title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_H1

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_H2
sample ID: 031706212
sample ID of_age- and cage-matched_mouse: 031706202

value: normal whole liver tissue, at time when breast tumor had reached 1 cm size


title: BaP 100 µM sample 2 [12987C]

status: Public on Oct 22 2010

type: RNA

city: Maastricht

first: Kevin

last: Hochstenbach

address: Universiteitssingel 50

department: Health Risk Analysis and Toxicology

country: Netherlands

institute: Maastricht University

hyb_protocol: Hybridization according to Agilent instructions.

scan_protocol: Slides were scanned on a GenePix® 4000B Microarray Scanner (Molecular Devices, Sunnyvale, USA). Cy3 and Cy5 were excited at wavelengths of 532 and 635 nm, respectively. Laser power was set to 100%. The photo multiplier tube gain was set to a saturation tolerance of 0.02% to minimize background and saturated spots. Photomultiplier gain was set to 587 (Cy3) and 705 (Cy5) for replicates 1 and 2, and 628 (Cy3) and 560 (Cy5) for replicates 3 and 4, based on automatic establishment of ideal scan settings. The images obtained (resolution 5 micron, 16 bit tiff image) were processed with Imagene 8.0.1 software (Biodiscovery, El Segundo, USA) to measure mean signal intensities for spots and local backgrounds followed by a quality control in Microsoft Excel.

data_processing: Data preparations were performed in GeneSight software (BioDiscovery) and included in chronological order: background subtraction, omission of bad spots (controls and irregularly shaped spots), LOWESS normalization, log (base=2) transformations, calculation of difference of test compound versus respective vehicle control.

molecule: total RNA

organism: Homo sapiens

source_name: control for 40_BaP_100%

label_protocol: The Two-Color Microarray-Based Gene Expression Analysis kit from Agilent Technologies (Amstelveen, The Netherlands) was used to generate Cyanine (Cy) labelled cRNA according to the manufacturer’s protocol.

growth_protocol: Isolated PBMC were resuspended in tissue culture medium RPMI 1640 supplemented with L-glutamine, 10% heat inactivated foetal calf serum (FCS) (Gibco, Paisley, UK) and 100 U/ml penicillin G and 0.1 mg/ml streptomycin (PAA Laboratories GmbH, Pasching, Austria) to a final concentration of 2,4*106  cells/ml.

extract_protocol: RNA was isolated from TRIzol® suspended cells according to the manufacturer’s protocol with minor modifications, followed by a clean up, using an RNeasy Mini Kit (Qiagen, Venlo, The Netherlands) with DNase treatment.

treatment_protocol: For analysis of whole genome gene expression by microarray PBMC from five independent donors per compound were exposed for 20 hours to three concentrations, i.e. the 100% and two serial ten-fold dilutions (10% and 1%), and a DMSO or PBS vehicle control. All exposures were performed in the presence of freshly prepared S9-mix.

tag: agent

value: vehicle control

tag: cell type

value: Human PBMC

tag: tox class

value: GTX

value: BaP

tag: concentration


title: normal liver from control mouse_sample_TL20070522_3_4_H2

city: Seattle

first: Regine

middle: M

last: Schoenherr

state: WA

address: 1100 Fairview Ave N, LE-360

country: USA

institute: Fred Hutchinson Cancer Research Center

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_H1
sample ID: 031706202
sample ID of_age- and cage-matched_mouse: 031706212

hyb_protocol: Biotinylated cRNA (600 ng/ul) was hybridized to GeneChip® Mouse 430 2.0 arrays (Affymetrix, Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: The arrays were washed and stained using a GeneChip® Fluidics Station and scanned using a GeneChip® Scanner 3000.

data_processing: Two sequential quality control checks were implemented to evaluate whether to include results from each of the GeneChips.  In the first step, recommendations made by Affymetrix were followed.(Zweig, M. H.; Campbell, G. Clin. Chem. 1993, 39, 561-577)  In the second step, we used the affyQCReport and affyPLM software in the Bioconductor package (http://www.bioconductor.org/) to search for poor-quality chips.(Pyeon, D.; et al. Cancer Res. 2007, 67, 4605-4619)  In total, 250 chips from both normal and cancer samples from 5 tissues passed these two steps of quality control evaluation. After passing the quality control checks, the DNA microarray data of each separate tissue type were subjected to a quartile normalization step (using Gene Pattern software version 3.0) where intensities of different arrays (but from the same tissue type) were adjusted to the same scale so that the intensity levels from the different arrays could be compared with one another.  The normalization was performed on log2 transformed data.

label: biotin

organism: Mus musculus

source_name: normal whole liver tissue, at time when breast tumor of matched tumor-bearing mouse had reached 1 cm size

label_protocol: Purified total RNA was normalized to 125ng/ul and reverse transcribed to produce double-stranded cDNA which was amplified, producing biotin-labeled cRNA using the GeneChip HT One-Cycle Target Labeling and Controls Kit (Affymetrix, Santa Clara, CA.)

growth_protocol: All mouse work was performed under IACUC regulations as approved by the Fred Hutchinson Cancer Research Center's animal use committee.  For these studies, a doxycycline-inducible, bitransgenic MMTV-rtTA/TetO-NeuNT (Her2/Neu) mouse model was used.  Corresponding control mice were transgenic for TetO-NeuNT only and were littermates of the bitransgenic mice.  The procedures for animal husbandry and tissue and plasma sample collection were previously reported in Whiteaker J.R., et al., J. Proteome Res. 2007, 10, 3962-3975 and Kelly-Spratt, K.S., et al., J. Proteome Res. 2008, 8, 3613-3618.  Briefly, all mice were fed standard laboratory chow (Harland Teklad, 8664) and acidified water ad libitum and kept on a 12 hour light-dark cycle.

extract_protocol: The tissues from thymus, spleen, liver, blood cells (blood with plasma fraction removed), and breast were homogenized, and total RNA was isolated using a standard Trizol (Invitrogen, Carlsbad, CA) and chloroform extraction protocol.

treatment_protocol: All mice received doxycycline (2 mg/mL + 5% sucrose) in the drinking water starting at 8 weeks of age.  Doxycycline was used to induce tumor development in the bitransgenic mice and breast tumors were allowed to develop to 1.0 cm in diameter after which each tumor-bearing mouse and its corresponding control littermate were euthanized by CO2 inhalation.  Tissue samples were collected when the tumors reached ~1 cm size and the samples were snap-frozen in liquid nitrogen.

tag: gender

value: female

tag: strain

value: FVB

tag: genotype

value: control mice transgenic for TetO-NeuNT only and littermates of the bitransgenic mice

tag: tissue


title: BaP 10 µM sample 4 [12988D]

source_name: control for 42_BaP_10%


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_H3

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_H4
sample ID: 102506225
sample ID of_age- and cage-matched_mouse: 102506235

source_name: normal whole liver tissue, at time when breast tumor had reached 1 cm size

value: doxycycline-inducible, bitransgenic MMTV-rtTA/TetO-NeuNT (Her2/Neu) mouse model


title: BaP 10 µM sample 1 [12987B]

source_name: control for 39_BaP_10%


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_G5

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_G6
sample ID: 121206223
sample ID of_age- and cage-matched_mouse: 121206233


title: PhIP 2.5 µM sample 5 [23878A]

source_name: control for 33_PhIP_1%

value: PhIP


title: PhIP 2.5 µM sample 4 [23877D]

source_name: control for 32_PhIP_1%


title: normal liver from control mouse_sample_TL20070522_3_4_G4

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_G3
sample ID: 102506214
sample ID of_age- and cage-matched_mouse: 102506203

value: normal whole liver tissue, at time when breast tumor of matched tumor-bearing mouse had reached 1 cm size


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_G3

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_G4
sample ID: 102506203
sample ID of_age- and cage-matched_mouse: 102506214


title: BaP 10 µM sample 3 [12988B]

source_name: control for 41_BaP_10%


title: normal liver from control mouse_sample_TL20070522_3_4_G2

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_G1
sample ID: 030306222
sample ID of_age- and cage-matched_mouse: 030306232


title: normal liver from control mouse_sample_TL20070522_3_4_G6

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_G5
sample ID: 121206233
sample ID of_age- and cage-matched_mouse: 121206223


title: TCDD 10 µM sample 4 [12986A]

source_name: control for 37_TCDD_100%

value: NGTX

value: TCDD


title: PhIP 2.5 µM sample 1 [23877A]

source_name: control for 28_PhIP_1%


title: TCDD 10 µM sample 5 [12986C]

source_name: control for 38_TCDD_100%


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_G1

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_G2
sample ID: 030306232
sample ID of_age- and cage-matched_mouse: 030306222


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_F5

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_F6
sample ID: 120806222
sample ID of_age- and cage-matched_mouse: 120806232


title: PhIP 2.5 µM sample 2 [23877B]

source_name: control for 30_PhIP_1%


title: normal liver from control mouse_sample_TL20070522_3_4_F4

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_F3
sample ID: 090706253
sample ID of_age- and cage-matched_mouse: 090706263


title: normal liver from control mouse_sample_TL20070522_3_4_F6

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_F5
sample ID: 120806232
sample ID of_age- and cage-matched_mouse: 120806222


title: PhIP 2.5 µM sample 3 [23877C]

source_name: control for 31_PhIP_1%


title: normal liver from control mouse_sample_TL20070522_3_4_F2

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_F1
sample ID: 030306202
sample ID of_age- and cage-matched_mouse: 030306212


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_F3

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_F4
sample ID: 090706263
sample ID of_age- and cage-matched_mouse: 090706253


title: TCDD 10 µM sample 1 [12984C]

source_name: control for 34_TCDD_100%


title: TCDD 1 µM sample 4 [12986B]

source_name: control for 37_TCDD_10%


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_F1

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_F2
sample ID: 030306212
sample ID of_age- and cage-matched_mouse: 030306202


title: normal liver from control mouse_sample_TL20070522_3_4_E6

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_E5
sample ID: 120806202
sample ID of_age- and cage-matched_mouse: 120806213


title: TCDD 1 µM sample 2 [12985B]

source_name: control for 35_TCDD_10%


title: TCDD 10 µM sample 3 [12985C]

source_name: control for 36_TCDD_100%


title: TCDD 1 µM sample 5 [12986D]

source_name: control for 38_TCDD_10%


title: TCDD 10 µM sample 2 [12985A]

source_name: control for 35_TCDD_100%


title: TCDD 1 µM sample 1 [12984D]

source_name: control for 34_TCDD_10%


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_E5

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_E6
sample ID: 120806213
sample ID of_age- and cage-matched_mouse: 120806202

source_name: normal whole liver tissue, at time when breast tumor had reached 1 cm size


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_E3

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_E4
sample ID: 090706233
sample ID of_age- and cage-matched_mouse: 090706243


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_E1

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_E2
sample ID: 021706202
sample ID of_age- and cage-matched_mouse: 021706213


title: normal liver from control mouse_sample_TL20070522_3_4_E2

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_E1
sample ID: 021706213
sample ID of_age- and cage-matched_mouse: 021706202

source_name: normal whole liver tissue, at time when breast tumor of matched tumor-bearing mouse had reached 1 cm size


title: normal liver from control mouse_sample_TL20070522_3_4_E4

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_E3
sample ID: 090706243
sample ID of_age- and cage-matched_mouse: 090706233


title: IQ 250 µM  sample 5 [13000A]

source_name: control for 61_IQ_100%

value: IQ


title: normal liver from tumor-bearing mouse_sample_TL20070522_5_D7

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_5_D8
sample ID: 011107233
sample ID of_age- and cage-matched_mouse: 011107223


title: normal liver from control mouse_sample_TL20070522_5_D8

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_5_D7
sample ID: 011107223
sample ID of_age- and cage-matched_mouse: 011107233


title: normal liver from tumor-bearing mouse_sample_TL20070523_3_4_D5

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_D6
sample ID: 120106223
sample ID of_age- and cage-matched_mouse: 120106233


title: normal liver from control mouse_sample_TL20070522_3_4_D6

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070523_3_4_D5
sample ID: 120106233
sample ID of_age- and cage-matched_mouse: 120106223


title: AA 0.5 mM sample 5 [23988C]

source_name: control for 68_AA_1%

value: AA


title: normal liver from control mouse_sample_TL20070522_3_4_D4

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070523_3_4_D3
sample ID: 090706213
sample ID of_age- and cage-matched_mouse: 090706202


title: AA 0.5 mM sample 2 [23987D]

source_name: control for 65_AA_1%


title: AA 0.5 mM sample 3 [23988A]

source_name: control for 66_AA_1%


title: EtOH 5 ‰ sample 4 [12993A]

source_name: control for 55_EtOH_100%

value: EtOH


title: EtOH 5 ‰ sample 3 [12992C]

source_name: control for 54_EtOH_100%


title: AA 0.5 mM sample 1 [23987C]

source_name: control for 64_AA_1%


title: TCDD 1 µM sample 3 [12985D]

source_name: control for 36_TCDD_10%


title: AA 0.5 mM sample 4 [23988B]

source_name: control for 67_AA_1%


title: EtOH 0.5 ‰ sample 4 [12993B]

source_name: control for 55_EtOH_10%


title: EtOH 5 ‰ sample 5 [12993C]

source_name: control for 57_EtOH_100%


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_D1

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070523_3_4_D2
sample ID: 012006203
sample ID of_age- and cage-matched_mouse: 012006215


title: normal liver from control mouse_sample_TL20070522_3_4_C6

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_C5
sample ID: 120106212
sample ID of_age- and cage-matched_mouse: 120106203


title: EtOH 5 ‰ sample 2 [12992A]

source_name: control for 51_EtOH_100%


title: normal liver from control mouse_sample_TL20070522_3_4_C4

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_C3
sample ID: 082406254
sample ID of_age- and cage-matched_mouse: 082406244


title: normal liver from tumor-bearing mouse_sample_TL20070523_3_4_D3

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_D4
sample ID: 090706202
sample ID of_age- and cage-matched_mouse: 090706213


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_C5

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_C6
sample ID: 120106203
sample ID of_age- and cage-matched_mouse: 120106212


title: EtOH 0.5 ‰ sample 3 [12992D]

source_name: control for 54_EtOH_10%


title: normal liver from control mouse_sample_TL20070523_3_4_D2

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_D1
sample ID: 012006215
sample ID of_age- and cage-matched_mouse: 012006203


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_C1

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_C2
sample ID: 011906101
sample ID of_age- and cage-matched_mouse: 011906111


title: normal liver from control mouse_sample_TL20070522_3_4_C2

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_C1
sample ID: 011906111
sample ID of_age- and cage-matched_mouse: 011906101


title: NDMA 67.5 mM sample 2 [13002C]

source_name: control for 70_DMNA_100%

value: DMNA


title: NDMA 67.5 mM sample 4 [13145C]

source_name: control for 72_DMNA_100%


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_C3

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_C4
sample ID: 082406244
sample ID of_age- and cage-matched_mouse: 082406254

source_name: normal whole liver tissue, at time when breast tumor had reached 1 cm size


title: normal liver from control mouse_sample_TL20070522_3_4_B6

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_B5
sample ID: 111706233
sample ID of_age- and cage-matched_mouse: 111706222

source_name: normal whole liver tissue, at time when breast tumor of matched tumor-bearing mouse had reached 1 cm size


title: NDMA 67.5 mM sample 3 [13145A]

source_name: control for 71_DMNA_100%


title: EtOH 0.5 ‰ sample 1 [13000D]

source_name: control for 50_EtOH_10%


title: EtOH 0.5 ‰ sample 2 [12992B]

source_name: control for 51_EtOH_10%


title: EtOH 5 ‰ sample 1 [13000C]

source_name: control for 50_EtOH_100%


title: NDMA 6.75 mM sample 4 [13135B]

source_name: control for 73_DMNA_10%


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_B3

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_B4
sample ID: 031706252
sample ID of_age- and cage-matched_mouse: 031706242

value: normal whole liver tissue, at time when breast tumor had reached 1 cm size


title: EtOH 0.5 ‰ sample 5 [12993D]

source_name: control for 57_EtOH_10%

value: vehicle control


title: NDMA 67.5 mM sample 5 [13135A]

source_name: control for 73_DMNA_100%

value: Human PBMC


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_B5

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_B6
sample ID: 111706222
sample ID of_age- and cage-matched_mouse: 111706233


title: PCB153 250 µM sample 5 [13137C]

source_name: control for 78_PCB_100%

value: PCB


title: NDMA 6.75 mM sample 1 [13002B]

source_name: control for 69_DMNA_10%

value: GTX


title: NDMA 6.75 mM sample 2 [13002D]

source_name: control for 70_DMNA_10%


title: normal liver from control mouse_sample_TL20070522_3_4_B4

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_B3
sample ID: 031706242
sample ID of_age- and cage-matched_mouse: 031706252

value: female


title: normal liver from control mouse_sample_TL20070522_3_4_B2

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_B1
sample ID: 122105218
sample ID of_age- and cage-matched_mouse: 122105202

value: FVB


title: NDMA 6.75 mM sample 3 [13145B]

source_name: control for 71_DMNA_10%


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_A5

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_A6
sample ID: 111706202
sample ID of_age- and cage-matched_mouse: 111706213


title: normal liver from control mouse_sample_TL20070522_3_4_A4

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_A3
sample ID: 031706232
sample ID of_age- and cage-matched_mouse: 031706222

value: control mice transgenic for TetO-NeuNT only and littermates of the bitransgenic mice


title: PCB153 250 µM sample 3 [13136C]

source_name: control for 76_PCB_100%


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_B1

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_B2
sample ID: 122105202
sample ID of_age- and cage-matched_mouse: 122105218

value: doxycycline-inducible, bitransgenic MMTV-rtTA/TetO-NeuNT (Her2/Neu) mouse model


title: normal liver from control mouse_sample_TL20070522_3_4_A2

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_A1
sample ID: 121505205
sample ID of_age- and cage-matched_mouse: 121505216


title: Diseased canine retina, 7 weeks, Z239

city: Philadelphia

first: Sem

last: Genini

state: PA

address: 3900 Delancey Street

department: Clinical Studies

institute: University of Pennsylvania

description: scan was part of a reference design study comparing retinal expression of normal and affected dogs at different time points

hyb_protocol: Hybridization followed the 3DNA Array Kit, Genesphere, Inc. Hatfield, PA Hybridized to array version 2.

scan_protocol: GenePix 4000B Scanner using GenePix Pro v.6.0

data_processing:
Provided data are raw data (not normalized).
For each channel, the signal was measured and corrected against the background for that particular channel.

organism: Canis lupus familiaris

source_name: Retina

label_protocol: 10ug of RNA was labeled using 3DNA Array Kit, Genesphere, Inc. Hatfield, PA (Paez et al., Mol Vis, 2006)

extract_protocol: Trizol extraction, followed by RNeasy mini Kit (Qiagen, Valencia, CA)

tag: disease state

value: diseased

tag: age

value: 7 weeks

source_name: Brain Pool

tag: reference

value: RNA from normal canine brain (equal parts temporal, occipital, and frontal lobe)

value: 16 weeks


title: PCB153 250 µM sample 4 [13137A]

source_name: control for 77_PCB_100%

value: NGTX


title: Diseased canine retina, 7 weeks, Z240


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_A1

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_A2
sample ID: 121505216
sample ID of_age- and cage-matched_mouse: 121505205

source_name: normal whole liver tissue, at time when breast tumor had reached 1 cm size


title: normal breast from control mouse_sample_TL20070522_5_H4

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_H3
sample ID: 102506232
sample ID of_age- and cage-matched_mouse: 102506222

source_name: normal whole breast tissue, at time when matched tumor-bearing mouse had 1 cm breast tumor


title: breast_tumor_sample_TL20070522_5_H5

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_H6
sample ID: 011107210
sample ID of_age- and cage-matched_mouse: 011107200

source_name: tumor whole breast tissue, at 1 cm tumor size


title: PCB153 250 µM sample 1 [13135C]

source_name: control for 74_PCB_100%


title: normal breast from control mouse_sample_TL20070522_5_H2

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_H1
sample ID: 031706200
sample ID of_age- and cage-matched_mouse: 031706210

value: normal whole breast tissue, at time when matched tumor-bearing mouse had 1 cm breast tumor


title: PCB153 25 µM sample 5 [13137D]

source_name: control for 78_PCB_10%


title: breast_tumor_sample_TL20070522_5_H3

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_H4
sample ID: 102506222
sample ID of_age- and cage-matched_mouse: 102506232

value: tumor whole breast tissue, at 1 cm tumor size


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_A3

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_A4
sample ID: 031706222
sample ID of_age- and cage-matched_mouse: 031706232


title: Diseased canine retina, 7 weeks, Z236


title: normal breast from control mouse_sample_TL20070522_5_H6

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_H5
sample ID: 011107200
sample ID of_age- and cage-matched_mouse: 011107210


title: Normal canine retina, 7 weeks, M159

value: normal


title: PCB153 25 µM sample 4 [13137B]

source_name: control for 77_PCB_10%


title: Normal canine retina, 7 weeks, M157


title: breast_tumor_sample_TL20070522_5_H1

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_H2
sample ID: 031706210
sample ID of_age- and cage-matched_mouse: 031706200


title: PCB153 25 µM sample 3 [13136D]

source_name: control for 76_PCB_10%


title: PCB153 25 µM sample 2 [13136B]

source_name: control for 75_PCB_10%


title: normal breast from control mouse_sample_TL20070522_5_G4

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_G3
sample ID: 102506211
sample ID of_age- and cage-matched_mouse: 102506200


title: Normal canine retina, 7 weeks, M158


title: breast_tumor_sample_TL20070522_5_G1

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_G2
sample ID: 030306230
sample ID of_age- and cage-matched_mouse: 030306220


title: normal breast from control mouse_sample_TL20070522_5_G2

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_G1
sample ID: 030306220
sample ID of_age- and cage-matched_mouse: 030306230


title: breast_tumor_sample_TL20070522_5_G3

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_G4
sample ID: 102506200
sample ID of_age- and cage-matched_mouse: 102506211


title: PCB153 25 µM sample 1 [13135D]

source_name: control for 74_PCB_10%


title: AFB1 1.25 mM sample 5 [23989D]

source_name: control for 83_AFB1_1%


title: normal breast from control mouse_sample_TL20070522_5_G6

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_G5
sample ID: 121206230
sample ID of_age- and cage-matched_mouse: 121206220


title: breast_tumor_sample_TL20070522_5_G5

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_G6
sample ID: 121206220
sample ID of_age- and cage-matched_mouse: 121206230


title: normal breast from control mouse_sample_TL20070522_5_F6

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_F5
sample ID: 120806230
sample ID of_age- and cage-matched_mouse: 120806220


title: Diseased canine retina, 16 weeks, Z232


title: Diseased canine retina, 16 weeks, Z230


title: Diseased canine retina, 16 weeks, Z233


title: normal breast from control mouse_sample_TL20070522_5_F4

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_F3
sample ID: 090706250
sample ID of_age- and cage-matched_mouse: 090706260


title: AFB1 1.25 mM sample 2 [23989A]

source_name: control for 80_AFB1_1%


title: AFB1 1.25 mM sample 4 [23989C]

source_name: control for 82_AFB1_1%


title: AFB1 1.25 mM sample 3 [23989B]

source_name: control for 81_AFB1_1%


title: breast_tumor_sample_TL20070522_5_F5

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_F6
sample ID: 120806220
sample ID of_age- and cage-matched_mouse: 120806230


title: normal breast from control mouse_sample_TL20070522_5_F2

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_F1
sample ID: 030306200
sample ID of_age- and cage-matched_mouse: 030306210


title: normal breast from control mouse_sample_TL20070522_5_E6

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_E5
sample ID: 120806200
sample ID of_age- and cage-matched_mouse: 120806210


title: Normal canine retina, 16 weeks, 5615

description: scan was part of a reference design study comparing retinal expression of normal and affected dogs at different time points

hyb_protocol: Hybridization followed the 3DNA Array Kit, Genesphere, Inc. Hatfield, PA Hybridized to array version 1.

source_name: Brain pool


title: Normal canine retina, 16 weeks, M490

source_name: Retina


title: breast_tumor_sample_TL20070522_5_F1

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_F2
sample ID: 030306210
sample ID of_age- and cage-matched_mouse: 030306200


title: breast_tumor_sample_TL20070522_5_E3

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_E4
sample ID: 090706230
sample ID of_age- and cage-matched_mouse: 090706240


title: breast_tumor_sample_TL20070522_5_E5

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_E6
sample ID: 120806210
sample ID of_age- and cage-matched_mouse: 120806200


title: normal breast from control mouse_sample_TL20070522_5_E4

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_E3
sample ID: 090706240
sample ID of_age- and cage-matched_mouse: 090706230


title: breast_tumor_sample_TL20070522_5_F3

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_F4
sample ID: 090706260
sample ID of_age- and cage-matched_mouse: 090706250


title: Normal canine retina, 16 weeks, 5617

source_name: Brain Pool


title: normal breast from control mouse_sample_TL20070522_5_E2

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_E1
sample ID: 021706211
sample ID of_age- and cage-matched_mouse: 021706200


title: MDA 30.5 mM sample 4 [12995C]

source_name: control for 62_MDA_100%

value: MDA


title: normal breast from control mouse_sample_TL20070522_5_D6

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_D5
sample ID: 120106230
sample ID of_age- and cage-matched_mouse: 120106220


title: 0 vs. 15 days. Replicate 3

city: Villamayor

first: Daniel

last: Osuna

state: Salamanca

address: Río Duero, 12

department: Fisiología Vegetal, Universidad de Salamanca.

country: Spain

institute: Centro Hispano-Luso de Investigaciones Agrarias.

description: Biological replicate 3 of 3. Control non-aged seeds vs. 15 days aged seeds.

hyb_protocol: Cy5 and Cy3 amplified RNA (aRNA) fragmented probes were mixed (200 pmol of each label) with 20 µg of PolyA (Sigma) and 20 µg of yeast tRNA (Sigma) in a final volume of 90 µl of hybridization buffer (50% formamide, 6X SSC, 0.5% SDS, 5X Denhardt’s). The probe was denatured at 95ºC for 5 minutes and applied to the slide using a LifterSlip (Erie Scientific). Slides were then incubated at 42ºC for 16h in hybridization chambers (Array-It). After incubation, slides were washed twice with 0.5X SSC, 0.1% SDS for 5 minutes each, twice with 0.5X SSC for 5 minutes and finally in 0.05X SSC for 5 minutes. Slides were dried by centrifugation at 563g for 1 minute.

scan_protocol: Images from Cy3 and Cy5 channels were equilibrated and captured with a GenePix 4000B (Axon) and spots quantified using GenPix software (Axon).

data_processing: Background correction and normalization of expression data were performed using LIMMA (Smyth and Speed, 2003; Smyth, 2004). LIMMA is part of Bioconductor, an R language project (Ihaka and Gentleman, 1996). First, the data set was filtered based on the spot quality. A strategy of adaptive background correction was used that avoids exaggerated variability of log-ratios for low-intensity spots. For local background correction the normexp method in LIMMA to adjust the local median background was used. The resulting log-ratios were print-tip loess normalized for each array (Smyth and Speed, 2003). To have similar distribution across arrays and to achieve consistency among arrays, log-ratio values were scaled using as scale estimator the median-absolute-value (Smyth and Speed, 2003). Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic (Smyth, 2004). To control the false discovery rate p-values were corrected by using the method of Benjamani and Hochberg (1995). The expected false discovery rate was controlled to be less than 5% or 10% where specified. Only reproducible expression values (present in at least two gene replicates and FDR<0.05) were considered and normalized log2 ratios were averaged.

organism: Lathyrus oleraceus

label_protocol: Total RNA (1 µg of each) was amplified and aminoallyl-labelled using MessageAmpTM II aRNA kit (Ambion) and 5-(3-aminoallyl)-2’deoxyuridine-5’-triphosphate (aa-dUTP, Ambion) following the manufacturer´s instructions. Approximately, 40-50 µg of aRNA was obtained. For each sample, 7.5 µg of aminoallyl-labelled aRNA was resuspended in 0.1 M Na2CO3 (pH 9.0) and labelled with either Cy3 or Cy5 Mono NHS Ester (CyTMDye Post-labelling Reactive Dye Pack, Amersham). The samples were purified following the manufacturer´s instructions for MegaclearTM (Ambion). Cy3 and Cy5 incorporation was measured using 1 µl of the probe in a Nanodrop spectrophotometer (Nanodrop Technologies Inc.). For each hybridization 200 pmol of Cy3 and Cy5 probes were mixed, dried in speed-vac, and resuspended in 9 µl of RNase-free water. Labelled aRNA was fragmented by adding 1 µl of 10X Fragmentation buffer (Ambion) and incubating at 70ºC for 15 minutes. The reaction was stopped with 1 µl of Stop solution (Ambion). Integrity and average size of Total RNA, aRNA and fragmented aRNA were evaluated using a Bioanalyzer 2100 (Agilent). Average size of aRNAs was about 1000 nucleotides and of fragmented aRNAs 100 nucleotides. The final volume of the probe was diluted to 100 µl in hybridization solution.

growth_protocol: Germination tests were performed on 1 % water agar at 25 °C under warm white fluorescent light (15 umol m-2 s-1) at a day / night cycle (8 /16h). Germination was defined as radical emergence by at least 2 mm.

extract_protocol: Total RNA was isolated from 30-50 mg ground seed powder following protocols of Oñate-Sánchez and Vicente-Carbajosa (2008)

treatment_protocol: Seeds of Pisum sativum L. cv Alaska Early (‘Abundant Life Seed Foundation’, Port Townsend, USA) were equilibrated at 20 ± 1 °C for ~5 weeks over non-saturated LiCl of 60% relative humidity (Hay et al., 2008) until their MC was stable at 12%. Relative humidity was recorded with a Rotronic AWVC-D10 Hygropalm and MC measured gravimetrically after drying for 17 h at 103 °C. These equilibrated seeds are referred to as ‘non-aged controls’. Seeds of 12 % MC were artificially aged in sealed bottles at 50 °C. Viability was lost after 55 d, during which time seed MC did not change significantly. At intervals, germination tests were performed on 1 % water agar at 25 °C at a day (15 umol m-2 s-1) / night cycle of 8 /16h. Germination was defined as radical emergence by >2 mm. For molecular analyses, 3-5 replicates of 20 pea seeds each were taken at each ageing interval, immediately frozen in liquid nitrogen, freeze dried and ground to a fine powder in hermetically closed, liquid nitrogen-cooled Teflon capsule using a laboratory mill (Braun Microdismembrator). The powder was stored at - 70 °C in humidity-proof vials until use in all assays

tag: cultivar

value: Alaska Early

value: Seeds

value: Non-aged control

value: Aged 15 days


title: 0 vs. 15 days. Replicate 1

description: Biological replicate 1 of 3. Control non-aged seeds vs. 15 days aged seeds.

source_name: Seeds of Pisum sativum L. cv Alaska Early (‘Abundant Life Seed Foundation’, Port Townsend, USA)


title: breast_tumor_sample_TL20070522_5_E1

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_E2
sample ID: 021706200
sample ID of_age- and cage-matched_mouse: 021706211

value: female


title: normal breast from control mouse_sample_TL20070522_5_D4

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_D3
sample ID: 090706210
sample ID of_age- and cage-matched_mouse: 090706200

source_name: normal whole breast tissue, at time when matched tumor-bearing mouse had 1 cm breast tumor

value: FVB


title: 0 vs. 15 days. Replicate 2

description: Biological replicate 2 of 3. Control non-aged seeds vs. 15 days aged seeds.


title: breast_tumor_sample_TL20070522_5_D5

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_D6
sample ID: 120106220
sample ID of_age- and cage-matched_mouse: 120106230

source_name: tumor whole breast tissue, at 1 cm tumor size


title: breast_tumor_sample_TL20070522_5_D1

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_D2
sample ID: 012006200
sample ID of_age- and cage-matched_mouse: 012006212


title: 0 vs. 12 days. Replicate 3

description: Biological replicate 3 of 3. Control non-aged seeds vs. 12 days aged seeds.

value: Aged 12 days


title: breast_tumor_sample_TL20070522_5_D3

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_D4
sample ID: 090706200
sample ID of_age- and cage-matched_mouse: 090706210

value: doxycycline-inducible, bitransgenic MMTV-rtTA/TetO-NeuNT (Her2/Neu) mouse model


title: MDA 30.5 mM sample 5 [12996A]

source_name: control for 63_MDA_100%

value: vehicle control

value: Human PBMC

value: GTX


title: MDA 30.5 mM sample 2 [12994C]

source_name: control for 58_MDA_100%


title: MDA 30.5 mM sample 1 [12994A]

source_name: control for 56_MDA_100%


title: normal breast from control mouse_sample_TL20070522_5_C6

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_C5
sample ID: 120106210
sample ID of_age- and cage-matched_mouse: 120106200

value: control mice transgenic for TetO-NeuNT only and littermates of the bitransgenic mice


title: normal breast from control mouse_sample_TL20070522_5_D2

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_D1
sample ID: 012006212
sample ID of_age- and cage-matched_mouse: 012006200


title: MDA 3.05 mM sample 5 [12996B]

source_name: control for 63_MDA_10%


title: 0 vs. 12 days. Replicate 2

description: Biological replicate 2 of 3. Control non-aged seeds vs. 12 days aged seeds.


title: AFB1 1.25 mM sample 1 [23988D]

source_name: control for 79_AFB1_1%


title: MDA 30.5 mM sample 3 [12995A]

source_name: control for 59_MDA_100%


title: 0 vs. 12 days. Replicate 1

description: Biological replicate 1 of 3. Control non-aged seeds vs. 12 days aged seeds.


title: normal breast from control mouse_sample_TL20070522_5_C4

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_C3
sample ID: 082406251
sample ID of_age- and cage-matched_mouse: 082406241


title: MDA 3.05 mM sample 4 [12995D]

source_name: control for 62_MDA_10%


title: breast_tumor_sample_TL20070522_5_C3

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_C4
sample ID: 082406241
sample ID of_age- and cage-matched_mouse: 082406251


title: normal breast from control mouse_sample_TL20070522_5_C2

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_C1
sample ID: 011906215
sample ID of_age- and cage-matched_mouse: 011906205


title: breast_tumor_sample_TL20070522_5_C5

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_C6
sample ID: 120106200
sample ID of_age- and cage-matched_mouse: 120106210


title: 0 vs. 8 days. Replicate 3

description: Biological replicate 3 of 3. Control non-aged seeds vs. 8 days aged seeds.

value: Aged 8 days


title: 0 vs. 8 days. Replicate 2

description: Biological replicate 2 of 3. Control non-aged seeds vs. 8 days aged seeds.


title: NDMA 67.5 mM sample 1 [13002A]

source_name: control for 69_DMNA_100%

value: DMNA


title: breast_tumor_sample_TL20070522_5_C1

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_C2
sample ID: 011906205
sample ID of_age- and cage-matched_mouse: 011906215

value: tumor whole breast tissue, at 1 cm tumor size


title: 0 vs. 8 days. Replicate 1

description: Biological replicate 1 of 3. Control non-aged seeds vs. 8 days aged seeds.


title: MDA 3.05 mM sample 3 [12995B]

source_name: control for 59_MDA_10%


title: normal breast from control mouse_sample_TL20070522_5_B6

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_B5
sample ID: 111706230
sample ID of_age- and cage-matched_mouse: 111706220

value: normal whole breast tissue, at time when matched tumor-bearing mouse had 1 cm breast tumor


title: breast_tumor_sample_TL20070522_5_B5

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_B6
sample ID: 111706220
sample ID of_age- and cage-matched_mouse: 111706230


title: normal breast from control mouse_sample_TL20070522_5_B4

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_B3
sample ID: 031706240
sample ID of_age- and cage-matched_mouse: 031706250


title: normal breast from control mouse_sample_TL20070522_5_B2

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_B1
sample ID: 122105214
sample ID of_age- and cage-matched_mouse: 122105200


title: normal breast from control mouse_sample_TL20070522_5_A8

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_A7
sample ID: 011107220
sample ID of_age- and cage-matched_mouse: 011107230


title: breast_tumor_sample_TL20070522_5_B3

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_B4
sample ID: 031706250
sample ID of_age- and cage-matched_mouse: 031706240


title: normal breast from control mouse_sample_TL20070522_5_A6

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_A5
sample ID: 111706210
sample ID of_age- and cage-matched_mouse: 111706200


title: breast_tumor_sample_TL20070522_5_B1

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_B2
sample ID: 122105200
sample ID of_age- and cage-matched_mouse: 122105214


title: PCB153 250 µM sample 2 [13136A]

source_name: control for 75_PCB_100%

value: NGTX

value: PCB


title: breast_tumor_sample_TL20070522_5_A7

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_A8
sample ID: 011107230
sample ID of_age- and cage-matched_mouse: 011107220


title: 4-HNE 32.05 µM sample 4 [23945B]

source_name: control for 87_4-HNE_10%


title: breast_tumor_sample_TL20070522_5_A5

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_A6
sample ID: 111706200
sample ID of_age- and cage-matched_mouse: 111706210


title: MDA 3.05 mM sample 2 [12994D]

source_name: control for 58_MDA_10%

value: MDA


title: normal liver from control mouse_sample_TL20070522_3_4_A6

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_A5
sample ID: 111706213
sample ID of_age- and cage-matched_mouse: 111706202

source_name: normal whole liver tissue, at time when breast tumor of matched tumor-bearing mouse had reached 1 cm size


title: normal breast from control mouse_sample_TL20070522_5_A4

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_A3
sample ID: 031706230
sample ID of_age- and cage-matched_mouse: 031706220


title: ob/ob TBP-2-/-

city: Kyoto

first: Hiroshi

last: Masutani

address: 53, Kawaharacho, Shogoin, Sakyo

country: Japan

institute: Institute for Virus Research, Kyoto University

description: Gene expresion in skeletal muscle of ob/ob TBP-2-/-  at 10 weeks age

hyb_protocol: Hybridization and washing were performed using Gene Expression Hybridization Kit <5188-5242> and Gene Expression Wash Buffer 1 & 2 <5188-5327> (Agilent Technologies) according to the manufacture's instruction. Cy-3labelled cRNA was fragmented at 60℃ for 30 min

scan_protocol: Slides (Whole Mouse genome, G4122F, Agilent Technologies) were scanned immediately after washing on the scaner (G2505B, Agilent Technologies)

data_processing: The scaned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent Technology). The obtained data were analyzed with GenespringGX. Per-chip normalizations were set to the 75th percentile, and per-gene normalizations to the median and specific samples.

source_name: fed ad lib skeletal muscle ob/ob TBP-2-/-

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5μg RNA using the Quick Amp labeling kit, one-color <5190-0442> and Agilent RNA Spike-In Kit (Agilent Technology) accordinfg to the manufacture's recommendations.

growth_protocol: skeletal muscle from 10 weeks aged mice

extract_protocol: Total RNA was extracted from the skeletal muscle of WT, TBP-2-/-, ob/ob, ob/ob TBP-2-/- mice using an Rneasy Fibrous Tissue Mini Kit (Qiagen)

treatment_protocol: The fresh skeletal from WT, TBP-2-/-, ob/ob ob/ob TBP-2-/- at 10 weeks age were desected and were immidiately treated with RNAlater solution at overnight

value: skeletal muscle

tag: genotype/variation

value: ob/ob TBP-2-/-

value: 10 weeks


title: ob/ob

description: Gene expresion in skeletal muscle of ob/ob at 10 weeks age

source_name: fed ad lib skeletal muscle Tob/ob

value: Tob/ob


title: 4-HNE 32.05 µM sample 3 [23944D]

source_name: control for 86_4-HNE_10%


title: 4-HNE 32.05 µM sample 2 [23944B]

source_name: control for 85_4-HNE_10%


title: breast_tumor_sample_TL20070522_5_A1

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_A2
sample ID: 121505214
sample ID of_age- and cage-matched_mouse: 121505200

source_name: tumor whole breast tissue, at 1 cm tumor size

value: female

value: FVB


title: WT

description: Gene expresion in skeletal muscle of WT at 10 weeks age

source_name: fed ad lib skeletal muscle WT

value: WT


title: TBP-2-/-

description: Gene expresion in skeletal muscle of TBP-2-/- at 10 weeks age

source_name: fed ad lib skeletal muscle TBP-2-/-


title: 4-HNE 32.05 µM sample 5 [23945D]

source_name: control for 88_4-HNE_10%

value: vehicle control

value: Human PBMC


title: anti-miR treated liver metastasis sample R3

status: Public on Oct 21 2010

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

country: France

institute: IARC WHO

hyb_protocol: 10 micrograms of cRNA generated by the IVT procedure was hybridized for 16 hr to the Affymetrix array according to the manufacturer's manual. Genechips® were processed using protocol EukGE_WS2v4 450 for Genechip® fluidics station 450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using GeneSpring GX11 program. No further adjustments were made to the data in the table.

source_name: Total RNA of anti-miR treated metastasis

label_protocol: 100 ng of total cellular RNA was converted to cDNA/cRNA and labeled using the Affymetrix 3'IVT Express Kit.

growth_protocol: Human melanoma cells A375 metastatic to liver treated with either control or anti-miR-182 using a mouse model.

extract_protocol: Total RNA was extracted using RNeasy micro-elute columns (QIAGEN), according to manufacturer's instructions.

treatment_protocol: In vivo liver metastasis model treated with either anti-miR-182 or control administered intraperitoneal twice weekly over 4 weeks.

tag: treatment


title: MDA 3.05 mM sample 1 [12994B]

source_name: control for 56_MDA_10%

value: GTX


title: control treated liver metastasis sample R1

source_name: Total RNA of control treated liver metastasis

value: Control


title: anti-miR treated liver metastasis sample R2


title: control treated liver metastasis sample R2


title: 4-HNE 32.05 µM sample 1 [23943D]

source_name: control for 84_4-HNE_10%


title: control treated liver metastasis sample R4


title: normal breast from control mouse_sample_TL20070522_5_A2

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_A1
sample ID: 121505200
sample ID of_age- and cage-matched_mouse: 121505214

source_name: normal whole breast tissue, at time when matched tumor-bearing mouse had 1 cm breast tumor

value: control mice transgenic for TetO-NeuNT only and littermates of the bitransgenic mice


title: anti-miR treated liver metastasis sample R4


title: control treated liver metastasis sample R3


title: breast_tumor_sample_TL20070522_5_A3

description:
Dataset Name: Whole breast array
sample name of age- and cage-matched_mouse: TL20070522_5_A4
sample ID: 031706220
sample ID of_age- and cage-matched_mouse: 031706230

value: doxycycline-inducible, bitransgenic MMTV-rtTA/TetO-NeuNT (Her2/Neu) mouse model

value: tumor whole breast tissue, at 1 cm tumor size


title: anti-miR treated liver metastasis sample R1


title: Normal_stromal_3

city: Indianapolis

first: Brittney-Shea

last: Herbert

state: IN

address: 975 W. Walnut st.

department: Medical & Molecular Genetics

institute: Indiana University School of Medicine

hyb_protocol: Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.

scan_protocol: The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.

data_processing: The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.

source_name: breast stromal cells

label_protocol: Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual

growth_protocol: All cells were tested at the same log phase of cell growth and at similar passages.  Four independent cultures of each sample cell line were collected for RNA extraction.  HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO).  Medium was changed every 2-3 days.  HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].

extract_protocol: Total RNA extracted using RNeasy mini-kit from Qiagen

tag: phenotype

value: normal

tag: ID

value: stromal


title: LiFraumeni_stromal_50_1

value: Li-Fraumeni


title: LiFraumeni_stromal_50_4


title: LiFraumeni_stromal_IUSM_2

value: IUSM


title: LiFraumeni_stromal_IUSM_4


title: Normal_stromal_4


title: LiFraumeni_stromal_50_2


title: LiFraumeni_stromal_IUSM_3


title: LiFraumeni_stromal_IUSM_1


title: LiFraumeni_stromal_50_3


title: LiFraumeni_epithelial_IUSM_4

source_name: breast epithelial cells

value: epithelial


title: LiFraumeni_epithelial_IUSM_3


title: Normal_stromal_1


title: Normal_stromal_2


title: LiFraumeni_epithelial_IUSM_2


title: LiFraumeni_epithelial_50_3


title: LiFraumeni_epithelial_50_2


title: LiFraumeni_epithelial_50_1


title: LiFraumeni_epithelial_IUSM_1


title: Normal_epithelial_4


title: Normal_epithelial_3


title: Normal_epithelial_1


title: LiFraumeni_epithelial_50_4


title: LX_ND_10_8_36_CH12LX_T_4_013009_Mouse430_2_RSTMSU601_9

city: Research Triangle Park

first: Russell

middle: Scott

last: Thomas

state: NC

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

description: Sample Type: B cell line, Number of Cells Seeded: 1X10^5/ml, 3ml W of 6W plate, 4 or 2 wells per treatment depending on timepoint, Cell Type: CH12. LX, Harvest Time Point: 8, Units of Harvest Time Point: hr

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix GCOS 1.0

source_name: TCDD, 8hr

label_protocol: standard Affymetrix protocol

growth_protocol: Growth Media: RPMISAdvance, HIFBS, HEPES, Pen/Strepp, L Glutamine, Mercaptoethanol, Amount of Media: 3, Units of Media: ml

extract_protocol:
Extraction Method: RNeasy
Additional Purification Method: Concentrated on Speed Vac

treatment_protocol: in vitro Treatment: TCDD, Treatment Duration: 8, Units of Duration: hr, Vehicle for Chemical: DMSO, Route of Exposure: media, Dose or Concentration: 10, Units of Dose or Concentration: nM

value: B cells

tag: cell line

tag: array type

tag: amount to core

tag: units of amount

value: ug

tag: ratio

tag: sample preservation

value: -20 in Nuclease free dH2O (RNeasy kit)


title: LX_ND_10_8_14_CH12LX_T_2_120408_Mouse430_2_RSTMSU601_9

tag: cell type


title: LX_ND_10_36_42_CH12LX_T_4_013009_Mouse430_2_RSTMSU601_9

description: Sample Type: B cell line, Number of Cells Seeded: 1X10^5/ml, 3ml W of 6W plate, 4 or 2 wells per treatment depending on timepoint, Cell Type: CH12. LX, Harvest Time Point: 36, Units of Harvest Time Point: hr

source_name: TCDD, 36hr

treatment_protocol: in vitro Treatment: TCDD, Treatment Duration: 36, Units of Duration: hr, Vehicle for Chemical: DMSO, Route of Exposure: media, Dose or Concentration: 10, Units of Dose or Concentration: nM


title: Normal_epithelial_2


title: LX_ND_10_24_7_CH12LX_T_1_111908_Mouse430_2_RSTMSU601_9

description: Sample Type: B cell line, Number of Cells Seeded: 1X10^5/ml, 3ml W of 6W plate, 4 or 2 wells per treatment depending on timepoint, Cell Type: CH12. LX, Harvest Time Point: 24, Units of Harvest Time Point: hr

source_name: TCDD, 24hr

treatment_protocol: in vitro Treatment: TCDD, Treatment Duration: 24, Units of Duration: hr, Vehicle for Chemical: DMSO, Route of Exposure: media, Dose or Concentration: 10, Units of Dose or Concentration: nM


title: LX_ND_10_48_22_CH12LX_T_2_120408_Mouse430_2_RSTMSU601_9

description: Sample Type: B cell line, Number of Cells Seeded: 1X10^5/ml, 3ml W of 6W plate, 4 or 2 wells per treatment depending on timepoint, Cell Type: CH12. LX, Harvest Time Point: 48, Units of Harvest Time Point: hr

source_name: TCDD, 48hr

treatment_protocol: in vitro Treatment: TCDD, Treatment Duration: 48, Units of Duration: hr, Vehicle for Chemical: DMSO, Route of Exposure: media, Dose or Concentration: 10, Units of Dose or Concentration: nM


title: LX_ND_10_8_3_CH12LX_T_1_111908_Mouse430_2_RSTMSU601_9


title: LX_ND_10_36_31_CH12LX_T_3_121508_Mouse430_2_RSTMSU601_9


title: LX_ND_10_24_29_CH12LX_T_3_121508_Mouse430_2_RSTMSU601_9


title: LX_ND_10_48_33_CH12LX_T_3_121508_Mouse430_2_RSTMSU601_9


title: LX_ND_10_24_40_CH12LX_T_4_013009_Mouse430_2_RSTMSU601_9


title: LX_ND_10_8_25_CH12LX_T_3_121508_Mouse430_2_RSTMSU601_9


title: LX_ND_10_36_9_CH12LX_T_1_111908_Mouse430_2_RSTMSU601_9


title: LX_ND_10_36_20_CH12LX_T_2_120408_Mouse430_2_RSTMSU601_9


title: LX_ND_10_48_11_CH12LX_T_1_111908_Mouse430_2_RSTMSU601_9


title: LX_ND_10_48_44_CH12LX_T_4_013009_Mouse430_2_RSTMSU601_9


title: LX_ND_10_12_5_CH12LX_T_1_111908_Mouse430_2_RSTMSU601_9

description: Sample Type: B cell line, Number of Cells Seeded: 1X10^5/ml, 3ml W of 6W plate, 4 or 2 wells per treatment depending on timepoint, Cell Type: CH12. LX, Harvest Time Point: 12, Units of Harvest Time Point: hr

source_name: TCDD, 12hr

treatment_protocol: in vitro Treatment: TCDD, Treatment Duration: 12, Units of Duration: hr, Vehicle for Chemical: DMSO, Route of Exposure: media, Dose or Concentration: 10, Units of Dose or Concentration: nM


title: LX_ND_10_12_38_CH12LX_T_4_013009_Mouse430_2_RSTMSU601_9


title: LX_ND_10_12_27_CH12LX_T_3_121508_Mouse430_2_RSTMSU601_9


title: LX_ND_10_12_16_CH12LX_T_2_120408_Mouse430_2_RSTMSU601_9


title: LX_ND_0_8_2_CH12LX_D_1_111908_Mouse430_2_RSTMSU601_9

source_name: DMSO, 8hr

treatment_protocol: in vitro Treatment: DMSO, Treatment Duration: 8, Units of Duration: hr, Vehicle for Chemical: DMSO, Route of Exposure: media, Dose or Concentration: 0, Units of Dose or Concentration: nM


title: LX_ND_0_8_13_CH12LX_D_2_120408_Mouse430_2_RSTMSU601_9


title: LX_ND_0_8_35_CH12LX_D_4_013009_Mouse430_2_RSTMSU601_9


title: LX_ND_0_8_24_CH12LX_D_3_121508_Mouse430_2_RSTMSU601_9


title: LX_ND_0_48_43_CH12LX_D_4_013009_Mouse430_2_RSTMSU601_9

source_name: DMSO, 48hr

treatment_protocol: in vitro Treatment: DMSO, Treatment Duration: 48, Units of Duration: hr, Vehicle for Chemical: DMSO, Route of Exposure: media, Dose or Concentration: 0, Units of Dose or Concentration: nM


title: LX_ND_0_48_21_CH12LX_D_2_120408_Mouse430_2_RSTMSU601_9


title: LX_ND_0_48_32_CH12LX_D_3_121508_Mouse430_2_RSTMSU601_9


title: LX_ND_0_48_10_CH12LX_D_1_111908_Mouse430_2_RSTMSU601_9


title: LX_ND_0_36_41_CH12LX_D_4_013009_Mouse430_2_RSTMSU601_9

source_name: DMSO, 36hr

treatment_protocol: in vitro Treatment: DMSO, Treatment Duration: 36, Units of Duration: hr, Vehicle for Chemical: DMSO, Route of Exposure: media, Dose or Concentration: 0, Units of Dose or Concentration: nM


title: LX_ND_0_12_26_CH12LX_D_3_121508_Mouse430_2_RSTMSU601_9

source_name: DMSO, 12hr

treatment_protocol: in vitro Treatment: DMSO, Treatment Duration: 12, Units of Duration: hr, Vehicle for Chemical: DMSO, Route of Exposure: media, Dose or Concentration: 0, Units of Dose or Concentration: nM


title: LX_ND_0_36_8_CH12LX_D_1_111908_Mouse430_2_RSTMSU601_9


title: LX_ND_10_24_18_CH12LX_T_2_120408_Mouse430_2_RSTMSU601_9


title: LX_ND_0_24_17_CH12LX_D_2_120408_Mouse430_2_RSTMSU601_9

source_name: DMSO, 24hr

treatment_protocol: in vitro Treatment: DMSO, Treatment Duration: 24, Units of Duration: hr, Vehicle for Chemical: DMSO, Route of Exposure: media, Dose or Concentration: 0, Units of Dose or Concentration: nM


title: LX_ND_0_24_39_CH12LX_D_4_013009_Mouse430_2_RSTMSU601_9


title: LX_ND_0_0_34_CH12LX_UN_4_013009_Mouse430_2_RSTMSU601_9

description: Sample Type: B cell line, Number of Cells Seeded: 1X10^5/ml, 3ml W of 6W plate, 4 or 2 wells per treatment depending on timepoint, Cell Type: CH12. LX, Harvest Time Point: 0, Units of Harvest Time Point: hr

source_name: Untreated, 0hr

treatment_protocol: in vitro Treatment: Untreated, Treatment Duration: 0, Units of Duration: hr, Vehicle for Chemical: DMSO, Route of Exposure: media, Dose or Concentration: 0, Units of Dose or Concentration: nM


title: WT brain (cerebellum) microvascular fragments, 2 months old, biological rep 3

city: Stockholm

first: Elisabet

last: Wallgard

address: Nobels väg 12A, PO Box 281

department: Dept. of Medical Epidemiology and Biostatistics

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from microvascular fragments

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GCRMA package in the bioconductor project (R version 2.4.1, gcrma version 2.6.0).

source_name: Mouse brain

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

extract_protocol: Extraction of total RNA was performed according to manufacturer's instructions using the RNeasy Mini Kit (Qiagen). RNA was DNase (Invitrogen) treated and samples were cleaned using RNeasy Minelute Cleanup Kit (Qiagen)

tag: strain

tag: gender

value: male

value: 2 months

value: brain microvascular fragments


title: WT Brain (cerebellum) microvascular fragments, 2 months old, biological rep 2

value: female

tag: tissue


title: LX_ND_0_0_23_CH12LX_UN_3_121508_Mouse430_2_RSTMSU601_9


title: WT brain (cerebrum) microvascular fragments, 2 months old, biological rep 1

tag: age


title: LX_ND_0_0_1_CH12LX_UN_1_111908_Mouse430_2_RSTMSU601_9


title: LX_ND_0_36_30_CH12LX_D_3_121508_Mouse430_2_RSTMSU601_9


title: LX_ND_0_24_6_CH12LX_D_1_111908_Mouse430_2_RSTMSU601_9


title: LX_ND_0_12_15_CH12LX_D_2_120408_Mouse430_2_RSTMSU601_9


title: LX_ND_0_12_4_CH12LX_D_1_111908_Mouse430_2_RSTMSU601_9


title: WT Brain (cerebrum) microvascular fragments, 2 months old, biological rep 2


title: WT brain (cerebrum) microvascular fragments, 2 months old, biological rep 3


title: LX_ND_0_24_28_CH12LX_D_3_121508_Mouse430_2_RSTMSU601_9


title: LX_ND_0_0_12_CH12LX_UN_2_120408_Mouse430_2_RSTMSU601_9

treatment_protocol: in vitro Treatment: Untreated, Treatment Duration: 0, Vehicle for Chemical: DMSO, Route of Exposure: media, Dose or Concentration: 0, Units of Dose or Concentration: nM


title: LX_ND_0_36_19_CH12LX_D_2_120408_Mouse430_2_RSTMSU601_9


title: Tie2Cre, R26P+/0, pdgfb-/- brain (cerebellum) microvascular fragments, 1 year old, biological rep 4

value: C57/SV129 (mixed background) Tie2Cre, R26P+/0, pdgfb-/-


title: LX_ND_0_12_37_CH12LX_D_4_013009_Mouse430_2_RSTMSU601_9


title: WT brain (cerebellum) microvascular fragments, 2 months old, biological rep 1


title: Tie2Cre, R26P+/0, pdgfb-/- brain (cerebrum) microvascular fragments, 1 year old, biological rep 4


title: Tie2Cre, R26P+/0, pdgfb-/- brain (cerebellum) microvascular fragments, 1 year old, biological rep 3


title: Tie2Cre, R26P+/0, pdgfb-/- brain (cerebrum) microvascular fragments, 1 year old, biological rep 3


title: Tie2Cre, R26P+/0, pdgfb-/- brain (cerebellum) microvascular fragments, 1 year old, biological rep 2


title: Tie2Cre, R26P+/0, pdgfb-/- brain (cerebrum) microvascular fragments, 1 year old, biological rep 2


title: Tie2Cre, R26P+/0, pdgfb-/- brain (cerebrum) microvascular fragments, 1 year old, biological rep 1


title: R26P+/0, pdgfb+/+ brain (cerebellum) microvascular fragments, 1 year old, biological rep 4

value: C57/SV129 (mixed background) R26P+/0, pdgfb+/+


title: Tie2Cre, R26P+/0, pdgfb-/- brain (cerebellum) microvascular fragments, 1 year old, biological rep 1


title: R26P+/0, pdgfb+/+ brain (cerebrum) microvascular fragments, 1 year old, biological rep 4


title: R26P+/0, pdgfb+/+ brain (cerebrum) microvascular fragments, 1 year old, biological rep 3


title: R26P+/0, pdgfb+/+ brain (cerebellum) microvascular fragments, 1 year old, biological rep 3


title: R26P+/0, pdgfb+/+ brain (cerebellum) microvascular fragments, 1 year old, biological rep 2


title: R26P+/0, pdgfb+/+ brain (cerebrum) microvascular fragments, 1 year old, biological rep 2


title: R26P+/0, pdgfb+/+ brain (cerebellum) microvascular fragments, 1 year old, biological rep 1


title: pdgfbret/ret brain microvascular fragments, 7 months old, biological rep 4

value: C57/B6/J pdgfbret/ret

value: 7 months


title: R26P+/0, pdgfb+/+ brain (cerebrum) microvascular fragments, 1 year old, biological rep 1


title: C.j. 11168 versus NW Dye Swap of DNA Comparison #2

type: genomic

city: East Lansing

first: Linda

middle: S.

last: Mansfield

state: MI

address: 181 Food Safety Bldg.

department: Microbiology and Molecular Genetics

institute: Michigan State University

description: Biological replicate 4 of 4: genomic DNA content comparison, dye swap.

hyb_protocol: Ambion SlideHyb solution was added to the denatured, labeled and combined samples.  Hybridized in cassettes in 54 degree water bath overnight

scan_protocol: GenePix 4000B scanner was used to scan arrays for fluorescence intensity, maximizing gains for sample clarity

data_processing: After GenePix was used for spot sizing and evaluation, gpr files were generated for each test/sample.  GACK analysis was then performed to evaluate presence/absence of each ORF

molecule: genomic DNA

organism: Campylobacter jejuni

source_name: C.j. 11168 genomic DNA

label_protocol: DNA was labeled with aminoallyl-dUTP using the BioPrime random priming DNA labeling kit (Invitrogen, Carlsbad, CA).

growth_protocol: Each strain was streaked from frozen stock on two tryptose soya agar plates containing 5% defibrinated sheeps’ blood; plates were incubated for 48 hours at 37 C in 5% CO2.  A single isolated colony from each plate was chosen and streaked onto another plate (biological replicates).

extract_protocol: Genomic DNA was isolated using the Qiagen Dneasy blood and tissue kit according to manufacturer's instructions.  20 ug. Of DNA was sheared using the GeneMachine Hydroshear to a length of 5.2 kb prior to labeling

treatment_protocol: Growth from each of the second plates was harvested separately.

tag: disease state

value: Enteritis-producing

source_name: C.j. NW genomic DNA

value: NW


title: C.j. 11168 versus NW DNA Comparison #2

description: Biological replicate 3 of 4: genomic DNA content comparison.


title: C.j. 11168 versus NW DNA Comparison #1

description: Biological replicate 1 of 4: genomic DNA content comparison.


title: C.j. 11168 versus 33560 Dye Swap of DNA Comparison #2

source_name: C.j. 33560 genomic DNA

value: Non-colonizing


title: C.j. 11168 versus NW Dye Swap of DNA Comparison #1

description: Biological replicate 2 of 4: genomic DNA content comparison, dye swap.


title: C.j. 11168 versus 33560 DNA Comparison #2


title: C.j. 11168 versus 33560 Dye Swap of DNA Comparison #1


title: C.j. 11168 versus 33560 DNA Comparison #1


title: C.j. 11168 versus D2600 Dye Swap of DNA Comparison #2

source_name: C.j. D2600 genomic DNA

value: Colonizing, no enteritis


title: C.j. 11168 versus D2600 DNA Comparison #2


title: pdgfbret/ret brain microvascular fragments, 7 months old, biological rep 3


title: pdgfbret/ret brain microvascular fragments, 7months old, biological rep 2


title: pdgfbret/ret brain microvascular fragments, 10 months old, biological rep 1

value: 10 months


title: C.j. 11168 versus D2600 Dye Swap of DNA Comparison #1


title: C.j. 11168 versus D2586 Dye Swap of DNA Comparison #1

source_name: C.j. D2586 genomic DNA


title: C.j. 11168 versus D2586 DNA Comparison #2


title: pdgfbret/+ brain microvascular fragments, 10 months old, biological rep 4

value: C57/B6/J pdgfbret/+


title: C.j. 11168 versus D2586 Dye Swap of DNA Comparison #2


title: C.j. 11168 versus D2600 DNA Comparison #1


title: pdgfbret/+ brain microvascular fragments, 8 months old, biological rep 3

value: 8 months


title: pdgfbret/+ brain microvascular fragments, 8 months old, biological rep 2


title: C.j. 11168 versus D2586 DNA Comparison #1


title: C.j. 11168 versus D0835 DNA Comparison #2

source_name: C.j. D0835 genomic DNA


title: C.j. 11168 versus D0835 Dye Swap of DNA Comparison #2


title: pdgfbret/+ brain microvascular fragments, 8 months old, biological rep 1


title: C.j. 11168 versus D0835 DNA Comparison #1


title: PC346Flu2 vs. PC346C rep4

city: Rotterdam

first: Rute

last: Marques

address: Dr Molewaterplein 50

institute: Erasmus MC

description: Not applicable

hyb_protocol: Before the hybridization, microarray slides were prehybridized in 5x SSC, 0.05% SDS, 4% BSA solution for 30 min at 45°C, washed twice with RNAse-free water for 2 min, rinsed with isopropanol and spin-dried for 3 min at 1500g. Microarray hybridizations were performed overnight at 45°C, with continuous agitation, in a HS4800 Hybridization Station (Tecan Benelux BV). Finally, the arrays were washed automatically in the Hybridization Station using: 2x SSC/0.05% SDS (at 45°C), 1x SSC and 0.2x SSC (at room temperature), and dried under a stream of N2, before scanning.

scan_protocol: Arrays were scanned in a ScanArray Express HT scanner (Perkin Elmer, Nederland BV) and spot intensities were quantified using Imagene software (Bio Discovery Inc, El Sequndo, CA, USA).

data_processing: Loewess normalization per subarray was performed using limma-package (http://bioinf.wehi.edu.au/limma/) from Bioconductor (http://www.bioconductor.org), followed by background substraction. To scale between arrays, the global median intensity per array was set at 1000. Dye intensities below 200 were then thresholded at 200, to minimize noise and make fold-change on the low-intensity range more robust against outliers. Spots with intensities below the threshold (200) for both Cy3 and Cy5 channels in more than 2 of the 4 arrays performed per subline were flagged and excluded from the analysis. Sample to reference ratios were then calculated and 2log transformed. Spots that showed opposite effects for the dye-swap/biological replicates were excluded from further analysis

source_name: PC346C cell line

label_protocol: Cy3- or Cy5-labelled RNA probes were produced by incorporating amino-allyl UTP during RNA amplification, followed by coupling to N-hydroxysuccinimide modified dye. Finally, 2 µg of the contra-labelled RNA probes were combined and purified/concentrated using Microcon-YM 30. Probe was collected in 5-15 ml final volume and resuspended in 80 µl Ambion hybridization buffer number 1.

growth_protocol: The basic culture medium used in the maintenance of PC346 cell lines consisted of DMEM-F12 medium (Cambrex BioWhitaker, Belgium) supplemented with 2% fetal calf serum (FCS; PAN Biotech GmbH, Aidenbach, Germany), 1% insulin-transferrin-selenium (Gibco BRL), 0.01% bovine serum albumin (Boehringer Mannheim, Germany), 10 ng/ml epidermal growth factor (Sigma-Aldrich), penicillin/streptomycin antibiotics (100 U/ml penicillin, 100 mg/ml streptomycin; BioWhitaker, Belgium); plus the following additions: 100 ng/ml fibronectin (Harbor Bio-Products, Tebu-bio, The Netherlands), 20 mg/ml fetuine (ICN Biomedicals, The Netherlands), 50 ng/ml choleratoxin, 0.1 mM phosphoethanolamine, 0.6 ng/ml triiodothyronine and 500 ng/ml dexametason (all from Sigma). Cells were grown in T25 PrimariaTM tissue culture flasks (BD Biosciences Benelux N.V, The Netherlands) at 37oC under 5% CO2 humidified atmosphere.

extract_protocol: Cells were seeded in their respective selection medium to reach ~50% confluency and allowed to grow for 2 days.  Total RNA was isolated with RNAzol B reagent (Campro Scientific, Veenendaal, The Netherlands) and further purified through RNeasy columns (Qiagen) with on-column DNA digestion, according to the manufacturer’s protocol.

treatment_protocol: PC346C cells were maintained in culture in the complete medium described above, supplemented with 0.1 nM 17-methyltrienolone (R1881; NEN, Boston MA, USA). PC346DCC selection medium was supplemented as described above, but depleted from androgens by using dextran-coated charcoal (DCC) treated FCS. PC346Flu1 and PC346Flu2 culture medium was also androgen depleted by using 2% DCC-FCS, and supplemented with 1 μM of hydroxyflutamide (OH-flutamide, Schering-Plough Research Institute, New Jersey, USA).

tag: selection medium

value: medium supplemented with 1nM R1881

source_name: PC346Flu2 cell line

value: steroid-stripped medium supplemented with 1uM hydroxyflutamide


title: C.j. 11168 versus D0121 Dye Swap of DNA comparison #2

source_name: C.j. D0121 genomic DNA


title: PC346Flu2 vs. PC346C rep3

description: Not applicable


title: Melanoma cell line_SKMEL103 [SNP]

city: New York

first: Iman

last: Osman

state: NY

address: 522 First Avenue, SML405

department: Urology

institute: New York University School of Medicine

description: Hybridized to SNP6.0 Arrays

hyb_protocol: DNA was restriction digested, PCR purified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files were generated using the GeneChip Command Console software (Affymetrix), and the Birdseed v2 algorithm (Korn et al. Nat Genet, 2008. PMID 18776909) was used to make the genotype calls and summarize the probe-set intensity (SPI) values for ensuing copy number analysis. A single normal reference genome profile assayed in the same batch was created using values from the 2 normal melanocytes cultured from infant foreskin (HEM-N and HEM-LP).
Primary data description: 1. 22 CHP files for melanoma and melanocyte cell lines 2. Data table that includes the Genotype Call (AA, AB, BB, NC, and NoCall) and the intensity signal for signal A and signal B in 22 cell lines.

source_name: Melanoma cell line_SKMEL103

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines derived from primary tumors were cultured in Mel 2% medium (Fang et al.Cancer Res, 2005. PMID 16230395), and metastatic cell lines were cultured as previously described (Segura et al. Proc Natl Acad Sci USA, 2009. PMID 19188590  ).

extract_protocol: Melanoma and melanocyte DNA was extracted using the Qiagen QIAmp DNA Mini kit (Qiagen Valencia, CA). DNA quantity was assessed by UV spectrophotometry and quality was assayed by agarose gel electrophoresis.

tag: histological subtype

value: Metastatic melanoma

value: Melanoma cell line, SKMEL103


title: Melanoma cell line_SKMEL173 [SNP]

description: Hybridized to SNP6.0 Arrays

data_processing:
CEL files were generated using the GeneChip Command Console software (Affymetrix), and the Birdseed v2 algorithm (Korn et al. Nat Genet, 2008. PMID 18776909) was used to make the genotype calls and summarize the probe-set intensity (SPI) values for ensuing copy number analysis. A single normal reference genome profile assayed in the same batch was created using values from the 2 normal melanocytes cultured from infant foreskin (HEM-N and HEM-LP).
1. 22 CHP files for melanoma and melanocyte cell lines 2. Data matrix that includes the Genotype Call (AA, AB, BB, NC, and NoCall) and the intensity signal for signal A and signal B in 22 cell lines.

source_name: Melanoma cell line_SKMEL173

value: Melanoma cell line, SKMEL173


title: C.j. 11168 versus D0835 Dye Swap of DNA Comparison #1


title: Melanoma cell line_WM39 [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Melanoma cell line_WM39

value: Primary nodular melanoma

value: Melanoma cell line, WM39


title: PC346Flu2 vs. PC346C rep2

description: Not applicable


title: Melanoma cell line_SKMEL19 [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Melanoma cell line_SKMEL19

value: Melanoma cell line, SKMEL19


title: C.j. 11168 versus D6849 Dye Swap of DNA comparison #2

source_name: C.j. D6849 genomic DNA


title: Melanoma cell line_SKMEL94 [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Melanoma cell line_SKMEL94

value: Melanoma cell line, SKMEL94


title: C.j. 11168 versus D0121 DNA comparison #1


title: C.j. 11168 versus D0121 Dye Swap of DNA comparison #1


title: Melanoma cell line_SKMEL85 [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Melanoma cell line_SKMEL85

value: Melanoma cell line, SKMEL85


title: C.j. 11168 versus D6849 Dye Swap of DNA comparison #1

value: Enteritis-producing


title: Melanoma cell line_WM1552c [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Melanoma cell line_WM1552c

value: Primary superficial spreading melanoma

value: Melanoma cell line, WM1552c


title: Melanoma cell line_LU451 [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Melanoma cell line_LU451

value: Metastatic nodular melanoma

value: Melanoma cell line, LU451


title: C.j. 11168 versus D0121 DNA comparison #2

value: Non-colonizing

source_name: C.j. 11168 genomic DNA


title: Melanoma cell line_A375 [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Melanoma cell line_A375

value: Melanoma cell line, A375


title: Melanoma cell line_SKMEL147 [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Melanoma cell line_SKMEL147

value: Melanoma cell line, SKMEL147


title: C.j. 11168 versus D6849 DNA comparison #1


title: Melanoma cell line_501 Mel [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Melanoma cell line_501 Mel

value: Melanoma cell line, 501 Mel


title: PC346Flu1 vs. PC346C rep4

description: Not applicable

value: medium supplemented with 1nM R1881

source_name: PC346Flu1 cell line

value: steroid-stripped medium supplemented with 1uM hydroxyflutamide


title: Immortalized melanocyte_Hermes2B [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Immortalized melanocyte_Hermes2B

value: Immortalized melanocyte

value: Immortalized melanocyte, Hermes2B


title: Melanoma cell line_SKMEL192 [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Melanoma cell line_SKMEL192

value: Metastatic melanoma

value: Melanoma cell line, SKMEL192


title: C.j. 11168 versus D6848 DNA comparison #2

source_name: C.j. D6848 genomic DNA


title: Melanoma cell line_SKMEL187 [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Melanoma cell line_SKMEL187

value: Melanoma cell line, SKMEL187


title: C.j. 11168 versus D6848 DNA comparison #1


title: C.j. 11168 versus D6848 Dye Swap of DNA comparison #2


title: C.j. 11168 versus D6847 Dye Swap of DNA comparison #2

source_name: C.j. D6847 genomic DN


title: Immortalized melanocyte_Hermes1 [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Immortalized melanocyte_Hermes1

value: Immortalized melanocyte, Hermes1


title: Melanoma cell line_WM278 [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Melanoma cell line_WM278

value: Primary nodular melanoma

value: Melanoma cell line, WM278


title: Melanoma cell line_WM35 [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Melanoma cell line_WM35

value: Primary superficial spreading melanoma

value: Melanoma cell line, WM35


title: Normal human melanocyte_HEM-N [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Normal human melanocyte_HEM-N

value: Normal melanocyte

value: Normal human melanocyte, HEM-N


title: Melanoma cell line_SKMEL100 [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Melanoma cell line_SKMEL100

value: Melanoma cell line, SKMEL100


title: Melanoma cell line_SKMEL29 [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Melanoma cell line_SKMEL29

value: Melanoma cell line, SKMEL29


title: C.j. 11168 versus D6849 DNA comparison #2

source_name: C.j. D6849 genomic DNA

value: Enteritis-producing


title: Control_2

city: Kamakura

first: Toshihiko

last: Kuroda

institute: Toray industries inc.

description: The raw data of each spot with a signal intensity greater than mean intensity plus 2 standard deviations (SD) of the background signal was considered to be valid.

hyb_protocol: See TORAY website for 3D-Gene Human miRNA Oligo chip : http://www.3d-gene.com/products/pro_007.html

scan_protocol: After stringent washes, fluorescent signals were scanned with the ScanArray Express Scanner (PerkinElmer, Waltham, MA).

data_processing: Fuorescent signals were scanned with the ScanArray Express Scanner (PerkinElmer, Waltham, MA) and analyzed using GenePix Pro version 5.0 (Molecular Devices, Sunnyvale, CA).

label_protocol: RNA was labeled with Cy5 using the Label IT miRNA labeling kit　(Takara Bio, Otsu, Japan)　according to the manufacturer’s　instructions.

extract_protocol: Total RNA was extracted from the snap frozen tissue specimens using TRIzol reagent (Invitrogen Japan, Tokyo, Japan) according to the manufacturer’s　instructions, and small RNA was purified and isolated from total RNA using the PureLink miRNA isolation kit (Invitrogen Japan).

value: Normal skeletal muscle


title: Control_4


title: Control_3


title: C.j. 11168 versus D6847 DNA comparison #2

source_name: C.j. D6847 genomic DNA

source_name: C.j. 11168 genomic DNA


title: C.j. 11168 versus D6847 DNA comparison #1


title: C.j. 11168 versus D6846 Dye Swap of DNA comparison #2

source_name: C.j. D6846 genomic DNA


title: C.j. 11168 versus D6847 Dye Swap of DNA comparison #1


title: PC346Flu1 vs. PC346C rep1

description: Not applicable

value: steroid-stripped medium supplemented with 1uM hydroxyflutamide

source_name: PC346C cell line

value: medium supplemented with 1nM R1881


title: Control_1


title: PC346DCC vs. PC346C rep4

description: Not applicable

source_name: PC346DCC cell line

value: steroid-stripped medium


title: Ewing tumor_5

source_name: Ewing tumor_5

value: Ewing tumor


title: PC346Flu1 vs. PC346C rep2

description: Not applicable

source_name: PC346Flu1 cell line


title: PC346Flu2 vs. PC346C rep1

description: Not applicable

source_name: PC346Flu2 cell line


title: PC346Flu1 vs. PC346C rep3

description: Not applicable


title: Ewing tumor_3

source_name: Ewing tumor_3


title: Ewing tumor_4

source_name: Ewing tumor_4


title: C.j. 11168 versus D6846 DNA comparison #2


title: C.j. 11168 versus D6846 Dye Swap of DNA comparison #1


title: Ewing tumor_2

source_name: Ewing tumor_2


title: PC346DCC vs. PC346C rep2

description: Not applicable


title: PC346DCC vs. PC346C rep3

description: Not applicable


title: Ewing tumor_1

source_name: Ewing tumor_1


title: Synovial sarcoma_10

source_name: Synovial sarcoma_10

value: Synovial sarcoma


title: R2-2 Cy5 hrpL 6h

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

description: Analysis used wild-type aerobic steady state RNA as control samples for comparison to the hrpL mutant experimental samples taken 6 h post-inoculation

hyb_protocol: The hybridization, wash, and dry were carried out in a LucideaTM Slidepro hybridization chamber (GEhealthcare, Piscataway, NJ, U.S.A.). After hybridization for 17 h at 60°C, the arrays were washed for 1 min each with wash solution I (6x SSPE [1x SSPE is 0.18 M NaCl, 10 mM NaH2PO4, and 1 mM EDTA, pH 7.7] 0.005% N-lauroylsarcosine), followed by wash solution II (0.06x SSPE, 0.005% N-lauroylsarcosine).

scan_protocol: Arrays were scanned using an GenePix 4200A scanner (Molecular Devices, Sunnyvale, CA, U.S.A.) with appropriate exposure settings for Cy3 (595 nm) and Cy5 (685 nm) at a 10-µm resolution, generating separate TIFF images.

data_processing: Microarray data with intensities reproducibly higher than background from 10 array results of three biological replicate experiments were selected for analysis. Following local background subtraction, the signal for each spot was normalized based on the median value of the median intensity of all the spots for each array. Each ratio (hrpL mutant/ 3937 wild-type) was converted to its log2 value for Significance Analysis of Microarrays (SAM) software analysis (Tusher et al., 2001). Genes showing differential expression in the microarray assays were determined by setting the number of falsely called genes to less than one for the significant gene list output. Significant genes are compared to the geomean of the ratios from ten arrays, genes were considered as HrpL-up-regulated if their level of transcription in the hrpL mutant WPP96 was no more than two-thirds of that observed in the corresponding 3937 wild-type . Genes were considered HrpL-down-regulated if their level of transcription was at least 1.5 times higher in the hrpL mutant WPP96 than that of wild-type 3937.

organism: Dickeya dadantii

label_protocol: 12 µg of total RNA was labeled in a 45-µL labeling reaction with 10 µL of a combination of 1 µL of spike RNA mix (GEhealthcare, Piscataway, NJ, U.S.A.), 1.8 µL of 25x amino allyl deoxynucleoside triphosphate (dNTP) mixture [5µL each of dATP, dCTP, dGTP (100 mM), 2µL dTTP (100 mM), 6µL aminoallyl dUTP, and 17µL SDW], 4.5 µL of dithiothreitol (0.1 M), 2 µL of 1mg/mL Oligo dT18 primers (Ambion, Austin, TX, U.S.A.), and 2 µL of reverse transcriptase in reaction buffer (Ambion, Austin, TX, U.S.A.). Primers and RNA were heated to 70°C for 10 min and then cooled on ice following incubation for 2 h at 42°C. The remaining RNA was denatured with 15 µL of 1 M NaOH and 15 µL of 0.5 M EDTA (pH 8.0) at 65°C for 10 min following neutralization with 15 µL of 1 M HCl. Purification of cDNA was done as described by the supplier (Qiagen, Valencia, CA, U.S.A.). One microliter of the appropriate Cy dye ester suspended in dimethyl sulfoxide (GEhealthcare, Piscataway, NJ, U.S.A.) and 2.0 µL of 1 M sodium carbonate were added to the purified cDNA in amber tubes and incubated for 1 h at room temperature in the dark. To the labeled cDNA, 3.0 µL of 4.0 M hydroxylamine hydrochloride was added and incubation was extended for another 30 min in the dark. The labeled targets were combined and mixed with distilled water and further purified with a QIAGEN MiniElute column (Qiagen, Valencia, CA, U.S.A.). The labeling efficiency was estimated with 1 µL of the cDNA using a NanoDrop ND-100 spectrophotometer (NanoDrop Technologies, Wilmington, DE, U.S.A.).

growth_protocol: The strains 3937 and hrpL mutant WPP96 were grown in T3SS-inducing minimum medium for 6 h

extract_protocol: Total RNA isolated using a Bio-Rad Aurum Total RNA Mini Kit

tag: genotype

value: hrpL mutant WPP96


title: C.j. 11168 versus D6846 DNA comparison #1


title: C.j. 11168 versus D6845 DNA comparison #2

source_name: C.j. D6845 genomic DNA


title: C.j. 11168 versus D6845 DNA comparison #1


title: C.j. 11168 versus D6845 Dye Swap of DNA comparison #2


title: C.j. 11168 versus D6844 Dye Swap of DNA comparison #2

source_name: C.j. D6844 genomic DNA


title: PC346DCC vs. PC346C rep1

description: Not applicable


title: C.j. 11168 versus D6844 Dye Swap of DNA comparison #1

description: Biological replicate 3 of 4: genomic DNA content comparison, dye swap.


title: Synovial sarcoma_9

source_name: Synovial sarcoma_9


title: C.j. 11168 versus D6845 Dye Swap of DNA comparison #1


title: C.j. 11168 versus D6844 DNA comparison #1


title: C.j. 11168 versus D6844 DNA comparison #2

description: Biological replicate 2 of 4: genomic DNA content comparison.


title: R2-2 Cy3 WT 6h

value: wild-type Ech3937


title: R2-1 Cy5 hrpL 6h


title: Synovial sarcoma_8

source_name: Synovial sarcoma_8


title: F3-2 Cy3 WT 6h


title: R2-1 Cy3 WT 6h


title: Normal human melanocyte_HEM-LP [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Normal human melanocyte_HEM-LP

value: Normal human melanocyte, HEM-LP


title: Embryo_48hpf_rep2

city: Woods Hole

first: Jared

last: Goldstone

state: MA

address: Redfield 3-52 MS#32

department: Biology

institute: Woods Hole Oceanographic Institution

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Custom Zebrafish Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x  mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The data were then normalized using the non-linear scaling method based on rank invariant probes. Briefly, this method finds the microarray with the overall median Cy3 signal for use as a baseline microarray (here 12 hpf, replicate C) to which all other microarrays are normalized. For normalization, microarrays are each separately normalized to the baseline microarray by finding Rank Invariant probes between the two microarrays. Prior to normalization any Cy3 values below 5 were set to 5 and after normalization the average normalized signal was calculated for probes duplicated on the microarray. Probes were removed from consideration when they exhibited saturation in any instance among the microarrays and duplicate probes, or when signals were not above background, in all instances among the microarrays and duplicate probes.

organism: Danio rerio

source_name: 100 pooled whole embryos

extract_protocol: RNA was prepared using the Bio-Rad Aurum Fatty and Fibrous Tissue kit. RNA samples were checked for quality using a NanoDrop ND-1000 spectrophotometer and an Agilent 2100 BioAnalyzer

treatment_protocol: Zebrafish embryos were maintained in 0.3X Daneau's solution refreshed every 24 hours. Each of 4 biological replicates consisted of 100 embryos. Embryos were sampled at 3, 6, 12, 24, 36, and 48 hours post fertilization.

tag: developmental hours post fertilization


title: Synovial sarcoma_6

source_name: Synovial sarcoma_6


title: Control_5


title: Embryo_48hpf_rep4


title: F3-1 Cy5 hrpL 6h


title: Embryo_48hpf_rep1


title: Embryo_48hpf_rep3


title: Synovial sarcoma_4

source_name: Synovial sarcoma_4


title: Embryo_36hpf_rep3


title: Synovial sarcoma_3

source_name: Synovial sarcoma_3


title: F3-1 Cy3 WT 6h


title: F3-2 Cy5 hrpL 6h


title: Synovial sarcoma_7

source_name: Synovial sarcoma_7


title: Embryo_36hpf_rep2


title: Synovial sarcoma_5

source_name: Synovial sarcoma_5


title: Embryo_36hpf_rep4


title: F2-2 Cy3 WT 6h


title: Embryo_36hpf_rep1


title: F2-2 Cy5 hrpL 6h


title: Embryo_24hpf_rep4


title: Melanoma cell line_SKMEL197 [SNP]

description: Hybridized to SNP6.0 Arrays

source_name: Melanoma cell line_SKMEL197

value: Metastatic melanoma

value: Melanoma cell line, SKMEL197


title: F2-1 Cy3 WT 6h


title: Embryo_12hpf_rep3


title: Embryo_24hpf_rep3


title: Embryo_24hpf_rep2


title: Embryo_12hpf_rep4


title: Embryo_12hpf_rep2


title: Embryo_24hpf_rep1


title: Embryo_12hpf_rep1


title: Synovial sarcoma_2

source_name: Synovial sarcoma_2

extract_protocol: Total RNA was extracted from the snap frozen tissue specimens using TRIzol reagent (Invitrogen Japan, Tokyo, Japan) according to the manufacturer’s　instructions, and  small RNA was purified and isolated from total RNA using the PureLink miRNA isolation kit (Invitrogen Japan).


title: Synovial sarcoma_1

source_name: Synovial sarcoma_1


title: R1-2 Cy5 hrpL 6h


title: F2-1 Cy5 hrpL 6h


title: R1-1 Cy5 hrpL 6h


title: R1-2 Cy3 WT 6h


title: F1-2 Cy5 hrpL 6h


title: Embryo_6hpf_rep1


title: Embryo_6hpf_rep2


title: R1-1 Cy3 WT 6h


title: F1-2 Cy3 WT 6h


title: Embryo_3hpf_rep1


title: Embryo_6hpf_rep3


title: HFD 5

city: Wallace Wurth Building, Sydney

first: Margaret

middle: J

last: Morris

state: NSW

address: University of New South Wales

department: School of Medical Sciences

country: Australia

institute: University of New South Wales

description: Gene expression from islet

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene ST 1.0 GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The data is then normalised using RMA in log 2 space and differentially expressed genes were selected based on ANOVA of chow (Control) vs high fat diet (HFD).

organism: Rattus norvegicus

source_name: islet from female offspring of fathers fed on high fat diet

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

growth_protocol: At 15 weeks of age, fathers were mated with normal females consuming chow, to generate the F1 offspring.

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

treatment_protocol: Fathers fed on HFD vs control, mate with females on normal chow then the female offspring's islet transcriptomics were analysed through microarray analysis

value: Female

value: Sprague-Dawley


title: Embryo_3hpf_rep4


title: Embryo_6hpf_rep4


title: WT_KLS_12-13wks_rep4

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

institute: Washington University in St.Louis

hyb_protocol: Labeled targets were hybridized to Mouse Exon 1.0ST arrays (Affymetrix, Santa Clara, CA).

scan_protocol: Gene chips were scanned using Affymetrix GeneArray scanner GS 3000.

data_processing:
Raw data were processed with the RMA algorithm in Affymetrix Expression ConsoleTM version1.1 (Affymetrix Inc., USA).
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: Bone marrow

label_protocol: Amplified cDNA was biotin labeled using the EncoreTM Biotin Module (NuGen Technologies, San Carlos, CA) according to the manufacturer’s instructions.

extract_protocol: Total cellular RNA was purified using Trizol reagent, quantified using UV spectroscopy (Nanodrop Technologies, Wilmington,DE) and qualitatively assessed using an Experian Bioanalyzer (Hercules,CA).Amplified cDNA was prepared from 20ng of total RNA using the whole transcript WT-Ovation TM RNA Amplification System.

value: Bl/6 Taconic

tag: genotype/variation

value: wild type

value: Bone marrow

value: KLS

tag: time of progression

value: 12 wks


title: mCG-PR_KLS_6wks_rep2

value: mCG-PR N17

value: 6 wks


title: WT_SLAM_6wks_rep1

value: SLAM


title: F1-1 Cy3 WT 6h


title: Embryo_3hpf_rep2


title: WT_SLAM_6wks_rep2


title: HFD 3

description: Gene expression from islet


title: WT_KLS_12-13wks_rep3


title: Chow 5

description: Gene expression from islet

source_name: islet from female offspring of fathers fed on chow


title: Embryo_3hpf_rep3


title: Chow 6

description: Gene expression from islet


title: HFD 4

description: Gene expression from islet


title: mCG-PR_KLS_6wks_rep3


title: F1-1 Cy5 hrpL 6h


title: WT-Xylan 24h Replicate 1

city: Ribeirao Preto

first: Wagner

middle: Rodrigo

last: de Souza

state: Sao Paulo

address: Av do Cafe

department: Pharmaceutical Sciences

country: Brazil

institute: University of Sao Paulo

description: Biological replicate 1 of 2. WT A. niger strain treated with xylan for 24h in minimal medium, no additional carbon source.

hyb_protocol: For the hybridization, 825 ng of each labeled cRNA was mixed with Agilent™ Fragmentation Mix and incubated at 60°C for exactly 30 minutes to fragment RNA. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 100 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in an oven (Agilent G2545A Hybridization Oven) set to 65°C for 17 hours. After, microarray slides were washed according to Agilent’s instructions.

scan_protocol: Scanned using the GenePix® 4000B microarray scanner (Molecular Devices, USA).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. Then, data were processed using the TIGR platform. Data were visualized using TMeV from TIGR, and the same software was used for statistical analysis (t test).

organism: Aspergillus niger

source_name: A. niger mycelia xylan-treated 24h

label_protocol: Prior to labeling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 (for untreated samples) or Cyanine-5 (for xylan-treated samples) for 2 hours at 40oC.

growth_protocol: The A. niger WT strain was initially grown on minimal medium with fructose for 24 hours at 30oC.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions, followed by DNAse treatment and purification using the RNeasy® Mini Kit  (Qiagen).

treatment_protocol: Mycelia from the WT strain was transferred to minimal medium containing xylan 1% (w/v) with no additional carbon source for 6, 12 and 24 h at 30oC.

value: WT

value: mycelia

tag: agent

value: xylan

tag: time point

value: 24 hours

source_name: WT strain treated with fructose for 24h

value: fructose


title: HFD 2

description: Gene expression from islet


title: HFD 1

description: Gene expression from islet


title: mCG-PR_KLS_6wks_rep1


title: Chow 4

description: Gene expression from islet


title: mCG-PR_KLS_13wks_rep1

value: 13 wks