title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M12_Georgia_04


title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M10_Georgia_04

status: Public on Jun 06 2008

type: RNA

city: Lausanne

first: John

last: Wang

address: Batiment Biophore

department: Department of Ecology and Evolution

country: Switzerland

institute: University of Lausanne

description: Adult workers were randomly collected from the foraging area and frozen individually. RNA from 7-10 workers of the same genotype were pooled.

hyb_protocol: Hybridization buffer (3x SSC, 0.18% SDS, 200 ng/μl yeast tRNA, 200 ng/µl polyA DNA; final concentration) was added to samples; samples were denatured, applied to microarrays, and hybridized overnight at 64°C. After hybridization, slides were washed sequential.

scan_protocol: Scanner: Agilent Technologies microarray scanner. Image quantification GenePix 5.1

data_processing: printTipLoess normalization (marray, Bioconductor)

molecule: total RNA

organism: Solenopsis invicta

source_name: Reference RNA batch 2004

label_protocol: Total RNA was amplified using the Ambion Message Amp II kit. Amplified RNA plus Alien spike control RNAs (Stratagene) were labeled using the indirect aa-dUTP labeling method. Reverse transcription primers: random 9mers.

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

tag: Pooled 25% of the amplified RNA from each experimental sample

source_name: Adult workers homozygote BB Gp9 monogyne

tag: Genotype

value: homozygote BB

tag: Colony form

value: monogyne

tag: Source population

value: Georgia


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P08_Georgia_06

source_name: Reference RNA batch 2006

extract_protocol: Total RNA extracted using Qiagen RNeasy Kit following manufacturer's instructions

tag: Amplified total RNA isolated en masse from hundreds of adult workers collected from the foraging area of 30 colonies (eight and seven of each social form from Georgia and Louisiana, respectively)

source_name: Adult workers heterozygote Bb Gp9 polygyne

value: heterozygote Bb

value: polygyne


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P06_Georgia_06


title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M02_Georgia_06


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P01_Louisiana_06

value: Louisiana


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P06_Georgia_06

source_name: Adult workers homozygote BB Gp9 polygyne


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P01_Georgia_04


title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M08_Georgia_04


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P02_Georgia_04


title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M40_Georgia_06


title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M11_Georgia_04


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P01_Georgia_06


title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M13_Georgia_06


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P01_Louisiana_06


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P01_Georgia_06


title: TLOM1

type: other

city: Bethesda

first: Man Lung

last: Yeung

state: MD

address: 9000 Rockville Pike

country: USA

institute: NIH

description: each probe recognizing one species of miRNA is spotted 5 times

hyb_protocol: Samples are hybridizied at 37 degree celsius overnight using MAUI hybridization system

scan_protocol: Datapoints collected from GenePix 4000B (Molecular Devices)

data_processing: data are exported to BRBarray tools for log2 transformation and median calculation (developed by Richard Simon and Amy Peng Lam; http://linus.nci.nih.gov/BRB-ArrayTools.html).

molecule: other

organism: Homo sapiens

source_name: HTLV-1 cell lines

label_protocol: After hybridization, excessive RNA was removed by washing in 0.1 X SSC. Unhybridized probes were removed using exonuclease I (NEB) for 3 hours. Since the probe design contains a stretch of thymidine, polyadenylation from the 3’end of the hybridized miRNAs were achieved by addition of biotin-label dATP (Enzo Life Sciences). Detection of the labeled miRNA under the 532 nm wavelength was facilitated by addition of streptavidin-conjugated Alexa-flur-555.

extract_protocol: Small RNAs (< 200 nt) are extracted from the HTLV-1 infected PBMCs using mirVana Small RNA isolation kit (Ambion) following the manufacturer's protocol.

tag: Small RNAs isolated from HTLV-1 infected cell lines


title: MT-1


title: ED


title: ATL-2


title: ATL55T


title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M01_Georgia_04


title: Pt4 Hseb-03-33

source_name: HTLV-1 infected PBMCs

tag: Small RNAs isolated from HTLV-1 infected PBMCs


title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M04_Georgia_04


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P07_Louisiana_06


title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M07_Georgia_04


title: 43T


title: ATL48T


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P08_Georgia_04


title: Pt3 Hseb-03-34


title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M02_Louisiana_06


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P07_Louisiana_06


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P04_Georgia_06


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P04_Georgia_04


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P08_Georgia_04


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P03_Georgia_06


title: Pt2 Hseb-03-29


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P03_Georgia_06


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P04_Georgia_04


title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M04_Georgia_06


title: Pt1 Hseb-03-30


title: PBMC Hseb-03-37

source_name: Normal human PBMC

extract_protocol: Small RNAs (< 200 nt) are extracted from the normal PBMCs using mirVana Small RNA isolation kit (Ambion) following the manufacturer's protocol.

tag: Small RNAs isolated from normal PBMCs


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P02_Georgia_06


title: PBMC Hseb-03-36


title: PBMC Hseb-03-35


title: WM_KIDNEY_76

status: Public on Jun 05 2008

city: Grand Rapids

first: Eric

last: Kort

state: MI

address: 333 Bostwick NE

institute: Van Andel Research Institute

description: Clear cell, chromophobe, papillary (types 1 and 2), oncocytoma, and Wilms tumor were compared to normal kidney tissue.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G

data_processing: The data were analyzed with custom CDF environments created by the MBNI - The version 6 entrez gene ID CDF was used.  Data were then rma normalized using R and the bioconductor suite of analysis tools (eset <- rma(ab))

label: SAPE

source_name: Renal Tumor

label_protocol: 10 ug of Qiagen-purified total RNA was labeled with 6ul of 1mg/ml R-Phycoerythrin Streptavidin (SAPE)

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer's protocol

tag: Age

value: Unknown

tag: Gender

value: F

tag: Stage

tag: Renal Tumor


title: BW25113 sdiA mutant LB with 1 mM indole 7-h 30C biofilm cell

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description:
RNA extracted from biofilm cells of E. coli K-12 sdiA mutant after 7 hours of growth in LB with glasswool at 30ºC with 1 mM
indole presence.

hyb_protocol: Prepared hybridization cocktail for Single Probe Array (169 Format) with total 80 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 0.6 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS)

scan_protocol: After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

label: biotin

organism: Escherichia coli

source_name: Channel 1

label_protocol: cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181)

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) and 1 mM indole for forming biofilm. After incubation for 7 h at 30°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).


title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M42_Georgia_06


title: WM_KIDNEY_78

value: M


title: WM_KIDNEY_73


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P04_Georgia_06


title: WM_KIDNEY_77


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P02_Georgia_06


title: BW25113 sdiA mutant LB with DMF 7-h 30C biofilm cell

description: RNA extracted from biofilm cells of E. coli K-12 sdiA mutant after 7 hours of growth in LB with glasswool at 30ºC with DMF presence.

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) and DMF for forming biofilm. After incubation for 7 h at 30°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).


title: WM_KIDNEY_75


title: WM_KIDNEY_74


title: WM_KIDNEY_79


title: WM_KIDNEY_70


title: WM_KIDNEY_72


title: WM_KIDNEY_69


title: WM_KIDNEY_68


title: WM_KIDNEY_67


title: WM_KIDNEY_64


title: WM_KIDNEY_63


title: WM_KIDNEY_65


title: WM_KIDNEY_66


title: WM_KIDNEY_62


title: WM_KIDNEY_71


title: WM_KIDNEY_53


title: WM_KIDNEY_56


title: WM_KIDNEY_61


title: P2_KIDNEY_13


title: WM_KIDNEY_55


title: WM_KIDNEY_54


title: WM_KIDNEY_60


title: P2_KIDNEY_12


title: WM_KIDNEY_58


title: WM_KIDNEY_59


title: P2_KIDNEY_11


title: WM_KIDNEY_57


title: P1_KIDNEY_9


title: P2_KIDNEY_2


title: P2_KIDNEY_3


title: P2_KIDNEY_4


title: P1_KIDNEY_18


title: P1_KIDNEY_19


title: P1_KIDNEY_8


title: P1_KIDNEY_6


title: Wilms_30_H7

description: Samples from Clear Cell RCC, Papillary RCC, Chromophobe RCC, Oncocytoma, and Wilms Tumor subtypes compared to pooled normal kidney samples.

hyb_protocol: Per LC Sciences protocol.

scan_protocol: Axon GenePix 4000B Microarray Scanner. Pixel size 10 µm.

data_processing: ArrayPro. Lowess Global Normalization.

source_name: Pooled normal kidney

label_protocol: Per LC Sciences protocol.

extract_protocol: Total RNA was extracted from samples with the mirVana miRNA isolation kit (Ambion) according to manufacturers protocol.  The samples were then processed by LC Sciences

tag: Normal tissue

source_name: Wilms

tag: Tumor Tissue


title: Wilms_27_H7


title: Wilms_28_H7


title: Wilms_29_H7


title: P1_KIDNEY_3


title: Chromophobe_25_H7

source_name: Chromophobe


title: Chromophobe_23_H7


title: P1_KIDNEY_4


title: P1_KIDNEY_5


title: P1_KIDNEY_1


title: P1_KIDNEY_2


title: Chromophobe_24_H7


title: P1_KIDNEY_11


title: Oncocytoma_20_H7

source_name: Oncocytoma


title: Oncocytoma_19_H7


title: Chromophobe_22_H7


title: ON_KIDNEY_7


title: hESC_KSR_SLG_1

city: New York

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: Illumina human ref-8V2.0

hyb_protocol: 750ng of labeled cRNA were hybridized on the Illumina Human Ref-8 V2.0 arrays according to Illumina's instructions.

scan_protocol: according to manufacturer

data_processing: The raw gene level Signal's where normalized using the standard quantile normalization from the bioconductor limma package. Then the data was transformed using the generalized logarithm function glog(x)=(asinh(x)-log(2))/log(2). Note: the (1/log(2)) term makes this glog asymptotically equivalent to log base 2.

source_name: NIH WA-09 (H9 hESCs)

label_protocol: 200ng ot total RNA were labeled using the Illumina Total Prep RNA Amplification Kit (Ambion, cat#AMIL1791) according the manufacturer's instructions

extract_protocol: total RNA was extracted from cell pellet using Trizol (invitrogen)

tag: status after 24hrs treatment

tag: KSR (serum-replacement medium 15%)

tag: Differentiation Assay

tag: SLG


title: hESC_KSR_DMSO_2

description: Illumina human ref-8V2.0


title: Oncocytoma_18_H7


title: Oncocytoma_17_H7


title: ON_KIDNEY_6


title: ON_KIDNEY_5


title: Papillary_14_H7

source_name: Papillary


title: Papillary_15_H7


title: hESC_CM_FGF2_4

description: Illumina human ref-8V2.0

tag: CM (conditioned hESC medium)

tag: Self-renewal Assay

tag: bFGF


title: hESC_KSR_SLG_2

description: Illumina human ref-8V2.0


title: ON_KIDNEY_4


title: Papillary_12_H7


title: hESC_KSR_control_3

description: Illumina human ref-8V2.0

tag: control


title: hESC_KSR_DMSO_1

description: Illumina human ref-8V2.0


title: ON_KIDNEY_2


title: ON_KIDNEY_3


title: hESC_CM_FGF2_3

description: Illumina human ref-8V2.0


title: Papillary_13_H7


title: Clear Cell_09_H7

source_name: Clear Cell


title: Clear Cell_10_H7


title: hESC_HES_FGF2_3

description: Illumina human ref-8V2.0

tag: HES (hESC medium)


title: NO_KIDNEY_12

source_name: Normal kidney

tag: Normal kidney


title: Clear Cell_07_H7


title: Wilms_08_H9


title: Clear Cell_08_H7


title: hESC_CM_control_3

description: Illumina human ref-8V2.0


title: Wilms_07_H9


title: hESC_KSR_SRM_2

description: Illumina human ref-8V2.0

tag: SRM


title: hESC_HES_control_3

description: Illumina human ref-8V2.0


title: hESC_KSR_RA_2

description: Illumina human ref-8V2.0

tag: RA


title: hESC_KSR_CYM_2

description: Illumina human ref-8V2.0

tag: CYM


title: hESC_HES_GTFX_2

description: Illumina human ref-8V2.0

tag: GTFX


title: hESC_HES_SNM_2

description: Illumina human ref-8V2.0

tag: SNM


title: Wilms_06_H9

tag: Normal tissue

tag: Age

tag: Gender

tag: Stage


title: Clear Cell_05_H7

tag: Tumor Tissue


title: Wilms_04_H9


title: Wilms_05_H9


title: Clear Cell_04_H7


title: CHR_KIDNEY_11

tag: Renal Tumor


title: hESC_HES_FBP_2

description: Illumina human ref-8V2.0

tag: status after 24hrs treatment

tag: FBP


title: hESC_HES_THEA_2

description: Illumina human ref-8V2.0

tag: Self-renewal Assay

tag: Thea


title: hESC_CM_FGF2_2

description: Illumina human ref-8V2.0

tag: CM (conditioned hESC medium)

tag: bFGF


title: Wilms_03_H9


title: Clear Cell_03_H7


title: ON_KIDNEY_8


title: CHR_KIDNEY_7


title: CHR_KIDNEY_9


title: Wilms_02_H9

tag: Unknown


title: hESC_CM_control_2

description: Illumina human ref-8V2.0

tag: control


title: hESC_KSR_control_2

description: Illumina human ref-8V2.0

tag: KSR (serum-replacement medium 15%)

tag: Differentiation Assay


title: Clear Cell_02_H7


title: Wilms_01_H9


title: hESC_HES_control_2

description: Illumina human ref-8V2.0

tag: HES (hESC medium)


title: hESC_HES_FGF2_2

description: Illumina human ref-8V2.0


title: CHR_KIDNEY_1


title: hESC_KSR_CYM_1

description: Illumina human ref-8V2.0

tag: CYM


title: CHR_KIDNEY_2


title: CC_KIDNEY_8


title: CC_KIDNEY_9


title: CC_KIDNEY_10


title: hESC_HES_GTFX_1

description: Illumina human ref-8V2.0

tag: GTFX


title: hESC_KSR_SRM_1

description: Illumina human ref-8V2.0

tag: SRM


title: CHR_KIDNEY_4

tag: Gender


title: CC_KIDNEY_7

tag: Stage


title: CC_KIDNEY_6

tag: Renal Tumor


title: hESC_HES_FBP_1

description: Illumina human ref-8V2.0

tag: status after 24hrs treatment


title: hESC_HES_SNM_1

description: Illumina human ref-8V2.0

tag: SNM


title: hESC_CM_FGF2_1

description: Illumina human ref-8V2.0

tag: Self-renewal Assay


title: hESC_KSR_control_1

description: Illumina human ref-8V2.0


title: hESC_CM_control_1

description: Illumina human ref-8V2.0


title: CC_KIDNEY_4


title: hESC_KSR_RA_1

description: Illumina human ref-8V2.0

tag: RA


title: CC_KIDNEY_2


title: CC_KIDNEY_1


title: hESC_HES_FGF2_1

description: Illumina human ref-8V2.0


title: CC_KIDNEY_3


title: CC_KIDNEY_5


title: hESC_HES_THEA_1

description: Illumina human ref-8V2.0

tag: Thea


title: array #1740115250_F, Tumor Liver RNA Patient 1

status: Public on Jun 04 2008

city: Calgary

first: Mark

last: Bieda

state: AB

address: 3330 Hospital Dr NW

department: Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

description: Note PMT1 settings

hyb_protocol: Illumina HumanRef-8 BeadChips were hybridized, washed, stained and scanned according to Illumina’s protocol using the updated wash procedure

scan_protocol: Processed arrays were read using Illumina BeadReader according to the manufacturer's instructions.

data_processing: Data were extracted with Illumina BeadStudio software using background subtraction and cubic spline normalization. Data were then adjusted by shifting the absolute minimum value for each array to be equal to 1; and then log2 transformed.

source_name: Tumor Liver

label_protocol: Targets were prepared from 200 ng total RNA using Illumina TotalPrep RNA Amplification Kit (Ambion, catalog #AMIL1791)

extract_protocol: RNA samples were prepared using Qiagen RNeasy Micro Kit (Qiagen) and then assayed using the Agilent Systems Bioanalyzer 2100 to ensure that high-quality RNA was used for the array experiments.

tag: Tumor Liver from Patient 1 of Acevedo et al., 2008 (PMID


title: array #1740115250_A, Purified Normal Hepatocytes, patient 5

description: Note PMT1 settings

source_name: Normal Liver

tag: Normal Liver from Patient 1 of Acevedo et al., 2008 (PMID


title: array #1740115250_G, Normal Liver RNA patient 3

description: Note PMT1 settings

tag: Normal Liver from Patient 3 of Acevedo et al., 2008 (PMID


title: hESC_HES_control_1

description: Illumina human ref-8V2.0

tag: control


title: 282_LU_1

city: Amsterdam

first: Oscar

middle: Leonard

last: Volger

state: Noor Holland

address: Meibergdreef 15

department: Cardiology

country: Netherlands

institute: Academic Medical Center

description: See the methods section of the linked publication for additional information.

hyb_protocol: Each cRNA sample (1 micrograms; Cy5-labeled) was hybridized in duplicate against a common reference cRNA sample (1 micrograms; Cy3-labeled), for 16 hours at 40 degrees Celsius.

scan_protocol: Agilent scanner: resolution: 10 micrometer, scan area: 60 x 21.6 mm, PMT: 50%, Laser power: 50%

data_processing: After print-tip Loess-normalization (Loess span: 0.3; limma package, Bioconductor, available online: http://www.bioconductor.org), and background subtraction, the microarray intensity data imported in the Rosetta Resolver database.

molecule: polyA RNA

source_name: common reference

label_protocol: Within these cRNAs the molar ratio of incorporated aminoallyl-rUTP (A5660, Sigma, St. Louis, MO) to rUTP was 1:1. Cy3 mono-reactive dyes (PA23001, Amersham Biosciences, Piscataway, NJ) were coupled according to the manufacturer’s instructions. Labeled cRNA was purified using the RNeasy purification kit (Qiagen GmbH, Hilden, Germany).

extract_protocol: Total RNA of each one of the three reference components was isolated by Trizol, and treated with DNAse-I. Thereafter, mRNA of each component was linearly amplified for one round (MessageAmp aRNA kit, #1750, Ambion), synthesizing antisense cRNAs.

tag: The common reference cRNA sample comprised equal quantities of the following three components

value: (1) human umbilical cord endothelial cells (HUVEC), stimulated with TNF-alpha (50 microgram/ml, 6 hrs); (2) THP-1 cell line stimulated for 24 hours with phorbyl myristate (PMA, 100 microgram/ml), and subsequently for 6 hours with lipopolysaccharide (LPS, 1 microgram/ml), and (3) a mix of whole mount human aorta and iliac artery.

label_protocol: Within these cRNAs the molar ratio of incorporated aminoallyl-rUTP (A5660, Sigma, St. Louis, MO) to rUTP was 1:1. Cy5 mono-reactive dyes (PA25001, Amersham Biosciences, Piscataway, NJ) were coupled according to the manufacturer’s instructions. Labeled cRNA was purified using the RNeasy purification kit (Qiagen GmbH, Hilden, Germany).

extract_protocol: Macrophages were isolated from Broncheo Alveolar Lavage (BAL) fluid. After isolation of total RNA molecules, the samples were linearly amplified(MessageAmp aRNA kit, #1750, Ambion), synthesizing antisense cRNAs.

tag: Lung macrophages


title: 275_LU_2

extract_protocol: mRNA molecules from liver macrophages were linearly amplified (MessageAmp aRNA kit, #1750, Ambion), synthesizing antisense cRNAs.

tag: Macrophages were isolated from Broncheo Alveolar Lavage (BAL) fluid. After isolation of total RNA molecules, the samples were linearly amplified (MessageAmp aRNA kit, #1750, Ambion), synthesizing antisense cRNAs.


title: 282_LI_2

tag: Liver macrophages


title: 275_SP_2

extract_protocol: mRNA molecules from splenic macrophages were linearly amplified (MessageAmp aRNA kit, #1750, Ambion), synthesizing antisense cRNAs.

tag: Splenic macrophages


title: 282_LU_2


title: 275_SP_1


title: 275_LU_1


title: array #1740115250_H, Tumor Liver RNA patient 3

description: Note PMT1 settings

tag: Tumor Liver from Patient 3 of Acevedo et al., 2008 (PMID


title: 275_LI_1


title: 275_LI_2


title: 282_CA_1

tag: Macrophages were isolated from human carotid artery plaque by Laser Capture Microdissection (Arcturus LCM system). After isolation of total RNA molecules, the samples were linearly amplified (MessageAmp aRNA kit, #1750, Ambion), synthesizing antisense cRNAs.


title: array #1740115250_E, Normal Liver RNA Patient 1

description: Note PMT1 settings


title: 275_CA_1

extract_protocol: Macrophages were isolated from human carotid artery plaque by Laser Capture Microdissection (Arcturus LCM system). After isolation of total RNA molecules, the samples were linearly amplified (MessageAmp aRNA kit, #1750, Ambion), synthesizing antisense cRNAs.


title: 282_LI_1

tag: mRNA molecules from liver macrophages were linearly amplified (MessageAmp aRNA kit, #1750, Ambion), synthesizing antisense cRNAs.


title: 275_CA_2


title: 282_CA_2


title: Cervical cancer_T-56-04

type: genomic

first: Murty

last: Vundavalli

address: 1130 St Nicholas Ave

department: Pathology

institute: Columbia University Medical Center

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: GCOS

molecule: genomic DNA

source_name: Cervical cancer, squamous cell carcinoma

label_protocol: Affymetrix

extract_protocol: Phenol-chloroform

tag: Cervical Cancer, squamous cell carcinoma, Stage IB2, microdissected, age 45, HPV negative


title: Cervical cancer_T-98-04

tag: Cervical Cancer, squamous cell carcinoma, Stage IB1, microdissected, age 38, HPV 18, HPV 45


title: Cervical cancer_T-20-04

source_name: Cervical cancer, adenocarcinoma

tag: Cervical Cancer, Adenocarcinoma, Stage IB2, microdissected, age 46, HPV 16


title: Normal Liver, Patient 1, 3meK9 1 Array, array 1531602

description: Normal Liver. Note Promoter 1 of 2 5 kb promoter array; complement is 1557302

hyb_protocol: The hybridization of DNA samples for ChIP-ChIP analysis was performed by NimbleGen Systems, Inc. Briefly, 13ug of the Cy5-labeled ChIP sample and 13ug of the Cy3-labeled total sample were mixed, dried down, and resuspended in 40 ul of NimbleGen Hybridization Buffer (NimbleGen Systems) plus 1.5 ug of human COT1 DNA. After denaturation, hybridization was carried out in a MAUI Hybridization System (BioMicro Systems) for 18 h at 42°C. The arrays were washed using NimbleGen Wash Buffer System (NimbleGen Systems), dried by centrifugation.

scan_protocol: The arrays were scanned at 5-um resolution using the GenePix 4000B scanner (Axon Instruments).

data_processing: raw, log base 2 ratios

label_protocol: The labeling of DNA samples for ChIP-ChIP analysis was performed by NimbleGen Systems, Inc. Briefly, each DNA sample (1 ug) was denatured in the presence of 5'-Cy3- or Cy5-labeled random nonamers (TriLink Biotechnologies) and incubated with 100 units (exo-) Klenow fragment (NEB) and dNTP mix [6 mM each in TE buffer (10 mM Tris/1 mM EDTA, pH 7.4; Invitrogen)] for 2 h at 37°C. Reactions were terminated by addition of 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water.

extract_protocol: Performed following the 'Chromatin Immunoprecipitation Assay (ChIPs)' protocol provided at http://genomics.ucdavis.edu/farnham

label_protocol: see labeling protocol for channel 1

extract_protocol: see extract protocol for channel 1

tag: control total input


title: Tumor Liver, Patient 1, POLII 1 Array, array 88346

description: Tumor Liver. Note Promoter 1 of 2 5 kb promoter array; complement is 89050


title: Normal Liver, Patient 1, H3me3K27 1 Array, array 88349

description: Normal Liver. Note Promoter 1 of 2 5 kb promoter array; complement is 95587


title: Normal Liver, Patient 1, H3me3K27 1 Array, array 81601

description: Normal Liver. Note Promoter 1 of 2 5 kb promoter array; complement is 85219


title: Cervical cancer_T-1907

tag: Cervical Cancer, squamous cell carcinoma, Stage IV, microdissected, age 33, HPV 16


title: Cervical cancer_T-1900

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 57, HPV 18


title: Array 88345 Promoter 1/Patient2/POLII ab

description: ChIP-chip experiment; POLII in normal liver; array 1 of 2 for 5 kb promoter array

source_name: Normal Liver, Patient 2, POLII

tag: normal liver

source_name: normal background DNA, Patient 2

tag: normal liver DNA from patient; control background channel


title: Normal Liver, Patient 1, POLII 1 Array, array 87639

description: Normal Liver. Note Promoter 1 of 2 5 kb promoter array; complement is 85233


title: Normal Liver, Patient 4, H3me3K27 1 Array, array 1860402

description: Normal Liver. Note Promoter 1 of 2 5 kb promoter array; complement is 1860702


title: Normal Liver, Patient 2, 3meK9 1 Array, array 1528902

description: Normal Liver. Note Promoter 1 of 2 5 kb promoter array; complement is 1558102


title: Normal Liver, Patient 2, me3K27 Promoter 1 Array, array 88819

description: Normal Liver. Note array 1 of 2 5 kb promoter array; complement is 81470


title: Normal Liver, Patient 1, POLII 1 Array, array 89040

description: Normal Liver. Note Promoter 1 of 2 5 kb promoter array; complement is 95568


title: Cervical cancer_T-1898

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 64, HPV 18


title: Tumor Liver, Patient 2, 3meK9 1 Array, array 1528802

description: Tumor Liver. Note Promoter 1 of 2 5 kb promoter array; complement is 1558302


title: Cervical cancer_T-2035

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 59, HPV 18


title: Tumor Liver, Patient 2, me3K27 Promoter 1 Array, array 88452

description: Tumor Liver. Note array 1 of 2 5 kb promoter array; complement is 87651


title: Tumor Liver, Patient 1, H3me3K27 1 Array, array 88833

description: Tumor Liver. Note Promoter 1 of 2 5 kb promoter array; complement is 96083


title: Tumor Liver, Patient 1, POLII 1 Array, array 85230

description: Tumor Liver. Note Promoter 1 of 2 5 kb promoter array; complement is 87658


title: Cervical cancer_T-1981

tag: Cervical Cancer, squamous cell carcinoma, Stage IB, microdissected, age 63, HPV 16, HPV 18


title: Promoter 1/Patient2/POLII Tumor liver

description: ChIP-chip experiment; POLII in tumor liver; array 1 of 2 for 5 kb promoter array

source_name: POLII ChIP tumor liver

tag: liver cancer; tumor liver sample

source_name: tumor liver background DNA

tag: liver cancer tumor liver DNA


title: Tumor Liver, Patient 1, 3meK9 1 Array, array 1531402

description: Tumor Liver. Note Promoter 1 of 2 5 kb promoter array; complement is 1558902


title: Normal Liver, Patient 4, H3me3K9 1 Array, array 1860902

description: Normal Liver. Note Promoter 1 of 2 5 kb promoter array; complement is 1861102


title: Normal Liver, Patient 4, POLII 1 Array, array 1859302

description: Normal Liver. Note Promoter 1 of 2 5 kb promoter array; complement is 1859702


title: Dll1 C3H_brain_rep6

status: Public on Jan 01 2009

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.0: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

organism: Mus musculus

source_name: Dll1 C3H brain

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: Dll1 C3H, male, brain, +/-, age

value: 15 weeks, Mouse ID 30051705

source_name: C3H brain

tag: C3H, male, brain, age


title: Tumor Liver, Patient 1, H3me3K27 1 Array, array 85222

description: Tumor Liver. Note Promoter 1 of 2 5 kb promoter array; complement is 81475


title: Cervical cancer_T-1875-2

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 36, HPV 16


title: Cervical cancer_T-966

tag: Cervical Cancer, squamous cell carcinoma, Stage IB, microdissected, age 71, HPV 16


title: Cervical cancer_T-954

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 64, HPV 33


title: Cervical cancer_T-224

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 38, HPV 6, HPV 39


title: Cervical cancer_T-940

source_name: cervical cancer, squamous cell carcinoma

tag: Cervical Cancer, squamous cell carcinoma, Stage IA1, microdissected, age 66, HPV 16


title: Cervical cancer_T-984

tag: Cervical Cancer, squamous cell carcinoma, Stage IB, microdissected, age 65, HPV 45


title: Cervical cancer_T-1721

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 70, HPV negative


title: Cervical cancer_T-892

source_name: Cervical cancer, sqaumous cell carcinoma

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 34, HPV 16


title: Cervical cancer_T-1798

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 33, HPV 16


title: Cervical cancer_T-222

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 32, HPV 16


title: Cervical cancer_T-1798-2

source_name: Cervical cancer, Squamous cell carcinoma


title: Cervical cancer_T-1068

tag: Cervical Cancer, squamous cell carcinoma, Stage IB, microdissected, age 41, HPV 16


title: Cervical cancer_T-1509

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 69, HPV 16


title: Cervical cancer_T-222-2


title: Cervical cancer_T-968

source_name: Cervical cancer, Adenocarcinoma

tag: Cervical Cancer, adenocarcinoma, Stage IIB, microdissected, age 57, HPV 16, HPV 18


title: Cervical cancer_T-841

tag: Cervical Cancer, squamous cell carcinoma, Stage IIA, microdissected, age 58, HPV 16


title: Cervical cancer_T-218-2

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 40, HPV 16


title: Cervical cancer_T-654

tag: Cervical Cancer, squamous cell carcinoma, Stage IA, microdissected, age 40, HPV 45


title: Cervical cancer_T-1051

tag: Cervical Cancer, squamous cell carcinoma, Stage IB, microdissected, age 42, HPV 16


title: Cervical cancer_T-939

tag: Cervical Cancer, adenocarcinoma, Stage IIIB, microdissected, age 39, HPV 18


title: Cervical cancer_T-869

tag: Cervical Cancer, Adenocarcinoma, Stage IB, microdissected, age 52, HPV 16


title: Cervical cancer_T-218


title: Cervical cancer_T-214

source_name: Cervial cancer, squamous cell carcinoma

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 43, HPV 16


title: Cervial cancer_T-214-2

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 43, HPV 16


title: Cervical cancer_T-194

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 66, HPV 16


title: Cervical cancer_T-190

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 28, HPV 18


title: Cervical cancer_T-188

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 77, HPV 58


title: Cervical cancer_T-205

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 45, HPV 16


title: Cervical cancer_T-194-2


title: Cervical cancer_T-207

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 54, HPV 16


title: Cervical cancer_T-169

label: Biotin

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 34, HPV 45


title: MGAS5005 vs ∆ccpA #3 Cy3/Cy5

city: College Park

first: Kevin

middle: S

last: McIver

address: 3124 Biociences Research Bldg. (413)

department: Cell Biology and Molecular Genetics

institute: University of Maryland, College Park

description: Details located in Kinkel et al, 2008

hyb_protocol: 50C overnight

scan_protocol: genepix 6.1

data_processing: ratio-based Pearson Centered normalization using Acuity 4.0

organism: Streptococcus pyogenes

label_protocol: Amersham CyScribe Post labeling kit

growth_protocol: 37C in closed cap tubes to mid log phase (Klett 65)

extract_protocol: Triton-X 100

tag: M1 MGAS5005 isogenic ∆ccpA strain

label_protocol: Amersham CyScribe post labeling kit

growth_protocol: 37C in closed cap tubes to mid-log phase (Klett 65)

tag: M1 MGAS5005 wild-type


title: MGAS5005 vs ∆ccpA #3 Cy5/Cy3

description: Details located in Kinkel et al, 2008

tag: M1 MGAS5005 ∆ccpA isogenic mutant


title: Cervical cancer_T-167

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 39, HPV 16


title: Cervical cancer_T-137

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 42, HPV 16


title: MGAS5005 vs ∆ccpA #2 Cy5/Cy3

description: Details located in Kinkel et al, 2008

source_name: M1 MGAS5005

tag: MGAS5005 Isogenic ∆ccpA mutant


title: Cervical cancer_T-161

tag: Cervical Cancer, squamous cell carcinoma, Stage IB1, microdissected, age 39, HPV 16


title: Cervical cancer_T-140-2

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 41, HPV 16


title: MGAS5005 vs ∆ccpA #2 Cy3/Cy5

description: Details located in Kinkel et al, 2008

tag: M1 MGAS5005 Isogenic ∆ccpA mutant

tag: M1 MGAS5005 Wild-type


title: Cervical cancer_T-163-2

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 62, HPV 16


title: Cervical cancer_T-148

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 60, HPV negative


title: MGAS5005 vs ∆ccpA #1 Cy5/Cy3

description: details located in Kinkel et al, Infection and Immunity 2008

extract_protocol: TritonX-100 isolation protocol

tag: serotype M1 strain MGAS5005 wild-type

tag: serotype M1 strain MGAS5005 ∆ccpA


title: Cervical cancer_T-135

tag: Cervical Cancer, squamous cell carcinoma, Stage IB1, microdissected, age 48, HPV 26, HPV35


title: Cervical cancer_T-138

source_name: Cervical cancer, squamouscell carcinoma


title: Cervical cancer_T-141

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 37, HPV 16


title: Cervical cancer_T-166

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 37, HPV 59


title: Cervical cancer_T-160

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 39, HPV type 39


title: Cervical cancer_T-146

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 51, HPV 18


title: MGAS5005 vs ∆ccpA #1 Cy3/Cy5

description: Details located in Kinkel et al, 2008

tag: M1 MGAS5005 ∆ccpA isogenic mutant

tag: M1 MGAS5005 wild-type


title: Cervical cancer_T-134

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 58, HPV 39, HPV 68


title: Cervical cancer_T-133

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 38, HPV 16


title: Cervical cancer_T-140

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB , microdissected, age 41, HPV 16


title: Cervical canceer_T-132

tag: Cervical Cancer, squamous cell carcinoma, Stage IB1, microdissected, age 39, HPV 18


title: Cervical cancer_T-128

source_name: Cervical cancer, squmous cell carcinoma

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 55, HPV 16


title: Cervical cancer_T-127

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 65, HPV 16


title: Cervical cancer_T-124

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 62, HPV 18


title: Cervical cancer_T-117

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 48, HPV 16


title: Cervical cancer_T-126

source_name: Cervial cancer, squmous cell carcinoma

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 28, HPV 45


title: Cervical cancer_T-130

source_name: Cervical cancer, squamous cell carcinoma

tag: Cervical Cancer, squamous cell carcinoma, Stage IIA, microdissected, age 40, HPV 16


title: Cervical cancer_T-116

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 50, HPV 16, HPV 35


title: Cervical cancer_T-107

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 48, HPV 16, HPV 68


title: Cervical cancer_T-98

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 39, HPV type 45


title: Cervical cancer_T-114

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 57, HPV type 16


title: Cervical cancer_T-118

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 42, HPV 52


title: Cervical cancer_T-106

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 50, HPV type 16


title: Cervical cancer_T-103

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 31, HPV type 16


title: Cervical cancer_T-80

source_name: Cervical cancer, sqamous cell carcinoma

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB , microdissected, age 36, HPV type 16


title: Cervical cancer_T-92

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 28, HPV type 67


title: Cervical cancer_T-87

tag: Cervical Cancer, squamous cell carcinoma, Stage IB2, microdissected, age 27, HPV type 45


title: Cervical cancer_T-78

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 51, HPV type 16 and 31


title: Cervical cancer_T-108

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 30, HPV type 16


title: Cervical cancer_T-79

source_name: Cervical cancer, squamous cell cancer

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 46, HPV type 16


title: Cervical cancer_T-86

tag: Cervical Cancer, squamous cell carcinoma, Stage IIB, microdissected, age 73, HPV type 56


title: Cervical cancer_T-75

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 40, HPV type 16


title: Cervical cancer_T-66

tag: Cervical Cancer, squamous cell carcinoma, Stage IB2, microdissected, age 39, HPV type 66


title: Cervical cancer_T-55

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB , microdissected, age 33, HPV type 16


title: Cervical cancer_T-57

tag: Cervical Cancer, Adenocarcinoma, Stage IB, microdissected, age 35, HPV type 16


title: Normal Liver RNA (not cancer-related), Patient 4_replicate

description: Note PMT1 settings

hyb_protocol: Illumina Human 6 BeadChips were hybridized, washed, stained and scanned according to Illumina’s protocol using the updated wash procedure

source_name: Normal Liver (not cancer-related)

tag: Normal Liver (not cancer-related) from Patient 4 of Acevedo et al., 2008 (PMID


title: Normal Liver RNA (not cancer-related), Patient 4

description: Note PMT1 settings


title: Cervical cancer_T-52-2

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 32, HPV type 16


title: Cervical cancer_T-24-3

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 36, HPV type 16


title: Cervical cancer_T-24


title: Cervical cancer_T-21-3

tag: Cervical Cancer, squamous cell carcinoma, Stage IIIB, microdissected, age 34, HPV type 16


title: Cervical cancer_T-21

source_name: Cervical cancer, microdissected squamous cell carcinoma


title: SW756_cervical cancer cell line

source_name: Cervical cancer cell line, ATCC

growth_protocol: ATCC

tag: Cell line


title: SiHa_cervical cancer cell line


title: MS751_cervical cancer cell line


title: 99089_TN_K27_Rep2

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

description: H3K27me3 ChIP terminal pyramidal neurons, Replicate 2

hyb_protocol: Hybridization was performed by NimbleGen Inc. according to standard procedures.

scan_protocol: Scanning was performed by NimbleGen Inc. according to standard procedures.

data_processing: log2 (ChIP/Input) ratios, not normalized

source_name: Total input from terminal pyramidal neurons

label_protocol: Labeling was performed by NimbleGen Inc. according to standard procedures.

extract_protocol: Genomic DNA prepared from sonicated input chromatin and amplified by ligation-mediated PCR

tag: Terminal pyramidal neurons derived from mouse embryonic stem cells, Gender

value: male

source_name: H3K27me3 ChIP from terminal pyramidal neurons

extract_protocol: Genomic DNA associated with H3K27me3 modified histones prepared by ChIP using Upstate 07-449 antibody and amplified by ligation-mediated PCR


title: ME-180_cervical cancer cell line

tag: Cell lien


title: 99151_TN_K27_Rep1

description: H3K27me3 ChIP terminal pyramidal neurons, Replicate 1


title: 109810_NP_K27_Rep1

description: H3K27me3 ChIP neuronal progenitor cells, Replicate 1

source_name: Total input from neuronal progenitor cells

tag: Neuronal progenitor cells derived from mouse embryonic stem cells, Gender

source_name: H3K27me3 ChIP from neuronal progenitor cells


title: 112119_ES_K27_Rep4

description: H3K27me3 ChIP ES cells, Replicate 4

source_name: Total input from embryonic stem cells

tag: Mouse embryonic stem cells isolated form mixed 129-C57Bl/6 background, Gender

source_name: H3K27me3 ChIP from mouse embryonic stem cells


title: 109809_NP_K27_Rep2

description: H3K27me3 ChIP neuronal progenitor cells, Replicate 2


title: HT-3_cervical cancer cell line


title: Normal Liver, Patient 1, POLII 2 Array, array 95568

description: Normal Liver. Note Promoter 2 of 2 5 kb promoter array; complement is 89040

source_name: Normal Liver

tag: control total input


title: 89472_ES_K27_Rep3

description: H3K27me3 ChIP ES cells, Replicate 3


title: 103469_TN_K4_Rep2

description: H3K4me2 ChIP terminal pyramidal neurons, Replicate 2

source_name: H3K4me2 ChIP from terminal pyramidal neurons

extract_protocol: Genomic DNA associated with H3K4me2 modified histones prepared by ChIP using Upstate 07-030 antibody and amplified by ligation-mediated PCR


title: 114106_ES_K27_Rep2

description: H3K27me3 ChIP ES cells, Replicate 2


title: 96363_ES_K27_Rep1

description: H3K27me3 ChIP ES cells, Replicate 1


title: Normal Liver, Patient 1, POLII 2 Array, array 85233

description: Normal Liver. Note Promoter 2 of 2 5 kb promoter array; complement is 87639


title: HeLa_cervical cancer cell line


title: 102381_TN_K4_Rep1

description: H3K4me2 ChIP terminal pyramidal neurons, Replicate 1


title: Tumor Liver, Patient 1, 3meK9 2 Array, array 1558902

description: Tumor Liver. Note Promoter 2 of 2 5 kb promoter array; complement is 1531402

source_name: Tumor Liver


title: 2749502_NP_K4_Rep2

description: H3K4me2 ChIP neuronal progenitor cells, Replicate 2

source_name: H3K4me2 ChIP from neuronal progenitor cells


title: 99149_ES_K4_Rep1

description: H3K4me2 ChIP ES cells, Replicate 1

source_name: H3K4me2 ChIP from mouse embryonic stem cells


title: C-4I_cervical cancer_cell line

source_name: Cervical cancer cellline, ATCC

tag: Cervical cancer cell line


title: 2748202_NP_K4_Rep1

description: H3K4me2 ChIP neuronal progenitor cells, Replicate 1


title: C-33A_Cervical Cancer_Cell Line

tag: cervical cancer cell line


title: CaSki_cervical cancer cell line


title: 99146_ES_K4_Rep2

description: H3K4me2 ChIP ES cells, Replicate 2


title: Tumor Liver, Patient 2, 3meK9 2 Array, array 1558302

description: Tumor Liver. Note Promoter 2 of 2 5 kb promoter array; complement is 1528802


title: 03-5611_normal cervix

source_name: Normal cervix, squamous epithelium

tag: Normal cervix, squamous epithelium, microdissected, age 44


title: 97882_TN_Pol2_Rep2

description: Pol2 ChIP terminal pyramidal neurons, Replicate 2

source_name: RNA Pol2 ChIP from terminal pyramidal neurons

extract_protocol: Genomic DNA bound to RNA polymerase 2 prepared by ChIP using Santa Cruz Biotechnology SC899 antibody and amplified by ligation-mediated PCR


title: 103782_TN_Pol2_Rep1

description: Pol2 ChIP terminal pyramidal neurons, Replicate 1


title: Tumor Liver, Patient 1, H3me3K27 2 Array, array 81475

description: Tumor Liver. Note Promoter 2 of 2 5 kb promoter array; complement is 85222


title: Tumor Liver, Patient 1, POLII 2 Array, array 87658

description: Tumor Liver. Note Promoter 2 of 2 5 kb promoter array; complement is 85230


title: 03-5438_normal cervix

tag: Normal cervix, squamous epithelium, microdissected, age 54


title: 03-4986_normal cervix

tag: Normal cervix, squamous epithelium, microdissected, age 42


title: 03-4508 normal cervix

tag: Normal cervix, squamous epithelium, microdissected, age 48


title: 3007002_NP_Pol2_Rep1

description: Pol2 ChIP neuronal progenitor cells, Replicate 1

source_name: RNA Pol2 ChIP from neuronal progenitor cells


title: 5113202_NP_Pol2_Rep2

description: Pol2 ChIP neuronal progenitor cells, Replicate 2


title: 05-446 normal cervix

tag: Normal cervix, squamous epithelium, microdissected, age 50


title: 96170_ES_Pol2_Rep2

description: Pol2 ChIP ES cells, Replicate 2

source_name: RNA Pol2 ChIP from mouse embryonic stem cells


title: Normal Liver, Patient 2, 3meK9 2 Array, array 1558102

description: Normal Liver. Note Promoter 2 of 2 5 kb promoter array; complement is 1528902


title: Normal Liver, Patient 1, H3me3K27 2 Array, array 95587

description: Normal Liver. Note Promoter 2 of 2 5 kb promoter array; complement is 88349


title: 82627_ES_Pol2_Rep1

description: Pol2 ChIP ES cells, Replicate 1


title: Tumor Liver, Patient 1, POLII 2 Array, array 89050

description: Tumor Liver. Note Promoter 2 of 2 5 kb promoter array; complement is 88346


title: GP05-15 Normal cervix

source_name: Normal cervical epithelium

tag: Female, Age 64, normal cervical epithelium, microdissected


title: 63481_TN_5mC_Rep2

description: MeDIP terminal pyramidal neurons, Replicate 2

data_processing: log2 (MeDIP/Input) ratios, not normalized

source_name: Total input sonicated genomic DNA from terminal pyramidal neurons

extract_protocol: Genomic DNA was prepared form 10e7 cells by incubating 8h at 55°C in lysis buffer (10mM Tris-HCl pH 7.5, 2mM EDTA, 10mM NaCl, 0.5% SDS) supplemented with 0.5mg/ml Proteinase K followed by phenol/chloroform extraction and ethanol precipitation. Genomic DNA was treated with RNase A to completely remove RNA contamination and sonicated to an average size of 500bp.

source_name: Methylated DNA from terminal pyramidal neurons enriched by MeDIP

extract_protocol: MeDIP was performed as previously described (Weber et al, 2007) using 3ug sonicated genomic DNA as starting material and 10ug antibody against 5-methylcytidine (Eurogentec, BI-MECY-1000).


title: RH RRE2 WT B VS QW434 B 6D 3

status: Public on Jun 25 2008

city: Austin

first: Rasika

last: Harshey

state: TX

department: Section of Molecular Genetics and Microbiology

institute: Institute of Cellular and Molecular Biology

description: No

hyb_protocol: 42 degree overnight

scan_protocol: Genepix 4000B

data_processing: Genepix Pro 4.0, normalized so that the mean of the ratio of medians of all the features was equal to one

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Wildtype 14028

label_protocol: reverse transcription

extract_protocol: Biorad Auapure RNA Isolation Kit

tag: from LB at log phase

extract_protocol: BioRad Aquapure RNA isolation kit


title: 05-31 normal cervix

source_name: Normal cervix, micridissected epithelium


title: Normal Liver, Patient 1, 3meK9 2 Array, array 1557302

description: Normal Liver. Note Promoter 2 of 2 5 kb promoter array; complement is 1531602


title: Monocyte ATV rep 2

status: Public on Jun 03 2008

city: Barcelona

first: Marta

last: Alegret

address: Diagonal 643

country: Spain

institute: University of Barcelona

description: No additional information

hyb_protocol: Affymetrix standard protocol

scan_protocol: GeneChip arrays were washed and scanned using a GeneArray Scanner, and scanned images were quantified according to Affymetrix standard procedures

data_processing:
Raw expression values were preprocessed using the RMA method , a three-step process which integrates background correction, normalization and summarization of probe values. These normalized values were the basis for all the analysis.
Previous to any analysis data were submitted to non-specific filtering to remove low signal genes and low variability genes (those genes whose standard deviation between all samples did not exceed a minimum threshold).

source_name: Monocyte human familial combined hyperlipidemia after treatment with atorvastatin (ATV) sample

label_protocol: Affymetrix standard protocol

growth_protocol: No growth protool, extraction just after separation

extract_protocol: Total RNA was isolated from monocytes using Trizol (Invitrogen Corp), was further purified by using RNeasy kit (Qiagen Inc, Valencia, USA), and was quantified by spectrometry at 260 nm; purity was assessed by the ratio of absorbances at 260-280 nm. RNA integrity was assessed after agarose gel electrophoresis.

treatment_protocol: Centrifugation of whole blood. Separation of mononuclear cells. Separation of moncoytes by plastic attachment .

tag: Human male subjects with familial combined hyperlipidemia  after treatment with atorvastatin (ATV), peripheral blood monocytes


title: 82897_TN_5mC_Rep3

description: MeDIP terminal pyramidal neurons, Replicate 3


title: Monocyte ATV rep 3

description: No additional information


title: Monocyte FCH rep 3

description: No additional information

source_name: Monocyte human familial combined hyperlipidemia (FCH) sample

tag: Human male subjects with familial combined hyperlipidemia (FCH), peripheral blood monocytes


title: Tumor Liver, Patient 1, H3me3K27 2 Array, array 96083

description: Tumor Liver. Note Promoter 2 of 2 5 kb promoter array; complement is 88833


title: Normal Liver, Patient 4, H3me3K27 2 Array, array 1860702

description: Normal Liver. Note Promoter 2 of 2 5 kb promoter array; complement is 1860402

source_name: Normal Liver


title: Monocyte FCH rep 1

description: No additional information


title: Monocyte control rep 1

description: No additional information

source_name: Monocyte human control sample

tag: Human healthy male subjects, peripheral blood monocytes


title: Monocyte control rep 2

description: No additional information


title: Th-/- hypoxic pool 3: E12.5 fetal ICR mouse RNA

city: Durham

first: Alisa

last: Ray

state: NC

address: DUMC Box 3209

department: Neurobiology

institute: Duke University

description: Th+/- dams were mated and E12.5 fetuses were dissected free of yolk sacs and frozen.  Pools of three fetus from different litters were pooled for each sample.

hyb_protocol: Fluorescent array images were obtained with an Axon slide scanner 4000B and GenePix Pro 3 software (Axon Instruments Inc.) at a resolution of 10microns.

data_processing: Data was analysed with GeneSpring 7 data software package (Silicon Genetics). Each data set was transformed into log base 2 expression ratios and normalised using lowness intensity-dependent normalisation.

label_protocol: Please refer to the web site, http://microarray.genome.duke.edu/services/spotted-arrays/protocols for a detailed protocol, used direct labeling procedure

extract_protocol: Total RNA isolated with RNA STAT-60 (Tel-Test, Inc, Friendswood, TX) extraction according to manufacturer's instructions  followed by RNAeasy Mini Kit extraction (Qiagen, Valencia, CA

tag: Th null E12.5 fetus

tag: hypoxic heterzygous dam exposed to  8% oxygen for 6 hr prior to E12.5 of gestation

source_name: Stratagene Universal Mouse Reference RNA

tag: RNA obtain from Stratagene

tag: Pooled RNA from 11 mouse cell lines


title: Monocyte FCH rep 2

description: No additional information


title: T3_MUTANT_15_YA0403#03_263

status: Public on Jun 20 2008

city: Birmingham

first: Nicklas

last: Bonander

address: Aston University

department: LHS -Life and Health Science

country: United Kingdom

institute: Aston university

hyb_protocol: Wistar Institute Hybridization protocol

scan_protocol: Wistar Institute scan protocol

data_processing: Wistar Institute nMD: normalized Median Density method

organism: Saccharomyces cerevisiae

source_name: Mutant V5.TM6*P strain media glucose concentration 26.3 g/L

label_protocol: Wistar Institute label protocol

extract_protocol: Wistar Institute extract protocol

treatment_protocol: Transformants were selected by growth on glucose. The resulting ura3 strain is referred to as V5.TM6*. The auxotrophic V5 wild type and V5.TM6* used in this study were made prototrophic by integration of URA3 [3] and are referred to as the V5 wild-type strain and V5.TM6*P, respectively. The growth media in the bioreactor was 5 × defined minimal medium [4], stirring was 1000rpm; Temp  30C; Aeriation 0.5 vvm; pH 5.

tag: Compare a wild type Saccaromyces cerevisise strain V5 strain (=V), with a mutant strain where glucose transport has been reduced by at least 30% in the strain V5.TM6*P (=T), mutant is lacking 7 hexose transporters HXT1, HXT2, HXT3, HXT4, HXT5, HXT6, HXT7, the plasma membrane contains a HXT1-HXT7 fusion protein. This construct is a combination of a low and high affinity glucose transporters. The glucose concentration in the culture media of each array is the parameter that can be how the arrays are sorted.

tag: Yeast cells grown in bioreactors monitoring, pH (=5) temp (=30ºC) and pO2>50% as well as O2 and CO2 in outlet gas. Growth media is YNB-CSM starting at 5% glucose. No detectable or small levels of glycerol (0g/g-starting glucose concentration) and ethanol (<2.5g/g-starting glucose concentration) after glucose depletion in the V5.TM6*P supporting the claim that V5.TM6*P grows fully respiratory on glucose. Result 1

value: V5 to V5.TM6*P RNA transition induce genes typical for respiratory growth. Result 2:There is a glucose dependence in the array signal of 20 genes (e.g HXT1, RGS2, ADH7, CHA4 and GLK1) in wild type V5 strain is not seen in the V5.TM6*P strain, this is an evidence for that glucose sensing occurs inside the yeast cell. That is, an intact glucose plasma membrane transport system is required for responding to a change in glucose concentration in the range 40 to 5g/L glucose. Last three letters of title is glucose concentration in media, in units g/L if divided by 10 (e.g. T1_MUTANT_13_YA0403#22_365, the residual glucose concentration of this sample is 36.5g/L).


title: Monocyte control rep 3

description: No additional information


title: 103783_NP_5mC_Rep3

description: MeDIP neuronal progenitor cells, Replicate 3

hyb_protocol: Hybridization was performed by NimbleGen Inc. according to standard procedures

scan_protocol: Scanning was performed by NimbleGen Inc. according to standard procedures

source_name: Total input sonicated genomic DNA from neuronal progenitor cells

label_protocol: Labeling was performed by NimbleGen Inc. according to standard procedures

extract_protocol: Genomic DNA was prepared form 10e7 cells by incubating 8h at 55°C in lysis buffer (10mM Tris-HCl pH 7.5, 2mM EDTA, 10mM NaCl, 0.5% SDS) supplemented with 0.5mg/ml Proteinase K followed by phenol/chloroform extraction and ethanol precipitation. Genomic DNA was treated with RNase A to completely remove RNA contamination and sonicated to an average size of 500bp

tag: Neuronal progenitor cells derived from mouse embryonic stem cells, Gender

source_name: Methylated DNA from neuronal progenitor cells enriched by MeDIP

extract_protocol: Methylated DNA was precipitated by MeDIP as previously described (Weber et al, 2007) using 3ug sonicated genomic DNA as starting material and 10ug antibody against 5-methylcytidine (Eurogentec, BI-MECY-1000)


title: 63243_TN_5mC_Rep1

description: MeDIP terminal pyramidal neurons, Replicate 1

tag: Terminal pyramidal neurons derived from mouse embryonic stem cells, Gender


title: Normal Liver, Patient 4, POLII 2 Array, array 1859702

description: Normal Liver. Note Promoter 2 of 2 5 kb promoter array; complement is 1859302

extract_protocol: Performed following the 'Chromatin Immunoprecipitation Assay (ChIPs)' protocol provided at http://genomics.ucdavis.edu/farnham

extract_protocol: see extract protocol for channel 1

tag: control total input


title: Tumor Liver, Patient 2, me3K27 Promoter 2 Array, array 87651

description: Tumor Liver. Note array 2 of 2 5 kb promoter array; complement is 88452

source_name: Tumor Liver


title: Monocyte ATV rep 1

description: No additional information


title: Th-/- hypoxic pool 1: E12.5 fetal ICR mouse RNA

scan_protocol: Fluorescent array images were obtained with an Axon slide scanner 4000B and GenePix Pro 3 software (Axon Instruments Inc.) at a resolution of 10microns.

tag: Th-/- 8% from E12.5 fetuses HC857, HC868, HC883


title: Th+/+ hypoxic pool 2: E12.5 fetal ICR mouse RNA

tag: wt E12.5 fetus

tag: Th+/+ 8%  from E12.5 fetuses HC866, HC964, HC977


title: Th-/- hypoxic pool 2: E12.5 fetal ICR mouse RNA

tag: Th-/- 8% from E12.5 fetuses HC856, HC965, HC884


title: Th+/+ hypoxic pool 3: E12.5 fetal ICR mouse RNA

tag: Th+/+ 8% from E12.5 fetuses HC864, HC878, HC977


title: Th-/- normoxic pool 2: E12.5 fetal ICR mouse RNA

tag: normoxic heterozygous dam


title: Th-/- normoxic pool 3: E12.5 fetal ICR mouse RNA


title: Th+/+ normoxic pool 3: E12.5 fetal ICR mouse RNA


title: Th+/+ normoxic pool 2: E12.5 fetal ICR mouse RNA

tag: Th+/+ 21% from E12.5 fetuses HC678, HC698 HC736


title: Promoter 2/Patient2/POLII Tumor liver

description:
ChIP-chip experiment; POLII in tumor liver; array 2 of 2 for 5 kb promoter array
Note that 88818 is paired with 88820 in that they are a set.

source_name: ChIP POLII tumor liver

tag: liver cancer patient; this is tumor liver sample

source_name: background DNA liver tumor

tag: liver cancer; tumor DNA sample


title: 82620_ES_5mC_Rep3

description: MeDIP ES cells, Replicate 3

source_name: Total input sonicated genomic DNA from embryonic stem cells

tag: Mouse embryonic stem cells isolated form mixed 129-C57Bl/6 background, Gender

source_name: Methylated DNA from embryonic stem cells enriched by MeDIP


title: 37324 MTS Mix 2

status: Public on May 24 2008

city: Thousand Oaks

first: Tiffany

last: Day

state: CA

address: One Amgen Center Drive

institute: Amgen

description: 37324 MTS Mix 2

hyb_protocol: To increase hybridization efficiency (~16 h at 45C with rotation at 50rpm), cRNA samples were fragmented according to standard Affymetrix protocols, before being incubated overnight with the GeneChip(r) Rat Genome 230 2.0 Array (Affymetrix, Santa Clara, CA).  Arrays were washed and stained using the antibody amplification and staining protocol according to the vendor's instructions.

scan_protocol: Scanned on Affymetrix GeneChip 3000 scanner.

data_processing: cel files were normalized with ‘mas5’ function of the Bioconductor package ‘affy’ in R

organism: Rattus norvegicus

source_name: Rat Mixed Tissue Sample, Mix 2

label_protocol: Biotinylated cRNA was generated using the BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY).

extract_protocol: Qiagen RNeasy maxi kits

tag: Sprague Dawley rat; Gender

value: male; Tissue:Mix 2. Liver:kidney:testes:brain =  2:2:4:2


title: Normal Liver, Patient 2, me3K27 Promoter 2 Array, array 81470

description: Normal Liver. Note array 2 of 2 5 kb promoter array; complement is 88819; see Acevedo et al., 2008 Cancer Res in press


title: Normal Liver, Patient 4, H3me3K9 2 Array, array 1861102

description: Normal Liver. Note Promoter 2 of 2 5 kb promoter array; complement is 1860902


title: 35311 MTS Mix 2

description: 35311 MTS Mix 2


title: 36018 MTS Mix 2

description: 36018 MTS Mix 2


title: 98672_NP_5mC_Rep2

description: MeDIP neuronal progenitor cells, Replicate 2


title: 81232_NP_5mC_Rep1

description: MeDIP neuronal progenitor cells, Replicate 1


title: 63608_ES_5mC_Rep1

description: MeDIP ES cells, Replicate 1


title: Array 87597 Promoter 2/Patient2/POLII ab

description: ChIP-chip experiment; POLII in normal liver; array 2 of 2 for 5 kb promoter array

source_name: liver POLII ChIP DNA

tag: normal liver

source_name: background DNA liver normal


title: Th+/+ normoxic pool 1: E12.5 fetal ICR mouse RNA

tag: Th+/+ 21% from E12.5 fetuses HC690, HC714 HC733

tag: RNA obtain from Stratagene

tag: Pooled RNA from 11 mouse cell lines


title: 34931 MTS Mix 2

description: 34931 MTS Mix 2


title: 34261 MTS Mix 2

description: 34261 MTS Mix 2


title: Th+/+ hypoxic pool 1: E12.5 fetal ICR mouse RNA

tag: Th+/+ from E12.5 fetuses HC861, HC876, HC885

tag: hypoxic heterzygous dam exposed to  8% oxygen for 6 hr prior to E12.5 of gestation


title: 34104 MTS Mix 2

description: 34104 MTS Mix 2


title: 34856 MTS Mix 2

description: 34856 MTS Mix 2


title: 32237 MTS Mix 2

description: 32237 MTS Mix 2


title: 31680 MTS Mix 2

description: 31680 MTS Mix 2


title: Normal Liver, Patient 1, H3me3K27 2 Array, array 85219

description: Normal Liver. Note Promoter 2 of 2 5 kb promoter array; complement is 81601

tag: control total input


title: 30816 MTS Mix 2

description: 30816 MTS Mix 2


title: 12hMesoOA_Oil_3

status: Public on Jun 19 2008

city: Cincinnati

first: William

middle: J

last: Scott

state: OH

address: 3333 Burnet Ave

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

description: Samples used for hybridization consisted of non-pooled (NP) RNA extracts from 8 groups in each of two time periods after drug administration: oil vehicle treated control embryonic limb bud mesoderm and ectoderm, phosphate buffered saline vehicle control embryonic limb bud mesoderm and ectoderm, acetazolamide treated embryonic limb bud mesoderm and ectoderm, and cadmium sulfate treated embryonic limb bud mesoderm and ectoderm. Forty-eight hybridization experiments were on non-pooled (NP) individual RNA extracts.

hyb_protocol: Full Protocol Description: Create a hybridization cocktail for a single probe array that contains  0.067 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg.mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Ivitrogen), and 1X Hybridization Buffer.  Heat hybridization cocktail to 99C for 5 minutes, to 45C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45?C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45?C for 16 hrs in the Hybridization Oven rotating at 60 rpm. Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual

scan_protocol: Images were scanned using a Genechip scanner 3000 [Affymetrix]

data_processing:
Affymetrix murine U74Av2 gene chips were used.  GeneChip CEL  files were subjected to  RMAExpress  quantile normalization  using  the  GeneSpring GX 7.1; Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring 7.1 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering.

Reference normalization sample for the 12h;Meso;acetazolamide group

label_protocol: Standard Affymetrix one-cycle target labeling protocol.

extract_protocol:
Total RNA was extracted from the murine ectoderms and mesoderms using Trizol kit (Invitrogen) and then purified two times using RNeasy columns (Qiagen)
Quality control steps:   RNA quality was assessed by using the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA) and only those samples with 28S/18S ratios between 1.3 and 2 were subsequently used

treatment_protocol: pregnant mice injected, ip, with either 400 mg/kg of acetazolamide suspended in vegetable oil or 4 mg/kg of Cadmium sulfate in phosphate buffered saline on gestation day 9.5. Three and twelve hours post-treatment, embryos collected.  The right forelimb buds were removed, treated with 2% Crude trypsin in PBS, the ectoderm and mesoderm separated.  The mesoderm and ectoderms of severals litters were pooled to obtain RNA.

tag: embryonic limb bud mesoderm

tag: oil vehicle-treated control


title: 63237_ES_5mC_Rep2

description: MeDIP ES cells, Replicate 2


title: 29681 MTS Mix 2

description: 29681 MTS Mix 2


title: 29750 MTS Mix 2

description: 29750 MTS Mix 2


title: 29014 MTS Mix 2

description: 29014 MTS Mix 2


title: 29605 MTS Mix 2

description: 29605 MTS Mix 2


title: 36020 MTS Mix 1

description: 36020 MTS Mix 1

source_name: Rat Mixed Tissue Sample, Mix 1

value: male; Tissue:Mix 1. Liver:kidney:testes:brain =  3:2:1:4


title: 28914 MTS Mix 2

description: 28914 MTS Mix 2


title: 32240 MTS Mix 1

description: 32240 MTS Mix 1


title: 30255 MTS Mix 2

description: 30255 MTS Mix 2


title: 34938 MTS Mix 1

description: 34938 MTS Mix 1


title: 34914 MTS Mix 1

description: 34914 MTS Mix 1


title: 35317 MTS Mix 1

description: 35317 MTS Mix 1


title: 37323 MTS Mix 1

description: 37323 MTS Mix 1


title: 28141 MTS Mix 2

description: 28141 MTS Mix 2


title: 36779 MTS Mix 1

description: 36779 MTS Mix 1


title: Th-/- normoxic pool 1: E12.5 fetal ICR mouse RNA

tag: Th null E12.5 fetus

tag: Th-/- 21% from E12.5 fetuses HC684, HC711 HC731


title: 34250 MTS Mix 1

description: 34250 MTS Mix 1


title: 29488 MTS Mix 2

description: 29488 MTS Mix 2


title: 31741 MTS Mix 1

description: 31741 MTS Mix 1


title: 31002 MTS Mix 1

description: 31002 MTS Mix 1


title: 34148 MTS Mix 1

description: 34148 MTS Mix 1


title: 30821 MTS Mix 1

description: 30821 MTS Mix 1


title: 29539 MTS Mix 2

description: 29539 MTS Mix 2


title: 30282 MTS Mix 1

description: 30282 MTS Mix 1


title: 36791 MTS Mix 2

description: 36791 MTS Mix 2


title: 29684 MTS Mix 1

description: 29684 MTS Mix 1


title: 29617 MTS Mix 1

description: 29617 MTS Mix 1


title: 29003 MTS Mix 1

description: 29003 MTS Mix 1


title: 29001 MTS Mix 1

description: 29001 MTS Mix 1


title: 29549 MTS Mix 1

description: 29549 MTS Mix 1


title: 29757 MTS Mix 1

description: 29757 MTS Mix 1


title: Leaf type O_wind effect_Replicate3

status: Public on Apr 03 2008

city: Seibersdorf

first: Silvia

last: Fluch

address: Campus Seibersdorf

department: Biogenetics/Natural Resources

country: Austria

institute: Austrian Research Centers GmbH

description: Biological replicate 3 out of 3

hyb_protocol: For hybridization the probes were mixed with hybridisation buffer (Amersham Biosciences) and Formamide at the ratio of 1:1:2 (v/v), respectively. Hybridizations were carried out using a Tecan HS 400 Hybridization Station (Tecan Austria GmbH, Austria) at 42°C for 15 h. The arrays were washed with 1x SSC for 30sec at RT, 1x SSC, 0,2% SDS for 20min at 50°C, 0,1x SSC, 0,2% SDS for 10min at RT and 0,2x SSC twice for 5min at RT.

scan_protocol: Microarray images were acquired on a Tecan LS 200 Scanner (Tecan Austria GmbH, Austria).

data_processing: Quantitation of signals was done using GenePix® Pro 5.0 software (Axon Instruments, Foster City, US, California). Differentially expressed clones were selected by pair-wise comparison of the samples from control and wind-blown leaves of the same developmental stage using the limma package (Smyth, 2004) of Bioconductor.

label: AlexaFluor® 555

organism: Populus nigra

source_name: leaf O

label_protocol: 5 μg of total RNA was reverse transcribed using Anchored Oligo(dT)20 Primer, amino-modified nucleotides and SuperScriptTM  RT (Superscript Plus indirect cDNA labeling System,  Invitrogen, Carlsbad, US California) according to manufacturer instructions. The first-strand cDNA was purified using the Qiagen PCR Purification Kit and subsequently coupled to AlexaFluor® 555 or AlexaFluor® 647 reactive Dye. The fluorescently labelled probes were purified using the same kit as written above.

growth_protocol: A clone of Populus nigra (E10), originating from a natural stand in Eferding (Upper Austria; Longitude: 14°05´, Latitude: 48°18´), was multiplied via cuttings in January 2005. Cuttings were rooted in small pots in standard soil and cultivated in greenhouse for 12 weeks. After this time the plants were well established they were transferred into bigger pots (Ø 30cm) and grown for further 6 weeks till the shoots were approx. 50cm in length. The plants were exposed to natural daily sunlight; humidity of the air was 67%. The daily temperature cycle was 18°C between 6 p.m. and 6 a.m. and 22°C between 6 a.m. and 6 p.m.

extract_protocol: The method of Chang et al. (1993) was used to extract RNA from Y-, E-, M- and O-aged leaves of 3 control and 3 wind-treated poplar leaves.

treatment_protocol: In the first week of July 2005 the poplar plants were split into two groups. One set of poplar plants were positioned into two curved rows opposite each other in a chamber of the greenhouse. At both ends of the parallel rows a fan was positioned that produced permanent and soft wind perturbation laterally across the plants, causing moderate leaf shaking, but no stem shaking. The wind speed determined with an anemometer (MPM 2000, Solomat, CT, USA) at plant level was 0.5 to 1.9 m/s. The wind-treatment was performed for 8 weeks.  The second set of poplar plants served as the control group and was grown in another chamber of the greenhouse under exactly the same conditions except the wind treatment.

tag: control

label: AlexaFluor® 647


title: Leaf type O_wind effect_swap_Replicate2

description: Biological replicate 2 out of 3

tag: wind-treated


title: Leaf type O_wind effect_swap_Replicate1

description: Biological replicate 1 out of 3


title: 29487 MTS Mix 1

description: 29487 MTS Mix 1


title: PI_20_AS_Q1_pool_2_48

status: Public on May 25 2008

city: Santa Clara

middle: R

last: Gingeras

address: 3380 Central Expressway

institute: Affymetrix, Inc.

description: 5' and 3' RACE reactions were performed using using the BD SMARTTM RACE cDNA amplification kit (BD Clontech Cat. No.634914) following the manufacturer's instructions. RACE oligonucleotides were designed with primer3(http://frodo.wi.mit.edu/cgi-bin/primer3/primer3.cgi) with the following parameters: 23 <= primer size <= 27, optimal size = 25, 68oC <= primer Tm <= 72oC, optimal Tm = 70oC,50% = primer GC percentage = 70%.

hyb_protocol: The labeled products were used directly for hybridization to Affymetrix Chromosome 21/22 2.0R Array for 18 h at 450C in a 3 M tetramethyl ammonium chloride/1x MES-based solution containing 100ug/mL Herring Sperm DNA, 0.02% Triton and 30pM of biotinylated control oligo B2 (Affymetrix). All reagents were from Invitrogen, except where noted otherwise.

scan_protocol: Standard Affymetrix protocols

data_processing: The maps of probe intensities versus the genomic positions were generated using Tiling array Software(TAS; http://www.affymetrix.com/support/developer/downloads/TilingArrayTools/index.affx).The graphs were generated without smoothing and median scaling. Each value on the graph represents intensity of the perfect match (PM) probe minus the intensity of the cognate mismatch (MM) probe. The coordinates of the probe always represent the ”left” genomic coordinate of a 25-mer.All data is in the coordinates of the hs.NCBIv35 version of the human genome. To minimize the number of falsely positive probes arising from cross-hybridization on the tiling array, we discard all positive probes having more than one perfect hit without gap in the whole genome. RACEfrags were built using a 99.7% percentile in the probe intensity value as a threshold. Two probes are included in the same RACEfrag if they are less than 25 nucleotides away (maxgap), and the minimum length of a RACEfrag (minrun) is 25 nucleotides.

label: Affymetrix DNA labeling reagent (#900542).

label_protocol: The pooled amplicons were then fragmented to ~ 50-100 nucleotides using DNAse I (Epicenter) at concentration of 0.00625U/ug of DNA for 8 minutes at 37oC followed by boiling for 10 min and cooling on ice. The fragmented amplicons were labeled in the following conditions: 1X terminal transferase(TdT) reaction buffer (Roche); 2.5mM CoCl2, DNA labeling reagent (DLR; Affymetrix; 1.125nmol per 1ug of fragmented DNA) and 200 units of recombinant TdT (Roche) for 3 hours at 37oC

extract_protocol: The products of RACE PCR reactions were pooled and purified by ethanol precipitation.

tag: The sample characteristics which is specific to each pool is detailed in http://genome.imim.es/datasets/racearrays2007


title: Leaf type O_wind effect_swap_Replicate3

description:
Biological replicate 1 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278858
Biological replicate 1 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278859
Biological replicate 2 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278860
Biological replicate 2 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278861
Biological replicate 3 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278862
Biological replicate 3 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278863
Biological replicate 1 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278864
Biological replicate 1 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278865
Biological replicate 2 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278866
Biological replicate 2 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278867
Biological replicate 3 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278868
Biological replicate 3 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278869
Biological replicate 1 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278870
Biological replicate 1 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278871
Biological replicate 2 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278872
Biological replicate 2 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278873
Biological replicate 3 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278874
Biological replicate 3 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278875
Biological replicate 1 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278876
Biological replicate 1 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278877
Biological replicate 2 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278878
Biological replicate 2 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278879
Biological replicate 3 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.^SAMPLE = GSM278880
Biological replicate 3 out of 3
The following developmental stages were defined for the experiment: Y - "youngest leaf" including the shoot tip = smallest fully enrolled leaf; E - "expanded leaf" = oldest leaf that had not reached full leaf thickness; M - "mature leaf" = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O - "old leaf" = 5th leaf below E.


title: Leaf type Y_wind effect_Replicate3

description: Biological replicate 3 out of 3

source_name: leaf Y


title: Leaf type Y_wind effect_swap_Replicate2

description: Biological replicate 2 out of 3


title: Leaf type O_wind effect_Replicate1

description: Biological replicate 1 out of 3


title: PI_20_AS_Q1_pool_1_48


title: Leaf type O_wind effect_Replicate2

description: Biological replicate 2 out of 3


title: Leaf type Y_wind effect_swap_Replicate1

description: Biological replicate 1 out of 3


title: Leaf type Y_wind effect_swap_Replicate3

description: Biological replicate 3 out of 3


title: Leaf type Y_wind effect_Replicate1

description: Biological replicate 1 out of 3


title: 28133 MTS Mix 1

description: 28133 MTS Mix 1


title: Leaf type E_wind effect_Replicate3

description: Biological replicate 3 out of 3

source_name: leaf E


title: Leaf type E_wind effect_swap_Replicate3

description: Biological replicate 3 out of 3


title: Leaf type E_wind effect_swap_Replicate2

description: Biological replicate 2 out of 3


title: Leaf type M_wind effect_swap_Replicate3

description: Biological replicate 3 out of 3

source_name: leaf M


title: Leaf type Y_wind effect_Replicate2

description: Biological replicate 2 out of 3


title: Leaf type M_wind effect_Replicate3

description: Biological replicate 3 out of 3


title: 31014 MTS Mix 2

description: 31014 MTS Mix 2


title: Leaf type E_wind effect_Replicate2

description: Biological replicate 2 out of 3


title: Leaf type M_wind effect_Replicate2

description: Biological replicate 2 out of 3


title: Leaf type E_wind effect_Replicate1

description: Biological replicate 1 out of 3


title: Leaf type E_wind effect_swap_Replicate1

description: Biological replicate 1 out of 3


title: Leaf type M_wind effect_Replicate1

description: Biological replicate 1 out of 3


title: Leaf type M_wind effect_swap_Replicate1

description: Biological replicate 1 out of 3


title: Leaf type M_wind effect_swap_Replicate2

description: Biological replicate 2 out of 3


title: X59333_Sty_51

status: Public on Mar 17 2008

city: South San Francisco

first: Peter

last: Haverty

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

hyb_protocol: Mapping 500K arrays were hybridized according to the Affymetrix protocol (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005) using an Affymetrix model 640 hybridization oven.

scan_protocol: Mapping 500K arrays were scanned according to the Affymetrix protocol (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005) using a GS3000 scanner.

data_processing: Affymetrix 500K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization.  Forty-eight normal samples were downloaded from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=500k) and analyzed at the same time.  One CEL file for each set (Sty and Nsp) with the median signal intensity across the set was selected as the reference array.   The dChip-normalized signal intensities were converted to log2 ratios and segmented as follows.  For each autosomal probe set, the log2 tumor/normal ratio of each tumor sample was calculated using the average intensity for each probe set in the normal set.  For Chromosome X, the average of the 20 normal female samples was used.   Each probe set was mapped to the genome, NCBI assembly version 35, using annotation provided by the Affymetrix web site.  The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment.

label_protocol: Following restriction enzyme digestion, biotin labeled DNA was prepared according to the Affymetrix protocol from 500ng of starting DNA (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005). The fluidics station model FS450 was used.

extract_protocol: A small piece of frozen tissue was removed from a sample of frozen tissue and incubated in a proteinase K digestion solution followed by cleanup using the Qiagen M48 robotics protocol.

tag: Primary malignant neoplasm of female breast; BREAST, LUMPECTOMY

value: INVASIVE DUCTAL CARCINOMA OF BREAST (2.5 CM), ACCOMPANIED BY LOBULAR CARCINOMA IN SITU.  METASTASES TO 4 OF 7 REGIONAL NODES IDENTIFIED.  NOTE: TUMOR STAGING IS ACCORDING TO THE 6TH EDITION OF THE AJCC CANCER STAGING MANUAL., 75-90


title: X41110_Sty_49

source_name: breast-met

tag: Secondary malignant neoplasm of lymph node; SENTINEL AXILLARY LYMPH NODE

value: METASTATIC INFILTRATING DUCTAL CARCINOMA OF BREAST.  RECEPTOR STATUS OF PRIMARY TUMOR NOT STATED., 75-90


title: X55140_Sty_50

tag: Primary malignant neoplasm of female breast; BREAST, MASTECTOMY

value: INVASIVE METAPLASTIC CARCINOMA WITH SARCOMATOID FEATURES (SUBMITTED SAMPLE) AND ASSOCIATED DUCTAL CARCINOMA IN SITU.  SEPARATE FOCUS OF INVASIVE AND IN SITU DUCTAL CARCINOMA IS IDENTIFIED.  NOTE: STAGE IS THAT AT TIME OF INITIAL DIAGNOSIS 2 YRS PRIOR.  TUMOR STAGING IS ACCORDING TO THE 6TH EDITION OF THE AJCC CANCER STAGING MANUAL.  INITIAL PRIMARY DIAGNOSED AS INFILTRATING DUCTAL CARCINOMA.  DONOR PREVIOUSLY TREATED WITH CHEMOTHERAPY., >90


title: X37777_Sty_42

tag: Primary malignant neoplasm of female breast; MASTECTOMY

value: INFILTRATING DUCTAL CARCINOMA, 2.3 CM DIAMETER, NUCLEAR GRADE 3, HISTOLOGIC GRADE 3, METASTATIC TO 3 REGIONAL NODES., 75-90


title: X37770_Sty_41

tag: Primary malignant neoplasm of female breast; BREAST, EXCISIONAL BIOPSY

value: INFILTRATING DUCTAL CARCINOMA, 3 CM DIAMETER, NUCLEAR GRADE 2-3/3, HISTOLOGIC GRADE 2-3/3, MITOTIC RATE 3/3.  NO REPORT ON REGIONAL NODE STATUS., 75-90


title: X41108_Sty_48

tag: Primary malignant neoplasm of female breast; PER SUBMITTED REPORT, MASTECTOMY

value: INFILTRATING CARCINOMA WITH DUCTAL AND LOBULAR FEATURES, 3.5 CM DIAMETER, METASTATIC TO ONE REGIONAL NODE.  ON GLGC PATHOLOGY REVIEW, FAVOR INTERPRETATION AS INFILTRATING DUCTAL CARCINOMA., 75-90


title: X20059_Sty_38

value: INFILTRATING DUCT CARCINOMA OF BREAST (3.0 CM), METASTATIC TO 1 OF 23 LEVEL I NODES.  ALL 8 LEVEL II NODES NEGATIVE FOR TUMOR.  20% IN SITU COMPONENT PRESENT., 75-90


title: X41106_Sty_47

tag: Secondary malignant neoplasm of lung; LUNG, LUL LOBECTOMY

value: POORLY DIFFERENTIATED CARCINOMA C/W METASTASIS FROM PREVIOUS PRIMARY MEDULLARY CARCINOMA OF BREAST APPROXIMATELY NINE YEARS PRIOR.  NOTE: DONOR PREVIOUSLY TREATED WITH CHEMOTHERAPY., 75-90


title: X41073_Sty_43

value: INFILTRATING DUCTAL CARCINOMA, MULTIFOCAL, BLOOM-RICHARDSON GRADE 3, WITH ULCERATION OF SKIN; METASTASIS TO AXILLARY NODES WITH EXTENSION INTO PERINODAL SOFT TISSUE., 75-90


title: X37760_Sty_40

tag: Secondary malignant neoplasm of ovary; OVARY

value: METASTATIC CARCINOMA C/W METASTASIS FROM PRIMARY OF BREAST 28 MONTHS PREVIOUSLY.  PRIMARY WAS NUCLEAR GRADE 2, HISTOLOGIC GRADE 3, METASTATIC TO REGIONAL NODE AND LIVER AT INITIAL DIAGNOSIS; DONOR IS S/P HORMONAL THERAPY., 75-90


title: X41078_Sty_45

tag: Primary malignant neoplasm of female breast; COMPLETION MASTECTOMY

value: RECURRENT INFILTRATING DUCTAL CARCINOMA, 7 YEARS AFTER PARTIAL MASTECTOMY FOR INITIAL PRIMARY TUMOR.  STAGING IS FOR INITIAL PRIMARY;  AT TIME OF RECURRENCE, ONE RESIDUAL AXILLARY NODE PRESENT, NEGATIVE FOR TUMOR.  INITIAL PRIMARY WAS ER+ PR+ HER2/NEU WEAK+; RECURRENCE (REPORTED IN CLINICAL DATA FOR THIS SAMPLE) IS ER- PR- HER2/NEU MODERATE+., 75-90


title: X06010_Sty_28

tag: Primary malignant neoplasm of female breast; BREAST

value: INFILTRATING DUCTAL CARCINOMA.  STAGE IV., 75-90


title: X16683_Sty_37

tag: Primary malignant neoplasm of female breast; MODIFIED RADICAL MASTECTOMY

value: IN SITU AND INFILTRATING DUCT CARCINOMA OF BREAST (4.1 CM).  REGIONAL NODES NEGATIVE FOR TUMOR., 75-90


title: X07220_Sty_30

value: INFILTRATING DUCTAL CARCINOMA, 4 CM DIAMETER., >90


title: X41103_Sty_46

value: INFILTRATING DUCTAL CARCINOMA, 5 CM DIAMETER, METASTATIC TO 2 REGIONAL NODES.  PATIENT IS S/P MASTECTOMY AND RADIATION TREATMENT FOR INFILTRATING DUCTAL CARCINOMA OF OPPOSITE BREAST 13 YEARS PREVIOUSLY.  PRIOR TUMOR WAS ER+ PR+ (HER2/NEU NOT ASSESSED AT THAT TIME).  CURRENT TUMOR IS ER BORDERLINE +  PR+  HER2/NEU -.  TUMOR ARISES IN A BACKGROUND OF FIBROCYSTIC DISEASE OF BREAST., 75-90


title: X07287_Sty_33

value: INFILTRATING DUCTAL CARCINOMA, 2 CM DIAMETER., 75-90


title: X12894_Sty_35

tag: Secondary malignant neoplasm of lymph node; AXILLARY NODE

value: METASTATIC INFILTRATING LOBULAR CARCINOMA OF BREAST.  DONOR PREVIOUSLY TREATED WITH CHEMOTHERAPY., >90


title: X07461_Sty_34

value: INFILTRATING DUCTAL CARCINOMA AND DUCTAL CARCINOMA IN SITU., >90


title: X14460_Sty_36

value: INFILTRATING DUCTAL CARCINOMA, 8 CM DIAMETER, ULCERATING SKIN WITH EXTENSIVE LYMPHOVASCULAR INVASION, DISCRETE AXILLARY TUMOR NODULE PRESENT (? REPLACED LYMPH NODE); SYNCHRONOUS METASTASIS TO LUNG; ER- PR- HER2/NEU STRONG+., 75-90


title: X06196_Sty_29

value: INFILTRATING DUCTAL CARCINOMA.  STAGE IV., >90


title: X20109_Sty_39

tag: Secondary malignant neoplasm of brain; BRAIN (CEREBELLUM), BIOPSY

value: METASTATIC ADENOCARCINOMA, C/W BREAST PRIMARY (ALTHOUGH OTHER PRIMARY SITES NOT EXCLUDED)., 75-90


title: X06006_Sty_26

value: INFILTRATING DUCTAL CARCINOMA.  STAGE I., >90


title: X07246_Sty_32

tag: Primary malignant neoplasm of female breast; BREST

value: INFILTRATING DUCTAL CARCINOMA, 4 CM DIAMETER., 75-90


title: X06003_Sty_25


title: X06008_Sty_27

value: INFILTRATING DUCTAL CARCINOMA., 75-90


title: X41074_Sty_44

tag: Primary malignant neoplasm of female breast; PARTIAL MASTECTOMY

value: INFILTRATING DUCTAL CARCINOMA, PAPILLARY TYPE, 3.5 CM DIAMETER.  INCOMPLETE INFORMATION FOR BLOOM-RICHARDSON GRADING, AND NO REPORT ON NODAL STATUS.  TUMOR ARISES IN FIBROCYSTIC BACKGROUND., 75-90


title: X05895_Sty_22

value: INFILTRATING DUCTAL CARCINOMA.  STAGE III., 75-90


title: X07226_Sty_31

value: INFILTRATING DUCTAL CARCINOMA, 4.5 CM DIAMETER., 75-90


title: X05907_Sty_23


title: X05893_Sty_21

value: INFILTRATING DUCTAL CARCINOMA.  STAGE II., >90


title: X06002_Sty_24

value: INFILTRATING DUCTAL CARCINOMA.  STAGE II., 75-90


title: X04866_Sty_17

value: INFILTRATING DUCTAL CARCINOMA., >90


title: X04857_Sty_15


title: X04873_Sty_18


title: X03344_Sty_6

tag: Primary malignant neoplasm of female breast; INFILTRATING DUCTAL CARCINOMA OF BREAST.  , 75-90


title: X04837_Sty_12

value: INFILTRATING DUCTAL CARCINOMA.., >90


title: X04834_Sty_10


title: X04835_Sty_11

value: INFILTRATING APOCRINE CARCINOMA (SUBTYPE OF INFILTRATING DUCTAL CARCINOMA)., 75-90


title: X03239_Sty_5

tag: Primary malignant neoplasm of female breast; INFILTRATING DUCTAL CARCINOMA OF BREAST., >90


title: X55140_Nsp_50

value: INVASIVE METAPLASTIC CARCINOMA WITH SARCOMATOID FEATURES (SUBMITTED SAMPLE) AND ASSOCIATED DUCTAL CARCINOMA IN SITU.  SEPARATE FOCUS OF INVASIVE AND IN SITU DUCTAL CARCINOMA IS IDENTIFIED.  NOTE: STAGE IS THAT AT TIME OF INITIAL DIAGNOSIS 2 YRS PRIOR.  TUMOR STAGING IS ACCORDING TO THE 6TH EDITION OF THE AJCC CANCER STAGING MANUAL.  INITIAL PRIMARY DIAGNOSED AS INFILTRATING DUCTAL CARCINOMA.  DONOR PREVIOUSLY TREATED WITH CHEMOTHERAPY., >90


title: X04832_Sty_9


title: X04839_Sty_13


title: X03235_Sty_4


title: X04877_Sty_19

value: INFILTRATING DUCTAL CARCINOMA  WITH DOMINANT INTRADUCTAL COMPONENT., >90