title: BRAF/MEK inhibitor resistance melanoma cells treated with PAK inhibitor PF3758309 array

status: Public on Jul 31 2017

city: Toronto

first: Hezhe

last: Lu

state: Ontario

address: 600 University Ave

country: Canada

institute: The Lunenfeld-Tanenbaum Research Institute

organism: Homo sapiens

technology: spotted peptide or protein

distribution: non-commercial

manufacturer: RPPA Core Facility, MD Anderson Cancer Center

manufacture_protocol: We stained slides for more than 200 unique antibodies and 3 secondary antibody negative controls which were analyzed on Array-Pro then by supercurve Rx64 3.1.1. There were 12 sets of replicated antibodies among slides. We performed QC test for each antibody staining (slide). The QC Score (Probability) values were also included in the data spreadsheet for your references. QC score above 0.8 indicates good antibody staining. We only included in the data for the all individual antibodies with QC Scores higher than 0.80 in the Heatmaps.  In the case of antibodies with replicates, the one with the highest QC Score was used.  For samples of tissue origin, we removed 7 antibodies cross react with damaged components (with unknown mechanism). There are 51 individual mouse antibodies (labeled -M) that will be removed for mouse tissue or xenograft samples, unless you specifically indicated for inclusion in your sample submission form.


title: BRAF/MEK inhibitor resistance melanoma cells treated with PAK inhibitor PF3758309 CR array

manufacture_protocol: We stained slides for more than 200 unique antibodies and 3 secondary antibody negative controls which were analyzed on Array-Pro then by supercurve Rx64 3.1.1. There were 12 sets of replicated antibodies among slides. We performed QC test for each antibody staining (slide). The QC Score (Probability) values were also included in the data spreadsheet for your references. QC score above 0.8 indicates good antibody staining. We only included in the data for the all individual antibodies with QC Scores higher than 0.80 in the Heatmaps.  In the case of antibodies with replicates, the one with the highest QC Score was used.  For samples of tissue origin, we removed 7 antibodies cross react with "damaged components" (with unknown mechanism). There are 51 individual mouse antibodies (labeled "-M") that will be removed for mouse tissue or xenograft samples, unless you specifically indicated for inclusion in your sample submission form.


title: Arraystar Human LncRNA Pathway microarray (Metabolism) [Mycroarray]

status: Public on Mar 31 2017

city: Rockville

first: Panos

last: Pan

state: MD

address: 9430 Key West Avenue

country: USA

institute: Arraystar Inc.

technology: in situ oligonucleotide

distribution: custom-commercial

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


title: Agilent-045717 Phaeodactylum 8x60k

city: Grenoble

first: Valeria

last: Villanova

address: 14 avenue Albert 1er de Belgique

department: LPCV

country: France

institute: CEA

organism: Phaeodactylum tricornutum

description:
Arrays of this design have barcodes that begin with 16045717 or 2545717.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

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


title: Illumina HiSeq 2500 (Synechocystis sp. PCC 6803)

last: GEO

organism: Synechocystis sp. PCC 6803

technology: high-throughput sequencing

distribution: virtual


title: Illumina Genome Analyzer (Solanum pimpinellifolium)

status: Public on Mar 29 2017

organism: Solanum pimpinellifolium


title: Ion Torrent PGM (Synechocystis sp. PCC 6803)


title: Illumina NextSeq 500 (Patiria miniata)

status: Public on Mar 30 2017

organism: Patiria miniata


title: Illumina HiSeq 2500 (Solanum lycopersicum x Solanum pennellii)


title: Agilent-014716 and Agilent-014717 Mouse Promoter ChIP-on-Chip Set 244K, Microarray 1 and 2 of 2 (Probe Name version)

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Department of Regenerative Biology

institute: University of Wisconsin

organism: Mus musculus

description:
Combined data from GPL14573 and GPL14597

Mouse Promoter ChIP-on-Chip Set 244K combined platform (Agilent-014716 and Agilent-014717)


title: Agilent-048820 FU-Steppuhn Solanum dulcamara 60K v1.0

status: Public on Apr 23 2017

city: Berlin

first: Tobias

last: Lortzing

state: Berlin

address: Haderslebener Str. 9

department: Biology

country: Germany

institute: Freie Universität Berlin

organism: Solanum dulcamara

manufacture_protocol: For manufacturing details, see Agilent website (http://www.agilent.com).


title: Applied Biosystems Taqman Low Density Array Human microRNA Card A+B v3.0

status: Public on Mar 28 2017

city: Kensington

first: Daniel

middle: D

last: Murray

state: NSW

address: The Kirby Institute, Wallace Wurth Building, UNSW Australia

department: Immunovirology and pathogenesis program

country: Australia

institute: Kirby Institute

technology: RT-PCR

description:
catalog number 4444913
All known miRNAs PCR assay

manufacture_protocol: see manufacturer's website


title: MRA-1001B1C Human miRNA Array [miRHuman_16]

city: Hohhot

first: yong

middle: ping

last: mu

address: No1,Tongdao North Street

country: China

institute: Inner Mongolia Medical University

description:
miRHuman_11_HUST_121206

Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579-596; (b) Zhu, Q., Hong, A., Sheng, N., Zhang, X., Jun, K.-Y., Srivannavit, O., Gulari, E., Gao, X., and Zhou, X. (2007) Microfluidic biochip for nucleic acid and protein analysis. in Methods Mol. Biol. Ed. Rampal, J. B. 382:287-312.;Bolstad, B. M., Irizarry, R. A., Astrandand, M., Speed, T. P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinfo. 19, 185-193.


title: [MoGene-2_1-st] Affymetrix Mouse Gene 2.1 ST Array [CDF: moGene21st_Mm_ENSG_19.0.0]

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: This array is identical to GPL17400 but the data were analyzed with a custom CDF environment.

relation: Alternative to: GPL17400 (Alternative CDF [official])

manufacture_protocol: see manufacturer's web site


title: Illumina HiSeq 2000 (Quercus robur)

organism: Quercus robur


title: RiboArray IncDETECT Rat Array 1X12K

city: Nantong

first: cheng

last: xiang

address: Qixiu Road NO.19

institute: Nantong University

organism: Rattus norvegicus

description: RiboArray™IncDETECT™ Rat Array 1X12K


title: [FinGene-1_1] Zebra Finch Gene 1.0 ST Array [transcript (gene) version]

status: Public on Mar 23 2017

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Taeniopygia guttata

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

No Affymetrix CSV annotations available as of March 23, 2017.

distribution: commercial

manufacture_protocol: See manufacturer's web site


title: Agilent-020599 SCRI_Hv35_44k_v1

status: Public on Mar 27 2017

city: Freising

first: Ralph

last: Hueckelhoven

department: Chair of Phytopathology

institute: TU München

organism: Hordeum vulgare

description:
Designed to HarvEST35 unigene set
Arrays of this design have barcodes that begin with 16020599 or 2520599.
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 Probe Name.
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: IlluminaHumanOmni5Exome-4 v1 B1

city: St. Augustine

first: Rajini

last: Haraksingh

address: The University of the West Indies

department: Life Sciences

country: Trinidad and Tobago

institute: The University of the West Indies

technology: oligonucleotide beads


title: AB SOLiD 4 System (Strongylocentrotus purpuratus)

organism: Strongylocentrotus purpuratus


title: [Axiom_CgiSNP] Affymetrix Oyster SNP

status: Public on Mar 21 2017

city: Qingdao

first: Haigang

last: Qi

state: Shandong

address: 7 Nanhai Rd.

department: Key Laboratory of Experimental Marine Biology

institute: Institute of Oceanology, Chinese Academy of Sciences

organism: Magallana gigas


title: LC_MRA-1004_miRZebrafish_13.0_090309 [miRNA ID version]

city: Changsha

first: zhang

last: fangliang

state: hunan

address: Changsha City Kaifu District

institute: Changsha University

organism: Danio rerio

description:
http://miRBase.org

Part No.MRA-1004C
Zebrafish miRNA Array
Version No. miRZebrafish_19_CSU_121127
Based on Sanger miRBase Release 19


title: Illumina NextSeq 500 (Strongylocentrotus purpuratus)

status: Public on Mar 22 2017


title: Semiotik mouse glycan array

city: Hospitalet de Llobregat

first: Rafael

last: Manez

state: Barcelona

address: Feixa Llarga s/n

country: Spain

institute: HUB

technology: other


title: IlluminaHumanOmni5-4 v1.0 D


title: Applied Biosystems Human Taqman MicroRNA Array v3.0 (330)

status: Public on Mar 16 2017

city: Shanghai

first: Lingyan

last: Zhu

address: 2901 Caolang Road, Jin Shan District

institute: Shanghai Public Health Clinical Center, Fudan University

description:
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards (2 per sample). Quantitative real-time PCR was performed for 768 features, 774 of which represent primate miRNAs.
qRT-PCR TaqMan Low-Density Array


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [gene-level release 33.1 version]

status: Public on Mar 17 2017

city: Seattle

first: G. Adam

last: Whitney

state: WA

address: 401 Terry Ave.

department: Bioinformatics

institute: PreCyte

description: Similar to GPL5175, but newer annotation file [annotated by release 33.1 of the Affymetrix human annotation file]


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

organism:
Homo sapiens
human gammaherpesvirus 4


title: AB 5500xl Genetic Analyzer (Caenorhabditis elegans)

organism: Caenorhabditis elegans


title: Illumina HiSeq 2000 (Isodon rubescens)

organism: Isodon rubescens


title: Illumina HiSeq 2000 (Acropora millepora)

organism: Acropora millepora


title: Illumina MiSeq (Clostridium perfringens)

organism: Clostridium perfringens


title: AB 5500xl Genetic Analyzer (Enterobacter lignolyticus SCF1)

status: Public on Mar 20 2017

organism: [Enterobacter] lignolyticus SCF1


title: IlluminaHumanOmni2.5Exome-8 v1.0 B

organism: Homo sapiens


title: Illumina HiSeq 2500 (Taeniopygia guttata)


title: Illumina HiSeq 2000 (Acropora gemmifera)

organism: Acropora gemmifera


title: ABI Mouse Genome Survey Microarray v.2.0

city: Stockholm

first: Eva

last: Severinson

address: Svante Arrhenius väg 20C

department: MBW

country: Sweden

institute: Stockholm University

organism: Mus musculus

technology: spotted oligonucleotide


title: Illumna HumanCoreExome-12_v1.1_C

manufacture_protocol: See manufacturer's website


title: Agilent_074976 Porphyromonas gingivalis Microarray

city: Madrid

first: Patricia

last: Romero Lastra

address: Plaza de Ramon y Cajal s/n

institute: Universidad Complutense de Madrid

organism: Porphyromonas gingivalis


title: [MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [gene-level version]

description: The probe to gene mapping file 'probeToGeneLUT.txt' is linked as supplementary file.


title: LC Sciences MRA-1001LCB_miRHuman_20

status: Public on Mar 11 2017

city: Nanjing

first: Li

last: Yang

state: Jiangsu

address: Dingjiaqiao 87

department: Pharmacology

institute: Southeast University


title: Illumina HiSeq 2000 (Callorhinchus milii)

last: GEO

organism: Callorhinchus milii


title: Illumina HiSeq 2500 (Thlaspi arvense)

organism: Thlaspi arvense


title: AB 5500xl Genetic Analyzer (Escherichia coli)

organism: Escherichia coli


title: Illumina Genome Analyzer IIx (Mycobacterium tuberculosis H37Ra)

status: Public on Mar 15 2017

organism: Mycobacterium tuberculosis H37Ra


title: Illumina HiSeq 2500 (Enterococcus faecalis)

status: Public on Mar 10 2017

organism: Enterococcus faecalis


title: Illumina Genome Analyzer IIx (Oreochromis niloticus)

status: Public on Mar 09 2017

organism: Oreochromis niloticus


title: Rattus norvegicus 5K

city: Estado de México

first: Ronquillo Sánchez

middle: Sánchez

last: María Dolores

state: Tlalnepantla

address: Av. De los Barrios No. 1, Los Reyes, Iztacala

department: Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala

country: Mexico

institute: Universidad Nacional Autónoma de México

organism: Rattus norvegicus

manufacture_protocol: Rattus norvegicus 70-mer oligo library from OPERON Oligo Sets (http://omad.operon.com/) It contains 5,000 gene specific oligonucleotide probes representing the better known genes, were resuspended to 40µM in Micro Spotting solution (Telechem International Inc.). SuperAmine coated slides 25x75 mm (TeleChem International INC) were printed in two copies, and fixed at 80°C for 4 hours. For pre-hybridization the slides were re-hydrated with water vapor at 60°C, and fixed with two cycles of UV light (1200J). After boiling for two minutes at 92°C, slides were washed with 95% ethanol for one minute and prehybridzed in 5X SSC, 0.1% SDS and 1% BSA for one hour at 42°C .The slides were washed and dried for further hybridization.


title: Illumina HiSeq 2500 (Mimulus peregrinus)

status: Public on Mar 07 2017

organism: Mimulus peregrinus


title: Illumina HiSeq 2500 (Anguilla marmorata)

status: Public on Mar 08 2017

organism: Anguilla marmorata


title: Agilent-027763 Amp and URv2 (Feature Number version)

status: Public on Mar 14 2017

city: Cambridge

first: Terry

middle: L.

last: Orr-Weaver

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

organism: Drosophila melanogaster

description:
AmpandURv2
Arrays of this design have barcodes that begin with 16027763 or 2527763.
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 NextSeq 500 (Homo sapiens)


title: Illumina HiSeq 2500 (Erythranthe lutea x Erythranthe guttata)

organism: Erythranthe lutea x Erythranthe guttata


title: Illumina MiSeq (Influenza B virus (B/Malaysia/2506/2004))


title: Illumina HiSeq 2500 (Erythranthe guttata)

organism: Erythranthe guttata


title: Illumina HiSeq 2500 (Erythranthe lutea)

organism: Erythranthe lutea


title: Illumina HiSeq 2000 (Brucella abortus)

status: Public on Mar 06 2017

organism: Brucella abortus


title: Illumina HiSeq 2500 (Aspergillus flavus)

organism: Aspergillus flavus


title: Illumina MiSeq (Chlorella vulgaris)

organism: Chlorella vulgaris


title: Illumina HiSeq 2500 (Cryptococcus neoformans var. grubii H99)

status: Public on Mar 13 2017

organism: Cryptococcus neoformans H99


title: Illumina HiSeq 2500 (Proteus mirabilis)

organism: Proteus mirabilis


title: Miltenyi Biotec miRXplore miRNA Microarray

city: Boston

first: Danesh

last: Moazed

state: Massachusetts

address: 240 Longwood Ave

department: Cell Biology

institute: Harvard Medical School

technology: spotted DNA/cDNA

manufacture_protocol: protocol according to Miltenyi Biotec (http://www.miltenyibiotec.com)


title: Agilent-079141 PPCD1-3_loci G4126A 8X60 array (Probe name version)

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

institute: Stein Eye Institute, UCLA

organism: Homo sapiens

description: Agilent-079141 PPCD1-3_loci  G4126A


title: Human 12x135K lncRNA expression array

status: Public on Mar 03 2017

first: Xi

last: Chen

address: 8th Panshan Road

institute: Second Military Medical University

description: All probes were re-mapped to Ensembl GRCh38.82 to aquire more accurate annotation. Probes perfectly annotated to a unique gene were retained and subjected to further analysis.

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


title: Illumina HiSeq 2000 (Temnothorax pilagens)

status: Public on Mar 02 2017

organism: Temnothorax pilagens


title: Illumina HiSeq 2000 (Temnothorax longispinosus)

organism: Temnothorax longispinosus


title: Illumina HiSeq 2000 (Temnothorax curvispinosus)

organism: Temnothorax curvispinosus


title: Illumina HiSeq 2000 (Temnothorax duloticus)

organism: Temnothorax duloticus


title: Illumina HiSeq 2000 (Temnothorax americanus)

organism: Temnothorax americanus


title: Illumina HiSeq 2000 (Temnothorax ambiguus)

organism: Temnothorax ambiguus


title: Illumina HiSeq 4000 (Xenopus tropicalis)

organism: Xenopus tropicalis


title: RiboArray™ Custom Lnc Array

status: Public on Mar 01 2017

city: guangzhou

first: jiafan

last: liu

address: No. 601 West Whampoa Road, Tianhe District, guangzhou

institute: Jinan University

organism: Mus musculus

description: This array contains probes for both protein coding and non-protein coding genes.

manufacture_protocol: Manufacture protocol not provided.


title: Illumina HiSeq 2500 (Aspergillus fumigatus)

organism: Aspergillus fumigatus


title: NanoString nCounter® Gene Expression CodeSet for mouse inflammation genes

city: Hamilton

first: Premysl

last: Bercik

address: 1280 Main Street West

department: Medicine

institute: McMaster University

manufacture_protocol: according to the manufacturer’s protocol


title: Illumina BovineSNP50 v3.0

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

organism: Bos taurus

description: 53,714 SNPs


title: Illumina BovineSNP50 v2.0

description: 54,609 SNPs


title: Illumina HumanOmni 2.5M 4v1-H SNP array

status: Public on Mar 05 2017

city: Philadelphia, PA

first: Richard

last: Aplenc

state: PA

address: 3501 Civic Center Blvd

department: Division of Oncology

institute: Children's Hospital of Philadelphia

manufacture_protocol: see Illumina web site


title: Illumina HumanOmni 2.5M 4v1-D SNP array


title: Illumina HumanHT-12 V4.0 expression beadchip

city: Pisa

first: Romina

last: D'Aurizio

state: PI

address: via Moruzzi 1

department: IIT

country: Italy

institute: CNR

manufacture_protocol: See manufacturer's website.


title: UHNMAC Yeast 6.4 K array (Y6.4K) version 7

city: Paterna

first: Roberto

last: Pérez

state: Valencia

address: Av Agustín Escardino 7

institute: Centro Superior de Investigaciones Científicas

organism: Saccharomyces cerevisiae

description:
spotted DNA/cDNA (double-spotted array containing 6240 yeast ESTs derived from PCR amplification of synthetic EST clones, plus 320 control spots of Arabidopsis totalling 6.4K).
Grid rows: 12; grid columns: 4; rows: 17; columns: 16, grid to grid distance: 4500 um; spot to spot distance: 200 um; spot size: 100 um.

manufacturer: Microarray Centre - University Health Network - Toronto - Canada

manufacture_protocol:
Microarrays are printed on UltraGAPS slides (Corning Inc.) using hihg-precision robotics. Printed arrays are processed following Corning's protocol and are ready-to-use.
1. Acquisition of bacterial clone set — our Yeast 6.4k clone set is derived from Research Genetics Genepairs. Detailed information about the ORFs and sequences can be found at http://www.yeastgenome.org/
2. Clone set is PCR amplified and DNA purified in working 96 well plates.
3. The purified DNA is then transferred to 384 well source plates with DNA concentration ranging from 0.10ug/ul to 0.25ug/ul.  These are used for spotting.
4. Microarrays are printed on UltraGAPS ™  slides (Corning Inc.) using hihg-precision robotics (up to 48 pins or print heads). Printed arrays are processed following Corning's protocol and are ready-to-use.
Up to 120 slides are printed in each batch and batches that result in greater than 95% printing fidelity are selected for post printing quality control tests
(measuring spot morphology, quality of background and signal intensity in a real hybridization using yeast total RNA, vector probe labeling method and terminal transferase tailing method).


title: [RAE230A] Affymetrix Rat Expression 230A Array

status: Public on Jun 23 2003

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Rattus norvegicus

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 01, 2016: annotation table updated with netaffx build 35

relation: Alternative to: GPL8627 (Alternative CDF)

relation: Alternative to: GPL14122 (Alternative CDF)

manufacture_protocol:
see manufacturer's web site

Array A of GeneChip Rat Expression Set 230
Has 15923 entries and was indexed 09-Apr-2003
Sequences used in the design of the array were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from Build 99 of UniGene (June 2002) and refined by analysis and comparison with a number of other publicly available databases including the Baylor College of Medicine Human Genome Sequencing Center's preliminary rat genome assembly (June 2002). In addition, sequences were analyzed for untrimmed low-quality sequence information, correct orientation, false clustering, alternative splicing and alternative polyadenylation.


title: miRCURYTM LNA Array (v.11.0)

city: Dalian

first: Ying

last: Gao

state: Liaoning

address: Linghai Road 1

institute: Dalian Maritime university

organism: Caenorhabditis elegans

manufacture_protocol: Exiqon


title: Illumina HiSeq 2500 (Streptococcus pneumoniae)

organism: Streptococcus pneumoniae


title: Illumina HiSeq 2500 (Eogystia hippophaecolus)

status: Public on Dec 21 2016

organism: Eogystia hippophaecolus


title: [100718_Cele_EXP] Nimblegen

manufacture_protocol: NimbleGen


title: NimbleGen Sporobolus stapfianus 53K

city: Columbia

first: Abou

last: Yobi

state: Missouri

address: 214 Curtis Hall

department: Plant Genetics Unit

institute: USDA-ARS

organism: Sporobolus stapfianus


title: Illumina HiSeq 4000 (Neurospora crassa)

organism: Neurospora crassa


title: Agilent-030439 LBLGC-Ptrichocarpa-CH3

status: Public on Jan 01 2014

city: Uppsala

first: Clement

last: Lafon-Placette

address: Almas Allé 5

institute: SLU

organism: Populus trichocarpa

description:
LBLGC-Ptrichocarpa-CH3

Arrays of this design have barcodes that begin with 16030439 or 2530439.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

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


title: Illumina HiSeq 4000 (Gossypium hirsutum)

organism: Gossypium hirsutum


title: CCDTM-miRNA850-version 4p1.4

status: Public on Jun 30 2015

city: Guangzhou

first: Xin

last: Li

state: Province

address: Southern medical university

department: Cancer research institute

institute: Southern medical university

organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human gammaherpesvirus 8
Macacine gammaherpesvirus 4
Betapolyomavirus macacae

description: This is a miRNA expression profiling using an updated platform (CCDTM-miRNA850-version 4p1.4) based on the Platform GPL7089 (CCDTM-miRNA850-version 4).

manufacturer: NIH Clinical Center, Dept. of Transfusion Medicine, Immunogenetics Section (NIH/CC/DTM)

manufacture_protocol: Oligos sythesized by Operon with 3' amine modification and purified by desalting. Oligos are adjusted to the same concentration and resuspend in 2mM phosphate buffer at 25mM oligo concentration and spotted on CodeLink(TM) Activated Slides (GE Healthcare) using an Omnigrid robotic arrayer (Genomic Solutions).


title: [Mm35b_P02R] Affymetrix Mouse Tiling 2.0R Set, Array 2

status: Public on Feb 01 2008

description:
Tiling array 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 GeneChip® Mouse Tiling 2.0R Array Set is designed for chromatin immunoprecipitation (ChIP) experiments. This set of seven arrays contains approximately 45 million oligonucleotide probes to interrogate the mouse genome. Each array in the set contains over 6.5 million perfect match probes to specifically interrogate genomic regions.
Sequences used in the design of the Mouse Tiling 2.0R Array Set were selected from NCBI mouse genome assembly (Build 33). Repetitive elements were removed by RepeatMasker. The Mouse Tiling 2.0R Array Set is available either as a whole-genome set of seven arrays (P/N 900852), or individual arrays from the set may be purchased separately.
Probes are tiled at an average resolution of 35 base pairs, as measured from the central position of adjacent 25-mer oligos, leaving a gap of approximately 10bp between probes. Oligonucleotide probes are synthesized in situ complementary to each corresponding sequence.

BPMAP and other files can be downloaded from the Affymetrix Web site below.


title: SMD Print_1430 hr1

status: Public on Mar 01 2013

city: Stanford

first: Stephen

last: Popper

department: Division of Infectious Diseases, Dept. of Medicine

institute: Stanford University

organism: Homo sapiens

manufacturer: Stanford Functional Genomics Facility, Stanford School of Medicine

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


title: Illumina HiSeq 1500 (Schizosaccharomyces pombe)

status: Public on Nov 16 2016

last: GEO

organism: Schizosaccharomyces pombe


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

status: Public on Jan 18 2011

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

RaGene-1_1-st-v1.na31.rn4.transcript.csv
#%create_date=Fri Sep 17 11:36:51 2010 PDT
#%chip_type=RaGene-1_1-st-v1
#%lib_set_name=RaGene-1_1-st
#%lib_set_version=v1
#%genome-species=Rattus norvegicus
#%genome-version=rn4
#%genome-version-ucsc=rn4
#%genome-version-ncbi=Rnor3.4
#%genome-version-create_date=2004-11-00
#%genome-lifted_from-species=Rattus norvegicus
#%genome-lifted_from-version-ucsc=rn4
#%genome-lifted_from-version-ncbi=Rnor3.4
#%netaffx-annotation-date=2009-11-23
#%netaffx-annotation-netaffx-build=31

relation: Alternative to: GPL22130 (ragene11st_Rn_ENTREZG_17.1.0)

relation: Alternative to: GPL23181 (ragene11st_Rn_ENTREZG_19.0.0)

manufacture_protocol: see manufacturer's web site


title: [Hs35b_P01R] Affymetrix Human Tiling 2.0R Set, Array 1

status: Public on Mar 29 2007

description:
Tiling array 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 GeneChip® Human Tiling 2.0R Array Set is designed for chromatin immunoprecipitation (ChIP) experiments. This set of seven arrays contains approximately 45 million oligonucleotide probes to interrogate the human genome. Each array in the set contains over 6.5 million perfect match probes to specifically interrogate genomic regions.
Sequences used in the design of the Human Tiling 2.0R Array Set were selected from NCBI human genome assembly (Build 34). Repetitive elements were removed by RepeatMasker. The Human Tiling 2.0R Array Set is available either as a whole-genome set of seven arrays (P/N 900772), or individual arrays from the set may be purchased separately. The GeneChip® Human Promoter 1.0R Array is a subset of the Human Tiling 2.0R Tiling Array Set, and the content was chosen specifically to analyze protein/DNA interactions within promoter regions.
Probes are tiled at an average resolution of 35 base pair, as measured from the central position of adjacent 25-mer oligos, leaving a gap of approximately 10bp between probes. Oligonucleotide probes are synthesized in situ complementary to each corresponding sequence.

BPMAP and other files can be downloaded from the Affymetrix Web site below.

manufacture_protocol: See manufacturer's web site


title: Agilent-047069 CATMAv7 [Probe Name Version]

status: Public on May 01 2015

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

organism: Arabidopsis thaliana

description:
sens agilent gene: triplicate no_gene: single
Arrays of this design have barcodes that begin with 16047069 or 2547069.


title: Phalanx Human OneArray Ver. 7 Release 1

status: Public on Mar 30 2016

city: Carlsbad

first: Sagar

middle: S

last: Damle

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

manufacture_protocol: See http://www.phalanxbiotech.com/ for updated protocols


title: Illumina HumanRef-8 v3.0 expression beadchip

status: Public on May 21 2008

description:
The HumanRef-8 v3.0 Expression BeadChip features up-to-date content derived from the National Center for Biotechnology Information Reference Sequence (NCBI RefSeq) database (Build 36.2, 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

relation: Alternative to: GPL10399 (gene-centered version)

relation: Alternative to: GPL18405 (addtnl control probes)

manufacture_protocol: see manufacturer's website


title: Agilent-021850 SurePrint G3 Human CGH Microarray (Feature Number version)

status: Public on Dec 10 2009

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
SurePrint G3 Human CGH Microarray 2x400K

Arrays of this design have barcodes that begin with 16021850 or 2521850.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

*** The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL887.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL19387.


title: Illumina MiSeq (Rattus norvegicus)

status: Public on Aug 06 2014


title: [MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [probe set (exon) version]

status: Public on Nov 30 2007

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

#%create_date=Wed Mar 11 17:52:51 2009 PDT
#%chip_type=MoEx-1_0-st-v1
#%lib_set_name=MoEx-1_0-st
#%lib_set_version=v1
#%genome-species=Mus musculus
#%genome-version=mm9
#%genome-version-ucsc=mm9
#%genome-version-ncbi=37
#%genome-version-create_date=2007-07
#%netaffx-annotation-date=2009-03-16
#%netaffx-annotation-netaffx-build=28


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

status: Public on Nov 21 2015

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 Probe Name.

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 Feature Number in the ID column is assigned accession number GPL21810.