered potential gene products located near the previously identified transgene insertion and translocation points on chromosomes 11 and 16. This custom array was designated Chr11/16.


title: DKFZ Homo sapiens 8k BAC array

first: Stefan

last: Pfister

address: INF 580

department: Molecular Genetics

institute: German Cancer Research Center

manufacturer: Division Molecular Genetics, German Cancer Research Center Heidelberg

first: Marc

last: Remke

first: Axel

last: Benner

first: Wiebke

last: Werft

first: Bernhard

last: Radlwimmer

first: Peter

last: Lichter

manufacture_protocol: DOP-PCR products were spotted in triplicate onto NexterionTM Slide E epoxysilane-coated slides (PEQLAB, Erlangen, Germany) using a spotting robot (VersArray ChipWriterTM Pro system, BioRad, Munich, Germany) at 20°C and 40% humidity. After spotting, slides were cross-linked, baked for 1 hr at 80°C, and cross-linked again.


title: MPSS tags from techical comparison of SAGE and MPSS

status: Public on Aug 02 2007

city: Oxford

first: Edward

last: Evans

state: Oxfordshire

address: HIU, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital

department: Nuffield Dept. Clinical Medicine

institute: University of Oxford

technology: MPSS

description: A list of all tags obtained in a set of MPSS libraries used to analyse the transcriptome of a CD4+ T cell clone.

first: Lawrence

last: Hene

first: Sreenu

last: Vattipally

first: Simon

last: Davis


title: DKFZ Homo sapiens array-CGH 6k BAC array

city: Heidelberg

manufacturer: German Cancer Reserach Center Heidelberg, Division Molecular Genetics

first: Frank

last: Mendrzyk

first: Grischa

last: Toedt


title: UCSF Homo sapiens 2.5K

status: Public on Aug 06 2007

city: Chiba

first: Akira

last: Nakagawara

address: 666-2 Nitona, Chuoh-ku

institute: Chiba Cancer Center Research Institute


title: Agilent Custom Mouse 44K Alternative Splicing Oligo Microarray

first: Qun

last: Pan

address: 160 College St.

description: A microarray platform to profile alternative splicing levels for 3707 cassette-type alternative exons across a diverse spectrum of mouse tissues.

first: Matthew

last: Fagnani

first: Yoseph

last: Barash

first: Joanna

last: Ip

first: Christine

last: Misquitta

first: Arneet

last: Saltzman

first: Ofer

last: Shai

first: Leo

last: Lee

first: Aviad

last: Rozenhek

first: Naveed

last: Mohammad

first: Sandrine

last: Willaime-Morawek

first: Tomas

last: Babak

first: Wen

last: Zhang

first: Timothy

last: Hughes

first: Derek

last: van der Kooy

first: Brendan

last: Frey

first: Benjamin

last: Blencowe

manufacture_protocol: 60-mer ink-jet Agilent microarray


title: LLHoyer_Calbicans_6k_v1.0

city: Urbana

first: Lois

last: Hoyer

state: IL

address: 2001 S Lincoln Ave

institute: University of Illinois

organism: Candida albicans

manufacturer: LLHoyer Laboratory, University of Illinois, Urbana, IL and Microarrays Inc., Nashville, TN

manufacture_protocol: Two separate rounds of PCR were performed on the ORF sequences.  The products were combined and the purity and length of PCR products were viewed by agarose gel electrophoresis.  Samples were dried and resuspended in 3x SSC with an approximate concentration of 0.1 µg/µl of DNA in each PCR well.  A total of 6392 PCR products were spotted (proprietary techniques created by Microarrays Inc., Nashville, TN) in duplicate onto SuperAmine Substrate slides (Telechem Intl).  Controls included Arabidopsis thaliana Spot Report Genes and mammalian DNA fragments (Stratagene), C. albicans genes of known expression profiles, and buffer blanks.


title: UNMC_Homo sapiens_10K_chipB

first: Javeed

last: Iqbal

first: Karen

last: Dybkaer

first: Guimei

last: Zhou

first: Huimin

last: Geng

first: Li

last: Xiao

first: Alexander

last: Schmitz

first: Wing

last: Chan


title: Cotton_oligonucleotide_array_v2.0

status: Public on Feb 06 2007

first: Alan

last: Gingle

organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

description:
Comment:  This is the second version of the cotton nucleotide platform. Three independently designed sets of IDT (Coralville, IA, USA) oligonucleotides are included on this microarray platform.  The first set of 1,152 oligonulceotides were designed by the Chen lab formerly located at Texas A&M.  A second set of 12,006 oligonucleotides was designed by the Wendel lab located at Iowa State University.  The third set of oligonucleotides (9,629) was designed by The Institute for Genomic Research (TIGR) in collaboration with the Chen Lab at The University of Texas using the latest TIGR cotton EST assembly (CGI8).  Version 1 (GEO#  GPL4305) included dual spotted oligonucleotides from only the first two sets of oligonucleotides.  We have not distinguished which features were specifically designed from each of the different Gossypium species because all probes were designed from an assembly of Gossypium ESTs.  An effort to do so may have been misleading, since all probes are expected to hybridize equally well to homologs across the different species, due to their limited coding sequence divergence.
The oligo probes have been annotated with GenBank accession identifiers based on any one of the following criteria.
1) GB_ACC: A probe was specifically designed to target a particular mRNA with associated GenBank accession identifier.
2) GB_LIST1: A high quality alignment (length >= 60 and percent identities >= 92%) to a member of either the ESTother or nt databases.
3) GB_LIST2: A high quality alignment (length >= 60 and percent identities >= 92%) to a contig member of the estinformatics (http://www.estinformatics.org/) assembly for Gossypium (assembly date: 12/31/2006).  These annotations are based on EST membership in the aligned contig and not on direct high quality alignment to any member EST.  Therefore, the number of associated accessions can be quite large.
A number of probes failed to meet any of these criteria and, therefore, have not been annotated with GenBank accession identifiers.  However, their available information can be accessed at http://cottonevolution.info/microarray.

first: Joshua

last: Udall

first: Andrew

middle: W

last: Woodward

first: Foo

last: Cheung

first: Jordan

last: Swanson

first: Lex

last: Flagel

first: Ran

last: Hovav

first: Ryan

last: Rapp

first: Dan

last: Nettleton

first: Jinsuk

last: Lee

first: Christopher

middle: D

last: Town

first: Rod

last: Wing

first: Cari

last: Soderlund

last: Paterson

first: Jeffrey

last: Chen

first: Jonathan

last: Wendel

manufacture_protocol: An aliquot of 384-well plates from all three sets (see description) of oligonucleotides was hydrated in water and diluted to the printing concentration with 3X SSC.  A single spot of each oligo from a single pin-dip was printed on each Corning epoxy slide at the Washington University Microarray Core facility using a locally constructed linear servo arrayer (after the DeRisi model, http://derisilabs.ucsf.edu/).  After printing, slides were allowed to dry in 50-70% humidity for 12-16 hrs at room temperature and subsequently cross-linked at 150 mJoules in a Strata-linker (Stratagene, Inc., La Jolla, CA, USA).  Two slides from each print batch are assessed for quality using SpotCheck (Genetix).  Batches of printed cotton microarrays and associated quality data are publicly available at http://cottonevolution.info.


title: 01_Drosophila_16K_Universitat_Barcelona

status: Public on Oct 23 2006

city: Barcelona

first: Sergi

last: Beltran

address: Baldiri Reixac 10

department: Serveis Cientificotècnics

country: Spain

institute: Universitat de Barcelona

organism: Drosophila melanogaster

description: Oligonucleotide Drosophila microarray platform containing virtually all genes from the genome. In addition to the Operon Drosophila Genome Oligo Set Version 1.1, a number of positive and negative controls have been printed so that quality of hybridizations and analysis procedures can be assessed.

manufacturer: Departament de Genètica (Universitat de Barcelona) i Plataforma de Transcriptòmica (SCT-PCB-UB)

first: Montserrat

last: Corominas

manufacture_protocol: Microarrays were printed on Corning UltraGAPS slides with a Genetix QArray using a 16 pin head, yielding a microarray with 48 Blocks and 16416 spots. The oligonucleotides printed are from the Drosophila Genome Oligo Set Version 1.1 (Operon Biotechnologies, Inc), a collection of 14593 probes representing 13577 Drosophila genes with Flybase ID. Additionaly, ten Arabidopsis thaliana 70mer sequences from TIGR (Wang et al., 2003) and spots with no material or with buffer were also printed to be used as spike-in and negative controls, respectively. Spike-in controls were printed on each block (total of 640 spots) so that print-tip and spatial variation along the microarray can be assessed. Twelve Drosophila genes have been printed 17 times to assess reproducibility of hybridization. All oligonucleotides were ressuspended in Pronto! Universal Spotting Solution (Corning).


title: University of Pennsylvania/Nathanson Lab_HomoSapiens_3315 unique BACS_FGA100101

status: Public on Apr 27 2007

city: Philadelphia

first: Carmen

last: Oquendo

address: 421 Curie Blvd

institute: University of Pennsylvania

description: ULTRA GAPS (Gama Amino Propyl Silane)

manufacture_protocol:
This BAC array platform consisted of 3315 unique BACs spotted in-house on CorningCMT Ultra-Gap slides (Corning, USA) using two replicates printed on each slide. Details of array construction are described elsewhere (Greshock et al., 2004)
Greshock J, Naylor TL, Margolin A, Diskin S, Cleaver SH, Futreal PA, deJong PJ, Zhao S, Liebman M, Weber BL. 2004. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res 14(1):179-87.