title: Basal epidermal cells, Sample 1

source_name: Human epidermis from brest reduction

value: Basal epidermal cells


title: PCT SHBG S42L_testosterone_rep1

status: Public on Dec 15 2010

type: RNA

city: Vancouver

first: Geoffrey

middle: L

last: Hammond

state: British Columbia

address: 950 West 28th Ave

department: OB/Gyn

country: Canada

institute: University of British Columbia

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization with the BeadStudio Program from Illumina.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: PCT cells constitutively expressing the human SHBG S42L mutant, 24h testosterone

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

growth_protocol: To generate PCT cells that constitutively express wild-type human SHBG or the human SHBG mutant deficient in steroid-binding, we transfected PKSV-PCT cells with cDNA constructs within pRC/CMV. Cell lines expressing human SHBG (PCT-SHBG) or a human SHBG mutant (PCT-SHBG S42L) with no detectable steroid-binding activity were obtained by limiting dilution cloning and screening the culture medium for secreted SHBG using an ultra-sensitive time-resolved fluorescence immunoassay. Cells were cultured in DMEM/F12 medium supplemented with 2% fetal bovine serum, insulin (5 μg/ml), dexamethasone (5 x 10-8M), selenium (60nM), transferrin (5 μg/ml), triiodothyronine (5 x 10-8M), EGF (10 ng/ml), D-glucose (20 mM), penicillin (100 U/mol), and streptomycin (100 μg/ml).

extract_protocol: RNA was extracted with the QIAGEN RNeasy mini kit with DNaseI treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyser.

treatment_protocol: 100 nM Testosterone or 100 nM 5a-dihydrotestosterone treatment of cells for 24 hours followed by 3 days in steroid-free medium.

tag: cell line

value: PKSV-PCT

tag: shbg expression

value: SHBG S42L mutant

tag: treatment

value: testosterone


title: D.rerio_GFP+ cells vs GFP- cells from 48hpf embryos tails_1 Replicate 1

city: Bethesda

first: Viviana

last: Gallardo

state: MD

address: 50 South Dr. Bldg 50. Room 5535

country: USA

institute: NHGRI/NIH

hyb_protocol: 200 picomoles of Cy3 and 100 picomoles of Cy5 labeled cRNAs are put in a total volume of 24 ul (qsp with DEPC H20) and 6 microliter of 5x fragmentation buffer from Affymetrix. the mixture is incubated at 94 ¡C for 15 minutes. Then, 25 ul of 2X hybridization buffer (250 _l Formamide, 250 _l 20xSSC and 20 _l 10%SDS). The mixture is then denatured for 2 minutes and applied on the Maui (BioMicro Systems, Inc) hybridization chamber/ array slide sandwich. The hybridization is performed at 45 degre for 20 hours.

scan_protocol: Microarray slides were scanned with a confocal laser (Agilent Technologies, Palo Alto, CA)

data_processing: PLab/DeArray. Data points with quality values below 0.7 were eliminated and the datasets were Lowess normalized. Normalized data were log-transformed and GFP+ and GFP- values were separately averaged over the eight experiments. Fold differences were calculated from log averages and Student’s t-test with Benjamini and Hochberg correction to generate p-values that were used to determined statistical significance. FileMaker Pro 9 (FileMaker, Inc.) and GeneSifter (http://www.genesifter.net/) softwares were used.

organism: Danio rerio

source_name: D.rerio_GFP-cells from 48hpf embryo tails_1 rep1

label_protocol: Approximately 500 ng to 800 ng RNA was linearly amplified by using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion) with yields ranging from 12 to 30 µg of aRNA. aRNA samples were split and labeled, half with Cy3 mono NHS ester and half with Cy5 mono NHS ester (CyDyes from GE Healthcare; post-labeling reagents from the MessageAmp II kit).

growth_protocol: Embryos were grown at 28.5°C in E3 medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4, and 0.1% Methylene Blue)

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: We used the tails of the Cldnb:gfp transgenic embryos in order to avoid recovering GFP-expressing cells in tissues other than the lateral line. Fish were anaesthetized and the tail was transected with a sharp scalpel adjacent to the end of the yolk extension. Tails of embryos were recovered from 36 hpf (for isolating primordium cells) or from 48 hpf (for neuromast cells) embryos, then transferred to Hank's medium containing 0.25% trypsin and 1mM EDTA and incubated for 15 to 30 min at room temperature during which they were dissociated mechanically by pipetting them up and down every 5 minutes. The digestion was stopped by adding fetal bovine serum to 10% and cell suspensions were then filtered through 40 µm nylon mesh, washed twice with PBS, pelleted by centrifugation at 600Xg for 2 minutes and resuspended in L-15 medium supplemented with 10% fetal bovine serum. FACS of single cell suspensions (GFP+ cell fraction and GFP- cell fraction) was performed at room temperature using a FACSAria.

tag: developmental stage

value: 48 hpf zebrafish embryo

tag: cell type

value: GFP- cell from embryonic tails

tag: genotype

value: Cldnb:gfp transgenic

source_name: D.rerio_GFP+cells from 48hpf embryo tails_1 rep1

value: GFP+ cell from embryonic tails


title: T1C3 vs IC8 melanoma cell line

city: LYON

first: Jerome

last: Lamartine

address: 7 passage du Vercors

country: France

institute: Université Lyon I

description: RNA from T1C3 and IC8 cells cultured to 70% confluency, hybridization T1C3 vs IC8

hyb_protocol: Direct hybridization sample (Cy5 vs Cy3)

scan_protocol: Axon 4000B Genepix software

data_processing: Loess normalization

organism: Homo sapiens

source_name: T1C3 melanoma cell line

label_protocol: Ambion / Amino Allyl MessageAmp II aRNA kit

extract_protocol: Tripure extraction Reagent

value: T1C3 melanoma cells

source_name: IC8 melanoma cell line

value: IC8 melanoma cells


title: 45C_REP1

city: Quebec

first: Eve-Lyne

last: Sylvestre

state: Quebec

address: 2440 Boul Hochelaga

institute: Université Laval

description:
Library was constructed with RNA extracted from 14 GV oocytes (CREATOR SMART, Clontech)
13724624_45°C_547

hyb_protocol: Sample probe was hybridized in technical replicate (2 replicates single-channel, on two slides) in SlideHyb™ Glass Array Hybridization Buffer #1 (Ambion, Streetville, Canada) for 18 hours at 45, 50, and 55°C respectively. Glass slides were then washed respectably at either 45, 50, or 55°C twice with 2X SCC/0.5% SDS for 15 min, twice with 0.5X SSC/0.5% SDS for 15 min, and rapidly washed in 1X SSC and H2O.

scan_protocol: Slides were scanned using the VersArray ChipReader System (Bio-Rad) at 5 microns resolution and analyzed using the ChipReader and ArrayPro Analyzer software (Media Cybernetics, San Diego, CA).

data_processing: Data processed/normalized with ChipReader and ArrayPro Analyzer software (Media Cybernetics, San Diego, CA).  Data were first normalized by Loess (by replicate within a same T°C), and signal was defined as present if intensity was above the threshold, calculated as negative and exogen DNA control cells mean  intensity plus 1x standard deviation (GFP, plant and Alien DNA (Stratagene), SSC) for each array.

source_name: human oocyte cDNA library 45°C

label_protocol: 2µg  of cDNAs  Purified PCR were then labelled using ULS Labeling Kit Alexafluor 547 and 647 dye pack (Kreatech, Amsterdam, The Netherlands); Diagnostics) according to manufacturer's instructions and unincorporated dyes were removed with Qiaquick PCR purification kit.

extract_protocol: Total RNA was isolated from 14 GV using PicoPure RNA isolation kit (Molecular Devices, Sunnyvale, CA) following manufacturer's instruction. DNase treatment was performed with Rnase-free DNase I (Qiagen, Missisauga, On, Canada). RNA quantification and integrity were assessed with a 2100 BioAnalyzer apparatus (Agilent, Mississauga, On, Canada) using the RNA 6000 Picochip a Bioanalyzer (Agilent). The full-length human oocyte cDNA library was generated using the Creator SMART cDNA Library Construction Kit (Clontech, Mountain View, CA). a unique human probe was generated from plasmid library by PCR amplification using 50X Advantage 2 polymerase Mix (Clontech), and primers corresponding to pDNR-LIB sequence (Up : 5’- AGTCGACGGTACCGGACATA-3’, Low : 5’-GCCAAACGAATGGTCTAGAAA-3’) for 17 thermal cycles.

tag: library

value: Human GV full-length oocyte cDNA library

tag: hybridization temperature


title: D.rerio_GFP+ cells vs GFP- cells from 36hpf embryos tails_2 Replicate 3

source_name: D.rerio_GFP-cells from 36hpf embryo tails_2 rep3

value: 36 hpf zebrafish embryo

source_name: D.rerio_GFP+cells from 36hpf embryo tails_2 rep3


title: D.rerio_GFP+ cells vs GFP- cells from 36hpf embryos tails_2 Replicate 4

source_name: D.rerio_GFP-cells from 36hpf embryo tails_2 rep4

source_name: D.rerio_GFP+cells from 36hpf embryo tails_2 rep4


title: 45C_REP2

description:
Library was constructed with RNA extracted from 14 GV oocytes (CREATOR SMART, Clontech)
13724625_45°C_647


title: T1C3 vs IC8 melanoma cell line swap

source_name: T1C3 malanoma cell line


title: PCT SHBG_DHT_rep1

source_name: PCT cells constitutively expressing wild-type human SHBG, 24h DHT

value: wild-type SHBG

value: 5a-dihydrotestosterone (DHT)


title: D.rerio_GFP+ cells vs GFP- cells from 48hpf embryos tails_1 Replicate 3

source_name: D.rerio_GFP-cells from 48hpf embryo tails_1 rep3

source_name: D.rerio_GFP+cells from 48hpf embryo tails_1 rep3


title: D.rerio_GFP+ cells vs GFP- cells from 36hpf embryos tails_2 Replicate 2

source_name: D.rerio_GFP-cells from 36hpf embryo tails_2 rep2

source_name: D.rerio_GFP+cells from 36hpf embryo tails_2 rep2


title: D.rerio_GFP+ cells vs GFP- cells from 36hpf embryos tails_2 Replicate 1

source_name: D.rerio_GFP-cells from 36hpf embryo tails_2 rep1

source_name: D.rerio_GFP+cells from 36hpf embryo tails_2 rep1


title: PCT SHBG S42L_DHT_rep3

source_name: PCT cells constitutively expressing the human SHBG S42L mutant, 24h DHT


title: Basal epidermal cells, Sample 2

city: New York

first: Miroslav

last: Blumenberg

state: NY

address: 455 First Ave #874

department: Dermatology

institute: NYU School of Medicine

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: MAS 5.0

label: Biotin

source_name: Human epidermis from brest reduction

label_protocol: Standard Affymetrix protocol

extract_protocol: Standard Affymetrix protocol

tag: donor


title: Histidine decarboxylase null myeloid-derived suppressor cell from colon tumor, rep2

first: XIANGDONG

last: YANG

address: 1130 St Nicholas Ave

department: Medicine

institute: Columbia University

description:
MDSC HDCKO-colon tumor-R
Technical replicate 2 of 2.

Differentially expressed genes of CD11b+Gr-1+ IMCs in the colonic tumors of HDC-EGFP/HDC-KO mice.

hyb_protocol: 12 μg of RNA dissolved in 300 μL of buffer was hybridized to Mouse Genome 430. 2.0 GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the GCRMA algorithm as implemented in Bioconductor/R.

source_name: CD11b+Gr-1+ myeloid cells sorted from the colon tumors of HDC-EGFP/HDC-KO transgenic mice induced with AOM/DSS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: HDC-deficient (HDC-KO) and HDC-EGFP mice were injected intraperitoneally with one dose of a genotoxic colonic carcinogen, azoxymethane (AOM), followed by 10 days of a non-genotoxic carcinogen, dextran sodium sulfate (DSS) oral exposure. 22-24 weeks later colon tumors were collected and CD11b+Gr-1+ myeloid cells were sorted.

tag: strain

value: HDC-EGFP/HDC-KO

tag: age

value: 7 months

tag: tissue

value: colon tumor

value: CD11b+Gr-1+ myeloid cells in the tumor stroma


title: Wild-type myeloid-derived suppressor cell from colon tumor, rep2

description:
MDSC WT-colon tumor-R
Technical replicate 2 of 2.

Differentially expressed genes of CD11b+Gr-1+ IMCs in the colonic tumors of HDC-EGFP mice.

source_name: CD11b+Gr-1+ myeloid cells sorted from the colon tumors of HDC-EGFP transgenic mice induced with AOM/DSS

value: HDC-EGFP


title: Bacteriophage c2 Infected Lactococcus lactis IL1403 Cell vs. Control Replicate 2

city: Fermoy

first: Vincenzo

last: Fallico

address: Moorepark

country: Ireland

institute: Teagasc Food Research Centre

description:
Biological replicate 2 of 2. Control L. lactis IL1403 cells, untreated.
Biological replicate 2 of 2. Experimental L. lactis IL1403 cells, infected with bacteriophage c2, harvested 10 min after infection.

hyb_protocol: The two differentially labelled cDNA probes were pooled, dried in a speed vac, and resuspended in 120 microliters of a preheated salt-based hybridization buffer (Ocimum Biosolutions, India) at 42 °C. Microarray slides were pre-hybridized in a solution containing 5X saline-sodium citrate (SSC) buffer, 0.1% sodium dodecyl sulphate (SDS), and 1% bovine serum albumin (BSA) at 42 °C for 60 min. After two washes with RT double-distilled water for 10 min, arrays were dried by centrifugation at 1,000 rpm for 5 min. The cDNA probe was denatured by heating at 95 °C for 3 min and cooled on ice for 1 min. After addition of 40 microliters of the background blocker KREAblock (Kreatech Biotechnology, The Netherlands), the hybridization mixture was heated at 42 °C before application to the microarray. The applied probe was kept in place with a coverslip, placed in a metal chamber, and incubated in a water bath at 42 °C for 24 h. Following overnight hybridization, slides were washed under gentle agitation for 1 min in preheated 5X SSC, 0.1% SDS buffer at 42°C, followed by washes at RT for 2 min in 2X SSC, 2 min in 1X SSC, and 1 min in 0.2X SSC. Slides were quickly rinsed in RT double-distilled water and dried in 50-ml conical-bottom tubes by centrifugation at 1,000 rpm for 5 min at RT.

scan_protocol: Microarrays were scanned with an Affymetrix 428TM Array Scanner (Affymetrix, USA) by using laser lights at wavelengths of 532 nm and 635 nm to excite Cy3 and Cy5 dye, respectively. Images were captured as 16-bit TIFF files by using Affymetrix Array Reader v.1.1 (Affymetrix, USA).

data_processing: Microarrays were analyzed using ImaGene v.7.5 (BioDiscovery Inc., USA) which uses a patented automatic segmentation algorithm to differentiate between signal and background values, and a complex tool including seven different criteria for spot fail/pass test to detect and flag low-quality spots. Presence of additional poor or empty spots not detected automatically was checked manually and flagged spots were excluded from quantification analysis. Background correction was applied globally by using the median of the signal values of all negative-control spots. A locally weighted regression scatter plot smoothing (LOWESS)-based procedure was applied globally, using all spots, to normalize background-corrected microarray data. The experiments were biologically replicated twice. Considering that each biological replicate also contained two technical duplicates on the array, the two hybridizations generated eight data points from both channels for each gene. The statistical significance of differential gene expression was calculated with the Significance Analysis of Microarray software by using a minimal two-fold change in expression ratio and maximal false discovery rate (FDR) of 1%.

organism: Lactococcus lactis

label_protocol: Purified single-stranded cDNA was dried in a speed vac, resuspended in 60 microliters of 0.1 M sodium bicarbonate buffer (pH 9.0), and labelled by incubation with Cy3 (reference) or Cy5 (experimental) mono NHS ester (GE Healthcare, UK) at room temperature (RT) for 90 min in the dark. Labelling reaction was quenched by addition of 5 microliters of 3 M sodium acetate (pH 5.2) followed by incubation at RT for 15 min in the dark. Uncoupled dye was removed by using the QIAquick PCR purification kit (QIAGEN, Germany) and the buffers provided with the kit, according to manufacturer's instructions. The efficiency of labelling was determined by reading the absorbance at 260 nm for cDNA concentration, the absorbance at 550 nm for Cy3 incorporation, and the absorbance at 650 nm for Cy5 incorporation.

growth_protocol: IL1403 cells grown in GM17 broth at 30 °C to mid-log phase (OD600 = 0.4). IL1403 cells split in two aliquots (experimental and reference). Addition of phage c2 (MOI = 800) and 10 mM CaCl2 to experimental sample. Addition of phage c2 (MOI = 800) and TMN buffer to reference sample. Incubated at 30 °C for additional 10 min. Infection stopping by immersion in -80 °C ethanol bath for 5 min.

extract_protocol: After centrifugation at 6,000 rpm for 5 min, cell pellets were re-suspended in 200  microliters of Tris-EDTA buffer (pH 8.0) containing 6 mg/ml lysozyme and incubated at 37 °C for 10 min. Total RNA was extracted by using the RiboPureTM-Bacteria kit (Ambion, USA) and contaminating DNA was removed with a DNA-free kit (Ambion, USA), according to manufacturer's recommendations. Total RNA samples (50 micrograms) were enriched for mRNA by using the mRNA-ONLYTM Prokaryotic mRNA Isolation kit (Epicentre Biotechnologies, USA). Reverse transcription of enriched mRNA into single-stranded cDNA was initiated by adding 9 micrograms of random hexamers (Invitrogen, USA) and 2 microliters of a 50X aminoallyl-deoxynucleoside triphosphate stock mixture (25 mM dATP, dGTP, dCTP, 10 mM dTTP, and 15 mM aminoallyl-dUTP). The volume was adjusted to 34 microliters with RNase-free water before the mixture was incubated at 70 °C for 10 min followed by 10 min at 25 °C to allow primers annealing. After addition of 12 microliters of 5X First Strand buffer (Invitrogen, USA), 3 microliters of 0.1 M dithiothreitol (Invitrogen, USA), 3 microliters of SUPERase-In (20 U/microliters; Ambion, USA), and 6 microliters of SuperScript III Reverse Transcriptase (200 U/microliters; Invitrogen, USA), the mixture was first incubated at 25 °C for 10 min and then at 42 °C for 24 h. cDNA synthesis was stopped by heating at 95 °C for 10 min and the RNA template was removed by alkaline treatment with 20 microliters of 0.5 M NaOH and 10 microliters of 0.5 M EDTA at 65°C for 30 min. Ten microliters of 1 M HCl were added to neutralize the cDNA mixture, which was then purified by using the QIAquick PCR purification kit (QIAGEN, Germany) according to manufacturer's instructions, except that the free amines-containing wash and elution buffer were replaced with an ethanol-based phosphate wash buffer (80% ethanol, 5 mM KPO4, pH 8.5) and a phosphate elution buffer (4 mM KPO4, pH 8.5), respectively.

treatment_protocol: The IL1403 culture was split in two 20-ml aliquots (experimental and reference), to which were added phage c2 (MOI = 800) (experimental) or TMN buffer (reference), and 10 mM CaCl2 to allow efficient phage adsorption. After incubation at 30 °C for 10 min to allow phage adsorption on IL1403 cells, samples were immersed in a -80 °C ethanol bath for 5 min to prevent any changes in gene expression profiles.

tag: infection status

value: uninfected

organism:
Lactococcus lactis
Ceduovirus c2

value: infected with bacteriophage c2


title: T0

city: Biella

first: caterina

last: Peraldo Neia

state: Biella

address: via Malta 3

department: Laboratory of  Cancer Genomics

country: Italy

institute: Fondazione Edo ed Elvo Tempia

description: technical replicate of SKBR3_NORM (dye swapped)

hyb_protocol: Samples were hybridized on 44K glass arrays (Agilent Technologies) using the In Situ Hybridization kit-plus (Agilent Technologies) according to the 60-mer oligo microarray processing protocol (Agilent Technologies). Slides were washed using the SSPE wash procedure.

scan_protocol: Slides were scanned using a dual-laser microarray scanner Agilent G2505B.

data_processing: Images were analyzed using Feature Extraction software (Agilent Technologies) version 7.6. Output files containing feature and background intensities and the related statistical parameters for red and green signals were then loaded into the Resolver SE System (Rosetta Biosoftware, Seattle, WA) together with the scan images and the Agilent Human Whole Genome pattern file. Data processing and normalization were performed using the Agilent Human Whole Genome platform-specific error model. Replicate expression profiles were combined to form ratio experiments where each gene is associated to an expression fold-change and a p-value to assess the statistical significance of its modulation in the sample compared to the reference. New ratio experiments were also built by applying the “ratio split with common reference” option and calculating ratios over the average of non tumor samples (CMN). A “weight by error” divisive clustering algorithm available within the Rosetta Resolver system (with cosine correlation as similarity metrics) was applied to such new ratios to compare their expression profiles. At the same time, data treatment with the LIMMA (LInear Models for MicroArray data) package available within Bioconductor (http://www.bioconductor.org/) was also performed applying normexp background calculation, lowess within-array and A-quantile between-array normalization methods.

source_name: SKBR3 sensitive

label_protocol: mRNA was amplified starting from 1μg using MessageAmp II aRNA Amplification kit (Ambion Inc. Austin TX, USA). Ammino-allyl modified nucleotides were incorporated in in vitro transcription step according to the manufacturer’s protocol.  Labeling was performed using NHS (N-hydroxysuccinimidyl) ester Cy3 or Cy5 dies (GE Healthcare Europe GMBH, Upsala - Sweden) able to react with the modified RNA. At least 5 μg of mRNA, for each sample, were labeled and purified with columns respectively. The Dye-Swap replication procedure was applied, in order to increase the accuracy of results. Samples were hybridized on 44K glass arrays (Agilent Technologies).

growth_protocol: T100 cells were obtained by chronically treating SKBR3 cells (American Type Culture Collection  Rockville, MD) with trastuzumab 100 µg/mL in RPMI 1640 medium (Invitrogen, Paisley, UK) with 10% fetal bovine serum (FBS), 1% Penn-strep + L-glutamine for 12 months. Parental SKBR3 cells sensitive to trastuzumab were named T0.

extract_protocol: Total RNA was isolated from T0 and T100 using TRIZOL reagent (Life Technologies, Gathersburg, MD) and quantified by Bioanalyzer 2100 (Agilent Technologies)

value: breast cancer

source_name: SKBR3 resistant to trastuzumab and lapatinib

tag: genome/variation

value: HER2 overexpressing


title: PCT SHBG S42L_DHT_rep2

value: PKSV-PCT

value: SHBG S42L mutant


title: Histidine decarboxylase null myeloid-derived suppressor cell from bone marrow, rep2

description:
HDC+ MDSC-HDCKO-BM-R
Technical replicate 2 of 2.

Differentially expressed genes of CD11b+Gr-1+ IMCs in the bone marrow of HDC-EGFP/HDC-KO mice.

source_name: HDC-expressing CD11b+Gr-1+ myeloid cells sorted from the bone marrow of HDC-EGFP/HDC-KO transgenic mice

treatment_protocol: Bone marrow-derived cells (BMDCs) from the femur and tibia of euthanized mice were flushed with ice-cold Hanks' Balanced Salt Solution (GIBCO) and depleted of red blood cells (RBCs) using RBC lysing buffer (BD Biosciences). Anti-CD11b and anti-Gr-1 labeled myeloid cells were sorted in three HDC-EGFP and three HDCEGFP/HDCKO mice (3-4 months).

value: 3-4 months

value: bone marrow

value: bone marrow CD11b+Gr-1+ myeloid cells


title: Wild-type myeloid-derived suppressor cell from bone marrow, rep2

description:
HDC+ MDSC-WT-BM-R
Technical replicate 2 of 2.

Differentially expressed genes of CD11b+Gr-1+ IMCs in the bone marrow of HDC-EGFP mice.

source_name: HDC-expressing CD11b+Gr-1+ myeloid cells sorted from the bone marrow of HDC-EGFP transgenic mice


title: dig1-mChLacI_LacOFUS1_xF_1

type: genomic

city: San Francisco

first: Hiten

last: Madhani

state: CA

department: Biochemistry and Biophysics

institute: University of California, San Francisco

description: No further information

hyb_protocol: arrays blocked with Agilent aCGH blocking buffer and each probe was hybridized 1:1 using Agilent hybridization buffer.  Hybes were allowed to proceed for 40hrs at 65 degrees.

scan_protocol: Scanned with GenePix 4000B at 5uM

data_processing: Median background subtracted first, then normalized using a loess algorithm

molecule: genomic DNA

organism: Saccharomyces cerevisiae

label_protocol: DNA was amplified using strand displacement amplification.  Random 9-mers were used to prime followed by amplification with dNTPs and exo- Klenow.  During the last amplification step, a mix of aadUTP:dTTP was used to generate amino-allyl-DNA probe that could be labeled with Cy3 or Cy5 dye.

growth_protocol: Cells were diluted from saturated cultures into -Ura media for 4hrs.  Cells were again diluted into YPAD, grown for another 4hrs and collected after treatment with 5uM alpha factor for 1hr.  All growth done at 30 degrees.

extract_protocol: Culture was crosslinked with 1.5mM EGS for 30min followed by 1% formaldehyde for 30min.  Crosslinking was quenched with 0.125M glycine for 5min.  DNA was extracted by bead beating 6x1min followed by light sonication (2x5min on low setting).  mCherry-LacI was immunoprecipitated using an anti-DsRed polyclonal antibody (1:100 dilution).

value: Ste12-eGFP-HYGMX, lacoarray-hismx-pfus1-fus1 at fus1 locus, mcherry-laci, dig1::KANMX

tag: sample type

value: IP

value: input


title: Histidine decarboxylase null myeloid-derived suppressor cell from colon tumor, rep1

description:
MDSC HDCKO-colon tumor
Technical replicate 1 of 2.

Differentially expressed genes of CD11b+Gr-1+ IMCs in the colonic tumors of HDC-EGFP/HDC-KO mice.

value: HDC-EGFP/HDC-KO


title: PCT SHBG S42L_DHT_rep1

value: 5a-dihydrotestosterone (DHT)


title: T100

description: technical replicate of SKBR3_DS


title: D.rerio_GFP+ cells vs GFP- cells from 36hpf embryos tails_1 Replicate 4

source_name: D.rerio_GFP-cells from 36hpf embryo tails_1 rep4

value: 36 hpf zebrafish embryo

value: GFP- cell from embryonic tails

value: Cldnb:gfp transgenic

source_name: D.rerio_GFP+cells from 36hpf embryo tails_1 rep4

value: GFP+ cell from embryonic tails


title: Histidine decarboxylase null myeloid-derived suppressor cell from bone marrow, rep1

description:
HDC+ MDSC-HDCKO-BM
Technical replicate 1 of 2.

Differentially expressed genes of CD11b+Gr-1+ IMCs in the bone marrow of HDC-EGFP/HDC-KO mice.


title: HUVEC_unspread_VEGF_rep3

city: Philadelphia

first: Colette

last: Shen

state: PA

address: 210 S. 33rd St., 510 Skirkanich Hall

institute: University of Pennsylvania

description: Gene expression data from HUVECs with changes in ECM adhesion and soluble VEGF stimulation

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Human Affymetrix U133+ v2.0 arrays. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin.  Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: The data were analyzed using GC-RMA.

source_name: HUVECs restricted in spreading, with VEGF exposure

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2ug total RNA.

growth_protocol: HUVECs were cultured in full growth medium (M199+20%FBS+ 50mg/ml ECGS+100mg/ml heparin+100units/ml penicillin+100 mg/ml streptomycin) on gelatin-coated surfaces prior to treatment.

extract_protocol: Total RNA was extrated using the Qiagen RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: HUVECs were cultured on micropatterned islands of fibronectin or allowed to spread fully on fibronectin for 2 hrs and then stimulated with 50ng/ml VEGF or no growth factor for 18 hrs in starve media (5% FBS in M199).

value: primary HUVECs

tag: cell passage

value: passage 3


title: Bacteriophage c2 Infected Lactococcus lactis IL1403 Cell vs. Control Replicate 1

description:
Biological replicate 1 of 2. Control L. lactis IL1403 cells, untreated.
Biological replicate 1 of 2. Experimental L. lactis IL1403 cells, infected with bacteriophage c2, harvested 10 min after infection.

value: uninfected

value: infected with bacteriophage c2


title: HUVEC_unspread_VEGF_rep2


title: Wild-type myeloid-derived suppressor cell from colon tumor, rep1

description:
MDSC WT-colon tumor
Technical replicate 1 of 2.

Differentially expressed genes of CD11b+Gr-1+ IMCs in the colonic tumors of HDC-EGFP mice.

value: HDC-EGFP

value: 7 months

value: colon tumor

value: CD11b+Gr-1+ myeloid cells in the tumor stroma


title: HUVEC_unspread_VEGF_rep1


title: HUVEC_unspread_noVEGF_rep3

source_name: HUVECs restricted in spreading, no VEGF exposure


title: MH-S_LPS_rep02

city: Baltimore

first: Joshua

middle: J

last: Reece

address: 615 N. Wolfe Street

department: MMI

institute: Johns Hopkins University BSPH

description: Intensity of hybridization for each probe pair was computed by GCOS 1.2 software (Affymetrix). (For more detailed methods, please refer to the website of the Malaria Research Institute Gene Array Core Facility (MRI-GACF) at the Johns Hopkins Bloomberg School of Public Health http://jhmmi.jhsph.edu)

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures using affy GCS3000

data_processing: Affymetrix Microarray Suite version 5.0

source_name: ATCC_CRL-2019, LPS treated

label_protocol: standard Affymetrix procedures

extract_protocol: trizol extraction followed by qiagen RNeasy total RNA cleanup protocol

tag: strain:BALB/c Mouse', 'cell type:alveolar macrophage', 'source

value: cell culture', 'condition:LPS treated


title: D.rerio_GFP+ cells vs GFP- cells from 36hpf embryos tails_1 Replicate 1

source_name: D.rerio_GFP-cells from 36hpf embryo tails_1 rep1

source_name: D.rerio_GFP+cells from 36hpf embryo tails_1 rep1


title: HUVEC_spread_noVEGF_rep3

source_name: HUVECs fully spread, no VEGF exposure


title: MH-S_LPS_rep03


title: D.rerio_GFP+ cells vs GFP- cells from 36hpf embryos tails_1 Replicate 3

source_name: D.rerio_GFP-cells from 36hpf embryo tails_1 rep3

source_name: D.rerio_GFP+cells from 36hpf embryo tails_1 rep3


title: HUVEC_unspread_noVEGF_rep2


title: HUVEC_spread_noVEGF_rep1


title: HUVEC_spread_VEGF_rep2

source_name: HUVECs fully spread, with VEGF exposure


title: HUVEC_spread_VEGF_rep3


title: MH-S_CON_rep01

source_name: ATCC_CRL-2019, uninfected control

value: cell culture', 'condition:uninfected control


title: MH-S_CON_rep02


title: HUVEC_unspread_noVEGF_rep1


title: MH-S_IL-4_rep02

source_name: ATCC_CRL-2019, IL-4 treated

value: cell culture', 'condition:IL-4 treated


title: MH-S_IL-4_rep01


title: HUVEC_spread_noVEGF_rep2


title: MH-S_LPS_rep01


title: D.rerio_GFP+ cells vs GFP- cells from 36hpf embryos tails_1 Replicate 2

source_name: D.rerio_GFP-cells from 36hpf embryo tails_1 rep2

source_name: D.rerio_GFP+cells from 36hpf embryo tails_1 rep2


title: Wild-type myeloid-derived suppressor cell from bone marrow, rep1

description:
HDC+ MDSC-WT-BM
Technical replicate 1 of 2.

Differentially expressed genes of CD11b+Gr-1+ IMCs in the bone marrow of HDC-EGFP mice.

value: 3-4 months

value: bone marrow

value: bone marrow CD11b+Gr-1+ myeloid cells


title: HUVEC_spread_VEGF_rep1


title: MH-S_IL-4_rep03


title: adult_1y2m_male_rep2

status: Public on Dec 14 2010

city: Zagreb

first: Tomislav

last: Domazet-Loso

address: Bijenicka cesta 54

department: Division of Molecluar Biology

country: Croatia

institute: Ruder Boskovic Institute

description:
Agilent Feature Extraction file:
US84303580_251916110562_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish adult, 1y2m, male, biological replicate 2.

hyb_protocol: 1650 ng of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul  following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Zebrafish (V2) Gene Expression Microarray slides (4x44K) (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 34°C GE Wash buffer 2 (Agilent), then dried 1 minute at room temperature.

scan_protocol: Slides were scanned immediately after washing and drying on the Agilent High-Resolution Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction 10.7 Image Analysis Software (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 019161_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: adult, 1y2m, male, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 400 ng RNA using the Agilent one-color Quick Amp Labeling Kit protocol according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Zebrafish (Danio rerio) were kept in 12L flow-through tanks at 26.5 °C (around 60 animals per tank). For accurate staging, fertilized eggs were collected within 15 min intervals and incubated in Petri dishes at 28.5°C with water changes every 2-6 hours. After hatching, larvae were transferred to 1L tanks and kept at 28.5 °C.

extract_protocol: Frozen tissues were homogenized in TRIZOL (Invitrogen) by shaking samples 4 min together with a 5mm steel bead in a bead mill (TissueLyser II, Qiagen) at 30 Hz (embryos and smaller larve) or by disruption (larger larvae, juveniles and adults) using rotor-stator homogenizer (Tissue Ruptor, Qiagen). Total RNA was isolated using TRIZOL plus protocol from Invitrogen and the quality and the yield was determined by BioAnalyzer 2100 (Agilent) and NanoDrop ND-1000 spectrophotometer (Thermo scientific)

treatment_protocol: Staging was done according to post-fertilization time. Embryos were additionally staged under the dissecting microscope according to ref. 1 to check for the consistency of post-fertilization timing and morphological development at standard temperature (28.5 °C). Only healthy animals that showed the expected morphological features for a given post-fertilization time were sampled. Each sample contained around 50 individuals until the 1 day and 3 hour embryo stage, 15 individuals until the 10 day larval stage, 10 individuals until the 18 day larval stage, 5 individuals until the 45 day juvenile stage, while in later juvenile and adult stages we sampled males and females separately and each sample contained 2 individuals. All samples were snap frozen in liquid nitrogen and stored at -80 °C until RNA extraction. To avoid severe biases due to the excess of unfertilized eggs, we squeezed eggs from adult females before freezing them in liquid nitrogen. 1. (Kimmel CB, Ballard WW, Kimmel SR, Ullmann B, Schilling TF. Stages of embryonic development of the zebrafish. Dev Dyn. 1995 Jul;203(3):253-310.)

value: wild type

value: adult

tag: developmental timing

tag: gender

value: male

tag: number of individuals per sample


title: adult_1y6m_male_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110562_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish adult, 1y6m, male, biological replicate 2.

source_name: adult, 1y6m, male, replicate 2

tag: developmental stage


title: adult_9m_male_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110386_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish adult, 9m, male, biological replicate 1.

source_name: adult, 9m, male, replicate 1


title: adult_1y9m_mixed_rep3

description:
Agilent Feature Extraction file:
US84303580_251916110387_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish adult, 1y9m, mixed sex, biological replicate 3.

source_name: adult, 1y9m, mixed sex, replicate 3

value: mixed


title: adult_1y6m_male_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110387_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish adult, 1y6m, male, biological replicate 1.

source_name: adult, 1y6m, male, replicate 1


title: adult_1y9m_mixed_rep4

description:
Agilent Feature Extraction file:
US84303580_251916110562_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish adult, 1y9m, mixed sex, biological replicate 4.

source_name: adult, 1y9m, mixed sex, replicate 4


title: adult_3m15d_male_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110561_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish adult, 3m15d, male, biological replicate 2.

source_name: adult, 3m15d, male, replicate 2


title: MH-S_CON_rep03


title: adult_1y2m_male_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110387_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish adult, 1y2m, male, biological replicate 1.

source_name: adult, 1y2m, male, replicate 1


title: adult_90d_male_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110576_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish adult, 90d, male, biological replicate 2.

source_name: adult, 90d, male, replicate 2


title: adult_7m_male_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110386_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish adult, 7m, male, biological replicate 1.

source_name: adult, 7m, male, replicate 1


title: adult_4m_male_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110386_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish adult, 4m, male, biological replicate 1.

source_name: adult, 4m, male, replicate 1


title: adult_90d_male_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110385_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish adult, 90d, male, biological replicate 1.

source_name: adult, 90d, male, replicate 1


title: adult_65d_male_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110576_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish adult, 65d, male, biological replicate 2.

source_name: adult, 65d, male, replicate 2


title: adult_80d_male_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110576_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish adult, 80d, male, biological replicate 2.

source_name: adult, 80d, male, replicate 2


title: adult_65d_male_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110572_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish adult, 65d, male, biological replicate 1.

source_name: adult, 65d, male, replicate 1


title: adult_55d_male_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110572_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish adult, 55d, male, biological replicate 1.

source_name: adult, 55d, male, replicate 1


title: adult_1y2m_female_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110409_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish adult, 1y2m, female, biological replicate 1.

source_name: adult, 1y2m, female, replicate 1

value: female


title: adult_1y9m_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110409_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish adult, 1y9m, mixed sex, biological replicate 1.

source_name: adult, 1y9m, mixed sex, replicate 1


title: adult_1y9m_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110558_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish adult, 1y9m, mixed sex, biological replicate 2.

source_name: adult, 1y9m, mixed sex, replicate 2


title: adult_3m15d_male_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110386_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish adult, 3m15d, male, biological replicate 1.

source_name: adult, 3m15d, male, replicate 1


title: adult_4m_male_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110561_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish adult, 4m, male, biological replicate 2.

source_name: adult, 4m, male, replicate 2


title: adult_1y6m_female_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110558_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish adult, 1y6m, female, biological replicate 2.

source_name: adult, 1y6m, female, replicate 2


title: adult_55d_male_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110576_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish adult, 55d, male, biological replicate 2.

source_name: adult, 55d, male, replicate 2


title: adult_9m_female_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110408_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish adult, 9m, female, biological replicate 1.

source_name: adult, 9m, female, replicate 1


title: adult_9m_male_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110561_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish adult, 9m, male, biological replicate 2.

source_name: adult, 9m, male, replicate 2


title: adult_9m_female_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110558_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish adult, 9m, female, biological replicate 2.

source_name: adult, 9m, female, replicate 2


title: adult_1y2m_female_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110558_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish adult, 1y2m, female, biological replicate 2.

source_name: adult, 1y2m, female, replicate 2


title: adult_7m_female_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110556_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish adult, 7m, female, biological replicate 2.

source_name: adult, 7m, female, replicate 2


title: adult_7m_female_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110408_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish adult, 7m, female, biological replicate 1.

source_name: adult, 7m, female, replicate 1


title: adult_3m15d_female_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110408_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish adult, 3m15d, female, biological replicate 2.

source_name: adult, 3m15d, female, replicate 2


title: adult_4m_female_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110408_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish adult, 4m, female, biological replicate 1.

source_name: adult, 4m, female, replicate 1


title: adult_90d_female_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110556_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish adult, 90d, female, biological replicate 2.

source_name: adult, 90d, female, replicate 2


title: adult_1y6m_female_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110409_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish adult, 1y6m, female, biological replicate 1.

source_name: adult, 1y6m, female, replicate 1


title: adult_90d_female_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110407_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish adult, 90d, female, biological replicate 1.

source_name: adult, 90d, female, replicate 1


title: adult_4m_female_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110556_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish adult, 4m, female, biological replicate 2.

source_name: adult, 4m, female, replicate 2


title: adult_80d_male_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110385_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish adult, 80d, male, biological replicate 1.

source_name: adult, 80d, male, replicate 1


title: juvenile_80d_female_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110555_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish juvenile, 80d, female, biological replicate 2.

source_name: juvenile, 80d, female, replicate 2

value: juvenile


title: juvenile_80d_female_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110407_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish juvenile, 80d, female, biological replicate 1.

source_name: juvenile, 80d, female, replicate 1


title: adult_3m15d_female_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110556_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish adult, 3m15d, female, biological replicate 1.

source_name: adult, 3m15d, female, replicate 1


title: juvenile_65d_female_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110407_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish juvenile, 65d, female, biological replicate 1.

source_name: juvenile, 65d, female, replicate 1


title: juvenile_65d_female_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110555_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish juvenile, 65d, female, biological replicate 2.

source_name: juvenile, 65d, female, replicate 2


title: juvenile_55d_female_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110407_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish juvenile, 55d, female, biological replicate 1.

source_name: juvenile, 55d, female, replicate 1


title: juvenile_55d_female_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110555_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish juvenile, 55d, female, biological replicate 2.

source_name: juvenile, 55d, female, replicate 2


title: juvenile_45d_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110555_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish juvenile, 45d, mixed sex, biological replicate 2.

source_name: juvenile, 45d, mixed sex, replicate 2


title: larva_40d_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110406_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish larva, 40d, mixed sex, biological replicate 1.

source_name: larva, 40d, mixed sex, replicate 1

value: larva


title: juvenile_45d_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110406_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish juvenile, 45d, mixed sex, biological replicate 1.

source_name: juvenile, 45d, mixed sex, replicate 1


title: larva_30d_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110405_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish larva, 30d, mixed sex, biological replicate 1.

source_name: larva, 30d, mixed sex, replicate 1


title: larva_18d_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110405_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish larva, 18d, mixed sex, biological replicate 1.

source_name: larva, 18d, mixed sex, replicate 1


title: larva_24d_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110554_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish larva, 24d, mixed sex, biological replicate 2.

source_name: larva, 24d, mixed sex, replicate 2


title: larva_30d_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110554_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish larva, 30d, mixed sex, biological replicate 2.

source_name: larva, 30d, mixed sex, replicate 2


title: larva_40d_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110554_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish larva, 40d, mixed sex, biological replicate 2.

source_name: larva, 40d, mixed sex, replicate 2


title: larva_14d_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110553_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish larva, 14d, mixed sex, biological replicate 2.

source_name: larva, 14d, mixed sex, replicate 2


title: larva_24d_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110405_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish larva, 24d, mixed sex, biological replicate 1.

source_name: larva, 24d, mixed sex, replicate 1


title: larva_4d_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110552_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish larva, 4d, mixed sex, biological replicate 2.

source_name: larva, 4d, mixed sex, replicate 2


title: hatching_2d_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110552_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish hatching, 2d, mixed sex, biological replicate 2.

source_name: hatching, 2d, mixed sex, replicate 2

value: hatching


title: larva_4d_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110404_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish larva, 4d, mixed sex, biological replicate 1.

source_name: larva, 4d, mixed sex, replicate 1


title: larva_6d_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110404_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish larva, 6d, mixed sex, biological replicate 1.

source_name: larva, 6d, mixed sex, replicate 1


title: hatching_3d_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110406_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish hatching, 3d, mixed sex, biological replicate 1.

source_name: hatching, 3d, mixed sex, replicate 1


title: hatching_2d12h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110403_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish hatching, 2d12h, mixed sex, biological replicate 1.

source_name: hatching, 2d12h, mixed sex, replicate 1


title: hatching_2d12h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110552_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish hatching, 2d12h, mixed sex, biological replicate 2.

source_name: hatching, 2d12h, mixed sex, replicate 2


title: larva_8d_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110553_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish larva, 8d, mixed sex, biological replicate 2.

source_name: larva, 8d, mixed sex, replicate 2


title: larva_10d_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110553_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish larva, 10d, mixed sex, biological replicate 2.

source_name: larva, 10d, mixed sex, replicate 2


title: larva_10d_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110406_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish larva, 10d, mixed sex, biological replicate 1.

source_name: larva, 10d, mixed sex, replicate 1


title: larva_14d_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110405_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish larva, 14d, mixed sex, biological replicate 1.

source_name: larva, 14d, mixed sex, replicate 1


title: larva_18d_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110554_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish larva, 18d, mixed sex, biological replicate 2.

source_name: larva, 18d, mixed sex, replicate 2


title: hatching_3d_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110552_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish hatching, 3d, mixed sex, biological replicate 2.

source_name: hatching, 3d, mixed sex, replicate 2


title: larva_6d_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110553_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish larva, 6d, mixed sex, biological replicate 2.

source_name: larva, 6d, mixed sex, replicate 2


title: larva_8d_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110404_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish larva, 8d, mixed sex, biological replicate 1.

source_name: larva, 8d, mixed sex, replicate 1


title: pharyngula_1d18h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110403_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish pharyngula, 1d18h, mixed sex, biological replicate 1.

source_name: pharyngula, 1d18h, mixed sex, replicate 1

value: pharyngula


title: pharyngula_1d10h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110551_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish pharyngula, 1d10h, mixed sex, biological replicate 2.

source_name: pharyngula, 1d10h, mixed sex, replicate 2


title: pharyngula_1d1h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110401_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish pharyngula, 1d1h, mixed sex, biological replicate 1.

source_name: pharyngula, 1d1h, mixed sex, replicate 1


title: pharyngula_1d14h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110402_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish pharyngula, 1d14h, mixed sex, biological replicate 1.

source_name: pharyngula, 1d14h, mixed sex, replicate 1


title: pharyngula_1d1h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110570_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish pharyngula, 1d1h, mixed sex, biological replicate 2.

source_name: pharyngula, 1d1h, mixed sex, replicate 2


title: segmentation_23h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110570_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish segmentation, 23h, mixed sex, biological replicate 2.

source_name: segmentation, 23h, mixed sex, replicate 2

value: segmentation


title: pharyngula_1d6h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110402_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish pharyngula, 1d6h, mixed sex, biological replicate 1.

source_name: pharyngula, 1d6h, mixed sex, replicate 1


title: pharyngula_1d18h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110551_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish pharyngula, 1d18h, mixed sex, biological replicate 2.

source_name: pharyngula, 1d18h, mixed sex, replicate 2


title: pharyngula_1d3h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110402_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish pharyngula, 1d3h, mixed sex, biological replicate 1.

source_name: pharyngula, 1d3h, mixed sex, replicate 1


title: segmentation_23h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110401_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish segmentation, 23h, mixed sex, biological replicate 1.

source_name: segmentation, 23h, mixed sex, replicate 1


title: pharyngula_1d10h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110402_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish pharyngula, 1d10h, mixed sex, biological replicate 1.

source_name: pharyngula, 1d10h, mixed sex, replicate 1


title: pharyngula_1d3h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110570_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish pharyngula, 1d3h, mixed sex, biological replicate 2.

source_name: pharyngula, 1d3h, mixed sex, replicate 2


title: hatching_2d_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110403_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish hatching, 2d, mixed sex, biological replicate 1.

source_name: hatching, 2d, mixed sex, replicate 1


title: segmentation_22h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110401_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish segmentation, 22h, mixed sex, biological replicate 1.

source_name: segmentation, 22h, mixed sex, replicate 1


title: segmentation_20h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110569_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish segmentation, 20h, mixed sex, biological replicate 2.

source_name: segmentation, 20h, mixed sex, replicate 2


title: Uveal Melanoma MU217

city: Paris Cedex 05

first: Cecile

last: Laurent

address: 26 rue d'ulm

institute: Institut Curie

description: Gene expression data from Uveal Melanoma

hyb_protocol: Following fragmentation, 10 ug of labelled cRNA were hybridized for 16 hr on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip GCS3000 scanner.

data_processing: Raw data were controlled using Genechip Operating Software and Affymetrix MAS5 algorithm to control the quality of hybridization and synthesis steps. Raw data were analysed using R/Bioconductor and normalized by GC-RMA method.

source_name: Eye

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix two round amplification  protocol from 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. A cleanup with RNAII Nucleospin was conducted according Macherey Nagel recommendations

value: Uveal Melanoma (eye)

tag: eye

value: left

tag: tumor location

value: on equator

tag: tumor diameter (mm)

tag: tumor thickness (mm)

tag: tumor cell type

tag: retinal detachment

value: no

tag: extrascleral extension

tag: chromosome 3 status

value: monosomy

tag: months to endpoint

tag: metastasis

value: yes


title: segmentation_21h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110401_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish segmentation, 21h, mixed sex, biological replicate 1.

source_name: segmentation, 21h, mixed sex, replicate 1

tag: strain


title: adult_7m_male_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110561_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish adult, 7m, male, biological replicate 2.

source_name: adult, 7m, male, replicate 2


title: segmentation_21h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110569_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish segmentation, 21h, mixed sex, biological replicate 2.

source_name: segmentation, 21h, mixed sex, replicate 2


title: Uveal Melanoma MU218

tag: tissue

tag: age

value: right


title: segmentation_20h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110400_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish segmentation, 20h, mixed sex, biological replicate 1.

source_name: segmentation, 20h, mixed sex, replicate 1

value: wild type

tag: developmental timing


title: segmentation_19h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110569_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish segmentation, 19h, mixed sex, biological replicate 2.

source_name: segmentation, 19h, mixed sex, replicate 2

tag: gender


title: pharyngula_1d14h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110551_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish pharyngula, 1d14h, mixed sex, biological replicate 2.

source_name: pharyngula, 1d14h, mixed sex, replicate 2

tag: number of individuals per sample


title: segmentation_22h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110570_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish segmentation, 22h, mixed sex, biological replicate 2.

source_name: segmentation, 22h, mixed sex, replicate 2

tag: developmental stage


title: Uveal Melanoma MU213

tag: eye

value: epithelioid

value: disomy


title: Uveal Melanoma MU215

value: male

tag: tumor location

value: mixed


title: segmentation_19h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110400_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish segmentation, 19h, mixed sex, biological replicate 1.

source_name: segmentation, 19h, mixed sex, replicate 1


title: Uveal Melanoma MU214

value: female

tag: tumor diameter (mm)


title: Uveal Melanoma MU216

tag: tumor thickness (mm)


title: Uveal Melanoma MU212

tag: tumor cell type


title: Uveal Melanoma MU211

tag: retinal detachment


title: segmentation_18h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110400_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish segmentation, 18h, mixed sex, biological replicate 1.

source_name: segmentation, 18h, mixed sex, replicate 1


title: segmentation_17h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110568_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish segmentation, 17h, mixed sex, biological replicate 2.

source_name: segmentation, 17h, mixed sex, replicate 2


title: segmentation_17h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110400_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish segmentation, 17h, mixed sex, biological replicate 1.

source_name: segmentation, 17h, mixed sex, replicate 1


title: segmentation_18h_mixed_rep3

description:
Agilent Feature Extraction file:
US84303580_251916110569_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish segmentation, 18h, mixed sex, biological replicate 3.

source_name: segmentation, 18h, mixed sex, replicate 3


title: Uveal Melanoma MU209

tag: extrascleral extension


title: Uveal Melanoma MU206

value: posterior to equator

tag: chromosome 3 status


title: segmentation_18h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110572_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish segmentation, 18h, mixed sex, biological replicate 2.

source_name: segmentation, 18h, mixed sex, replicate 2


title: segmentation_16h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110414_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish segmentation, 16h, mixed sex, biological replicate 1.

source_name: segmentation, 16h, mixed sex, replicate 1


title: Uveal Melanoma MU210

tag: months to endpoint


title: segmentation_15h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110568_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish segmentation, 15h, mixed sex, biological replicate 2.

source_name: segmentation, 15h, mixed sex, replicate 2


title: Uveal Melanoma MU208

tag: metastasis


title: segmentation_14h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110568_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish segmentation, 14h, mixed sex, biological replicate 2.

source_name: segmentation, 14h, mixed sex, replicate 2

tag: strain


title: segmentation_15h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110414_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish segmentation, 15h, mixed sex, biological replicate 1.

source_name: segmentation, 15h, mixed sex, replicate 1


title: segmentation_14h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110414_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish segmentation, 14h, mixed sex, biological replicate 1.

source_name: segmentation, 14h, mixed sex, replicate 1


title: Uveal Melanoma MU197

description: Gene expression data from Uveal Melanoma

source_name: Eye

tag: tissue


title: Uveal Melanoma MU205

tag: age


title: Uveal Melanoma MU185


title: segmentation_12h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110567_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish segmentation, 12h, mixed sex, biological replicate 2.

source_name: segmentation, 12h, mixed sex, replicate 2

tag: developmental timing


title: Uveal Melanoma MU173

tag: gender


title: Uveal Melanoma MU174


title: pharyngula_1d6h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110551_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish pharyngula, 1d6h, mixed sex, biological replicate 2.

source_name: pharyngula, 1d6h, mixed sex, replicate 2

tag: number of individuals per sample


title: segmentation_13h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110414_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish segmentation, 13h, mixed sex, biological replicate 1.

source_name: segmentation, 13h, mixed sex, replicate 1

tag: developmental stage


title: Uveal Melanoma MU195

tag: eye


title: segmentation_13h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110567_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish segmentation, 13h, mixed sex, biological replicate 2.

source_name: segmentation, 13h, mixed sex, replicate 2


title: Uveal Melanoma MU192

tag: tumor location

value: posterior and on equator


title: segmentation_12h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110398_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish segmentation, 12h, mixed sex, biological replicate 1.

source_name: segmentation, 12h, mixed sex, replicate 1


title: Uveal Melanoma MU175

tag: tumor diameter (mm)


title: segmentation_11h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110567_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish segmentation, 11h, mixed sex, biological replicate 2.

source_name: segmentation, 11h, mixed sex, replicate 2


title: segmentation_10h20min_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110398_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish segmentation, 10h20min, mixed sex, biological replicate 1.

source_name: segmentation, 10h20min, mixed sex, replicate 1


title: segmentation_11h40min_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110567_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish segmentation, 11h40min, mixed sex, biological replicate 2.

source_name: segmentation, 11h40min, mixed sex, replicate 2


title: Uveal Melanoma MU153

tag: tumor thickness (mm)


title: Uveal Melanoma MU167

value: anterior to equator

tag: tumor cell type


title: segmentation_11h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110398_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish segmentation, 11h, mixed sex, biological replicate 1.

source_name: segmentation, 11h, mixed sex, replicate 1

value: segmentation


title: Uveal Melanoma MU164

value: Uveal Melanoma (eye)

tag: retinal detachment


title: Uveal Melanoma MU152

value: left

tag: extrascleral extension


title: Uveal Melanoma MU131

value: on equator

tag: chromosome 3 status


title: Uveal Melanoma MU166

value: no

tag: months to endpoint


title: gastrula_10h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110560_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish gastrula, 10h, mixed sex, biological replicate 2.

source_name: gastrula, 10h, mixed sex, replicate 2

value: gastrula


title: gastrula_9h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110560_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish gastrula, 9h, mixed sex, biological replicate 2.

source_name: gastrula, 9h, mixed sex, replicate 2


title: Uveal Melanoma MU132

tag: metastasis


title: Uveal Melanoma MU129


title: Uveal Melanoma MU109

value: monosomy

value: yes


title: gastrula_10h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110413_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish gastrula, 10h, mixed sex, biological replicate 1.

source_name: gastrula, 10h, mixed sex, replicate 1

tag: strain

value: wild type


title: Uveal Melanoma MU151

tag: tissue

value: right

value: partial monosomy


title: Uveal Melanoma MU130

tag: age

value: male

value: disomy


title: gastrula_8h_mixed_rep3

description:
Agilent Feature Extraction file:
US84303580_251916110560_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish gastrula, 8h, mixed sex, biological replicate 3.

source_name: gastrula, 8h, mixed sex, replicate 3

tag: developmental timing

value: mixed


title: gastrula_9h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110413_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish gastrula, 9h, mixed sex, biological replicate 1.

source_name: gastrula, 9h, mixed sex, replicate 1

tag: gender


title: gastrula_7h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110559_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish gastrula, 7h, mixed sex, biological replicate 2.

source_name: gastrula, 7h, mixed sex, replicate 2

tag: number of individuals per sample


title: segmentation_11h40min_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110398_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish segmentation, 11h40min, mixed sex, biological replicate 1.

source_name: segmentation, 11h40min, mixed sex, replicate 1

tag: developmental stage


title: Uveal Melanoma MU87

description: Gene expression data from Uveal Melanoma

source_name: Eye

value: female

tag: eye


title: gastrula_7h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110412_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish gastrula, 7h, mixed sex, biological replicate 1.

source_name: gastrula, 7h, mixed sex, replicate 1


title: gastrula_6h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110559_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish gastrula, 6h, mixed sex, biological replicate 2.

source_name: gastrula, 6h, mixed sex, replicate 2


title: gastrula_6h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110412_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish gastrula, 6h, mixed sex, biological replicate 1.

source_name: gastrula, 6h, mixed sex, replicate 1


title: Uveal Melanoma MU89

tag: tumor location

value: epithelioid


title: gastrula_5h20min_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110559_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish gastrula, 5h20min, mixed sex, biological replicate 2.

source_name: gastrula, 5h20min, mixed sex, replicate 2


title: Uveal Melanoma MU88

tag: tumor diameter (mm)


title: gastrula_8h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110572_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish gastrula, 8h, mixed sex, biological replicate 2.

source_name: gastrula, 8h, mixed sex, replicate 2


title: gastrula_8h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110413_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish gastrula, 8h, mixed sex, biological replicate 1.

source_name: gastrula, 8h, mixed sex, replicate 1


title: Uveal Melanoma MU108

value: posterior to equator

tag: tumor thickness (mm)


title: Uveal Melanoma MU111

tag: tumor cell type


title: Uveal Melanoma MU107

tag: retinal detachment


title: segmentation_10h20min_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110560_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish segmentation, 10h20min, mixed sex, biological replicate 2.

source_name: segmentation, 10h20min, mixed sex, replicate 2

value: segmentation


title: Uveal Melanoma MU66

value: Uveal Melanoma (eye)

tag: extrascleral extension


title: Uveal Melanoma MU67

value: left

tag: chromosome 3 status


title: gastrula_5h20min_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110412_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish gastrula, 5h20min, mixed sex, biological replicate 1.

source_name: gastrula, 5h20min, mixed sex, replicate 1


title: Uveal Melanoma MU85

value: all over the eye

tag: months to endpoint


title: dsr1 SA treated  biological rep 1

city: Wembley

first: Cynthia

last: Gleason

state: WA

address: Private Bag #5

department: Plant Industry

country: Australia

institute: CSIRO

description: Gene expression data from dsr1 seedlings that contain the GSTF8::LUC reporter treated with salicylic acid

hyb_protocol: cRNA was hybridized to the GeneChip® Arabidopsis ATH1 Genome Array using a Genechip instrument system with scanner 3000 7G and autoloader for expression array processing and analysis, following manufacturer's protocol.  Labeling, hybing and scanning were performed at the Australian Genome Research Facility.

scan_protocol: Genechips were scanned Affymetrix GeneChip scanner 3000 7G

data_processing: The raw data files underwent background correction, normalization, probe specific correction, and summary value computation using the Robust Multichip Average (RMA) method in the Bioconductor package.  To find the differentially expressed genes we utilized the limma package for R to calculate the Log2 fold change, the moderate t-statistic, B value, and the adjusted p value (Benjamini–Hochberg FDR) for each array probe.

organism: Arabidopsis thaliana

source_name: whole seedlings, SA treated, 10 hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: WT (a Columbia line containing a -800GSTF8::LUC reporter) and dsr1 (an EMS mutant of the Columbia line containing a -800GSTF8::LUC reporter) Arabidopsis seeds were stratified for 3 days at 4ºC.  They were germinated on MS-media and grown in a  21ºC growth room with a 16 hour light/ 8 hour dark cycle.  4 day old seedlings were used in this experiment.

extract_protocol: Total RNA was extracted using the Qiagen Rneasy kit, following manufacturer's instructions

treatment_protocol: 5 ml of either water (mock) or 1 mM salicylic acid (SA) was poured onto 56 mm Petri dishes containing 4-day old seedlings. After 40 min of incubation at room temperature, the excess liquid was discarded.  Ten hours after treatment, samples were collected.

value: Whole seedling

tag: genotype

tag: agent

value: salicylic acid

tag: genetic background


title: Uveal Melanoma MU86

tag: tissue

tag: age

value: posterior and on equator

value: monosomy

tag: metastasis


title: Uveal Melanoma MU110

tag: gender

value: on equator

value: yes

value: no


title: blastula_3h20min_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110394_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish blastula, 3h20min, mixed sex, biological replicate 2.

source_name: blastula, 3h20min, mixed sex, replicate 2

tag: strain

value: wild type

tag: developmental stage

value: blastula

tag: developmental timing

tag: number of individuals per sample


title: blastula_2h45min_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110394_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish blastula, 2h45min, mixed sex, biological replicate 2.

source_name: blastula, 2h45min, mixed sex, replicate 2

value: mixed


title: Uveal Melanoma MU48

value: female

tag: eye

tag: tumor location

tag: tumor diameter (mm)

tag: tumor thickness (mm)


title: blastula_4h40min_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110559_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish blastula, 4h40min, mixed sex, biological replicate 2.

source_name: blastula, 4h40min, mixed sex, replicate 2


title: blastula_4h40min_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110412_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish blastula, 4h40min, mixed sex, biological replicate 1.

source_name: blastula, 4h40min, mixed sex, replicate 1


title: blastula_4h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110394_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish blastula, 4h, mixed sex, biological replicate 2.

source_name: blastula, 4h, mixed sex, replicate 2


title: dsr1 SA treated  biological rep 2


title: Uveal Melanoma MU64

value: male

tag: tumor cell type

tag: retinal detachment

tag: extrascleral extension

tag: chromosome 3 status


title: Uveal Melanoma MU63

value: disomy

tag: months to endpoint


title: blastula_4h_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110411_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish blastula, 4h, mixed sex, biological replicate 1.

source_name: blastula, 4h, mixed sex, replicate 1


title: dsr1 SA treated  biological rep 3

tag: tissue

tag: genotype

tag: agent

tag: genetic background


title: blastula_3h20min_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110411_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish blastula, 3h20min, mixed sex, biological replicate 1.

source_name: blastula, 3h20min, mixed sex, replicate 1

tag: strain

tag: gender


title: Uveal Melanoma MU65

description: Gene expression data from Uveal Melanoma

source_name: Eye

tag: age

tag: metastasis


title: Uveal Melanoma MU62

tag: eye

value: right


title: blastula_2h45min_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110411_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish blastula, 2h45min, mixed sex, biological replicate 1.

source_name: blastula, 2h45min, mixed sex, replicate 1

tag: developmental stage

tag: developmental timing

tag: number of individuals per sample


title: WT SA treated  biological rep 1

description: Gene expression data from WT seedlings that contain the GSTF8::LUC reporter treated with salicylic acid

value: WT


title: blastula_2h15min_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110394_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish blastula, 2h15min, mixed sex, biological replicate 2.

source_name: blastula, 2h15min, mixed sex, replicate 2


title: Uveal Melanoma MU207

value: Uveal Melanoma (eye)

tag: tumor location

tag: tumor diameter (mm)

tag: tumor thickness (mm)

tag: tumor cell type

value: epithelioid


title: Uveal Melanoma MU40

value: left

tag: retinal detachment

tag: extrascleral extension

tag: chromosome 3 status

tag: months to endpoint


title: segmentation_16h_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110568_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish segmentation, 16h, mixed sex, biological replicate 2.

source_name: segmentation, 16h, mixed sex, replicate 2

value: segmentation


title: Uveal Melanoma MU44

tag: tissue


title: human erythroid progenitors scramble replicate 4

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

description: pro-erythroblasts scr 4

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: The data were analyzed with RMA as background correction, summarization & normalization method.

source_name: peripheral blood, human erythroid progenitors scramble

label_protocol: Whole transcript sense target labeling assay

growth_protocol: CD34+ cells were cultured in a modified serum-free medium (M-C Giarratana et al., Nature Biotechnology, 2005) with the modification of using 20% BIT (StemCell Technologies, Canada) which contains pre-tested batches of 50 mg/ml bovine serum albumin, 50 mg/ml rh insulin and 1 mg/ml human transferrin (iron-saturated) in s MDM instead of separate components. The amplification procedure was based on a four-step expansion culture of CD34+ cells, in IMDM (Invitrogen) media supplemented with 20% BIT, 4 mM L-glutamine (Gibco), 1% (v/v) penicilin/streptomycin, 40 mg/ml inositol, 10 mg/ml folic acid, 0.16 mM monothioglycerol, 900 ng/ml ferrous sulfate and 90 ng/ml ferric nitrate, by sequential supply of the culture with hydrocortisone (all from Sigma-Aldrich) and specific combinations of cytokines. In the first step (days 0-8), 5 x 104/ml CD34+ cells were cultured in the presence of 10-6 M hydrocortisone, 100 ng/ml stem cell factor (SCF), 3 IU/ml erythropoietin (EPO) and 5 ng/ml interleukin-3 (IL-3) (R&D Systems, Cedarlane Laboratories, Hornby, Ontario, Canada). On day 4, cells were diluted at 4 x 104/ml in fresh medium containing hydrocortisone and the same cytokines. On day 8, cells were washed and resuspended at a final concentration of 2x105 cells/ml in fresh medium containing only SCF and EPO. In the second step (days 11-15) cells were harvested, washed to remove growth factors and metabolites and resuspended at a final concentration of 2x105 cells/ml and co-cultured on mouse, bone marrow stromal cells (MS-5) (HyperCLDB, depositor : Prof. Dr. W. Ostertag, Heinrich-Pette-Institut, Hamburg, Germany) in fresh medium supplemented with erythropoietin. In the third step (day 15-18) all non adherent cells were harvested, washed to remove the residual Epo and cultured on MS-5 stromal layer in fresh medium without cytokines. In the fourth step (day 18-26) cells were resuspended at 5-7x106/ ml in a fresh media supplemented with 10% FBS and transferred in a new stromal layer to allow a better preservation of the cultured of red blood cells.

extract_protocol: RNeasy Mini Kit (Qiagen)

tag: protocol

value: control [scramble (scr) shRNA]


title: human erythroid progenitors scramble replicate 2

description: pro-erythroblasts scr 2


title: Uveal Melanoma MU14

tag: gender

value: monosomy


title: Uveal Melanoma MU47

tag: age

value: on equator

value: partial monosomy


title: Uveal Melanoma MU38

value: posterior to equator

value: yes

tag: metastasis


title: human erythroid progenitors scramble replicate 3

description: pro-erythroblasts scr 3


title: O157_CL MC fraction vs control

city: Aurora

first: Ki-Suk

last: Kim

state: CO

department: Pediatrics

institute: University of Colorado Anschutz Medical Campus

description: Gene expression after exposure to CL MC fraction

hyb_protocol: Array hybridization and staining were carried out according to instructions provided in the Agilent hybridization system. During the cDNA synthesis process, fluorescent incorporation labeled cDNA have hybridized with Agilent Escherichia coli 8X 15K array.

scan_protocol: Processed arrays were scanned with Agilent GeneSpring GX.

data_processing: Data analysis was carried out using the Agilent GeneSpring GX. Robust Multi-array Average (RMA) normalization performed using of signal intensity spot data which obtained by scanning process and it is indicated as a scatter plot data. Distribution of all genes which obtained result of the experiment is indicated as a histogram. Accuracy of the results of the experiment was determined through comparison of the histogram with the scatter plot data.

organism: Escherichia coli

source_name: EDL932 exposure to CL MC fraction

label_protocol: cDNA was synthesized from 12µg of total RNA using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) following the Agilent E. coli 8X 15K arrays protocol (Agilent Technologies). Spike controls containing RNA transcripts from several Bacillus subtilis genes were included in the RNA mixtures as internal controls to monitor the efficiency of labeling, hybridization and staining. The reaction mixture was incubated at 25℃ for 10 minutes, 37℃ for 60 minutes and 42℃ for 60 minutes followed by inactivation of the enzyme at 70℃ for 10 minutes. Purification of cDNA was carried out using the QIAquick PCR purification kit (Qiagen, Inc.). The cDNA was fragmented at 37℃ for 10 minutes in a reaction mixture consisting of purified cDNA and DNase I (Roche Applied Science) in One-Phor-All buffer (Invitrogen) in the order of 0.06 U DNase/µl of cDNA. The quality of fragmented cDNA was examined using the RNA 6000 Nano Labchip with an Agilent 2100 bioanalyzer. Labeling of the 3’termini of fragmented cDNA was performed using the Enzo BioArray terminal labeling kit with Biotin-ddUTP.

growth_protocol: The bacterial cells were grown at 37℃ for 17 hours on Luria-Bertani (LB) agar plate. An isolated colony was picked and inoculated into 100ml of sterilized LB broth (10g of tryptone, 5g of yeast extract and 10g of sodium chloride per liter) and incubated overnight for 17 hours at 37℃ with shaking at 250 rpm. A 1:100 dilution of the culture was performed using pre-warmed LB broth. The diluted culture was incubated at 37℃ with shaking at 250rpm until a final optical density (OD600) of 0.8 (early logarithmic phase) was attained. A further 1:10 dilution was performed using LB broth and incubated at 37℃ with shaking at 250 rpm.

extract_protocol: 50µl of total RNA of the cells affected by the Chrysanthemum herba methyl chloride fraction was isolated. The RNA extraction procedure was carried out using the RNeasy mini kit (Qiagen, Inc.) according to the manufacturer’s instructions. Briefly, 1ml of bacterial culture was added to 2ml of RNA protect bacteria reagent (Qiagen, Inc.). Centrifugation (5000 g for 10 minutes) of the mixture was performed to precipitate the cells. The harvested cells were incubated in TE buffer with 1 mg/ml lysozyme (Fisher Scientific). Total RNA was eluted in 50ml of RNase free water (Ambion Inc.) using the NanoDrop Spectrophotometer (NanoDrop Technologies, Inc.). RNA quality was examined using the RNA 6000 Nano Labchip with an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: 200µl of prepared E.coli O157 cells within LB broth is spreaded to LB agar plate, and sterilized 6mm filtered paper disk was placed on the plate tightly, where E.coli O157 is spreaded. Each filtered fractions are injected to each paper disk and Distilled water and Ampicillin were used as negative- and positive control each and then cultured at 37℃ for 24 hours. Finally the diameter of the cleared zone arisen around the paper disk was measured.

tag: strain

value: E.coli O157:H7 EDL 932

source_name: EDL932 unexposed


title: cleavage_1h45min_mixed_rep3

description:
Agilent Feature Extraction file:
US84303580_251916110562_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish cleavage, 1h45min, mixed sex, biological replicate 3.

source_name: cleavage, 1h45min, mixed sex, replicate 3

value: wild type

tag: developmental stage

value: cleavage

value: mixed


title: WT mock treated  biological rep 1

description: Gene expression data from WT seedlings that contain the GSTF8::LUC reporter treated with water (mock)

source_name: whole seedlings, mock treated, 10 hr

value: Whole seedling

tag: genotype

tag: agent

value: mock

tag: genetic background


title: human erythroid progenitors TAL1 knock down replicate 4

description: TAL1 KD 4

source_name: peripheral blood, human erythroid progenitors TAL1 knock down

value: TAL1 knockdown


title: dsr1 mock treated  biological rep 2


title: blastula_2h15min_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110411_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish blastula, 2h15min, mixed sex, biological replicate 1.

source_name: blastula, 2h15min, mixed sex, replicate 1

value: blastula

tag: developmental timing

tag: number of individuals per sample


title: cleavage_1h45min_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110393_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish cleavage, 1h45min, mixed sex, biological replicate 2.

source_name: cleavage, 1h45min, mixed sex, replicate 2


title: human erythroid progenitors TAL1 knock down replicate 3

description: TAL1 KD 3


title: Jurkat_T_Cells_stimulated_12H_Pol-II_rep1_slide2of2

city: Forest Hill

first: Russell

middle: Leigh

last: McInnes

state: Vic

address: 347 Burwood Hwy

department: LSCA

institute: Agilent Technologies

description: Biological replicate 1 of 2 on the second of the two slides that comprise a single 2-colour ChIP-chip experiment

hyb_protocol: Labelling, hybridization and scanning were performed as described in the Mammalian ChIP-on-chip protocol (version 9.1; Agilent Technologies)

scan_protocol: Scanned on Agilent G2565BA Scanner

data_processing: Scanned images were quantified with Agilent Feature Extraction software under the default chip-chip protocol (version 9.5.3).

source_name: Total IP 12H

growth_protocol: Human Jurkat T cells were cultured in RPMI 1640 medium (Gibco) supplemented with 10% FCS, 2mM L-glutamine, 9 mM HEPES and antibiotics. Jurkat T cells were maintained in suspension at a density of 5 x 10^5 cells/ml. Cells were stimulated with 20 ng/ml of phorbol 12-myristate 13-acetate (P) (Boehringer Mannheim) and 1 µM Ca 2+ ionophore A23187 (I) (Sigma-Aldrich) for the times indicated.

extract_protocol: Pooled ChIP samples were subsequently amplified based on one round of the whole genome amplification method using the WGA2 kit (Sigma-Aldrich), as described previously (O'Geen, Hollenhorst, Dindot)

treatment_protocol: ChIP assays were performed following the protocol supplied by Upstate Biotechnology, as previously detailed (MCB 2009).

tag: cell line

value: Jurkat T Cells - stimulated

value: 12 hours

source_name: Pol-II 12H

tag: antibody

value: anti-Pol II (8WG16)

tag: sample type

value: DNA pooled from five independent ChIP assay experiments


title: Uveal Melanoma MU13

value: Uveal Melanoma (eye)

value: male

tag: eye

value: right

tag: tumor location

tag: tumor diameter (mm)

tag: tumor thickness (mm)

tag: tumor cell type

tag: retinal detachment

value: no

tag: extrascleral extension

tag: chromosome 3 status

value: disomy


title: cleavage_1h45min_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110410_S01_GE1_105_Dec08_1_4.txt.
Gene expression in wild type zebrafish cleavage, 1h45min, mixed sex, biological replicate 1.

source_name: cleavage, 1h45min, mixed sex, replicate 1

tag: strain

tag: developmental stage

tag: gender


title: Uveal Melanoma MU12

tag: tissue

tag: age

value: left

value: on equator

value: yes

tag: months to endpoint

tag: metastasis


title: Jurkat_T_Cells_stimulated_4H_PKC-theta_rep2_slide2of2

description: Biological replicate 2 of 2 on the second of the two slides that comprise a single 2-colour ChIP-chip experiment

source_name: Total IP 4H

label_protocol: Labelling, hybridization and scanning were performed as described in the Mammalian ChIP-on-chip protocol (version 9.1; Agilent Technologies)

tag: cell line

value: 4 hours

source_name: PKC-theta 4H

tag: antibody

value: anti-PKC-theta


title: Jurkat_T_Cells_stimulated_12H_Pol-II_rep2_slide2of2

tag: sample type


title: Jurkat_T_Cells_stimulated_4H_PKC-theta_rep2_slide1of2

description: Biological replicate 2 of 2 on the first of the two slides that comprise a single 2-colour ChIP-chip experiment


title: cleavage_1h15min_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110393_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish cleavage, 1h15min, mixed sex, biological replicate 2.

source_name: cleavage, 1h15min, mixed sex, replicate 2

value: wild type

value: cleavage

tag: developmental timing

value: mixed

tag: number of individuals per sample


title: Jurkat_T_Cells_stimulated_4H_PKC-theta_rep1_slide1of2

description: Biological replicate 1 of 2 on the first of the two slides that comprise a single 2-colour ChIP-chip experiment

value: Jurkat T Cells - stimulated


title: Jurkat_T_Cells_stimulated_12H_Pol-II_rep2_slide1of2

value: 12 hours


title: Uveal Melanoma MU11

source_name: Eye

tag: eye

tag: tumor location

tag: tumor diameter (mm)

tag: tumor thickness (mm)

value: epithelioid

value: monosomy


title: cleavage_1h15min_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110410_S01_GE1_105_Dec08_1_3.txt.
Gene expression in wild type zebrafish cleavage, 1h15min, mixed sex, biological replicate 1.

source_name: cleavage, 1h15min, mixed sex, replicate 1


title: cleavage_45min_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110410_S01_GE1_105_Dec08_1_2.txt.
Gene expression in wild type zebrafish cleavage, 45min, mixed sex, biological replicate 1.

source_name: cleavage, 45min, mixed sex, replicate 1


title: Jurkat rep6

description: Jurkat 6

source_name: Jurkat lines expressing a Dox-inducible shRNA against TAL1 without Dox addition

growth_protocol: Growth medium: RPMI 1640 supplemented with 10% (v/v) fetal bovine serum, 100 units/ml of penicillin and 100 mg/ml of streptomycin, blasticidin and G418 at 1 mg/ml.

tag: protocol

value: control (no Dox)


title: zygote_15min_mixed_rep2

description:
Agilent Feature Extraction file:
US84303580_251916110393_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish zygote, 15min, mixed sex, biological replicate 2.

source_name: zygote, 15min, mixed sex, replicate 2

tag: strain

value: zygote


title: Jurkat +Dox rep5

description: Jurkat Dox+5

source_name: Jurkat lines expressing a Dox-inducible shRNA against TAL1 with added Dox

value: TAL1 knockdown


title: human erythroid progenitors TAL1 knock down replicate 2

description: TAL1 KD 2


title: Jurkat rep5

description: Jurkat 5


title: Silver_ion_treatment_1b_1/2h

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

description: Gene expression of B. cereus with silver ion treatment 30 mins

hyb_protocol: 600 ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner G Model G2565BA at 5 micron resolution.

data_processing: The normalization was done using GeneSpring GX 11 Software. Recommended Percentile Shift Normalization.

organism: Bacillus cereus

label_protocol: Poly (A)-tails were added to the 3’-end of RNA by using A-plus Poly (A) polymerase tailing kit (Epicentre Biotechnologies).Then  the samples  were labeled using Agilent Quick Amp Kit PLUS (Part number: 5190-0442).  Five hundred nanograms each of the samples were incubated with reverse trancription mix at 42°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for aRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity

growth_protocol: Overnight culture was innoculated into the LB broth and incubated it 37°C with agitation of 200 rpm until the O.D reach upto 0.5

extract_protocol: RNA was prepared using (QIAGEN MINI Rneays kit) followed according to the manufacturer's instructions

treatment_protocol: Exponentially grown bacterial cells were treated with 1 mM silver nitrate and incubated it for two different time points 30 and 60 mins at 37°C with agitation of 200 rpm.

tag: class

value: Gram-positive bacteria


title: Uveal Melanoma MU10

description: Gene expression data from Uveal Melanoma

value: Uveal Melanoma (eye)

tag: gender

value: male

value: right

tag: tumor cell type

tag: retinal detachment

tag: extrascleral extension

value: no

tag: chromosome 3 status

value: disomy


title: Silver_ion_treatment_2b_1h

description: Gene expression of B. cereus with silver ion treatment 60 mins


title: No_silver_ion__2b_1h

description: Gene expression of B. cereus without silver ion treatment 60 mins


title: Uveal Melanoma MU6

tag: tissue

tag: age

value: posterior to equator

value: yes

tag: months to endpoint

tag: metastasis


title: zygote_15min_mixed_rep1

description:
Agilent Feature Extraction file:
US84303580_251916110410_S01_GE1_105_Dec08_1_1.txt.
Gene expression in wild type zebrafish zygote, 15min, mixed sex, biological replicate 1.

source_name: zygote, 15min, mixed sex, replicate 1

value: wild type

tag: developmental stage

tag: developmental timing

tag: number of individuals per sample


title: Silver_ion_treatment_2a_1h

source_name: B. cereus with silver ion treatment 60 mins


title: Jurkat_T_Cells_stimulated_4H_PKC-theta_rep1_slide2of2

tag: cell line

value: 4 hours

tag: antibody

value: anti-PKC-theta

tag: sample type

value: DNA pooled from five independent ChIP assay experiments


title: Uveal Melanoma MU4

tag: eye

tag: tumor location

value: on equator

tag: tumor diameter (mm)

tag: tumor thickness (mm)


title: Uveal Melanoma MU8

tag: gender

value: anterior to equator

tag: tumor cell type

tag: retinal detachment

value: monosomy