title: LC-13

status: Public on Sep 09 2005

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

organism: Homo sapiens

technology: spotted DNA/cDNA

distribution: non-commercial

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


title: 2005-09-28_Crawford_HG17_Set32

status: Public on Nov 18 2007

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

technology: in situ oligonucleotide

distribution: custom-commercial

first: Gregory

middle: E

last: Crawford

manufacture_protocol: Oligonucleotides spaced approximately every 100 base pairs across the entire non-repetitive human genome were synthesized in situ on a 38-array set.


title: 2005-09-28_Crawford_HG17_Set34


title: Whole rice locus 44K array 1

status: Public on Nov 27 2007

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

country: Japan

institute: NARO/HARC

organism: Oryza sativa

description:
Keyword: Oryza sativa ssp. Japonica cv. Nipponbare
Keyword: rice full-length cDNA sequences
Keyword: TIGR pseudomolecules release 4

first: Koji

last: Suzuki

first: Shoshi

last: Kikuchi

manufacture_protocol:
For design probes, FL-clone sequences (FLcDNAs and FLESTs) were mapped on TIGR Pseudomolecules release 2 using the BLAT program (determinination of FL-locus)After this mapping, we selected nucleotide sequences from the FL-locus and CDS of TIGR annoatiton release 2 for probe design and about 82K kinds of 60-mer probe candidates were designed by Agilent Technologies on the basis of such factors as GC content and melting Temperature of oligo and were spotted on two slides (41K probes per slide).
In our investigation, we used the information of TIGR Pseudomolecules release 4 (TIGR4), so, these designed probes were re-mapped on TIGR4 by BLAT according to the criterion (>95% identity, >90% coverage, non-redundant highest score). 63455 probes were mapped on Fl-locus and/or TIGR-locus based on TIGR pseudomolecules release 4.


title: 2005-09-28_Crawford_HG17_Set36


title: Drosophila microarray sheet

status: Public on Nov 19 2007

city: Baltimore

first: Haruyoshi

last: Yamaza

address: 6200 Seaforth Street

department: Laboratory of Experimental Gerontology

institute: National Institute on Aging

organism: Drosophila melanogaster

manufacturer: Laboratory of Experimantal Gerontology, National Institute on Aging

first: Ming

last: Zhan

first: Yu

last: Sun

first: Jason

last: Sinclair

first: Huai

last: Li

first: Sige

last: Zou

manufacture_protocol: PCR products of 14,151 predicted or known genes in D. melanogaster were used to generate DNA microarray. The length of each PCR amplicon was 100-600 bp. cDNA was amplified with universal primers (AATGCAGGTTAACCTGGCTTATCG and AACGCGGCTACAATTAATACATAACC). PCR products were printed on 3-D slides (Full Moon Biosystems Inc.).


title: 2005-09-28_Crawford_HG17_Set38


title: SHGB

status: Public on Jan 25 2006

manufacturer: Stanford Functional Genomics Facility,  Stanford School of Medicine


title: 2005-09-28_Crawford_HG17_Set29


title: LC-27

status: Public on Dec 30 2005


title: 2005-09-28_Crawford_HG17_Set33


title: 2005-09-28_Crawford_HG17_Set35


title: UKU_trout_1.8K_v1

status: Public on Nov 22 2007

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

organism: Oncorhynchus mykiss

first: Heikki

last: Koskinen

manufacture_protocol: Inserts were PCR amplified in a 96-well format with universal primers in detergent-free buffer and products were purified. Materials were consolidated to 384-well plates and spotting buffer was added. Spotting was conduced using R-ray microarray printer, a home-made spotter at Finninsh DNA Microarray Centre.


title: LC-36

status: Public on Jul 09 2005

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


title: UW_Homo_sapiens_array_hg18_NimbleGen

city: Madison

first: Victor

last: Ruotti

state: WI

address: 425 Henry Mall

department: Biotechnology

institute: UW Madison

description:
Standard 60-mer hg18 gene expression array

The Platform data table reflects a condensed representation of the replicate (8x) 60-mer oligo features.
The full array layout (GPL5876_full_array_layout.txt) is linked as a Supplementary file at the foot of this record.
The design (.ndf) file is also linked as a Supplementary file.

first: Junying

last: Yu

first: Maxim

middle: A

last: Vodyanik

first: Kim

last: Smuga-Otto

first: Jennifer

middle: L

last: Frane

first: Shulan

last: Tian

first: Gudrun

last: Jonsdottir

first: Ron

last: Stewart

first: Igor

middle: I

last: Slukvin

first: James

last: Thomson

manufacture_protocol: Standard NimbleGen maskless array synthesis for standard 60-mer hg17 gene expression array


title: MML

status: Public on Aug 05 2005

last: Stanford Microarray Database

organism: Mus musculus


title: Yale/Duman cDNA spotted array

status: Public on Nov 30 2007

first: Joshua

last: Hunsberger

address: 35 Convent Drive MSC3711

institute: NIH

manufacture_protocol: spotted cDNA


title: Wistar Illumina Human V6 Array

city: Philadelphia

first: Louise

middle: C

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

technology: oligonucleotide beads

first: Michael

first: Wenhwai

last: Horng

manufacture_protocol: Illumina Beads


title: 2005-09-28_Crawford_HG17_Set31

first: Sean

last: Davis

first: Gregory

last: Crawford


title: Homo sapiens 0.4K miChip v8

status: Public on Nov 21 2007

city: Heidelberg

first: Mirco

last: Castoldi

address: Im Neuenheimer Feld 156

department: Department of Pediatric Oncology, Hematology and Immunology

country: Germany

institute: University of Heidelberg

technology: spotted oligonucleotide

description:
miChip v8.0 annotation was done for human. miChip v8.0 contains capture probe matching several mouse and rat microRNAs that were not validated in human (miRbase v 8.0)
miChip array are spotted on CodeLink, GE Life Science, cat. no. 30001100). Codelink glass slides are coated with N-hydroxysuccinimide

manufacturer: Array were spotted by the Genomics Core Facility, EMBL, Germany. LNA-modified capture probes were manufactured by Exiqon, Denmark

first: Vladimir

last: Benes

first: Sabine

last: Schimidt

first: Martina

middle: U

last: Muckenthaler

first: Matthias

middle: W

last: Hentze

manufacture_protocol:
LNA-modified oligonucleotide (Exiqon) capture probes are designed to have a close to uniform Tm of 72 Celsius against their complementary targets. This is achieved by adjustment of LNA content and length of capture probes (miRCURY Array probes, Exiqon). A C6-amino linker is added to the 5’end of all capture probes. The desiccated capture probe set is available in a 384-well plate format. Capture probes are printed onto N-hydroxysuccinimide glass surfaces (Codelink, GE Healthcare Life Science) using the Lucidea Array Spotter (GE Healthcare Life Science).
Additional material required for array preparation: post-coupling blocking solution [50 mM ethanolamine, 0.1 M Tris (pH 9)], post-coupling washing solution (4 XSSC, 0.1% SDS), a water bath (50 C) and a tabletop centrifuge (Eppendorf, 5810R) fitted with rotor (A4-62) adaptors for microplate carriers or for 50 ml tubes
miRCURY Array probes (Exiqon) are diluted to a final concentration of 20 uM in 3X•printing buffer [(150 mM sodium phosphate (pH 8.5)] prior to spotting. Probe set are spotted on CodeLink, (GE Healthcare Life Science), where slides are printed using the Lucidea array spotter (GE Healthcare Life Science) with 65% humidity and a temperature of 21 C.
Each spot measures about 120 um in diameter with a center-to-center spacing between spots of 300 um. To obtain a reliable read out each capture probe is printed in quadruplicate using a re-dip after four slides. Spotted glass slides are subjected to post processing as recommended by the manufacturer. In brief, CodeLink slides are designed to covalently immobilize amine-modified oligonucleotides for microarrays. However, the reactive groups are moisture sensitive and slides must be stored desiccated, hence the coupling of C6-amino linker oligonucleotides to the surface takes place in a humid environment following printing. Consequently, following printing, arrays are collected and introduced into bottom-sealed racks (e.g. microscope slide racks) that are placed in boxes containing a saturated solution of sodium chloride.
(Note. To prepare a saturated solution of sodium chloride, add as much solid NaCl to water as needed to form a 1 cm deep slurry in the bottom of the box). Boxes are sealed with saran wrap or airtight lids, and stored overnight at room temperature. Next Day, printed arrays are transferred into glass racks and residual reactive groups on the CodeLink surface are inactivated by incubation with post-coupling blocking solution (pre-warmed to 50 C) for 30 min in the water bath (50 C). Then the slides are rinsed twice with deionized water and a third time with post-coupling washing solution (pre-warmed to 50 C) for 30 min on the shaker. Slides are then briefly rinsed with deionized water. Subsequently, the racks are placed into microplate carriers, and centrifuged for 2 min at 1500 rpm.
Ready-to-hybridize slides can be stored for up to 6 month at room temperature in a desiccator.


title: LC-23

status: Public on Nov 23 2005


title: UKU_trout_1.3K_v2

first: Aleksei

last: Krasnov

first: Heikki

last: Koskinen


title: Agilent-014695 Mouse Genome CGH Microarray 244A (G4415A) - alternative version

status: Public on Nov 24 2007

city: Manchester

first: Catriona

last: Rennie

address: Oxford Rd

department: Faculty of Life Sciences

country: United Kingdom

institute: The University of Manchester

description:
This is an alternative version of the official Agilent platform assigned accession number GPL4092.

The ID column represents the Agilent Probe names.

This microarray is Agilent’s premium product for mouse DNA copy-number profiling. Over 235,000 60-mer oligonucleotide probes, specifically optimized for copy-number measurement, span coding and non-coding genomic sequences with median spacing of 6.2 kb and 15.2 kb respectively. This microarray is designed for use with Agilent’s optimized assay protocols, enabling researchers to use nanogram levels of total genomic DNA without complexity reduction.

distribution: commercial

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


title: 2005-09-28_Crawford_HG17_Set37


title: Illumina_human_517

city: Jyväskylä

first: Eija

last: Pöllänen

address: PO Box 35/Viveca

department: Department of Health Sciences

country: Finland

institute: University of Jyväskylä


title: 2005-09-28_Crawford_HG17_Set27


title: SHDB

status: Public on Aug 25 2005


title: 2005-09-28_Crawford_HG17_Set28


title: 2005-09-28_Crawford_HG17_Set26


title: CATMA_CIG_Arabidopsis_25K_V1

city: Lausanne

first: Keith

last: Harshman

address: Genopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

organism: Arabidopsis thaliana

technology: mixed spotted oligonucleotide/cDNA

manufacturer: DNA Array Facility, Center for Integrative Genomics, Genopode, University of Lausanne

manufacture_protocol: The Arabidopsis thaliana microarray contains gene specific tags (GSTs) that have been designed by the Complete Arabidopsis Transcriptome MicroArray Project (CATMA Project). As described on the CATMA project webpage, the probes spotted on the array are collection consisting primarily of PCR products but also including oligonucleotids. The spotting buffer is 3xSSC 1,5M betaïne, the spotting robot is a GeneMachines OmniGrid300. DNA was spotted on aldehyde slides.


title: 2005-09-28_Crawford_HG17_Set23


title: 2005-09-28_Crawford_HG17_Set21


title: 2005-09-28_Crawford_HG17_Set22


title: Whole rice locus 44K array 2

first: Kouji

last: Satoh

first: Koji

last: Suzuki

first: Shoshi

last: Kikuchi


title: 2005-09-28_Crawford_HG17_Set20


title: 2005-09-28_Crawford_HG17_Set17


title: 2005-09-28_Crawford_HG17_Set19


title: 2005-09-28_Crawford_HG17_Set18


title: 2005-09-28_Crawford_HG17_Set13


title: 2005-09-28_Crawford_HG17_Set11


title: 2005-09-28_Crawford_HG17_Set12


title: 2005-09-28_Crawford_HG17_Set24


title: 2005-09-28_Crawford_HG17_Set15


title: 2005-09-28_Crawford_HG17_Set09


title: 2005-09-28_Crawford_HG17_Set10


title: 2005-09-28_Crawford_HG17_Set08


title: 2005-09-28_Crawford_HG17_Set07


title: 2005-09-28_Crawford_HG17_Set16


title: 2005-09-28_Crawford_HG17_Set03


title: 2005-09-28_Crawford_HG17_Set05


title: 2005-09-28_Crawford_HG17_Set06


title: 2005-09-28_Crawford_HG17_Set01


title: 2006-02-27_Crawford_HG17_Set32


title: 2005-09-28_Crawford_HG17_Set02


title: 2006-02-27_Crawford_HG17_Set34


title: 2006-02-27_Crawford_HG17_Set36


title: 2006-02-27_Crawford_HG17_Set38


title: 2006-02-27_Crawford_HG17_Set37


title: 2006-02-27_Crawford_HG17_Set35


title: 2006-02-27_Crawford_HG17_Set31


title: 2006-02-27_Crawford_HG17_Set33


title: 2005-09-28_Crawford_HG17_Set04


title: 2006-02-27_Crawford_HG17_Set29


title: 2006-02-27_Crawford_HG17_Set30


title: 2006-02-27_Crawford_HG17_Set27


title: 2006-02-27_Crawford_HG17_Set25


title: 2006-02-27_Crawford_HG17_Set28


title: 2006-02-27_Crawford_HG17_Set23


title: 2006-02-27_Crawford_HG17_Set26


title: 2005-09-28_Crawford_HG17_Set14


title: 2006-02-27_Crawford_HG17_Set24


title: 2006-02-27_Crawford_HG17_Set22


title: 2006-02-27_Crawford_HG17_Set21


title: 2006-02-27_Crawford_HG17_Set19


title: 2006-02-27_Crawford_HG17_Set20


title: 2006-02-27_Crawford_HG17_Set18


title: LC-18

status: Public on Nov 16 2005

last: Stanford Microarray Database


title: 2006-02-27_Crawford_HG17_Set17


title: 2006-02-27_Crawford_HG17_Set15


title: 2006-02-27_Crawford_HG17_Set16


title: 2006-02-27_Crawford_HG17_Set14


title: 2006-02-27_Crawford_HG17_Set12


title: 2006-02-27_Crawford_HG17_Set13


title: 2006-02-27_Crawford_HG17_Set11


title: 2006-02-27_Crawford_HG17_Set09


title: 2006-02-27_Crawford_HG17_Set04


title: 2006-02-27_Crawford_HG17_Set10


title: 2006-02-27_Crawford_HG17_Set08


title: 2006-02-27_Crawford_HG17_Set05


title: 2006-02-27_Crawford_HG17_Set06


title: 2006-02-27_Crawford_HG17_Set02


title: 2006-02-27_Crawford_HG17_Set03


title: 2006-02-27_Crawford_HG17_Set07


title: 2006-02-27_Crawford_HG17_Set01


title: CGH-CHORI-32K-Chr. 18 19 20 21 22

status: Public on Nov 14 2007

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: The array contains 3045 distinct BAC and PAC sequences. The bacs were printed in 2 replicates. In total the array design contains 7744 features printed in a layout of 4 meta rows, 4 meta columns, 20 rows per block and 20 columns per block.This grid is printed twice on the glass slides allowing for two microarray arrays per slide

first: Paul

last: Van Hummelen

first: Guy

last: Froyen

first: Joris

middle: R

last: Vermeesch

manufacture_protocol:
MicroGrid Printing ProtocolEquipment:
1. Microgrid (Genomics Solutions, UK).
2. 384 microtiter plates (X7022, Genetix)
3. 4x4 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 Na-Phosphate (pH 8.45) buffer, 0.000125% sarcosyl at concentrations of 300 ng/ul.
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 20 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.
7. Incubate the slides in humid chamber with saturated NaCl for 24 to 72 hours.
8. Block 1%NH4OH.


title: CGH-CHORI-32K-Chr. 3 11

description: The array contains 3629 distinct BAC and PAC sequences. The bacs were printed in 2 replicates. In total the array design contains 7392 features printed in a layout of 4 meta rows, 4 meta columns, 21 rows per block and 22 columns per block.This grid is printed twice on the glass slides allowing for two microarray arrays per slide.

manufacture_protocol:
MicroGrid Printing ProtocolEquipment:
1. Microgrid (Genomics Solutions, UK).
2. 384 microtiter plates (X7022, Genetix)
3. 4x4 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 Na-Phosphate (pH 8.45) buffer, 0.000125% sarcosyl at concentrations of 300 ng/ul.
2. Set spotter settings for 2 arrays of 4x4 blocks printed with 16 pins: column pitch = 185 um, row pitch = 185 um; Humidity 55%; 85 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 20 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.
7. Incubate the slides in humid chamber with saturated NaCl for 24 to 72 hours.
8. Block 1%NH4OH.


title: CGH-CHORI-32K-Chr. 4 15 16

description: The array contains 3835 distinct BAC and PAC sequences. The bacs were printed in 2 replicates. 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 arrays per slide.

manufacture_protocol:
MicroGrid Printing ProtocolEquipment:
1. Microgrid (Genomics Solutions, UK).
2. 384 microtiter plates (X7022, Genetix)
3. 4x4 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 Na-Phosphate (pH 8.45) buffer, 0.000125% sarcosyl at concentrations of 300 ng/ul.
2. Set spotter settings for 2 arrays of 4x4 blocks printed with 16 pins: column pitch = 185 um, row pitch = 185 um; Humidity 55%; 70 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 20 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.
7. Incubate the slides in humid chamber with saturated NaCl for 24 to 72 hours.
8. Block 1%NH4OH.


title: Spectral Chip 2600 BAC array

status: Public on Nov 15 2007

city: New York

first: James

last: Korkola

state: NY

address: 1275 York Ave

department: Cell Biology

institute: Memorial Sloan-Kettering

manufacturer: Spectral Genomics (now part of Perkin Elmer)

manufacture_protocol: Commercial chip; 48 subarrays (12X4), each containing 120 spotted BAC clones (10X12); duplicate clones within each subarray; 2600 BAC clones total (~1Mb resolution)


title: CGH-CHORI-32K-Chr. 1 9

description: The array contains 3713 distinct BAC and PAC sequences. The bacs were printed in 2 replicates. 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 arrays per slide.

manufacture_protocol:
MicroGrid Printing ProtocolEquipment:
1. Microgrid (Genomics Solutions, UK).
2. 384 microtiter plates (X7022, Genetix)
3. 4x4 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 Na-Phosphate (pH 8.45) buffer, 0.000125% sarcosyl at concentrations of 300 ng/ul.
2. Set spotter settings for 2 arrays of 4x4 blocks printed with 16 pins: column pitch = 185 um, row pitch = 185 um; Humidity 55%; 81 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 20 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.
7. Incubate the slides in humid chamber with saturated NaCl for 24 to 72 hours.
8. Block 1%NH4OH.


title: CGH-CHORI-32K-Chr. 8 10 17

description: The array contains 3794 distinct BAC and PAC sequences. The bacs were printed in 2 replicates. 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 arrays per slide.


title: CGH-CHORI-32K-CHr. 2 14

description: The array contains 3708 distinct BAC and PAC sequences. The bacs were printed in 2 replicates. 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 arrays per slide.


title: CGH-CHORI-32K-Chr. 6 7

description: The array contains 3756 distinct BAC and PAC sequences. The bacs were printed in 2 replicates. 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 arrays per slide.

manufacture_protocol:
MicroGrid Printing ProtocolEquipment:
1. Microgrid (Genomics Solutions, UK).
2. 384 microtiter plates (X7022, Genetix)
3. 4x4 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 Na-Phosphate (pH 8.45) buffer, 0.000125% sarcosyl at concentrations of 300 ng/ul.
2. Set spotter settings for 2 arrays of 4x4 blocks printed with 16 pins: column pitch = 185 um, row pitch = 185 um; Humidity 55%; 80 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 20 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.
7. Incubate the slides in humid chamber with saturated NaCl for 24 to 72 hours.
8. Block 1%NH4OH.


title: RussellDG-Mtb-Rv+CDC1551 spotted oligo array

city: Ithaca

first: Kyle

middle: Herman

last: Rohde

address: Vet. Med. Center, C5 101

department: Microbiology and Immunology

institute: Cornell University

organism: Mycobacterium tuberculosis

manufacturer: Oligo library designed/synthesized by Operon, Inc.  Arrays printed by Center For Gene Expression Profiling (CGEP) at the Boyce Thompson Institute

middle: H

first: Robert

middle: B

last: Abramovitch

first: David

middle: G

last: Russell

manufacture_protocol: The version 1.1 Mtb 70-mer oligo library was used.  It contains a totall of 4320 70-mers, including targets for 3,924 ORFs annotated for strain H37Rv by Sanger plus an additional 371 ORFs from strain CDC1551 (TIGER) with less than 97% homology to H37Rv.  Oligos are Tm normalized to 79C +/- 5 degrees C.  Negative controls are 25 randomized 70-mers.  Positive control - mix of 4295 Mtb specific 70-mers.  Oligos were spotted using a Genomic Solutions (previously BioRobotics), MicroGrid Pro arrayer equipped with Micro-Spot 2500 pins (BioRobotics) onto Corning UltraGap slides. Each target wass spotted in duplicate  After spotting slides were UV irradiated at 200 milli-Joules in a BioRad UV box and then baked  for 1-2 hours at 85C.  They were then washed with 1%SDS for 2 minutes, then 2X Milli-Q water wash, dunk in 100% ethanol for 10 seconds and dried by centrifugation at 600RPM for 3 minutes.


title: MHP Human Chromosome 1 tile path CGH array version 2

status: Public on Nov 09 2007

city: Cambridge

first: Koichi

last: Ichimura

address: Addenbrooke's Hospital Box 231

department: Pathology

institute: University of Cambridge

description: The chromosome 1 tile path array clone set has been assembled by the Mapping Core, Map Finishing and Microarray Facility groups of the Wellcome Trust Sanger Institute, Hinxton, UK. Additional chromosome 1 clones were kindly supplied by the Wellcome Trust Sanger Institute. The 5Mb clone set has been selected from the 1Mb clone set assembled in the Wellcome Trust Sanger Institute. The array has 24 subarrays (6 rows by 4 columns), each subarray consisted of 18 rows by 17 columns.

manufacturer: Department of Pathology, Univeristy of Cambridge

first: Danita

middle: M

last: Pearson

last: Carter

first: Anthony

last: Brown

first: V

middle: P

last: Collins

manufacture_protocol:
1.BAC/PAC clones were grown in 2xTY medium in a deep-well titre plate at 37°C overnight with chloramphenicol 25µg/ml (BAC) or kanamycin 20µg/ml (PAC).
2. DNA was extracted from BAC or PAC clone using modified alkali-lysis method (microprepping).
3. Approximately 5ng of BAC/PAC DNA was PCR-amplified using three DOP-primers (Fiegler H, Genes Chromosomes Cancer 36:361-374, 2003).
4. Two microlitre of the DOP-PCR products was further amplified using 5'-Aminolink universal primer (Fiegler H, Genes Chromosomes Cancer 36:361-374, 2003).
5. Three volumes of the Amino-PCR products were mixed with one volume of 4xSpotting buffer (1M Sodium phosphate buffer, pH8.5, 0.001% Sarkosyl) to make a spotting mix.
6. The spotting mix was filtered through Corning 96 well white polystyrene filter plate with modified styrene insert (0.2µm PVDF) by centrifugation.
7. The filtered spotting mix was transferred to a 384-well plate.
8. The spotting mix was printed printed in duplicate onto a CodeLink slide (GE Healthcare) using a MicroGrid II robot (Genomic Solutions, Huntingdon, UK) in 4x4 subarrays.
9. The printed slides were incubated at room temperature for 24-72 hours in a humidified chamber.
10. The slides were treated with 1% ammonium hydroxide at room temperature for 5 min, then with 0.1% SDS at room temperature for 5min.
11. The slides were heat-denatured in a boiling water for 2 min, cooled, rinsed with water and dried.


title: CGH-CHORI-32K-Chr. 5 13

description: The array contains 3634 distinct BAC and PAC sequences. The bacs were printed in 2 replicates. In total the array design contains 7392 features printed in a layout of 4 meta rows, 4 meta columns, 21 rows per block and 22 columns per block.  This grid is printed twice on the glass slides allowing for two microarray arrays per slide.


title: Affymetrix Plasmodium falciparum 5K (SrcMalaria )

status: Public on Nov 10 2007

city: Bronx

first: Johanna

middle: Patricia

last: Daily

address: 1301 Morris Park Avenue, Price Center

department: Medicine (Infectious Disease)

institute: Albert Einstein College of Medicine

organism: Plasmodium falciparum

description: chip provided by Karine Gaelle Le Roch (University of California, Riverside)

manufacture_protocol: see Manufacturer's website


title: MHP Human Chromosome 1 tile path CGH array version 1

description: The chromosome 1 tile path array clone set has been assembled by the Mapping Core, Map Finishing and Microarray Facility groups of the Wellcome Trust Sanger Institute, Hinxton, UK. The array has 24 subarrays (6 rows by 4 columns), each subarray consisted of 18 rows by 18 columns.

first: Cordelia

middle: F

last: Langford

first: Simon

last: Gregory

first: Rachel

last: Cooper

manufacture_protocol: As described in Fiegler H et al. Genes Chromosomes Cancer 36:361-374, 2003


title: Keck Glycine max 18kB cDNA array_prints 201-206

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

organism: Glycine max

description: see Vodkin et al., BMC Genomics 5:73 (2004) for details of cDNAs represented on the arrays and Thibaud-Nissen et al., Plant Physiol 132:118-136 (2003); Zou et al. Mol Plant Microbe Interat 18:1161-1174 (2005); Zabala and Vodkin, Plant Cell 17: 2619-2632 (2005) for use of cDNA arrays in soybean.

manufacturer: Vodkin laboratory, University of Illinois and W.M. Keck Center, University of Illinois

first: L

middle: O

first: D

last: Gonzalez

first: A

last: Khanna

first: R

last: Shealy

first: S

middle: J

last: Clough

first: G

last: Zabala

first: J

last: Tuteja

first: M

last: Stromvik

last: Jones

last: Bari

last: Band

last: Gong

last: Liu

manufacture_protocol: PCR amplified cDNA inserts printed with Genemachines Omnigrid


title: Eurogentec S. pombe ORF array (A170F)

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

organism: Schizosaccharomyces pombe

manufacture_protocol:
rimary PCR: The PCR reactions are performed using tagged genome specific primers in the presence of genomic DNA (provided by your laboratory). We normally achieve a success rate of 93 % of PCR reactions. For the failed PCR reactions we perform three different protocols of PCR conditions, which include different MgCl2 concentrations and different Taq polymerase. We should normally get an additional 2 % working and reach a success rate of 95 % in total. We check 5 % of the total oligos by Mass Spectrometry and will re-synthesize maximum 2 % of the oligos based on a newly designed primer. We will perform the PCR reactions with the new designed oligonucleotides with the standard PCR protocol. Following this process we reach usually 97 % success rate.
Secondary PCR: amplifications will be performed using a single pair of primers annealing to tag sequences introduced on primary PCR primers. These PCR amplifications will also be controlled by agarose gel electrophoresis and repeated if required reaching a minimum of 95 % success rate. The final PCR products will contain an amino group at their 5' end to promote the attachment of the predicted gene coding DNA strand to the treated glass slides.


title: Illumina HumanHap300 array

status: Public on Nov 06 2007

city: Brisbane

first: Stuart

last: Macgregor

state: Queensland

address: 300 Herston Road

department: Genetic Epidemiology

country: Australia

institute: Queensland Institute of Medical Research

description: HumanHap300 Genotyping BeadChip provides genome-wide coverage using >318,000 tag SNPs chosen from the International HapMap Project.

manufacture_protocol: see the manufacturer's website


title: U. Toronto Saccharomyces cerevisiae y6.4k2.gal cDNA array

status: Public on Nov 02 2007

city: Boston

first: Suzanne

last: Komili

state: MA

address: 44 Binney St.

institute: Harvard University

organism: Saccharomyces cerevisiae

first: Natalie

last: Farny

first: Frederick

last: Roth

first: Pamela

middle: A

last: Silver

manufacture_protocol: Double-spotted array containing 6,240 yeast ORFS (plus control spots totalling 6.4k)


title: Nimblegen Homo sapiens 4 array Tiling Set

city: King of Prussia

first: Joel

last: Greshock

address: 2301 Renaissance Blvd.

department: Translational Medicine, Oncology

institute: GlaxoSmithKline

description:
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
Build: HG18, NCBI 36

first: Bin

last: Feng

first: Barbara

middle: L

last: Weber

first: Lynda

last: Chin

manufacture_protocol:
Oligonucleotide arrays were designed as described by Selzer et al. (2005).  As part of the probe design process, regions targeted for coverage were repeat-masked and covered by 50-75 mer oligos spaced at ~1.5 kb intervals.  Probes were generated from both strands, and replicated on the array 3 times. This platorm consists of 4 arrays that collectively tile the entire human genome, each of which is broadly organized by chromosome.  These were constructed by maskless array synthesis technology (NimbleGen Systems Inc.), containing 385,000 oligonucleotides per array.  Each was synthesized by photolithography.
Selzer, R. R. et al. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44, 305-19 (2005).


title: MGDP Zea mays Unigene 01_01_05

city: Mississippi State

first: Rowena

middle: Yvette

last: Kelley

state: MS

address: 810 Highway 12 East

department: Corn Host Plant Resistance Research Unit (CHPRRU)

institute: USDA-ARS

organism: Zea mays

manufacture_protocol: The maize Unigene I arrays fabricated by the Maize Gene Discovery Project contain 5376 ESTs (for more information, see http://www.maizegdb.org/). Within these arrays, the cDNA samples are printed three times next to each other; consequently, average signal intensities and the ratio between co-hybridized samples could be assessed multiple times within each microarray and within experiments. These arrays contain cDNAs recovered from libraries of mixed adult tissues (707 and 945), mixed stages of embryo development (687), and salt-stressed roots (603).


title: INDAC Drosophila melanogaster 15K v5.0

city: Los Angeles

first: Thomas

middle: Daniel

last: Goldman

address: 1050 Childs Way Room 201B

department: Molecular and Computational Biology

institute: University of Southern California

manufacture_protocol: 15,158 oligonucleotide probes representing all known and predicted open-reading-frames, based on release 4.1 of the Drosophila melanogaster genome were synthesized. The long oligonucleotide sequences were designed by the International Drosophila Array Consortium (INDAC) using a custom implementation of OligoArray2. The oligonucleotides were designed with size ranges between 65-69 nucleotides, a minimal Tm window, bias towards the 3’-ends of transcripts, and minimal sequence similarity to other genes. The oligonucleotide sequences can be downloaded from Flymine


title: Agilent Homo sapiens 185K array

manufacture_protocol:
see manufacturer's web site at http://www.agilent.com/
Test array -- final design is Agilent-014068


title: NIAID Ecab -- E. coli 6.5K

status: Public on Nov 01 2007

city: Bethesda

first: Timothy

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

organism: Escherichia coli

manufacturer: NIAID Microarray Research Facility (NIH/NIAID)

first: Guojian

last: Jiang

first: Michael

last: Wilson

manufacture_protocol:
Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions (http://www.genomicsolutions.com) that is fitted with a printhead and 16 SMP3 print tips from Telechem (http://www.arrayit.com).
The E. coli microarray (Ecab) probe set is based on 70mer oligonucleotides from Operon's E. coli Genome Oligo Set Version 1.0 (http://omad.operon.com/download/index.php).
Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl) to a normaliz
The Ecab microarray spot densities are 200 microns (center-to-center).
The microarrays are printed on Epoxy Slides from Corning (Catalog # 40042) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: JCVI PFGRC Streptococcus pneumoniae 13K v2 array designed primarily based on strain TIGR4

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Streptococcus pneumoniae

description: This set includes 2852 reporters, has 13824 spots distributed in 96 blocks.

manufacture_protocol: 2QSP, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 5369763, pen id 10181, pen cycles -1, operator Jon, humidity control On, humidity set point65


city: Tsukuba

first: Emiko

last: Kitagawa

state: Ibaraki

address: Onogawa 16-1

institute: National Institute of Advanced Industrial Science and Technology

description:
Hitachisoft Hypergene Yeast Chip Ver. 0 (lot 60)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.

manufacture_protocol: see manufacturer's web site


title: Hitachisoft Hypergene Yeast Chip Ver. 0 (lot 89-94)

description:
Hitachisoft Hypergene Yeast Chip Ver. 1 (lot 89-94)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


title: Myxococcus xanthus Microarray consortium 6.7K cDNA array

city: Marburg

first: Lotte

last: Sogaard-Andersen

address: Karl-von-Frisch-Str.

department: Ecophysiology

institute: Max Planck Institute for Terrestrial Microbiology

organism: Myxococcus xanthus

manufacture_protocol: spotted cDNA array


description:
Hitachisoft Hypergene Yeast Chip Ver. 0 (lot 55)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


description:
Hitachisoft Hypergene Yeast Chip Ver. 0 (lot 53,54,56,57,58)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


title: TIGR PFGRC Aspergillus fumigatus v2 array designed primarily based on strain Af293

city: Ribeirao Preto

first: Gustavo

middle: Henrique

state: Sao Paulo

address: Avenida do Café, s/n

department: Departament of Pharmaceutical Sciences

country: Brazil

institute: Faculty of Pharmaceutical Sciences of Ribeirao Preto

organism: Aspergillus fumigatus

description:
This set includes 9674 oligonucleotides, has 22176 spots distributed in 48 blocks.

The condensed array layout file (ie, 1x representation of oligos) is linked below as a supplementary file.

manufacturer: TIGR PFGRC (The Pathogen Functional Genomics Resource Center)

first: Frederico

last: Soriani

first: Iran

last: Malavazi

manufacture_protocol: 2QAF, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


description:
Hitachisoft Hypergene Yeast Chip Ver. 0 (lot 46)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


description:
Hitachisoft Hypergene Yeast Chip Ver. 0 (lot 70)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


description:
Hitachisoft Hypergene Yeast Chip Ver. 0 (lot 49)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


description:
Hitachisoft Hypergene Yeast Chip Ver. 2.0 (lot 01-37)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


description:
Hitachisoft Hypergene Yeast Chip Ver. 0 (lot 50)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


description:
Hitachisoft Hypergene Yeast Chip Ver. 0 (lot 41,42,43,44)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


description:
Hitachisoft Hypergene Yeast Chip Ver. 0 (lot 33,35,36)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


description:
Hitachisoft Hypergene Yeast Chip Ver. 0 (lot 25,26,27,28)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


title: Hitachisoft Hypergene Yeast Chip Ver. 1-1 (Lot55)

description:
Hitachisoft Hypergene Yeast Chip Ver. 1-1 (48 block Lot55)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


title: FHCRC Immunology Chicken 4.2k cDNA microarray

city: Seattle

first: Ryan

last: Basom

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

organism: Gallus gallus

description:
FHCRC Immunology Chicken cDNA Microarray (Neiman,
et. al, PNAS, 98: 6378-6383 (2001)).  The annotation for this platform was generated during November of 2003.

manufacture_protocol: The array was constructed by mechanically spotting PCR products onto standard glass microscope slides.


title: Hitachisoft Hypergene Yeast Chip Ver. 1-1 (Lot06-13)

description:
Hitachisoft Hypergene Yeast Chip Ver. 1-1 (48 block Lot06-13)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


description:
Hitachisoft Hypergene Yeast Chip Ver. 0 (lot 29,30,31)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


title: Hitachisoft Hypergene Yeast Chip Ver. 1-1 (Lot27-28)

description:
Hitachisoft Hypergene Yeast Chip Ver. 1-1 (48 block Lot27-28)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


title: Hitachisoft Hypergene Yeast Chip Ver. 1-1 (Jan)

description:
Hitachisoft Hypergene Yeast Chip Ver. 1-1 (48 block Jan)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


title: Streptococcus pneumoniae TIGR4 Eurogentec Microarrays

city: Toulouse

first: Julien

last: Storai

address: 135 avenue de Rangueil

country: France

institute: CNRS

last: Storaï

first: Bernard

last: Martin

first: Chantal

last: Granadel

first: Jean-Pierre

last: Claverys

first: Nic

last: Lindley

manufacture_protocol:
Streptococcus pneumoniae MicroArray was designed and developed in close collaboration with the Molecular Genetics group at the University of Groningen, The Netherlands (Prof. Dr. O.P. Kuipers, Dr. J. Kok) and Laboratory of Pediatrics, Erasmus Medical Center, Rotterdam (Dr. P.W.M. Hermans, Prof. Dr. R. de Groot). The genome sequence of the gram-positive pathogenic bacterium Streptococcus pneumoniae has been released and the sequence information can be obtained at ftp://ftp.tigr.org/pub/data/s_pneumoniae/. From 2105 unique sequences provided on the web site we select 2085 ORFs. Specific primers were designed to amplify all 2085 putative ORFs. The primers were selected carefully to amplify only a specific region of each ORF. Universal sequences of 15 bases were incorporated on the 5' of each specific forward and reverse primer. The PCR reactions were performed in two rounds using 96-well plates in a 100 ml reaction volume. The first round of PCR reaction (primary PCR) was done using 10 ng of DNA genomic as template and the specific part of the oligo. The second round of PCR reactions (secondary PCR) was performed in the presence of 5 ul of 40-fold diluted primary PCR products and the C12-NH2 modified universal primers. The entire primary and the secondary PCR reactions were controlled on standard gel electrophoresis for yield and for the expected size. Using these two-step methods we have successfully amplified up to 96 % of 2085 S. pneumoniae ORFs. The 5'-aminated PCR products were purified using Millipore 96-well purification kit, concentrated to 200 to 500 ng per microliter and then covalently immobilization onto aldehyde coated glass slide through a well-known Schiff base reaction.
S. pneumoniae MicroArrays are manufactured by printing PCR amplicons suspended in optimized spotting buffer for high coupling efficiency of DNA to the most consistent aldehyde coated glass slides. This spotting chemistry provides us the highest hybridization intensities, which is a consequence of a better binding of the probe to the slides and their accessibility to the cDNA targets. We use ChipWriter™ Pro (Virtek) which is a high precision dispensing robot to spot the PCR products onto aldehyde glass slides. The robot is designed to collect 100 nl of DNA solution and to deposit 0.6 nl per spot. For S. pneumoniae MicroArray, we use simultaneously 16 pins to place the spots in area of 1.8 x 1.8 cm. In order to generate high quality spots, the printing procedure is performed under a tight controlled humidity and temperature environment. This allows having the complete control on the spot morphology, the spot diameter and uniformity. This configuration of the robot generates 16 blocks, each containing 15 x 15 dots with 200 microns spacing center to center with a spot diameter of 100 microns. Note that the pattern of spotting could be different from the one mentioned above.


description:
Hitachisoft Hypergene Yeast Chip Ver. 0 (lot 21)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


title: NIA 15K Mouse (AGRF Nov 2001)

status: Public on Oct 16 2007

city: Parkville

first: Stephen

last: Nutt

state: Vic

address: 1G Royal Pde

department: Molecular Medicine

institute: Walter and Eliza Hall Institute of Medical Research

first: Clare

last: Pridans

first: Melissa

last: Holmes

first: Matthew

last: Polli

first: James

last: Wettenhall

first: Aleksandar

last: Dakic

first: Lynn

last: Corcoran

first: Gordon

middle: K

last: Smyth

first: Steve

manufacture_protocol: Spotted NIA 15k cDNA clones


title: Nimblegen Hg18 Promoter (2 of 2)

city: Davis

first: Kimberly

middle: Rose

last: Blahnik

address: GBSF 1 Shields Ave

department: Genome and Biomedical Sciences

institute: University of California Davis

organism: Homo sapiens

description: Promoter Tiling Array

manufacture_protocol: as described on Nimblegen website


title: NICHE Human ENL and LNCaP v1.0

city: Coleraine

first: Mark

middle: John

last: McCann

state: Northern Ireland

address: Cromore road

department: Northern Ireland Centre for Food and Health

institute: University of Ulster

description: The Oligo GEArray® Human Prostate Cancer Biomarkers Microarray profiles the expression of 263 genes useful as molecular markers in the prognosis and diagnosis of prostate cancer.

first: Chris

middle: I

last: Gill

first: Hugh

last: McGlynn

first: Ian

middle: R

last: Rowland

manufacture_protocol:
The LNCaP cell line was obtained from the European Collection of Cell Cultures (ECACC, Salisbury UK) and cultured in RPMI 1640 medium (Gibco Life Technologies, Paisley UK) supplemented with 2.0mM l-glutamine (Gibco), 10.0mM HEPES (Sigma), 1% penicillin-streptomycin (Gibco), 1% of a 45% glucose solution (Sigma), and 10% foetal bovine serum (Gibco), with the media refreshed every ninety-six hours. Enterolactone (CAS 78473-71-9, Fluka, Schelldorf Germany) was prepared at 60μM in cell-line specific media (0.72% DMSO v/v). All control treatments were cell-line specific media adjusted to contain 0.72% DMSO (v/v).
The cells were grown to 70% confluence as triplicate independent experiments and treated with either enterolactone or media, before incubation for 72 hours under standard cell culture conditions. The total RNA was isolated using RNeasy Mini kit and treated with DNase I (Qiagen, Crawley UK) following the manufacturers guidelines. RNA purity and concentration was measured using the NanoDrop spectrophotometer and all RNA purities were between 1.8 and 2.0.
The total RNA from treated and untreated cells extracted previously was sent in dry ice by overnight courier to SuperArray Bioscience Corporation (Frederick, USA) for microarray analysis using the Oligo GEArray® Human Prostate Cancer Biomarkers Microarray (OHS-403). The experiment was performed in triplicate. The microarray data was analysed for significance using the students’ t-test, with a value of p=0.05 taken as significant.
Manufacturer details (ref Superarray)
Quality Control:
Suspend in 10 mM Tris pH 8.0 @ > 0.1 mg/ml
A260/A280 > 2.0 and A260/A230 > 1.7 in Tris pH 8.0
For Total RNA, 28S:18S agarose gel band intensity ~ 2:1
Experimental format
EXP1 Control  and enterolactone
EXP2 Control  and enterolactone
EXP3 Control  and enterolactone
Dye swaping used
Expression data calculated from mean of experiments.
Experimental outline available at the SuperArray website (Oligo GEArray Gene Expresssion Array Protocol)
Agarose Gel or BioAnalyzerElectropherogram


title: Nimblegen Hg18 Promoter (1 of 2)

description: Promoter Tiling Array


title: MMX

status: Public on Sep 14 2007

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

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


title: SHGE


title: SHGC


title: MMAJ

status: Public on Aug 15 2007


title: MMAG


title: Streptococcus pneumoniae  TIGR4 v6 codY

status: Public on Apr 17 2007

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

organism: Streptococcus pneumoniae TIGR4

last: de Jong

manufacture_protocol: Amplicon array on ArrayIt superamine slides


title: SHFS

status: Public on Aug 09 2007


title: SHFA


title: SHEU


title: MIT/WI Bartel D. melanogaster 454 2007

status: Public on Jun 10 2007

city: San Francisco

middle: Graham

last: Ruby

address: 1700 4th Street QB3 s404

department: Biochemistry

institute: UCSF

organism: Drosophila melanogaster

technology: other

distribution: virtual

manufacture_protocol: see www.454.com


title: MMAF

status: Public on Nov 10 2006


title: UCSF-CCC Homo sapiens 2.5K HumArray2.0 (2464 BAC clones each printed in triplicate)

status: Public on Mar 06 2007

first: Antoine

last: Snijders

address: 2340 Sutter Street

department: Cancer Research Institute

institute: University of California San Francisco

first: Marlies

last: Nowee

first: Jane

last: Fridlyand

first: Jurgen

last: Piek

first: Josephine

last: Dorsman

first: Ajay

last: Jain

first: Daniel

last: Pinkel

first: Paul

last: van Diest

first: Rene

last: Verheijen

first: Donna

last: Albertson

manufacture_protocol:
Isolation of BAC/P1 DNA.  We inoculated 0.1ul of a glycerol stock of BAC or P1 containing bacteria into 5 ml LB media containing chloramphenicol (10 ug/ml) or kanamycin (50 ug/ml) for BACs or P1s, respectively and incubated the cultures overnight (~16 h) at 37  degrees C with agitation at 225 rpm.  We prepared larger cultures for DNA isolation, by inoculating 25 ml
LB media, containing the appropriate antibiotic with 200 ul of the previously grown overnight culture and incubating in a shaking incubator at 37  degrees C at 225 rpm overnight (~16 h).  We monitored bacterial growth by measuring the OD of a 1:10 dilution, which preferably ranged between 0.25 and 0.35 at a wavelength of 600 nm.  We used the Qiagen Plasmid Mini kit to isolate DNA, following a modified version of the Qiagen Plasmid Mini Purification protocol.  We transferred the 25 ml cultures into 50 ml tubes and centrifuged them for 15 min at 4000 rcf at 4  degrees C to pellet the bacteria.   We re-suspended the pellet in Qiagen buffer P1 (1.5 ml), containing RNase A at the manufacturer’s recommended concentration and then added buffer P2 (1.5 ml).  We mixed the tubes extremely gently by inversion and incubated at room temperature for 5 min. Then, we added buffer P3 (1.5 ml), again mixed very gently by inversion and incubated on ice for 10 min.  We inverted each tube once and centrifuged at 4000 rpm at 4  degrees C until the supernatant became clear (45 to 60 min).  We filtered the supernatant through a 35-micron nylon mesh prior to loading onto Qiagen-tip 20 columns, which had been equilibrated following the manufacturer’s protocol.  We followed the manufacturer’s protocol for the DNA isolation steps with the exception that the elution buffer QF was heated to 65  degrees C before it was added to the column.  After elution, we added 0.56 ml isopropanol to the DNA and incubated overnight at 4  degrees C.  We collected the DNA pellet by centrifugation for 45 min at 14000 rpm at 4  degrees C.  After aspirating the supernatant, we allowed the pellet to dry in air for at most 30 min before re-suspending the DNA in 50 ul of H2O.  We determined the DNA concentration using a fluorometer.  The yield typically ranged between 60-100 ng/ul (i.e. 3-5 ug per isolation). To ascertain DNA purity, we digested each BAC (200 ng) with HindIII and electrophoresed the digest through a 0.75% agarose gel.  We discarded DNA preparations that showed a significant contamination with host bacterial DNA, seen as a background smear of degraded DNA in the gel.
Preparation of BAC/P1 DNA representations by ligation-mediated PCR.  We digested the DNA with MseI by incubating overnight at 37  degrees C in a 5 ul reaction containing 1.5 ul DNA (20 to 600 ng), 0.4 U/ul MseI (New England Biolabs), and 0.4x One-Phor-All-Buffer-Plus (Amersham).  For ligation of adapters, we diluted 1 ul of each digest to a final concentration of 1 ng/ul with H2O and then mixed 1 ng of the digested DNA with 0.5 ul One-Phor-All-Buffer-Plus (10x, Amersham), 0.5 ul of 100 uM Primer 1 (TAACTAGCATGC), 0.5 ul of 100 uM Primer 2 (5’ aminolinker AGTGGGATTCCGCATGCTAGT) and 5.5 ul H2O. We incubated the mixture at 65  degrees C for 1 min after which we ramped the temperature down to 15  degrees C with a ramp-speed of 1.3  degrees C per minute.  When the temperature reached 15  degrees C, we added 1 ul of 10 mM ATP and 1 ul T4-DNA ligase (5 U/ul, Gibco BRL) and continued incubation at 15  degrees C overnight.  To initiate the first round of PCR amplification, we added a 40 ul mixture, consisting of 3 ul PCR Buffer 1 (Expand Long Template PCR System, Roche), 2 ul of a mixture of each nucleotide (10 mM) and 35 ul H2O to the ligation reaction.  Before we started the PCR program, we incubated the reaction at 68  degrees C for 4 min and then added 1 ul DNA polymerase (3.5 U/ul, Expand Long Template PCR System, Roche).  We carried out thermal cycling in a Perkin-Elmer Gene Amp PCR System 9700 block as follows: 94  degrees C for 40 s, 57  degrees C for 30 s, 68  degrees C for 1.25 min for 14 cycles, followed by, 94  degrees C for 40 s, 57  degrees C for 30 s, 68  degrees C for 1.75 min for 34 cycles and 94  degrees C for 40 s, 57  degrees C for 30 s and 68  degrees C for 5 min for the final cycle.   We electrophoresed 3.5 ul of the PCR product through a 1% agarose gel to determine the size range of the amplified DNA, which ideally ranged from 100 to 2000 bp.  To make the DNA for spotting on the arrays, we carried out a second round of amplification in a 100 ul reaction containing 1 ul of the primary PCR product, 4 uM Primer 2, TAQ-buffer II (1x; Perkin Elmer), 0.2 mM dNTP mix, 5.5 mM MgCl2 (Perkin Elmer), 2.5 U Amplitaq Gold (Perkin Elmer) and H2O. We carried out an initial incubation at 95  degrees C for 10 min in a MJ Research Peltier Thermal Cycler 225, followed by 95  degrees C for 30 s, 50  degrees C for 30 s and 72  degrees C for 2 min for 45 cycles and finally 7 min at 72  degrees C.  This reaction yields ~10 ug of DNA, with each fragment containing a 5’ amino linker.
Preparation of DNA spotting solutions.  We evaporated the amplification reaction (100 ul) to a final volume of 50 ul by incubation at 45  degrees C in a hybridization oven (Techne, Hybridizer HB-1D) for approximately 75 min and then added 2.5 volumes of ice-cold ethanol and 0.1 volumes of 3 M NaOAc to precipitate the DNA.  (The use of ethanol precipitation proved superior to isopropanol precipitation.)  We inverted the tubes and chilled them at –20  degrees C for 15 min before collecting the precipitate by centrifugation at 1699 rcf for 90 min.  We washed the pellets with 70% ethanol (150 ul) and collected them by centrifugation at 1699 rcf for 45 min.  We air-dried the pellets for approximately 60 to 90 min and then re-suspended them in 12 ul of 20% DMSO in H2O (~0.8 ug/ul).  We transferred the DNA solutions into 864 well microtitre plates for robotic arraying.  Previously, we prepared DNA for spotting in 80% DMSO and 0.3 ug/ul nitrocellulose.  However, we subsequently evaluated spotting solutions containing various concentrations of dimethyl formamide, formamide or DMSO, with or without nitrocellulose.  We determined that nitrocellulose was not required for spotting DNA prepared by PCR using primers with 5’amino linkers and that spotting solutions made with 20% DMSO performed well.  We have also generated representations of large insert clones for arraying by using degenerate oligonucleotide primed PCR and by amplification of mixtures of subclones from BACs, but found the ligation-mediated PCR procedure to be superior.
Array printing.  We used a custom built printer, employing a 4 x 4 array of quartz capillary tubes spaced on 3 mm centers to print ~70-100 μm diameter spots on 130 μm centers.  We printed each DNA solution in triplicate to create an array of ~7500 elements in a 12 mm square area.  We printed the arrays on chromium coated microscope slides (PTI or Nanofilm) for these studies, but also routinely print the arrays on glass slides (Corning GAPs).  We allowed the printed slides to dry overnight, then exposed the slides to UV light (65 mJ) in a UV Stratalinker 2400 (Stratagene).  We hybridized to these slides without additional treatment, except for the pre-hybridization slide blocking described below.  We found no indication of DNA loss from the spots at any stage of the procedure when we performed hybridization in formamide buffers at 37 °C.


title: JCVI PFGRC Mycobacterium smegmatis 30K v2 array designed primarily based on strain MC2 155

status: Public on Feb 10 2007

first: PFGRC

last: JCVI

organism: Mycolicibacterium smegmatis

description: This set includes 6158 oligonucleotides, has 30000 spots distributed in 48 blocks.

manufacture_protocol: 2QMS, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: moc

status: Public on Jul 17 2007

organism: Mus musculus


title: SHEW

status: Public on Oct 18 2006


title: JCVI PFGRC Aspergillus fumigatus 22K v3 array designed primarily based on strain Af293

status: Public on Jun 05 2007

description: This set includes 9674 oligonucleotides, has 22176 spots distributed in 48 blocks.

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


title: mob


title: PulseChip 2

city: Raleigh

first: Tristan

last: Coram

state: NC

address: 4118 Williams Hall, NC State University

institute: USDA-ARS, NC State University

organism:
Cicer arietinum
Lathyrus sativus

manufacturer: RMIT University, School of Applied Sciences, Bundoora AUSTRALIA

middle: E

first: Eddie

last: Pang

first: Nitin

last: Mantri

manufacture_protocol:
Coram TE and Pang ECK. 2006. Expression profiling of chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Published in Plant Biotechnology Journal.
A total of 715 ESTs and 12 controls were used in the construction of 727-feature microarrays according to minimum information about a microarray experiment guidelines (MIAME). Of the 715 ESTs, 516 were obtained from a previously synthesized and characterized EST collection constructed from cDNA of the ascochyta blight resistant ICC3996 chickpea genotype. Briefly, 1021 ESTs were generated from stem/leaf tissue of ICC3996 harvested after inoculation with A. rabiei spores, and assembled into 516 unigenes employed in the construction of this microarray. A single clone was selected to represent each contig. A further 43 chickpea cDNAs whose sequencing reactions had previously failed were also included in this microarray. The remaining 156 ESTs represent potential defence-related ESTs from a grasspea (Lathyrus sativus) cDNA library constructed from the Mycosphaerella pinodes resistant genotype ATC80878.  The 12 controls included negative, printing, and blank buffer controls. All samples were dried in 384-well plates before being resuspended in 10 µL 50% (v/v) dimethylsulphoxide:water at 250 ng/µL, and arrayed onto amino-silanized slides (Corning Incorporated Life Sciences, Acton, MA) using a BioRobotics® MicroGrid II Compact (Genomic Solutions, Ann Arbor, MI) with four Microspot 2500 pins (Genomic Solutions, Ann Arbor, MI). Blank buffer spots, digested vector and PCR primer were also incorporated as negative controls, as well as Cy5-10T as a printing control. Each element was deposited six times with a volume of approximately 6 nL and diameter of 200 µm. Slides were pre-hybridised by blocking in 5X SSC, 0.1% SDS, 25% Formamide, 1% BSA for 45 min at 42ºC, rinsed in distilled water and dried.


title: MMO

status: Public on Oct 04 2006

last: Stanford Microarray Database


title: SHGJ


title: SHFR


title: Judelson/Syngenta_Phytophthora infestans_15645_V.1

status: Public on Mar 30 2007

city: Riverside

first: Howard

middle: S

last: Judelson

address: Boyce Hall

department: Plant Pathology

institute: University of California

organism: Phytophthora infestans

description: The GeneChip is not available commercially.

first: Waraporn

last: Prakob

manufacture_protocol: The Phytophthora GeneChip array was manufactured by Affymetrix under contract with Syngenta Corporation.  This was a PM/MM design which covers genes predicted from a combination of EST sequencing and genomic sequencing.  Each predicted gene is interrogated with 20 probe pairs each (25mers).  Other details of the chip design are proprietary.


title: MMP

status: Public on Oct 03 2006


title: MMS


title: JCVI PFGRC Trypanosoma brucei 37K v2 array designed primarily based on strain TREU927

status: Public on Sep 21 2006

organism: Trypanosoma brucei

description: This set includes 8381 oligonucleotides, has 37632 spots distributed in 48 blocks.

manufacture_protocol: 2QTB, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Trypanosoma cruzi 26K v1 array designed primarily based on strain CL Brener

organism: Trypanosoma cruzi

description: This set includes 11141 oligonucleotides, has 26496 spots distributed in 48 blocks.

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


title: JCVI PFGRC Vibrio cholerae 19K v2 array designed primarily based on strain El Tor N16961

organism: Vibrio cholerae

description: This set includes 3811 oligonucleotides, has 19008 spots distributed in 96 blocks.

manufacture_protocol: 2QVC, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 5885507, pen id 0, pen cycles -1, operator Jon, humidity control On, humidity set point65


title: JCVI PFGRC Streptococcus pneumoniae 17K v4 array designed primarily based on strain TIGR4

status: Public on Sep 19 2006

description: This set includes 3312 oligonucleotides, has 17280 spots distributed in 96 blocks.

manufacture_protocol: 4QSP, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 5886915, pen id 0, pen cycles -1, operator Jon, humidity control On, humidity set point65


title: MMJ


title: JCVI PFGRC Trypanosoma brucei 9K v1 array designed primarily based on strain TREU927

description: This set includes 8381 oligonucleotides, has 9672 spots distributed in 24 blocks.

manufacture_protocol: QTB, with arrayer LUCIDEA, mode Normal, replicates 1, repeats 1, slide_dips 25, machine cycles 4622083, pen id 10179, pen cycles -1, operator Kathy/Jon, humidity control On, humidity set point65


title: JCVI PFGRC Streptococcus pneumoniae 17K v4 array designed primarily based on strain R6


title: JCVI PFGRC Streptococcus pneumoniae 17K v4 array designed primarily based on strain G54


title: JCVI PFGRC Staphylococcus aureus 32K v5 array designed primarily based on strain pLW043

status: Public on Sep 15 2006

organism: Staphylococcus aureus

description: This set includes 4531 oligonucleotides, has 32448 spots distributed in 48 blocks.

manufacture_protocol: 5QSA, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Staphylococcus aureus 32K v5 array designed primarily based on strain N315


title: JCVI PFGRC Staphylococcus aureus 32K v5 array designed primarily based on strain MSSA476


title: JCVI PFGRC Staphylococcus aureus 22K v4.1 array designed primarily based on strain MW2

description: This set includes 4531 oligonucleotides, has 22080 spots distributed in 96 blocks.

manufacture_protocol: 4QSA, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 1785606, pen id 0, pen cycles -1, operator Jon, humidity control On, humidity set point65


title: JCVI PFGRC Staphylococcus aureus 32K v5 array designed primarily based on strain MRSA252


title: JCVI PFGRC Staphylococcus aureus 32K v5 array designed primarily based on strain COL


title: JCVI PFGRC Staphylococcus aureus 22K v4.1 array designed primarily based on strain MSSA476


title: JCVI PFGRC Staphylococcus aureus 22K v4.1 array designed primarily based on strain pLW043


title: JCVI PFGRC Staphylococcus aureus 32K v5 array designed primarily based on strain Mu50


title: JCVI PFGRC Staphylococcus aureus 22K v4.1 array designed primarily based on strain COL


title: JCVI PFGRC Staphylococcus aureus 22K v4.1 array designed primarily based on strain Mu50


title: JCVI PFGRC Neisseria gonorrhoeae 30K v2 array designed primarily based on strain MC58

status: Public on Sep 13 2006

organism: Neisseria gonorrhoeae

description: This set includes 5387 oligonucleotides, has 30000 spots distributed in 48 blocks.

manufacture_protocol: 2QNG, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: 2005-09-28_Crawford_HG17_Set25

status: Public on Nov 18 2007

first: Sean

last: Davis

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

first: Gregory

last: Crawford

manufacture_protocol: Oligonucleotides spaced approximately every 100 base pairs across the entire non-repetitive human genome were synthesized in situ on a 38-array set.


title: JCVI PFGRC Staphylococcus aureus 32K v5 array designed primarily based on strain MW2


title: JCVI PFGRC Neisseria gonorrhoeae 14K v1 array designed primarily based on strain Z2491

description: This set includes 5387 oligonucleotides, has 14688 spots distributed in 48 blocks.

manufacture_protocol: QNG, with arrayer LUCIDEA, mode Normal, replicates 2, repeats 1, slide_dips -1, machine cycles 993646, pen id 10164, pen cycles -1, operator Shamria/Robin, humidity control On, humidity set point65


title: JCVI PFGRC Staphylococcus aureus 22K v4.1 array designed primarily based on strain MRSA252


title: JCVI PFGRC Neisseria gonorrhoeae 30K v2 array designed primarily based on strain Z2491


title: JCVI PFGRC Neisseria gonorrhoeae 14K v1 array designed primarily based on strain MC58


title: JCVI PFGRC Neisseria gonorrhoeae 14K v1 array designed primarily based on strain FA1090


title: JCVI PFGRC Salmonella typhimurium 31K v4 array designed primarily based on strain Ty2

organism: Salmonella enterica subsp. enterica serovar Typhimurium

description: This set includes 5459 oligonucleotides, has 31200 spots distributed in 48 blocks.

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: JCVI PFGRC Staphylococcus aureus 22K v4.1 array designed primarily based on strain N315 [FULL_FEATURE_LAYOUT]


title: JCVI PFGRC Treponema denticola 13K v1 array designed primarily based on strain ATCC 35405

organism: Treponema denticola

description: This set includes 2744 oligonucleotides, has 13824 spots distributed in 96 blocks.

manufacture_protocol: QTD, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 7449021, pen id 10189, pen cycles -1, operator Kathy, humidity control On, humidity set point65


title: JCVI PFGRC Porphyromonas gingivalis 10K v2 array designed primarily based on strain W83

organism: Porphyromonas gingivalis

description: This set includes 1903 oligonucleotides, has 10752 spots distributed in 96 blocks.

manufacture_protocol: 2QPG, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 7245441, pen id 10175, pen cycles -1, operator BJ, humidity control On, humidity set point65


title: JCVI PFGRC Rickettsia prowazekii 9K v1 array designed primarily based on strain Wilmington

organism: Rickettsia prowazekii

description: This set includes 1393 oligonucleotides, has 9216 spots distributed in 96 blocks.

manufacture_protocol: QRP, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 1879974, pen id 0, pen cycles -1, operator Jon, humidity control On, humidity set point65


title: JCVI PFGRC Salmonella typhimurium 31K v4 array designed primarily based on strain LT2; SGSC 1412; ATCC 700720


title: JCVI PFGRC Rickettsia prowazekii 9K v1 array designed primarily based on strain Madrid E


title: JCVI PFGRC Salmonella typhimurium 31K v4 array designed primarily based on strain CT18


title: JCVI PFGRC Pseudomonas aeruginosa 18K v1 array designed primarily based on strain PAO1

organism: Pseudomonas aeruginosa

description: This set includes 5552 oligonucleotides, has 18720 spots distributed in 72 blocks.

manufacture_protocol: QPA, with arrayer LUCIDEA, mode Normal, replicates 3, repeats 1, slide_dips 38, machine cycles 3165894, pen id 10184, pen cycles -1, operator Jon, humidity control On, humidity set point65


title: JCVI PFGRC Neisseria gonorrhoeae 30K v2 array designed primarily based on strain FA1090


title: JCVI PFGRC Plasmodium falciparum 31K v2 array designed primarily based on strain 3D7

organism: Plasmodium falciparum

description: This set includes 5204 oligonucleotides, has 31200 spots distributed in 48 blocks.

manufacture_protocol: 2QPF, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Candida albicans 23K v1 array designed primarily based on strain SC5314

status: Public on Sep 08 2006

organism: Candida albicans

description: This set includes 7001 oligonucleotides, has 23232 spots distributed in 48 blocks.

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


title: JCVI PFGRC Listeria monocytogenes 27K v2 array designed primarily based on strain 4b H7858

status: Public on Sep 09 2006

organism: Listeria monocytogenes

description: This set includes 6228 oligonucleotides, has 27648 spots distributed in 48 blocks.

manufacture_protocol: 2QLM, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: SHEB

status: Public on Sep 11 2006

organism: Homo sapiens

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


title: JCVI PFGRC Chlamydia pneumoniae 10K v2 array designed primarily based on strain CWL029

status: Public on Aug 30 2006

organism: Chlamydia pneumoniae

description: This set includes 2059 oligonucleotides, has 10752 spots distributed in 96 blocks.

manufacture_protocol: 2QCP, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 7178241, pen id 10188, pen cycles -1, operator bj, humidity control On, humidity set point65


title: JCVI PFGRC Listeria monocytogenes 27K v2 array designed primarily based on strain EGD-e


title: JCVI PFGRC Listeria monocytogenes 13K v1 array designed primarily based on strain EGD-e

description: This set includes 6228 oligonucleotides, has 13872 spots distributed in 48 blocks.

manufacture_protocol: QLM, with arrayer LUCIDEA, mode Normal, replicates 2, repeats 1, slide_dips 38, machine cycles 3617783, pen id 10175, pen cycles -1, operator MICROARRAY, humidity control On, humidity set point65


title: JCVI PFGRC Chlamydia pneumoniae 10K v2 array designed primarily based on strain J138


title: JCVI PFGRC Francisella tularensis 12K v1 array designed primarily based on strain F6168

organism: Francisella tularensis

description: This set includes 2331 oligonucleotides, has 12288 spots distributed in 96 blocks.

manufacture_protocol: QFT, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 1747430, pen id 0, pen cycles -1, operator Jon, humidity control On, humidity set point65


title: JCVI PFGRC Fusobacterium nucleatum 30K v2 array designed primarily based on strain ATCC10953

organism: Fusobacterium nucleatum

description: This set includes 4230 oligonucleotides, has 30000 spots distributed in 48 blocks.

manufacture_protocol: 2QFN, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Listeria monocytogenes 13K v1 array designed primarily based on strain 4b H7858


title: JCVI PFGRC Helicobacter pylori 13K v2.1 array designed primarily based on strain J99

organism: Helicobacter pylori

description: This set includes 2571 oligonucleotides, has 13824 spots distributed in 96 blocks.

manufacture_protocol: 2QHP, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 5881667, pen id 0, pen cycles -1, operator Jon, humidity control On, humidity set point65


title: JCVI PFGRC Listeria monocytogenes 13K v1 array designed primarily based on strain 1/2a F6854


title: JCVI PFGRC Francisella tularensis 12K v1 array designed primarily based on strain Schu4


title: JCVI PFGRC Yersinia pestis 11K v1 array designed primarily based on strain CO92

organism: Yersinia pestis

description: This set includes 4645 oligonucleotides, has 11520 spots distributed in 48 blocks.

manufacture_protocol: QYP, with arrayer LUCIDEA, mode Normal, replicates 2, repeats 1, slide_dips 50, machine cycles 2714963, pen id 0, pen cycles -1, operator microarray, humidity control On, humidity set point65


title: JCVI PFGRC Listeria monocytogenes 27K v2 array designed primarily based on strain 1/2a F6854


title: JCVI PFGRC Fusobacterium nucleatum 30K v2 array designed primarily based on strain ATCC_25586


title: JCVI PFGRC Mycobacterium tuberculosis 22K v2.1 array designed primarily based on strain CDC1551

status: Public on Sep 12 2006

organism: Mycobacterium tuberculosis

description: This set includes 4742 oligonucleotides, has 22080 spots distributed in 96 blocks.

manufacture_protocol: 2QMT, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 1783814, pen id 0, pen cycles -1, operator Jon, humidity control On, humidity set point65


title: JCVI PFGRC Listeria monocytogenes 27K v2 array designed primarily based on strain 4b F2365


title: JCVI PFGRC Mycobacterium tuberculosis 32K v3 array designed primarily based on strain CDC1551

description: This set includes 4742 oligonucleotides, has 32448 spots distributed in 48 blocks.

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


title: JCVI PFGRC Yersinia pestis 11K v1 array designed primarily based on strain KIM


title: JCVI PFGRC Listeria monocytogenes 13K v1 array designed primarily based on strain 4b F2365


title: JCVI PFGRC Francisella tularensis 12K v1 array designed primarily based on strain LVS


title: JCVI PFGRC Chlamydia pneumoniae 10K v2 array designed primarily based on strain D/UW-3/CX


title: JCVI PFGRC Helicobacter pylori 13K v2.1 array designed primarily based on strain 26695


title: JCVI PFGRC Clostridium botulinum 17K v2 array designed primarily based on strain Hall_strain_A

organism: Clostridium botulinum

description: This set includes 3617 oligonucleotides, has 17280 spots distributed in 96 blocks.

manufacture_protocol: 2QCB, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 1779334, pen id 0, pen cycles -1, operator Jon, humidity control On, humidity set point65


title: JCVI PFGRC Chlamydia pneumoniae 10K v2 array designed primarily based on strain AR39


title: JCVI PFGRC Aspergillus fumigatus 22K v2.1 array designed primarily based on strain Af293

organism: Aspergillus fumigatus

description: This set includes 9674 oligonucleotides, has 22176 spots distributed in 48 blocks.

manufacture_protocol: 2QAF, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Burkholderia mallei 32K v1 array designed primarily based on strain K96243

organism: Burkholderia mallei

description: This set includes 9826 oligonucleotides, has 32448 spots distributed in 48 blocks.

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


title: JCVI PFGRC Aspergillus fumigatus 11K v1 array designed primarily based on strain Af293

description: This set includes 9657 oligonucleotides, has 11160 spots distributed in 24 blocks.

manufacture_protocol: QAF, with arrayer LUCIDEA, mode Normal, replicates 1, repeats 1, slide_dips -1, machine cycles 5156742, pen id 10180, pen cycles -1, operator Jon/Kathy, humidity control On, humidity set point65


title: JCVI PFGRC Burkholderia mallei 32K v1 array designed primarily based on strain ATCC 23344


title: JCVI PFGRC Bacillus anthracis 13K v1 array designed primarily based on strain Ames

organism: Bacillus anthracis

description: This set includes 5602 oligonucleotides, has 13056 spots distributed in 48 blocks.

manufacture_protocol: QBA, with arrayer LUCIDEA, mode Normal, replicates 2, repeats 1, slide_dips 38, machine cycles 3050982, pen id 10186, pen cycles -1, operator MICROARRAY, humidity control On, humidity set point65


title: CDS-Chlamy-1.1

status: Public on Aug 18 2006

organism: Chlamydomonas reinhardtii

manufacturer: Janos,,Demeter; Dept. Genetics, CCSR 2255, Stanford, CA, USA, 94305; 726-0075; jdemeter@genome.stanford.edu


title: JCVI PFGRC Bacillus anthracis 27K v2 array designed primarily based on strain A2012

description: This set includes 5821 oligonucleotides, has 27648 spots distributed in 48 blocks.

manufacture_protocol: 2QBA, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: PulseChip 1

status: Public on Aug 01 2006

organism:
Cicer arietinum
Lathyrus sativus
Lens culinaris

first: Edwin

middle: C

first: Barkat

middle: M

last: Mustafa

manufacture_protocol:
Coram TE and Pang ECK. 2006. Expression profiling of chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Published in Plant Biotechnology Journal.

A total of 715 ESTs, 41 RGA DNA sequences, and 12 controls were used in the construction of 768-feature microarrays according to minimum information about a microarray experiment guidelines (MIAME). Of the 715 ESTs, 516 were obtained from a previously synthesized and characterized EST collection constructed from cDNA of the ascochyta blight resistant ICC3996 chickpea genotype. Briefly, 1021 ESTs were generated from stem/leaf tissue of ICC3996 harvested after inoculation with A. rabiei spores, and assembled into 516 unigenes employed in the construction of this microarray. A single clone was selected to represent each contig. A further 43 chickpea cDNAs whose sequencing reactions had previously failed were also included in this microarray. The remaining 156 ESTs represent potential defence-related ESTs from a grasspea (Lathyrus sativus) cDNA library constructed from the Mycosphaerella pinodes resistant genotype ATC80878. Finally, the 41 RGA sequences were isolated from lentil (Lens culinaris) genotypes ILL6002 (A. lentis susceptible) and ILL7537 (A. lentis resistant). The 12 controls included negative, printing, and blank buffer controls. All samples were dried in 384-well plates before being resuspended in 10 µL 50% (v/v) dimethylsulphoxide:water at 250 ng/µL, and arrayed onto amino-silanized slides (Corning Incorporated Life Sciences, Acton, MA) using a BioRobotics® MicroGrid II Compact (Genomic Solutions, Ann Arbor, MI) with four Microspot 2500 pins (Genomic Solutions, Ann Arbor, MI). Blank buffer spots, digested vector and PCR primer were also incorporated as negative controls, as well as Cy5-10T as a printing control. Each element was deposited six times with a volume of approximately 6 nL and diameter of 200 µm. Slides were pre-hybridised by blocking in 5X SSC, 0.1% SDS, 25% Formamide, 1% BSA for 45 min at 42ºC, rinsed in distilled water and dried.


title: JCVI PFGRC Bacillus anthracis 27K v2 array designed primarily based on strain Ames


title: JCVI PFGRC Burkholderia mallei 32K v1 array designed primarily based on strain GB8 horse 4


title: JCVI PFGRC Burkholderia mallei 32K v1 array designed primarily based on strain 1710b


title: JCVI PFGRC Yersinia pestis 30K v2 array designed primarily based on strain CO92

status: Public on Jun 22 2006

description: This set includes 4826 oligonucleotides, has 30000 spots distributed in 48 blocks.

manufacture_protocol: 2QYP, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Actinobacillus actinomycetemcomitans 12K v1 array designed primarily based on strain HK1651

organism: Aggregatibacter actinomycetemcomitans

description: This set includes 2303 oligonucleotides, has 12288 spots distributed in 96 blocks.

manufacture_protocol: QAA, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 7392081, pen id 10179, pen cycles -1, operator Susie, humidity control On, humidity set point65


title: SHDW

status: Public on Mar 08 2006

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


title: University of Pisa Dugesia japonica Dj600-chip

status: Public on Jul 19 2006

city: Pisa

first: Leonardo

last: Rossi

address: Via Volta 4

department: Morfologia Umana e Biologia Applicata

country: Italy

institute: University of Pisa

organism: Dugesia japonica

manufacturer: Immunogenetics Section, Department of Transfusion Medicine, Clinical Center, NIH

first: Alessandra

last: Salvetti

first: Francesco

last: Marincola

first: Annalisa

last: Lena

first: Paolo

last: Deri

first: Linda

last: Mannini

first: Renata

last: Batistoni

first: Ena

last: wang

first: Vittorio

last: Gremigni

manufacture_protocol: 612 gene specific 60 mer sense oligonucleotides (Tm from 79 to 88) were synthesized by Invitrogen. Oligonucleotides were re-suspended in 3XSSC at the concentration of 0.5 μg/μl (25 μM) and spotted onto poly-D-lysine coated slides with a configuration of 4 x 13 x 13 using OmniGrid robotic printer (Genemachine). Printed slides were kept in a desiccator at room temperature for 15 days. After UV cross-linking, slides were blocked with succinic anhydride for 15 minutes rinsed in distilled water and denatured in boiling water for 2 minutes. After quick dehydrate in 95% ethanol, slides were dried by centrifugation at 800 rpm for 3 minutes and stored in a desiccators until use.


title: JCVI PFGRC Bacillus anthracis 13K v1 array designed primarily based on strain A2012

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

institute: J. Craig Venter Institute


title: LC-33

status: Public on May 23 2006


title: SHET


title: SHEV


title: SMG

status: Public on May 24 2006

organism: Mus musculus

manufacturer: Gavin,,Sherlock; School of Medicine, Department of Genetics, Stanford, CA, United States, 94305; 650-498-6012; sherlock@genome.stanford.edu


title: SHER


title: SHAF

status: Public on Feb 25 2006


title: SHEH


title: SHGT


title: JBB

manufacturer: Tina,,Boussard; School of Medicine, Department of Genetics, Stanford, CA, United States, 94305; 650-736-0077; boussard@genome.stanford.edu


title: SHFM

status: Public on Mar 15 2006


title: SHEG


title: SHDE


title: SHGG


title: SVK

status: Public on Mar 04 2006


title: SHGA


title: SHBU

status: Public on Feb 01 2006


title: CE_printW

status: Public on Jan 28 2006

organism: Caenorhabditis elegans

manufacturer: John,,Matese; Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Room 135, Princeton, NJ, United States; (609) 258-8309; jcmatese@genomics.princeton.edu


title: ECD3

status: Public on Jan 31 2006

organism: Escherichia coli


title: CE_printY

status: Public on Jan 25 2006


title: CE_printT


title: SHEE

organism: Homo sapiens


title: LC-24

status: Public on Jan 11 2006


title: CE_printS

status: Public on Feb 03 2006


title: SHEK


title: SHEM


title: Print_872


title: SHDV

status: Public on Jan 21 2006


title: SHDO

status: Public on Jan 07 2006


title: SHES

status: Public on Jan 10 2006


title: SHDR


title: SHEP


title: SHDQ

status: Public on Jan 19 2006


title: LC-26


title: CE_printV

status: Public on Jan 06 2006


title: SHDU


title: SHDN


title: SHEI


title: SHBD


title: SHDS

status: Public on Dec 30 2005


title: SHCO


title: SHCT

status: Public on Dec 29 2005


title: SHBF


title: print_122


title: SHEJ


title: SHCM

status: Public on Dec 21 2005


title: MMH


title: SHBL


title: MMA


title: JCVI PFGRC Yersinia pestis 30K v2 array designed primarily based on strain KIM

status: Public on Aug 30 2006


title: SHCZ


title: SHBW


title: SHDL


title: SHDF


title: SHCR


title: SHBO


title: SHCN


title: MSU2_12-00

status: Public on Dec 03 2005

organism: Arabidopsis thaliana

manufacturer: Jeremy,,Gollub; CCSR 2255, Stanford, California  94305; 650-736-0075; jgollub@genome.stanford.edu


title: SHCW


title: Print_108


title: CIW-5_09-01

status: Public on Dec 20 2005


title: SHDM


title: LC-14

status: Public on Dec 17 2005


title: SHCI

status: Public on Nov 24 2005


title: Cohen-31k-b

status: Public on Dec 31 2005


title: LC-21

status: Public on Nov 23 2005


title: SHDD


title: SHBI


title: SHBS


title: MMF


title: SHCK

status: Public on Dec 15 2005


title: SHBC


title: MMG


title: Print_79

status: Public on Nov 26 2005


title: MMD


title: Print_78

status: Public on Nov 19 2005


title: Print_127


title: CE_printP


title: LC-25


title: SHAU

status: Public on Nov 03 2005


title: SHCQ

status: Public on Nov 04 2005


title: SHBK


title: MMM


title: SHCV


title: LC-11

status: Public on Nov 16 2005


title: LC-30


title: LC-12


title: SHQ

status: Public on Oct 25 2005


title: SHAG


title: SHAN


title: SHAQ

status: Public on Oct 22 2005


title: Print_122


title: LC-31


title: SHCE


title: SHBG


title: LC-19


title: SHAB


title: SHBA


title: SHY


title: SHAI


title: SHAE

status: Public on Oct 13 2005


title: LC-20

status: Public on Oct 18 2005


title: Cohen-31K1a

status: Public on Oct 20 2005


title: SHBJ


title: SHBY


title: SHW


title: SHAW


title: SHAO


title: SHAD

status: Public on Oct 15 2005


title: SHAL


title: SHAS


title: SHAY


title: SHAV

status: Public on Sep 23 2005


title: SHAH

status: Public on Sep 30 2005


title: SHP


title: Cohen-20K1a


title: SHAP


title: SHAX


title: SHAM


title: DM-11_00_2000

status: Public on Sep 10 2005

organism: Drosophila melanogaster


title: DM-07_02_2000


title: ecoli_12

manufacturer: Catherine,,Ball; Stanford University School of Medicine, Department of Genetics, CCSR Room 2255b, Stanford, CA, USA, 94305; 650-498-6012; ball@genome.stanford.edu


title: MMAC

status: Public on Sep 17 2005

manufacturer: Stanford Functional Genomics Facility,  Stanford School of Medicine


title: DM-07_2000-25col


title: SHU


title: DM-03_00_2000


title: SHR


title: MME

status: Public on Nov 23 2005


title: CIW2.5Kv4

status: Public on Sep 09 2005


title: ECD1a-list1


title: LC-39


title: SHAK


title: OSUrbt Oncorhynchus mykiss 1.6K v2.0

status: Public on Sep 06 2005

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

organism: Oncorhynchus mykiss

description: 4 X 4 pin arrangement Microspot 2500 pins (quill design)

first: S.

first: L.

middle: G

last: Gerwick

first: C.

last: Rosato

last: Givan

first: G.

last: Bailey

middle: J

last: Bayne

first: D.

last: Williams

manufacture_protocol: Oligonucleotides were resuspended in spotting buffer (3X SSC and 1.5 M betaine) at 25 uM final concentration and were printed onto Corning UltraGap slides (Acton, MA) using a Biorobotics Microgrid II arrayer (Genomic Solutions, Ann Arbor, MI) with 16 pins.  The trout 70-mers were each printed in duplicate and a set of ten SpotReport Alien Oligos (Stratagene, La Jolla, CA) were printed 16 times (once per block) on the array.  After printing, slides were desiccated for 24-48 hrs and cross-linked with UV Stratalinker (Stratagene) at 600 mJ.


title: CIW-6_11-01

status: Public on Aug 26 2005

last: Stanford Microarray Database

state: CA


title: ecoli_10


title: LC-9

status: Public on Aug 27 2005


title: MSU-2_03-00


title: CIW-7_02-02


title: SVJ

status: Public on Aug 25 2005


title: CIW-4_08-01


title: SVI


title: HA27


title: SHAC


title: CE_printL

status: Public on Aug 13 2005


title: CIW-4_09-01


title: TGC

organism: Toxoplasma gondii


title: ecoli_9.0


title: TGB


title: CE_printR

status: Public on Aug 20 2005


title: SHCG (2)

status: Public on Jul 30 2005


title: CDS-Chlamy-1.0

status: Public on Jul 28 2005


title: SHBV


title: SHAA

status: Public on Jul 23 2005


title: ToxoGondii_1


title: SHAJ


title: SVL_SVM_SVN_SVO


title: MMAB


title: CE_PrintJ

status: Public on Jul 22 2005


title: SHX

status: Public on Jul 21 2005


title: MMU

status: Public on Jul 16 2005


title: MMC

status: Public on Jul 29 2005


title: CE_printU

status: Public on Jul 20 2005


title: ce_printD


title: CE_printG_H_I


title: SCA-B

organism: Saccharomyces cerevisiae

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


title: CE_printK


title: TGD


title: Cohen-HJ3


title: Yeast Splicing Chip v4.0

status: Public on Apr 02 2002

city: Santa Cruz

first: Manuel

last: Ares

institute: UC Santa Cruz

description:
This is an oligonucleotide microarray designed to measure splicing in yeast.  Each intron containing gene has 3 features (Splice Junction, Intron, Exon2).  The SJ oligo symmetrically spans the splice junction with 20nt on each side.  The SJ, Int, and Ex2 oligos are custom designed 40-mers.  The array also contains about 1000 70-mers from the Operon Yeast Genome Set.  All of the SJ, Int, and Ex2 oligos are printed 4 times, the Operon 70-mers are printed only once.
Keywords = Splicing

first: Tyson

middle: A

last: Clark

first: Charles

middle: W

last: Sugnet


title: y15

status: Public on Feb 12 2002

description:
Tip Configuration: Standard 16-tip
Columns per Sector: 24
Column Spacing: 175
Row Spacing: 175


title: 2005-09-28_Crawford_HG17_Set30

status: Public on Nov 18 2007

city: Bethesda

first: Sean

last: Davis

state: MD

first: Gregory

last: Crawford

manufacture_protocol: Oligonucleotides spaced approximately every 100 base pairs across the entire non-repetitive human genome were synthesized in situ on a 38-array set.