title: Dnmt1-/- (p53-/-)

city: Cambridge

first: Jamie

last: Hackett

address: Tennis Court Road

country: United Kingdom

institute: Gurdon Institue

data_processing: Average Normalisation, Background subtracted

source_name: KO cells

label_protocol: TotalPrep RNA amplification kit

growth_protocol: Cells were maintained in Dulbecco's modified Eagle's medium supplemented with l-glutamine, non-essential amino acids, sodium pyruvate, β-mercapto-ethanol, and 15% foetal calf serum

extract_protocol: Total RNA was extracted with TRIZOL

value: Embryonic Fibroblasts

tag: genotype

tag: genetic background


title: DLBCL GEP data N0068

status: Public on Aug 01 2012

type: RNA

city: Pleasanton

first: Yan

last: Li

state: CA

address: 4300 Hacienda Dr

department: Bioinformatics

country: USA

institute: Roche Molecular Systems

description:
DLBCL GEP data
Gene expression data from DLBCL lymphoma FFPET sample

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: Data pre-processing included a summarization and quantile normalization step to generate probe set level signal intensities for each microarray experiment and was performed as previously published by Liu WM et al. PQN and DQN: algorithms for expression microarrays. J.Theor.Biol. 2006;243:273-278. The signal used was DQN3, i.e., DQN signal normalized with quantiles of the beta distribution with parameters p=1.2 and q=3

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: DLBCL patient sample

label_protocol: 50 ng of FFPE total RNA was used as input amount for amplification by WT-Ovation FFPE System (NuGEN Cat.# 3400) according to manufacturer’s instructions.  5 μg of the amplified cDNA was fragmentated and biotin labeled by FL-Ovation™ cDNA Biotin Module V2 (NuGEN Cat.# 4200) according to manufacturer’s instructions.

extract_protocol: FFPE RNA was isolated by HighPure Paraffin RNA extraction kit (Roche Applied Science Cat # 03270289001 X) according to manufacturer’s instructions

treatment_protocol: The standard therapy for these patients is rituximab combined with cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP).

tag: gene expression profiling subgroup

value: ABC

tag: immunohistochemistry subgroup


title: DLBCL GEP data N0067

value: UC


title: Splenic Marginal Zone Lymphoma P22 50XbaI

type: genomic

city: Pamplona

first: Vicente

middle: Jose

last: Fresquet

state: Navarra

address: Av Pio XII 55

department: Division of Oncology

country: Spain

institute: Center for Applied Medical Research (Cima)

description: Hybridized to 50K_Xba

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The CEL files were analyzed using the aroma.affymetrix package of R/Bioconductor (CRLMM-algorithm to produce genotype calls and SNPRMA to produce the summarized signal).

label: Biotin

molecule: genomic DNA

source_name: Splenic Marginal Zone Lymphoma P22

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% FBS

extract_protocol: Genomic DNA was extracted from mononuclear cells and cell lines using the Qiagen DNA Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

treatment_protocol: Not treatment

tag: tissue

value: Splenic Marginal Zone Lymphoma


title: DLBCL GEP data N0065


title: Peripheral T cell lymphoma 5

city: Madrid

first: Esperanza

last: Martín-Sánchez

address: Melchor Fernandez Almagro 3

institute: Spanish National Cancer Research Centre (CNIO)

description:
PTCL 5
Biological replicate 5 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Technologies, Inc.) were added, and samples were applied to microarrays enclosed in Agilent hybridization chambers. After hybridization, slides were sequentially washed.

scan_protocol: Microarray slides were scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Bioconductor's limma package was employed for preprocessing and normalization. Thus, background was corrected using the normexp method and data were normalized using the loess and quantiles method for within-array and inter-array normalization, respectively.

source_name: Human lymph node from a peripheral T cell lymphoma patient

label_protocol: 500 ng of total RNA were primed with the T7 promoter primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of MMLV RT. Then, the resulting cDNA was transcribed and labeled into cRNA using T7 RNA polymerase, NTPs and a fraction of Cy3-CTP (for the RNA reference) and Cy5-CTP (for the samples) for 2 h at 40ºC (all reagents were obtained from Agilent Technologies, Inc.).

growth_protocol: Lymph nodes were frozen to preserve the RNA properties.

extract_protocol: Total RNA was extracted using Trizol, precipitated with isopropanol and purified with the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer's instructions.

value: lymph node

tag: disease status

value: peripheral T cell lymphoma (PTCL)

source_name: Universal Human Reference RNA

tag: cell line

value: 10 human tumor cell lines

tag: sample type

value: reference


title: p53-/-

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

organism: Mus musculus

tag: cell type


title: DLBCL GEP data N0066


title: Normal 3

city: Aveiro

first: Patrícia

middle: Matos

last: Pereira

address: Campus Universitário de Santiago

department: Biology

country: Portugal

institute: University of Aveiro

hyb_protocol: Hybridisation of labelled RNA was done on miRNAChip_human_V2 at 42ºC for 16h. The normal gastric pooled reference sample was labelled and hybridised four times to check arrays’ reproducibility.

scan_protocol: Slides were scanned using an Agilent G2565AA microarray scanner

data_processing: Microarray images were analyzed using Quantarray v3.0 software (PerkinElmer). Manually flagged bad spots were eliminated and the Cy3 median pixel intensity values were  background subtracted, followed by the averaging of quadruplicate features on the array. Data points were removed when intensity values were below 100 (2 times the background signal). A global median normalization of human gastric cancer microarray data was applied using BRB-ArrayTools v3.4.0 software. Log-transformed (base 2) cy3 intensities were obtained. Differentially expressed miRNAs from each sample were identified using the Multiple Experiment Viewer Mev software version 4.6.2. A nonparametric Wilcoxon rank sum (Mann-Whitney) test at a critical value of P=0.05 and FDR=0.05 was performed to identify miRNAs that demonstrated statistically significant difference in expression between normal gastric mucosa and tumour tissue.

source_name: 10 Normal Gastric Mucosas

label_protocol: Two μg of total RNA from primary gastric tumors and normal gastric reference sample were labelled with Cy3-ULS using the ULSTM miRNA labelling kit (Kreatech) followed by purification and monitoring of dye incorporation by UV-visible spectroscopy.

extract_protocol: Total RNA was isolated from tumours and normal gastric mucosas using the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Ambion Inc, Austin, TX) according to manufacturer’s protocol. RNA quantity and integrity were assessed using the Nanodrop and Agilent 2100 bioanalyzer systems, respectively.  The 10 normal gastric mucosa RNA samples were pooled to obtain the normal gastric reference sample. All tumour samples were histologically verified to contain a minimum of 70% of neoplastic cells.

value: Normal Gastric Mucosa

tag: lauren histology

value: Normal


title: Peripheral T cell lymphoma 4

description:
PTCL 4
Biological replicate 4 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Mm 265-95

city: Boston

first: Charles

last: Lee

state: MA

address: 221 Longwood Ave., EBRC-422

department: Pathology

institute: Brigham and Women's Hospital/Harvard Medical School

hyb_protocol: Agilent recommended protocol

scan_protocol: scan at 3 uM resolution

data_processing: Agilent Feature Extraction software. Dye bias correction was performed using default settings in Agilent Feature Extraction. The Log2 ratios were calculated using the ratio of rProcessedSignal to gProcessedSignal from the Feature Extraction files.

organism: Macaca mulatta

source_name: rhesus macaque_B cell line

label_protocol: Agilent recommended protocol

growth_protocol: standard for B cell lines

extract_protocol: standard DNA extraction from B cell lines using cell lysis

tag: commercial source of sample

value: Yerkes-not available for purchase

source_name: human_reference_B cell line

tag: reference


title: TC-1+MSCV+miR-144+miR-451 retrovirus – Influenza 24 h rep3

city: seattle

first: madhumati

last: gundapuneni

address: 401 Terry avenue North

institute: Institute for systems biology

description: TC-1 cell line (CRL-2785) MSCV+miR retrovirus – Influenza

hyb_protocol: Labeled, fragmented cDNA was hybridized for 16 hours at 45 deg C and 60rpm to a Affymetrix GeneChip. Washing was performed on the Fluidics with protocol FS450_0001.

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: RMA normalization was done using the  Affymetrix Power Tools (APT) software package.

label_protocol: Samples were labeled according to the Affymetrix Whole Transcript Sense Target Labeling Assay, including the RiboMinus rRNA depletion step

growth_protocol: cells were cultured in DMEM + 10% heat-inactivated FBS + 2 mM L-glutamine + penicillin and streptomycin in the presence of 2 ug/mL puromycin

extract_protocol: Trizol, according to the manufacturer's instructions.

tag: strain

value: Type I lung epithelial cell


title: TC-1+MSCV+miR-144+miR-451 retrovirus – Influenza 24 h rep2


title: Normal 2


title: Normal 1


title: TC-1+MSCV+miR-144+miR-451 retrovirus – Influenza 24 h rep1


title: DLBCL GEP data N0064

value: GCB


title: TC-1+MSCV retrovirus – Influenza 24 h rep3

description: TC-1 cell line (CRL-2785) MSCV retrovirus – Influenza

source_name: TC-1+MSCV retrovirus – Influenza 24 h


title: Patient 43

source_name: Primary Gastric Tumor

value: Primary Gastric Tumor

value: Diffuse


title: Patient 42


title: PR00053_Coriell

data_processing: Agilent Feature Extraction software. Dye bias correction was peformed using a subset of probes with 100% sequence identity across human, chimpanzee, gorilla, orangutan, and rhesus macaque reference genomes. The Log2 ratios were calculated using the ratio of rProcessedSignal to gProcessedSignal from the Feature Extraction files.

organism: Gorilla beringei

source_name: gorilla_B cell line

value: Coriell


title: Peripheral T cell lymphoma 2

description:
PTCL 2
Biological replicate 2 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Mm173-02


title: Reactive lymph node 6

description:
LN 6
Biological replicate 6 of 6. Reactive lymph node as a control non-tumoral tissue.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.

source_name: Human reactive lymph node from a non-lymphoma patient

value: non-lymphoma


title: TC-1+MSCV retrovirus – Influenza 24 h rep2


title: Patient 41


title: Peripheral T cell lymphoma 1

description:
PTCL 1
Biological replicate 1 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Reactive lymph node 5

description:
LN 5
Biological replicate 5 of 6. Reactive lymph node as a control non-tumoral tissue.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: PR001103_Coriell


title: DLBCL GEP data N0063


title: DLBCL GEP data N0062


title: PR00724_Coriell

organism: Pongo abelii

source_name: orangutan_B cell line


title: DLBCL GEP data N0061


title: TC-1+MSCV retrovirus – Influenza 24 h rep1


title: AG18358_Coriell

organism: Pan troglodytes

source_name: chimpanzee_B cell line

value: Coriell-no longer available for purchase


title: DLBCL GEP data N0060

value: ABC


title: TC-1+MSCV+miR-144+miR-451 retrovirus – unstimulated

description: TC-1 cell line (CRL-2785) MSCV+miR – unstim


title: Patient 38

value: Intestinal


title: Mm118-99


title: AG18359_Coriell


title: Patient 39


title: S003659_Coriell


title: Reactive lymph node 3

description:
LN 3
Biological replicate 3 of 6. Reactive lymph node as a control non-tumoral tissue.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Patient 37


title: NA19238_HapMap

source_name: human_B cell line


title: Reactive lymph node 1

description:
LN 1
Biological replicate 1 of 6. Reactive lymph node as a control non-tumoral tissue.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: NA19239_HapMap


title: S003641_Coriell


title: Patient 35


title: Patient 34


title: Patient 36


title: DLBCL GEP data N0059


title: Mm256-95


title: DLBCL GEP data N0055


title: TC-1+MSCV retrovirus – unstimulated

description: TC-1 cell line (CRL-2785) MSCV retrovirus – unstim

source_name: TC-1+MSCV retrovirus – unstimulated


title: normal (grade 1) cartilage, mid zone, rep 4

city: La Jolla

first: Shawn

middle: Patrick

last: Grogan

address: 10550 N. Torrey Pines Road, MEM161

department: MEM

institute: TSRI

hyb_protocol: 5 ug post fragmentation and labeling product was hybridized overnight following the NuGEN Encore Biotin Module protocol.  Hybridization and scanning of samples to arrays was performed using the standard NuGEN Hybridization, Cocktail Assembly, and Fluidics Protocols using Affymetrix’s GeneChip Hybridization, Wash, and Stain Kit (Affymetrix P/N 900720), according to NuGEN Encore Biotin Module protocol

scan_protocol: Chips were scanned using the Affymetrix GeneChip Scanner 3000 7G with default settings and a target intensity of 250 for scaling.

data_processing:
Data was normalized using both RMA and dCHIP
Log2 RMA signals are presented in the data table below.
Log2 dCHIP signals can be found in a supplementary file linked to the Series record.
The normalized data have filtered out the Affymetrix Control probes and the 30% lowest variant probesets.

source_name: donor 93, cartilage, middle zone

label_protocol: Five nanograms (5 ng) of total RNA was amplified using the NuGEN Ovation Pico WTA System version 1.0.  Post amplification, 4ug of the purified cDNA product was processed with the NuGEN WT-Ovation Exon Module version 1.0.  Post Exon, 5ug of the purified cDNA product was fragmented and labeled using NuGEN Encore Biotin Module.

growth_protocol: Normal human knee joints were procured by tissue banks and processed within 24-60 hours post mortem.

extract_protocol: Total RNA was isolated from cartilage zones using the Qiagen Rneasy kit with Dnase digestion following the manufacturer's instructions. Total RNA was quantified using NanoDrop (ND-1000).  Sample quality was checked with the Agilent 2100 Bioanalyzer using the RNA 6000 Pico LabChip (Agilent Cat. # 5065-4473). Only samples with RIN > 6 were used.

treatment_protocol: Osteochondral cores were obtained from the medial and lateral femoral condyles of normal knee joints.  The bone portion of each osteochondral core was embedded in paraffin in a standard plastic cassette to allow fixation of the plug in the microtome. The entire cartilage was sliced into 50 μm thick sections from the cartilage surface downwards to the calcified cartilage using a microtome (Microm HM 325, Thermo Scientific, Walldorf, Germany).  Each section was transferred to one well of a 96-well plate filled with RNAlater (Qiagen). The sections were segregated into zones for RNA isolation as follows: The upper 10% of zonal slices were allocated to the SZ, the middle 40% were allocated to the MZ and the lower 30% were allocated to the DZ. To avoid overlap between zones, regions of approximately 200 μm between the SZ and MZ and between the MZ and DZ were discarded.

tag: donor

tag: age

value: 24 yo

tag: gender

value: Male

value: cartilage, middle zone


title: DLBCL GEP data N0058


title: PHF8 shRNA3

city: Barcelona

first: Elena

last: Asensio

state: Select a State or Province

address: Baldiri Reixac 4-8

department: Molecular Genomics

hyb_protocol: After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples. The data was normalized using AFM 4.0 toolbox. !Sample_data_row_count = 48803

source_name: HeLa

label_protocol: 500 ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the Quick Amp Labeling kit (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)

extract_protocol: Total RNAs were extracted with Trizol reagent (Invitrogen) according to manufacturer’s protocol

tag: genotype/variation

value: PHF8 shRNA

value: HeLa

value: 31 years adult

value: female

tag: ethnicity

value: Black


title: PHF8 shRNA2


title: Reactive lymph node 2

description:
LN 2
Biological replicate 2 of 6. Reactive lymph node as a control non-tumoral tissue.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.

value: lymph node

value: 10 human tumor cell lines

value: reference


title: PHF8 shRNA1


title: normal (grade 1) cartilage, superficial zone, rep 4

source_name: donor 93, cartilage, superficial zone

value: cartilage, superficial zone


title: DLBCL GEP data N0054

source_name: DLBCL patient sample

value: GCB


title: DLBCL GEP data N0057

value: UC


title: normal (grade 1) cartilage, deep zone, rep 4

source_name: donor 93, cartilage, deep zone

value: cartilage, deep zone


title: Patient 33

value: Primary Gastric Tumor


title: Control shRNA3

value: Control shRNA


title: NA18502_HapMap

value: Coriell


title: Patient 32

value: Diffuse


title: Peripheral T cell lymphoma 3

description:
PTCL 3
Biological replicate 3 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.

source_name: Human lymph node from a peripheral T cell lymphoma patient

value: peripheral T cell lymphoma (PTCL)

source_name: Universal Human Reference RNA


title: normal (grade 1) cartilage, mid zone, rep 3

source_name: donor 91, cartilage, middle zone

value: 23 yo

value: Female

value: cartilage, middle zone


title: Patient 31

value: Intestinal


title: DLBCL GEP data N0056


title: Reactive lymph node 4

description:
LN 4
Biological replicate 4 of 6. Reactive lymph node as a control non-tumoral tissue.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.

value: non-lymphoma


title: normal (grade 1) cartilage, superficial zone, rep 3

source_name: donor 91, cartilage, superficial zone


title: Patient 30


title: Patient 29


title: normal (grade 1) cartilage, deep zone, rep 3

source_name: donor 91, cartilage, deep zone


title: Anti-HMGA2 siRNA treated Y79 cells (Replicate treated3)

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression after 48hrs of transient transfection

hyb_protocol: 800ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327) and scanned using the Agilent Microarray Scanner G2505C at 3 micron resolution.

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: The normalization was done using GeneSpring GX 11 Software using 75th percentile shift-normalization.

source_name: Anti-HMGA2 siRNA treated Y79 cells

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: 5% CO2 ,20%FBS in RPMI medium,1640

extract_protocol: RNA was prepared using the Qiagen RNeasy mini kit (Qiagen GmbH, Hilden) following the manufacturer's recommendations. RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 200nm of Anti-HMGA2 trated to Y79 cells and incubated for 48 hours.

tag: origin


title: Patient 28

source_name: Primary Gastric Tumor


title: DLBCL GEP data N0052

description:
DLBCL GEP data
Gene expression data from DLBCL lymphoma FFPET sample

tag: gene expression profiling subgroup


title: Patient 27


title: DLBCL GEP data N0044

value: ABC

tag: immunohistochemistry subgroup


title: Control shRNA1

value: HeLa

value: 31 years adult

value: female

value: Black


title: DLBCL GEP data N0048

value: GCB


title: Control shRNA2


title: DLBCL GEP data N0047


title: normal (grade 1) cartilage, mid zone, rep 2

source_name: donor 77, cartilage, middle zone

value: 46 yo

value: Male

tag: tissue


title: Untreated y79 cells (Replicate control3)

source_name: Untreated y79 cells


title: normal (grade 1) cartilage, superficial zone, rep 2

source_name: donor 77, cartilage, superficial zone

value: cartilage, superficial zone


title: DLBCL GEP data N0042


title: DLBCL GEP data N0045


title: Patient 26

value: Primary Gastric Tumor


title: DLBCL GEP data N0039


title: Patient 24

value: Mixed


title: Anti-HMGA2 siRNA treated Y79 cells (Replicate treated2)


title: NA18517_HapMap

source_name: human_B cell line

value: Coriell

source_name: human_reference_B cell line


title: normal (grade 1) cartilage, superficial zone, rep 1

source_name: donor 71, cartilage, superficial zone

value: 44 yo


title: Patient 23


title: Patient 22


title: Anti-HMGA2 siRNA treated Y79 cells (Replicate treated1)


title: DLBCL GEP data N0037


title: Patient 21


title: Untreated y79 cells (Replicate control2)


title: Untreated y79 cells (Replicate control1)


title: Patient 20

value: Diffuse


title: DLBCL GEP data N0035


title: Patient 19


title: DLBCL GEP data N0038

value: UC


title: normal (grade 1) cartilage, mid zone, rep 1

source_name: donor 71, cartilage, middle zone

value: cartilage, middle zone


title: Patient 18


title: normal (grade 1) cartilage, deep zone, rep 1

source_name: donor 71, cartilage, deep zone

value: cartilage, deep zone


title: DLBCL GEP data N0031

source_name: DLBCL patient sample


title: DLBCL GEP data N0029


title: normal (grade 1) cartilage, deep zone, rep 2

source_name: donor 77, cartilage, deep zone


title: Healthy control LT-HSC 3

city: Bronx

first: Britta

last: Will

state: NY

address: 1300 Morris Park Avenue

department: Cell Biology

institute: Albert Einstein College of Medicine

hyb_protocol: Following fragmentation, ~5 microg of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Gene 1.0 ST microarray (Affymetrix). GeneChips were washed and stained in an Affymetrix Fluidics Station

scan_protocol: GeneChip® Scanner 3000 7G system (Affymetrix) according to standard protocols.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings; CEL files were generated. CEL files processed/normalized using DNA-Chip Analyzer (dChip) to generate probeset-level signal intensity data.

source_name: sorted HSCs from bone marrow

label_protocol: Biotinylated cRNA were prepared using the GeneChip® WT terminal labeling kit (Affymetrix) according to the manufacturer's instructions.

growth_protocol: uncultured primary cells

extract_protocol: Total mRNA was extracted using Qiagen's RNAesy Micro kit according to the manufacturer's instructions; After checking the quality of RNA with an Agilent 2100 Bioanalyzer, total RNA was amplified utilizing Single Primer Isothermal Amplification (SPIA®Nugen Ovation pico WTA) system according to the manufacturer’s instructions.

tag: disease state

value: control

value: Lin-CD34+CD38-CD90+ cells


title: DLBCL GEP data N0034

value: ABC


title: Healthy control LT-HSC 2


title: Healthy control ST-HSC 3

value: Lin-CD34+CD38-CD90- cells


title: DLBCL GEP data N0036


title: Patient 15


title: Patient 16


title: DLBCL GEP data N0030


title: Healthy control ST-HSC 1


title: Healthy control ST-HSC 2


title: Patient 14


title: Patient 13

value: Intestinal


title: DLBCL GEP data N0027

value: GCB


title: Patient 12


title: DLBCL GEP data N0028


title: Patient 11


title: Healthy control LT-HSC 1


title: MDS LT-HSC 2

value: MDS


title: Patient 8


title: MDS ST-HSC 2


title: MDS ST-HSC 1


title: DLBCL GEP data N0025


title: Patient 5


title: Patient 6


title: DLBCL GEP data N0026


title: storm PM treated samples collected at D4 after exposure #2

city: New York

first: Hong

last: Sun

address: 341 East 25 Street

department: Medicine

institute: NYU School of Medicine

hyb_protocol: Samples were hybridized with Affymetrix Human Gene 1.0 ST Arrays and scanned at the NYU Cancer Institute Genomics Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Data analysis was performed using GeneSpring v12 (Agilent Technologies)
probe_group_file: HuGene-1_0-st-v1.r4.pgf
meta-probeset_file: HuGene-1_0-st-v1.r4.mps

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Normal human bronchial epithelial BEAS-2B cells were cultured in DMEM (Invitrogen) supplemented with 10% FBS and 100 U/ml penicillin and 100 mg/ml streptomycin (Invitrogen).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen). The isolated T.RNA was subjected to a colum purification using Rneasy Plus Micro Kit (Qiagen)

treatment_protocol: BEAS-2B cells were treated with particles (50 μg/cm3) that were collected either during normal or storm weather conditions for 1- or 4- days.

value: bronchial epithelial cell

tag: treatment

value: storm PM treated

tag: timepoint


title: DLBCL GEP data N0021


title: storm PM treated samples collected at D4 after exposure #1

tag: cell type


title: Patient 3

value: Primary Gastric Tumor

tag: lauren histology


title: DLBCL GEP data N0024


title: MDS LT-HSC 1


title: untreated control samples collected at D4 #2


title: DLBCL GEP data N0019


title: normal PM treated samples collected at D4 after exposure #1

value: PM treated


title: normal PM treated samples collected at D4 after exposure #2


title: DLBCL GEP data N0020


title: DLBCL GEP data N0023


title: untreated control samples collected at D4 #1


title: Patient 1


title: Patient 2


title: storm PM treated samples collected at D1 after exposure #2


title: storm PM treated samples collected at D1 after exposure #1


title: DLBCL GEP data N0018


title: DLBCL GEP data N0016


title: normal PM treated samples collected at D1 after exposure #2


title: DLBCL GEP data N0012


title: normal PM treated samples collected at D1 after exposure #1


title: Synechocystis PCC6803, 72h, rep1

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

country: Germany

institute: University of Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.65 µg of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09 and GE1-v1_95_Feb07 for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensity was background corrected (normexp) and quantile normalized.

organism: Synechocystis sp. PCC 6803

source_name: Synechocystis PCC6803, 72h after iron limitation stress induction by DFB addition

label_protocol: The RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: Synechocystis wild type strain was grown at 30 °C in a modified version of BG11 medium (YBG11) containing a higher amount of EDTA (16 μM instead of 2.8 μM in BG11) and a lower iron concentration (Shcolnick, Shaked et al. 2007). Light intensity was adjusted to 50 μmol photons m−2·s−1 of white light. Cultures were aerated with normal air.

extract_protocol: Synechocystis cells (40 to 50 ml) were collected at different time points by rapid ﬁltration (Pall Supor 800 Filter, 0.8 mm). The filters with the collected cells were transferred to a tube containing 2 ml of PGTX (Pinto et al. 2009), immediately frozen in liquid nitrogen and stored at -80°C until extraction. RNA was extracted following the protocol by  Pinto et al., 2009 (Pinto, Thapper et al. 2009)

treatment_protocol: Desferrioxamine B (endconcentration 100µM) was added to the liquid cultures, and samples were taken before treatment, 3,12, 24, 48 and 72 h after DFB addition.

tag: stress

value: iron limitation

tag: time


title: DLBCL GEP data N0010


title: DLBCL GEP data N0009


title: DLBCL GEP data N0011


title: DLBCL GEP data N0014


title: Synechocystis PCC6803, 72h, rep2


title: DLBCL GEP data N0013


title: Synechocystis PCC6803, 48h, rep2

source_name: Synechocystis PCC6803, 48h after iron limitation stress induction by DFB addition


title: Nalm6_MondoA_knockdown_3

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

institute: Technische Universität München

hyb_protocol: Affymetrix GeneChip Hybridization, Wash, and Stain Kit. cRNA was hybridized to Affymetrix Human Gene 1.0 ST arrays

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Affymetrix Expression Console 1.1 using Affymetrix default analysis settings and RMA as normalization method.

source_name: MondoA shRNA

label_protocol: Total RNA (200 ng) was amplified and labeled using Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit.

growth_protocol: Cells were grown in plastic cell culture flasks in a humidified incubator at 37°C in 5% CO2 atmosphere in RPMI 1640 media containing 20% heat-inactivated fetal bovine serum, 1% glutamine, 100 µg/mL gentamycin and 200 mg/dl D-glucose .

extract_protocol: RNA was isolated using the RNeasy RNA isolation kit according to the manufacturer´s instructions.

tag: cell line

value: leukemia


title: Synechocystis PCC6803, 48h, rep1


title: Nalm6_MondoA_knockdown_2


title: DLBCL GEP data N0008


title: DLBCL GEP data N0006


title: Synechocystis PCC6803, 12h, rep2

source_name: Synechocystis PCC6803, 12h after iron limitation stress induction by DFB addition


title: Synechocystis PCC6803, 24h, rep2

source_name: Synechocystis PCC6803, 24h after iron limitation stress induction by DFB addition


title: DLBCL GEP data N0007


title: Nalm6_MondoA_knockdown_1


title: Synechocystis PCC6803, 24h, rep1


title: Synechocystis PCC6803, 3h, rep1

source_name: Synechocystis PCC6803, 3h after iron limitation stress induction by DFB addition


title: Recovery

description: 14 days recovery after 5aza-dC exposure

treatment_protocol: 1uM 5aza-dC was added and replaced daily for 3 days.

value: Fibroblasts

value: 1uM 5aza-dC then 14 days recovery


title: Synechocystis PCC6803, 0h, rep2

source_name: Synechocystis PCC6803 culture raised under control conditions

value: control conditions


title: Synechocystis PCC6803, 3h, rep2


title: DLBCL GEP data N0004


title: Nalm6_control_2

source_name: nonsense shRNA


title: DLBCL GEP data N0002


title: Synechocystis PCC6803, 12h, rep1


title: DLBCL GEP data N0005


title: untreated control samples collected at D1 #2


title: DLBCL GEP data N0001


title: DLBCL GEP data N0003


title: Nalm6_control_1


title: Mock

description: Mock treated

value: mock


title: Synechocystis PCC6803, 0h, rep1


title: 5aza-dC

description: 1uM 5aza-dC

value: 1uM 5aza-dC


title: 200mg/kg-liver-rat3

status: Public on Jul 24 2012

city: North Chicago

first: Rita

last: Ciurlionis

state: IL

address: 1 North Waukegan Road

institute: Abbvie

description: Gene expression data from liver of rats treated for 5 days orally with A-998679 at 300 mg/kg/day

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230_2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

data_processing: Log intensity and p values generated in Rosetta Resolver (version 7.2) based on imported Affymetrix .cel files with mean scaling (controls and flagged spots excluded, trim percentage of '10.0') and standard (untransformed) detrending algorithm for non-linearity correction (max bins = '40'; trim percentage = '20.0'). Fold change; all gene expression changes with fold change at least +/-1.5 and p<0.05 in at least one sample; changes not meeting these parameters are considered unchanged (FC=1).

organism: Rattus norvegicus

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

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

treatment_protocol: livers from vehicle and compound treated rats were flash frozen in LN2 at necropsy

tag: strain

value: Sprague Dawley

value: male

tag: weight

value: liver


title: Olig1-KO#38

status: Public on Jul 28 2012

first: John

last: Alberta

address: 450 Brookline Ave.

institute: Dana-Farber Cancer Institute

description: Gene expression from embryonic day 14.5 Olig1-KO mouse ganglionic eminence cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430A 2.0 array.

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

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

source_name: mouse E14.5 ganglionic eminences

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

growth_protocol: Serum-free neural stem cell media supplemented with EGF

value: neural stem cell

tag: genotype

value: Olig1 KO

tag: genetic background


title: 30mg/kg-liver-rat2

description: Gene expression data from liver of rats treated for 5 days orally with A-998679 at 30 mg/kg/day

tag: gender


title: DGM-10132 [gene_expr]

status: Public on Jun 20 2012

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: small airway epithelium from healthy nonsmokers or smokers with COPD

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

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

tag: department of genetic medicine id

tag: smoking status

value: S

tag: copd status

value: yes


title: 100mg/kg-liver-rat1

description: Gene expression data from liver of rats treated for 5 days orally with A-998679 at 100 mg/kg/day

tag: tissue


title: 30mg/kg-liver-rat3


title: 100mg/kg-liver-rat3


title: 200mg/kg-liver-rat2


title: 100mg/kg-liver-rat2


title: DGM-00471 [gene_expr]


title: vehicle-liver-rat3

description: Gene expression data from liver of rats treated for 5 day orally with 0.2% HPMC at 10 ml/kg/day

source_name: vehicle


title: DGM-10404 [gene_expr]


title: DGM-10152 [gene_expr]


title: DGM-00632 [gene_expr]


title: DGM-10139 [gene_expr]


title: vehicle-liver-rat2


title: 200mg/kg-liver-rat1


title: Patient 4

source_name: Primary Gastric Tumor

value: Intestinal


title: DGM-00262 [gene_expr]


title: LNCaP-Control-RNAi cells replicate1

status: Public on Jul 10 2012

city: Chiba

first: Yukie

last: Yoshii

address: Anagawa 4-9-1, Inage

country: Japan

institute: National Institute of Radiological Sciences

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: LNCaP-Control-RNAi cells_replicate1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were incubated in a humidified atmosphere of 5% CO2 in air at 37°C. RPMI 1640 medium (Gibco, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum and antibiotics was used for growth medium. Exponentially growing cells were used for the experiments. Cells were trypsinized, and the number of viable cells was counted by the trypan blue dye-exclusion method.

extract_protocol: Total RNA isolation was performed with a Micro-to-Midi total RNA purification system (Invitrogen). The integrity of total RNAs was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells (1 × 10^4) were plated in 100 ul growth medium per well on 96-well plates and incubated overnight. The medium was then changed to growth medium containing hexadimethrine bromide (Sigma) at a final concentration of 8 ug/ml to enhance the transduction efficiency. Lentiviral particles (5-50 ul, 0.5-5 multiplicity of infection) were added and the plates were incubated overnight. Thereafter, we selected stable transductants expressing the shRNAs with puromycin.

value: LNCaP

tag: transfection

value: control-RNAi


title: 30mg/kg-liver-rat1


title: vehicle-liver-rat1


title: LNCaP-FASN-RNAi cells replicate1

source_name: LNCaP-FASN-RNAi cells_replicate1

value: FASN-RNAi


title: LNCaP-FASN-RNAi cells replicate2

source_name: LNCaP-FASN-RNAi cells_replicate2


title: DGM-00061 [gene_expr]


title: DGM-00028 [gene_expr]


title: DGM-00060 [gene_expr]


title: LNCaP-Control-RNAi cells replicate2

source_name: LNCaP-Control-RNAi cells_replicate2


title: DGM-00171 [gene_expr]


title: DGM-00136 [gene_expr]

source_name: small airway epithelium from healthy nonsmokers or healthy smokers

tag: ethnicity

value: Eur


title: DGM-00231 [gene_expr]


title: DGM-10131 [gene_expr]


title: DGM-00791 [gene_expr]


title: DU145_XMRV-infected_24h_rep2

status: Public on May 06 2012

city: Bethesda

first: Krishna

last: Ketha

state: MD

address: 8800 Rockville Pike

department: Division of Hematology

institute: CBER/FDA

description:
DV24B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

hyb_protocol: The Hy3-labeled samples and Hy5-labeled reference RNA samples were mixed pair-wise and hybridized to the miRCURY LNA microRNA array (5th Gen-has,mmu and rno; Exiqon, Inc.).

scan_protocol: The miRCURY LNA microarray slides were scanned using the Agilent G2565BA Micorarray Scanner System (ImaGene 9.0 Software).

data_processing: The quantified signals were background corrected and normalized using the Lowess regression algorithm. Agilent software was used for the analysis. When clustering samples and miRNAs, 133 of 1277 miRNA passed the filtering criteria on variation across sample comparisons; SD >1.0. These miRNA were used in the two-way hierarchical clustering of miRNAs. Only miRNAs with 24 values (no 'null's accepted) across samples were included in the analysis. The microRNAs have been sorted on the basis of the high-to-low SD values, with the highest differential expression on top. When calling of a particular miRNA failed on an array, this is indicated by null in the row containing this miRNA and in the column corresponding to this array. In the expression matrix, all capture probes with both Hy3 and Hy5 signals lower than 1.5x of the median signal intensity of the given slide are excluded as indicated by the “null”. The values are all log2(Hy3/Hy5) ratios.

source_name: DU145, virus-infected, 24h

label_protocol: 1000 ng total RNA from each sample and reference pool (pool of all 24 samples in each experiment) was labeled using the miRCURY LNA microRNA HiPower Labeling kit, Hy3/Hy5 (Exiqon, Inc.).

extract_protocol: Total RNA was extracted using the miRCURY RNA isolation kit (Exiqon, Inc.) at 6h, 24h and 48h.

treatment_protocol: PBLs, MDMs, LNCaP and DU145 cells were mock-treated or infected with XMRV.

value: prostate cancer cell line

tag: treatment

value: XMRV-infected

tag: time post-infection

source_name: Reference pool of 24 samples

tag: sample type

value: reference


title: DU145_XMRV-infected_48h_rep2

description:
DV48B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: DU145, virus-infected, 48h

tag: cell type


title: DGM-00601 [gene_expr]

value: Afr


title: untreated control samples collected at D1 #1

value: bronchial epithelial cell

tag: timepoint


title: DGM-00313 [gene_expr]


title: DGM-00776 [gene_expr]


title: DU145_Mock_48h_rep2

description:
DM48B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: DU145, mock, 48h

tag: cell line

value: mock infected


title: DU145_Mock_6h_rep2

description:
DM6B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: DU145, mock, 6h


title: LNCaP_XMRV-infected_24h_rep2

description:
LV24B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: LNCaP, virus-infected, 24h


title: DU145_Mock_24h_rep2

description:
DM24B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: DU145, mock, 24h


title: LNCaP_XMRV-infected_48h_rep2

description:
LV48B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: LNCaP, virus-infected, 48h


title: LNCaP_Mock_48h_rep2

description:
LM48B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: LNCaP, mock, 48h


title: DU145_XMRV-infected_6h_rep2

description:
DV6B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: DU145, virus-infected, 6h


title: LNCaP_Mock_6h_rep2

description:
LM6B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: LNCaP, mock, 6h


title: MDM_XMRV-infected_24h_rep2

description:
MV24B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: MDMs, virus-infected, 24h

value: primary monocyte-derived macrophages (MDMs)


title: MDM_XMRV-infected_48h_rep2

description:
MV48B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: MDMs, virus-infected, 48h


title: LNCaP_Mock_24h_rep2

description:
LM24B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: LNCaP, mock, 24h


title: MDM_Mock_48h_rep2

description:
MM48B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: MDMs, mock, 48h


title: PBL_XMRV-infected_24h_rep2

description:
PV24B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: PBLs, virus-infected, 24h

value: primary peripheral blood lymphocytes (PBLs)


title: MDM_Mock_6h_rep2

description:
MM6B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: MDMs, mock, 6h


title: LNCaP_XMRV-infected_6h_rep2

description:
LV6B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: LNCaP, virus-infected, 6h


title: PBL_XMRV-infected_6h_rep2

description:
PV6B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: PBLs, virus-infected, 6h

source_name: Reference pool of 24 samples


title: PBL_Mock_48h_rep2

description:
PM48B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: PBLs, mock, 48h


title: PBL_Mock_6h_rep2

description:
PM6B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: PBLs, mock, 6h


title: PBL_Mock_24h_rep2

description:
PM24B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: PBLs, mock, 24h


title: DU145_XMRV-infected_48h_rep1

description:
DV48A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: DU145, virus-infected, 48h


title: DGM-00038 [gene_expr]

source_name: small airway epithelium from healthy nonsmokers or smokers with COPD


title: MDM_XMRV-infected_6h_rep2

description:
MV6B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: MDMs, virus-infected, 6h


title: DU145_XMRV-infected_24h_rep1

description:
DV24A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: DU145, virus-infected, 24h


title: DU145_XMRV-infected_6h_rep1

description:
DV6A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: DU145, virus-infected, 6h


title: LNCaP_XMRV-infected_48h_rep1

description:
LV48A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: LNCaP, virus-infected, 48h


title: PBL_XMRV-infected_48h_rep2

description:
PV48B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: PBLs, virus-infected, 48h


title: MDM_Mock_24h_rep2

description:
MM24B
Experiment B

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: MDMs, mock, 24h


title: LNCaP_XMRV-infected_6h_rep1

description:
LV6A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).


title: LNCaP_Mock_48h_rep1

description:
LM48A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: LNCaP, mock, 48h


title: LNCaP_Mock_6h_rep1

description:
LM6A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: LNCaP, mock, 6h


title: MDM_XMRV-infected_48h_rep1

description:
MV48A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: MDMs, virus-infected, 48h


title: DU145_Mock_24h_rep1

description:
DM24A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: DU145, mock, 24h


title: DU145_Mock_48h_rep1

description:
DM48A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: DU145, mock, 48h


title: MDM_Mock_48h_rep1

description:
MM48A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: MDMs, mock, 48h

source_name: Reference pool of 24 samples


title: LNCaP_XMRV-infected_24h_rep1

description:
LV24A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: LNCaP, virus-infected, 24h


title: MDM_Mock_24h_rep1

description:
MM24A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).


title: MDM_XMRV-infected_6h_rep1

description:
MV6A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).


title: MDM_Mock_6h_rep1

description:
MM6A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: MDMs, mock, 6h


title: MDM_XMRV-infected_24h_rep1

description:
MV24A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: MDMs, virus-infected, 24h


title: LNCaP_Mock_24h_rep1

description:
LM24A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: LNCaP, mock, 24h


title: PBL_XMRV-infected_48h_rep1

description:
PV48A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).


title: PBL_XMRV-infected_24h_rep1

description:
PV24A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: PBLs, virus-infected, 24h


title: PBL_Mock_24h_rep1

description:
PM24A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: PBLs, mock, 24h


title: PBL_Mock_6h_rep1

description:
PM6A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: PBLs, mock, 6h


title: PBL_Mock_48h_rep1

description:
PM48A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: PBLs, mock, 48h


title: DU145_Mock_6h_rep1

description:
DM6A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: DU145, mock, 6h


title: PBL_XMRV-infected_6h_rep1

description:
PV6A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).

source_name: PBLs, virus-infected, 6h


title: cluster thinned, replicate 1, end of véraison

status: Public on Mar 05 2012

city: Bologna

first: Chiara

last: Pastore

address: Viale Fanin, 46

country: Italy

institute: University of Bologna

description: Cluster thinned first biological replicate

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: The microarray was scanned using a ScanArray 4000XL   (Perkin-Elmer) at 532 nm (Cy-3 absorption peak) and   GenePix Pro7 software (Molecular Devices, Sunnyvale,   CA, USA) according to the manufacturers’ instructions.   Images were analyzed using NimbleScan v2.5 software   (Roche).

data_processing: NimbleScan v2.5 software (Roche), produces Pair Files containing the raw signal intensity data for each probe and Calls Files with normalized expression data.

organism: Vitis vinifera

source_name: Sangiovese berry

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Adult Sangiovese  (Vitis vinifera L.) vines, clone 12T grafted to SO4, planted in the field in a   vineyard in Bologna, Italy (44°30’N, 11°24’E), with North-  South oriented rows (vine spacing 1 m × 2.8 m, vertical   shoot positioned spur pruned cordon training system.

extract_protocol: Total RNA was extracted from the berry tissue without seeds using    the Spectrum™ Plant Total RNA kit (Sigma-Aldrich, St.  Louis, MO). RNA quality and quantity were determined   using a Nanodrop 2000 instrument (Thermo Scientific,   Wilmington, DE) and a Bioanalyzer Chip RNA 7500 series   II (Agilent, Santa Clara, CA).

treatment_protocol: Nine vines per treatment, with the same   cluster number at flowering (16 per vine), were selected in   a single uniform row and each vine was randomly assigned   in three blocks to the two following groups: control (C, no   treatment) and cluster thinning (CT, removal of 50% of   total clusters per vine at veraison, JD 211).

tag: cultivar

value: Sangiovese

tag: developmental stage

value: end of véraison

tag: protocol

value: cluster thinned

value: berries


title: cluster thinned, replicate 3, end of véraison

description: Cluster thinned third biological replicate


title: control, untreated, replicate 1, harvest

description: Control first biological replicate

value: harvest

value: control


title: CBSM-6 mo WI4T2

status: Public on Jan 01 2012

city: Los Angeles

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

institute: UCLA School of Medicine

description: Illumina HT-12 v4 expression arrays

hyb_protocol: Standard Illumina beadarray hybridization protocol for gene expression profiling (carried out in UCLA Southern California Genotyping Consortium Core Laboratory).

scan_protocol: Standard Illumina beadarray scan protocol for gene expression profiling (carried out in UCLA Southern California Genotyping Consortium Core Laboratory).

data_processing: Gene expression values derived from Illumina GenomeStudio software were subject to quantile normalization, and log2-transformed for statistical analysis.

source_name: Peripheral blood mononuclear cells

label_protocol: Standard Illumina beadarray probe synthesis for gene expression profiling (carried out in UCLA Southern California Genotyping Consortium Core Laboratory).

extract_protocol: Human peripheral blood leukocytes were isolated and total RNA was extracted using Qiagen RNEasy.

value: Cognitive behavioral stress management-6 mo

value: peripheral blood mononuclear cell

tag: disease state

value: breast cancer

value: female


title: Control-6 mo ZC1T2

description: Illumina HT-12 v4 expression arrays

value: Control-6 mo

tag: gender


title: control, untreated, replicate 3, harvest

description: Control third biological replicate


title: CBSM-6 mo VI2T2

description: Illumina HT-12 v4 expression arrays


title: cluster thinned, replicate 2, harvest

description: Cluster thinned second biological replicate


title: cluster thinned, replicate 1, harvest


title: cluster thinned, replicate 3, harvest


title: control, untreated, replicate 2, end of véraison

description: Control second biological replicate


title: Control-6 mo ZC6T2

description: Illumina HT-12 v4 expression arrays


title: Control-12 mo TC4T3

description: Illumina HT-12 v4 expression arrays

value: Control-12 mo


title: CBSM-6 mo TI1T2

description: Illumina HT-12 v4 expression arrays


title: control, untreated, replicate 3, end of véraison

description: Control third biological replicate


title: Control-12 mo WCIT3

description: Illumina HT-12 v4 expression arrays


title: control, untreated, replicate 2, harvest

description: Control second biological replicate


title: control, untreated, replicate 2, beginning of véraison

description: Control second biological replicate

value: beginning of véraison


title: Control-6 mo WC3T2

description: Illumina HT-12 v4 expression arrays


title: control, untreated, replicate 1, end of véraison

description: Control first biological replicate


title: cluster thinned, replicate 1, beginning of véraison


title: cluster thinned, replicate 3, beginning of véraison


title: CBSM-12 mo ZI4T3

description: Illumina HT-12 v4 expression arrays

value: Cognitive behavioral stress management-12 mo


title: cluster thinned, replicate 2, beginning of véraison


title: control, untreated, replicate 3, beginning of véraison

description: Control third biological replicate


title: control, untreated, replicate 1, beginning of véraison

description: Control first biological replicate


title: cluster thinned, replicate 2, end of véraison


title: Control-6 mo UC1T2

description: Illumina HT-12 v4 expression arrays


title: Control-12 mo VC1T3

description: Illumina HT-12 v4 expression arrays


title: CBSM-6 mo JI4T2

description: Illumina HT-12 v4 expression arrays


title: CBSM-12 mo SI5T3

description: Illumina HT-12 v4 expression arrays


title: Control-6 mo HC2T2

description: Illumina HT-12 v4 expression arrays


title: CBSM-6 mo II6T2

description: Illumina HT-12 v4 expression arrays


title: Control-6 mo TC1T2

description: Illumina HT-12 v4 expression arrays


title: Control-6 mo GGC2T2

description: Illumina HT-12 v4 expression arrays


title: CBSM-6 mo GGI1T2

description: Illumina HT-12 v4 expression arrays


title: CBSM-6 mo GI4T2

description: Illumina HT-12 v4 expression arrays


title: Control-12 mo GC1T3

description: Illumina HT-12 v4 expression arrays


title: CBSM-6 mo EI6T2

description: Illumina HT-12 v4 expression arrays


title: CBSM-6 mo II7T2

description: Illumina HT-12 v4 expression arrays


title: CBSM-6 mo EI1T2

description: Illumina HT-12 v4 expression arrays


title: CBSM-12 mo EI7T2

description: Illumina HT-12 v4 expression arrays


title: Control-6 mo FC3T2

description: Illumina HT-12 v4 expression arrays


title: Control-6 mo IC4T2

description: Illumina HT-12 v4 expression arrays


title: Control-6 mo HC6T2

description: Illumina HT-12 v4 expression arrays


title: Control-12 mo HC1T3

description: Illumina HT-12 v4 expression arrays


title: Control-6 mo HC3T2

description: Illumina HT-12 v4 expression arrays


title: Control-6 mo HC4T2

description: Illumina HT-12 v4 expression arrays


title: CBSM-6 mo EEI3T2

description: Illumina HT-12 v4 expression arrays


title: CBSM-6 mo GI3T2

description: Illumina HT-12 v4 expression arrays


title: Control-6 mo EEC3T2

description: Illumina HT-12 v4 expression arrays


title: Control-6 mo EC2T2

description: Illumina HT-12 v4 expression arrays


title: Control-6 mo EC3T2

description: Illumina HT-12 v4 expression arrays


title: CBSM-6 mo GI1T2

description: Illumina HT-12 v4 expression arrays


title: CBSM-6 mo DDI6T2

description: Illumina HT-12 v4 expression arrays


title: Control-6 mo EC1T2

description: Illumina HT-12 v4 expression arrays


title: DGM-00167 [gene_expr]

status: Public on Oct 27 2011

source_name: small airway epithelium from healthy nonsmokers or smokers with COPD

tag: department of genetic medicine id

value: S

value: yes


title: CBSM-6 mo GGI3T2

description: Illumina HT-12 v4 expression arrays


title: CBSM-6 mo CI3T2

description: Illumina HT-12 v4 expression arrays


title: Control-6 mo FC4T2

description: Illumina HT-12 v4 expression arrays


title: Control-6 mo FC2T2

description: Illumina HT-12 v4 expression arrays


title: CBSM-12 mo CI2T3

description: Illumina HT-12 v4 expression arrays


title: CBSM-6 mo EI3T2

description: Illumina HT-12 v4 expression arrays


title: CBSM-12 mo EEI6T3

description: Illumina HT-12 v4 expression arrays


title: CBSM-6 mo EI2T2

description: Illumina HT-12 v4 expression arrays


title: CBSM-12 mo BBI2T3

description: Illumina HT-12 v4 expression arrays


title: spt3-del-1-a

status: Public on May 23 2011

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

country: Netherlands

institute: UMC Utrecht

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction

data_processing:
as genes, no bg corr, but followed by gene-specific dye bias correction. Identical to genes, no bg corr if the dye bias correction is 0.0, which is the default. So far (jan 2008), we have only  dye-bias corrections for yeast.
limma, A software package for the analysis of gene expression microarray data, especially the use of linear models for analysing designed experiments and the assessment of differential expression. Author(s): Gordon Smyth.    The limma R package version 2.12.0 is used. P-values are Benjamini-Hochberg FDR corrected.

organism: Saccharomyces cerevisiae

source_name: refpool

label_protocol: robot amplification and labeling v1.0

extract_protocol: yeast RNA isolation for robotic amplification v1.0

tag: strain

tag: genotype

value: wild type


title: ubp8-del-1-b


title: ubp8-del-1-a


title: spt7-del-2-b


title: spt20-del-1-b


title: CBSM-6 mo DI1T2

description: Illumina HT-12 v4 expression arrays


title: spt20-del-1-a


title: CBSM-6 mo DDI3T2

description: Illumina HT-12 v4 expression arrays


title: CBSM-12 mo BBI3T3

description: Illumina HT-12 v4 expression arrays


title: CBSM-6 mo CI5T2

description: Illumina HT-12 v4 expression arrays


title: Control-12 mo DC1T3

description: Illumina HT-12 v4 expression arrays


title: sgf29-del-1-a


title: hfi1-del-matA-1-a


title: Psoriasis-10 +IFN-γ

status: Public on Nov 30 2011

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: GeneChip Two-Cycle cDNA Synthesis  Kit (Affymetrix )

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: Psoriasis-10 +IFN-γ

extract_protocol: Whole skin punch biopsies were homogenized in RLT with Beta-2-mercaptoethanol, RNA was extracted using RNeasy-Micro kit (QIAGEN, Valencia, CA).

value: psoriasis

tag: group

value: IFN-γ


title: sgf73-del-1-b


title: sus1-del-1-a


title: spt7-del-2-a


title: sgf73-del-1-a


title: CBSM-12 mo BBI6T3

description: Illumina HT-12 v4 expression arrays


title: spt8-del-1-a


title: spt3-del-1-b


title: ngg1-del-1-a


title: Hyp_Con_M4

status: Public on Apr 17 2011

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

hyb_protocol: Agilent one color protocol; Microarrays were washed the following day according to the supplemental Agilent protocol “Preventing Ozone-Related Problems”.  Slides were washed in GE Wash Buffer 1 at room temperature for 1 min, followed by GE Wash Buffer 2 at 37ºC for 1 min, acetonitrile wash at room temperature for 1 min, and Stabilizing and Drying Solution wash at room temperature for 30 s.

scan_protocol: Microarrays were kept in the dark until scanned at 5 μm at both 10 and 100 PMT (Agilent G2505 B Microarray Scanner).  Agilent Feature Extraction Software (v9.5) formed a composite of the two scans and calculated parameters for Extended Dynamic Range.

data_processing: Normalized signal intensity provided in VALUE column is Loess Normalization. Data were also normalized using Quanitle normalization for the manuscript (GSE27963_Quantile_Normalized_data.txt). Data anlyzed with JMP Genomics (JMP® Genomics v3.2)

organism: Micropterus salmoides

source_name: hypothalamus; LMB sexually mature (April)

label_protocol: Agilent one color protocol for Cy3

extract_protocol: STAT60 protocol for total RNA

treatment_protocol: Largemouth bass fed a diet chemically modified with dieldrin and estrogen.

value: male

tag: diet

tag: tissue

value: hypothalamus


title: Hyp_Con_M3


title: gcn5-del-1-a


title: Hyp_Con_F3


title: spt8-del-1-b


title: ada2-del-1-b


title: sgf29-del-1-b


title: sus1-del-1-b


title: sgf11-del-2-b

extract_protocol: yeast HTP RNA isolation for robot v2.0


title: sgf11-del-2-a


title: Hyp_Con_F4


title: ada2-del-1-a


title: Hyp_Con_M2


title: gcn5-del-1-b


title: ngg1-del-1-b


title: Hyp_Dld_E2_M1 3.0 mg/dieldrin + 0.7 mg/kg E2

value: 3.0 mg/dieldrin + 0.7 mg/kg E2


title: Hyp_Dld_M3 3.0 mg/dieldrin

value: 3.0 mg/dieldrin


title: Hyp_Dld_F4 3.0 mg/dieldrin


title: hfi1-del-matA-1-b


title: Hyp_Dld_E2_M2 3.0 mg/dieldrin + 0.7 mg/kg E2


title: Hyp_Con_M1

value: control


title: Hyp_Con_F2


title: Hyp_Dld_M1 3.0 mg/dieldrin


title: Hyp_Con_F1


title: Hyp_Dld_F2 3.0 mg/dieldrin


title: Hyp_Dld_M4 3.0 mg/dieldrin


title: Hyp_Dld_E2_M4 3.0 mg/dieldrin + 0.7 mg/kg E2


title: Hyp_Dld_E2_M3 3.0 mg/dieldrin + 0.7 mg/kg E2


title: Hyp_Dld_M2 3.0 mg/dieldrin


title: Hyp_Dld_F1 3.0 mg/dieldrin


title: Hyp_Dld_F3 3.0 mg/dieldrin


title: Patient_OC1217

status: Public on Mar 11 2011

city: Navi Mumbai

first: Manoj

middle: Balkrishna

last: Mahimkar

state: Maharashtra

address: Sector-22, Owe Village, Kharghar Node

institute: Cancer Research Institute, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre

description: Biological replicate

hyb_protocol: 5 micrograms of cy3 and cy5 labeled samples were hybridized.  Hybridizations were done using the aCGH Hybridization kit of Agilent (Part Number: 5190-0404). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 40 hours

scan_protocol: The hybridized slides were washed using Agilent aCGH wash buffers (Part No: 5188-5221/22) and scanned using the Agilent Microarray Scanner G2505C

data_processing: The Analysis was done using Agilent DNA Analytics Software. Significant abberations were identified. (CY5 Treated vs. Cy3 Control)

source_name: Pooled Genomic DNA Male

label_protocol: The samples for Comparative Genomic DNA Hybridization were labeled using Agilent Genomic DNA labeling Kit (Part Number: 5190-0453). 1 Micrograms of each sample was digested using Alu1 and Rsa1. This restricted DNA was then labeled with Cy3 and Cy5 dUTP using random primer labeling method. The labeled DNA was then concentrated and quality assessed for yields and specific activity.

extract_protocol: DNA was extracted by standard phenol chloroform method. Quantity and quality of DNA was monitored using NanoDrop-1000 spectrophotometer and by running agarose gel electrophoresis respectively.

treatment_protocol: Freshly collected oral tissues from oral cancer patients and peripheral blood lymhocytes from healthy donors were kept at -80°C till DNA was extracted.

value: Male

value: Peripheral Blood Lymphocytes

value: Pooled Genomic DNA Male

source_name: Oral Tumor Tissue

value: Oral Tumor

tag: age

tag: site

value: Tongue

tag: Stage


title: Patient_OC1001

description: Biological replicate

tag: cell type

tag: sample type

value: Gingivobuccal complex


title: Patient_OC1025

description: Biological replicate


title: Patient_OC1159

description: Biological replicate


title: Patient_OC849

description: Biological replicate


title: Patient_OC398

description: Biological replicate


title: Patient_OC498

description: Biological replicate


title: Patient_OC1004

description: Biological replicate


title: Patient_OC860

description: Biological replicate

source_name: Pooled Genomic DNA Female

value: Female

value: Pooled Genomic DNA Female


title: Patient_OC811

description: Biological replicate


title: Patient_OC939

description: Biological replicate


title: Patient_OC672

description: Biological replicate


title: Patient_OC588

description: Biological replicate


title: Patient_OC105

description: Biological replicate


title: Patient_OC1367

description: Biological replicate


title: Patient_OC1331

description: Biological replicate


title: Patient_OC1667

description: Biological replicate


title: Patient_OC996

description: Biological replicate


title: Patient_OC739

description: Biological replicate


title: Patient_OC561

description: Biological replicate


title: Patient_OC519

description: Biological replicate


title: Patient_OC187

description: Biological replicate


title: Patient_OC344

description: Biological replicate


title: Patient_OC1666

description: Biological replicate


title: Patient_OC1508

description: Biological replicate


title: Patient_OC1418

description: Biological replicate


title: Patient_OC1371

description: Biological replicate


title: Patient_OC1665

description: Biological replicate


title: Patient_OC1496

description: Biological replicate


title: Patient_OC1501

description: Biological replicate


title: Patient_OC1750

description: Biological replicate


title: Patient_OC1721

description: Biological replicate


title: Patient_OC1462

description: Biological replicate


title: Patient_OC1440

description: Biological replicate


title: Patient_OC1426

description: Biological replicate


title: Patient_OC1718

description: Biological replicate


title: Patient_OC1405

description: Biological replicate


title: Patient_OC1662

description: Biological replicate


title: Patient_OC1664

description: Biological replicate


title: Patient_OC1649

description: Biological replicate


title: Patient_OC1323

description: Biological replicate


title: Patient_OC0542

description: Biological replicate


title: Patient_OC1507

description: Biological replicate


title: Patient_OC1294

description: Biological replicate


title: Patient_OC1726

description: Biological replicate


title: Patient_OC1722

description: Biological replicate


title: Patient_OC1747

description: Biological replicate


title: Patient_OC1652

description: Biological replicate


title: Patient_OC1464

description: Biological replicate


title: Patient_OC1487

description: Biological replicate


title: Patient_OC0547

description: Biological replicate


title: Patient_OC1663

description: Biological replicate


title: Patient_OC1656

description: Biological replicate


title: Patient_OC1719

description: Biological replicate


title: Patient_OC1647

description: Biological replicate


title: Patient_OC1658

description: Biological replicate


title: MS3

status: Public on Mar 02 2011

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

description: Major salivary glands sample (parotid, submandibular, and sublingual gland) Male mouse control sample, Replicate #3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the v2 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with RMA Express using the default settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

source_name: Major salivary glands sample (parotid, submandibular, and sublingual gland). Male mouse control sample.

tag: Sex

value: female

value: BALB/c

value: Major salivary glands (parotid, submandibular, and sublingual gland)


title: MLN1

description: Submandibular lymph node sample. Male mouse control sample, Replicate #1

source_name: Submandibular lymph node sample. Male mouse control sample.

value: Submandibular lymph node


title: MLN2

description: Submandibular lymph node sample. Male mouse control sample, Replicate #2

value: male


title: P48s

description: Major salivary glands sample (parotid, submandibular, and sublingual gland) Progesterone (P4) dissolved in sesame oil vehicle, Replicate #1

source_name: Major salivary glands sample (parotid, submandibular, and sublingual gland) Progesterone (P4) dissolved in sesame oil vehicle.


title: P49s

description: Major salivary glands sample (parotid, submandibular, and sublingual gland) Progesterone (P4) dissolved in sesame oil vehicle, Replicate #2


title: E28s

description: Major salivary glands sample (parotid, submandibular, and sublingual gland). Endogenous estrogen (E2) dissolved in sesame oil vehicle, Replicate #1

source_name: Major salivary glands sample (parotid, submandibular, and sublingual gland) - Endogenous estrogen (E2) dissolved in sesame oil vehicle


title: E29s

description: Major salivary glands sample (parotid, submandibular, and sublingual gland). Endogenous estrogen (E2) dissolved in sesame oil vehicle, Replicate #2


title: E210s

description: Major salivary glands sample (parotid, submandibular, and sublingual gland). Endogenous estrogen (E2) dissolved in sesame oil vehicle, Replicate #3


title: MLN3

description: Submandibular lymph node sample. Male mouse control sample, Replicate #3


title: E2P48s

description: Major salivary glands sample (parotid, submandibular, and sublingual gland) Both endogenous estrogen (E2) and progesterone (P4) dissolved in sesame oil vehicle, Replicate #1

source_name: Major salivary glands sample (parotid, submandibular, and sublingual gland) Both endogenous estrogen (E2) and progesterone (P4) dissolved in sesame oil vehicle.


title: Oil10s

description: Major salivary glands sample (parotid, submandibular, and sublingual gland) Treatment control - sesame oil vehicle only, Replicate #3

source_name: Major salivary glands sample (parotid, submandibular, and sublingual gland) Treatment control - sesame oil vehicle only.


title: E2P49s

description: Major salivary glands sample (parotid, submandibular, and sublingual gland) Both endogenous estrogen (E2) and progesterone (P4) dissolved in sesame oil vehicle, Replicate #2


title: MS2

description: Major salivary glands sample (parotid, submandibular, and sublingual gland) Male mouse control sample, Replicate #2


title: MS1

description: Major salivary glands sample (parotid, submandibular, and sublingual gland) Male mouse control sample, Replicate #1


title: Patient_OC1645

description: Biological replicate


title: P410LN

description: Submandibular lymph node sample. Progesterone (P4) dissolved in sesame oil vehicle, Replicate #3

source_name: Submandibular lymph node sample. Progesterone (P4) dissolved in sesame oil vehicle.


title: Patient_OC1653

description: Biological replicate


title: Patient_OC1651

description: Biological replicate


title: P410s

description: Major salivary glands sample (parotid, submandibular, and sublingual gland) Progesterone (P4) dissolved in sesame oil vehicle, Replicate #3


title: E2P410s

description: Major salivary glands sample (parotid, submandibular, and sublingual gland) Both endogenous estrogen (E2) and progesterone (P4) dissolved in sesame oil vehicle, Replicate #3


title: E2P48LN

description: Submandibular lymph node sample. Both endogenous estrogen (E2) and progesterone (P4) dissolved in sesame oil vehicle, Replicate #3

source_name: Submandibular lymph node sample. Both endogenous estrogen (E2) and progesterone (P4) dissolved in sesame oil vehicle.


title: Oil8s

description: Major salivary glands sample (parotid, submandibular, and sublingual gland) Treatment control - sesame oil vehicle only, Replicate #1


title: Oil9s

description: Major salivary glands sample (parotid, submandibular, and sublingual gland) Treatment control - sesame oil vehicle only, Replicate #2


title: E2P47LN

description: Submandibular lymph node sample. Both endogenous estrogen (E2) and progesterone (P4) dissolved in sesame oil vehicle, Replicate #2


title: E27LN

description: Submandibular lymph node sample. Endogenous estrogen (E2) dissolved in sesame oil vehicle, Replicate #3

source_name: Submandibular lymph node sample. Endogenous estrogen (E2) dissolved in sesame oil vehicle.


title: E26LN

description: Submandibular lymph node sample. Endogenous estrogen (E2) dissolved in sesame oil vehicle, Replicate #2


title: E2P46LN

description: Submandibular lymph node sample. Both endogenous estrogen (E2) and progesterone (P4) dissolved in sesame oil vehicle, Replicate #1


title: OIL8LN

description: Submandibular lymph node sample. Treatment control - sesame oil vehicle only, Replicate #2

source_name: Submandibular lymph node sample.Treatment control - sesame oil vehicle only.


title: E25LN

description: Submandibular lymph node sample. Endogenous estrogen (E2) dissolved in sesame oil vehicle, Replicate #1


title: OIL9LN

description: Submandibular lymph node sample. Treatment control - sesame oil vehicle only, Replicate #3


title: P4LN2

description: Submandibular lymph node sample. Progesterone (P4) dissolved in sesame oil vehicle, Replicate #1


title: E2P410ut

description: Uteri sample (uterine horns and cervix). Both endogenous estrogen (E2) and progesterone (P4) dissolved in sesame oil vehicle, Replicate #3

source_name: Uteri sample (uterine horns and cervix). Both endogenous estrogen (E2) and progesterone (P4) dissolved in sesame oil vehicle.

value: Uteri (uterine horns and cervix)


title: OIL5LN

description: Submandibular lymph node sample. Treatment control - sesame oil vehicle only, Replicate #1


title: P4LN13

description: Submandibular lymph node sample. Progesterone (P4) dissolved in sesame oil vehicle, Replicate #2


title: E2P48ut

description: Uteri sample (uterine horns and cervix). Both endogenous estrogen (E2) and progesterone (P4) dissolved in sesame oil vehicle, Replicate #1


title: E2P49ut

description: Uteri sample (uterine horns and cervix). Both endogenous estrogen (E2) and progesterone (P4) dissolved in sesame oil vehicle, Replicate #2


title: Patient_OC1644

description: Biological replicate


title: E210ut

description: Uteri sample (uterine horns and cervix). Endogenous estrogen (E2) dissolved in sesame oil vehicle, Replicate #3.

source_name: Uteri sample (uterine horns and cervix). Endogenous estrogen (E2) dissolved in sesame oil vehicle.


title: E28ut

description: Uteri sample (uterine horns and cervix). Endogenous estrogen (E2) dissolved in sesame oil vehicle, Replicate #1.


title: P48ut

description: Uteri sample (uterine horns and cervix). Progesterone (P4) dissolved in sesame oil vehicle, Replicate #1

source_name: Uteri sample (uterine horns and cervix). Progesterone (P4) dissolved in sesame oil vehicle.


title: P410ut

description: Uteri sample (uterine horns and cervix). Progesterone (P4) dissolved in sesame oil vehicle, Replicate #3


title: OIL23ut

description: Uteri sample (uterine horns and cervix). Only sesame oil vehicle (treatment control), Replicate #3

source_name: Uteri sample (uterine horns and cervix). Only sesame oil vehicle (treatment control).


title: P49ut

description: Uteri sample (uterine horns and cervix). Progesterone (P4) dissolved in sesame oil vehicle, Replicate #2


title: OIL8ut

description: Uteri sample (uterine horns and cervix). Only sesame oil vehicle (treatment control), Replicate #1


title: OIL10ut

description: Uteri sample (uterine horns and cervix). Only sesame oil vehicle (treatment control), Replicate #2


title: E29ut

description: Uteri sample (uterine horns and cervix). Endogenous estrogen (E2) dissolved in sesame oil vehicle, Replicate #2.


title: 182 IN2

status: Public on Sep 08 2009

city: Toronto

first: Bekim

last: Sadikovic

state: Ontario

address: 555 University Avenue

country: Canada

institute: The SickKids Hospital and Princess Margaret Hospital

description: Input DNA - Replicate 2

hyb_protocol: The uracil glycosilase treatment, streptavidin/phycoerythrin labeling, hybridization and microarray scanning were performed as per Affymetrix Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/products/arrays/specific/human_promoter.affx) at The Centre for Applied Genomics (The Hospital for Sick Children, Toronto, ON, Canada)

data_processing: The Me-DIP-chip .cel files for osteoblasts and tumour samples (2 IP and 2 IN) were log2 transformed, normalized and imported into PGS. We baseline normalized the signal using the matched-pair normalization tool in PGS, by subtracting log2 IN signal intensity at each of 4.2 million from cell type-matched IP signals resulting in 6 corrected datasets (IP1 cor. and IP2 cor. for each cell line). In order to determine the relative enrichment of IP cor. signals in tumours relative to  osteoblasts, we used the PGS 1-way ANOVA tool and calculated the fold change using the geometric mean (for log-transformed data) for individual tumours, or alternatively for all tumours vs. osteoblasts in cumulative analysis.  Thus generated signals represented baseline-normalized, osteoblast-relative, and cancer cell-specific enrichment levels for each of 4.2 million probes. Significant region detection (both enrichment/hypermethylation and depletion/hypomethylation) was performed using Hidden Markov Model (HMM) tool in PGS by applying it to the fold change data for individual tumour or cumulative analysis. In order to capture significant differences in enrichment in tumours vs. normal osteoblast across shorter genomic regions (min. ~350 nucleotides) with robust enrichment differences as well as intermediate (min. ~500 nucleotides) and large regions (min. 1400 nucleotides), three HMM algorithms were applied (s-HMM, m-HMM, and l-HMM). Following cut-offs were used: s-HMM (min. probes: 10, detection states: -5,5, ignore state: 0, max. probability: 0.99, genomic decay: 10,000, sigma: 2), m-HMM (min. probes: 15, detection states: -3,3, ignore state: 0, max. probability: 0.99, genomic decay: 10,000, sigma: 1), and l-HMM  (min. probes: 40, detection states: -1.5,1.5, ignore state: 0, max. probability: 0.99, genomic decay: 10,000, sigma: 1). Significantly enriched/hypermethylated and depleted/hypomethylated HMM regions were annotated to the corresponding genes present on the Affymetrix Gene 1.0 Array using the  HuGene-1_0-st-v1.na24.hg18.transcriptmod.csv file which was annotated to detect regions associated with specific genes 10 Kb 5’ and 3 Kb 3’ from transcriptional start sites to correspond to the coverage on the Affy Promoter 1.0R Array.

label: streptavidin/phycoerythrin

source_name: osteosarcoma tissue sample 182

growth_protocol: Normal human osteoblasts (HOB) are primary osteoblasts from the hip bone of a normal male donor that were purchased from PromoCell (Heidelberg, Germany, Catalogue # C-12760) and maintained in medium provided by the manufacturer and used at culture passage 3. Three days after plating (~80% confluent), cells where harvested for DNA or RNA extractions.

extract_protocol: DNA was extracted by phenol-chloroform extraction and subsequent precipitation in 100% ethanol. DNA precipitate was washed with 70% ethanol then eluted in DNAse free water

treatment_protocol: Cells were harvested with Tripsin (Invitrogen) as per manifacturers instructions

value: pediatric osteosarcoma


title: 182 IP1

description: Methyl-Cytosine Immunoprecipitated fraction - Replicate 1

scan_protocol: The uracil glycosilase treatment, streptavidin/phycoerythrin labeling, hybridization and microarray scanning were performed as per Affymetrix Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/products/arrays/specific/human_promoter.affx) at The Centre for Applied Genomics (The Hospital for Sick Children, Toronto, ON, Canada)


title: 182 IP2

description: Methyl-Cytosine Immunoprecipitated fraction - Replicate 2

label_protocol: The uracil glycosilase treatment, streptavidin/phycoerythrin labeling, hybridization and microarray scanning were performed as per Affymetrix Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/products/arrays/specific/human_promoter.affx) at The Centre for Applied Genomics (The Hospital for Sick Children, Toronto, ON, Canada)


title: 182 IN1

description: Input DNA - Replicate 1


title: 180 IP2

source_name: osteosarcoma tissue sample 180


title: 180 IN1

description: Input DNA - Replicate 1


title: 180 IN2

description: Input DNA - Replicate 2


title: 180 IP1


title: 179 IN1

description: Input DNA - Replicate 1

source_name: osteosarcoma tissue sample 179


title: 179 IP2


title: 178 IP2

source_name: osteosarcoma tissue sample 178


title: 179 IP1


title: 178 IP1


title: 177 IP2

source_name: osteosarcoma tissue sample 177


title: 177 IN2

description: Input DNA - Replicate 2


title: 179 IN2

description: Input DNA - Replicate 2


title: 178 IN1

description: Input DNA - Replicate 1


title: 177 IN1

description: Input DNA - Replicate 1


title: 178 IN2

description: Input DNA - Replicate 2


title: PB_CD34+_2

status: Public on Jun 10 2010

city: Boston

first: Hu

last: Li

address: 3 Blackfan Circle

institute: Wyss Institute

description: Gene expression data obtained from PB CD34+ blood

hyb_protocol: cDNA was fragmented and 10ug hybridized to an Affymetrix U133 Plus 2.0 array for 16 hours. Arrays were washed and stained using the Affy 450 Fluidics Station according to the manufacturer's protocol

scan_protocol: Arrays were scanned using a GeneChip 3000 scanner according to the manufacturers recommendation

data_processing: RMA (Bioconductor Affy and RMA Packages).

source_name: human  peripheral blood derived CD34+ cells

label_protocol: Preparation of biotinylated cDNA was performed according to the standard Nugen amplification sample preparation protocol, starting with 100ng of total RNA

growth_protocol: Normal peripheral blood CD34+ (PB CD34+) and mononuclear cells (PBMCs) were either maintained in medium described previously (Loh et al. 2009) or grown in dendritic cell medium supplemented with SCF and GM-CSF

extract_protocol: Trizol isolation followed by Rneasy (Qiagen) column purification were performed according to manufacturer's specifications

value: peripheral blood derived CD34+ cells (PB_CD34+)


title: dH1F_Fibro_2

description: Gene expression data obtained from fibroblasts

source_name: human fibroblast

growth_protocol: Fibroblasts were grown in DMEM containing 10 % inactivated fetal serum (IFS), 50 U/ml penicillin, 50 mg/ml streptomycin, and 1 mM L-glutamine

value: fibroblast

tag: cell line

value: GM04981 from Coriell


title: 177 IP1


title: PB34_iPS1_1

description: Gene expression data obtained from PB CD34+ blood iPS

source_name: iPS

growth_protocol: For feeder-free culture of iPSCs, the plate was coated with 0.3mg/ml Matrigel (BD-Bioscience, San Jose, CA) and mTeSR (StemCell Technologies, Vancouver, Canada) was used according to the manufacturer’s instruction.

value: iPS cells

tag: iPS derived from

value: PB CD34+ blood


title: PBMCs_1

description: Gene expression data obtained from PBMCs blood

source_name: human peripheral blood derived mononuclear cells (PBMCs)


title: 180 replicate 1

description: gene expression data 180 bioreplicate 1

hyb_protocol: Labeling, hybridization and scanning were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 4 (P/N 701880 Rev 4). (http://www.affymetrix.com/support/technical/byproduct.affx?product=hugene-1_0-st-v1).

data_processing: Data from RNA expression array experiments in the form of .cel files (GCOS 1.3 software) were imported into and analysed using the Partek Genomic Suite Software (PGS). The expression array .cel files for osteoblasts and tumour samples (2 arrays each) were imported using PGS Gene Expression Workflow tool (subject to RMA normalization and log2 transformation). The significantly over- and under-expressed genes in tumours compared to normal osteoblasts were detected using 1-way ANOVA tool at p<0.01 and +/- 2-fold enrichment, either specifically for each tumour sample or cumulatively (i.e. mean signal of all tumours vs. osteoblasts). Significantly over- and under-expressed regions were annotated to the corresponding genes present on the Affymetrix Gene 1.0 Array using the HuGene-1_0-st-v1.na24.hg18.transcript.csv file.

label: TdT labeling kit

source_name: osteosarcoma tumor 180

extract_protocol: Total RNA from tumours cells and HOB was extracted using the TRIzol reagent method as per manifacturers instructions (Invitrogen, Osaka, Japan).


title: 180 replicate 2

description: gene expression data 180 bioreplicate 2

scan_protocol: Labeling, hybridization and scanning were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 4 (P/N 701880 Rev 4). (http://www.affymetrix.com/support/technical/byproduct.affx?product=hugene-1_0-st-v1).


title: 178 replicate 1

description: gene expression data 178 bioreplicate 1

source_name: osteosarcoma tumor 178

label_protocol: Labeling, hybridization and scanning were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 4 (P/N 701880 Rev 4). (http://www.affymetrix.com/support/technical/byproduct.affx?product=hugene-1_0-st-v1).


title: 183 replicate 1

description: gene expression data 183 bioreplicate 1

source_name: osteosarcoma tumor 183


title: 182 replicate 2

description: gene expression data 182 bioreplicate 2

source_name: osteosarcoma tumor 182


title: 177 replicate 2

description: gene expression data 177 bioreplicate 2

source_name: osteosarcoma tumor 177


status: Public on Sep 01 2009

city: Charlotte

last: Zagorski

state: NC

address: 1542 Garden Terrace, 301

department: Emergency Medicine

institute: Carolinas Medical Center

description: Experimental pulmonary embolism:  Week 6 PE2.0 rat, heart right ventricle apex, biological rep4

hyb_protocol: 25 microg of fragmented cRNA was hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 v2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned twice using an Agilent Gene Array Scanner G2500A

data_processing: The data were generated with Affymetrix GeneChip Operating Software using a scaling target of 500, user defined normalization of 1.0, no probe mask, no baseline, and default "parameter" settings.

source_name: Gene expression data from right ventricle apex RNA after 6 weeks of microsphere treatment.

label_protocol: Biotinylated cRNA was prepared according to Affymetrix protocols from 5 microgram total RNA (Carolinas Medical Center-modified Affymetrix "Expression Analysis Technical Manual", 2001 using Superscript II cDNA module, Affymetrix IVT module, Affymetrix/Qiagen sample clean-up module).

growth_protocol: Rat was euthanized 6 weeks after vehicle treatment. Heart was excised surgicaly and briefly perfused with saline buffer on a Langendorff heart perfusion apparatus. The right venticle was disected and separated into outflow tract (base) and apex samples. This sample is "A" for apex.

extract_protocol: Heart tissue was snap frozen in liquid nitrogen and crushed to a fine powder with a mortar and pestle in liquid nitrogen. Aliquots of powders were homogenized in guanidinium isothiocyanate and extracted with acidic phenol/chloroform. Crude RNA was collected by ethanol precipitation and purified using Qiagen RNeasy spin columns.

treatment_protocol: Rat was injected in the right jugular vein with 2 million (25 micron) polystyrene microspheres/100 grams weight at a concentration of 13 million microspheres/ml in 0.01% tween-20.

value: Sprague Dawley

tag: weight

value: approximately 350 grams at time of experiment


title: 178 replicate 2

description: gene expression data 178 bioreplicate 2


title: 182 replicate 1

description: gene expression data 182 bioreplicate 1


title: 179 replicate 1

description: gene expression data 179 bioreplicate 1

source_name: osteosarcoma tumor 179


description: Experimental pulmonary embolism:  Week 6 PE2.0 rat, heart right ventricle apex, biological rep3


description: Experimental pulmonary embolism: Week 6 PE2.0 rat, heart right ventricle outflow, biological rep5

source_name: Gene expression data from right ventricle outflow RNA after 6 weeks of microsphere treatment.

growth_protocol: Rat was euthanized 6 weeks after vehicle treatment. Heart was excised surgicaly and briefly perfused with saline buffer on a Langendorff heart perfusion apparatus. The right venticle was disected and separated into outflow tract (base) and apex samples. This sample is "O" for outflow tract.


description: Experimental pulmonary embolism: Week 6 PE2.0 rat, heart right ventricle outflow, biological rep4


title: 179 replicate 2

description: gene expression data 179 bioreplicate 2


title: 183 replicate 2

description: gene expression data 183 bioreplicate 2


description: Experimental pulmonary embolism:  Week 6 PE2.0 rat, heart right ventricle apex, biological rep2


description: Experimental pulmonary embolism: Week 6 PE2.0 rat, heart right ventricle outflow, biological rep3


title: 177 replicate 1

description: gene expression data 177 bioreplicate 1


description: Experimental pulmonary embolism:  Week 6 PE2.0 rat, heart right ventricle apex, biological rep1


description: Experimental pulmonary embolism: Week 6 PE2.0 rat, heart right ventricle outflow, biological rep2


description: Experimental pulmonary embolism:  Week 6 PE2.0 rat, heart right ventricle apex, biological rep5


description: Experimental pulmonary embolism: Week 6 PE2.0 rat, heart right ventricle outflow, biological rep1


description: Experimental pulmonary embolism: Week 6 vehicle control rat, heart right ventricle outflow, biological rep3

source_name: Gene expression data from right ventricle outflow RNA after 6 weeks of vehicle treatment.

treatment_protocol: Rat was injected in the right jugular vein with 0.15 ml/100 grams weight of 0.01% Tween-20 as "vehicle" control treatment