title: Testis_UF_Control_rep3

status: Public on Aug 11 2010

city: Providence

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit, according to the manufacturer's protocol (G4140-90040)

scan_protocol: Scanning was performed using the Agilent 2505B DNA Microarray Scanner, according to the manufacturer's protocol (G4140-90040)

data_processing: Data were processed using JMP Genomics v3.1.  gProcessedSignal data were imported from the raw data files, non-uniform spots were removed using Agilent's feature flagger, and rows not containing at least 2 data points for a row (probe) were deleted.  Data were loess-normalized (1 iteration, smoothing parameter = 0.2) using JMP Genomics.

organism: Pimephales promelas

source_name: testis, UF control water, exposed 48 h

label_protocol: Labeling with Cy3 was performed using the Agilent Low Input Linear Amplification Kit, according to the manufacturer's protocol (G4140-90040)

growth_protocol: Reproductively mature male FHM were acclimated for 48 h in aquaria prior to beginning the experiments.

extract_protocol: Total RNA was extracted from 30-50 mg FHM testis or liver tissue using RNA STAT-60 reagent (Tel-Test) and subsequently DNase-treated using TURBO DNA-free (Ambion).

treatment_protocol: Site water was transported to UF in fiberglass containers for sites A, B, and E, and reference sites C and D.  UF control water was carbon-filtered, dechlorinated tap water.  Exposures were conducted in static conditions in glass aquaria with water renewal every 12 hours for 48 hours.

value: testis


title: Testis_E_Exposed_rep3

type: RNA

first: Daniel

country: USA

molecule: total RNA

source_name: testis, site E water, exposed 48 h

tag: tissue


title: Testis_D_Ref_rep4

source_name: testis, reference site D water, exposed 48 h


title: DN3_rep1

status: Public on Aug 15 2010

city: Stanford

first: Jun

last: Seita

state: CA

address: Lokey Stem Cell Building #G3101, 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip 3000 7G with GCOS version 1.4.0.036.

data_processing: The data were analyzed with R/Bioconductor.

label: biotin

organism: Mus musculus

source_name: thymocyte

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: progenitor population

tag: strain

tag: age

value: 2 month

tag: gender

value: male


title: Testis_B_Exposed_rep2

source_name: testis, site B water, exposed 48 h


title: Testis_E_Exposed_rep4


title: Testis_E_Exposed_rep2


title: Testis_A_Exposed_rep4

source_name: testis, site A water, exposed 48 h


title: Testis_A_Exposed_rep2


title: DN1_rep1


title: Testis_B_Exposed_rep1


title: DN3_rep3


title: Testis_UF_Control_rep4


title: Testis_B_Exposed_rep4


title: DN2_rep3


title: Testis_UF_Control_rep2


title: Testis_B_Exposed_rep3


title: DN1_rep2


title: GMP_rep3

source_name: bone marrow

value: GMP


title: DN1_rep3


title: Testis_E_Exposed_rep1


title: Testis_D_Ref_rep3


title: Testis_A_Exposed_rep3


title: Liver_E_Exposed_rep4

source_name: liver, site E water, exposed 48 h

value: liver


title: Testis_A_Exposed_rep1


title: DN3_rep2


title: DN2_rep2


title: Testis_D_Ref_rep1


title: Liver_A_Exposed_rep4

source_name: liver, site A water, exposed 48 h


title: Testis_UF_Control_rep1


title: Liver_E_Exposed_rep3


title: Liver_B_Exposed_rep2

source_name: liver, site B water, exposed 48 h


title: DN2_rep1


title: Liver_UF_Control_rep3

source_name: liver, UF control water, exposed 48 h


title: Liver_D_Ref_rep3

source_name: liver, reference site D water, exposed 48 h


title: Liver_UF_Control_rep4


title: Liver_E_Exposed_rep2


title: Liver_B_Exposed_rep4


title: Liver_A_Exposed_rep3


title: Liver_A_Exposed_rep2


title: Liver_UF_Control_rep1


title: Liver_B_Exposed_rep3


title: Liver_B_Exposed_rep1


title: Liver_D_Ref_rep2


title: Liver_UF_Control_rep2


title: Liver_D_Ref_rep1


title: Liver_A_Exposed_rep1


title: FSGS-3

status: Public on May 26 2010

city: Valenzano-Bari

first: Sharon

middle: Natasha

last: Cox

department: Renal Lab

country: Italy

institute: Schena Foundation

description: After hybridization, the microarray chips were washed using the Affymetrix fluidics station in a buffer containing biotinylated antistreptavidin antibody and stained with streptavidin-PE.

hyb_protocol: After a step of purification, 15 ug of newly synthesized cRNA were fragmented by metal-induced hydrolisis and hybridized for 16 hours at 45°C to the GeneChip Human Genome U133A oligonucleotide microarray (Affymetrix, Santa Clara, CA, USA).

scan_protocol: The intensity of the fluorescence was measured with an Affymetrix scanner

data_processing: Scaled gene expression values were calculated using the default setting of Affymetrix Microarray Suite (MAS) software version 5.0

label: Biotin

organism: Homo sapiens

source_name: Whole Blood: FSGS patient with normal renal function

label_protocol: cDNA was obtained using the GeneChip One-Cycle cDNA Synthesis kit with globin peptide nucleic acid (PNAs) inclusion (Affymetrix, Santa Clara, California). After that an in vitro transcription was performed to generate biotinylated cRNA to be hybridized on microarrays using the Gene Chip IVT Labelling kit (Affymetrix). The T7 fagus promoter triggered the process of transcription.

extract_protocol: Peripheral blood was collected with PaxGene tubes (Qiagen, Valencia, CA, USA), which stabilize and protect RNA. Total RNA was extracted immediately using PaxGene blood RNA isolation kit (PreAnalytiX).

tag: creatinine clearance

value: >90 ml/min/1.73 m2 body surface area (evaluated by Cockcroft-Gault formula)

tag: serum creatinine

tag: clinical follow up

value: at least 7 years


title: FSGS-1

source_name: Whole Blood: FSGS-1 patient with normal renal function

value: At least 7 years


title: FSGS-2

value: female


title: MPGN-1

source_name: Whole Blood: MPGN-I patient with normal renal function


title: MPGN-2

source_name: Whole Blood: MPGN-2 patient with normal renal function


title: Np63 pathway activated 8

status: Public on Apr 12 2010

city: Boston

first: Adam

last: Gustafson

state: MA

address: 44 Cummington St

institute: Boston University

hyb_protocol: Affymetrix Suggested Protocol

scan_protocol: Affymetrix Suggested Protocol

data_processing: RMA normalized using Affymetrix Expression Console

source_name: Mammary Epithelial Culture

label_protocol: Affymetrix Suggested Protocol

extract_protocol: Affymetrix Suggested Protocol

tag: protocol

value: cell culture treated with adenovirus to activate NP63 pathway


title: MPGN-3

source_name: Whole Blood: MPGN- I patient with normal renal function


title: Np63 pathway activated 7


title: Np63 pathway activated 5


title: Np63 pathway activated 4


title: Np63 pathway activated 3


title: Np63 pathway activated 2


title: GFP control 6

value: cell culture treated with adenovirus to activate GFP


title: GFP control 11


title: Np63 pathway activated 6


title: PI3K pathway activated 8

value: cell culture treated with adenovirus to activate PI3K pathway


title: GFP control 10


title: GFP control 7


title: PI3K pathway activated 6


title: PI3K pathway activated 5


title: GFP control 9


title: GFP control 4


title: GFP control 8


title: GFP control 3


title: GFP control 2


title: GFP control 5


title: PI3K pathway activated 3


title: PI3K pathway activated 2


title: GFP control 1


title: Np63 pathway activated 1


title: MDA 231-2

status: Public on Sep 09 2009

city: Savannah

first: Nagendra

last: Ningaraj

state: GA

address: 4700 Waters Avenue

department: Anderson Cancer Institute

institute: Memorial University Medical Center

description: RMA expression value derived from Expression Console software; core-gene analysis

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the Memorial University Medical Center Genomics Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Background correction and normalization was done using Expression Console (Affimetrix). Gene level expression values (probeset intensity analysis) were derived using RMA alogrithm using core annotation level for transcripts. Exon array data was further analyzed using Partek Genomic Suite 6.4 software (Partek Inc., St. Louis, MO). Gene-level data was then filtered to include only those probesets that are in the ‘core’ meta-probe list, which represents 17 800 RefSeq genes and full-length GenBank mRNAs. Analysis of Variance (ANOVA) and multi test correction for P-values in Partek Genomic Suite were used to identify differentially expressed genes, using tissue type (primary versus metastatic tissue) as the candidate variable in the ANOVA model to obtain metastatic specific genes.

source_name: Metastatic Breast Tumor

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Cell lines were grown according to conditions recommended by ATCC.

extract_protocol: RNA was isolated from cells using TRIzol reagent (Invitrogen), according to the manufacturer’s instructions.

tag: cell line

tag: tumor type

value: Metastatic Breast Tumor

tag: sex

value: Female


title: MDA 231-1


title: MDA 231-3


title: MDA 361-3

source_name: Metastatic Breast Tumor to Brain

value: Metastatic Breast Tumor to Brain


title: MDA 361-1


title: MCF7-3

source_name: Primary Breast Tumor

value: Primary Breast Tumor


title: MDA 361-2


title: 2_NK Kit-

status: Public on Mar 01 2009

city: Bonn

first: Joachim

middle: L

last: Schultze

address: Carl-Troll-Str. 31

department: LIMES Institute

country: Germany

institute: University of Bonn

description: NK-Kit- cells

hyb_protocol: 1.5 µg cRNA was hybridized for 16 h to Sentrix Mouse-6 Expression BeadChips (Illumina) according to the Sentrix Beadchip hybridization protocol of the Illumina Beadstation 500X System manual.

scan_protocol: Samples were scanned using Illumina´s Direct-Hyb-Protocol on Illumina Beadstation 500X.

data_processing:
Raw data were extracted using Illumina Beadstudio Software V 3.1.1.0
Quantile normalization was performed using the IlluminaGUI R-package
(http://IlluminaGUI.dnsalias.org).

source_name: NK cell subsets from C57Bl/6 mice

label_protocol: Biotin-labeled cRNA was synthesized according to the instruction manual of the Illumina® TotalPrep™ RNA Amplification Kit (Applied Biosystems, Darmstadt, Germany) using 50 – 100 ng total RNA.

extract_protocol: NK kit+ and NK kit- subsets are stocked at -80°C in Trizol and then used for isolation of RNA. RNA isolation was performed according the manufacturer´s protocol. Total RNA was subsequently purified with Qiagen MinElute Cleanup Kit according to the manufacturer´s protocol.

treatment_protocol: Two subpopulations of NK cells are sorted from mouse spleens with a FACS Vantage instrument (BD Bioscience). NK kit+ are defined as CD3-NK1.1+CD117+ cells and NK kit- as CD3-NK1.1+CD117- cells. Splenocytes from C57Bl/6 mice were sorted in two steps. First, they were enriched in NK cells (NK1.1+/CD3-) by a magnetic separation using NK cell Isolation Kit (Miltenyi Biotec). Second, enriched NK cells were stained with FITC-conjugated anti-CD117 (c-kit) and PE-conjugated anti-NK1.1 monoclonal antibodies to allow a sorting of NK kit+ and NK kit- cells. Antibodies were purchased from Pharmingen, San Diego, CA or eBioscience, San Diego, CA. The purity of NK cells was around 98% after cell sorting.

tag: CD3-NK1.1+CD117+ NK cells compared to CD3-NK1.1+CD117- NK cells from spleen. Strain

value: C57Bl/6. Gender:female. Age:7 weeks. C57Bl/6 mice were obtained from C.River Laboratories (L’Arbresle, France) and the Centre d’Elevage Janvier (Le Genest-st-Isle, France).


title: 1_NK Kit-

description: NK Kit- cells


title: MCF7-2


title: 2_NK Kit+

description: NK-Kit+ cells


title: PI3K pathway activated 7


title: 3_NK Kit+

description: NK-Kit+ cells


title: 3_NK Kit-

description: NK-Kit- cells


title: Liver_C_week10

status: Public on Dec 01 2007

city: Singapore

first: Mei Yen

last: Chan

state: Singapore

address: 5 Lower Kent Ridge Road

department: Pediatrics

country: Singapore

institute: Yong Loo Lin School of Medicine, National University of Singapore

description: Liver tissue from C57BL/6J mice fed on control diet

hyb_protocol: Following fragmentation, the labeled cRNA were hybridized to the Affymetrix GeneChip® Mouse Genome 430 2.0 chip according to the protocol provided by the manufacturer.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner G2500A

data_processing: The GeneChip Operating Software Version 1.2.0.037 (Affymetrix) was used to analyze the scanned image. The normalization target was set to 500.

source_name: Liver, control

label_protocol: Biotinylated cRNA were prepared using the Genechip IVT Labelling Kit (Affymetrix, 900182), according to manufacturer's protocol.

extract_protocol: Total RNA was isolated from the frozen liver tissue of each mouse using Trizol reagent (Life Technologies, 15596-018) and purified using RNeasy Mini Kit (Qiagen, 74104), according to manufacturer's protocol.

treatment_protocol: Liver samples comprising identical lobes were quickly removed from each mouse. The liver samples were immediately snap-frozen in liquid nitrogen and stored at -80°C.

tag: Female mice


title: 1_NK Kit+

description: NK-Kit+ cells


title: Melanoma metastatic cell line A375, P6, biol rep6 (LeiFidler)

status: Public on Oct 02 2007

city: cambridge

first: steve

last: shen

address: 77 mass ave

institute: MIT

description: human melanoma metastatic cell line A375

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on one U133A human chip and one test chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: raw data (CEL file) were normalized with RMA and further analyzied with GenePatter comparative marker selection module.

source_name: A375 parental cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (701025, Revision 3).

extract_protocol: Rneasy mini kit

tag: Genotype

value: poorly metastatic

tag: Age


title: Melanoma metastatic cell line A375, P10, biol rep10 (LeiFidler)


title: Melanoma metastatic cell line A375, P5, biol rep5 (LeiFidler)


title: Melanoma metastatic cell line A375, P1, biol rep1 (LeiFidler)


title: Melanoma metastatic cell line A375, P4, biol rep4 (LeiFidler)


title: Melanoma metastatic cell line A375, P8, biol rep8 (LeiFidler)


title: Liver_C_week2


title: PI3K pathway activated 4


title: Liver_HF_week2

description: Liver tissue from C57BL/6J mice fed on high-fat diets

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner G2500A.

source_name: Liver, high-fat


title: Melanoma metastatic cell line A375, P2, biol rep2 (LeiFidler)


title: Melanoma metastatic cell line A375, P7, biol rep7 (LeiATCC)


title: Melanoma metastatic cell line A375, P8, biol rep8 (LeiATCC)


title: Melanoma metastatic cell line A375, P11, biol rep11 (LeiATCC)


title: Liver_D_Ref_rep4


title: Melanoma metastatic cell line A375, P7, biol rep7 (LeiFidler)


title: Liver_HF_week10


title: Melanoma metastatic cell line A375, P9, biol rep9 (LeiFidler)


title: Melanoma metastatic cell line A375, P5, biol rep5 (LeiATCC)


title: Melanoma metastatic cell line A375, P6, biol rep6 (LeiATCC)


title: Melanoma metastatic cell line A375, P4, biol rep4 (LeiATCC)


title: Melanoma metastatic cell line A375, P3, biol rep3 (LeiATCC)


title: Melanoma metastatic cell line A375, P3, biol rep3 (LeiFidler)


title: Melanoma metastatic cell line A375, P2, biol rep2 (LeiATCC)


title: Melanoma metastatic cell line A375, P1, biol rep1 (LeiATCC)


title: PAX sample 6

status: Public on Apr 30 2007

description: Blood samples from apparently healthy blood donors were collected in  PAXgeneTM collection tubes. RNA was prepared with the PAXgene Blood RNA kit according to the manufacturer´s instruction including an optional DNAse digestion step. Gene expression profiles were assessed using HG-U133A arrays.

hyb_protocol: Affymetrix hybridization protocol

scan_protocol: Affymetrix protocol for HGU133A arrays

data_processing: Cell files were imported in dCHIP and normalized to mean intensity

source_name: whole blood

label_protocol: Affymetrix IVT labeling kit

extract_protocol: PAXgene


title: PAX sample 9


title: PAX sample 7


title: PAX sample 10


title: PAX sample 11


title: PAX sample 14


title: Melanoma metastatic cell line A375, P9, biol rep9 (LeiATCC)


title: PAX sample 5


title: MCF7-1


title: PAX sample 8


title: PAX sample 3


title: PAX sample 13


title: PAX sample 4


title: PAX sample 2


title: PAX sample 12


title: GRP sample 12

description: Blood samples from apparently healthy blood donors were collected in  PAXgeneTM collection tubes. RNA was prepared with the PAXgene Blood RNA kit according to the manufacturer´s instruction including an optional DNAse digestion step. Globin reduction was performed according to the Affymetrix technical note. Gene expression profiles were assessed using HG-U133A arrays.


title: PAX sample 1


title: GRP sample 14


title: GRP sample 11


title: GRP sample 10


title: GRP sample 13


title: GRP sample 9


title: GRP sample 8


title: PI3K pathway activated 1


title: GRP sample 6


title: GRP sample 5


title: GRP sample 4


title: GRP sample 7


title: GRP sample 3


title: 9-A

status: Public on Oct 01 2006

city: Rockville

first: Maryanne

last: Vahey

state: MD

address: 1600 East Gude Drive

institute: Walter Reed Army Institute of Research

description: acute malaria-Cameroon

data_processing: The data were analyzed with MAS5.0 using Affymetrix default settings.

source_name: acute malaria-Cameroon

tag: Malaria, Human, PBMC, in vivo


title: 6-U

description: baseline uninfected

source_name: baseline uninfected


title: 8-A

description: acute malaria-Cameroon


title: 9-U

description: baseline uninfected


title: 8-I

description: experimental malaria-infected

source_name: experimental malaria-infected


title: 6-I

description: experimental malaria-infected


title: 7-A

description: acute malaria-Cameroon


title: GRP sample 1

data_processing: Cell files were imported in dCHIP and normalized to mean intensity.


title: 5-A

description: acute malaria-Cameroon


title: 5-Rx

description: treated malaria-Cameroon

source_name: treated malaria-Cameroon


title: 8-U

description: baseline uninfected


title: 7-I

description: experimental malaria-infected


title: 5-I

description: experimental malaria-infected


title: 4-I

description: experimental malaria-infected


title: GRP sample 2


title: 8-Rx

description: treated malaria-Cameroon


title: 5-U

description: baseline uninfected


title: 7-U

description: baseline uninfected


title: 4-U

description: baseline uninfected


title: 23-Rx

description: treated malaria-Cameroon


title: 3-U

description: baseline uninfected


title: 9-I

description: experimental malaria-infected


title: 3-I

description: experimental malaria-infected


title: 23-A

description: acute malaria-Cameroon


title: 22-U

description: baseline uninfected


title: Melanoma metastatic cell line A375, P10, biol rep10 (LeiATCC)


title: 21-U

description: baseline uninfected


title: 20-Rx

description: treated malaria-Cameroon


title: 20-I

description: experimental malaria-infected


title: 22-I

description: experimental malaria-infected


title: 20-A

description: acute malaria-Cameroon


title: 21-I

description: experimental malaria-infected


title: 18-I

description: experimental malaria-infected


title: 19-U

description: baseline uninfected


title: 18-U

description: baseline uninfected


title: 9-Rx

description: treated malaria-Cameroon


title: 2-U

description: baseline uninfected


title: 20-U

description: baseline uninfected


title: 19-I

description: experimental malaria-infected


title: 22-A

description: acute malaria-Cameroon


title: 16-A

description: acute malaria-Cameroon


title: 18-A

description: acute malaria-Cameroon


title: 17-I

description: experimental malaria-infected


title: 16-U

description: baseline uninfected


title: 16-I

description: experimental malaria-infected


title: 16-Rx

description: treated malaria-Cameroon


title: 15-I

description: experimental malaria-infected


title: 15-U

description: baseline uninfected


title: 17-U

description: baseline uninfected


title: 14-Rx

description: treated malaria-Cameroon


title: 14-A

description: acute malaria-Cameroon


title: 14-U

description: baseline uninfected


title: 14-I

description: experimental malaria-infected


title: 13-I

description: experimental malaria-infected


title: 13-U

description: baseline uninfected


title: 12-A

description: acute malaria-Cameroon


title: 12-U

description: baseline uninfected


title: 12-I

description: experimental malaria-infected


title: 12-Rx

description: treated malaria-Cameroon


title: 11-A

description: acute malaria-Cameroon


title: 11-Rx

description: treated malaria-Cameroon


title: 11-U

description: baseline uninfected


title: 10-U

description: baseline uninfected


title: 10-I

description: experimental malaria-infected


title: 11-I

description: experimental malaria-infected


title: 10-A

description: acute malaria-Cameroon


title: 10-Rx

description: treated malaria-Cameroon


title: 1-I

description: experimental malaria-infected


title: 6-A

description: acute malaria-Cameroon


title: 1-A

description: acute malaria-Cameroon


title: 1-Rx

description: treated malaria-Cameroon


title: 1-U

description: baseline uninfected


title: CH2113

status: Public on Dec 15 2005

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

country: United Kingdom

institute: University of Bristol

description: Sample represents the supraoptic nucleus from 5 dehydrated animals (3 Days)

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: GCOS version 1.2

label: MessageAmpII aRNA Amplification kit (Ambion)

organism: Rattus norvegicus

source_name: Supraoptic nucleus_3d dehydrated

label_protocol: Protocol available at http://www.AMBION.com/catalog/CatNum.php?1753

extract_protocol: Tissue was dissected in an RNase free manner and stored in RNAlater (Ambion) at -20C for no more than 1 month. Homogenisation in QIAzol was conducted mechanically and the aqueous phase separated using a PLG column (Eppendorf). RNA was further purified using RNeasy minelute cleanup kit  (Qiagen). RNA quality was confirmed using nanodrop and bioanylizer 2100 (Agilent).

tag: Strain

value: Sprague Dawley

tag: Gender

value: Male

value: 10-12 weeks

tag: Tissue

value: Hypothalamic Supraoptic nucleus


title: CH2123

status: Public on Dec 01 2005

description: Sample represents the supraoptic nucleus from 5 control animals

source_name: Supraoptic nucleus_control


title: CH2111

label_protocol:
Protocol available at http://www.AMBION.com/catalog/CatNum.php?1753

500ng total RNA was used initially


title: CH2120


title: CH2112

label_protocol:
Protocol available at http://www.AMBION.com/catalog/CatNum.php?1753
500ng total RNA was used initially


title: CH2121


title: CH2110

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures


title: 7-Rx

description: treated malaria-Cameroon


title: CH2124


title: CH2114


title: CH2122


title: 2-I

description: experimental malaria-infected