title: N5

source_name: naive B-cells donor 5

treatment_protocol: cells were isolated from peripheral blood of five healthy adult donors. blood samples were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 naïve B cells were isolated by magnetic cell separation, depleting CD27+ (memory B cells, T cell subpopulation) and CD11b+ (monocytes, macrophages, granulocytes, NK cells) cells, using the MACS system (Miltenyi Biotech, Bergisch Gladbach, Germany) followed by fluorescence-activated cell sorting (FACS) of IgD+ CD27- cells.

tag: naive B cell, isolated from peripheral blood of healthy donors by fluorescence-activated cell sorting


title: CC1

status: Public on Oct 01 2008

type: RNA

city: Essen

first: Ralf

last: Küppers

address: Virchowstr. 173

department: Institute for Cell Biology (Tumor Research)

country: Germany

institute: University of Duisburg-Essen, Medical School

description: Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.

hyb_protocol: Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.

scan_protocol: Scanning was performed according to the Affymetrix protocol.

data_processing: Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: centrocytes donor 1

label_protocol: The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).

extract_protocol: The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.

treatment_protocol: Tonsils for the isolation of centrocytes (CC) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar centrocytes were isolated by FACS-sorting according to the following marker expression: CD20high CD38+ CD77-.

tag: centrocytes, isolated from tonsils by fluorescence-activated cell sorting


title: M2

source_name: memory B cells donor 2

treatment_protocol: cells were isolated from peripheral blood of five healthy adult donors. blood samples were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 memory B cells were isolated by MACS depletion of CD11b+ and CD3+ cells followed by FACS-sorting of CD20+ CD27+ cells.

tag: memory B cells, isolated from peripheral blood of healthy donors by fluorescence-activated cell sorting


title: N1

source_name: naive B-cells donor 1


title: CC4

source_name: centrocytes donor 4


title: N2

source_name: naive B-cells donor 2


title: CB3

source_name: centroblasts donor 3

treatment_protocol: Tonsils for the isolation of centroblasts (CB) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar centroblasts were isolated by FACS-sorting according to the following marker expression: CD20high CD38+ CD77+.

tag: centroblasts, isolated from tonsils by fluorescence-activated cell sorting


title: N4

source_name: naive B-cells donor 4


title: Ecotype Col0 RNA sample3

status: Public on Oct 02 2008

city: Wageningen

first: Bart

last: Thomma

state: Gelderland

address: Binnenhaven 5

department: Plant Sciences

country: Netherlands

institute: Wageningen University

description: Each replicate consists of either 10 Avr2-expressing or 10 Col-0 Arabidopsis plants.

hyb_protocol: Standard affymetrix

scan_protocol: Standard affymetrix

data_processing: MAS5.0 algorithm

organism: Arabidopsis thaliana

source_name: Foliar tissue from wild type Arabidopsis

label_protocol: Affymetrix 1 cycle target

extract_protocol: Trizol+Machery nagel Kit

tag: Green plant


title: N3

source_name: naive B-cells donor 3


title: M1

source_name: memory B cells donor 1


title: CC5

source_name: centrocytes donor 5


title: DLBCL10

source_name: diffuse large B-cell lymphoma case 10

treatment_protocol: Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.

tag: primary lymphoma cells laser-microdissected from a patient diagnosed with diffuse large B-cell lymphoma (DLBCL)


title: DLBCL11

source_name: diffuse large B-cell lymphoma case 11


title: DLBCL6

source_name: diffuse large B-cell lymphoma case 6


title: DLBCL8

source_name: diffuse large B-cell lymphoma case 8


title: DLBCL7

source_name: diffuse large B-cell lymphoma case 7


title: DLBCL9

source_name: diffuse large B-cell lymphoma case 9


title: DLBCL5

source_name: diffuse large B-cell lymphoma case 5


title: DLBCL2

source_name: diffuse large B-cell lymphoma case 2


title: BL4

source_name: Burkitt lymphoma case 4

tag: primary lymphoma cells laser-microdissected from a patient diagnosed with Burkitt lymphoma (BL)


title: BL3

source_name: Burkitt lymphoma case 3


title: FL5

source_name: follicular lymphoma case 5

tag: primary lymphoma cells laser-microdissected from a patient diagnosed with follicular lymphoma (FL)


title: TCRBL2

source_name: T-cell rich B-cell lymphoma case 2

treatment_protocol: Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.

tag: primary lymphoma cells laser-microdissected from a patient diagnosed with T-cell rich B-cell lymphoma (TCRBL)


title: FL1

source_name: follicular lymphoma case 1


title: BL5

source_name: Burkitt lymphoma case 5


title: FL2

source_name: follicular lymphoma case 2


title: cHL12

source_name: classical Hodgkin lymphoma case 12

tag: primary lymphoma cells laser-microdissected from a patient diagnosed with classical Hodgkin lymphoma (cHL)


title: DLBCL4

source_name: diffuse large B-cell lymphoma case 4


title: BL1

source_name: Burkitt lymphoma case 1


title: FL3

source_name: follicular lymphoma case 3


title: TCRBL3

source_name: T-cell rich B-cell lymphoma case 3


title: TCRBL4

source_name: T-cell rich B-cell lymphoma case 4


title: NLPHL1

source_name: nodular lymphocte-predominant Hodgkin lymphoma case 1

tag: primary lymphoma cells laser-microdissected from a patient diagnosed with nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL)


title: DLBCL3

source_name: diffuse large B-cell lymphoma case 3


title: NLPHL4

source_name: nodular lymphocte-predominant Hodgkin lymphoma case 4


title: NLPHL5

source_name: nodular lymphocte-predominant Hodgkin lymphoma case 5


title: TCRBL1

source_name: T-cell rich B-cell lymphoma case 1


title: NLPHL3

source_name: nodular lymphocte-predominant Hodgkin lymphoma case 3


title: DLBCL1

source_name: diffuse large B-cell lymphoma case 1


title: NLPHL2

source_name: nodular lymphocte-predominant Hodgkin lymphoma case 2


title: FL4

source_name: follicular lymphoma case 4


title: BL2

source_name: Burkitt lymphoma case 2


title: cHL10

source_name: classical Hodgkin lymphoma case 10


title: cHL11

source_name: classical Hodgkin lymphoma case 11


title: cHL8

source_name: classical Hodgkin lymphoma case 8


title: cHL1

source_name: classical Hodgkin lymphoma case 1


title: cHL2

source_name: classical Hodgkin lymphoma case 2


title: cHL3

source_name: classical Hodgkin lymphoma case 3


title: cHL5

source_name: classical Hodgkin lymphoma case 5


title: cHL4

source_name: classical Hodgkin lymphoma case 4


title: cHL6

source_name: classical Hodgkin lymphoma case 6


title: Human Hepatocytes_Control, Donor 5

city: Hannover

first: Jürgen

last: Borlak

address: Nikolai-Fuchs-Strasse 1

institute: Fraunhofer Institut

description: no additional information

hyb_protocol: Ten µg of biotinylated fragmented cRNA were hybridized onto the GeneChip® Array according to the manufacturer's recommendation. In case that the yield of biotinylated cRNA was less than 10 µg, the in vitro transcription was repeated using as template the same cDNA as had been used in the failed reaction. In case there was no sufficient cDNA left, a new cDNA synthesis was initiated. The hybridization was performed for 16 hours at 60 rpm and 45 °C in a GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays was done on a Gene Chip® Fluidics Station 400 (Affymetrix) according to the manufacturer's recommendation. The antibody signal amplification, washing and staining protocol (Affymetrix) was used to stain the arrays with streptavidin R-phycoerythrin (SAPE; Invitrogen, USA). To amplify staining, SAPE solution was added twice with a biotinylated anti-streptavidin antibody (Vector Laboratories, CA) staining step in between.

scan_protocol: The arrays were scanned using a GeneChip® Scanner 3000. Scanned image files were visually inspected for artifacts and then analyzed, each image being scaled to the same target value for comparison between chips. The GeneChip® Operating Software (GCOS) was used to control the fluidics station and the scanner, to capture probe array data, and to analyze hybridization intensity data. Default parameters provided in the Affymetrix data analysis software package were applied for analysis.

data_processing: Affymetrix .CEL files were uploaded into our database ArrayTrack, which is a toxicogenomics software for microarray data management and analysis. Significant gene lists were prepared in ArrayTrack by using the Welch t-test, applying the following criteria: p-values < 0.05, mean channel intensities > 50, abs fold-change > 1.2.

source_name: Primary human hepatocytes

label_protocol: One to 15 µg of total RNA were used as starting material to prepare cDNA. Synthesis of double-stranded cDNA was performed using a GeneChip® one-cycle cDNA Kit (Affymetrix). The cleanup of double-stranded cDNA was done using a GeneChip® Sample Cleanup module (Affymetrix). Depending on the starting amount of total RNA, 12 (1 to 8 µg total RNA) or 6 µl (8 to 15 µg total RNA) of cDNA solution were used for in vitro transcription. The in vitro transcription was conducted with a GeneChip® IVT Labeling Kit (Affymetrix). The total amount of the reaction product was purified with a GeneChip® Sample Cleanup module (Affymetrix). Purified cRNA was quantified and checked for quality using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer. Purified cRNA was cleaved into fragments of 35-200 bases by metal-induced hydrolysis. The degree of fragmentation and the length distribution of the fragmented biotinylated cRNA were checked by capillary electrophoresis using Agilent 2100 Bioanalyzer.

growth_protocol: Primary hepatocytes were cultured enclosed between two layers of collagen. One ml collagen solution containing 1.1 mg/ml collagen was used for coating one 60-mm Petri dish (Greiner, Frickenhausen, Germany). The pH of the collagen was adjusted to 7.4 using a 10x DMEM concentrate (Biochrom, Berlin, Germany). The 2 x 106 hepatocytes per dish were seeded. Two hours after seeding and attachment of the cells, culture medium was removed along with nonadherent cells. After 24-48 hours in culture, the medium was aspirated and a second layer of collagen was pipetted on top of the cells. After gelation of this second layer, culture medium was added. Culture medium (2 ml) was changed daily. The total volume of cell culture supernatant was 4 ml, including the hydrated collagen matrix volume of 2 ml.

extract_protocol: Transcriptome analysis was done according to the manufacturer's recommendation (Affymetrix GeneChip® Expression Analysis Technical Manual (Santa Clara, CA, USA)), using GeneChip® Human Expression Array HG-U133 plus 2.0 covering over 47,000 transcripts and variants, which represent approximately 39,000 of the best characterized human genes. Total RNA was isolated from the hepatocytes using RNeasy total RNA isolation kit (QIAGEN). A second cleanup of isolated RNA was done using RNeasy Mini Kit (Qiagen). RNA was checked for quantity, purity, and integrity of the 18S and 28S ribosomal bands by capillary electrophoresis using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer.

treatment_protocol: Prior to exposure, cells were allowed to recover from the isolation procedure for 4 to 5 days. Cells were harvested 5 days after daily treatment with doxorubicin (0.1 µg/ml, 0.172 µM) or untreated (control). Secondary antibody (0.5 µg/ml) was added in each case. Goat affinity purified antibody to human IgG Fc (secondary antibody) was purchased from MP Biomedicals, Heidelberg, Germany (Cat no. 55071, lot no. 04715).

tag: Human hepatocytes isolated from specimens obtained from patients undergoing hepatic resections

tag: sex

value: female; age:57; reason for liver resection:Epitheloidal angiolipoma


title: Human Hepatocytes_Trovafloxacin, Donor_4

description: no additional information

hyb_protocol: Ten µg of biotinylated fragmented cRNA were hybridized onto the GeneChip® Array according to the manufacturer's recommendation. In case that the yield of biotinylated cRNA was less than 10 µg, the in-vitro transcription was repeated using the same cDNA as template as had been used in the failed reaction. In case there was no sufficient cDNA left, a new cDNA synthesis was initiated. The hybridization was performed for 16 hours at 60 rpm and 45 °C in a GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays was done on a Gene Chip® Fluidics Station 400 (Affymetrix) according to the manufacturer's recommendation. The antibody signal amplification, washing and staining protocol (Affymetrix) was used to stain the arrays with streptavidin R-phycoerythrin (SAPE; Invitrogen, USA). To amplify staining, SAPE solution was added twice with a biotinylated anti-streptavidin antibody (Vector Laboratories, CA) staining step in between.

scan_protocol: The arrays were scanned using a GeneChip® Scanner 3000. Scanned image files were visually inspected for artifacts and then analyzed, each image being scaled to the same target value for comparison between chips. The GeneChip® Operating Software (GCOS) was used to control the fluidics station and the scanner, to capture probe array data and to analyze hybridization intensity data. Default parameters provided in the Affymetrix data analysis software package were applied for analysis.

data_processing: Affymetrix .CEL files were uploaded into our database ArrayTrack, which is a toxicogenomics software for microarray data management and analysis. Significant gene lists were prepared in ArrayTrack by using the Welch t-test, applying the following criteria: p-values < 0.05, mean channel intensities > 100, abs fold-change > 2.5.

label_protocol: One to 15 µg of total RNA were used as starting material to prepare cDNA. Synthesis of double-stranded cDNA was performed using a GeneChip® one-cycle cDNA Kit (Affymetrix). The cleanup of double-stranded cDNA was done using a GeneChip® Sample Cleanup module (Affymetrix). Depending on the starting amount of total RNA, 12 (1 to 8 µg total RNA) or 6 µl (8 to 15 µg total RNA) of cDNA solution were used for in-vitro transcription. The in-vitro transcription was conducted with a GeneChip® IVT Labeling Kit (Affymetrix). The total amount of the reaction product was purified with a GeneChip® Sample Cleanup module (Affymetrix). Purified cRNA was quantified and checked for quality using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer. Purified cRNA was cleaved into fragments of 35-200 bases by metal-induced hydrolysis. The degree of fragmentation and the length distribution of the fragmented biotinylated cRNA was checked by capillary electrophoresis using Agilent 2100 Bioanalyzer.

growth_protocol: Primary hepatocytes were cultured enclosed between two layers of collagen. One ml collagen solution containing 1.1 mg/ml collagen was used for coating one 60-mm Petri dish (Greiner, Frickenhausen, Germany). The pH of the collagen was adjusted to 7.4 using a 10x DMEM concentrate (Biochrom, Berlin, Germany). The 2 x 106 hepatocytes per dish were seeded. Two hours after seeding and attachment of the cells, culture medium was removed along with nonadherent cells. After 24-48 h in culture, the medium was aspirated and a second layer of collagen was pipetted on top of the cells. After gelation of this second layer, culture medium was added. Culture medium (2 ml) was changed daily. The total volume of cell culture supernatant was 4 ml, including the hydrated collagen matrix volume of 2 ml.

extract_protocol: Total RNA was isolated from the hepatocytes using RNeasy total RNA isolation kit (QIAGEN). A second cleanup of isolated RNA was done using RNeasy Mini Kit (Qiagen). RNA was checked for quantity, purity and integrity of the 18S and 28S ribosomal bands by capillary electrophoresis using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer.

treatment_protocol: Prior to exposure, cells were allowed to recover from the isolation procedure for 4 to 5 days. Cells were harvested after treatment with 100 µg/ml of trovafloxacin and after 72 hours of treatment.

value: male; age:65; reason for liver resection:colorectal liver metastasis


title: Human Hepatocytes_Control, Donor 4

description: no additional information

value: male; age:76; reason for liver resection:Hepatocellular carcinoma


title: Human Hepatocytes_Control, Donor 1

description: no additional information

value: male; age:67; reason for liver resection:Liver metastasis, stomach cancer


title: Human Hepatocytes_Control, Donor 2

description: no additional information

value: male; age:72; reason for liver resection:Liver metastasis, gastrointestinal stromal tumor


title: Human Hepatocytes_Control, Donor_4

description: no additional information


title: Human Hepatocytes_Doxorubicin, Donor 4

description: no additional information


title: Human Hepatocytes_Control, Donor_1

description: no additional information

value: male; age:63; reason for liver resection:liver metastasis, kidney carcinoma


title: Human Hepatocytes_Control, Donor 3

description: no additional information

value: male; age:69; reason for liver resection:Colorectal liver metastasis


title: Human Hepatocytes_Trovafloxacin, Donor_3

description: no additional information

value: female; age:43; reason for liver resection:liver adenoma


title: Human Hepatocytes_Control, Donor_2

description: no additional information

value: female; age:60; reason for liver resection:liver metastasis, mamma carcinoma


title: Human Hepatocytes_Doxorubicin, Donor 3

description: no additional information


title: cHL7

source_name: classical Hodgkin lymphoma case 7


title: moDC_candida+_control_3

city: Tampere

first: Niko

middle: Kristian

last: Sillanpaa

address: Papinkatu 14 A 10

department: Molecular immunology

country: Finland

institute: National Institute of Health, Finland

description: Matrix: candida pos

hyb_protocol: 15 μg of biotin-labeled cRNA were fragmented according to the Affymetrix eukaryotic sample protocol and hybridized to the U133 Plus 2.0 chip (Affymetrix). Hybridization, staining and washing were performed using the Affymetrix Fluidics Station 450 and Hybridization Oven 640 under standard conditions.

scan_protocol: Scanning was performed according to the standard Affymetrix protocol.

data_processing: The raw data was first processed with the Affymetrix Microarray Suite 5 (Affymetrix) software in order to create lists of good quality genes. The initial selection procedure utilized Affymetrix expression level flags (present, marginal, absent). Genes that were flagged either present or marginally expressed in all replicates were considered expressed and genes that were flagged absent in all replicates were considered absent. Genes with inconsistent flagging were not included in the analysis. Further, a cross gene error model was devised with the GeneSpring GX 7.3.1 (Agilent Technologies) software in order to calculate the lowest reliable expression value for each set of chips and to filter away the genes with unreliably low intensities. The raw data was then reprocessed with GeneSpring GX 7.3.1 using the GC-RMA algorithm with default parameters. The pre-processed intensities that had a magnitude lower than 0.01 were set to 0.01. The intensities of individual genes were normalized by dividing by the median intensity of a set of appropriate replicates. The resulting data was log2-transformed and geometrical means were calculated to give one expression value for a set of replicates.

source_name: mature, candida albicans stimulated moDCs from healthy control

label_protocol: One microgram of total cellular RNA was treated according to the conventional Affymetrix eukaryotic RNA labeling protocols (Affymetrix, Santa Clara, CA) and then used to prepare biotinylated cRNA with the Enzo Bioarray High Yield RNA transcript labelling kit (Enzo, Life sciences, Farmingdale, NY).

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated from 70-100 ml of EDTA blood over Ficoll–Paque gradient. PBMCs  were plated at a cell density of 10×106 cells/ml onto six-well, 24-well or 96-well plates. Monocytes were allowed to adhere for 2 h at 37°C, after which non-adherent  cells were removed by washing with phosphate-buffered saline (PBS). Monocytes were differentiated into moDCs in RPMI supplemented with 2 mM L-glutamine, 20  mM HEPES, 10% fetal calf serum (FCS) and containing 20 ng/ml IL-4 and 10 ng/ml GM-CSF. Fresh medium was added every two days.

extract_protocol: Total RNA was extracted from DCs using the RNeasy Mini kit (Qiagen, Venlo, The Netherlands). Quantity of RNA was determined with spectrophotometer and the quality was controlled using the Agilent Bioanalyzer 2100.

treatment_protocol: The samples labelled candida_pos were co-cultured with candida albicans using a cell-to-candida ratio of 1:1 (MOI of 1).

tag: Gender

value: female


title: moDC_candida+_control_1

description: Matrix: candida pos


title: moDC_candida+_control_2

description: Matrix: candida pos


title: Human Hepatocytes_Control, Donor_3

description: no additional information


title: Human Hepatocytes_Doxorubicin, Donor 5

description: no additional information


title: Human Hepatocytes_Doxorubicin, Donor 1

description: no additional information


title: moDC_candida-_control_2

description: Matrix: candida neg

source_name: mature moDCs from healthy control


title: Human Hepatocytes_Doxorubicin, Donor 2

description: no additional information


title: Human Hepatocytes_Trovafloxacin, Donor_2

description: no additional information


title: Human Hepatocytes_Trovafloxacin, Donor_1

description: no additional information


title: moDC_candida+_patient_3

description: Matrix: candida pos

source_name: mature, candida albicans stimulated moDCs from APECED patient


title: moDC_candida+_patient_1

description: Matrix: candida pos


title: moDC_candida+_patient_2

description: Matrix: candida pos


title: moDC_candida-_control_3

description: Matrix: candida neg


title: moDC_candida-_control_1

description: Matrix: candida neg


title: moDC_candida-_patient_3

description: Matrix: candida neg

source_name: mature moDCs from APECED patient


title: PBMCs_untreated_biorep2

city: Greifswald

first: Sandra

last: Scharf

address: F.-L.-Jahn-Str. 15a

department: Department of Functional Genomics

institute: Ernst Moritz Arndt University Greifswald, Institute for Genetics and Functional Genomics

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

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

data_processing: Raw data were generated with GCOS 1.4 (MAS algorithm) without scaling. Normalization was performed with GeneSpring GX 7.3.1 (Agilent) and included data transformation of signals below 10 to 10 as well as per chip and per gene median normalisation.

source_name: PBMCs untreated donor2

label_protocol: Preparation of biotinylated cRNA followed the Affymetrix standard protocol starting from 2.5 µg total RNA (GeneChip Expression Analysis Technical Manual, 2004, Affymetrix)

growth_protocol: Purified PBMCs were cultured in RPMI containing 10% FCS.

extract_protocol: TRIzol extraction of total RNA, subsequent purification of RNA with Qiagen RNeasy Micro Kit and precipitation of RNA with Sodium acetate and ethanol.

treatment_protocol: Human PBMCs were purified from buffy coats of healthy blood donors and stimulated for 6h with the recombinant SAgs SEB or SEI.

tag: donor 2

tag: medium control untreated


title: moDC_candida-_patient_1

description: Matrix: candida neg


title: PBMCs_SEB-treated_biorep2

source_name: PBMCs SEB-treated donor2

tag: treated with SEB 100pg/ml


title: moDC_candida-_patient_2

description: Matrix: candida neg


title: PBMCs_SEB-treated_biorep1

source_name: PBMCs SEB-treated donor1

tag: donor 1


title: Col-0 seedling biological replicate 3

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

country: Switzerland

institute: UNIL

description: Gene expression data from seedlings 10 days after germination

hyb_protocol: 10ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to a Arabidopsis ATH1 microarrays for 16 hours at 45ºC; Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.

scan_protocol: Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000.

data_processing: Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Quality Reporter.

label: Biotin

source_name: Arabidopsis seedling 10 days after germination

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

growth_protocol: Arabidopsis pvip1 pvip2 mutants and corresponding Col-0 wild type seed were germinated on MS agar plates and cultivated at 21°C (16h light).

extract_protocol: TRI reagent (Sigma) extraction of total RNA was performed according to the manufacturer instructions; further clean-up of RNA was performed with RNeasy Plant Mini columns (Qiagen) according to manufacturer’s instructions.

treatment_protocol: 10 days after germination seedlings were harvested; roots of wild type seedlings were removed; vestigial hypocotyl of mutants was cut to control for wounding effects.

tag: Wild type seedlings


title: pvip1 pvip2 seedling biological replicate 3

tag: Rootless seedlings - wounded


title: PBMCs_SEI-treated_biorep1

source_name: PBMCs SEI-treated donor1

tag: treated with SEI 100pg/ml


title: PBMCs_untreated_biorep1

source_name: PBMCs untreated donor1


title: Col-0 seedling biological replicate 1


title: pvip1 pvip2 seedling biological replicate 2


title: PBMCs_SEI-treated_biorep2

source_name: PBMCs SEI-treated donor2


title: Adipose tissue_421_obese_rep4

city: GRANADA

first: Concepcion

middle: María

last: Aguilera

state: Granada

address: Ramon y Cajal, 4

department: Intitute of Nutrition and Food Technology

country: Spain

institute: University of Granada

description: Normal

hyb_protocol: Following fragmentation, cRNA were hybridized on the GeneChip Human U133 plus 2.0 array according to Affymetrix recomendations

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with robust multi-array (RMA) for background correction, normalization and polishing

source_name: Omental adipose tissue, obese, child

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: Total RNA was prepared using the RNeasy Lipid Tissue Midi Kit (Qiagen)

tag: tissue

value: omental adipose

tag: group

value: obese

tag: gender

value: M

tag: age

value: 9 years

tag: z score bmi


title: cHL9

source_name: classical Hodgkin lymphoma case 9

tag: primary lymphoma cells laser-microdissected from a patient diagnosed with classical Hodgkin lymphoma (cHL)


title: PBMCs_untreated_biorep3

source_name: PBMCs untreated donor3

tag: donor 3


title: Adipose tissue_418_obese_rep1

description: Normal

value: 11 years


title: PBMCs_SEB-treated_biorep3

source_name: PBMCs SEB-treated donor3


title: Adipose tissue_425_control_rep2

description: Normal

source_name: Omental adipose tissue, normal weight, child

value: normal weight

value: 7 year


title: Col-0 seedling biological replicate 2


title: PBMCs_SEI-treated_biorep3

source_name: PBMCs SEI-treated donor3


title: Adipose tissue_427_control_rep4

description: Normal

value: 10 year


title: Adipose tissue_423_control_rep1

description: Normal


title: Adipose tissue_419_obese_rep2

description: Normal


title: pvip1 pvip2 seedling biological replicate 1


title: Adipose tissue_429_control_rep6

description: Normal


title: Adipose tissue_420_obese_rep3

description: Normal

value: 12 years


title: Adipose tissue_426_control_rep3

description: Normal

value: F

value: 8 year


title: Adipose tissue_422_obese_rep5

description: Normal

value: 10 years


title: Adipose tissue_428_control_rep5

description: Normal


title: Patient 19 (expression)

status: Public on Sep 30 2008

city: Leiden

first: Marloes

last: van Kester

address: Einthovenweg 20

department: Dermatology

institute: Leiden University Medical Center

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner System 3000

data_processing: The array images were quantified utilizing the Genechip operating system (GCOS) v1.2 software (Affymetrix). The average fluorescence intensity was determined for each microarray and then the output of each experiment was globally scaled to a target value of 200. Further normalization and variance stabilization was performed using VSN in the R statistical software package

source_name: MF tumor biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA

extract_protocol: RNA was extracted from 25 x 50 μM frozen sections using the RNeasy kit (Qiagen), yielding 25-60 μg total RNA

value: skin

tag: Stage

value: transformed


title: Patient 18 (expression)


title: Patient 10 (expression)


title: Patient 21 (expression)


title: Patient 9 (expression)


title: Patient 11 (expression)


title: Patient 16 (expression)


title: Patient 15 (expression)


title: Patient 20 (expression)


title: Patient 1 (expression)


title: Patient 14 (expression)


title: Patient 8 (expression)


title: Patient 3 (expression)


title: Patient 7 (expression)


title: Patient 17 (expression)


title: Patient 22 (expression)


title: Patient 12 (expression)


title: Patient 4 (expression)


title: Patient 5 (expression)


title: Patient 2 (expression)


title: Patient7_PB

city: Hong Kong

first: Alice

last: Cheung

address: 21 Sassoon Road, Pokfulam

department: Medicine

country: China

institute: HKU

hyb_protocol: After fragmentation, 15ug of cRNA was hybridized to the GeneChip array for 16 hours. The GeneChips were washed and stained using the GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned with the GeneChip Scanner 3000 (both from Affymetrix Inc., Santa Clara, CA, USA).

data_processing: Data were analysed using the GeneChip Operating Software Version 1.4.0.036. (Affymetrix Inc., Santa Clara, CA, USA). For comparison across different arrays, the data for each array were normalized by a global scaling strategy (MAS5), using a scaling target intensity of 500.

source_name: Patient7_PB CD34+

label_protocol: double-stranded cDNA was generated by reverse transcription from 1 ug of total RNA with an oligo(dT) primer bearing a T7 promoter. The double-stranded cDNA was used as a template for in vitro transcription to generate biotin-labeled cRNA using MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion Inc., Austin, TX, USA).

growth_protocol: Paired BM and PB samples were prospectively collected from patients with AML. Mononuclear cells (MNC) were purified by density gradient centrifugation.

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

treatment_protocol: CD34+ cells were isolated by immunomagnetic methods

tag: AML subtypes

tag: Sex/Age


title: Patient6_BM

source_name: Patient6_BM CD34+


title: Patient8_BM

source_name: Patient8_BM CD34+

value: MLD


title: Patient7_BM

source_name: Patient7_BM CD34+


title: Patient5_PB

source_name: Patient5_PB CD34+

value: Not classifiable


title: Patient 13 (expression)


title: Patient9_BM

source_name: Patient9_BM CD34+

value: MDS


title: Patient6_PB

source_name: Patient6_PB CD34+


title: Patient8_PB

source_name: Patient8_PB CD34+


title: Patient9_PB

source_name: Patient9_PB CD34+


title: Patient5_BM

source_name: Patient5_BM CD34+


title: Patient 6 (expression)


title: Myometrium_preterm labor_T53

status: Public on Sep 27 2008

city: Kansas City

first: Carl

middle: P

last: Weiner

state: KS

address: 3901 Rainbow Boulevard, MS 2028

country: USA

institute: University of Kansas Medical Center

description: All microarray procedures were performed according to Affymetrix standard protocol (Affymetrix genechip expression analysis technical manual).

hyb_protocol: A hybridization cocktail is prepared, including the fragmented target cRNA, probe array controls, BSA, and herring sperm DNA.  It is then hybridized to the probe array during a 16 hour incubation using Affymetrix hybridization oven 640.  Immediately following hybridization, the probe array undergoes automated washing and staining protocol (Affymetrix genechip expression analysis technical manual) on the Affymetrix Fluidics Station 400.

scan_protocol: Probe array was then scanned using the Affymetrix GeneChip Scanner 3000 according to standard protocol (Affymetrix genechip expression analysis technical manual).

data_processing: Oligonucleotide microarrays were analyzed using the Affymetrix Expression Console™.  Gene expression levels were normalized using the R Statistical package and software available through the Bioconductor Project. Normalization was carried out using a background adjustment procedure and a sequence-specific expression method (GC-RMA).  A detection P value was used to make a reliable call of gene expression (present, marginal, or absent).  Genes present in only one of the three patient samples were classified as absent overall.

source_name: Myometrium_preterm labor_T53

label_protocol: Labeled cRNA was produce according to manufacturers standard procdures (Affymetrix genechip expression analysis technical manual).  cDNA is synthesized from total RNA.  An In vitro transcription reaction is then done to produce biotin-labeled cRNA from the cDNA.  The cRNA is fragmented before hybridization.

extract_protocol: Total RNA was isolated using TRIzol™ Reagent (Invitrogen™, Carlsbad, CA) according to the manufacturer’s protocol.  RNA qunatity and quality was reassessed prior to spotting using the Agilent 2100 Bioanalyzer™ (Agilent Technologies, Palo Alto, CA)

tag: Tissue

value: myometrium, Gender:female, Gestational age:31 weeks, Condition:preterm labor


title: Myometrium_term no labor_T16

source_name: Myometrium_term no labor_T16

value: myometrium, Gender:female, Gestational age:39 weeks, Condition:term labor


title: Myometrium_preterm no labor_T36

source_name: Myometrium_preterm no labor_T36

value: myometrium, Gender:female, Gestational age:29 weeks, Condition:preterm no labor


title: Myometrium_preterm labor_N20

source_name: Myometrium_preterm labor_N20


title: Microvascular Fragments, 1 year old, biological rep1

city: Stockholm

first: Liqun

last: He

address: Scheelesvag 2

country: Sweden

institute: Karolinska Institute

description: Gene expression data from microvascular Fragments at 1year

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

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

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

organism: Mus musculus

source_name: Mouse brain

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

extract_protocol: Extraction of total RNA was performed according to manufacturer's instructions (RNeasy Micro Kit (Qiagen, cat.# 74004) for embryonic tissue and RNeasy Mini Kit (Qiagen, cat.# 74104) for adult tissue)

tag: Strain

value: C57/SV129 (mixed background), Gender:male, Age:1 year old, Tissue:brain microvascular fragments


title: Microvascular Fragments, 1 year old, biological rep2

value: C57/SV129 (mixed background), Gender:female, Age:1 year old, Tissue:brain microvascular fragments


title: Myometrium_preterm no labor_T18

source_name: Myometrium_preterm no labor_T18


title: Myometrium_preterm no labor_T25

source_name: Myometrium_preterm no labor_T25


title: Microvascular Fragments, Embryonic day 18.5, biological rep3

description: Gene expression data from microvascular Fragments at Embryonic day 18.5

value: NMRI, Gender:N/A, Age:18.5 embryonic days, Tissue:brain microvascular fragments


title: Myometrium_term no labor_Mem72

source_name: Myometrium_term no labor_Mem72


title: Myometrium_preterm labor_T84

source_name: Myometrium_preterm labor_T84


title: Rest Of the Brain, Embryonic day 18.5, biological rep2

description: Gene expression data from rest brain at Embryonic day 18.5

value: NMRI, Gender:N/A, Age:18.5 embryonic days, Tissue:brain tissue without microvascular fragments


title: Microvascular Fragments, Embryonic day 18.5, biological rep2


title: Myometrium_term labor_Flap35

source_name: Myometrium_term labor_Flap35


title: Rest Of the Brain, Embryonic day 18.5, biological rep1


title: Rest Of the Brain, Embryonic day 18.5, biological rep3

description: Gene expression data from rest brain at Embryonic day 18.10


title: Myometrium_term labor_Flap29

source_name: Myometrium_term labor_Flap29


title: Microvascular Fragments, Embryonic day 18.5, biological rep1


title: Myometrium_term labor_Flap28

source_name: Myometrium_term labor_Flap28


title: Microvascular Fragments, 1 year old, biological rep3


title: 76N RhoA T37A1

status: Public on Sep 26 2008

city: Chicago

first: Simon

last: Lin

state: IL

department: Bioinformatics Core

institute: Northwestern University

description: gene expression data from mutant RhoA ( T37A) immortalized human mammary epithelial cells

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

source_name: Mutant RhoA (T37A) immortalized human mammary epithelial cells

label_protocol: standard Affymetrix protocol

growth_protocol: Reduction mammoplasty-derived human mammary epithelial cell strains, 76N and RhoA immortalized 76N cells  were grown in the DFCI-1 medium

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.For each cell line,  RNA was isolated in three independent experiments.

treatment_protocol: No treatment. Logarithmically growing cells were collected for RNA extraction.

tag: Reduction mammoplasty


title: 76N RhoA WT3

description: Gene expression data from wild type RhoA immortalized human mammary epithelial cells

source_name: Wild type RhoA immortalized human mammary epithelial cells


title: 76N RhoA T37A3


title: control plus

city: Bunkyo-ku

first: naomi

last: takahashi

state: Tokyo

address: 1-5-45 Yushima

department: Department of Pediatrics and Developmental Biology

country: Japan

institute: Tokyo Medical and Dental University

description: Gene expression data from aCD28/aCD3 stimulated CD4+ T cells of a healthy control.

hyb_protocol: The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip® Human Genome U133 plus 2.0 probe arrays (Affymetrix).

scan_protocol: The Affymetrix GeneChip scanner using default settings.

data_processing: Data analysis was performed with GeneSpring software version 7.2 (Agilent Technologies).  To normalize the variations in staining intensity among chips, the 'Average Difference' values for all genes on a given chip were divided by the median value for expression of all genes on the chip.  To eliminate genes containing only a background signal, genes were selected only if the raw values of the 'Average Difference' were more than 50, and expression of the gene was judged to be 'Present' by the GeneChip Operating Software version 1.4 (Affymetrix).

source_name: CD4+ T cells, aCD28+aCD3, 24hr

label_protocol: Labeling using GeneChip IVT Labeling kit (Affymetrix)

growth_protocol: RPMI 1640, 10% FBS, anti-CD28 mAb (at 1mg/mL) with plate-bound anti-CD3 mAb, 24hr

extract_protocol: Total RNA was extracted using RNeasy mini kit with DNase (QIAGEN).

treatment_protocol: CD4 T-cells were negatively selected with a StemSep device (StemCell Technologies) from the PBMCs.

tag: healthy volumteer


title: 76N RhoA G14V3

description: gene expression data from constitutively active form of RhoA ( G14V) immortalized human mammary epithelial cells

source_name: Constitutively active form of RhoA ( G14V) immortalized human mammary epithelial cells


title: 76N RhoA T37A2


title: patient#1 plus

description: Gene expression data from aCD28/aCD3 stimulated CD4+ T cells of a patient#1.


title: control minus

description: Gene expression data from unstimulated CD4+ T cells of a healthy control.

source_name: CD4+ T cells, minus tiimuli, 24hr

treatment_protocol: CD4 T-cells were negatively selected with a StemSep device (StemCell


title: patient#2 plus

description: Gene expression data from aCD28/aCD3 stimulated CD4+ T cells of a patient#2.


title: 76N RhoA WT2


title: 76N2

description: Gene expression data from normal human mammary epithelial cells

source_name: Normal human mammary epithelial cells


title: patient#2 minus

description: Gene expression data from unstimulated CD4+ T cells of a patient#2.


title: 76N RhoA G14V2


title: patient#1 minus

description: Gene expression data from unstimulated CD4+ T cells of a patient#1.


title: 76N1


title: Wilms' tumor; WT_RK42

status: Public on Sep 25 2008

city: Rotterdam

first: Dmitry

last: Zubakov

state: ZH

address: Dr. Molewaterplein, 50

department: FMB

institute: Erasmus Medical Centre Rotterdam

description: gene expression data for renal tumor

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: renal tissue

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

treatment_protocol: Biopsy material was stored in liquid nitrogen until RNA extraction

tag: renal tumor


title: Wilms' tumor; WT_RK16

description: gene expression data for renal tumor


title: Wilms' tumor; WT_RK34

description: gene expression data for renal tumor


title: renal oncocytoma; RO_HD37

description: gene expression data for renal tumor


title: papillary renal cell cancer; pRCCb_HD38b

description: gene expression data for renal tumor


title: Wilms' tumor; WT_RK20

description: gene expression data for renal tumor


title: rhabdoid tumor of kidney; RhT_HD4

description: gene expression data for renal tumor


title: renal oncocytoma; RO_HD171A

description: gene expression data for renal tumor


title: renal oncocytoma; RO_HD1175

description: gene expression data for renal tumor


title: papillary renal cell cancer; pRCCb_HA454a

description: gene expression data for renal tumor


title: papillary renal cell cancer; pRCCb_HD38a

description: gene expression data for renal tumor


title: papillary renal cell cancer; pRCCb_HA393B

description: gene expression data for renal tumor


title: papillary renal cell cancer; pRCCb_HA454b

description: gene expression data for renal tumor


title: papillary renal cell cancer; pRCCb_HD183

description: gene expression data for renal tumor


title: papillary renal cell cancer; pRCCb_FR503

description: gene expression data for renal tumor


title: papillary renal cell cancer; pRCCb_HA456a

description: gene expression data for renal tumor


title: papillary renal cell cancer; pRCCb_HD11

description: gene expression data for renal tumor


title: papillary renal cell cancer; pRCCa_HD95

description: gene expression data for renal tumor


title: Myometrium_term no labor_Prot12

source_name: Myometrium_term no labor_Prot12


title: renal oncocytoma; RO_HD30

description: gene expression data for renal tumor


title: papillary renal cell cancer; pRCCa_HD208

description: gene expression data for renal tumor


title: papillary renal cell cancer; pRCCa_HD193A

description: gene expression data for renal tumor


title: papillary renal cell cancer; pRCCa_HD193B

description: gene expression data for renal tumor


title: papillary renal cell cancer; pRCCa_HD21

description: gene expression data for renal tumor


title: papillary renal cell cancer; pRCCa_HD101

description: gene expression data for renal tumor


title: papillary renal cell cancer; pRCCa_HD1562T1

description: gene expression data for renal tumor


title: papillary renal cell cancer; pRCCa_HD108

description: gene expression data for renal tumor


title: papillary renal cell cancer; pRCCa_HD100

description: gene expression data for renal tumor


title: papillary renal cell cancer; pRCCa_HD1562T2

description: gene expression data for renal tumor


title: adult normal kidney; NK1a_AK1

description: gene expression data for normal kidney

tag: normal kidney


title: adult normal kidney; NK1b_AK1

description: gene expression data for normal kidney


title: fetal normal kidney; Fkfemale_FKF

description: gene expression data for normal kidney


title: adult normal kidney; NK2b_AK2

description: gene expression data for normal kidney


title: conventional renal cell cancer; cRCCb_HD214

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCb_HA463

description: gene expression data for renal tumor


title: renal lipoma ; LP_HD1847

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCb_HD115A

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCb_HA312

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCb_HD49B

description: gene expression data for renal tumor


title: fetal normal kidney; FKmale_FKM

description: gene expression data for normal kidney


title: conventional renal cell cancer; cRCCb_HD2

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCa_HD42

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCb_HD12

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCb_HD110B

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCa_HD63

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCb_HA306

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCa_HD33

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCb_HA181

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCa_HD44

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCa_HD212

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCb_HA344

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCb_HD93

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCa_HD172B

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCa_HD18

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCa_HD34

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCb_HD58

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCa_HD172A

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCa_HD140

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCa_HD114

description: gene expression data for renal tumor


title: conventional renal cell cancer; cRCCa_HA322

description: gene expression data for renal tumor


title: chromophobe renal cell cancer; chRCC_HD29

description: gene expression data for renal tumor


title: chromophobe renal cell cancer; chRCC_HA88

description: gene expression data for renal tumor


title: WT-drought-2, biological rep 2

city: Beijing

first: Wenying

last: Xu

address: Datun Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences

description: Gene expression data from droughted treated leaf of WT plants

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degree on GeneChip Arabidopsis ATH1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with GCOS software (Microarray Suite version 5.0, MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: leaf of WT mutant after drought treatment

growth_protocol:
WT plants were grown under normal watering conditions for 24 days and then stressed by completely depriving of irrigation for 10 days. Arabidopsis rosette leaves samples were homogenized in liquid nitrogen prior to RNA isolation
Arabidopsis plants were grown   in soil under long-day conditions (16 hr light; 8 hr dark) at 22 degree

extract_protocol: total RNA was isolated by RNAplant reagent ((Tiangen Biotech))and  purified by Qiagen RNeasy kit.

tag: genotype

value: arabidopsis Columbia

value: WT plants were grown under normal watering conditions for 24 days and then stressed  for 10 days.


title: chromophobe renal cell cancer; chRCC_HA315

description: gene expression data for renal tumor


title: WT-ck-1, biological rep 1

description: Gene expression data from leaf of WT plants under control condition

source_name: leaf of WT mutant under control

growth_protocol:
WT plants were grown under normal watering conditions for 34 days. Arabidopsis rosette leaves samples were homogenized in liquid nitrogen prior to RNA isolation
Arabidopsis plants were grown   in soil under long-day conditions (16 hr light; 8 hr dark) at 22 degree

extract_protocol: total RNA was isolated and  purified by Qiagen RNeasy kit


title: dor-ck-2, biological rep 2

description: Gene expression data from leaf of S29 mutant under control condition

source_name: leaf of dor mutant under control

growth_protocol:
dor plants were grown under normal watering conditions for 34 days. Arabidopsis rosette leaves samples were homogenized in liquid nitrogen prior to RNA isolation
Arabidopsis plants were grown   in soil under long-day conditions (16 hr light; 8 hr dark) at 22 degree

value: arabidopsis Columbia, SALK T-DNA insertion (Salk-050074)


title: WT-ck-2, biological rep 2

value: WT plants were grown under normal watering conditions for 34 days.


title: dor-drought-1, biological rep 1

description: Gene expression data from droughted treated leaf of S29 mutant

source_name: leaf of dor mutant after drought treatment

growth_protocol:
dor  plants were grown under normal watering conditions for 24 days and then stressed by completely depriving of irrigation for 10 days. Arabidopsis rosette leaves samples were homogenized in liquid nitrogen prior to RNA isolation
Arabidopsis plants were grown in soil under long-day conditions (16 hr light; 8 hr dark) at 22 degree

value: dor plants were grown under normal watering conditions for 24 days and then stressed  for 10 day


title: dor-drought-2, biological rep 2

growth_protocol:
dor plants were grown under normal watering conditions for 24 days and then stressed by completely depriving of irrigation for 10 days. Arabidopsis rosette leaves samples were homogenized in liquid nitrogen prior to RNA isolation
Arabidopsis plants were grown   in soil under long-day conditions (16 hr light; 8 hr dark) at 22 degree

value: dor plants were grown under normal watering conditions for 24 days and then stressed  for 10 days.


title: conventional renal cell cancer; cRCCa_HA343

description: gene expression data for renal tumor


title: clear cell sarcoma of the kidney; CCSK_HA302

description: gene expression data for renal tumor


title: collecting duct carcinoma; CDC_HD85

description: gene expression data for renal tumor


title: chromophobe renal cell cancer; chRCC_HA417

description: gene expression data for renal tumor


title: WT-drought-1, biological rep 1

growth_protocol:
WT plants were grown under normal watering conditions for 24 days and then stressed by completely depriving of irrigation for 10 days. Arabidopsis rosette leaves samples were homogenized in liquid nitrogen prior to RNA isolation
Arabidopsis plants were grown in soil under long-day conditions (16 hr light; 8 hr dark) at 22 degree

value: WT plants were grown under normal watering conditions for 24 days and then stressed  for 10 days


title: dor-ck-1, biological rep 1

value: dor plants were grown under normal watering conditions for 34 days.


title: collecting duct carcinoma; CDC_HD91

description: gene expression data for renal tumor


title: Control_RNAi_3hr_2

status: Public on Sep 24 2008

city: Boston

first: Yingxi

state: MA

address: Enders 250, 300 Longwood Avenue

department: Neurology/Neurobiology

institute: Children' Hospital/Harvard Medical School

description: E16 mouse embryonic hippocampal neuron cultures were infected with lentivirus expression shRNA @ 3DIV and depolarized with 55 mM KCl @ 8DIV for 0, 1, 3 and 6 hours.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized to the Affymetrix MOE-430-2.0 chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using Affymetrix GeneArray Scanner.

data_processing: The data were processed with MAS 5.0. The normalization target was set to 500.

source_name: Mouse E16 Hippocampal Neurons, KCl, 3 hr

label_protocol: Biotinylated cRNA were prepared from 200 ng total RNA using the Enzo IVT labeling kit (Enzo, Farmingdale, NY).

extract_protocol: Total RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

tag: Mouse E16 Hippocampal Neurons

tag: control RNAi @ 3 DIV

tag: KCl @ 8 DIV

tag: 3 hr


title: Control_RNAi_1hr_1

source_name: Mouse E16 Hippocampal Neurons, KCl, 1 hr

tag: 1 hr


title: Control_RNAi_0hr_2

source_name: Mouse E16 Hippocampal Neurons, KCl, 0 hr

tag: 0 hr


title: Control_RNAi_0hr_3


title: Control_RNAi_3hr_3


title: Control_RNAi_1hr_3


title: Npas4_RNAi_3hr_2

data_processing: The data were processed with MAS 4.0. The normalization target was set to 500.

tag: Npas4 RNAi @ 3 DIV


title: Control_RNAi_3hr_1


title: Control_RNAi_0hr_1


title: Npas4_RNAi_1hr_3


title: Npas4_RNAi_6hr_3

source_name: Mouse E16 Hippocampal Neurons, KCl, 6 hr

tag: 6 hr


title: Npas4_RNAi_3hr_3


title: Control_RNAi_6hr_3


title: Control_RNAi_6hr_2


title: human umbilical cord blood derived endothelial progenitor cell

city: Seoul

first: Young-Guen

last: Kwon

address: 262 Seongsanno, Seodaemun-Gu

department: Dppartment of Biochemistry

country: South Korea

institute: Yonsei University

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized to the Affymetrix HG-U133A chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 7GPLUS

data_processing: Expression data were analyzed using Microarray Suite version 5.0 (Affymetrix) and GenPlex v2.4 software (ISTECH Inc. Korea).

molecule: polyA RNA

source_name: endothelial progenitor cell

label_protocol: Biotinylated cRNA were prepared from 2 microg total RNA using the BioArray-High-Yield-RNA-Transcript-Labeling-Kit (Enzo, Farmingdale, NY).

extract_protocol: EPCs from human umbilical cord blood (HUCB) were cultured on fibronectin coated plate for 7 days . RNA was extracted using the Invisorb RNA Kit II (Invitek, Berlin, Germany) according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).


title: Npas4_RNAi_6hr_2


title: Outgrowth endothelial cell differentiated from endothelial progenitor cell

description: Outgrowth endothelial cell differentiated from human umbilical cord blood derived-endothelial progenitor cell

source_name: Outgrowth endothelial cell

extract_protocol: OEC naturally differentiated from human umbilical cord blood-derived EPCs. RNA was extracted using the Invisorb RNA Kit II (Invitek, Berlin, Germany) according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).


title: Npas4_RNAi_0hr_3


title: Npas4_RNAi_1hr_2


title: Npas4_RNAi_3hr_1


title: Control_RNAi_1hr_2


title: Control_RNAi_6hr_1


title: Npas4_RNAi_0hr_2


title: Npas4_RNAi_6hr_1


title: Npas4_RNAi_1hr_1


title: Lymphoblastoid cell line TK6 rep 1

status: Public on Sep 23 2008

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

description: Gene expression data from lymphoblastoid cell line

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.100

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3100

data_processing: PLIER normalization

source_name: lymphoblastoid cell line

growth_protocol: Lymphoblastoid cell line grown to mid log phase

extract_protocol: rna easy extraction

treatment_protocol: Lyphoblastoid cell line untreated

tag: Lymphoblastoid cell line from NIHPDR collection

tag: Lymphoblastoid cell line


title: Lymphoblastoid cell line TK6 treated with MNNG rep 1

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.102

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3102

treatment_protocol: Lyphoblastoid cell lines were exposed to MNNG


title: Lymphoblastoid cell line TK6 treated with MNNG rep 2

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.103

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3103


title: Lymphoblastoid cell line TK6 rep 2

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.101

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3101


title: Lymphoblastoid cell line MT1 rep 1

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.96

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3096


title: Npas4_RNAi_0hr_1


title: Lymphoblastoid cell line 24 rep 2, Coriell GM15061

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.93

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3093


title: Lymphoblastoid cell line MT1 treated with MNNG rep 2

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.99

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3099


title: Lymphoblastoid cell line 23 treated with MNNG rep 1, Coriell GM15386

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.90

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3090


title: Lymphoblastoid cell line MT1 rep 2

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.97

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3097


title: Lymphoblastoid cell line 22 treated with MNNG rep 2, Coriell GM15324

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.87

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3087


title: Lymphoblastoid cell line 23 rep 1, Coriell GM15386

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.88

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3088


title: Lymphoblastoid cell line MT1 treated with MNNG rep 1

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.98

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3098


title: Lymphoblastoid cell line 24 treated with MNNG rep 1, Coriell GM15061

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.94

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3094


title: Lymphoblastoid cell line 23 treated with MNNG rep 2, Coriell GM15386

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.91

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3091


title: Lymphoblastoid cell line 22 rep 2, Coriell GM15324

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.85

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3085


title: Lymphoblastoid cell line 21 treated with MNNG rep 1, Coriell GM15268

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.82

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3082


title: Lymphoblastoid cell line 24 rep 1, Coriell GM15061

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.92

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3092


title: Lymphoblastoid cell line 20 treated with MNNG rep 2, Coriell GM15242

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.79

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3079


title: Lymphoblastoid cell line 22 rep 1, Coriell GM15324

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.84

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3084


title: Lymphoblastoid cell line 24 treated with MNNG rep 2, Coriell GM15061

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.95

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3095


title: Lymphoblastoid cell line 20 treated with MNNG rep 1, Coriell GM15242

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.78

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3078


title: Lymphoblastoid cell line 21 rep 2, Coriell GM15268

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.81

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3081


title: Lymphoblastoid cell line 19 rep 2, Coriell GM15226

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.73

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3073


title: Lymphoblastoid cell line 18 treated with MNNG rep 1, Coriell GM15216

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.70

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3070


title: Lymphoblastoid cell line 19 rep 1, Coriell GM15226

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.72

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3072


title: Lymphoblastoid cell line 19 treated with MNNG rep 2, Coriell GM15226

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.75

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3075


title: Lymphoblastoid cell line 20 rep 2, Coriell GM15242

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.77

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3077


title: Lymphoblastoid cell line 19 treated with MNNG rep 1, Coriell GM15226

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.74

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3074


title: Lymphoblastoid cell line 18 rep 1, Coriell GM15216

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.68

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3068


title: Lymphoblastoid cell line 18 treated with MNNG rep 2, Coriell GM15216

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.71

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3071


title: Lymphoblastoid cell line 17 rep 2, Coriell GM15144

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.65

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3065


title: Lymphoblastoid cell line 21 treated with MNNG rep 2, Coriell GM15268

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.83

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3083


title: Lymphoblastoid cell line 22 treated with MNNG rep 1, Coriell GM15324

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.86

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3086


title: Lymphoblastoid cell line 20 rep 1, Coriell GM15242

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.76

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3076


title: Lymphoblastoid cell line 23 rep 2, Coriell GM15386

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.89

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3089


title: Lymphoblastoid cell line 21 rep 1, Coriell GM15268

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.80

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3080


title: Lymphoblastoid cell line 18 rep 2, Coriell GM15216

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.69

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3069


title: Lymphoblastoid cell line 16 treated with MNNG rep 1, Coriell GM15072

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.62

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3062


title: Lymphoblastoid cell line 17 treated with MNNG rep 2, Coriell GM15144

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.67

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3067


title: Lymphoblastoid cell line 17 treated with MNNG rep 1, Coriell GM15144

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.66

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3066


title: Lymphoblastoid cell line 17 rep 1, Coriell GM15144

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.64

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3064


title: Lymphoblastoid cell line 15 rep 2, Coriell GM15056

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.57

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3057


title: Lymphoblastoid cell line 16 rep 2, Coriell GM15072

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.61

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3061


title: Lymphoblastoid cell line 16 rep 1, Coriell GM15072

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.60

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3060


title: Lymphoblastoid cell line 15 treated with MNNG rep 1, Coriell GM15056

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.58

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3058


title: Lymphoblastoid cell line 15 treated with MNNG rep 2, Coriell GM15056

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.59

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3059


title: Lymphoblastoid cell line 14 treated with MNNG rep 1, Coriell GM15038

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.54

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3054


title: Lymphoblastoid cell line 14 treated with MNNG rep 2, Coriell GM15038

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.55

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3055


title: Lymphoblastoid cell line 13 treated with MNNG rep 2, Coriell GM15590

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.51

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3051


title: Lymphoblastoid cell line 14 rep 1, Coriell GM15038

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.52

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3052


title: Lymphoblastoid cell line 13 treated with MNNG rep 1, Coriell GM15590

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.50

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3050


title: Lymphoblastoid cell line 13 rep 1, Coriell GM15590

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.48

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3048


title: Lymphoblastoid cell line 15 rep 1, Coriell GM15056

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.56

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3056


title: Lymphoblastoid cell line 14 rep 2, Coriell GM15038

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.53

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3053


title: Lymphoblastoid cell line 12 treated with MNNG rep 2, Coriell GM15385

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.47

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3047


title: Lymphoblastoid cell line 12 rep 2, Coriell GM15385

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.45

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3045


title: Lymphoblastoid cell line 13 rep 2, Coriell GM15590

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.49

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3049


title: Lymphoblastoid cell line 11 treated with MNNG rep 1, Coriell GM15227

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.42

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3042


title: Lymphoblastoid cell line 16 treated with MNNG rep 2, Coriell GM15072

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.63

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3063


title: Lymphoblastoid cell line 12 treated with MNNG rep 1, Coriell GM15385

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.46

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3046


title: Lymphoblastoid cell line 11 rep 2, Coriell GM15227

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.41

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3041


title: Lymphoblastoid cell line 12 rep 1, Coriell GM15385

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.44

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3044


title: Lymphoblastoid cell line 10 rep 1, Coriell GM15221

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.36

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3036


title: Lymphoblastoid cell line 11 treated with MNNG rep 2, Coriell GM15227

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.43

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3043


title: Lymphoblastoid cell line 10 treated with MNNG rep 2, Coriell GM15221

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.39

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3039


title: Lymphoblastoid cell line 9 rep 2, Coriell GM15213

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.33

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3033


title: Lymphoblastoid cell line 9 rep 1, Coriell GM15213

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.32

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3032


title: Lymphoblastoid cell line 8 treated with MNNG rep 1, Coriell GM15510

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.30

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3030


title: Lymphoblastoid cell line 8 rep 2, Coriell GM15510

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.29

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3029


title: Lymphoblastoid cell line 10 treated with MNNG rep 1, Coriell GM15221

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.38

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3038


title: Lymphoblastoid cell line 11 rep 1, Coriell GM15227

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.40

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3040


title: Lymphoblastoid cell line 10 rep 2, Coriell GM15221

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.37

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3037


title: Lymphoblastoid cell line 7 treated with MNNG rep 2, Coriell GM15236

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.27

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3027


title: Lymphoblastoid cell line 9 treated with MNNG rep 2, Coriell GM15213

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.35

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3035


title: Lymphoblastoid cell line 9 treated with MNNG rep 1, Coriell GM15213

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.34

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3034


title: Lymphoblastoid cell line 8 treated with MNNG rep 2, Coriell GM15510

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.31

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3031


title: Lymphoblastoid cell line 8 rep 1, Coriell GM15510

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.28

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3028


title: Lymphoblastoid cell line 7 treated with MNNG rep 1, Coriell GM15236

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.26

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3026


title: Lymphoblastoid cell line 6 treated with MNNG rep 2, Coriell GM15224

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.23

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3023


title: Lymphoblastoid cell line 7 rep 2, Coriell GM15236

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.25

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3025


title: Lymphoblastoid cell line 7 rep 1, Coriell GM15236

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.24

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3024


title: Lymphoblastoid cell line 6 treated with MNNG rep 1, Coriell GM15224

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.22

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3022


title: Lymphoblastoid cell line 5 treated with MNNG rep 2, Coriell GM15245

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.19

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3019


title: Lymphoblastoid cell line 5 rep 1, Coriell GM15245

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.16

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3016


title: gun5_norflurazon_3

city: La Jolla

first: Joanne

last: Chory

state: CA

address: 10010 N. Torrey Pines Road.

department: Plant Biology Laboratory

institute: The Salk Institute for Biological Studies

description: 5 day old light grown

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Data manipulations were performed in R (http://www.r-project.org/). Standard Affymetrix quality-control procedures were carried out using the BioConductor packages simpleaffy and affyPLM. Expression was normalized and estimated using the gcRMA package of BioConductor. The quality of data from replicate samples was checked using least square regression (R2) and scatter plots for each condition studied. The normalized data were filtered, using two criteria: (1) detectable expression under at least one condition as defined by a MAS5 (Affymetrix) and normalized expression larger than 60 units and variable expression across conditions (p value < 0.01 from ANOVA modeling)

source_name: gun5 NF treated

label_protocol: Affymetrix

growth_protocol: Seeds were surface sterilized and plated on 1/2 LS plates supplemented with 1% sucrose and grown at 21o C under continous light (100µmol*m-2*sec-1).

extract_protocol: RNeasy (Qiagen; Hilden, Geramny) according to manufacturer's protocol

treatment_protocol: Sedds were grown on plates with or without 5µM Norflurazon

tag: whole seedling


title: gun5_norflurazon_2

description: 5 day old light grown


title: gun5_norflurazon_1

description: 5 day old light grown


title: gun5_control_2

description: 5 day old light grown

source_name: gun5 untreated


title: Lymphoblastoid cell line 4 treated with MNNG rep 2, Coriell GM15223

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.15

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3015


title: Lymphoblastoid cell line 6 rep 2, Coriell GM15224

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.21

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3021


title: Lymphoblastoid cell line 5 treated with MNNG rep 1, Coriell GM15245

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.18

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3018


title: Lymphoblastoid cell line 3 treated with MNNG rep 1, Coriell GM15215

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.10

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3010


title: gun5_control_3

description: 5 day old light grown


title: gun5_control_1

description: 5 day old light grown


title: Lymphoblastoid cell line 5 rep 2, Coriell GM15245

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.17

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3017


title: Lymphoblastoid cell line 6 rep 1, Coriell GM15224

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.20

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3020


title: gun1-9_norflurazon_2

description: 5 day old light grown

source_name: gun1-9 NF treated


title: Lymphoblastoid cell line 4 rep 1, Coriell GM15223

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.12

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3012


title: Lymphoblastoid cell line 3 treated with MNNG rep 2, Coriell GM15215

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.11

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3011


title: Lymphoblastoid cell line 4 treated with MNNG rep 1, Coriell GM15223

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.14

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3014


title: gun1-9_norflurazon_1

description: 5 day old light grown


title: Lymphoblastoid cell line 3 rep 2, Coriell GM15215

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.9

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3009


title: gun1-9_control_3

description: 5 day old light grown

source_name: gun1-9 untreated


title: gun1-9_norflurazon_3

description: 5 day old light grown


title: Lymphoblastoid cell line 3 rep 1, Coriell GM15215

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.8

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3008


title: Lymphoblastoid cell line 4 rep 2, Coriell GM15223

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.13

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3013


title: gun1-9_control_1

description: 5 day old light grown


title: Lymphoblastoid cell line 2 treated with MNNG rep 1, Coriell GM15036

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.6

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3006


title: gun1-9_control_2

description: 5 day old light grown


title: Col-0_control_2

description: 5 day old light grown

source_name: Col-0 untreated


title: Vasectomised epididimus,47years-old, cauda segment

status: Public on Sep 22 2008

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

description:
Gene expression data from Normal epididimus,50 years-old, head segment
biological rep 1

hyb_protocol: Following fragmentaion, 15 µg of cRNA were hybridized for 16h at 45°C to GeneChip U133 Plus 2.0 Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (EukGE-WS2v5_450).

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 G7 and extracted by GCOS 1.2 software (Affymetrix).

data_processing: The data were analyzed with LimmaGUI software (Bioconductor). Data was normalized by RMA method.

label_protocol: Biotinylated cRNA were prepared accordind to the standard Affymetrix protocol from 10 µg total  RNA (Expression Analysis technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted by Trizol reagent according to manufacturer’s instructions.

treatment_protocol: Dissection protocol: Tissues were collected under optimum conditions while artificial circulation was maintained to preserve organs assigned for transplantation. Epididymides were dissected in caput, corpus and cauda epididymidis and immediately frozen in liquid nitrogen and stored at -80°C until used for RNA extraction

tag: Epididymis


title: Col-0_norflurazon_1

description: 5 day old light grown

source_name: Col-0 NF treated


title: Col-0_norflurazon_2

description: 5 day old light grown


title: Lymphoblastoid cell line 1 treated with MNNG rep 2, Coriell GM15029

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.3

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3003


title: Lymphoblastoid cell line 2 rep 1, Coriell GM15036

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.4

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3004


title: Lymphoblastoid cell line 2 treated with MNNG rep 2, Coriell GM15036

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.7

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3007


title: Col-0_control_3

description: 5 day old light grown

hyb_protocol: Affymetrix

scan_protocol: Affymetrix


title: Vasectomised epididimus,45 years-old, cauda segment

description:
Gene expression data from Normal epididimus,47 years-old, head segment
biological rep 1


title: Lymphoblastoid cell line 1 rep 1, Coriell GM15029

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.0

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3000


title: Col-0_norflurazon_3

description: 5 day old light grown


title: Lymphoblastoid cell line 1 treated with MNNG rep 1, Coriell GM15029

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.2

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3002


title: Lymphoblastoid cell line 1 rep 2, Coriell GM15029

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.1

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3001


title: Vasectomised epididimus,47 years-old, caput segment

description:
Gene expression data from Normal epididimus,50 years-old, tail segment
biological rep 3


title: Vasectomised epididimus,1980, corpus segment

description:
Gene expression data from Normal epididimus, 26 years-old, corpus segment
biological rep 2


title: Col-0_control_1

description: 5 day old light grown


title: vastus lateralis, protein intake: 1.00 g/kg, old, subject 21

city: West Lafayette

first: Wayne

last: Campbell

state: IN

address: 700 West State Street

department: Foods and Nutrition

institute: Purdue University

description: Gene expression for older male following two weeks of dietary protein intake 1.00 g/kg

hyb_protocol: Affymetrix protocol

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

data_processing: The raw data were summarized using Affymetrix Microarray Suite (MAS) 5.0 software

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from a minimum of 5 ug total RNA

extract_protocol: Total RNA was isolated from the frozen muscle sample using Tri-Reagent following the manufacturerÆs instructions.  Isolated total RNA was further purified using RNeasy Mini Kits following manufacturerÆs protocol

treatment_protocol: Three randomized controlled feeding trials with protein intakes of 63% (P63: 0.50 g/kg-1/d-1), 94% (P94: 0.75 g/kg-1/d-1), and 125% (P125: 1.00 g/kg-1/d-1) of the recommended dietary allowance (RDA).

tag: Protein intake

tag: Trial

tag: Sex

value: Male

tag: Age


title: vastus lateralis, protein intake: 1.00 g/kg, old, subject 22


title: Vasectomised epididimus,1980, cauda segment

description:
Gene expression data from Normal epididimus,26 years-old, head segment
biological rep 1


title: Vasectomised epididimus,45 years-old, corpus segment

description:
Gene expression data from Normal epididimus,47 years-old, corpus segment
biological rep 2


title: Lymphoblastoid cell line 2 rep 2, Coriell GM15036

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.5

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3005


title: vastus lateralis, protein intake: 1.00 g/kg, old, subject 20


title: vastus lateralis, protein intake: 1.00 g/kg, old, subject 19


title: Vasectomised epididimus,47 years-old, corpus segment

description:
Gene expression data from Normal epididimus,50 years-old, corpus segment
biological rep 2


title: Vasectomised epididimus,45 years-old, caput segment

description:
Gene expression data from Normal epididimus,47 years-old, tail segment
biological rep 3


title: Vasectomised epididimus,1980, caput segment

description:
Gene expression data from Normal epididimus,26 years-old, tail segment
biological rep 3


title: vastus lateralis, protein intake: 1.00 g/kg, old, subject 17


title: vastus lateralis, protein intake: 1.00 g/kg, old, subject 18


title: vastus lateralis, protein intake: 1.00 g/kg, old, subject 16


title: vastus lateralis, protein intake: 1.00 g/kg, old, subject 15


title: vastus lateralis, protein intake: 0.75 g/kg, old, subject 21

description: Gene expression for older male following 2 weeks of dietary protein intake of 0.75 g/kg


title: vastus lateralis, protein intake: 0.75 g/kg, old, subject 16


title: Murine normal cells_rep 2

city: Oxford

first: Dilair

last: Baban

address: Roosevelt Drive

department: Wellcome Trust Centre Human Genetics

country: United Kingdom

institute: University of Oxford

description: Here we have investigated the invasion of lymphatic vessels as a key step in the metastasis of primary tumour cells to draining lymph nodes by comparing the gene expression profile of normal dermal lymphatic endothelial cells (LEC) with those isolated from tumours of murine T-241/VEGF-C metastatic fibrosarcoma.

hyb_protocol: Fragmented labeled cRNA (15 µg) was used in 300 µl hybridization cocktail containing spiked controls (Affymetrix #900299). A 200 µl sample of this hybridization cocktail was used on the chip and incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v5, Affymetrix) of double-staining and post-hybridizations washes.

scan_protocol: Fluorescent images were captured using gene Array Scanner 3000 and GCOS1.2 software (Affymetrix).

data_processing: We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 45,101 probe sets (transcripts) on each of these arrays.

source_name: Normal dermal LEC were isolated from C57BL/6 mice.

label_protocol: 50ng total RNA used in Affymetrix two cycle labelling kit cat. no. 900494

growth_protocol: Mouse LEC were grown in gelatin-coated tissue culture flasks in EGM-2 medium at 37ºC, 5 % CO2 in a humidified atmosphere.

extract_protocol: Total RNA extracted using Qiagen RNeasy.

treatment_protocol: Normal dermal LEC were isolated from the tail skin of 8-week old female C57Bl6 mice. Skin was incubated at 4°C overnight in PBS containing 2mg/ml dispase before removing the epidermis. The dermis was then scraped to release endothelial cells, which were collected by centrifugation before culture. LEC were purified, after lifting with accutase®, by immunomagnetic selection with rabbit anti-mouse LYVE-1 and goat anti-rabbit MACS® beads according to the manufacturers instructions

tag: Normal dermal LEC were isolated from the tail skin of 8-week old female C57BL/6 mice.


title: Murine normal cells_rep 3


title: Murine fibrosarcoma tumor cells_rep 2

hyb_protocol: Fragmented labeled cRNA (15 µg) was used in 300 µl hybridization cocktail containing spiked controls (Affymetrix #900299). A 200 µl sample of this hybridization cocktail was used on the chip and incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v5, Affymetrix) of double-staining and post-hybridisations washes.

source_name: Tumour LEC were isolated from C57BL/6 mice injected with T241/VEGF-C/GFP fibrosarcomas.

growth_protocol: Mouse LEC were grown in gelatin-coated tissue culture flasks in EGM-2 medium.

treatment_protocol: Tumours were minced and shaken in PBS containing collagenase, elastase, hyaluronidase and DNAse (0.1%, 0.01%, 0.2% and 0.01% w/v respectively) for 1 hour at 37°C. The dispersed tissue was then filtered and washed before being cultured. The majority of contaminating tumour cells were removed by lifting with PBS/5mM EDTA, prior to detachment of the strongly adherent LEC with accutase® and their isolation by incubated at 4°C overnight in PBS containing 2mg/ml dispase before removing the epidermis. The dermis was then scraped to release endothelial cells, which were collected by centrifugation before culture. LEC were purified, after lifting with accutase®, by immunomagnetic selection with rabbit anti-mouse LYVE-1 and goat anti-rabbit MACS® beads according to the manufacturers instructions.

tag: LEC were isolated from primary tumours growing in the dorsal skin of 8-week old female C57BL/6 mice injected with T241/VEGF-C/GFP cells. Cells were suspended (2xmillion/ml) in sterile PBS before injection (100microlitter) subcutaneously to the right of mid-dorsum below the shoulder of C57Bl/6 mice. Mice were checked daily for primary tumour growth and killed before the tumour size reached ethical limits within 2-4 weeks.


title: vastus lateralis, protein intake: 0.75 g/kg, old, subject 15


title: vastus lateralis, protein intake: 0.75 g/kg, old, subject 18


title: vastus lateralis, protein intake: 0.75 g/kg, old, subject 22


title: vastus lateralis, protein intake:0.50 g/kg, old, subject 18

description: Gene expression for older male following two weeks of dietary protein intake of 0.50 g/kg

tag: Protein intake:0.50 g/kg


title: vastus lateralis, protein intake: 0.75 g/kg, old, subject 17


title: Murine fibrosarcoma tumor cells_rep 3


title: vastus lateralis, protein intake: 1.00 g/kg, young, subject 13

description: Gene expression for younger male following two weeks of dietary protein intake 1.00 g/kg


title: vastus lateralis, protein intake:0.50 g/kg, old, subject 20


title: Murine fibrosarcoma tumor cells_rep 1


title: vastus lateralis, protein intake:0.50 g/kg, old, subject 15


title: vastus lateralis, protein intake:0.50 g/kg, old, subject 17


title: vastus lateralis, protein intake: 0.75 g/kg, old, subject 19


title: vastus lateralis, protein intake:0.50 g/kg, old, subject 22


title: vastus lateralis, protein intake: 0.75 g/kg, old, subject 20


title: vastus lateralis, protein intake:0.50 g/kg, old, subject 21


title: vastus lateralis, protein intake: 1.00 g/kg, young, subject 9


title: vastus lateralis, protein intake:0.50 g/kg, old, subject 19


title: vastus lateralis, protein intake: 1.00 g/kg, young, subject 8


title: vastus lateralis, protein intake: 1.00 g/kg, young, subject 10


title: vastus lateralis, protein intake: 1.00 g/kg, young, subject 11


title: vastus lateralis, protein intake: 1.00 g/kg, young, subject 12


title: vastus lateralis, protein intake:0.50 g/kg, old, subject 16


title: vastus lateralis, protein intake: 1.00 g/kg, young, subject 7


title: vastus lateralis, protein intake: 1.00 g/kg, young, subject 5


title: vastus lateralis, protein intake: 1.00 g/kg, young, subject 14


title: vastus lateralis, protein intake: 1.00 g/kg, young, subject 6


title: vastus lateralis, protein intake: 0.75 g/kg, young, subject 13

description: Gene expression for younger male following 2 weeks of dietary protein intake of 0.75 g/kg


title: vastus lateralis, protein intake: 0.75 g/kg, young, subject 12


title: vastus lateralis, protein intake: 0.75 g/kg, young, subject 11


title: vastus lateralis, protein intake: 0.75 g/kg, young, subject 14


title: vastus lateralis, protein intake: 0.75 g/kg, young, subject 10


title: vastus lateralis, protein intake: 0.75 g/kg, young, subject 6