title: 48h p.i. MAH10091 [mRNA]

city: Berlin

first: Soroush

last: Sharbati

address: Oertzenweg 19b

department: Institute of Veterinary Biochemistry

country: Germany

institute: Freie Universitaet Berlin

description:
6_#11#14_Ausw
data from replicate microarrays: colums were combined before data analysis; dye swap experiments: data was converted and treated like data from replicate arrays

hyb_protocol: Automated hybridization and washings were carried out in the aHyb™ Hybridization Station (Miltenyi Biotec). Buffers for prehybridization, hybridization and wash were supplied with the PIQOR™ Microarray Kit (Miltenyi Biotec) and protocols were followed according to the manufacturer’s instructions.

scan_protocol: The microarrays were scanned at 10 µm resolution using a GenePix 4000B scanner (Molecular Devices).

data_processing: Microarray image analysis and ratio-based normalisation of the microarray data was conducted using the software package GenePix Pro 6.1 (Molecular Devices). Data was filtered with respect to background-subtracted signal intensity, signal to noise ratio and Spot diameter. Using Acuity 4.0 data was further processed: the dye swap column operation was applied to dye swap data, so that every log 2 ratio was replaced by its negative. After assessment of reproducibility and evaluation of dye swap experiments, replicate microarray data was combined by calculating the mean of respective log 2 ratios for subsequent analysis.

label: Alexa Fluor 647

source_name: 48h post infection (MAH10091)

label_protocol: aRNA was converted into cDNA and fluorescently labeled using the SuperScript™ Plus Indirect cDNA Labeling System (Life Technologies) and Alexa Fluor® Dyes. 15 µg aRNA and anchored oligo (dT) were used for reverse transcription according to the manufacturer’s protocol. Sample cDNA (infected) was labeled fluorescently with Alexa Fluor® 647, while the control (non-infected) was labeled with Alexa Fluor® 555. One dye swap experiment was performed (5_#6#10_DS).

growth_protocol: Monocytes were isolated from buffy coats using Percoll gradient centrifugation, suspended in IMDM medium (PAA) with 3% human AB serum and incubated at 37 °C and in 5% CO2. Cells were allowed to adhere overnight, non-adherent cells were removed.

extract_protocol: Total RNA was isolated from infected as well as non infected adherent cells using the mirVana miRNA Isolation Kit (Life Technologies). The described procedure was performed in triplicate using the buffy coats from three independent healthy donors. RNA amplification was employed using MessageAmp II aRNA Amplification Kit (Life Technologies) according to the manufacturor’s instructions. Pools of total RNA from three independent infection experiments were prepared for MAH strains 104 and 10091/06 and non-infected controls relating to each point in time (6, 24 and 48 h post infection).

treatment_protocol: The cells were allowed to differentiate during three days in IMDM with 3% AB serum and then infected for 4 h with MAH 104 or MAH 10091/06 at a multiplicity of infection (MOI) of 25. The negative control was not inoculated. After Amikacin treatment samples were taken for RNA isolation after 6 h, 24 h and 48 h post infection.

value: monocyte-derived macrophage

tag: infection

tag: time

label: Alexa Fluor 555

source_name: non-infected control

value: non-infected control


title: Bevacizumab (Avastin) 17.1 (HumanWG-6)

status: Public on Apr 22 2011

type: RNA

city: Houston

first: Tina

last: Cascone

state: TX

address: 1515 Holcombe Blvd.

department: Cancer Medicine

country: USA

institute: UT MD Anderson Cancer Center

hyb_protocol: Each of 1.5 ug of biotinylated cRNAs was hybridized to both Illumina Human WG-6 V3 and Mouse WG-6 V2 microarrays at the same time.

scan_protocol: Signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Health care Bio-Sciences, Little Chalfont, UK). Gene expression data were collected by using Illumina bead Array Reader confocal scanner (BeadStation 500GXDW; Illumina Inc.)

data_processing: Read out files from the Illumina scanner were normalized using RMA and log2base transformed using the BRB-ArrayTools developed by Richard Simon and the BRB-Tools development team. Class comparison between vehicle and drug-treated mice was performed by the BRB-ArrayTools using a p-value statistical cut-off and estimation of the false discovery rate.

label: Biotin labeled

molecule: total RNA

organism: Homo sapiens

source_name: Subcutaneous xenograft (murine) from a mouse treated with bevacizumab (10mg/kg) 17.1

label_protocol: Biotin labeled cRNA samples for hybridization were prepared by using Illumina Total Prep RNA Amplification Kit (Ambion Inc., Austin, TX). One microgram of total RNA was used for the synthesis of cDNA and followed by an amplification and biotin labeling.

extract_protocol: Total RNA was isolated from the cancer tissues by using mirVanaTM miRNA isolation Kit (Ambion Inc., Austin, TX) according to manufacturer’s protocol.

tag: strain

value: Athymic nude mouse

tag: gender

value: male

tag: age

value: 5-8 weeks

tag: xenografts

value: 2 million human H1975 NSCLC cells

tag: tissue

value: lung adenocarcinoma

tag: treatment

value: bevacizumab


title: 48h p.i. MAH104 [mRNA]

source_name: 48h post infection (MAH104)

tag: cell type


title: MCF10A_Keap1 siNA_rep1

city: Baltimore

first: Abena

last: Agyeman

state: MD

address: 615 N Wolfe St

department: Biochemistry and Molecular Biology

institute: Johns Hopkins School of Public Health

description: Gene expression after 24hr Keap1 siRNA exposure

hyb_protocol: Cy3-labeled samples (0.825 ug) were used for hybridization at 65ºC for 17 hours in a hybridization oven with rotation. After hybridization, microarrays were washed and dried in a walk-in ozone-controlled enclosure according to the Agilent microarray processing protocol.

scan_protocol: Microarrays were scanned using an Agilent G2565A Scanner controlled by Agilent Scan Control 7.0 software.

data_processing: Data were extracted with Agilent Feature Extraction 9.5.3.1 software.

source_name: non tumorigenic human breast epithelial MCF10A cell line: Keap1 siNA_rep1

label_protocol: Sample amplification and labeling procedures were carried out using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) with minor modifications. Briefly, 0.4 µg total RNA was reverse-transcribed into cDNA by MMLV-RT using an oligo dT primer (System Biosciences, Mountain View, CA) that incorporates a T7 promoter sequence. The cDNA was then used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine-3 labeled CTP (Perkin Elmer, Waltham, MA). The labeled cRNA was purified using RNeasy mini kit (Qiagen). RNA spike-in controls (Agilent Technologies) were added to RNA samples before amplification and labeling according to the manufacturer’s protocol.

growth_protocol: MCF10A (American Type Culture Collection, Manassas, VA) cells were cultured in (DMEM)/F12 minus L-lysine and L-arginine for SILAC. Medium was supplemented with 5% horse serum, 20ng/ml epidermal Growth Factor, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin and 10 µg/ml insulin at 37°C in a humidified environment with 5% CO2. For light medium 12C6 L-lysine:2HCL and 12C6 L-arginine-HCl were supplemented and for heavy medium 13C6 L-lysine:2HCl and 13C6 L-arginine:HCl were added (Cambridge Isotope Laboratories, Andover, MA).

extract_protocol: Total MCF10A RNA was isolated from cell pellets using TriZol reagent (Invitrogen), followed by RNeasy mini kit with DNase on-column digestion (Quiagen, Valencia, CA). MCF10A RNA was quantified with a NanoDrop ND-1000 (Thermo Scientific) followed by quality assessment with a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s protocol.

treatment_protocol: Cells were transfected with 30nM KEAP1 or non targeting control (NTC) siRNA in heavy and light SILAC media respectively by reverse transfection.  Cells were treated with 15 µM sulforaphane (SFN) or acetonitrile vehicle in heavy and light medium respectively 24 hours after plating. RNA was collected 24 hours after plating. The SFN treatment and KEAP1 knockdown experiments each had four biological replicates

tag: cell line

tag: treatment protocol

value: Keap1 siRNA


title: Bevacizumab (Avastin) 19.1 (HumanWG-6)

source_name: Subcutaneous xenograft (murine) from a mouse treated with bevacizumab (10 mg/kg) 19.1


title: 6h p.i. MAH104 [mRNA]

source_name: 6h post infection (MAH104)


title: 24h p.i. MAH10091 [mRNA]

source_name: 24h post infection (MAH10091)


title: MDA-MB-231_Paclitaxel_Rep1

city: Washington DC

first: Nesrin

last: Rechache

state: Washington DC

address: W401 Research Building  Georgetown University Medical Center  3970 Reservoir Rd NW

institute: Georgetown University

description: Gene expression data from MDA-MB-231 cells grown in normal growth media with 1uM Verapamil and 7nM of Paclitaxel

hyb_protocol: 10 ug of fragmented cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scan protocol Standard Protocol for Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Affymetrix Expression Console version 1.1.2 using Affymetrix default analysis settings and PLIER workflow as normalization method.

label: biotin

source_name: Verapamil and Paclitaxel

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

extract_protocol: RNA isolated from three independent passages of sensitive, Docetaxel and Paclitaxel resistant cell lines using Trizol (Invitrogen; Carlsbad, CA), 2 ml per T-75 flask, followed by Qiagen RNeasy cleanup protocol.

treatment_protocol: Cells were grown in T75 flasks and cultured in normal growth media with 1µM Verapamil for the sensitive cells, 7nM Paclitaxel for Paclitaxel resistant cells and 2nM Docetaxel for Docetaxel resistant cells.

tag: source tissue

value: mammary gland

value: adherant epithelial cells


title: 24h p.i. MAH104 [mRNA] (dye-swap)

description:
4_#6#10_Ausw
data from replicate microarrays: colums were combined before data analysis; dye swap experiments: data was converted and treated like data from replicate arrays

label: Alexa Fluor 647, Alexa Fluor 555

source_name: 24h post infection (MAH104)


title: MCF10A_NTC siRNA_rep4

description: Gene expression after 24hr NTC siRNA exposure

source_name: non tumorigenic human breast epithelial MCF10A cell line: NTC siRNA_rep4

value: non targeting control (NTC) siRNA


title: MDA-MB-231_Docetaxel_Rep1

description: Gene expression data from MDA-MB-231 cells grown in normal growth media with 1uM Verapamil and 2nM Docetaxel

source_name: Verapamil and Docetaxel


title: MCF10A_NTC siRNA_rep3

source_name: non tumorigenic human breast epithelial MCF10A cell line: NTC siRNA_rep3


title: MDA-MB-231_Docetaxel_Rep3


title: Vehicle 7.1 (PBS) control (HumanWG-6)

source_name: Subcutaneous xenograft (murine) from a mouse treated with control (PBS) vehicle 7.1

value: PBS


title: MDA-MB-231_Docetaxel_Rep2


title: MCF10A_NTC siRNA_rep1

source_name: non tumorigenic human breast epithelial MCF10A cell line: NTC siRNA_rep1


title: MCF10A_NTC siRNA_rep2

source_name: non tumorigenic human breast epithelial MCF10A cell line: NTC siRNA_rep2


title: Vehicle 2.1 (PBS) control (HumanWG-6)

source_name: Subcutaneous xenograft (murine) from a mouse treated with control (PBS) vehicle 2.1


title: MDA-MB-231_Verapamel_Rep3

description: Gene expression data from MDA-MB-231 cells grown in normal growth media with 1uM Verapamil

source_name: Verapamil only_control


title: Vehicle 5.2 (PBS) control (HumanWG-6)

source_name: Subcutaneous xenograft (murine) from a mouse treated with control (PBS) vehicle 5.2


title: 48h p.i. MAH104 [miRNA]

hyb_protocol: Fully automated hybridisation and washings were carried out in the aHyb™ Hybridization Station (Miltenyi Biotec). Buffers were supplied with the miRCURY LNA miRNA Array kit. Slides were prehybridised at 56 °C for 5 min. Fluorescently labeled samples were hybridized for 16 hours at 56 °C. The slides were washed twice for 1 minute with buffer A at 56 °C followed by two successive washes at 23 °C using buffers B and C, respectively. Afterwards, dipped in bi-distilled water dried by brief centrifugation.

data_processing:
Microarray image analysis and ratio-based normalisation of the microarray data was conducted using the software package GenePix Pro 6.1 (Molecular Devices). Data was filtered with respect to background-subtracted signal intensity, signal to noise ratio and Spot diameter. Using Acuity 4.0 data was further processed: the dye swap column operation was applied to dye swap data, so that every log 2 ratio was replaced by its negative. After assessment of reproducibility and evaluation of dye swap experiments, replicate microarray data was combined by calculating the mean of respective log 2 ratios for subsequent analysis.
Note that microRNA from only one single cell population was quantified (human macrophages). Furthermore, we used very stringent conditions for hybridization as well as filtering of data in order to assure validity.

label_protocol: Samples (RNA from infected cells) were labelled with Hy5, while the control (RNA from non infected cells) was labelled with Hy3, except for the dye swap experiment (P#6#10_0365_DS_7). miRCURY LNA miRNA Array Power Labeling kit (Exiqon) was used according to the manufacturor's protocol.

extract_protocol: Total RNA was isolated from infected as well as non infected adherent cells using the mirVana miRNA Isolation Kit (Life Technologies). The described procedure was performed in triplicate using the buffy coats from three independent healthy donors. Pools of total RNA from three independent infection experiments were prepared for MAH strains 104 and 10091/06 and non-infected controls relating to each point in time (6, 24 and 48 h post infection).

source_name: non-infected control


title: 48h p.i. MAH10091 [miRNA]

source_name: 48h post infection (MAH10091)


title: 6h p.i. MAH10091 [mRNA]

source_name: 6h post infection (MAH10091)


title: MCF10A_SFN_rep3

description: Gene expression after 24hr SFN treatment

source_name: non tumorigenic human breast epithelial MCF10A cell line: SFN_rep3

value: SFN


title: MDA-MB-231_Verapamel_Rep2


title: 24h p.i. MAH104 [miRNA] (dye-swap)

description: data from replicate microarrays: colums were combined before data analysis; dye swap experiments: data was converted and treated like data from replicate arrays


title: 24h p.i. MAH10091 [miRNA]


title: WT 3

city: Cambridge

first: Sergiy

last: Libert

state: MA

address: 77 Mass ave

institute: MIT

hyb_protocol: Standard protocol recommended by manufacturer Affymetrix

data_processing: We used Agilent GeneSpring GX v.11.0 for the analysis of the data. We used Robust Multichip Average (RMA) algorithm as the initial method for chip summarization.

organism: Mus musculus

source_name: Brain of WT mice

extract_protocol: Trizol, according to manufacturer’s manual, followed by purification with Quigen RNA easy kit.

value: Males

value: 3 months old

value: Brain


title: 6h p.i. MAH10091 [miRNA]

value: monocyte-derived macrophage


title: BSKO 3

scan_protocol: Standard protocol recommended by manufacturer Affymetrix

source_name: Brain of BSKO mice


title: MDA-MB-231_Verapamel_Rep1


title: MCF10A_SFN_rep4

source_name: non tumorigenic human breast epithelial MCF10A cell line: SFN_rep4


title: MCF10A_Vehicle_rep3

description: Gene expression after 24hr Vehicle treatment

source_name: non tumorigenic human breast epithelial MCF10A cell line: Vehicle_rep3

value: Vehicle


title: BSKO 4

label_protocol: Standard protocol recommended by manufacturer Affymetrix


title: WT 4


title: MCF10A_Vehicle_rep1

source_name: non tumorigenic human breast epithelial MCF10A cell line: Vehicle_rep1


title: BSKO 2


title: WT 2


title: 6h p.i. MAH104 [miRNA]

source_name: 6h post infection (MAH104)

value: non-infected control


title: MCF10A_SFN_rep2

source_name: non tumorigenic human breast epithelial MCF10A cell line: SFN_rep2


title: CD4 14 MOG 0

city: Lodz

first: Marcin

middle: P

last: Mycko

address: Kopcinskiego 22

department: Department of Neurology

country: Poland

institute: Medical University of Lodz

description: Exiqon 10.0

hyb_protocol: Using Tecan hybridization stations the hybridization and washing steps are fully automated for excellent reproducibility  (Exiqon).

scan_protocol: Arrays are scanned with highly sensitive equipment in ozone free environment to reduce day-to-day variation to a minimum. Image Analysis is then performed to quantify the signals on the arrays (Exiqon).

data_processing:
Normalization method: LOWESS. The data obtained is normalized using methods applicable to the performed experiment (Exiqon).
Depending on the experimental setup and the size of the project customized data analysis is provided (including heat map/Unsupervised Hierarchical Clustering, PCA-plots etc based on TTests or ANOVA) (Exiqon).

source_name: CD4+ T cells

label_protocol: Our miRCURY™ LNA Array Power labeling kit allows highly efficient and uniform labeling of microRNAs with minimal sequence bias (Exiqon).

growth_protocol: CD4+ T cells have been magnetics beads purified from peripheral lymph nodes of Cd57Bl/6 mice that has been immunized with 150 ug of MOG peptide 35-55 in CFA.

extract_protocol: mirVana kit (Ambion)

treatment_protocol: Cells were either unstimulated (0) or stimulated in vitro for 14 days with 50 ug/ml of MOG peptide 35-55 (14)

value: MOG35-55 in CFA

source_name: Common reference pool


title: CD4 14 CFA 0

description: Exiqon 10.0

value: CFA


title: CD4 14 CFA 3

description: Exiqon 10.0


title: CD4 14 MOG 3

description: Exiqon 10.0


title: MCF10A_SFN_rep1

source_name: non tumorigenic human breast epithelial MCF10A cell line: SFN_rep1


title: MCF10A_Vehicle_rep2

source_name: non tumorigenic human breast epithelial MCF10A cell line: Vehicle_rep2


title: WT 1


title: BSKO 1


title: MCF10A_Vehicle_rep4

source_name: non tumorigenic human breast epithelial MCF10A cell line: Vehicle_rep4


title: blastomere_triplet_2_small_B

status: Public on Apr 21 2011

city: Regensburg

first: Matthias

last: Maneck

address: Franz-Josef-Strauß-Allee 11

department: Department of Pathology

institute: University of Regensburg

hyb_protocol: Murine Operon 70mer oligonucleotide arrays (Version 4) were prehybridized with 5x SSC + 0.1% SDS + 0.1% BSA at 42°C and hybridized in an Array-booster hybridization station (Implen, Munich) at 42°C overnight. Washing steps following hybridization were twice in 2x SSC+0.1% SDS for 5 min at 42°C, twice in 0.1x SSC+0.1% SDS for 10 min at room temperature, and twice in 0.1x SSC for 2.5 min. Unspecific binding of labelled proteins was blocked with 1% blocking reagent for nucleic acid hybridization (Roche) followed by a staining procedure with anti-Dig-Cy5 and Streptavidin-Cy3 (each 16 µg/ml, Jackson Laboratories). Excess antibody/streptavidin was removed with two washings in 4x SSC + 0.2% Tween-20 for 10 min and final washing in 10 mM Tris.

scan_protocol: Slides were scanned on a GenePix 4000B scanner (Molecular Devices). Images were gridded and spots were quantified using GenePix Pro 3.0 software (Molecular Devices). Features and areas of obvious defects were manually flagged and excluded.

data_processing:
Raw probe intensities were background corrected by applying the normexp method of limma. Loess normalization was used in M vs. A plots of individual intensities of transcripts in one array and the median intensity across all arrays of the same transcript. Log2-ratios were calculated from the normalized intensities and quantile normalization was applied for normalization across arrays.
Although the raw data are two channel, only the Cy5 signal of each file was analyzed. The Cy5 channel for each gene is normalized to the average Cy5 intensity of the gene across all samples.

source_name: blastomere of 3 cell embryo

label_protocol: Primary cDNA amplification products were labelled in the presence of 3% formamide, 2.4 µM CP2-BGL primer (TCAGAATTCATGCCGCCCCCCCGGCCC), dNTPs (0.35 mM dATP and dGTP, 0.3 mM dTTP and dCTP) and 0.05 mM labelled nucleotides. Sample cDNA was labelled with digoxygenin-dUTP (Roche) and aminodigoxygenin-dCTP (PerkinElmer, Rodgau-Jügesheim), reference cDNA with biotin-dUTP (Roche) and biotin-dCTP (Invitrogen). Universal reference cDNA was pooled from various murine tissues and cell lines. Labeling was performed as following: 12 cycles of 15 s at 94°C, 4 min at 68°C and 3 cycles with an elongation of the extension time of 10 s and a final elongation step of 7 min at 68°C. The primers were removed by a digest with 30 U BglI (Fermentas, St Leon-Rot) and the samples purified on a purification column (Qiagen, Hilden).

growth_protocol: Culture of oocytes and embryos in vitro was for the minimum time, in KSOM medium as described in Amanai et al., Biol. Reprod. 75, 877-884 (2006).

extract_protocol: Isolated single cells were placed in 4,4 µl of lysis buffer (Active Motif, Rixensart, Belgium) supplemented with 10 ng of E. coli tRNA (Roche, Mannheim) and stored on dry ice and -80°C, prior to processing. mRNA isolation and global amplification of 1st strand cDNA was carried out as as previously published (Hartmann CH, Klein CA. Gene expression profiling of single cells on large-scale oligonucleotide arrays. Nucleic Acids Res 2006, 34(21):e143.). The proteolytic digest was performed by adding of 2 µl of lysis solution, containing 1 µl of lysis buffer, supplemented with 1 µg of protease (Active Motif, Rixensart, Belgium), and 1 µl of 60 µM biotinylated oligo-dT peptide nucleic acids (PNAs) (Active Motif, Rixensart, Belgium) and incubating at 45°C for 10 min, followed by 1 min at 70°C and 15 min at 22°C for PNA annealing. mRNA was isolated with 4 µl streptavidin-conjugated magnetic beads (Active Motif, Rixensart, Belgium) during 45 min rotation (to avoid sedimentation of beads) at room temperature. Ten microliters of cDNA wash buffer 1 (50 mM Tris–HCl pH 8.3, 75 mM KCl, 3 mM MgCl2, 10 mM DTT and 0.25% Igepal) were added and the tubes placed into a magnetic rack, to pellet the beads. The supernatant containing the genomic DNA was collected and the beads were washed using 20 µl of cDNA wash buffer 2 (50 mM Tris–HCl pH 8.3, 75 mM KCl, 3 mM MgCl2, 10 mM DTT, 0.5% Tween-20). The supernatant was removed and the step repeated with 20 µl of cDNA wash buffer 1. Reverse transcription was carried out under rotation (to avoid sedimentation of beads) for 45 min at 44°C in a mix containing 0.5 mM dNTPs, 200 U Superscript II (Invitrogen, Karlsruhe), 30 µM CFL15CN8 primer (C15GTCTAGAN8), 15 µM CFL15CT24 primer (C15GTCTAGAT24VN), 0.25% Igepal, 10 mM DTT (Invitrogen, Karlsruhe) and the RT buffer supplied by the manufacturer, in a final volume of 20 µl. Primers were annealed at room temperature for 10 min before addition of the enzyme. After completing the reverse transcription, beads were washed in 20 µl of tailing wash buffer (50 mM KH2PO4 pH 7, 1 mM DTT, 0.25% Igepal) and resuspended in 10 µl of tailing buffer (10 mM KH2PO4 pH 7, 4 mM MgCl2, 0.1 mM DTT, 200 µM dGTP). After denaturation of the cDNA–mRNA hybrids at 94°C for 4 min, samples were chilled on ice, and 10 U of Terminal deoxynucleotide transferase (Amersham, Freiburg) were added and the samples incubated at 37°C for 60 min for the G-tailing reaction. After inactivation of the tailing enzyme (70°C, 5 min), 35 µl of PCR mix I [4 µl buffer 1 (Expand Long Template, Roche), 3% deionized formamide, and water] was added to each sample. A hotstart PCR was performed adding 5.5 µl PCR mix II [350 mM dNTPs, 1.2 µM CP2 primer (TCAGAATTCATGC15) and 5 U PolMix (Expand Long Template)]. Forty cycles were run in a MJ research PCR thermal cycler: 20 cycles of 15 s at 94°C, 30 s at 65°C, 2 min at 68°C and 20 cycles with an elongation of the extension time of 10 s and a final elongation step of 7 min at 68°C.

treatment_protocol: IVF was performed according to Amanai et al., Biol. Reprod. 75, 877-884 (2006). Spindle microsurgery was within 3 min of samples being removed from culture media. Blastomeres were separated by trituration through a blunted pipette immediately after cleavage, determined by observing pools of embryos incubated in separate dishes. This process is described in detail in VerMilyea et al., 2011.

tag: type

value: blastomere triplet


title: blastomere_triplet_5_small_B


title: blastomere_triplet_7_small_B


title: blastomere_triplet_3_small_B


title: blastomere_triplet_4_small_B


title: blastomere_triplet_4_small_A


title: blastomere_triplet_5_small_A


title: blastomere_triplet_3_small_A


title: blastomere_triplet_6_small_B


title: blastomere_triplet_7_small_A


title: blastomere_triplet_6_small_A


title: blastomere_triplet_8_small_A


title: blastomere_triplet_1_small_B


title: 1-CD4-4-S

city: Chicago

first: Albert

last: Bendelac

state: IL

address: 929 East 57th Street, GCIS W506

department: Pathology

institute: The University of Chicago

hyb_protocol: 12µg of fragmented cRNA was hybridized to the array for 16 hours at 45°C and 60 rpm.  The array was washed and stained with streptavidin phycoerythrin according to the Affymetrix GeneChip protocol.

scan_protocol: The array was scanned using the Affymetrix Gene Chip Scanner 3000 7G and the CEL intensity files was generated using Gene Chip Operating Software (MicroArray Suite 5.0).

data_processing: Data was generated using MicroArray Suite 5.0 and scaled to a median intensity of 500.

label: Biotin

source_name: Individual #1, CD4 T cell clone #4, stimulated

label_protocol: Biotin-labeled cRNA was generated using the Genechip Expression 3´ amplification IVT labeling kit (Affymetrix).

extract_protocol: Trizol protocol (Invitrogen) followed by the RNeasy Mini kit (Qiagen)

treatment_protocol: Stimulated 3 days prior to analysis with feeder cells consisting of irradiated allogenic PBMC (50,000/well) and irradiated EBV-transformed cells (5,000/well), in medium containing 1μg/ml PHA and 100U/ml human IL-2.

value: CD4 T cell clone


title: blastomere_triplet_8_large


title: blastomere_triplet_7_large


title: blastomere_triplet_1_small_A


title: blastomere_triplet_6_large


title: blastomere_triplet_2_small_A


title: blastomere_triplet_2_large


title: blastomere_triplet_8_small_B


title: blastomere_triplet_5_large


title: blastomere_triplet_4_large


title: blastomere_pair_22_B

source_name: blastomere of 2 cell embryo

value: blastomere pair


title: blastomere_triplet_1_large


title: blastomere_pair_19_B


title: blastomere_pair_20_B


title: blastomere_pair_14_B


title: blastomere_pair_21_B


title: blastomere_pair_15_B


title: blastomere_pair_10_B


title: blastomere_pair_16_B


title: blastomere_pair_17_B


title: blastomere_pair_12_B


title: blastomere_pair_9_B


title: blastomere_pair_8_B


title: blastomere_pair_7_B


title: blastomere_triplet_3_large


title: blastomere_pair_5_B


title: blastomere_pair_3_B


title: blastomere_pair_18_B


title: blastomere_pair_6_B


title: blastomere_pair_4_B


title: blastomere_pair_11_B


title: blastomere_pair_2_B


title: blastomere_pair_1_B


title: CD4 0

description: Exiqon 10.0

value: unstimulated


title: blastomere_pair_21_A


title: blastomere_pair_22_A


title: blastomere_pair_18_A


title: blastomere_pair_13_B

description: 080201-8 rescan


title: blastomere_pair_17_A


title: blastomere_pair_19_A


title: blastomere_pair_14_A


title: blastomere_pair_10_A


title: blastomere_pair_20_A


title: blastomere_pair_15_A


title: blastomere_pair_13_A

description: 080201-7 rescan


title: blastomere_pair_11_A


title: blastomere_pair_6_A


title: blastomere_pair_7_A


title: blastomere_pair_3_A


title: blastomere_pair_2_A


title: blastomere_pair_4_A


title: blastomere_pair_9_A


title: oocyte_pair_10

source_name: oocyte with removed spindle

value: oocyte


title: oocyte_pair_8


title: oocyte_pair_9


title: blastomere_pair_16_A


title: oocyte_pair_5


title: blastomere_pair_5_A


title: oocyte_pair_2


title: oocyte_pair_1


title: oocyte_pair_6


title: spindle_pair_8

source_name: spindle removed from oocyte

value: spindle


title: oocyte_pair_4


title: spindle_pair_6


title: spindle_pair_4


title: spindle_pair_10


title: blastomere_pair_1_A


title: spindle_pair_5


title: oocyte_pair_3


title: blastomere_pair_12_A


title: blastomere_pair_8_A


title: oocyte_pair_7


title: spindle_pair_9


title: spindle_pair_7


title: spindle_pair_1


title: polarbody_pair_11

source_name: polar body 3h after IVF start

value: pbs


title: polarbody_pair_15


title: spindle_pair_2


title: polarbody_pair_14


title: spindle_pair_3


title: polarbody_pair_13


title: polarbody_pair_12


title: polarbody_pair_9


title: polarbody_pair_8


title: polarbody_pair_6


title: polarbody_pair_4


title: polarbody_pair_2


title: polarbody_pair_7


title: zygote_pair_11

source_name: zygote 3h after IVF start

value: zygote


title: zygote_pair_8


title: polarbody_pair_3


title: zygote_pair_13


title: zygote_pair_12


title: polarbody_pair_16


title: polarbody_pair_10


title: zygote_pair_10


title: zygote_pair_16


title: zygote_pair_9


title: polarbody_pair_5


title: zygote_pair_7


title: polarbody_pair_1


title: zygote_pair_14


title: zygote_pair_5


title: zygote_pair_3


title: zygote_pair_4


title: zygote_pair_6


title: zygote_pair_2


title: zygote_pair_1


title: DD DAY 3 TIME 04:00 Replicate 3

city: Ramat Gan

first: Oren

last: Levy

address: Max and Anna Web

department: The Mina and Everard Goodman Faculty of Life Sciences

country: Israel

institute: Bar Ilan University

description: Biological replicate 3 of 3

hyb_protocol: Microarrays were pre-hybridized and hybridized with the labeled samples using the Genisphere 3DNA-900 microarray kit following the manufacturer’s instructions and using a dynamic hybridization system (MAUI, BioMicro Systems). Prior to and post hybridization the microarray slides were washed three times (wash 1: 2 x SSC 0.2 % SDS at 65°C for 15 min, Wash 2: 2 x SSC at room temperature for 10 min, Wash 3: 0.2 x SSC at room temperature for 10 min)

scan_protocol: Slides were scanned using a GenePix ® 4200 scanner (Axon Instruments) and image acquisition was performed using the software GenePix ® Pro 5.

data_processing: Both within-slide and between-slides normalizations were performed. Within-slide normalization included:   (1) Background correction. Whenever the foreground intensities were higher then the background intensities, the latter were subtracted from the foreground. In the other cases the foreground intensities were corrected according to Edwards (2003, Bioinformatics).    (2) Correction of spatial variation. In each print-tip steps 3&4 of the normalization were done separately (Yang et al., 2002, Nucleic Acids Res). Finally, step 5 guarantied that all the print-tips had the same median absolute deviation (MAD).  (3) Total intensity normalization. The mean logarithm of the expression ratios ('log ratios') was fixed to zero by subtracting a constant from the log ratios.    (4) Correction of intensity-dependent biases. The Lowess method was utilized in order to correct intensity-dependent biases in the log ratios.    (5) Within-slide MAD regularization. While steps 3 and 4 adjust the mean log ratios to zero, the variance in the log ratios can vary between different print-tip. To overcome this problem all the different print-tips where normalized together using the MAD scale (Yang et al., 2002, Nucleic Acids Res).    Between-slide normalization included:   (6) Between-slide MAD regularization. The variance in the log ratios vary between slides. Again, the MAD scale normalization was used to fix this problem.     (7) Averaging over replicates. The probes had their log ratios averaged between replicates.

organism: Acropora millepora

source_name: Coral colony, under constant darkness (DD), day 3, time 04:00

label_protocol: cDNA probe synthesis was performed from 1000 ng total RNA using Superscript Reverse Transcriptase (Invitrogen) and 2 pmol of chimeric reverse transcription primer (Genisphere). We used a reference two-colour microarray design, where for each array the sample was labeled with Cy5 and the reference, consisting of pooled RNA from all treatments and time points, was labeled with Cy3.

extract_protocol: Total RNA was extracted from each sample using Trizol (Invitrogen) following manufacturer’s instructions. The integrity and quality of total RNA was assessed using a Bioanalyzer (Agilent Technology). Only samples showing intact RNA were used for probe construction.

tag: coral colony

tag: light conditions

value: constant darkness (DD)

tag: day

tag: sample type

value: reference (i.e., pooled RNA from all treatments and time points)


title: DD DAY 3 TIME 04:00 Replicate 1

description: Biological replicate 1 of 3

source_name: pooled RNA from all treatments and time points


title: DD DAY 2 TIME 24:00 Replicate 3

description: Biological replicate 3 of 3

source_name: Coral colony, under constant darkness (DD), day 2, time 24:00


title: DD DAY 2 TIME 20:00 Replicate 2

description: Biological replicate 2 of 3

source_name: Coral colony, under constant darkness (DD), day 2, time 20:00


title: DD DAY 2 TIME 20:00 Replicate 3

description: Biological replicate 3 of 3


title: DD DAY 2 TIME 20:00 Replicate 1

description: Biological replicate 1 of 3


title: DD DAY 2 TIME 24:00 Replicate 2

description: Biological replicate 2 of 3


title: DD DAY 3 TIME 04:00 Replicate 2

description: Biological replicate 2 of 3


title: DD DAY 2 TIME 12:00 Replicate 3

description: Biological replicate 3 of 3

source_name: Coral colony, under constant darkness (DD), day 2, time 12:00


title: 4712R

type: genomic

city: Los Angeles

first: Sven

last: Bocklandt

state: California

address: Gonda 5524, 695 Charles Young Drive S

department: Department of Human Genetics

institute: UCLA

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

source_name: saliva sample

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from saliva samples collected with the Oragene DNA system, according to Genotek's standard instructions

tag: pair id number

value: Heterosexual

tag: race

value: White


title: DD DAY 2 TIME 16:00 Replicate 1

description: Biological replicate 1 of 3

source_name: Coral colony, under constant darkness (DD), day 2, time 16:00

tag: time


title: DD DAY 2 TIME 16:00 Replicate 3

description: Biological replicate 3 of 3


title: DD DAY 2 TIME 12:00 Replicate 2

description: Biological replicate 2 of 3


title: DD DAY 2 TIME 16:00 Replicate 2

description: Biological replicate 2 of 3


title: 912R


title: 4511R

value: Homosexual


title: 5611R

value: Af Am


title: 112R2


title: 6211R


title: 3211R


title: DD DAY 2 TIME 24:00 Replicate 1

description: Biological replicate 1 of 3


title: 112R1


title: 111R2


title: 6212R


title: DD DAY 2 TIME 08:00 Replicate 3

description: Biological replicate 3 of 3

source_name: Coral colony, under constant darkness (DD), day 2, time 08:00


title: DD DAY 2 TIME 08:00 Replicate 1

description: Biological replicate 1 of 3


title: DD DAY 2 TIME 08:00 Replicate 2

description: Biological replicate 2 of 3


title: DD DAY 2 TIME 12:00 Replicate 1

description: Biological replicate 1 of 3


title: zygote_pair_15


title: DD DAY 2 TIME 04:00 Replicate 2

description: Biological replicate 2 of 3

source_name: Coral colony, under constant darkness (DD), day 2, time 04:00


title: DD DAY 2 TIME 04:00 Replicate 1

description: Biological replicate 1 of 3


title: 7412


title: 111R1


title: DD DAY 1 TIME 24:00 Replicate 3

description: Biological replicate 3 of 3

source_name: Coral colony, under constant darkness (DD), day 1, time 24:00


title: 5612R


title: 7411


title: 7312


title: DD DAY 1 TIME 24:00 Replicate 2

description: Biological replicate 2 of 3


title: 6511


title: 6512


title: 6212


title: 6211


title: 5912


title: DD DAY 1 TIME 20:00 Replicate 1

description: Biological replicate 1 of 3

source_name: Coral colony, under constant darkness (DD), day 1, time 20:00


title: 7311


title: DD DAY 1 TIME 20:00 Replicate 3

description: Biological replicate 3 of 3


title: DD DAY 1 TIME 20:00 Replicate 2

description: Biological replicate 2 of 3


title: 5911


title: DD DAY 1 TIME 16:00 Replicate 2

description: Biological replicate 2 of 3

source_name: Coral colony, under constant darkness (DD), day 1, time 16:00


title: DD DAY 1 TIME 24:00 Replicate 1

description: Biological replicate 1 of 3


title: DD DAY 1 TIME 16:00 Replicate 3

description: Biological replicate 3 of 3


title: 4711R


title: 5712


title: 5711


title: DD DAY 1 TIME 12:00 Replicate 3

description: Biological replicate 3 of 3

source_name: Coral colony, under constant darkness (DD), day 1, time 12:00


title: DD DAY 1 TIME 12:00 Replicate 1

description: Biological replicate 1 of 3


title: DD DAY 1 TIME 16:00 Replicate 1

description: Biological replicate 1 of 3


title: DD DAY 1 TIME 08:00 Replicate 1

description: Biological replicate 1 of 3

source_name: Coral colony, under constant darkness (DD), day 1, time 08:00


title: DD DAY 1 TIME 12:00 Replicate 2

description: Biological replicate 2 of 3


title: DD DAY 1 TIME 08:00 Replicate 3

description: Biological replicate 3 of 3


title: 5511


title: DD DAY 1 TIME 08:00 Replicate 2

description: Biological replicate 2 of 3


title: 5312


title: LD DAY 3 TIME 04:00 Replicate 3

description: Biological replicate 3 of 3

source_name: Coral colony, under an ambient light/dark (LD) cycle, day 3, time 04:00

value: ambient light/dark (LD) cycle


title: 5412


title: 5411


title: LD DAY 2 TIME 24:00 Replicate 3

description: Biological replicate 3 of 3

source_name: Coral colony, under an ambient light/dark (LD) cycle, day 2, time 24:00


title: LD DAY 3 TIME 04:00 Replicate 1

description: Biological replicate 1 of 3


title: 5612


title: LD DAY 2 TIME 24:00 Replicate 2

description: Biological replicate 2 of 3


title: 5611


title: 5512


title: 4912


title: LD DAY 2 TIME 20:00 Replicate 3

description: Biological replicate 3 of 3

source_name: Coral colony, under an ambient light/dark (LD) cycle, day 2, time 20:00


title: 5311


title: 4911


title: LD DAY 2 TIME 24:00 Replicate 1

description: Biological replicate 1 of 3


title: LD DAY 2 TIME 16:00 Replicate 2

description: Biological replicate 2 of 3

source_name: Coral colony, under an ambient light/dark (LD) cycle, day 2, time 16:00


title: 4812


title: 5112


title: 4811


title: LD DAY 2 TIME 20:00 Replicate 1

description: Biological replicate 1 of 3

source_name: pooled RNA from all treatments and time points


title: 4712


title: LD DAY 2 TIME 12:00 Replicate 3

description: Biological replicate 3 of 3

source_name: Coral colony, under an ambient light/dark (LD) cycle, day 2, time 12:00


title: LD DAY 2 TIME 12:00 Replicate 2

description: Biological replicate 2 of 3


title: 4611


title: 4711


title: 4612


title: 4512


title: LD DAY 2 TIME 16:00 Replicate 1

description: Biological replicate 1 of 3


title: LD DAY 2 TIME 08:00 Replicate 2

description: Biological replicate 2 of 3

source_name: Coral colony, under an ambient light/dark (LD) cycle, day 2, time 08:00


title: LD DAY 2 TIME 12:00 Replicate 1

description: Biological replicate 1 of 3


title: LD DAY 2 TIME 04:00 Replicate 2

description: Biological replicate 2 of 3

source_name: Coral colony, under an ambient light/dark (LD) cycle, day 2, time 04:00


title: LD DAY 2 TIME 08:00 Replicate 1

description: Biological replicate 1 of 3


title: LD DAY 2 TIME 04:00 Replicate 3

description: Biological replicate 3 of 3


title: 4312

source_name: saliva sample


title: 4411


title: LD DAY 2 TIME 04:00 Replicate 1

description: Biological replicate 1 of 3


title: 4311


title: 4211


title: 4414


title: LD DAY 2 TIME 20:00 Replicate 2

description: Biological replicate 2 of 3


title: 4212


title: 4012


title: LD DAY 1 TIME 24:00 Replicate 2

description: Biological replicate 2 of 3

source_name: Coral colony, under an ambient light/dark (LD) cycle, day 1, time 24:00


title: LD DAY 1 TIME 24:00 Replicate 1

description: Biological replicate 1 of 3


title: 3812


title: DD DAY 2 TIME 04:00 Replicate 3

description: Biological replicate 3 of 3


title: 4412


title: LD DAY 1 TIME 24:00 Replicate 3

description: Biological replicate 3 of 3


title: 4511


title: LD DAY 1 TIME 20:00 Replicate 3

description: Biological replicate 3 of 3

source_name: Coral colony, under an ambient light/dark (LD) cycle, day 1, time 20:00


title: LD DAY 2 TIME 08:00 Replicate 3

description: Biological replicate 3 of 3


title: 3811


title: 3212


title: 4011


title: LD DAY 1 TIME 20:00 Replicate 1

description: Biological replicate 1 of 3


title: LD DAY 1 TIME 20:00 Replicate 2

description: Biological replicate 2 of 3


title: LD DAY 1 TIME 12:00 Replicate 3

description: Biological replicate 3 of 3

source_name: Coral colony, under an ambient light/dark (LD) cycle, day 1, time 12:00


title: 3112

value: Latino


title: LD DAY 1 TIME 16:00 Replicate 1

description: Biological replicate 1 of 3

source_name: Coral colony, under an ambient light/dark (LD) cycle, day 1, time 16:00


title: 3211


title: LD DAY 1 TIME 16:00 Replicate 3

description: Biological replicate 3 of 3


title: LD DAY 1 TIME 16:00 Replicate 2

description: Biological replicate 2 of 3


title: 3012


title: 3011


title: 2512


title: 3111


title: 2511


title: LD DAY 1 TIME 12:00 Replicate 1

description: Biological replicate 1 of 3


title: 94-4_Tumor

city: Taipei

first: Chien-Wei

last: Tseng

address: No. 1, Sec. 4, Roosevelt Road

country: Taiwan

institute: National Taiwan University

hyb_protocol: The labeled RNA was hybridized to Agilent human miRNA microarrays for 20 hours at 55°C.

scan_protocol: The hybridized microarrays were washed and scanned using an Agilent G2565A scanner. Data were extracted from the scanned images using Agilent Feature Extraction software image analysis.

data_processing: Scanned images were analyzed by Feature extraction 9.1 software (Agilent Technologies, U.S.A.), and an image analysis and normalization software was used to quantify signal and background intensity for each feature. The data were substantially normalized by the rank-consistency-filtering LOWESS method. The normalized value was obtained from the ratio of each gene's signal in normal tissue to its signal in tumor tissue (data can be found on Series record; GSE28700.txt).

source_name: tumor tissue

label_protocol: Each sample was prepared according to the Agilent's miRNA Microarray System protocol. Total RNA (100 ng) from normal or tumor tissues was dephosphorylated with 11.2 units of calf intestine alkaline phosphatase (GE Healthcare Life Sciences, Sweden),  denatured with dimethyl sulfoxide and labeled with pCp-Cy3 using T4 RNA ligase (GE Healthcare Europe GmbH, Otelfingen, Switzerland).

extract_protocol: MicroRNA was extracted by the miRNeasy Mini Kit (Qiagen, Inc.) following manufacturer's instructions. The quality of the purified RNA was determined using a BioAnalyzer (Agilent Technologies, Palo Alto, CA).

tag: disease state

value: tumor


title: LD DAY 1 TIME 12:00 Replicate 2

description: Biological replicate 2 of 3


title: LD DAY 1 TIME 08:00 Replicate 3

description: Biological replicate 3 of 3

source_name: Coral colony, under an ambient light/dark (LD) cycle, day 1, time 08:00


title: LD DAY 1 TIME 08:00 Replicate 1

description: Biological replicate 1 of 3


title: 2111

tag: age


title: 2311


title: LD DAY 1 TIME 08:00 Replicate 2

description: Biological replicate 2 of 3


title: 2411


title: 2312


title: 2012


title: 2112


title: 94-4_Normal

source_name: normal tissue

value: normal


title: 94-20_Normal


title: 94-35_Normal


title: 94-20_Tumor


title: 94-21_Tumor


title: 94-35_Tumor


title: 94-21_Normal


title: 2011


title: 1411


title: 94-2_Normal


title: 94-46_Tumor


title: 1012


title: 1412


title: 94-44_Tumor


title: 94-2_Tumor


title: 94-46_Normal


title: 1011


title: 912


title: LD DAY 3 TIME 04:00 Replicate 2

description: Biological replicate 2 of 3


title: 812


title: LD DAY 2 TIME 16:00 Replicate 3

description: Biological replicate 3 of 3


title: 93-31_Tumor


title: 5111


title: 911


title: 94-44_Normal


title: 93-31_Normal


title: Lcn2_Hepa_1hD

city: Bethesda

first: Myong-Hee

last: Sung

address: 41 Library Dr

department: NCI

institute: NIH

description:
411633
Lipocalin 2 (Lcn2) 4C from cell line Hepa1C1C7; subset E.
Pool of 2 biological replicates.

hyb_protocol: 25-30 µg of the Cy5-labeled 4C DNA was mixed with an equal amount of Cy3-labeled genomic DNA and precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol. DNA was recovered and hybridized in 39ul hybridization buffer following chromatin immunoprecipitation (ChIP)-chip protocols (Nimblegen Systems; chapter 4 in http://www.nimblegen.com/products/lit/NG_ChIP-chip_Guide_v6p2.pdf). Arrays were sealed with Maui mixer SL and hybridized in Maui hybridization stations for 16 h at 42C. Arrays were washed at room temperature in 6X SSPE/5x10E-3 % Sodium N-lauroylsarcosinate for 5 minutes and two 5 minutes washes with 0.06% SSPE.

scan_protocol: Arrays were scanned on an Agilent G2939A scanner per manufacturer's protocol.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2 ChIP data extraction. LogRatios of PAIR file values were taken; then quantile normalization was applied to each subset A,...,E (a batch of 4C samples) separately to generate the Sample data table values. The normalization was performed using a custom-written code in the statistical programming language R.

source_name: Lcn2 4C, dexamethasone 60m

label_protocol: 1 µg purified 4C DNA was labeled with Cy5. Genomic DNA from the corresponding cell cut with HindIII and Csp6I was similarly labeled with Cy3 as a control for hybridization efficiency. Labeling was done according to standard chromatin immunoprecipitation (ChIP)-chip protocols (Nimblegen Systems; chapter 3 in http://www.nimblegen.com/products/lit/NG_ChIP-chip_Guide_v6p2.pdf).

extract_protocol:
2x10E7 adherent cells were fixed with 2% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS, scraped and collected in a 50ml tube. Nuclei were isolates in 10 ml of lysis buffer (0.2% NP-40, 10 mM NaCl, 10 mM Tris pH8.0) for 1hr on ice. Following centrifugation, the nuclei were suspended in 1ml 1.2X HindIII buffer (New England Biolabs buffer 2).  The nuclei were incubated in 0.3% SDS for 1hr at 3C (60 ul 20% SDS) and then SDS was quenched by incubation in 2% Triton X-100 for 1hr at 3C (200 ul 10% Triton X-100. Digestion was done with 800 U of HindIII (New England Biolabs) overnight at 3C while shaking gently. Before ligation, the HindIII was inactivated at 65C for 20 minutes, and the chromatin was ligated in 14 ml with 200 U T4 DNA ligase (Roche) for 4hr at 16C. To reverse the crosslinks, the sample was incubated overnight at 16C with 600 Âµg Proteinase K, following by RNA elimination by incubation with 600Âµg RNAse for 45 minutes at 3C. The 3C DNA was purified by phenol-chloroform extraction and ethanol precipitation. This 3C DNA sample was further cut with 150 U Csp6I (Fermantas) overnight at 3C. The restriction enzyme was inactivated at 65C for 20 minutes and removed by phenol-chloroform extraction. Ligation was performed as in the previous step to favor circularization of the DNA molecules in 14 ml with 200 U T4 DNA ligase (Roche) for 4hr at 16C. Ligation products were phenol-chloroform extracted and ethanol precipitated. Digested products were purified using a QIAquick PCR purification kit (Qiagen). The bait (Lcn2, Arrdc2, or Anxa5) contact loci were amplified by inverse PCR using bait-specific primers using the Expand Long Template PCR system (Roche). For each experiment (repeat), PCR was performed in 16 PCR reactions of 50 ul using 200ng 4C DNA as template in each reaction. PCR conditions were as follows: 94C for 2 min, 30 cycles of 94C for 15 s, 60C for 1 min and 68C for 3 min; followed by a final step of 68 C for 7 min. Primer sequences that were used to PCR amplify 4C DNA:
Lcn2_4CF 5'-GGGAGGTTAGTCACAGGGA-3'
Lcn2_4CR 5'-AGGGAGGATGACTTAAGGAG-3'
Arrdc2_4CF 5'-CAAATGCCAAAAGGAAGGAA-3'
Arrdc2_4CR 5'-TCAGTCAACATGCATCTCAGAA-3'
Anxa5_4CF 5'-CACCAGTTAACTAGCTTGCTTGC-3'
Anxa5_4CR 5'-TGAACAGGTCAGTCACATTGG-3'.
All 16 PCR reactions were pooled and purified this 4C template using QIAquick PCR purification kit (Qiagen).

treatment_protocol: Dexamethasone for 60 minutes.

value: hepatocytes

value: Lcn2 4C DNA

value: dexamethasone

tag: treatment duration

value: 1 hr

source_name: Control

treatment_protocol: None.

value: input


title: 612


title: 111


title: 112


title: 611


title: Lcn2_Hepa_0h

description:
411632H
Lipocalin 2 (Lcn2) 4C from cell line Hepa1C1C7; subset E.
Pool of 2 biological replicates.

source_name: Lcn2 4C, dexamethasone 0m


title: Arrdc2 4C-Dex60m-rep2

description:
268507
Arrestin domain containing 2 (Arrdc2) 4C from cell line 3134; subset B.

source_name: Arrdc2 4C, dexamethasone 60m

value: mammary epithelial cells

value: Arrdc2 4C DNA


title: Arrdc2 4C-Dex0m-rep1

description:
268915
Arrestin domain containing 2 (Arrdc2) 4C from cell line 3134; subset B.

source_name: Arrdc2 4C, dexamethasone 0m


title: Arrdc2 4C-Dex60m-rep1

description:
268580
Arrestin domain containing 2 (Arrdc2) 4C from cell line 3134; subset B.


title: Pancreatic cancer tumor specimen 43

first: Jih-Hsiang

last: Lee

address: 9000 Rockville Pike, building 10 8N254

department: Medical oncology branch

institute: National Cancer Institute

hyb_protocol: According to ULS labeling kit protocol version 3 November 2008

scan_protocol: Scanned on an Agilent G25056 scanner.

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

source_name: pancreatic cancer tumor specimen

label_protocol: The labeling procedure was conducted using the Genomic DNA ULS labeling kit (Agilent)

extract_protocol: FFPE tumor specimens were assessed for quality and adequacy of fixation and storage. A Hematoxylin & Eosin stained slide was prepared for each sample. A pathologist verified the presence of tumor tissue and marked the areas with more than 50% cancer cells on the paraffin blocks. The DNA was extracted using DNeasy kit (Qiagen, Inc., Valencia, CA) according to Genomic DNA ULS labeling kit protocol (Agilent Technologies, Inc., Palo Alto, CA)

tag: gender

value: male

tag: age (yr)

tag: overall survival (months)

source_name: reference: Promega Genomic DNA

tag: reference

value: Promega genomic DNA


title: Lcn2_10minD

description:
411636
Lipocalin 2 (Lcn2) 4C from cell line 3134; subset C.
Pool of 2 biological replicates.

source_name: Lcn2 4C, dexamethasone 10m

treatment_protocol: Dexamethasone for 10 minutes.

tag: cell line

tag: cell type

tag: treatment

value: 10 min


title: Lcn2 4C-Dex0m-rep1

description:
7414202
Lipocalin 2 (Lcn2) 4C from cell line 3134; subset A.


title: Pancreatic cancer tumor specimen 42


title: Pancreatic cancer tumor specimen 44


title: Anxa5_1hD

description:
411632
Annexin A5 (Anxa5) 4C from cell line 3134; subset D.
Pool of 2 biological replicates.

source_name: Anxa5 4C, dexamethasone 60m

value: Anxa5 4C DNA


title: 811

source_name: saliva sample

value: Homosexual

value: White


title: 2412

value: Heterosexual


title: Lcn2 4C-Dex60m-rep2

description:
7164302
Lipocalin 2 (Lcn2) 4C from cell line 3134; subset A.


title: Pancreatic cancer tumor specimen 41

value: female


title: Pancreatic cancer tumor specimen 40


title: 93-26_Tumor

value: tumor


title: 93-26_Normal

value: normal


title: Lcn2_30minD

description:
317990
Lipocalin 2 (Lcn2) 4C from cell line 3134; subset C.
Pool of 2 biological replicates.

source_name: Lcn2 4C, dexamethasone 30m

treatment_protocol: Dexamethasone for 30 minutes.

value: 30 min


title: Liver Tumor Tissue LCS-190A

first: Xin

middle: Wei

last: Wang

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

description: No additional information.

hyb_protocol: Hybridization Protocol Other: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Scanning Protocol Other: GeneChips were scanned using GeneChip® Scanner 3000 by Affymetrix.

data_processing:
Data Processing Protocol
Calculation Method: The CEL files from the two Affymetrix series were combined using the matchprobes package in the R programming environment. Thereafter, the RMA method in the R affy package was used to obtain probe set expression summaries.

label_protocol:
Biotinylated cRNA Labeling Protocol
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, P/N 702232 Rev. 2, Affymetrix).

extract_protocol:
TRIzol Extraction Protocol
Other: Total RNA was isolated from microdissected fresh frozen tissues using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's protocol. RNA integrity for each sample was confirmed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: tissue

value: Liver Tumor Tissue

value: Hepatocellular carcinoma (HCC)

tag: individual


title: Lcn2 4C-Dex0m-rep2

description:
7164102
Lipocalin 2 (Lcn2) 4C from cell line 3134; subset A.

value: Lcn2 4C DNA


title: Anxa5_0hD

description:
411636A
Annexin A5 (Anxa5) 4C from cell line 3134; subset D.
Pool of 2 biological replicates.

source_name: Anxa5 4C, dexamethasone 0m

value: input


title: 94-19_Tumor


title: 94-19_Normal


title: Liver Non-Tumor Tissue LCS-181B

description: No additional information.

value: Liver Non-Tumor Tissue


title: 94-18_Tumor


title: 94-18_Normal


title: Pancreatic cancer tumor specimen 38


title: 94-16_Tumor


title: Liver Non-Tumor Tissue LCS-168B

description: No additional information.


title: 94-16_Normal


title: Pancreatic cancer tumor specimen 36


title: Pancreatic cancer tumor specimen 37


title: Pancreatic cancer tumor specimen 34


title: 94-14_Tumor


title: Pancreatic cancer tumor specimen 33


title: Pancreatic cancer tumor specimen 35


title: Pancreatic cancer tumor specimen 39


title: Pancreatic cancer tumor specimen 32


title: Lcn2 4C-Dex60m-rep1

description:
7159202
Lipocalin 2 (Lcn2) 4C from cell line 3134; subset A.

value: mammary epithelial cells

value: dexamethasone

value: 1 hr


title: Liver Non-Tumor Tissue LCS-026B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-128B

description: No additional information.


title: 94-14_Normal


title: Liver Non-Tumor Tissue LCS-003B

description: No additional information.


title: Pancreatic cancer tumor specimen 31

value: male

value: Promega genomic DNA


title: Liver Non-Tumor Tissue X02-362B

description: No additional information.


title: Pancreatic cancer tumor specimen 30


title: Liver Tumor Tissue X02-362A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-006B

description: No additional information.


title: Pancreatic cancer tumor specimen 29


title: Pancreatic cancer tumor specimen 28


title: 94-1_Tumor


title: 94-1_Nomral


title: 93-29_Tumor


title: 93-29_Normal


title: 95-3_Tumor


title: 95-3_Normal


title: Liver Non-Tumor Tissue X02-342B

description: No additional information.


title: 95-10_Tumor


title: Pancreatic cancer tumor specimen 27


title: Pancreatic cancer tumor specimen 26


title: 95-10_Normal


title: 94-10_Tumor


title: Efaecalis_V583_Stationary

city: Caen

first: jean-christophe

last: giard

address: esplanade de la paix

country: France

institute: Université de Caen

hyb_protocol: Production, hybridization and data collecting were carried out by Febit biomed GmbH Company (Heidelberg, Germany).

scan_protocol: Production, hybridization and data collecting carried out by Febit biomed GmbH Company (Heidelberg, Germany) on the Febit Geniom platform.

data_processing: Genedata Expressionist software (version 5.3) was used for data processing. Raw data were Quantile normalized applying standard settings  (Averaging: Logarithmic Mean) of Expressionist Analyst.

organism: Enterococcus faecalis V583

source_name: Cells were grown at 37°C im M17 0.5% glucose medium, collected at 24h stationary phase

label_protocol: Fractionated RNA labelled using mirVana labelling kit (Applied Biosystems) hybridized onto the tiling array.

growth_protocol: E. faecalis V583 strain cells were grown at 37ºC in M17 0.5% glucose medium and collected at exponential phase (OD600 = 0.5) and at 24h stationary phase.

extract_protocol: For total RNA extraction cells were resuspended into 200 µl of “max bacterial enhancement reagent” (Invitrogen), transferred into micro tubes containing glass beads and 400 µl acid phenol (Ambion, Austin, TX) followed by  mechanically lysation in Mixer Mill 200 (30/s, 30 min, Retsch, Haan, Germany). After centrifugation 10 min at 14,000 g at 4ºC, aqueous phase  transferred to 2 ml tubes containing 1 ml Trizol reagent, 5 min incubation at room temperature (RT). Added 200 µl chloroform, mixed, incubated for 3 min at RT. Centrifugation for 15 min at 12,000 g at 4ºC; aqueous phase transferred into 2 ml tubes containing 200 µl chloroform, mixed gently and centrifuged again. RNAs contained in the Aqueous phase with RNAs precipitated by addition of 500 µl isopropanol, incubated for 10 min at RT. After centrifugation, RNA pellets washed with 75% ethanol, dried at RT. RNA pellets resuspended in DEPC-treated pure water. To enrich sncRNAs, 10µg RNA fractionated using flashPAGE Fractionator (Applied Biosystems, Foster City, CA).

treatment_protocol: Harvested by centrifugation

tag: strain

tag: phase

value: stationary


title: VHL-related pheochromocytoma replicate 5_FFPE

city: Budapest

first: Zsófia

last: Tömböl

address: Szentkirályi u. 46.

department: 2nd Department of Medicine

country: Hungary

institute: Semmelweis University

hyb_protocol: Samples were hybridized to Agilent Human miRNA Microarray Rel12.0 (Agilent Tech. Inc.) at 55oC, for 20 hours according to the manufacturer’s instructions.

scan_protocol: After washing microarray slides array scanning  was performed by Agilent DNA Microarray Scanner G2565BA (Agilent Tech. Inc.).

data_processing: Feature extraction and data processing was performed  with default scenario for Agilent Human MiRNA Microarray Rel12.0 by Feature Extraction Software 9.5.3 (Agilent Tech. Inc.) to calculate gProcessed signal

source_name: VHL-related, human pheochromocytoma, FFPE sample

label_protocol: Total RNA of 100 nanograms was dephosphorylated, denaturated and Cyanine3-pCp ligated according to the manufacturer’s instructions using miRNA Complete Labeling and Hyb Kit (Agilent Tech. Inc.). Labeled RNA was purified on Micro Bio-Spin P-6 Columns (Bio-Rad Laboratories, Hercules, CA, USA).

extract_protocol: Total RNA isolation was carried out after 100% xylene deparaffinization from altogether 5 slices of FFPE tissue sections with 15 μm thickness by Ambion RecoverAll Total Nucleic Acid Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer’s protocol. If required, extended deparaffinization and protease digestion at 50oC was performed. Total RNA extraction from fresh-frozen samples was performed after tissue homogenization with Qiagen miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) completed with optional on-column DNase digestion carried out by RNase-Free DNase Set (Qiagen GmbH).

treatment_protocol: A total of 21 formalin-fixed paraffin-embedded (FFPE) pheochromocytoma tissue samples were collected from pathological archives. From three patients fresh frozen tissue samples were obtained, as well. After surgical removal these three tissue samples were immediately snap frozen in liquid nitrogen and stored at -80oC until RNA isolation. Histological diagnoses were confirmed in all FFPE and frozen tissue samples.

tag: tumor localization

value: adrenal

tag: hereditary or sporadic

value: hereditary

tag: germline mutations

tag: age at the time of surgery (years)

tag: time until recurrence (years)

tag: type of starting material

value: formalin-fixed paraffin-embedded tissue block

tag: age of starting material (years)


title: VHL-related pheochromocytoma replicate 4_FFPE

tag: gender

value: female


title: Pancreatic cancer tumor specimen 24

tag: age (yr)

tag: overall survival (months)


title: Liver Tumor Tissue X02-342A

description: No additional information.

tag: disease state


title: Pancreatic cancer tumor specimen 22

tag: reference


title: Pancreatic cancer tumor specimen 25


title: Pancreatic cancer tumor specimen 23


title: 93-32_Tumor

source_name: tumor tissue

value: tumor


title: Efaecalis_V583_Exponential

source_name: Cells were grown at 37°C im M17 0.5% glucose medium, collected at exponential phase (OD600=0.5)

value: exponential


title: VHL-related pheochromocytoma replicate 2_FFPE


title: Pancreatic cancer tumor specimen 20


title: VHL-related pheochromocytoma replicate 1_FFPE


title: Pancreatic cancer tumor specimen 21


title: 94-10_Normal

source_name: normal tissue

value: normal


title: VHL-related pheochromocytoma replicate 3_FFPE


title: 93-32_Normal


title: Pancreatic cancer tumor specimen 19


title: Sample 39 - MLL/AF10

city: Padova

first: Andrea

last: Zangrando

address: Via Giustiniani, 3

department: Woman and Child's Health

country: Italy

institute: University of Padova

description: Gene expression data from acute myeloid leukemia with MLL/AF10 translocations at diagnosis

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000 7G

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org]

source_name: Peripheral Blood cells

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix IVT express protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).

extract_protocol: Total RNA extracted using Trizol

value: AML samples

tag: cells

value: Peripheral Blood


title: Pancreatic cancer tumor specimen 15


title: SC105_Tumor


title: Arrdc2 4C-Dex0m-rep2

description:
268842
Arrestin domain containing 2 (Arrdc2) 4C from cell line 3134; subset B.

tag: cell line

tag: cell type

tag: sample type

value: Arrdc2 4C DNA

source_name: Control

value: input


title: Sample 40 - MLL/AF10


title: Pancreatic cancer tumor specimen 17


title: MEN2-related pheochromocytoma replicate 5_FFPE

source_name: MEN2-related, human pheochromocytoma, FFPE sample

value: RET:GC609TCC (Cys-Ser)


title: Pancreatic cancer tumor specimen 16


title: MEN2-related pheochromocytoma replicate 4_FFPE

value: RET:TGC634CGC (Cys-Arg)


title: SC105_Normal


title: Pancreatic cancer tumor specimen 18


title: Pancreatic cancer tumor specimen 14


title: 93-6_Tumor


title: 92-8_Normal


title: MEN2-related pheochromocytoma replicate 2_Frozen

source_name: MEN2-related, human pheochromocytoma, fresh-frozen sample

value: RET:TGC611TAC (Cys-Tyr)

value: fresh-frozen tumor tissue


title: MEN2-related pheochromocytoma replicate 1_FFPE


title: MEN2-related pheochromocytoma replicate 3_FFPE

value: RET:TGC634TGG (Cys-Trp)


title: Sporadic recurring pheochromocytoma replicate 4_FFPE

source_name: Sporadic recurring, human pheochromocytoma (first tumor), FFPE sample

value: sporadic

value: male


title: 93-6_Normal


title: 92-8_Tumor


title: MEN2-related pheochromocytoma replicate 2_FFPE

value: adrenal

value: hereditary


title: Sporadic recurring pheochromocytoma replicate 3_FFPE

value: formalin-fixed paraffin-embedded tissue block


title: Sporadic recurring pheochromocytoma replicate 2_FFPE

value: female


title: Pancreatic cancer tumor specimen 9

source_name: pancreatic cancer tumor specimen

value: Promega genomic DNA


title: Pancreatic cancer tumor specimen 10

source_name: reference: Promega Genomic DNA


title: Pancreatic cancer tumor specimen 12


title: Sporadic recurring pheochromocytoma replicate 5_FFPE


title: Pancreatic cancer tumor specimen 13


title: Sporadic benign pheochromocytoma replicate 6_FFPE

source_name: Sporadic benign, human pheochromocytoma, FFPE sample


title: Pancreatic cancer tumor specimen 11


title: Pancreatic cancer tumor specimen 3


title: Pancreatic cancer tumor specimen 5


title: Sporadic benign pheochromocytoma replicate 5_Frozen

source_name: Sporadic benign, human pheochromocytoma, fresh-frozen sample


title: gmi1-1 seedlings, gamma-irradiated, biological rep3

city: Vienna

first: Gudrun

last: Boehmdorfer

address: Dr. Bohr-Gasse 3

country: Austria

institute: GMI – Gregor Mendel Institute of Molecular Plant Biology

description: Gene expression data from 5d old gamma-irradiated gmi1-1 seedlings

hyb_protocol: Biotin Labelled cRNA using Affymetrix GeneChip Hybridization, Wash and Stain Kit, according to guidelines set out by Affymetrix, Santa Clara, CA

scan_protocol: Affymetrix MAS 5.0 Standard Scanning

data_processing: Probe level normalization for different backgrounds and overall hybridization intensities of individual chips, using an iterative 20%-trimmed least squares fit of a generative model with additive-multiplicative noise [Huber, W., von Heydebreck, A., Sültmann, H., Poustka, A. & Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18, S96 (2002)] using vsnMatrix and an asinh scale asymptotically compatible with a log base 2 transform (custom scale calibration). Removal of both probe-specific background and adjusting perfect-match signal intensities for probe-specific affinities using gcrma with custom parameters selecting the Empirical Bayes ‘affinities’ model  [Wu, Z., Irizarry, R.A., Gentleman, R., Martinez Murillo, F. & Spencer, F. A Model based background adjustment for oligonucleotide expression arrays. J. Am. Stat. Assoc. 99, 909–917 (2004)] and employing a custom CDF based on TAIR-8 (following Dai et al  [Dai, M. et al. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucl. Acids Res. 33, e175 (2005)] plus removing probes perfectly matching multiple chromosomal locations yielding 16,949 probe sets with 3 to 25 probes per target). Probe summarization by robust fit of a linear multi-chip probe-level model was used to compute transcript expression estimates by affyPLM  [Bolstad, B. Low Level Analysis of High-density Oligonucleotide array data: Background, normalization and summarization. Dissertation. University of California, Berkeley. (http://bmbolstad.com/) (2004)]. Robust linear model fit using lmFit with regularized t-statistic and self-consistent prior. Benjamini-Yekutieli correction for multiple testing.

organism: Arabidopsis thaliana

source_name: gmi1-1 seedlings, gamma-irradiated

label_protocol: Labelled using protocol described in manual Affymetrix GeneChip Expression Analysis Technical Manual, One-Cycle target labelling

growth_protocol: Seeds were sterilized and plated on ½ MS plates. After 2 days stratification at 4°C, plates were incubated in continuous light (100 µmol/m2/s; Percival CU-36/L4, USA) at 21C for 5 days.

extract_protocol: Plantlets were frozen in liquid nitrogen, grinded and the RNA was isolated with Tri-Reagent (Sigma), DNase treated (TurboDNase, Ambion), and purified via PCI extraction followed by EtOH precipitation.

treatment_protocol: For gamma-irradiation, a Co-60-gamma source (Gamma-cell 220, Nordion International, Canada) was used to irradiate the seedlings with 100Gy at a dose rate between 27 to 34 Gy/min. After irradiation, plants were returned into the growth invubator and finally harvested 1.5h post irradiation.

tag: ecotype

tag: genotype

tag: tissue

value: 5 day old seedlings


title: Pancreatic cancer tumor specimen 7


title: Pancreatic cancer tumor specimen 6


title: Sporadic benign pheochromocytoma replicate 5_FFPE

tag: tumor localization

tag: hereditary or sporadic

tag: germline mutations


title: Pancreatic cancer tumor specimen 1


title: Pancreatic cancer tumor specimen 2


title: Pancreatic cancer tumor specimen 8


title: gmi1-1 seedlings, gamma-irradiated, biological rep1


title: wildtype seedlings, gamma-irradiated, biological rep2

description: Gene expression data from 5d old gamma-irradiated wildtye seedlings

source_name: wildtype seedlings, gamma-irradiated

value: wildtype


title: Sporadic recurring pheochromocytoma replicate 4_Frozen

source_name: Sporadic recurring, human pheochromocytoma (first tumor), fresh-frozen sample

tag: age at the time of surgery (years)

tag: time until recurrence (years)

tag: type of starting material


title: gmi1-1 seedlings, gamma-irradiated, biological rep2


title: Pancreatic cancer tumor specimen 4

tag: gender

tag: age (yr)


title: Sporadic benign pheochromocytoma replicate 4_FFPE

tag: age of starting material (years)


title: Sporadic recurring pheochromocytoma replicate 1_FFPE


title: Sporadic benign pheochromocytoma replicate 2_FFPE


title: wildtype seedlings, gamma-irradiated, biological rep3


title: wildtype seedlings, gamma-irradiated, biological rep1


title: gmi1-1 seedlings, untreated, biological rep3

description: Gene expression data from 5d old gmi1-1 seedlings

source_name: gmi1-1 seedlings, untreated


title: Sporadic benign pheochromocytoma replicate 1_FFPE


title: wt, biological rep3

city: Durham

first: Alejandro

last: Aballay

state: North Carolina

address: 268 Jones

department: Molecular Genetics and Microbiology

institute: Duke University

description: Gene expression data from L4 animals

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

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

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

organism: Caenorhabditis elegans

source_name: Wild-type animals infected with P. aeruginosa PA14 for 4 hours at 25°C (total transcripts)

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: Gravid adult wild-type and tag-24/octr-1 animals were lysed using a solution of sodium hydroxide and bleach (ratio of 5:2), washed and the eggs were synchronized for 22 hours in S basal liquid medium at room temperature. Synchronized L1 larval animals were placed onto NGM plates seeded with E. coli OP50 and grown at 20°C until the animals had reached the L4 larval stage.

extract_protocol: After 4 hours, animals were collected and washed with M9 buffer, and RNA was extracted using TRIzol reagent (Invitrogen). Residual genomic DNA was removed by DNase treatment (Ambion Austin, TX).

treatment_protocol: Animals were collected and washed with M9 buffer before transferring to NGM plates containing P. aeruginosa PA14 for 4 hours at 25°C.

value: whole animals

value: wild type

tag: developmental stage

value: L4 animals

tag: infection

value: P. aeruginosa PA14

tag: genetic background


title: tag-24, biological rep1

description: Gene expression data from L4 animals

source_name: tag-24 animals infected with P. aeruginosa PA14 for 4 hours at 25°C (total transcripts)

value: tag-24 mutant


title: gmi1-1 seedlings, untreated, biological rep2


title: wildtype seedlings, untreated, biological rep2

description: Gene expression data from 5d old wildtye seedlings

source_name: wildtype seedlings, untreated


title: Sporadic benign pheochromocytoma replicate 3_FFPE


title: wt, biological rep2

description: Gene expression data from L4 animals


title: gmi1-1 seedlings, untreated, biological rep1


title: tag-24, biological rep2

description: Gene expression data from L4 animals


title: tag-24, biological rep3

description: Gene expression data from L4 animals


title: wt, biological rep1

description: Gene expression data from L4 animals


title: wildtype seedlings, untreated, biological rep1


title: rat parietal cortex, aged , subject 6

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling (target intensity = 500) for quality control. gcRMA ( justgcRMA function in bioconductor in R v.2.7.1) was run on all chips simultaneously to generate probe set signal intensities

label: Standard Affymetrix

organism: Rattus norvegicus

source_name: rat

label_protocol: Standard Affymetrix

extract_protocol: Standard Affymetrix

tag: strain

value: Fischer 344

value: Male

tag: subject

value: frontal cortex

tag: age

value: 21 to 23 months old (aged)


title: rat parietal cortex, aged , subject 1


title: rat parietal cortex, aged , subject 3


title: rat parietal cortex, young , subject 6

value: 3 to 5 months old (young)


title: rat parietal cortex, aged , subject 4


title: rat parietal cortex, aged , subject 2


title: wildtype seedlings, untreated, biological rep3

tag: ecotype

tag: genotype


title: rat parietal cortex, aged , subject 5

tag: tissue


title: Penfield_2-6_ft1-20-degrees-long-day_Rep3_ATH1

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

hyb_protocol: Biotin Labelled cRNA using "Affymetrix GeneChip Hybridization, Wash and Stain Kit", according to guidelines set out by Affymetrix, Santa Clara, CA

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system

source_name: Glabra

label_protocol: Labelled using protocol described in Affymetrix manual "3' IVT Express Kit User Manual"

growth_protocol: Plants were grown in long 16h days at 20 degrees celcius under white fluorescent light at 80-100umol m-2 sec-2. Mature seed was collected from dehisced siliques.  Levington seed compost  Intercept  I plant per P40 insert daily 20 °C average, 20 °C day, 20 °C night 80 % average, unknown % day, unknown % night

extract_protocol: Qiagen RNAeasy kit protocol

value: ft-1 mutant

value: seeds

tag: stock code

value: N65 Genetic background:Ler Genetic variation:Single marker


title: rat parietal cortex, young , subject 5


title: rat parietal cortex, young , subject 4


title: CagA positive gastric epithelial cells

city: Suita

first: yoshito

last: hayashi

state: Osaka

address: 2-2 Yamadaoka

department: Department of Gastroenterology and Hepatology

country: Japan

institute: Osaka University Graduate School of Medicine

description: Mixture with equal deal of TC(+) and TC(-) cells

hyb_protocol: The labeled microRNA was hybridized to the array for approximately 17 hours at 45 C

scan_protocol: The arrays were scanned with a Agilent Technologies Microarray scanner (Agilent Technologies).

data_processing: The signal data of each array were analyzed using an GeneSpring GX (Agilent Technologies). The array data were corrected by global normalization.

source_name: CagA expressing RGM1 cells

label_protocol: The purified microRNA was labeled using the miVana miRNA Labeling kit (Applied Biosystems) and a CyeDye Mono-Reactive Dye Pack (Amersham Biosciences).

growth_protocol: Cells weremaintained in Dulbecco’s Modified Eagle Medium and Ham`s F12 (DMEM/F12; Invitrogen, Carlsbad, CA, USA) containing 10% fetal bovine serum (FBS; ICN Pharmaceuticals, Costa Mesa, CA, USA) and 1% antibiotic-antimycotic (Invitrogen, Carlsbad, CA, USA

extract_protocol: Total RNA including microRNA was extracted with mirVana miRNA Isolation Kit (Applied Biosystems).

treatment_protocol: We used a tetracycline (tet)-off system containing vectors pTet-off and pTRE (BD Biosciences Clontech, Palo Alto, CA, USA) to control cagA gene expression in RGM1 cells. These vectors produce reverse tetracycline-dependent transactivator (rtTA) and tetracycline-responsive element (TRE). After the removal of doxycycline from the culture medium, rtTA binds TRE, which induces a target gene expression downstream of the TRE gene. cagA gene isolated from the H. pylori strain NCTC 11637 (ABCCC, Western type) was inserted downstream of the TRE gene. Cell clones were generated with the tet-off system according to the previously described procedure. They were then maintained in the medium with 1.0μg/mL doxycycline (Takara, Japan).

tag: cell line

tag: cell type

value: gastric epitherial cells

source_name: control


title: LN443/control vs LN443/PDGF-A

city: PITTSBURGH

first: HAIZHONG

last: FENG

state: PA

address: 5117 CENTRE AVE

institute: UNIVERSITY OF PITTSBURGH

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. 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.

source_name: Control LN443/GFP

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Standard gene expression techniques were used to express human PDGF-A gene encoded by a retroviral pMXI-gfp vector in glioma cells.  Stable expressing cell lines were selected by FACS sorting for GFP=positive cell popultions.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Glioma cells were grown to ~ 80% confluence in DMEM media containg 10% FBS, then subjected t serum starvation for 24 hr before total RNA preparation.

value: glioma cells

tag: transfection

value: GFP

source_name: transfected cells: LN444/PDGF-A

value: PDGF-A


title: CagA negative gastric epithelial cells

source_name: CagA non-expressing RGM1 cells

growth_protocol: Cells weremaintained in Dulbecco’s Modified Eagle Medium and Ham`s F12 (DMEM/F12; Invitrogen, Carlsbad, CA, USA) containing 10% fetal bovine serum (FBS; ICN Pharmaceuticals, Costa Mesa, CA, USA) and 1% antibiotic-antimycotic (Invitrogen, Carlsbad, CA, USA).


title: rat parietal cortex, young , subject 2

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling (target intensity = 500 ) for quality control. gcRMA ( justgcRMA function in bioconductor in R v.2.7.1 ) was run on all chips simultaneously to generate probe set signal intensities


title: LN444/control vs LN444/PDGF-A

source_name: Control LN444/GFP


title: rat parietal cortex, young , subject 1

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling (target intensity = 500) for quality control. gcRMA ( justgcRMA function in bioconductor in R v.2.7.1) was run on all chips simultaneously to generate probe set signal intensities.


title: rat parietal cortex, young , subject 3


title: Scr_shRNA

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

country: China

institute: Fudan Univ, Shanghai, China

description: Gene expression data from E14 ES cells treated with scramble shRNA and selected with puromycin.

hyb_protocol: Hybridization was performed according to the manufacturer's instructions at Expression Analysis, Inc. (http://www.expressionanalysis.com)

scan_protocol: Scanning was performed at Expression Analysis, Inc. (http://www.expressionanalysis.com)

data_processing: The data were analyzed with the MATLAB (R2009b) Bioinformatics toolbox affygcrma function with default analysis settings.

source_name: mouse embryonic stem cells, Scr shRNA

label_protocol: Biotinylated cRNA were prepared using the Affymetrix One Cycle kit according to the standard Affymetrix protocol at Expression Analysis, Inc. (http://www.expressionanalysis.com)

growth_protocol: E14 ES cells were feeder-free cultured.

extract_protocol: Total RNA was extracted by Trizol. At the final step of purification, RNA was loaded onto an RNeasy column (Qiagen) and treated with RNAse-free DNAse I.

treatment_protocol: E14 ES cells were infected with Scr shRNA, Tet1 shRNA2863 or Tet1 shRNA3387 containing lentivirus and harvested after 4-days selection with puromycin.

value: mouse embryonic stem (MES) cells

tag: treatment

value: scramble shRNA


title: Tet1_shRNA3387

description: Gene expression data from E14 ES cells treated with Tet1 shRNA3387 and selected with puromycin.

source_name: mouse embryonic stem cells, Tet1 shRNA3387

value: Tet1 shRNA3387


title: Tet1_siRNA

description: Gene expression data from J1 ES cells transfected with Tet1 siRNA.

source_name: mouse embryonic stem cells, Tet1 siRNA

growth_protocol: J1 ES cells were cultured with MEF feeder cells.

treatment_protocol: J1 ES cells were transfected with control siRNA or Tet1 siRNA and harvested four days after transfection.

value: Tet1 siRNA


title: Control_siRNA

description: Gene expression data from J1 ES cells transfected with control siRNA.

source_name: mouse embryonic stem cells, control siRNA

value: control siRNA


title: E12_1

status: Public on Apr 20 2011

city: Hangzhou

first: Jiang

last: Hong

state: Zhe Jiang

address: Yuhangtang Road,NO.388

department: life science

institute: Zhejiang University

description: Embryo kidney on gestation 12_tech rep 1

hyb_protocol: a. Prepare Target Hybridization Mix: Add 4 to 20 µg of biotin-labeled cRNA target prepared using the TrueLabeling-AMP kit to 0.75 ml of pre-wPCR-Gradearmed GEAhyb Hybridization Solution. Mix well, and keep the Target Hybridization Mix at 60°C.   Note: We suggest starting with 6 µg of cRNA target. However, this amount may be decreased if the resulting signals are too intense or increased if resulting signals are too weak. Levels of cRNA target above 10 µg may saturate more abundant messages on the Oligo GEArray.   b. Discard the pre-hybridization solution from the hybridization tube. Add the Target Hybridization Mix containing the labeled cRNA target to the tube.   c. Hybridize overnight at 60°C with continuous agitation at 5 to 10 rpm.

scan_protocol: X-ray film, exposed to the chemiluminescent array, was scanned on a flatbed scanner to obtain a digital image.

data_processing: Positive and negative controls are included within the array. Final images were saved in either .tiff or .jpg, and uploaded for further analysis as described below. Data analysis was conducted using online with GEArray Expression Analysis Suite at www.SuperArray.com.

source_name: Embryo kidney on gestation 12

label_protocol: cDNA template was reverse-transcribed from total RNA followed by amplification and biotin-16-labeling using the Oligo GEArray TrueLabeling-AMP™ 2.0 Kit (SABiosciences) according to the manufacturers protocol. Resulting cDNA was further purified using cRNA clean-up kit (SABiosciences) following the manufacturers procedure.  http://www.sabiosciences.com/support_manual.php

extract_protocol: Total RNA was isolated using TRIzol Reagent (Invitrogen) following the manufacturers instructions.  http://tools.invitrogen.com/content/sfs/manuals/trizol_reagent.pdf

value: Embryo kidney

tag: gestation stage

value: gestation 12


title: E14_2

description: Embryo kidney on gestation 14_tech rep 2

source_name: Embryo kidney on gestation 14

value: gestation 14


title: E13_3

description: Embryo kidney on gestation 13_tech rep 3

source_name: Embryo kidney on gestation 13

value: gestation 13


title: E14_1

description: Embryo kidney on gestation 14_tech rep 1


title: E18_2

description: Embryo kidney on gestation 18_tech rep 2

source_name: Embryo kidney on gestation 18

value: gestation 18


title: E13_1

description: Embryo kidney on gestation 13_tech rep 1


title: E18_1

description: Embryo kidney on gestation 18_tech rep 1


title: E16_2

description: Embryo kidney on gestation 16_tech rep 2

source_name: Embryo kidney on gestation 16

value: gestation 16


title: E16_1

description: Embryo kidney on gestation 16_tech rep 1


title: E12_2

description: Embryo kidney on gestation 12_tech rep 2


title: E12_3

description: Embryo kidney on gestation 12_tech rep 3


title: E13_2

description: Embryo kidney on gestation 13_tech rep 2


title: C. crescentus DSigU cells incubated in M2 in the absence of glucose for 15 min

city: Stanford

first: Leticia

last: Britos

state: CA

address: 279 Campus Dr.

institute: Stanford University

description: Gene expression data for C. crescentus LS3547 cells incubated in M2 media in the absence of glucose for 15 min

hyb_protocol: Following fragmentation, 1.9 ug of cDNA were hybridized overnight at 50 deg C on GeneChip CauloHi1, using the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol ProkGE_WS2v3_450.

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

data_processing: The RMA statistical algorithm [78], available under the Bioconductor software package of R, was used for background noise removal, normalization and summarization of the microarray data corresponding to two independent experiments for each condition (cells starved for carbon for 30 and 60 min, and the respective controls). A Significance Analysis of Microarrays (SAM) [76] was applied to the dataset, with the following parameters: unpaired, logged, median centered, T statistic. A 2-fold minimum change was selected as cutoff, and a delta value yielding a false discovery rate lower than 1%.

organism: Caulobacter vibrioides

label_protocol: cDNA was synthesized using Super Script II (Invitrogen) with random hexamers, according to the manufacturer’s instructions. After reverse transcription, RNA was removed by 30 min NaOH incubation at 65 °C and cDNA was purified using MinElute columns (Qiagen). Purified cDNA was fragmented by a 5 min incubation with DNAseI (Invitrogen; 0.6U/μg cDNA) in a thermocycler, followed by 15 min enzyme inactivation at 98 °C. DNAseI activity was previously titrated, and the same batch of enzyme and thermocycler were used across all experiments to obtain reproducible fragmentation. RNA 6000 Nano kit (Agilent) on a Agilent 2100 Bioanalyzer was used to control for homogeneous fragmentation (50-200 bp range) of samples. Fragmented cDNA was biotinylated at the 3’ termini with GeneChip DNA Labeling Reagent (Affymetrix).

growth_protocol: Cells were grown in M2G medium (never reaching OD600nm greater than 0.4)

extract_protocol: Total RNA was extracted from cells using the Purelink Mini Total RNA Purification System (Invitrogen), according to the manufacturer’s instructions for on-column DNAse treatment to remove contaminating DNA

treatment_protocol: Cells were collected by centrifugation (5 min at 9,000xg) and washed twice with a large volume of ice-cold M2 medium, resuspending by gentle pipetting. Control cells were mock-washed with ice-cold M2 with 0.2% glucose. Washed cells were resuspended in pre-warmed M2 or M2G media and incubated at 28 °C in a water bath with shaking. Samples were collected at 30 and 60 minutes, frozen in liquid nitrogen and stored at -80 °C.

value: delta-SigU

tag: growth media

value: carbon starvation


title: C. crescentus DSigU cells in M2G

description: Gene expression data for C. crescentus LS3547 cells incubated in complete M2G media for 15 min

value: mock


title: C. crescentus DSigT cells in M2G

description: Gene expression data for C. crescentus LS3554 cells incubated in complete M2G media for 15 min

value: delta-SigT


title: C. crescentus wild-type cells incubated in M2 in the absence of glucose for 15 min

description: Gene expression data for C. crescentus wild-type cells incubated in M2 media in the absence of glucose for 15 min

value: wild type


title: C. crescentus wild-type cells in M2G

description: Gene expression data for C. crescentus wild-type cells incubated in complete M2G media for 15 min


title: C. crescentus DSigT cells incubated in M2 in the absence of glucose for 15 min

description: Gene expression data for C. crescentus LS3554 cells incubated in M2 media in the absence of glucose for 15 min


title: C. crescentus mixed population in M2 60 min, biological replicate 2

description: Gene expression datas for C. crescentus cells incubated in the absence of glucose for 60 min

hyb_protocol: Following fragmentation, 2.9 ug (for biological replicates 1) and 3.6 ug (for biological replicates 2) of cDNA were hybridized overnight at 50 deg C on GeneChip CauloHi1, using the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol ProkGE_WS2v3_450.

growth_protocol: Cells were grown overnight in small cultures in M2G medium (never reaching OD600nm greater than 0.4) . These cultures were used to inoculate 1200 ml cultures, which were incubated at 28 °C until they had reached an OD600 nm of 0.3-0.4.

tag: time

value: 60 min


title: C. crescentus swarmer cells in M2G media

description: Gene expression data for freshly isolated C. crescentus swarmer cells

growth_protocol: Cells were grown in M2G medium (never reaching OD600nm greater than 0.4). Cultures were cooled on ice, pelleted at 9,000 x g at 4°C, and resuspended in 300 μl of ice-cold M2G. After adjusting the volume to 1ml, one volume of ice-cold Percoll was added and mixed thoroughly. The suspension was centrifuged at 11,000 x g for 20 min at 4°C, to separate the swarmer cells (lower band) from the rest of the population (top band). To obtain the stalked cells samples, the synchronization procedure was performed as described above, swarmers were resuspended in M2G , and allowed to differentiate for 60 min at 28°C. At that point, loss of motility of the majority of the population was confirmed by microscopy.

treatment_protocol: Cells were collected by centrifugation (5 min at 9,000xg) and washed twice with a large volume of ice-cold M2 medium, resuspending by gentle pipetting. Control cells were mock-washed with ice-cold M2 with 0.2% glucose. Washed cells were resuspended in pre-warmed M2 or M2G media and incubated at 28 °C in a water bath with shaking. Samples were collected after 15 minutes, frozen in liquid nitrogen and stored at -80 °C.

tag: developmental stage

value: swarmer cells


title: C. crescentus swarmer cells after 15min in M2 media in the absence of glucose

description: Gene expression data for C. crescentus swarmer cells incubated in M2 medium in the absence of glucose for 15 min


title: Gene expression profiling of NtPT1-trasngenic rice (PT 1-7-8) treated with low phosphorus_3rd

city: Suwon

first: Myoung Ryoul

last: Park

address: 126 Suin-ro

country: South Korea

institute: National Institute of Crop Science

description: This experiment was performed with three independent biological replicates (1st, 2nd and 3rd ). The whole genome microarray consisting of a total of 64,896 oligonucleotides was printed on two separate slides (Slides A and B).

hyb_protocol: Equal amounts of Cy5- and Cy3-labeled samples were combined, dried by speed-vac centrifugation and then dissolved in 1x hybridization buffer composed of 5X SSC, 0.1% SDS, 0.2 mg/ml of yeast tRNA, 0.2 mg/ml of polyadenylic acid and 25% super-pure formamide. Hybridization was performed by applying the labeled mixture of control and transgenic rice samples onto the area of the microarray slide corresponding to the spot matrix and then covered with cover slip (Lifterslip by Erie/Fisher Scientific). The hybridization assembly was mounted in sealed and humidified hybridization chamber (Genomictree). The chamber was submerged into 42C water from 18 to 20 hours. Following hybridization, the cover slips were gently peeled-off and the slides were washed in three stringency buffer solutions: Buffer 1, 2x SSC (3M sodium chloride, 0.3M sodium citrate) plus 0.1% SDS; Buffer 2, 0.1x SSC plus 0.1% SDS; Buffer 3, 0.1x SSC. Washing with buffers 1 and 2 was performed at 42C, and with buffer 3 at room temperature. All washing were carried out for 10 minutes each step.

scan_protocol: The microarray was scanned with ArrayWoRx Biochip Reader-Standard (AppliedPrecision, USA).

data_processing: Quality flagging was performed on the microarray scans using Imagene 5.0 (BioDiscovery, USA) and Genesight 3.2 (BioDiscovery, USA). A complex quality control query was used to identify and select high quality spots (features) from the entire microarray matrix. This query was formulated to exclude features that belong to any of the following filter criteria: 1) The feature intensity is near background level; 2) The feature is irregular or not uniform (spotting irregularity); and 3) The background around the feature is not uniform (hybridization irregularity). Only the features that passed these stringent filter criteria were included in subsequent bioinformatics analysis of the gene expression data. Gene expression data in each image was normalized globally (see VALUE below) prior to high level analysis.

organism: Oryza sativa

source_name: Control NtPT1-trasngenic rice (PT 1-7-8) seedlings

label_protocol: The target RNA sample was processed in a multi-step procedure using the MessageAmp II aRNA amplification method (Ambion). The cDNA synthesis reaction was primed with oligo-dT catalyzed by ArrayScript reverse transcriptase (Ambion). The resulting cDNA was used as template for in vitro transcription using T7 enzyme cocktail (Ambion) producing up to 20 ug of aRNA per reaction labeled with aminoallyl-dUTP, The resulting aRNA molecules were chemically labeled with Cy3 fluorescent dye.

extract_protocol: Total RNA was isolated from NtPT1-trasngenic rice (PT 1-7-8) seedlings treated with normal P using the TriZol extraction method according to manufacturer's (Invitrogen) protocol.

value: NtPT1-trasngenic rice (PT 1-7-8)

value: normal P (320μM Pi)

value: seedling

source_name: Treated NtPT1-trasngenic rice (PT 1-7-8) seedlings

label_protocol: The target RNA sample was processed in a multi-step procedure using the MessageAmp II aRNA amplification method (Ambion). The cDNA synthesis reaction was primed with oligo-dT catalyzed by ArrayScript reverse transcriptase (Ambion). The resulting cDNA was used as template for in vitro transcription using T7 enzyme cocktail (Ambion) producing up to 20 ug of aRNA per reaction labeled with aminoallyl-dUTP, The resulting aRNA molecules were chemically labeled with Cy5 fluorescent dye.

extract_protocol: Total RNA was isolated from NtPT1-trasngenic rice (PT 1-7-8) seedlings treated with low P using the TriZol extraction method according to manufacturer's (Invitrogen) protocol.

value: low P (32μM Pi)


title: C. crescentus mixed population in M2 30 min, biological replicate 1

description: Gene expression datas for C. crescentus cells incubated in the absence of glucose for 30 min

value: 30 min


title: C. crescentus mixed population in M2G 60 min, biological replicate 2

description: Gene expression datas for C. crescentus cells incubated in complete media for 60 min


title: C. crescentus stalked cells after 15min in M2 media in the absence of glucose

description: Gene expression data for C. crescentus stalked cells incubated in M2 medium in the absence of glucose for 15 min

value: stalked cells


title: small airways, COPD 162

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: airway epithelial cells obtained by bronchoscopy and brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: sex

value: M

tag: ethnic group

value: white

tag: smoking status

value: COPD, GOLD-I, 26 pack-years


title: C. crescentus mixed population in M2 30 min, biological replicate 2

tag: strain


title: small airways, COPD 176

tag: age

value: black

value: COPD, GOLD-II, 24 pack-years


title: C. crescentus mixed population in M2G 30 min, biological replicate 1

description: Gene expression data for C. crescentus cells incubated in complete media for 30 min


title: Gene expression profiling of NtPT1-trasngenic rice (PT 1-7-8) treated with low phosphorus_2nd