title: Spleen_infected_7weeks_rep2

city: Herston

first: Melissa

middle: Louise

last: Burke

state: QLD

address: 300 Herston Road

department: Division of Infectious Diseases and Immunology

institute: Queensland Institute of Medical Research

description: Gene expression in the spleen of C57BL/6 mice 7 weeks post infection with Schistosoma japonicum

hyb_protocol: cRNA was hybridised to Illumina mouse-6 v1.1 expression beadchips according to the manufacturers instructions

scan_protocol: Microarrays were scanned using a Beadstation 500 at Green factor level 2

data_processing: Data was analysed using BeadStudio and Genespring GX; Values reported were derived using Illumina BeadStudio v3 and represent relative signal intensity normalized to background, Genespring GX was used to normalise each chip to the 50th percentile and each gene to the median and uninfected controls, measurements less than 0.01 were set to 0.01

source_name: Spleen homogenate, infected, 7 weeks

label_protocol: cRNA was synthesised from 250ng of pooled total RNA with an Illumina Total Prep RNA Amplification Kit (Ambion Inc., USA) according to the manufacturers instructions

extract_protocol: Total RNA was extracted from spleen tissue by phase separation with Trizol (Invitrogen, USA) and column chromatography using an Rneasy Mini kit (Qiagen Inc, USA), RNA quantity was measured using a Nanodrop (Nanodrop Technologies, USA) and quality was assessed using an Agilent Bioanalyzer Nanochip (Agilent Technologies, USA)

treatment_protocol: Mice were euthanized and spleen tissue was collected and stored in RNAlater for microarray analysis

value: Female

value: 6 weeks

value: Spleen

tag: infection/agent

value: Schistosoma japonicum

tag: time point

value: 7 weeks post infection 20 cercariae


title: Colon_PostNatalDay3_rep1

status: Public on Dec 18 2009

type: RNA

city: Lausanne

first: Peter

middle: I

last: Duncan

address: Vers-chez-les-Blanc

department: Nutrition & Health

country: Switzerland

institute: Nestlé Research Center

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Quality control of the data was performed on all samples with a Pearson correlation matrix and a Principal Component Analysis. The data were normalised using quantile normalisation with IlluminaGUI

molecule: total RNA

organism: Rattus norvegicus

source_name: colon, day 3

label_protocol: Biotinylated cRNA was synthesized, labelled and purified according to the Illumina TotalPrep RNA amplification protocol.

extract_protocol: Total RNA was extracted and purified with the RNAdvance tissue kit (Agencourt) extraction. RNA was quantified with the RiboGreen RNA Quantification Kit (Molecular Probes) and monitored for quality on an Agilent 2100 Bioanalyser.

treatment_protocol: tissue was snap frozen in liquid nitrogen and stored at -80°C.

tag: strain

value: Sprague Dawley

tag: age

value: postnatal day 3

tag: tissue

value: colon


title: Colon_PostNatalDay2_rep5

description: replicate 5

source_name: colon, day 2

value: postnatal day 2


title: Spleen_infected_7weeks_rep1

country: Australia

organism: Mus musculus

tag: gender


title: Spleen_infected_6weeks_rep2

description: Gene expression in the spleen of C57BL/6 mice 6 weeks post infection with Schistosoma japonicum

source_name: Spleen homogenate, infected, 6 weeks

value: 6 weeks post infection 20 cercariae


title: Spleen_infected_6weeks_rep1


title: Colon_PostNatalDay5_rep4

description: replicate 4

source_name: colon, day 5

value: postnatal day 5


title: Spleen_infected_4weeks_rep2

description: Gene expression in the spleen of C57BL/6 mice 4 weeks post infection with Schistosoma japonicum

source_name: Spleen homogenate, infected, 4 weeks

value: 4 weeks post infection 20 cercariae


title: Colon_PostNatalDay2_rep3

description: replicate 3


title: Colon_PostNatalDay2_rep2

description: replicate 2


title: Spleen_uninfected_control_rep1

description: Gene expression in the spleen of normal C57BL/6 mice

source_name: Spleen homogenate, uninfected


title: Colon_PostNatalDay1_rep5

description: replicate 5

source_name: colon, day 1

value: postnatal day 1


title: Spleen_infected_4weeks_rep1


title: Spleen_uninfected_control_rep2


title: Colon_PostNatalDay1_rep3

description: replicate 3


title: Colon_PostNatalDay2_rep1

description: replicate 1


title: Colon_PostNatalDay1_rep4

description: replicate 4


title: Colon_PostNatalDay2_rep4

description: replicate 4


title: Colon_PostNatalDay3_rep2

description: replicate 2


title: Colon_Embryo_Day21_rep5

description: replicate 5

source_name: embryo, day 21, colon

value: embryo, day 21


title: Colon_PostNatalDay1_rep2

description: replicate 2


title: Colon_PostNatalDay1_rep6

description: replicate 6


title: Colon_Embryo_Day21_rep2

description: replicate 2


title: Colon_Embryo_Day21_rep4

description: replicate 4


title: Ponkan fruit under cold storage, 30-day

city: Wuhan

first: An

middle: dan

last: Zhu

state: Hubei

address: Shizishan street NO.1

department: College of Horticulture and Forestry Science

country: China

institute: Huazhong agricultural university

description: Gene expression data from postharvest ponkan pulp under cold storage at 30-day.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on GeneChip Citrus Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: The data were first analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default parameters and RMA was used to pre-process, normalize raw data, and calculate expression values.

label: biotin

organism: Citrus reticulata

source_name: Ponkan pulp at 30-day under cold storage

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

growth_protocol: Postharvest ponkan fruits were stored at 4ºC under controlled humidity.

extract_protocol: About 5 g of frozen pulp was grinded into fine powder with liquid nitrogen for RNA extraction. RNA was extracted as described by Tao et al. (Nengguo Tao, 2004).

treatment_protocol: All fruits were uniform in size and free of any peel defect. After washing and air-drying, fruits were stored at 4ºC.

value: pulp

tag: treatment

value: cold storage

tag: time

value: 30 days


title: Colon_PostNatalDay1_rep1

description: replicate 1


title: Ponkan fruit under cold storage, 90-day

description: Gene expression data from postharvest ponkan pulp under cold storage at 90-day.

source_name: Ponkan pulp at 90-day under cold storage

value: 90 days


title: Ponkan fruit under cold storage, 0-day

description: Gene expression data from postharvest ponkan pulp under cold storage at 0-day (control).

source_name: Ponkan pulp at 0-day

value: 0 days


title: Colon_Embryo_Day21_rep6

description: replicate 6


title: Ponkan fruit under cold storage, 60-day

description: Gene expression data from postharvest ponkan pulp under cold storage at 60-day.

source_name: Ponkan pulp at 60-day under cold storage

value: 60 days


title: WT42 vs DrsbK42

status: Public on Dec 17 2009

city: Wageningen

first: Mark

middle: de

last: Been

address: Bomenweg 2

department: Agrotechnology and Food Sciences Group

country: Netherlands

institute: Wageningen UR

description: No extra description.

hyb_protocol: The target was denatured by boiling for 1 min and immediate cooling on ice prior to hybridization. A total of 300ng of both samples was mixed and applied with the Agilent hybridization buffer to the microarray, according to the Agilent manual. Hybridization was performed at 60 °C. The slide was washed according to the Agilent microarray wash protocol.

scan_protocol: Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2565BA using the extended dynamic range scan mode, according to the Agilent protocol.

data_processing: Lowess-normalization, performed with Agilent Feature Extract software.

organism: Bacillus cereus ATCC 14579

source_name: WT 42 degrees 10 min

label_protocol: Complementary DNA was synthesized and labeled using 15 μg of total RNA, and the CyScribe Post-Labeling kit (Amersham Biosciences Europe GmbH) according to the supplier's instructions.

extract_protocol: RNA was extracted as described by Van Schaik et al., 2007

tag: B. cereus ATCC 14579 cells were grown to mid-exponential growth phase (OD600 = 0.5-0.6) (BHI, 30 degrees Celcius, 200 rpm) and then exposed to a 42 degrees mild heat shock for 10 min.

source_name: DrsbK 42 degrees 10 min

tag: B. cereus FM1404 (delta-bc1008) cells were grown to mid-exponential growth phase (OD600 = 0.5-0.6) (BHI, 30 degrees Celcius, 200 rpm) and then exposed to a 42 degrees mild heat shock for 10 min.


title: Colon_Embryo_Day21_rep3

description: replicate 3


title: DrsbK42 vs WT42

description: No extra description.

source_name: DrsbK 42 degrees 10 min (ii)

source_name: WT 42 degrees 10 min (ii)


title: WT30 vs WT42

description: No extra description.

source_name: WT 30 degrees (ii)

tag: B. cereus ATCC 14579 cells were grown to mid-exponential growth phase (OD600 = 0.5-0.6) (BHI, 30 degrees Celcius, 200 rpm).


title: 15(S)-HETE + LPS, biological rep3, DWW32

city: Nashville

first: David

middle: W

last: Wright

state: TN

address: SC Stevenson Center 7, Station B 351822

department: Chemistry

country: USA

institute: Vanderbilt University

description: 15S-HETE, biological replicate 3

hyb_protocol: All hybridization reagents, hybridization controls, wash reagents, and chemiluminescent reagents were provided in the ABI CL Detection Kit, part#4342142, and the manufacturer’s protocol was followed.  Briefly, the arrays were equilibrated to room temperature and then pre-hybridized with a 1ml volume for 60’ with agitation (100RPM) at 55C per manufacturer’s protocol.  During the pre-hybridization, the DIG-labelled targets were fragmented and then stored on ice until the pre-hyb was completed.  Once pre-hyb was completed the targets were mixed with the appropriate reagents, including Hybridization controls, and the 0.5ml target was added to the pre-hybridization through the port on the array chamber.  The arrays were immediately returned to the 55C Hybridization oven and agitated exactly 16 hours at 100RPM.  The arrays were then washed and incubated with Anti-Dig-APAntibody for 20 minutes.  Following antibody washes, the arrays were incubated with Chemiluminescence Enhancing Solution, washed a final time and then stored in the last wash buffer at room temperature. Substrate for the chemiluminescence reaction was added to each array individually and then the array was immediately imaged on the 1700 Chemiluminescent Analyzer.

scan_protocol: Following addition of the chemiluminescence reaction substrate, each array was immediately imaged on the 1700 Chemiluminescent Analyzer. Each imaging was completed in approximately 15 minutes and the images were assessed for QC/QA and a primary analysis was completed by the AB1700 Expression Array System Software (v 1.1.1).

data_processing: Signal intensities across microarrays were quantile normalized

label: Digoxigenin

label_protocol: All RNA Preps were run on an Agilent 2100 Bioanalyzer to assess RNA integrity. Those samples meeting minimum requirements of RIN value of 7.0 and greater were used to generate targets for hybridization to ABI arrays. One (1) ug of Total RNA (30ng mRNA) was used to generate First Strand cDNA using the NanoAmp RT-IVT labeling kit according to manufacturer’s protocol (ABI, Cat#4365715).  Following first strand synthesis, second strand synthesis was completed.  The resulting cDNA was then purified using an ABI kit provided column and the entire reaction was used in an IVT reaction to generate DIG labeled cRNA.  The cRNA was then purified using a kit provided column and assessed for quality on an Agilent Bioanalyzer.  All reactions meeting ABI criteria in terms of quantity and size of target produced were fragmented and then hybridized to the appropriate array for 16 hours with agitation at 55C.

growth_protocol: Cells were cultured under standard incubation conditions (37 ºC, 5% CO2) and grown in RPMI supplemented with 5% FBS and 1μg/mL P/S

extract_protocol: Cells were harvested at 24 h using Versagene RNA purification and DNase treatment kits. Six wells of a 6-well plate were pooled for each sample.

treatment_protocol: Samples were treated with 40 uM 15(S)-HETE. Immediately following treatment, lipopolysaccharide (LPS) was added at a final concentration of 1 μg/mL

tag: cell line


title: 15(S)-HETE + LPS, biological rep2, DWW31

description: 15S-HETE, biological replicate 2


title: 15(S)-HETE + LPS, biological rep1, DWW30

description: 15S-HETE, biological replicate 1


title: Brain_PostNatalDay3_rep5

description: replicate 5

source_name: brain, right hemisphere, day 3

value: brain, right hemisphere


title: control 23

type: genomic

city: Heidelberg

first: Rongxi

last: Yang

address: Im Neuenheimer Feld 580

country: Germany

institute: German Cancer Research Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data analysis and normalization were done using the standard analysing algorithms implemented in the methylation analysis module of the Illumina beadstudio software.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

label_protocol: The EpiTect Bisulfite kit (Qiagen) was applied for bisulfite conversion of all DNA samples according to the manufacturer’s recommendations. For each conversion, 800 ng of genomic DNA was used. Bisulfite-converted genomic DNA was vacuum-dried and resuspended in 10 ul H2O for the subsequent methylation array experiments.

extract_protocol: Genomic DNA was prepared by the Qiagen DNA Blood Mini Kit from peripheral blood cells of patient 1 (d 0 and month 27) and 25 healthy controls including 12 males and 13 females. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: control/case

value: control

value: Female


title: Patient 1 (d 0)

value: male


title: control 21

description: Christoph


title: Patient 1 (month 27)


title: control 25


title: control 24


title: control 17


title: control 18


title: control 19


title: control 20


title: control 14


title: control 16


title: control 22

description: Phililip


title: Sample 1 GPL 001

city: Chongqing

first: yi

last: qing

state: Chongqing

address: No.10 Changjiangzhi Rd

department: Daping Hospital and Research Institute of Surgery

institute: Third Military Medical University

description: GEArray Q Series Human DNA Damage Signaling Pathway gene array kit was designed to profile the expression of 96 key genes involved in DNA damage signaling pathways. The genes featured are those associated with the ATR/ATM signaling network and transcriptional targets of DNA damage response. These DNA damage-signaling pathways can be categorized into three functional groups: cell cycle arrest, apoptosis, and genome stability & repair pathways. Through a simple side-by-side hybridization, using your RNA samples and the arrays and reagents provided in the kit, you can simultaneously determine the expression profile of these 96 genes.

hyb_protocol: Pre-wet the array membrane were prehybridized for 2 h at 60C with 2 ml of pre-warmed GEAhyb Hybridization Solution and vortex the tube briefly. Then add 4 to 20 µg of biotin-labeled cRNA target prepared using the TrueLabeling-AMP kit to 0.75 ml of pre-warmed GEAhyb Hybridization Solution. Hybridize overnight at 60 °C with continuous agitation at 5 to 10 rpm.

scan_protocol: After the CDP-Star incubation, the GEArray is now ready for image acquisition. The chemiluminescent array image can be captured using X-ray film and a flatbed desktop scanner. We recommend starting with an initial exposure of 1-2 min on X-ray film. Adjust the exposure time after and based on the initial recording. We recommend collecting the chemiluminescent signal as soon as possible. However, The CDP-Star® substrate reaches peak light emission between 2-4 hr. Thus, there is ample time to collect several images with various exposure settings.

data_processing:
No matter which medium you choose to capture the image, save all images as electronic files in grayscale (8 or 16 bit) and preferably in TIFF format or alternatively in JPEG format. If using X-ray film, be sure to use the software for your flatbed desktop scanner to convert the image of the film into this format. Use the web-based completely integrated GEArray Expression Analysis Suite to complete your data analysis. Refer to the software’s User Guide for more information and further instructions.
The original data subtracts the background data, and divides the data of housekeeper gene, so we can obtain the normalized data. This is the normalization algorithm.

source_name: HeLa cell

label_protocol: cDNA synthesize and linear amplification of RNA & cRNA synthesize with TrueLabeling-AMP™ Linear RNA Amplification Kit. cRNA purificate with SuperArray ArrayGrade cRNA Cleanup Kit (Catalog Number: GA-012).

extract_protocol: Lyse cells in TRIZOL Reagent by repetitive pipetting. Use 1 ml of the reagent per 5-10 × 106 of cells.RNA extraction with TRIZOL.

value: HeLa


title: control 15


title: Sample 3 GPL 003

source_name: HeLaXR cell

value: subline HeLaXR


title: control 13


title: control 12


title: Sample 2 GPL 002

source_name: HeLaNR cell

value: subline HeLaNR


title: control 11


title: control 10


title: control 8


title: control 6


title: control 7


title: control 5


title: control 2


title: control 3


title: control 1


title: TKO-2-crypts

city: Columbus

first: Gustavo

last: Leone

state: OH

address: 640 west 12th avenue

department: 840A Biomedical Research Tower

institute: The Ohio State University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Agilent GeneArray 3000 with 7G upgrade.

data_processing: BRB-array tools developed by Dr. Richard Simon and Amy Peng Lam of the National Cancer Institute

source_name: crypts from E2f1-/-;E2f2-/-;E2f3-/- small intestines

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

growth_protocol: Mice were maintained with normal diet in the mouse facility.

extract_protocol: Trizol (invitrogen) extraction of total RNA

treatment_protocol: Small intestines were harvested 7 days after mice were injected intraperitoneally with beta-napthoflavone.

value: small intestines

value: 2 month old


title: TKO-3-crypts


title: TKO-2-villi

source_name: villi from E2f1-/-;E2f2-/-;E2f3-/- small intestines


title: Rb-3-villi

source_name: villi from Rb-/- small intestines


title: QKO-2-villi

source_name: villi from E2f1-/-;E2f2-/-;E2f3-/-;Rb-/- small intestines


title: TKO-1-crypts


title: QKO-1-villi


title: QKO-3-crypts

source_name: crypts from E2f1-/-;E2f2-/-;E2f3-/-;Rb-/- small intestines


title: QKO-3-villi


title: Rb-1-villi


title: WT-3-villi

source_name: villi from wild-type small intestines


title: TKO-1-villi


title: Rb-2-villi


title: TKO-3-villi


title: QKO-2-crypts


title: QKO-1-crypts


title: WT-1-villi


title: Rb-3-crypts

source_name: crypts from Rb-/- small intestines


title: WT-2-villi


title: WT-3-crypts

source_name: crypts from wild-type small intestines


title: Rb-2-crypts


title: WT-2-crypts


title: Rb-1-crypts


title: WT42 vs WT30

description: No extra description.

source_name: WT 42 degrees 10 min

source_name: WT 30 degrees


title: WT-1-crypts


title: control 9


title: M.bovis-NO vs M.bovis_rep4

city: Valdivia

first: Germán

last: Rehren

state: Valdivia

address: Campus Isla Teja

department: Biochemistry

country: Chile

institute: Universidad Austral de Chile

description: Synthesis and hybridization of labelled samples was performed as described in previously published protocols (Walters et al. Mol Microbiol (2006) 60(2):312-330).

hyb_protocol: Total purified cDNA was added to the arrays in a hybridization solution containing a final concentration of 0.5 ug/ul tRNA, 2.0x SSC, 0.25% formamide and 0.1% SDS. For each array, cDNA prepared from the M. tuberculosis RNA was mixed with cDNA from M. bovis. The slides were covered by a flat 22 x 22 mm coverslip and hybridized in sealed hybridization chambers for sixteen hours at 50°C in a water bath.

scan_protocol: Prepared slides were immediately scanned using an Axon 4000A Scanner (Axon Instruments). Fluorescence intensities of Cy3 and Cy5 dies at each spot were quantified using the GenePix Pro 4.0 software.

data_processing: Intensity values obtained from spots on the chip were corrected by background subtraction. Corrected data were then normalized using the Lowess implementation included in GeneSpring 7.2 software (Silicon Genetics). The values are expressed as log2 (NO/untreated) ratios determined from the normalized fluorescence intensity.

organism: Mycobacterium tuberculosis variant bovis

source_name: M. bovis culture

growth_protocol: Culture grew in Middlebrook 7H9 media supplemented with ADS, pyruvate and Tween 80.

extract_protocol:
Mid-log phase culture was shortly centrifuged and the pellet quickly frozen with dry ice. RNA was extracted according to published protocols.
Manganelli et al. Mol Microbiol (2001) 41(2):423-437

treatment_protocol: No treatment

value: Ravenel (TMC 401)

source_name: M. bovis-NO culture

extract_protocol:
After NO exposure, culture was shortly centrifuged and the pellet quickly frozen with dry ice. RNA was extracted according to published protocols.
Manganelli et al. Mol Microbiol (2001) 41(2):423-437

treatment_protocol: Mid-log phase cultures were exposed to 50 uM diethylenetriamine/nitric oxide adduct (DETA/NO) for 40 minutes.

value: nitric oxide


title: Strain_ju322_vs_N2

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

hyb_protocol: The sample was rehydrated in 40 l of NimbleGen Hybridization Buffer (NimbleGen Systems, Inc.), denatured at 95°C for 5 min, and then cooled to 42°C. Hybridizations were carried out for 18 hr at 42°C in the NimbleGen Service Laboratory. The arrays were washed using a NimbleGen Wash Buffer System (NimbleGen Systems, Inc.) and immediately dried down by centrifugation. See Selzer, R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319 (PMID 16075461).

scan_protocol: The scanner used was an Axon Scanner (Model # 4000B) . See Selzer, R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319 (PMID 16075461).

data_processing: The raw log2 intensity ratio were normalized with the LOESS regression.

organism: Caenorhabditis elegans

label_protocol: Cy3 dye-labeled random 9mers (TriLink BioTechnologies, Inc.) were diluted to 1 O.D./42 µl of buffer containing 0.125M Tris-HCl (pH 8.0), 0.125M MgCl2, 1.75 µl/ml β-Mercaptoethanol. 1 µg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 ºC and then chilled on ice in 0.2 ml PCR tubes. 10 µl of 50X dNTP mixture (1X TE buffer, 10 mM each of dATP, dCTP, dGTP and dTTP), 8 µl DI water and 100 U Klenow fragment (exo-) was added to each tube and mixed well with a pipet. Samples were centrifuged and incubated at 37 ºC for 2 hours. 10 µl 0.5 M EDTA was added and mixed well to stop the labeling reaction. DNA was precipitated by adding 11.5 µl 0.5 M NaCl and 110 µl isopropanol, vortexing, incubating in the dark for 10 minutes at room temperature, and centrifuging at 12,000X G for 10 minutes. The supernatant was removed and the DNA pellet was washed with 500 µl 80% ethanol. After centrifugation at 12,000X G for 2 minutes, the supernatant was removed and the pellet was dried in a SpeedVac on low heat for 5 minutes before being rehydrated in 25 µl DI water. DNA concentration was measured using a spectrophotometer.

extract_protocol: DNA was prepared either by standard phenol-chloroform extraction followed by ethanol precipitation, or with the Puregene DNA Purification Kit (D-7000A, Gentra Systems) using the solid tissue protocol.

value: hermaphrodite

value: whole animals

source_name: Wild-type N2

label_protocol: Cy5 dye-labeled random 9mers (TriLink BioTechnologies, Inc.) were diluted to 1 O.D./42 µl of buffer containing 0.125M Tris-HCl (pH 8.0), 0.125M MgCl2, 1.75 µl/ml β-Mercaptoethanol. 1 µg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 ºC and then chilled on ice in 0.2 ml PCR tubes. 10 µl of 50X dNTP mixture (1X TE buffer, 10 mM each of dATP, dCTP, dGTP and dTTP), 8 µl DI water and 100 U Klenow fragment (exo-) was added to each tube and mixed well with a pipet. Samples were centrifuged and incubated at 37 ºC for 2 hours. 10 µl 0.5 M EDTA was added and mixed well to stop the labeling reaction. DNA was precipitated by adding 11.5 µl 0.5 M NaCl and 110 µl isopropanol, vortexing, incubating in the dark for 10 minutes at room temperature, and centrifuging at 12,000X G for 10 minutes. The supernatant was removed and the DNA pellet was washed with 500 µl 80% ethanol. After centrifugation at 12,000X G for 2 minutes, the supernatant was removed and the pellet was dried in a SpeedVac on low heat for 5 minutes before being rehydrated in 25 µl DI water. DNA concentration was measured using a spectrophotometer.

tag: genotype

value: wild-type


title: Strain_rw7000_vs_N2


title: Strain_kr314_vs_N2


title: M.bovis-NO vs M.bovis_rep2

label_protocol: Walters et al. Mol Microbiol (2006) 60(2):312-330


title: M.bovis-NO vs M.bovis_rep3


title: EGTA treatment time-point 8, IC90

status: Public on Dec 16 2009

city: Singapore

first: Guangan

last: Hu

address: 60 Nanyang Drive

department: School of biological sciences

country: Singapore

institute: Nanyang Technological Unversity

description: no additional information

hyb_protocol: Microarray hybridizations were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Scanning as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

data_processing: Data processing as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, Normalization and subsequent filtering for quality control were carried out using NOMAD database (http://derisilab.ucsf.edu). Spots were considered of good quality when they were unflagged and had a median intensity greater than the local background plus 2 times the standard deviation of the background for each dye channel. The values presented in the sample data represent log2-transformed ratios of the measurement in the sample channel (Cy5) divided by the corresponding measurement in the reference channel (Cy3, P. falciparum RNA reference pool).

organism: Plasmodium falciparum

source_name: Dd2, start 34hpi, 8hr after treatment

label_protocol: RNA extraction, cDNA synthesis and labeling as well as microarray hybridizations of the four samples representing time points 1, 2, 3, and 4 against a reference RNA pool were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.

growth_protocol: Laboratory strain 3D7 and Dd2, sorbitol synchronized. Parasites grow in a 2% suspension of purified human RBCs and RPMI 1640 media supplemented with 0.25% Albumax, 2 g/l sodium bicarbonate, 0.1 mM hypoxanthine, 25 mM HEPES (pH 7.4), and 50 μg/l gentamycin, at 37°C, 5% O2, and 6% CO2. The 3D7 parasites for microarray reference pool were mixed with 6 time-series samples (every 8hrs through a 48hr life cycle), harvested from a 6 liter biofermenter synchronized culture.

treatment_protocol: Synchronzied parasite cultures are splitted into proper number flasks (75ml culture/flask). Total number is double number of time points for one experiment. Half flasks are treated with one compound with the final concentration of IC50 or IC90, and half flasks are negative controls. After the treatment of different time points, parasites in each flask were harvested for total RNA isolation and microarray hybridizations.

tag: treatment group

value: EGTA IC90

value: 8 hr

source_name: reference pool


title: Strain_my2_vs_N2


title: H3K4me3 replicate1b

city: Nijmegen

first: Gert Jan

last: Veenstra

address: Geert Grooteplein 28

department: Molecular Developmental Biology

institute: Radboud University

description: ChIP-chip of H3K4me3 in Xenopus tropicalis embryos

hyb_protocol: According to manufacturer's protocol (Roche Nimblegen)

data_processing: ChIP/input log2 ratio, scaled using Tukey's biweight

organism: Xenopus tropicalis

source_name: H3K4me3 ChIP DNA from Xenopus tropicalis embryos, Nieuwkoop-Faber stage 11-12

extract_protocol: Xenopus tropicalis embryos were obtained from a natural mating procedure after human chorion gonadotropin injection, dejellied in 2% cysteine and collected at stage 11-12. Chromatin (300 embryos) was fixed in 1% formaldehyde, sheared using a Branson sonifier, immunoprecipitated using 1-5 µg of antibody ( α-H3K4me3 (Abcam) or α-TBP (SL33)), washed, decrosslinked, DNA was purified and amplified using the T7 amplification protocol.

tag: chip antibody

tag: developmental stage

value: Nieuwkoop-Faber stage 11-12

value: whole embryo

source_name: Input DNA from Xenopus tropicalis embryos, Nieuwkoop-Faber stage 11-12

value: none, input DNA


title: Strain_ju263_vs_N2


title: M.bovis-NO vs M.bovis_rep1


title: Strain_ju258_vs_N2


title: Strain_cb4853_vs_N2


title: Strain_cb4854_vs_N2


title: EGTA treatment time-point 9, IC90

description: no additional information

source_name: Dd2, start 34hpi, 9hr after treatment

extract_protocol: RNA extraction, cDNA synthesis and labeling as well as microarray hybridizations of the four samples representing time points 1, 2, 3, and 4 against a reference RNA pool were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.

value: 9 hr


title: EGTA treatment time-point 10, IC90

description: no additional information

source_name: Dd2, start 34hpi, 10hr after treatment

value: 10 hr


title: EGTA treatment time-point 3, IC90

description: no additional information

source_name: Dd2, start 34hpi, 3hr after treatment

value: 3 hr


title: EGTA treatment time-point 4, IC90

description: no additional information

source_name: Dd2, start 34hpi, 4hr after treatment

value: 4 hr


title: EGTA treatment time-point 7, IC90

description: no additional information

source_name: Dd2, start 34hpi, 7hr after treatment

value: 7 hr


title: EGTA treatment time-point 5, IC90

description: no additional information

source_name: Dd2, start 34hpi, 5hr after treatment

value: 5 hr


title: Strain_cb3191_vs_N2


title: EGTA treatment time-point 2, IC90

description: no additional information

source_name: Dd2, start 34hpi, 2hr after treatment

value: 2 hr


title: H3K4me3 replicate1g

scan_protocol: According to manufacturer's protocol (Roche Nimblegen)


title: Strain_cb4856_vs_N2


title: Strain_ab1_vs_N2


title: EGTA treatment time-point 7, IC50

description: no additional information

value: EGTA IC50


title: Strain_cb4858_vs_N2


title: EGTA treatment time-point 8, IC50

description: no additional information


title: EGTA treatment time-point 9, IC50

description: no additional information


title: EGTA treatment time-point 4, IC50

description: no additional information


title: EGTA treatment time-point 3, IC50

description: no additional information


title: EGTA treatment time-point 6, IC50

description: no additional information

source_name: Dd2, start 34hpi, 6hr after treatment

value: 6 hr


title: EGTA treatment time-point 5, IC50

description: no additional information


title: EGTA treatment time-point 1, IC50

description: no additional information

source_name: Dd2, start 34hpi, 1hr after treatment

value: 1 hr


title: Control time-point 10 for EGTA treatment

description: no additional information

source_name: Dd2, negative controls, start 34hpi, 10hr

value: control for EGTA


title: Control time-point 9 for EGTA treatment

description: no additional information

source_name: Dd2, negative controls, start 34hpi, 9hr


title: Control time-point 8 for EGTA treatment

description: no additional information

source_name: Dd2, negative controls, start 34hpi, 8hr


title: Control time-point 7 for EGTA treatment

description: no additional information

source_name: Dd2, negative controls, start 34hpi, 7hr


title: Control time-point 6 for EGTA treatment

description: no additional information

source_name: Dd2, negative controls, start 34hpi, 6hr


title: Control time-point 4 for EGTA treatment

description: no additional information

source_name: Dd2, negative controls, start 34hpi, 4hr

source_name: reference pool


title: Control time-point 5 for EGTA treatment

description: no additional information

source_name: Dd2, negative controls, start 34hpi, 5hr


title: Control time-point 2 for EGTA treatment

description: no additional information

source_name: Dd2, negative controls, start 34hpi, 2hr


title: Control time-point 1 for EGTA treatment

description: no additional information

source_name: Dd2, negative controls, start 34hpi, 1hr


title: EGTA treatment time-point 1, IC90

description: no additional information


title: Trichostatin treatment time-point 4,IC90

description: no additional information

value: Trichostatin IC90


title: Trichostatin treatment time-point 5,IC90

description: no additional information


title: Trichostatin treatment time-point 6,IC90

description: no additional information

source_name: Dd2, start 34hpi, 8hr after treatment


title: Control time-point 3 for EGTA treatment

description: no additional information

source_name: Dd2, negative controls, start 34hpi, 3hr


title: Trichostatin treatment time-point 1,IC90

description: no additional information


title: H3K4me3 replicate1f

source_name: H3K4me3 ChIP DNA from Xenopus tropicalis embryos, Nieuwkoop-Faber stage 11-12

label_protocol: According to manufacturer's protocol (Roche Nimblegen)

source_name: Input DNA from Xenopus tropicalis embryos, Nieuwkoop-Faber stage 11-12


title: Trichostatin treatment time-point 5,IC50

description: no additional information

value: Trichostatin IC50


title: Trichostatin treatment time-point 2,IC90

description: no additional information

source_name: Dd2, start 34hpi, 2hr after treatment


title: TBP

description: ChIP-chip of TBP in Xenopus tropicalis embryos

source_name: TBP ChIP DNA from Xenopus tropicalis embryos, Nieuwkoop-Faber stage 11-12

value: TBP


title: Trichostatin treatment time-point 6,IC50

description: no additional information

value: 8 hr


title: Trichostatin treatment time-point 4,IC50

description: no additional information

source_name: Dd2, start 34hpi, 4hr after treatment


title: Control time-point 6 for Trichostatin treatment

description: no additional information

value: control for Trichostatin


title: Trichostatin treatment time-point 2,IC50

description: no additional information


title: Trichostatin treatment time-point 1,IC50

description: no additional information

source_name: Dd2, start 34hpi, 1hr after treatment


title: Control time-point 4 for Trichostatin treatment

description: no additional information


title: Control time-point 5 for Trichostatin treatment

description: no additional information


title: Trichostatin treatment time-point 3,IC90

description: no additional information

source_name: Dd2, start 34hpi, 3hr after treatment


title: Control time-point 3 for Trichostatin treatment

description: no additional information


title: Control time-point 1 for Trichostatin treatment

description: no additional information


title: Apicidin treatment 2 (Schiz) time-point 5, IC90

description: no additional information

source_name: Dd2, start 34hpi, 5hr after treatment

value: Apicidin treatment 2 (Schiz) IC90


title: Control time-point 2 for Trichostatin treatment

description: no additional information


title: Apicidin treatment 2 (Schiz) time-point 4, IC90

description: no additional information


title: Apicidin treatment 2 (Schiz) time-point 3, IC90

description: no additional information


title: H3K4me3 replicate3

value: Nieuwkoop-Faber stage 11-12

value: whole embryo

value: none, input DNA


title: Apicidin treatment 2 (Schiz) time-point 1, IC90

description: no additional information


title: Apicidin treatment 2 (Schiz) time-point 2, IC90

description: no additional information


title: EGTA treatment time-point 6, IC90

description: no additional information

source_name: Dd2, start 34hpi, 6hr after treatment

value: EGTA IC90


title: H3K4me3 replicate1d


title: H3K4me3 replicate2


title: EGTA treatment time-point 2, IC50

description: no additional information


title: H3K4me3 replicate1c


title: Apicidin treatment 2 (Schiz) time-point 3, IC50

description: no additional information

value: Apicidin treatment 2 (Schiz) IC50

value: 3 hr


title: Control time-point 4 for Apicidin treatment 2

description: no additional information

value: control for Apicidin treatment 2

value: 4 hr


title: Apicidin treatment 2 (Schiz) time-point 1, IC50

description: no additional information


title: Apicidin treatment 2 (Schiz) time-point 2, IC50

description: no additional information

value: 2 hr


title: Apicidin treatment 2 (Schiz) time-point 5, IC50

description: no additional information

value: 5 hr


title: Control time-point 3 for Apicidin treatment 2

description: no additional information


title: Control time-point 2 for Apicidin treatment 2

description: no additional information


title: Apicidin treatment 2 (Schiz) time-point 4, IC50

description: no additional information


title: Control time-point 1 for Apicidin treatment 2

description: no additional information

value: 1 hr


title: EGTA treatment time-point 10, IC50

description: no additional information

source_name: Dd2, start 34hpi, 10hr after treatment

value: EGTA IC50

value: 10 hr


title: Apicidin treatment 1 (Troph) time-point 3, IC90

description: no additional information

source_name: Dd2, start 18hpi, 3hr after treatment

value: Apicidin treatment 1 (Troph) IC90


title: Apicidin treatment 1 (Troph) time-point 2, IC90

description: no additional information

source_name: Dd2, start 18hpi, 2hr after treatment

source_name: reference pool


title: H3K4me3 replicate1e


title: Apicidin treatment 1 (Troph) time-point 4, IC90

description: no additional information

source_name: Dd2, start 18hpi, 4hr after treatment


title: Apicidin treatment 1 (Troph) time-point 5, IC90

description: no additional information

source_name: Dd2, start 18hpi, 5hr after treatment


title: Apicidin treatment 1 (Troph) time-point 6, IC90

description: no additional information

source_name: Dd2, start 18hpi, 6hr after treatment

value: 6 hr


title: Apicidin treatment 1 (Troph) time-point 6, IC50

description: no additional information

value: Apicidin treatment 1 (Troph) IC50


title: Apicidin treatment 1 (Troph) time-point 3, IC50

description: no additional information


title: Apicidin treatment 1 (Troph) time-point 1, IC90

description: no additional information

source_name: Dd2, start 18hpi, 1hr after treatment


title: Apicidin treatment 1 (Troph) time-point 4, IC50

description: no additional information


title: Apicidin treatment 1 (Troph) time-point 2, IC50

description: no additional information


title: Apicidin treatment 1 (Troph) time-point 5, IC50

description: no additional information


title: Control time-point 5 for Apicidin treatment 2

description: no additional information

source_name: Dd2, negative controls, start 34hpi, 5hr


title: Control time-point 3 for Apicidin treatment 1

description: no additional information

source_name: Dd2, negative controls, start 18hpi, 3hr

value: control for Apicidin treatment 1


title: Control time-point 4 for Apicidin treatment 1

description: no additional information

source_name: Dd2, negative controls, start 18hpi, 4hr


title: Control time-point 5 for Apicidin treatment 1

description: no additional information

source_name: Dd2, negative controls, start 18hpi, 5hr


title: Leupeptine treatment time-point 5,IC50

description: no additional information

source_name: Dd2,start 33hpi, 4hr after treatment

value: Leupeptine


title: Control time-point 6 for Apicidin treatment 1

description: no additional information

source_name: Dd2, negative controls, start 18hpi, 6hr


title: Leupeptine treatment time-point 4,IC50

description: no additional information

source_name: Dd2,start 33hpi, 3hr after treatment


title: Leupeptine treatment time-point 3,IC50

description: no additional information

source_name: Dd2,start 33hpi, 2hr after treatment


title: E64 treatment time-point 5,IC50

description: no additional information


title: Control time-point 2 for Apicidin treatment 1

description: no additional information

source_name: Dd2, negative controls, start 18hpi, 2hr


title: Apicidin treatment 1 (Troph) time-point 1, IC50

description: no additional information


title: Control time-point 1 for Apicidin treatment 1

description: no additional information

source_name: Dd2, negative controls, start 18hpi, 1hr


title: H3K4me3 replicate1a

source_name: H3K4me3 ChIP DNA from Xenopus tropicalis embryos, Nieuwkoop-Faber stage 11-12

value: Nieuwkoop-Faber stage 11-12

value: whole embryo

source_name: Input DNA from Xenopus tropicalis embryos, Nieuwkoop-Faber stage 11-12


title: Trichostatin treatment time-point 3,IC50

description: no additional information

source_name: Dd2, start 34hpi, 3hr after treatment

value: Trichostatin IC50

source_name: reference pool


title: Leupeptine treatment time-point 1,IC50

description: no additional information

source_name: Dd2,start 33hpi, 0.5hr after treatment


title: E64 treatment time-point 1,IC50

description: no additional information


title: Leupeptine treatment time-point 2,IC50

description: no additional information

source_name: Dd2,start 33hpi, 1hr after treatment


title: PMSF treatment time-point 3,IC50

description: no additional information

value: PMSF


title: PMSF treatment time-point 4,IC50

description: no additional information

value: 3 hr


title: E64 treatment time-point 4,IC50

description: no additional information


title: E64 treatment time-point 2,IC50

description: no additional information


title: Retinol A treatment time-point 4,IC50

description: no additional information

value: Retinol A


title: PMSF treatment time-point 5,IC50

description: no additional information

value: 4 hr


title: E64 treatment time-point 3,IC50

description: no additional information

value: 2 hr


title: PMSF treatment time-point 1,IC50

description: no additional information


title: PMSF treatment time-point 2,IC50

description: no additional information


title: Retinol A treatment time-point 5,IC50

description: no additional information


title: Control time-point 3 for Retinol A/PMSF/E64/Leupeptine

description: no additional information

source_name: Dd2, negative controls, start 33hpi, 2hr

value: control for Retinol A/PMSF/E64/Leupeptine


title: control 4

source_name: peripheral blood

value: control

value: Female


title: Retinol A treatment time-point 2,IC50

description: no additional information

value: 1 hr


title: Staurosporine 2 treatment time-point 4,IC50

description: no additional information

value: Staurosporine 2


title: Control time-point 5 for Retinol A/PMSF/E64/Leupeptine

description: no additional information

source_name: Dd2, negative controls, start 33hpi, 4hr


title: Staurosporine 2 treatment time-point 5,IC50

description: no additional information


title: Retinol A treatment time-point 3,IC50

description: no additional information


title: Control time-point 2 for Retinol A/PMSF/E64/Leupeptine

description: no additional information

source_name: Dd2, negative controls, start 33hpi, 1hr


title: Control time-point 4 for Retinol A/PMSF/E64/Leupeptine

description: no additional information

source_name: Dd2, negative controls, start 33hpi, 3hr


title: Staurosporine 2 treatment time-point 2,IC50

description: no additional information


title: Colchicine treatment time-point 4,IC50

description: no additional information

value: Colchicine


title: Retinol A treatment time-point 1,IC50

description: no additional information


title: Control time-point 1 for Retinol A/PMSF/E64/Leupeptine

description: no additional information

source_name: Dd2, negative controls, start 33hpi, 0.5hr


title: Colchicine treatment time-point 5,IC50

description: no additional information

source_name: Dd2,start 33hpi, 4hr after treatment


title: Colchicine treatment time-point 2,IC50

description: no additional information


title: Colchicine treatment time-point 1,IC50

description: no additional information


title: Na3VO4 treatment time-point 3,IC50

description: no additional information


title: Na3VO4 treatment time-point 4,IC50

description: no additional information

source_name: Dd2,start 33hpi, 3hr after treatment


title: Na3VO4 treatment time-point 2,IC50

description: no additional information


title: Na3VO4 treatment time-point 1,IC50

description: no additional information


title: Control time-point 3 for Na3VO4/Colchicine/Staurosporne 2

description: no additional information

value: control for Na3VO4/Colchicine/Staurosporne 2


title: Control time-point 5 for Na3VO4/Colchicine/Staurosporne 2

description: no additional information


title: Colchicine treatment time-point 3,IC50

description: no additional information

source_name: Dd2,start 33hpi, 2hr after treatment


title: Staurosporine 2 treatment time-point 1,IC50

description: no additional information


title: Na3VO4 treatment time-point 5,IC50

description: no additional information


title: Staurosporine 2 treatment time-point 3,IC50

description: no additional information


title: Control time-point 2 for Na3VO4/Colchicine/Staurosporne 2

description: no additional information


title: Control time-point 4 for Na3VO4/Colchicine/Staurosporne 2

description: no additional information


title: Chloroquine 2 treatment time-point 5,2*IC90

description: no additional information

source_name: 3D7, start 18hpi, 8hr after treatment

value: Chloroquine 2 IC90

value: 8 hr


title: Chloroquine 2 treatment time-point 2,2*IC90

description: no additional information

source_name: 3D7, start 18hpi, 2hr after treatment


title: Chloroquine 2 treatment time-point 4,2*IC90

description: no additional information

source_name: 3D7, start 18hpi, 6hr after treatment

value: 6 hr


title: Chloroquine 2 treatment time-point 5,IC90

description: no additional information


title: Chloroquine 2 treatment time-point 3,2*IC90

description: no additional information

source_name: 3D7, start 18hpi, 4hr after treatment


title: Chloroquine 2 treatment time-point 3,IC90

description: no additional information


title: Control time-point 1 for Na3VO4/Colchicine/Staurosporne 2

description: no additional information


title: Chloroquine 2 treatment time-point 2,IC90

description: no additional information


title: Chloroquine 2 treatment time-point 1,IC90

description: no additional information

source_name: 3D7, start 18hpi, 1hr after treatment


title: Chloroquine 2 treatment time-point 6,2*IC90

description: no additional information

source_name: 3D7, start 18hpi, 10hr after treatment

value: 10 hr

source_name: reference pool


title: Chloroquine 2 treatment time-point 6,IC90

description: no additional information


title: Chloroquine 2 treatment time-point 1,2*IC90

description: no additional information


title: Chloroquine 2 treatment time-point 1,IC50

description: no additional information

value: Chloroquine 2 IC50


title: Chloroquine 2 treatment time-point 3,IC50

description: no additional information


title: Control time-point 5 for Chloroquine 2

description: no additional information

source_name: 3D7, negative controls, start 18hpi, 8hr

value: control for Chloroquine 2


title: Control time-point 4 for Chloroquine 2

description: no additional information

source_name: 3D7, negative controls, start 18hpi, 6hr


title: Chloroquine 2 treatment time-point 6,IC50

description: no additional information


title: Control time-point 6 for Chloroquine 2

description: no additional information

source_name: 3D7, negative controls, start 18hpi, 10hr


title: Artemisinin treatment time-point 4,IC50

description: no additional information

source_name: Dd2, start 18hpi, 6hr after treatment

value: Artemisinin


title: Control time-point 3 for Chloroquine 2

description: no additional information

source_name: 3D7, negative controls, start 18hpi, 4hr


title: Artemisinin treatment time-point 6,IC50

description: no additional information

source_name: Dd2, start 18hpi, 10hr after treatment


title: Control time-point 2 for Chloroquine 2

description: no additional information

source_name: 3D7, negative controls, start 18hpi, 2hr


title: Control time-point 1 for Chloroquine 2

description: no additional information

source_name: 3D7, negative controls, start 18hpi, 1hr


title: Artemisinin treatment time-point 2,IC50

description: no additional information

source_name: Dd2, start 18hpi, 2hr after treatment


title: Febrifugine treatment time-point 3,IC50

description: no additional information

source_name: Dd2, start 18hpi, 4hr after treatment

value: Febrifugine


title: Febrifugine treatment time-point 4,IC50

description: no additional information


title: Chloroquine 2 treatment time-point 4,IC90

description: no additional information


title: Febrifugine treatment time-point 1,IC50

description: no additional information

source_name: Dd2, start 18hpi, 1hr after treatment


title: Febrifugine treatment time-point 6,IC50

description: no additional information


title: Artemisinin treatment time-point 1,IC50

description: no additional information


title: Chloroquine 2 treatment time-point 4,IC50

description: no additional information


title: Chloroquine 1 treatment time-point 6,IC50

description: no additional information

value: Chloroquine 1


title: Artemisinin treatment time-point 3,IC50

description: no additional information

value: 4 hr


title: Febrifugine treatment time-point 5,IC50

description: no additional information

source_name: Dd2, start 18hpi, 8hr after treatment


title: Chloroquine 1 treatment time-point 5,IC50

description: no additional information


title: Chloroquine 2 treatment time-point 2,IC50

description: no additional information

source_name: 3D7, start 18hpi, 2hr after treatment

value: 2 hr


title: Artemisinin treatment time-point 5,IC50

description: no additional information


title: Febrifugine treatment time-point 2,IC50

description: no additional information


title: Quinine treatment time-point 6,IC50

description: no additional information

value: Quinine


title: Quinine treatment time-point 1,IC50

description: no additional information


title: Chloroquine 1 treatment time-point 3,IC50

description: no additional information


title: Quinine treatment time-point 3,IC50

description: no additional information


title: Chloroquine 2 treatment time-point 5,IC50

description: no additional information

source_name: 3D7, start 18hpi, 8hr after treatment


title: Chloroquine 1 treatment time-point 1,IC50

description: no additional information


title: Quinine treatment time-point 5,IC50

description: no additional information


title: Quinine treatment time-point 4,IC50

description: no additional information


title: Control time-point 6 for Quinine/Chloroquine 1/febrifugine/artemisinin

description: no additional information

source_name: Dd2, negative controls, start 18hpi, 10hr

value: control for Quinine/Chloroquine 1/febrifugine/artemisinin


title: Chloroquine 1 treatment time-point 2,IC50

description: no additional information


title: Control time-point 3 for Quinine/Chloroquine 1/febrifugine/artemisinin

description: no additional information

source_name: Dd2, negative controls, start 18hpi, 4hr


title: Quinine treatment time-point 2,IC50

description: no additional information

source_name: reference pool


title: Control time-point 5 for Quinine/Chloroquine 1/febrifugine/artemisinin

description: no additional information

source_name: Dd2, negative controls, start 18hpi, 8hr


title: Roscovitine A treatment time-point 3,IC50

description: no additional information

source_name: Dd2, start 33hpi, 4hr after treatment

value: Roscovitine A


title: Control time-point 4 for Quinine/Chloroquine 1/febrifugine/artemisinin

description: no additional information

source_name: Dd2, negative controls, start 18hpi, 6hr


title: Roscovitine A treatment time-point 6,IC50

description: no additional information

source_name: Dd2, start 33hpi, 10hr after treatment


title: Roscovitine A treatment time-point 5,IC50

description: no additional information

source_name: Dd2, start 33hpi, 8hr after treatment


title: Roscovitine A treatment time-point 1,IC50

description: no additional information

source_name: Dd2, start 33hpi, 1hr after treatment

value: 1 hr


title: Roscovitine A treatment time-point 4,IC50

description: no additional information

source_name: Dd2, start 33hpi, 6hr after treatment


title: Control time-point 2 for Quinine/Chloroquine 1/febrifugine/artemisinin

description: no additional information

source_name: Dd2, negative controls, start 18hpi, 2hr


title: Roscovitine A treatment time-point 2,IC50

description: no additional information

source_name: Dd2, start 33hpi, 2hr after treatment


title: FK506 treatment time-point 8,IC50

description: no additional information

source_name: Dd2, start 33hpi, 14hr after treatment

value: 14 hr


title: FK506 treatment time-point 6,IC50

description: no additional information


title: CyclosporineA treatment time-point 8,IC50

description: no additional information

value: CyclosporineA


title: FK506 treatment time-point 5,IC50

description: no additional information


title: FK506 treatment time-point 3,IC50

description: no additional information


title: FK506 treatment time-point 2,IC50

description: no additional information


title: FK506 treatment time-point 1,IC50

description: no additional information


title: Control time-point 1 for Quinine/Chloroquine 1/febrifugine/artemisinin

description: no additional information

source_name: Dd2, negative controls, start 18hpi, 1hr


title: Control time-point 7 for CyclosporineA/FK506/RoscovitineA

description: no additional information

source_name: Dd2, negative controls, start 33hpi, 12hr

value: 12 hr


title: CyclosporineA treatment time-point 1,IC50

description: no additional information


title: Control time-point 6 for CyclosporineA/FK506/RoscovitineA

description: no additional information

source_name: Dd2, negative controls, start 33hpi, 10hr


title: CyclosporineA treatment time-point 5,IC50

description: no additional information

value: 8 hr


title: Control time-point 8 for CyclosporineA/FK506/RoscovitineA

description: no additional information

source_name: Dd2, negative controls, start 33hpi, 14hr


title: Control time-point 4 for CyclosporineA/FK506/RoscovitineA

description: no additional information

source_name: Dd2, negative controls, start 33hpi, 6hr

value: 6 hr


title: Roscovitine A treatment time-point 7,IC50

description: no additional information

source_name: Dd2, start 33hpi, 12hr after treatment


title: CyclosporineA treatment time-point 2,IC50

description: no additional information

source_name: reference pool


title: Control time-point 5 for CyclosporineA/FK506/RoscovitineA

description: no additional information

source_name: Dd2, negative controls, start 33hpi, 8hr


title: Control time-point 3 for CyclosporineA/FK506/RoscovitineA

description: no additional information

source_name: Dd2, negative controls, start 33hpi, 4hr


title: CyclosporineA treatment time-point 7,IC50

description: no additional information


title: Roscovitine A treatment time-point 8,IC50

description: no additional information


title: CyclosporineA treatment time-point 6,IC50

description: no additional information

value: 10 hr


title: Staurosporine 1treatment time-point 7,IC50

description: no additional information

source_name: Dd2, start 32hpi, 12hr after treatment

value: Staurosporine 1


title: Control time-point 2 for CyclosporineA/FK506/RoscovitineA

description: no additional information

source_name: Dd2, negative controls, start 33hpi, 2hr


title: Staurosporine 1treatment time-point 6,IC50

description: no additional information

source_name: Dd2, start 32hpi, 10hr after treatment


title: Chloroquine 1 treatment time-point 4,IC50

description: no additional information

source_name: Dd2, start 18hpi, 6hr after treatment


title: Control time-point 1 for CyclosporineA/FK506/RoscovitineA

description: no additional information

source_name: Dd2, negative controls, start 33hpi, 1hr


title: FK506 treatment time-point 7,IC50

description: no additional information


title: CyclosporineA treatment time-point 4,IC50

description: no additional information

source_name: Dd2, start 33hpi, 6hr after treatment


title: Staurosporine 1treatment time-point 2,IC50

description: no additional information

source_name: Dd2, start 32hpi, 2hr after treatment


title: CyclosporineA treatment time-point 3,IC50

description: no additional information

source_name: Dd2, start 33hpi, 4hr after treatment


title: Staurosporine 1treatment time-point 4,IC50

description: no additional information

source_name: Dd2, start 32hpi, 6hr after treatment


title: KN93 treatment time-point 7,IC50

description: no additional information


title: Staurosporine 1treatment time-point 5,IC50

description: no additional information

source_name: Dd2, start 32hpi, 8hr after treatment


title: Staurosporine 1treatment time-point 3,IC50

description: no additional information

source_name: Dd2, start 32hpi, 4hr after treatment


title: Staurosporine 1treatment time-point 1,IC50

description: no additional information

source_name: Dd2, start 32hpi, 1hr after treatment


title: KN93 treatment time-point 4,IC50

description: no additional information


title: KN93 treatment time-point 6,IC50

description: no additional information


title: ML7 treatment time-point 5,IC50

description: no additional information


title: ML7 treatment time-point 7,IC50

description: no additional information


title: ML7 treatment time-point 2,IC50

description: no additional information


title: ML7 treatment time-point 3,IC50

description: no additional information


title: W7 treatment time-point 6,IC50

description: no additional information


title: KN93 treatment time-point 3,IC50

description: no additional information


title: ML7 treatment time-point 6,IC50

description: no additional information


title: ML7 treatment time-point 4,IC50

description: no additional information


title: W7 treatment time-point 5,IC50

description: no additional information


title: ML7 treatment time-point 1,IC50

description: no additional information


title: KN93 treatment time-point 1,IC50

description: no additional information


title: W7 treatment time-point 4,IC50

description: no additional information


title: KN93 treatment time-point 2,IC50

description: no additional information


title: W7 treatment time-point 1,IC50

description: no additional information


title: W7 treatment time-point 2,IC50

description: no additional information


title: W7 treatment time-point 3,IC50

description: no additional information


title: Control time-point 4 for ML7/W7/KN7/Staurosporine1

description: no additional information

source_name: Dd2, negative controls, start 32hpi, 6hr

value: control for ML7/W7/KN7/Staurosporine1


title: Control time-point 3 for ML7/W7/KN7/Staurosporine1

description: no additional information

source_name: Dd2, negative controls, start 32hpi, 4hr


title: Control time-point 2 for ML7/W7/KN7/Staurosporine1

description: no additional information

source_name: Dd2, negative controls, start 32hpi, 2hr

source_name: reference pool


title: Control time-point 1 for ML7/W7/KN7/Staurosporine1

description: no additional information

source_name: Dd2, negative controls, start 32hpi, 1hr


title: Control time-point 7 for ML7/W7/KN7/Staurosporine1

description: no additional information

source_name: Dd2, negative controls, start 32hpi, 12hr


title: KN93 treatment time-point 5,IC50

description: no additional information


title: W7 treatment time-point 7,IC50

description: no additional information

source_name: Dd2, start 32hpi, 12hr after treatment


title: Control time-point 5 for ML7/W7/KN7/Staurosporine1

description: no additional information

source_name: Dd2, negative controls, start 32hpi, 8hr


title: Control time-point 6 for ML7/W7/KN7/Staurosporine1

description: no additional information

source_name: Dd2, negative controls, start 32hpi, 10hr


title: DLBCL18

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: Human Promega control

hyb_protocol: Scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

label_protocol: manufacturer's instructions

extract_protocol: manufacturer's instructions

treatment_protocol: Total DNA extracted using manufacturer's instructions

value: male

value: 58 years

source_name: Human Promega control

tag: type

value: male Pomega control


title: DLBCL14

description: Human Promega control

value: 44 years


title: DLBCL20

description: Human Promega control

value: 63 years


title: DLBCL12

description: Human Promega control

value: 24 years


title: DLBCL17

description: Human Promega control

value: female

value: 28 years

value: female Pomega control


title: DLBCL5

description: Human Promega control

value: 57 years


title: DLBCL8

description: Human Promega control

value: 66 years


title: DLBCL13

description: Human Promega control

value: 30 years


title: DLBCL9

description: Human Promega control

value: 86 years


title: DLBCL16

description: Human Promega control


title: DLBCL2

description: Human Promega control

value: 37 years


title: DLBCL19

description: Human Promega control

value: 56 years


title: DLBCL3

description: Human Promega control

value: 72 years


title: DLBCL6

description: Human Promega control

value: 33 years


title: DLBCL1

description: Human Promega control

value: 59 years


title: DLBCL4

description: Human Promega control

value: male

value: 45 years


title: DLBCL11

description: Human Promega control

value: 53 years

value: male Pomega control


title: DLBCL10

description: Human Promega control

value: 46 years


title: DLBCL15

description: Human Promega control

value: female

value: 65 years


title: MR337

description: Human Promega control

value: 9 years


title: MR382

description: Human Promega control

value: 6 years

value: female Pomega control


title: MR279

description: Human Promega control

value: 8 years


title: MR374

description: Human Promega control


title: MR102

description: Human Promega control

value: 3 years


title: MR99

description: Human Promega control

value: 5 years


title: MR112

description: Human Promega control


title: muscle_subject 22_post suppliment_rep1

city: Novato

first: Simon

last: Melov

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

description:
Muscle Biopsy from Left Leg (Control)
4051956127_C

hyb_protocol: Labeled cRNA samples were hybridized to Human Ref-8 BeadChips (Illumina) according to the manufacturer's instructions, using equipment specified by the manufacturer (Illumina).

scan_protocol: Processed arrays were read using a BeadStation array reader (Illumina) according to the manufacturer's instructions.

data_processing: Gene array data analyses were done comparing baseline, post supplementation, 3 and 48 hours post exercise using simple paired t-test on log2 expression ratios.  Genes were ranked by p-value and the inference reported following adjustment for multiple testing using the FDR and the Benjamini and Hochberg method. Among those genes with an adjusted q-value (based on FDR) of <0.05, we used hierarchical clustering (based on the HOPACH algorithm to find groups of genes with similar profiles across the subjects.

source_name: vastus lateralis muscle, post supplement

label_protocol: Samples which passed quality were amplified one round and biotin-labeled, using the Illumina TotalPrep Kit (Ambion) according to the manufacturer's instructions. Concentration and quality were assessed using the  Nanodrop Spectrophotometer and the Agilent Bioanalyzer Nano Chip System.

extract_protocol: Total RNA was extracted by homogenizing ~30 mg of skeletal muscle in 2 mL of Trizol Reagent, followed by phase separation using 200 μL of chloroform and precipitation using 500 μL of isopropyl alcohol. The RNA pellet was then washed three times in 75% ethanol and re-suspended in 15 μL DEPC-treated water. Concentration and purity was determined using a UV spectrophotometer at the absorbance of 260/280 nm (measurements were done in duplicate). RNA integrity was assessed in a randomly chosen subset of samples using agarose gel electrophoresis. RNA samples were then treated with DNA-free recombinant DNase I (Ambion Inc, Austin, TX) according to the manufacturer’s instructions. Total RNA concentration and purity were assessed by using a Nanodrop Spectrophotometer and the Agilent Bioanalyzer Nano Chip System.

value: Male

tag: supplement

value: Placebo

value: skeletal muscle


title: DLBCL7

description: Human Promega control

value: 44 years


title: muscle_subject 22_post exercise_48hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956105_H

source_name: vastus lateralis muscle, post exercise, 48hours


title: muscle_subject 22_baseline_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956126_H

source_name: vastus lateralis muscle, baseline


title: muscle_subject 22_post exercise_3hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956048_H

source_name: vastus lateralis muscle, post exercise, 3hours


title: MR84

description: Human Promega control


title: muscle_subject 21_post suppliment_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956107_F


title: muscle_subject 20_post exercise_3hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956108_A

value: Estradiol


title: MR15

description: Human Promega control

value: male

value: 4 years


title: muscle_subject 17_post exercise_48hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956107_D


title: MR4

description: Human Promega control

value: 17 years

value: male Pomega control


title: muscle_subject 17_baseline_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956071_G


title: MR24

description: Human Promega control


title: muscle_subject 20_post exercise_48hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956121_H


title: muscle_subject 21_baseline_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956071_D


title: MR90

description: Human Promega control

value: 2 years


title: muscle_subject 20_baseline_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956105_A


title: muscle_subject 20_post suppliment_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956048_D


title: MR22

description: Human Promega control


title: muscle_subject 17_post suppliment_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956048_F


title: muscle_subject 21_post exercise_48hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956126_F


title: muscle_subject 17_post exercise_3hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956121_B


title: muscle_subject 16_baseline_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956121_F


title: muscle_subject 21_post exercise_3hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956108_E


title: muscle_subject 16_post suppliment_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956105_F


title: HBEGF 8h

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description: Normal human bronchial epithelial cells  HBEGF 8h

hyb_protocol: Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.

scan_protocol: Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.

data_processing: All 17 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.

label: Biotin

source_name: Normal human bronchial epithelial cells

label_protocol: In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.

extract_protocol: Total RNA was purified from cell lysates (Rneasy; Qiagen). Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).

tag: cell type

value: bronchial epithelial cells

tag: hybridization batch


title: HBEGF 3h

description: Normal human bronchial epithelial cells  HBEGF 3h


title: Pressure + AG1478 8h

description: Normal human bronchial epithelial cells  Pressure + AG1478 8h


title: HBEGF 1h

description: Normal human bronchial epithelial cells  HBEGF 1h


title: muscle_subject 16_post exercise_48hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956108_G

tag: age

tag: tissue


title: Pressure + AG1478 1h

description: Normal human bronchial epithelial cells  Pressure + AG1478 1h


title: muscle_subject 15_baseline_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956127_F

tag: gender


title: AG1478 8h

description: Normal human bronchial epithelial cells  AG1478 8h


title: muscle_subject 15_post exercise_3hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956105_G


title: muscle_subject 15_post suppliment_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956108_F


title: muscle_subject 13_post suppliment_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956121_E


title: muscle_subject 11_baseline_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956048_C


title: muscle_subject 13_baseline_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956048_A


title: AG1478 0h

description: Normal human bronchial epithelial cells  AG1478 0h


title: muscle_subject 13_post exercise_3hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956105_C


title: Pressure + AG1478 3h

description: Normal human bronchial epithelial cells  Pressure + AG1478 3h


title: muscle_subject 15_post exercise_48hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956121_D


title: AG1478 1h

description: Normal human bronchial epithelial cells  AG1478 1h


title: muscle_subject 11_post suppliment_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956126_E


title: Control 3h

description: Normal human bronchial epithelial cells  Control 3h


title: muscle_subject 11_post exercise_3hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956127_D


title: Pressure 3h

description: Normal human bronchial epithelial cells  Pressure 3h


title: muscle_subject 16_post exercise_3hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956107_C


title: Control 0h

description: Normal human bronchial epithelial cells  Control 0h


title: muscle_subject 13_post exercise_48hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956126_A


title: AG1478 3h

description: Normal human bronchial epithelial cells  AG1478 3h


title: muscle_subject 11_post exercise_48hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956071_F


title: Control 1h

description: Normal human bronchial epithelial cells  Control 1h


title: Control 8h

description: Normal human bronchial epithelial cells  Control 8h


title: Pressure 1h

description: Normal human bronchial epithelial cells  Pressure 1h


title: Pressure 8h

description: Normal human bronchial epithelial cells  Pressure 8h


title: Non-infant ALL PRED resistant 13

city: Rotterdam

first: Ronald

last: Stam

address: Dr. Molewaterplein 60

institute: Erasmus MC - Sophia Children's Hospital

description: Gene expression data primary childhood ALL cells

hyb_protocol: Fragmented cRNA was hybridized to Affymetrix HU133A microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Gene expression data were normalized using dChip, and filtered with a max-min=100, and max/min=4.

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone resistant 13

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

extract_protocol: Total RNA was extracted from leukemic cells using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Primary ALL samples were obtained at diagnosis (before treatment) and processed within 24 hours after sampling. All samples contained >90% leukemic blasts.

tag: sex

value: female

value: Child

value: >1 year old

value: Precursor B-cells

tag: disease status

value: acute lymphoblastic leukemia (ALL)

tag: clinical response factor

value: prednisolone resistant


title: Non-infant ALL PRED resistant 11

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone resistant 11


title: muscle_subject 9_post suppliment_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956126_C

value: Male


title: Non-infant ALL PRED resistant 9

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone resistant 9


title: muscle_subject 10_post suppliment_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956121_A

value: Placebo


title: Non-infant ALL PRED resistant 12

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone resistant 12


title: muscle_subject 10_baseline_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956108_H

value: skeletal muscle


title: muscle_subject 9_baseline_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956108_B


title: muscle_subject 10_post exercise_3hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956071_H


title: Non-infant ALL PRED resistant 7

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone resistant 7


title: Non-infant ALL PRED resistant 10

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone resistant 10


title: muscle_subject 9_post exercise_48hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956105_B


title: muscle_subject 9_post exercise_3hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956127_A


title: Non-infant ALL PRED resistant 8

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone resistant 8


title: Non-infant ALL PRED resistant 6

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone resistant 6


title: muscle_subject 7_baseline_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956127_B


title: Non-infant ALL PRED resistant 5

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone resistant 5


title: muscle_subject 7_post suppliment_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956105_D


title: muscle_subject 10_post exercise_48hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956048_G


title: muscle_subject 7_post exercise_3hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956107_G


title: muscle_subject 7_post exercise_48hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956071_C


title: muscle_subject 6_baseline_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956121_C


title: Non-infant ALL PRED resistant 4

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone resistant 4


title: Non-infant ALL PRED resistant 2

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone resistant 2


title: Non-infant ALL PRED resistant 3

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone resistant 3


title: Non-infant ALL PRED resistant 1

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone resistant 1


title: Non-infant ALL PRED sensitive 14

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone sensitive 14

value: prednisolone sensitive


title: muscle_subject 5_post suppliment_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956071_E

source_name: vastus lateralis muscle, post supplement


title: muscle_subject 6_post suppliment_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956108_C


title: Non-infant ALL PRED sensitive 7

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone sensitive 7


title: muscle_subject 5_baseline_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956107_H

source_name: vastus lateralis muscle, baseline


title: Non-infant ALL PRED sensitive 13

description: Gene expression data primary childhood ALL cells

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone sensitive 13


title: muscle_subject 4_baseline_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956126_D

value: Estradiol


title: Non-infant ALL PRED sensitive 9

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone sensitive 9

value: male


title: muscle_subject 6_post exercise_3hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956071_B

source_name: vastus lateralis muscle, post exercise, 3hours


title: Non-infant ALL PRED sensitive 8

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone sensitive 8


title: muscle_subject 5_post exercise_3hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956126_G


title: muscle_subject 5_post exercise_48hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956127_E

source_name: vastus lateralis muscle, post exercise, 48hours


title: Non-infant ALL PRED sensitive 12

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone sensitive 12


title: muscle_subject 4_post suppliment_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956107_E


title: muscle_subject 6_post exercise_48hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956048_B


title: Non-infant ALL PRED sensitive 6

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone sensitive 6


title: Non-infant ALL PRED sensitive 10

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone sensitive 10


title: Non-infant ALL PRED sensitive 11

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone sensitive 11


title: Infant ALL MLL-AF4 positive sample 28

description: Gene expression profiling data (HU133plus2.0) primary infant ALL cells

hyb_protocol: Fragmented cRNA was hybridized to Affymetrix HU133plus 2.0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The CEL files represent the raw (unscaled; scaling factor = 1) gene expression data. Raw (unscaled) array data was collectively normalized using variance-stabilizing normalization (VSN), performed in the statistical environment R (version 2.10.1) using Bioconductor packages.

source_name: Primary infant (<1 year of age) ALL cells at diagnosis (untreated) (>90% blasts)

value: Acute Lymphoblastic Leukemia cells (>90% blasts)

tag: genome/variation

tag: age (months)

value: Precursor B-cell acute lymphoblastic leukemia (ALL)


title: Non-infant ALL PRED sensitive 4

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone sensitive 4


title: muscle_subject 4_post exercise_48hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956127_H


title: muscle_subject 3_post suppliment_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956071_A


title: muscle_subject 3_baseline_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956107_A


title: Non-infant ALL PRED sensitive 2

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone sensitive 2


title: Non-infant ALL PRED sensitive 3

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone sensitive 3


title: Non-infant ALL PRED sensitive 5

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone sensitive 5


title: muscle_subject 3_post exercise_48hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956108_D


title: Non-infant ALL PRED sensitive 1

source_name: Primary non-infant (childhood) ALL cells in vitro prednisolone sensitive 1

value: <1 year old


title: muscle_subject 4_post exercise_3hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956121_G


title: muscle_subject 1_post exercise_48hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956107_B


title: Infant ALL PRED resistant 9

description: Gene expression data primary infant ALL cells

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone resistant 9

value: Infant


title: muscle_subject 1_baseline_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956105_E

source_name: vastus lateralis muscle, baseline


title: Bract at S0, biological rep1

city: Ya'an

first: Guangsheng

last: Yuan

state: Sichuan Province

address: Xinkang Road 46

department: Maize Research Institute

institute: Sichuan Agricultural University

description: Gene expression data from maize bract uninfected control in Ye478.

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

scan_protocol: GeneChips were scanned using the Scanner 3000 7G.

data_processing: The data were analyzed with GeneChip Operating SoftwareVersion1.4 using Affymetrix default analysis settings and global scaling as normalization method.

organism: Zea mays

source_name: Maize bract uninfection in Ye478

growth_protocol: Both cultivars resistant Bt-1 and susceptible Ye478, were planted in experimental field i. The spores of Fusarium moniliforme were cultured on potato dextrose agar (PDA) media for 15 d prior to collection for inoculations.

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

treatment_protocol: Inoculum of Fusarium moniliforme was prepared by washing conidia from the cultures and diluting  in water. Milky stage maize plants were inoculated with Fusarium moniliforme on each bract by injection, and bract tissues were collected at 4 days after inoculation.

tag: genetic background

value: Susceptible maize (Ye478) inbred

value: maize bract


title: muscle_subject 3_post exercise_3hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956048_E


title: Infant ALL PRED resistant 6

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone resistant 6

value: female


title: muscle_subject 1_post exercise_3hours_rep1

description:
Muscle Biopsy from Right Leg (Exercised)
4051956126_B

source_name: vastus lateralis muscle, post exercise, 3hours


title: muscle_subject 1_post suppliment_rep1

description:
Muscle Biopsy from Left Leg (Control)
4051956127_G

source_name: vastus lateralis muscle, post supplement


title: Bract at ST, biological rep1

description: Gene expression data from maize bract 4 days post infected  in Ye478.

source_name: Maize bract 4 days post infection in Ye478


title: Bract at ST, biological rep2


title: Bract at S0, biological rep2


title: Infant ALL PRED resistant 10

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone resistant 10


title: Infant ALL PRED resistant 12

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone resistant 12


title: Infant ALL PRED resistant 8

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone resistant 8


title: Infant ALL PRED resistant 5

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone resistant 5


title: Infant ALL PRED resistant 4

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone resistant 4


title: Infant ALL PRED resistant 11

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone resistant 11


title: Infant ALL PRED resistant 2

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone resistant 2


title: Infant ALL PRED resistant 3

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone resistant 3


title: Bract at R0, biological rep1

description: Gene expression data from maize bract uninfected control in Bt-1.

source_name: Maize bract uninfection in Bt-1

value: Resistant maize (Bt-1) inbred


title: Bract at R0, biological rep2


title: Infant ALL PRED resistant 1

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone resistant 1

value: Precursor B-cells


title: caudal non-5HT neurons (C-) biological replicate 3

city: Cleveland

first: Evan

middle: S.

last: Deneris

address: 2109 Adlebert Road

department: Neurosciences

institute: Case Western Reserve University

description:
gene expression data from rostral 5HT neurons (R+), rostral non-5HT neurons (R-), caudal 5HT neurons (C+), and caudal non-5HT neurons (C-)
61 den20

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

scan_protocol: GeneChips were scanned using the Affymetrix High Density Genechip Scanner 3000.

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

source_name: caudal non-5HT neurons (C-)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200,000 sorted cells for reach replicate using one round of amplication.

growth_protocol: E12.5 ePet-EYFP neural tubes were dissected into rostral and caudal portions by making incisions at the pontine flexure, mesecephalic flexure, and spinal cord.

treatment_protocol: Cells were dissociated by mild trypsin and mechanical trituration with a glass pipette into single cell suspensions. Cells were sorted and 4 populations collected directly into Trizol: (R+. R-, C+, and C).

value: caudal non-5HT neurons

tag: genotype

value: ePet-EYFP


title: Infant ALL PRED sensitive 13

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone sensisitve 13

value: acute lymphoblastic leukemia (ALL)


title: Infant ALL PRED resistant 7

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone resistant 7

value: prednisolone resistant


title: Infant ALL PRED sensitive 12

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone sensisitve 12


title: Bract at RT, biological rep2

description: Gene expression data from maize bract 4 days post infected  in Bt-1.

source_name: Maize bract 4 days post infection in Bt-1


title: Bract at RT, biological rep1


title: Infant ALL PRED sensitive 11

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone sensisitve 11


title: Infant ALL PRED sensitive 8

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone sensisitve 8


title: rostral 5HT neurons (R+) biological replicate 3

description:
gene expression data from rostral 5HT neurons (R+), rostral non-5HT neurons (R-), caudal 5HT neurons (C+), and caudal non-5HT neurons (C-)
61 den17

source_name: rostral 5HT neurons (R+)

value: rostral 5HT neurons


title: Infant ALL PRED sensitive 5

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone sensisitve 5

value: prednisolone sensitive


title: rostral non-5HT neurons (R-) biological replicate 3

description:
gene expression data from rostral 5HT neurons (R+), rostral non-5HT neurons (R-), caudal 5HT neurons (C+), and caudal non-5HT neurons (C-)
61 den18

source_name: rostral non-5HT neurons (R-)

value: rostral non-5HT neurons


title: Infant ALL PRED sensitive 10

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone sensisitve 10


title: Infant ALL PRED sensitive 9

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone sensisitve 9


title: caudal non-5HT neurons (C-) biological replicate 2

description:
gene expression data from rostral 5HT neurons (R+), rostral non-5HT neurons (R-), caudal 5HT neurons (C+), and caudal non-5HT neurons (C-)
61 den16


title: Infant ALL PRED sensitive 4

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone sensisitve 4

value: male


title: Infant ALL PRED sensitive 3

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone sensisitve 3


title: rostral non-5HT neurons (R-)biological replicate 2

description:
gene expression data from rostral 5HT neurons (R+), rostral non-5HT neurons (R-), caudal 5HT neurons (C+), and caudal non-5HT neurons (C-)
61 den14


title: Infant ALL PRED sensitive 7

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone sensisitve 7


title: caudal non-5HT neurons (C-)biological replicate 1

description:
gene expression data from rostral 5HT neurons (R+), rostral non-5HT neurons (R-), caudal 5HT neurons (C+), and caudal non-5HT neurons (C-)
61 den12


title: rostral 5HT neurons (R+) biological replicate 2

description:
gene expression data from rostral 5HT neurons (R+), rostral non-5HT neurons (R-), caudal 5HT neurons (C+), and caudal non-5HT neurons (C-)
61 den13


title: Infant ALL PRED sensitive 2

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone sensisitve 2


title: rostral 5HT neurons (R+) biological replicate 1

description:
gene expression data from rostral 5HT neurons (R+), rostral non-5HT neurons (R-), caudal 5HT neurons (C+), and caudal non-5HT neurons (C-)
61 den09


title: Infant ALL PRED sensitive 1

description: Gene expression data primary infant ALL cells

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone sensisitve 1


title: caudal 5HT neurons (C+)biological replicate 1

description:
gene expression data from rostral 5HT neurons (R+), rostral non-5HT neurons (R-), caudal 5HT neurons (C+), and caudal non-5HT neurons (C-)
61 den11

source_name: caudal 5HT neurons (C+)

value: caudal 5HT neurons


title: caudal 5HT neurons (C+) biological replicate 3

description:
gene expression data from rostral 5HT neurons (R+), rostral non-5HT neurons (R-), caudal 5HT neurons (C+), and caudal non-5HT neurons (C-)
61 den19


title: rostral non-5HT neurons (R-) biological replicate 1

description:
gene expression data from rostral 5HT neurons (R+), rostral non-5HT neurons (R-), caudal 5HT neurons (C+), and caudal non-5HT neurons (C-)
61 den10


title: Trout exposed to 2 mg/L crude oil for 96 h then allowed to recover for 96 h, liver replicate 2,1

status: Public on Dec 15 2009

city: Bangor

first: Sharon

middle: E.

last: Hook

state: NSW

address: Private Mail Bag 7

department: Centre for Environmental Contaminants Research

institute: CSIRO

description: Biological replicate 2, Technical replicate 1

hyb_protocol: Samples were mixed with 20 µg tRNA and 20 µg Herring Sperm DNA to prevent non specific hybridization, then mixed with 35 µl of modified Genisphere hybridization buffer (50% formamide, 40% 20x SSC, 9% Denhardt’s solution, 1% SDS). This mixture was then applied to the arrays and allowed to hybridize overnight (16 hr) at 45 o C. After hybridization, arrays were washed in SSC/SDS buffers with descending stringency to remove any unhybridized or weakly (nonspecifically) hybridized cDNAs.

scan_protocol: Arrays were scanned using a Perkin Elmer ScanArray Express, with laser power and PMT gain varied to equalize fluorescence intensity between channels and to prevent over saturation of signal intensity.

data_processing: Data were extracted using ScanArray Express software (Perkin Elmer). The median fluorescence intensity with background subtracted was imported Genespring microarray analysis software for further analysis. Data were LOWESS normalized and spots that did not meet a minimum signal intensity were removed.

label: Alexa Fluor 555

organism: Oncorhynchus mykiss

source_name: liver (control)

label_protocol: Labelled using I\nvitrogen’s Superscript cDNA Indirect Labeling kit and the manufacturer's protocol, and Alexa fluors.

extract_protocol: Trizol extraction following the manufacturer's protocol

treatment_protocol: Juvenile Rainbow trout were exposed to the WAF of Crude oil at the specified dose

tag: treatment

value: control

tag: harvested at what time

label: Alexa Fluor 647

source_name: liver (exposed)

value: 2 mg/L Crude Oil


title: Trout exposed to 2 mg/L crude oil for 96 h then allowed to recover for 96 h, liver replicate 3,1

description: Biological replicate 3, Technical replicate 1


title: Trout exposed to 2 mg/L crude oil for 96 h then allowed to recover for 96 h, liver replicate 2,2

description: Biological replicate 2, Technical replicate 2


title: Trout exposed to 2 mg/L crude oil for 96 h then allowed to recover for 96 h, liver replicate 1,2

description: Biological replicate 1, Technical replicate 2


title: Trout exposed to 2 mg/L crude oil for 96 h, liver replicate 3,2

description: Biological replicate 3, Technical replicate 2


title: Trout exposed to 2 mg/L crude oil for 96 h, liver replicate 1,1

description: Biological replicate 1, Technical replicate 1


title: Trout exposed to 2 mg/L crude oil for 96 h then allowed to recover for 96 h, liver replicate 3,2


title: Trout exposed to 2 mg/L crude oil for 96 h, liver replicate 1,2


title: Trout exposed to 2 mg/L crude oil for 24 h, liver replicate 2,2


title: Trout exposed to 10 mg/L crude oil for 96 h then allowed to recover for 96 h, liver replicate 3,1

value: 10 mg/L Crude Oil


title: Trout exposed to 2 mg/L crude oil for 96 h, liver replicate 2,1


title: Trout exposed to 10 mg/L crude oil for 96 h then allowed to recover for 96 h, liver replicate 3,2


title: Trout exposed to 2 mg/L crude oil for 24 h, liver replicate 2,1


title: Trout exposed to 2 mg/L crude oil for 96 h, liver replicate 3,1


title: Trout exposed to 2 mg/L crude oil for 24 h, liver replicate 1,1


title: Trout exposed to 2 mg/L crude oil for 96 h, liver replicate 2,2


title: Trout exposed to 2 mg/L crude oil for 24 h, liver replicate 1,2


title: Trout exposed to 2 mg/L crude oil for 24 h, liver replicate 3,1


title: Trout exposed to 2 mg/L crude oil for 96 h then allowed to recover for 96 h, liver replicate 1,1


title: Trout exposed to 10 mg/L crude oil for 96 h then allowed to recover for 96 h, liver replicate 1,2


title: Trout exposed to 10 mg/L crude oil for 96 h, liver replicate 3,1


title: Trout exposed to 2 mg/L crude oil for 24 h, liver replicate 3,2


title: Trout exposed to 10 mg/L crude oil for 96 h, liver replicate 2,1


title: Trout exposed to 10 mg/L crude oil for 96 h then allowed to recover for 96 h, liver replicate 1,1


title: Trout exposed to 10 mg/L crude oil for 96 h, liver replicate 2,2


title: Trout exposed to 10 mg/L crude oil for 96 h, liver replicate 1,2


title: Trout exposed to 10 mg/L crude oil for 96 h, liver replicate 1,1


title: Trout exposed to 10 mg/L crude oil for 96 h, liver replicate 3,2