title: amnion mesenchymal cells, 8h interleukin-1-beta, biological rep2

city: Columbus

first: Douglas

middle: A.

last: Kniss

state: OH

address: 395 W. 12th Avenue

department: OB/GYN

institute: The Ohio State University

description:
Gene expression data from amnion mesenchymal cells treated with interleukin-1-beta for 8h
AMC_8h-1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Genome U133A 2.0 Arrays (Platform GPL571). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with R statistics package version 2.7.1 using robust multichip average (RMA) as normalization method.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (GeneChip Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Primary cultures of human amnion mesenchymal cells were prepared from amnion membranes obtained prior to labor at term.  Cells were cultured in DMEM (25 mM glucose) supplemented with 10% fetal bovine serum, 2mM L-glutamine, 1mM sodium pyruvate, 50 ug/ml of gentamicin sulfate, and 0.5 mg/ml of amphotericin B at 37C in a 5% CO2 atmosphere.

extract_protocol: Total RNA from control and experimental groups were extracted using Trizol reagent and the RNeasy Mini Kit (Qiagen) as according to the manufacturer's instructions.

treatment_protocol: Early passage cells at confluence were treated with interleukin-1-beta (10 ng/ml) for 1 or 8 h, whereas control cells were treated with serum-free medium only.

value: amnion

tag: cell type

value: mesenchymal

tag: agent

tag: time

value: 8 hr


title: genotype: Williams 82 - rep4

status: Public on Jun 02 2011

type: RNA

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

country: USA

institute: Iowa State University

description: BPMV vector control 4

hyb_protocol: Soybean probe hybridization protocol

scan_protocol: Affy soybean scanning protocol

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

label: biotin

molecule: total RNA

organism: Glycine max

source_name: The top fully expanded trifoliolate leaves, petioles and stem segments. (genotype: Williams 82)

label_protocol: Affymetrix one-cycle target labeling

extract_protocol: Affy soybean extraction protocol

tag: williams 82 (germplasm name); ud

value: 0000075 The top fully expanded trifoliolate leaves, petioles and stem segments., (Organism Part); UD:0000076 35 day old plant (Development Stage); field soil (Growth Media).


title: genotype: Williams 82 - rep1

description: BPMV vector control 1


title: Bone met sample 7

city: UMEÅ

first: Pernilla

last: Wikström

address: Department of Medical biosciences, Buildning 6M, 2nd floor

department: Medical biosciences, Pathology

country: Sweden

institute: Umeå University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using the cubic spline algorithm (GenomeStudio software, version 2009.1) and probes with all signals lower than two-times the mean background were excluded.

organism: Homo sapiens

source_name: Patient 7

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays. Quality control was performed with Agilent Bioanalyser.

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

tag: disease stage

value: Castration-resistant prostate cancer

tag: tissue

value: Bone metastases

tag: ar-v expression level

value: low (others)


title: genotype: Williams 82 - rep2

description: BPMV vector control 2


title: Bone met sample 10

source_name: Patient 10


title: Prdm1+/+_9

city: Oxford

first: Arne

middle: Wyndham

last: Mould

state: Oxfordshire

address: Warneford Hospital

department: Psychiatry

country: United Kingdom

institute: Oxford University

description: Prdm1CA/+ biological replicate 9

data_processing: Rank invariant normalisation with background subtraction using the Gene Expression Module V1.6.0 of Illumina GenomeStudio V2009.2

organism: Mus musculus

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

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: strain

value: Mixed

tag: developmental stage

value: embryonic (E18.5)

tag: prdm1 genotype

value: small intestine


title: amnion mesenchymal cells, 1h interleukin-1-beta, biological rep3

description:
Gene expression data from amnion mesenchymal cells treated with interleukin-1-beta for 1h
AMC_1h-3

value: 1 hr


title: Bone met sample 15

source_name: Patient 15


title: siAP-2γ (First Base)-transfected MCF-7, 12h E2

city: Singapore

first: SI KEE

last: TAN

address: 60 Biopolis Street #02-01 Genome

department: Cancer biology and Pharmacology

country: Singapore

institute: Genomic Institute of Singapore

description: 4671881066_A, 4671881068_A, 4671881069_A

hyb_protocol: 750ng of cRNA were hybridized to the Sentrix HumanRef-8 v3 Expression BeadChip Kit (Illumina) according to the manufacturer protocol.

scan_protocol: BeadChips were scanned using the BeadArray Reader.

data_processing:
Raw data was analyzed using GeneSpring GX 11.0 software. Dataset was normalized using percentile shift normalization and baseline transformed to median of control samples.
Triplicates were generated for the experiment and analyses were performed using the average of the triplicates (after normalization). Raw data provided as supplementary file (filename: GSE26740_non-normalized.txt.gz)

source_name: MCF-7 breast cancer cells

label_protocol: Biotinylated cRNA were prepared from 500ng total RNA using Illumina TotalPrep-96 RNA Amplification Kit (Ambion).

growth_protocol: MCF-7 breast cancer cells were maintained in DMEM (Invitrogen/Gibco) supplemented with 5% fetal bovine serum (FBS), penicillin, streptomycin, and gentamycin in a 37°C incubator with 5% CO2.

extract_protocol: RNA was harvested using Trizol reagent (Sigma) and purified according to manufacturer protocol in PureLink RNA Mini Kit (Invitrogen).

treatment_protocol: ~400,000 cells were seeded in phenol red-free DMEM/F12 containing 5% charcoal stripped FBS (Hyclone) with penicillin, streptomycin and gentamycin. Within 24h after seeding, cells were transfected with NC or siRNA targeting AP-2γ (from Dharmacon and First Base). Transfection was repeated the next day to achieve double knockdown. After 96h from the first transfection, hormone-depleted cells were treated with E2 to a final concentration of 10 nM for 12h before harvesting for RNA.  Cells treated with an equal volume vehicle, ETOH (ethanol) for 12h are used as controls.

tag: cell line

tag: condition

value: siAP-2γ (First Base)-transfected MCF-7, E2


title: amnion mesenchymal cells, 1h interleukin-1-beta, biological rep2

description:
Gene expression data from amnion mesenchymal cells treated with interleukin-1-beta for 1h
AMC_1h-2


title: Bone met sample 8

source_name: Patient 8


title: siAP-2γ (First Base)-transfected MCF-7, 12h ETOH

description: 4671881066_B, 4671881068_B, 4671881069_B

value: siAP-2γ (First Base)-transfected MCF-7, ETOH


title: amnion mesenchymal cells, 8h interleukin-1-beta, biological rep1

source_name: amnion mesenchymal cells treated with interleukin-1-beta for 8h


title: amnion mesenchymal cells, 8h interleukin-1-beta, biological rep3


title: Bone met sample 3

source_name: Patient 3


title: Bone met sample 2

source_name: Patient 2


title: heart from wt mice after sham surgery

city: Dallas

first: Qingjun

last: Zhang

address: 5323 Harry Hines Blvd,NB11.110

institute: UT Southwestern

description: replicate 1

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: mouse heart

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina® TotalPrep RNA Amplification kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment. Quality control was performed with Agilent Bioanalyser.

tag: genetic bacground

value: FvB

tag: age

value: 8 week

tag: surgery

value: sham

tag: genotype

value: wild type

value: heart


title: Bone met sample 1

source_name: Patient 1


title: amnion mesenchymal cells, no treatment, biological rep1

description:
Gene expression data from amnion mesenchymal cells with no treatment
AMC_veh-1

value: amnion

value: mesenchymal

value: vehicle

value: control


title: Braak V-VI, APOE e4+ temporal cortex astrocytes

status: Public on Jun 01 2011

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

description: Gene expression data from human astrocytes

hyb_protocol: 7µg of cRNA molecules were heat fragmented and applied to the Human Genome HGU133 Plus 2.0 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

data_processing: The data were using Array Assist 3 software

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

extract_protocol: PicoPure RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions

treatment_protocol:
7um frozen temporal cortex sections were fixed in acetone and immunostained for GFAP using a rapid staining protocol. They were then washed and dehydrated through graded ethanol concentrations (70%, 95%, 100%) and cleared in xylene.
From each individual case, approximately 1500 astrocytes were isolated using a PixCell II laser-capture microdissection system (Arcturus Bioscience)

value: temporal cortex

value: astrocytes

tag: braak stage

value: Braak V-VI

tag: apoe status

value: APOE e4+


title: Braak V-VI, APOE e4+ sample 3

tag: cell type


title: siAP-2γ (Dharmacon)-transfected MCF-7, 12h ETOH

description: 4671881066_D, 4671881068_D, 4671881069_D

value: siAP-2γ (Dharmacon)-transfected MCF-7, ETOH


title: Braak III-IV, APOE e4- sample 2

value: Braak III-IV

value: APOE e4-


title: Braak III-IV, APOE e4- temporal cortex astrocytes


title: Braak V-VI, APOE e4- sample 3


title: NC-transfected MCF-7, 12h ETOH

description: 4671881066_F, 4671881068_F, 4671881069_F

value: NC-transfected MCF-7, ETOH


title: Braak V-VI, APOE e4- sample 2


title: Braak V-VI, APOE e4- sample 1


title: Braak III-IV, APOE e4+ sample 3


title: NC-transfected MCF-7, 12h E2

description: 4671881066_E, 4671881068_E, 4671881069_E

value: NC-transfected MCF-7, E2


title: amnion mesenchymal cells, no treatment, biological rep2

description:
Gene expression data from amnion mesenchymal cells with no treatment
AMC_veh-2

tag: agent

tag: time


title: amnion mesenchymal cells, no treatment, biological rep3

description:
Gene expression data from amnion mesenchymal cells with no treatment
AMC_veh-3


title: 4101_1

city: Aurora

first: Michael

middle: J

last: Schurr

state: CO

department: Microbiology

institute: University of Colorado School of Medicine

data_processing:
Microarray data were generated using Affymetrix protocols as previously described (Frisk et al., 2004, Lizewski et al., 2004, Morici et al., 2007). Absolute expression transcript levels were normalized for each chip by globally scaling all probe sets to a target signal intensity of 500. Three statistical algorithms (detection, change call, and signal log ratio) were then used to identify differential gene expression in experimental and control samples. The detection metric (presence, absence, or marginal) for a particular gene was determined using default parameters in MAS software (version 5.0; Affymetrix). Batch analysis was performed in MAS to make pairwise comparisons between individual experimental and control GeneChips in order to generate change calls and a signal log ratio for each transcript. These data were imported into Data Mining Tools (version 3.0; Affymetrix). Transcripts that were absent under both control and experimental conditions were eliminated from further consideration. Statistical significance of signals between the control and experimental conditions (P < 0.05) for individual transcripts was determined using the t test. We defined a positive change call as one in which greater than 50% of the transcripts had a call of increased (I) or marginally increased (MI) for up-regulated genes and decreased (D) or marginally decreased (MD) for down-regulated genes. Finally, the mean value of the signal log ratios from each comparison file was calculated.  Only those genes that met the above criteria and had a mean signal log ratio of greater than or equal to 1 for up-regulated transcripts and less than of equal to 1 for down-regulated transcripts were kept in the final list of genes. Signal log ratio values were converted from log2 and expressed as fold changes.

Frisk, A., J. R. Schurr, G. Wang, D. C. Bertucci, L. Marrero, S. H. Hwang, D. J. Hassett & M. J. Schurr, (2004) Transcriptome analysis of Pseudomonas aeruginosa after interaction with human airway epithelial cells. Infect. Immun. 72: 5433-5438.
Lizewski, S. E., J. R. Schurr, D. W. Jackson, A. Frisk, A. J. Carterson & M. J. Schurr, (2004) Identification of AlgR-regulated genes in Pseudomonas aeruginosa by use of microarray analysis. J. Bacteriol. 186: 5672-5684.
Morici, L. A., A. J. Carterson, V. E. Wagner, A. Frisk, J. R. Schurr, K. H. zu Bentrup, D. J. Hassett, B. H. Iglewski, K. Sauer & M. J. Schurr, (2007) Pseudomonas aeruginosa AlgR represses the Rhl quorum-sensing system in a biofilm-specific manner. J. Bacteriol. 189: 7752-7764.

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa delta PA4101 (bfmR) grown in a flow-through bioflm

label_protocol: Ten micrograms of total RNA was used for cDNA synthesis, fragmentation, and labeling according to the Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol. End labeled with biotin-ddUTP with use of the Enzo BioArray Terminal Labeling kit (Affymetrix).

growth_protocol: P. aeruginosa and P. aeruginosa delta PA4101 (bfmR) were grown in a flow-through bioflm on minimal medium with 10 mM glutamate for 6 days.

extract_protocol: Cells were treated with RNAprotect (Qiagen), and total RNA was extracted using an RNeasy mini purification kit (Qiagen) per the manufacturer’s instructions.  RNA quality and the presence of residual DNA were checked on an Agilent Bioanalyzer 2100 electrophoretic system pre- and post-DNase treatment.

treatment_protocol: None.

value: PAO1 delta bfmR

tag: growth condition

value: biofilm


title: Braak III-IV, APOE e4- sample 3

tag: tissue


title: Braak I-II, APOE e4- sample 2

value: Braak I-II


title: 4101_2

hyb_protocol: Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.


title: 4101_3

scan_protocol: Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.


title: Braak I-II, APOE e4+ sample 3


title: Braak I-II, APOE e4+ sample 2


title: Braak I-II, APOE e4+ temporal cortex astrocytes


title: Braak III-IV, APOE e4+ temporal cortex astrocytes


title: Braak V-VI, APOE e4+ sample 2


title: Braak III-IV, APOE e4+ sample 2


title: amnion mesenchymal cells, 1h interleukin-1-beta, biological rep1

description:
Gene expression data from amnion mesenchymal cells treated with interleukin-1-beta for 1h
AMC_1h-1

value: 1 hr


title: Braak I-II, APOE e4- sample 3


title: Braak I-II, APOE e4- temporal cortex astrocytes


title: CLL B cells high miR-155 mutated  IgVH CLL, CLL44

city: NEW YORK

first: Piali

last: Mukherjee

state: New York

department: Medicine

institute: Weill Cornell Medicine

hyb_protocol: The biotin labeled cDNA was fragmented and hybridized on Human U133 Plus 2 arrays.  GeneChips were washed and stained according to manufacturer's protocol

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000 7G

data_processing: MAS 5.0

source_name: Chronic lymphocytic leukemia

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 5 mg total RNA (Expression Analysis Technical Manual, Affymetrix)

extract_protocol: Total RNA was extracted by Trizol and purified using the Rneasy minikit (Qiagen, Valencia, CA) according to the manufacturer's instructions

value: purified CLL B cells, peripheral blood

tag: expression

value: high miR-155

tag: mutation

value: mutated  IgVH


title: CLL B cells high miR-155 mutated  IgVH CLL, CLL1


title: CLL B cells high miR-155 unmutated  IgVH CLL, CLL7

value: unmutated  IgVH


title: Breast Cancer Pleural Effusion E24334

city: Boston

first: Adam

last: Gustafson

state: MA

address: 44 Cummington St

institute: Boston University

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Standard Affymetrix Protocol

source_name: Breast Cancer Pleural Effusion

label_protocol: Standard Affymetrix Protocol

extract_protocol: Standard Affymetrix Protocol

value: Pleural Effusion

tag: prediction

value: resistant to valproic acid


title: CLL B cells high miR-155 mutated  IgVH CLL, CLL37


title: CLL B cells low miR-155 mutated  IgVH CLL, CLL42

value: low miR-155


title: CLL B cells low miR-155 mutated  IgVH CLL, CLL18


title: CLL B cells low miR-155 unmutated  IgVH CLL, CLL15


title: CLL B cells high miR-155 unmutated  IgVH CLL, CLL62


title: CLL B cells high miR-155 unmutated  IgVH CLL, CLL20


title: Breast Cancer Pleural Effusion H10161

value: sensitive to valproic acid


title: B. subtilis_argon treated_replicate3

city: Greifswald

first: Ulrike

last: Mäder

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

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

description: B. subtilis grown in LB medium

hyb_protocol: 500 ng of Cy5-labeled cDNA and 500 ng of Cy3-labeled cDNA were hybridized to the microarray following Agilent’s hybridization, washing and scanning protocol (Two-Color Microarray-based Gene Expression Analysis, version 5.5).

scan_protocol: The microarray was scanned using an Agilent Microarray Scanner G2565CA (Agilent Technologies).

data_processing: Data were extracted using the Agilent Feature Extraction software (version 10.5, Agilent Technologies).

organism: Bacillus subtilis

source_name: pooled RNA (equal amounts of RNA from all samples)

label_protocol: For cDNA synthesis, 10 µg of total RNA were mixed with random primers (Promega) and spike-ins (Two-Color RNA Spike-In Kit, Agilent Technologies). The RNA/primer mixture was incubated at 70 °C for 10 min followed by 5 min incubation on ice. Then, the following reagents were added: 10 µl of 5x First Strand Buffer (Invitrogen), 5 µl of 0.1 M DTT (Invitrogen), 0.5 µl of a dNTP mix (10 mM dATP, dGTP, and dTTP, 2.5 mM dCTP), 1.25 µl of Cy3-dCTP or Cy5-dCTP (GE Healthcare) and 2µl of SuperScript II reverse transcriptase (Invitrogen). The reaction mixture was incubated at 42 °C for 60 min and then heated to 70 °C for 10 min. After 5 min on ice, the RNA was degraded by incubation with 2 units of RNaseH (Invitrogen) at room temperature for 30 min. Labeled cDNA was then purified using the CyScribe GFX Purification Kit (GE Healthcare). The individual samples were labeled with Cy5, whereas the reference pool was labeled with Cy3.

growth_protocol: The Bacillus subtilis 168 wild type strain was grown aerobically at 37 °C in LB medium.

extract_protocol: Total RNA was isolated by the mechanical cell disruption/ acid phenol method (Eymann et al., 2002, PMID: 11948165).

treatment_protocol: At OD540 of 0.5, cells were treated with argon gas and argon plasma (with a discharge power of 5 W), respectively, for 15 min. Samples were taken 5 min after the treatment.

value: wild type

source_name: argon gas treated


title: CLL B cells high miR-155 mutated  IgVH CLL, CLL9


title: CLL B cells low miR-155 unmutated  IgVH CLL, CLL24


title: CLL B cells low miR-155 mutated  IgVH CLL, CLL32


title: B. subtilis_argon plasma treated_replicate2

description: B. subtilis grown in LB medium

source_name: argon plasma treated


title: CLL B cells low miR-155 unmutated  IgVH CLL, CLL3


title: CLL B cells high miR-155 mutated  IgVH CLL, CLL5


title: CLL B cells low miR-155 unmutated  IgVH CLL, I08-108


title: B. subtilis_argon plasma treated_replicate3

description: B. subtilis grown in LB medium


title: CLL B cells low miR-155 mutated  IgVH CLL, CLL56


title: CLL B cells low miR-155 unmutated  IgVH CLL, I07-4971

value: purified CLL B cells, spleen


title: CLL B cells high miR-155 unmutated  IgVH CLL, I08-130


title: CLL B cells high miR-155 unmutated  IgVH CLL, I05-13


title: CLL B cells high miR-155 unmutated  IgVH CLL, I08-597

value: purified CLL B cells, lymph node


title: Breast Cancer Pleural Effusion H24458


title: CLL B cells low miR-155 mutated  IgVH CLL, CLL50


title: CLL B cells low miR-155 unmutated  IgVH CLL, CLL30


title: Breast Cancer Pleural Effusion G22372

value: intermediate sensitivity to valproic acid


title: siAP-2γ (Dharmacon)-transfected MCF-7, 12h E2

description: 4671881066_C, 4671881068_C, 4671881069_C

value: siAP-2γ (Dharmacon)-transfected MCF-7, E2


title: B. subtilis_argon treated_replicate2

description: B. subtilis grown in LB medium


title: SZ84T

type: genomic

city: London

first: Wei

last: Dai

address: Du Cane Road

department: Sugery and Cancer

institute: Imperial College London

description: patient Z84

hyb_protocol: see Nouzova M et al. J Pharmacol Exp Ther 311:968-81, 2004

scan_protocol: Scan on Agilent C scanner at 5µm resolution and features were extracted using Agilent feature extraction v9.5.3.1 using CGH-v4_95_Feb07

data_processing: Probes with high (>650000) and low (lower than mean+1.96SD of negative controls) signal intensities were excluded and intra-array normalisation was done with the background-corrected signals from two channels using MLDA package (see Dai et al. BMC Bioinformatics 9:337, 2008) tailored for DMH dataset. The flagged probes were treated as missing data points (about 3%) and imputed by KNN algorithm (k=10)

molecule: genomic DNA

source_name: McrBC undigested sample

label_protocol: The McrBC digested sample was labelled by Cy5 and McrBC mock disgested sample was labelled by Cy3

extract_protocol: see Strathdee G et al. Oncogene 18: 2335-41, 1999

treatment_protocol: McrBC undigested sample

value: primary ovarian tumor

source_name: McrBC digested sample

treatment_protocol: McrBC digested sample


title: Breast Cancer Pleural effusion E21518

source_name: Pleural Effusion breast cancer


title: SZ91Tb

description: patient Z91


title: Peripheral blood cells from healthy control with low serum Sema4A level, biological rep2

city: Kobe

first: Akiko

last: Matsui

address: 6-7-5, Minatojima-Minamimachi, Chuo-ku

department: Department of Molecular & Cellular Biology

country: Japan

institute: Nippon Boehringer Ingelheim, Co. Ltd

description: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. GeneChips were scanned using the  GeneChip Scanner 3000 and GCOS.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using GeneSpring GX 11.0.1.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

extract_protocol: Extraction with QIAamp RNA blood Mini Kit (QIAGEN) was performed according to the manufacturer's instructions.

treatment_protocol: No treatment performed.

tag: gender

value: female

value: peripheral blood

tag: disease state

value: healthy

tag: serum level

value: low serum Sema4A level


title: Peripheral blood cells from MS patients with low serum Sema4A level, biological rep1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the  GeneChip Scanner 3000 and GCOS.

source_name: Peripheral blood cells from multiple sclerosis patients with low serum Sema4A level, biological rep1

value: multiple sclerosis


title: SZ80Tb

description: patient Z80


title: SZ76T

description: patient Z76


title: Peripheral blood cells from MS patients with high serum Sema4A level, biological rep3

source_name: Peripheral blood cells from multiple sclerosis patients with high serum Sema4A level, biological rep3

value: high serum Sema4A level


title: B. subtilis_argon plasma treated_replicate1

description: B. subtilis grown in LB medium


title: B. subtilis_argon treated_replicate1

description: B. subtilis grown in LB medium


title: Peripheral blood cells from healthy control with low serum Sema4A level, biological rep4


title: Breast cancer Pleural effusion I27253


title: SZ91T

description: patient Z91


title: SZ75Tb

description: patient Z75


title: SZ7Tb

description: patient Z7


title: SZ76Tb

description: patient Z76


title: SZ84Tb

description: patient Z84


title: Peripheral blood cells from healthy control with low serum Sema4A level, biological rep1


title: Peripheral blood cells from MS patients with high serum Sema4A level, biological rep2

source_name: Peripheral blood cells from multiple sclerosis patients with high serum Sema4A level, biological rep2


title: Peripheral blood cells from MS patients with low serum Sema4A level, biological rep2

source_name: Peripheral blood cells from multiple sclerosis patients with low serum Sema4A level, biological rep2


title: Peripheral blood cells from MS patients with high serum Sema4A level, biological rep1

source_name: Peripheral blood cells from multiple sclerosis patients with high serum Sema4A level, biological rep1


title: BLM Pcad

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: non-invasive P-cadherin over-expression variant of the invasive BLM melanoma cell line

hyb_protocol: A mixture of purified and fragmented biotinylated cRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in the GeneChip® fluidics station 400 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using the GeneChip® scanner 3000 (Affymetrix).

data_processing: MAS 5.0 normalization was applied. The data were base 2 log-transformed.

source_name: Human melanoma cells; LZRS-P-cadherin-IRES-EGFP transduced

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technolgies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 2 µg of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was converted and amplified to double stranded cDNA in a 1-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturers protocol (Affymetrix). All amplification and labeling reactions were performed on a Biomek 3000 ArrayPlex Workstation (Beckman Coulter).

growth_protocol: Cells were grown and maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco BRL, Belgium) containing 10% heat-inactivated fetal bovine serum (Greiner Bio-One, Belgium), 100 IU per mL penicillin, 100 µg per mL streptomycin and 2,5 µg per mL amphotericin B. Cells were continuously incubated at 37°C in a 10% CO2 atmosphere. Culture media were refreshed once a week and cells were divided upon 90% confluency.

extract_protocol: RNeasy minikit, Qiagen; RNA was extracted according to the manufacturers' instructions. Prior to RNA extraction, cells were collected and snap-frozen in liquid nitrogen. RNA was stored at -80°C.

tag: cell line

value: Human BLM (Bowes Lung Metastases) melanoma cells

tag: protocol

value: P-cadherin overexpression

tag: genotype/variation


title: SZ7T

description: patient Z7


title: SZ75T

description: patient Z75


title: BLMLIE (L)

description: invasive BLM melanoma cell line

source_name: Human melanoma cells; LZRS-IRES-EGFP transduced

value: control

value: invasive BLM melanoma cell line


title: SZ80T

description: patient Z80


title: SZ6Tb

description: patient Z6


title: Peripheral blood cells from MS patients with low serum Sema4A level, biological rep3

source_name: Peripheral blood cells from multiple sclerosis patients with low serum Sema4A level, biological rep3


title: Peripheral blood cells from healthy control with low serum Sema4A level, biological rep3


title: SZ64Tb

description: patient Z64


title: SZ6T

description: patient Z6


title: SZ58Tb

description: patient Z58


title: SZ64T

description: patient Z64


title: SZ62T

description: patient Z62


title: SZ57Tb

description: patient Z57


title: SZ58T

description: patient Z58


title: prefrontal/orbito-frontal cortex, left side, 17 gestational weeks

city: Brussels

first: Vincent

last: Detours

address: 808 Route de Lennik

department: School of Medicine

institute: Free University of Brussels

hyb_protocol: cDNAs were prepared and hybridized according to manufacturer's instructions (Affymetrix HGU133+v2.0).

scan_protocol: Affymetrix protocol

data_processing: RMA

extract_protocol: RNA was extracted from each sample using RNeasy kit (Qiagen).

value: prefrontal/orbito-frontal cortex

tag: side of brain

value: left

tag: age

value: 17 gestational weeks


title: prefrontal/orbito-frontal cortex, left side, 19 gestational weeks

label_protocol: cDNAs were prepared and hybridized according to manufacturer's instructions (Affymetrix HGU133+v2.0).

value: 19 gestational weeks


title: parieto-temporal cortex, left side, 17 gestational weeks

value: parieto-temporal cortex


title: SZ56Tb

description: patient Z56


title: SZ57T

description: patient Z57


title: prefrontal/orbito-frontal cortex, right side, 17 gestational weeks

value: right


title: prefrontal/orbito-frontal cortex, right side, 19 gestational weeks


title: SZ56T

description: patient Z56

value: primary ovarian tumor


title: parieto-temporal cortex, right side, 19 gestational weeks


title: Control 04852

description: no additional information

hyb_protocol: Standard affymetrix protocol

scan_protocol: Affymetrix gene chip scanner

source_name: Pleural effusion from triple negative breast cancer. Grown in 3D culture.

label_protocol: Standard affymetrix protocol

extract_protocol: Standard affymetrix protocol

value: not sensitive to valproic acid

value: Pleural Effusion


title: SZ35Tb

description: patient Z35


title: SZ51Tb

description: patient Z51


title: Control 03766

description: no additional information


title: SZ62Tb

description: patient Z62


title: Control 01056

description: no additional information


title: Tomato fruit PBS control 2

city: Rehovot

first: Robert

last: Fluhr

department: Plant Sciences

country: Israel

institute: Weizmann Institute of Science

description: Tomato breaker fruit parenchyma PBS control

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45 degrees C on Affymetrix Tomato GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GC3000 7G.

data_processing: RMA via PARTEK software.

organism: Solanum lycopersicum

source_name: Tomato breaker fruit parenchyma cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix), in the Weizmann Institute microarray unit.

growth_protocol: The plants were grown in pots filled with a peat-vermiculite (4:1, v/v) mixture containing slow-release high-N Multicote 4 with microelements (0.3% w/w; Haifa Chemicals, Haifa Bay, Israel). Average temperatures in the greenhouse during the growth period fluctuated from 18 to 25˚C.

extract_protocol: Total RNA was prepared from the fruit pericarp, of 10 mm diameter and 3-4 mm deep. Each biological repeat consisted of 20 infection or treatments front pericarp of 10 mm diameter and 3-4 mm deep from at least five different fruit. For RNA isolation one grams of tissue was ground in liquid nitrogen, transferred to 4ml extraction buffer (100mM Tris-HCl at pH 9.0, 200mM NaCl, 15mM EDTA at pH 8.0, 0.5% sarkosyl) and homogenized, 4ml phenol was added flowed by 280µl of 3M sodium-acetate and homogenized. The extraction was subjected to 10min centrifuge at 10000rpm and 4ml of tri-reagent was added to the supernatant and flowed by another centrifuge. 4ml of isopropanol was added to the supernatant and kept in ice for an hour flowed by another centrifuge. The resulted pellet was resuspended with 1ml DEPC water, 0.5ml of 8N Licl was added and kept on ice for overnight. The resuspended pellet was centrifuge, treated with 70% ethanol and dried. The RNA pellet was treated with DNase (Turbo-DNA Free; Ambion, Austin, Texas). Followed by RNA cleanup with RNAeasy Plant Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: The fruits had been surface-sterilized in 0.3% (v/v) hypochlorite for 10 min, rinsed thoroughly with water and dried. A 0.5mm thick, 10-mm diameter of the peel tissue was removed from the tomato fruit. 50 µl of PBS buffer was pipette directly on the wounded tissue every 4 hours. fruits were incubated at 22°C and 95% RH in covered plastic containers.The samples were collected 24 hours post treatment.

tag: cultivar

value: Hazera 1402

value: pericarp


title: SZ2T

description: patient Z2


title: BLMP-cad (P)

value: non-invasive P-cadherin over-expression variant


title: SZ35T

description: patient Z35


title: Control 00918

description: no additional information


title: PE1

description: no additional information

value: sensitive to valproic acid


title: SZ51T

description: patient Z51


title: Tomato fruit ammonium treatment

description: Tomato breaker fruit parenchyma ammonium treatment

treatment_protocol: The fruits had been surface-sterilized in 0.3% (v/v) hypochlorite for 10 min, rinsed thoroughly with water and dried. A 0.5mm thick, 10-mm diameter of the peel tissue was removed from the tomato fruit. 50 µl of 5mM ammonium-chloride in PBS buffer was pipette directly on the wounded tissue every 4 hours. fruits were incubated at 22°C and 95% RH in covered plastic containers.The samples were collected 24 hours post treatment.


title: Tomato fruit PBS control


title: SZ29Tb

description: patient Z29


title: Tomato fruit ammonium treatment 2


title: PE5

description: no additional information


title: SZ29T

description: patient Z29


title: PE4

description: no additional information


title: PE2

description: no additional information


title: Tomato fruit wound control 2

description: Tomato breaker fruit parenchyma wound control

treatment_protocol: The fruits had been surface-sterilized in 0.3% (v/v) hypochlorite for 10 min, rinsed thoroughly with water and dried. A 0.5mm thick, 10-mm diameter of the peel tissue was removed from the tomato fruit.


title: SZ25Tb

description: patient Z25


title: Tomato fruit wound inoculation by Colletotrichum coccodes 2

description: Tomato breaker fruit parenchyma cells wound inoculation by C. coccodes

treatment_protocol: The fruits had been surface-sterilized in 0.3% (v/v) hypochlorite for 10 min, rinsed thoroughly with water and dried. Fruit inoculation was carried out on the pericarp. A 0.5mm thick, 10-mm diameter of the peel tissue was removed from the tomato fruit and replaced by a 0.5mm thick hyphal disk of Colletotrichum coccodesmycelia (Alkan et al., 2008). This hyphal disk was obtained by growing spores for 3 days on primary media and transferred to 1 day growth on secondary media (“hyphal mat infection method”) (Alkan et al., 2008).


title: SZ30Tb

description: patient Z30


title: SZ2Tb

description: patient Z2


title: SZ30T

description: patient Z30


title: Tomato fruit wound control


title: SZ24Tb

description: patient Z24


title: SZ21T

description: patient Z21


title: Tomato fruit wound inoculation by Colletotrichum coccodes

description: Tomato fruit wound inoculation by C. coccodes

data_processing: RMA via PARTEK software

source_name: tomato breaker fruit parenchyma cells


title: SZ24T

description: patient Z24


title: SZ18T

description: patient Z18


title: Sen1-TAP_rep3

city: Montréal

first: François

last: Robert

state: Québec

address: 110, avenue des Pins Ouest

department: Chromatin and Genomic Expression

country: Canada

institute: Institut de recherches cliniques de Montréal (IRCM)

description: Biological replicate 3 of 3. Sen1 occupancy measured by the IP/Input ratio in WT cells.

hyb_protocol: Resuspend Cy5 labeled IP in 4ul of water and combine with corresponding Cy3 labeled sample. Mix to 450ul of the hybridization buffer for each slide (45ul 0.5M Mes NaOH (pH 6.9), 135ul Formamide, 58.5ul 5M NaCl, 45ul 5% N-Lauroylsarcosine (FLUKA), 1ul 250 ug/ml Salmon Sperm DNA, 10ul 8 mg/ml yeast tRNA, 5.4ul 0.5 M EDTA, 150.1ul mQH2O). Boil samples for 3 minutes in 100ºC heat block. Transfer to 40ºC heat block for another 10 minutes. Follow standard Agilent chamber hybridization protocols. Incubate overnight at 40C in hybridization oven. Post-Hybridization Washes: Separate coverslip and slide in Wash buffer #1. Wash slides in Wash buffer #1 for 5 minutes at room temperature on an orbital shaker (cover the dish to avoid light on the slides). Wash in 31C Wash buffer #2 for 5 minutes on an orbital shaker. Take slides out of the buffer slowly to dry them. Wash Buffer #1: 6x SSPE, 0.005% N-lauroylsarcosine. Wash Buffer #2: 0.06x SSPE.    Stripping is done in 1 L of 5 mM Potassium phosphate buffer pH 6.6. 1. Use a 2L beaker, which can fit a slide rack. Pour the stripping buffer, submerge the rack with slides (from 1 to 10) and heat it up slowly while stirring with a stir bar until the liquid boils with big bubbles. Do not overboil it. Remove the rack and briefly rinse in a container with water. Slowly remove the rack from the liquid. Cy5 channel will be stripped much better than Cy3, but this does not affect the performance of subsequent hybridizations. Stock solution of 1M Potassium phosphate buffer, pH 6.6: Mix 3.81 ml of 1M K2HPO4 + 6.19 ml of 1M KH2PO4. Dilute 2.5 ml of this 1M solution in 500 ml Milli-Q water to obtain 5mM Potassium phosphate buffer, pH 6.6.

scan_protocol: Axon GenePix 4000B scanner and the GenePix Pro extraction software were used. Scan at 100% laser power for both channels. Set the Pixel Size to 5um / pixel. Set the Lines to average to 1. Set the Focus Position to 0um. Adjust PMTs so that approximately 1-2% spots are saturated. This is done to ensure full dynamic range utilization. Adjust PMTs so that the intensity ratio is 0.9 - 1.1 when looking at intensity values greater than or equal to 3000 on the Intensity / Frequence histogram. Images were quantified using Axon GenePix (version 6.1.0.4).

data_processing: The raw data were corrected (foreground-background) then normalized using the limma's loess function (Yang et al.,2002) in BioConductor (from the ArrayPipe Analysis Pipeline (Hokamp et al., 2004)) and replicates were combined using a weighted average method as described previously (Pokholok et al., 2005).

organism: Saccharomyces cerevisiae

label_protocol: Blunting: Do everything on ice! Add 70uL of the blunting solution (11uL NEB Buffer #2, 0.5uL BSA 10mg/mL, 0.5uL 20mM dNTPs, 0.2uL T4 DNA Polymerase 3U/uL, 57.8uL ddH2O) to 40uL of the resuspended DNA obtained at the end of the cleanup step. For WCEs, use 2uL + 38uL ddH2O instead of 40uL. Incubate 20 minutes at 12C. Add 11.5uL 3M NaOAc, pH 5.2, and 0.5uL Glycogen 20mg/mL and vortex briefly. Extract with 120uL Phenol/Chloroform/Isoamyl alcohol (25:24:1). Transfer 110uL to a new tube, and add 230uL -20C 100% EtOH. Put at -80C for 30min, then spin 20 minutes at 4C. Wash the pellet with 500uL -20C 70% EtOH and spin 15 minutes at 4C. Resuspend the pellet in 25uL ddH2O and place on ice.     Ligation: Thaw everything on ice, and do all manipulations on ice. Add 25uL of ligase mix (10uL 5x T4 Ligase Buffer, 6.7uL 15uM unidirectional linkers, 0.5uL T4 DNA Ligase, High Concentration, 8uL ddH2O) to the resuspended pellet from the blunting step. Incubate overnight at 16C. Add 6uL 3M NaOAc, pH 5.2, and vortex. Add 130uL -20C 100% EtOH and centrifuge 20 minutes at 4C. Wash the pellet (should be a smear on the side of the tube) with 500uL -20C 70% EtOH. Spin 15 minutes at 4C. Dry the pellet and resuspend in 25uL ddH2O.     Labeling: Add 15uL of PCR Labeling mix (4uL 10x ThermoPol Buffer, 2uL 5mM aa-dUTP mix, 1.25uL Oligo FR1, 7.75uL ddH2O) to the pellet from the ligation step. Start the PCR program, and during the first step (4 minutes at 55C), add 10uL of the polymerase mix (1uL 10x ThermoPol buffer, 1uL Taq Polymerase 5U/uL, 0.01uL Pfu Polymerase Turbo 2.5U/uL, 8uL ddH2O). PCR cycling conditions: 1) 5:00 at 55C 2) 5:00 at 72C 3) 2:00 at 95C 4) 0:30 at 95C 5) 0:30 at 55C 6) 1:00 at 72C 7) Repeat steps 4-6 31 more times. 8) 4:00 at 72C 9) Forever at 4C Purify PCR reactions with Qiagen PCR Cleanup kits, following their protocol BUT use a phosphate wash buffer and a phosphate elution buffer instead of their buffers PE and EB, respectively. Also, wash the columns only once, and elute twice with 30uL elution buffer. Speed-vac the eluate to dryness. Resuspend the pellets with fresh 4.5uL 0.1M Sodium Carbonate Buffer, pH 9.0. Add 4.5uL of the appropriate NHS-ester Cy-dye. Fresh tubes of NHS-ester Cy-dye should be resuspended in 73uL DMSO. Mix well, and incubate at room temperature in the dark for one hour. Add 35uL 0.1M NaOAc, pH 5.2. Purify using the Qiagen PCR Cleanup protocol using all their buffers, but wash only once and elute twice in 30uL. It is a good idea to elute both samples of a pair (Cy5 and Cy3) in the same tube to avoid DNA loss upon later resuspension. Speed-vac until 10-20uL are left, or to dryness. Phosphate Wash Buffer (100mL): 0.5mL 1M KPO4, pH 8.5 15.25mL ddH2O 84.25mL 95% EtOH Solution will be cloudy upon mixing. Phosphate Elution Buffer (10mL): 0.04mL 1M KPO4, pH 8.5 9.96mL ddH2O 1M KPO4, pH 8.5 (10mL): 9.5mL 1M K2HPO4 0.5mL 1M KH2PO4 1M Sodium Carbonate Buffer, pH 9.0 (100mL): 10.8g Na2CO3 80mL ddH2O pH to 9.0 with concentrated HCl Adjust volume to 100mL with ddH2O DILUTE 1:10 WHEN USING! Solution will change composition over time. Use only if less than a month old. Reference: Drouin S., Robert F. Methods (in press).B38

growth_protocol: Cells containing TAP-tagged SEN1 or NRD1 (Ghaemmaghami et al, 2003) were grown in 50mL YPD overnight to OD600 0.8-1.0 by inoculation of a single colony. For downregulation of Sen1, the Sen1tetO7 (MATa his3Δ leu2Δ met15Δ ura3Δ URA3::CMV-tTA kanR TetO7-SEN1) (Mnaimneh et al., 2004) and its corresponding wt strains were grown in YPD containing 10ug.ml doxycycline.  A volume of 5 ml of 11% formaldehyde in 0.1M NaCl, 1mM EDTA, 50 mM Hepes-KOH, pH 7.5 was added to the cultures and shaken on a rotating wheel at room temperature for 20min.  Crosslinking was stopped by addition of 9 mL 3M Glycine in 20mM Tris base and incubation for 5min at room temperature.

extract_protocol: Crosslinked cells were pelleted at 3.7k RPM in Beckman centrifuge (GS 6R Rotor 3.8), then washed twice with 40mL ice cold TBS and once with 10ml ChiP lysis buffer with 1Complete tablet (50mM Hepes-KOH, pH 7.5, 150mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium Deoxycholate, 0.1% SDS) before being quick-frozen by immersion in liquid nitrogen. Cells were thawed on ice, and resuspended in 1mL lysis buffer adjusted to 0.5% SDS with protease inhibitors and transferred to 1.5 ml screw cap tubes. 500uL of acid-washed glass beads (Sigma) were added, and the cells were lysed using the bead-beater (6x2.5min cycles, with 5min breaks on ice). The tubes are pierced with a 18-gauge syringe needle to allow elution of lysate, but not of beads. The pierced tubes were put in 2mL collection tubes and spun briefly to 6000 RPM. The lysate was then clarified by centrifugation for 15min at max speed in a refrigerated microfuge. The pellet was then washed with 1ml of lysis buffer containing 0.1% SDS. The pellet is then resuspended in  1ml of lysis buffer containing 0.1% SDS and the homogenate was sonicated 8x 30sec (in a ice-water bath) with a 1 minute break between sonication cycles. The sonicated lysates were centrifuged in a refrigerated centrifuge as before. After adjusting salt concentration to 275mM, the supernatant was frozen at -80C, or used immediately for ChIP.    For the immunoprecipitation, 500ul of chromatin was incubated with constant agitation at 4oC overnight with either   10ul of IgG-sepharose beads prewashed with TE, for the immunoprecipitation of TAP tagged proteins or, with 1.25ul of 8WG16 monoclonal antibody prepared in house, for RNAPII immunoprecipitation. In the latter case, 20ul protein A sepharose beads were added next day and incubated for 2 hours for the collection of the immune complexes.  In each case, beads containing chromatin were washed once for 4 min with rotation with 1.4 ml of the following solutions:  FA lysis buffer /0.1% SDS/ 275mM NaCl (250ul 5M NaCl in 10ml).  FA lysis buffer /0.1% SDS/ 500mM NaCl (700ul 5M NaCl in 10ml).  10mM Tris-HCl, pH 8.0, 0.25M LiCl, 1mM EDTA, 0.5% NP-40, 0.5% Na Deoxycholate.  TE (10mM Tris-HCl, pH 8.0, 1mM EDTA).  The bound proteins were eluted by incubating the beads at 65ºC for 20 minutes in 100ul of TE-SDS1%. Beads were washed with 100ul and the two eluates were combined. At this step, 20 ul of input chromatin was combined with 180uL TE + 1% SDS and treated similarly with the immunoprecipiated chromatin fraction. Chromatin fractions are deproteinized by incubation with 10ul of 10mg/ml of Proteinase K for 2hr at 37oC, followed by 6 hr at 65oC for the reversal of the crosslinks.    To clean-up the DNA, Uncrosslinked chromatin fractions were then cleaned up using Qiagen QIAquick PCR Purification Kit according to the manufacturer’s instructions.

tag: strain

tag: antibody

value: IgG-sepharose beads


title: Nrd1-TAP_rep1

description: Biological replicate 1 of 3. Nrd1 occupancy measured by the IP/Input ratio in WT cells.


title: SZ17Tb

description: patient Z17


title: RNAPII_tetO7:sen1_rep1

description: Biological replicate 1 of 2. RNAPII occupancy measured by the IP/Input ratio in tetO7:sen1 cells.

value: 8WG16 anti-CTD of Rpb1 (monoclonal antibody prepared in house)


title: Nrd1-TAP_rep2

description: Biological replicate 2 of 3. Nrd1 occupancy measured by the IP/Input ratio in WT cells.


title: Sen1-TAP_rep2

description: Biological replicate 2 of 3. Sen1 occupancy measured by the IP/Input ratio in WT cells.


title: SZ18Tb

description: patient Z18


title: RNAPII_tetO7:sen1_rep2

description: Biological replicate 2 of 2. RNAPII occupancy measured by the IP/Input ratio in tetO7:sen1 cells.


title: SZ21Tb

description: patient Z21


title: HUES6 hESCs biological rep 3 [mRNA]

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description:
M6-3
Gene expression data from SSEA4+ HUES6 hESC line

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX ref8 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina BeadArray Reader scanner

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings.

source_name: hESCs with SSEA4+

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

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

value: HUES6 hESC line


title: SZ17T

description: patient Z17


title: SZ16T

description: patient Z16


title: Nrd1-TAP_rep3

description: Biological replicate 3 of 3. Nrd1 occupancy measured by the IP/Input ratio in WT cells.


title: Sen1-TAP_rep1

description: Biological replicate 1 of 3. Sen1 occupancy measured by the IP/Input ratio in WT cells.


title: SZ15Tb

description: patient Z15


title: RNAPII_WT_rep1

description: Biological replicate 1 of 2. RNAPII occupancy measured by the IP/Input ratio in WT cells.


title: SZ25T

description: patient Z25


title: SZ15T

description: patient Z15


title: BLM LIE

description: invasive BLM melanoma cell line

value: Human BLM (Bowes Lung Metastases) melanoma cells

value: control

value: invasive BLM melanoma cell line


title: RNAPII_WT_rep2

description: Biological replicate 2 of 2. RNAPII occupancy measured by the IP/Input ratio in WT cells.


title: SZ14Tb

description: patient Z14


title: I6 hESCs biological rep 3 [mRNA]

description:
I6-3
Gene expression data from SSEA4+ I6 hESC line

value: I6 hESC line


title: SZ16Tb

description: patient Z16


title: HUES6 hESCs biological rep 2 [mRNA]

description:
M6-2
Gene expression data from SSEA4+ HUES6 hESC line


title: I4 hESCs biological rep 3 [mRNA]

description:
I4-3
Gene expression data from SSEA4+ I4 hESC line

value: I4 hESC line


title: I4 hESCs biological rep 2 [mRNA]

description:
I4-2
Gene expression data from SSEA4+ I4 hESC line


title: SZ125T

description: patient Z125


title: SZ125Tb

description: patient Z125


title: H9 hESCs biological rep 3 [mRNA]

description:
H9-3
Gene expression data from SSEA4+ H9 hESC line

value: H9 hESC line


title: SZ122T

description: patient Z122


title: H9 hESCs biological rep 2 [mRNA]

description:
H9-2
Gene expression data from SSEA4+ H9 hESC line


title: I6 hESCs biological rep 1-1 [mRNA]

description:
HK_I6ESC
Gene expression data from SSEA4+ I6 hESC line


title: SZ120Tb

description: patient Z120


title: SZ121T

description: patient Z121


title: SZ118Tb

description: patient Z118


title: HUES6 hESCs biological rep 1-2 [mRNA]

description:
HK_HUES6ESC2
Gene expression data from SSEA4+ HUES6 hESC line


title: SZ112T

description: patient Z112


title: I6 hESCs biological rep 1-2 [mRNA]

description:
HK_I6ESC2
Gene expression data from SSEA4+ I6 hESC line


title: SZ122Tb

description: patient Z122


title: H9 hESCs biological rep 1-2 [mRNA]

description:
HK_H9ESC2
Gene expression data from SSEA4+ H9 hESC line


title: I4 hESCs biological rep 1-1 [mRNA]

description:
HK_I4ESC
Gene expression data from SSEA4+ I4 hESC line


title: SZ118T

description: patient Z118


title: SZ112Tb

description: patient Z112


title: HUES6 hESCs biological rep 1-1 [mRNA]

description:
HK_HUES6ESC
Gene expression data from SSEA4+ HUES6 hESC line


title: SZ14T

description: patient Z14


title: H9 hESCs biological rep 1-1 [mRNA]

description:
HK_H9ESC
Gene expression data from SSEA4+ H9 hESC line


title: I4 hESCs biological rep 1-2 [mRNA]

description:
HK_I4ESC2
Gene expression data from SSEA4+ I4 hESC line


title: SZ105T

description: patient Z105


title: SZ121Tb

description: patient Z121


title: I6 hESCs biological rep 2 [mRNA]

description:
I6-2
Gene expression data from SSEA4+ I6 hESC line


title: SZ105Tb

description: patient Z105


title: SZ120T

description: patient Z120


title: parieto-temporal cortex, left side, 19 gestational weeks

value: parieto-temporal cortex

value: left

value: 19 gestational weeks


title: SZ102T

description: patient Z102

value: primary ovarian tumor


title: SZ102Tb

description: patient Z102


title: SZ101T

description: patient Z101


title: SS9Tb

description: patient S9


title: SZ101Tb

description: patient Z101


title: SS5Tb

description: patient S5


title: SS9T

description: patient S9


title: SS5T

description: patient S5


title: MSC_Mock_a

city: Rotterdam

first: Jeroen

last: van de Peppel

address: 's Gravendijkwal 230

country: Netherlands

institute: ErasmusMC

description: Bone marrow derived Mesenchymal Stem cells transduced over night with Mock and osteogenic differentiated for 7 days, replicate 1

data_processing: The data was background subtracted, vst transformation and a quantile normalization was applied. Probes that were detected at least 5 times in the experiments (illumina detection p-value <0.01), were considered to be expressed and further analyzed for differential expression using Limma.

source_name: MSC transduced with Mock

label_protocol: cDNA and Biotinylated cRNA were prepared with the Illumina Totalprep RNA Amplification kit (Ambion)

growth_protocol: alphaMEM, 20mM HEPES, strep/pen, 1.8 mM CaCl2, 10% FCS, 10 mM beta-glycerophosphate, 100 nM dexamethasone

extract_protocol: Total RNA extracted using Trizol (invitrogen)

treatment_protocol: shRNAi transduction

value: Male

value: Bone Marrow


title: MSC_Mock_b

description: Bone marrow derived Mesenchymal Stem cells transduced over night with Mock and osteogenic differentiated for 7 days, replicate 2


title: MSC_Mock_d

description: Bone marrow derived Mesenchymal Stem cells transduced over night with Mock and osteogenic differentiated for 7 days, replicate 4


title: SS3Tb

description: patient S3


title: SS3T

description: patient S3


title: SS2T

description: patient S2


title: MSC_Mock_c

description: Bone marrow derived Mesenchymal Stem cells transduced over night with Mock and osteogenic differentiated for 7 days, replicate 3


title: MSC_tGFP_a

description: Bone marrow derived Mesenchymal Stem cells transduced over night with tGFP and osteogenic differentiated for 7 days, replicate 1

source_name: MSC transduced with tGFP


title: MSC_shC_c

description: Bone marrow derived Mesenchymal Stem cells transduced over night with shC and osteogenic differentiated for 7 days, replicate 3

source_name: MSC transduced with shC


title: MSC_tGFP_b

description: Bone marrow derived Mesenchymal Stem cells transduced over night with tGFP and osteogenic differentiated for 7 days, replicate 2


title: MSC_shC_b

description: Bone marrow derived Mesenchymal Stem cells transduced over night with shC and osteogenic differentiated for 7 days, replicate 2


title: MSC_tGFP_c

description: Bone marrow derived Mesenchymal Stem cells transduced over night with tGFP and osteogenic differentiated for 7 days, replicate 3


title: SS28T

description: patient S28

source_name: McrBC undigested sample

source_name: McrBC digested sample


title: SS28Tb

description: patient S28


title: SS26Tb

description: patient S26


title: MSC_shC_d

description: Bone marrow derived Mesenchymal Stem cells transduced over night with shC and osteogenic differentiated for 7 days, replicate 4


title: SS2Tb

description: patient S2


title: MSC_GPM6Bsh2_d

description: Bone marrow derived Mesenchymal Stem cells transduced over night with sh2 and osteogenic differentiated for 7 days, replicate 4

source_name: MSC transduced with sh2


title: MSC_GPM6Bsh3_c

description: Bone marrow derived Mesenchymal Stem cells transduced over night with sh3 and osteogenic differentiated for 7 days, replicate 3

source_name: MSC transduced with sh3


title: MSC_shC_a

description: Bone marrow derived Mesenchymal Stem cells transduced over night with shC and osteogenic differentiated for 7 days, replicate 1


title: MSC_GPM6Bsh3_a

description: Bone marrow derived Mesenchymal Stem cells transduced over night with sh3 and osteogenic differentiated for 7 days, replicate 1


title: SS26T

description: patient S26


title: MSC_GPM6Bsh3_d

description: Bone marrow derived Mesenchymal Stem cells transduced over night with sh3 and osteogenic differentiated for 7 days, replicate 4


title: MSC_GPM6Bsh3_b

description: Bone marrow derived Mesenchymal Stem cells transduced over night with sh3 and osteogenic differentiated for 7 days, replicate 2


title: SS22Tb

description: patient S22


title: SS25Tb

description: patient S25


title: SS25T

description: patient S25


title: MSC_GPM6Bsh2_b

description: Bone marrow derived Mesenchymal Stem cells transduced over night with sh2 and osteogenic differentiated for 7 days, replicate 2


title: SS22T

description: patient S22


title: SS14Tb

description: patient S14


title: SS16T

description: patient S16


title: MSC_GPM6Bsh2_c

description: Bone marrow derived Mesenchymal Stem cells transduced over night with sh2 and osteogenic differentiated for 7 days, replicate 3


title: MSC_GPM6Bsh2_a

description: Bone marrow derived Mesenchymal Stem cells transduced over night with sh2 and osteogenic differentiated for 7 days, replicate 1


title: MSC_GPM6Bsh1_c

description: Bone marrow derived Mesenchymal Stem cells transduced over night with sh1 and osteogenic differentiated for 7 days, replicate 3

source_name: MSC transduced with sh1


title: MSC_GPM6Bsh1_a

description: Bone marrow derived Mesenchymal Stem cells transduced over night with sh1 and osteogenic differentiated for 7 days, replicate 1


title: SS16Tb

description: patient S16


title: SS14T

description: patient S14


title: MSC_GPM6Bsh1_d

description: Bone marrow derived Mesenchymal Stem cells transduced over night with sh1 and osteogenic differentiated for 7 days, replicate 4


title: SS13T

description: patient S13


title: MSC_GPM6Bsh1_b

description: Bone marrow derived Mesenchymal Stem cells transduced over night with sh1 and osteogenic differentiated for 7 days, replicate 2


title: SS11Tb

description: patient S11


title: SS12T

description: patient S12


title: SS13Tb

description: patient S13


title: SS12Tb

description: patient S12


title: SS11T

description: patient S11


title: parieto-temporal cortex, right side, 17 gestational weeks

value: right

value: 17 gestational weeks


title: QM9414 strain deleted for Cre1 under carbon catabolite repression versus under carbon catabolite derepression dye switch

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

country: France

institute: École normale supérieure

hyb_protocol: 1.5µg of labelled cDNA is mixed with one volume of 2X GE buffer (Agilent) and 10% of blocking agent. The hybridization sample volume is dispense on the selected microarray and incubated overnight at 65°C in a hybridization oven (Agilent). The array slides are washed 1 minute in "wash 1 buffer" at room temperature and one minute in "wash 2 buffer" at 37°C. The array slides are then air dryed and ready for scaning.

scan_protocol: The hybridized microarrays were scanned using Genepix 4000B (Molecular Devices, Sunnyvale, CA, USA) and the resulting image files analyzed by GenePix Pro 6.1 software (Axon).

data_processing: For each GenePix output file, two filters were applied, one to clear out flagged spots and another one to discard saturating spots where the median foreground intensity was greater than 60,000 in one of the two channels. The resulting median foreground intensities were normalized, without background signal subtraction, using a global Lowess correction followed by a print-tip median normalization step (Lemoine et al., 2006).

organism: Trichoderma reesei

source_name: Total RNA extracted from T reesei QM9414 strain deleted for Cre1 under carbon catabolite derepression.

label_protocol: 1 µg RNA are retro transcribed using Superscript III retro transcriptase. The cDNA are purified using QiaQuick column (Quiagen) and incubated 1 hour at room temperature in presence of 0,05M NaBicarbonate and NHS-ester Cy.The coupling is stoped by addition of hydroxylamine to a final concentration of 0,6M. Labeled cDNA are purified using QiaQuick column.

extract_protocol: Fungal mycelia were harvested by filtration, washed with distilled cold water, frozen and ground under liquid nitrogen. For extraction of total RNA purification kits (SV Total RNA Isolation System, Promega) were used according to the manufacturer’s protocol.

treatment_protocol: Chemostat cultures with D-glucose as the limiting carbon source at 0.025 gram/hour  which have previously been shown to lead to CCR derepression (Karaffa et al. 2006)

value: QM9141 deleted for Cre1

tag: condition

value: Carbon Catabolite Derepression

source_name: Total RNA extracted from T reesei QM9414 strain deleted for Cre1 under carbon catabolite repression.

treatment_protocol: Chemostat cultures with D-glucose as the limiting carbon source at 0.07 gram/hour  which have previously been shown to lead to CCR repression (Karaffa et al. 2006)

value: Carbon Catabolite Repression


title: QM9414 strain deleted for Cre1 under carbon catabolite repression versus under carbon catabolite derepression


title: QM9414 strain deleted for Cre1 versus QM9411 strain under carbon catabolite derepression dye switch

treatment_protocol: Chemostat cultures with D-glucose as the limiting carbon source at 0.025 gram/hour  which have previously been shown to lead to CCR repression (Karaffa et al. 2006)

value: QM9141 deleted fro Cre1

source_name: Total RNA extracted from T reesei QM9414 strain under carbon catabolite derepression.


title: QM9414 strain deleted for Cre1 versus QM9411 strain under carbon catabolite repression dye switch

source_name: Total RNA extracted from T reesei QM9414 strain under carbon catabolite repression.


title: QM9414 strain under carbon catabolite repression versus under carbon catabolite derepression dye switch


title: SS10T

description: patient S10


title: QM9414 strain deleted for Cre1 versus QM9411 strain under carbon catabolite derepression


title: QM9414 strain under carbon catabolite repression versus under carbon catabolite derepression


title: patient 5

city: Providence

first: Sara

last: Pacheco

state: RI

address: 70 Ship Street, Room 510

department: Pathology and Lab Medicine

institute: Brown University

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

source_name: sperm

label_protocol: Standard Illumina Protocol

growth_protocol: Preparing Semen Samples for Separation  1. Determine the number of tubes needed for isolations based on the volume used for DNA/RNA. You will use ¼ of the total semen volume for DNA isolation and the remaining ¾ for RNA isolations.  a. Up to 1 ml of semen can be used per conical tube  b. Example: 4 mls semen  i. 1 ml is for DNA → therefore 1 conical tube is required for  DNA analysis prep  ii. 3 mls for RNA → therefore 3 conical tubes are required for RNA analysis prep  2. Label tubes with sample number and either “RNA” or “DNA”    Sperm Separation: Percolling:  1. When preparing Percoll and 2x PBS, do under sterile conditions to keep the Percoll sterile.  a. Add up to 1 ml 2x PBS and 1 ml Percoll to a 15 ml conical tube.  2. Gently pipette up to 1 ml semen sample on top.  3. Spin samples at 1200 rpm for 40 min → will see visible pellet at the bottom  4. Remove supernatant until the interface layer right before the pellet in bleach.    Sperm Separation: Washing:  1. Combine sperm pellets and remaining supernatant from DNA and RNA tubes, respectively, to reduce the number of tubes you are working with.  2. Add 1x PBS to a total volume of 10 ml.  3. Spin samples at 2000 rpm for 7 minutes and remove as much supernatant as you can without disrupting sperm.  4. Repeat washes 2x.  5. Resuspend pellet in 1 ml 1x PBS.  6. Add suspensions to properly labeled tubes for DNA and RNA.  7. Spin DNA tube at max speed to pellet the cells.  8. Remove supernatant, flash freeze pellets in liquid nitrogen, and store in -80 freezer.  9. Continue with RNA isolation protocol.

extract_protocol: DNA was isolated from the sperm of the 21 men using a modified protocol in which sperm pellets were lysed for 16 hours in a solution containing Tris (Fisher Scientific, Pittsburgh, PA, USA), DTT (Promega Corporation, Madison, WI, USA), NaCl (EMD Chemicals, Inc., the North American Affiliate of Merck KGaA, Darmstadt, Germany), EDTA (Fisher Scientific, Pittsburgh, PA, USA), SDS (Fisher Scientific, Pittsburgh, PA, USA), Proteinase K (Promega Corporation, Madison, WI, USA), and beta-mercaptoethanol (Sigma-Aldrich, St. Louis, MO, USA) [32]. The DNA was then extracted using phenol/chloroform (Sigma-Aldrich, St. Louis, MO, USA), ethanol precipitated, and bisulfite modified using the EZ DNA Methylation kit (Zymo Research Corporation, Orange, CA, USA).

tag: count

tag: motility

tag: morphology


title: SOT478b

description: patient OT478

tag: tissue


title: patient 11


title: SOT478

description: patient OT478


title: SS10Tb

description: patient S10


title: QM9414 strain deleted for Cre1 versus QM9411 strain under carbon catabolite repression


title: SAH

description: patient AH


title: SAHb

description: patient AH


title: SOT450b

description: patient OT450


title: patient 8


title: SOT450

description: patient OT450


title: patient 10


title: S89

description: patient 89


title: S87b

description: patient 87


title: S89b

description: patient 89


title: S91

description: patient 91


title: S91b

description: patient 91


title: patient 22


title: S87

description: patient 87


title: patient 33


title: patient 28


title: S81b

description: patient 81


title: patient 9


title: patient 36


title: patient 37


title: patient 40


title: patient 29


title: patient 31


title: patient 41


title: S81

description: patient 81


title: patient 13


title: patient 16


title: S82

description: patient 82


title: patient 23


title: S82b

description: patient 82


title: patient 34


title: patient 32


title: S79b

description: patient 79


title: S79

description: patient 79


title: patient 35


title: patient 26


title: S73b

description: patient 73


title: Endoderm_Rep3_vs_BleachedRef

city: NICE

first: Cecile

last: Sabourault

address: Faculte des Sciences, Parc Valrose, BP 71

department: Biology

institute: University of Nice

description: Sample 7

hyb_protocol: 500 ng of each labelled cDNA were diluted in Hi-RPM Gene Expression Hyb buffer (Agilent) and hybridized on the array overnight at 47°C. Dye-swapping hybridizations were performed for each condition.

scan_protocol: Slides were scanned using an AXON 4000B scanner (Molecular Devices). Image acquisition and quality control was performed using the software GenePix ® Pro 6.0.

data_processing: Analyses were carried out using the LimmaGUI package for the R system. Normexp + offset (positive offset of 50) method was performed as background correction. Print-tip loess normalization was performed for each slide. Quantile normalisation was applied to mean-log intensities in order to make the distributions essentially equivalent across arrays.

organism: Anemonia viridis

label_protocol: 5µg of total RNA was labelled using the ChipShotTM Direct labelling system then purified using a Clean-up system (Promega), according to the manufacturer's instructions. 5ng of a Lux mRNA exogenous standard was added to each sample before labelling.

extract_protocol: Total RNA extracted using Trizol® Reagent (Invitrogen) following Chomczynski and Mackey procedure (BioTechniques, 1995). RNA was subjected to a DNase treatment (RQ1-DNAse, Promega), then resuspended in nuclease-free water. RNA quantity and quality were assessed using a NanoDrop ND-1000 spectrophotometer and a Bioanalyzer 2100 (Agilent Technology), respectively.

tag: specimen

value: Endoderm

value: VBl reference

value: tentacle (ectoderm+endoderm)


title: Endoderm_Rep1_vs_BleachedRef

description: Sample 5


title: Endoderm_Rep2_vs_BleachedRef

description: Sample 6


title: Ectoderm_Rep2_vs_BleachedRef

description: Sample 2

value: Ectoderm


title: Ectoderm_Rep3_vs_BleachedRef

description: Sample 3


title: Ectoderm_Rep4_vs_BleachedRef

description: Sample 4


title: S73

description: patient 73


title: S66b

description: patient 66


title: Ectoderm_Rep1_vs_BleachedRef

description: Sample 1


title: Endoderm_Rep4_vs_BleachedRef

description: Sample 8


title: Bleached_Rep5_vs_BleachedRef

description: Sample 10

treatment_protocol: MOMM1, MOMM2, MOMP1 are naturally occuring bleached specimens. AC5temp and AC6temp are bleached specimens resulting from a heat stress. VBl is the bleached reference specimen, which has been treated by a catalase inhibitor.

value: Bleached


title: Bleached_Rep4_vs_BleachedRef

description: Sample 9


title: Bleached_Rep3_vs_BleachedRef

description: Sample 8


title: Bleached_Rep2_vs_BleachedRef

description: Sample 7


title: S60

description: patient 60


title: S6

description: patient 6


title: S42b

description: patient 42


title: S44b

description: patient 44


title: S60b

description: patient 60


title: S44

description: patient 44


title: Bleached_Rep1_vs_BleachedRef

description: Sample 6


title: S66

description: patient 66


title: S38b

description: patient 38


title: S38

description: patient 38


title: S37

description: patient 37


title: Symbiotic_Rep3_vs_BleachedRef

description: Sample 3

value: Symbiotic


title: Symbiotic_Rep4_vs_BleachedRef

description: Sample 4


title: Symbiotic_Rep5_vs_BleachedRef

description: Sample 5


title: S31

description: patient 31


title: S6b

description: patient 6


title: Symbiotic_Rep2_vs_BleachedRef

description: Sample 2


title: S42

description: patient 42


title: S271b

description: patient 271


title: S31b

description: patient 31


title: ref RNA3 Val Set

city: Atlanta

first: Gregory

last: Doho

state: GA

address: 1365B Clifton Rd NE

institute: Emory University

description: ref RNA_Ctrl

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: SAMs were scanned using Illumina BeadArray Scanner

data_processing: The data were normalized using quantile-normalization with GenomeStudio V2010.1

source_name: Commercial

label_protocol: PCR product was prepared with standard Illumina protocol for arrays

extract_protocol: Ambion Recoverall on MagMax Express 96 as described in Abramovitz et al, Biotechniques, 44(3): 417-23.

tag: group

value: ref RNA


title: ref RNA2 Val Set

description: ref RNA_Ctrl


title: Pca_PCS-000473 Val Set

description: Prostate Cancer

source_name: Prostate

value: Prostate Cancer

tag: biochemical recurrence

value: Unknown

tag: time f/u

tag: time no bcr

tag: time bcr

tag: time clin rec

tag: time met rec

tag: psa

tag: gleason score

tag: tumor stage

tag: patient number


title: S268

description: patient 268

value: primary ovarian tumor


title: Pca_PCS-000472.3 Val Set

description: Prostate Cancer


title: ref RNA1 Val Set

description: ref RNA_Ctrl


title: S37b

description: patient 37


title: S271

description: patient 271


title: Symbiotic_Rep1_vs_BleachedRef

description: Sample 1


title: Pca_PCS-000472 Val Set

description: Prostate Cancer


title: S268b

description: patient 268


title: S267b

description: patient 267


title: S264

description: patient 264


title: S267

description: patient 267


title: Pca_PCS-000293 Val Set

description: Prostate Cancer

value: Recurrence


title: S263b

description: patient 263


title: S264b

description: patient 264


title: Pca_PCS-000478 Val Set

description: Prostate Cancer


title: S263

description: patient 263


title: S257b

description: patient 257


title: Pca_PCS-000472.2 Val Set

description: Prostate Cancer


title: Pca_PCS-000289 Val Set

description: Prostate Cancer

value: Non-Recurrence


title: Pca_PCS-000282 Val Set

description: Prostate Cancer


title: Pca_PCS-000273 Val Set

description: Prostate Cancer


title: Pca_PCS-000280 Val Set

description: Prostate Cancer


title: Pca_PCS-000278 Val Set

description: Prostate Cancer


title: Pca_PCS-000252 Val Set

description: Prostate Cancer


title: Pca_PCS-000269 Val Set

description: Prostate Cancer


title: Pca_PCS-000248 Val Set

description: Prostate Cancer


title: Pca_PCS-000257 Val Set

description: Prostate Cancer


title: Pca_PCS-000265 Val Set

description: Prostate Cancer


title: S252

description: patient 252


title: S245b

description: patient 245


title: S257

description: patient 257


title: Pca_PCS-000246 Val Set

description: Prostate Cancer


title: S243b

description: patient 243


title: Pca_PCS-000239 Val Set

description: Prostate Cancer


title: S245

description: patient 245


title: S252b

description: patient 252


title: S243

description: patient 243


title: S242b

description: patient 242


title: S238b

description: patient 238


title: Pca_PCS-000233.3 Val Set

description: Prostate Cancer


title: Pca_PCS-000237 Val Set

description: Prostate Cancer


title: S227b

description: patient 227


title: S238

description: patient 238


title: S227

description: patient 227


title: S242

description: patient 242


title: Pca_PCS-000233.2 Val Set

description: Prostate Cancer


title: Pca_PCS-000233 Val Set

description: Prostate Cancer


title: Pca_PCS-000225 Val Set

description: Prostate Cancer


title: Pca_PCS-000230 Val Set

description: Prostate Cancer


title: Pca_PCS-000222.2 Val Set

description: Prostate Cancer


title: Pca_PCS-000222.3 Val Set

description: Prostate Cancer


title: Pca_PCS-000196.2 Val Set

description: Prostate Cancer


title: Pca_PCS-000215 Val Set

description: Prostate Cancer


title: Pca_PCS-000218 Val Set

description: Prostate Cancer


title: Pca_PCS-000200 Val Set

description: Prostate Cancer


title: Pca_PCS-000209 Val Set

description: Prostate Cancer


title: Pca_PCS-000222 Val Set

description: Prostate Cancer


title: Pca_PCS-000196.3 Val Set

description: Prostate Cancer


title: S218

description: patient 218


title: S222b

description: patient 222


title: S203

description: patient 203


title: S203b

description: patient 203


title: S219b

description: patient 219


title: Pca_PCS-000185 Val Set

description: Prostate Cancer


title: Pca_PCS-000186.2 Val Set

description: Prostate Cancer


title: Pca_PCS-000180.3 Val Set

description: Prostate Cancer


title: Pca_PCS-000186.3 Val Set

description: Prostate Cancer


title: Pca_PCS-000184 Val Set

description: Prostate Cancer


title: Pca_PCS-000193 Val Set

description: Prostate Cancer


title: Pca_PCS-000186 Val Set

description: Prostate Cancer


title: Pca_PCS-000196 Val Set

description: Prostate Cancer


title: S219

description: patient 219


title: S184

description: patient 184


title: S218b

description: patient 218


title: S204

description: patient 204


title: S195b

description: patient 195


title: S195

description: patient 195


title: Pca_PCS-000180.2 Val Set

description: Prostate Cancer


title: S183b

description: patient 183


title: S222

description: patient 222


title: S188

description: patient 188


title: S212

description: patient 212


title: S2

description: patient 2


title: S2b

description: patient 2


title: S183

description: patient 183


title: S204b

description: patient 204


title: S188b

description: patient 188


title: S184b

description: patient 184


title: S212b

description: patient 212


title: Pca_PCS-000176 Val Set

description: Prostate Cancer


title: Pca_PCS-000180 Val Set

description: Prostate Cancer


title: S182b

description: patient 182


title: Pca_PCS-000170 Val Set

description: Prostate Cancer


title: Pca_PCS-000139 Val Set

description: Prostate Cancer


title: Pca_PCS-000133 Val Set

description: Prostate Cancer


title: Pca_PCS-000136 Val Set

description: Prostate Cancer


title: Pca_PCS-000135 Val Set

description: Prostate Cancer


title: Pca_PCS-000130 Val Set

description: Prostate Cancer


title: Pca_PCS-000129 Val Set

description: Prostate Cancer


title: Pca_PCS-000166 Val Set

description: Prostate Cancer


title: Pca_PCS-000123 Val Set

description: Prostate Cancer


title: Pca_PCS-000120 Val Set

description: Prostate Cancer


title: Pca_PCS-000116.3 Val Set

description: Prostate Cancer


title: Pca_PCS-000119 Val Set

description: Prostate Cancer


title: Pca_PCS-000116.2 Val Set

description: Prostate Cancer


title: S177

description: patient 177


title: S167b

description: patient 167


title: S170b

description: patient 170


title: S182

description: patient 182


title: S175

description: patient 175


title: S161

description: patient 161


title: S170

description: patient 170


title: S161b

description: patient 161


title: S177b

description: patient 177


title: Pca_PCS-000125 Val Set

description: Prostate Cancer


title: S165

description: patient 165


title: S15b

description: patient 15


title: S156

description: patient 156


title: Pca_PCS-000116 Val Set

description: Prostate Cancer


title: S165b

description: patient 165


title: S156b

description: patient 156


title: Pca_PCS-000095 Val Set

description: Prostate Cancer


title: Pca_PCS-000115 Val Set

description: Prostate Cancer


title: Pca_PCS-000086 Val Set

description: Prostate Cancer


title: Pca_PCS-000083.2 Val Set

description: Prostate Cancer


title: S15

description: patient 15


title: S146

description: patient 146


title: Pca_PCS-000081.2 Val Set

description: Prostate Cancer


title: Pca_PCS-000081 Val Set

description: Prostate Cancer


title: Pca_PCS-000083 Val Set

description: Prostate Cancer


title: Pca_PCS-000081.3 Val Set

description: Prostate Cancer


title: Pca_PCS-000077 Val Set

description: Prostate Cancer


title: Pca_PCS-000066.3 Val Set

description: Prostate Cancer


title: S175b

description: patient 175


title: S145

description: patient 145


title: Pca_PCS-000074 Val Set

description: Prostate Cancer


title: S145b

description: patient 145


title: Pca_PCS-000062.3 Val Set

description: Prostate Cancer


title: Pca_PCS-000064.3 Val Set

description: Prostate Cancer


title: S131

description: patient 131


title: S139b

description: patient 139


title: S139

description: patient 139


title: S146b

description: patient 146


title: Pca_PCS-000060.3 Val Set

description: Prostate Cancer


title: S131b

description: patient 131


title: S119b

description: patient 119


title: S128

description: patient 128


title: S128b

description: patient 128


title: S167

description: patient 167


title: S125b

description: patient 125


title: S119

description: patient 119


title: S125

description: patient 125


title: Pca_PCS-000060.2 Val Set

description: Prostate Cancer


title: Pca_PCS-000063.3 Val Set

description: Prostate Cancer


title: Pca_PCS-000060 Val Set

description: Prostate Cancer


title: Pca_PCS-000057.2 Val Set

description: Prostate Cancer


title: Pca_PCS-000057.3 Val Set

description: Prostate Cancer


title: Pca_PCS-000057 Val Set

description: Prostate Cancer


title: Pca_PCS-000053.2 Val Set

description: Prostate Cancer


title: Pca_PCS-000053 Val Set

description: Prostate Cancer


title: Pca_PCS-000042 Val Set

description: Prostate Cancer


title: Pca_PCS-000051 Val Set

description: Prostate Cancer


title: Pca_PCS-000037 Val Set

description: Prostate Cancer


title: Pca_PCS-000038 Val Set

description: Prostate Cancer


title: gDNA2 Val Set

value: gDNA


title: Pca_PCS-000005 Val Set

description: Prostate Cancer


title: Pca_PCS-000013 Val Set

description: Prostate Cancer


title: S118b

description: patient 118


title: Pca_PCS-000053.3 Val Set

description: Prostate Cancer


title: S105b

description: patient 105


title: S118

description: patient 118


title: S106

description: patient 106


title: S106b

description: patient 106


title: Pca_PCS-000055 Val Set

description: Prostate Cancer


title: gDNA3 Val Set


title: S108

description: patient 108


title: S100b

description: patient 100


title: S10b

description: patient 10


title: gDNA1 Val Set


title: S105

description: patient 105


title: N_WCIPC-000186

description: Normal

tag: disease state

value: Normal

value: normal prostate

tag: time clinical recurrence

tag: time metastatic recurrence


title: S108b

description: patient 108


title: S100

description: patient 100


title: S10

description: patient 10


title: Pca_PCS-000017 Val Set

description: Prostate Cancer


title: F98902pl18_2 with array type maize from Affymetrix

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

description: Maize, Zea mays, is one of the most widely grown crops in the world as it provides cereal grain for human purposes and feedstock for cattle. Maize is increasingly used as a biomass fuel, such as ethanol. Studies have shown that maize stem is made up of different lignified cell types: epidermis, sclerenchyma (a few layers under the epidermis and surrounding vascular bundles in the rind), parenchyma (mostly lignified near the epidermis). One of the aims of this work is to find out if it is the proportion of these different cell types or their number (especially for vascular bundles) which influences the degree of digestibility of maize lines. For that the objective of our work is to develop a genomic strategic approach allowing an improvement of traits involved in cell wall degradability. The work will include the mapping of genes considered as strategic in the cell wall biosynthesis, the search of new genes of interest through bio-analysis, the functional analysis of genes suspected to be of importance in cell wall pathway, the search of candidate underlying QTL, and transcriptomic approaches in order to find genes co-regulation, transcription, and eQTL.

hyb_protocol: labelled extract quantity: 10ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Zea mays

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: aerial - terreau BF4 treff light cycle 16/8 and natural light hygrometry: 50%

tag: cell line

tag: dev. stage (boyes et al. plant cell 2001)

value: flower development


title: N_WCIPC-000185

description: Normal

tag: tissue


title: F98902pl6_1 with array type maize from Affymetrix


title: N_WCIPC-000184

description: Normal

tag: group


title: N_WCIPC-000182

description: Normal

tag: biochemical recurrence


title: Cm489pl10_2 with array type maize from Affymetrix


title: Pca_WCIPC-000175

description: Prostate Cancer

value: Prostate cancer tumor

tag: time f/u


title: N_WCIPC-000178

description: Normal

tag: time no bcr


title: Pca_WCIPC-000176

description: Prostate Cancer

tag: time bcr


title: Pca_WCIPC-000172

description: Prostate Cancer


title: N_WCIPC-000179

description: Normal


title: Pca_WCIPC-000167

description: Prostate Cancer


title: N_WCIPC-000180

description: Normal


title: TJF_1 with array type maize from Affymetrix

tag: age

value: 21 day

tag: dev.stage (boyes et al. plant cell 2001)

value: 7 leaves stage


title: TJF_2 with array type maize from Affymetrix


title: Cm489pl9_1 with array type maize from Affymetrix


title: Pca_WCIPC-000161

description: Prostate Cancer

tag: psa


title: Pca_WCIPC-000159

description: Prostate Cancer

tag: gleason score


title: Pca_WCIPC-000154

description: Prostate Cancer

tag: tumor stage


title: Pca_WCIPC-000163

description: Prostate Cancer

tag: patient number


title: Pca_WCIPC-000166

description: Prostate Cancer

tag: disease state


title: Pca_WCIPC-000150

description: Prostate Cancer

tag: time clinical recurrence


title: Hey3Met2_MutatantRnaset2_rep1

city: Ispra (VA)

first: marco

last: fabbri

address: Via E. Fermi, 2749

department: Institute for Health and Consumer Protection

country: Italy

institute: European Commission - Joint Research Centre

description: Gene expression after transfection with mutated RNASET2

hyb_protocol: standard Agilent protocol

scan_protocol: Scanned with the Agilent G2565BA Microarray Scanner (Agilent)

data_processing: The fluorescence intensities on scanned images were extracted and preprocessed by Agilent Feature Extraction Software (v10.5.1.1).

source_name: Hey3Met2 transfected with mutant RNASET2

label_protocol: standard Agilent protocol

growth_protocol: The Hey3Met2 ovarian cancer cell line was maintained in DMEM/F12 medium with 10% FBS and 1% GlutaMax (Gibco)

extract_protocol: Fourteen days  after transfection, cells were harvested and total RNA extracted using RNeasy Plus kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: Expression vectors human  wildtype  RNASET2 cDNA or catalitically impaired mutant RNASET2 cloned in pcDNA3  were transfected into Hey3Met2 cells

tag: cell type

tag: transfection

value: mutant RNASET2


title: Hey3Met2_control_rep3

description: Gene expression after transfection with empty vector

source_name: Hey3Met2 transfected with empty vector

value: empty vector


title: Hey3Met2_MutatantRnaset2_rep2


title: TJCM_1 with array type maize from Affymetrix

tag: cell line


title: TJCM_2 with array type maize from Affymetrix


title: Pca_WCIPC-000147

description: Prostate Cancer

tag: tissue

tag: time metastatic recurrence


title: Hey3Met2_control_rep2


title: Hey3Met2_WTRnaset2_rep3

description: Gene expression after transfection with wildtype RNASET2

source_name: Hey3Met2 transfected with wildtype  RNASET2

value: wildtype  RNASET2


title: Hey3Met2_MutatantRnaset2_rep3


title: Hey3Met2_WTRnaset2_rep2


title: Hey3Met2_control_rep1


title: Hey3Met2_WTRnaset2_rep1


title: Pca_WCIPC-000145

description: Prostate Cancer

tag: group

tag: biochemical recurrence


title: Pca_WCIPC-000144

description: Prostate Cancer

tag: time f/u

tag: time no bcr


title: Pca_WCIPC-000136

description: Prostate Cancer

tag: time bcr


title: Pca_WCIPC-000138

description: Prostate Cancer


title: Pca_WCIPC-000141

description: Prostate Cancer


title: Pca_WCIPC-000134

description: Prostate Cancer


title: Patient fibroblast (P6)

city: Prague

first: Viktor

last: Stranecky

address: Ke Karlovu 2

department: 1st Faculty of Medicine

country: Czech Republic

institute: Charles University

description:
Agilent Feature Extraction file:
US45103058_251485035149_S01_GE2_105_Dec08_1_3.txt

hyb_protocol: 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17 hrs in a 65° C, according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene expression Analysis, Agilent) .

scan_protocol: The hybridized slides were scanned with Agilent G2565AA scanner (Agilent) . Agilent Feature Extraction software version 10.5 (Agilent) was used for image analysis the of TIFF files, as generated by the scanner.

data_processing: Data from individual arrays were background corrected (using normexp method), log transformed and normalized using Loess and G-quantile functions. Normalization was performed in R statistic environment using Limma package.

source_name: Total RNA from patient fibroblast labeled with Cyanine-5 (red)

label_protocol: 500 ng of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).  500 ng of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).  Total RNA (500 ng) was reverse transcribed, labeled and hybridized onto Agilent 44k human genome microarray using Two-color Microarray Based Gene Expression Analysis Kit (Agilent, Santa Clara, CA). All 9 patient samples and 3 controls (Cy5-labeled) were hybridized against to common reference RNA (Cy3-labeled).

growth_protocol: Human skin fibroblast  were cultured at 37 °C in 5 % atmosphere of CO2 in the DMEM medium (with L-Glutamine, Sodium Pyruvate and high glucose concentration 4.5 g/l ) supplemented by 10 % fetal bovine serum, 20 mM HEPES pH 7.5  and in presence of penicillin (10 U/ml) and streptomycin (10 µg/ml).

extract_protocol: Total RNA was isolated from patient and control cultured cells using the TRIZOL solution (Invitrogen, Carlsbad, Ca).

treatment_protocol: Cells were harvested using 0.05 % trypsin and 0.02 % EDTA.

value: fibroblast

tag: genotype/variation

value: SURF1 mutation

source_name: Total RNA from reference HeLa cell lines labeled with Cyanine-3 (green)

tag: reference

value: HeLa


title: Pca_WCIPC-000129

description: Prostate Cancer

value: Prostate Cancer

value: Unknown

tag: psa

tag: gleason score


title: Pca_WCIPC-000133

description: Prostate Cancer

value: Recurrence

tag: tumor stage

tag: patient number


title: Patient fibroblast (P9)

description:
Agilent Feature Extraction file:
US45103058_251485035150_S01_GE2_105_Dec08_1_2.txt


title: Patient fibroblast (P8)

description:
Agilent Feature Extraction file:
US45103058_251485035149_S01_GE2_105_Dec08_1_2.txt


title: Patient fibroblast (P4)

description:
Agilent Feature Extraction file:
US45103058_251485035147_S01_GE2_105_Dec08_1_4.txt


title: Pca_WCIPC-000124

description: Prostate Cancer

tag: disease state

value: Non-Recurrence

tag: time clinical recurrence


title: Pca_WCIPC-000125

description: Prostate Cancer


title: Patient fibroblast (P3)

description:
Agilent Feature Extraction file:
US45103058_251485035148_S01_GE2_105_Dec08_1_1.txt

tag: cell type


title: Pca_WCIPC-000126

description: Prostate Cancer


title: Pca_WCIPC-000117

description: Prostate Cancer


title: Pca_WCIPC-000115

description: Prostate Cancer


title: Pca_WCIPC-000127

description: Prostate Cancer


title: Patient fibroblast (P5)

description:
Agilent Feature Extraction file:
US45103058_251485035148_S01_GE2_105_Dec08_1_3.txt


title: Patient fibroblast (P2)

description:
Agilent Feature Extraction file:
US45103058_251485035148_S01_GE2_105_Dec08_1_2.txt


title: Patient fibroblast (P7)

description:
Agilent Feature Extraction file:
US45103058_251485035147_S01_GE2_105_Dec08_1_3.txt


title: Control fibroblast (C2)

description:
Agilent Feature Extraction file:
US45103058_251485035150_S01_GE2_105_Dec08_1_3.txt

source_name: Total RNA from control fibroblast labeled with Cyanine-5 (red)

value: control


title: Pca_WCIPC-000114

description: Prostate Cancer


title: Pca_WCIPC-000113

description: Prostate Cancer


title: Pca_WCIPC-000112

description: Prostate Cancer


title: MCF7_+_Dox_0hr_E2_2

city: Madison

last: Xu

state: WI

address: 1400 University Ave

institute: UW-Madison

description: Dox treat, no E2 treat

hyb_protocol: Hybridization was perform at 65C for 17 hours according to Agilent Tecan HS Pro Hybridization Protocol

scan_protocol: The scan setting is 5um resolution, sigle pass using GenePix 4000A scanner. The data was extracted using Agilent Feature Extraction Software.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Total mRNA was labeled using Agilent’s Quick Amp Labeling Kit.

growth_protocol: MCF7-tet-on-CARM1shRNA cells were grown in DMEM in 10% FBS. Three days before E2 treatment, the cells were switched to phenol-red free DMEM with 5% 6X charcoal stripped FBS.

extract_protocol: Total mRNA were extracted from cells using Qiagen Rneasy Kit

treatment_protocol: When the cells were treated with Dox, they were treated with 1ug/ml Dox for 5 days to induce knockingdown CARM1. The medium were changed to phenol-red free DMEM+charcoal stripped FBS for 3 days before treating with E2 (10nM)

tag: treatment

value: Dox

tag: treatment time

value: 4 h


title: Pca_WCIPC-000121

description: Prostate Cancer

tag: tissue

tag: time metastatic recurrence


title: Pca_WCIPC-000111

description: Prostate Cancer

tag: group

tag: biochemical recurrence


title: MCF7_+_Dox_0hr_E2_3

description: Dox treat, no E2 treat


title: Pca_WCIPC-000108

description: Prostate Cancer

tag: time f/u

tag: time no bcr


title: Control fibroblast (C3)

description:
Agilent Feature Extraction file:
US45103058_251485035150_S01_GE2_105_Dec08_1_1.txt

tag: genotype/variation


title: MCF7_+_Dox_0hr_E2_1

description: Dox treat, no E2 treat


title: Patient fibroblast (P1)

description:
Agilent Feature Extraction file:
US45103058_251485035149_S01_GE2_105_Dec08_1_1.txt

tag: reference


title: MCF7_-_Dox_0hr_E2_3

description: no Dox treat, no E2 treat

value: untreated


title: MCF7_-_Dox_0hr_E2_2

description: no Dox treat, no E2 treat


title: Pca_WCIPC-000107

description: Prostate Cancer

value: Prostate cancer tumor

tag: time bcr

tag: psa


title: Pca_WCIPC-000101

description: Prostate Cancer

tag: gleason score

tag: tumor stage


title: Pca_WCIPC-000100

description: Prostate Cancer

tag: disease state

tag: patient number


title: MCF7_+_Dox_4hr_E2_1

description: Dox pre-treat, E2 4h

value: Dox + E2


title: Pca_WCIPC-000096

description: Prostate Cancer

tag: time clinical recurrence


title: MCF7_+_Dox_4hr_E2_2

description: Dox pre-treat, E2 4h

tag: treatment


title: Control fibroblast (C1)

description:
Agilent Feature Extraction file:
US45103058_251485035150_S01_GE2_105_Dec08_1_4.txt

tag: cell type


title: Pca_WCIPC-000089

description: Prostate Cancer

tag: tissue


title: Pca_WCIPC-000087

description: Prostate Cancer

tag: time metastatic recurrence


title: MCF7_-_Dox_4hr_E2_1

description: no Dox treat, E2 4h

tag: treatment time


title: Pca_WCIPC-000081

description: Prostate Cancer

tag: group

tag: biochemical recurrence


title: Pca_WCIPC-000084

description: Prostate Cancer

tag: time f/u

tag: time no bcr


title: MCF7_+_Dox_4hr_E2_3

description: Dox pre-treat, E2 4h


title: Pca_WCIPC-000063

description: Prostate Cancer


title: Pca_WCIPC-000064

description: Prostate Cancer


title: Pca_WCIPC-000079

description: Prostate Cancer


title: Pca_WCIPC-000073

description: Prostate Cancer


title: MCF7_-_Dox_4hr_E2_3

description: no Dox treat, E2 4h


title: MCF7_-_Dox_4hr_E2_2

description: no Dox treat, E2 4h


title: PYO Treated - repeat 3 - mAdbID:103985

city: Rockville

first: Balazs

last: Rada

state: MD

address: 12441 Parklawn Drive

department: NIAID

institute: NIH

description: mAdb experiment ID: 103985

hyb_protocol: Agilent Hybridization Protocol Other: Labeled RNA were hybridized to the microarrays using the TECAN HS Pro 4800 hybridization station with Agilent 2x Gene expression hybridization HI-RPM buffer and 10x Blocking Reagent at 65°C for 17 hours, and washed with Agilent Gene Expression Wash Buffer 1 at room temperature and Gene Expression Wash Buffer 2 at 37°C. Automation program “Agilent GE Protocol HPR“ included final drying step with nitrogen gas for 3 minutes.

scan_protocol: Agilent Scanning Protocol Other: The slides were imaged using an Agilent high-resolution DNA microarray scanner G2505C at 5 um resolution and 100/10% PMT XDR. Agilent Feature Extraction software, protocol "GE2 105 Dec08", was used for image analysis.

data_processing:
JMP Genomics Data Processing
Calculation Method: Using MedianSignal column from Feature Extraction output, lowess normalization was used followed by re-centering all samples by subtracting the sample log2 median from each log2 expression measure. Normalized values were subjected to mixed-effects ANOVA with treatment as the fixed effect, array_id as the random effect.

source_name: Untreated

label_protocol:
Cy3 Direct Labeling Protocol
Other: Total RNA (40 ug) was reverse transcribed to cDNA using oligo dT primers and SuperScript II RT. Double-stranded cDNA was synthesized using DNA polymerase with cy3-labeled dUTP with for direct dye incorporation. Clean-up was done with Vivaspin (Qiagen) column, washed four times, resuspended in RNase-free water.

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was isolated using Trizol (Invitrogen) and an additional clean-up step was introduced using Qiagen "RNeasy mini-kit" RNA isolation kit.

tag: agent

value: Untreated

tag: cell line

value: epithelial

source_name: PYO Treated

label_protocol:
Cy5 Direct Labeling Protocol
Other: Total RNA (40 ug) was reverse transcribed to cDNA using oligo dT primers and SuperScript II RT. Double-stranded cDNA was synthesized using DNA polymerase with cy5-labeled dUTP with for direct dye incorporation. Clean-up was done with Vivaspin (Qiagen) column, washed four times, resuspended in RNase-free water.

treatment_protocol:
Treatment type: compound
Agent: pyocyanin
Treatment dose: 8 uM
Treatment time: 48 hours

value: PYO Treated


title: PYO Treated - repeat 4 - mAdbID:103986

description: mAdb experiment ID: 103986


title: PYO Treated - repeat 1 - mAdbID:103983

description: mAdb experiment ID: 103983


title: PYO Treated - repeat 2 - mAdbID:103984

description: mAdb experiment ID: 103984


title: Pca_WCIPC-000043

description: Prostate Cancer

tag: time bcr

tag: psa


title: Pca_WCIPC-000058

description: Prostate Cancer

tag: gleason score

tag: tumor stage


title: MCF7_-_Dox_0hr_E2_1

description: no Dox treat, no E2 treat


title: Pca_WCIPC-000001

description: Prostate Cancer

tag: disease state

tag: patient number