title: TMV*rep vs. TMV*CP.MP_6 hr_Replicate 2

city: Taipei

first: Cheng-En

last: Chen

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

country: Taiwan

institute: National Taiwan University

description: Biological replicate 2 of 2. Analysis used TMV*rep transfected cells as control samples for comparison to the TMV*CP.MP transfected samples taken at 6 hour.

hyb_protocol: For preparation of hybridization solution, 44.28 μl probes were mixed with 6.23 μl yeast tRNA (2 μg/μl), 12.60 μl 20X SSC and 11.90 μl 2% SDS. Hybridized slides were incubated in a 65°C water bath. Let hybridize for 16 hrs. Detail methods were described in http://ipmb.sinica.edu.tw/microarray/protocol.htm.

scan_protocol: The hybridization signals were acquired with the use of Axon GenePix 4000B and analyzed by use of GenePix 4.0 (Axon Instruments, Foster City, CA, USA).

data_processing: The software GeneSpring GX 11.2 (Agilent Technologies, Santa Clara, California, USA) were used. Using the LOWESS algorithm to remove intensity dependent effects within the calculated values. Normalised values were used to calculate the Cy3/Cy5 fluorescence ratios.

organism: Arabidopsis thaliana

source_name: TMV*rep inoculated protoplasts at 6 hpi

label_protocol: The protocol used for preparation of Cy3 and Cy5 labelled cDNA is originally developed by Michael B. Eisen and Patrick O. Brown. 1999. DNA Arrays for Analysis of Gene Expression. In Methods in Enzymology (Weissman SM, ed.) 303: pp179-205. Academic Press, San Diego, CA. with some modification. Detail methods were described in http://ipmb.sinica.edu.tw/microarray/protocol.htm.

growth_protocol: Wild-type A. thaliana ecotype Col-0 were grown at 22C under long-day conditions (16-hr light/8-hr dark, 100-150 µE).

extract_protocol: Total RNA extracted using the Pine Tree Method (Chang et al., 1993. Plant Mol. Biol. Rep. 11:113-116.) as previously described.

treatment_protocol: Protoplasts were isolated from 6- to 7-week-old A. thaliana expanded leaves. In vitro transcription prepared RNA of TMV*rep and TMV*CP.MP were used to inoculated protoplasts.

tag: ecotype

value: protoplasts

source_name: TMV*CP.MP inoculated protoplasts at 6 hpi


title: TMV*rep vs. TMV*CP.MP_6 hr_Replicate 1

status: Public on Apr 15 2013

type: RNA

description: Biological replicate 1 of 2. Analysis used TMV*rep transfected cells as control samples for comparison to the TMV*CP.MP transfected samples taken at 6 hour.

molecule: total RNA

tag: cell type


title: Osteosarcoma 44 (RNA)

city: Amsterdam

first: Joeri

last: Both

state: Noord Holland

address: Meibergdreef 9

department: Genome Analysis

country: Netherlands

institute: Amsterdam Medical Center

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio

label: biotin

organism: Homo sapiens

source_name: resection

label_protocol: The Illumina TotalPrep RNA amplification Kit (Ambion, art. No. AM-IL1791) was used to synthesize biotine labeled

growth_protocol: The pHobs sample was grown under recommended culture conditions in basis osteoblast growth medium with growth supplement

extract_protocol: The RNA was isolated using a standard Trizol method after which an automated version of the Qiagen Rneasy mini kit was used to further clean the RNA. Only samples with RIN score of 7 or higher were used (assayed on BioAnalyzer)

tag: location

value: humerus

tag: type of material

value: resection

tag: tissue

value: osteosarcoma tumor


title: ADC17

city: Seville

first: Sonia

last: Molina-Pinelo

address: Avda. MAnuel Siurot s/n

country: Spain

institute: IBIS

description: test

data_processing: Relative quantification of gene expression was determined using the comparative cycle threshold method (2(-ddCt)) as previously described Ref : Livak, K. J., and T. D. Schmittgen. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25:402-408. .

label: FAM

source_name: Tumoral tissue

label_protocol: FAM

extract_protocol: Total RNA, containing small RNA, was extracted from tumour tissue sample by mirVana miRNA isolation kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions.

value: NSCLC

tag: histologic subtype in nsclc

value: Lung adenocarcinoma


title: ADC20

description: test


title: ADC18

description: test


title: ADC19

description: test


title: ADC15

description: test


title: Osteosarcoma 45 (RNA)

scan_protocol: Standard Illumina hybridization protocol

value: tibia


title: TMV*rep vs. TMV*CP.MP_4 hr_Replicate 1

description: Biological replicate 1 of 2. Analysis used TMV*rep transfected cells as control samples for comparison to the TMV*CP.MP transfected samples taken at 4 hour.

source_name: TMV*rep inoculated protoplasts at 4 hpi

source_name: TMV*CP.MP inoculated protoplasts at 4 hpi


title: ADC16

description: test


title: TMV*rep vs. TMV*CP.MP_0.5 hr_Replicate 2

description: Biological replicate 2 of 2. Analysis used TMV*rep transfected cells as control samples for comparison to the TMV*CP.MP transfected samples taken at 0.5 hour.

source_name: TMV*rep inoculated protoplasts at 0.5 hpi

source_name: TMV*CP.MP inoculated protoplasts at 0.5 hpi


title: osteosarcoma 8 (SNP)

type: genomic

description: Genomic DNA extracted from osteosarcomas was genotyped using HumanCNV370-Quad BeadChips (Illumina).

hyb_protocol: Standard hyb protocol (Illumina)

scan_protocol: Standard scan protocol (Illumina)

data_processing: standard Illumina protocol

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: osteosarcoma

label_protocol: Standard label protocol (Illumina), 200 ng of genomic DNA as start material

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and high salt precipitation, washed with EtOH, air dried, resuspended in TE.

tag: gender

value: Male

value: femur


title: ADC14

description: test


title: Osteosarcoma 46 (RNA)

source_name: biopsy

value: ilium

value: biopsy


title: TMV*rep vs. TMV*CP.MP_0.5 hr_Replicate 1

description: Biological replicate 1 of 2. Analysis used TMV*rep transfected cells as control samples for comparison to the TMV*CP.MP transfected samples taken at 0.5 hour.


title: Osteosarcoma 42 (RNA)


title: Osteosarcoma 41 (RNA)

value: mandibula


title: Osteosarcoma 43 (RNA)

value: ulna


title: Osteosarcoma 39 (RNA)


title: osteosarcoma 3 (SNP)

value: Female

value: metastasis

value: lung

value: metastatic lung osteosarcoma tumor


title: ADC13

description: test


title: TMV*rep vs. TMV*CP.MP_4 hr_Replicate 2

description: Biological replicate 2 of 2. Analysis used TMV*rep transfected cells as control samples for comparison to the TMV*CP.MP transfected samples taken at 4 hour.

value: protoplasts


title: Osteosarcoma 35 (RNA)


title: Osteosarcoma 40 (RNA)


title: osteosarcoma 6 (SNP)


title: ADC12

description: test


title: Osteosarcoma 36 (RNA)

value: humerus


title: Osteosarcoma 37 (RNA)


title: ADC11

description: test


title: ADC10

description: test


title: Osteosarcoma 19 (RNA)


title: Osteosarcoma 17 (RNA)

value: resection


title: Osteosarcoma 16 (RNA)

value: osteosarcoma tumor


title: ADC9

description: test

value: NSCLC


title: Osteosarcoma 13 (RNA)


title: ADC8

description: test

value: Lung adenocarcinoma


title: Osteosarcoma 15 (RNA)


title: Osteosarcoma 18 (RNA)

value: tibia


title: Osteosarcoma 20 (RNA)


title: ADC7

description: test


title: ADC5

description: test


title: ADC6

description: test


title: Osteosarcoma 14 (RNA)


title: Osteosarcoma 11 (RNA)


title: ADC4

description: test


title: Osteosarcoma 38 (RNA)


title: osteosarcoma 4 (SNP)

value: Male


title: Osteosarcoma 7 (RNA)

value: femur


title: ADC1

description: test


title: Osteosarcoma 9 (RNA)

source_name: metastasis


title: primary fetal human osteoblasts (RNA)

source_name: cultured cells

value: cultured cells

value: primary fetal human osteoblasts


title: Osteosarcoma 28 (RNA)

value: ilium

value: biopsy


title: Osteosarcoma 34 (RNA)


title: Osteosarcoma 12 (RNA)


title: Osteosarcoma 3 (RNA)


title: Osteosarcoma 33 (RNA)


title: Osteosarcoma 6 (RNA)


title: Osteosarcoma 4 (RNA)


title: ADC2

description: test


title: osteosarcoma 2 (SNP)


title: ADC3

description: test


title: Peripheral Serum_Post Surgery_vcb 0033-2 [dataset 2]

city: Vancouver

first: Sara

last: MacLellan

state: British Columbia

address: 675 West 10 Ave

country: Canada

institute: BC Cancer Research Centre

description:
Test
miRNA profiling

data_processing:
Cp values and ROX reference dye normalization were calculated using Viia7 Software (Applied Biosystems). All assays were inspected for distinct melting curves and those assays with more than one Tm and those detected within five Cp’s of the negative control (Cp >35) were excluded from analysis.
The qRT-PCR results were exported to GenEx (MultiD Analyses AB) and normalized using inter-plate calibrators located on the miRNA Ready-to-Use panels.
We used the mean expression value of all expressed miRNAs in a given sample as a normalization factor (global mean method). Normalized value (∆Cp) = Global mean-assay Cp.
The miRNAs that gave no signal (null in matrix non-normalized) in any samples were removed before normalization.
Fold Change worksheet reports  (2^(pre-surgery∆Cp - post-surgery∆Cp)). Linked as supplementary file on Series record.

label: SYBR Green

source_name: Peripheral Serum

label_protocol: A fixed volume of eluted RNA (19.2 μL for 768 reactions) was used for miRNA expression assays. Total RNA was reverse transcribed using the miRCURY LNA Universal RT miRNA PCR, Polyadenylation and cDNA synthesis kit (Exiqon Inc.). The cDNA was then quantified by quantitative real-time PCR (qRT-PCR) on the miRNA Ready-to-Use PCR, Human panel I and panel II with the miRCURY LNA Universal RT miRNA PCR, SYBR Green master mix according to the manufacturer’s protocol (Exiqon Inc.).

extract_protocol: Total RNA was extracted from 200 μL of serum using miRNeasy Mini Kit (Qiagen) according to manufacturer instructions, except that 1.25 μL of MS2 carrier RNA (Roche Applied Science) per 200 μL of serum was added to the QIAzol Lysis Reagent prior to RNA purification.

value: Peripheral Serum

value: non-cellular fraction

tag: activation agent

tag: disease state

value: HRL

tag: disease status

value: Post surgery (Squamous cell carcinoma)

tag: time

value: 6 months post-surgery


title: Peripheral Serum_Post Surgery_vcb-7036-2 [dataset 2]

description:
Test
miRNA profiling
'vcb 7036 and scc 7036' are the same sample, and vcb-7036-2 (same as 7036-2) is the post-surgery sample for that pair.


title: Peripheral Serum_Post Surgery_7035-0035-2 [dataset 2]

description:
Test
miRNA profiling


title: Osteosarcoma 5 (RNA)


title: H1650  ID-1 Si EGF

city: Tampa

first: Jonathan

last: Nguyen

state: FL

department: Tumor Biology

country: USA

institute: Moffitt Cancer Centre & Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to the Affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scaner.

data_processing: The data were analyzed with the Affymetrix GCOS 1.4 software using the MAS 5.0 alorighthm with default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.  Additonal analysis was performed by by log2 transformation of the expression values, and the mean center expression level for each gene was determined

source_name: H1650  ID-1 Si EGF

label_protocol: Biotinylated cRNA were prepared according to the Ambion Message Amp Premier protocl using 100 ng of total RNA (Ambion).

growth_protocol: Human NSCLC cell lines A549 (k-Ras mutanat) and H1650 (EGFR mutant) were used in this study. These cell lines were maintained in Ham’s F-12K(Cellgro) and RPMI-1640 (Mediatech Cellgro) supplemented with 10% FBS (Cellgro). Nicotine and EGF used in the studies were 1µM and 100 ng/ml for 18-24 hrs, depending on the experiment. The cells were grown to 70 % confluency in complete medium with serum for 24 hours and rendered quiescent by serum starvation for 48 hours and stimulated with nicotine and EGF for 18 hrs irrespective of each cell lines. RNA was prepared from the treated samples with Qiagen RNeasy Kit and then sent for microarray analysis. The RNA samples were subjected to heat inactivation to check the purity and validated the same on 1%  agarose gel by electrophoresis. Total RNA extracted  were used to generate cRNA targets, which were subsequently hybridized to Human Genome U133A plus 2.0 oligonucleotide probe arrays (Affymetrix, Santa Clara, CA) according to standard protocols. Raw data was processed by log2 transformation of the expression values. Genes with significant expression levels above 2 fold downregulated or upregulated were chosen for further study.

extract_protocol: Isolation of total RNA was performed using the Qiagen RNEasy column according to the manufacturer's instructions.

tag: treatment

value: EGF

tag: cell line

tag: knockdown


title: H1650 Control Si Nicotine

source_name: H1650 Control Si Nicotine

value: nicotine

value: control


title: Osteosarcoma 10 (RNA)

value: resection

value: osteosarcoma tumor


title: Osteosarcoma 1 (RNA)

value: lung

value: metastasis

value: metastatic lung osteosarcoma tumor


title: A549 Control Si

source_name: A549 Control Si


title: A549 ID-1 Si EGF

source_name: A549 ID-1 Si EGF


title: Osteosarcoma 2 (RNA)

value: femur


title: Peripheral Serum_Post Surgery_7054-0054-2 [dataset 2]

description:
Test
miRNA profiling


title: Peripheral Serum_Post Surgery_7044-2 [dataset 2]

description:
Test
miRNA profiling


title: A549 Control Si Nicotine

source_name: A549 Control Si Nicotine


title: A549 Control Si EGF

source_name: A549 Control Si EGF


title: osteosarcoma 1 (SNP)

value: Female


title: Osteosarcoma 8 (RNA)

source_name: resection


title: H1650  ID-1 Si Nicotine

source_name: H1650  ID-1 Si Nicotine


title: Peripheral Serum_Post Surgery_4211-0060-2 [dataset 2]

description:
Test
miRNA profiling


title: Peripheral Serum_Post Surgery_3182-0023-2 [dataset 2]

description:
Test
miRNA profiling


title: Peripheral Serum_Post Surgery_7026-2 [dataset 2]

description:
Test
miRNA profiling


title: Peripheral Serum_Post Surgery_2014-2 [dataset 2]

description:
Test
miRNA profiling


title: Peripheral Serum_Post Surgery_1727-2 [dataset 2]

description:
Test
miRNA profiling


title: Peripheral Serum_Pre Surgery_vcb 0033 [dataset 2]

description:
Test
miRNA profiling
'VBC-0033 and cis 0033' are the same sample.

value: carcinoma in situ

value: Pre-surgery


title: Peripheral Serum_Pre Surgery_vbc 0036_scc 7036 [dataset 2]

value: Peripheral Serum

value: Squamous cell carcinoma


title: H1650 Control Si EGF

source_name: H1650 Control Si EGF


title: Peripheral Serum_Pre Surgery_7026-0026 [dataset 2]

description:
Test
miRNA profiling
'7026-0026 and scc 7026-0026' are the same sample.

value: non-cellular fraction

value: HRL


title: Peripheral Serum_Pre Surgery_7035-0035 [dataset 2]

description:
Test
miRNA profiling
'7035-0035 and cis 7035-0035' are the same sample.


title: Peripheral Serum_Pre Surgery_7044 [dataset 2]

description:
Test
miRNA profiling
'7044 and cis 7044' are the same sample.


title: Peripheral Serum_Pre Surgery_7054-0054 [dataset 2]

description:
Test
miRNA profiling
'7054-0054 and cis 7054-0054' are the same sample.


title: H1650 Control Si

source_name: H1650 Control Si


title: Peripheral Serum_Pre Surgery_1727 [dataset 2]

description:
Test
miRNA profiling
'1727 and cis 1727' are the same sample.


title: Peripheral Serum_Pre Surgery_4211-0060 [dataset 2]

description:
Test
miRNA profiling
'4211-0060 and cis 4211-0060' are the same sample.


title: Peripheral Serum_Pre Surgery_3182-0023 [dataset 2]

description:
Test
miRNA profiling
'3182-0023 and scc 3182-0023' are the same sample.


title: lung_YP_4hr_rep2

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Gene expression profiling after 4hrs YP

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: YP 4hr

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from harvested lungs using Trizol/phenol chloroform extraction followed by precipitation.  RNA quality assessed using Agilent Bioanalyzer.

treatment_protocol: Balb/c mice exposed via intranasal inoculation of F. tularensis SchuS4, F. tularensis LVS, Y. pestis, avirulent Y. pestis, L. pneumophila, or P. aeruginosa  for 4, 24 or 48hrs.

tag: strain

value: Balb/c

value: Lung

tag: infection

value: Y. pestis

tag: time point


title: A549 ID-1 Si Nicotine

source_name: A549 ID-1 Si Nicotine

value: nicotine


title: lung_YP_4hr_rep1

description: Gene expression profiling after 4hrs YP


title: lung_aYP_4hr_rep2

description: Gene expression profiling after 4hrs aYP

source_name: aYP 4hr

value: Y. pestis avirulent


title: Peripheral Serum_Pre Surgery_2014 [dataset 2]

description:
Test
miRNA profiling
'2014 and cis 2014' are the same sample.


title: lung_YP_4hr_rep3

description: Gene expression profiling after 4hrs YP


title: lung_aYP_4hr_rep1


title: lung_aYP_4hr_rep3


title: lung_Mock_4hr_rep1

description: Gene expression profiling after 4hrs Mock

source_name: Mock 4hr

value: Mock


title: Peripheral Serum_Pre-Surgery_scc 7075-0075 [dataset 1]

description:
Test
miRNA profiling


title: Peripheral Serum_Pre-Surgery_scc 7080-0080 [dataset 1]

description:
Test
miRNA profiling


title: lung_Mock_4hr_rep3


title: Peripheral Serum_Pre-Surgery_scc 7064-0064 [dataset 1]

description:
Test
miRNA profiling


title: Peripheral Serum_Pre-Surgery_cis 7073 [dataset 1]

description:
Test
miRNA profiling


title: Gastrulation +24h-D, replicate 3

city: Talence

first: angela

last: tingaud-sequeira

address: avenue des Facultés

country: France

institute: Université Bordeaux 1

hyb_protocol: Sample hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Scanning performed by Max Planck Institute in Berlin

data_processing: The raw fluorescence intensity data were processed and normalised using quantile normalisation.  Differential expression between timepoints and groups was assessed by using linear models and empirical Bayes unpaired moderated t-statistics.  Fold changes (FCs) and their corresponding moderated bayes p-values were obtained for he studied pairwise comparisons.  Determinations of false discovery rates (FDR computation using Benjamini-Hochberg procedure) were performed.  All computations were done using Limma R-package (Smyth 2005).  The significance level was set at 0.01.

organism: Fundulus heteroclitus

source_name: Gastrulation +24h-D

label_protocol: Sample labeling with Cy3-dCTP was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol

growth_protocol: At 3 hpf (50% epiboly), pools of embryo were incubated in air or in water.

extract_protocol: total RNA was extracted by using Qiagen RNasy Minikit

value: embryo

tag: incubation

value: air

tag: developmental stage

value: 29 hpf


title: Peripheral Serum_Pre-Surgery_ scc 7074 [dataset 1]

description:
Test
miRNA profiling

tag: cell type


title: Peripheral Serum_Pre-Surgery_scc 7071-0071 [dataset 1]

description:
Test
miRNA profiling


title: Peripheral Serum_Pre-Surgery_scc 7067-0067 [dataset 1]

description:
Test
miRNA profiling


title: lung_Mock_4hr_rep2


title: Gastrulation +24h-D, replicate 1


title: Peripheral Serum_Pre-Surgery_cis 7068-0068 [dataset 1]

description:
Test
miRNA profiling


title: Gastrulation +24h-D, replicate 2


title: Gastrulation +24h-C, replicate 3

source_name: Gastrulation +24h-C

value: water


title: Peripheral Serum_Pre-Surgery_cis 7061-0061 [dataset 1]

description:
Test
miRNA profiling

source_name: Peripheral Serum


title: Peripheral Serum_Pre-Surgery_scc 7057-0057 [dataset 1]

description:
Test
miRNA profiling


title: Peripheral Serum_Pre-Surgery_scc 7059-0059 [dataset 1]

description:
Test
miRNA profiling


title: Gastrulation +24h-C, replicate 1


title: Gastrulation +12h-D, replicate 3

source_name: Gastrulation +12h-D

value: 17 hpf


title: lung_FT SchuS4_4hr_rep3

description: Gene expression profiling after 4hrs FT SchuS4

source_name: FT Schu4 4hr

value: F. tularensis SchuS4


title: Peripheral Serum_Pre-Surgery_cis 7054-0054 [dataset 1]

value: carcinoma in situ

value: Pre-surgery


title: Gastrulation +24h-C, replicate 2


title: lung_FT SchuS4_4hr_rep2


title: Peripheral Serum_Pre-Surgery_cis 7055-0055 [dataset 1]

description:
Test
miRNA profiling

value: Peripheral Serum


title: Peripheral Serum_Pre-Surgery_scc 7051-0051 [dataset 1]

description:
Test
miRNA profiling

value: non-cellular fraction

value: Squamous cell carcinoma


title: Peripheral Serum_Pre-Surgery_ cis 7044 [dataset 1]

value: HRL


title: Gastrulation +12h-D, replicate 2


title: lung_FT SchuS4_4hr_rep1

value: Balb/c

value: Lung


title: Peripheral Serum_Pre-Surgery_scc 7047 [dataset 1]

description:
Test
miRNA profiling


title: Peripheral Serum_Pre-Surgery_cis 7035-0035 [dataset 1]


title: Gastrulation +12h-D, replicate 1


title: Peripheral Serum_Pre-Surgery_scc 7036 [dataset 1]

description:
Test
miRNA profiling
vcb 7036 and scc 7036' are the same sample, and vcb-7036-2 is the post-surgery sample for that pair.


title: Peripheral Serum_Pre-Surgery_cis 0033 [dataset 1]


title: Peripheral Serum_Pre-Surgery_scc 7026-0026 [dataset 1]


title: lung_FT LVS_4hr_rep3

description: Gene expression profiling after 4hrs FT LVS

source_name: FT LVS 4hr

value: F. tularenesis LVS


title: Gastrulation +12h-C, replicate 3

source_name: Gastrulation +12h-C


title: lung_FT LVS_4hr_rep2


title: lung_FT LVS_4hr_rep1


title: Peripheral Serum_Pre-Surgery_cis 7020-0020 [dataset 1]

description:
Test
miRNA profiling


title: Gastrulation +12h-C, replicate 2


title: lung_LP_4hr_rep3

description: Gene expression profiling after 4hrs LP

source_name: LP 4hr

value: L. pneumophila


title: Peripheral Serum_Pre-Surgery_scc 7005-0005 [dataset 1]

description:
Test
miRNA profiling


title: Gastrulation +12h-C, replicate 1


title: Peripheral Serum_Pre-Surgery_cis 4211-0060 [dataset 1]


title: Gastrulation +6h-D, replicate 3

source_name: Gastrulation +6h-D

value: 11 hpf


title: Peripheral Serum_Pre-Surgery_scc 3182-0023 [dataset 1]


title: lung_LP_4hr_rep2

description: Gene expression profiling after 4hrs LP


title: lung_LP_4hr_rep1

description: Gene expression profiling after 4hrs LP


title: lung_PA_4hr_rep3

description: Gene expression profiling after 4hrs PA

source_name: BA PA 4hr

value: P. aeruginosa


title: Peripheral Serum_Pre-Surgery_cis 2014 [dataset 1]


title: Peripheral Serum_Pre-Surgery_cis 3178-0010 [dataset 1]

description:
Test
miRNA profiling


title: Gastrulation +6h-D, replicate 2

value: embryo

value: air


title: Gastrulation +6h-D, replicate 1


title: Peripheral Serum_Pre-Surgery_scc 1442-0024 [dataset 1]

description:
Test
miRNA profiling


title: Peripheral Serum_Pre-Surgery_scc 1252-0027 [dataset 1]

description:
Test
miRNA profiling


title: Gastrulation +6h-C, replicate 2

source_name: Gastrulation +6h-C

value: water


title: lung_PA_4hr_rep1

description: Gene expression profiling after 4hrs PA


title: lung_PA_4hr_rep2

description: Gene expression profiling after 4hrs PA


title: Gastrulation +3h-D, replicate 3

source_name: Gastrulation +3h-D

value: 8 hpf


title: lung_YP_48hr_rep3

description: Gene expression profiling after 48hrs YP

source_name: YP 48hr

value: Y. pestis


title: Gastrulation +6h-C, replicate 3


title: Gastrulation +6h-C, replicate 1


title: Peripheral Serum_Pre-Surgery_cis 78 [dataset 1]

description:
Test
miRNA profiling

value: carcinoma in situ


title: Peripheral Serum_ctrl 163 [dataset 1]

description:
Control
miRNA profiling

value: normal control

value: non-cancer

value: Control


title: Peripheral Serum_Pre-Surgery_cis 1727 [dataset 1]

value: Peripheral Serum

value: non-cellular fraction

value: Pre-surgery


title: lung_aYP_48hr_rep3

description: Gene expression profiling after 48hrs aYP

source_name: aYP 48hr

value: Balb/c

value: Lung

value: Y. pestis avirulent


title: Peripheral Serum_ctrl152 [dataset 1]

description:
Control
miRNA profiling


title: lung_YP_48hr_rep2


title: lung_aYP_48hr_rep2


title: lung_Mock_48hr_rep3

description: Gene expression profiling after 48hrs Mock

source_name: Mock 48hr

value: Mock


title: lung_YP_48hr_rep1


title: Gastrulation +3h-D, replicate 2


title: lung_Mock_48hr_rep2


title: Gastrulation +3h-C, replicate 2

source_name: Gastrulation +3h-C


title: Cells transfected with p-27-5p mimic, rep2

first: Hsueh-Fen

last: Juan

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

department: institute of molecular and cellular biology

institute: National Taiwan university

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G.

data_processing:
Samples were analyzed using the Partek Genomics suite. RMA expression values were quantile normalized.

Core exons were included in the analysis.
Genome build: hg18
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: T-47D breast cancer cell line, p-27-5p mimic

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: The T-47D cell line was cultured in DMEM with 10% FBS.

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

treatment_protocol: For transfection assays, cells were plated in antibiotic-free media and transfected with TurboFect (Fermantas, California, USA) according to the manufacturer's instructions. p-27-5p mimic was transfected at a 200nM concentration.

value: breast cancer cells

value: miRNA p-27-5p mimic


title: Cells transfected with pre-miR negative control, rep2

source_name: T-47D breast cancer cell line, control

value: pre-miR negative control


title: Cells transfected with pre-miR negative control, rep1


title: Cells transfected with p-27-5p mimic, rep1


title: Peripheral Serum_ctrl 0192 [dataset 1]

description:
Control
miRNA profiling


title: Peripheral Serum_ctrl 0169 [dataset 1]

description:
Control
miRNA profiling


title: Peripheral Serum_ctrl 0060 [dataset 1]

description:
Control
miRNA profiling


title: Peripheral Serum_ctrl 4947 [dataset 1]

description:
Control
miRNA profiling


title: Peripheral Serum_ctrl 0077 [dataset 1]

description:
Control
miRNA profiling


title: Gastrulation +1h-D, replicate 3

source_name: Gastrulation +1h-D

value: embryo

value: air

value: 6 hpf


title: Gastrulation +3h-C, replicate 3

value: water

value: 8 hpf


title: Gastrulation +3h-D, replicate 1


title: Gastrulation +1h-D, replicate 2


title: Peripheral Serum_ctrl 4927 [dataset 1]

description:
Control
miRNA profiling

source_name: Peripheral Serum

value: normal control

value: non-cancer


title: HDR vs. LDR 3

city: Oslo

first: Nina

middle: Frederike Jeppesen

last: Edin

address: Sem Sælandsvei 24

department: Physics

country: Norway

institute: University of Oslo

description:
Biological replicate 3 of 3.
ch1: T-47D cells irradiated at high-dose rate, harvested after 24 h.
ch2: T-47D cells irradiated at low-dose rate, harvested after 2 months.

hyb_protocol: Two-color Microarray-Based Gene Expression Analysis using a 44K Human Whole Genome Oligo Microarray Kit from Agilent Technologies.

scan_protocol: Agilent Feature Extraction Software (version 9.1.3.1) was used to quantify images scanned on Agilent Technologies Scanner G2505B US22502537.

data_processing: All analysis was performed using the Bioconductor package LIMMA, including global loess normalization. Differentially expressed genes between LDR and T-47D (with HDR as reference) were identified using a linear model with a modified t-test between the two groups. The p-values were corrected for multiple testing using Benjamini and Hochberg FDR. The same procedure was used when comparing LDR to HDR (where T-47D was used as reference).

source_name: T-47D breast cancer cells, HDR irradiated

label_protocol: Two-color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) using a 44K Human Whole Genome Oligo Microarray Kit from Agilent Technologies.

growth_protocol: T-47D cells were grown with 2 weekly reseedings.

extract_protocol: Total RNA was purified from cell pellets using the Qiagen RNeasy Mini Kit (Qiagen 74104, Germany).

treatment_protocol: T-47D cells were irradiated with 0.3 Gy at either 0.3 Gy/h or 35 Gy/h, and then cultured for 2 months or 24h, respectively. The cells were scraped into RNAlater.

value: Irradiated with 0.3 Gy at 35 Gy/h 24 h before harvest

source_name: T-47D breast cancer cells, LDR irradiated

tag: cell treatment

value: Irradiated 1h at 0.3 Gy/h, then cultured for 2 months


title: HDR vs. LDR 2

description:
Biological replicate 2 of 3.
ch1: T-47D cells irradiated at high-dose rate, harvested after 24 h.
ch2: T-47D cells irradiated at low-dose rate, harvested after 2 months.


title: Gastrulation +3h-C, replicate 1

tag: tissue


title: lung_FT SchuS4_48hr_rep3

description: Gene expression profiling after 48hrs FT SchuS4

source_name: FT Schu4 48hr

value: F. tularensis SchuS4


title: lung_Mock_48hr_rep1

value: Balb/c


title: HDR vs. Control 2

description:
Biological replicate 2 of 4.
ch1: T-47D cells irradiated at high-dose rate, harvested after 24 h.
ch2: Control T-47D cells, untreated, harvested after several passages.

source_name: T-47D breast cancer cells, unirradiated control


title: HDR vs. Control 4

description:
Biological replicate 4 of 4.
ch1: T-47D cells irradiated at high-dose rate, harvested after 24 h.
ch2: Control T-47D cells, untreated, harvested after several passages.


title: Peripheral Serum_ctrl 4549 [dataset 1]

description:
Control
miRNA profiling

value: Peripheral Serum

value: non-cellular fraction

value: Control


title: HDR vs. LDR 1

description:
Biological replicate 1 of 3.
ch1: T-47D cells irradiated at high-dose rate, harvested after 24 h.
ch2: T-47D cells irradiated at low-dose rate, harvested after 2 months.

value: breast cancer cells


title: lung_LP_48hr_rep1

description: Gene expression profiling after 48hrs LP

source_name: LP 48hr

value: Lung

value: L. pneumophila


title: HDR vs. Control 3

description:
Biological replicate 3 of 4.
ch1: T-47D cells irradiated at high-dose rate, harvested after 24 h.
ch2: Control T-47D cells, untreated, harvested after several passages.


title: Gastrulation +1h-C, replicate 2

source_name: Gastrulation +1h-C

value: embryo


title: Gastrulation +1h-D, replicate 1

value: air


title: lung_FT SchuS4_48hr_rep1


title: LDR vs. Control 3

description:
Biological replicate 3 of 4.
ch1: T-47D cells irradiated at low-dose rate, harvested after 2 months.
ch2: Control T-47D cells, untreated, harvested after several passages.


title: HDR vs. Control 1

description:
Biological replicate 1 of 4.
ch1: T-47D cells irradiated at high-dose rate, harvested after 24 h.
ch2: Control T-47D cells, untreated, harvested after several passages.


title: Gastrulation +1h-C, replicate 1

value: 6 hpf


title: Gastrulation +1h-C, replicate 3

value: water


title: LDR vs. Control 4

description:
Biological replicate 4 of 4.
ch1: T-47D cells irradiated at low-dose rate, harvested after 2 months.
ch2: Control T-47D cells, untreated, harvested after several passages.


title: LDR vs. Control 2

description:
Biological replicate 2 of 4.
ch1: T-47D cells irradiated at low-dose rate, harvested after 2 months.
ch2: Control T-47D cells, untreated, harvested after several passages.


title: lung_FT SchuS4_48hr_rep2


title: Peripheral Serum_ctrl 4513 [dataset 1]

description:
Control
miRNA profiling


title: lung_FT LVS_48hr_rep3

description: Gene expression profiling after 48hrs FT LVS

source_name: FT LVS 48hr

value: F. tularenesis LVS


title: lung_FT LVS_48hr_rep2


title: Peripheral Serum_ctrl 4473 [dataset 1]

description:
Control
miRNA profiling

value: normal control


title: Gastrulation +30min-D, replicate 3

source_name: Gastrulation +30min-D

value: 5.5 hpf


title: Peripheral Serum_ctrl 4368 [dataset 1]

description:
Control
miRNA profiling

value: non-cancer


title: Gastrulation +30min-D, replicate 2


title: lung_FT LVS_48hr_rep1


title: lung_PA_48hr_rep3

description: Gene expression profiling after 48hrs PA

source_name: PA 48hr

value: P. aeruginosa


title: Gastrulation +30min-D, replicate 1


title: LDR vs. Control 1

description:
Biological replicate 1 of 4.
ch1: T-47D cells irradiated at low-dose rate, harvested after 2 months.
ch2: Control T-47D cells, untreated, harvested after several passages.

value: Irradiated 1h at 0.3 Gy/h, then cultured for 2 months


title: lung_PA_48hr_rep2

value: Balb/c


title: Peripheral Serum_ctrl 4366 [dataset 1]

description:
Control
miRNA profiling

value: Peripheral Serum


title: Peripheral Serum_ctrl 4357 [dataset 1]

description:
Control
miRNA profiling

value: non-cellular fraction


title: Peripheral Serum_ctrl 4364 [dataset 1]

description:
Control
miRNA profiling

value: Control


title: Peripheral Serum_ctrl 4363 [dataset 1]

description:
Control
miRNA profiling


title: Peripheral Serum_ctrl 4355 [dataset 1]

description:
Control
miRNA profiling


title: Peripheral Serum_ctrl 4356 [dataset 1]

description:
Control
miRNA profiling


title: Gastrulation +30min-C, replicate 3

source_name: Gastrulation +30min-C


title: Gastrulation +30min-C, replicate 2


title: Gastrulation +30min-C, replicate 1


title: Gastrulation, replicate 3

source_name: Gastrulation

value: 5 hpf


title: lung_aYP_48hr_rep1

description: Gene expression profiling after 48hrs aYP

source_name: aYP 48hr

value: Lung

value: Y. pestis avirulent


title: OG1delta-EF2638_2011

city: Milwaukee

first: Dusanka

last: Vesic

state: Wisconsin

address: 8701 Watertown Plank Road

department: Microbiology and Molecular Genetics

institute: Medical College of Wisconsin

description: This sample is of Enterococcus faecalis OG1delta-EF2638. It is the first of two wild-type biological replicates, each from independent cultures. Three technical replicates performed.

hyb_protocol: Hybridization was performed at the Carver Center for Genomics (University of Iowa) following the standard operating protocol for Nimblegen arrays. See www.nimblegen.com.

scan_protocol: Scanning was performed at the Carver Center for Genomics (University of Iowa), following the standard operating protocol for Nimblegen arrays. 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: Enterococcus faecalis OG1RF

source_name: Enterococcus faecalis OG1delta-EF2638

label_protocol: Labeling was performed at the Carver Center for Genomics (University of Iowa) following the standard operating protocol for Nimblegen arrays. See www.nimblegen.com.

growth_protocol: Enterococcus faecalis wild-type OG1 and mutant OG1 delta-EF2638 were grown to exponential phase (OD600=0.16) aerobically at 225 rpm, 37 °C in MH broth.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by treatment with Turbo DNase (Ambion). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Carver Center for Genomics at the University of Iowa.

treatment_protocol: Total RNA was used in the study. RNAProtect reagent (Qiagen) was first used to kill the bacteria and stabilize the RNA. Cell pellets were lysed with mutanolysin and lysozyme treatment and subsequently processed with RNeasy Mini Kit (Qiagen) to isolate total RNA.

tag: genotype

value: Deletion mutant delta-EF2638

tag: phenotype

value: Growth defect present when grown with aeration

tag: accession for complete og1rf genome


title: OG1delta-EF2638_2012

description: This sample is of Enterococcus faecalis OG1delta-EF2638. It is the second of two wild-type biological replicates, each from independent cultures. Three technical replicates performed.


title: Peripheral Serum_ctrl 4354 [dataset 1]

description:
Control
miRNA profiling

tag: activation agent

tag: disease state


title: Gastrulation, replicate 2

value: embryo


title: OG1_2012

description: This sample is of wild-type Enterococcus faecalis OG1. It is the second of two wild-type biological replicates, each from independent cultures. Three technical replicates performed.

source_name: Enterococcus faecalis wild-type OG1

value: wild-type


title: OG1_2011

description: This sample is of wild-type Enterococcus faecalis OG1. It is the first of two wild-type biological replicates, each from independent cultures. Three technical replicates performed.


title: Gastrulation, replicate 1

value: water


title: 2-4 cells, replicate 3

source_name: 2-4 cells

value: 1 hour post-fertilisation (hpf)


title: Peripheral Serum_ctrl 4351 [dataset 1]

description:
Control
miRNA profiling

value: normal control

tag: disease status

tag: time


title: Peripheral Serum_ctrl 4345 [dataset 1]

description:
Control
miRNA profiling

value: non-cancer


title: Peripheral Serum_ctrl 4353 [dataset 1]

description:
Control
miRNA profiling


title: lung_YP_24hr_rep1

description: Gene expression profiling after 24hrs YP

source_name: YP 24hr

value: Y. pestis


title: lung_YP_24hr_rep3


title: 2-4 cells, replicate 1


title: 2-4 cells, replicate 2


title: lung_PA_48hr_rep1

value: P. aeruginosa


title: lung_YP_24hr_rep2

value: Balb/c


title: lung_Mock_24hr_rep3

description: Gene expression profiling after 24hrs Mock

source_name: Mock 24hr

value: Mock


title: lung_aYP_24hr_rep3

description: Gene expression profiling after 24hrs aYP

source_name: aYP 24hr


title: lung_aYP_24hr_rep1


title: lung_Mock_24hr_rep1


title: lung_Mock_24hr_rep2


title: lung_aYP_24hr_rep2


title: Peripheral Serum_ctrl 4343 [dataset 1]

description:
Control
miRNA profiling

source_name: Peripheral Serum

value: Peripheral Serum

value: non-cellular fraction


title: Peripheral Serum_ctrl 4331 [dataset 1]

description:
Control
miRNA profiling

value: Control


title: Peripheral Serum_ctrl 4335 [dataset 1]

description:
Control
miRNA profiling


title: Peripheral Serum_ctrl 4325 [dataset 1]

description:
Control
miRNA profiling


title: lung_LP_24hr_rep3

description: Gene expression profiling after 24hrs LP

source_name: LP 24hr

value: Lung

value: L. pneumophila


title: lung_LP_24hr_rep4


title: lung_LP_24hr_rep2


title: lung_FT SchuS4_24hr_rep3

description: Gene expression profiling after 24hrs FT SchuS4

source_name: FT Schu4 24hr

value: F. tularensis SchuS4


title: H2009_shNKX2-1_clone_Dox_treated_Rep3

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: The fragmented cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to GeneChip Human Gene 1.0 ST Array chips overnight at 45°C (performed by the Dana-Farber Cancer Institute Microarray Core). A fluidics instrument was used with FS450_0007 protocol by the core to perform washes to remove cDNA that had not hybridized to its complementary oligonucleotide probe. The bound cDNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were subsequently added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: A confocal laser scanner was used for excitation and measurement of cDNAs bound to complementary oligonucleotides by the Dana-Farber Cancer Institute Microarray Core.

data_processing: Raw expression values were normalized by RMA using a gene centric CDF.

source_name: cell line, pLKO-Tet-Op-shNKX2-1 infected, single cell cloned, Dox treated 48h

label_protocol: Fragmented single-stranded cDNA was end-labeled with a biotinylated nucleotide-analog by the Dana-Farber Cancer Institute Microarray Core.

extract_protocol: Total RNA was extracted with QIAGEN's RNeasy kit.

treatment_protocol: Doxycycline 50ng/ml for 48 hours

tag: cell line

tag: expression

tag: treatment

value: Dox treated 48h

tag: sample type

value: single cell clone


title: H2009_shNKX2-1_Dox_treated_Rep3

source_name: cell line, pLKO-Tet-Op-shNKX2-1 infected, Dox treated 48h

value: pooled population


title: lung_LP_24hr_rep1

tag: strain

tag: infection

tag: time point


title: H2009_shNKX2-1_clone_Dox_treated_Rep2


title: lung_FT LVS_24hr_rep3

description: Gene expression profiling after 24hrs FT LVS

source_name: FT LVS 24hr

value: F. tularenesis LVS


title: lung_FT SchuS4_24hr_rep1


title: H2009_shNKX2-1_clone_Dox_treated_Rep1


title: lung_PA_24hr_rep1

description: Gene expression profiling after 24hrs PA

source_name: PA 24hr


title: lung_FT SchuS4_24hr_rep2


title: H2009_shNKX2-1_Dox_treated_Rep2


title: lung_PA_24hr_rep2


title: H2009_shGFP_Dox_treated_Rep2

source_name: cell line, pLKO-Tet-Op-shGFP infected, Dox treated 48h

value: pLKO-Tet-Op-shGFP


title: H2009_shGFP_Dox_treated_Rep3


title: H2009_shGFP_Dox_treated_Rep4


title: H2009_shNKX2-1_Dox_treated_Rep1


title: lung_FT LVS_24hr_rep2


title: lung_PA_24hr_rep4


title: Serrated Adenoma, sample 6

status: Public on Apr 14 2013

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

description: serrated 12

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the manufacturer's protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to the manufacturer's protocol.

data_processing: Expression data (CEL files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix).

source_name: serrated adenoma

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with the One-Cycle cDNA synthesis Kit (Affymetrix) according to the manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to the manufacturer's protocol.

value: serrated adenoma


title: lung_FT LVS_24hr_rep1


title: lung_PA_24hr_rep3


title: H2009_shGFP_Dox_treated_Rep1


title: Serrated Adenoma, sample 3

description: serrated 15


title: Serrated Adenoma, sample 2

description: serrated 14


title: Serrated Adenoma, sample 1

description: serrated 10


title: Serrated Adenoma, sample 5

description: serrated 11


title: Serrated Adenoma, sample 4

description: serrated 16


title: Tubular Adenoma, sample 6

source_name: tubular adenoma

value: tubular adenoma


title: Tubular Adenoma, sample 5


title: Tubular Adenoma, sample 4


title: MEF_Dox_8TF_A2B5sorted

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

description: gene expression data of mouse embryo fibroblasts infected with inducible lentiviral vectors expressing Olig2, Nkx6-2, Sox10, Nkx2-2, Myt1, Olig1, ST18, and Myrf treated with doxycycline for 21d in OPC conditions then FACS sorted for A2B5

hyb_protocol: Labeled cRNA (10 ug) was hybridized for 17 hours at 45 degrees C on Affymetrix Mouse Gene 1.0 ST arrays, washed, and stained in the Affymetrix Fluidics Station 450

scan_protocol: Arrays were scanned using Affymetrix Scanner 3000 7G

data_processing: Cel files were generated with the Affymetrix GeneChip Command Console 2.0 and the data were normalized with the RMA method using the default settings in Expression Console Software (Affymetrix)

source_name: mouse embryo fibroblasts, doxycycline, 8TF, 21d, A2B5 sorted

label_protocol: Biotinylated cRNA was prepared from 150ng of total RNA using the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay according to the manufacturer's instructions

growth_protocol: MEFs were cultured in DMEM +10% FBS and transitioned to OPC growth conditions (N2B27 +FGF2 and PDGFaa)

extract_protocol: Total RNA prepared using the RNeasy Plus Kit (Qiagen) according to the manufacturer’s protocol

treatment_protocol: MEFs were infected with inducible lentiviral vectors and doxycycline was added for 21 days

tag: cell type

value: MEFs

tag: genotype/variation

value: rtTA, Plp1:GFP


title: OPCs_undifferentiated

description: gene expression data of oligodendrocyte progenitor cells

source_name: oligodendrocyte progenitor cells


title: Tubular Adenoma, sample 7

tag: tissue


title: MEF_Dox_3TF_21d

description: gene expression data of mouse embryo fibroblasts infected with inducible lentiviral vectors expressing Olig2, Nkx6-2, and Sox10 treated with doxycycline for 21d in OPC conditions

source_name: mouse embryo fibroblasts, doxycycline, 3TF, 21d


title: Tubular Adenoma, sample 2


title: MEF_untreated

description: gene expression data of mouse embryo fibroblasts, untreated

source_name: mouse embryo fibroblasts, untreated


title: MEF_Dox_8TF_21d

description: gene expression data of mouse embryo fibroblasts infected with inducible lentiviral vectors expressing Olig2, Nkx6-2, Sox10, Nkx2-2, Myt1, Olig1, ST18, and Myrf treated with doxycycline for 21d in OPC conditions

source_name: mouse embryo fibroblasts, doxycycline, 8TF, 21d


title: Tubular Adenoma, sample 1


title: S2* cells, with 20E, replicate 1

status: Public on Apr 13 2013

city: Lausanne

first: Thomas

last: Flatt

address: UNIL Sorge, Biophore

department: Department of Ecology and Evolution

country: Switzerland

institute: University of Lausanne

hyb_protocol: cDNA products were hybridized at the Brown University Genomics Core Facility to Affymetrix GeneChip Drosophila_2.0 Genome Arrays (3 replicate chips per treatment)

scan_protocol: GeneChips were scanned using the Affymetrix Gene Scanner 3000 7G at the Brown University Genomics Core Facility

data_processing: Expression data were processed and analyzed with dCHIP software (http://www.hsph.harvard.edu/cli/complab/dchip/); raw data were normalized across chips by the invariant difference selection algorithm with gene expression given by the model-based expression index.

organism: Drosophila melanogaster

source_name: S2* cells_1 µM of 20E for 24 hrs

label_protocol: standard Affymetrix protocol

growth_protocol: Drosophila S2* cells were grown in Schneider's medium (Gibco) with 10% fetal bovine serum, 1% Gluta-MAX (Gibco), and 0.2% penicillin-streptomycin (Gibco) at 27C.

treatment_protocol: Cells were either treated with 1 microMolar 20-hydroxy-ecdysone (20E) (Sigma) for 24 hours or left untreated (control)

value: S2* cells

tag: treated with

value: 1 microMolar steroid hormone 20-hydroxy-ecdysone (20E) for 24hr


title: S2* cells, without 20E, replicate 1

source_name: Untreated S2* cells (control)

value: none (untreated control)


title: S2* cells, with 20E, replicate 3


title: JJN3_3_POM_24h

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression profiling data of Pomalidomide (CC-4047) treated JJN3 cell line replicate 3

hyb_protocol: Biotin labeled cRNA target was hybridized on GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix Inc., Santa Clara, CA, USA) according to the standard Affymetrix protocol. The arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The GeneChip® Human Genome U133 Plus 2.0 arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix Inc., Santa Clara, CA).

data_processing: Expression values were extracted from cell intensity files, using GeneAnnot custom chip definition files. The CDF Packages for R/Bioconductor (http://www.bioconductor.org/) version 2.2.0 was based on GeneAnnot annotation Version 2.0 and publicly available at http://www.xlab.unimo.it/GA_CDF/. The data were normalized using Robust Multi-array Average procedure.

source_name: JJN3 Multiple Myeloma cell line

label_protocol: Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols.

growth_protocol: JJN3 cell line was maintained in culture in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum (FBS), Penicillin (100U/ml), Streptomycin (100µg/ml), L-Glutamine (2mM) and Fungizone antimycotic (2,5µg/ml) (Invitrogen Life Technologies, Milan, Italy).

extract_protocol: Total RNA was extracted from the cells using the RNeasy total RNA isolation kit (Qiagen, Valencia, CA), and then quantified using a Nanodrop ND-100 (Celbio S.p.A., Milan, Italy).

treatment_protocol: JJN3 cells were cultured in presence of 100 µM Pomalidomide (CC-4047) for 24 hours.

value: Pomalidomide (CC-4047) (100 µM, 24h)


title: S2* cells, with 20E, replicate 2


title: S2* cells, without 20E, replicate 2


title: HUVECs overexpressing miR-146a, rep1

city: Shanghai

first: Kai

last: Zhu

address: 136 Yi Xue Yuan Road

country: China

institute: liver cancer institute, Fudan University

description:
Examine genome expression changes of HUVECs overexpressing miR-146a.
S31_H004

hyb_protocol: Fluorescent targets were hybridized to the Phalanx Human OneArray v6.1 with Phalanx hybridization buffer using Phalanx Hybridization System.

scan_protocol: The scanned images were analyzed with Agilent Scanner and processing by GenePix software 4.1 to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Using Rosetta Resolver System (Rosetta Biosoftware) Error Model to calculate normalized intensity, CV, log2 ratio and p-value (differential expressed). Briefly, exclude probes which flag are -50 within all arrays, squeeze replicated probes within one chip and averaged, then normalize intensities by median scaling and take average of normalized intensity (mean).

source_name: HUVECs overexpressing miR-146a

label_protocol: Cyanine-5 (Cy5) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human umbilical vein endothelial cells (HUVECs) (8000, Sciencell, Carlsbad, CA) were maintained in EGM-2 medium (CC-4147, Lonza, Switzerland).

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations. The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion. Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: To obtain stable miR-146a overexpressing cells, HUVECs were infected with viruses carrying a miR-146a precursor (pre-146a) sequence (PMIRH146aPA-1, System Biosciences).

value: human umbilical vein endothelial cells (HUVECs)

tag: overexpression


title: JJN3_2_POM_24h

description: Gene expression profiling data of Pomalidomide (CC-4047) treated JJN3 cell line replicate 2


title: HUVECs overexpressing miR-146a, rep3

description:
Examine genome expression changes of HUVECs overexpressing miR-146a.
S33_H006


title: HUVECs control, rep2

description:
Examine genome expression changes of HUVECs overexpressing miR-146a.
N2_H002

source_name: HUVECs control

value: control


title: HUVECs control, rep1

description:
Examine genome expression changes of HUVECs overexpressing miR-146a.
N1_H001


title: HUVECs overexpressing miR-146a, rep2

description:
Examine genome expression changes of HUVECs overexpressing miR-146a.
S32_H005


title: MEF_Dox_21d

description: gene expression data of mouse embryo fibroblasts treated with doxycycline for 21d in OPC conditions

source_name: mouse embryo fibroblasts, doxycycline, 21d


title: JJN3_1_POM_24h

description: Gene expression profiling data of Pomalidomide (CC-4047) treated JJN3 cell line replicate 1


title: JJN3_2_LEN_24h

description: Gene expression profiling data of Lenalidomide (CC-5013) treated JJN3 cell line replicate 2

treatment_protocol: JJN3 cells were cultured in presence of 100 µM Lenalidomide (CC-5013) for 24 hours.

value: Lenalidomide (CC-5013) (100 µM, 24h)


title: HUVECs control, rep3

description:
Examine genome expression changes of HUVECs overexpressing miR-146a.
N3_H003


title: plasma-HC 2

city: Kyoto

first: Koichi

last: Murata

state: Kyoto

address: 54, Kawahara-cho, Shogoin, Sakyo-ku

department: Orthopaedics

country: Japan

institute: Kyoto University

description: Control

data_processing: The SDS2.2.2 automatically caluculated the uploaded raw threshold cycle data. Normalization was carried out with the average Ct value of all miRNAs. Relative quantification of miRNA expression was calculated with the 2−ΔΔCt Ct method. The data was presented as log10 of the relative quantity of each miRNA. Fold Change worksheet reports test/control (i.e., RA/HC) ratios.

source_name: plasma-HC

label_protocol: see manufacturer's website: http://www.appliedbiosystems.com/

extract_protocol: RT2 qPCR-Grade miRNA isolation kit (SABiosciences, Frederick, MD) after twice extration using with Sepasol-RNA II (Nacalai Tesque, Kyoto, Japan), a phenol-based reagent for liquid sample.

tag: gender

value: female

tag: age (yrs)

tag: diagnosis

value: healthy

value: plasma


title: JJN3_1_LEN_24h

description: Gene expression profiling data of Lenalidomide (CC-5013) treated JJN3 cell line replicate 1


title: JJN3_3_LEN_24h

description: Gene expression profiling data of Lenalidomide (CC-5013) treated JJN3 cell line replicate 3


title: S2* cells, without 20E, replicate 3


title: plasma-HC 3

description: Control


title: plasma-HC 1

description: Control

value: male


title: Tubular Adenoma, sample 3


title: JJN3_3_CTR_24h

description: Gene expression profiling data of untreated JJN3 cell line replicate 3

treatment_protocol: JJN3 cells were cultured in presence of vehicle (DMSO) for 24 hours.

value: untreated


title: JJN3_2_CTR_24h

description: Gene expression profiling data of untreated JJN3 cell line replicate 2


title: plasma-RA 3

description: Test

source_name: plasma-RA

value: rheumatoid arthritis


title: vAbl transformed cells +Tamox 3

city: Berkeley

first: Kwan

last: Chow

state: CA

address: 439 LSA

institute: UC Berkeley

description: vAbl transformed cells Foxo1 knockout

hyb_protocol: Following fragmentation, 5 ug of fragmented cRNA was hybridized for 18 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: data was processed using GenePattern (Broad Institute) platform with ceiling threshold set as 20000

source_name: vAbl transformed pro-B cells

label_protocol: Integrity of total RNAs were checked with Bioanalyzer. Biotinylated cRNA were prepared from the total RNA according to the manufacturer's recommendation (NuGen, San Carlos, CA) from 200ng of total RNA.

growth_protocol: vAbl transformed cells were cultured in RPMI 1640 medium supplemented with 5% (vol/vol) FCS, L-glutamine (2 mM), penicillin (100 g/ml), streptomycin (100 g/ml), and 2-mercaptoethanol (50 mM)

extract_protocol: total RNA was extracted using TRIZOL reagent, then purified with QIAGEN RNAeasy mini kit columns

treatment_protocol: Half the cells were treated with 1uM tamoxifen for 2 days, the other half untreated

tag: genotype

value: Foxo1f/f; ERCre

value: 1uM tamoxifen for 2 days


title: plasma-RA 2

description: Test


title: plasma-RA 1

description: Test


title: vAbl transformed cells +Tamox 2

description: vAbl transformed cells Foxo1 knockout


title: vAbl transformed cells untreated 2

description: vAbl transformed cells WT


title: JJN3_1_CTR_24h

description: Gene expression profiling data of untreated JJN3 cell line replicate 1


title: vAbl transformed cells untreated 1

description: vAbl transformed cells WT


title: vAbl transformed cells untreated 3

description: vAbl transformed cells WT


title: vAbl transformed cells +Tamox 1

description: vAbl transformed cells Foxo1 knockout


title: CD8+ KLRG1low KO cells, biological rep2

city: La Jolla

first: Rodrigo

middle: A

last: Hess

address: 9500 Gilman Dr

department: Cellular and Molecular Medicine

institute: University of California San Diego

description: Gene expression data from Mouse CD8+ KLRG1low KO cells, day8 post infection

hyb_protocol: cRNA was hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data was analyzed with GenePattern software suite.

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix protocol.

extract_protocol: total RNA extraction was performed by RNeasy Mini Kit from Qiagen according to the manufacturer's instructions.

treatment_protocol: We carried out gene deletion in Rosa26Cre-ERT2 Foxo1f/f (Foxo1-/-) P14 mice just prior to adoptive transfer (Kerdiles et al., 2009), and transfer equal numbers (10x104) of P14 CD8+ cells from the spleens of KO (Foxo1-/- P14) and WT P14 mice. Mice were infected with LCMV-Armstrong and RNA isolated from KLRG1low and KLRG1high FACS-sorted congenically-marked WT and Foxo1-/- P14 cells eight days post-infection.

value: Spleen

tag: age

value: 8-12 weeks


title: CD8+ KLRG1high KO cells

description: Gene expression data from Mouse CD8+ KLRG1high KO cells, day8 post infection


title: CD8+ KLRG1low WT cells, biological rep2

description: Gene expression data from Mouse CD8+ KLRG1low WT cells, day8 post infection


title: CD8+ KLRG1low KO cells, biological rep1

source_name: Mouse CD8+ KLRG1low KO cells, day8 post infection


title: Bmi1Ink4a_2

status: Public on Apr 12 2013

city: San Francisco

first: Brian

last: Biehs

address: 505 Parnassus Ave

institute: UCSF

hyb_protocol: Hybridizations were performed for 17 hrs, according to the manufacturers protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner and raw signal intensities were extracted with Feature Extraction v10.6 software.

data_processing: This dataset was normalized using the quantile normalization method that is proposed by Bolstad et al (2003).  No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.

source_name: colony derivied from dental epithelia

label_protocol: RNA was amplified using the Sigma whole transcriptome amplification kits following the manufacturer’s protocol (Sigma-Aldrich, St Louis, MO), and subsequent Cy3-CTP labeling was performed using NimbleGen one-color labeling kits (Roche-NimbleGen Inc, Madison, WI). Labeled Cy3-cDNA was assessed using the Nandrop ND-8000 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome.

extract_protocol: Qiagen Rneasy mini kit

value: dental stem cell colony derivied from dental epithelia

tag: genetic background

value: mixed


title: Bmi1Ink4a_3


title: CD8+ KLRG1low WT cells, biological rep1

source_name: Mouse CD8+ KLRG1low WT cells, day8 post infection


title: CD8+ KLRG1high WT cells

description: Gene expression data from Mouse CD8+ KLRG1high WT cells, day8 post infection


title: WT_3

value: WT


title: Bmi1_4


title: Bmi1_1


title: Bmi1Ink4a_1


title: Bmi1_3


title: WT_4


title: WT_5


title: Bmi1Ink4a_4


title: WT_1


title: Bmi1_2


title: peripheral white blood cell PO720

first: Yi

last: Zhang

state: WI

address: 8701 W Watertown Plank Rd

department: Medicine

description: Illumina Human WG-6 v3 expression

hyb_protocol: A total of 1.5 µg aRNA was hybridized to Illumina HumanWG-6 version 2 or version 3 chips

scan_protocol: Samples were scanned on the Illumina BeadArray 500GX Reader using Illumina BeadScan image data acquisition software (version 2.3.0.13).

data_processing: Illumina GenomeStudio software (version 2010.3) was used for preliminary data analysis with standard background normalization.

source_name: peripheral white blood cell

label_protocol: Biotin-16-UTP (Roche) labeled aRNA was synthesized using Ambion’s proprietary MEGAscript in vitro transcription IVT)  technology and T7 RNA Polymerase. Purification of aRNA samples was carried out using QIAGEN’s RNeasy 96 protocol for RNA cleanup using spin technology.

extract_protocol: 2.5ml blood was collected into a PAXgene® Blood RNA Tube (BD, Franklin Lakes, NJ) following an overnight fast. Total RNA was isolated from each tube using the PAXgene Blood RNA Kit (Qiagen, Valencia, CA) and anti-sense RNA (aRNA) was synthesized using the MessageAmp II-Biotin aRNA kit (Ambion, Austin, TX)

tag: race

value: Caucasian

tag: leptin

tag: adiponectin


title: peripheral white blood cell PO385

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell PO717

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell U5074W1

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell PO716

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP98

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell PO380

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell PO384

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell PO376

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell PO379

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP94

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP97

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP92

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP96

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP89

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP86

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP8

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP83

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP73

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP77

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP75

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP90

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP70

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP69

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP85

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP93

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP78

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP76

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP72

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP80

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP88

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP67

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP7

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP74

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP68

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP53

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP64

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP55

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP65

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP52

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP60

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP66

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP51

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP43

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP47

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP54

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP63

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP49

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP62

description: Illumina Human WG-6 v3 expression


title: case number 9-Non-Hodgkin Lymphoma

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

country: Belgium

institute: KULeuven

description: Hybridized to Affymetrix Cytogenetics Array

hyb_protocol: DNA was whole-genome amplified, purified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: CEL files generated by Affymetrix Command Console and CYCHP files generated byAffymetrix Chromosome Analysis Suite software (ChAS).  DNA copy number and allele analysis were performed using Affymetrix ChAS, which compares all hybridization intensities against a built-in reference data set

source_name: tumor DNA

label_protocol: Biotin, affymetrix protocol for the  Cytogenetics array 2.7M

growth_protocol: No culture-just DNA from frozen tissue

extract_protocol: Qiagen kit for DNA extraction

treatment_protocol: no previous treatment

tag: disease state

value: Non-Hodgkin Lymphoma

value: tumor


title: peripheral white blood cell NP44

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP32

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP42

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP3

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP38

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP22

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP20

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP18

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP21

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP25

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP33

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP29

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP24

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP28

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP26

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP31

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP37

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP40

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP27

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP19

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP17

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP122

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP153

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP149

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP13

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP150

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP145

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP144

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP151

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP124

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP12

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP116

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP117

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP108

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP111

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP109

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NP101

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK89

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK9

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK80

description: Illumina Human WG-6 v3 expression

tag: fatmass(kg)

tag: fatmass(pct)

tag: leanmass(kg)

tag: leanmass(pct)


title: peripheral white blood cell NK77

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK91

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK76

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK72

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK96

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK8

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK84

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK82

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK85

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK74

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK83

description: Illumina Human WG-6 v3 expression


title: EBF1-2

city: Philadelphia

first: David

last: Allman

state: PA

address: 36th & Hamilton Walk, 230 John Morgan Building

institute: University of Pennsylvania

hyb_protocol: Biotinylated targets were heated at 99 °C for 5 min and hybridized for 16 h at 45 °C. The microarrays were then washed at low (6× SSPE) and high (100 mM MES, 0.1 M 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: GeneChips were scanned using the GeneArray Scanner 3000 7G.

data_processing: The data were analysed using Partek Genomics Suite, version 6.5 (Partek). Robust multichip average (RMA) with default settings was used to normalize data.

label_protocol: Protocols were conducted as described in the Affymetrix GeneChip Expression Analysis Technical Manual. Quality and quantity of extracted RNA was tested on a bioanalyser by UPENN Microarray Core Facility. the resulting cDNA was fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling. cDNA yields ranged from 5-9ug

growth_protocol: Ebf1-/- progenitors were propagated and maintained on OP9 stromal cells in Opti-MEM, 10% FCS, primatone, L-glutamine, and Pen/Strep supplemented with 10 ng/ml each of IL-7, flt3-ligand (FL) and stem cell factor (SCF).

extract_protocol: Target preparation and hybridization protocols were conducted as described in the Ovation Pico WTA System V2 User Guide (NuGEN) and the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, [50ng] of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated an RNA priming region.  Second-strand cDNA synthesis was followed by ribo-SPIA linear amplification of each transcript using an isothermal reaction with RNase, RNA primer and DNA polymerase, and the resulting cDNA was fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling. cDNA yields ranged from 5-9ug

treatment_protocol: High titer virus was generated using a CaPO4 transfection protocol. Cultures were supplemented with fresh medium at 12h post-infection and harvested for downstream applications at indicated time points post-infection.

tag: cell type

value: Ebf1-/- pre-pro-B cell line

tag: transduction

value: MigY-EBF1 virus


title: EBF1-1


title: Pax5-1

value: MigR-Pax5 virus


title: peripheral white blood cell NK70

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK60

description: Illumina Human WG-6 v3 expression

value: female


title: peripheral white blood cell NK59

description: Illumina Human WG-6 v3 expression

value: male


title: peripheral white blood cell NP34

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK67

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK62

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK66

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK6

description: Illumina Human WG-6 v3 expression


title: Control-2

source_name: Control

value: control MigR1 virus


title: Pax5-2


title: Control-1


title: peripheral white blood cell NK53

description: Illumina Human WG-6 v3 expression


title: Xu 6 control

city: Atlanta

first: Benem-Orom

middle: Andrew

last: Davids

state: ga

address: 720 Westview Drive SW

department: Neurobiology

institute: Morehouse School of Medicine

description: naïve brain

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings for MAS5

organism: Rattus norvegicus

source_name: naïve brain

growth_protocol: All animals used in these studies were treated humanely and with regard for alleviation of suffering and pain and all protocols involving animals were approved by the IACUCs of Morehouse School of Medicine and/or The Georgia Institute of Technology prior to the initiation of experimentation. Adult male Sprague-Dawley rats (290-300g; Charles River Laboratories International, Inc., USA) were housed individually in standard plastic cages in a temperature-controlled room (22 ± 2C) on a 12 h reverse light-dark cycle.  Food and water were provided ad libitum.

extract_protocol: The ipsilateral hemi-brain tissue at the site of the injury, the corresponding contralateral hemi-brain tissue, and naïve (control) brain tissue (n=3 for each) were used for RNA isolation. Total RNA was extracted with TRIzol Reagent (Life Technologies, Rockville, MD, USA) and cleaned (RNAqueous Kit, Ambion, Austin, TX, USA). The RNA was prepared for microarray hybridization with the GeneChip® 3’ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA) aRNA amplification procedure. Briefly, total RNA was reverse transcribed to synthesize first-strand cDNA containing a T7 promoter sequence. The single-stranded cDNA was converted into a double-stranded DNA template for transcription. The reaction employed DNA polymerase and RNase H to simultaneously degrade the RNA and synthesize second-strand cDNA. In vitro transcription generated multiple copies of biotin-modified aRNA from the double-stranded cDNA templates (this was the amplification step). aRNA Purification removed unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the biotin-modified aRNA. Finally, the labeled aRNA was fragmented to prepare the target for hybridization to GeneChip® 3’ expression arrays

treatment_protocol: Under isoflurane anesthesia, rats received a unilateral controlled cortical impact (CCI/TBI) using the Pittsburgh Precision Instruments, Inc. device. A craniotomy was made with the center 4 mm posterior and 3-4 mm lateral to bregma using a 6 mm diameter trephan drill bit. The impact was done at an angle of 15° from vertical with a velocity of 3 m/s to a depth of 2 mm using a 5 mm diameter impact tip.  The rats were sacrificed 24 h post-injury and the brains were removed for RNA isolation.

tag: tissue

value: Brain

value: 6.5-9 weeks

tag: weight

tag: strain

value: Sprague-Dawley

tag: treatment

value: naïve


title: Todd 3C

description: Gene expression data from contralateral hemi-brain after brain injury

source_name: contralateral hemi-brain

value: contralateral to traumatic brain injury


title: peripheral white blood cell NK48

description: Illumina Human WG-6 v3 expression

tag: gender


title: peripheral white blood cell NK39

description: Illumina Human WG-6 v3 expression

tag: age


title: NAIVE 6

type: protein

city: Irvine

first: Elisabeth

last: Baum

address: Med Surge II

institute: University of California Irvine

hyb_protocol: Serum samples were diluted 1:200 (human) or 1:100 (P. leucopus) in Protein Array Blocking (PAB) buffer (Whatman Inc, Sanford, ME) supplemented with 10% (vol/vol) DH5alpha E. coli lysate (MCLAB, San Francisco, CA). This suspension was incubated for 30 min at 22°C, with gentle constant shaking. Arrays were re-hydrated with PAB buffer for 30 min at 22°C. Primary antibody was placed on re-hydrated array pads and incubated for 12 h at 4°C on a rocker platform (Bellco, Vineland, NJ). Pads were rinsed 6 times, followed by three 5-minute washes in Tween-TBS. Cy3-conjugated secondary antibody, goat anti-human IgG heavy and light chain or goat anti-Peromyscus leucopus IgG heavy and light chain (KPL, Gaithersburg, MD), were diluted 1:200 in PAB buffer, and incubated with pads in the dark for 1 h at 22°C on a rocking platform. Arrays were washed in Tween-TBS as described above and this process repeated with TBS alone.

scan_protocol: Slides were dismounted from their frames, rinsed in double-distilled H2O and centrifuged 20 min at 500 x g to dry. Probed array slides were scanned in a Perkin Elmer ScanArray Express HT at a wavelength of 670 nm, at 95% laser power and 55% PMT. The output RGB TIFF files generated by the scanner were quantitated using ProScanArray Express software (Perkin Elmer, Waltham, MA) with spot-specific background correction.

data_processing: For analysis of antibody binding to OspC proteins on the microarray the following steps were taken: (i) raw values of antibody binding measured as the mean pixel intensity of spots of printed protein were log10-transformed; raw values less than 1.0 were set to 0; (ii) the mean, standard deviation, 95% confidence intervals and z-scores of antibody binding intensity to each OspC type were calculated for the human LD patient, P. leucopus and respective control sera groups.  Inclusion criterion for cross-reactivity analysis was a minimum reactivity corresponding to a z score of 2 to at least one OspC protein.

molecule: protein

organism: Peromyscus leucopus

source_name: serum

tag: serum type

value: control

tag: lyme disease stage

value: Not Applicable

tag: infecting ospc type


title: NAIVE 7


title: peripheral white blood cell NK34

description: Illumina Human WG-6 v3 expression

tag: race

tag: leptin

tag: adiponectin


title: peripheral white blood cell NK37

description: Illumina Human WG-6 v3 expression

tag: fatmass(kg)

tag: fatmass(pct)


title: NAIVE 5


title: peripheral white blood cell NK40

description: Illumina Human WG-6 v3 expression

tag: leanmass(kg)

tag: leanmass(pct)


title: peripheral white blood cell NP139

description: Illumina Human WG-6 v3 expression


title: Xu 13 control

description: naïve brain


title: Todd 1C


title: Todd 1I

description: Gene expression data from ipsilateral hemi-brain after brain injury

source_name: ipsilateral hemi-brain

value: traumatic brain injury


title: peripheral white blood cell NK52

description: Illumina Human WG-6 v3 expression

value: Caucasian


title: peripheral white blood cell NK4

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK41

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK38

description: Illumina Human WG-6 v3 expression


title: Xu 2 control

description: naïve brain


title: 2C Todd


title: peripheral white blood cell NK31

description: Illumina Human WG-6 v3 expression


title: 2I Todd


title: NAIVE 4


title: peripheral white blood cell NK36

description: Illumina Human WG-6 v3 expression


title: NAIVE 3


title: peripheral white blood cell NK28

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK32

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK30

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK29

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK3

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK27

description: Illumina Human WG-6 v3 expression


title: NAIVE 2


title: NAIVE 1


title: WQR 5

value: infected

value: T


title: WQR 3


title: WQR 2


title: peripheral white blood cell NK25

description: Illumina Human WG-6 v3 expression


title: WQR 1


title: peripheral white blood cell NK24

description: Illumina Human WG-6 v3 expression


title: TBO2 4

value: N


title: peripheral white blood cell NK23

description: Illumina Human WG-6 v3 expression


title: TBO2 5


title: peripheral white blood cell NK2

description: Illumina Human WG-6 v3 expression


title: TBO2 3


title: TBO2 1


title: TBO2 2


title: SH2 1

value: K


title: peripheral white blood cell NK20

description: Illumina Human WG-6 v3 expression


title: SH2 3


title: peripheral white blood cell NK199

description: Illumina Human WG-6 v3 expression


title: IDS 5

value: A and N


title: IDS 3


title: IDS 4


title: SH2 4


title: IDS 1


title: HB19 4

value: I


title: peripheral white blood cell NK187

description: Illumina Human WG-6 v3 expression

value: female


title: peripheral white blood cell NK182

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK177

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK179

description: Illumina Human WG-6 v3 expression


title: HB19 3


title: peripheral white blood cell NK18

description: Illumina Human WG-6 v3 expression

value: male


title: peripheral white blood cell NK193

description: Illumina Human WG-6 v3 expression


title: IDS 2


title: peripheral white blood cell NK22

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK191

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK19

description: Illumina Human WG-6 v3 expression


title: HB19 2


title: peripheral white blood cell NK180

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK176

description: Illumina Human WG-6 v3 expression


title: HB19 1


title: peripheral white blood cell NK170

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK174

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK17

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK165

description: Illumina Human WG-6 v3 expression


title: 27577 5

value: F


title: peripheral white blood cell NK164

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK167

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK162

description: Illumina Human WG-6 v3 expression


title: Steere 60


title: peripheral white blood cell NK163

description: Illumina Human WG-6 v3 expression


title: Steere 5


title: Steere 56


title: Steere 52


title: Steere 59


title: Steere 53


title: peripheral white blood cell NK150

description: Illumina Human WG-6 v3 expression


title: 27577 4


title: Steere 49


title: Steere 44


title: Steere 38


title: Steere 45


title: Steere 32


title: Steere 34


title: Todd 3I

value: Brain

value: 6.5-9 weeks


title: peripheral white blood cell NK149

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK146

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK139

description: Illumina Human WG-6 v3 expression


title: Steere 28


title: Steere 19


title: Steere 23


title: peripheral white blood cell NK133

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK131

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK14

description: Illumina Human WG-6 v3 expression


title: Steere 2


title: peripheral white blood cell NK127

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK121

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK161

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK137

description: Illumina Human WG-6 v3 expression


title: Steere 14


title: Steere 36


title: Steere 11


title: peripheral white blood cell NK132

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK13

description: Illumina Human WG-6 v3 expression


title: Steere 10


title: peripheral white blood cell NK118

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK115

description: Illumina Human WG-6 v3 expression


title: 900878


title: peripheral white blood cell NK117

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK110

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK113

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK119

description: Illumina Human WG-6 v3 expression


title: 900877


title: peripheral white blood cell NK108

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK106

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell NK123

description: Illumina Human WG-6 v3 expression


title: 900874


title: 900875


title: 900876


title: Steere 6

value: Lyme Arthritis

value: unknown


title: Steere 8


title: Steere 57


title: Steere 58

value: Disseminated or Late


title: Steere 50


title: Steere 54


title: Steere 47


title: Steere 46


title: peripheral white blood cell NK105

description: Illumina Human WG-6 v3 expression


title: Steere 42


title: Steere 43


title: Steere 41


title: peripheral white blood cell KO379

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell KO376

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell KO374

description: Illumina Human WG-6 v3 expression


title: Steere 35


title: peripheral white blood cell KO365

description: Illumina Human WG-6 v3 expression


title: Steere 37


title: peripheral white blood cell KO375

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell KO360

description: Illumina Human WG-6 v3 expression


title: Steere 31


title: Steere 33


title: peripheral white blood cell NK1

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell K0007

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell KO368

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell KO378

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell KO363

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell 16332

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell 16288

description: Illumina Human WG-6 v3 expression


title: Steere 39


title: peripheral white blood cell 16325

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell 16329

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell 16287

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell K0008

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell 16302

description: Illumina Human WG-6 v3 expression


title: Steere 27


title: Steere 22


title: Steere 24


title: Steere 30


title: Steere 25


title: Steere 21


title: peripheral white blood cell 16280

description: Illumina Human WG-6 v3 expression


title: Steere 18


title: Steere 20


title: Steere 13


title: Steere 12


title: 940880

value: Late


title: 940357

value: Disseminated


title: Steere 17


title: 930206

value: Early


title: 921982

value: infected


title: peripheral white blood cell 10247

description: Illumina Human WG-6 v3 expression

value: Caucasian


title: peripheral white blood cell 3987

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell 3975

description: Illumina Human WG-6 v3 expression


title: 911847


title: peripheral white blood cell 3971

description: Illumina Human WG-6 v3 expression


title: 931414


title: peripheral white blood cell 6011

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell 3962

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell 16175

description: Illumina Human WG-6 v3 expression


title: 911841


title: 920057


title: peripheral white blood cell 3980

description: Illumina Human WG-6 v3 expression


title: 911353


title: peripheral white blood cell 3974

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell 3875

description: Illumina Human WG-6 v3 expression


title: 911351


title: peripheral white blood cell 3871

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell 3833

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell 2077

description: Illumina Human WG-6 v3 expression


title: 911350


title: peripheral white blood cell 3967

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell 3958

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell 3876

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell 3831

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell 2072

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell 2075

description: Illumina Human WG-6 v3 expression


title: 911348


title: peripheral white blood cell 3837

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell 1316

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell 3872

description: Illumina Human WG-6 v3 expression


title: 911347


title: peripheral white blood cell 1329

description: Illumina Human WG-6 v3 expression


title: 911349


title: peripheral white blood cell 1270

description: Illumina Human WG-6 v3 expression


title: 911104


title: 910943


title: peripheral white blood cell 1269

description: Illumina Human WG-6 v3 expression


title: 910900


title: peripheral white blood cell 1268

description: Illumina Human WG-6 v3 expression


title: 910544


title: peripheral white blood cell 1042

description: Illumina Human WG-6 v3 expression


title: 910533


title: peripheral white blood cell 1267

description: Illumina Human WG-6 v3 expression


title: 910532


title: 910531


title: Bmi1KO.2088

source_name: Mouse incisor dental epithelia

label_protocol: standard Agilent protocol

extract_protocol: Whole incisors were incubated in accumax, dental epithlial were mechanically separated from mesenchyme and total RNA was extracted using the Qiagen Rneasy mini kit.

tag: genotype

value: incisor dental epithelia

tag: genetic background

value: mixed


title: peripheral white blood cell 1040

description: Illumina Human WG-6 v3 expression


title: peripheral white blood cell 586

description: Illumina Human WG-6 v3 expression


title: 910794


title: peripheral white blood cell 1030

description: Illumina Human WG-6 v3 expression


title: 902668


title: Bmi1KO.2087

tag: tissue


title: 902622


title: BmiKO.2089


title: 902436


title: peripheral white blood cell 583

description: Illumina Human WG-6 v3 expression


title: 902111