title: LongSAGE analysis of transcriptome changes, Botrytis cinerea conidia germination

status: Public on Apr 06 2010

type: SAGE

anchor: NlaIII

city: Beijing

first: Shangwu

last: Chen

address: Qing Hua Dong Lu No. 17

country: China

institute: China Agricultural University

description: Botrytis cinerea M4 spore were harvested in PS medium (37.5 g potato, 20 g sugar for 1 liter medium), been diluted to the concentration of 5.0×105 conidia/ml, then added ethanol to a final concentration of 4% (V/V) for further experiment.

molecule: polyA RNA

organism: Botrytis cinerea

source_name: spore

extract_protocol: Total RNA was prepared from the frozen materials using TRIZOL reagent (Invitrogen) and digested by RNase-free DNase I. LongSAGE libraries were constructed using ISAGE™ Long Kits (Invitrogen) according to the instructions of manufacturer. Transforming clones were sequenced with ABI PRIZM 3730 DNA sequencer.

tag: M4 strain


title: Donor 3 - Monocytes Untreated - mAdbID:83688

status: Public on Apr 01 2010

type: RNA

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 83688

hyb_protocol: Sample Hybrization Protocol Wash procedure: Washing: 1. Wash with 2x SSC + 0.1% SDS to remove coverslip. 2. Wash with 1x SSC for 1 min. 3. Wash with 0.2x SSC for 1 min. 4. Wash with 0.05x SSC for 10-20 seconds. 5. Centrifuge slide at 80-100 g for 3 min. Other: Hybridization: Combine Cy3 and Cy5 labeled target (adjust the color to purple) and complete dry the sample by speed vacuum . Add 37ul of the following mixture to the dried target (for 20x40mm slide): 1ul 50x Denhardt’s blocking solution (Sigma Cat# 2532) 1ul poly dA (8mg/ml Pharmacia Cat# 27-7988-01) 1ul yeast tRNA (4mg/ml Sigma Cat# R8759) 10ul Human Cot I DNA (1mg/ml Gibco BRL Cat# 15279-011) 3ul 20X SSC 1ul 10% SDS 20ul of DEPC H2O Heat for 2 min at 99oC and Cool to RT. Apply target mixture to array slide, add coverslip, place in humidified hyb chamber, and hybridize at 65oC over night.

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.26;; 4.58 Temperature: 32.31

data_processing:
BRBArrayTools
Calculation Method: Fluorescence intensities generated by Cy5 and Cy3 probes hybridized onto the microarray slides were scanned were scanned on a GenePix 4000 (Axon Instruments, Union City, CA) at variable PMT voltage to obtain maximal signal intensities with < 1% probe saturation. Data were uploaded to National Institute of Health, NCI/CCR µArray database (http://nciarray.nci.nih.gov). Raw data were retrieved in BRB-ArrayTools(http://linus.nci.nih.gov/BRBArrayTools.html) format for analysis and normalization. Following filter criteria was applied to the data set: 1. spots were excluded if intensity < 300, and spot size less than 25um 2. genes were filtered out if >80% of experiment with missing data values. 3. log2 transformed data were normalized using lowess smoother, and intensity ratios were truncated if greater than 64. Transcriptional data were process by averaging results in replicate experiments for the same genes. Hierchical clustering analysis was performed on BRBArray tools using centered correlation as similarity metric and centroid linkage method: Cluster 3:0. Heat maps were generated using Eisen’s TreView Software.

molecule: total RNA

organism: Homo sapiens

source_name: Pooled Normal Donor PBMC

label_protocol:
Cy3 Sample Labeling Protocol
Other: Target labeling by reverse transcription: 4ul First strand buffer 1ul dN6 primer (8ug/ul; Boehringer Mannheim Cat# 1034731 resuspended in 250ul DEPC H2O) 2ul 10X low T - dNTP (5mM A, C and GTP, 2mM dTTP) 2ul Cy-dUTP (1mM Cy3) 2ul 0.1 M DTT 1ul RNasin 3-6ug amplified mRNA in 7 ul DEPC H2O Mix well and heat to 65C for 5min then cool down to 42C. Add 1.5ul SSII and Incubate for 90 min at 42C. Add 2.5ul 500mM EDTA and heat to 65C for 1min. Add 5ul 1M NaOH and incubate at 65C for 15min to hydrolyze RNA. Add 12.5ul 1M Tris immediately to neutralize the pH. Add 35ul of 1xTE. Target clean up: Prepare Bio-6 column and run target solution through it. Collect flow through and add 200ul 1xTE. Concentrate target to ~20ul using a microcon YM-30 column (Millipore Cat# 42410).

extract_protocol:
RNA extraction with TRIZOL
Extraction method: TRIZOL
Other: Cells were lysed with TRIzol reagent (Invitrogen, Carlsbad, CA) and total RNA was isolated according to the manufacturers instructions. RNA integrity was assessed by the presence of 28S and 18S bands using Agilent bioanalyzer and quantified using nanodrop with A260/A280 ratios > 2.0 after dilution in DEPC water.

tag: Tissue

value: blood

tag: Cell type

value: PBMC

source_name: Monocytes Untreated

label_protocol:
Cy5 Sample Labeling Protocol
Other: Target labeling by reverse transcription: 4ul First strand buffer 1ul dN6 primer (8ug/ul; Boehringer Mannheim Cat# 1034731 resuspended in 250ul DEPC H2O) 2ul 10X low T - dNTP (5mM A, C and GTP, 2mM dTTP) 2ul Cy-dUTP (1mM Cy5) 2ul 0.1 M DTT 1ul RNasin 3-6ug amplified mRNA in 7 ul DEPC H2O Mix well and heat to 65C for 5min then cool down to 42C. Add 1.5ul SSII and Incubate for 90 min at 42C. Add 2.5ul 500mM EDTA and heat to 65C for 1min. Add 5ul 1M NaOH and incubate at 65C for 15min to hydrolyze RNA. Add 12.5ul 1M Tris immediately to neutralize the pH. Add 35ul of 1xTE. Target clean up: Prepare Bio-6 column and run target solution through it. Collect flow through and add 200ul 1xTE. Concentrate target to ~20ul using a microcon YM-30 column (Millipore Cat# 42410).

value: Monocytes


title: Donor 7 - NK cell Untreated - mAdbID:83685

description: mAdb experiment ID: 83685

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.55 Temperature: 32.28

source_name: NK cell Untreated

value: NK cell


title: LongSAGE analysis of transcriptome changes, Botrytis cinerea conidia germination treated with resveratrol

description: After conidia were aseptically harvested, they were diluted to the concentration of 5.0×105 conidia/ml with P.S (37.5 g potato, 20 g sugar for 1 liter medium), resveratrol was quickly added as ethanolic solutions to the nongerminated conidial suspensions at a concentration of 140 µg/ml and the final ethanol concentration is 4% (V/V).


title: Donor 7 - Monocytes Untreated - mAdbID:83684

description: mAdb experiment ID: 83684

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.53 Temperature: 32.22


title: Donor 6 - Monocytes Untreated - mAdbID:83679

description: mAdb experiment ID: 83679

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.26;; 4.62 Temperature: 32.46


title: Donor 6 - NK cell Untreated - mAdbID:83680

description: mAdb experiment ID: 83680

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.26;; 4.64 Temperature: 32.52


title: Donor 3 - NK cell Untreated - mAdbID:83689

description: mAdb experiment ID: 83689

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.26;; 4.59 Temperature: 32.34


title: Donor 6 - T cell Untreated - mAdbID:83682

description: mAdb experiment ID: 83682

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 3.96 Temperature: 30.08

source_name: T cell Untreated

value: T cell


title: Donor 5 - NK cell Untreated - mAdbID:83672

description: mAdb experiment ID: 83672

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.24;; 3.97 Temperature: 30.51


title: Donor 7 - B cell Untreated - mAdbID:83683

description: mAdb experiment ID: 83683

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.26;; 4.6 Temperature: 32.4

source_name: B cell Untreated

value: B cell


title: Donor 7 - T cell Untreated - mAdbID:83686

description: mAdb experiment ID: 83686

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.57 Temperature: 32.28


title: Donor 5 - Monocytes Untreated - mAdbID:83671

description: mAdb experiment ID: 83671

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 3.96 Temperature: 29.96


title: Donor 4 - T cell Untreated - mAdbID:83669

description: mAdb experiment ID: 83669

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.49 Temperature: 31.88


title: Donor 4 - NK cell Untreated - mAdbID:83667

description: mAdb experiment ID: 83667

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.46 Temperature: 31.79


title: Donor 4 - B cell Untreated - mAdbID:83665

description: mAdb experiment ID: 83665

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.52 Temperature: 31.94


title: Donor 2 - T cell Untreated - mAdbID:83664

description: mAdb experiment ID: 83664

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.1 Temperature: 31.27


title: Donor 3- B cell Untreated - mAdbID:83687

description: mAdb experiment ID: 83687

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.26;; 4.55 Temperature: 32


title: Donor 5 - B cell Untreated - mAdbID:83670

description: mAdb experiment ID: 83670

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.26;; 4.41 Temperature: 31.64


title: Donor 2 - Monocytes Untreated - mAdbID:83662

description: mAdb experiment ID: 83662

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.07 Temperature: 31.12


title: Donor 5 - T cell Untreated - mAdbID:83674

description: mAdb experiment ID: 83674

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.24;; 3.99 Temperature: 30.72


title: Donor 2 - B cell Untreated - mAdbID:83592

description: mAdb experiment ID: 83592

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 4.01 Temperature: 30.69


title: Donor 4 - Monocytes Untreated - mAdbID:83666

description: mAdb experiment ID: 83666

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.43 Temperature: 31.64


title: Donor 2 - NK cell Untreated - mAdbID:83663

description: mAdb experiment ID: 83663

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 3.99 Temperature: 30.51


title: Donor 3- T cell Untreated - mAdbID:83690

description: mAdb experiment ID: 83690

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 4.4 Temperature: 29.41


title: Donor 7 - CD133 - GCSF plus AMD3100 - mAdbID:81760

description: mAdb experiment ID: 81760

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.5 Temperature: 32.25

source_name: CD133 - GCSF plus AMD3100 Mobilized

treatment_protocol:
Treatment type: compound
Agent: GCSF plus AMD3100
Treatment dose: 10 ug / kg (GCSF); 240ug / kg (AMD3100)
Treatment time: 5 days (GCSF); 12 hours (AMD3100)
In-vivo treatment: Healthy donors recieved GCSF for 5 days. On the 5th day donors recieved one dose of AMD3100. Then the PBSC were collected by aphoresis.


title: Donor 8 - CD133 - AMD3100 - mAdbID:81761

description: mAdb experiment ID: 81761

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 4.75 Temperature: 29.35

source_name: CD133 - AMD3100 Mobilized

treatment_protocol:
Treatment type: compound
Agent: AMD3100
Treatment dose: 240ug / kg (AMD3100)
Treatment time: 12 hours
In-vivo treatment: Healthy donors recieved one dose of AMD3100. Then the PBSC were collected by aphoresis.


title: D3-Monocyte - mAdbID:83158

description: mAdb experiment ID: 83158

hyb_protocol: Sample Hybridization Protocol Other: Small RNA was enriched from 10ug total RNA by flashPAGE (Pre-cast Gel,Type A) (Ambion, Austin, TX, USA) and purified using flashPAGE reaction clean-up kit (Ambion, Austin, TX, USA) according to manufacture’s instruction. The same procedures were applied to obtain small RNA from the Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines that was used as the reference for the miRNA expression array assay. Fragmented small RNA were 3’-end tailed with amine-modified nucleotides and chemically coupled to CyDye fluors (Amersham Biosciences, piscatway, NJ, USA), which sample with Cy5 and the reference with Cy3 respectively, using the mirVana miRNA Labeling Kit (Ambion) following the recommended protocol by the manufactures’ instruction. After labeling, the samples and the reference were co-hybridized to the miRNA array at room temperature over night. Both the processed cDNA and the miRNA array slides were scanned by GenePix scanner Pro 4.0 (Axon, Sunnyvale, CA, USA).

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 100;; 100 LaserPower: 3.44;; 3.6 Temperature: 32.43

data_processing:
BRBArrayTools
Calculation Method: Fluorescence intensities generated by Cy5 and Cy3 probes hybridized onto the microarray slides were scanned were scanned on a GenePix 4000 (Axon Instruments, Union City, CA) at variable PMT voltage to obtain maximal signal intensities with < 1% probe saturation. Data were uploaded to National Institute of Health, NCI/CCR µArray database (http://nciarray.nci.nih.gov). Raw data were retrieved in BRB-ArrayTools(http://linus.nci.nih.gov/BRBArrayTools.html) format for analysis and normalization. Following filter criteria was applied to the data set: 1. spots were excluded if intensity < 100, and spot size less than 10um 2. genes were filtered out if >80% of experiment with missing data values. 3. log2 transformed data were normalized using lowess smoother, and intensity ratios were truncated if greater than 64. Transcriptional data were process by averaging results in replicate experiments for the same genes. Hierchical clustering analysis was performed on BRBArray tools using centered correlation as similarity metric and centroid linkage method: Cluster 3:0. Heat maps were generated using Eisen’s TreView Software.

label_protocol:
Cy5 Sample Labeling Protocol
Other: Small RNA was enriched from 10ug total RNA by flashPAGE (Pre-cast Gel,Type A) (Ambion, Austin, TX, USA) and purified using flashPAGE reaction clean-up kit (Ambion, Austin, TX, USA) according to manufacture’s instruction. The same procedures were applied to obtain small RNA from the Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines that was used as the reference for the miRNA expression array assay. Fragmented small RNA were 3’-end tailed with amine-modified nucleotides and chemically coupled to CyDye fluors (Amersham Biosciences, piscatway, NJ, USA), which sample with Cy5 and the reference with Cy3 respectively, using the mirVana miRNA Labeling Kit (Ambion) following the recommended protocol by the manufactures’ instruction. After labeling, the samples and the reference were co-hybridized to the miRNA array at room temperature over night. Both the processed cDNA and the miRNA array slides were scanned by GenePix scanner Pro 4.0 (Axon, Sunnyvale, CA, USA).

organism:
Homo sapiens
human gammaherpesvirus 4

source_name: EBV-infected B cell line

label_protocol:
Cy3 Sample Labeling Protocol
Other: Small RNA was enriched from 10ug total RNA by flashPAGE (Pre-cast Gel,Type A) (Ambion, Austin, TX, USA) and purified using flashPAGE reaction clean-up kit (Ambion, Austin, TX, USA) according to manufacture~Rs instruction. The same procedures were applied to obtain small RNA from the Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines that was used as the reference for the miRNA expression array assay. Fragmented small RNA were 3~R-end tailed with amine-modified nucleotides and chemically coupled to CyDye fluors (Amersham Biosciences, piscatway, NJ, USA), which sample with Cy5 and the reference with Cy3 respectively, using the mirVana miRNA Labeling Kit (Ambion) following the recommended protocol by the manufactures~R instruction. After labeling, the samples and the reference were co-hybridized to the miRNA array at room temperature over night. Both the processed cDNA and the miRNA array slides were scanned by GenePix scanner Pro 4.0 (Axon, Sunnyvale, CA, USA).

value: EBV-infected B cell


title: Donor 2 - CD133 - GCSF plus AMD3100 - mAdbID:81755

description: mAdb experiment ID: 81755

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.12 Temperature: 32.03


title: Donor 4 - CD133 - AMD3100 - mAdbID:81757

description: mAdb experiment ID: 81757

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 3.97 Temperature: 30.11


title: Donor 1 - Monocytes Untreated - mAdbID:83589

description: mAdb experiment ID: 83589

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.26;; 4.08 Temperature: 31.91


title: D6-Monocyte - mAdbID:83855

description: mAdb experiment ID: 83855

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.24;; 4.07 Temperature: 28.49


title: Donor 1 - NK cell Untreated - mAdbID:83590

description: mAdb experiment ID: 83590

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.24;; 4.03 Temperature: 30.84


title: Donor 3 - CD34 - GCSF - mAdbID:81763

description: mAdb experiment ID: 81763

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.29 Temperature: 32.13

source_name: CD34 - GCSF Mobilized

treatment_protocol:
Treatment type: compound
Agent: GCSF
Treatment dose: 10 ug / kg
Treatment time: 5 days
In-vivo treatment: Healthy people recieved GCSF for 5 days. Then the PBSC were collected by aphoresis.


title: Donor 1 - B cell Untreated - mAdbID:83588

description: mAdb experiment ID: 83588

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 5.15 Temperature: 27.79


title: Donor 1 - CD133 - GCSF plus AMD3100 - mAdbID:81754

description: mAdb experiment ID: 81754

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.27;; 4.68 Temperature: 32.95


title: Donor 1 - CD34 - GCSF - mAdbID:81753

description: mAdb experiment ID: 81753

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.3 Temperature: 32.19


title: Donor 6 - CD133 - GCSF plus AMD3100 - mAdbID:81759

description: mAdb experiment ID: 81759

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 3.97 Temperature: 29.68


title: Donor 5 - CD34 - GCSF - mAdbID:81762

description: mAdb experiment ID: 81762

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 5.07 Temperature: 28.31


title: D7-B Cell - mAdbID:83151

description: mAdb experiment ID: 83151

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.32;; 3.2 Temperature: 31.97


title: Donor 5 - CD133 - AMD3100 - mAdbID:81758

description: mAdb experiment ID: 81758

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.53 Temperature: 32.34


title: D6-B Cell - mAdbID:83143

description: mAdb experiment ID: 83143

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.31;; 3.23 Temperature: 31.85


title: D6-T cell - mAdbID:83144

description: mAdb experiment ID: 83144

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.31;; 3.23 Temperature: 31.91


title: D2-Monocyte - mAdbID:83854

description: mAdb experiment ID: 83854

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 4.12 Temperature: 28.16


title: D1-Monocyte - mAdbID:83853

description: mAdb experiment ID: 83853

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 4.17 Temperature: 27.88


title: D7-Monocyte - mAdbID:83856

description: mAdb experiment ID: 83856

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.24;; 4.05 Temperature: 28.8


title: D5-NK cell - mAdbID:83141

description: mAdb experiment ID: 83141

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.31;; 3.22 Temperature: 31.7


title: D5-B Cell - mAdbID:83139

description: mAdb experiment ID: 83139

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.27;; 3.28 Temperature: 31.24


title: D4-B Cell - mAdbID:83129

description: mAdb experiment ID: 83129

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.25;; 3.51 Temperature: 30.57


title: D4-T cell - mAdbID:83130

description: mAdb experiment ID: 83130

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.28;; 3.36 Temperature: 32.61


title: D1-NK cell - mAdbID:83123

description: mAdb experiment ID: 83123

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.25;; 3.47 Temperature: 29.78


title: D4-Monocyte - mAdbID:83132

description: mAdb experiment ID: 83132

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.28;; 3.31 Temperature: 31.7


title: D3-T cell - mAdbID:83156

description: mAdb experiment ID: 83156

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 100;; 100 LaserPower: 3.43;; 3.6 Temperature: 32.4


title: D3-NK cell - mAdbID:83157

description: mAdb experiment ID: 83157

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 100;; 100 LaserPower: 3.43;; 3.6 Temperature: 32.37


title: Donor 1 - T cell Untreated - mAdbID:83591

description: mAdb experiment ID: 83591

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.26;; 4.11 Temperature: 32


title: D1-B Cell - mAdbID:83119

description: mAdb experiment ID: 83119

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.24;; 3.55 Temperature: 29.17


title: D7-T cell - mAdbID:83152

description: mAdb experiment ID: 83152

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.31;; 3.22 Temperature: 32.03


title: D7-NK cell - mAdbID:83153

description: mAdb experiment ID: 83153

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 100;; 100 LaserPower: 3.43;; 3.6 Temperature: 32.43


title: D1-T cell - mAdbID:83122

description: mAdb experiment ID: 83122

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.23;; 3.57 Temperature: 28.68


title: D3-CD34-G-CSF - mAdbID:83110

description: mAdb experiment ID: 83110

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.26;; 3.27 Temperature: 29.04


title: Donor 3 - CD133 -AMD3100 - mAdbID:81756

description: mAdb experiment ID: 81756

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.58 Temperature: 32.52


title: D6-NK cell - mAdbID:83145

description: mAdb experiment ID: 83145

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.32;; 3.23 Temperature: 31.97


title: D5-CD133-AMD3100 - mAdbID:82736

description: mAdb experiment ID: 82736

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.22;; 3.43 Temperature: 27.76

treatment_protocol:
Treatment type: compound
Agent: AMD3100
Treatment dose: 240ug / kg (AMD3100)
Treatment time: 12 hours
Other: Healthy donors recieved one dose of AMD3100. Then the PBSC were collected by aphoresis.


title: Donor 2 - CD34 - GCSF - mAdbID:81748

description: mAdb experiment ID: 81748

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 4.88 Temperature: 28.98


title: D4-CD133-AMD3100 - mAdbID:82735

description: mAdb experiment ID: 82735

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.62 Temperature: 27.12


title: Donor 6 - B cell Untreated - mAdbID:83676

description: mAdb experiment ID: 83676

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 4.32 Temperature: 29.59


title: D6-CD133-G-CSF+AMD3100 - mAdbID:82737

description: mAdb experiment ID: 82737

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.23;; 3.39 Temperature: 28.01

treatment_protocol:
Treatment type: compound
Agent: GCSF plus AMD3100
Treatment dose: 10 ug / kg (GCSF); 240 ug / kg (AMD3100)
Treatment time: 5 days (GCSF); 12 hours (AMD3100)
In-vivo treatment: Healthy donors recieved GCSF for 5 days. On the 5th day donors recieved one dose of AMD3100. Then the PBSC were collected by aphoresis.


title: D2-CD34-G-CSF - mAdbID:83109

description: mAdb experiment ID: 83109

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.25;; 3.58 Temperature: 28.28


title: D1-CD133-G-CSF+AMD3100 - mAdbID:82732

description: mAdb experiment ID: 82732

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.19;; 3.59 Temperature: 25.23


title: D5-Monocyte - mAdbID:83142

description: mAdb experiment ID: 83142

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.18;; 3.4 Temperature: 25.75


title: D5-T cell - mAdbID:83140

description: mAdb experiment ID: 83140

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.31;; 3.2 Temperature: 31.76


title: Donor 4 - CD34 - GCSF - mAdbID:81746

description: mAdb experiment ID: 81746

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 5 Temperature: 28.65


title: D4-NK cell - mAdbID:83131

description: mAdb experiment ID: 83131

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 33 LaserPower: 3.29;; 3.28 Temperature: 31.82


title: D2-B Cell - mAdbID:83125

description: mAdb experiment ID: 83125

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.24;; 3.5 Temperature: 29.44


title: D2-T cell - mAdbID:83126

description: mAdb experiment ID: 83126

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.26;; 3.4 Temperature: 30.29


title: D2-NK cell - mAdbID:83127

description: mAdb experiment ID: 83127

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.26;; 3.43 Temperature: 30.11


title: D5-CD34-G-CSF - mAdbID:83118

description: mAdb experiment ID: 83118

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.25;; 3.26 Temperature: 29.35


title: D4-CD34-G-CSF - mAdbID:83115

description: mAdb experiment ID: 83115

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.26;; 3.29 Temperature: 28.83


title: D7-CD133-G-CSF+AMD3100 - mAdbID:82738

description: mAdb experiment ID: 82738

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.25;; 3.33 Temperature: 28.59


title: D8-CD133-AMD3100 - mAdbID:82739

description: mAdb experiment ID: 82739

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.24;; 3.35 Temperature: 28.37


title: D1-CD34-G-CSF - mAdbID:83108

description: mAdb experiment ID: 83108

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.25;; 3.58 Temperature: 28.46


title: D3-CD133-AMD3100 - mAdbID:82734

description: mAdb experiment ID: 82734

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.62 Temperature: 26.75


title: D2-CD133-G-CSF+AMD3100 - mAdbID:82733

description: mAdb experiment ID: 82733

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.19;; 3.6 Temperature: 26.17


title: D3-B Cell - mAdbID:83155

description: mAdb experiment ID: 83155

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.31;; 3.33 Temperature: 32.4


title: W8 vs B8 Rep2 (18Kb)

status: Public on Mar 24 2010

city: Urbana

first: min

last: li

state: IL

address: Rm230 1101 W peabody Dr

country: USA

institute: University of Illinois at Urbana-Champaign

description: Replicate 2

hyb_protocol: Hegde P. et al. Biotechniques 2000 29:548-56

scan_protocol: Scanner: Perkin-Elmer ScanArray Express Software: ScanArray Express v2.1

data_processing:
Spot raw data from GenePix v5.0
in-house PERL programs to format data and remove spots weaker than negative control
log2 transformation and GLowess in R/MAANOVA

organism: Glycine max

source_name: Pooled the 3 leaflets of the primary trifoliate leaf

label_protocol: Indirect incorporation using aa-dUTP

growth_protocol:
Greenhouse (25C)
16h daylength

extract_protocol: Trizol Phase-Lock Gel RNA Extraction

treatment_protocol:
Water control with adjuvant
1% v/v Herbimax, Loveland Industries
8 hr post application

tag: tissue

value: leaflet

tag: genotype

value: Cultivar Williams 82

tag: development stage

value: V1 stage (about 2 weeks old)

treatment_protocol:
Bentazon 22-25 mM mist spray
8 hr post application


title: W4 vs W8 Rep3 (18Kb)

description: Replicate 3

treatment_protocol:
Water control with adjuvant
1% v/v Herbimax, Loveland Industries
4 hr post application


title: A4 vs W4 Rep3 (18Kb)

description: Replicate 3

treatment_protocol:
Atrazine 22-25 mM mist spray
4 hr post application


title: A2 vs B2 Rep3 (18Kb)

description: Replicate 3

treatment_protocol:
Atrazine 22-25 mM mist spray
2 hr post application

treatment_protocol:
Bentazon 22-25 mM mist spray
2 hr post application


title: B1 vs W1 Rep3 (18Kb)

description: Replicate 3

treatment_protocol:
Bentazon 22-25 mM mist spray
1 hr post application

treatment_protocol:
Water control with adjuvant
1% v/v Herbimax, Loveland Industries
1 hr post application


title: B8 vs A8 Rep3 (18Kb)

description: Replicate 3

treatment_protocol:
Atrazine 22-25 mM mist spray
8 hr post application


title: W8 vs B8 Rep3 (18Kb)

description: Replicate 3


title: B2 vs B4 Rep2 (18Kb)

description: Replicate 2

treatment_protocol:
Bentazon 22-25 mM mist spray
4 hr post application


title: B2 vs B4 Rep3 (18Kb)

description: Replicate 3


title: A8 vs A1 Rep2 (18Kb)

description: Replicate 2

treatment_protocol:
Atrazine 22-25 mM mist spray
1 hr post application


title: W1 vs W2 Rep2 (18Kb)

description: Replicate 2

treatment_protocol:
Water control with adjuvant
1% v/v Herbimax, Loveland Industries
2 hr post application


title: W2 vs A2 Rep3 (18Kb)

description: Replicate 3


title: B4 vs A4 Rep3 (18Kb)

description: Replicate 3


title: A8 vs A1 Rep3 (18Kb)

description: Replicate 3


title: B8 vs A8 Rep1 (18Kb)

description: Replicate 1


title: W4 vs W8 Rep2 (18Kb)

description: Replicate 2


title: A1 vs B1 Rep3 (18Kb)

description: Replicate 3


title: A4 vs W4 Rep2 (18Kb)

description: Replicate 2


title: B8 vs A8 Rep2 (18Kb)

description: Replicate 2


title: B4 vs A4 Rep2 (18Kb)

description: Replicate 2


title: A8 vs A1 Rep1 (18Kb)

description: Replicate 1


title: W1 vs W2 Rep3 (18Kb)

description: Replicate 3


title: B4 vs A4 Rep1 (18Kb)

description: Replicate 1


title: W8 vs B8 Rep1 (18Kb)

description: Replicate 1


title: W4 vs W8 Rep1 (18Kb)

description: Replicate 1


title: A2 vs B2 Rep2 (18Kb)

description: Replicate 2


title: W2 vs A2 Rep2 (18Kb)

description: Replicate 2


title: B1 vs W1 Rep2 (18Kb)

description: Replicate 2


title: W2 vs A2 Rep1 (18Kb)

description: Replicate 1


title: B8 vs A8 Rep3 (18Ka)

description: Replicate 3


title: B2 vs B4 Rep1 (18Kb)

description: Replicate 1


title: A1 vs B1 Rep2 (18Kb)

description: Replicate 2


title: W8 vs B8 Rep3 (18Ka)

description: Replicate 3


title: A2 vs B2 Rep3 (18Ka)

description: Replicate 3


title: A1 vs B1 Rep1 (18Kb)

description: Replicate 1


title: B1 vs W1 Rep3 (18Ka)

description: Replicate 3


title: B4 vs A4 Rep3 (18Ka)

description: Replicate 3


title: A4 vs W4 Rep1 (18Kb)

description: Replicate 1


title: A4 vs W4 Rep2 (18Ka)

description: Replicate 2


title: A8 vs A1 Rep3 (18Ka)

description: Replicate 3


title: A2 vs B2 Rep1 (18Kb)

description: Replicate 1


title: W4 vs W8 Rep2 (18Ka)

description: Replicate 2


title: W1 vs W2 Rep3 (18Ka)

description: Replicate 3


title: A8 vs A1 Rep2 (18Ka)

description: Replicate 2


title: B4 vs A4 Rep2 (18Ka)

description: Replicate 2


title: W4 vs W8 Rep3 (18Ka)

description: Replicate 3


title: A1 vs B1 Rep3 (18Ka)

description: Replicate 3


title: A4 vs W4 Rep3 (18Ka)

description: Replicate 3


title: B2 vs B4 Rep3 (18Ka)

description: Replicate 3


title: B1 vs W1 Rep1 (18Kb)

description: Replicate 1


title: W8 vs B8 Rep2 (18Ka)

description: Replicate 2


title: W2 vs A2 Rep3 (18Ka)

description: Replicate 3


title: A8 vs A1 Rep1 (18Ka)

description: Replicate 1


title: B2 vs B4 Rep2 (18Ka)

description: Replicate 2


title: A2 vs B2 Rep2 (18Ka)

description: Replicate 2


title: B8 vs A8 Rep2 (18Ka)

description: Replicate 2


title: W2 vs A2 Rep2 (18Ka)

description: Replicate 2


title: W4 vs W8 Rep1 (18Ka)

description: Replicate 1


title: B4 vs A4 Rep1 (18Ka)

description: Replicate 1


title: A2 vs B2 Rep1 (18Ka)

description: Replicate 1


title: W8 vs B8 Rep1 (18Ka)

description: Replicate 1


title: A1 vs B1 Rep1 (18Ka)

description: Replicate 1


title: A4 vs W4 Rep1 (18Ka)

description: Replicate 1


title: W1 vs W2 Rep2 (18Ka)

description: Replicate 2


title: B1 vs W1 Rep2 (18Ka)

description: Replicate 2


title: A1 vs B1 Rep2 (18Ka)

description: Replicate 2


title: B2 vs B4 Rep1 (18Ka)

description: Replicate 1


title: W2 vs A2 Rep1 (18Ka)

description: Replicate 1


title: B8 vs A8 Rep1 (18Ka)

description: Replicate 1


title: W1 vs W2 Rep1 (18Ka)

description: Replicate 1


title: B1 vs W1 Rep1 (18Ka)

description: Replicate 1


title: T14 R vs. T14 S rep3 (18Ka)

status: Public on Mar 23 2010

description: Replicate 3

data_processing:
Spot raw data from GenePix v4.1
in-house PERL programs to format data and remove spots weaker than negative control
log2 transformation and RLowess in R/MAANOVA

source_name: top one inch going from just under unifoliate node down towards cotyledon node

growth_protocol:
Growth Chamber (23C)
Light 160-180 umol photons/m2/sec
12h daylength for 14 days, then 16h

treatment_protocol:
14 hrs post inoculation
Sclerotinia sclerotiorum 105HT
overnight growth on potato dextrose agar
agar plug of growing front of colony, mycelia-side down on fresh cut stem
stem was cut just below the first unifoliate node

value: Plant Introduction PI194639

tag: age

value: 15 days


title: T8 R vs. T14 R rep3 (18Ka)

description: Replicate 3

treatment_protocol:
8 hrs post inoculation
Sclerotinia sclerotiorum 105HT
overnight growth on potato dextrose agar
agar plug of growing front of colony, mycelia-side down on fresh cut stem
stem was cut just below the first unifoliate node


title: T14 S vs. T8 S rep3 (18Ka)

description: Replicate 3


title: T14 R vs. T14 S rep2 (18Ka)

description: Replicate 2


title: T8 R vs. T14 R rep2 (18Ka)

description: Replicate 2


title: T8 R vs. T14 R rep1 (18Ka)

description: Replicate 1


title: T8 S vs. T8 R rep3 (18Ka)

description: Replicate 3


title: T8 S vs. T8 R rep2 (18Ka)

description: Replicate 2


title: T14 S vs. T8 S rep2 (18Ka)

description: Replicate 2


title: T14 R vs. T14 S rep1 (18Ka)

description: Replicate 1


title: T14 S vs. T8 S rep1 (18Ka)

description: Replicate 1


title: T0 S vs. R rep1A (18Ka)

description: Replicate 1A

treatment_protocol: No treatment


title: T8 S vs. T8 R rep1 (18Ka)

description: Replicate 1


title: T0 S vs. R rep1B (18Ka)

description: Replicate 1B


title: T0 S vs. R rep3B (18Ka)

description: Replicate 3B


title: T0 S vs. R rep2B (18Ka)

description: Replicate 2B


title: W1 vs W2 Rep1 (18Kb)

description: Replicate 1


title: T0 S vs. R rep3A (18Ka)

description: Replicate 3A


title: T0 S vs. R rep2B (18Kb)

description: Replicate 2B


title: T0 S vs. R rep2A (18Ka)

description: Replicate 2A


title: T14 R vs. T14 S rep2 (18Kb)

description: Replicate 2


title: T8 R vs. T14 R rep3 (18Kb)

description: Replicate 3


title: T0 S vs. R rep3A (18Kb)

description: Replicate 3A


title: T0 S vs. R rep3B (18Kb)

description: Replicate 3B


title: T0 S vs. R rep1B (18Kb)

description: Replicate 1B


title: T14 R vs. T14 S rep1 (18Kb)

description: Replicate 1


title: T8 S vs. T8 R rep3 (18Kb)

description: Replicate 3


title: T14 R vs. T14 S rep3 (18Kb)

description: Replicate 3


title: T8 S vs. T8 R rep2 (18Kb)

description: Replicate 2


title: T14 S vs. T8 S rep2 (18Kb)

description: Replicate 2


title: male 2_R574

status: Public on Mar 20 2010

city: Lausanne

first: James

last: Holzwarth

state: Vaud

address: vers chez les blanc

department: Bioanalytical Sciences

country: Switzerland

institute: Nestle Research Center

description: no additional information

hyb_protocol: 5 µg of RNA from each sample were then independently amplified, labeled and hybridized to the HG-U133A Affymetrix chip (Affymetrix, High Wycombe, UK), according to the manufacturer’s instructions.

scan_protocol: The chips were scanned at 488 nm with an Argon-ion laser (Agilent Biotechnologies and Affymetrix).

data_processing: Expression signals were generated using the MAS 5.0 algorithm (Affymetrix), unscaled data.

label: biotin

source_name: transverse colon

label_protocol: The samples were labeled according to the manufacturer's instructions (Affymetrix, High Wycombe, UK).

extract_protocol: Total RNA was extracted using the TriPure Isolation reagent (Roche Diagnostics AG, Rotkreuz, Switzerland) and Dnase-I treated and purified with the Nucleospin kit (Macherey-Nagel AG, Oensingen, Switzerland). RNA quality was assessed with the Agilent 2100 Bioanalyzer and the RNA 6000 Nano LabChip kit (Agilent Biotechnologies, Waldbronn, Germany).

tag: Age

value: 23 years


title: T0 S vs. R rep1A (18Kb)

description: Replicate 1A


title: T0 S vs. R rep2A (18Kb)

description: Replicate 2A


title: male 2_R573

description: no additional information

source_name: ileum


title: T8 R vs. T14 R rep2 (18Kb)

description: Replicate 2


title: T8 R vs. T14 R rep1 (18Kb)

description: Replicate 1


title: T14 S vs. T8 S rep3 (18Kb)

description: Replicate 3


title: male 2_R570

description: no additional information

source_name: antrum


title: male 2_R571

description: no additional information

source_name: duodenum


title: male 1_R553

description: no additional information

value: 22 years


title: male 1_R552

description: no additional information

source_name: jejunum


title: female 2_R539

description: no additional information

value: 25 years


title: female 2_R537

description: .CEL file not available for this Sample


title: T14 S vs. T8 S rep1 (18Kb)

description: Replicate 1


title: male 1_R550

description: no additional information


title: female 2_R536

description: .CEL file not available for this Sample


title: female 2_R538

description: no additional information


title: male 1_R551

description: no additional information


title: male 1_R554

description: no additional information


title: T8 S vs. T8 S rep1 (18Kb)

description: Replicate 1


title: female 2_R535

description: no additional information


title: female 1_R478

description: no additional information

value: 24 years


title: female 1_R476

description: no additional information


title: female 1_R477

description: no additional information


title: female 1_R475

description: no additional information


title: wt Mthfd colon, biological rep1

city: Ithaca

first: David

last: Lin

state: NY

address: T2 006A VRT

institute: Cornell University

description:
MessageAmp II amplified
Mthfd-wt-26

hyb_protocol: Amplified material was applied to Affymetrix 430A 2.0 chips, hybridized, and washed on a 430A fluidics station as per manufacturer's directions.

scan_protocol: Samples were scanned on an Affymetrix GeneChip 3000 scanner.

data_processing: Raw array data was processed using GCOS software. Signal values were scaled to a default target of 500 and summarized in a pivot table. Further statistical analysis was performed in R. Signal values were log2-transformed after offset by 32.  Gene filtering was applied to include only 17259 probe sets having at least 1 present call.  A two-sample t test was applied on the normalized log ratio of each probe set.  At a p-value of 0.05, 920 differential genes were selected.  After further applying a 1.5 fold change cutoff, the top 132 differential genes were selected.

organism: Mus musculus

source_name: proximal colon, wild-type mouse fed control diet

label_protocol: One microgram of total RNA from each colon sample was amplified using the MessageAmp II Biotin Enhanced  amplification kit (Ambion) as per manufacturer's directions.

growth_protocol: Mthfd heterozygous mice were obtained as gene-trap mice from BayGenomics. Wild-type and heterozygote mice were weaned at three weeks onto a standard control diet (AIN-93G) and maintained on this diet for five weeks.

extract_protocol: Colon samples were removed from RNALater and total RNA was isolated with Trizol as per manufacturer's directions This total RNA was then further purified using a Qiagen RNEasy column as per manufacturer's directions.

treatment_protocol: Colons were flushed with PBS, and tissue from the proximal third of each colon was opened longitudinally. Samples were rinsed with PBS and frozen in RNALater at -80.

value: wt

value: proximal colon

value: 8 weeks

tag: diet

value: control diet for 5 weeks from weaning


title: het Mthfd colon, biological rep2

description:
MessageAmp II amplified
Mthfd-het-33

source_name: proximal colon, Mthfd heterozygous mouse fed control diet


title: wt Mthfd colon, biological rep3

description:
MessageAmp II amplified
Mthfd-wt-28


title: het Mthfd colon, biological rep1

description:
MessageAmp II amplified
Mthfd-het-32


title: wt Mthfd colon, biological rep2

description:
MessageAmp II amplified
Mthfd-wt-27


title: Diff_POD+CD24+GCTM2Neg_rep1

status: Public on Mar 16 2010

city: St Lucia

first: Sean

last: Grimmond

state: Q

address: Services Rd

department: Institute for Molecular Bioscience

country: Australia

institute: University of Queensland

description:
HES4 differentiated and Podocalyxin+ CD24+ GCTM-2 Negative subpopulation replicate 1
1911480077_D

hyb_protocol: llumina Human 6 BeadChips were hybridized, washed, stained and scanned according to Illuminas protocol

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

data_processing: Data were first extracted with Illumina BeadStudio software without normalisation.  Data was then uploaded into R, where RMA background adjustment and Quantile normalisation was performed using the BeadExplorer package

source_name: Embryonic Stem Cells

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

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

tag: cell type


title: hESC_undiff_rep3

description:
HES4 hESC undifferentiated replicate 3
1911480102_C

value: HES4 hESC undifferentiated


title: het Mthfd colon, biological rep3

description:
MessageAmp II amplified
Mthfd-het-34


title: female 1_R479

description: no additional information


title: hESC_undiff_rep2

description:
HES4 hESC undifferentiated replicate 2
1911480077_E


title: Diff_rep3

description:
HES4 differentiated replicate 3
1911480102_D

value: HES4 differentiated


title: Diff_POD+CD24+GCTM2Neg_rep2

description:
HES4 differentiated and Podocalyxin+ CD24+ GCTM-2 Negative subpopulation replicate 2
1911480102_B


title: Diff_rep2

description:
HES4 differentiated replicate 2
1911480077_F


title: Diff_POD+CD24+GCTM2Neg_rep3

description:
HES4 differentiated and Podocalyxin+ CD24+ GCTM-2 Negative subpopulation replicate 3
1911480102_F


title: Diff_POD+CD24+GCTM2Low_rep1

description:
HES4 differentiated and Podocalyxin+ CD24+ GCTM-2 Low subpopulation replicate 1
1911480077_C


title: Diff_POD+CD24+GCTM2Low_rep2

description:
HES4 differentiated and Podocalyxin+ CD24+ GCTM-2 Low subpopulation replicate 2
1911480102_A


title: Diff_POD+CD24+GCTM2Low_rep3

description:
HES4 differentiated and Podocalyxin+ CD24+ GCTM-2 Low subpopulation replicate 3
1911480102_E


title: beta-ZAL-treated Cells Replicate 3

status: Public on Mar 11 2010

city: Tokyo

first: zhu

last: yun

address: takanawa 4-21-12

country: Japan

institute: scinet company

hyb_protocol: Hybridization buffer (5×SSC, 0.5% SDS) was added, and samples were applied to microarrays and incubated in  HYBCHAMBERS (GeneMachines). After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an ChipReader (Virtek) scanner. Images were quantified using IPLab (Scanalytics).

data_processing: Data processing was carried out using Microsoft Excel software. For each spot, the ratio of Cy3 and Cy5 signal intensities was calculated and log2-trasformed. Each log2 value was normalized by dividing with the average of log2 values for internal control genes.

source_name: MCF-7 cells

label_protocol: 5 µg aliquots of total RNA were amplified using RiboAmp RNA Amplification Kit (ARCTURUS), and  labeled using Atlas PowerScript Fluorescent Labeling Kit (Clontech); Cy3 or Cy5 labeled.

growth_protocol: Cells were maintained in phenol red-free RPMI 1640 medium containing 10% dextran-coated charcoal-treated FBS for 3 days.

extract_protocol: Total RNA extracted using Isogen following manufacturer's instructions.

treatment_protocol: treated for three days with beta-ZAL

value: MCF-7 cells

treatment_protocol: control cells treated for three days with DMSO


title: beta-ZAL-treated Cells Replicate 2


title: beta-ZAL-treated Cells Replicate 1


title: MNP Treated Rep3

status: Public on Mar 13 2010

city: Delhi

first: Jameel

middle: Ahmad

last: Khan

state: Delhi

address: Mall Road

country: India

institute: Institute Of Genomics and Integrative Biology (CSIR)

description: HeLa Cells treated with 2 mg/ml MNP

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using Rank invariant normalization in Bead Studio 3.0 software from Illumina Inc.

source_name: Hela Cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion's Illumina® TotalPrep™ RNA Amplification Kit

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Denaturing agarose gel electrophoresis and OD 260/280

tag: cell line

value: HeLa

tag: agent

value: Magnetite (Fe3O4) Nanoparticles


title: alpha-ZAL-treated Cells Replicate 3

treatment_protocol: treated for three days with alpha-ZAL


title: Control Rep3

description: HeLa Cells treated with sterile water

value: control


title: Control Rep2

description: HeLa Cells treated with sterile water


title: MNP Treated Rep1

description: HeLa Cells treated with 2 mg/ml MNP


title: hESC_undiff_rep1

description:
HES4 hESC undifferentiated replicate 1
1911480077_A


title: Control Rep1

description: HeLa Cells treated with sterile water


title: alpha-ZAL-treated Cells Replicate 2


title: MNP Treated Rep2

description: HeLa Cells treated with 2 mg/ml MNP


title: alpha-ZAL-treated Cells Replicate 1


title: Diff_rep1

description:
HES4 differentiated replicate 1
1911480077_B


title: ZAL-treated Cells Replicate 1

treatment_protocol: treated for three days with ZAL


title: ZAL-treated Cells Replicate 3


title: beta-ZEA-treated Cells Replicate 3

treatment_protocol: treated for three days with beta-ZEA


title: ARPE-19 42h-2 TNF

city: Kisarazu

first: Rui

last: Ose

state: Chiba

address: 2-6-7 Kazusa-Kamatari

department: Department of Human Genome Research

institute: Kazusa DNA Research Institute

description: ARPE-19 treated with TNF for 42hour

hyb_protocol: Refer to the Affymetrix Expression Analysis Technical Manual

label: Biotin

label_protocol: IVT labeling Kit

extract_protocol: Qiagen RNeasy Mini Kit

value: ARPE-19 human retinal pigment epithelium (RPE) cell line

value: TNF

tag: time

value: 42 hour


title: alpha-ZEA-treated Cells Replicate 2

treatment_protocol: treated for three days with alpha-ZEA


title: alpha-ZEA-treated Cells Replicate 3


title: beta-ZEA-treated Cells Replicate 2


title: male 2_R572

description: no additional information

value: 23 years


title: ZAL-treated Cells Replicate 2


title: ARPE-19 42h-1 TNF

description: ARPE-19 treated with TNF for 42hour

scan_protocol: Refer to the Affymetrix Expression Analysis Technical Manual


title: ARPE-19 42h-2 TGF

description: ARPE-19 treated with TGF for 42hour

value: TGF


title: ARPE-19 42h-1 TGF

description: ARPE-19 treated with TGF for 42hour


title: ARPE-19 42h-0 TNF

description: ARPE-19 treated with TNF for 42hour


title: ARPE-19 42h-0 TGF

description: ARPE-19 treated with TGF for 42hour


title: ZEA-treated Cells Replicate 3

treatment_protocol: treated for three days with ZEA


title: E2-treated Cells Replicate 2

treatment_protocol: treated for three days with E2


title: beta-ZEA-treated Cells Replicate 1


title: ARPE-19 6h-1 TGF

description: ARPE-19 treated with TGF for 6hour

value: 6 hour


title: alpha-ZEA-treated Cells Replicate 1


title: ARPE-19 6h-1 TNF

description: ARPE-19 treated with TNF for 6hour


title: ARPE-19 6h-0 TNF

description: ARPE-19 treated with TNF for 6hour


title: ZEA-treated Cells Replicate 1


title: ARPE-19 6h-0 TGF

description: ARPE-19 treated with TGF for 6hour


title: E2-treated Cells Replicate 1


title: ARPE-19 6h-2 TNF

description: ARPE-19 treated with TNF for 6hour


title: ZEA-treated Cells Replicate 2


title: ARPE-19 6h-2 TGF

description: ARPE-19 treated with TGF for 6hour


title: liver-11weeks-BxA-152

status: Public on Mar 10 2010

city: Bar Harbor

first: Gary

last: Churchill

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: gene expression data from the F2 progeny produced by a B6 x A/J cross

hyb_protocol: Fifteen micrograms of biotin-labeled and fragmented cRNA was then hybridized onto Mouse Genome 430 2.0 GeneChip arrays (Affymetrix) for 16 hours at 45C.  Post-hybridization staining and washing were performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 laser confocal slide scanner.

data_processing:
Data was normalized with FARMS using a custom CDF mm430mmentrezgcdf.
The experimental variable measurements TG (triglycerides), HDL (high-density lipoproteins), and bodyweight were all log transformed prior to analysis to achieve symmetric distributions and to stabilize variance across the range of measured values.

source_name: 11 weeks, liver

label_protocol: In an in vitro transcription (IVT) reaction with T7 RNA polymerase, the cDNA was linearly amplified and labeled with biotinylated nucleotides (Enzo Diagnostics, Farmingdale, NY).

growth_protocol: Mice were sacrificed at 11 weeks of age. Livers were immediately collected and flash-frozen in liquid nitrogen.

extract_protocol: RNA extraction was carried out using TRIzol reagent following the manufacturer's guidelines (Invitrogen, Carlsbad, California, USA).  Samples were homogenized, using a Polytron homogenizer for one minute. RNA quality was assessed using a 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Palo Alto, CA). Following reverse transcription with an oligo(dT)-T7 primer (Affymetrix, Santa Clara, CA), double-stranded cDNA was synthesized with the superscript double-stranded cDNA synthesis custom kit (Invitrogen).

value: liver

value: 11 weeks

tag: other

value: F2 progeny produced by a B6 x A/J cross

tag: tg (triglycerides) level

value: 94 micrograms/deciliter

tag: hdl (high-density lipoproteins) level

value: 76.4 micrograms/deciliter

tag: bodyweight

value: 31.45 grams


title: liver-11weeks-BxA-148

value: 93 micrograms/deciliter

value: 74.2 micrograms/deciliter

value: 26.73 grams


title: liver-11weeks-BxA-150

value: 62 micrograms/deciliter

value: 51 micrograms/deciliter

value: 25.89 grams


title: liver-11weeks-BxA-149

value: 84 micrograms/deciliter

value: 70 micrograms/deciliter

value: 29.75 grams


title: liver-11weeks-BxA-147

value: 98 micrograms/deciliter

value: 84.7 micrograms/deciliter

value: 31.7 grams


title: liver-11weeks-BxA-249

value: liver

value: 11 weeks

value: 89 micrograms/deciliter

value: 67.9 micrograms/deciliter

value: 33.36 grams


title: liver-11weeks-BxA-140

value: F2 progeny produced by a B6 x A/J cross

value: 81 micrograms/deciliter

value: 66.7 micrograms/deciliter

value: 29.92 grams


title: liver-11weeks-BxA-312

value: 76 micrograms/deciliter

value: 67.5 micrograms/deciliter

value: 23.61 grams


title: liver-11weeks-BxA-158

value: 118 micrograms/deciliter

value: 92.7 micrograms/deciliter

value: 42.36 grams


title: liver-11weeks-BxA-159

value: 87 micrograms/deciliter

value: 73.2 micrograms/deciliter

value: 30.77 grams


title: liver-11weeks-BxA-204

value: liver

value: 11 weeks

value: 80 micrograms/deciliter

value: 68 micrograms/deciliter

value: 29.09 grams


title: liver-11weeks-BxA-141

value: F2 progeny produced by a B6 x A/J cross

value: 83 micrograms/deciliter

value: 64.8 micrograms/deciliter

value: 30.15 grams


title: liver-11weeks-BxA-154

value: 99 micrograms/deciliter

value: 81.8 micrograms/deciliter

value: 34.51 grams


title: liver-11weeks-BxA-153

value: 86 micrograms/deciliter

value: 69.7 micrograms/deciliter

value: 33.4 grams


title: liver-11weeks-BxA-157

value: 106 micrograms/deciliter

value: 90.4 micrograms/deciliter

value: 36.25 grams


title: liver-11weeks-BxA-144

value: liver

value: 11 weeks

value: 89 micrograms/deciliter

value: 71 micrograms/deciliter

value: 28.27 grams


title: liver-11weeks-BxA-136

value: F2 progeny produced by a B6 x A/J cross

value: 81.6 micrograms/deciliter

value: 28.76 grams


title: liver-11weeks-BxA-145

value: 62 micrograms/deciliter

value: 53.2 micrograms/deciliter

value: 23.11 grams


title: liver-11weeks-BxA-132

value: 75 micrograms/deciliter

value: 64 micrograms/deciliter

value: 25.31 grams


title: liver-11weeks-BxA-155

value: 97 micrograms/deciliter

value: 79.5 micrograms/deciliter

value: 33.95 grams


title: liver-11weeks-BxA-139

value: liver

value: 90 micrograms/deciliter

value: 72.1 micrograms/deciliter

value: 31.41 grams


title: liver-11weeks-BxA-130

value: 11 weeks

value: 80 micrograms/deciliter

value: 67.5 micrograms/deciliter

value: 29.86 grams


title: liver-11weeks-BxA-146

value: F2 progeny produced by a B6 x A/J cross

value: 85 micrograms/deciliter

value: 70.4 micrograms/deciliter

value: 34.97 grams


title: liver-11weeks-BxA-127

value: 91 micrograms/deciliter

value: 71.1 micrograms/deciliter

value: 25.81 grams


title: liver-11weeks-BxA-143

value: 57 micrograms/deciliter

value: 42.9 micrograms/deciliter

value: 25.47 grams


title: liver-11weeks-BxA-126

value: liver

value: 79 micrograms/deciliter

value: 68.2 micrograms/deciliter

value: 30.54 grams


title: liver-11weeks-BxA-129

value: 11 weeks

value: 86 micrograms/deciliter

value: 71.9 micrograms/deciliter

value: 28.6 grams


title: liver-11weeks-BxA-125

value: F2 progeny produced by a B6 x A/J cross

value: 99 micrograms/deciliter

value: 82.7 micrograms/deciliter

value: 32.96 grams


title: liver-11weeks-BxA-128

value: 98 micrograms/deciliter

value: 84 micrograms/deciliter

value: 34.54 grams


title: liver-11weeks-BxA-131

value: 72.8 micrograms/deciliter

value: 29.79 grams


title: liver-11weeks-BxA-116

value: liver

value: 91 micrograms/deciliter

value: 74.4 micrograms/deciliter

value: 29.43 grams


title: liver-11weeks-BxA-104

value: 11 weeks

value: 93 micrograms/deciliter

value: 78.1 micrograms/deciliter

value: 33.86 grams


title: liver-11weeks-BxA-121

value: F2 progeny produced by a B6 x A/J cross

value: 73 micrograms/deciliter

value: 59.1 micrograms/deciliter

value: 27.02 grams


title: liver-11weeks-BxA-114

value: 73.7 micrograms/deciliter

value: 29.25 grams


title: liver-11weeks-BxA-120

value: 86 micrograms/deciliter

value: 67.1 micrograms/deciliter

value: 34.08 grams


title: liver-11weeks-BxA-103

value: liver

value: 68 micrograms/deciliter

value: 56.9 micrograms/deciliter

value: 28.14 grams


title: liver-11weeks-BxA-107

value: 11 weeks

value: 78 micrograms/deciliter

value: 65.4 micrograms/deciliter

value: 34.89 grams


title: liver-11weeks-BxA-119

value: F2 progeny produced by a B6 x A/J cross

value: 77 micrograms/deciliter

value: 61.9 micrograms/deciliter

value: 29.69 grams


title: liver-11weeks-BxA-94

value: 91 micrograms/deciliter

value: 70.4 micrograms/deciliter

value: 31.37 grams


title: liver-11weeks-BxA-122

value: 66 micrograms/deciliter

value: 56.4 micrograms/deciliter

value: 27.04 grams


title: liver-11weeks-BxA-100

value: liver

value: 104 micrograms/deciliter

value: 82.4 micrograms/deciliter

value: 33.93 grams


title: liver-11weeks-BxA-108

value: 11 weeks

value: 75 micrograms/deciliter

value: 64 micrograms/deciliter

value: 30.21 grams


title: liver-11weeks-BxA-95

value: F2 progeny produced by a B6 x A/J cross

value: 48.1 micrograms/deciliter

value: 24.46 grams


title: liver-11weeks-BxA-102

value: 96 micrograms/deciliter

value: 74.8 micrograms/deciliter

value: 32.96 grams


title: liver-11weeks-BxA-123

value: 85 micrograms/deciliter

value: 72.6 micrograms/deciliter

value: 23.74 grams


title: liver-11weeks-BxA-101

value: liver

value: 72 micrograms/deciliter

value: 51.2 micrograms/deciliter

value: 26.16 grams


title: liver-11weeks-BxA-118

value: 11 weeks

value: 106 micrograms/deciliter

value: 89.7 micrograms/deciliter

value: 31.11 grams


title: liver-11weeks-BxA-92

value: F2 progeny produced by a B6 x A/J cross

value: 81 micrograms/deciliter

value: 66.3 micrograms/deciliter

value: 25.59 grams


title: liver-11weeks-BxA-87

value: 96 micrograms/deciliter

value: 77.3 micrograms/deciliter

value: 30.48 grams


title: liver-11weeks-BxA-86

value: 66 micrograms/deciliter

value: 54.4 micrograms/deciliter

value: 30.7 grams


title: liver-11weeks-BxA-84

value: liver

value: 74 micrograms/deciliter

value: 57.5 micrograms/deciliter

value: 32.41 grams


title: liver-11weeks-BxA-89

value: 11 weeks

value: 97 micrograms/deciliter

value: 76.3 micrograms/deciliter

value: 34.77 grams


title: liver-11weeks-BxA-81

value: F2 progeny produced by a B6 x A/J cross

value: 60 micrograms/deciliter

value: 49.7 micrograms/deciliter

value: 28.4 grams


title: liver-11weeks-BxA-80

value: 70 micrograms/deciliter

value: 57.1 micrograms/deciliter

value: 29.41 grams


title: liver-11weeks-BxA-79

value: 71 micrograms/deciliter

value: 58.5 micrograms/deciliter

value: 35.6 grams


title: liver-11weeks-BxA-88

value: liver

value: 93 micrograms/deciliter

value: 77 micrograms/deciliter

value: 34.31 grams


title: liver-11weeks-BxA-83

value: 11 weeks

value: NA micrograms/deciliter

value: 67.2 micrograms/deciliter

value: 36.94 grams


title: liver-11weeks-BxA-105

value: F2 progeny produced by a B6 x A/J cross

value: 82 micrograms/deciliter

value: 66.9 micrograms/deciliter

value: 32.41 grams


title: liver-11weeks-BxA-91

value: 84 micrograms/deciliter

value: 64.6 micrograms/deciliter

value: 33.94 grams


title: liver-11weeks-BxA-93

value: 98 micrograms/deciliter

value: 79.7 micrograms/deciliter

value: 33.91 grams


title: liver-11weeks-BxA-71

value: liver

value: 65.6 micrograms/deciliter

value: 33.19 grams


title: liver-11weeks-BxA-78

value: 11 weeks

value: 48 micrograms/deciliter

value: 40 micrograms/deciliter

value: 25.82 grams


title: liver-11weeks-BxA-72

value: F2 progeny produced by a B6 x A/J cross

value: 86 micrograms/deciliter

value: 64.3 micrograms/deciliter

value: 26.74 grams


title: liver-11weeks-BxA-69

value: 72 micrograms/deciliter

value: 56.2 micrograms/deciliter

value: 32.35 grams


title: liver-11weeks-BxA-75

value: 56 micrograms/deciliter

value: 41.3 micrograms/deciliter

value: 30.88 grams


title: liver-11weeks-BxA-67

value: liver

value: 68 micrograms/deciliter

value: 51.2 micrograms/deciliter

value: 29.56 grams


title: liver-11weeks-BxA-61

value: 11 weeks

value: NA micrograms/deciliter

value: 56.4 micrograms/deciliter

value: 22.58 grams


title: liver-11weeks-BxA-68

value: F2 progeny produced by a B6 x A/J cross

value: 73 micrograms/deciliter

value: 29.52 grams


title: liver-11weeks-BxA-54

value: 79 micrograms/deciliter

value: 62.2 micrograms/deciliter

value: 28.51 grams


title: liver-11weeks-BxA-77

value: 75 micrograms/deciliter

value: 58.3 micrograms/deciliter

value: 28.27 grams


title: liver-11weeks-BxA-64

value: liver

value: 100 micrograms/deciliter

value: 76.7 micrograms/deciliter

value: 32.67 grams


title: liver-11weeks-BxA-48

value: 11 weeks

value: 96 micrograms/deciliter

value: 74.5 micrograms/deciliter

value: 33.6 grams


title: liver-11weeks-BxA-44

value: F2 progeny produced by a B6 x A/J cross

value: 70 micrograms/deciliter

value: 52.1 micrograms/deciliter

value: 33.17 grams


title: liver-11weeks-BxA-66

value: 67 micrograms/deciliter

value: 51.8 micrograms/deciliter

value: 29.35 grams


title: liver-11weeks-BxA-43

value: 73.5 micrograms/deciliter

value: 32.75 grams


title: liver-11weeks-BxA-42

value: liver

value: 80 micrograms/deciliter

value: 59 micrograms/deciliter

value: 31.82 grams


title: liver-11weeks-BxA-59

value: 11 weeks

value: NA micrograms/deciliter

value: 62.7 micrograms/deciliter

value: 28.95 grams


title: liver-11weeks-BxA-38

value: F2 progeny produced by a B6 x A/J cross

value: 86 micrograms/deciliter

value: 66.4 micrograms/deciliter

value: 34.38 grams


title: liver-11weeks-BxA-50

value: 92 micrograms/deciliter

value: 71.2 micrograms/deciliter

value: 38.94 grams


title: liver-11weeks-BxA-46

value: 68.4 micrograms/deciliter

value: 29.55 grams


title: liver-11weeks-BxA-41

value: liver

value: 93 micrograms/deciliter

value: 72.2 micrograms/deciliter

value: 32.67 grams


title: liver-11weeks-BxA-40

value: 11 weeks

value: 96 micrograms/deciliter

value: 74.4 micrograms/deciliter

value: 34.71 grams


title: liver-11weeks-BxA-62

value: F2 progeny produced by a B6 x A/J cross

value: NA micrograms/deciliter

value: 65.1 micrograms/deciliter

value: 32.37 grams


title: liver-11weeks-BxA-55

value: 83 micrograms/deciliter

value: 64.3 micrograms/deciliter

value: 38.44 grams


title: liver-11weeks-BxA-57

value: 71.8 micrograms/deciliter

value: 31.4 grams


title: liver-11weeks-BxA-76

value: liver

value: 88 micrograms/deciliter

value: 66 micrograms/deciliter

value: 31.7 grams


title: liver-11weeks-BxA-60

value: 11 weeks

value: 68.2 micrograms/deciliter

value: 33.37 grams


title: liver-11weeks-BxA-35

value: 82 micrograms/deciliter

value: 65.6 micrograms/deciliter

value: 36.36 grams


title: liver-11weeks-BxA-33

value: F2 progeny produced by a B6 x A/J cross

value: 105 micrograms/deciliter

value: 82.6 micrograms/deciliter

value: 35.52 grams


title: liver-11weeks-BxA-36

value: 107 micrograms/deciliter

value: 85 micrograms/deciliter

value: 33.69 grams


title: liver-11weeks-BxA-32

value: liver

value: 76 micrograms/deciliter

value: 56.8 micrograms/deciliter

value: 31.99 grams


title: liver-11weeks-BxA-37

value: 11 weeks

value: 94 micrograms/deciliter

value: 76.1 micrograms/deciliter

value: 34.52 grams


title: liver-11weeks-BxA-34

value: 73.3 micrograms/deciliter

value: 35.83 grams


title: liver-11weeks-BxA-27

value: F2 progeny produced by a B6 x A/J cross

value: 83 micrograms/deciliter

value: 64.8 micrograms/deciliter

value: 31.86 grams


title: liver-11weeks-BxA-26

value: 91 micrograms/deciliter

value: 73.1 micrograms/deciliter

value: 30.13 grams


title: liver-11weeks-BxA-28

value: liver

value: 75 micrograms/deciliter

value: 55.5 micrograms/deciliter

value: 31.57 grams


title: liver-11weeks-BxA-19

value: 11 weeks

value: 69 micrograms/deciliter

value: 49.5 micrograms/deciliter

value: 31.04 grams


title: liver-11weeks-BxA-21

value: 104 micrograms/deciliter

value: 73.2 micrograms/deciliter

value: 34.88 grams


title: liver-11weeks-BxA-22

value: F2 progeny produced by a B6 x A/J cross

value: 88 micrograms/deciliter

value: 66.2 micrograms/deciliter

value: 34.41 grams


title: liver-11weeks-BxA-11

value: 66.7 micrograms/deciliter

value: 28.86 grams


title: liver-11weeks-BxA-16

value: liver

value: 52 micrograms/deciliter

value: 37.81 grams


title: liver-11weeks-BxA-18

value: 82 micrograms/deciliter

value: 56.6 micrograms/deciliter

value: 30.81 grams


title: liver-11weeks-BxA-25

value: 11 weeks

value: 84 micrograms/deciliter

value: 62.7 micrograms/deciliter

value: 29.92 grams


title: liver-11weeks-BxA-5

value: 101 micrograms/deciliter

value: 73.1 micrograms/deciliter

value: 40.07 grams


title: liver-11weeks-BxA-9

value: F2 progeny produced by a B6 x A/J cross

value: 100 micrograms/deciliter

value: 80.5 micrograms/deciliter

value: 38.01 grams


title: liver-11weeks-BxA-17

value: liver

value: 76 micrograms/deciliter

value: 53 micrograms/deciliter

value: 32.22 grams


title: liver-11weeks-BxA-24

value: 71 micrograms/deciliter

value: 48.2 micrograms/deciliter

value: 33.27 grams


title: liver-11weeks-BxA-12

value: 11 weeks

value: 90 micrograms/deciliter

value: 63.9 micrograms/deciliter

value: 30.64 grams


title: liver-11weeks-BxA-14

value: 82 micrograms/deciliter

value: 59.3 micrograms/deciliter

value: 29.71 grams


title: liver-11weeks-BxA-8

value: F2 progeny produced by a B6 x A/J cross

value: 106 micrograms/deciliter

value: 73.7 micrograms/deciliter

value: 33.06 grams


title: liver-11weeks-BxA-20

value: liver

value: 61 micrograms/deciliter

value: 36.4 micrograms/deciliter

value: 27.46 grams


title: liver-11weeks-BxA-10

value: 103 micrograms/deciliter

value: 66.1 micrograms/deciliter

value: 31.52 grams


title: liver-11weeks-BxA-3

value: 11 weeks

value: 74 micrograms/deciliter

value: 53.1 micrograms/deciliter

value: 34.04 grams


title: liver-11weeks-BxA-7

value: 95 micrograms/deciliter

value: 72.9 micrograms/deciliter

value: 38.83 grams


title: liver-11weeks-BxA-6

value: F2 progeny produced by a B6 x A/J cross

value: 90 micrograms/deciliter

value: 72.5 micrograms/deciliter

value: 30.12 grams


title: liver-11weeks-BxA-51

value: liver

value: 73 micrograms/deciliter

value: 52.2 micrograms/deciliter

value: 36.99 grams


title: liver-11weeks-BxA-4

value: 66.7 micrograms/deciliter

value: 29.83 grams


title: liver-11weeks-BxA-2

value: 11 weeks

value: 79 micrograms/deciliter

value: 61.5 micrograms/deciliter

value: 31.9 grams


title: liver-11weeks-BxA-1

value: 86 micrograms/deciliter

value: 62.9 micrograms/deciliter

value: 35.47 grams


title: lung_Met

status: Public on Mar 05 2010

city: Vancouver

first: Kim

middle: Marie

last: Lonergan

state: British Columbia

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

country: Canada

institute: British Columbia Cancer Research Centre

description: Biopsy material

source_name: lung

extract_protocol: MicroSAGE protocol: annealing to oligo (dT) magnetic beads

tag: Metaplastic bronchial epithelium


title: lung_Dys

description: Biopsy material

tag: Dysplastic bronchial epithelium


title: lung_SqCC-4

description: Biopsy material

tag: Non-small cell lung cancer

value: invasive squamous cell carcinoma


title: lung_SqCC-5

description: Biopsy material


title: lung_SqCC-6

description: Biopsy material


title: lung_SqCC-3

description: Biopsy material


title: lung_SqCC-2

description: Biopsy material


title: lung_CIS-3

description: Biopsy material

value: squamous cell carcinoma-in-situ


title: lung_CIS-5

description: Biopsy material


title: lung_CIS-4

description: Biopsy material


title: lung_SqCC-1

description: Biopsy material


title: HeLa cisplatin resistant cell line 1_replicate 2

city: Kwei-San

first: Ching-Kuey

middle: Chuck

last: Chao

state: Tao-Yuan

address: 259, Wen-Hwa 1 Rd

department: Biochemistry and Molecular Biology

country: Taiwan

institute: Chang-Gung University

hyb_protocol: 15.5 hrs @65 degree C

scan_protocol: Scanner=GenePix 4000B [82719] PixelSize=10 PMTVolts=690, 710 Creator=GenePix Pro 3.0.5.56 LaserPower=4.03, 4.3 RatioFormulation=W1/W2 (635 nm/532 nm)

data_processing: Raw Data were input to SMA package in R environment. A within and between slides LOWESS normalization method were used to adjust Cy5 and Cy3 signals. Ratios were calculated from adjusted Cy5 and Cy3 signals.

source_name: HeLa cisplatin resistant cell line 1

label_protocol: Genisphere 3 DNA

extract_protocol: Trizol (Invitrogen Inc.)

value: HeLa cisplatin resistant cell line 1

source_name: HeLa

value: HeLa


title: HeLa cisplatin resistant cell line 3_replicate 2

source_name: HeLa cisplatin resistant cell line 3

value: HeLa cisplatin resistant cell line 3


title: lung_CIS-1

description: Biopsy material


title: HeLa cisplatin resistant cell line 2_replicate 2

source_name: HeLa cisplatin resistant cell line 2

value: HeLa cisplatin resistant cell line 2


title: HeLa cisplatin resistant cell line 2_replicate 1


title: PR9692 metastasizing cell line, replicate 3

city: Basel

first: Robert

last: Ivanek

address: Hebelstrasse 20

department: Department of Biomedicine

institute: University of Basel

description: Gene expression data from sarcoma derived PR9692 metastatic cell line in culture

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Chicken Genome 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 Bioconductor (version 2.3) using Affymetrix default annotation and GC-RMA as normalization method.

organism: Gallus gallus

source_name: Sarcoma derived PR9692 metastatic cell line in culture

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

extract_protocol: Approximately 10 millions cultured cells were dissolved in 2 ml TRIzol reagent and total RNA was extracted according to manufacturer's protocol.


title: lung_CIS-2

description: Biopsy material

extract_protocol: MicroSAGE protocol:  annealing to oligo (dT)  magnetic beads


title: HeLa cisplatin resistant cell line 1_replicate 1


title: PR9692-E9 non-metastasizing cell line, replicate 2

description: Gene expression data from sarcoma derived PR9692-E9 non-metastatic cell line in culture

source_name: Sarcoma derived PR9692-E9 non-metastatic cell line in culture


title: PR9692-E9 non-metastasizing cell line, replicate 1

value: Sarcoma derived PR9692-E9 non-metastatic cell line


title: PR9692-E9-EGR1 metastasizing cell line, replicate 3

description: Gene expression data from sarcoma derived PR9692-E9-EGR1 metastatic cell line in culture

source_name: Sarcoma derived PR9692-E9-EGR1 metastatic cell line in culture


title: HeLa cisplatin resistant cell line 3_replicate 1


title: PR9692-E9-EGR1 metastasizing cell line, replicate 2

value: Sarcoma derived PR9692-E9-EGR1 metastatic cell line


title: PR9692-E9-EGR1 metastasizing cell line, replicate 1


title: PR9692-E9 non-metastasizing cell line, replicate 3


title: PR9692 metastasizing cell line, replicate 2

value: Sarcoma derived PR9692 metastatic cell line


title: PR9692 metastasizing cell line, replicate 1


title: Subject4_buttock full skin_no irritation_ammonium thiocyanate (matrix 2)

status: Public on Mar 03 2010

city: Odense

first: Mads

last: Thomassen

address: Soender Boulevard 9

department: Clinical Genetics (KKA)

country: Denmark

institute: Odense University Hospital

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

data_processing: dCHIP

label_protocol: For the microarray experiment, RNA from 16 buttocks full thickness skin samples and 13 epidermal samples was amplified with the MessageAmp II Enhanced kit (Applied biosystems/Ambion), following the manufacturer’s instructions for single-round amplification using 500 ng total RNA.

extract_protocol: Samples were thawed for 30 min and carefully transferred to new 2.0 mL microtubes containing one stainless steel bead (Qiagen) and 350 mL of buffer RLT (supplied with the RNeasy Micro Kit) according to the manufacturer’s instructions.   Next, the new microtubes were placed in a TissueLyser® (Qiagen) bead beater to homogenize the tissue for 2 x 2 min (epidermis) or 2 x 3 min (dermis) at 30 Hz. RNA was extracted using the RNeasy Micro Kit (Qiagen) following the manufacturer’s instructions. For dermal samples a protein digestion step (proteinase K, Qiagen) was added as recommended in the fibrous tissue protocol.

treatment_protocol: Large Finn® chambers (Ø=16 mm) containing filter paper discs saturated with 25 µL sodium lauryl sulphate (SLS, Sigma-Aldrich) 2% (aq.) or SLS 5% (aq.) were placed on the upper buttock skin in 4 healthy volunteers. After 24 h exposure the patches were removed and visual scoring was performed. Equally irritated sites with a 1+ score were selected for biopsy.

tag: tissue type

value: buttock full skin

tag: condition

value: adjacent normal skin

tag: subject

value: adult subject 4


title: Subject2_buttock full skin_no irritation_RNAlater (matrix 2)

value: adult subject 2


title: Subject3_buttock full skin_no irritation_RNAlater (matrix 2)

value: adult subject 3


title: Subject3_buttock full skin_no irritation_RNAlater (matrix 1)


title: Subject2_buttock full skin_no irritation_ammonium thiocyanate (matrix 2)


title: Subject4_buttock full skin_no irritation_RNAlater (matrix 2)


title: Subject1_buttock full skin_no irritation_RNAlater (matrix 2)

value: adult subject 1


title: Subject3_buttock full skin_no irritation_ammonium thiocyanate (matrix 2)


title: Subject4_buttock full skin_no irritation_ammonium thiocyanate (matrix 1)


title: Subject2_buttock full skin_no irritation_RNAlater (matrix 1)


title: Subject2_buttock full skin_no irritation_ammonium thiocyanate (matrix 1)


title: Subject3_buttock full skin_no irritation_ammonium thiocyanate (matrix 1)


title: Subject1_buttock full skin_no irritation_ammonium thiocyanate (matrix 2)


title: Subject4_buttock full skin_24h SLS_RNAlater (matrix 1)

source_name: buttock full skin_24h SLS_RNAlater

value: inflamed skin


title: Subject4_buttock full skin_no irritation_RNAlater (matrix 1)


title: Subject1_buttock full skin_no irritation_RNAlater (matrix 1)


title: Subject2_buttock full skin_24h SLS_RNAlater (matrix 1)


title: Subject1_buttock full skin_no irritation_ammonium thiocyanate (matrix 1)


title: MCH115150_HIV-LRN_p24_stimulated

status: Public on Mar 02 2010

city: Boston

first: Paul

last: McLaren

state: MA

address: 77 Avenue Louis Pasteur, NRB150

department: Medicine

institute: Harvard Medical School

description: Gene expression data from HIV p24 stimulated CD4+ T cells of an HIV negative non-commercial sex-worker from Nairobi, Kenya

hyb_protocol: Hybridization of microarrays was carried out for 18 hours at 42C with rotation in a hybridization oven.

scan_protocol: Arrays were exposed to phosphorimaging screens for 24 hours and screens were scanned on a BioRad Personal FX imager using Quantity One software

data_processing: Quantified data were log transformed, batch corrected (using Partek software), and normalized using a combination of RMA and an in house EMD-based method to remove remaining non-bilogical variation

label_protocol: cDNA was generated from 1ug of total RNA and labeled with 33P dCTP using Qiagen LabelStar Array kits following manufacturers instructions

growth_protocol: PBMC isolated from whole blood were cultured for 24 hours in RPMI+10%FCS, 2% pen/strep at 37C and 5% CO2

extract_protocol: Total RNA was extracted using Qiagen RNeasy mini kit plus kits following manufacturers instructions

treatment_protocol: PBMC were either left unstiulated or treated with PHA (5ug/ml) C albicans (10ug/ml) flu peptide (2ug/ml) or HIV p24 (1ug/ml). After stimulation PBMC were negatively selected for being CD4+ by magentic bead purification

tag: HIV low-risk negative

tag: stimulation

value: Hiv p24


title: MCH114277_HIV-LRN_p24_stimulated


title: Subject1_buttock full skin_24h SLS_ammonium thiocyanate (matrix 1)


title: Subject4_buttock full skin_24h SLS_ammonium thiocyanate (matrix 1)


title: Subject3_buttock full skin_24h SLS_ammonium thiocyanate (matrix 1)


title: Subject1_buttock full skin_24h SLS_RNAlater (matrix 1)


title: MCH117436_HIV-LRN_p24_stimulated


title: MCH116641_HIV-LRN_p24_stimulated


title: MCH117066_HIV-LRN_p24_stimulated


title: liver-11weeks-BxA-47

tag: tissue

value: liver

tag: age

value: 11 weeks

value: F2 progeny produced by a B6 x A/J cross

value: 111 micrograms/deciliter

value: 84.7 micrograms/deciliter

value: 28.89 grams


title: Subject3_buttock full skin_24h SLS_RNAlater (matrix 1)


title: Subject2_buttock full skin_24h SLS_ammonium thiocyanate (matrix 1)


title: MCH112499_HIV-LRN_p24_stimulated


title: MCH111757_HIV-LRN_p24_stimulated


title: MCH107058_HIV-LRN_p24_stimulated


title: MCH105452_HIV-LRN_p24_stimulated


title: MCH102749_HIV-LRN_p24_stimulated


title: ML887_HIV-R_p24_stimulated

description: Gene expression data from HIV p24 stimulated CD4+ T cells of an HIV resistant commercial sex-worker from Nairobi, Kenya

tag: HIV resistant


title: ML881_HIV-R_p24_stimulated


title: ML1997_HIV-R_p24_stimulated


title: ML1960_HIV-R_p24_stimulated


title: ML466_HIV-R_p24_stimulated


title: ML893_HIV-R_p24_stimulated


title: ML556_HIV-R_p24_stimulated


title: ML767_HIV-R_p24_stimulated


title: ML1952_HIV-R_p24_stimulated


title: ML1803_HIV-R_p24_stimulated


title: ML1796_HIV-R_p24_stimulated


title: ML1643_HIV-R_p24_stimulated


title: ML1498_HIV-R_p24_stimulated


title: ML1430_HIV-R_p24_stimulated


title: ML1482_HIV-R_p24_stimulated


title: ML1260_HIV-R_p24_stimulated


title: ML1072_HIV-R_p24_stimulated


title: MCH112499_HIV-LRN_flu_stimulated

description: Gene expression data from flu peptide stimulated CD4+ T cells of an HIV negative non-commercial sex-worker from Nairobi, Kenya

value: flu peptide


title: MCH114277_HIV-LRN_flu_stimulated


title: MCH117436_HIV-LRN_flu_stimulated


title: MCH116641_HIV-LRN_flu_stimulated


title: MCH117066_HIV-LRN_flu_stimulated


title: MCH111757_HIV-LRN_flu_stimulated


title: MCH107058_HIV-LRN_flu_stimulated


title: MCH115150_HIV-LRN_flu_stimulated


title: MCH105452_HIV-LRN_flu_stimulated


title: MCH102749_HIV-LRN_flu_stimulated


title: ML893_HIV-R_flu_stimulated

description: Gene expression data from flu peptide stimulated CD4+ T cells of an HIV resistant commercial sex-worker from Nairobi, Kenya


title: ML887_HIV-R_flu_stimulated


title: ML1803_HIV-R_flu_stimulated


title: ML1960_HIV-R_flu_stimulated


title: ML881_HIV-R_flu_stimulated


title: ML1997_HIV-R_flu_stimulated


title: ML1952_HIV-R_flu_stimulated


title: ML767_HIV-R_flu_stimulated


title: ML1796_HIV-R_flu_stimulated


title: ML1643_HIV-R_flu_stimulated


title: ML1498_HIV-R_flu_stimulated


title: ML556_HIV-R_flu_stimulated


title: ML1430_HIV-R_flu_stimulated


title: MCH115150_HIV-LRN_C_albicans_stimulated

description: Gene expression data from C albicans stimulated CD4+ T cells of an HIV negative non-commercial sex-worker from Nairobi, Kenya

value: C albicans


title: ML466_HIV-R_flu_stimulated


title: ML1482_HIV-R_flu_stimulated


title: ML1072_HIV-R_flu_stimulated


title: MCH112499_HIV-LRN_C_albicans_stimulated


title: MCH117436_HIV-LRN_C_albicans_stimulated


title: MCH116641_HIV-LRN_C_albicans_stimulated


title: MCH117066_HIV-LRN_C_albicans_stimulated


title: MCH114277_HIV-LRN_C_albicans_stimulated


title: ML1260_HIV-R_flu_stimulated


title: MCH111757_HIV-LRN_C_albicans_stimulated


title: ML893_HIV-R_C_albicans_stimulated

description: Gene expression data from C albicans stimulated CD4+ T cells of an HIV resistant commercial sex-worker from Nairobi, Kenya


title: ML887_HIV-R_C_albicans_stimulated


title: MCH102749_HIV-LRN_C_albicans_stimulated


title: MCH105452_HIV-LRN_C_albicans_stimulated


title: MCH107058_HIV-LRN_C_albicans_stimulated


title: ML881_HIV-R_C_albicans_stimulated


title: ML556_HIV-R_C_albicans_stimulated


title: ML767_HIV-R_C_albicans_stimulated


title: ML1997_HIV-R_C_albicans_stimulated


title: ML466_HIV-R_C_albicans_stimulated


title: ML1796_HIV-R_C_albicans_stimulated


title: ML1960_HIV-R_C_albicans_stimulated


title: ML1803_HIV-R_C_albicans_stimulated


title: ML1952_HIV-R_C_albicans_stimulated


title: ML1643_HIV-R_C_albicans_stimulated


title: ML1482_HIV-R_C_albicans_stimulated


title: ML1498_HIV-R_C_albicans_stimulated


title: ML1430_HIV-R_C_albicans_stimulated


title: MCH111757_HIV-LRN_PHA_stimulated

description: Gene expression data from PHA stimulated CD4+ T cells of an HIV negative non-commercial sex-worker from Nairobi, Kenya

value: PHA


title: MCH112499_HIV-LRN_PHA_stimulated


title: MCH114277_HIV-LRN_PHA_stimulated


title: MCH116641_HIV-LRN_PHA_stimulated


title: MCH117066_HIV-LRN_PHA_stimulated


title: MCH117436_HIV-LRN_PHA_stimulated


title: ML893_HIV-R_PHA_stimulated

description: Gene expression data from PHA stimulated CD4+ T cells of an HIV resistant commercial sex-worker from Nairobi, Kenya


title: MCH107058_HIV-LRN_PHA_stimulated


title: ML466_HIV-R_PHA_stimulated


title: ML887_HIV-R_PHA_stimulated


title: ML556_HIV-R_PHA_stimulated


title: MCH105452_HIV-LRN_PHA_stimulated


title: ML767_HIV-R_PHA_stimulated


title: ML881_HIV-R_PHA_stimulated


title: MCH102749_HIV-LRN_PHA_stimulated


title: ML1260_HIV-R_C_albicans_stimulated


title: ML1072_HIV-R_C_albicans_stimulated


title: ML1997_HIV-R_PHA_stimulated


title: MCH115150_HIV-LRN_PHA_stimulated


title: ML1960_HIV-R_PHA_stimulated


title: ML1803_HIV-R_PHA_stimulated


title: ML1796_HIV-R_PHA_stimulated


title: ML1498_HIV-R_PHA_stimulated


title: ML1643_HIV-R_PHA_stimulated


title: MCH117436_HIV-LRN_media_alone

description: Gene expression data from unstimulated CD4+ T cells of an HIV negative non-commercial sex-worker from Nairobi, Kenya

value: media


title: ML1430_HIV-R_PHA_stimulated


title: ML1482_HIV-R_PHA_stimulated


title: ML1260_HIV-R_PHA_stimulated


title: ML1072_HIV-R_PHA_stimulated


title: ML1952_HIV-R_PHA_stimulated


title: MCH117066_HIV-LRN_media_alone


title: MCH115150_HIV-LRN_media_alone


title: MCH107058_HIV-LRN_media_alone


title: MCH116641_HIV-LRN_media_alone


title: MCH112499_HIV-LRN_media_alone


title: MCH114277_HIV-LRN_media_alone


title: ML1997_HIV-R_media_alone

description: Gene expression data from unstimulated CD4+ T cells of an HIV resistant commercial sex-worker from Nairobi, Kenya


title: ML1960_HIV-R_media_alone


title: ML893_HIV-R_media_alone


title: MCH111757_HIV-LRN_media_alone


title: ML466_HIV-R_media_alone


title: MCH105452_HIV-LRN_media_alone


title: ML887_HIV-R_media_alone


title: ML1796_HIV-R_media_alone


title: ML556_HIV-R_media_alone


title: ML767_HIV-R_media_alone


title: ML881_HIV-R_media_alone


title: MCH102749_HIV-LRN_media_alone


title: ML1803_HIV-R_media_alone


title: ML1643_HIV-R_media_alone


title: ML1482_HIV-R_media_alone


title: ML1498_HIV-R_media_alone


title: ML1952_HIV-R_media_alone


title: ML1072_HIV-R_media_alone


title: ML1260_HIV-R_media_alone


title: ML1430_HIV-R_media_alone


title: CD44-/CD24+ cells rep 4

status: Public on Mar 01 2010

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

description: CD44-/CD24+ cells rep 4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C onto Human HGU133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanned using Affymetrix GeneChip® Scanner 3000 7G

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 1000.

source_name: immortalized breast epithelial cell line

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix standard single cycle 3' IVT protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were maintained in DMEM/F12 with 5% horse serum, 10 microgram/ml Insulin, 20 ng/ml epidermal growth factor, 100 ng/ml cholera toxin, 0.5 microgram/ml hydrocortisone.

extract_protocol: Qiagen Rneasy

treatment_protocol: Cells were stained with CD44-FITC and CD24-PE antibodies and CD44+/CD24- and CD44-/CD24+ cells were collected by flow cytometry sorting. Sorted cells were plated and grown for 4 days

value: Breast epithelial immortalized cell line

tag: cell surface markers

value: CD44 negative, CD24 positive


title: CD44-/CD24+ cells rep 2

description: CD44-/CD24+ cells rep 2


title: CD44-/CD24+ cells rep 1

description: CD44-/CD24+ cells rep 1


title: CD44+/CD24- cells rep 2

description: CD44+/CD24- cells rep 2

value: CD44 positive, CD24 negative


title: gln3deletion_3AT_rep#4

first: Ron

last: Wek

address: 635 Barnhill Dr. MS4065

department: Biochemistry & Molecular Biology

description: Gene expression data from yeast.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on HGU133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with Affymetrix Gene Chip Operating Software (GCOS) using the MAS 5.0 algorithm using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

organism: Saccharomyces cerevisiae

source_name: gln3 deletion, 3AT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix, 2004).

growth_protocol: Cells were cultured in synthetic medium (SD) containing 2% dextrose and 0.5% ammonium sulfate and supplemented with all amino acids except histidine (SC).

extract_protocol: Total RNA was purified using the hot phenol method.

treatment_protocol: Microarray analysis was carried out using RNA prepared from cells treated for 1 hour with 10 mM 3-amino-1,2,4-triazole (3-AT), 200 nM rapamycin, or no stress, as indicated.

tag: treatment

tag: strain

tag: genotype

value: gln3 deletion


title: CD44+/CD24- cells rep 4

description: CD44+/CD24- cells rep 4


title: WT rice root vs. GS1;1 mutant rice root

city: Sendai

first: Tomoyuki

last: Yamaya

address: 1-1Tsutsumidori-Amamiyamachi, Aoba-ku

department: Gladuate School of Agricultural Science

institute: Tohoku University

description: Comparison of gene expression between a GS1;1 mutant and wild-type plants in root at the 18-day-old.

hyb_protocol: hybridization_Kit: in situ hybridization plus hybridization_Manufacturer: Agilent Technologies hybridization_Manual: Agilent Technologies

scan_protocol: Scanner: Agilent DNA microarray Scaner (G2565AA) Manufacturer: Agilent Technologies Software: Scanner Control software Manual: Agilent Technologies

data_processing:
Software: Feature Extraction Software Version A.7.5.1
Manufacturer: Agilent Technologies
Manual: Agilent Technologies

organism: Oryza sativa

source_name: WT rice root

label_protocol: The total RNA extracted (750 ng) from root was labeled with Cy-3 using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent, USA).

growth_protocol:
growth: hydroponic culture
growth enviroment: greenhouse
growth substrates: The germinated seedlings were grown hydroponically in one-fourth concentration of the hydroponic culture solution in the presence of 1.0 mM NH4Cl as nitrogen source. The culture solution was replaced as new one every morning at 10:00 am.

extract_protocol: Total RNA was isolated from root using the RNeasy plant mini kit (Qiagen). RNA profile and integrity of RNA was checked by Agilent’s Bioanalyzer.

tag: cultivar

value: Nipponbare

value: 18 days after sowing

value: root

source_name: GS1;1 mutant rice root

label_protocol: The total RNA extracted (750 ng) from root was labeled with Cy-5 using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent, USA).

value: Nipponbare GS1;1 knock out mutant

tag: mutant line

value: Tos17 insertion mutant NC2373


title: CD44-/CD24+ cells rep 3

description: CD44-/CD24+ cells rep 3


title: gcn4gln3deletion_3AT_rep#4

description: Gene expression data from yeast.

source_name: gcn4 gln3 deletion, 3AT

value: gcn4 gln3 deletion


title: gcn4gln3deletion_untreated_rep#4

description: Gene expression data from yeast.

source_name: gcn4 gln3 deletion, untreated

value: untreated


title: gcn2gln3deletion_3AT_rep#4

description: Gene expression data from yeast.

source_name: gcn2 gln3 deletion, 3AT

value: gcn2 gln3 deletion


title: gln3deletion_Rap_rep#4

description: Gene expression data from yeast.

source_name: gln3 deletion, Rap

value: Rapamycin


title: gcn2gln3deletion_untreated_rep#4

description: Gene expression data from yeast.

source_name: gcn2 gln3 deletion, untreated


title: CD44+/CD24- cells rep 1

description: CD44+/CD24- cells rep 1


title: gcn4gln3deletion_Rap_rep#4

description: Gene expression data from yeast.

source_name: gcn4 gln3 deletion, Rap


title: WT rice leaf blade vs. GS1;1 mutant rice leaf blade, dye-swap

description: Comparison of gene expression between a GS1;1 mutant and wild-type plants in leaf blade at the 18-day-old.

source_name: GS1;1 mutant rice leaf blade

label_protocol: The total RNA extracted (750 ng) from leaf blade was labeled with Cy-3 using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent, USA).

extract_protocol: Total RNA was isolated from leaf blade using the RNeasy plant mini kit (Qiagen). RNA profile and integrity of RNA was checked by Agilent’s Bioanalyzer.

value: 3rd leaf blade

source_name: WT rice leaf blade

label_protocol: The total RNA extracted (750 ng) from leaf blade was labeled with Cy-5 using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent, USA).


title: gcn2gln3deletion_Rap_rep#4

description: Gene expression data from yeast.

source_name: gcn2 gln3 deletion, Rap


title: WT rice leaf sheath vs. GS1;1 mutant rice leaf sheath

description: Comparison of gene expression between a GS1;1 mutant and wild-type plants in leaf sheath at the 18-day-old.

source_name: WT rice leaf sheath

label_protocol: The total RNA extracted (750 ng) from leaf sheath was labeled with Cy-3 using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent, USA).

extract_protocol: Total RNA was isolated from leaf sheath using the RNeasy plant mini kit (Qiagen). RNA profile and integrity of RNA was checked by Agilent’s Bioanalyzer.

value: 3rd leaf sheath

source_name: GS1;1 mutant rice leaf sheath

label_protocol: The total RNA extracted (750 ng) from leaf sheath was labeled with Cy-5 using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent, USA).


title: CD44+/CD24- cells rep 3

description: CD44+/CD24- cells rep 3


title: WT rice leaf sheath vs. GS1;1 mutant rice leaf sheath, dye-swap


title: gcn4deletion_Rap_rep#4

description: Gene expression data from yeast.

source_name: gcn4 deletion, Rap

value: gcn4 deletion


title: gln3deletion_untreated_rep#4

description: Gene expression data from yeast.

source_name: gln3 deletion, untreated


title: WT rice root vs. GS1;1 mutant rice root, dye-swap


title: WT rice leaf blade vs. GS1;1 mutant rice leaf blade


title: wild-type_Rap_rep#4

description: Gene expression data from yeast.

source_name: wild-type, Rap

value: wild-type


title: gcn2deletion_untreated_rep#4

description: Gene expression data from yeast.

source_name: gcn2 deletion, untreated

value: gcn2 deletion


title: gcn2deletion_3AT_rep#4

description: Gene expression data from yeast.

source_name: gcn2 deletion, 3AT


title: wild-type_3AT_rep#4

description: Gene expression data from yeast.

source_name: wild-type, 3AT


title: gln3deletion_3AT_rep#3

description: Gene expression data from yeast.

source_name: gln3 deletion, 3AT


title: gcn2deletion_Rap_rep#4

description: Gene expression data from yeast.

source_name: gcn2 deletion, Rap


title: gcn2gln3deletion_untreated_rep#3

description: Gene expression data from yeast.


title: gcn2gln3deletion_Rap_rep#3

description: Gene expression data from yeast.


title: gcn4deletion_untreated_rep#4

description: Gene expression data from yeast.

source_name: gcn4 deletion, untreated


title: gcn4gln3deletion_Rap_rep#3

description: Gene expression data from yeast.


title: gln3deletion_untreated_rep#3

description: Gene expression data from yeast.


title: wild-type_untreated_rep#4

description: Gene expression data from yeast.

source_name: wild-type, untreated


title: gcn4gln3deletion_3AT_rep#3

description: Gene expression data from yeast.

source_name: gcn4 gln3 deletion, 3AT


title: wild-type_Rap_rep#3

description: Gene expression data from yeast.


title: gcn2gln3deletion_3AT_rep#3

description: Gene expression data from yeast.

source_name: gcn2 gln3 deletion, 3AT


title: gcn2deletion_untreated_rep#3

description: Gene expression data from yeast.


title: gcn4gln3deletion_untreated_rep#3

description: Gene expression data from yeast.

source_name: gcn4 gln3 deletion, untreated


title: wild-type_3AT_rep#3

description: Gene expression data from yeast.


title: gcn4deletion_untreated_rep#3

description: Gene expression data from yeast.


title: gcn2deletion_3AT_rep#3

description: Gene expression data from yeast.


title: gcn4gln3deletion_Rap_rep#2

description: Gene expression data from yeast.

source_name: gcn4 gln3 deletion, Rap


title: gcn4gln3deletion_3AT_rep#2

description: Gene expression data from yeast.


title: gcn2deletion_Rap_rep#3

description: Gene expression data from yeast.


title: gln3deletion_Rap_rep#2

description: Gene expression data from yeast.

source_name: gln3 deletion, Rap


title: gcn2gln3deletion_Rap_rep#2

description: Gene expression data from yeast.

source_name: gcn2 gln3 deletion, Rap


title: gln3deletion_Rap_rep#3

description: Gene expression data from yeast.


title: gcn2gln3deletion_3AT_rep#2

description: Gene expression data from yeast.


title: wild-type_untreated_rep#3

description: Gene expression data from yeast.


title: gcn2deletion_Rap_rep#2

description: Gene expression data from yeast.


title: gcn4deletion_untreated_rep#2

description: Gene expression data from yeast.


title: gcn2gln3deletion_untreated_rep#2

description: Gene expression data from yeast.

source_name: gcn2 gln3 deletion, untreated


title: gcn4deletion_3AT_rep#2

description: Gene expression data from yeast.

source_name: gcn4 deletion, 3AT


title: gcn2deletion_3AT_rep#2

description: Gene expression data from yeast.


title: gcn4gln3deletion_Rap_rep#1

description: Gene expression data from yeast.


title: wild-type_untreated_rep#2

description: Gene expression data from yeast.


title: gcn4gln3deletion_untreated_rep#2

description: Gene expression data from yeast.


title: gcn4gln3deletion_untreated_rep#1

description: Gene expression data from yeast.


title: gln3deletion_untreated_rep#2

description: Gene expression data from yeast.

source_name: gln3 deletion, untreated


title: wild-type_3AT_rep#2

description: Gene expression data from yeast.


title: gcn4deletion_Rap_rep#2

description: Gene expression data from yeast.

source_name: gcn4 deletion, Rap


title: wild-type_Rap_rep#2

description: Gene expression data from yeast.

source_name: wild-type, Rap


title: gln3deletion_Rap_rep#1

description: Gene expression data from yeast.


title: gcn4gln3deletion_3AT_rep#1

description: Gene expression data from yeast.


title: gcn2gln3deletion_Rap_rep#1

description: Gene expression data from yeast.


title: gln3deletion_3AT_rep#1

description: Gene expression data from yeast.


title: gcn2deletion_untreated_rep#2

description: Gene expression data from yeast.

source_name: gcn2 deletion, untreated


title: gcn2gln3deletion_3AT_rep#1

description: Gene expression data from yeast.


title: gcn2gln3deletion_untreated_rep#1

description: Gene expression data from yeast.


title: gln3deletion_untreated_rep#1

description: Gene expression data from yeast.


title: gcn2deletion_untreated_rep#1

description: Gene expression data from yeast.


title: gcn4deletion_Rap_rep#1

description: Gene expression data from yeast.