title: 00-010L_LN CRPC metastasis [CGH]

description:
00-010L CRPC lymph node metastasis
00-010L_LN

value: LN

tag: androgen deprivation therapy (adt)

tag: secondary ar pathway antagonism (arpa)

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F

tag: chemotherapy


title: Foxo1(-/-)/VEGF(-)-3

status: Public on Feb 16 2016

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

molecule: total RNA

organism: Mus musculus

source_name: ES cell-derived endothelial cells

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: For the induction of ECs, ES cells were seeded on OP9 stromal cell layer and cultured in alpha-MEM supplemented with 10% FCS and 0.05 mM 2-mercaptoethanol for 6.5 days.

extract_protocol: Total RNA samples were extracted from cells using RNeasy Plus Mini Kit (QIAGEN #74134).

treatment_protocol: For VEGF stimulation, recombinant murine VEGF-A (10 ng/ml) was added in the medium during the last two days (4.5–6.5 days).

tag: genotype

tag: treatment

value: no treatment

tag: cell type

value: ES cell-derived endothelial cells


title: Foxo1(+/+)/VEGF(+)-1

value: wild-type

value: VEGF treated


title: 00-010M_LN CRPC metastasis [CGH]

type: genomic

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

country: USA

institute: Fred Hutchinson Cancer Center

description:
00-010M CRPC lymph node metastasis
00-010M_LN

hyb_protocol: Cy3 and Cy5 probes were combined and hybridized to Agilent 2x400K SurePrint G3 CGH Microarrays and washed following the manufacturer’s specifications.

scan_protocol: Fluorescent array images were collected using the Agilent DNA microarray scanner G2505C and Agilent Feature Extraction software.

data_processing: Agilent Feature Extraction software version 10.7.3.1 was used to grid and extract the data using the CGH_107_Sep09 protocol with default settings. Feature Extraction Grid_GenomicBuild was hg18:NCBI36:Mar2006. Control probes were removed, duplicate probes averaged, and log2 ratios defined as gProcessedSignal/rProcessedSignal.

molecule: genomic DNA

organism: Homo sapiens

source_name: A pool of reference normal male DNA

label_protocol: One microgram of high molecular weight genomic DNA from each sample was labeled by random priming using the Agilent Genomic DNA Enzymatic Labeling Kit (Cy3-dUTP.)  A pool of reference normal male DNA (Promega, Part No. G1471) was labeled with Cy5-dUTP following manufacturer's suggest protocols

tag: gender

value: male

tag: tissue

extract_protocol:
Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.
Genomic DNA was isolated from OCT sections of localized and metastatic tissues with ≥50% tumor content, 1mm punches from frozen bone metastases as well as patient-matched normal tissues using the Qiagen QiaAmp DNA Micro kit incorporating RNAse-treatment. DNA quality was assessed by agarose gel electrophoresis.

tag: patient

tag: tumor type

value: CRPC metastasis

tag: tumor site

tag: age (yrs)

tag: psa ng/ml

value: L=LHRH agonist; O=orchiectomy:L

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:M


title: 00-029N9_LN CRPC metastasis [CGH]

description:
00-029N9 CRPC lymph node metastasis
00-029N9_LN

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: L=LHRH agonist; O=orchiectomy:O

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:N


title: Foxo1(-/-)/VEGF(-)-1


title: Foxo1(-/-)/VEGF(-)-2


title: 00-029J2_LN CRPC metastasis

description: 00-029J2 CRPC lymph node metastasis

hyb_protocol: Hybridizations to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2505C (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software versions 10.7.3.1 were used to grid and extract the data using the GE2_105_Jan09 protocols with default settings. Data was loess normalized within arrays (normexp background correction with offset 50) and quantile normalized between arrays in R using the Limma Bioconductor package by batch. Control probes were removed, duplicate probes averaged, and spots flagged by Agilent Feature Extraction software as being foreground feature nonuniformity or population outliers were assigned a value of NA. Data was normalized separately for LuCaP xenografts and CRPC metastases. CRPC metastases were subject to an additional normalization step to remove systematic batch effects due to date of RNA-amplification by application of the ComBat function within the sva Bioconductor package to the log2 Cy3 signal intensities. Batches are indicated in the ch2: characteristics: batch field and indicates RNA-amplification batch. Batch normalization was applied to a larger set of CRPC samples than those that appear in this study.

label_protocol: amplified amino-allyl aRNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl aRNA was labeled with Cy5) following the manufacturer’s suggested protocols.

extract_protocol: To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA).  Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl incorporation in the second round using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

extract_protocol: Eight-micron thick sections from soft tissue CRPC frozen metastases in Optimal Cutting Temperature compound (OCT; Tissue-Tek) were cut using a Leica CM3050S cryostat, collected on PEN Membrane Frame Slides (Life Technologies) and immediately fixed in 95% ethanol. Sections were briefly stained with hematoxylin then dehydrated in 100% ethanol. 5,000-10,000 tumor cells per sample were laser capture microdissected with an Arcturus Veritas instrument and collected on CapSure® Macro LCM Caps (Life Technologies). Digital photographs were taken of tissue sections before, during, and after LCM and assessed by a pathologist to confirm the tumor content. RNA was isolated using the Arcturus PicoPure RNA Isolation Kit and the samples were DNAse treated using the Qiagen RNase-Free DNase Set. Total RNA was amplified two rounds with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

tag: batch

tag: ne group

tag: erg group

value: ERG negative group


title: Foxo1(+/+)/VEGF(-)-1


title: 07-042H2_LN CRPC metastasis

description: 07-042H2 CRPC lymph node metastasis

value: CHGA positive/ SYP positive/ AR positive group

value: ERG positive group


title: Subject6_Day_2

city: RTP

first: Pierre

middle: Robert

last: Bushel

state: NC

department: Biostatistics and Computational Biology Branch

institute: NIEHS

hyb_protocol: For each two-color comparison, 750 ng of each Cy3 and Cy5 cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hrs in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing and scanning.

scan_protocol: Gene expression pixel intensities were extracted by scanning the microarrays with an Agilent Scanner (Agilent Technologies, Wilmington, DE).

data_processing: The log base 2 pixel intensity values from the Cy3 and Cy5 channels were background subtracted, corrected for dye bias and normalized across arrays via systematic variation normalization (SVN) as described in Chou JW, Paules RS, Bushel PR. Systematic variation normalization in microarray data to get gene expression comparison unbiased. Journal of bioinformatics and computational biology 2005; 3(2): 225-241.  Then the data was corrected for batch effects using an empirical Bayes model with the classification of the subjects and before or after dosing as covariates and parametric estimation of priors such as decribed in Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007; 8(1): 118-127.

source_name: Stratagene human universal reference

label_protocol: 500 ng of total RNA (universal reference and subject samples) was amplified, labeled (with cytofluor reversal) using the Agilent Low RNA Input Fluorescent Linear Amplification Kit, according to manufacturer’s protocol.

extract_protocol: Each day peripheral blood (7.5 mls) was drawn into PAXgene™ blood RNA collection tubes (3 tubes @ 2.5 mls). Samples were mixed and RNA was isolated according to the manufacturer’s protocol, including the optional on-column DNase digestion. RNA quality was assessed with an Agilent Bioanalyzer™ and only samples with intact 18S and 28S ribosomal RNA peaks were used for microarray analysis.

treatment_protocol: Individuals given placebos were classified as within the Placebo group.  Responders:  Individuals with a 2-fold increase in serum ALT from their respective baseline value and greater than 2x the upper limit of normal (as defined by historical data from the UNC hospital: females = 30 IU/L; males = 40 IU/L) in response to acetaminophen.  Non-responders: Individuals receiving acetaminophen but not meeting the “Responder” criteria.  The baseline for normal was defined as the mean of the daily ALT measurements obtained in the 3 days before the start of acetaminophen dosing (the acclimation period).

tag: reference composition

value: 10 human cell lines

tag: individual

value: Whole Blood

value: Male

tag: ethnicity (c= caucasian, h=hispanic, aa=african american, a=asian)

value: C/H

tag: age

tag: response

value: Non-responder

value: Acetaminophen

tag: time

value: Day 2


title: 00-090T3_LN CRPC metastasis

description: 00-090T3 CRPC lymph node metastasis

value: male

value: CRPC metastasis

value: LN


title: 00-010N_CAP CRPC primary/localized tumor

description: 00-010N CRPC prostate primary/localized tumor

data_processing: Agilent Feature Extraction software versions 10.1.1.1 were used to grid and extract the data using the GE2-v5_10_Apr08 protocols with default settings. Data was loess normalized within arrays (normexp background correction with offset 50) and quantile normalized between arrays in R using the Limma Bioconductor package by batch. Control probes were removed, duplicate probes averaged, and spots flagged by Agilent Feature Extraction software as being foreground feature nonuniformity or population outliers were assigned a value of NA. Data was normalized separately for LuCaP xenografts and CRPC metastases. CRPC metastases were subject to an additional normalization step to remove systematic batch effects due to date of RNA-amplification by application of the ComBat function within the sva Bioconductor package to the log2 Cy3 signal intensities. Batches are indicated in the ch2: characteristics: batch field and indicates RNA-amplification batch. Batch normalization was applied to a larger set of CRPC samples than those that appear in this study.

extract_protocol: Eight-micron thick sections from CRPC localized tumors in Optimal Cutting Temperature compound (OCT; Tissue-Tek) were cut using a Leica CM3050S cryostat, collected on PEN Membrane Frame Slides (Life Technologies) and immediately fixed in 95% ethanol. Sections were briefly stained with hematoxylin then dehydrated in 100% ethanol. 5,000-10,000 tumor cells per sample were laser capture microdissected with an Arcturus Veritas instrument and collected on CapSure® Macro LCM Caps (Life Technologies). Digital photographs were taken of tissue sections before, during, and after LCM and assessed by a pathologist to confirm the tumor content. RNA was isolated using the Arcturus PicoPure RNA Isolation Kit and the samples were DNAse treated using the Qiagen RNase-Free DNase Set. Total RNA was amplified two rounds with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: CRPC primary/localized

value: PROSTATE


title: 00-029O6_LN CRPC metastasis

description: 00-029O6 CRPC lymph node metastasis

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines


title: Foxo1(+/+)/VEGF(-)-2

tag: genotype

value: wild-type

tag: treatment

value: no treatment

tag: cell type

value: ES cell-derived endothelial cells


title: 01-087QQ1_BONE CRPC metastasis

description: 01-087QQ1 CRPC bone metastasis

tag: gender

tag: tissue

extract_protocol: The bone metastases which were frozen in OCT blocks were sampled using 1 mm diameter tissue punch in a -20oC cryostat. The sample was obtained from the region of the block where there was tumor based upon a section of an adjacent decalcified FFPE block. RNA was isolated from the tissue cores using RNeasy Plus Micro Kit (Qiagen Inc.). Tissue cores were placed in the kit’s Buffer RLT Plus, to which β-mercaptoethanol had been added, and homogenized with a disposable hard tissue homogenizer tip (Omni International). Total RNA was amplified two rounds with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

value: CHGA positive/ SYP positive/ AR positive group

value: BONE

tag: patient


title: 00-010N_CAP CRPC primary/localized tumor [CGH]

description:
00-010N CRPC prostate primary/localized tumor
00-010N_CAP

value: A pool of reference normal male DNA (Promega, Part No. G1471)

tag: tumor type

tag: tumor site

tag: age (yrs)

tag: androgen deprivation therapy (adt)

value: L=LHRH agonist; O=orchiectomy:L

tag: secondary ar pathway antagonism (arpa)

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F

tag: chemotherapy

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:M


title: 00-029P7_LUNG CRPC metastasis

description: 00-029P7 CRPC lung metastasis

tag: batch

value: LUNG


title: 04-101L3_LN CRPC metastasis

description: 04-101L3 CRPC lymph node metastasis

value: male

tag: ne group

tag: erg group


title: 07-042EE1_BONE CRPC metastasis

description: 07-042EE1 CRPC bone metastasis

value: ERG positive group

value: CRPC metastasis


title: 05-144EE1_BONE CRPC metastasis

description: 05-144EE1 CRPC bone metastasis

value: CHGA positive/ SYP positive/ AR negative group


title: 99-069G1_PERITONEUM CRPC metastasis

description: 99-069G1 CRPC peritoneum metastasis

value: PERITONEUM


title: A549 CSE 1% 5 weeks, biological rep 1

city: Mexico City

first: Marco

last: Checa

address: Calada de Tlalpan 4502, Colonia XVI Delegación Tlalpan

department: Pulmonary Fibrosis

country: Mexico

institute: Instituto Nacional de Enfermedades Respiratorias

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 1% for 5 week.
CSE1%5w.R1

hyb_protocol: The labeled cDNA product was heated to 95°C and hybridized to the Human Gene 1.0 ST microarray (Affymetrix Inc.) for 17 + 1 hr at 45°C. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain

scan_protocol: A confocal scanner (Affymetrix GeneChip Scanner 3000 7G plus) was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature

data_processing: The statistical analyses were performed with R 2.11.0. All samples were normalized and summarized by Robust Multiarray Average (RMA). Times series analysis was carried out using bioconductor timecourse package. Differential expression analysis between NK cells non stimulated and LPG-stimulated was performed using LIMMA. The Benjamini and Hochberg multiple hypothesis testing correction procedure was applied to control the false discovery rate (FDR). Data were filtered to include only genes that had a 2-fold-change difference between the groups and an adjusted p value of 0.05

label: Biotin

source_name: Human alveolar epithelial cells (A549) exposed to CSE 1% for 5 weeks.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA

growth_protocol: Human alveolar epithelial cells (A549) at 80% confluence were left in culture medium without serum 24 hours before the start of the experiment followed by incubation with CSE 1%, 5% and 10% in DMEM plus 1% of FBS (fetal bovine serum).

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

treatment_protocol: CSE media was refreshed every 24 hrs. The cell cultures were maintained for a week, and sub-cultured each time at a density of 6.0 x 106 cells per 100mm dish, until completing 3 and 5 weeks of stimuli respectively.

tag: cell line

value: alveolar epithelial cell line A549

tag: agent

value: CSE

tag: dose

value: 5 weeks


title: Foxo1(+/+)/VEGF(-)-3

tag: genotype

value: wild-type

tag: treatment

value: no treatment

value: ES cell-derived endothelial cells


title: A549 CSE 10% 5 weeks, biological rep 3

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 10% for 5 week.
CSE10%5w.R3

source_name: Human alveolar epithelial cells (A549) exposed to CSE 10% for 5 weeks.

tag: time


title: A549 CSE 1% 5 weeks, biological rep 3

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 1% for 5 week.
CSE1%5w.R3


title: A549 CSE 5% 5 weeks, biological rep 2

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 5% for 5 week.
CSE5%5w.R2

source_name: Human alveolar epithelial cells (A549) exposed to CSE 5% for 5 weeks.


title: A549 CSE 5% 3 weeks, biological rep 3

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 5% for 3 week.
CSE5%3w.R3

source_name: Human alveolar epithelial cells (A549) exposed to CSE 5% for 3 weeks.

value: 3 weeks


title: 00-029T2_CAP CRPC primary/localized tumor

description: 00-029T2 CRPC pelvic_mass primary/localized tumor

tag: gender

tag: tissue

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

value: CRPC primary/localized


title: A549 CSE 10% 5 weeks, biological rep 1

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 10% for 5 week.
CSE10%5w.R1


title: 00-010L_LN CRPC metastasis

description: 00-010L CRPC lymph node metastasis

tag: tumor type

value: LN

tag: patient


title: A549 CSE 5% 5 weeks, biological rep 3

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 5% for 5 week.
CSE5%5w.R3


title: A549 CSE 5% 3 weeks, biological rep 2

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 5% for 3 week.
CSE5%3w.R2


title: A549 CSE 5% 5 weeks, biological rep 1

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 5% for 5 week.
CSE5%5w.R1


title: A549 CSE 10% 5 weeks, biological rep 2

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 10% for 5 week.
CSE10%5w.R2


title: 05-221MM1_BONE CRPC metastasis

description: 05-221MM1 CRPC bone metastasis

value: CHGA positive/ SYP positive/ AR positive group

tag: tumor site

value: BONE


title: A549 CSE 5% 3 weeks, biological rep 1

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 5% for 3 week.
CSE5%3w.R1


title: 01-087MM_BONE CRPC metastasis

description: 01-087MM CRPC bone metastasis

value: male


title: A549 CSE 1% 5 weeks, biological rep 2

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 1% for 5 week.
CSE1%5w.R2


title: 08-037F1_LIVER CRPC metastasis

description: 08-037F1 CRPC liver metastasis

value: CHGA positive/ SYP negative group

value: ERG negative group

value: CRPC metastasis

value: LIVER


title: 03-192A1_LIVER CRPC metastasis

description: 03-192A1 CRPC liver metastasis

value: CHGA positive/ SYP positive/ AR negative group


title: 05-144E1_LIVER CRPC metastasis

description: 05-144E1 CRPC liver metastasis


title: 03-192D2_LN CRPC metastasis

description: 03-192D2 CRPC lymph node metastasis


title: A549 CSE 10% 3 weeks, biological rep 3

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 10% for 3 week.
CSE10%3w.R3

source_name: Human alveolar epithelial cells (A549) exposed to CSE 10% for 3 weeks.

value: alveolar epithelial cell line A549

value: CSE


title: A549 CSE 10% 3 weeks, biological rep 1

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 10% for 3 week.
CSE10%3w.R1


title: 05-144HH1_BONE CRPC metastasis

description: 05-144HH1 CRPC bone metastasis


title: 06-081H5_LN CRPC metastasis

description: 06-081H5 CRPC lymph node metastasis


title: 07-062F2_LUNG CRPC metastasis

description: 07-062F2 CRPC lung metastasis

value: LUNG


title: A549 CSE 10% 3 weeks, biological rep 2

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 10% for 3 week.
CSE10%3w.R2


title: A549 CSE 5% 1 week, biological rep 2

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 5% for 1 week.
CSE5%1w.R2

value: 1 week


title: A549 CSE 5% 1 week, biological rep 3

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 5% for 1 week.
CSE5%1w.R3


title: 05-165K5_LUNG CRPC metastasis

description: 05-165K5 CRPC lung metastasis


title: A549 CSE 1% 3 weeks, biological rep 3

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 1% for 3 week.
CSE1%3w.R3

source_name: Human alveolar epithelial cells (A549) exposed to CSE 1% for 3 weeks.

value: 3 weeks


title: A549 CSE 10% 1 weeks, biological rep 1

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 10% for 1 week.
CSE10%1w.R1


title: A549 CSE 1% 3 weeks, biological rep 1

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 1% for 3 week.
CSE1%3w.R1


title: 06-047H1_LN CRPC metastasis

description: 06-047H1 CRPC lymph node metastasis

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines


title: A549 CSE 10% 1 weeks, biological rep 3

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 10% for 1 week.
CSE10%1w.R3


title: A549 CSE 1% 3 weeks, biological rep 2

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 1% for 3 week.
CSE1%3w.R2


title: 05-165M1_LN CRPC metastasis

description: 05-165M1 CRPC lymph node metastasis

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.


title: 99-091I_LN CRPC metastasis

description: 99-091I CRPC lymph node metastasis

value: CHGA negative group


title: 05-116F_LUNG CRPC metastasis

description: 05-116F CRPC lung metastasis


title: 05-148E3_LIVER CRPC metastasis

description: 05-148E3 CRPC liver metastasis


title: 06-081E2_LIVER CRPC metastasis

description: 06-081E2 CRPC liver metastasis


title: A549 CSE 10% 1 weeks, biological rep 2

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 10% for 1 week.
CSE10%1w.R2


title: 00-140FF_BONE CRPC metastasis

description: 00-140FF CRPC bone metastasis


title: A549 CSE 1% 1 week, biological rep 1

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 1% for 1 week.
CSE1%1w.R1


title: A549 CSE 1% 1 week, biological rep 3

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 1% for 1 week.
CSE1%1w.R3


title: 99-064N_LN CRPC metastasis

description: 99-064N CRPC lymph node metastasis

value: LN


title: A549 Ctrl 5 weeks, biological rep 3

description:
Gene expression data from Human alveolar epithelial cells (A549) seeded 3 weeks without exposure to CSE
CT5w.R3

source_name: Human alveolar epithelial cells (A549) seeded 5 weeks without exposure to CSE

value: Ctrl


title: 98-362B1_LN CRPC metastasis

description: 98-362B1 CRPC lymph node metastasis


title: 99-091C_LIVER CRPC metastasis

description: 99-091C CRPC liver metastasis


title: 98-372L_LN CRPC metastasis

description: 98-372L CRPC lymph node metastasis


title: A549 CSE 1% 1 week, biological rep 2

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 1% for 1 week.
CSE1%1w.R2


title: A549 Ctrl 5 weeks, biological rep 2

description:
Gene expression data from Human alveolar epithelial cells (A549) seeded 3 weeks without exposure to CSE
CT5w.R2


title: A549 Ctrl 3 weeks, biological rep 3

description:
Gene expression data from Human alveolar epithelial cells (A549) seeded 3 weeks without exposure to CSE
CT3w.R3


title: 98-362K2_LUNG CRPC metastasis

description: 98-362K2 CRPC lung metastasis


title: A549 CSE 5% 1 week, biological rep 1

description:
Gene expression data from Human alveolar epithelial cells (A549) exposed to CSE 5% for 1 week.
CSE5%1w.R1


title: A549 Ctrl 5 weeks, biological rep 1

description:
Gene expression data from Human alveolar epithelial cells (A549) seeded 3 weeks without exposure to CSE
CT5w.R1


title: 98-328H_APPENDIX CRPC metastasis

description: 98-328H CRPC appendix metastasis

value: APPENDIX


title: A549 Ctrl 3 weeks, biological rep 2

description:
Gene expression data from Human alveolar epithelial cells (A549) seeded 3 weeks without exposure to CSE
CT3w.R2


title: 98-328K_PERITONEUM CRPC metastasis

description: 98-328K CRPC peritoneum metastasis

value: male

value: PERITONEUM


title: 08-020HH1_BONE CRPC metastasis

description: 08-020HH1 CRPC bone metastasis

value: ERG positive group

value: BONE


title: 08-006TT1_BONE CRPC metastasis

description: 08-006TT1 CRPC bone metastasis

value: CRPC metastasis


title: A549 Ctrl 1 week, biological rep 3

description:
Gene expression data from Human alveolar epithelial cells (A549) seeded 1 week without exposure to CSE
CT1w.R3


title: 07-050XX1_BONE CRPC metastasis

description: 07-050XX1 CRPC bone metastasis

value: ERG negative group


title: 08-020Y6_KIDNEY CRPC metastasis

description: 08-020Y6 CRPC kidney metastasis

value: KIDNEY


title: A549 Ctrl 3 weeks, biological rep 1

description:
Gene expression data from Human alveolar epithelial cells (A549) seeded 3 weeks without exposure to CSE
CT3w.R1

value: alveolar epithelial cell line A549


title: A549 Ctrl 1 week, biological rep 1

description:
Gene expression data from Human alveolar epithelial cells (A549) seeded 1 week without exposure to CSE
CT1w.R1


title: 08-006H1_LN CRPC metastasis

description: 08-006H1 CRPC lymph node metastasis


title: Monocytes/macrophages With MEC1 21d F

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

country: Italy

institute: IRCCS, Ospdale San Raffaele

description:
mouse F
#9323675050_F

hyb_protocol: Biotin-labeled cRNA was hybridized on MouseWG-6 v2.0 Expression BeadChip (harboring probes for ~45k transcript) for 16 hours. The BeadChip underwent a washing and streptavidin-Cy3 (GE Healthcare Bio-Sciences) conjugate staining protocol

scan_protocol: Illumina BeadArray Reader

data_processing: The data were normalized using the quantile algorithm implemented in the Illumina® GenomeStudio software

source_name: Murine bone marrow

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep Amplification kit (Ambion-Life technologies)

extract_protocol: QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit

tag: genotype/variation

tag: strain

value: BALB/c

tag: age

value: 11 weeks

value: Bone marrow

value: injected intravenously with MEC1 cells


title: 07-044KK5_BONE CRPC metastasis

description: 07-044KK5 CRPC bone metastasis

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

tag: batch


title: A549 Ctrl 1 week, biological rep 2

description:
Gene expression data from Human alveolar epithelial cells (A549) seeded 1 week without exposure to CSE
CT1w.R2


title: antagomir-132 4

city: Leiden

first: Roel

last: Bijkerk

address: Albinusdreef 2

department: Nephrology

country: Netherlands

institute: LUMC

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Genomestudio

label: biotin

source_name: Renal FoxD1-derivative cells, 10 days after UUO

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

extract_protocol: RNA was extracted with standard Trizol-chloroform protocol.

treatment_protocol: FoxD1-GC;tdTomato were used, antagomir-132 or scramblemir was injected i.v. at 40 mg/kg bodyweight, and unilateral ureter obstruction was performed. 10 days after surgery, mice were sacrificed, kidneys removed and dissociated followed by FACS-mediated isolation of Tomato-positive cells, as described in corresponding manuscript.

value: kidney

tag: sex and age

value: 8 weeks

tag: diagnosis

value: fibrotic


title: Monocytes/macrophages With MEC1 21d D

description:
mouse D
#9323675050_D


title: 06-134H1_LN CRPC metastasis

description: 06-134H1 CRPC lymph node metastasis

value: male

tag: ne group

value: CHGA negative group

tag: erg group

value: LN


title: Monocytes/macrophages With MEC1 21d E

description:
mouse E
#9323675050_E


title: antagomir-132 2

description: replicate 2


title: 07-050EE1_BONE CRPC metastasis

description: 07-050EE1 CRPC bone metastasis

value: BONE


title: scramblemir 4

description: replicate 4


title: Monocytes/macrophages No MEC1 21d C

description:
mouse C
#9323675050_C


title: 06-131BB1_BONE CRPC metastasis

description: 06-131BB1 CRPC bone metastasis

value: CRPC metastasis


title: 06-047QQ1_BONE CRPC metastasis

description: 06-047QQ1 CRPC bone metastasis


title: antagomir-132 3

description: replicate 3


title: antagomir-132 1

description: replicate 1


title: 05-217L3_LUNG CRPC metastasis

description: 05-217L3 CRPC lung metastasis

value: LUNG


title: Monocytes/macrophages No MEC1 21d A

description:
mouse A
#9323675050_A


title: 05-217F1_LN CRPC metastasis

description: 05-217F1 CRPC lymph node metastasis


title: scramblemir 2

description: replicate 2


title: 05-187J3_LN CRPC metastasis

description: 05-187J3 CRPC lymph node metastasis

value: ERG positive group


title: scramblemir 1

description: replicate 1


title: 05-214BB2_BONE CRPC metastasis

description: 05-214BB2 CRPC bone metastasis


title: 04-149E2_LN CRPC metastasis

description: 04-149E2 CRPC lymph node metastasis

value: ERG negative group


title: 05-116LL_BONE CRPC metastasis

description: 05-116LL CRPC bone metastasis


title: Sample-bGL1-22-stimulated

city: New Haven

first: Rakesh

last: Verma

state: CT

address: 333 Cedar St.

department: Yale Cancer Center

institute: Yale University

description: Gene expression data from b-GL122-expanded T cells from healthy donor-Peripheral blood mononuclear cells (PBMCs) that were sorted with CD1d tetramer loaded with  b-GL122.

hyb_protocol: RNA was amplified, labeled, and hybridized on the Affymetrix Human Genome U133 Plus 2.0 microarray chips at the Yale Center for Genome Anlaysis (YCGA) Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) at the Yale Center for Genome Anlaysis (YCGA) Microarray Core Facility.

data_processing: The data were analyzed with GeneSpring GX 12.5 (Agilent Technologies)

source_name: Peripheral blood mononuclear cells (PBMCs) from healthy donors

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA at the Yale Center for Genome Anlaysis (YCGA) Microarray Core Facility.

growth_protocol: Lipids and CD1d tetramer loading:   NKT ligand a-galactosyl-ceramide (a-GalCer) was kindly provided by  Kirin Breweries (Tokyo, Japan). b-D-GlcCer d18:1-C24:1(15Z),C12:0 was  from Avanti Polar Lipids. b-D-GlcCer d18:1-C22:0 (thin-layer chromatography  purity .98%) and lysoglucocerebroside (thin-layer chromatography  purity .98%) were from Matreya. Human empty CD1d tetramer  were obtained from the National Institutes of Health (NIH) tetramer facility  (Atlanta, GA). A molar loading ratio (lipid to CD1d) of 200:1 was used for  tetramerization studies for human tetramers. The unloaded multimer control was prepared by mixing CD1d  tetramer with the carrier only.

treatment_protocol: Stimulation of NKT cells in culture:  For stimulation with anti-CD3/CD28 beads (Miltenyi Biotec), sorted  tetramer-positive cells were stimulated with anti-CD3/CD28 beads in a 96-  well U-bottom plate. For some experiments, sorted bGL1-22/LGL1/  a-GalCer tetramer-positive cells were cultured with CD1d-expressing cell  line (C1rd cells; kindly provided by Dr Mark Exley, Boston) or mock transfected  control cells at a T-cell: antigen-presenting cell (APC) ratio of  1: 0, with or without lipid pulsing.

tag: cell type

value: CD1d tetramer-sorted b-GL122-specific T cells

tag: protocol

value: stimulated


title: 05-011D2_LN CRPC metastasis

description: 05-011D2 CRPC lymph node metastasis


title: 05-214E1_LN CRPC metastasis

description: 05-214E1 CRPC lymph node metastasis


title: nsEP U937, biological rep 3

city: San Antonio

first: Caleb

last: Roth

state: Texas

address: 7703 Floyd Curl

department: Radiology

institute: UTHSCSA

description: Gene expression data from U-937 cells 4hr post nsEP exposure

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained with streptavidin-conjugated phycoerythrin in the Affymetrix Fluidics Station 450 following Affymetrix standard procedures.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 30007G using Affymetrix’ GeneChip Operating Software to generate raw and averaged image files (.DAT and .CEL).

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.  Arrays were scaled to target intensity value of 500. The normalization, and log base 2 transformation of gene signals were carried out using Quantile Normalization. For statistical analysis, one-way ANOVA was used for multiple group comparison across all samples in the experiment, followed by multiple testing correction to determine the false discovery rate.  Genes with a FDR-adjusted p-value of < 0.05 were considered differentially expressed genes (DEG).  Pair-wise comparisons were then performed for all DEG.  For each pair of treatments, a two-sample t-test was carried out for every gene, followed by multiple testing correction to determine FDR.  Genes with a FDR-adjusted p-value of < 0.05 were considered statistically significant.  The resulting list of genes and associated p-values were graphically represented by hierarchical clustering, principal components analysis, and volcano plots

source_name: U-937 cells 4hr post nsEP exposure

label_protocol: Biotin-labeled cRNA were prepared a modified MessageAmp procedure (Life Technologies, Inc.) from 1 ug total RNA.

growth_protocol: U-937 cells were grown according to ATCC protocol; 37 C/5 % CO2/95 % humidity; grown in RMPI media supplemented with 10% FBS and 1% pen/strep

extract_protocol: total RNA was extracted with the Qiagen Rneasy mini kit according to the manufacturers protocol

treatment_protocol: cells were harvested by centrifugation, counted, and concentration adjusted to 1200 cells/ μl and then placed in an electroporation cuvette and either SHAM, or nsEP or heat shock exposed

value: Pleura/pleural effusion, lymphocyte, Myeloid

tag: cell line


title: Monocytes/macrophages No MEC1 21d B

description:
mouse B
#9323675050_B

value: BALB/c

value: 11 weeks

value: Bone marrow

tag: treatment


title: Sample-aGAL-stimulated

description: Gene expression data from a-GALCER-expanded T cells from healthy donor-Peripheral blood mononuclear cells (PBMCs) that were sorted with CD1d tetramer loaded with  a-GALCER.

value: CD1d tetramer-sorted a-GALCER-specific T cells


title: heat shock U937, biological rep 2

description: Gene expression data from U-937 cells 4hr post heat shock exposure


title: Sample-LGL1-stimulated

description: Gene expression data from LGL1-expanded T cells from healthy donor-Peripheral blood mononuclear cells (PBMCs) that were sorted with CD1d tetramer loaded with LGL1.

value: CD1d tetramer-sorted LGL1-specific T cells


title: nsEP U937, biological rep 2


title: Sample-LGL1-unstimulated-control

value: unstimulated (control)


title: 05-011G4_LUNG CRPC metastasis

description: 05-011G4 CRPC lung metastasis

tag: gender

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.


title: heat shock U937, biological rep 1

source_name: U-937 cells 4hr post heat shock exposure


title: 04-050L1_LN CRPC metastasis

description: 04-050L1 CRPC lymph node metastasis

tag: tissue

value: CHGA negative group

value: LN


title: 05-092I1_LN CRPC metastasis

description: 05-092I1 CRPC lymph node metastasis

tag: tumor type

value: CRPC metastasis


title: 03-163S4_LIVER CRPC metastasis

description: 03-163S4 CRPC liver metastasis

value: LIVER

tag: patient


title: scramblemir 3

description: replicate 3

value: kidney

value: 8 weeks

value: fibrotic


title: SHAM U937, biological rep 3

description: Gene expression data from U-937 cells 4hr post SHAM exposure

source_name: U-937 cells 4hr post SHAM exposure

value: Pleura/pleural effusion, lymphocyte, Myeloid


title: nsEP U937, biological rep 1


title: 05-092E7_LIVER CRPC metastasis

description: 05-092E7 CRPC liver metastasis

tag: tumor site


title: Sample-bGL1-22-unstimulated-control

value: CD1d tetramer-sorted b-GL122-specific T cells


title: 04-112H3_LN CRPC metastasis

description: 04-112H3 CRPC lymph node metastasis

value: ERG negative group


title: Sample-aGAL-unstimulated-control


title: SHAM U937, biological rep 1


title: heat shock U937, biological rep 3


title: SHAM U937, biological rep 2


title: heat shock Jurkat, biological rep 3

description: Gene expression data from Jurkat cells 4hr post heat shock exposure

growth_protocol: Jurkat cells were grown according to ATCC protocol; 37 C/5 % CO2/95 % humidity; grown in RMPI media supplemented with 10% FBS and 1% pen/strep

value: cell line (T lymphocyte)

value: Jurkat


title: heat shock Jurkat, biological rep 2

source_name: Jurkat cells 4hr post heat shock exposure


title: nsEP Jurkat, biological rep 3

description: Gene expression data from Jurkat cells 4hr post nsEP exposure

source_name: Jurkat cells 4hr post nsEP exposure


title: 03-082H1_LIVER CRPC metastasis

description: 03-082H1 CRPC liver metastasis


title: SHAM Jurkat, biological rep 1

description: Gene expression data from Jurkat cells 4hr post SHAM exposure

source_name: Jurkat cells 4hr post SHAM exposure


title: 03-139E3_RETROPERITONEAL CRPC metastasis

description: 03-139E3 CRPC retroperitoneal metastasis

value: RETROPERITONEAL


title: SHAM Jurkat, biological rep 2


title: 03-027P2_LIVER CRPC metastasis

description: 03-027P2 CRPC liver metastasis


title: heat shock HDFA, biological rep 3

description: Gene expression data from HDFA cells 4hr post heat shock exposure

source_name: HDFA cells 4hr post heat shock exposure

growth_protocol: HDFA cells were grown according to Cascade Biologics protocol; 37 C/5 % CO2/95 % humidity; grown in Medium 106 supplemented with Low Serum Growth Supplement (LSGS)

value: Primary human dermal fibroblasts isolated from adult skin


title: nsEP Jurkat, biological rep 2


title: SHAM Jurkat, biological rep 3


title: nsEP Jurkat, biological rep 1


title: SHAM HDFA, biological rep 2

description: Gene expression data from HDFA cells 4hr post SHAM exposure

source_name: HDFA cells 4hr post SHAM exposure


title: nsEP HDFA, biological rep 3

description: Gene expression data from HDFA cells 4hr post nsEP exposure

source_name: HDFA cells 4hr post nsEP exposure


title: 02-083E1_LN CRPC metastasis

description: 02-083E1 CRPC lymph node metastasis

value: male


title: 02-142II_BONE CRPC metastasis

description: 02-142II CRPC bone metastasis

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: BONE


title: 01-095N1_LN CRPC metastasis

description: 01-095N1 CRPC lymph node metastasis

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

value: CHGA negative group


title: 01-181AA_BONE CRPC metastasis

description: 01-181AA CRPC bone metastasis

value: ERG positive group

value: CRPC metastasis


title: 01-120C1_LN CRPC metastasis

description: 01-120C1 CRPC lymph node metastasis

value: LN


title: nsEP HDFA, biological rep 2


title: heat shock HDFA, biological rep 2


title: heat shock Jurkat, biological rep 1


title: heat shock HDFA, biological rep 1


title: SHAM HDFA, biological rep 3


title: nsEP HDFA, biological rep 1


title: 01-120A1_LIVER CRPC metastasis

description: 01-120A1 CRPC liver metastasis

value: LIVER


title: 01-095C6_LIVER CRPC metastasis

description: 01-095C6 CRPC liver metastasis


title: SHAM HDFA, biological rep 1


title: 01-002G1_LN CRPC metastasis

description: 01-002G1 CRPC lymph node metastasis


title: 03-130L_RETROPERITONEAL CRPC metastasis

description: 03-130L CRPC retroperitoneal metastasis


title: human MEC1 CLL cell line in vitro B

description:
in vitro replicate 2
#8803836015_B

hyb_protocol: Biotin-labeled cRNA was hybridized on HumanHT-12 v4 BeadChip (harboring probes for ~47k transcript) for 16 hours. The BeadChip underwent a washing and streptavidin-Cy3 (GE Healthcare Bio-Sciences) conjugate staining protocol

source_name: human CLL cell line from in vitro culture

value: CLL

tag: sample type

value: in vitro


title: human MEC1 CLL cell line xeno-transplanted 21d F

description:
mouse n11
#8803836015_L

source_name: human CLL cell line from murine bone marrow

value: xeno-transplanted 21d

tag: mouse strain

value: Rag2-/-γc-/- on BALB/c background

tag: mouse age

value: 11 weeks

tag: mouse tissue

value: Bone marrow


title: 00-029N9_LN CRPC metastasis

description: 00-029N9 CRPC lymph node metastasis

tag: batch


title: IPF151-ctrl

city: Los Angeles

first: ting

last: Xie

state: CA

address: 127 San Vicente Blvd

department: Pulmonary

institute: Cedars-Sinai Medical Center

description:
IPF151-ctrl
Gene expression data from cultured IPF151 lung fibroblasts.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array.

scan_protocol: GeneChips were scanned by GenePix 4000B scanner.

data_processing: Robust multi-chip analysis (RMA) normalization was done on the entire data set using Partek Genomics Suite 6.5. Multi-way ANOVA and fold change were performed to select target genes that were differentially expressed between 5'-Aza and Ctrl. Differentially expressed genes between groups, selected with following cutoff: p<=0.05, fold change >= 1.5 (data available in supplementary file GSE69764_differentially_expressed.txt).

source_name: IPF151 lung fibroblasts, control

label_protocol: Affymetrix® FlashTag™ Biotin HSR RNA Labeling Kits.

growth_protocol: 3 human IPF fibroblasts were cultured in growth medium. The cells were passage 4.

extract_protocol: Qiagen RNeasy mini kit.

tag: disease state

value: idiopathic pulmonary fibrosis (IPF)

value: lung fibroblast

value: control


title: human MEC1 CLL cell line xeno-transplanted 21d E

description:
mouse n10
#8803836015_K


title: 00-090G2_LUNG CRPC metastasis

description: 00-090G2 CRPC lung metastasis

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

tag: ne group

value: LUNG


title: human MEC1 CLL cell line xeno-transplanted 21d D

description:
mouse n8
#8803836015_J

tag: age


title: IPF159-5Aza

description:
IPF159-5Aza
Gene expression data from cultured IPF159 lung fibroblasts treated with 5'-azacytidine.

source_name: IPF159 lung fibroblasts, control

treatment_protocol: Cells were treated with 5'-azacytidine 5 uM for 24 hours.

tag: cell type

value: 5'-azacytidine (5uM, 24hr)


title: T59

status: Public on Feb 15 2016

city: Heidelberg

first: Christel

last: Herold-Mende

address: Im Neuenheimer Feld 400

department: Department of Neurosurgery

country: Germany

institute: Heidelberg University Hospital

data_processing: Raw-intensity data were obtained after image analysis of the fluorescent spot intensity reads. All preprocessing and normalization steps were performed in the R programming environment [www.r-project.org]. Inter-array normalization was conducted using qspline normalization in the affy package. Probe sets belonging to one gene were median summarized leading to a reduced number of probes in the normalized data set. Next, a linear model was fitted to account for different batches (limma package). Lastly, intra-array normalization was performed by means of median-centering data and followed by log2 transformation.

source_name: meningioma tissue

label_protocol: Standard labeling protocol of Genomic Core Facility of the German Cancer Research Center (DKFZ, Heidelberg, Germany)

extract_protocol: Total RNA was extracted from tissue using the AllPrep Kit (Qiagen) according to manufacturer's instructions. RNA integrity was assessed by the Agilent 2100 Bioanalyzer.

tag: subtype


title: 00-140J9_LN CRPC metastasis

description: 00-140J9 CRPC lymph node metastasis

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

value: CHGA negative group

tag: erg group

value: ERG negative group


title: IPF151-5Aza

description:
IPF151-5Aza
Gene expression data from cultured IPF151 lung fibroblasts treated with 5'-azacytidine.

source_name: IPF151 lung fibroblasts, 5'-azacytidine treatment

tag: treatment


title: human MEC1 CLL cell line in vitro C

description:
in vitro replicate 3
#8803836015_G

tag: cell line


title: T61


title: 00-010K_LIVER CRPC metastasis

description: 00-010K CRPC liver metastasis

tag: gender

tag: tissue

value: CRPC metastasis

value: LIVER


title: T56


title: human MEC1 CLL cell line in vitro A

description:
in vitro replicate 1
#8803836015_A

value: CLL

value: in vitro


title: 00-140G1_LIVER CRPC metastasis

description: 00-140G1 CRPC liver metastasis

tag: tumor type

tag: patient


title: T62


title: IPF159-ctrl

description:
IPF159-ctrl
Gene expression data from cultured IPF159 lung fibroblasts.

source_name: IPF159 lung fibroblasts, 5'-azacytidine treatment


title: 05-187E1_LIVER CRPC metastasis

description: 05-187E1 CRPC liver metastasis

tag: tumor site


title: IPF157-ctrl

description:
IPF157-ctrl
Gene expression data from cultured IPF157 lung fibroblasts.

source_name: IPF157 lung fibroblasts, 5'-azacytidine treatment


title: T54


title: T60


title: 00-010M_LN CRPC metastasis

description: 00-010M CRPC lymph node metastasis

value: LN


title: T57


title: T52


title: T53


title: IPF157-5Aza

description:
IPF157-5Aza
Gene expression data from cultured IPF157 lung fibroblasts treated with 5'-azacytidine.

source_name: IPF157 lung fibroblasts, control


title: T47


title: T50


title: T55


title: T43


title: T58


title: T46


title: T48


title: T51


title: T49


title: T44


title: T45


title: T37


title: T35


title: T38


title: T39


title: T32


title: T31


title: T40


title: T34


title: T30


title: T27


title: T41


title: T26


title: T36


title: T29


title: T33


title: T24


title: T42


title: T19


title: T25


title: T22


title: T20


title: T15


title: T28


title: T12


title: T16


title: T13


title: T23


title: T18


title: T17


title: T21


title: T9


title: T7


title: T8


title: T10


title: T6


title: T14


title: T4


title: T2


title: T1


title: T11


title: Heart, Infarcted, rep6

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description: 12 week old mice, border zone of infarct, 2 weeks after surgery

hyb_protocol: Arrays (Affymetrix, Santa Clara , CA, USA) were hybridized with 2.7μg of biotinylated target, at  45°C for 17 hours washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix)

data_processing: Background subtraction, quantile normalization and probeset summarization was performed using the Affymetrix Power Tools apt-probeset-summarize command with the -rma option

source_name: Heart, Infarcted

label_protocol: 200ng of total RNA were used to perform target preparation using the WT Expression Kit (Life Technologies). 5.5 μg of each fragmented cDNA was end-labeled with biotin

extract_protocol: Total RNA was isolated using Trizol (Invitrogen). RNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 Bioanalyzer.

tag: strain

value: heart

value: 12 week-old


title: V583 Δtdc (test) compared to V583 (reference) Replicate 1

city: Villaviciosa

first: Victor

last: Ladero

state: Select if applicable

address: Paseo Rio Linares S/N

department: Technology and Biotechnology of dairy products

country: Spain

institute: IPLA-CSIC

description: Biological replicate 1 of 2.

hyb_protocol: Three hundred ng of DyLight 550- and three hundred ng of DyLight 650-labelled cDNA were mixed and hybridized for 17 h at 60°C in the E. faecalis V583 DNA microarray using the In situ Hybridization Kit Plus, the Hybridization Gasket Slide and the Agilent G2534A Microarray Hybridization Chamber (Agilent Technologies). Slides were washed using the washing buffers indicated by the manufacturer.

scan_protocol: Microarrays were scanned using a GenePix 4200A Microarray Scanner (Molecular Devices, Sunnyvale, CA)

data_processing: Slide images were analyzed using GenePix Pro v.6.0 software. Background subtraction and LOWESS (locally weighted scatterplot smoothing) normalization were done using the standard routines provided by GENOME2D software available at http://server.molgenrug.nl/index.php/analysis-pipeline.

label: DyLight 650

organism: Enterococcus faecalis

source_name: Enterococcus faecalis V583 Δtdc grown with 15 mM tyrosine

label_protocol: Total cDNA was synthesized from 20 µg of RNA using the SuperScript® III Reverse Transcriptase kit (Life Technologies, Bleiswijk, Netherlands). The cDNA was purified using the NucleoSpin Gel and PCR Clean-up kit (Macherey-Nager, Landsmeer, The Netherlands) following the manufacturer instructions. Twenty µg of the purified cDNA was immediately labeled with DyLight 550 or DyLight 650 using the DyLight® Amine-Reactive Dyes kit (Thermo Scientific) as the manufacturer indicated. Quality and quantity of cDNA and DyLight 550 and DyLight 650 labelling were checked on a NanoDrop spectrophotometer (Thermo Scientific, Landsmeer, The Netherlands).

growth_protocol: Both strains E. faecalis V583 and E. faecalis V583 Δtdc were grown in 30 mL of M17 culture medium (Oxoid, UK) supplemented with 0.5% glucose (w/v) (GM17) and 15 mM tyrosine (Sigma-Aldrich, Barcelona, Spain) for 5 h at 37°C without aereation. After a centrifugation at 16,000 x g for 1 min at 4˚C, the supernatants were discarded and cell pellets were frozen in liquid nitrogen and stored at -80°C.

extract_protocol: Cell pellets were resuspended in 400 µl of TE buffer (10 mM Tris-HCl, 1 mM EDTA pH 8.0) and 50 µl of 10% SDS, 500 µl of phenol:chloroform:isoamyl alcohol (25:24:1) (Sigma-Aldrich), 500 mg of glass beads (75–150 µm) (Sigma-Aldrich), and 175 µl of Macaloid suspension (Bentone MA, Rheox Inc., Scotland, United Kingdom) were added. Cells were mechanically disrupted in a bead beater at 4˚C with two cycles of 60 s. During the shaking intervals the cells were kept on ice for 1 min. The samples were then centrifuged at 16,000 x g for 1 min at 4˚C. The upper phase was transferred to fresh tubes containing 500 µl chloroform: isoamyl alcohol (24:1) and centrifuged for 5 min at 4˚C. Total RNA was isolated with the High Pure RNA Isolation Kit (Roche Diagnostics GmbH, Mannheim, Germany) following the instructions provided by the manufacturer. The concentration and quality of the RNA was determined on a NanoDrop spectrophotometer (Thermo Scientific, Landsmeer, The Netherlands).

value: V583 Δtdc

tag: tyramine producer

value: No

label: DyLight 550

source_name: Enterococcus faecalis V583 grown with 15 mM tyrosine

value: Yes


title: V583 Δtdc (test) compared to V583 (reference) Replicate 2

description: Biological replicate 2 of 2. Dye swap


title: Heart, Sham, rep4

description: 12 week old mice, border zone of sham infarct, 2 weeks after surgery

source_name: Heart, Sham


title: T3


title: V583 Δtdc (test) compared to V583 (reference) Replicate 3

description: Technical replicate 1 of 1.


title: Heart, Sham, rep6


title: Heart, Infarcted, rep2


title: Heart, Sham, rep5


title: Meristem_Arbosana_biorep3

city: Zagreb

first: Juan Jose

last: Gonzalez Plaza

address: Mirogojska 8

department: Research Department

country: Croatia

institute: University Hospital for Infectious Diseases "Dr. Fran Mihaljevic"

description: Olive tree meristems from different cultivars with specific canopies or architectural features

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Olea europaea

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

growth_protocol: Adult trees were growing in the field, at IFAPA (Cordoba, Spain)

extract_protocol: RNA was isolated from olive meristems using a previously reported protocol (Bilgin, D.D., DeLucia, E.H. and Clough, S.J. (2009) A robust plant RNA isolation method suitable for Affymetrix GeneChip analysis and quantitative real-time RT-PCR. Nat. Protoc. 4, 333-340.) All samples were treated with DNAse using RNase-free DNAse I (TAKARA BIO INC., Japan), following the instructions provided by the manufacturer. RNA quality was tested by electrophoresis and using NANODROP spectrophotometer (THERMO FISHER SCIENTIFIC, USA), which was also used to quantify the RNA concentration. An aliquot of RNA was tested by PCR to ensure no trace of contaminating genomic DNA was detectable. Genomic DNA, used as a PCR positive control, was extracted using the JET FLEX EXTRACTION KIT (GENOMED, Germany).  Olive cDNA was synthesized using TRANSCRIPTOR FIRST STRAND cDNA SYNTHESIS KIT (ROCHE, Germany) with random hexanucleotides (PROMEGA, USA). After synthesis, cDNAs were diluted 1:5 in molecular grade biology water and were used as template in RT-qPCR. Arabidopsis cDNA synthesis was carried out using SUPERSCRIPTII reverse transcriptase (LIFE TECHNOLOGIES, USA), and the iScript (BIORAD, USA).

treatment_protocol: Harvesting was carried out between 8:00 to 11:00 a.m., at the end of Spring. Samples were immediately frozen in liquid nitrogen, and maintained afterwards at -80 ºC. Samples of the Picual x Arbequina seedlings used to generate pools were harvested individually and 0.2 g of tissue per individual mixed and processed together to obtain RNA to be used for microarray analysis.

tag: cultivar

value: Arbosana

value: Active meristems

tag: feature

value: Arbosana canopy


title: Meristem_Chiquitita_biorep3

value: Chiquitita

value: Chiquitita canopy


title: Heart, Infarcted, rep3


title: Heart, Sham, rep3


title: Meristem_Bsi_biorep3

value: Chiquitita x Arbosana

value: Simple branching pattern


title: Heart, Infarcted, rep1


title: Meristem_Bram_biorep3

value: Complex branching pattern


title: Heart, Infarcted, rep5


title: Meristem_EL_biorep3

value: Picual x Arbequina

value: Long internode length


title: Heart, Sham, rep2


title: Meristem_ChilLike_biorep3

value: Chiquitita like canopy


title: Meristem_EK_biorep1

value: Short internode length


title: Meristem_Pactive_biorep1

value: Picual

value: Picual canopy


title: Meristem_Arbequina_biorep1

value: Arbequina

value: Arbequina canopy


title: Meristem_DG_biorrep2

value: Large trunk diameter


title: Heart, Sham, rep1

value: heart

value: 12 week-old


title: Meristem_Bram_biorep1

value: Active meristems


title: Meristem_Pactive_biorep2


title: Meristem_Arbequina_biorep2


title: Meristem_DG_biorrep1


title: Meristem_Pdormant_biorep2

value: Dormant meristems


title: Meristem_Chiquitita_biorep2

value: Chiquitita

value: Chiquitita canopy


title: Meristem_EL_biorep2


title: Meristem_Pdormant_biorep3


title: Meristem_Arbosana_biorep1

value: Arbosana

value: Arbosana canopy


title: Meristem_DK_biorep3

value: Picual x Arbequina

value: Short internode


title: Meristem_Pactive_biorep3


title: Meristem_ChilLike_biorep1

value: Chiquitita x Arbosana

value: Chiquitita like canopy


title: Meristem_Chiquitita_biorep1


title: Meristem_Arbequina_biorep3


title: Meristem_DK_biorep2

value: Short internode length


title: Meristem_DG_biorrep3


title: Meristem_EK_biorep2


title: Meristem_Arbosana_biorep2


title: Meristem_Bram_biorep2

value: Complex branching pattern


title: Meristem_Bsi_biorep2

value: Simple branching pattern


title: Meristem_EL_biorep1

value: Long internode length


title: Meristem_Pdormant_biorep1

value: Picual

value: Picual canopy


title: Meristem_Bsi_biorep1


title: Meristem_ChilLike_biorep2


title: Meristem_EK_biorep3


title: Meristem_DK_biorep1

value: Small trunk diameter


title: T5

tag: batch


title: H-1-PMNs

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

hyb_protocol: Hybridize 12-Sample Beadchip

scan_protocol: SentrixScanVersion 2.3.0.13  (This information is in the .XML file)

data_processing: The data were analysed using GenomeStudio version 1.1.1 using the average chip normalization method.

source_name: Polymorphonuclear cells from healthy donor

label_protocol: Biotinylated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion

extract_protocol: Tempus Spin Isolation Kit

tag: disease state

value: healthy control

tag: individual

value: Polymorphonuclear cells

value: Male

tag: ethnicity

value: Not Hispanic

tag: race

value: African American


title: H-2-CD8

source_name: CD8 T cells from healthy donor

tag: cell type

value: CD8 T cells

tag: age

value: White


title: AHI-4-NK

source_name: NK cells from AHI patient

value: Acute human immunodeficiency virus (HIV) infection (AHI)

value: NK cells


title: AHI-1-Monos

source_name: Monocytes from AHI patient

value: Monocytes


title: Heart, Infarcted, rep4

value: heart

value: 12 week-old


title: AHI-1-NK


title: AHI-2-B

source_name: B cells from AHI patient

value: B cells


title: AHI-4-CD4

source_name: CD4 T cells from AHI patient

value: CD4 T cells


title: AHI-1-PMNs

source_name: Polymorphonuclear cells from AHI patient


title: H-1-NK

source_name: NK cells from healthy donor


title: AHI-3-PMNs

value: other


title: AHI-4-CD8

source_name: CD8 T cells from AHI patient


title: H-1-CD8


title: H-4-PMNs


title: H-3-Monos

source_name: Monocytes from healthy donor

value: Female


title: AHI-1-B


title: H-2-CD4

source_name: CD4 T cells from healthy donor


title: AHI-2-CD4


title: AHI-1-CD8


title: H-2-PMNs


title: H-3-CD4


title: H-1-CD4


title: H-2-Monos


title: AHI-1-CD4


title: H-4-CD4


title: H-4-Monos


title: H-4-NK


title: AHI-2-Monos


title: H-2-NK


title: H-1-B

source_name: B cells from healthy donor


title: AHI-3-CD8


title: H-1-Monos


title: H-3-B


title: s_JF_thy_036_P

city: Boston

first: Iñigo

last: Landa

state: Massachusetts

address: 77 Avenue Louis Pasteur, 4BF Building, Room 645A

department: Medicine/Endocrinology

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

hyb_protocol: not provided

scan_protocol: not provided

data_processing: gcRMA method

source_name: Poorly-differentiated thyroid tumor

label_protocol: not provided

growth_protocol: Tumor resection

extract_protocol: Standard RNA extraction

value: male

value: Thyroid

value: Primary


title: s_JF_thy_037_P

source_name: Anaplastic thyroid tumor

value: female

value: Recurrent tumor in neck


title: AHI-4-B

value: Male

value: Not Hispanic


title: s_JF_thy_034_P


title: AHI-3-B


title: AHI-2-CD8

value: CD8 T cells

value: White


title: s_JF_thy_026_P


title: s_JF_thy_032_P


title: s_JF_thy_030_P


title: AHI-2-NK

value: Acute human immunodeficiency virus (HIV) infection (AHI)

value: NK cells


title: s_JF_thy_033_P

value: Primary (residual)


title: s_JF_thy_035_P


title: s_JF_thy_027_P


title: AHI-4-Monos

value: Monocytes


title: s_JF_thy_028_P


title: s_JF_thy_031_P


title: s_JF_thy_029_P


title: s_JF_thy_025_P


title: s_JF_thy_023_P


title: s_JF_thy_020_P


title: s_JF_thy_022_P


title: s_JF_thy_021_P


title: s_JF_thy_018_P

value: Recurrent tumor


title: s_JF_thy_019_P


title: s_JF_thy_024_P


title: s_JF_thy_017_P


title: s_JF_thy_016_P


title: Vietnam_Malaria_BH026d7_PFS

city: Liverpool

first: Michael

last: Griffiths

address: 8 West Derby Street

country: United Kingdom

institute: Institute of Infection and Global Health, University of Liverpool

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64782.gif

scan_protocol: Scanner Model: GenePix 4200A

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Stratagene 1 Round Amplification 2.8 ug

extract_protocol: not provided

tag: reference

value: Stratagene Universal Human Ref RNA

tag: time

value: Whole blood


title: s_JF_thy_014_P

tag: gender

tag: tissue

value: Metastasis


title: Vietnam_Malaria_BH417d0_PFU

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64803.gif


title: Vietnam_Malaria_BH073d7_PFS

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64788.gif


title: Vietnam_Malaria_BH417d28_PFU

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64804.gif


title: s_JF_thy_015_P

tag: tumor type


title: Vietnam_Malaria_BH400d28_PFU

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64793.gif


title: Vietnam_Malaria_BH011d7_PFS

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64776.gif


title: s_JF_thy_011_P

value: male


title: s_JF_thy_008_P

value: Thyroid


title: s_JF_thy_012_P

value: Recurrent/persistent metastasic tumor to lymph node


title: s_JF_thy_010_P

value: female


title: s_JF_thy_007_P

value: Primary


title: Vietnam_Malaria_BH041d31_PFS

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64790.gif


title: s_JF_thy_013_P


title: s_JF_thy_009_P


title: Vietnam_Malaria_BH054d7_PFS

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64785.gif


title: Vietnam_Malaria_BH026d0_PFS

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64780.gif


title: Vietnam_Malaria_BH405d6_PFU

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64799.gif


title: Vietnam_Malaria_BH011d0_PFS

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64775.gif


title: Vietnam_Malaria_BH405d0_PFU

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64798.gif


title: s_JF_thy_002_P


title: s_JF_thy_006_P


title: s_JF_thy_003_P


title: s_JF_thy_005_P


title: s_JF_thy_004_P


title: s_JF_thy_001_P


title: Vietnam_Malaria_BR416d0_health

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64817.gif

value: Healthy


title: Vietnam_Malaria_BH024d7_PFS

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64779.gif


title: Vietnam_Malaria_BH073d0_PFS

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64786.gif


title: Vietnam_Malaria_BH428d0_PFU

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64810.gif


title: Vietnam_Malaria_BR418d0_health

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64818.gif


title: Vietnam_Malaria_BH424d31_PFU

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64808.gif


title: Vietnam_Malaria_BH054d0_PFS

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64783.gif


title: antiCD40-IL4_bio-rep-4

city: Montreal

first: Bruce

middle: David

last: Mazer

state: Quebec

address: 1001 boul. Décarie

department: RESP

country: Canada

institute: RI-MUHC

description: Gene expression data from B cells cultured under Th2-skewing conditions

hyb_protocol: Following fragmentation, target cRNA was hybridized for 16 hours at 45°C to Affymetrix Human Genome U133 Plus 2.0 array. Arrays were stained and washed using the GeneChips Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000. Images were processed using GeneChip Operating Software (GCOS) to generate CEL files.

data_processing: Raw data was read using the Bioconductor oligo package. Probe intensities were normalized across all arrays by the robust multi-array average (RMA) algorithm.

source_name: B lymphocytes, treated with antiCD40 and IL4

label_protocol: 50 ng of total RNA were subjected to two rounds of amplification using Affymetrix GeneChip two-cycle target labeling and control reagents according to the manufacturer's protocols

growth_protocol: Tonsillar B cells were cultured for 24 hours in RPMI 1640 10% FBS with 2 mM L-glutamine, 50 U/mL penicillin, 50 µg/mL streptomycin, 1 mM sodium pyruvate and 15mM HEPES

extract_protocol: RNA was extracted with TRIzol reagent (Life Technologies) and cleaned with RNeasy Mini silica-gel membrane columns (Qiagen).

treatment_protocol: Cells were cultured in the presence or absence of 10 µg/mL anti-CD40 antibody (clone G28-5) and 100 U/mL recombinant human IL-4

value: Tonsil

value: B lymphocytes


title: Vietnam_Malaria_BH403d7_PFU

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64797.gif


title: antiCD40-IL4_bio-rep-3


title: Vietnam_Malaria_BH400d7_PFU

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64794.gif


title: Control_bio-rep-3

description: Gene expression data from unstimulated B cells

source_name: B lymphocytes, unstimulated


title: antiCD40-IL4_bio-rep-2


title: Vietnam_Malaria_BH400d0_PFU

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64792.gif


title: Control_bio-rep-4


title: Vietnam_Malaria_BH041d1_PFS

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64789.gif


title: Control_bio-rep-2


title: Vietnam_Malaria_BH041d6_PFS

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64791.gif


title: Vietnam_Malaria_BH024d0_PFS

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64777.gif


title: Control_bio-rep-1


title: Vietnam_Malaria_BH424d1_PFU

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64807.gif


title: Vietnam_Malaria_BR409d0_health

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64816.gif


title: antiCD40-IL4_bio-rep-1


title: Vietnam_Malaria_BH073d31_PFS

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64787.gif


title: Vietnam_Malaria_BH424d7_PFU

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64809.gif


title: Vietnam_Malaria_BH024d35_PFS

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64778.gif


title: Vietnam_Malaria_BH026d30_PFS

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64781.gif


title: PFkhi_59213A

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60158.gif

scan_protocol: Scanner Model: GenePix 4000A

source_name: Stratagene Universal Human Ref RNA, 1st rnd amp AW and SP 11/01/01, 3ug

value: Acute


title: Vietnam_Malaria_BH054d28_PFS

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64784.gif


title: PFkhi_59213C

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60173.gif

value: Convalescent


title: PFkhi_53614A

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60141.gif


title: PFkhi_60116A

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60160.gif


title: Vietnam_Malaria_BH403d0_PFU

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64795.gif


title: PFkhi_55544A

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60146.gif


title: Vietnam_Malaria_BH403d28_PFU

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64796.gif


title: PFkhi_53768C

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60174.gif


title: PFkhi_54476C

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60143.gif


title: Vietnam_Malaria_BH428d7_PFU

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64812.gif


title: Vietnam_Malaria_BH428d28_PFU

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64811.gif


title: 5_cont_rbc_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77908.gif

scan_protocol: GenePix Results 3

source_name: Stratagene Human ref. 1 Round Amplification 7ug(input)_4ug(couple)

source_name: 1 round amplification 15ug(input)_5_cont_rbc_9hrs

value: red blood cells

value: 9 h

tag: infection

value: no

value: NoHxMal


title: 10_cont_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77312.gif

value: Stratagene Universal Human Ref RNA

source_name: 1 round amplification 15ug(input)_10_cont_rbc_5hrs

value: 5 h


title: PFkhi_53768A

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60170.gif

value: Whole blood


title: PFkhi_54124C

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60157.gif


title: PFkhi_58826C

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60132.gif


title: 4_pat_A4_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77905.gif

source_name: 1 round amplification 15ug(input)_4_pat_A4_9hrs

value: yes

value: PrevHxMal


title: 4_pat_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77329.gif

source_name: 1 round amplification 15ug(input)_4_pat_A4_5hrs


title: 11_pat_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77872.gif

source_name: 1 round amplification 15ug(input)_11_pat_rbc_5hrs


title: PFkhi_53641Az

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60189.gif


title: PFkhi_53701A

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60130.gif


title: PFkhi_58988A

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60172.gif


title: 6_pat_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77349.gif

source_name: 1 round amplification 15ug(input)_6_pat_A4_5hrs


title: 6_cont_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77310.gif

source_name: 1 round amplification 15ug(input)_6_cont_rbc_5hrs


title: PFkhi_54234A

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60128.gif


title: PFkhi_58826A

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60096.gif


title: 14_pat_A4_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77880.gif

source_name: 1 round amplification 15ug(input)_14_pat_A4_9hrs


title: PFkhi_55037A

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60260.gif


title: PFkhi_59226A

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60145.gif


title: PFkhi_54476A

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60171.gif


title: 9_cont_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77338.gif

source_name: 1 round amplification 15ug(input)_9_cont_rbc_5hrs


title: PFkhi_53701Cz

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60190.gif


title: PFkhi_59167A

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60144.gif


title: 8_cont_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77348.gif

source_name: 1 round amplification 15ug(input)_8_cont_rbc_5hrs


title: 1_cont_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77351.gif

source_name: 1 round amplification 15ug(input)_1_cont_A4_5hrs


title: PFkhi_54124A

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60142.gif


title: 10_cont_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77311.gif

source_name: 1 round amplification 15ug(input)_10_cont_A4_5hrs


title: 16_cont_rbc_5hrs_wide cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77354.gif

source_name: 1 round amplification 15ug(input)_16_cont_rbc_5hrs


title: 8_pat_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77318.gif

source_name: 1 round amplification 15ug(input)_8_pat_rbc_5hrs


title: 12_cont_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77341.gif

source_name: 1 round amplification 15ug(input)_12_cont_A4_5hrs


title: PFsev_BH60d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60118.gif

source_name: Stratagene Universal Human Ref RNA, 1st rnd amp AW and SP 11/01/01, 3ug


title: PFkhi_59226C

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60159.gif


title: PFsev_BH8d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60151.gif


title: PF_BH417d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60059.gif

scan_protocol: Scanner Model: GenePix 4000B


title: 4_pat_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77330.gif

source_name: Stratagene Human ref. 1 Round Amplification 7ug(input)_4ug(couple)

source_name: 1 round amplification 15ug(input)_4_pat_rbc_5hrs


title: 6_pat_A4_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77911.gif

source_name: 1 round amplification 15ug(input)_6_pat_A4_9hrs


title: PFsev_BH38d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60156.gif


title: PFkhi_53641C

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60098.gif


title: PFsev_BH15d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60178.gif


title: 5_pat_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77343.gif

source_name: 1 round amplification 15ug(input)_5_pat_A4_5hrs


title: 5_pat_A4_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77909.gif

source_name: 1 round amplification 15ug(input)_5_pat_A4_9hrs


title: 13_pat_rbc_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77878.gif

source_name: 1 round amplification 15ug(input)_13_pat_rbc_9hrs


title: PFsev_BH36d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60180.gif


title: PFsev_BH24d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60179.gif


title: 5_cont_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77315.gif

source_name: 1 round amplification 15ug(input)_5_cont_A4_5hrs


title: 5_cont_A4_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77907.gif

source_name: 1 round amplification 15ug(input)_5_cont_A4_9hrs


title: HD_MC3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60087.gif


title: 4_cont_A4_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77903.gif

source_name: 1 round amplification 15ug(input)_4_cont_A4_9hrs


title: 12_cont_A4_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77873.gif

source_name: 1 round amplification 15ug(input)_12_cont_A4_9hrs


title: 15_cont_rbc_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77886.gif

source_name: 1 round amplification 15ug(input)_15_cont_rbc_9hrs


title: PFkhi_54234C

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60100.gif


title: 9_cont_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77337.gif

source_name: 1 round amplification 15ug(input)_9_cont_A4_5hrs


title: PF_BH406d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60055.gif


title: PFsev_BH46d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60120.gif


title: PFsev_BH72d000z

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60202.gif


title: HD_BR443d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60123.gif


title: PFsev_BH57d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60122.gif


title: PFsev_BH26d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60155.gif


title: 16_pat_A4_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77888.gif

source_name: 1 round amplification 15ug(input)_16_pat_A4_9hrs


title: HD_MC1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60229.gif


title: 7_pat_A4_5hrs_narrow cover slip_rpt

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77331.gif

source_name: 1 round amplification 15ug(input)_7_pat_A4_5hrs


title: 3_pat_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77319.gif

source_name: 1 round amplification 15ug(input)_3_pat_A4_5hrs


title: 12_cont_rbc_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77874.gif

source_name: 1 round amplification 15ug(input)_12_cont_rbc_9hrs


title: PF_BH405d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60054.gif

source_name: Stratagene Universal Human Ref RNA, 1st rnd amp AW and SP 11/01/01, 3ug


title: 14_pat_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77334.gif

source_name: Stratagene Human ref. 1 Round Amplification 7ug(input)_4ug(couple)

source_name: 1 round amplification 15ug(input)_14_pat_rbc_5hrs


title: HD_MC2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60068.gif


title: 15_cont_A4_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77885.gif

source_name: 1 round amplification 15ug(input)_15_cont_A4_9hrs


title: 5_pat_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77344.gif

source_name: 1 round amplification 15ug(input)_5_pat_rbc_5hrs


title: PFsev_BH73d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60124.gif


title: PF_BH413d000amp1hyb2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60084.gif


title: PFsev_BH10d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60164.gif


title: HD_MC4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60111.gif


title: PF_BH421d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60085.gif


title: 6_pat_rbc_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77912.gif

source_name: 1 round amplification 15ug(input)_6_pat_rbc_9hrs


title: 13_pat_A4_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77876.gif

source_name: 1 round amplification 15ug(input)_13_pat_A4_9hrs


title: PF_BH415d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60105.gif


title: PF_BH422d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60107.gif


title: 6_cont_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77309.gif

source_name: 1 round amplification 15ug(input)_6_cont_A4_5hrs


title: 5_cont_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77316.gif

source_name: 1 round amplification 15ug(input)_5_cont_rbc_5hrs


title: 17_cont_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77325.gif

source_name: 1 round amplification 15ug(input)_17_cont_A4_5hrs


title: HD_BR410d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60073.gif


title: 16_pat_rbc_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77890.gif

source_name: 1 round amplification 15ug(input)_16_pat_rbc_9hrs


title: 17_cont_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77326.gif

source_name: 1 round amplification 15ug(input)_17_cont_rbc_5hrs


title: PFsev_BH13d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60177.gif


title: PFsev_BH9d000z

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60187.gif


title: 11_pat_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77871.gif

source_name: 1 round amplification 15ug(input)_11_pat_A4_5hrs


title: 14_pat_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77333.gif

source_name: 1 round amplification 15ug(input)_14_pat_A4_5hrs


title: 6_pat_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77350.gif

source_name: 1 round amplification 15ug(input)_6_pat_rbc_5hrs


title: PFsev_BH25d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60262.gif


title: 2_cont_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77346.gif

source_name: 1 round amplification 15ug(input)_2_cont_rbc_5hrs


title: PFsev_BH41d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60181.gif


title: PFsev_BH14d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60165.gif


title: HD_BR413d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60075.gif


title: PFsev_BH54d000z

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60201.gif


title: PF_BH428d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60086.gif


title: PFsev_BH42d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60166.gif


title: 17_cont_rbc_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77893.gif

source_name: 1 round amplification 15ug(input)_17_cont_rbc_9hrs


title: 12_cont_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77342.gif

source_name: 1 round amplification 15ug(input)_12_cont_A4_5hrs


title: 2_cont_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77345.gif

source_name: Stratagene Human ref. 1 Round Amplification 7ug(input)_4ug(couple)

source_name: 1 round amplification 15ug(input)_2_cont_A4_5hrs


title: PF_BH412d000amp1hyb2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60057.gif

source_name: Stratagene Universal Human Ref RNA, 1st rnd amp AW and SP 11/01/01, 3ug


title: 4_cont_rbc_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77904.gif

source_name: 1 round amplification 15ug(input)_4_cont_rbc_9hrs


title: 3_pat_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77320.gif

source_name: 1 round amplification 15ug(input)_3_pat_rbc_5hrs


title: 15_cont_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77336.gif

source_name: 1 round amplification 15ug(input)_15_cont_rbc_5hrs


title: HD_BR411d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60121.gif


title: PFsev_BH11d000

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60152.gif


title: 12_pat_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77313.gif

source_name: 1 round amplification 15ug(input)_12_pat_A4_5hrs


title: 11_cont_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77339.gif

source_name: 1 round amplification 15ug(input)_11_cont_A4_5hrs


title: 5_pat_rbc_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77910.gif

source_name: 1 round amplification 15ug(input)_5_pat_rbc_9hrs


title: 1_cont_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77352.gif

source_name: 1 round amplification 15ug(input)_1_cont_rbc_5hrs


title: 3_cont_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77902.gif

source_name: 1 round amplification 15ug(input)_3_cont_rbc_5hrs


title: 15_cont_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77335.gif

source_name: 1 round amplification 15ug(input)_15_cont_A4_5hrs


title: 3_cont_A4_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77901.gif

source_name: 1 round amplification 15ug(input)_3_cont_A4_5hrs


title: 14_pat_rbc_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77883.gif

source_name: 1 round amplification 15ug(input)_14_pat_rbc_9hrs


title: 7_cont_rbc_5hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77914.gif

source_name: 1 round amplification 15ug(input)_7_cont_rbc_5hrs


title: 17_cont_A4_9hrs_narrow cover slip

description:
Simple  annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77891.gif

source_name: 1 round amplification 15ug(input)_17_cont_A4_9hrs