title: genotype: Stander - time: 3 days - rep3

description: Stander grains after 3 days of germination replication 3


title: genotype: Robust - time: 3 days - rep2

status: Public on Oct 07 2010

type: RNA

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

country: USA

institute: Iowa State University

description: Robust grains after 3 days of germination replication 2

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

label: biotin

molecule: total RNA

organism: Hordeum vulgare

source_name: seed (genotype: Robust - time: 3 days)

label_protocol: Affymetrix one-cycle target labeling

extract_protocol: Trizol RNA extraction followed by RNeasy purification

tag: germplasm name

value: hv cv. robust

tag: organism part

tag: development stage

tag: growth media

value: not specified

tag: age

value: 3 days


title: genotype: Morex - time: 3 days - rep1

description: Morex grains after 3 days of germination replication 1

source_name: seed (genotype: Morex - time: 3 days)

value: hv cv. morex


title: genotype: Stander - time: 0 days - rep1

description: Stander grains after steeping replication 1

source_name: seed (genotype: Stander - time: 0 days)

value: hv cv. stander

value: 0 days


title: genotype: Manker - time: 0 days - rep3

description: Manker grains after steeping replication 3

source_name: seed (genotype: Manker - time: 0 days)

value: hv cv. manker


title: Lung Mesenchymal Stomal Cells 1

status: Public on Oct 08 2010

city: Ann Arbor

first: Marc

middle: B

last: Hershenson

state: MI

address: 1150 W Medical Center Dr

department: Pediatrics

institute: University of Michigan Medical School

description: Biological Replicate 1

hyb_protocol: Per standard Illumina hybridization protocol, cRNA was hybridized to HumanRef-8 v3 Expression BeadChips for 16 hours at 58 degrees

scan_protocol: Per standard Illumina hybridization protocol, BeadChips were scanned using an Illumina BeadArray Reader to generate .idat files which were analyzed with the GenomeStudio Data Analysis Software with Gene Expression Module (Illumina, Inc.).

data_processing: The data were normalised using average normalisation with the Illumina GenomeStudio Gene Expression Analysis Module v1.7.0.  Software framework: Illumina GenomeStudioV2010.2.

label: Biotin

organism: Homo sapiens

source_name: Lung

label_protocol: Total RNA was used to generate biotinylated amplified cRNA with the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems)

extract_protocol: QIAGEN RNeasy Mini Kit

tag: cell type

value: Mesenchymal Stomal Cells

tag: tissue

value: Lung

tag: chip#


title: genotype: Manker - time: 0 days - rep2

description: Manker grains after steeping replication 2


title: genotype: Manker - time: 3 days - rep1

description: Manker grains after 3 days of germination replication 1

source_name: seed (genotype: Manker - time: 3 days)


title: genotype: Manker - time: 0 days - rep1

description: Manker grains after steeping replication 1


title: genotype: M78 - time: 0 days - rep1

description: M78 grains after steeping replication 1

source_name: seed (genotype: M78 - time: 0 days)

value: hv cv. m78


title: genotype: M78 - time: 3 days - rep2

description: M78 grains after 3 days of germination replication 2

source_name: seed (genotype: M78 - time: 3 days)


title: genotype: M66 - time: 3 days - rep3

description: M66 grains after 3 days of germination replication 3

source_name: seed (genotype: M66 - time: 3 days)

value: hv cv. m66


title: genotype: M66 - time: 0 days - rep3

description: M66 grains after steeping replication 3

source_name: seed (genotype: M66 - time: 0 days)


title: genotype: M78 - time: 3 days - rep1

description: M78 grains after 3 days of germination replication 1


title: genotype: M55 - time: 3 days - rep2

description: M55 grains after 3 days of germination replication 2

source_name: seed (genotype: M55 - time: 3 days)

value: hv cv. m55


title: genotype: M78 - time: 3 days - rep3

description: M78 grains after 3 days of germination replication 3


title: genotype: M66 - time: 3 days - rep1

description: M66 grains after 3 days of germination replication 1


title: genotype: M66 - time: 0 days - rep2

description: M66 grains after steeping replication 2


title: genotype: M66 - time: 3 days - rep2


title: genotype: M66 - time: 0 days - rep1

description: M66 grains after steeping replication 1


title: genotype: Manker - time: 3 days - rep3

description: Manker grains after 3 days of germination replication 3


title: genotype: M46 - time: 3 days - rep1

description: M46 grains after 3 days of germination replication 1

source_name: seed (genotype: M46 - time: 3 days)

value: hv cv. m46


title: genotype: M55 - time: 0 days - rep2

description: M55 grains after steeping replication 2

source_name: seed (genotype: M55 - time: 0 days)


title: genotype: M55 - time: 3 days - rep1

description: M55 grains after 3 days of germination replication 1


title: genotype: M55 - time: 3 days - rep3

description: M55 grains after 3 days of germination replication 3


title: genotype: M55 - time: 0 days - rep3

description: M55 grains after steeping replication 3


title: genotype: M46 - time: 0 days - rep2

description: M46 grains after steeping replication 2

source_name: seed (genotype: M46 - time: 0 days)


title: genotype: M55 - time: 0 days - rep1

description: M55 grains after steeping replication 1


title: genotype: M78 - time: 0 days - rep2

description: M78 grains after steeping replication 2


title: genotype: M46 - time: 0 days - rep3

description: M46 grains after steeping replication 3


title: genotype: M46 - time: 3 days - rep2

description: M46 grains after 3 days of germination replication 2


title: LNCaP

type: genomic

city: Zuerich

first: Mark

last: Robinson

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

country: Switzerland

institute: University of Zuerich

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing: Data were processed through the R/aroma.affymetrix package using the CRMA algorithm (See http://aroma-project.org/vignettes/CRMAv2).

molecule: genomic DNA

source_name: LNCaP cells

label_protocol: Affymetrix standard procedure

growth_protocol: 37 deg C with 5% CO2

extract_protocol: Genomic DNA was extracted using the Puregene extraction kit (Gentra Systems) according to the manufacturer's protocol.

value: cell line

tag: cell line

value: LNCaP cells


title: PrEC

source_name: PrEC cells

value: PrEC cells


title: genotype: M78 - time: 0 days - rep3

description: M78 grains after steeping replication 3


title: genotype: M46 - time: 3 days - rep3

description: M46 grains after 3 days of germination replication 3


title: necrotic synthetic wheat-seedling shoot meristem with low temperature-rep1

city: Kobe

first: Shigeo

last: Takumi

state: Hyogo

address: Rokkodai 1-1, Nada

department: Graduate School of Agricultural Science

country: Japan

institute: Kobe University

description: Gene expression in shoot apical meristem under low temperature

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

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

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

organism: Triticum aestivum

source_name: synthetic hexaploid wheat

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

extract_protocol: Total RNA was extracted, using an RNeasy Plant Mini kit (Qiagen). RNA quality was checked using an Agilent 2100 BioAnalyzer.

treatment_protocol: Plants were grown at 23°C for 3 weeks, and then incubated at 4°C for 6 weeks.

value: shoots containig shoot apical meristem

tag: phenotype

value: cold-induced hybrid necrosis


title: genotype: M44 - time: 3 days - rep2

description: M44 grains after 3 days of germination replication 2

source_name: seed (genotype: M44 - time: 3 days)

value: hv cv. m44

value: not specified


title: genotype: M44 - time: 0 days - rep1

description: M44 grains after steeping replication 1

source_name: seed (genotype: M44 - time: 0 days)


title: genotype: M1 - time: 3 days - rep3

description: M1 grains after 3 days of germination replication 3

source_name: seed (genotype: M1 - time: 3 days)

value: hv cv. m1

value: 3 days


title: genotype: M1 - time: 0 days - rep1

description: M1 grains after steeping replication 1

source_name: seed (genotype: M1 - time: 0 days)

value: 0 days


title: genotype: M44 - time: 3 days - rep1

description: M44 grains after 3 days of germination replication 1


title: genotype: Lacey - time: 0 days - rep2

description: Lacey grains after steeping replication 2

source_name: seed (genotype: Lacey - time: 0 days)

value: hv cv. lacey


title: genotype: Lacey - time: 0 days - rep3

description: Lacey grains after steeping replication 3


title: MALT_Lymphoma_Translocation Negative_24

city: London

first: Rifat

last: Hamoudi

address: 67-73 Riding House Street

department: Surgery

country: United Kingdom

institute: University College London

description: Gene expression data was obtained from fresh forzen biopsy at diagnosis.

hyb_protocol: Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 B GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned  at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000.

data_processing: Batch MAS5 Normalisation on all 24 MALT lymphoma samples ran on the HG-U133B GeneChips was carried out using the MAS5() function within the affy library version 1.20.0 in Bioconductor version 2.0. All MAS5 data were scaled to a target intensity of 100. Bioconductor was run on R version 2.8.0 (2008-10-20). The file was written out and split into each individual sample file with one column for probe and another for the MAS5 normalised value.

source_name: Gastric MALT lymphoma

label_protocol: Linear amplification of RNA was carried out using tagged T7 and T3 primers using in house method. This was done to amplify the amount of RNA from 5-10ng to 5-6ug.This was followed by biotin labelling of the cRNA was carried out using the Enzo labelling kit (Enzo life sciences) from 5ug of linearly amplified RNA.

extract_protocol: RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion).

tag: lymphoma type

value: Gastric MALT lymphoma

tag: translocations


title: MALT_Lymphoma_Translocation Negative_22


title: MALT_Lymphoma_Translocation Negative_21


title: genotype: M44 - time: 0 days - rep2

description: M44 grains after steeping replication 2


title: genotype: M1 - time: 3 days - rep1

description: M1 grains after 3 days of germination replication 1


title: genotype: M46 - time: 0 days - rep1

description: M46 grains after steeping replication 1


title: genotype: M44 - time: 0 days - rep3

description: M44 grains after steeping replication 3


title: genotype: M44 - time: 3 days - rep3

description: M44 grains after 3 days of germination replication 3


title: genotype: M1 - time: 0 days - rep3

description: M1 grains after steeping replication 3


title: genotype: M1 - time: 3 days - rep2

description: M1 grains after 3 days of germination replication 2


title: genotype: Lacey - time: 3 days - rep1

description: Lacey grains after 3 days of germination replication 1

source_name: seed (genotype: Lacey - time: 3 days)


title: genotype: Lacey - time: 3 days - rep3

description: Lacey grains after 3 days of germination replication 3


title: MALT_Lymphoma_Translocation Negative_23


title: genotype: Lacey - time: 0 days - rep1

description: Lacey grains after steeping replication 1


title: genotype: M1 - time: 0 days - rep2

description: M1 grains after steeping replication 2


title: wild type synthetic wheat-seedling shoot meri with low temperature-rep2

value: wild-type


title: genotype: Stander - time: 0 days - rep2

description: Stander grains after steeping replication 2

source_name: seed (genotype: Stander - time: 0 days)

value: hv cv. stander


title: genotype: Excel - time: 3 days - rep2

description: Excel grains after 3 days of germination replication 2

source_name: seed (genotype: Excel - time: 3 days)

value: hv cv. excel


title: MALT_Lymphoma_Translocation Negative_20


title: wild type synthetic wheat-seedling leaf with low temperature-rep1

description: Gene expression in 3-week-old seedling leaves under low temperature

treatment_protocol: Plants were grown at 23°C for 3 weeks, and then incubated at 4°C for 12 weeks.

value: leaf


title: MALT_Lymphoma_Translocation Negative_19


title: genotype: Excel - time: 0 days - rep2

description: Excel grains after steeping replication 2

source_name: seed (genotype: Excel - time: 0 days)


title: genotype: Excel - time: 0 days - rep3

description: Excel grains after steeping replication 3


title: MALT_Lymphoma_t(11;18)/API2-MALT1_13

tag: translocation


title: MALT_Lymphoma_t(14;18)/IGH-MALT1_15

source_name: Hepatic MALT lymphoma

value: Hepatic MALT lymphoma


title: genotype: Lacey - time: 3 days - rep2

description: Lacey grains after 3 days of germination replication 2


title: MALT_Lymphoma_Translocation Negative_16


title: genotype: Excel - time: 3 days - rep1

description: Excel grains after 3 days of germination replication 1


title: MALT_Lymphoma_Translocation Negative_17


title: MALT_Lymphoma_Translocation Negative_18


title: genotype: Excel - time: 3 days - rep3

description: Excel grains after 3 days of germination replication 3


title: MALT_Lymphoma_t(11;18)/API2-MALT1_11


title: MALT_Lymphoma_t(11;18)/API2-MALT1_12


title: MALT_Lymphoma_t(11;18)/API2-MALT1_10


title: MALT_Lymphoma_t(11;18)/API2-MALT1_9

source_name: Pulmonary MALT lymphoma

value: Pulmonary MALT lymphoma


title: MALT_Lymphoma_t(1;14)/BCL10-IGH_2


title: MALT_Lymphoma_t(14;18)/IGH-MALT1_14

source_name: Occular MALT lymphoma

value: Occular Adnexa MALT lymphoma


title: MALT_Lymphoma_t(1;14)/BCL10-IGH_3


title: MALT_Lymphoma_t(11;18)/API2-MALT1_5


title: genotype: Excel - time: 0 days - rep1

description: Excel grains after steeping replication 1


title: MALT_Lymphoma_t(11;18)/API2-MALT1_8


title: genotype: Dickson - time: 0 days - rep3

description: Dickson grains after steeping replication 3

source_name: seed (genotype: Dickson - time: 0 days)

value: hv cv. dickson


title: genotype: Dickson - time: 3 days - rep3

description: Dickson grains after 3 days of germination replication 3

source_name: seed (genotype: Dickson - time: 3 days)


title: genotype: Dickson - time: 0 days - rep2

description: Dickson grains after steeping replication 2


title: MALT_Lymphoma_t(11;18)/API2-MALT1_6

description: Gene expression data was obtained from fresh forzen biopsy at diagnosis.


title: genotype: Dickson - time: 3 days - rep1

description: Dickson grains after 3 days of germination replication 1


title: MALT_Lymphoma_t(1;14)/BCL10-IGH_4


title: MALT_Lymphoma_t(11;18)/API2-MALT1_7


title: genotype: Dickson - time: 3 days - rep2

description: Dickson grains after 3 days of germination replication 2


title: Healthy Donor 20

city: Boston

first: Michael

middle: Richard

last: Green

state: MA

address: 44 Binney Street

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
References:
1 beckwith m et al., j natl cancer inst 82: 501-509 (1990).
2 drexler hg et al., dsmz catalogue of cell lines 2005: http://www.dsmz.de/mutz/mutzhome.htm.
3 li cc et al., leukemia 9: 650-655 (1995).

hyb_protocol: According to manufacturer’s protocol.

scan_protocol: According to manufacturer’s protocol.

data_processing: Raw data (CEL files) were used for input into GenePattern GISTIC pipeline (http://genepattern.broadinstitute.org/gp/pages/login.jsf).  GISTIC scores (output) are provided as a supplementary file on the Series record.

source_name: Peripheral blood lymphocytes

label_protocol: According to manufacturer’s protocol.

extract_protocol: After homogenization using lysing matrix A tubes (MP Biomedicals) genomic DNA was extracted using Qiagen DNeasy Blood and Tissue Kit according to the manufacturers recommendation (Qiagen Genomic DNA Handbook) (Takeyama et al. (2008) Oncogene 27:318-322).

value: Peripheral blood lymphocytes obtained from a healthy donor.


title: MALT_Lymphoma_t(1;2)/BCL10-IGK_1

description: t(1;2)(p22;q32) translocation which is identical to the t(1;14) translocation.


title: Healthy Donor 19


title: genotype: Dickson - time: 0 days - rep1

description: Dickson grains after steeping replication 1


title: Healthy Donor 18


title: Helathy Donor 15


title: Healthy Donor 16


title: Healthy Donor 17


title: Healthy Donor 13


title: Healthy Donor 14


title: Healthy Donor 12


title: Healthy Donor 11


title: Healthy Donor 10


title: Healthy Donor 8


title: Healthy Donor 7


title: Healthy Donor 9


title: Control-1

city: Potsdam

first: Jens

last: Schwachtje

address: Am Mühlenberg 1

department: Energy Metabolism

country: Germany

institute: Max-Planck-Institute for Molecular Plant Physiology

hyb_protocol: Hybridization solution was prepared according to Affymetrix´ GeneChip Expression Analysis Technical Manual. The final concentration of cRNA was 60 ng/μl. Hybridization was performed for 16-18 hours at 45°C and 60 rpm in a rotating hybridization oven (Hybridization Oven 640, Affymetrix).

scan_protocol: Scanning was performed with the GeneChip Scanner 3000 7G (Affymetrix), which is controlled by Affymetrix´ software GeneChip Operating System (GCOS) v1.4.

data_processing: Data (.cel files) were quality-checked and normalized using robust multi array averaging (rma) with ROBIN software (Lohse et al. 2010) and analyzed with MapMan software (Usadel et al. 2005).

organism: Arabidopsis thaliana

source_name: Whole Arabidopsis seedlings, 18 days old

label_protocol: cDNA synthesis and in vitro-transcription was done with Ambion´s Message Amp II 96 Kit (Cat. No. 1819), starting with 1 μg of total RNA

growth_protocol: One or two Arabidopsis seedlings were grown in 1.5 ml Eppendorf tubes, from which the tip was cut off. The tubes contained sandy soil and were placed on peat substrate. Light conditions were 12 light/12 dark at 20°C and 18 °C, respectively.

extract_protocol: Twenty-five seedlings were pooled for each of three  replicates per treatment. RNA was extracted from seedlings with RNeasy Mini Kit from Quiagen according to the manufacturer´s protocol.

treatment_protocol: Six hours before harvesting 18-day old seedlings, 500 µl of P. sp. G62 (OD 0.5 in 10 mM MgSO4), or MgSO4 only for controls was applied to the medium.

value: whole seedling

tag: ecotype

value: 18 days

tag: treatment group

value: control


title: Healthy Donor 6


title: Pseudomonas-treatment 3

value: pseudomonas treated


title: genotype: Cree - time: 3 days - rep1

description: Cree grains after 3 days of germination replication 1

source_name: seed (genotype: Cree - time: 3 days)

value: hv cv. cree

value: not specified

value: 3 days


title: Pseudomonas-treatment 1


title: genotype: Cree - time: 0 days - rep2

description: Cree grains after steeping replication 2

source_name: seed (genotype: Cree - time: 0 days)

value: 0 days


title: genotype: Cree - time: 0 days - rep1

description: Cree grains after steeping replication 1


title: Healthy Donor 5


title: Healthy Donor 4


title: genotype: Cree - time: 3 days - rep2

description: Cree grains after 3 days of germination replication 2


title: genotype: Cree - time: 0 days - rep3

description: Cree grains after steeping replication 3


title: Healthy Donor 3


title: genotype: Bonanza - time: 3 days - rep2

description: Bonanza grains after 3 days of germination replication 2

source_name: seed (genotype: Bonanza - time: 3 days)

value: hv cv. bonanza


title: Normal Donor 02


title: genotype: Bonanza - time: 3 days - rep3

description: Bonanza grains after 3 days of germination replication 3


title: Control-3


title: WSU-NHL

source_name: DLBCL Cell Line

growth_protocol: McCoy's 5A medium with 20% heat-inactivated fetal bovine serum (FBS), 10mM HEPES buffer, 4 mM L-glutamine, 50 U/mL penicillin and 50 U/mL streptomycin.

value: Mature EBV-negative B-cell line established from B-NHL (diffuse large cell lymphoma).


title: Normal Donor 1


title: SUP-HD-1

source_name: HL Cell Line

value: EBV-negative cell line derived from classical Hodgkin lymphoma (nodular sclerosis).


title: SUD-HL-8

growth_protocol: RPMI medium with 10% heat-inactivated fetal bovine serum (FBS), 10mM HEPES buffer, 4 mM L-glutamine, 50 U/mL penicillin and 50 U/mL streptomycin.


title: SUD-HL-10

value: Mature EBV-negative B-cell line established from B-NHL ("diffuse histiocytic").


title: SUD-HL-7

value: Mature EBV-negative B-cell line derived from B-NHL (follicular lymphoma).


title: SUD-HL-5

value: Mature EBV-negative B-cell line derived from B-NHL (diffuse large cell lymphoma).


title: SUD-HL-6


title: SUD-HL-4


title: Toledo

value: Diffuse large cell lymphoma; non-Hodgkin's B cell lymphoma


title: genotype: Bonanza - time: 3 days - rep1

description: Bonanza grains after 3 days of germination replication 1


title: genotype: Bonanza - time: 0 days - rep3

description: Bonanza grains after steeping replication 3

source_name: seed (genotype: Bonanza - time: 0 days)


title: genotype: Bonanza - time: 0 days - rep2

description: Bonanza grains after steeping replication 2


title: Control-2


title: genotype: Bonanza - time: 0 days - rep1

description: Bonanza grains after steeping replication 1


title: OCI-Ly19

growth_protocol: IMDM medium with 10% heat-inactivated fetal bovine serum (FBS), 10mM HEPES buffer, 4 mM L-glutamine, 50 U/mL penicillin and 50 U/mL streptomycin.

value: Mature EBV-positive B-cell line derived from B-NHL (diffuse large cell lymphoma).


title: OCI-Ly18


title: Pfeiffer


title: Uterus HPTE 2h rep2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: gene expression in ovariectomized HPTE 2 hour treated uterus

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

organism: Mus musculus

source_name: uterus, HPTE treated 2 hours

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: frozen uterine tissue was pulverized and each uterus was homogenized in 800 ul of Trizol (Invitrogen) with 250 ug/ml glycogen. Extraction proceeded as descibed in manufacturer's protocol. Following resuspension of RNA pellet, a second preciptation was done with NaAcetate and ethanol. This pellet was then resuspended in depc treated water, treated with DNAse and cleaned up using the Qiagen RNeasy kit clean up protocol. RNA concentration and A260/280 was checked and quality was evaluated by formaldehyde gel.

treatment_protocol: ovariectomized mice were allowed to rest for 10-14 days, then injected with 100 ul sesame oil or 250 ng estradiol in 100 ul sesame oil or 750 ug BPA or HPTE in sesame oil subcutaneously. Uterine tissue was collected 2 or 24 hours after injection and frozen in liquid nitrogen

tag: strain

value: adult (10+ weeks)

tag: gender

value: ovariectomized female

value: uterus

tag: treatment

value: 2 hours

tag: time

value: HPTE treated


title: Uterus HPTE 2h rep3


title: Uterus HPTE 2h rep1


title: Uterus HPTE 24h rep1

description: gene expression in ovariectomized HPTE 24 hour treated uterus

source_name: uterus, HPTE treated 24 hours

value: 24 hours


title: ATZ_rep3 (part 2)

city: seoul

first: hyun-jung

last: koo

address: hoegi-dong,dongdaemun-gu

country: South Korea

institute: Kyung Hee University

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized by quantile normalization using the Avadis 4.3 software (Strand Genomics).

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

growth_protocol: The cells were cultured in DMEM/F12 supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml in a humidified atmosphere at 37℃ with 5% CO₂.

extract_protocol: Total RNA from SH-SY5Y cells (n=3) was isolated using TRIzol (Invitrogen, Karlsruhe, Germany) and quantified with NanoDrop spectrophotometer (NanoDrop Technologies, Inc.).

value: atrazine


title: Uterus BPA 24h rep3

description: gene expression in ovariectomized BPA 24 hour treated uterus

source_name: uterus, BPA treated 24 hours

value: BPA treated


title: OCI-Ly8

description:
References:
1 beckwith m et al., j natl cancer inst 82: 501-509 (1990).
2 drexler hg et al., dsmz catalogue of cell lines 2005: http://www.dsmz.de/mutz/mutzhome.htm.
3 li cc et al., leukemia 9: 650-655 (1995).

value: Mature EBV-negative B-cell line derived from B-NHL (immunoblastic lymphoma).


title: OCI-Ly7


title: OCI-Ly10

growth_protocol: IMDM medium with 20% heat-inactivated fetal bovine serum (FBS), 10mM HEPES buffer, 4 mM L-glutamine, 50 U/mL penicillin and 50 U/mL streptomycin.


title: OCI-Ly4


title: Uterus HPTE 24h rep3


title: OCI-Ly3


title: ATZ_rep2 (part 2)

description: replicate 2


title: DMSO_rep3 (part 2)

description: replicate 3

value: DMSO


title: Uterus BPA 24h rep1


title: ATZ_rep1 (part 2)

description: replicate 1


title: Uterus BPA 24h rep2


title: OCI-Ly-1


title: L-1236


title: DMSO_rep1 (part 2)

description: replicate 1


title: L-540


title: DMSO_rep2 (part 2)

description: replicate 2


title: Tuni_rep3 (part 1)

description: replicate 3

data_processing: The data were normalized by quantile normalization using Avadis 4.3 software (Strand Genomics).

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

value: tunicamycin


title: Tuni_rep2 (part 1)

description: replicate 2


title: Uterus BPA 2h rep2

description: gene expression in ovariectomized BPA 2 hour treated uterus

source_name: uterus, BPA treated 2 hours


title: Uterus BPA 2h rep3


title: L-428

value: EBV-negative cell line derived from classical Hodgkin lymphoma (nodular sclerosis).


title: Thap_rep2 (part 1)

description: replicate 2

value: thapsigargin


title: KM-H2


title: Tuni_rep1 (part 1)

description: replicate 1


title: Thap_rep3 (part 1)

description: replicate 3


title: Uterus estradiol 24h rep3

description: gene expression in ovariectomized E2 24 hour treated uterus

source_name: uterus, E2 treated 24 hours

value: E2 treated


title: Uterus estradiol 24h rep2


title: Uterus estradiol 2h rep3

description: gene expression in ovariectomized E2 2 hour treated uterus

source_name: uterus, E2 treated 2 hours


title: Uterus estradiol 2h rep2


title: KARPAS-1106P

source_name: MLBCL Cell Line

growth_protocol: RPMI medium with 20% heat-inactivated fetal bovine serum (FBS), 10mM HEPES buffer, 4 mM L-glutamine, 50 U/mL penicillin and 50 U/mL streptomycin.

value: Mature EBV-negative B-cell line derived from mediastinal lymphoblastic B-NHL.


title: DMSO_rep3 (part 1)

description: replicate 3


title: Thap_rep1 (part 1)

description: replicate 1


title: HD-LM-2


title: HT

value: Mature EBV-negative B-cell line derived from B-NHL (diffuse mixed small/large cell lymphoma).


title: FARAGE

value: Mature EBV-positive B-cell line derived from B-NHL (diffuse large cell lymphoma).


title: DMSO_rep2 (part 1)

description: replicate 2


title: Uterus BPA 2h rep1

value: adult (10+ weeks)


title: DB

description:
Human cell line model for Diffuse Large B-cell Lymphoma.
References:
1 beckwith m et al., j natl cancer inst 82: 501-509 (1990).
2 drexler hg et al., dsmz catalogue of cell lines 2005: http://www.dsmz.de/mutz/mutzhome.htm.
3 li cc et al., leukemia 9: 650-655 (1995).

value: Mature EBV-negative B-cell line derived from B-NHL (diffuse large cell lymphoma).


title: Uterus estradiol 2h rep1

value: ovariectomized female

value: uterus


title: KARPAS-422


title: MALT_Lymphoma_Translocation Negative_20

description: Gene expression data was obtained from fresh forzen biopsy at diagnosis.

hyb_protocol: Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 A GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned  at pixel value 3um, wavelength 570 nm using the argon laser scanner the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Batch MAS5 Normalisation on all 24 MALT lymphoma samples ran on the HG-U133A GeneChips was carried out using the MAS5() function within the affy library version 1.20.0 in Bioconductor version 2.0. All MAS5 data were scaled to a target intensity of 100. Bioconductor was run on R version 2.8.0 (2008-10-20). The file was written out and split into each individual sample file with one column for probe and another for the MAS5 normalised value.

source_name: Gastric MALT lymphoma

label_protocol: Biotin labelling of the cRNA was carried out using the Enzo labelling kit (Enzo life sciences) from 5ug total RNA.

value: Gastric MALT lymphoma


title: DMSO_rep1 (part 1)

description: replicate 1


title: Uterus sesame oil 24h rep1

description: gene expression in ovariectomized sesame oil vehicle treated uterus

source_name: uterus, sesame oil control

value: control


title: Follicular_Lymphoma_5

hyb_protocol: Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400.

data_processing: Batch MAS5 Normalisation on all 7 follicular lymphoma and 8 mantle cell lymphoma samples ran on the HG-U133 plus2 GeneChips was carried out using the MAS5() function within the affy library version 1.20.0 in Bioconductor version 2.0. All MAS5 data were scaled to a target intensity of 100. Bioconductor was run on R version 2.8.0 (2008-10-20). The file was written out and split into each individual sample file with one column for probe and another for the MAS5 normalised value.

source_name: Lymph node from follicular lymphoma patient

label_protocol: Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA.

value: Follicular lymphoma


title: Array 1_4: 4106a_4 cy5 + 5191A_4 cy3

city: Harpenden

first: Chris

last: Bass

state: Hertfordshire

address: West Common

department: Biological Chemistry

institute: Rothamsted Research

description: US45102835_252518810001_S01_GE2-v5_10_Apr08_1_4

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5).

data_processing: Agilent Feature Extraction Software (v 10.5) was used for background subtraction and LOWESS normalization.

organism: Myzus persicae

source_name: ten whole aphids 15 days old

label_protocol: Two micrograms of each RNA sample was used to generate labeled cRNA, this was prepared, hybridized onto arrays and these were washed and scanned exactly as described in the Agilent Quick Amp Labeling Protocol (Version 5.7) which can be downloaded from http://www.chem.agilent.com/en-US/products/instruments/dnamicroarrays/pages/gp11617.aspx

growth_protocol: Both M. persicae clones used in this study were originally established from a single parthenogenetic female collected from a field populations and reared on Chinese cabbage leaves (Brassica napus L var chinensis cv Tip-Top) in small plastic box-cages maintained at 18°C under a 16:8 h light:dark regime. Aphids of similar age were regularly transferred to new boxes in order to rear them as distinct cohorts.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. Genomic DNA was removed by DNase I digestion using the DNA-free DNase Treatment and Removal Reagent (Ambion).

treatment_protocol: Clones reared as above (both clones were untreated)

tag: clone


title: Array 1_1: 4106a_1 cy5 + 5191A_1 cy3

description: US45102835_252518810001_S01_GE2-v5_10_Apr08_1_1

hyb_protocol: as described in the Agilent Quick Amp Labeling Protocol (Version 5.7) which can be downloaded from http://www.chem.agilent.com/en-US/products/instruments/dnamicroarrays/pages/gp11617.aspx


title: Pool of normal mammary tissue

status: Public on Oct 06 2010

city: Brussels

first: Olivier

last: Feron

address: 53 Avenue E. Mounier, bte B1.53.09

department: Pole of Pharmacology and Therapeutics (FATH)  Institute of Experimental and Clinical Research (IREC)

country: Belgium

institute: Université catholique de Louvain

hyb_protocol: After array saturation with salmon sperm, biotinylated cDNA (denaturated for 2 minutes at 94°C) were hybridized over night at 60°C under agitation, and then incubated in CDP-Stat Chemiluminescence Substrate (Super Array)

scan_protocol: The data were collected on ChemiDoc XRS Analyser (Biorad, Hercules, CA, USA). The picture used for analysis was the last one before the first saturation pixel appearance

data_processing: Macroarray data processing was performed on raw data of the 96 genes printed on the membranes and analyzed with Super Array Software using “whole gene median value” and “housekeeping gene mean value” normalization. The housekeeping genes was GAPDH, PPIA, RPL19 and ACTB. A local background subtraction was automatically performed. The results would be considered correct only if both normalizations gave the same results. The final results appeared as the mean of whole gene median value and housekeeping gene mean value normalizations.

source_name: Commercial RNA

label_protocol: One µg of total RNA was reverse transcribed with Ampolabeling (LPR) Kit L-03 (Super Array). cDNA were next amplified by PCR in presence of biotin-16-dUTP (Roche, Rosny-sous-Bois, France): 5 min initial 85°C denaturation step, 30 cycles of 1 min à 85°C, 1 min at 50°C and 1 min at 72°C. Before hybridization, quality of staining was verified according to manufacturer’s instructions.

extract_protocol: Total RNA was extracted from cell lines and tissue samples by using Qiagen Kit extraction (Hilden, Germany). The quantity of RNA was assessed spectrophotometrically at 260 nm and 280nm (the A260/A280 ratio of pure RNA is approximately 2). The quality of RNA was determined by visualization of the 18S and 28S RNA bands under UV light after Sybr Safe stained agarose gel electrophoresis. Reverse transcription was performed as described in reference: Arnal et al. Breast Cancer Res Treat. 2000; 61: 13-20.

value: Female

tag: tumor size

tag: grade

tag: er

tag: pr

tag: nodes

tag: clinical response 1

tag: clinical response 2

tag: histological response

tag: recurrence

tag: disease free survival (months)

tag: death

tag: overall survival (months)

tag: survivin

value: < Median


title: Breast carcinoma obtained before therapy 41

source_name: RNA from non treated breast carcinoma

tag: gender

tag: age

value: < 50 year old

value: Positive

value: No response

value: No

value: > Median


title: Array 1_3: 4106a_3 cy5 + 5191A_3 cy3

description: US45102835_252518810001_S01_GE2-v5_10_Apr08_1_3


title: MALT_Lymphoma_t(1;14)/BCL10-IGH_2

scan_protocol: GeneChips were scanned at pixel value 3um, wavelength 570 nm using the argon laser Hewlett-Packard GeneArray Scanner G2500A.

tag: lymphoma type

tag: translocation


title: Uterus sesame oil 24h rep3

tag: strain

tag: tissue

tag: treatment

tag: time


title: Follicular_Lymphoma_4


title: Array 1_2: 4106a_2 cy5 + 5191A_2 cy3

description: US45102835_252518810001_S01_GE2-v5_10_Apr08_1_2

tag: clone


title: MALT_Lymphoma_t(14;18)/IGH-MALT1_14

source_name: Occular MALT lymphoma

value: Occular Adnexa MALT lymphoma


title: IGFbp3-treated Id cKO

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

hyb_protocol: 5.5ug of fragmented and labeled single-stranded DNA were hybridized for 17 hr at 45C on GeneChip Mouse Gene ST 1.0 ST arrays.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: CEL files were processed using the Affymetrix Expression Console software and RMA normalization performed

source_name: Id conditional KO, 6 months, treated with mouse recombinant IGFbp3

label_protocol: Labeled fragmented single-stranded DNA were prepared according to the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual Version 4 from 300ng of total RNA

extract_protocol: Rneasy (Quiagen)

value: heart

value: 6 month adult


title: Tie2Cre+Id1-/-Id3+/-

source_name: Id control heart, 6 months


title: Array 1_2: 4106a_2 cy3 + 5191A_2 cy5

description: US45102835_252518810002_S01_GE2-v5_10_Apr08_1_2


title: Tie2Cre+Id1F/-Id3-/-

source_name: Id conditional KO, 6 months


title: Array 1_3: 4106a_3 cy3 + 5191A_3 cy5

description: US45102835_252518810002_S01_GE2-v5_10_Apr08_1_3


title: IGFbp3-untreated Id cKO

description: Diego_03-12-10_8(no treated)

source_name: Id conditional KO, 6 months, control not treated


title: Breast carcinoma obtained before therapy 40

value: > 50 year old

tag: tumor size

tag: grade

tag: er

tag: pr

tag: nodes

tag: clinical response 1

value: Yes


title: Array 1_4: 4106a_4 cy3 + 5191A_4 cy5

description: US45102835_252518810002_S01_GE2-v5_10_Apr08_1_4


title: Array 1_1: 4106a_1 cy3 + 5191A_1 cy5

description: US45102835_252518810002_S01_GE2-v5_10_Apr08_1_1


title: WT

source_name: WT heart, 6 months


title: Breast carcinoma obtained before therapy 38

tag: clinical response 2

tag: histological response

tag: recurrence

tag: disease free survival (months)

tag: death

tag: overall survival (months)


title: Breast carcinoma obtained before therapy 37

tag: gender

tag: age

value: Negative

tag: survivin


title: Breast carcinoma obtained before therapy 39


title: Breast carcinoma obtained before therapy 31


title: Breast carcinoma obtained before therapy 32


title: Breast carcinoma obtained before therapy 33

value: Partial response


title: Breast carcinoma obtained before therapy 34


title: Breast carcinoma obtained before therapy 35


title: Breast carcinoma obtained before therapy 27

value: Complete response


title: Breast carcinoma obtained before therapy 28


title: Breast carcinoma obtained before therapy 29


title: Breast carcinoma obtained before therapy 30


title: Uterus HPTE 24h rep2

description: gene expression in ovariectomized HPTE 24 hour treated uterus

source_name: uterus, HPTE treated 24 hours

tag: strain

value: adult (10+ weeks)

value: ovariectomized female

tag: tissue

value: uterus

tag: treatment

value: 24 hours

tag: time

value: HPTE treated


title: Breast carcinoma obtained before therapy 24

value: Female

value: < 50 year old

tag: tumor size

tag: grade

tag: er

value: Positive

value: < Median


title: Breast carcinoma obtained before therapy 25

tag: pr

tag: nodes

tag: clinical response 1

value: No

value: > Median


title: Breast carcinoma obtained before therapy 21

tag: clinical response 2

tag: histological response

value: No response

tag: recurrence


title: Breast carcinoma obtained before therapy 17

value: > 50 year old

tag: disease free survival (months)

tag: death

tag: overall survival (months)


title: Breast carcinoma obtained before therapy 18

tag: gender

tag: age

value: Yes

tag: survivin


title: Breast carcinoma obtained before therapy 20

value: Negative


title: Breast carcinoma obtained before therapy 19


title: Breast carcinoma obtained before therapy 22


title: Breast carcinoma obtained before therapy 23


title: Breast carcinoma obtained before therapy 14

value: Partial response


title: Breast carcinoma obtained before therapy 16


title: Breast carcinoma obtained before therapy 13


title: Breast carcinoma obtained before therapy 15


title: Breast carcinoma obtained before therapy 26


title: Breast carcinoma obtained before therapy 12


title: Breast carcinoma obtained before therapy 11


title: Breast carcinoma obtained before therapy 8


title: Breast carcinoma obtained before therapy 9


title: Breast carcinoma obtained before therapy 10


title: Breast carcinoma obtained before therapy 6


title: Breast carcinoma obtained before therapy 7


title: Breast carcinoma obtained before therapy 3


title: Breast carcinoma obtained before therapy 4


title: Breast carcinoma obtained before therapy 5

value: Complete response


title: Breast carcinoma obtained before therapy 2


title: Uterus sesame oil 24h rep2

tag: strain

value: adult (10+ weeks)

tag: tissue

tag: treatment

value: control


title: Breast carcinoma obtained before therapy 36

tag: tumor size

tag: grade


title: Breast carcinoma obtained before therapy 1

tag: er

tag: pr


title: crypt layer, wild type, mouse m81

city: Bronx

first: Georgia

last: Corner

state: NY

address: 111 East 210th Street

department: Oncology

institute: Albert Einstein Comprehensive Cancer Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 Array. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: RMA normalization of all 24 cel files was done with the R statistical package.

source_name: Cells isolated from crypt layer of large intestine, from C57Bl/6 mouse

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: Mice maintained as described in Mariadason et.al., Gastroenterology. 2005 Apr;128(4):1081-8

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

treatment_protocol: At age 6 months, mice were sacrificed and the large intestines dissected out.  Sequential elution was used to isolate the most superficial layer of cells and the crypt layer of cells from each intestine.  See Mariadason et.al., Gastroenterology. 2005 Apr;128(4):1081-8

tag: layer of epithelium

value: F10 (crypt)

tag: genotype

tag: mouse


title: crypt layer, wild type, mouse n10


title: crypt layer, APC mutant, mouse m05

source_name: Cells isolated from crypt layer of large intestine, from APC1638+/- mouse

value: APC-


title: crypt layer, p21 mutant, mouse j04

source_name: Cells isolated from crypt layer of large intestine, from p21-/- mouse


title: crypt layer, p21 mutant, mouse i49


title: crypt layer, p21 mutant, mouse i74


title: crypt layer, p21 mutant, mouse j29


title: crypt layer, APC mutant, mouse m64


title: crypt layer, wild type, mouse i28


title: Donor 3, seasonal H1N1-infected human type I-like alveolar epithelial cells at 8h

city: Hong Kong

first: SMY

last: Lee

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

description:
D3_H1
Gene expression data of seasonal H1N1 virus-infected type I-like alveolar epithelial cells at 8 h post-infection time.

hyb_protocol: The samples were hybridized to Human Gene 1.0 ST microarrays according to standardized protocols from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software using the Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

source_name: Differentiated human type I-like alveolar epithelial cells infected by seasonal H1N1 virus at 8h post-infection time

label_protocol: Total RNA was labeled employing the Whole Transcript (WT) Sense Target Labeling Assay according to the manufacturer’s instructions (Affymetrix).

growth_protocol:
Isolation of primary human alveolar type II alveolar epithelial cells: Primary type II alveolar epithelial cells were isolated using human non-malignant lung tissue obtained from patients undergoing lung resection. After removing visible bronchi, the lung tissue was minced into pieces of > 0.5 mm thickness using a tissue chopper and washed with balanced salt solution containing Hanks' balanced salt solution with 0.7 mM sodium bicarbonate at pH 7.4 for 3 times to partially remove macrophages and blood cells. The tissue was digested using a combination of 0.5% trypsin and 4 U/ml elastase for 40 min at 37°C in a shaking water-bath. The digestion was stopped by adding DMEM/F12 medium with 40% FBS in and DNase I (350 U/ml). Cell clumps were dispersed by repeatedly pipetting the cell suspension for 10 min. A disposable cell strainer (gauze size of 50 μm) was used to separate large undigested tissue fragments. The single cell suspension in the flow-through was centrifuged and resuspended in a 1:1 mixture of DMEM/F12 medium and small airway basal medium (SABM)supplemented with 0.5 ng/ml epidermal growth factor (hEGF), 500 ng/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 0.1 ng/ml retinoic acid, 6.5 ng/ml triiodothyronine, 0.5 μg/ml hydrocortisone, 30 μg/ml bovine pituitary extract and 0.5 mg/ml BSA together with 5% FBS and 350 U/ml DNase I. The cell suspension was plated on plastic flask and incubated in a 37°C water-jacketed incubator with 5% CO2 supply for 90 min. The non-adherent cells were layered on a discontinuous cold Percoll density gradient (densities 1.089 and 1.040 g/ml) and centrifuged at 25×g for 20 min without brake. The cell layer at the interface of the two gradients was collected and washed four times with BSS to remove the Percoll. The cell suspension was incubated with magnetic beads coated with anti-CD14 antibodies at room temperature for 20 min under constant mixing. After the removal of the beads using a magnet (MACS CD14 MicroBeads), cell viability was assessed by trypan-blue exclusion. The purified alveolar epithelial cell suspension was resuspended in small airway growth medium supplemented with 1% FBS, 100 U/ml penicillin and 100 μg/ml streptomycin. The cells were maintained in a humidified atmosphere (5% CO2, 37°C) under liquid-covered conditions, and growth medium was changed daily starting from 60 h after plating the cells.

Type I-like alveolar epithelial cell differentiation: The purified type II alveolar epithelial cell pellet (passage 1 or 2) was resuspended in medium and cultured for 14 to 20 days with the small airway culture medium SAGM. The cells spread to form a confluent monolayer and the culture medium was changed every 48 h before used for virus infection experiments.

extract_protocol: Total RNA was isolated by the RNEasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Differentiated type I-like alveolar epithelial cells were mock infected, or infected with pdmH1N1 or seasonal H1N1 at a multiplicity of infection (MOI) of two. Total RNA was extracted from cells after 8h post-infection.

tag: individual

value: donor 3

value: lung

tag: cell type

value: differentiated type I-like alveolar epithelial cells

tag: infection

value: seasonal H1N1 virus

tag: time point

value: 8h post-infection


title: Donor 1, seasonal H1N1-infected human type I-like alveolar epithelial cells at 8h

description:
D1_H1
Gene expression data of seasonal H1N1 virus-infected type I-like alveolar epithelial cells at 8 h post-infection time.

value: donor 1


title: Donor 2, mock-infected human type I-like alveolar epithelial cells at 8h

description:
D2_mock
Gene expression data of mock-infected type I-like alveolar epithelial cells at 8 h post-infection time.

source_name: Differentiated human type I-like alveolar epithelial cells mock infected at 8h post-infection time

value: donor 2

value: mock


title: Donor 2, seasonal H1N1-infected human type I-like alveolar epithelial cells at 8h

description:
D2_H1
Gene expression data of seasonal H1N1 virus-infected type I-like alveolar epithelial cells at 8 h post-infection time.


title: Donor 3, pdmH1N1-infected human type I-like alveolar epithelial cells at 8h

description:
D3_pdmH1
Gene expression data of pdmH1N1 virus-infected type I-like alveolar epithelial cells at 8 h post-infection time.

source_name: Differentiated human type I-like alveolar epithelial cells infected by pdmH1N1 virus at 8h post-infection time

value: pdmH1N1 virus


title: Donor 3, mock-infected human type I-like alveolar epithelial cells at 8h

description:
D3_mock
Gene expression data of mock-infected type I-like alveolar epithelial cells at 8 h post-infection time.


title: villus layer, wild type, mouse h85

source_name: Cells isolated from villus layer of large intestine, from C57Bl/6 mouse

value: F1 (villus)


title: crypt layer, wild type, mouse h85


title: Donor 1, pdmH1N1-infected human type I-like alveolar epithelial cells at 8h

description:
D1_pdmH1
Gene expression data of pdmH1N1 virus-infected type I-like alveolar epithelial cells at 8 h post-infection time.


title: villus layer, p21 mutant, mouse i49

source_name: Cells isolated from villus layer of large intestine, from p21-/- mouse


title: villus layer, p21 mutant, mouse i74


title: crypt layer, APC mutant, mouse m79


title: crypt layer, APC mutant, mouse n80


title: villus layer, p21 mutant, mouse j29


title: Donor 2, pdmH1N1-infected human type I-like alveolar epithelial cells at 8h

description:
D2_pdmH1
Gene expression data of pdmH1N1 virus-infected type I-like alveolar epithelial cells at 8 h post-infection time.


title: villus layer, wild type, mouse i28


title: Donor 1, mock-infected human type I-like alveolar epithelial cells at 8h

description:
D1_mock
Gene expression data of mock-infected type I-like alveolar epithelial cells at 8 h post-infection time.


title: villus layer, p21 mutant, mouse j04


title: canine retina, healthy, biol. rep5

city: Iowa City

first: Markus

middle: H

last: Kuehn

address: 375 Newton Road

department: Ophthalmology and Visual Sciences

institute: University of Iowa

hyb_protocol: cRNA was hybridized overnight to Affymetrix Canine 2.0 arrays in a Model 640 hybridization oven.  Chips were washed using a Model 450 GeneChip fluidics station.

scan_protocol: Data were obtained using a Model 3000 GeneArray scanner.

data_processing: RMAexpress

organism: Canis lupus familiaris

source_name: adult canine retina

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

extract_protocol: Retina was collected and RNA was extracted using Rneasy columns (Qiagen) including on-column DNA digests

treatment_protocol: Canine eyes were enucleated and immediately immersed in RNAlater (Ambion).  Eye were stored at -80C until retinal isolation and RNA extraction

tag: breed

value: Beagle

value: 4 years

value: retina

tag: disease state

value: healthy


title: canine retina, healthy, biol. rep4

tag: age


title: villus layer, wild type, mouse n10


title: villus layer, wild type, mouse m81


title: villus layer, APC mutant, mouse m05

source_name: Cells isolated from villus layer of large intestine, from APC1638+/- mouse


title: testis sterile F1 musculus/domesticus rep2

status: Public on Oct 05 2010

city: Leipzig

first: Thomas

last: Giger

address: Deutscher Platz 6

department: Evolutionary Genetics

institute: Max-Planck-Institute of Evolutionary Anthropology

description:
cross between one domseticus and one musculus strain
F1 Mus domesticus / Mus musculus

hyb_protocol: Arrays were hybridized, washed, and stained accoring to the array manufacturers instructions. Washing and stainig was performed on GeneChip fluidics station.

scan_protocol: The arrays were scanned using a GeneChip 3000 scanner.

data_processing: Updated transcript definition were downloaded (www.brainarray.org) and used instead of the chip description file provided by affymetrix. All data processing and analysis was done in R. Data analysis was performed using probe logarithmic intensity error estimation (PLIER) on the signal intensity measurements as implemented with the justPlier function in BioConductor. We only considered for analysis those genes with detectable expression in all individuals based on Wilcoxon signed rank tests (P < 0.01) between perfect versus mismatch signals. Expression values were quantile normalized. We considered genes to have significantly different expression between groups based on gene-by-gene students t-tests (P < 0.05), excluding genes with no variation between individuals.

organism: Mus musculus musculus x M. m. domesticus

source_name: testis, sterile

label_protocol: Biotinylated complementary RNA was generated from 5 μg of total RNA through reverse trasncription, second strand synthesis, and invitro transcription according to the array manufacturers instructions.

growth_protocol: All breeding colonies were established using individuals purchased from the Jackson Laboratory (Bar Harbor, ME). To represent M. domesticus, we used M. domesticus LEWES/EiJ and M. domesticus WSB/EiJ. Both were derived from natural populations in eastern North America. We used M. musculus CZECHII/EiJ and M. musculus PWK/PhJ to represent M. musculus, which were isolated from different localities within the Czech Republic. The mice were maintained at the University of Arizona Central Animal Facility following IACUC regulations. Breeding pairs were housed two per cage and pregnant females were isolated prior to giving birth. Male offspring were weaned at approximately 20 days postpartum, housed in sibling groups of up to four until 40 days postpartum, and then caged singly until being sacrificed at 60 days old

extract_protocol: We extracted total RNA from whole testis using an RNeasy Midi kit (QIAGEN Inc., Valencia, CA) with mortar and pestle disruption and syringe homogenization. RNA sample quality and quantification was determined with an RNA Nano LabChip on an Agilent Bioanalyzer 2100 (Santa Clara, CA). Only samples with an RNA integrity number of 10 were used.

treatment_protocol: Testis were immediately dissected after being euthanized. One testis was cross-sectioned, stored immediately in RNAlater (Ambion, Inc., Austin, TX), and archived at -80C

tag: cross

value: F1 PWK/PhJ X LEWES/EiJ

value: testis

tag: fertility

value: sterile


title: testis fertile M. domesticus rep2

description: cross between two domesticus strains

organism: Mus musculus domesticus

source_name: testis, fertile

value: F1 LEWES/EiJ X WSB/EiJ

tag: tissue

value: fertile


title: canine retina, glaucoma, biol. rep5

value: Dalmatian

value: 9 years

value: glaucoma


title: testis sterile F1 musculus/domesticus rep3


title: testis fertile F1 domesticus/musculus rep2

description:
cross between one musculus and one domesticus strain
F1 Mus musculus / Mus domesticus

value: F1 LEWES/EiJ X PWK/PhJ


title: Id1F/+Id3-/-

source_name: Id control heart, 6 months

tag: strain

value: heart

value: 6 month adult


title: canine retina, glaucoma, biol. rep2

value: Shiba Inu

value: 14 years


title: testis fertile M. musculus rep 1

description: cross between two musculus strains

value: F1 PWK/PhJ X CZECHII/EiJ


title: testis fertile M. musculus rep 3

description: cross between two musculus strains


title: canine retina, glaucoma, biol. rep3

value: Basset Hound

value: 5 years


title: testis fertile M. musculus rep 2

description: cross between two musculus strains


title: villus layer, APC mutant, mouse m79

value: F1 (villus)

value: APC-


title: testis fertile M. domesticus rep3

description: cross between two domesticus strains

value: testis


title: testis sterile F1 musculus/domesticus rep1

value: F1 PWK/PhJ X LEWES/EiJ

value: sterile


title: villus layer, APC mutant, mouse m64


title: testis fertile F1 domesticus/musculus rep3

value: fertile


title: canine retina, healthy, biol. rep3

value: Beagle

value: 4 years

value: retina

value: healthy


title: canine retina, healthy, biol. rep1


title: villus layer, APC mutant, mouse n80


title: testis fertile F1 domesticus/musculus rep1

value: F1 LEWES/EiJ X PWK/PhJ


title: canine retina, glaucoma, biol. rep4

value: 7 years

value: glaucoma


title: testis fertile M. domesticus rep1

description: cross between two domesticus strains

value: F1 LEWES/EiJ X WSB/EiJ


title: canine retina, glaucoma, biol. rep1

value: Shiba Inu


title: Glutamine_vs_Ammonia_rep3

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

hyb_protocol: Custom-made whole-genome DNA microarrays for C. glutamicum ATCC 13032 printed with 70-mer oligonucleotides were obtained from Operon (Cologne, Germany) and are based on the genome sequence entry NC_006958. Hybridisation and stringent washing of the microarrays were performed according to the instructions of the supplier. Hybridisation was carried out for 16 - 18 h at 42°C using a MAUI hybridization system (BioMicro Systems, Salt Lake City, USA).

scan_protocol: After washing the microarrays were dried by centrifugation (5 min, 1600 g) and fluorescence was determined at 532 nm (Cy3-dUTP) and 635 nm (Cy5-dUTP) with 10 µm resolution using an Axon GenePix 6000 laser scanner (Axon Instruments, Sunnyvale, U.S.A).

data_processing: Quantitative image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0, Axon Instruments). For data normalization, GPR-files were processed using the BioConductor/R-packages limma and marray (www.bioconductor.org). Processed and normalized data as well as experimental details (according to MIAME) were stored in the in-house microarray database for further analysis.

organism: Corynebacterium glutamicum ATCC 13032

source_name: Glutamine

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532

growth_protocol: Bacterial strains, media and growth conditions. The C. glutamicum type strain ATCC 13032 was used as wild type. For growth experiments and DNA microarray experiments, cells from a fresh LB agar plate were inoculated into 70 ml  LB medium in a 500 ml baffled shake flask and this first preculture was incubated at 30°C and 120 rpm. For DNA microarray experiments, cells were washed in culture medium without any carbon and nitrogen source and the second preculture and subsequently the main culture were inoculated to an optical density at 600 nm (OD600) of 0.1 and 0.5, respectively, in 60 ml CgXII minimal medium without urea and ammonium sulphate, which contained 0.03 g/l 3,4-dihydroxybenzoate and 0.2 mg/l biotin. For growth experiments the main culture was inoculated to an OD600 of 0.5 to 1. The medium contained 70 mM glucose as carbon and energy source. As sole nitrogen source either 150 mM ammonium sulphate or 70 mM glutamine were used.

extract_protocol: Preparation of total RNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532

treatment_protocol: see growth protocol

value: type strain ATCC 13032

tag: growth phase

value: exponential

source_name: Ammonia


title: canine retina, healthy, biol. rep2


title: comB4 merodiploid recA vs WT 1

status: Public on Oct 04 2010

city: Seattle

first: Nina

middle: Reda

last: Salama

state: WA

address: 1100 Fairview Ave. N

department: Division of Human Biology

institute: Fred Hutchinson Cancer Research Center

description:
NSH57 WT and comB4 merodiploid (comB4 at rdxA) recA- cells were grown in Brucella Broth to OD600=0.7-0.9 and collected.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82859.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Helicobacter pylori

source_name: WT

label_protocol: not provided

extract_protocol: not provided

value: WT

value: comB4 merodiploid recA-


title: recA untreated vs recA cipro-treated 2

description:
recA cells were grown in Brucella Broth to OD600=0.6 and treated for 2.5 hours with 1ug.ml cipro (10X MIC) or untreated.
Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81393.gif

source_name: recA RNA

value: recA-

tag: treatment

source_name: recA RNA plus cipro

value: cipro


title: comB10 addA vs WT 1

description:
NSH57 WT and comB10- addA- cells were grown in Brucella Broth to OD600=0.7-0.9 and collected.
Image: http://smd.stanford.edu/MicroArray/gifs/2008-10/81648.gif

source_name: WT RNA

source_name: msd23 RNA

value: comB10- addA- (msd23)


title: comB10 addA vs WT 3

description:
NSH57 WT and comB10- addA- cells were grown in Brucella Broth to OD600=0.7-0.9 and collected.
Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/81807.gif

source_name: comB10 addA

value: comB10- addA-


title: comB10 addA vs WT 4

description:
NSH57 WT and comB10- addA- cells were grown in Brucella Broth to OD600=0.7-0.9 and collected.
Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81537.gif


title: recA vs WT 1

description:
NSH57 WT and recA- cells were grown in Brucella Broth to OD600=0.7-0.9 and collected.
Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81391.gif

value: WT (NSH57)

value: recA mutant


title: WT untreated vs WT gentamycin-treated 2

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2009-09/84911.gif
Helicobacter pylori (strain NSH57) were grown to mid-log phase and treated for 2 hours with 10ug/ml gentamycin (10XMIC).

scan_protocol: GenePix 4000B

source_name: WT untreated

source_name: WT (MSD1) treated 2.5 h with 10ug/ml gentamycin


title: WT untreated vs WT gentamycin-treated 3

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2009-09/84912.gif
Helicobacter pylori (strain NSH57) were grown to mid-log phase and treated for 2 hours with 10ug/ml gentamycin (10XMIC).


title: comB4 merodiploid (MSD89) vs WT 1

description:
The NSH57 WT strain (G27) and the isogenic comB4 merodiploid (additional copy of comB4 inserted at the rdxA locus) were grown to mid-log phase (OD600=0.6-0.8) in brucella broth.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83023.gif

value: NSH57 WT (G27)

value: comB4 merodiploid


title: comB4 merodiploid recA vs WT 3

description:
NSH57 WT and comB4 merodiploid (comB4 at rdxA) recA- cells were grown in Brucella Broth to OD600=0.7-0.9 and collected.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82812.gif


title: recA untreated vs recA cipro-treated 3

description:
recA cells were grown in Brucella Broth to OD600=0.6 and treated for 2.5 hours with 1ug.ml cipro (10X MIC) or untreated.
Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81394.gif


title: comB4 merodiploid (MSD89) vs WT 2

description:
The NSH57 WT strain (G27) and the isogenic comB4 merodiploid (additional copy of comB4 inserted at the rdxA locus) were grown to mid-log phase (OD600=0.6-0.8) in brucella broth.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82751.gif


title: comB4 merodiploid recA vs WT 2

description:
NSH57 WT and comB4 merodiploid (comB4 at rdxA) recA- cells were grown in Brucella Broth to OD600=0.7-0.9 and collected.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82811.gif


title: recA vs WT 3

description:
NSH57 WT and recA- cells were grown in Brucella Broth to OD600=0.7-0.9 and collected.
Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81392.gif


title: y_AlMg_12_rep1

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

department: Medicine

institute: Univ of Alabama at Birmingham

description:
Gene expression in root of soybean seedling under aluminum plus magnesium treatments.
Y4

hyb_protocol: Hybridization of the GeneChips was carried out  following the manufacturer’s protocol. Briefly, the fragmented biotin labeled cRNA was mixed with 0.05nM control oligonucleotide B2, 20X Eukaryotic hybridization controls (bioB, bioC, bioD, cre), 0.1 mg/mL herring sperm DNA, 0.5 mg/mL BSA, 2X hybridization buffer (1X 100mM MES/1M NaCl/20mM EDTA/0.01% Tween-20) and 10% DMSO.  The hybridization cocktail was incubated at 99oC for 5 minutes to denature the herring sperm DNA and any secondary structure on the cRNA.  The cocktail was then equilibrated to 45oC for 5 minutes prior to addition to the GeneChip.  Hybridization was carried out in the Affymetrix Hybridization Oven 640 at 45oC with rotation at 60rpm for 16 hours.  Following the hybridization step the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following Fluidics Protocol Mini_euk2v3 as recommended by the manufacturer for this Chip type.  The GeneChips were first washed in a non-stringent wash buffer of 6X SSPE/0.01% Tween-20 followed by stringent wash with 100mM MES/0.1M NaCl/0.01% Tween-20.  The first staining of the GeneChips was done in 2X stain buffer (1X 100mM MES/1M NaCl/0.05% Tween-20), 2mg/mL BSA, and 0.01 mg/mL Streptavidin Phycoerythrin (SAPE).  The GeneChips were washed in non-stringent wash buffer.  A second stain comprised of 2X staining buffer, 2mg/mL BSA, 0.1mg/mL Goat IgG, and 0.003mg/mL of biotinylated antibody was conducted immediately followed by a third stain comprised of the SAPE solution (see above).  Finally, the GeneChips were washed in non-stringent wash buffer prior to scanning.

scan_protocol: Scanning of the GeneChips was done using the Affymetrix 3000 7G scanner as described by the manufacturer. The Fluidics station and Scanner were controlled using Affymetrix GeneChip Command Console (AGCC).

data_processing: ArrayAssist Enterprise (Agilent, CA).

organism: Glycine max

source_name: One centimeter long root tip of soybean genotype Young, Al + Mg, 12hr

label_protocol: The labeling of the RNA was done as per the manufacturer's instructions (Affymetrix, Santa Clara, CA).  Briefly, two microgram of total RNA was reverse transcribed using an oligo dT-T7 primer under standard conditions.  The resulting first strand cDNA was incubated with RNAse H, E. coli DNA ligase, and E. coli DNA polymerase, dNTPs and buffer to produce second-stranded cDNA.  The cDNA was purified using spin columns following the manufacturer’s instructions (Qiagen).  The purified cDNA was then used in an in vitro transcription assay to produce the target biotin labeled cRNA for hybridization using the 3’ IVT kit from Affymetrix following the manufacturer’s instructions.  The cRNA was purified using a spin column following the kit’s instructions (Qiagen), and fragmented prior to hybridization onto the GeneChips.

growth_protocol: Plants were grown in hydroponic conditions in a growth chamber at 28oC /16 hours light and 20oC/8 hours dark cycle.

extract_protocol: Total RNA was extracted using Qiagen plant RNeasy extraction kit according to manufacturer's protocol.

treatment_protocol: 10 µM Al or Al plus Mg.

value: Young

value: root

tag: aluminum sensitivity

value: tolerant

value: aluminum and magnesium

tag: treatment time


title: WT untreated vs WT gentamycin-treated 1b

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2009-09/84910.gif
Helicobacter pylori (strain NSH57) were grown to mid-log phase and treated for 2 hours with 10ug/ml gentamycin (10XMIC).


title: recR- mutant (MSD49) vs WT 2

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81538.gif
The Helicobacter pylori recR- mutant (MSD49, cat deletion, MSD57, kan deletion) and wild-type NSH57 cells were grown to OD600=0.8

source_name: recR- mutant (MSD49, cat deletion)

value: recR- mutant (MSD49, cat deletion)


title: WT untreated vs WT gentamycin-treated 1a

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2009-09/84909.gif
Helicobacter pylori (strain NSH57) were grown to mid-log phase and treated for 2 hours with 10ug/ml gentamycin (10XMIC).


title: y_AlMg_72_rep2

description:
Gene expression in root of soybean seedling under aluminum plus magnesium treatments.
Y11

source_name: One centimeter long root tip of soybean genotype Young, Al + Mg, 72hr

tag: genotype


title: y_Al_72_rep3c

description:
Gene expression in root of soybean seedling under aluminum only treatment.
Y9

source_name: One centimeter long root tip of soybean genotype Young, Al, 72hr

value: aluminum


title: y_AlMg_72_rep3

description:
Gene expression in root of soybean seedling under aluminum plus magnesium treatments.
Y12


title: y_AlMg_72_rep1

description:
Gene expression in root of soybean seedling under aluminum plus magnesium treatments.
Y10


title: WT untreated vs WT gentamycin-treated 4

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2009-09/84913.gif
Helicobacter pylori (strain NSH57) were grown to mid-log phase and treated for 2 hours with 10ug/ml gentamycin (10XMIC).


title: comB4 merodiploid (MSD89) vs WT 4

description:
The NSH57 WT strain (G27) and the isogenic comB4 merodiploid (additional copy of comB4 inserted at the rdxA locus) were grown to mid-log phase (OD600=0.6-0.8) in brucella broth.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82750.gif


title: comB4 merodiploid (MSD89) vs WT 3

description:
The NSH57 WT strain (G27) and the isogenic comB4 merodiploid (additional copy of comB4 inserted at the rdxA locus) were grown to mid-log phase (OD600=0.6-0.8) in brucella broth.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83024.gif


title: y_Al_72_rep2c

description:
Gene expression in root of soybean seedling under aluminum only treatment.
Y8


title: y_Al_12_rep3c

description:
Gene expression in root of soybean seedling under aluminum only treatment.
Y3

source_name: One centimeter long root tip of soybean genotype Young, Al, 12hr


title: y_AlMg_12_rep3

description:
Gene expression in root of soybean seedling under aluminum plus magnesium treatments.
Y6


title: p_AlMg_12_rep3

description:
Gene expression in root of soybean seedling under aluminum plus magnesium treatments.
Pl6

source_name: One centimeter long root tip of soybean genotype PI 416937, Al + Mg, 12hr

value: sensitive


title: p_AlMg_12_rep2

description:
Gene expression in root of soybean seedling under aluminum plus magnesium treatments.
Pl5


title: y_Al_12_rep1c

description:
Gene expression in root of soybean seedling under aluminum only treatment.
Y1


title: p_AlMg_72_rep1

description:
Gene expression in root of soybean seedling under aluminum plus magnesium treatments.
Pl10

source_name: One centimeter long root tip of soybean genotype PI 416937, Al + Mg, 72hr


title: p_Al_12_rep1c

description:
Gene expression in root of soybean seedling under aluminum only treatment.
Pl1

source_name: One centimeter long root tip of soybean genotype PI 416937, Al, 12hr


title: y_Al_12_rep2c

description:
Gene expression in root of soybean seedling under aluminum only treatment.
Y2


title: p_Al_12_rep3c

description:
Gene expression in root of soybean seedling under aluminum only treatment.
Pl3


title: p_AlMg_72_rep3

description:
Gene expression in root of soybean seedling under aluminum plus magnesium treatments.
Pl12


title: p_Al_72_rep3c

description:
Gene expression in root of soybean seedling under aluminum only treatment.
Pl9

source_name: One centimeter long root tip of soybean genotype PI 416937, Al, 72hr


title: p_AlMg_72_rep2

description:
Gene expression in root of soybean seedling under aluminum plus magnesium treatments.
Pl11


title: p_Al_12_rep2c

description:
Gene expression in root of soybean seedling under aluminum only treatment.
Pl2


title: y_AlMg_12_rep2

description:
Gene expression in root of soybean seedling under aluminum plus magnesium treatments.
Y5


title: p_AlMg_12_rep1

description:
Gene expression in root of soybean seedling under aluminum plus magnesium treatments.
Pl4


title: p_Al_72_rep1c

description:
Gene expression in root of soybean seedling under aluminum only treatment.
Pl7


title: p_Al_72_rep2c

description:
Gene expression in root of soybean seedling under aluminum only treatment.
Pl8


title: y_Al_72_rep1c

description:
Gene expression in root of soybean seedling under aluminum only treatment.
Y7


title: recA untreated vs recA cipro-treated 4

description:
recA cells were grown in Brucella Broth to OD600=0.6 and treated for 2.5 hours with 1ug.ml cipro (10X MIC) or untreated.
Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/80074.gif

source_name: MSD70 RNA

source_name: cipro RNA


title: comB10 addA vs WT 2

description:
NSH57 WT and comB10- addA- cells were grown in Brucella Broth to OD600=0.7-0.9 and collected.
Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/80076.gif

value: WT (MSD1)

source_name: mutant RNA


title: recA untreated vs recA cipro-treated 1

description:
recA cells were grown in Brucella Broth to OD600=0.6 and treated for 2.5 hours with 1ug.ml cipro (10X MIC) or untreated.
Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/80075.gif


title: recA vs WT 4

description:
NSH57 WT and recA- cells were grown in Brucella Broth to OD600=0.7-0.9 and collected.
Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/80073.gif

source_name: MSD1 RNA

value: WT


title: recR- mutant (MSD57) vs WT 3

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79849.gif
The Helicobacter pylori recR- mutant (MSD49, cat deletion, MSD57, kan deletion) and wild-type NSH57 cells were grown to OD600=0.8

source_name: WT

source_name: recR- mutant (MSD57, kan deletion)

value: recR- mutant (MSD57, kan deletion)


title: recR- mutant (MSD49) vs WT 1

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79086.gif
The Helicobacter pylori recR- mutant (MSD49, cat deletion, MSD57, kan deletion) and wild-type NSH57 cells were grown to OD600=0.8


title: addA vs WT 3

description:
NSH57 WT and addA- cells were grown in Brucella Broth to OD600=0.7-0.9 and collected
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78801.gif

source_name: WT RNA

source_name: addA RNA

value: addA-


title: addA vs WT 2

description:
NSH57 WT and addA- cells were grown in Brucella Broth to OD600=0.7-0.9 and collected
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78802.gif


title: In vivo common dendritic cell progenitor (In vivo CDP_2) sample 2

city: Aachen

first: Martin

last: Zenke

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

description: BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).

hyb_protocol: Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing GCRMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

source_name: In vivo common dendritic cell progenitor isolated from mouse bone marrow

label_protocol: Probe preparation was with 50 nanogram RNA using the Affymetrix GeneChip 3’IVT Express Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.

extract_protocol: Total RNA was extracted using RNeasy Micro kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.

value: bone marrow


title: Testis_normal_P.ID.015

city: Chieti

first: Florina

last: Raicu

state: Abruzzo

address: Via Colle dell'Ara

department: Aging Research Center (CESI)

country: Italy

institute: G. d’Annunzio University Foundation Chieti

description: Both Cy3 and Cy5 lasers were balanced before performing the scanning using the calibration control spots with different concentration scattered on the array.

hyb_protocol: Cy3 or cy5 labelled targets were resuspended in 80 μl of hybridization cocktail and incubated at 95°C for 5 minutes. Samples were cooled for 15 minutes at room temperature. Hybridization cocktail contains the following reagents: 5xSSC, 0,1% SDS, 50% formamide, 1% ssDNA (Ambion, Austin, TX, USA). Samples were quick applied to our microarray (Microcribi Padova), covered with a cover slip, placed in moisturized hybridization chambers (MWG) and incubated overnight (14 - 16 hours) at 42 °C. Prior to hybridization we performed the prehybridization of microarray slides in order to wash unbound DNA from the slides after the addition of the probes. The prehybridization cocktail contains the flollowing reagents: 5xSSC, 0,1% SDS, 50% formamide, 1%ssDNA (Ambion, Austin, TX, USA), 10% Denhardt solution (Eurobio, France).After 16 hours hybridization of labeled aRNA sample mix at 42oC, the hybridization chamber was removed from the water bath, the arrays were washed with gentle stirring with the first wash buffer (1× SSC, 0,2% SDS) for 4 min. The array was washed in the next two wash buffers (0,1× SSC, 0,2 % SSC and two times with 0.2× SSC respectively) as before. The array was dried at room temperature in the dark and scanned.

scan_protocol: Cy3-Cy5 fluorescent signals were captured by a Confocal Laser Scanner "ScanArray Express" (Packard BioScience) and analysed using the software "ScanArray Express - MicroArray Analysis System" version 3.0 (Perkin Elmer) using a 5 micron resolution .

data_processing: The values of the median signal intensity from each spot were subtracted from the local median background intensity. For each slide after local background subtraction, a LOWESS algorithm was used for row data normalization to evaluate signal to noise ratio and generate log ratios of experimental vs. control signal.

source_name: total RNA home made universal reference

label_protocol: To acquire the quantity of RNA needed for microarray analysis we amplified the RNA lineary using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (from Ambion Inc.). Reverse transcription uses an oligo(dT) primer bearing a T7 promoter using ArrayScript™, a reverse transcriptase (RT) engineered to produce higher yields of first strand cDNA than wild type enzymes . ArrayScript catalyzes the synthesis of virtually full-length cDNA, which is the best way to ensure production of reproducible microarray samples. The cDNA then undergoes second strand synthesis and clean-up to become a template for in vitro transcription (IVT) with T7 RNA Polymerase. The IVT is configured to incorporate the modified nucleotide, 5-(3-aminoallyl)-UTP (aaUTP) into the aRNA (the antisense amplified RNA is referred to as aRNA, in scientific literature it is also commonly called cRNA.) during in vitro transcription. aaUTP contains a reactive primary amino group on the C5 position of uracil that can be chemically coupled to N-hydroxysuccinimidyl ester-derivatized reactive dyes (NHS ester dyes), such as Cy™3 and Cy5, in a simple, efficient reaction.

extract_protocol: According to manufacture protocol (Clontech, Terra Bella, CA, USA). All Total Clontech RNAs have been meticulously prepared to ensure the highest degree of performance in every application.

tag: Control represented by an home-made RNA universal reference that consists of a from a collection of different commercial human purified tissue RNA pool (brain, liver, muscle and lung).(Clontech, Terra Bella, CA, USA).

source_name: normal testis biopsy obstructive azoospermia

extract_protocol: Total RNA from the testicular tissue types biopsies was extracted according to SVtotal RNA Izolation System kit (Promega, Madison, WI, USA).

tag: 3-5 mm fragments per testis were excised, processed for histological analysis, and at least one sample per testis was submerged in 2 ml of RNAlater (Ambion, Austin, TX, USA) for RNA extraction.


title: In vivo common dendritic cell progenitor (In vivo CDP_1) sample 1

tag: cell type

value: In vivo common dendritic cell progenitor isolated from mouse bone marrow


title: recA vs WT 2

description:
NSH57 WT and recA- cells were grown in Brucella Broth to OD600=0.7-0.9 and collected.
Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79846.gif

value: WT (NSH57)


title: TGF-beta1 treated (12 hours) common dendritic cell progenitor sample 2 (CDP_12h_2)

source_name: TGF-beta1 treated common dendritic cell progenitor amplified from mouse bone marrow for 12 hours

label_protocol: Probe preparation was with 250 nanogram RNA using the Affymetrix GeneChip 3’IVT Express Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.


title: TGF-beta1 treated (24 hours) common dendritic cell progenitor sample 1 (CDP_24h_1)

source_name: TGF-beta1 treated common dendritic cell progenitor amplified from mouse bone marrow for 24 hours


title: WT cipro-treated  vs WT untreated 3

description:
H. pylori strain NSH57 (G27 is the parent) was grown to logarithmic phase and treated with 10ug/ml ciprofloxacin (10XMIC) for 2.5 hours or left untreated.
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79175.gif

value: NSH57 WT

source_name: cipro 1ug RNA

value: cipro 1ug RNA


title: Testis_microdeleted AZFc SCOS_P.ID.008_replica 3

source_name: biopsy normal testis obstructive azoospermia

source_name: testis biopsy microdeleted AZFc Sertoli-Cell-Only Syndrome


title: Testis_microdeleted AZFc SCOS_P.ID.008


title: TGF-beta1 treated (24 hours) common dendritic cell progenitor sample 2 (CDP_24h_2)

value: TGF-beta1 treated common dendritic cell progenitor amplified from mouse bone marrow for 24 hours


title: addA vs WT 1

description:
NSH57 WT and addA- cells were grown in Brucella Broth to OD600=0.7-0.9 and collected
Image: http://smd.stanford.edu/MicroArray/gifs/2008-03/78878.gif


title: Testis_microdeleted AZFc oligozoo_P.ID.012_replica 1

scan_protocol: Cy3-Cy5 fluorescent signals were captured by a Confocal Laser Scanner "ScanArray Express" (Packard BioScience) and analysed using the software "ScanArray Express - MicroArray Analysis System" version 3.0 (Perkin Elmer) using a 5 micron resolution.

tag: 3-5 mm fragments per testis were excised, processed for histological analysis, and at least one sample per testis was submerged in 2 ml of RNAlater (Ambion, Austin, TX, USA) for RNA extraction. Y chromosome AZFc microdeleted.

source_name: testis biopsy microdeleted AZFc oligozoospermia


title: Testis_idiopathic oligozoo_P.ID.002

source_name: testis biopsy idiopathic oligozoospermia


title: HCM1HA+10hdoxy vs HCM1HA - Exp 2

city: Lleida

first: Cabiscol

last: Elisa

address: Montserrat Roig, 2

department: Ciencies mediques Basiques

country: Spain

institute: Universitat de Lleida

hyb_protocol: Prehybridizations of the DNA microarrays were carried out at 42 oC for 1 h in a solution containing 5x SSC, 0.1% SDS, 1% bovine serum albumin. For hybridization, dried Cy3-and Cy5-labelled probes were resuspended in 35 ul of hybridization solution (50% formamide, 5x SSC, 0.1% SDS) each and mixed. Five ug of salmon sperm DNA was added to the mix before denaturation for 3 min at 95 oC. DNA microarrays were hybridized in an ArrayBooster hybridization station (Sunergia Group) for 14 h at 42 oC.

scan_protocol: The scanner ScanArray 4000 (Packard) was used to obtain the Cy3 and Cy5 images with a resolution of 10 um.  The fluorescent intensity of the spots was measured and processed using the GenePix Pro 6.0 software (Molecular Devices)

data_processing: The GEPAS server (http://gepas3.bioinfo.cipf.es/) was used to preprocess the data: merge replicates and remove inconsistent replicates (Maximum distance to median of replicates=0.5). The data was normalized in each image so that the mean of the Median of Ratios of the normalization features is equal to 1.

organism: Saccharomyces cerevisiae

source_name: yeast cells grown exponentially in YPD

label_protocol: Fluorescent labeled cDNA was prepared from 8 ug of purified total RNA by the indirect dUTP-labeling method, using the CyScribe post-labeling kit (Amersham Biosciences)

growth_protocol: Grown at 30ºC in YPD rich medium until A600=0.5. 30 ml of yeast culture was harvested by centrifugation and washed with cold water. Dried cell pellet was kept at -80 oC until RNA purification

extract_protocol: Total RNA purification using the Ambion RiboPure™-Yeast Total RNA Isolation Kit

tag: strain/genotype variation

source_name: yeast cells grown exponentially in YPD and treated with doxycycline for 10 h

value: GRB2405:CML128 HCM1-3HA::natMX4 (HCM1HA + 10h doxy)


title: Testis_normal_P.ID.016


title: WT cipro-treated  vs WT untreated 1

description:
H. pylori strain NSH57 (G27 is the parent) was grown to logarithmic phase and treated with 10ug/ml ciprofloxacin (10XMIC) for 2.5 hours or left untreated.
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79174.gif

value: cipro


title: Testis_idiopathic oligozoo_P.ID.002_replica 2

source_name: normal testis  obstructive azoospermia


title: HCM1HA+10hdoxy vs HCM1HA - Exp 1


title: TGF-beta1 treated (12 hours) common dendritic cell progenitor sample 1 (CDP_12h_1)

value: TGF-beta1 treated common dendritic cell progenitor amplified from mouse bone marrow for 12 hours


title: Testis_microdeleted AZFc SCOS_P.ID.008_replica 2


title: WT cipro-treated  vs WT untreated 2

description:
H. pylori strain NSH57 (G27 is the parent) was grown to logarithmic phase and treated with 10ug/ml ciprofloxacin (10XMIC) for 2.5 hours or left untreated.
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79085.gif


title: TGF-beta1 treated (8 hours) common dendritic cell progenitor sample 1 (CDP_8h_1)

source_name: TGF-beta1 treated common dendritic cell progenitor amplified from mouse bone marrow for 8 hours


title: TGF-beta1 treated (4 hours) common dendritic cell progenitor sample 2 (CDP_4h_2)

source_name: TGF-beta1 treated common dendritic cell progenitor amplified from mouse bone marrow for 4 hours


title: Testis_microdeleted AZFc oligozoo_P.ID.013_replica 1


title: Testis_microdeleted AZFc SCOS_P.ID.009_replica 1


title: Testis_microdeleted AZFc oligozoo_P.ID.013_replica 2

tag: 3-5 mm fragments per testis were excised, processed for histological analysis, and at least one sample per testis was submerged in 2 ml of RNAlater (Ambion, Austin, TX, USA) for RNA extraction.Y chromosome AZFc microdelelted.


title: Testis_normal_P.ID.014


title: Testis_microdeleted AZFc oligozoo_P.ID.011


title: HCM1HA+4hdoxy vs HCM1HA - Exp 2

source_name: yeast cells grown exponentially in YPD and treated with doxycycline for 4 h

value: GRB2405:CML128 HCM1-3HA::natMX4 (HCM1HA + 4h doxy)


title: HCM1HA vs WT - Exp 1

value: CML128:MATa ura3-52 his4 leu2-3,112 trp1 (WT)


title: TGF-beta1 treated (4 hours) common dendritic cell progenitor sample 1 (CDP_4h_1)

value: TGF-beta1 treated common dendritic cell progenitor amplified from mouse bone marrow for 4 hours


title: HCM1HA+4hdoxy vs HCM1HA - Exp 1


title: tetHcm1HA vs tetHCM1HA + doxy - Exp 2

value: MJRC07:GRB2405 tetO7-HCM1-3HA::kanMX4 (tetHCM1HA + 10h doxy)


title: untreated common dendritic cell progenitor sample 2 (CDP_0h_2)

source_name: untreated common dendritic cell progenitor amplified from mouse bone marrow


title: Testis_idiopathic oligozoo_P.ID.007


title: Testis_idiopathic oligozoo_P.ID.005


title: untreated common dendritic cell progenitor sample 1 (CDP_0h_1)

value: untreated common dendritic cell progenitor amplified from mouse bone marrow


title: Plasmacytoid dendritic cell sample 2 (pDC_2)

source_name: Plasmacytoid dendritic cell differentiated from amplified progenitor cells from bone marrow

label_protocol: Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.


title: Conventional dendritic cell sample 2 (cDC_2)

source_name: Conventional dendritic cell differentiated from amplified progenitor cells mouse bone marrow


title: Plasmacytoid dendritic cell sample 1 (pDC_1)

value: Plasmacytoid dendritic cell differentiated from amplified progenitor cells


title: Conventional dendritic cell sample 1 (cDC_1)

value: Conventional dendritic cell differentiated from amplified progenitor cells


title: TCF-1 KO CD8 memory T cells, biological rep3

city: Nutley

first: Hai-Hui

last: Xue

state: NJ

address: 111 Ideation Way

department: Center for Discovery and Innovation

institute: Hackensack University Medical Center

description: Gene expression data from TCF-1-deficient memory CD8 T cells

hyb_protocol: 2.5 ug of labeld cDNA were hybridized on mouse GENE 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 complete with a 7G upgrade.

data_processing:
The data were analyzed with Partek GS v 6.4 using default RMA as normalization method.
Probe group file: MoGene-1_0-v1.r4.pgf
Meta-probeset file: MoGene-1_0-v1.r4.mps

source_name: Mouse TCF-1-deficient memory CD8 T cells

label_protocol: Biotinylated cDNA were prepared using NuGEN WT-Ovation PicoRNA amplification system, starting from 800 pg to 50 ng of total RNA.

growth_protocol: Naïve OT-I T cells were transferred into isogenic recipient mice and infected with Listeria monocytogenes. Memory T cells were isolated from these recipient mice at>80 days post infection.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by further purification on RNeasy columns.

treatment_protocol: Memory CD8 T cells were sorted directly into Trizol LS reagent.

value: isolated from spleen

value: memory CD8 T cells

tag: genome/variation

value: over 80 days after infection


title: TGF-beta1 treated (8 hours) common dendritic cell progenitor sample 2 (CDP_8h_2)

value: TGF-beta1 treated common dendritic cell progenitor amplified from mouse bone marrow for 8 hours

value: bone marrow


title: HCM1HA vs WT - Exp 2


title: tetHcm1HA vs tetHCM1HA + doxy - Exp 1


title: tetHCM1HA vs HCM1HA - Exp 2


title: tetHCM1HA vs HCM1HA - Exp 1


title: WT vs Δhcm1 - Exp 2

value: MJRC05:CML128 hcm1::natMX4 (Δhcm1)


title: WT vs Δhcm1 - Exp 1


title: Common dendritic cell progenitor sample 2 (CDP_2)

source_name: Common dendritic cell progenitor amplified from bone marrow

value: Common dendritic cell progenitor


title: Testis_microdeleted AZFc oligozoo_P.ID.013


title: Testis_idiopathic oligozoo_P.ID.003

source_name: normal testis biopsy obstructive azoospermia


title: TCF-1 KO CD8 memory T cells, biological rep2

tag: age


title: Testis_idiopathic oligozoo_P.ID.006


title: Testis_idiopathic oligozoo_P.ID.003_replica 1


title: Testis_idiopathic azoospermia_P.ID.001

source_name: testis biopsy idiopathic azoospermia


title: WT CD8 memory T cells, biological rep3

description: Gene expression data from WT memory CD8 T cells

source_name: Mouse WT memory CD8 T cells

value: wild type


title: Multipotent progenitor sample 1 (MPP_1)

source_name: Multipotent progenitor amplified from bone marrow

value: Multipotent progenitor


title: Common dendritic cell progenitor sample 1 (CDP_1)


title: WT CD8 memory T cells, biological rep2


title: Testis_microdeleted AZFc SCOS_P.ID.008_replica 1

source_name: biopsy normal testis obstructive azoospermia

source_name: testis biopsy microdeleted AZFc Sertoli-Cell-Only Syndrome

tag: Y chromosome AZFc microdeletion


title: TCF-1 KO CD8 memory T cells, biological rep1


title: WT CD8 memory T cells, biological rep1


title: Multipotent progenitor sample 2 (MPP_2)


title: MCA_0.1µM_120h_Replicate3

status: Public on Oct 02 2010

city: Hannover

first: Astrid

last: Rohrbeck

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Department of Toxicology

institute: Medizinische Hochschule Hannover

hyb_protocol: Following fragmentation, labeled cRNA of each sample was hybridized to Affymetrix GeneChip® Mouse Genome - 430 2.0 arrays covering approximately 36,000 full-length mouse gene transcripts and stained according to the manufacturer's instructions.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000.

data_processing: Array data was normalized using scaling or per-chip normalization to adjust the total or average intensity of each array to be approximately the same (GCOS). The Scale factor (SF) was according to the Affymetrix recommended setting SF=1 and the TGT value was 500 and were used to generate a microarray quality control and data report. A T-test analysis was performed using Data Mining Tool (DMT) 3.0 from Affymetrix. A stringent comparison between normal and tumoral tissues was performed according to the consistency of gene expression changes. A t-test and a ranking analysis with up- and down-regulated genes were performed and only genes that exhibit a 100% concordance in the change direction with a p-value < 0.05 (t-test) and a fold change (FC) *2/FC*-2 were reported.

source_name: embryonic mouse fibroblasts Balb/c 3T3 cell line

label_protocol: Total RNA (5µg) was used to generate biotin-labeled cRNA (10 µg) by means of GeneChip® One-Cycle cDNA Synthesis Kit and GeneChip® IVT Labeling Kit (Affymetrix). Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a Bioanalyzer (Agilent 2001 Biosizing, Agilent Technologies).

growth_protocol: The Balb/c 3T3 cell line was obtained from Cytotest Cell Research GmbH (RCC), Roßdorf, Germany. Cells were harvested and used within 9-10 passages to perform the experiments. Cells were cultured with M10F containing MEM (minimum essential medium) + 10% FBS and incubated at 37 °C and 5% CO2.

extract_protocol: RNA-extraction was performed with the RNeasy Mini Kit (RNeasy MidiKit Qiagen, Santa Clarita, CA, USA) according to the manufacturer’s instruction. A standard quality control of the total RNA was performed using the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Balb/c 3T3 cells were seeded at 200 cells in each 60 x 15 mm culture dish with 4 ml M10F, using six culture dishes for every treatment. When cells reached a confluence of 60-65%, the culture medium was removed and replaced with fresh medium containing all tested chemicals at a specific concentration and two time points (24 and 120h).   First we treated the cells both 24h and 120h with concentrations reported in the literature (0.5µM BaP, 50µM DAT, 25µM AAF and 2µM MCA). In a second approach IC20 concentrations were investigated for each chemical at both time points. The concentrations determined for IC20 ranged from 1.5 µM BaP to 700 µM DAT for 24h of treatment, and from 0.1 µM BaP or MCA to 10µM AAF for 120h of treatment. Balb/c 3T3 cells treated with 0.75% DMSO alone were kept as controls.

value: BALB/c

tag: cell line

value: 3T3 cell line

value: 3-methycholanthrene (MCA)

tag: dose

tag: time


title: MCA_0.1µM_120h_Replicate1

tag: strain


title: Testis_idiopathic oligozoo_P.ID.002_replica 1

source_name: testis biopsy idiopathic oligozoospermia


title: Testis_microdeleted AZFc oligozoo_P.ID.012

source_name: testis biopsy microdeleted AZFc oligozoospermia


title: MCA_0.1µM_120h_Replicate2

tag: treatment


title: Testis_idiopathic oligozoo_P.ID.004


title: MCA_20µM_24h_Replicate2


title: Control_DMSO_120h_E2_Replicate3

value: E2 = control of the second experimental approach


title: BaP_0.1µM_120h_Replicate2

value: benzo(a)pyrene (BaP)