title: [YG_S98] Affymetrix Yeast Genome S98 Array

status: Public on Mar 11 2002

city: Santa Clara

last: Affymetrix

state: CA

country: USA

institute: Affymetrix, Inc.

organism: Saccharomyces cerevisiae

technology: in situ oligonucleotide

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

June 03, 2009: annotation table updated with netaffx build 28
June 08, 2012: annotation table updated with netaffx build 32
: annotation table updated with netaffx build
July 01, 2016: annotation table updated with netaffx build 35

distribution: commercial

manufacture_protocol:
see manufacturer's web site

Has 9335 entries and was indexed 29-Jan-2002.
Contains probes for all known 6,400 yeast genes, and candidate open reading frames.  Based primarily upon the December 1998 version of the Saccharomyces Genome Database (SGD).
Corresponds to strain S288C.


title: [MG_U74B] Affymetrix Murine Genome U74B Array

status: Public on Jan 17 2002

organism: Mus musculus

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

The MG-U74 version 1 set comprises three arrays representing over 36,000 mouse genes and ESTs.

Keywords = high density oligonucleotide array
June 24, 2016: annotation table updated with netaffx build 35

manufacture_protocol: see manufacturer's web site


title: ehu/biozel_Chelonlabrosus_16kv2 [Agilent-022256 FISHtoTXIPs-II]

status: Public on Jul 31 2016

city: Leioa

first: Ibon

last: Cancio

address: B/sarriena s/n

country: Spain

institute: UPV/EHU

organism: Chelon labrosus

description:
Chelon labrosus,
Arrays of this design have barcodes that begin with 16022256 or 2522256.
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Feature Extraction feature number.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

distribution: custom-commercial

first: Oihane

last: Diaz de Cerio

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


title: [MG_U74C] Affymetrix Murine Genome U74C Array

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

The MG-U74 version 1 set comprises three arrays representing over 36,000 mouse genes and ESTs.

Keywords = high density oligonucleotide array
June 27, 2016: annotation table updated with netaffx build 35


title: Agilent-030447 UNMBIOCETI Biomphalaria glabrata 30K v1.0

status: Public on Jul 30 2016

city: Albuquerque

first: Coen

middle: M

last: Adema

state: NM

address: 1 University of New Mexico

department: CETI Biology MSC03 2020

institute: University of New Mexico

organism:
Schistosoma mansoni
Biomphalaria glabrata
Echinostoma paraensei

description:
Please note, this single spot/feature design (AMADID 030447) was superceded with a duplicate spot/feature design, using the same features.  The updated array design is AMADID 033677. For access to this platform, contact coenadem@unm.edu for collaborator status needed to purchase microarray from Agilent
Biomphalaria glabrata (fresh water planorbid snail), a small number of features derives from trematode parasites Schistosoma mansoni and Echinostoma paraensei

first: George

middle: H

last: Rosenberg

manufacture_protocol: Publicly available cDNA sequences (2010) for Biomphalaria glabrata were assembled using Mira. Transcripts were analyzed and as needed reverse complemented for longest continuous ORF. A total  of 30593 predicted transcripts, supplemented with 15 mitochondrial gene sequences from Biomphalaria glabrata, 26 (12 nuclear + 14 mitochondrial) gene sequences from Schistosoma mansoni and  12 (9 nuclear + 3 mitochondrial) gene sequences from Echinostoma paraensei) were used as targets for e-array (Agilent) design of unique 60-mer probe sequences. Single replicate probes were arranged in 8 x 60k custom microarray format with Agilent 60-mer SurePrint technology.  Design name Biomphalaria glabrata Transcriptomev1_28Sep10. Created date 28 Sep 2010. Feature layout: randomized. Design ID:030447.


title: Chipscreen/Operon Human Genome Array-Ready Oligo Set (Version 4.0)

status: Public on Mar 28 2017

city: Hefei

first: Rui

last: Li

state: Anhui

address: Huangshan Road 443, USTC West Campus

department: School of Life Sciences

country: China

institute: University of Science and Technology of China

organism: Homo sapiens

technology: spotted oligonucleotide

manufacturer: Operon Biotechnologies, Inc., Chipscreen Ltd.

manufacture_protocol:
Human whole genomic gene probe set (Operon AROS Version 4.0) were purchased from Operon biotechnologies, Inc., which composed of 91 plates in 384-well format and 34944 distinct probes (detailed as in the microarray gene list).
The PowerMatrix Slides were purchased from Fullmoon Biosciences, which designed to immobilize oligonucleotides for microarray applications. The slides were coated with proprietary polymer materials, which create a three dimensional matrix-like binding surface.
The probes were dissolved in 2 × printing buffer (from Fullmoon Biosciences) at a final concentration of 1 µg/µL and then ready for microarray printing.
The array format on the slide was composed of 48 small blocks (4 columns × 12 rows), each small block was composed of 729 probe spots (27 columns × 27 rows), so there are totally 34992 probe spots (48 blocks × 729 spots/block) on one slide. The diameter of each spot was about 125µM (plus 10% buffered area).
After printing, the microarray slides were incubated in a chamber with 65 – 75% relative humidity for 10-12 hours. Then the slides were mobilized by UV cross link at 400 mJ. Finally allow the slides to dry at room temperature for 30 minutes and then ready for use.


title: ehu/biozel_Chelonlabrosus_44kv1 [Agilent-026248 FISHtoTXIPs-III]

description:
chelon labrosus, thicklip grey mullet, TBT experimetn, pyrosequencing, high density
Arrays of this design have barcodes that begin with 16026248 or 2526248.
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Feature Extraction feature number.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Agilent-021146 Chelon labrosus Array [Probe Name version]


title: NADC MAP 70mer ver 1.0

status: Public on Jul 29 2016

city: Saint Paul

first: Elise

last: Lamont

state: MN

address: 1971 Commonwealth Avenue, Veterinary Science, Room 205

institute: University of Minnesota

organism: Mycobacterium avium subsp. paratuberculosis K-10

distribution: non-commercial

manufacturer: National Animal Disease Center, Ames, IA: Dr. John P. Bannantine

manufacture_protocol:
This is a protocol that works with the MicroGrid Compact array spotter from Apogent Discoveries.
Protocol uses poly-L-lysine coated slides from Fischer Thermo Scientific.
* Check the room humidity using the software. Ideally, want the chamber humidity around 45%. So if the room is above 55%, you might want to turn on the dehumidifier in the small room and close the door.
* Open the TAS application. The GRID file is pre set. Load this GRID file.
* Check to see if the reservoir tank needs filling. There is an indicator between the “fill” and “drain” buttons on the toolbar.
* Fill the two flat white reservoir trays with distilled water. The black one in the chamber is the main wash station. The reservoir will fill this one.
* The pins are stored in a white container that should be carefully removed away by pulling the pin assembly out sideways.
* Secure the pin assembly into the clamp above the sonicator bath and turn it on and let it run for 5 minutes. Then pull it out of the sonicator bath and spray compressed air on the pins. Put it back in the bath for another 5 minutes. No need to dry before putting it into the machine. Always degas the water prior to sonication.
* Within the application, click the green “Go” button on the menu bar. Now the software will prompt you as to what to do. Its initial instruction is to load the pin tool.
* Pull out the pin assembly and put it into the machine. The holder is spring loaded so push it up into the hole and twist a quarter turn. Once seated the empty pin holders should be toward the front.
* Put on gloves and open the sealed new packages of slides and place those on the slide tray in the machine.
* The first 8 slots on the top tray are reserved for the preblotting slides. The instrument is programmed to place 5 preblots on these slides before going over and doing the array slides to be used in experimental studies.
* The spotting buffer is 6 x SSC and 3M betaine. That is a 2x stock.
* Load slides from the back first then work toward the front. Be very careful as you get closer to the pin assembly. The slides should be placed in the hitches on the tray so that they are flush with the lower left tab. This makes the array location on each slide very consistent and helps when scanning.
* Once the top tray is completely loaded, close the lid, turn on the vacuum using the software and open the lid to check the seal on the vacuum by trying to move one of the slides. PUT THE FIRST SOURCE PLATE ON now as well, since you will not be prompted to do this later.
* Close the lid and click the okay button to make the second tray move forward. Load that tray with all remaining slides. Remember to date any excess slides you do store after removal from package and use those in the next run, if unexpired.
* For the MAP K-10 array, there are 15 source plates sealed and double bagged to prevent evaporation.
* Remove the tape of the first plate and seat it in the silver holder with the “A1” well in the lower left corner. Now you should be ready to click “ok” and you have about 20 minutes before needing to switch out the source plates.
* Machine is programmed as follows: wash #1, wash #2, black tray wash, dries, dips into source plate, pre-spots 5 times, then spots on slides. Does duplicate, then triplicate for each slide on the trays.
* For QC, check the initial spots shortly after the run begins. Shine a flashlight at an angle to see the spots. If they are not perfectly aligned, or you think there is a piece of lint that might be ruining the spotting, pull out either a single pin or the entire assembly and look at it under a dissecting microscope to find the problem. Then re-sonicate the problem pin or the entire assembly and try again. Check spotting frequently throughout the print run.
* When each source plate is completed, which takes about 20-22 minutes, then the computer indicates to put in the next source plate. Place it into the arrayer with the A1 well in the lower left corner, as before. Close the lid and click “OK” in the dialog box on the computer.
* After the last source plate is completed, the software prompts you to perform a series of clean-up steps.
* One thing you will be prompted to do is remove the printed slides. The first 8 preblotted slides should be disposed of. Collect the remaining slides, score the top left corner with a diamond pen, and place them in the box the manufacturer provided for storage.
* The pin tool can be removed for the sonication, air blowing and sonication treatment again. This time, give it a good air blow-drying at the very end before putting them back into the white container.
* In addition, empty the pins baths (flat white trays) and rinse them out and put them in the chamber upside down.


title: Illumina HiSeq 2500 (Arabidopsis thaliana; Cuscuta pentagona)

status: Public on Jul 28 2016

last: GEO

organism:
Arabidopsis thaliana
Cuscuta pentagona

technology: high-throughput sequencing

distribution: virtual


title: Rat oxidative stress and antioxidant defense RT2 profiler PCR array

city: Sheffield

first: Marta

last: Milo

state: South Yorkshire

address: Western Bank

department: Biomedical Science

country: United Kingdom

institute: University of Sheffield

organism: Rattus norvegicus

technology: RT-PCR

description:
DC-APC PCR assay panel
SABiosciences RT² Profiler panel of PCR assays.

manufacture_protocol: see manufacturer's website


title: Scophthalmus maximus clone id version [DesignID: 016528]

organism: Scophthalmus maximus

manufacturer: Facultad Veterinaria, Campus Universitario Pabellon IV 2 superior, Universidad Santiago Compostela

manufacture_protocol: An EST database from immune tissues was used to design the first high density turbot (Scophthalmus maximus) oligo-microarray with the aim of identifying candidate genes for tolerance to pathogens. Specific oligonucleotides (60mers) were successfully designed for 2716 out of 3482 unique sequences of the database.


title: Illumina HiSeq 2500 (Elodea nuttallii)

organism: Elodea nuttallii


title: Illumina HiSeq 2500 (Cuscuta pentagona)

organism: Cuscuta pentagona


title: Illumina HiSeq 3000 (Nitrobacter winogradskyi)

organism: Nitrobacter winogradskyi


title: NimbleGen Rice 3'-tiling 385K array

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

organism: Oryza sativa


title: [Mu11KsubA] Affymetrix Murine 11K SubA Array

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

June 03, 2009: annotation table updated with netaffx build 28
June 21, 2012: annotation table updated with netaffx build 32
July 08, 2016: annotation table updated with netaffx build 35

manufacture_protocol:
see manufacturer's web site

Has 13179 entries and was indexed 29-Jan-2002.


title: Full Moon Human Cell Cycle Control Phospho Antibody Array

city: Daejeon

first: Myung-Shin

last: Lee

address: Yongdu-dong, Jung-gu

department: Microbiology and Immunology

institute: Eulji University School of Medicine

technology: antibody

manufacture_protocol: See manufacturer's website (http://www.fullmoonbio.com/).


title: [MG_U74A] Affymetrix Murine Genome U74A Array

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

June 03, 2009: annotation table updated with netaffx build 28
June 21, 2012: annotation table updated with netaffx build 32
July 06, 2016: annotation table updated with netaffx build 35

manufacture_protocol:
see manufacturer's web site

The MG-U74 version 1 set comprises three arrays representing over 36,000 mouse genes and ESTs.


title: [Hu6800] Affymetrix Human Full Length HuGeneFL Array

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

Has 7129 entries and was indexed 29-Jan-2002.
Probes represent approximately 5,000 full-length human sequences.

Keywords = high density oligonucleotide array
July 08, 2016: annotation table updated with netaffx build 35


title: Illumina HiSeq 2500 (Solanum tuberosum)

organism: Solanum tuberosum


title: Agilent-036053 0GyP 4x180k CGH array [Feature Number version]

status: Public on Jul 27 2016

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

country: Japan

institute: Institute for Environmental Science

description:
Agilent-036053 0GyP

Arrays of this design have barcodes that begin with 16036053 or 2536053.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-036469 0GyQ 4x180k CGH array [Feature Number version]

description:
Agilent-036469 0GyQ

Arrays of this design have barcodes that begin with 16036469 or 2536469.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-035841 0GyO 4x180k CGH array [Feature Number version]

description:
Agilent-035841 0GyO

Arrays of this design have barcodes that begin with 16035841 or 2535841.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-031365 0GyE 4x180k CGH array [Feature Number version]

description:
Agilent-031365 0GyE

Arrays of this design have barcodes that begin with 16031365 or 2531365.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-033784 0GyH3 4x180k CGH array [Feature Number version]

description:
Agilent-033784 0GyH3

Arrays of this design have barcodes that begin with 16033784 or 2533784.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-031794 0GyG 4x180k CGH array [Feature Number version]

description:
Agilent-031794 0GyG

Arrays of this design have barcodes that begin with 16031794 or 2531794.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-032684 0GyI 4x180k CGH array [Feature Number version]

description:
Agilent-032684 0GyI

Arrays of this design have barcodes that begin with 16032684 or 2532684.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-045495 0GyU 4x180k CGH array [Feature Number version]

description:
Agilent-045495 0GyU

Arrays of this design have barcodes that begin with 16045495 or 2545495.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-031094 0Gy1D 8x60k CGH array [Feature Number version]

description:
Agilent-031094 0Gy1D

Arrays of this design have barcodes that begin with 16031094 or 2531094.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-039198 0GyA 4x180k CGH array [Feature Number version]

description:
Agilent-039198 0GyA

Arrays of this design have barcodes that begin with 16039198 or 2539198.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-039335 0GyC2 4x180k CGH array [Feature Number version]

description:
Agilent-039335 0GyC2

Arrays of this design have barcodes that begin with 16039335 or 2539335.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: [MG_U74Bv2] Affymetrix Murine Genome U74B Version 2 Array

manufacture_protocol:
see manufacturer's web site

The MG-U74 set includes 3 arrays with a total of 36899 entries and was indexed 29-Jan-2002.
The set represents ~36,000 full length genes and EST clusters derived from sequence clusters in Build 74 of the Mouse Unigene Database.


title: Agilent-031095 0GyD2 8x60k CGH array [Feature Number version]

description:
Agilent-031095 0GyD2

Arrays of this design have barcodes that begin with 16031095 or 2531095.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: [MG_U74Cv2] Affymetrix Murine Genome U74 Version 2 Array

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

June 03, 2009: annotation table updated with netaffx build 28
June 21, 2012: annotation table updated with netaffx build 32
June 24, 2016: annotation table updated with netaffx build 35


title: Agilent-060348 20mGyX 4x180k CGH array [Feature Number version]

description:
Agilent-060348 20mGyX

Arrays of this design have barcodes that begin with 16060348 or 2560348.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: [HG_U95A] Affymetrix Human Genome U95A Array

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

The Human Genome U95 (HG-U95) Set, consisting of five GeneChip arrays, contains almost 63,000 probe sets interrogating approximately 54,000 clusters derived from the UniGene database (Build 95).

Keywords = high density oligonucleotide array
July 08, 2016: annotation table updated with netaffx build 35


title: Agilent-060031 20mGyV 4x180k CGH array [Probe Name version]

description:
Agilent-060031 20mGyV

Arrays of this design have barcodes that begin with 16060031 or 2560031.


title: Agilent-059843 20mGyU 4x180k CGH array [Probe Name version]

description:
Agilent-059843 20mGyU

Arrays of this design have barcodes that begin with 16059843 or 2559843.


title: Agilent-039976 20mGyR 4x180k CGH array [Feature Number version]

description:
Agilent-039976 20mGyR

Arrays of this design have barcodes that begin with 16039976 or 2539976.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-039890 20mGyQ 4x180k CGH array [Feature Number version]

description:
Agilent-039890 20mGyQ

Arrays of this design have barcodes that begin with 16039890 or 2539890.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-038534 20mGyP 8x60k CGH array [Feature Number version]

description:
Agilent-038534 20mGyP

Arrays of this design have barcodes that begin with 16038534 or 2538534.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-038533 20mGyO 8x60k CGH array [Feature Number version]

description:
Agilent-038533 20mGyO

Arrays of this design have barcodes that begin with 16038533 or 2538533.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-037775 20mGyM 4x180k CGH array [Feature Number version]

description:
Agilent-037775 20mGyM

Arrays of this design have barcodes that begin with 16037775 or 2537775.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-037241 20mGyL 4x180k CGH array [Feature Number version]

description:
Agilent-037241 20mGyL

Arrays of this design have barcodes that begin with 16037241 or 2537241.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-032256 20mGyF 4x180k CGH array [Feature Number version]

description:
Agilent-032256 20mGyF

Arrays of this design have barcodes that begin with 16032256 or 2532256.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-039199 0GyB2 4x180k CGH array [Feature Number version]

description:
Agilent-039199 0GyB2

Arrays of this design have barcodes that begin with 16039199 or 2539199.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-034698 20mGyH 4x180k CGH array [Feature Number version]

description:
Agilent-034698 20mGyH

Arrays of this design have barcodes that begin with 16034698 or 2534698.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-031818 20mGyB 4x180k CGH array [Feature Number version]

description:
Agilent-031818 20mGyB

Arrays of this design have barcodes that begin with 16031818 or 2531818.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-031984 20mGyD 4x180k CGH array [Feature Number version]

description:
Agilent-031984 20mGyD

Arrays of this design have barcodes that begin with 16031984 or 2531984.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-032096 20mGyE 4x180k CGH array [Feature Number version]

description:
Agilent-032096 20mGyE

Arrays of this design have barcodes that begin with 16032096 or 2532096.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-047141 0GyZ 4x180k CGH array [Probe Name version]

description:
Agilent-047141 0GyZ

Arrays of this design have barcodes that begin with 16047141 or 2547141.


title: Agilent-033942 20mGyG 4x180k CGH array [Feature Number version]

description:
Agilent-033942 20mGyG

Arrays of this design have barcodes that begin with 16033942 or 2533942.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-046414 0GyX 4x180k CGH array [Probe Name version]

description:
Agilent-046414 0GyX

Arrays of this design have barcodes that begin with 16046414 or 2546414.


title: Agilent-038532 20mGyN 8x60k CGH array [Feature Number version]

description:
Agilent-038532 20mGyN

Arrays of this design have barcodes that begin with 16038532 or 2538532.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-045496 0GyV 4x180k CGH array [Feature Number version]

description:
Agilent-045496 0GyV

Arrays of this design have barcodes that begin with 16045496 or 2545496.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-035066 20mGyI 4x180k CGH array [Feature Number version]

description:
Agilent-035066 20mGyI

Arrays of this design have barcodes that begin with 16035066 or 2535066.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-063531 20mGyZ G4125A 4x180k CGH array [Feature Number version]

description:
Agilent-063531 20mGyZ G4125A

Arrays of this design have barcodes that begin with 16063531 or 2563531

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-063559 20mGyAA G4125A 4x180k CGH array [Feature Number version]

description:
Agilent-063559 20mGyAA G4125A

Arrays of this design have barcodes that begin with 16063559 or 2563559

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Illumina Genome Analyzer IIx (Ictidomys tridecemlineatus)

organism: Ictidomys tridecemlineatus


title: Agilent-031930 20mGyC 4x180k CGH array [Feature Number version]

description:
Agilent-031930 20mGyC

Arrays of this design have barcodes that begin with 16031930 or 2531930.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-032095 20mGyA 4x180k CGH array [Feature Number version]

description:
Agilent-032095 20mGyA

Arrays of this design have barcodes that begin with 16032095 or 2532095.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: [Pae_G1a] Affymetrix Pseudomonas aeruginosa Array

organism: Pseudomonas aeruginosa

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

This GeneChip probe array is a powerful tool for monitoring trascriptional regulation and antimicrobial agent response of P. aeruginosa. The array represents the annotated genome of P. aeruginosa strain PA01 and includes 5,549 protein-coding sequences, 18 tRNA genes, a representative of the ribosomal RNA cluster and 117 genes present in strains other than PA01.

In addition, 199 probe sets corresponding to all intergenic regions exceeding 600 base pairs have been included. The selected probes have been screened against sequence homologies in the existing database of human genes.

Keywords = high density oligonucleotide array
July 06, 2016: annotation table updated with netaffx build 35


title: Ion Torrent PGM (Gallus gallus)

organism: Gallus gallus


title: Agilent-046766 0GyY 4x180k CGH array [Probe Name version]

description:
Agilent-046766 0GyY

Arrays of this design have barcodes that begin with 16046766 or 2546766.


title: Ion Torrent Proton (Ciona robusta)

status: Public on Jul 26 2016

organism: Ciona robusta


title: [HG-Focus] Affymetrix Human HG-Focus Target Array

status: Public on Jul 18 2002

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

June 03, 2009: annotation table updated with netaffx build 28
June 21, 2012: annotation table updated with netaffx build 32
July 08, 2016: annotation table updated with netaffx build 35

manufacture_protocol:
see manufacturer's web site

Has 8793 entries and was indexed 13-May-2002.
Probe sets on this array represent gene sequences which are experimentally verified.


title: Agilent-046160 0GyW 4x180k CGH array [Probe Name version]

organism: Mus musculus

description:
Agilent-046160 0GyW

Arrays of this design have barcodes that begin with 16046160 or 2546160.


title: Illumina Genome Analyzer IIx (Medicago sativa)

organism: Medicago sativa


title: Agilent-036841 20mGyJ 4x180k CGH array [Feature Number version]

description:
Agilent-036841 20mGyJ

Arrays of this design have barcodes that begin with 16036841 or 2536841.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-040095 20mGyST 4x180k CGH array [Feature Number version]

description:
Agilent-040095 20mGyST

Arrays of this design have barcodes that begin with 16040095 or 2540095.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-061943 iTowgeN_3_131111

status: Public on Jul 25 2016

city: Sendai

first: Yoshinori

last: Kanayama

state: Miyagi

address: 1-1, Tsutsumidori-amamiyamachi, Aobaku

department: Graduate School of Agricultural Science

institute: Tohoku University

organism: Solanum lycopersicum

description:
tomato whole gene array from iTGA2.3

Arrays of this design have barcodes that begin with 16061943 or 2561943.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-065680 Hypericum perforatum array (Probe Name version)

city: Verona

first: Elisa

last: Gecchele

address: Strada Le Grazie

country: Italy

institute: University of Verona

organism: Hypericum perforatum

description: The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL22108.

relation: Alternative to: GPL22108 (feature number version)

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


title: Illumina HiSeq 2000 (Morus alba)

organism: Morus alba


title: Illumina Genome Analyzer IIx (Arvicanthis niloticus)

organism: Arvicanthis niloticus


title: Genotypic_Human_Hg19_CGH_2x400K_Array_068045

status: Public on Jul 22 2016

city: Singapore

first: Shumei

last: Chia

state: Singapore

country: Singapore

institute: Genome Institute of Singapore

organism: Homo sapiens


title: Agilent-048727 Symplocarpus renifolius custom microarray 4x44K

city: Miyazaki

first: Yasuko

last: Ito-Inaba

address: 1-1 Gakuenkibanadai-nishi

department: Organization for Promotion of Tenure Track

institute: University of Miyazaki

organism: Symplocarpus renifolius

description:
Agilent-048727 miyazaki_inaba_ozg_longseq
Arrays of this design have barcodes that begin with 16048727 or 2548727.
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Feature Extraction feature number.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Institute for Environmental Genomics Shewanella loihica Array

status: Public on Jul 21 2016

city: Norman

first: Ming

last: Xie

state: Oklahoma

address: 101 L DAVID BOREN BLVD

department: Microbiology and plant biology

institute: Institute for Environmental Genomics

organism: Shewanella loihica PV-4

manufacture_protocol: see site


title: Agilent-066133 20mGyW G4125A 4x180k CGH array [Probe Name version]

description:
Agilent-066133 20mGyW G4125A

Arrays of this design have barcodes that begin with 16066133 or 2566133


title: Custom Agilent C. albicans 8x15k Gene expression (AMADID: 026377) designed by Genotypic Technology Private LTD

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

organism: Candida albicans


title: Illumina HiSeq 3000 (Oryza sativa Japonica Group)

organism: Oryza sativa Japonica Group


title: Agilent-031721 0GyF 4x180k CGH array [Feature Number version]

description:
Agilent-031721 0GyF

Arrays of this design have barcodes that begin with 16031721 or 2531721.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Illumina HiSeq 2000 (Glehnia littoralis)

status: Public on Jul 20 2016

organism: Glehnia littoralis


title: SABiosciences  Mouse Wound Healing PCR Array assay panel

city: London

first: Miguel

middle: Angel

last: Burguillos

address: 4 Newark Street

institute: Queen Mary University of London

description:
PCR assay
SABiosciences RT² Profiler panel of PCR assays.


title: CustomArray Signaling Pathway 4x2k platform

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

technology: spotted DNA/cDNA

manufacture_protocol: CustomArray B3 synthesizer was used for oligonucleotide probe synthesis on CustomArray ECD 4X2K slides. Synthesis was performed according to manufacturer recommendations. Total 2227 unique oligonucleotide probes of 40 nucleotides in length  were placed on each of four arrays on the chip.


title: [AraGene-1_0-st] Arabidopsis Gene 1.1 ST Array [CDF: aragene10st_At_TAIRG version 18]

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

organism: Arabidopsis thaliana

manufacture_protocol: This is identical to GPL17416  but a custom CDF environment was used to extract data [Brainarray Version 18, aragene10st ]. CDF and other files can be downloaded at: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/18.0.0/tairg.asp


title: Illumina HiSeq 2000 (Dimocarpus longan)

status: Public on Jul 15 2016

organism: Dimocarpus longan


title: 017617 IMUL-Candida glabrata 8x15k [Probe name version]

status: Public on Jul 23 2016

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Nakaseomyces glabratus CBS 138

description:
The nucleotide sequences of the 5283 C. glabrata ORFs and the mitochondrial genome (release 2) were downloaded from the Génolevure Consortium (http://www.genolevures.org/). Following the Agilent eArray Design guidelines, two separate probe sets for each ORF were designed, each consisting of 60 base oligonucleotides. The probe selection was performed using the GE Probe Design Tool; probes were filtered following their base composition and distribution, cross-hybridization potential and melting temperature to yield two probes sets representing each 5210 nuclear and 6 mitochondrial ORFs. These probes cover more than 98% of the nuclear genome and represent 6 out of the 8 mitochondrial protein-encoding genes. For quality control and normalization purposes, 103 probes were selected randomly and spotted 20 times throughout each array in addition to standard Agilent controls. C. glabrata custom arrays were manufactured in the 8x15k format by Agilent Technologies.
Design ID 017617

relation: Alternative to: GPL10713 (gene name version)

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


title: Agilent-021146 Chelon labrosus FISHtoTXIPs array (Feature Number version)

city: Leioa

first: Ibon

last: Cancio

address: B/sarriena s/n

institute: UPV/EHU

organism: Chelon labrosus

description:
Chelon labrosus
Arrays of this design have barcodes that begin with 16021146 or 2521146.
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Feature Extraction feature number.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Illumina HiSeq 2500 (Postia placenta)

status: Public on Jul 18 2016

organism: Rhodonia placenta


title: Illumina HiSeq 2500 (Citrus trifoliata)

organism: Citrus trifoliata


title: Illumina HiSeq 2500 (Ulmus pumila)

organism: Ulmus pumila


title: Illumina HiSeq 2000 (Fusarium oxysporum f. sp. niveum)

status: Public on Jul 14 2016

organism: Fusarium oxysporum f. sp. niveum


title: Illumina HiSeq 2500 (Trichoderma reesei)

organism: Trichoderma reesei


title: Agilent-037725 HamArrayV2_exon_1323101544566_1323101884258 037724

status: Public on Jul 13 2016

city: Reus

first: Josep

middle: Maria

last: del Bas

state: Tarragona

address: Avd Universitat 1

institute: Centre tecnològic de Nutrició i Salut

organism: Mesocricetus auratus

description:
Segona versio del HamArray utilitzant sondes HamV3
Arrays of this design have barcodes that begin with 16037725 or 2537725.
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Feature Extraction feature number.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Illumina MouseWG-6 v2.0 R2 expression beadchip [gene symbol version]

organism: Mus musculus

technology: oligonucleotide beads

description:
The MouseWG-6 v2.0 Expression BeadChip offer the most up-to-date content for whole-genome expression profiling in the mouse. Featuring content derived from the National Center for Biotechnology Information Reference Sequence (NCBI RefSeq) database (Build 36, Release 22).
Please use the GEO Data Submission Report Plug-in v1.0 for Gene Expression which may be downloaded from https://icom.illumina.com/icom/software.ilmn?id=234 to format the normalized and raw data. These should be submitted as part of a GEOarchive. Instructions for assembling a GEOarchive may be found at http://www.ncbi.nlm.nih.gov/projects/geo/info/spreadsheet.html


title: NimbleGen Hydrogenobacter thermophilus TK-6 4X72K array Univ.of Tokyo v1.0

city: Tokyo

first: Masafumi

last: Kameya

state: No U.S. state/territory

address: 2-12-1, Ookayama, Meguro-ku

department: Earth-Life Science Institute

institute: Tokyo Institute of Technology

organism: Hydrogenobacter thermophilus TK-6

description:
Whole genome tiling array of Hydrogenobacter thermophilus TK-6 with 69,638 probe spaced every 25 bp along the genome. Probe sizes range from 50 to 74 bp. Probe sequences are available in the '2009-06-23_RDKK197_Hthe_expr.ndf' supplementary file.
2009-06-23_RDKK197_Hthe_expr.ndf
2009-06-23_RDKK197_Hthe_expr.ngd
2009-06-23_RDKK197_Hthe_expr.pos

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


title: [DrosGenome1] Affymetrix Drosophila Genome Array

status: Public on Mar 11 2002

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Drosophila melanogaster

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

Has 14010 entries and was indexed 29-Jan-2002
The sequences used to develop this array are accessible through FlyBase. Probes were synthesized in situ.
Contains >13,500 gene sequences predicted from annotation of the Drosophila genome version 1, >8000 sequences for which confirming EST or full-length cDNA evidence is available, ~3,000 genes identified using prediction algorithms, and ~2,500 genes that not only have a gene predicted algorithmically, but also show some homology to genes from other organisms.
For ~4,000 genes, expressed sequence alignment information from the Drosophila Gene Collection was used to modify the boundaries of the predicted transcript. In these cases, the probe sets correspond to the modified exon boundaries. In addition, several hundred ESTs close to predicted gene sequences, but lying outside of predetermined gene inclusion boundaries, are included.

Keywords = high density oligonucleotide array
July 06, 2016: annotation table updated with netaffx build 35

manufacture_protocol: see manufacturer's web site


title: Illumina MiSeq (Streptomyces venezuelae ATCC 10712)

status: Public on Jul 12 2016

last: GEO

organism: Streptomyces venezuelae ATCC 10712


title: Illumina HiSeq 2500 (Adeno-associated virus)

status: Public on Jul 19 2016

organism: Adeno-associated virus


title: Illumina MiSeq (Adeno-associated virus)


title: Illumina NextSeq 500 (Macaca nemestrina)

organism: Macaca nemestrina


title: Exiqon miRCURY LNA microRNA array, 6th generation [miRBase v17, condensed Probe_ID version]

city: Changsha

first: Hou-De

last: Zhou

state: Hunan

address: Renmin middle road 139

department: Department of Metabolism & Endocrinology

institute: The Second Xiangya Hospital, Central South University

description:
Supplier=Exiqon A/S
Product=miRCURY LNA microRNA Array, 6th generation - hsa, mmu & rno
ProductDate=November 2010
ProductNumber=208400,208401,208402
LotNumberRange=34101-34101
Organism(s)=Mus musculus, Mouse cytomegalovirus, Mouse gammaherpesvirus
GalFileCreationDate=2011-06-06 09:54
ArrayContents_DesignedFor=miRBase 16.0
ArrayContents_CurrentNameColumn=miRBase 17.0
ArrayContents_CurrentNameColumnCoverage=Mus musculus and related vira:94.26%


title: NimbleGen Human ChIP-chip 2.1M Deluxe Promoter Array [100718_HG19_Deluxe_Prom_ChIP_HX1]

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Homo sapiens

description:
Design ID: 537713
Design name: 100718_HG19_Deluxe_Prom_ChIP_HX1
Genome build: HG19

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


title: Human Disease-related LncRNA Profiler

status: Public on Jul 11 2016

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

institute: IRCCS-Policlinico San Donato

description:
catalog number: RA920D-1
PCR assay


title: Illumina Porcine SNP60v2 BeadChip

organism: Sus scrofa

manufacture_protocol: See manufacturer's website


title: Illumina HiSeq 2000 (Escherichia coli ATCC 8739)

organism: Escherichia coli ATCC 8739


title: Agilent-034519 Manihot esculenta microarray (probe name version)

city: Phayathai

first: Onsaya

last: Patanun

state: Bangkok

address: Rama6 rd. Phayathai

department: Biotechnology

country: Thailand

institute: Mahidol university

organism: Manihot esculenta

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


title: SABiosciences RT² Profiler PCR array-mouse chemokines & receptors assay panels [PAMM-022Z]

city: Guangzhou

first: Chong

last: Wu

address: 135 Xin Gang Xi Road

institute: Sun Yat-sen University

description:
RT² Profiler PCR array-mouse chemokines & receptors
SABiosciences RT² Profiler panel of PCR assays.

manufacture_protocol: see manufacturer's website


title: SABiosciences RT² Profiler PCR array-mouse common cytokines assay panels [PAMM-021Z]

description:
RT² Profiler PCR array-mouse common cytokines
SABiosciences RT² Profiler panel of PCR assays.


title: SABiosciences/Qiagen Human Cell Cycle RT2 Profiler PCR Array (PAHS-020Z)

city: Bunkyo-ku

first: Kyoko

last: Kojima-Aikawa

state: Tokyo

address: 2-1-1 Otsuka

department: Faculty of Core Research, Natural Science Division

institute: Ochanomizu University

description: PCR assay


title: Agilent-045283 0GyR 4x180k CGH array [Feature Number version]

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

address: Takahoko, Hacchasawa,

institute: Institute for Environmental Science

description:
Agilent-045283 0GyR

Arrays of this design have barcodes that begin with 16045283 or 2545283.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Illumina HiSeq 4000 (Homo sapiens; Human herpesvirus 4)

status: Public on Jul 10 2016

organism:
Homo sapiens
human gammaherpesvirus 4


title: Illumina HiSeq 2000 (Mus musculus musculus)

organism: Mus musculus musculus


title: Illumina HiSeq 2500 (Homo sapiens; Human herpesvirus 4)


title: Illumina HiSeq 2000 (Neotoma stephensi)

organism: Neotoma stephensi


title: CustomArray Signaling Pathway platform version 2

manufacture_protocol: CustomArray B3 synthesizer was used for oligonucleotide probe synthesis on CustomArray ECD 4X2K/12K slides. Synthesis was performed according to manufacturer recommendations. Two replicates of total 6000 unique oligonucleotide probes of 40 nucleotides in length  were placed on chip.


title: Agilent-029152 Unrestricted Mouse miRNA Microarray 028772 (miRBase release 18 Feature Number version)

description:
Grid Date: Dec-26-2011 (corresponding to miRBase release 18)

Arrays of this design have barcodes that begin with 16029152 or 2529152.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-030107 rat epilepsy array (Feature number version)

status: Public on Jul 06 2016

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

country: Canada

institute: McGill University

organism: Rattus norvegicus

description:
Annotations based on rn4:RGSCv3.4:Nov2004

Arrays of this design have barcodes that begin with 16030107 or 2530107.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-029152 Unrestricted Mouse miRNA Microarray 028772 (miRBase release 18 miRNA ID version)

description: Grid Date: Dec-26-2011 (corresponding to miRBase release 18)


title: Illumina HiSeq 4000 (Acinetobacter baumannii)

organism: Acinetobacter baumannii


title: Illumina HiSeq 2000 (Schizophyllum commune)

status: Public on Jul 07 2016

organism: Schizophyllum commune


title: [RaGene-1_1-st] Affymetrix Rat Gene 1.1 ST Array [transcript (gene) version] [CDF: ragene11st_Rn_ENTREZG_17.1.0]

status: Public on Jul 08 2016

relation: Alternative to: GPL11534 (alternative CDF [official])

manufacture_protocol: This is identical to GPL11534 but a custom CDF environment was used to extract data [ragene11st_Rn_ENTREZG_17.1.0]. CDF and other files can be downloaded at: http://mbni.org/customcdf/17.1.0/entrezg.download/ragene11st_Rn_ENTREZG_17.1.0.zip


title: Agilent-060349 20mGyY 4x180k CGH array [Feature Number version]

status: Public on Jul 27 2016

description:
Agilent-060349 20mGyY

Arrays of this design have barcodes that begin with 16060349 or 2560349.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Illumina HiSeq 4000 (Capra hircus)

organism: Capra hircus


title: Agilent-037581 rhesus promoter tiling 2011 array (Feature number version)

organism: Macaca mulatta

description:
Annotations based on rheMac2:BCMV1:Jan2006

Arrays of this design have barcodes that begin with 16037581 or 2537581.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-024757 human promoter and stress-related genes array (Feature number version)

description:
Annotations based on hg19:GRCh37:Feb2009

Arrays of this design have barcodes that begin with 16024757 or 2524757.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: NanoString nCounter human miRNA expression system

city: Chicago

first: Shiyuan

last: Cheng

state: IL

address: 303 E. Superior Street

department: Neurology

institute: Northwestern University

technology: other

manufacture_protocol: See manufacturer's website http://www.nanostring.com


title: Illumina Genome Analyzer (Tribolium castaneum)

organism: Tribolium castaneum


title: Illumina HiSeq 2000 (Lactuca sativa)

organism: Lactuca sativa


title: Illumina Genome Analyzer (Capra hircus)


title: NimbleGen Sus scrofa

city: Addlestone

first: Helen

middle: Elizabeth

last: Everett

state: Surrey

address: New Haw

department: Virology

institute: Animal and Plant Health Agency (APHA)

description:
Sus scrofa genome build v10.2
110627_Sscr_ref_miRNA_FS_exp
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are linked below as supplementary files.
NDF 110627 tab delim.xlsx
NGD 110627 tab delim.xlsx

manufacture_protocol: High-density 12x135K DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.


title: Equine host array 12x135k v1

city: Guildford

first: Falko

last: Steinbach

address: Daphne Jackson Road

institute: Univ of Surrey

organism: Equus caballus

description: Nimblegen design ID 569001 based on Equus caballus RefSeq data using 60mer oligos. A multi probe per gene design that includes random and other control probes

manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology.


title: Illumina MiSeq (Serratia marcescens)

status: Public on Jul 05 2016

organism: Serratia marcescens


title: Agilent-065680 Hypericum perforatum array

city: Verona

first: Elisa

last: Gecchele

address: Strada Le Grazie

institute: University of Verona

organism: Hypericum perforatum

relation: Alternative to: GPL22204 (Probe Name version)


title: PorcineSNP60v2

city: Chengdu

first: Mingzhou

last: Li

state: Sichuan

address: No.211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University


title: Agilent-030192 Rat Whole Genome 8x60k Gene Expression Microarray (AMADID:030192)

status: Public on Jul 01 2016

city: Bangalore

first: Genotypic

last: technology

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

institute: Genotypic Technology

description:
designed by Genotypic Technology Private Limited

*** The ID column includes the Agilent Probe Names.


title: Agilent B.subtilis Gene Expression  8x15k Array AMADID: 020941 designed by Genotypic Technology Private Limited.

organism: Bacillus subtilis subsp. subtilis str. 168


title: Agilent-034971 Migratory and Desert Locust EST Array

status: Public on Jul 02 2016

city: Leuven

first: Jozef

last: Vanden Broeck

address: Naamsestraat 59

department: Animal Physiology and Neurobiology

country: Belgium

institute: KU Leuven

organism:
Locusta migratoria
Schistocerca gregaria

description:
Agilent-034971 Locusta-Schisto-totalMA-110617

EST-based microarrays: 1. A set of unique Locusta ESTs (from LocustDB and the CNS database), 2. Schistocerca ESTs having no homolog in the unique Locusta set.

The microarray platform contains probes representing (i) all EST sequences retrieved from LocustDB [1], (ii) all EST sequences retrieved from the L. migratoria central nervous system deep-sequencing project [2] that did not appear to be represented in LocustDB and (iii) all S. gregaria EST sequences [3] having no ortholog in the L. migratoria set (blastn hits producing E < 1E-10 were considered orthologs). The locust microarrays were designed by means of the eArray system (Agilent Technologies). Probes were designed according to the following eArray criteria: (i) probe length: 60 nucleotides, (ii) two probes per target sequence (best probe methodology) and (iii) probe orientation: sense. Other parameters were set at default settings. The locust microarray platform was assayed by means of self-self hybridizations of pooled brain and midgut samples of 5th larval locusts in three different feeding conditions, i.e., normal fed, fed a diet supplemented with protease inhibitors, and starved. The aim of these gene expression studies was (i) to determine the genes that appear to be expressed in the tissues under study, and (ii) for each of these gene targets, to select the best-performing corresponding probe for platform optimization for future studies. For detailed information, we refer to the article corresponding to the associated data Series.

[1] Ma ZY, Yu J, Kang L (2006) LocustDB: a relational database for the transcriptome and biology of the migratory locust (Locusta migratoria). BMC Genomics 7: 11.
[2] Zhang Z, Peng ZY, Yi K, Cheng Y, Xia Y (2012) Identification of representative genes of the central nervous system of the locust, Locusta migratoria manilensis by deep sequencing. Journal of Insect Science 12: 86.
[3] Badisco L, Huybrechts J, Simonet G, Verlinden H, Marchal E et al. (2011) Transcriptome analysis of the desert locust central nervous system: production and annotation of a Schistocerca gregaria EST database. PLoS One 6: e17274.

Arrays of this design have barcodes that begin with 16034971 or 2534971.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-077006 Rhodococcus jostii RHA1 8x15K custom expression array (Systematic Name version)

city: Vicksburg

first: Dawn

middle: E

last: Hancock

state: Mississippi

address: 3909 Halls Ferry Road

department: Engineer Research and Development Center

institute: DEPARTMENT OF DEFENSE Army Corps of Engineers

organism: Rhodococcus jostii RHA1

description:
Agilent custom 8 x 15K microarray AMADID number  077006
Rhodococcus jostii RHA1 8x15k array with total 9074 probes and 50 genes replicated to fill the blank features
The Platform data table reflects a condensed representation of the expression array's replicate (gene number) features.
The Agilent design file (077006_D_GEO_20150722.txt) is attached.

manufacture_protocol: High-density DNA array prepared by Agilent technologies. See manufacturer's website at http://www.genomics.agilent.com/.


title: Agilent Human miRNA Microarray

city: Bethesda

first: Weixin

last: Wang

address: 9000 Rockville Pike

department: DLM/CC

institute: NIH

organism: Homo sapiens


title: Agilent-045111 Pinctada_1112 [Probe Name Version]

city: Haikou

first: Yaohua

last: Shi

address: 18 Renmin Road

department: The Ocean College

institute: Hainan University

organism: Pinctada imbricata

description: Arrays of this design have barcodes that begin with 16045111 or 2545111.

relation: Alternative to: GPL20647 (Feature Number Version)


title: Agilent-078298 human circRNA array V1.0 4X180K [Probe Name Version]

city: shanghai

first: qian

last: jin

address: libing road

institute: MSP


title: Agilent-045111 Pinctada_1112 [Feature Number Version]

description:
Arrays of this design have barcodes that begin with 16045111 or 2545111.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

relation: Alternative to: GPL20648 (Probe Name Version)


title: Custom Gene Expression plate from Bio-RAD

city: Silver Spring

first: Raj

middle: K

last: Puri

state: Maryland

address: 10903 New Hampshire Ave

institute: FDA

description: PCR assay


title: [HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [CDF: Brainarray HuGene11stv1_Hs_ENTREZG_15.1.0]

status: Public on Jun 26 2014

first: GEO

last: admin

institute: NCBI/NLM/NIH

description:
HuGene-1_1-st-v1.na32.hg19.transcript.csv
#%create_date=Tue Jun 21 17:41:46 2011 PDT
#%chip_type=HuGene-1_1-st-v1
#%lib_set_name=HuGene-1_1-st
#%lib_set_version=v1
#%genome-species=Homo sapiens
#%genome-version=hg19
#%genome-version-ucsc=hg19
#%genome-version-ncbi=GRCh37
#%genome-version-create_date=2009-02-00
#%genome-lifted-method=liftOver
#%genome-lifted_from-species=Homo sapiens
#%genome-lifted_from-version-ucsc=hg18
#%genome-lifted_from-version-ncbi=36.1
#%netaffx-annotation-date=2011-06-22
#%netaffx-annotation-netaffx-build=32

This identical to GPL11532 but a custom cdf environmnet was used to extract data.

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


title: Arraystar Human T-UCR Microarray [Agilent-038545]

status: Public on Apr 11 2014

city: Rockville

first: Panos

last: Pan

address: 9430 Key West Avenue

institute: Arraystar Inc.


title: NanoString nCounter miRNA expression assay (miRBase 21)

status: Public on Aug 15 2015

city: Iowa City

first: Ajit

last: Vikram

state: Iowa

address: 431 Newton Rd. 400 EMRB

department: Internal Medicine

institute: University of Iowa

organism: Mus musculus


title: Illumina HiSeq 4000 (Taenia solium)

last: GEO

organism: Taenia solium


title: Custom Agilent-066047 Bombyx mori Gene Expression 4x44k designed by Genotypic Technology Private Limited

organism: Bombyx mori

description: AMADID: 066047 designed  by Genotypic Technology Private Limited.


title: Fusarium fujikuroi annotation version 2 gene expression array [121227_Ffuji_v2_2_BT_expr_HX12]

status: Public on Jul 04 2016

city: Freising

first: Ulrich

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

institute: Technische Universität München

organism: Fusarium fujikuroi

description: NimbleGen design name 121227_Ffuji_v2_2_BT_expr

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


title: Agilent-046732 Multistrain detection CGH 4x180k Array

city: Poznan

first: Krzysztof

last: Krawczyk

state: Greater Poland

address: Wladyslawa Wegorka 20

department: Virology and Bacteriology

country: Poland

institute: Institute of Plant Protection-National Research Institute

organism:
Bacteria
Zea mays
Viruses

description:
Arrays of this design have barcodes that begin with 16046732 or 2546732.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: IMUL-Candida glabrata 8x15k

status: Public on Jul 24 2010

city: Lausanne

first: Dominique

last: Sanglard

address: Rue Bugnon 48

country: Switzerland

institute: University of Lausanne and University Hospital Center

organism: Nakaseomyces glabratus CBS 138

description: The nucleotide sequences of the 5283 C. glabrata ORFs and the mitochondrial genome (release 2) were downloaded from the Génolevure Consortium (http://www.genolevures.org/). Following the Agilent eArray Design guidelines, two separate probe sets for each ORF were designed, each consisting of 60 base oligonucleotides. The probe selection was performed using the GE Probe Design Tool; probes were filtered following their base composition and distribution, cross-hybridization potential and melting temperature to yield two probes sets representing each 5210 nuclear and 6 mitochondrial ORFs. These probes cover more than 98% of the nuclear genome and represent 6 out of the 8 mitochondrial protein-encoding genes. For quality control and normalization purposes, 103 probes were selected randomly and spotted 20 times throughout each array in addition to standard Agilent controls. C. glabrata custom arrays were manufactured in the 8x15k format by Agilent Technologies.

first: Sélène

last: Ferrari

relation: Alternative to: GPL22200 (Probe name version)


title: Agilent-029586 Haloferax mediterranei 15K array

city: San Vicente del Raspeig

first: Julia

last: Esclapez

state: Alicante

address: Crta San Vicente del Raspeig s/n

department: Biochemistry

institute: University of Alicante

organism: Haloferax mediterranei

description:
Arrays of this design have barcodes that begin with 16029586 or 2529586.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Illumina HiSeq 2000 (Hepatitis C virus; Homo sapiens)

status: Public on May 02 2016

organism:
Homo sapiens
Hepacivirus hominis


title: Agilent-020573 Bifidobacterium breve UCC2003 Agilent 4x44k format

status: Public on Feb 23 2011

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

organism: Bifidobacterium breve UCC2003

description: Custom 4x44k microarray design of B. breve UCC2003 with three unique probes replicated 5 times per 1 kb of gene sequence.

first: Douwe

last: van Sinderen

manufacture_protocol: Chemical In-situ oligonucleotide synthesis.


title: Illumina HiSeq 2000 (Streptococcus sp. 'group A')

status: Public on Jan 23 2015

country: USA

organism: Streptococcus sp. 'group A'


title: Agilent-016322 Yeast (V2) Gene Expression 8x15K Microarray (Feature Number version)

status: Public on Feb 18 2010

city: Palo Alto

last: Agilent Technologies

state: CA

institute: Agilent Technologies

organism: Saccharomyces cerevisiae

description:
15,208 S. cerevisiae (S288C strain) ORFs represented.
Contents sourced from Saccharomyces Genome Database (SGD), January, 2004.

This oligonucleotide microarray will enable researchers to simultaneously characterize expression of many thousands of yeast genes and identify gene activity during important biological processes, such as yeast growth, adaptation, and response to drug candidates.

Arrays of this design have barcodes that begin with 16016322 or 2516322.
Agilent part number (V2): G4813A

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

The ID column represents the Agilent Feature Extraction feature number.

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

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL16244

relation:
Alternative to: GPL13340
Alternative to: GPL16244

manufacture_protocol:
Agilent 60-mer SurePrint technology.
See manufacturer's web site at http://www.agilent.com/.


title: Agilent-079487 Arraystar Human LncRNA microarray V4 (Probe Name version)

status: Public on May 07 2016

state: MD


title: Illumina HiSeq 2500 (Homo sapiens; Mus musculus)

organism:
Homo sapiens
Mus musculus


title: Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray [Feature Number version]

status: Public on May 04 2016

description:
Catalog gene expression microarray for Mouse, v2 8x60K

Arrays of this design have barcodes that begin with 16074809 or 2574809.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL21163.