title: Input_B (1)

description: genomic DNA input from J1 cells expressing bfEZH1on B chip


title: Fl/Fl day -2 (b)

status: Public on Dec 29 2009

type: RNA

city: Boston

first: Xiaohua

last: Shen

state: MA

address: 44 Binney Street

department: Pediatric Oncology

country: USA

institute: Dana Farber Cancer Institute

description: Jmj (fl/fl) wild-type ES cells at day 2 of LIF withdrawal, biological rep 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with dChip.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: standard culture conditions were used to culture ES cells.

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

treatment_protocol: ES cell differentiation was induced by LIF withdrawal and cells were collected at various time points from day 0 to day 8.

tag: cell type

value: Jmj (fl/fl) wild-type embryonic stem (ES) cells


title: Input_C (1)

type: genomic

description: genomic DNA input from J1 cells expressing bfEZH1on C chip

hyb_protocol: About 2-4 ug of labeled DNA were hybridized for 16 hr at 45C on tiling arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing:
The data were analyzed with Model-based Analysis of Tiling-arrays for ChIP-chip (MAT) developed by the Liu lab and processed based on MM8 annotation.
MATScore, p value (in form of -10log10_Pvalue), fold-change, FDR, peak position and length were reported for each peak identified by MAT program.

molecule: genomic DNA

label_protocol: Fragmented DNA was labeled with biotin-N6-ddATP by terminal deoxynucleiotidyl transferase.

extract_protocol: pulled down chromatin was reversely crosslinked and DNA was precipitated by isopropanol.

treatment_protocol: mouse ES cells were fixed with 0.8% formaldehyde for 10 min at room temperature. Cell lydates were ChIP'ed by antibodies recognizing EZH2 (Ac22, Upstate), SUZ12 (P15, Santa Cruz), JMJ (Abcam) or by using streptavidin-Dyna beads (Invitrogen). DNA fragments were isolated and amplified by LM-PCR. Amplified DNA was fragmented and biotin labeled before hybridiztion.

tag: antibody


title: Input_B (3)

description: genomic DNA input from Ezh2-/- cells on B chip

source_name: genomic DNA input from Ezh2-/- cells


title: Fl/Fl day-0 (a)

description: Jmj (fl/fl) wild-type ES cells at day 0 (undifferentiated), biological rep 1


title: Fl/Fl day-0 (b)

description: Jmj (fl/fl) wild-type ES cells at day 0 (undifferentiated), biological rep 2


title: Input_C (2)

description: genomic DNA input from CJ7 cells on C chip

source_name: genomic DNA input from CJ7 cells


title: whole lung Fisher rat at PN14 replicate 3

status: Public on Dec 28 2009

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were standard background corrected and quantile normalized using the R Bioconductor package lumi.

organism: Rattus norvegicus

source_name: rat whole lung

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

extract_protocol: RNA from whole lung tissue and primary lung cells was isolated using Trizol reagent (Invitrogen, Burlington, ON, Canada) according to the manufacturer’s instructions. RNA was resuspended in 1x RNASecure (Ambion, Austin, TX, USA) and treated with the Turbo DNase-free kit (Ambion, Austin, TX, USA) to remove any traces of DNA.

tag: strain

value: Fisher

tag: age (pn postnatal days)

tag: tissue

value: whole lung

tag: beadchip sentrix barcode

tag: beadchip section

value: F

tag: microarray hybridization date

tag: number of detected genes (p<0.01)

tag: number of detected genes (p<0.05)


title: whole lung Lewis rat at PN14 replicate 2

value: Lewis

value: A


title: whole lung Brown Norway rat at PN14 replicate 2

value: Brown Norway

value: I


title: whole lung Brown Norway rat at PN14 replicate 3

value: J


title: Fl/Fl day-2 (a)

description: Jmj (fl/fl) wild-type ES cells at day 2 of LIF withdrawal, biological rep 1


title: whole lung Fisher rat at PN14 replicate 2

value: E


title: whole lung Brown Norway rat at PN7 replicate 4

value: K


title: whole lung Brown Norway rat at PN7 replicate 3


title: whole lung Brown Norway rat at PN14 replicate 1

value: H


title: whole lung Lewis rat at PN14 replicate 1

value: L


title: whole lung Lewis rat at PN14 replicate 4

value: C


title: whole lung Brown Norway rat at PN7 replicate 1


title: whole lung Brown Norway rat at PN7 replicate 2


title: whole lung Fisher rat at PN14 replicate 1

value: D


title: whole lung Fisher rat at PN14 replicate 4

value: G


title: whole lung Brown Norway rat at PN14 replicate 4


title: whole lung Lewis rat at PN14 replicate 3

value: B


title: whole lung Fisher rat at PN7 replicate 2


title: whole lung Lewis rat at PN7 replicate 4

description: whole lung Lewis rat at PN7 replicate 4


title: whole lung Fisher rat at PN7 replicate 3


title: whole lung Fisher rat at PN7 replicate 4


title: whole lung Lewis rat at PN7 replicate 3

description: whole lung Lewis rat at PN7 replicate 3


title: whole lung Fisher rat at PN7 replicate 1


title: whole lung Lewis rat at PN7 replicate 1

description: whole lung Lewis rat at PN7 replicate 1


title: whole lung Brown Norway rat at PN1 replicate 3


title: whole lung Brown Norway rat at PN1 replicate 4


title: whole lung Fisher rat at PN1 replicate 3


title: whole lung Brown Norway rat at PN1 replicate 5


title: whole lung Fisher rat at PN1 replicate 1


title: whole lung Lewis rat at PN1 replicate 1

description: whole lung Lewis rat at PN1 replicate 1


title: whole lung Brown Norway rat at PN1 replicate 1


title: whole lung Fisher rat at PN1 replicate 2


title: S. mutans spxAB mutant, replicate 4

status: Public on Dec 25 2009

city: Gainesville

first: Jessica

middle: K

last: Kajfasz

state: FL

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

description: spxAB 4

hyb_protocol: The slides were hybridized to a mixture containing equal amounts of test and reference cDNA for 16 h at 42°C in a MAUI hybridization chamber (BioMicro Systems), and the hybridized slides were washed.

scan_protocol: Slides were scanned using a GenePix scanner (Axon Instruments, Inc., Union City, CA).

data_processing: Data were analyzed using software available at the J. Craig Venter Institute PFGRC website.  Single-channel images of the slides were loaded into Spotfinder and overlaid.  A spot grid was created according to PFGRC specifications and manually adjusted to fit all spots.  The Microarray Data Analysis System (MIDAS) software was used to normalize the spot intensity data using LOWESS and iterative log mean centering with default setting.  MIDAS also utilized In-Slide Replicate Analysis to average the intensities of the spots that were replicated on the microarray slide.  Spots that were missing or labeled as “bad” during the upstream processes in 50% of the slides were cut off in the output files, which also did not include control spots printed on the slides.   Statistical analysis was carried out with BRB array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) with a cutoff P value of 0.001.

organism: Streptococcus mutans

source_name: spxAB mid-log RNA

label_protocol: Once RNA was purified as described above, cDNA was generated from 2ug RNA per sample as described by the protocol available from the Pathogen Functional Genomics Research Center (PFGRC) using Invitrogen Superscript III Reverse Transcriptase (Invitrogen, Gaithersburg, MD) to increase cDNA yields.  Purified cDNAs were coupled to  Cy3 (experimental samples) or Cy5 (reference cDNA).

growth_protocol: Cells were grown in Brain-Heart medium buffered to pH 7.0 with KPO4 buffer to OD600 of 0.4 in a 5% CO2 incubator at 37°C.

extract_protocol: RNA was isolated from homogenized S. mutans cells grown in BHI medium buffered to pH 7.0 to OD600 of 0.4 by repeated hot acid-phenol:chloroform extractions, and the nucleic acid was precipitated with 1 volume ice-cold isopropanol and one-tenth volume 3M sodium acetate (pH 5) at –20°C overnight.  RNA pellets were resuspended in 80 mL nuclease-free H2O, and treated with DNase I (Ambion) at 37°C for 30 minutes.  RNA concentrations were determined using a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA), and 1 mL samples were run on an agarose gel to verify RNA integrity.  The RNA was purified again using the RNeasy mini kit (Qiagen), including a second on-column DNase treatment that was performed as recommended by the supplier.  Final RNA concentrations were determined in triplicate.

tag: genotype

value: spxA,spxB double-mutant

tag: growth phase

value: mid-log

organism: Streptococcus mutans UA159

source_name: wild-type mid-log RNA

growth_protocol: Cells were grown in Brain-Heart medium to OD600 of 0.5 in a 5% CO2 incubator at 37°C.

value: wild type


title: S. mutans spxAB mutant, replicate 2

description: spxAB 2


title: S. mutans spxAB mutant, replicate 3

description: spxAB 3


title: whole lung Lewis rat at PN1 replicate 3

description: whole lung Lewis rat at PN1 replicate 3

value: whole lung


title: S. mutans spxAB mutant, replicate 1

description: spxAB 1


title: max3 seedlings_DMSO (mock)_rep2

city: Tokyo

first: kiyoshi

last: mashiguchi

address: 1-1-1 Yayoi, Bunkyo-ku

country: Japan

institute: University of Tokyo

description: We performed microarray analysis using SL-deficient mutants to compare gene expression profiles in response to GR24 to determine whether exogenous applied strigolactone would modulate gene expression.

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Summarization was performed by RMA using the original CEL files.

organism: Arabidopsis thaliana

source_name: max3 seedlings treated with DMSO (mock) for 90min

label_protocol: Total RNA was processed to produce biotinylated cRNA targets according to the manufacturer’s instructions.

extract_protocol: Total RNA was isolated and purified using RNeasy (Qiagen, Hilden, Germany) and the RNase-free DNase Set (Qiagen).

tag: agent

value: DMSO (mock)

tag: replicate

tag: tissue type

value: whole seedlings

value: Col

tag: age


title: whole lung Lewis rat at PN1 replicate 2

description: whole lung Lewis rat at PN1 replicate 2

value: Lewis


title: whole lung Lewis rat at PN7 replicate 2

description: whole lung Lewis rat at PN7 replicate 2

value: A


title: S. mutans spxB mutant, replicate 2

description: spxB 2

source_name: spxB mid-log RNA

value: spxB mutant


title: S. mutans spxB mutant, replicate 1

description: spxB 1


title: S. mutans spxB mutant, replicate 4

description: spxB 4


title: whole lung Brown Norway rat at PN1 replicate 2

value: Brown Norway

value: I


title: S. mutans spxA mutant, replicate 4

description: spxA 4

source_name: spxA mid-log RNA

value: spxA mutant


title: max3 seedlings_GR24 (1 uM)_rep2

source_name: max3 seedlings treated with with GR24 (1 uM) for 90min


title: whole lung Fisher rat at PN1 replicate 4

value: Fisher


title: max3 seedlings_DMSO (mock)_rep1


title: max3 seedlings_GR24 (1 uM)_rep1


title: S. mutans spxB mutant, replicate 3

description: spxB 3


title: S. mutans spxA mutant, replicate 3

description: spxA 3


title: S. mutans spxA mutant, replicate 2

description: spxA 2


title: S. mutans UA159 wild type, replicate 1

description: UA159 1


title: S. mutans UA159 wild type, replicate 2

description: UA159 2


title: S. mutans UA159 wild type, replicate 3

description: UA159 3


title: S. mutans spxA mutant, replicate 1

description: spxA 1


title: S. mutans UA159 wild type, replicate 4

description: UA159 4


title: HuAoSMC Serum Starved 48h_2

city: Stanford

first: Joshua

middle: M.

last: Spin

state: CA

address: 300 Pasteur Drive

institute: Stanford University

hyb_protocol: GE Blocking agent and Hi-RPM hybridization buffer were added to the samples, which were incubated at 100° C for 5 min, and transferred to an ice-water bath. Samples and arrays were then loaded using Agilent SureHyb chambers and gaskets, hybridized at 55° C for 20 hours, and washed (Gene Expression wash buffers 1 and 2).

scan_protocol: Arrays were scanned using an Agilent Microarray Scanner and Feature Extractor (software v 9.5.1).

data_processing:
The Sample data were normalized, background subtracted and processed using the Feature Extractor. However, replicates of the same miRNA were not averaged, a process that occurs when the data is properly uploaded to Genespring.  Control Flagged spots have been removed.

QC reports were generated by the Feature Extraction software, and the array data were analyzed with Genespring GX 10.0.2 (Agilent). Arrays were examined with Quality Control metrics, principal components analysis (PCA), and hierachical agglomerative clustering (HAC). One chip (6 arrays) clustered separately and was therefore excluded from further analysis. Two additional arrays were excluded for QC reasons. The remaining 10 arrays were subjected to one-way ANOVA at a cutoff of p < 0.05, with Benjamini-Hochberg correction for multiple testing. Significant miRNAs were required to show > 2.0-fold expression change from Control.

organism: Homo sapiens

source_name: Serum-Starved AoSMC, 48h

label_protocol: Per manufacturer’s protocol, 100 ng of total RNA per sample was dephosphorylated using calf intestine alkaline phosphatase at 37° C for 30 min, then denatured in DMSO at 100° C for 5 min and placed in an ice-water bath. Ligation to Cyanine 3-pCp was performed using T4 Ligase at 16° C for 2 hours, and labeled miRNA samples were purified using Micro Bio-spin 6 columns.

growth_protocol: Human aortic SMCs (Lonza Walkersville Inc., Walkersville, MD, passage #3) were propagated in growth media SmGM-2 with SingleQuot supplements and growth factors (Lonza) in 5% FBS per manufacturer’s instructions.

extract_protocol: Cell culture and homogenized aortic samples were harvested with QIAzol Lysis Reagent. Total RNA was isolated using the miRNeasy Mini Kit (Qiagen, Valencia, CA) per standard methods.  RNA was quantitated by Nanodrop, and RNA and miRNA quality and integrity were verified using the Agilent 2100 Bioanalyzer System (Agilent Technologies, Santa Clara, CA). RNA Integrity Numbers (RIN) for all samples ranged from 8.5 to 10.

treatment_protocol: Control plates were harvested for RNA extraction, and the remaining plates were serum starved for 48 (SS48) or 72 hours (SS72) in serum-free basal media (SmBM) to induce growth arrest and expression of SMC differentiation genes, according to conventional protocols.  Samples included cells from two separate lots, as well as two technical replicates/vial/time point.

value: aorta

value: smooth muscle cells

tag: treatment

value: serum-starved

tag: time


title: HuAoSMC Serum Starved 48h_3

tag: cell type


title: HuAoSMC Serum Starved 72h_2

source_name: Serum-Starved AoSMC, 72h


title: HuAoSMC Control_3

source_name: Control Serum-Fed AoSMC

value: serum-fed


title: HuAoSMC Control_1


title: HuAoSMC Serum Starved 72h_1


title: HuAoSMC Control_2


title: HuAoSMC Serum Starved 72h_3


title: P8 wt1

status: Public on Dec 24 2009

city: Naples

first: Vincenzo

middle: Alessandro

last: Gennarino

state: Italy

address: Via Pietro Castellino,111

department: TIGEM

country: Italy

institute: Telethon

description: Transcriptome analysis of Vax2 knockout mice

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: RMA

source_name: Mus musculus tissue

label_protocol: Standard Affymetrix protocol.

extract_protocol: Total RNA was obtained using the TRIzol (Invitrogen) according to the manufacturer’s instructions.

tag: genotype/variation

value: wt

value: Whole eye


title: Expression data of the thymus from 15 weeks old Hexb-/- mice

city: Yokohama City

first: Akira

last: Yamaguchi

state: Kanagawa

address: 3-9 Fukuura

department: Department of Pathology

institute: Yokohama City University School of Medicine

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis were calculated by  Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Thymus from 15 weeks old Hexb-/- mice

label_protocol: cDNA were synthesized by GeneChip T7-Oligo(dT) Promoter Primer Kit(Affymetrix) and TaKaRa cDNA Synthesis Kit (TaKaRa Bio) from 10 μg  total RNA. Biotinylated cRNA were synthesized by IVT Labeling Kit(Affymetrix).

extract_protocol: RNA extraction was performed using a Trizol Reagent (Invitrogen).

value: Thymus

value: Hexb-/-

tag: strain

value: 15 weeks old


title: P60 Vax2-/- 2

tag: tissue


title: HuAoSMC Serum Starved 48h_4


title: E16.5 Vax2-/- 2


title: P8 Vax2-/- 1


title: P8 Vax2-/- 2


title: P60 wt2


title: Expression data of the thymus from 15 weeks old Hexb+/- mice

source_name: Thymus from 15 weeks old Hexb+/- mice

value: Hexb+/-


title: E16.5 wt1


title: P8 wt2


title: P60 Vax2-/- 1


title: E16.5 wt2


title: P60 wt1


title: E16.5 Vax2-/- 1


title: E12.5 Vax2-/- 2

value: whole eye


title: 6/85 sample 3

city: Storrs

first: Steven

middle: J.

last: Geary

state: CT

address: 61 N. Eagleville Rd

department: Pathobiology and Veterinary Science

institute: University of Connecticut

description: Eight Arabidopsis-based negative control features were not included in the analysis but were used to verify specificity of hybridization signal.

hyb_protocol: DNA was hybridized to the microarray slides in hybridization chambers overnight at 42 C with shaking and washed with decreasing concentrations of SSC buffer the next day.  Excess sample and buffer was removed via centrifugation.

scan_protocol: Slides were scanned at a PMT gain of 700 using a GenePix 4000B scanner and signal intensity was determined for each feature using GenePix Pro 4.1 software.

data_processing: The background subtracted median pixel intensity of each feature was averaged between duplicate features from each slide and then averaged again across samples from the same strain.  Average signals from each feature from Rlow were divided by the signal of the same feature from F, ts-11, or 6/85 and log(2) transformed.  Features with a ratio of log(2)<-2 were considered to be divergent or absent.

organism: Mycoplasmoides gallisepticum

label_protocol: 4 ug of genomic DNA was labeled using BioPrime Array CGH genomic labeling system (Invitrogen) and labeled with Cy3 dye.

growth_protocol: M. gallisepticum cultures were grown to mid-log phase in Hayflick's medium and pelleted via centrifugation.

extract_protocol: Genomic DNA was extracted from pelleted cells using the Easy DNA kit per the instructions (Invitrogen).

tag: virulence phenotype

value: attenuated


title: HuAoSMC Serum Starved 48h_1


title: E12.5 wt1


title: E12.5 wt2


title: E10.5 Vax2-/- 2


title: E10.5 wt2


title: E12.5 Vax2-/- 1


title: E10.5 wt3


title: E10.5 Vax2-/- 1


title: ts-11 sample 2


title: ts-11 sample 1


title: ts-11 sample 3


title: F sample 1

source_name: F

value: F


title: F sample 3


title: F sample 2


title: 6/85 sample 2


title: 6/85 sample 1


title: Rlow sample 1

source_name: Rlow

value: Rlow

value: virulent


title: Rlow sample 2


title: Rlow sample 3


title: E10.5 Vax2-/- 3


title: HES3 BCM medium Matrigel 90day rep1

city: Singapore

first: Woon-Khiong

last: Chan

email: dbscwk@nus.edu.sg, g0500139@nus.edu.sg

address: S2-05-19, 14 Science Drive 4

department: Biological Sciences

country: Singapore

institute: National University of Singapore

description: replicate 1

hyb_protocol: 1.5 µg of biotinylated cRNA was used for each array in the Human WG-6 v3.0 BeadChip (Illumina). The BeadChips were hybridized at 58oC for 16 hours and washed according to the standard Illumina protocol.

scan_protocol: The arrays were scanned with the Illumina Beadstation 500GX using Scan Factor 1.0 and PMT 501.

data_processing: Scanned data were retrieved using BeadStudio Gene Expression Module v3.4 and inspected with the quality control parameters. Data was background corrected using the default settings prior to further processing. The background corrected raw data was pre-processed with Bioconductor/R using the ‘lumi’ package (Du et al. 2008. Bioinformatics 24, 1547-1548). The data was transformed using the VST method (Lin et al 2008. Nucleic Acids Res. 36, e11), quantile normalized and filtered with detection p-value <0.01. Quality control of the data was carried out before and after normalization with density plots, signal intensity boxplots and pairwise plots implemented with the ‘lumi’ package.

source_name: human embryonic stem cells

label_protocol: The Illumina® TotalPrep RNA Amplification Kit (Cat No. AMIL1791) was used for amplification of total RNA for microarray analysis. Briefly, 100 ng of total RNA was used for first strand reverse transcriptase (RT) reaction with T7 oligo (dT) primer which was carried out for 2 hours at 42oC, followed by a second strand cDNA synthesis at 16oC for 2 hours. Amplification of biotinylated cRNA was carried out by in vitro transcription with biotin UTP using purified the cDNA products at 37oC for 16 hours. 1.5 ul of the sample was run on Nanodrop to determine the concentration of the purified labeled cRNA. 100 ng of the sample was used to run on Agilent Bionalyzer 2100 with the Agilent RNA 6000 Nanochip (Cat No. 5067-1511) using the default settings to determine the integrity of the labeled sample.

extract_protocol: All the EBs harvested at the various time points were rinsed twice with PBS followed by extraction of total RNA using RNeasy® Plus Micro Kit (Cat. No- 74034). The eluate volume was 12 ul. 1.5 ul of the eluted sample was run on Nanodrop™ 1000 (Thermo Fisher Scientific) to determine the yield. 50 ng of the sample was used to run on Agilent Bionalyzer 2100 with the Agilent RNA 6000 Nanochip (Cat No. 5067-1511) using the default settings to determine the integrity of the labeled sample.

tag: cell line

tag: culture condition

value: BCM+MAT

tag: culture day


title: HES3 EB medium Matrigel 90day rep2

description: replicate 2

value: EB+MAT


title: HES3 EB medium Matrigel 90day rep1

description: replicate 1


title: HES3 EB medium 90day rep1

description: replicate 1

value: EB


title: HES3 BCM medium Matrigel 90day rep2

description: replicate 2


title: HES3 EB medium Matrigel 90day rep3

description: replicate 3


title: HES3 EB medium 90day rep2

description: replicate 2


title: HES3 EB medium 60day rep1

description: replicate 1


title: HES3 EB medium Matrigel 60day rep1

description: replicate 1


title: HES3 BCM medium Matrigel 30day rep1

description: replicate 1


title: HES3 BCM medium Matrigel 30day rep2

description: replicate 2


title: HES3 EB medium Matrigel 30day rep2

description: replicate 2


title: HES3 BCM medium 14day rep2

description: replicate 2

value: BCM


title: HES3 EB medium Matrigel 30day rep1

description: replicate 1


title: HES3 BCM medium Matrigel 14day rep2

description: replicate 2


title: HES3 EB medium 30day rep1

description: replicate 1


title: E10.5 wt1


title: HES3 EB medium Matrigel 14day rep3

description: replicate 3


title: HES3 BCM medium Matrigel 14day rep1

description: replicate 1


title: HES3 EB medium Matrigel 14day rep1

description: replicate 1


title: HES3 EB medium Matrigel 14day rep2

description: replicate 2


title: HES3 BCM medium 30day rep2

description: replicate 2


title: HES3 BCM medium 30day rep1

description: replicate 1


title: HES3 EB medium Matrigel 30day rep3

description: replicate 3


title: HES3 EB medium 30day rep2

description: replicate 2


title: HES3 EB medium 30day rep3

description: replicate 3


title: HES3 BCM medium 14day rep1

description: replicate 1


title: HES3 EB medium 14day rep3

description: replicate 3


title: HES3 EB medium 14day rep2

description: replicate 2


title: HES3 BCM medium 7day rep2

description: replicate 2


title: HES3 BCM medium Matrigel 7day rep2

description: replicate 2


title: HES3 BCM medium Matrigel 7day rep1

description: replicate 1


title: Sarcoma Prkar1a+/- Tp53+/--4

city: Bethesda

first: Madson

middle: Q

last: Almeida

state: MD

address: 10 Center Drive, MSC 1103

department: Section on Genetics and Endocrinology / NICHD

institute: NIH

description: Replicate 4

data_processing: Z score transformation for normalization was performed for each Illumina sample/array as previously described (Cheadle et al. J Mol Diagn, 5:73-81).

source_name: Sarcoma

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: cervival spine

tag: disease state

value: cervival spine osteosarcoma

value: (CD-1 x C57BL/6) F1 hybrid background

value: 12 months


title: HES3 EB medium 7day rep2

description: replicate 2


title: HES3 Undifferentiated rep3

description: replicate 3

value: control (undifferentiated)


title: HES3 Undifferentiated rep2

description: replicate 2


title: HES3 EB medium Matrigel 7day rep2

description: replicate 2


title: HES3 EB medium 7day rep1

description: replicate 1


title: HES3 EB medium 7day rep3

description: replicate 3


title: HES3 BCM medium 7day rep1

description: replicate 1


title: dB/dB Catalase-Tg, sample 2

city: Montreal

first: Nicolas

last: Godin

state: QC

address: 3850 St-Urbain

country: Canada

institute: Université de Montréal

description:
Gene expression data from proximal tubules of 20-week-old mice.
DB_CAT_2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with limma packages from bioconductor softwares suite, using the GC-RMA method of normalization.

source_name: Proximal tubules from 20-week-old dB/dB catalase-Tg mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 20-week-old mice were fed a normal diet and water.

treatment_protocol: Proximal tubules were isolated by Percoll centrifugation.

value: kidney proximal tubule

tag: genotype

value: dB/dB catalase-Tg

value: 20 weeks


title: HES3 EB medium 14day rep1

description: replicate 1


title: dB/dB Catalase-Tg, sample 3

description:
Gene expression data from proximal tubules of 20-week-old mice.
DB_CAT_3


title: HES3 EB medium Matrigel 7day rep1

description: replicate 1


title: HES3 EB medium Matrigel 7day rep3

description: replicate 3


title: HES3 Undifferentiated rep1

description: replicate 1


title: dB/dB, sample 1

description:
Gene expression data from proximal tubules of 20-week-old mice.
DB_1

source_name: Proximal tubules from 20-week-old dB/dB mice

value: dB/dB


title: dB/dB, sample 2

description:
Gene expression data from proximal tubules of 20-week-old mice.
DB_2


title: dB/dB Catalase-Tg, sample 1

description:
Gene expression data from proximal tubules of 20-week-old mice.
DB_CAT_1


title: Sarcoma Prkar1a+/- Tp53+/--1

description: Replicate 1

value: sacrum

value: sacrum ostesarcoma


title: Sarcoma Tp53+/--2

description: Replicate 2

value: lumbar spine

value: lumbar spine osteosarcoma


title: Sarcoma Prkar1a+/- Tp53+/--3

description: Replicate 3

value: left shoulder

value: left shoulder osteosarcoma


title: Sarcoma Tp53+/--1

description: Replicate 1

value: perineal soft tissue

value: perineal soft tissue sarcoma


title: Sarcoma Prkar1a+/- Tp53+/--2

description: Replicate 2

value: toe bone

value: toe osteosarcoma


title: Catalase-Tg, sample 3

description:
Gene expression data from proximal tubules of 20-week-old mice.
WT_Cat_3

source_name: Proximal tubules from 20-week-old catalase-Tg mice

value: catalase-Tg


title: Catalase-Tg, sample 2

description:
Gene expression data from proximal tubules of 20-week-old mice.
WT_Cat_2


title: dB/dB, sample 3

description:
Gene expression data from proximal tubules of 20-week-old mice.
DB_3


title: Wild Type, sample 3

description:
Gene expression data from proximal tubules of 20-week-old mice.
WT_3

source_name: Proximal tubules from 20-week-old wild-type mice

value: wild type


title: Thyroid Prkar1a+/- Rb1+/--1

description: Replicate 1

source_name: Thyroid tumor

value: thyroid gland

value: thyroid tumor

value: Prkar1a+/- Rb1+/-

value: (CD-1 x C57BL/6) F1 hybrid background

value: 12 months


title: Catalase-Tg, sample 1

description:
Gene expression data from proximal tubules of 20-week-old mice.
WT_Cat_1

value: kidney proximal tubule

value: 20 weeks


title: Thyroid Prkar1a+/- Rb1+/--2

description: Replicate 2


title: Wild Type, sample 2

description:
Gene expression data from proximal tubules of 20-week-old mice.
WT_2


title: Pituitary Prkar1a+/- Rb1+/--3

description: Replicate 3

source_name: Pituitary tumor

value: pituitary gland

value: pituitary tumor


title: Thyroid Rb1+/--1

description: Replicate 1


title: Thyroid Rb1+/--2

description: Replicate 2


title: Thyroid Prkar1a+/- Rb1+/--3

description: Replicate 3


title: CFSE+CD25- , patient 6

city: Melbourne

first: shuo

last: li

state: VIC

address: 85 Commercial road

country: Australia

institute: Burnet Institute

description: sorting protocol: Sorting of HCV peptide-stimulated CFSE-CD25+/CD25- co-cultures from HCV patients was performed using a FACSaria located in a PC3 facility.  The cultures were sorted on day 5 into 3 fractions as specified, based on their CFSE labelling and CD25 expression. The primary gate was set on lymphocytes based on SSC/FSC and an additional CD3 gate (for methylation analysis and microarray) or CD4 gate (for in vitro suppression assay) was introduced to the CFSE- population to refine the conventional T cell population.

data_processing: The data were normalised using quantile normalisation with BeadStudio Gene Expression Module v3.3 software

source_name: FACS sorted T cell fraction

growth_protocol: PBMC from patients were separated by Ficoll Paque centrifugation and CD25+ cells were isolated from PBMC using CD25 microbeads (MiltenyiBiotec Bergisch Gladbach, Germany) according to the manufacturer’s instructions. The CD25+ cells, typically 1-2 % of total PBMC, were labelled with CFSE (Sigma-Aldrich, St Louis, MO, USA) and mixed back with unlabeled CD25-depleted PBMC at a ratio 1:10. The CFSE-CD25+/CD25- co-culture was stimulated with or without genotype matched HCVpp in RPMI-1640, 2 mM L-glutamine, 100 IU/mL penicillin-streptomycin (Invitrogen Carlsbad, CA, USA) and 5% human AB serum (MP Biosciences, Aurora, CA, USA) in 24-well tissue culture plates (Interpath, Australia). Cells were harvested on day 5 for sorting.

extract_protocol: Total RNA from sorted cells (P5 = CD25+CFSE+, P6 = CD25-CFSE+ and P7 = CD3+CFSE-) was isolated using RNeasy Kit (QIAGEN) according to the manufacturer’s instructions. The RNA quality was ascertained by the Agilent Bioanalyser 2100 using the NanoChip protocol.

tag: disease

value: chronic HCV

tag: cell fraction

tag: time of sorting

value: on day 5 of culture

tag: patient


title: CFSE-, patient 1

value: CFSE-


title: CFSE-, patient 2


title: CFSE+CD25- , patient 3


title: CFSE-, patient 5


title: CFSE+CD25- , patient 5


title: CFSE+CD25- , patient 1


title: CFSE-, patient 6


title: Wild Type, sample 1

description:
Gene expression data from proximal tubules of 20-week-old mice.
WT_1

tag: age


title: Thyroid Rb1+/--3

description: Replicate 3


title: Pituitary Prkar1a+/- Rb1+/--2

description: Replicate 2


title: Pituitary Rb1+/--3

description: Replicate 3


title: CFSE+CD25- , patient 2


title: CFSE+CD25- , patient 4


title: Pituitary Prkar1a+/- Rb1+/--1

description: Replicate 1


title: CFSE-, patient 3


title: CFSE-, patient 4


title: CFSE+CD25+ , patient 6


title: Pituitary Rb1+/--1

description: Replicate 1


title: CFSE+CD25+ , patient 5


title: clock-727

status: Public on Dec 23 2009

city: Houston

first: Scott

middle: E

last: Evans

state: TX

address: 1400 Holcombe Blvd

department: Pulmonary Medicine - Unit 1462

institute: University of Texas-M.D. Anderson Cancer Center

description: k-ras, no treatment

hyb_protocol: cRNA was hybridized to BeadChips per Illumina instructions.

scan_protocol: Chips were scanned using level 3 signal using a BeadStation 500 scanner.

data_processing: Data was processed using Illumina BeadStudio v3. Matrix tables were generated both without normalization and with rank invariant normalization, using sham group as the reference group. Values reported were derived using Illumina BeadStudio v3 and are relative signal intensity normalized to background.

source_name: LR-CC

label_protocol: cRNA was hybridized to BeadChips prior to labeling with Cy3-Streptavidin per Illumina instructions.

extract_protocol: The lungs were mechanically homogenized, then total RNA was isolated from lung homogenates using the RNeasy system (Qiagen, Valencia, CA), and cRNA was synthesized and amplified from equal masses of total RNA using the Ilumina TotalPrep RNA amplification kit (Ambion, Austin, TX).

treatment_protocol: WT or CC-LR mice were either challenged with NTHi lysate or sensitized to ovalbumin by intraperitoneal injection weekly for two weeks, then challenged for 30 min to an aerosol of ovalbumin in 0.9% saline weekly for eight weeks. Mice from each group were euthanized on day one after the last exposure for comparison. To reduce the lung leukocyte burden, the pulmonary vasculature was perfused and the airways lavaged with PBS.

value: whole lung

tag: genome/variation

value: LR-CC (a Clara cell-targeted K-ras mutant)

tag: treatment group

value: no treatment

tag: treatment time

value: 1 d after last treatment


title: clock-675

description: k-ras, no treatment


title: WT-OVA-8-D1-3

description: WT, OVA treated

source_name: WT

value: WT

value: OVA treated


title: clock-675_2

description: k-ras, OVA treated


title: clock-680

description: k-ras, OVA treated


title: WT skin papilloma -2

description: Replicate 2

source_name: papilloma

treatment_protocol: 2-step skin carcinogenesis protocol

value: dorsal skin

value: skin papilloma

tag: genotype/variation

value: wildtype

value: 6 months


title: CFSE+CD25+ , patient 2


title: clock-682

description: k-ras, OVA treated


title: clock-300

description: k-ras, no treatment


title: WT-OVA-8-D1-2

description: WT, OVA treated


title: Prkar1a+/- skin papilloma -3

description: Replicate 3

tag: strain

value: (CD-1 x C57BL/6) F1 hybrid background


title: CFSE+CD25+ , patient 3


title: CFSE+CD25+ , patient 4


title: C-OVA-3

description: WT, no treatment

tag: tissue


title: C-OVA-1

description: WT, no treatment


title: C-OVA-2

description: WT, no treatment


title: Pituitary Rb1+/--2

description: Replicate 2

value: 12 months


title: Prkar1a+/- skin papilloma -2

description: Replicate 2


title: clock-428

description: k-ras, NTHi treated

value: NTHi treated


title: CH4-3

description: WT, no treatment


title: clock-426

description: k-ras, NTHi treated


title: clock-429

description: k-ras, NTHi treated


title: NW8D-2

description: WT, NTHi treated


title: WT-OVA-8-D1-1

description: WT, OVA treated


title: Prkar1a+/- skin papilloma -1

description: Replicate 1


title: CH4-1

description: WT, no treatment


title: CH4-2

description: WT, no treatment


title: NW8D-3

description: WT, NTHi treated


title: NW8D-1

description: WT, NTHi treated


title: WT skin papilloma -1

description: Replicate 1


title: Paired Normal tissue #227

first: Zhigang

middle: C

last: Wang

address: 44 Binney St SM936A

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: Hybridized to 10K SNP array

hyb_protocol: Following Affymetrix GenChip Xba131 hybridization protocol

data_processing: Copy number analysis using dChip software. Raw data in CEL file and txt file which provides genotypes.

label: Biotin

source_name: Normal, beast tissue

label_protocol: Following Affymetrix GenChip Xba131 target labelling protocol

extract_protocol: DNA was extracted by proteinase K digestion, phenol-chroloform extraction, and ethanol precipitation.

tag: histologic type

tag: grade

tag: er/pr/her


title: Paired Normal tissue #164

description: Hybridized to 10K SNP array


title: Paired Normal tissue #169

description: Hybridized to 10K SNP array

source_name: Normal, Blood buffy coat


title: clock-483

description: k-ras, no treatment


title: clock-479

description: k-ras, no treatment


title: Paired Normal tissue #230

description: Hybridized to 10K SNP array


title: Paired Normal tissue #192

description: Hybridized to 10K SNP array


title: Paired Normal tissue #199

description: Hybridized to 10K SNP array


title: Paired Normal tissue #58

description: Hybridized to 10K SNP array


title: CFSE+CD25+ , patient 1


title: Paired Normal tissue #34

description: Hybridized to 10K SNP array


title: clock-493

description: k-ras, no treatment


title: Paired Normal tissue #56

description: Hybridized to 10K SNP array


title: Paired Normal tissue #911

description: Hybridized to 10K SNP array


title: Paired Normal tissue #96

description: Hybridized to 10K SNP array


title: Paired Normal tissue #126

description: Hybridized to 10K SNP array


title: Paired Normal tissue #656

description: Hybridized to 10K SNP array


title: Paired Normal tissue #363

description: Hybridized to 10K SNP array


title: Paired Normal tissue #214

description: Hybridized to 10K SNP array


title: Pt6_HL_mock_rep1

city: Roma

first: Francesco

last: D'Alò

address: Largo A. Gemelli 8

department: Hematology

institute: Università Cattolica del Sacro Cuore

description: Gene expression data from bone marrow normal CD34+ cells after in vitro mock treatment for 72 hours

hyb_protocol: Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.

scan_protocol: GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software

data_processing: Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs  Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.

source_name: Pt6, HL, mock treatment

label_protocol: GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.

growth_protocol: Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.

extract_protocol: RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C.  A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for  the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for  72 hours, while the corresponding amount of solvent was added for the mock treated plates.

tag: cell type

value: bone marrow CD34+

tag: gender

value: female

value: HL

tag: karyotype

value: normal


title: Paired Normal tissue #148

description: Hybridized to 10K SNP array


title: Pt6_HL_Decitabine_rep3

description: Gene expression data from bone marrow normal CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours

source_name: Pt6, HL, 1 µM  decitabine

tag: disease


title: Paired Normal tissue #691

description: Hybridized to 10K SNP array


title: Paired Normal tissue #665

description: Hybridized to 10K SNP array


title: Paired Normal tissue #828

description: Hybridized to 10K SNP array


title: Paired Normal tissue #12

description: Hybridized to 10K SNP array


title: Paired Normal tissue #138

description: Hybridized to 10K SNP array


title: Paired Normal tissue #670

description: Hybridized to 10K SNP array


title: Paired Normal tissue #489

description: Hybridized to 10K SNP array


title: Paired Normal tissue #396

description: Hybridized to 10K SNP array


title: Pt6_HL_mock_rep2


title: Paired Normal tissue #558

description: Hybridized to 10K SNP array


title: Pt6_HL_Decitabine_rep2


title: Paired Normal tissue #609

description: Hybridized to 10K SNP array


title: Paired Normal tissue #664

description: Hybridized to 10K SNP array


title: Paired Normal tissue #590

description: Hybridized to 10K SNP array


title: Paired Normal tissue #613

description: Hybridized to 10K SNP array


title: Pt6_HL_Decitabine_rep1


title: Paired Normal tissue #524

description: Hybridized to 10K SNP array


title: Pt5_HL_mock_rep2

source_name: Pt5, HL, mock treatment

value: male


title: Paired Normal tissue #554

description: Hybridized to 10K SNP array


title: Pt5_HL_Decitabine_rep2

source_name: Pt5, HL, 1 µM  decitabine


title: Paired Normal tissue #498

description: Hybridized to 10K SNP array


title: Paired Normal tissue #343

description: Hybridized to 10K SNP array


title: Pt5_HL_Decitabine_rep1


title: Paired Normal tissue #417

description: Hybridized to 10K SNP array


title: Pt4_MDS_mock_rep1

description: Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro mock treatment for 72 hours

source_name: Pt4, MDS, mock treatment

value: MDS


title: sAML-F40_N_Mapping250K_Nsp

status: Public on Apr 29 2010

first: Motohiro

last: Kato

address: 7-3-1, Hongo, Bunkyo-ku

description: We have used anonymous normal references (own-lab-generated) for SNP array analysis.

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: CNAG/AsCNAR 3.0 After appropriate normalization of mean array intensities, signal ratios between tumours and anonymous normal references were calculated in an allele-specific manner, and allele-specific copy numbers were inferred from the observed signal ratios based on the hidden Markov model using CNAG/AsCNAR 3.0 software (http://www.genome.umin.jp).

label: biotin phytoerythrin

source_name: MPD specimens

label_protocol: Affymetrix standard

extract_protocol: standard DNA extraction

tag: disease category


title: Breast Cancer #227

description: Hybridized to 10K SNP array

source_name: Breast cancer

value: Ductal

value: III


title: Pt3_MDS_Decitabine_rep3

description: Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours

source_name: Pt3, MDS, 1 µM  decitabine

value: abnormal


title: Paired Normal tissue #330

description: Hybridized to 10K SNP array


title: Paired Normal tissue #312

description: Hybridized to 10K SNP array


title: Pt5_HL_Decitabine_rep3


title: Breast Cancer #56

description: Hybridized to 10K SNP array


title: Pt5_HL_mock_rep1


title: Pt4_MDS_Decitabine_rep1

source_name: Pt4, MDS, 1 µM  decitabine


title: Pt3_MDS_mock_rep2

source_name: Pt3, MDS, mock treatment


title: Paired Normal tissue #316

description: Hybridized to 10K SNP array


title: Pt3_MDS_Decitabine_rep2


title: Pt4_MDS_Decitabine_rep2


title: Pt4_MDS_mock_rep2


title: Pt3_MDS_mock_rep1


title: Breast Cancer #670

description: Hybridized to 10K SNP array


title: Pt2_MDS_mock_rep2

source_name: Pt2, MDS, mock treatment


title: Breast Cancer #664

description: Hybridized to 10K SNP array


title: Pt2_MDS_mock_rep1


title: Paired Normal tissue #325

description: Hybridized to 10K SNP array


title: Breast Cancer #609

description: Hybridized to 10K SNP array


title: Pt2_MDS_Decitabine_rep2

source_name: Pt2, MDS, 1 µM  decitabine


title: Pt1_MDS_mock_rep2

source_name: Pt1, MDS, mock treatment


title: Pt3_MDS_Decitabine_rep1


title: Pt1_MDS_mock_rep1


title: Pt1_MDS_Decitabine_rep1

source_name: Pt1, MDS, 1 µM  decitabine


title: Breast Cancer #126

description: Hybridized to 10K SNP array


title: Pt2_MDS_Decitabine_rep3


title: Breast Cancer #230

description: Hybridized to 10K SNP array


title: Pt1_MDS_Decitabine_rep3


title: Breast Cancer #558

description: Hybridized to 10K SNP array


title: Breast Cancer #72

description: Hybridized to 10K SNP array


title: Pt1_MDS_Decitabine_rep2


title: Breast Cancer #475

description: Hybridized to 10K SNP array


title: Breast Cancer #34

description: Hybridized to 10K SNP array


title: Breast Cancer #451

description: Hybridized to 10K SNP array


title: Pt4_MDS_Decitabine_rep3


title: Pt2_MDS_Decitabine_rep1


title: Breast Cancer #554

description: Hybridized to 10K SNP array


title: Breast Cancer #148

description: Hybridized to 10K SNP array


title: Breast Cancer #511

description: Hybridized to 10K SNP array

value: II


title: Breast Cancer #4

description: Hybridized to 10K SNP array


title: Breast Cancer #206

description: Hybridized to 10K SNP array

value: Mixed

value: +low/+low/-


title: Breast Cancer #656

description: Hybridized to 10K SNP array


title: Breast Cancer #58

description: Hybridized to 10K SNP array


title: Serum10-3

city: Guangzhou

first: Duanqing

last: Pei

state: Guangdong

address: Room 301, International Business Incubator, Guangzhou science park

department: Center for Molecular Medicine

country: China

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences(GIBH.CAS)

description: expression data from iPS cells at D3 post-retroviral infection

hyb_protocol: Following fragmentation and labeling, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip MoGene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Partek software.

source_name: iPS indcued by OKSM cultured in iPS-SF1 supplemented with FBS at D3 post-infection

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Whole Transcript (WT) Sense Target   Labeling Assay Manual, 2007, Affymetrix).

growth_protocol: Cultured in 37℃ with 5% CO2 in the media descripted in sample source name.

treatment_protocol: MEFs were infected with Oct4/Sox2/Klf4/c-Myc retrovirus and then cultured in indicated media.

tag: cell line

value: mouse embryonic fibroblast cells infected by Oct4/Sox2/Klf4/c-Myc


title: mES-3

source_name: iPS indcued by OKSM cultured in mES at D3 post-infection


title: Breast Cancer #489

description: Hybridized to 10K SNP array


title: Serum10-1


title: Serum10-2


title: Breast Cancer #524

description: Hybridized to 10K SNP array


title: WT v. KO d8-4

city: Salt Lake City

first: Matthew

last: Williams

state: UT

address: 15 N. Medical Dr. E.

department: Pathology

institute: University of Utah

description:
C57BL/6 mice (Thy1.2+) received adoptive transfer of 1 x 10^4 WT (Thy1.1+) and IL-2Ra-deficient (Thy1.1+Thy1.2+) i.v. Mice were infected one day later with 2 x 10^5 LCMV Arm i.p.
Spleens were harvested at day 8 post-infection.  CD8 T cells were enriched using magnetic beads (Miltenyi, per manufacturer's instructions) and stained with Thy1.1-FITC and Thy1.2 PE.  WT and KO CTL were FACS sorted from these samples using a FACSVantage (BDBiosciences).

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: d8 WT P14 CTL

label_protocol: 200 mcg total RNA was used in a linear amplification and labeling reaction to generate Cy3 or Cy5-labeled cRNA using a kit, per manufacturer's instructions (Agilent, Low RNA Input Fluorescent Linear Amplification Kit)

extract_protocol: RNA was extracted using Rneasy kits (Qiagen, per manufacturer's intrcuctions).

value: 8 weeks

value: CD8 T cell

tag: infectious agent

value: LCMV

tag: time point post-infection

tag: genetic background

tag: genotype

value: wild type

source_name: d8 IL2Ra-deficient P14 CTL

value: IL2Ra KO


title: Breast Cancer #12

description: Hybridized to 10K SNP array


title: WT v. KO d8-2

tag: age


title: iPSSF1-3

source_name: iPS indcued by OKSM cultured in iPS-SF1 at D3 post-infection

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


title: mES-2


title: Breast Cancer #828

description: Hybridized to 10K SNP array


title: Breast Cancer #330

description: Hybridized to 10K SNP array


title: Guangxi buffalo, longuissimus dorsi muscle at 36 months, biological rep 2

city: Yangling

first: Yingying

last: Zhang

address: No.22 Xinong Road, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China.

institute: National Beef Cattle Improvement Center

description: Gene expression data from Guangxi buffalo longuissimus dorsi muscle at 36 months.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Bovine Genome arrays using ArrayAffymetrix® GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.

data_processing: The data were analyzed with Affymetrix® GeneChip® Operating Software Version1.4 (GCOS1.4) using Affymetrix default analysis settings. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Bubalus bubalis

source_name: Guangxi buffalo, longuissimus dorsi muscle, 36 months

treatment_protocol: Cattle were slaughtered at 36 months of age. Longuissimus dorsi tissues were taken adjacent to the 12th section of the Longuissimus dorsi muscle, immediately frozen in liquid nitrogen, and conserved at -80C

tag: breed

value: Guangxi buffalo

value: longuissimus dorsi muscle

value: 36 months


title: Guangxi buffalo, longuissimus dorsi muscle at 36 months, biological rep 3


title: Breast Cancer #138

description: Hybridized to 10K SNP array

value: Lobular


title: mES-1


title: Qinghai yak, longuissimus dorsi muscle at 36 months, biological rep 2

description: Gene expression data from Qinghai yak longuissimus dorsi muscle at 36 months.

organism: Bos grunniens

source_name: Qinghai yak, longuissimus dorsi muscle, 36 months

value: Qinghai yak


title: BMP_Nog-3

source_name: iPS indcued by OKSM cultured in iPS-SF1 supplemented with BMP4 and Noggin at D3 post-infection


title: Guangxi buffalo, longuissimus dorsi muscle at 36 months, biological rep 1


title: WT v. KO d8-3


title: Breast Cancer #780

description: Hybridized to 10K SNP array

value: Ductal


title: Qinghai yak, longuissimus dorsi muscle at 36 months, biological rep 3


title: iPSSF1-1


title: Qinghai yak, longuissimus dorsi muscle at 36 months, biological rep 1


title: Breast Cancer #691

description: Hybridized to 10K SNP array


title: Qinchuan cattle, longuissimus dorsi muscle at 36 months, biological rep FM3

description: Gene expression data from Qinchuan cattle longuissimus dorsi muscle at 36 months.

organism: Bos taurus

source_name: Qinchuan cattle, longuissimus dorsi muscle, female, 36 months

value: Qinchuan

value: female


title: iPSSF1-2


title: necrotic synthetic wheat-seedling leaf-replicate1

city: Kobe

first: Shigeo

last: Takumi

state: Hyogo

address: Rokkodai 1-1, Nada

department: Graduate School of Agricultural Science

institute: Kobe University

description: Gene expression in 3-week-old seedling leaves

hyb_protocol: Hybridization of the Cy3-labeled cRNA to the microarrays and washing were performed using a Gene Expression Hybridization kit and Gene Expression Wash Pack (Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: Signal intensities were detected by Feature Extraction software (Agilent Technologies). Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Triticum aestivum

source_name: synthetic hexaploid wheat

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants were grown at 23°C for 3 weeks

extract_protocol: Total RNA was extracted from the 1st (lowest) leaves of WT and necrosis synthetic lines, using an RNeasy Plant Mini kit (Qiagen). RNA quality was checked using an Agilent 2100 BioAnalyzer.

value: leaf

tag: phenotype

value: hybrid necrosis


title: BMP_Nog-1


title: Qinchuan cattle, longuissimus dorsi muscle at 36 months, biological rep FM2

tag: tissue


title: wild type synthetic wheat-seedling leaf-replicate2


title: BMP_Nog-2


title: wild type synthetic wheat-seedling leaf-replicate1


title: BMP4-3

source_name: iPS indcued by OKSM cultured in iPS-SF1 supplemented with BMP4 at D3 post-infection


title: WT v. KO d8-1


title: BMP4-2


title: Breast Cancer #665

city: Boston

description: Hybridized to 10K SNP array

source_name: Breast cancer

tag: histologic type

value: III


title: BMP4-1

value: mouse embryonic fibroblast cells infected by Oct4/Sox2/Klf4/c-Myc


title: Qinchuan cattle, longuissimus dorsi muscle at 36 months, biological rep CM2

source_name: Qinchuan cattle, longuissimus dorsi muscle, castrated male, 36 months

value: castrated male


title: Breast Cancer #417

description: Hybridized to 10K SNP array

tag: grade


title: Qinchuan cattle, longuissimus dorsi muscle at 36 months, biological rep CM1


title: Breast Cancer #214

description: Hybridized to 10K SNP array

tag: er/pr/her


title: Breast Cancer #498

description: Hybridized to 10K SNP array


title: Qinchuan cattle, longuissimus dorsi muscle at 36 months, biological rep FM1


title: Breast Cancer #325

description: Hybridized to 10K SNP array


title: Qinchuan cattle, longuissimus dorsi muscle at 36 months, biological rep CM3


title: Breast Cancer #164

description: Hybridized to 10K SNP array


title: Qinchuan cattle, longuissimus dorsi muscle at 36 months, biological rep IM2

source_name: Qinchuan cattle, longuissimus dorsi muscle, intact male, 36 months

value: intact male


title: necrotic synthetic wheat-seedling leaf-replicate2


title: M19HEM20090605_simF3_melM5

city: Portland

first: Suzy

last: Renn

state: OR

address: 3203 SE Woodstock Blvd

department: Biology

institute: Reed College

description: Cy3= Drosophila simulans female genomic DNA Cy5= Drosophila melanogaster male genomic DNA

hyb_protocol: The samples were combined with hybridization buffer Ambion Hyb Buffer 1 and hybridized to the microarray at  48 degrees 12-16 hours

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=740_550_ ScanPower=100_100_

data_processing: After removing ""flagged"" and bad spots, only those spots were used whose average intensity was at least two standard deviations above the average background. Arrays were background corrected (method minimal) and normalized in R/Bioconductor with within-arrays loess (using a set of 1000 conserved genes) and intensity ratios were calculated.

organism: Drosophila simulans

source_name: Drosophila simulans female

label_protocol: dCTP incorporation with Klenow

growth_protocol: Grown in fly nutrient media

extract_protocol: ProteinaseK/Phenol Extraction

tag: sex

tag: species

value: sim

organism: Drosophila melanogaster

source_name: Drosophila melanogaster male

value: male

value: mel


title: Breast Cancer #590

description: Hybridized to 10K SNP array

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


title: Goat_mammarytissue_Swap6_SlideS12_6831_P70cy5_L40cy3

city: Jouy en Josas

first: Felicie

last: Faucon

address: Domaine de Vivert Bat 221

department: Genetique Animale

country: France

institute: INRA Jouy en Josas

description: All samples were associated following an even loop experimental design which was developed according to variance minimization (Kerr and Churchill, 2001; Kerr, 2003). In this experimental design every time point was compared to the four others excepted for the comparison P46 and L40  which were supposed too different developmental stages and could risk to increase the variance.

hyb_protocol: Prior to hybridization, microarrays were pre-hybridized for 30 minutes at 50°C in a filtered solution of 1% BSA, 3.5X SSC, 0.1% SDS and twice rinsed in ultra pure water for 5 minutes under orbital agitation. An evaluated amount of 380 ng of each labelled cDNA sample was fragmented for 30 minutes at 60°C in the [1x] Fragmentation Buffer (Agilent Technologies, Santa Clara, Ca, USA). So, the fragmented labelled cDNA samples were diluted in hybridization buffer (Agilent Technologies, Santa Clara, Ca, USA) and were hybridized to the microarrays for 20h at 60°C in a rotating hybridization oven (Agilent Technologies, Santa Clara, Ca, USA). After the hybridization was complete, microarrays were washed under orbital agitation twice for 5 minutes at 50°C in a (2X SSC, 0.1% SDS) solution and were successively washed twice for 5 minutes at room temperature in (0.5X SSC, 0.1% SDS) solution, in (0.1X SSC, 0.1% SDS) solution for 5 minutes, in (0.1X SSC) solution 3 times for 5 minutes and in ultra pure water for 1 minute. They were finally dried for 45 seconds in a mini-centrifuge system.

scan_protocol: Agilent - Agilent feature extraction software (Version 5-7.1)

data_processing: Data were normalized using the normalisation function of the anapuce package or R (http://www.bioconductor.org/). It performs an intensity dependant normalization using a global loess (Yang et al., 2002) followed by subtraction of the log-ratio median calculated over the values for an entire block from each individual log-ratio in order to correct an eventual print-tip effect.

organism: Capra hircus

source_name: Goat, mammary gland tissue, 70 days of pregnancy

label_protocol: RNA samples were labelled using SuperscriptTM Indirected cDNA labelling protocol (Invitrogen, Carlsbad, CA, USA). Briefly, 10 µg of total extracted RNA were first reverse transcribed using SuperScriptTM III Reverse Transcriptase enzyme and amino-modified dNTPs. The synthesized cDNA were separated from the non-incorporated amino-modified dNTPs on S.N.A.P.TM columns. They were labelled with Cy3TM or Cy5TM dyes (GE Healthcare, Europe) and further separated from non-incorporated dyes on S.N.A.P.TM Columns.

extract_protocol: Freeze samples were grinded in a Freezer Mill 6750 (Bioblock) in liquid nitrogen. RNA were extracted by mixing the resulting powder with Trizol reagent (Invitrogen, Carlsbad, CA, USA) and purify on QIAGEN RNeasy mini-columns. After DNaseI treatment (QIAGEN, Valencia, CA, USA) total RNA were eluted.

tag: Animal

value: Goat

tag: Developmental Stage

value: Pregnancy

tag: Days

tag: Tissue

value: mammary gland

tag: Acronym

source_name: Goat, mammary gland tissue, 40 days of lactation

value: Lactation


title: Qinchuan cattle, longuissimus dorsi muscle at 36 months, biological rep IM1

value: longuissimus dorsi muscle

tag: gender

value: 36 months


title: Qinchuan cattle, longuissimus dorsi muscle at 36 months, biological rep IM3

value: Qinchuan


title: Goat_mammarytissue_Swap6_SlideS11_6820_P70cy3_L40cy5


title: Goat_mammarytissue_Swap7_SlideS13_6817_P90cy3_P110cy5

source_name: Goat, mammary gland tissue, 90 days of pregnancy

source_name: Goat, mammary gland tissue, 110 days of pregnancy


title: Breast Cancer #636

description: Hybridized to 10K SNP array

value: Ductal


title: M18HEM20090605_melM3_simF5b

description: Cy3= Drosophila melanogaster male genomic DNA Cy5= Drosophila simulans female genomic DNA

value: female


title: Breast Cancer #333

description: Hybridized to 10K SNP array


title: Breast Cancer #396

description: Hybridized to 10K SNP array


title: Breast Cancer #911

description: Hybridized to 10K SNP array


title: M13HEM20090505_Sim3_Mel5

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=850_610_ ScanPower=100_100_


title: M17HEM20090604_melM3_simF5

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=740_500_ ScanPower=100_100_


title: Goat_mammarytissue_Swap5_SlideS10_6827_P70cy5_P110cy3


title: Goat_mammarytissue_Swap5_SlideS9_6819_P70cy3_P110cy5


title: Goat_mammarytissue_Swap4_SlideS8_6834_P70cy5_P90cy3


title: Breast Cancer #312

description: Hybridized to 10K SNP array


title: Breast Cancer #169

description: Hybridized to 10K SNP array


title: M15HEM20090616_YakF3_MelM5

description: Cy3= Drosophila yakuba female genomic DNA Cy5= Drosophila melanogaster male genomic DNA

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=740_610_ ScanPower=100_100_

organism: Drosophila yakuba

source_name: Drosophila yakuba female

value: yak


title: Breast Cancer #343

description: Hybridized to 10K SNP array

value: III


title: Breast Cancer #96

description: Hybridized to 10K SNP array


title: Goat_mammarytissue_Swap4_SlideS7_6828_P70cy3_P90cy5


title: Goat_mammarytissue_Swap3_SlideS6_6812_P46cy5_P110cy3

source_name: Goat, mammary gland tissue, 46 days of pregnancy


title: M16HEM20090616_YakF3_MelM5


title: pCs54scpr20060501_melF3M5_0071

description: Cy3= Drosophila melanogaster female genomic DNA Cy5= Drosophila melanogaster male genomic DNA

hyb_protocol: The samples were combined with hybridization buffer (3.4X SSC, 0.15% SDS, 1 mM DTT) and hybridized to the microarray at  70 degrees 12-16 hours

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=760_720_ ScanPower=100_100_

source_name: Drosophila melanogaster female


title: pCs55scpr20060501_melM3F5_70

description: Cy3= Drosophila melanogaster male genomic DNA Cy5= Drosophila melanogaster female genomic DNA


title: Breast Cancer #613

description: Hybridized to 10K SNP array


title: pCs51scpr20060501_melF3M5_67

hyb_protocol: The samples were combined with hybridization buffer (3.4X SSC, 0.15% SDS, 1 mM DTT) and hybridized to the microarray at  67 degrees 12-16 hours

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=760_740_ ScanPower=100_100_


title: Goat_mammarytissue_Swap3_SlideS5_6811_P46cy3_P110cy5


title: Goat_mammarytissue_Swap2_SlideS4_6821_P46cy5_P90cy3


title: Breast Cancer #362

description: Hybridized to 10K SNP array


title: Breast Cancer #192

description: Hybridized to 10K SNP array


title: Breast Cancer #363

description: Hybridized to 10K SNP array


title: pCs58scpr20060501_melF3M5_65

hyb_protocol: The samples were combined with hybridization buffer (3.4X SSC, 0.15% SDS, 1 mM DTT) and hybridized to the microarray at  65 degrees 12-16 hours


title: Breast Cancer #316

description: Hybridized to 10K SNP array


title: Goat_mammarytissue_Swap8_SlideS16_6836_P90cy5_L40cy3


title: Breast Cancer #199

description: Hybridized to 10K SNP array


title: pCs96_SR20090311_HEM0616

description: Cy3= Drosophila melanogaster male genomic DNA Cy5= Drosophila yakuba female genomic DNA

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=880_580_ ScanPower=100_100_


title: pCs93_HMCP20090313

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=980_680_ ScanPower=100_100_


title: Goat_mammarytissue_Swap9_SlideS18_6835_P110cy5_L40cy3


title: Breast Cancer #142

description: Hybridized to 10K SNP array


title: Goat_mammarytissue_Swap9_SlideS17_6256_P110cy3_L40cy5


title: Goat_mammarytissue_Swap2_SlideS3_6814_P46cy3_P90cy5


title: pCs91_DE20090313b_20090602

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=950_710_ ScanPower=100_100_


title: Goat_mammarytissue_Swap8_SlideS15_6833_P90cy3_L40cy5


title: Goat_mammarytissue_Swap7_SlideS14_6830_P90cy5_P110cy3


title: Goat_mammarytissue_Swap1_SlideS1_6813_P46cy3_P70cy5


title: pCs57scpr20060501_melM3F5_67

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=740_720_ ScanPower=100_100_


title: pCs59scpr20060501_melM3F5

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=750_720_ ScanPower=100_100_


title: pCs87_AO20090313_HEM0616

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=1000_710_ ScanPower=100_100_


title: Breast Cancer #452

description: Hybridized to 10K SNP array


title: Cambium_Re-hydrated vs Control_swap_Replicate1

status: Public on Dec 22 2009

city: Florence

first: Monica

last: Berta

address: Via Maragliano 77

department: Agricultural Biotechnology

institute: University of Florence

hyb_protocol: Hybridizations were carried out using CAMLAB micro-array hybrid chamber. The probes were mixed with hybridization buffer (Amersham Biosciences) and formamide at the ratio of 1:1:2 (by vol.), respectively. Hybridizations were carried out at 42°C for 15/18 h. To remove the lifter slip, the slides were rinsed briefly in water and then washed with 1x SSC, 0.2% SDS for 15 min at 50°C, 0.1x SSC, 0.2% SDS for 10 min at RT and 0.2x SSC twice for 5 min at RT.

scan_protocol: Microarray images were acquired on ScanArray Gx (PerkinElmer) with a 5 μm resolution. Quantitation of signals was done using “ScanArray Express” software (PerkinElmer).

data_processing: LOWESS normalized. The expression levels for all genes presented on the microarray were locally normalized by weighted print-tip-loess, followed by a scale-normalization between arrays, using the LIMMA package for R.

label: AlexaFluor® 647

organism: Populus alba

label_protocol: Starting from 15 μg of RNA, reverse transcription and indirect labelling with the two fluorescent probes (Alexa 555, Alexa 647) were performed by means of “SuperScriptTM Plus Indirect cDNA Labelling System” (INVITROGEN), following the manufacturer’s instructions.

growth_protocol: 32 one-years-old Populus alba L. plants, clone Marte, were selected for dimensional uniformity (height mean 139.3 ± 8.6 cm and mean stem diameter 4.8 ± 0.1 mm, average leaf number per plant 28.8 ± 0.6). During the experiment, plants were maintained in a greenhouse under natural day-light condition (750 m m-2 s-1, maximal photon flux density). The temperature was maintained in the range of 17 to 28.5°C  and a relative humidity (%) ranging between 55 and 90%.

extract_protocol: Total RNA was extracted from freeze-dried cambium following the extraction protocol of Kolosova et al. (2004)

treatment_protocol: Plants were divided in two homogeneous groups of 16 plants each and submitted to different watering regimes for 17 days. In control plants, soil moisture was maintained to field capacity (soil water content = 28%) whilst in treated plants, watering was suspended for 9 days (Tmax) and then was resumed for 8 days (Trec).

value: Cambium

tag: treatment

value: Control

label: AlexaFluor® 555

value: Re-hydreated


title: Cambium_Re-hydrated vs Control_swap_Replicate2

value: Re-hydrated


title: Cambium_Re-hydrated vs Stress_Replicate1

value: Stress


title: Cambium_Stress vs Control_Replicate2


title: Cambium_Re-hydrated vs Stress_swap_Replicate2


title: Cambium_Re-hydrated vs Control_Replicate2


title: Cambium_Stress vs Control_swap_Replicate2


title: Cambium_Stress vs Control_swap_Replicate1


title: Cambium_Re-hydrated vs Stress_Replicate2


title: Cambium_Re-hydrated vs Control_Replicate1


title: L-mock_sample #7

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

institute: Fondo Edo Tempia

description:
Technical replicates (normal and dye-swap) of L-mock_sample #7.
Normal: 7_L-mock_NORM
Dye-swap: 7_L-mock_DS

hyb_protocol: Equal amounts (0.75 ug) of labeled specimens from sample and reference were put together, fragmented and hybridized to oligonucleotide glass arrays representing 41K human unique genes and transcripts (Human Whole Genome Oligo Microarray Array, Agilent Technologies). All steps were performed using the In Situ Hybridization kit-plus (Agilent Technologies) and following the 60-mer oligo microarray processing protocol (Agilent Technologies). Then, slides were washed with the SSPE wash procedure. For each sample, a dye-swap replicate was performed.

scan_protocol: Slides were scanned with the 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. Replicated 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.

The raw and processed data output are from Feature Extraction Software version 7.6 (Agilent Technologies). Data from technical replicates (normal and dye-swap labelling) were combined and then the data was normalized. Log10 ratios representing test/reference are reported in the VALUE column of the Sample data tables.

label: Cy3, Cy5

source_name: Mock transfected CLL cells from patient #7

label_protocol: RNA isolated from each cell culture and from the human universal reference (BD™ Human Universal Reference Total RNA, Clontech, Palo Alto, CA) was amplified by means of the Amino Allyl MessageAmp II aRNA Kit (Ambion) to obtain amino allyl antisense RNA (aaRNA) following the method developed by Eberwine and coworkers. Two rounds of amplification were performed to obtain the necessary quantity of aaRNA for labeling. Briefly: mRNA was reverse transcribed in cDNA single strand; after the second strand synthesis (in the second round of amplification), cDNA was in vitro transcribed in aaRNA including amino allyl modified nucleotides (aaUTP). Both dsDNA and aaRNA underwent a purification step using columns provided with the kit. Labeling was performed using NHS ester Cy3 or Cy5 dyes (Amersham Biosciences, Buckinghamshire UK) able to react with the modified RNA. mRNA quality was checked by means of RNA 6000 nano chip assays (Agilent Technologies). At least 5 ug of mRNA for each sample were labeled and purified with columns.

extract_protocol: All the samples were homogenized (Ultra – TurraxT8, Ika – Werke, Staufen, Germany) and total RNA was isolated by using TriReagent (Sigma Aldrich). TotRNA quality was checked by means of RNA 6000 pico chip assays (Agilent Technologies, Palo Alto, CA) run on the Agilent 2100 bioanalyzer.

tag: Gender

value: F

tag: Age

source_name: commercial human universal reference

tag: Clontech human universal reference


title: L-mock_sample #5

description:
Technical replicates (normal and dye-swap) of L-mock_sample #5.
Normal: 5_L-mock_NORM
Dye-swap: 5_L-mock_DS

source_name: Mock transfected CLL cells from patient #5

value: M


title: Cambium_Stress vs Control_Replicate1


title: Cambium_Re-hydrated vs Stress_swap_Replicate1


title: L-mock_sample #6

description:
Technical replicates (normal and dye-swap) of L-mock_sample #6.
Normal: 6_L-mock_NORM
Dye-swap: 6_L-mock_DS

source_name: Mock transfected CLL cells from patient #6


title: Goat_mammarytissue_Swap1_SlideS2_6824_P46cy5_P70cy3

value: Goat

value: Pregnancy


title: L-mock_sample #2

description:
Technical replicates (normal and dye-swap) of L-mock_sample #2.
Normal: 2_L-mock_NORM
Dye-swap: 2_L-mock_DS

source_name: Mock transfected CLL cells from patient #2


title: L-mock_sample #4

description:
Technical replicates (normal and dye-swap) of L-mock_sample #4.
Normal: 4_L-mock_NORM
Dye-swap: 4_L-mock_DS

source_name: Mock transfected CLL cells from patient #4


title: L-mock_sample #3

description:
Technical replicates (normal and dye-swap) of L-mock_sample #3.
Normal: 3_L-mock_NORM
Dye-swap: 3_L-mock_DS

source_name: Mock transfected CLL cells from patient #3


title: L-mock_sample #1

description:
Technical replicates (normal and dye-swap) of L-mock_sample #1.
Normal: 1_L-mock_NORM
Dye-swap: 1_L-mock_DS

source_name: Mock transfected CLL cells from patient #1


title: L-CD31+_sample #9

description:
Technical replicates (normal and dye-swap) of L-CD31+_sample #9.
Normal: 9_L-CD31+_NORM
Dye-swap: 9_L-CD31+_DS

source_name: CD31+ transfected CLL cells from patient #9


title: L-CD31+_sample #8

description:
Technical replicates (normal and dye-swap) of L-CD31+_sample #8.
Normal: 8_L-CD31+_NORM
Dye-swap: 8_L-CD31+_DS

source_name: CD31+ transfected CLL cells from patient #8


title: L-mock_sample #10

description:
Technical replicates (normal and dye-swap) of L-mock_sample #10.
Normal: 10_L-mock_NORM
Dye-swap: 10_L-mock_DS

source_name: Mock transfected CLL cells from patient #10


title: L-CD31+_sample #6

description:
Technical replicates (normal and dye-swap) of L-CD31+_sample #6.
Normal: 6_L-CD31+_NORM
Dye-swap: 6_L-CD31+_DS

source_name: CD31+ transfected CLL cells from patient #6


title: L-CD31+_sample #4

description:
Technical replicates (normal and dye-swap) of L-CD31+_sample #4.
Normal: 4_L-CD31+_NORM
Dye-swap: 4_L-CD31+_DS

source_name: CD31+ transfected CLL cells from patient #4


title: L-CD31+_sample #3

description:
Technical replicates (normal and dye-swap) of L-CD31+_sample #3.
Normal: 3_L-CD31+_NORM
Dye-swap: 3_L-CD31+_DS

source_name: CD31+ transfected CLL cells from patient #3


title: L-CD31+_sample #5

description:
Technical replicates (normal and dye-swap) of L-CD31+_sample #5.
Normal: 5_L-CD31+_NORM
Dye-swap: 5_L-CD31+_DS

source_name: CD31+ transfected CLL cells from patient #5


title: L-CD31+_sample #1

description:
Technical replicates (normal and dye-swap) of L-CD31+_sample #1.
Normal: 1_L-CD31+_NORM
Dye-swap: 1_L-CD31+_DS

source_name: CD31+ transfected CLL cells from patient #1


title: L-CD31+_sample #10

description:
Technical replicates (normal and dye-swap) of L-CD31+_sample #10.
Normal: 10_L-CD31+_NORM
Dye-swap: 10_L-CD31+_DS

source_name: CD31+ transfected CLL cells from patient #10


title: L-CD31+_sample #2

description:
Technical replicates (normal and dye-swap) of L-CD31+_sample #2.
Normal: 2_L-CD31+_NORM
Dye-swap: 2_L-CD31+_DS

source_name: CD31+ transfected CLL cells from patient #2


title: basal_sample #8

description:
Technical replicates (normal and dye-swap) of basal_sample #8.
Normal: 8_basal_NORM
Dye-swap: 8_basal_DS

source_name: CLL cells from patient #8

source_name: commercial human universal reference


title: basal_sample #9

description:
Technical replicates (normal and dye-swap) of basal_sample #9.
Normal: 9_basal_NORM
Dye-swap: 9_basal_DS

source_name: CLL cells from patient #9


title: basal_sample #7

description:
Technical replicates (normal and dye-swap) of basal_sample #7.
Normal: 7_basal_NORM
Dye-swap: 7_basal_DS

source_name: CLL cells from patient #7


title: basal_sample #6

description:
Technical replicates (normal and dye-swap) of basal_sample #6.
Normal: 6_basal_NORM
Dye-swap: 6_basal_DS

source_name: CLL cells from patient #6


title: basal_sample #10

description:
Technical replicates (normal and dye-swap) of basal_sample #10.
Normal: 10_basal_NORM
Dye-swap: 10_basal_DS

source_name: CLL cells from patient #10


title: basal_sample #5

description:
Technical replicates (normal and dye-swap) of basal_sample #5.
Normal: 5_basal_NORM
Dye-swap: 5_basal_DS

source_name: CLL cells from patient #5


title: CCL153 MIR155 48h #1 345664

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description:
CCL153 NEG 48H #1 vs CCL153 MIR155 48H #1
Date:2008/03/14

hyb_protocol: Agilent : 750.0 ng at 62 degree_C during 18 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : printtiploess, Background norm. : none, Software used : limmagui --> VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: CCL153 NEG 48h #1

label_protocol: Ambion

extract_protocol: Qiagen

tag: Labeling_reference:CCL153 NEG 48H #1

value: CCL153 NEG 48H #1

value: fibroblast

value: human fetal pulmonary fibroblast (CCL153)

tag: Labeling_reference:CCL153 MIR155 48H #1


title: CCL153 MIR155 48h #2 345410

description:
CCL153 NEG 48H #2 vs CCL153 MIR155 48H #2
Date:2008/04/09

hyb_protocol: Agilent : 2000.0 ng at 62 degree_C during 18 hours

source_name: CCL153 NEG 48h #2

tag: Labeling_reference:CCL153 NEG 48H #2

value: CCL153 NEG 48H #2

tag: Labeling_reference:CCL153 MIR155 48H #2


title: basal_sample #2

description:
Technical replicates (normal and dye-swap) of basal_sample #2.
Normal: 2_basal_NORM
Dye-swap: 2_basal_DS

source_name: CLL cells from patient #2


title: basal_sample #1

description:
Technical replicates (normal and dye-swap) of basal_sample #1.
Normal: 1_basal_NORM
Dye-swap: 1_basal_DS

source_name: CLL cells from patient #1


title: CCL153 MIR155 24h #1 345265

description:
CCL153 MIR155 24H #1 vs CCL153 NEG 24H #1
Date:2008/03/14

tag: Labeling_reference:CCL153 MIR155 24H #1

source_name: CCL153 NEG 24h #1

tag: Labeling_reference:CCL153 NEG 24H #1

value: CCL153 NEG 24H #1


title: basal_sample #4

description:
Technical replicates (normal and dye-swap) of basal_sample #4.
Normal: 4_basal_NORM
Dye-swap: 4_basal_DS

source_name: CLL cells from patient #4


title: CCL153 MIR155 48h #2 345269

description:
CCL153 MIR155 48H #2 vs CCL153 NEG 48H #2
Date:2008/04/09


title: CCL153 MIR155 24h #1 345425

description:
CCL153 NEG 24H #1 vs CCL153 MIR155 24H #1
Date:2008/03/14

value: CCL153 NEG 24H


title: basal_sample #3

description:
Technical replicates (normal and dye-swap) of basal_sample #3.
Normal: 3_basal_NORM
Dye-swap: 3_basal_DS

source_name: CLL cells from patient #3


title: L-mock_sample #8

description:
Technical replicates (normal and dye-swap) of L-mock_sample #8.
Normal: 8_L-mock_NORM
Dye-swap: 8_L-mock_DS

source_name: Mock transfected CLL cells from patient #8


title: CCL153 MIR155 48h #1 345423

description:
CCL153 MIR155 48H #1 vs CCL153 NEG 48H #1
Date:2008/03/14


title: zf_ovary_hal_61941

city: Duluth

first: Daniel

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

institute: US EPA

description:
Sample 61941 - ovary from zebrafish exposed to 50 ug haloperidol/L (nominal) for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

hyb_protocol: All of the labeling and post labeling procedures were conducted in ozone-free enclosure to ensure the integrity of the label. Labeled materials were set up for the fragmentation reaction according to Agilent protocol described in their processing manual, and hybridized overnight in the rotating oven at 65°C in an ozone-free room. The Agilent Oligo Microarray Zebrafish slide, with approximately 21, 000 genes represented was used for the gene expression analyses (4 x 44K format, product 015064). Labeled samples (825 ng) were co-hybridized using sureHyb chambers from Agilent. Wash conditions used were as outlined in the Agilent processing manual (protocol version 4.0).

scan_protocol: The arrays were scanned using Agilent scanner (G2505B). Agilent feature extraction software was used for extracting array data; the initial data quality analyses were done using Rosetta Luminator software (Rosetta Biosoftware, Seattle, WA).

data_processing: Microarray image processing and data pre-processing were performed using Agilent's Feature Extraction Software (v 9.5). The intensity of each spot was summarized by mean pixel intensity. A log10 transformed signal ratio between the experimental (Cy5) and reference (Cy3) channel was calculated for each spot.

organism: Danio rerio

source_name: zf ovary, exposed to 50 ug haloperidol/L for 96 h

label_protocol: RNA from each condition of interest (treatment) was labeled with a Cy5 dye and hybridized onto arrays together with Cy3 labeled RNA taken from a standard reference pool of RNA extracted from sexually mature male and female gonads and brains, and female livers. For the microarray analyses, total RNA was amplified using Agilent low input linear amplification kit according to the process outlined by the manufacturer (Agilent Technologies). Amplified target cRNA (1-5 µg) was labeled with either cyanine-5 or cyanine-3 using ULS aRNA Flurorescent Labeling Kits from Kreatech according to the manufacturers protocol (Kreatech Biotechnology, Amsterdam, The Netherlands). Concentrations of labeled cRNA and the label incorporation was determined using Nanodrop-1000 spectrophotometer.

growth_protocol: 25 degrees C. 16:8 light:dark photoperiod. fed liver Artemia

extract_protocol: Ovary samples were transferred to TRI Reagent® (Sigma), homogenized, and extracted following the manufacturer’s protocol. Total RNA was quantified using a Nanodrop® ND-1000 spectrophotometer, and the integrity and purity of the RNA samples was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and a RNA Nano Chip Kit (Agilent). Optical density ratios (260/280 nm) for all samples were between 1.97 and 2.08 and RNA integrity numbers (RIN; Agilent) ranged from 5.7-9.3.

treatment_protocol: After 96 h, fish was humanely euthanized in buffered MS-222 (tricaine methanesulfonate) and weighed. Whole gonads were removed, weighed, and preserved in RNAlater.

value: female

tag: age

value: 5 months

tag: strain

value: ab wild-type strain

tag: tissue

value: gonad

tag: sample

source_name: Reference pool

growth_protocol: 25°C, 16:8 light:dark photoperiod, fed live Artemia

extract_protocol: Tissues were thawed, homogenized and total RNA extracted with TRI Reagent® (Sigma-Aldrich, St. Louis, MO) following the manufacturer’s protocol. Total RNA from all tissues and specimens was pooled together. Total RNA was quantified using a nanodrop ND-100 spectrophotometer (Nanodrop technologies, Wilmington, DE). Integrity and purity of RNA samples was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Paulo Alto, CA) and an RNA Pico Chip Kit (Agilent).

treatment_protocol: All fish humanely euthanized in buffered MS-222 (tricaine methanesulfonate)

value: Females and Males

value: 7 months

value: gonads and brains from males and females, livers from females


title: CCL153 MIR155 24h #2 345665

description:
CCL153 NEG 24H #2 vs CCL153 MIR155 24H #2
Date:2008/04/09

source_name: CCL153 NEG 24h #2

tag: Labeling_reference:CCL153 NEG 24H #2

value: CCL153 NEG 24H #2

tag: Tissue

tag: Labeling_reference:CCL153 MIR155 24H #2

value: fibroblastes


title: L-mock_sample #9

description:
Technical replicates (normal and dye-swap) of L-mock_sample #9.
Normal: 9_L-mock_NORM
Dye-swap: 9_L-mock_DS

source_name: Mock transfected CLL cells from patient #9

value: M

source_name: commercial human universal reference


title: HTCC1062_No_carbon_control_latelog_rep3

city: Madison

first: Michael

middle: S

last: Schwalbach

state: WI

address: 1550 Linden Dr

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin-Madison

description: amplified aRNA, one IVT reaction with modified nucleotides

hyb_protocol: 5 ug of labeled aRNA was hybridized to chips at 45˚C, rotate at 60rpm overnight for 16 hours

scan_protocol: The samples were scanned with an Affymetrix GeneChip Scanner 3000 7G with autoloader using AGCC software.

data_processing: RMA normalization conducted with Affymetrix ExpressionConsole software package, Statistical analyses performed in Multi-Experiment Viewer (MeV) software package (TIGR)

organism: Candidatus Pelagibacter ubique HTCC1062

source_name: Bacteria, HTCC1062, late log phase

label_protocol: RNA was labeled with biotin labeled nucleotides (perkin-elmer) during in vitro transcription (IVT) reaction.

growth_protocol: Cells grown 20C in dark, collected late log from seawater media via centrifugation.

extract_protocol: Total RNA was extracted using Rneasy kit (Qiagen) and amplified using MessageAmp-II-Bacteria RNA Amplification Kit (Ambion)

treatment_protocol: Cells were pelleted, treated with Bacteria Protect reagent (Qiagen) then frozen at -80C prior to extraction

tag: growth phase

value: late log


title: zf_ovary_hal_61919

description:
Sample 61919 - ovary from zebrafish exposed to 50 ug haloperidol/L (nominal) for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

tag: gender


title: CCL153 MIR155 24h #2 345411

description:
CCL153 MIR155 24H #2 vs CCL153 NEG 24H #2
Date:2008/04/09


title: zf_ovary_con_61935

description:
Sample 61935 - ovary from zebrafish exposed to control water for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

source_name: zf ovary, exposed to control water for 96 h


title: HTCC1062_No_carbon_control_latelog_rep2


title: zf_ovary_hal_61915

description:
Sample 61915 - ovary from zebrafish exposed to 50 ug haloperidol/L (nominal) for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: HTCC1062_No_carbon_control_latelog_rep1


title: HTCC1062_glucose30uM_latelog_rep3


title: HTCC1062_glucose30uM_latelog_rep1


title: zf_ovary_hal_61945

description:
Sample 61945 - ovary from zebrafish exposed to 50 ug haloperidol/L (nominal) for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: HTCC1062_glucose30uM_latelog_rep2


title: zf_ovary_con_61911

description:
Sample 61911 - ovary from zebrafish exposed to control water for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: Favorable Histology Wilms Tumor (WT00-346)

city: Chicago

first: Elizabeth

middle: J

last: Perlman

state: IL

address: 2373 North Lincoln Avenue, Room A.204

institute: Children's Memorial Research Center

hyb_protocol: The labeled, fragmented cRNA was hybridized to the Affymetrix HG - U133A oligonucleotide array for 16 hours at 45°C according to Affymetrix protocol. Staining was done in the GeneChip Fluidics Station using pre-programmed Affymetrix protocols.

scan_protocol: The arrays were scanned in an HP GeneArray Scanner.

data_processing: Data were normalized using robust multi-array average (RMA) method. This normalized value of each probeset for each tumor is provided in the file “All Normalized Data.”

source_name: Pretreatment tumor tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated by Trizol (Invitrogen, Carlsbad, CA) extraction and treated with DNase I (Roche, Indianapolis, IN).

tag: Pretreatment tumor tissue


title: Favorable Histology Wilms Tumor (WT00-342)


title: zf_ovary_con_61903

description:
Sample 61903 - ovary from zebrafish exposed to control water for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

growth_protocol: 25 degrees C.  16:8 light:dark photoperiod.  fed liver Artemia

extract_protocol: Tissues were thawed, homogenized and total RNA extracted with TRI Reagent® (Sigma-Aldrich, St. Louis, MO) following the manufacturer’s protocol.  Total RNA from all tissues and specimens was pooled together.  Total RNA was quantified using a nanodrop ND-100 spectrophotometer (Nanodrop technologies, Wilmington, DE). Integrity and purity of RNA samples was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Paulo Alto, CA) and an RNA Pico Chip Kit (Agilent).


title: Favorable Histology Wilms Tumor (WT00-345)


title: Favorable Histology Wilms Tumor (WT00-341)


title: Favorable Histology Wilms Tumor (WT00-339)


title: Favorable Histology Wilms Tumor (WT00-340)


title: zf_ovary_hal_61913

description:
Sample 61913 - ovary from zebrafish exposed to 50 ug haloperidol/L (nominal) for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: zf_ovary_hal_61939

description:
Sample 61939 - ovary from zebrafish exposed to 50 ug haloperidol/L (nominal) for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: Favorable Histology Wilms Tumor (WT00-311)


title: Favorable Histology Wilms Tumor (WT00-334)


title: Favorable Histology Wilms Tumor (WT00-276)


title: Favorable Histology Wilms Tumor (WT00-333)


title: Favorable Histology Wilms Tumor (WT00-331)


title: Favorable Histology Wilms Tumor (WT00-312)


title: Favorable Histology Wilms Tumor (WT00-263)


title: zf_ovary_con_61931

description:
Sample 61931 - ovary from zebrafish exposed to control water for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: Favorable Histology Wilms Tumor (WT00-247)


title: Favorable Histology Wilms Tumor (WT00-265)


title: Favorable Histology Wilms Tumor (WT00-271)


title: zf_ovary_con_61907

description:
Sample 61907 - ovary from zebrafish exposed to control water for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: Favorable Histology Wilms Tumor (WT00-232)


title: zf_ovary_con_61927

description:
Sample 61913 - ovary from zebrafish exposed to 50 ug haloperidol/L for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: Favorable Histology Wilms Tumor (WT00-243)


title: Favorable Histology Wilms Tumor (WT00-246)


title: Favorable Histology Wilms Tumor (WT00-178)


title: Favorable Histology Wilms Tumor (WT00-186)


title: Favorable Histology Wilms Tumor (WT00-196)


title: Favorable Histology Wilms Tumor (WT00-188)


title: Favorable Histology Wilms Tumor (WT00-185)


title: Favorable Histology Wilms Tumor (WT00-177)


title: Favorable Histology Wilms Tumor (WT00-086)


title: Favorable Histology Wilms Tumor (WT00-151)


title: Favorable Histology Wilms Tumor (WT00-160)


title: Favorable Histology Wilms Tumor (WT00-085)


title: Favorable Histology Wilms Tumor (WT00-058)


title: Favorable Histology Wilms Tumor (WT00-046)


title: Favorable Histology Wilms Tumor (WT00-082)


title: Favorable Histology Wilms Tumor (WT00-153)


title: Favorable Histology Wilms Tumor (WT00-127)


title: Favorable Histology Wilms Tumor (WT00-038)


title: Favorable Histology Wilms Tumor (WT00-002)


title: Favorable Histology Wilms Tumor (WT00-054)


title: Favorable Histology Wilms Tumor (WT00-026)


title: HCT-8_indole_24h_rep3

city: College Station

first: Tarun

last: Bansal

address: 3122 TAMU

department: Chemical Engineering

institute: Texas A & M University

description: Cells were grown in RPMI 1640 medium

hyb_protocol: CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection according to manufacturer's instructions http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf

scan_protocol: CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection according to manufacturer's instructions http://www.appliedmicroarrays.com/application_notes/63005079.pdf

data_processing: Median normalized values derived from CodeLink Expression Analysis Version 4.1.0.29054

label: biotin, Alexa-647 Streptavidin

source_name: HCT-8 cell monolayer treated with indole for 24 hr

label_protocol: CodeLink Gene Expression System: Manual Labelled cRNA Target Preparation according to manufacturer's instructions http://www.appliedmicroarrays.com/pdf/iexpress2006_web.pdf

extract_protocol: HCT-8 cells were grown in monolayers till 80% confluence. Indole was added to cells and they were incubated for further 4h or 24 h. RNA was extracted using Qiagen RNeasy Kit.

tag: Human colon-cancer cell line HCT-8