title: Small Cell Lung Cancer cell line H1930 (CL-H1930_N_A)

description: No additional description available for sample: CL-H1930_N_A

source_name: Small Cell Lung Cancer cell line: H1930


title: Small Cell Lung Cancer cell line LX22 (CL-LX22_Y_A)

status: Public on May 26 2009

type: RNA

city: Baltimore

first: Luigi

last: Marchionni

state: MD

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

country: USA

institute: Johns Hopkins University

description: No additional description available for sample: CL-LX22_Y_A

hyb_protocol: Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. The array was then washed and stained with streptavidin?phycoerythrin (Molecular Probes) using the GeneChip Fluidics Workstation 450 (Affymetrix).

scan_protocol: The gene chip was then scanned using a confocal laser scanner (Affymetrix GeneArray Scanner 3000)

data_processing: The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Small Cell Lung Cancer cell line: LX22

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 to 5 microg total RNA. In brief, double-stranded cDNA synthesis was prepared from 2.5 to 5 µg of total RNA (SuperScript double-stranded cDNA synthesis kit; Invitrogen). After purification (QIAquick, Qiagen AG), the cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High yield T7 DNA transcription kit, ENZO Life Sciences). The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG).

extract_protocol: Total RNA was purified using RNAzol (Invitrogen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 7.5 were profiled.

tag: cell line

tag: type

value: Cell culture

tag: disease state

value: Small Cell Lung Cancer


title: Small Cell Lung Cancer cell line H1618 (CL-H1618_N_A)

description: No additional description available for sample: CL-H1618_N_A

source_name: Small Cell Lung Cancer cell line: H1618


title: Small Cell Lung Cancer cell line H446 (CL-H446_N_A)

description: No additional description available for sample: CL-H446_N_A

source_name: Small Cell Lung Cancer cell line: H446


title: Small Cell Lung Cancer cell line H526 (CL-H526_N_A)

description: No additional description available for sample: CL-H526_N_A

source_name: Small Cell Lung Cancer cell line: H526


title: MDA-MB-468GFP-LN_BIOREP_1

city: London

first: Ann

last: Chambers

state: Ontario

address: 790 Commissioner's Road E

department: Victoria research labs

country: Canada

institute: London Regional Cancer program

description: Data were imported into genespring 7.0 for further analysis

hyb_protocol: Hybridization performed at the London regional cancer program (www.lrgc.ca) as per Affymetrix's hybridization protocol for this chip type (www.affymetrix.com)

scan_protocol: Scanning performed at the London regional cancer program (www.lrgc.ca) as per Affymetrix's scanning protocol for this chip type (www,affymetrix.com)

data_processing:
Data processes using MAS5.0 standard algorithm.
Alpha1: 0.05
Alpha2: 0.065
Tau:0.015
Noise (RawQ) 4.300
TGT Value: 150
Norm Factor (NF): 1.000

label: Biotin + SAPI

label_protocol: Labeling performed at the London regional cancer program (www.lrgc.ca) as per Affymetrix's standard one-cycle labeling protocol for this chip type (www,affymetrix.com)

growth_protocol: Cells grown in a-MEM supplemented with 10% FCS. 5% CO2, 37 deg.

extract_protocol: Used RNEasy RNA extraction kit (Qiagen) as per manufacturer's protocol

tag: MDA-MB-468GFP-LN_BIOREP_1. isolated from a lymph node metatasis of MDA-MB-468GFP.


title: MDA-MB-468GFP-LN_BIOREP_3

scan_protocol: Scanning performed at the London regional cancer program (www.lrgc.ca) as per Affymetrix's scanning protocol for this chip type (www.affymetrix.com)

tag: Derived from a lymph node metastasis of it parental line, MDA-MB-468GFP.


title: Small Cell Lung Cancer Primary xenograft, sample LX33 (X-LX33_Y_A)

description: No additional description available for sample: X-LX33_Y_A

source_name: Small Cell Lung Cancer Primary xenograft, sample: LX33

tag: sample

value: Tissue


title: MDA-MB-468GFP-LN_BIOREP_2

tag: Isolated from a lymphatic metastasis of it's parental cell line MDA-MB-468GFP.


title: MDA-MB-468GFP_biorep_1

description: Data were imported into Genespring 7.0 for further analysis.

hyb_protocol: Hybridization performed at the London Regional Genenomics Center (www.lrgc.ca) as per Affymetrix's standard hybridization protocol for this chip type (www.affymetrix.com)

scan_protocol: Scanning performed at the London Regional Genenomics Center (www.lrgc.ca) as per Affymetrix's standard scanning protocol for this chip type (www.affymetrix.com)

data_processing:
Data processed using MAS 5.0 standard algorithm.
Alpha1:		0.05
Alpha2:		0.065
Tau:		0.015
Noise (RawQ):	4.300
Scale Factor (SF):	0.514
TGT Value:		150
Norm Factor (NF):	1.000

label: Biotin + SApi (As per affymetrix standard protocol, www.affymetrix.com)

source_name: MDA-MB-468GFP parental cell line, Bio Rep 1

label_protocol: Labeling performed at the London Regional Genenomics Center (www.lrgc.ca) as per Affymetrix's standard one cycle labeling protocol for this chip type (www.affymetrix.com)

growth_protocol: Cells grown in a-MEM media supplemented with 10% FCS, 5% CO2, 37 deg

extract_protocol: Used RNeasy RNA extraction kit (Qiagen) as per Manufacturer's protocol.

tag: MDA-MB-468GFP parental cell line,

tag: Bio Rep 1

tag: Derivative of MDA-MB-468, a Breast Cancer Adenomcarcinoma cell line


title: MDA-MB-468GFP_biorep_3

source_name: MDA-MB-468GFP Parental cell line, Bio rep 3

tag: bio rep 3.  Derivative of MDA-MB-468 Breast adenocarcinoma cell line


title: MDA-MB-468GFP_biorep_2

hyb_protocol: Hybridization performed at the London regional cancer program (www.lrgc.ca) as per Affymetrix's hybridization protocol for this chip type (www,affymetrix.com)

tag: MDA-MB-468GFP parental cell line, Bio rep 2. derivative of MDA-MB-468, a breast cancer adenocarcinoma cell line


title: E16.5 WT Dorsal Skin 8

status: Public on May 20 2009

city: Irvine

first: Amelia

middle: Soto

last: Hopkin

state: CA

address: 250 Sprague Hall

department: Biological Chemistry & Medicine

institute: University of California Irvine

description: E16.5 WT dorsal skin

hyb_protocol: Following the recommended procedure, 0.54 ug of this fragmented target single-stranded cDNA was hybridized at 45c with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Gene 1.0 ST array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fludics Station 450 (Fluidics protocol FS450_007).

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G and GeneChip Operating Software v. 1.4 to produce .CEL intensity files.

data_processing:
These probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP).
(Algorithm: PLIER v 2.0; Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile).

label: Biotin

organism: Mus musculus

source_name: Dorsal Skin

label_protocol:
Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+mRNA present in the isolated total RNA (typically 100ng total RNA starting material each sample reaction) using the GeneChip WT cDNA synthesis Kit (Affymetrix, Inc., Santa Clara, CA) and random hexamers tagged with a T7 promoter sequence. The double-stranded cDNA is then used as a template to generate many copies of antisense cRNA from an in vitro transcription reaction (IVT) of 16hrs in the presence of T7 RNA Polymerase using the Affymetrix Genechip WT cDNA Amplification Kit. 10 ug of cRNA were input into the second cycle cDNA reaction with random hexamers that are used to reverse transcribe the cRNA from the first cycle to produce single-stranded DNA in the sense orientation.
The single-stranded DNA sample is fragmented (WT Terminal Labeling Kit, Affymetrix, Inc, Santa Clara, CA) to an average strand length of 60 bases (range 40-70bp) following prescribed protocols (Affymetrix GeneChip WT Sense Target Labeling Assay Manual). The fragmented single-stranded DNA is subsequently labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

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

tag: age

value: Embryonic day 16.5

tag: tissue

value: Dorsal Skin

tag: genotype

value: wild-type


title: E14.5 WT Dorsal Skin 1-3

description: E14.5 WT dorsal skin

value: Embryonic day 14.5


title: E18.5 WT Dorsal Skin 5-5

description: E18.5 WT dorsal skin

value: Embryonic day 18.5


title: E18.5 WT Dorsal Skin 6-4

description: E18.5 WT dorsal skin


title: E14.5 WT Bladder 1-6

description: E14.5 WT bladder

source_name: Bladder

value: Bladder


title: E16.5 WT Bladder 1-1

description: E16.5 WT bladder


title: E16.5 WT Bladder 1-2

description: E16.5 WT bladder


title: E16.5 WT Dorsal Skin 6

description: E16.5 WT dorsal skin


title: E18.5 WT Dorsal Skin 1-4

description: E18.5 WT dorsal skin


title: E16.5 WT Dorsal Skin 7

description: E16.5 WT dorsal skin


title: E14.5 WT Dorsal Skin 1-2

description: E14.5 WT dorsal skin

source_name: dorsal skin


title: E16.5 WT Bladder 1-3

description: E16.5 WT bladder


title: E14.5 WT Bladder 1-3

description: E14.5 WT bladder


title: E18.5 Get1 +/- Bladder 2-5

description: Get1 Het E18.5 bladder

source_name: bladder


title: E18.5 Get1 -/- Bladder 2-3

description: Get1 KO E 18.5 bladder


title: E18.5 Get1 -/- Bladder 2-2

description: Get1 KO bladder


title: E18.5 Get1 +/- Bladder 2-4

description: Get1 het E18.5 bladder


title: E18.5 Get1 -/- Bladder 1-1

description: Get1 KO E18.5 bladder

value: Embyronic day 18.5


title: Itk knockout CD4+ CD3-stimulated 2

city: Huddinge

first: Emelie

last: Blomberg

address: Novum level 5

department: Department of Laboratory Medicine, Clinical Research Center

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from mouse CD4+ Itk knockout T-cells with anti-CD3 stimulation

hyb_protocol: Following fragmentation, 100 ng of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChip® Scanner 3000 7G with AutoLoader.

data_processing: The data were analyzed with dChip, invariant set normalization, model-based expression signal values, 5th percentile of region (PM-only) background subtraction

source_name: CD3-stimulated CD4+ T-cells from Itk knockout C57BL/6 mice

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

growth_protocol: The stimulated CD3+ T-cells were grown at 37°C with 5% CO2 for 24 hrs. The unstimulated cells were after separation immediately used for RNA extraction.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Stimulations were done with anti-CD3 (1 mg/ml) for 24 hrs.

tag: C57BL/6 mice, thymus and spleen pooled


title: Itk knockout CD4+ CD3-stimulated 1


title: Itk knockout CD8+ unstimulated 2

description: Gene expression data from mouse CD8+ Itk knockout T-cells without stimulation

source_name: unstimulated CD8+ T-cells from Itk knockout C57BL/6 mice


title: Wild type CD8+ unstimulated

description: Gene expression data from mouse CD8+ Wt T-cells without stimulation

source_name: unstimulated CD8+ T-cells from Wt C57BL/6 mice


title: Itk knockout CD8+ CD3-stimulated

description: Gene expression data from mouse CD8+ Itk knockout T-cells with anti-CD3 stimulation

source_name: CD3-stimulated CD8+ T-cells from Itk knockout C57BL/6 mice


title: Itk knockout CD8+ unstimulated 1


title: Wild type CD8+ CD3-stimulated

description: Gene expression data from mouse CD8+ Wt T-cells with anti-CD3 stimulation

source_name: CD3-stimulated CD8+ T-cells from Wt C57BL/6 mice


title: Wild type CD4+ CD3-stimulated 2

description: Gene expression data from mouse CD4+ Wt T-cells with anti-CD3 stimulation

source_name: CD3-stimulated CD4+ T-cells from Wt C57BL/6 mice


title: Wild type CD4+ CD3-stimulated 1


title: Itk knockout CD4+ unstimulated 2

description: Gene expression data from mouse CD4+ Itk knockout T-cells without stimulation

source_name: unstimulated CD4+ T-cells from Itk knockout C57BL/6 mice


title: E18.5 Get1 +/- Bladder 2-6

description: Get1 Het E18.5 bladder


title: Itk knockout CD4+ unstimulated 3


title: Wild type CD3-stimulated and CsA-treated 1

description: Gene expression data from mouse CD3+ Wt T-cells with anti-CD3 stimulation and CsA-treatment

source_name: CD3-stimulated and CsA-treated CD3+ T-cells from Wt C57BL/6 mice

treatment_protocol: Stimulations were done with anti-CD3 (1 mg/ml) with or without anti-CD28 (3 mg/ml) in the presence or absence of CsA (1 mg/ml) for 24 hrs. The experiments with anti-CD3- and anti-CD3CD28 stimulations of Wt samples were done at two different occasions, explaining the day 1 and day 2 notes in the sample title.


title: Wild type CD4+ unstimulated 2

description: Gene expression data from mouse CD4+ Wt T-cells without stimulation

source_name: unstimulated CD4+ T-cells from Wt C57BL/6 mice


title: Itk knockout CD3CD28-stimulated 1

description: Gene expression data from mouse CD3+ Itk knockout T-cells with anti-CD3 and anti-CD28 stimulation

source_name: CD3CD28-stimulated CD3+ T-cells from Itk knockout C57BL/6 mice


title: Wild type CD3CD28-stimulated and CsA-treated 1

description: Gene expression data from mouse CD3+ Wt T-cells with anti-CD3 and anti-CD28 stimulation and CsA-treatment

source_name: CD3CD28-stimulated and CsA-treated CD3+ T-cells from Wt C57BL/6 mice


title: Wild type CD3CD28-stimulated and CsA-treated 2


title: Wild type CD3CD28-stimulated 3 day 1

description: Gene expression data from mouse CD3+ Wt T-cells with anti-CD3 and anti-CD28 stimulation

source_name: CD3CD28-stimulated CD3+ T-cells from Wt C57BL/6 mice


title: Itk knockout CD4+ unstimulated 1


title: Wild type CD3-stimulated and CsA-treated 2


title: Wild type CD3CD28-stimulated 2 day 2


title: Wild type CD4+ unstimulated 1


title: Wild type CD3CD28-stimulated 1 day 2


title: Wild type CD3-stimulated 2 day 2

description: Gene expression data from mouse CD3+ Wt T-cells with anti-CD3 stimulation

source_name: CD3-stimulated CD3+ T-cells from Wt C57BL/6 mice


title: Wild type CD3CD28-stimulated 1 day 1


title: Itk knockout CD3-stimulated 2

description: Gene expression data from mouse CD3+ Itk knockout T-cells with anti-CD3 stimulation

source_name: CD3-stimulated CD3+ T-cells from Itk knockout C57BL/6 mice


title: Wild type CD3-stimulated 1 day 2


title: Itk knockout CD3-stimulated 1


title: Itk knockout CD3CD28-stimulated 2


title: Wild type CD3CD28-stimulated 2 day 1


title: Wild type CD3-stimulated 3 day 1


title: Wild type unstimulated 3

description: Gene expression data from mouse CD3+ Wt T-cells without stimulation

source_name: unstimulated CD3+ T-cells from Wt C57BL/6 mice


title: Wild type CD3-stimulated 2 day 1


title: Wild type unstimulated 2


title: Itk knockout unstimulated 1

description: Gene expression data from mouse CD3+ Itk knockout T-cells without stimulation

source_name: unstimulated CD3+ T-cells from Itk knockout C57BL/6 mice


title: Itk knockout unstimulated 2


title: Wild type unstimulated 1


title: ML-DmBG3 cells:  RNAi Rad21 10 micrograms, 4 days biological rep3

status: Public on May 19 2009

city: Saint Louis

first: Dale

last: Dorsett

state: MO

address: 1100 South Grand Boulevard

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

description: Gene expression data from ML-DmBG3 cells; RNAi Rad21 10 micrograms, 4 days

hyb_protocol: Following fragmentation, 10 mg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 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

data_processing: The data were normalized using gc-RMA algorithms, which consist of background adjustment and quantile normalization, accounting for probe GC content; executed using  the R statistical environment and the BioConductor package.  Transcript levels from Rad21 and Nipped-B RNAi treatments were compared to those of Mock RNAi controls at 3 and >3 days (4 and 6 days) (N=4 per RNAi comparison; N=2 per treatment condition). A balanced 2-way ANOVA was performed on GCRMA-normalized log2 transformed signal intensities to assess gene expression variability with regard to RNAi treatment and treatment conditions (FDR ≤ 0.1).

organism: Drosophila melanogaster

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: ML-DmBG3 cells were cultured in Schneiders media with 10% FCS and 10 micrograms per ml insulin. Cells were passaged to keep them between 1 and 10 million cells per ml.

extract_protocol: Trizol extraction of total RNA then purified by Qiagen Rneasy Minelute columns.

treatment_protocol: For RNAi treatment, cells were plated at 5 million cells per 3 cm well. Media was replaced with 1 ml of Express Five SFM (Invitrogen) with 1% FCS, and 10 micrograms per ml insulin.  The indicated amount of dsRNA was added per well. Media was adjusted to 3 ml and 10% FCS with Schneider’s media after 2 hrs. Cells were replated as needed. Templates for dsRNA synthesis were made by PCR from cDNA templates using primers with T7 promoters (see primer table linked as a supplementary file to the Series GSE16152 record). Equal amounts of two dsRNAs against each target were used.

tag: cells

value: ML-DmBG3 cells (derived from central nervous system)

tag: rnai knockdown

tag: micrograms rnai

tag: time

value: 4 days


title: ML-DmBG3 cells:  RNAi Mock 0 micrograms, 3 days biological rep2

description: Gene expression data from ML-DmBG3 cells; RNAi Mock 0 micrograms, 3 days

value: Mock

value: 3 days


title: ML-DmBG3 cells:  RNAi Mock 0 micrograms, 3 days biological rep1


title: ML-DmBG3 cells:  RNAi Nipped-B 40 micrograms, 3 days biological rep1

description: Gene expression data from ML-DmBG3 cells; RNAi Nipped-B 40 micrograms, 3 days

value: Nipped-B


title: ML-DmBG3 cells:  RNAi Mock 0 micrograms, 4 days biological rep3

description: Gene expression data from ML-DmBG3 cells; RNAi Mock 0 micrograms, 4 days


title: ML-DmBG3 cells:  RNAi Nipped-B 10 micrograms, 4 days biological rep3

description: Gene expression data from ML-DmBG3 cells; RNAi Nipped-B 10 micrograms, 4 days


title: ML-DmBG3 cells:  RNAi Nipped-B 40 micrograms, 3 days biological rep2


title: ML-DmBG3 cells:  RNAi Rad21 40 micrograms, 3 days biological rep2

description: Gene expression data from ML-DmBG3 cells; RNAi Rad21 40 micrograms, 3 days


title: ML-DmBG3 cells:  RNAi Rad21 40 micrograms, 3 days biological rep1


title: ML-DmBG3 cells:  RNAi Rad21 10 micrograms, 6 days biological rep4

description: Gene expression data from ML-DmBG3 cells; RNAi Rad21 10 micrograms, 6 days

value: 6 days


title: ML-DmBG3 cells:  RNAi Mock 0 micrograms, 6 days biological rep4

description: Gene expression data from ML-DmBG3 cells; RNAi Mock 0 micrograms, 6 days


title: ML-DmBG3 cells:  RNAi Nipped-B 10 micrograms, 6 days biological rep4

description: Gene expression data from ML-DmBG3 cells; RNAi Nipped-B 10 micrograms, 6 days


title: A.thaliana mpk6-ko, H2O 4h rep2

status: Public on May 15 2009

city: Halle

first: Tino

last: Unthan

address: Weinberg

department: stress and developmental biology

country: Germany

institute: Leibniz Institue of Plant Biochemistry (IPB)

description: No

hyb_protocol: All hybridization, staining and washing steps have been done according Affymetrix using GeneChip Hybridization Oven 640 and the Affymetrix GeneChip Fluidics Station 450. GeneChips   have been hybridized with cRNA for 16 hours  at 45 C and 60 rpm.

scan_protocol: After washing and staining, the arrays were scanned in a Affymetrix GeneChip Scanner 3000 7G.

data_processing: Raw fluorescence data were used to calculate signal intensities for each oligonucleotide probe set by the accompanying software (GeneChip Operating System, Version 1.3; Affymetrix). The fluorescence intensity of each chip was linearly scaled to an average target intensity of 500, permitting reproducible interarray comparisons.

organism: Arabidopsis thaliana

source_name: plant leaf, H2O 4h

label_protocol: RNAs have been treated with the One-Cycle cDNA Synthesis Kit from Affymetrix (Santa Clara, CA) until dscDNA with T7 primer incorporation. Resulting “Target” dscDNA (double-stranded cDNA) has been purified  and served as a template in the subsequent in vitro trascription  (IVT) reaction for complimentary RNA (cRNA) amplification and biotin labeling. We used the GeneChip IVT labeling Kit from Affymetrix

growth_protocol: plants grown on soil under short day conditions (8h light 23°C and 16h dark 22°C)

extract_protocol: total RNA was extracted from plant tissue using the TRIZOL Method and afterwards RNA cleanup with RNeacsy Kit from Quiagen

treatment_protocol: H2O infiltrated in leaves, harvested 4h pi

tag: A. thaliana, mpk6-ko, 6 week old plants, leaf material


title: A.thaliana mpk6-ko, Flg22 4h rep2

description: No

source_name: plant leaf, Flg22 4h

treatment_protocol: 1µM Flg22 infiltrated in leaves, harvested 4h pi


title: A.thaliana mpk6-ko, H2O 4h rep1

description: No


title: A.thaliana mpk6-ko, H2O 4h rep3

description: No


title: A.thaliana mpk6-ko, Flg22 4h rep3

description: No


title: A.thaliana 35S::ERF104, H2O 4h rep1

description: No

tag: A. thaliana, ERF104 over expresser, 6 week old plants, leaf material


title: A.thaliana mpk6-ko, Flg22 4h rep1

description: No


title: A.thaliana 35S::ERF104, H2O 4h rep2

description: No


title: A.thaliana 35S::ERF104, Flg22 4h rep2

description: No


title: A.thaliana 35S::ERF104, Flg22 4h rep1

description: No


title: A.thaliana erf104-ko, H2O 4h rep3

description: No

tag: A. thaliana, erf104-ko, 6 week old plants, leaf material


title: A.thaliana 35S::ERF104, H2O 4h rep3

description: No


title: A.thaliana 35S::ERF104, Flg22 4h rep3

description: No


title: A.thaliana erf104-ko, H2O 4h rep2

description: No


title: Wild type CD3-stimulated 1 day 1


title: A.thaliana erf104-ko, H2O 4h rep1

description: No


title: A.thaliana erf104-ko, Flg22 4h rep3

description: No

treatment_protocol: Flg22 infiltrated in leaves, harvested 4h pi


title: A.thaliana erf104-ko, Flg22 4h rep2

description: No


title: A.thaliana Col-0, Flg22 4h rep2

description: No

label_protocol: RNAs have been treated with the One-Cycle cDNA Synthesis Kit from Affymetrix (Santa Clara, CA) until dscDNA with T7 primer incorporation. Resulting “Target” dscDNA (double-stranded cDNA) has been purified  and served as a template in the subsequent in vitro trascription   (IVT) reaction for complimentary RNA (cRNA) amplification and biotin labeling. We used the GeneChip IVT labeling Kit from Affymetrix.

tag: A. thaliana Col-0, 6 week old plants, leaf material


title: A.thaliana erf104-ko, Flg22 4h rep1

description: No


title: A.thaliana Col-0, H2O 4h rep1

description: No


title: A.thaliana Col-0, Flg22 4h rep3

description: No


title: A.thaliana Col-0, H2O 4h rep2

description: No


title: patient:14--location:ni--R:01

status: Public on May 13 2009

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

description: no additional information

hyb_protocol: Following fragmentation, 13 ug of biotin-labeled cRNA were hybridized for 16 h at 45 C on GeneChip Human Genome U133 Plus 2.0 arrays. Arrays were then washed using an Affymetrix Fluidics Station 450 FS450_001 protocol.

scan_protocol: Standard Affymetrix procedures

data_processing: Signal intensities were detected and analyzed with the Affymetrix gene chip operating software version 1.4 (GCOS; Affymetrix)

source_name: cold cup biopsy, 20mm3 size, IC non-ulcer tissue

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix protocol from 1 ug total-RNA.

extract_protocol: Total-RNA has been isolated with the RNeasy Mini Kit (QIAGEN) including an on column DNaseI digestion, according to the manufacturer's instructions.

treatment_protocol: Bladder biopsies have been stored in RNAlater (QIAGEN), according to the manufacturer's instructions.

value: bladder

tag: disease state

value: IC, non-ulcer tissue


title: A.thaliana Col-0, H2O 4h rep3

description: No


title: A.thaliana Col-0, Flg22 4h rep1

description: No


title: Blood sample from patient 179 at Day 180

status: Public on May 09 2009

city: Basel

first: Guillemette

last: Duchateau-Nguyen

address: Building 93

department: Pharma Research and Early Development

institute: F.Hoffmann-La Roche AG

description: Gene expression data from venous blood drawn in the morning from fasted subject.

hyb_protocol: The cRNA samples were hybridized overnight to Affymetrix U133 Plus 2.0 full genome oligonucleotide arrays and then stained with Streptavidin-Phycoerythrin according to the manufacturer’s instructions (Affymetrix Inc, CA, USA).

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: Gene signal intensities were computed using the MAS 5.0 algorithm (component of GCOS 1.0 software) using Affymetrix default analysis settings. Signal intensities were normalized using a quantile-quantile method [Bolstad, 2003].

source_name: Venous blood from healthy individual

label_protocol: One microgram of total RNA from each blood sample was used to generate biotinylated cRNA, using the Agilent Low RNA Input Linear Amplification procedure (Version 2), with minor modifications (Agilent Technologies GmbH; Waldbronn, Germany).

extract_protocol: Total RNA was extracted using the PAXgene 96 Blood RNA kit (Qiagen; Hilden, Germany) according to the manufacturer's instructions.

value: Blood

tag: patient identifier

tag: day

value: Day 180

tag: age (years)

tag: sex

value: Female


title: Blood sample from patient 180 at Day 1

value: Day 1


title: Blood sample from patient 180 at Day 90

value: Day 90


title: Blood sample from patient 179 at Day 90


title: Blood sample from patient 180 at Day 180


title: Blood sample from patient 179 at Day 28

value: Day 28


title: Blood sample from patient 180 at Day 14

value: Day 14


title: Blood sample from patient 179 at Day 1


title: Blood sample from patient 180 at Day 28


title: Blood sample from patient 173 at Day 1


title: Blood sample from patient 174 at Day 90


title: Blood sample from patient 173 at Day 180


title: Blood sample from patient 173 at Day 90


title: Blood sample from patient 179 at Day 14


title: Blood sample from patient 174 at Day 28


title: Blood sample from patient 174 at Day 14


title: Blood sample from patient 173 at Day 28


title: Blood sample from patient 173 at Day 14


title: Blood sample from patient 174 at Day 1


title: Blood sample from patient 172 at Day 180


title: Blood sample from patient 172 at Day 14


title: Blood sample from patient 172 at Day 90


title: Blood sample from patient 165 at Day 28


title: Blood sample from patient 172 at Day 28


title: Blood sample from patient 160 at Day 14


title: Blood sample from patient 163 at Day 14


title: Blood sample from patient 163 at Day 180


title: Blood sample from patient 163 at Day 90


title: Blood sample from patient 172 at Day 1


title: Blood sample from patient 165 at Day 14


title: Blood sample from patient 165 at Day 90


title: Blood sample from patient 165 at Day 180


title: Blood sample from patient 160 at Day 1


title: Blood sample from patient 165 at Day 1


title: Blood sample from patient 163 at Day 1


title: Blood sample from patient 159 at Day 14


title: Blood sample from patient 159 at Day 180


title: Blood sample from patient 159 at Day 90


title: Blood sample from patient 160 at Day 28


title: Blood sample from patient 154 at Day 1


title: Blood sample from patient 159 at Day 28


title: Blood sample from patient 154 at Day 180


title: Blood sample from patient 159 at Day 1


title: Blood sample from patient 163 at Day 28


title: Blood sample from patient 154 at Day 14


title: Blood sample from patient 154 at Day 28


title: Blood sample from patient 160 at Day 180


title: Blood sample from patient 148 at Day 180


title: Blood sample from patient 154 at Day 90


title: Blood sample from patient 160 at Day 90


title: Blood sample from patient 138 at Day 180

value: Male


title: Blood sample from patient 147 at Day 28


title: Blood sample from patient 148 at Day 28


title: Blood sample from patient 138 at Day 28


title: Blood sample from patient 147 at Day 180


title: Blood sample from patient 135 at Day 28


title: Blood sample from patient 147 at Day 14


title: Blood sample from patient 148 at Day 14


title: Blood sample from patient 138 at Day 14


title: Blood sample from patient 147 at Day 90


title: Blood sample from patient 135 at Day 1


title: Blood sample from patient 148 at Day 90


title: Blood sample from patient 135 at Day 90


title: Blood sample from patient 138 at Day 90


title: Blood sample from patient 148 at Day 1


title: Blood sample from patient 131 at Day 1


title: Blood sample from patient 123 at Day 1


title: Blood sample from patient 138 at Day 1


title: Blood sample from patient 123 at Day 28


title: Blood sample from patient 135 at Day 14


title: Blood sample from patient 135 at Day 180


title: Blood sample from patient 147 at Day 1


title: Blood sample from patient 131 at Day 14


title: Blood sample from patient 131 at Day 90


title: Blood sample from patient 131 at Day 180


title: Blood sample from patient 131 at Day 28


title: Blood sample from patient 123 at Day 90


title: Blood sample from patient 123 at Day 14


title: Blood sample from patient 123 at Day 180


title: Blood sample from patient 121 at Day 180


title: Blood sample from patient 121 at Day 90


title: Blood sample from patient 121 at Day 1


title: Blood sample from patient 121 at Day 14


title: Blood sample from patient 117 at Day 90


title: Blood sample from patient 114 at Day 180


title: Blood sample from patient 117 at Day 1


title: Blood sample from patient 117 at Day 180


title: Blood sample from patient 117 at Day 28


title: Blood sample from patient 114 at Day 90


title: Blood sample from patient 117 at Day 14


title: Blood sample from patient 121 at Day 28


title: Blood sample from patient 114 at Day 28


title: Blood sample from patient 114 at Day 14


title: Blood sample from patient 113 at Day 180


title: Blood sample from patient 114 at Day 1


title: Blood sample from patient 108 at Day 90


title: Blood sample from patient 113 at Day 14


title: Blood sample from patient 113 at Day 90


title: Blood sample from patient 108 at Day 180


title: Blood sample from patient 113 at Day 1


title: Blood sample from patient 106 at Day 14


title: Blood sample from patient 108 at Day 14


title: Blood sample from patient 113 at Day 28


title: Blood sample from patient 106 at Day 28


title: Blood sample from patient 108 at Day 1


title: Blood sample from patient 108 at Day 28


title: Blood sample from patient 106 at Day 180


title: Blood sample from patient 106 at Day 90


title: EtOH-2

status: Public on May 08 2009

first: Kevin

last: Yarema

address: 3400 N. Charles St., Clark Hall 106A

department: Biomedical Engineering

hyb_protocol: 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip human U133Plus 2.0 arrays for 16hr at 45 C with constant rotation (60 rpm).  Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA.  The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings.  For comparison between different chips, global scaling was used, scaling all probesets to a user defined target intensity (TGT) of 150.

data_processing: Image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings.  For comparison between different chips, global scaling was used following MAS5.0 algorithm, scaling all probesets to a user defined target intensity (TGT) of 150.

source_name: MDA-MB-231 breast cancer cells

label_protocol: RNA from control and experimental cells was processed using the RNA amplification protocol described by Affymetrix (Affymetrix Expression Manual). Briefly, 5 micrograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer (Proligo LLC, Boulder, Colorado) and the SuperScript Choice System (Invitrogen, Carlsbad, California).  Following the double stranded cDNA synthesis, the product was purified by phenol-chloroform extraction, and biotinilated anti-sense cRNA was generated through in vitro transcription using the BioArray RNA High Yield Transcript Labelling kit (ENZO Life Sciences Inc., Farmingdale, New York).

extract_protocol: Total RNA was isolated from cells using Trizol reagent (Invitrogen), following manufacturer's instructions.  Isolated RNA was purified using Turbo DNase (Ambion) and Mini Spin columns (Qiagen).

treatment_protocol: Cells were plated and grown for 3 days before being harvested for microarray analysis.  Growth medium (RPMI 1640 with 10% FBS) was supplemented with EtOH (final percentage = 0.40%) at the time of plating.

tag: no additional information


title: EtOH-1


title: EtOH-3


title: C1OH-Ac3ManNAc-2

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0(GCOS) software from Affymetrix, using the standard default settings.  For comparison between different chips, global scaling was used, scaling all probesets to a user defined target intensity (TGT) of 150.

treatment_protocol: Cells were plated and grown for 3 days before being harvested for microarray analysis.  Growth medium (RPMI 1640 with 10% FBS) was supplemented with C1OH-Ac3ManNAc (100 uM) at the time of plating.


title: C6OH-But3ManNAc-2

treatment_protocol: Cells were plated and grown for 3 days before being harvested for microarray analysis.  Growth medium (RPMI 1640 with 10% FBS) was supplemented with C6OH-But3ManNAc (30 uM) at the time of plating.


title: C1OH-But3GlcNAc-1

treatment_protocol: Cells were plated and grown for 3 days before being harvested for microarray analysis.  Growth medium (RPMI 1640 with 10% FBS) was supplemented with C1OH-But3GlcNAc (40 uM) at the time of plating.


title: C1OH-But3ManNAc-2

treatment_protocol: Cells were plated and grown for 3 days before being harvested for microarray analysis.  Growth medium (RPMI 1640 with 10% FBS) was supplemented with C1OH-But3ManNAc (30 uM) at the time of plating.


title: C1OH-But3GalNAc-2

treatment_protocol: Cells were plated and grown for 3 days before being harvested for microarray analysis.  Growth medium (RPMI 1640 with 10% FBS) was supplemented with C1OH-But3GalNAc (50 uM) at the time of plating.


title: Ac4ManNLev-2

treatment_protocol: Cells were plated and grown for 3 days before being harvested for microarray analysis.  Growth medium (RPMI 1640 with 10% FBS) was supplemented with Ac4ManNLev (75 uM) at the time of plating.


title: C1OH-Ac3ManNAc-1


title: C1OH-But3ManNAc-1


title: Ac4ManNLev-1


title: C6OH-But3ManNAc-1


title: C1OH-But3GlcNAc-2


title: Blood sample from patient 106 at Day 1

tag: tissue


title: MDMs  normoxia

status: Public on May 05 2009

city: sheffield

first: Hsin-Yu

last: Fang

address: Beech Hill Rd

department: Infection & Immunity,School of Medicine & BioMedical Sciences

country: United Kingdom

institute: University of Sheffield

description: human MDMs subjected to normoxia (20% O2)

hyb_protocol: Following fragmentation,  cRNA were hybridized for 16 hr at 45C on Human Genome U133A plus 2.0 gene chips arrays then genechips were washed and stained.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip scanner 3000

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.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChip  Expression Analysis Technical Manual, Affymetrix)

growth_protocol: Human Monocytes were isolated from Buffy coats and mononuclear cells was seeded in Iscove's Modified Dulbecco's Media  with 5% human AB serum  and 2mM L-Glutamine  and incubated at 37ºC, 5% CO2. After 2h, adherent cells were washed and cultured for 7 days to allow differentiation into MDMs.

extract_protocol: Total RNA was prepared using RNeasy kit (Qiagen) according to the manufacturer’s instructions

treatment_protocol: monocyte-derived macrophages (MDMs) were subjected to severe hypoxia (< 0.5% O2) or normoxia (20.9% O2) in 5% CO2 humidified multi-gas incubators

tag: cell type

value: macrophage


title: MDMs  hypoxia

description: human MDMs subjected to severe hypoxia (< 0.5% O2)


title: C1OH-But3GalNAc-1


title: Human MSCs added to the NOD/scid mouse lung in vitro (U133 Plus 2.0)

status: Public on May 07 2009

city: Temple

first: Joni

last: Ylostalo

state: TX

address: 5701 Airport Rd., Module C

department: Institute for Regenerative Medicine

institute: Texas A&M

description:
Cultured adult human MSCs.
NOD/scid mouse lung.
In vitro mixing of the tissues.
Sample is a mixture of human multipotent stromal cells (MSCs) and mouse lung.

hyb_protocol: Labeled cRNA was hybridized for 16 hours at 45C onto the HG-U133 Plus 2.0 array (Affymetrix). After washing, the array was stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR), amplified with biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA) and stained again with streptavidin-phycoerythrin.

scan_protocol: The array was scanned for fluorescence (GeneChip Scanner 3000, Affymetrix) using the GeneChip Operating software 1.0 (GCOS, Affymetrix

data_processing: The array was scaled to target value of 500.

organism:
Homo sapiens
Mus musculus

source_name: In vitro mix of human MSCs and NOD/scid mouse lung

label_protocol: 7 μg of total RNA was used to synthesize double-stranded cDNA (Superscript Choice System, GIBCO /BRL).  The double-stranded cDNA was purified by phenol/chloroform extraction (Phase Lock Gel, Eppendorf, Hamburg, Germany) and concentrated by ethanol precipitation. In vitro transcription was used to produce biotin-labeled cRNA (BioArray HighYield RNA Transcription Labeling Kit; Enzo Diagnostics, Farmingdale, NY).  The biotinylated cRNA was then cleaned (RNeasy Mini Kit) and fragmented.

growth_protocol: Human MSCs were isolated from 1– 4-ml bone marrow aspirates taken from the iliac crest of normal adult donors. Nucleated cells were isolated with a density gradient and resuspended in complete culture medium (CCM) consisting of alpha-minimal essential medium, 17% fetal bovine serum (FBS), 100 units/ml penicillin, 100 ug/ml streptomycin, and 2 mM L-glutamine. All of the nucleated cells were plated in 20 ml of medium in a 175-cm2 culture dish and incubated at 37°C with 5% CO2. After 24 hours, nonadherent cells were discarded, and adherent cells were thoroughly washed twice with phosphate-buffered saline (PBS). The cells were incubated 4 –11 days until approximately 70% confluent, harvested with 0.25% trypsin and 1 mM EDTA for 5 minutes at 37°C, and replated at 50 cells/cm2 in an intercommunicating system of cultureflasks. The cells were incubated 7–10 days until approximately 70% confluent, harvested with trypsin/EDTA, suspended at 1 million cells/ml in 5% dimethyl sulfoxide and 30% FBS, and frozen in 1-ml aliquots at -80°C overnight and then placed in liquid nitrogen (passage 1 cells). A frozen vial of MSCs was then thawed and cells were plated in a 145-cm2 culture dish in CCM. After 24-hour incubation at 37°C and 5% CO2, the medium was removed, cells were washed with PBS, and adherent viable cells were harvested with trypsin/EDTA. Recovered passage 1 MSCs were then plated at 100 cells/cm2 on 15cm plastic dishes. Cells were cultured for 7 days in CCM. About 1 X 106 hMSCs were added to lung from control mouse (NOD/scid) just before homogenization.

extract_protocol: RNA was isolated with Trizol (Invitrogen) and cleaned by RNeasy Mini Kit (Qiagen).

tag: sample type

value: mixture of cultured adult human MSCs and NOD/scid mouse lung


title: Healthy Twin 28a

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

institute: University Clinic of Schleswig Holstein

description: Gene expression data from healthy human twins (mucosal biopsies), male, age: 33a

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133 2.0 Plus Array (Affymetrix GeneChipHybridization Oven 640). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3036

data_processing: Sample data was processed using GCOS 1.3.0 (Affymetrix default settings) and normalized using GCRMA

source_name: Intestinal mucosa biopsy from healthy human individuals

label_protocol: Biotinylated cRNA were prepared using Message Amp II-Biotin (Ambion) and further processed using the standard Affymetrix protocol (Affymetrix manual 2005)

extract_protocol: Qiagen RNeasy mini extraction was performed according to the manufacturer's instructions.

tag: other

value: pair 28

tag: gender

value: male

tag: age

tag: genotype/variation

value: dizygotic twin


title: Healthy Twin 25a

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 22a

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3030

value: pair 25

value: female


title: Healthy Twin 27a

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 43a

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3034

value: pair 27


title: Healthy Twin 29b

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 32b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3039

value: pair 29


title: Healthy Twin 29a

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 32a

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3038


title: Healthy Twin 26b

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 30b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3033

value: pair 26


title: Healthy Twin 23b

description: Gene expression data from healthy human twins (mucosal biopsies), male, age: 20b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3027

value: pair 23


title: Healthy Twin 24b

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 36b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3029

value: pair 24


title: Healthy Twin 25b

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 22b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3031


title: Healthy Twin 27b

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 43b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3035


title: NOD/scid mouse lung (U133 Plus 2.0)

description: NOD/scid mouse lung.

scan_protocol: The array was scanned for fluorescence (GeneChip Scanner 3000, Affymetrix) using the GeneChip Operating software 1.0 (GCOS, Affymetrix)

source_name: NOD/scid mouse lung

tag: genotype

value: NOD/scid

value: lung


title: Healthy Twin 26a

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 30a

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3032


title: Healthy Twin 28b

description: Gene expression data from healthy human twins (mucosal biopsies), male, age: 33b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3037


title: Healthy Twin 24a

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 36a

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3028


title: NOD/scid mouse lung 10 h after IV infusion of human MSCs (U133 Plus 2.0)

description:
Cultured adult human MSCs.
NOD/scid mouse lung 10h after IV infusion of hMSCs.
NOD/scid mouse lung 10h after IV infusion of human multipotent stromal cells (hMSCs)

source_name: NOD/scid mouse lung 10 h after IV infusion of hMSCs

growth_protocol: Human MSCs were isolated from 1– 4-ml bone marrow aspirates taken from the iliac crest of normal adult donors. Nucleated cells were isolated with a density gradient and resuspended in complete culture medium (CCM) consisting of alpha-minimal essential medium, 17% fetal bovine serum (FBS), 100 units/ml penicillin, 100 ug/ml streptomycin, and 2 mM L-glutamine. All of the nucleated cells were plated in 20 ml of medium in a 175-cm2 culture dish and incubated at 37°C with 5% CO2. After 24 hours, nonadherent cells were discarded, and adherent cells were thoroughly washed twice with phosphate-buffered saline (PBS). The cells were incubated 4 –11 days until approximately 70% confluent, harvested with 0.25% trypsin and 1 mM EDTA for 5 minutes at 37°C, and replated at 50 cells/cm2 in an intercommunicating system of cultureflasks. The cells were incubated 7–10 days until approximately 70% confluent, harvested with trypsin/EDTA, suspended at 1 million cells/ml in 5% dimethyl sulfoxide and 30% FBS, and frozen in 1-ml aliquots at -80°C overnight and then placed in liquid nitrogen (passage 1 cells). A frozen vial of MSCs was then thawed and cells were plated in a 145-cm2 culture dish in CCM. After 24-hour incubation at 37°C and 5% CO2, the medium was removed, cells were washed with PBS, and adherent viable cells were harvested with trypsin/EDTA. Recovered passage 1 MSCs were then plated at 100 cells/cm2 on 15cm plastic dishes. Cells were cultured for 7 days in CCM. About 2 X 106 hMSCs were infused IV into NOD/scid mouse and lung RNA was isolated 10h after infusion.


title: Healthy Twin 12b

description: Gene expression data from healthy human twins (mucosal biopsies), male, age: 47b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3019

value: pair 12

value: monozygotic twin


title: Healthy Twin 20a

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 38a

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3020

value: pair 20


title: Healthy Twin 22b

description: Gene expression data from healthy human twins (mucosal biopsies), male, age: 43b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3025

value: pair 22


title: Healthy Twin 23a

description: Gene expression data from healthy human twins (mucosal biopsies), male, age: 20a

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3026


title: Healthy Twin 21a

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 24a

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3022

value: pair 21


title: Healthy Twin 22a

description: Gene expression data from healthy human twins (mucosal biopsies), male, age: 43a

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3024


title: Healthy Twin 20b

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 38b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3021


title: Healthy Twin 12a

description: Gene expression data from healthy human twins (mucosal biopsies), male, age: 47a

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3018


title: Healthy Twin 21b

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 24b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3023


title: Healthy Twin 11a

description: Gene expression data from healthy human twins (mucosal biopsies), male, age: 34a

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3016

value: pair 11


title: Healthy Twin 11b

description: Gene expression data from healthy human twins (mucosal biopsies), male, age: 34b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3017

value: male


title: Healthy Twin 08b

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 37b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3015

value: pair 08


title: Healthy Twin 06b

description: Gene expression data from healthy human twins (mucosal biopsies), male, age: 20b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3011

value: pair 06


title: Healthy Twin 07a

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 30a

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3012

value: pair 07

value: female


title: Healthy Twin 08a

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 37a

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3014


title: Healthy Twin 05b

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 53b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3009

value: pair 05


title: Healthy Twin 06a

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3010


title: Healthy Twin 05a

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 53a

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3008


title: Healthy Twin 04b

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 23b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3007

value: pair 04


title: Healthy Twin 03b

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 21b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3005

value: pair 03


title: Healthy Twin 01b

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 30b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

value: pair 01


title: Healthy Twin 02b

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 39b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3003

value: pair 02


title: Healthy Twin 04a

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 23a

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3006


title: Healthy Twin 07b

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3013


title: Healthy Twin 02a

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 39a

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3002


title: Healthy Twin 01a


title: Healthy Twin 03a

description: Gene expression data from healthy human twins (mucosal biopsies), female, age: 21a

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3004


title: Clone A cells treated with 5uM NIM811 and cultured for 48 hours rep4

status: Public on May 03 2009

city: Cambridge

first: Piroska

last: Devay

state: MA

address: 500 Technology Sq

department: Infectious Disease

institute: NIBRI

description: no additional information

hyb_protocol: Hybridization to Affymetrix U133 Plus 2 microarrays was carried out at 45˚ C for 18 hours, then washed and stained in Affymetrix GeneChip Fluidics Workstation 450.

scan_protocol: Arrays were scanned on GeneArray Scanner 3000 according to the manufacturer's protocol (Affymetrix Inc.)

data_processing: Raw data was normalized using RMA in the  Bioconductor package.

source_name: Huh7 cells with HCV replicon, treated with 5uM NIM811, cultured for 48 hours

label_protocol: After reverse transcription cDNA was fragmented and biotinylated according to the Affymetrix protocol.

growth_protocol: Huh7 cells or Clone A cells were cultured at 37˚ C (5% CO2) in DMEM with 10% Fetal Bovine Serum.

extract_protocol: RNA  was extracted with Purescript RNA Purification System  (Gentra) and RNeasy Mini Kit (Qiagen) according to the manufacturer protocol.

treatment_protocol: Cultured cells were treated with 1 or 5 uM NIM811 or CsA diluted in fresh medium.

tag: hcv genotype

value: genotype 1B

tag: agent

tag: concentration

tag: time

value: 48 hours


title: Clone A cells treated with 5uM CsA and cultured for 24 hours rep6

description: no additional information

source_name: Huh7 cells with HCV replicon, treated with 5uM CsA, cultured for 24 hours

value: CsA

value: 24 hours


title: Huh7 cells treated with 5uM CsA and cultured for 48 hours rep6

description: no additional information

source_name: Huh7 cells, treated with 5uM CsA, cultured for 48 hours


title: Huh7 cells treated with 5uM CsA and cultured for 48 hours rep5

description: no additional information


title: Clone A cells treated with 1uM NIM811 and cultured for 48 hours rep2

description: no additional information

source_name: Huh7 cells with HCV replicon, treated with 1uM NIM811, cultured for 48 hours


title: Huh7 cells treated with 5uM NIM811 and cultured for 48 hours rep6

description: no additional information

source_name: Huh7 cells, treated with 5uM NIM811, cultured for 48 hours


title: Clone A cells treated with 1uM NIM811 and cultured for 48 hours rep1

description: no additional information


title: Clone A  cells treated with 5uM CsA and cultured for 24 hours rep4

description: no additional information


title: Huh7 cells treated with 5uM CsA and cultured for 48 hours rep4

description: no additional information


title: Huh7 cells treated with 1uM NIM811 and cultured for48 hours rep2

description: no additional information

source_name: Huh7 cells, treated with 1uM NIM811, cultured for48 hours


title: Huh7 cells treated with 5uM NIM811 and cultured for 48 hours rep4

description: no additional information


title: Huh7 cells treated with 1uM NIM811 and cultured for 48 hours rep1

description: no additional information

source_name: Huh7 cells, treated with 1uM NIM811, cultured for 48 hours


title: Clone A cells treated with 1uM CsA and cultured for 24 hours rep3

description: no additional information

source_name: Huh7 cells with HCV replicon, treated with 1uM CsA, cultured for 24 hours


title: Huh7 cells treated with 1uM CsA and cultured for 48 hours rep3

description: no additional information

source_name: Huh7 cells, treated with 1uM CsA, cultured for 48 hours


title: Clone A  cells treated with 1uM CsA and cultured for 24 hours rep1

description: no additional information


title: Clone A cells treated with 5uM CsA and cultured for 24 hours rep5

description: no additional information


title: Huh7 cells treated with 1uM NIM811 and cultured for 48 hours rep3

description: no additional information


title: Huh7 cells treated with 1uM CsA and cultured for 48 hours rep2

description: no additional information


title: Clone A cells treated with 5uM NIM811 and cultured for 48 hours rep5

description: no additional information


title: Huh7 cells treated with 5uM NIM811 and cultured for48 hours rep5

description: no additional information

source_name: Huh7 cells, treated with 5uM NIM811, cultured for48 hours


title: Clone A cells treated with 1uM CsA and cultured for 24 hours rep2

description: no additional information


title: Clone A cells treated with 1uM NIM811 and cultured for 48 hours rep3

description: no additional information


title: Huh7 cells cultured for 48 hours rep4

description: no additional information

source_name: Huh7 cells, cultured for 48 hours

value: control


title: Huh7 cells treated with 1uM CsA and cultured for 48 hours rep1

description: no additional information


title: Clone A cells cultured for 48 hours rep6

description: no additional information

source_name: Huh7 cells with HCV replicon, cultured for 48 hours


title: Clone A cells cultured for 48 hours rep5

description: no additional information


title: Clone A cells cultured for 48 hours rep4

description: no additional information


title: Huh7 cells cultured for 48 hours rep6

description: no additional information


title: Clone A cells treated with 5uM CsA and cultured for 48 hours rep3

description: no additional information

source_name: Huh7 cells with HCV replicon, treated with 5uM CsA, cultured for 48 hours


title: Huh7 cells cultured for 48 hours rep5

description: no additional information


title: Clone A cells treated with 5uM NIM811 and cultured for 48 hours rep2

description: no additional information


title: Clone A cells treated with 5uM NIM811 and cultured for 48 hours rep1

description: no additional information


title: Clone A cells cultured for 24 hours rep2

description: no additional information

source_name: Huh7 cells with HCV replicon, cultured for 24 hours


title: Clone A cells treated with 5uM NIM811 and cultured for 48 hours rep3

description: no additional information


title: Clone A cells cultured for 48 hours rep2

description: no additional information


title: Clone A  cells treated with 5uM CsA and cultured for 24 hours rep1

description: no additional information


title: Clone A  cells treated with 5uM CsA and cultured for 48 hours rep1

description: no additional information


title: Clone A cells treated with 5uM CsA and cultured for 24 hours rep2

description: no additional information


title: Clone A cells cultured for 24 hours rep1

description: no additional information


title: Clone A  cells treated with 5uM CsA and cultured for 12 hours rep1

description: no additional information

source_name: Huh7 cells with HCV replicon, treated with 5uM CsA, cultured for 12 hours

value: 12 hours


title: Clone A cells treated with 5uM NIM811 and cultured for 12 hours rep3

description: no additional information

source_name: Huh7 cells with HCV replicon, treated with 5uM NIM811, cultured for 12 hours


title: Clone A cells treated with 5uM CsA and cultured for 24 hours rep3

description: no additional information


title: Clone A cells treated with 5uM CsA and cultured for 12 hours rep2

description: no additional information


title: Clone A cells cultured for 48 hours rep3

description: no additional information


title: Clone A cells treated with 5uM NIM811 and cultured for 24 hours rep3

description: no additional information

source_name: Huh7 cells with HCV replicon, treated with 5uM NIM811, cultured for 24 hours


title: Clone A cells treated with 5uM NIM811 and cultured for 12 hours rep2

description: no additional information


title: Clone A cells cultured for 12 hours rep2

description: no additional information

source_name: Huh7 cells with HCV replicon, cultured for 12 hours


title: Clone A cells treated with 5uM CsA and cultured for 48 hours rep2

description: no additional information


title: Clone A cells treated with 5uM NIM811 and cultured for 24 hours rep1

description: no additional information


title: Clone A cells cultured for 48 hours rep1

description: no additional information


title: Clone A cells cultured for 12 hours rep1

description: no additional information


title: Huh7 cells treated with 5uM CsA and cultured for 48 hours rep3

description: no additional information


title: Clone A cells treated with 5uM CsA and cultured for 12 hours rep3

description: no additional information


title: Huh7 cells treated with 5uM CsA and cultured for 48 hours rep2

description: no additional information


title: Clone A cells cultured for 12 hours rep3

description: no additional information


title: Clone A cells treated with 5uM NIM811 and cultured for 24 hours rep2

description: no additional information


title: Clone A cells cultured for 24 hours rep3

description: no additional information


title: Clone A cells treated with 5uM NIM811 and cultured for 12 hours rep1

description: no additional information


title: Huh7 cells treated with 5uM CsA and cultured for 48 hours rep1

description: no additional information


title: Huh7 cells treated with 5uM NIM811 and cultured for 48 hours rep3

description: no additional information


title: Huh7 cells treated with 5uM NIM811 and cultured for 48 hours rep1

description: no additional information


title: Huh7 cells treated with 5uM CsA and cultured for 24 hours rep2

description: no additional information

source_name: Huh7 cells, treated with 5uM CsA, cultured for 24 hours


title: Huh7 cells treated with 5uM NIM811 and cultured for 24 hours rep1

description: no additional information

source_name: Huh7 cells, treated with 5uM NIM811, cultured for 24 hours


title: Huh7 cells treated with 5uM CsA and cultured for 24 hours rep1

description: no additional information


title: Huh7 cells cultured for 48 hours rep3

description: no additional information


title: Huh7 cells treated with 5uM NIM811 and cultured for48 hours rep2

description: no additional information


title: Huh7 cells cultured for 48 hours rep1

description: no additional information


title: Huh7 cells treated with 5uM NIM811 and cultured for 12 hours rep3

description: no additional information

source_name: Huh7 cells, treated with 5uM NIM811, cultured for 12 hours


title: Huh7 cells treated with 5uM CsA and cultured for 12 hours rep2

description: no additional information

source_name: Huh7 cells, treated with 5uM CsA, cultured for 12 hours


title: Huh7 cells treated with 5uM CsA and cultured for 12 hours rep1

description: no additional information


title: Huh7 cells cultured for 12 hours rep2

description: no additional information

source_name: Huh7 cells, cultured for 12 hours


title: Huh7 cells cultured for 12 hours rep1

description: no additional information


title: Huh7 cells treated with 5uM NIM811 and cultured for 24 hours rep3

description: no additional information


title: Huh7 cells treated with 5uM NIM811 and cultured for 12 hours rep2

description: no additional information


title: Huh7 cells treated with 5uM CsA and cultured for 12 hours rep3

description: no additional information


title: Huh7 cells cultured for 24 hours rep2

description: no additional information

source_name: Huh7 cells, cultured for 24 hours


title: H295R_Group_C_Dose_100_TIMEPT1_031

status: Public on May 02 2009

city: Salem

first: William

last: Loging

state: CT

address: 73 Skyline Dr

institute: CETP Project Team

description: no additional information

hyb_protocol: According to standard Affymetrix protocol.

data_processing: RMA

source_name: H295R adrenocortical carcinoma cells

extract_protocol: RNA was extracted with the RNeasy 96 kit (QIAGEN) per the manufacturer’s instructions.

tag: cell line

value: H295R adrenocortical carcinoma cells

value: Cells derived from Adrenal gland

value: test compound CP-529414 (CETP+ /BP+ THQ+)

tag: dose

value: 3 hr


title: Huh7 cells treated with 5uM NIM811 and cultured for 12 hours rep1

description: no additional information


title: Huh7 cells cultured for 12 hours rep3

description: no additional information


title: Huh7 cells treated with 5uM NIM811 and cultured for 24 hours rep2

description: no additional information


title: H295R_Group_B_Dose_100_TIMEPT1_009

description: no additional information

scan_protocol: According to standard Affymetrix protocol.

value: angiotensin II


title: H295R_Group_B_Dose_100_TIMEPT1_008

description: no additional information

label_protocol: According to standard Affymetrix protocol.


title: Huh7 cells cultured for 24 hours rep1

description: no additional information


title: H295R_Group_C_Dose_100_TIMEPT1_032

description: no additional information


title: H295R_Group_B_Dose_100_TIMEPT1_007

description: no additional information


title: H295R_Group_C_Dose_100_TIMEPT1_033

description: no additional information


title: H295R_Group_A_Dose_NA_TIMEPT1_002

description: no additional information

value: DMSO (control)


title: Huh7 cells cultured for 24 hours rep3

description: no additional information


title: Huh7 cells cultured for 48 hours rep2

description: no additional information


title: H295R_Group_A_Dose_NA_TIMEPT1_001

description: no additional information


title: H295R_Group_A_Dose_NA_TIMEPT1_003

description: no additional information


title: Testis 13.9 Weeks Gestation rep1

status: Public on May 01 2009

city: Pullman

first: Lizhong

last: Yang

state: WA

address: 531 Fulmer Hall/POB 644660

department: School of Molecular Biosciences

institute: Washington State University

description: gene expression data from normal human fetal testes between 9 weeks and 20 weeks of gestation

hyb_protocol: The labeled cDNA was fragmented, hybridized to Human Genome U133A Plus arrays (Affymetrix, Santa Clara, CA) and stained in accordance with the manufacturer's standard protocol.

scan_protocol: The arrays were washed utilizing the Affymetrix GeneChip Fluidics Station 400 and scanned using a GeneArray Scanner 2500A (Agilent, Palo Alto, CA).

data_processing: Analysis of data was conducted within the R statistical computing environment (www.R-project.org).  Visual inspection of 49 scanned images and output from the “affyQCreport” package of Bioconductor (www.bioconductor.org) revealed 34 of 49 arrays were within acceptable limits.  The 15 arrays that were unacceptable had significant degradation as determined by poor 3’/5’ ratios of Affy control probe sets present on each array.  For the remaining 34 arrays, probe sets were filtered on the following two criteria:  probe sets not classified as present in any array were eliminated and two separate normalizations of the data (MAS5 and RMA) were then performed.   The background intensity values for each normalization routine was determined using probe sets labeled absent in all microarrays and only those probe sets above the 99th percentile of the background were retained for further analysis.

source_name: Human Testis 13.9 Weeks Gestation rep1

label_protocol: Ovation Biotin RNA Amplification and Labeling System by NuGEN (San Carlos, CA)

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Protect Mini/midi Kit®.

value: Human fetal testis

tag: fetus age

value: 13.9 weeks


title: Testis 12.6 Weeks Gestation

source_name: Human Testis 12.6 Weeks Gestation

value: 12.6 weeks


title: MCF-7 transfected with human SOX2 expression construct,biological rep1

city: Beijing

first: Yupeng

last: Chen

address: Haidian District 38

country: China

institute: Peking University Health Science Center

description: Gene expression data from MCF-7 transfected with SOX2

hyb_protocol: Hybridization was performed at 45°C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640). The GeneChip arrays were washed and then stained (streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: The hybridization data were analyzed using GeneChip Operating software (GCOS 1.4). The scanned images were firstly assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of GCOS 1.4. A global scaling factor of 500 was used to normalize the different arrays.

source_name: Hman Breast Cancer MCF-7 Cells, transfected with Human SOX2 Expression Construct

label_protocol: 2 μg of total RNA was used to synthesize double-stranded cDNA, then to produce biotin-tagged cRNA using MessageAmp™ II aRNA Amplification Kit.

growth_protocol: The MCF-7 cells were grown in Dulbecco's modified Eagle's medium (Invitrogen) supplemented with 10% fetal bovine serum (Gibco BRL). The cells were maintained in a humidified 37°C incubator with 5% CO2, fed every 3 days with complete medium, and subcultured when confluence was reached.

treatment_protocol: Cells were transfected with the control and SOX2 expression plasmids by using Lipofectamine 2000 reagent (Invitrogen) in accordance with the manufacturer's protocol. The cells were harvested at 24 hours after transfection.

tag: Human Breast Cancer Cells


title: Testis 16.1 Weeks Gestation rep2

source_name: Human Testis 16.1 Weeks Gestation rep2

value: 16.1 weeks


title: Testis 17.2 Weeks Gestation

source_name: Human Testis 17.2 Weeks Gestation

value: 17.2 weeks


title: Testis 16.1 Weeks Gestation rep1

source_name: Human Testis 16.1 Weeks Gestation rep1


title: Testis 18.6 Weeks Gestation

source_name: Human Testis 18.6 Weeks Gestation

value: 18.6 weeks


title: MCF-7 transfected with pcDNA3.1

description: Gene expression data from MCF-7 transfected with pcDNA3.1

source_name: Hman Breast Cancer MCF-7 Cells, transfected with pcDNA3.1


title: Testis 12 Weeks Gestation

source_name: Human Testis 12 Weeks Gestation

value: 12 weeks


title: Testis 13.9 Weeks Gestation rep2

source_name: Human Testis 13.9 Weeks Gestation rep2


title: Testis 18.9 Weeks Gestation

source_name: Human Testis 18.9 Weeks Gestation

value: 18.9 weeks


title: Testis 13.6 Weeks Gestation

source_name: Human Testis 13.6 Weeks Gestation

value: 13.6 weeks


title: Testis 19.9 Weeks Gestation

source_name: Human Testis 19.9 Weeks Gestation

value: 19.9 weeks


title: Testis 9.1 Weeks Gestation

source_name: Human Testis 9.1 Weeks Gestation

value: 9.1 weeks


title: Testis 11 Weeks Gestation rep1

source_name: Human Testis 11 Weeks Gestation rep1

value: 11 weeks


title: Testis 9 Weeks Gestation

source_name: Human Testis 9 Weeks Gestation

value: 9 weeks


title: Testis 11 Weeks Gestation rep2

source_name: Human Testis 11 Weeks Gestation rep2


title: Testis 9.9 Weeks Gestation

source_name: Human Testis 9.9 Weeks Gestation

value: 9.9 weeks


title: Ovary 16.9 Weeks Gestation rep2

description: gene expression data from normal human fetal ovaries between 9 weeks and 20 weeks of gestation

source_name: Human Ovary 16.9 Weeks Gestation rep2

value: Human fetal ovary

value: 16.9 weeks


title: Ovary 18.1 Weeks Gestation

source_name: Human Ovary 18.1 Weeks Gestation

value: 18.1 weeks


title: Ovary 17.1 Weeks Gestation

source_name: Human Ovary 17.1 Weeks Gestation

value: 17.1 weeks


title: Testis 11.7 Weeks Gestation

source_name: Human Testis 11.7 Weeks Gestation

value: Human fetal testis

value: 11.7 weeks


title: MCF-7 transfected with human SOX2 expression construct,biological rep2

source_name: Hman Breast Cancer MCF-7 Cells, transfected with Human SOX2 Expression Construct


title: Ovary 16.4 Weeks Gestation

source_name: Human Ovary 16.4 Weeks Gestation

value: 16.4 weeks


title: Ovary 13.6 Weeks Gestation rep2

source_name: Human Ovary 13.6 Weeks Gestation rep2


title: Ovary 14.4 Weeks Gestation

source_name: Human Ovary 14.4 Weeks Gestation

value: 14.4 weeks


title: Ovary 16.9 Weeks Gestation rep1

source_name: Human Ovary 16.9 Weeks Gestation rep1


title: Ovary 13.6 Weeks Gestation rep1

source_name: Human Ovary 13.6 Weeks Gestation rep1


title: Ovary 12 Weeks Gestation

source_name: Human Ovary 12 Weeks Gestation


title: Ovary 13.9 Weeks Gestation

source_name: Human Ovary 13.9 Weeks Gestation

value: 13.9 weeks


title: Ovary 11 Weeks Gestation

source_name: Human Ovary 11 Weeks Gestation


title: Ovary 16.1 Weeks Gestation

source_name: Human Ovary 16.1 Weeks Gestation

value: 16.1 weeks


title: Ovary 9.6 Weeks Gestation rep2

source_name: Human Ovary 9.6 Weeks Gestation rep2

value: 9.6 weeks


title: Ovary 9.6 Weeks Gestation rep1

source_name: Human Ovary 9.6 Weeks Gestation rep1


title: Ovary 12.9 Weeks Gestation

source_name: Human Ovary 12.9 Weeks Gestation

value: 12.9 weeks


title: Ovary 9.1 Weeks Gestation

source_name: Human Ovary 9.1 Weeks Gestation


title: Ovary 9.6 Weeks Gestation rep3

source_name: Human Ovary 9.6 Weeks Gestation rep3


title: 14568T (U133plus2): Brain metastasis

city: Houston

first: Xiang

last: Zhang

address: One Baylor Plaza, BCM600

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

description: Brain metastasis

hyb_protocol: Test3 arrays (Affymetrix), standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA algorithm

source_name: Brain

label_protocol: Biotinylated nucleotides (Enzo Biochem), standard Affymetrix protocol

extract_protocol: TRIzol (GIBCO/BRL)

tag: Breast cancer


title: 115463T (U133plus2): Bone metastasis

description: Bone metastasis

source_name: Bone


title: 15112T (U133plus2): Lung metastasis

description: Lung metastasis

source_name: Lung


title: 11993T (U133plus2): Lung metastasis

description: Lung metastasis


title: 12370T (U133plus2): Brain metastasis

description: Brain metastasis


title: 114112T (U133plus2): Bone metastasis

description: Bone metastasis


title: 14891T (U133plus2): Bone metastasis

description: Bone metastasis


title: 13685T (U133plus2): Brain metastasis

description: Brain metastasis


title: 116610T (U133plus2): Brain metastasis

description: Brain metastasis


title: 112397T (U133plus2): Bone metastasis

description: Bone metastasis


title: 11887T (U133plus2): Bone metastasis

description: Bone metastasis


title: 112403T (U133plus2): Brain metastasis

description: Brain metastasis


title: 113471T (U133plus2): Brain metastasis

description: Brain metastasis


title: 111276T (U133plus2): Brain metastasis

description: Brain metastasis


title: 113542T (U133plus2): Brain metastasis

description: Brain metastasis


title: 110032T (U133plus2): Brain metastasis

description: Brain metastasis


title: 109714T (U133plus2): Brain metastasis

description: Brain metastasis


title: 110312T (U133plus2): Brain metastasis

description: Brain metastasis


title: 110783T (U133plus2): Lung metastasis

description: Lung metastasis


title: In vivo control_2

first: Edward

last: Oakeley

address: Maulbeerstrasse 66

institute: FMI

description: tumor lysate from MDA-MB-231/control xenograft

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: GCRMA generated using Genedata's Refiner 5.0 software tool

label_protocol: Affymetrix protocol

growth_protocol: Three MDA-MB-231/sFRP1 clones and three MDA-MB-231/control clones were cultured in DMEM 10% FCS with 1mg/ml G-418. In parallel, the three sFRP1+ clones and the three control clones were pooled and injected to fat pads of nude mice. A few – several weeks after, mice were sacrificed and tumors arising from these cells were taken to isolate RNA.

extract_protocol: Cultured cells were collected when plates were 70-80% confluent and RNA was extracted using RNeasy Mini kit (Qiagen, Venlo, The Netherlands). To extract the RNA from tumours, dissected tumours were put in RNAlater (Qiagen) over night at 4°C, followed by RNA extraction using TRIzol reagent (Invitrogen) and washing using the RNAeasy Mini kit according to manufacturer’s instructions.

treatment_protocol: RNA was taken from cell lysates and tumor lysates

tag: Strain

value: Balb/c nude, Sex:female, Tissue:xenografted mammary tumor


title: 109506T (U133plus2): Brain metastasis

description: Brain metastasis


title: In vivo sFRP1_5

description: tumor lysate from MDA-MB-231/sFRP1 xenograft


title: In vivo control_5

source_name: tumor lysate from MDA-MB-231/control xenograft


title: In vivo sFRP1_4

source_name: tumor lysate from MDA-MB-231/sFRP1 xenograft


title: In vitro control_3

description: cultured MDA-MB-231/control cell

source_name: cultured MDA-MB-231/control cell

tag: MDA-MB-231/control cells


title: In vivo sFRP1_1


title: 104406T (U133plus2): Brain metastasis

description: Brain metastasis


title: In vivo sFRP1_6


title: In vivo control_4


title: In vivo control_1


title: In vitro control_2

description: cultured MDA-MB-231/control cell


title: 107696T (U133plus2): Bone metastasis

description: Bone metastasis


title: 107502T (U133plus2): Brain metastasis

description: Brain metastasis


title: In vivo control_3


title: 107961T (U133plus2): Bone metastasis

description: Bone metastasis


title: In vivo sFRP1_3


title: 102962T (U133plus2): Brain metastasis

description: Brain metastasis


title: 109594T (U133plus2): Bone metastasis

description: Bone metastasis


title: In vitro sFRP1_3

description: cultured MDA-MB-231/sFRP1 cell

source_name: cultured MDA-MB-231/sFRP1 cell

tag: MDA-MB-231/sFRP1 cells


title: In vitro sFRP1_2

description: cultured MDA-MB-231/sFRP1 cell


title: In vitro control_1

description: cultured MDA-MB-231/control cell


title: 5381T (U133plus2): Lung metastasis

description: Lung metastasis


title: In vivo sFRP1_2


title: In vitro sFRP1_1

description: cultured MDA-MB-231/sFRP1 cell


title: patient:4--location:ni--R:01

description: no additional information

scan_protocol: Standard Affymetrix procedures

source_name: cold cup biopsy, 20mm3 size, IC non-ulcer tissue

tag: tissue

value: bladder

tag: disease state

value: IC, non-ulcer tissue


title: patient:4--location:ulcus--R:01

description: no additional information

source_name: cold cup biopsy, 20mm3 size, IC ulcer

value: IC, ulcer


title: Expressional Response to Acute Hypoxia in Drosophila (NC3)

status: Public on Apr 30 2009

city: La Jolla

first: Dan

last: Zhou

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

institute: University of California, San Diego, School of Medicine

description: Control Sample 3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 7G

data_processing: The data were analyzed with GCOS1.4 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Drosophila melanogaster: Control group 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix)

extract_protocol: Total RNA was extracted using RNeasy Micro kit (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: 25 males and females (5-6 days old adult) flies exposed to 2.5 hours of normoxia kept in the same room so exposed to same level of light and noise

tag: strain

value: Canton-S

tag: developmental stage

value: Adult

value: Whole organism


title: Expressional Response to Acute Hypoxia in Drosophila (IH1)

description: IH treated group 1

source_name: Drosophila melanogaster treated with intermittent hypoxia, group 1

treatment_protocol: 25 males and females (5-6 days old adult) flies exposed to 2.5 hours of 1% intermittent hypoxia (cycle- 4 min. 1% O2 alternating with 4 min 21% O2).


title: patient:9--location:healthy--R:01

description: no additional information

source_name: cold cup biopsy, 20mm3 size, healthy

value: no


title: Expressional Response to Acute Hypoxia in Drosophila (CH1)

description: CH treated group 1

source_name: Drosophila melanogaster treated with constant hypoxia, group 1

treatment_protocol: 25 males and females (5-6 days old adult) flies exposed to 2.5 hours of constant hypoxia (1% O2).


title: patient:15--location:ulcus--R:01

description: no additional information


title: patient:5--location:healthy--R:01

description: no additional information


title: Expressional Response to Acute Hypoxia in Drosophila (NC1)

description: Control Sample 1

source_name: Drosophila melanogaster: control group 1


title: Expressional Response to Acute Hypoxia in Drosophila (IH3)

description: IH treated group 3

source_name: Drosophila melanogaster treated with intermittent hypoxia, group 3


title: Expressional Response to Acute Hypoxia in Drosophila (CH2)

description: CH treated group 2

source_name: Drosophila melanogaster treated with constant hypoxia, group 2


title: patient:14--location:ulcus--R:01

description: no additional information


title: patient:11--location:healthy--R:01

description: no additional information


title: Expressional Response to Acute Hypoxia in Drosophila (NC2)

description: Control Sample 2

source_name: Drosophila melanogaster: control group 2


title: patient:13--location:ni--R:01

description: no additional information


title: patient:7--location:healthy--R:01

description: no additional information


title: patient:15--location:ni--R:01

description: no additional information


title: Expressional Response to Acute Hypoxia in Drosophila (CH3)

description: CH treated group 3

source_name: Drosophila melanogaster treated with constant hypoxia, group 3


title: patient:10--location:healthy--R:01

description: no additional information


title: Expressional Response to Acute Hypoxia in Drosophila (IH2)

description: IH treated group 2

source_name: Drosophila melanogaster treated with intermittent hypoxia, group 2


title: patient:13--location:ulcus--R:01

description: no additional information


title: Insulin sensitive patient 4 - omental adipose tissue

status: Public on Apr 24 2009

city: Worcester

first: Olga

middle: Theresa

last: Hardy

address: 373 Plantation Street, Biotech Two, Suite 100

department: Molecular Medicine

institute: University of Massachusetts

description: Gene expression data from human adipose tissue obtained during gastric bypass surgery.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000, with 7G upgrade

data_processing: The data were analyzed with the Bioconductor statistical environment using RMA and Expression Console software using RMA. Gene Set Analysis method in Significance Analysis of Microarrays (SAM, Palo Alto, CA) with 1000 permutations of the data was applied for analysis of Gene Ontology (GO) Molecular Function Gene Sets.

source_name: Obese female

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

extract_protocol:
Paired samples of omental and subcutaneous adipose were obtained from fasting patients during gastric bypass surgery. Whole adipose tissue was dissected to remove fibrotic tissue and obvious vasculature, and frozen in 0.5 cm3 sections in liquid nitrogen.
Total RNA was isolated from frozen human tissues by homogenizing the tissue in TRIzol. RNA quality was assessed using a denaturing agarose gel.  Total RNA was purified using RNeasy Mini-Kit.

value: omental adipose

tag: gender

value: female

tag: metabolic status

value: insulin sensitive


title: patient:12--location:ni--R:01

description: no additional information


title: Insulin sensitive patient 2 - omental adipose tissue


title: Insulin sensitive patient 3 - omental adipose tissue


title: Insulin sensitive patient 5 - omental adipose tissue


title: patient:12--location:ulcus--R:01

description: no additional information


title: Insulin resistant patient 1 - omental adipose tissue

source_name: Obese male

value: male

value: insulin resistant


title: Insulin sensitive patient 3 - subcutaneous adipose tissue

value: subcutaneous adipose


title: Insulin sensitive patient 5 - subcutaneous adipose tissue


title: Insulin resistant patient 5 - omental adipose tissue


title: Insulin resistant patient 2 - omental adipose tissue


title: Insulin resistant patient 4 - omental adipose tissue


title: Insulin resistant patient 5 - subcutaneous adipose tissue


title: Insulin sensitive patient 1 - subcutaneous adipose tissue


title: Insulin resistant patient 3 - subcutaneous adipose tissue


title: Insulin resistant patient 4 - subcutaneous adipose tissue


title: Insulin resistant patient 3 - omental adipose tissue


title: Insulin sensitive patient 2 - subcutaneous adipose tissue


title: Insulin sensitive patient 1 - omental adipose tissue


title: Insulin sensitive patient 4 - subcutaneous adipose tissue


title: 105079T (U133plus2): Bone metastasis

description: Bone metastasis

source_name: Bone


title: Insulin resistant patient 1 - subcutaneous adipose tissue


title: 112282T (U133plus2): Bone metastasis

description: Bone metastasis


title: 48h_LPS_IFNg

status: Public on Apr 22 2009

city: Vienna

first: Alexander

last: Dohnal

address: Kinderspitalgasse 6

department: Tumour Immunology

country: Austria

institute: St. Anna Children's Cancer Research Institute

description: Monocyte derived dendritic cells from a healthy donor activated for 6 hours with LPS IFNg analyzed after 48 hours

hyb_protocol: according to standard Affymetrix procedures

source_name: dendritic cells_LPS IFNg_48h

extract_protocol: RNeasy kit (Qiagen, Hilden, Germany)


title: iDC_12h

description: Monocyte derived dendritic cells from a healthy donor, unstimulated control analyzed after 12 hours

scan_protocol: according to standard Affymetrix procedures


title: tfl1-1-23ºC-RepA

status: Public on Apr 18 2009

city: Ciudad de Buenos Aires

first: Pablo

middle: Diego

last: Cerdan

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

description: tfl1-1 seeds were sterilized overnight by exposure to clorine vapour in a close container. Afterwards seeds were plated on MS salts, Agar 1.2%, and stratified for 3 days in the dark at 4ºC. Plates were moved to a plant incubator and grown for ten days at 23ºC, under continuous cool fluorescent light of 80 micromoles/sec m2. Then seedlings were harvested an inmediately frozen in liquid nitrogen

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

source_name: 10-day old tfl1-1 seedlings, grown on MS salts agar plates, at 23ºC under continuous cool-white fluorescent light, 80 micromoles/sec m2

label_protocol: Affymetrix

growth_protocol:
Seed sterilization: clorine vapour O/N
Plating: MS Salts, 1.2 % Agar
Stratification: 3 days at 4ºC
Growth conditions: 10 days at 23ºC, under continuous cool-white fluorescent light, 80 micromoles/sec m2

extract_protocol: Qiagen RNAeasy kit

value: 10-day old seedlings

tag: genotype

tag: growth conditions


title: tfl1-1-23ºC-RepB


title: iDC_24h

description: Monocyte derived dendritic cells from a healthy donor, unstimulated control analyzed after 24 hours

label_protocol: according to standard Affymetrix procedures


title: iDC_48h

description: Monocyte derived dendritic cells from a healthy donor, unstimulated control analyzed after 48 hours


title: 12h_LPS_IFNg

description: monocyte derived dendritic cells from a healthy donor activated for 6 hours with LPS IFNg analyzed after 12 hours

source_name: dendritic cells_LPS IFNg_12h


title: elf3-7-23ºC-RepC

description: elf3-7 seeds were sterilized overnight by exposure to clorine vapour in a close container. Afterwards seeds were plated on MS salts, Agar 1.2%, and stratified for 3 days in the dark at 4ºC. Plates were moved to a plant incubator and grown for ten days at 23ºC, under continuous cool fluorescent light of 80 micromoles/sec m2. Then seedlings were harvested an inmediately frozen in liquid nitrogen

source_name: 10-day old elf3-7 seedlings, grown on MS salts agar plates, at 23ºC under continuous cool-white fluorescent light, 80 micromoles/sec m2


title: 6h_LPS_IFNg

description: monocyte derived dendritic cells from a healthy donor activated for 6 hours with LPS IFNg analyzed after 6 hours

source_name: dendritic cells_LPS IFNg_6h


title: elf3-7-16ºC-RepA

description: elf3-7 seeds were sterilized overnight by exposure to clorine vapour in a close container. Afterwards seeds were plated on MS salts, Agar 1.2%, and stratified for 3 days in the dark at 4ºC. Plates were moved to a plant incubator and grown for ten days at 16ºC, under continuous cool fluorescent light of 80 micromoles/sec m2. Then seedlings were harvested an inmediately frozen in liquid nitrogen

source_name: 10-day old elf3-7 seedlings, grown on MS salts agar plates, at 16ºC under continuous cool-white fluorescent light, 80 micromoles/sec m2

growth_protocol:
Seed sterilization: clorine vapour O/N
Plating: MS Salts, 1.2 % Agar
Stratification: 3 days at 4ºC
Growth conditions: 10 days at 16ºC, under continuous cool-white fluorescent light, 80 micromoles/sec m2


title: WT-23ºC-RepC

description: WT Col seeds were sterilized overnight by exposure to clorine vapour in a close container. Afterwards seeds were plated on MS salts, Agar 1.2%, and stratified for 3 days in the dark at 4ºC. Plates were moved to a plant incubator and grown for ten days at 23ºC, under continuous cool fluorescent light of 80 micromoles/sec m2. Then seedlings were harvested an inmediately frozen in liquid nitrogen

source_name: 10-day old WT Col seedlings, grown on MS salts agar plates, at 23ºC under continuous cool-white fluorescent light, 80 micromoles/sec m2

value: Columbia (WT)


title: iDC_6h

description: Monocyte derived dendritic cells from a healthy donor, unstimulated control analyzed after 6h hours

source_name: dendritic cells_unstimulated control_6h


title: tfl1-1-23ºC-RepC


title: tfl1-1-16ºC-RepC

description: tfl1-1 seeds were sterilized overnight by exposure to clorine vapour in a close container. Afterwards seeds were plated on MS salts, Agar 1.2%, and stratified for 3 days in the dark at 4ºC. Plates were moved to a plant incubator and grown for ten days at 16ºC, under continuous cool fluorescent light of 80 micromoles/sec m2. Then seedlings were harvested an inmediately frozen in liquid nitrogen

source_name: 10-day old tfl1-1 seedlings, grown on MS salts agar plates, at 16ºC under continuous cool-white fluorescent light, 80 micromoles/sec m2


title: WT-23ºC-RepB


title: WT-23ºC-RepA


title: 24h_LPS_IFNg

description: monocyte derived dendritic cells from a healthy donor activated for 6 hours with LPS IFNg analyzed after 24 hours

source_name: dendritic cells_LPS IFNg_24h


title: elf3-7-23ºC-RepA


title: elf3-7-23ºC-RepB


title: Round5 A2780 (cisplatin-resistant), biological rep3

status: Public on Apr 17 2009

city: Bloomington

first: Meng

last: Li

state: IN

address: 1001 E 3rd Street

department: Medical Sciences

institute: Indiana University

description: Gene expression data from Round5 A2780 cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human U133 plus 2.0  GeneChips. 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 median target intensity of each array was arbitrarily set to 1000.

source_name: Round5 A2780 cells (GI50 = 35uM)

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: Cells were maintained in RPMI 1640 media with 2 mM L-glutamine, 50 U/ml penicillin, 50 mg/ml streptomycin, and 10% fetal bovine serum, at 30o C

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

value: Round5 A2780


title: Round5 A2780 (cisplatin-resistant), biological rep1


title: Round5 A2780 (cisplatin-resistant), biological rep4


title: Round5 A2780 (cisplatin-resistant), biological rep5


title: parental A2780 (cisplatin-sensitive), biological rep3

description: Gene expression data from parental A2780 cells

source_name: parental A2780 cells (GI50 = 5uM)

value: parental A2780


title: Round5 A2780 (cisplatin-resistant), biological rep2


title: parental A2780 (cisplatin-sensitive), biological rep4


title: patient:2--location:healthy--R:01

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

description: no additional information

hyb_protocol: Following fragmentation, 13 ug of biotin-labeled cRNA were hybridized for 16 h at 45 C on GeneChip Human Genome U133 Plus 2.0 arrays. Arrays were then washed using an Affymetrix Fluidics Station 450 FS450_001 protocol.

source_name: cold cup biopsy, 20mm3 size, healthy

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix protocol from 1 ug total-RNA.

value: bladder


title: WT-16ºC-RepC

description: WT Columbia seeds were sterilized overnight by exposure to clorine vapour in a close container. Afterwards seeds were plated on MS salts, Agar 1.2%, and stratified for 3 days in the dark at 4ºC. Plates were moved to a plant incubator and grown for ten days at 16ºC, under continuous cool fluorescent light of 80 micromoles/sec m2. Then seedlings were harvested an inmediately frozen in liquid nitrogen

source_name: 10-day old Columbia (WT) seedlings, grown on MS salts agar plates, at 16ºC under continuous cool-white fluorescent light, 80 micromoles/sec m2

extract_protocol: Qiagen RNAeasy Kit


title: elf3-7-16ºC-RepB


title: WT-16ºC-RepA

description: 10-day old Columbia (WT) seedlings, grown on MS salts agar plates, at 16ºC under continuous cool-white fluorescent light, 80 micromoles/sec m2


title: parental A2780 (cisplatin-sensitive), biological rep1


title: elf3-7-16ºC-RepC


title: tfl1-1-16ºC-RepB


title: WT-16ºC-RepB

description: WT Columbia seeds were sterilized overnight by exposure to clorine vapour in a close container. Afterwards seeds were plated on MS salts, Agar 1.2%, and stratified for 3 days in the dark at 4ºC. Plates were moved to a plant incubator and grown for ten  at 16ºC, under continuous cool fluorescent light of 80 micromoles/sec m2. Then seedlings were harvested an inmediately frozen in liquid nitrogen

source_name: WT10 d-old, continuous WL, 80 micromoles/sec m2, 16ºC, RepB


title: hepatoma_wt_TCDD_rep1

city: Ann Arbor

first: Maureen

middle: A

last: Sartor

state: MI

address: 2017 Palmer Commons-100 Washtenaw Ave.

institute: University of Michigan

hyb_protocol: Affymetrix GeneChip Mouse Genome Arrays were hybridized with 15 mg of fragmented aRNA for 16 hr at 45oC.  Hybridization, staining, and washing were carried out using the Affymetrix GeneChip Hybridization Wash and Stain Kit following the manufacturer’s protocols.

scan_protocol: Scanned according to Affymetrix protocols.

data_processing: Data was pre-processed with RMA.

source_name: hepatoma wildtype cells, TCDD 8hr

label_protocol: Ambion Biotin-Enhanced Message Amp II kit (Austin, Texas), following the manufacturer’s protocols

growth_protocol: Grown in alpha MEM medium with 5% fetal bovine serum

extract_protocol: Total RNA was extracted using NucleoSpin RNA II columns (Macherey-Nagel) according to the manufacturer’s instructions.  RNA extracts were validated on preparation for quality and integrity using the Agilent 2100 Bioanalyzer.  All RNA samples had RNA Integrity Number greater than 7.0.

treatment_protocol: Treatment with 2,3,7,8-tetrachlorodibenzo-p-dioxin in DMSO for 8 hr.

tag: Gender

value: Male

tag: Cell line

tag: Tissue

value: Liver tumor


title: tfl1-1-16ºC-RepA


title: hepatoma_wt_TCDD_rep3


title: parental A2780 (cisplatin-sensitive), biological rep5

tag: cell line


title: hepatoma_wt_DMSO_rep3

source_name: hepatoma wildtype cells, DMSO 8hr

treatment_protocol: No treatment in DMSO for 8 hr.


title: hepatome_wt_TCDD_rep2


title: hepatoma_wt_DMSO_rep1


title: parental A2780 (cisplatin-sensitive), biological rep2


title: hepatoma_wt_BaP_rep1

source_name: hepatoma wildtype cells, BaP 8hr

treatment_protocol: Treatment with 5 micromolar Benzo[a]pyrene in DMSO for 8 hr.


title: hepatoma_wt_BaP_rep2


title: hepatoma_wt_BaP_rep3


title: hepatoma_mutant_TCDD_rep3

source_name: hepatoma mutant cells, TCDD 8hr

treatment_protocol: Treatment with 5 nanomolar 2,3,7,8-tetrachlorodibenzo-p-dioxin in DMSO for 8 hr.

value: Hepa-1c1c7 mutant derivative with AHR unable to bind DNA


title: hepatoma_wt_DMSO_rep2


title: hepatoma_mutant_DMSO_rep2

source_name: hepatoma mutant cells, DMSO 8hr

value: Hepa-1c1c7 derivative with AHR unable to bind DNA


title: hepatoma_mutant_TCDD_rep2


title: hepatoma_mutant_BaP_rep3

source_name: hepatoma mutant cells, BaP 8hr

treatment_protocol: Treated with 5 micromolar benzo[a]pyrene in DMSO for 8 hr.

value: C57BL/6 derived


title: hepatoma_mutant_TCDD_rep1


title: hepatoma_mutant_BaP_rep1


title: hepatoma_mutant_DMSO_rep1


title: hepatoma_mutant_BaP_rep2

value: hepa-1c1c7 mutant derivative with AHR unable to bind DNA