title: S1-H36

description: log2 gene expression data

value: Breast cancer

tag: gender

tag: race

tag: set

tag: er

tag: pr

tag: triple-negative status

tag: tumor grade

tag: tumor size

tag: positive nodes

tag: tnbc subtype

value: Basal-Like Immune-Activated (BLIA)


title: PMEC_17

status: Public on Dec 18 2015

type: RNA

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data was analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor.

label: biotin

molecule: total RNA

organism: Sus scrofa

source_name: PMEC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: Primary cell cultures were established from mammary glands of three lactating sows of commercial herds. 4.4 x 10E5 of the isolated mammary epithelial cells from every individual (three biological replicates) were seeded and cultured in collagen-coated 6-well plates in complete medium without APS (three technical replicates per individual and treatment condition).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

treatment_protocol: Primary mammary epithelial cells (PMEC) were treated with 10E7/ml heat-inactivated S. aureus and E. coli, respectively, for 3 h and for 24 h.

tag: biological replicates

value: ANIMAL_3 II

tag: treatment

value: S. aureus

tag: time


title: UCMD patient  repl2

city: Barcelona

first: Susana

last: Kalko

state: BARCELONA

address: c/Rosello 153

department: Bioinformatics Platform

country: Spain

institute: IDIBAPS

hyb_protocol: Following cRNA fragmentation the sample was hybridized on The GeneChip HT HG-U219 Array Plate

scan_protocol: Hybridization, washes and scanning were processed in the Gene Titan instrument, a fully automated array system

data_processing: Raw expression measures were summarized after background correction and normalization steps using the rma methodology in the Expression Console™ Software 1.2.1.20.

organism: Homo sapiens

source_name: Fibroblast

label_protocol: Sample preparation for microarray hybridization was performed following Affymetrix’s protocols.   The GeneChip3’IVT Express Protocol was used for sample labeling.Briefly from 150 ng total RNA a  biotin labeled cRNA was generated by reverse transcription, followed by an IVT

extract_protocol: Total RNA was extracted from fibroblasts cultures with RNeasy Fibrous Tissue mini kit following the manufacturer's instructions. Quantity and quality of RNA obtained was determined with Nanodrop 8000 Spectrophotometer (Thermo Scientific, Schwerte, Germany) and its integrity with Agilent 2100 Bioanalyzer (Agilent technologies, Waldbronn, Germany). In all samples RNA integrity numbers (RIN) were >8 and 260/280 ratios near 2.0.

tag: cell type

value: dermal fibroblasts

tag: disease state

value: UCMD


title: UCMD patient with AA repl2

value: ascorbic acid


title: RH, biological rep2

city: Wageningen

first: Anderson Tadeu

last: Silva

state: Gelderland

address: Droevendaalsesteeg 1

department: Plant Physiology

country: Netherlands

institute: Wageningen University

description: Gene expression data from germinated Arabidopsis seeds at the stage of root hair

hyb_protocol: Following fragmentation, 2.5 ug of ss-cDNA were hybridized on the Affymetrix ARAGene 1.1ST Array plates. Plates were washed and stained by the GeneTitan machine using the Affymetrix HWS Kit for the GeneTitan.

scan_protocol: Plates were scanned using the Affymetrix GeneTitan scanner operated by the software program Affymetrix GeneChip Command Console.

data_processing: The Robust Multichip Analysis (RMA-Sketch for gene level analysis) algorithm was used for the summarization. Signal intensities were extracted and analysed using the Bioconductor packages of R. The data was normalized using the RMA algorithm with the TAIRG v17 cdf file.

organism: Arabidopsis thaliana

source_name: Germinated seeds at the stage of root hair

label_protocol: Biotin-labeled cDNA was prepared using the Affymetrix NuGEN Ovation PicoSL WTA and Biotin Module from 50ng total RNA according to the manufacturer's specifications.

growth_protocol: Seeds were cold stratified for 72 h at 4˚C in 9 cm Petri dishes on two layers of blue filter paper and 10 ml of distilled water. After stratification, seeds were transferred to germination cabinets with constant white light at 22 ˚C.

extract_protocol: Total RNA was extracted following the hot borate protocol modified from Wan and Wilkins (1994) (Maia et al, Plos ONE 2011)

treatment_protocol: Three thousand seeds at each developmental stage were selected using a stereomicoscope.

tag: cultivar

tag: plant organ

value: seeds

tag: developmental stage


title: S1-H38

city: Houston

first: Suzanne

last: Fuqua

state: Texas

address: 1 Baylor Plaza

country: USA

institute: Baylor College of Medicine

description: log2 gene expression data

hyb_protocol: Standard Affymetix protocol for 3' IVT design

scan_protocol: Scanner GCS3000 7G

data_processing:
The data were analyzed with  Affy package in R, RMA method
Expressions estimated using RMA signal method

source_name: Human breast cancer

label_protocol: 3' IVT express

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

treatment_protocol: breast tumor samples, flash frozen

tag: tissue

tag: age (years)

tag: gender

value: Female

tag: race

value: Caucasian

tag: body mass index

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

value: Validation TN

value: Negative

value: TN

tag: metastases

value: No mets

value: Mesenchymal (MES)


title: S1-H35B

description: log2 gene expression data

tag: set

tag: er

tag: pr

tag: triple-negative status

tag: tumor grade

value: Poorly Differentiated

tag: tumor size

tag: positive nodes

tag: tnbc subtype


title: RH, biological rep3

tag: cultivar

tag: plant organ

tag: developmental stage

value: Germinated seeds at the stage of root hair


title: RH, biological rep1


title: PMEC_14

tag: biological replicates

value: ANIMAL_2 II

tag: treatment

tag: time


title: PMEC_13

value: ANIMAL_2 I


title: PMEC_12

value: ANIMAL_1 III

value: S. aureus


title: RP, biological rep1

description: Gene expression data from germinated Arabidopsis seeds at the stage of radicle protrusion

source_name: Germinated seeds at the stage of radicle protrusion


title: RP, biological rep3

value: Germinated seeds at the stage of radicle protrusion


title: RP, biological rep2


title: Healthy Control  repl7

description: This sample has not been analyzed in this publication.

tag: cell type

value: dermal fibroblasts

tag: disease state

value: healthy control


title: S1-H29

description: log2 gene expression data

tag: tissue

value: Breast cancer

tag: age (years)

tag: gender

value: Female

tag: race

tag: body mass index

tag: menopausal status

value: Post-Menopausal

tag: histology group

tag: histology

tag: ajcc stage (7th edition, 2010)


title: UCMD patient with AA repl1

value: UCMD

value: ascorbic acid


title: UCMD patient  repl1


title: PMEC_15

value: ANIMAL_2 III


title: PMEC_11

value: ANIMAL_1 II


title: S1-H31

description: log2 gene expression data

value: Caucasian

value: Infiltrating Ductal Carcinoma

tag: set

value: Validation TN

tag: er

value: Negative

tag: pr

tag: triple-negative status

value: TN

tag: tumor size

value: any size with direct extension

tag: positive nodes

tag: tnbc subtype

value: Mesenchymal (MES)


title: S1-H2B

description: log2 gene expression data

tag: tumor grade

value: Moderately Differentiated

tag: metastases

value: No mets

value: Luminal-AR (LAR)


title: PMEC_25

tag: biological replicates

value: ANIMAL_3 I

tag: treatment

value: unbehandelt

tag: time


title: Healthy Control  repl6

tag: cell type

value: dermal fibroblasts

tag: disease state

value: healthy control


title: Healthy Control with AA repl6

value: ascorbic acid


title: PMEC_9

value: ANIMAL_3 III

value: E. coli


title: PMEC_10

value: ANIMAL_1 I

value: S. aureus


title: PMEC_8

value: ANIMAL_3 II


title: Healthy Control  repl4


title: PMEC_7


title: TR, biological rep1

description: Gene expression data from Arabidopsis seeds at the stage of testa rupture

source_name: Testa rupture stage

tag: cultivar

tag: plant organ

value: seeds

tag: developmental stage

value: Testa rupture stage


title: TR, biological rep3


title: S1-H19

description: log2 gene expression data

tag: tissue

value: Breast cancer

tag: age (years)

tag: gender

value: Female

tag: race

value: Caucasian

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Validation TN

value: Negative

value: TN

value: Poorly Differentiated


title: 6H, biological rep3

description: Gene expression data from Arabidopsis seeds imbibed for 6 hours

source_name: 6 hours imbibed seeds

value: 6 hours imbibed seeds


title: PMEC_4

value: ANIMAL_2 I


title: Healthy Control  repl3

value: dermal fibroblasts

value: healthy control


title: S1-H10

description: log2 gene expression data

tag: body mass index

tag: menopausal status

value: Post-Menopausal

tag: er

tag: pr

tag: triple-negative status

tag: tumor size

tag: positive nodes

tag: metastases

value: No mets

tag: tnbc subtype

value: Mesenchymal (MES)


title: S1-H28

description: log2 gene expression data

tag: tissue

tag: tumor grade

value: Basal-Like Immune-Suppressed (BLIS)


title: 6H, biological rep1

tag: cultivar

tag: plant organ

value: seeds

tag: developmental stage


title: PMEC_5

tag: biological replicates

value: ANIMAL_2 II

tag: treatment

value: E. coli

tag: time


title: DS, biological rep3

description: Gene expression data from Arabidopsis matured dry seeds

source_name: Mature dry seeds

value: Mature dry seeds


title: S1-H27

description: log2 gene expression data

value: Breast cancer

tag: age (years)

tag: gender

value: Female

tag: race

value: Caucasian

tag: body mass index

value: Pre-menopausal

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set


title: PMEC_6

value: ANIMAL_2 III


title: S1-H14

description: log2 gene expression data

tag: menopausal status

value: Validation TN

tag: er

value: Negative

tag: pr

tag: triple-negative status

value: TN

value: Poorly Differentiated

tag: tumor size

tag: positive nodes

tag: metastases

tag: tnbc subtype

value: Basal-Like Immune-Activated (BLIA)


title: S1-H20B

description: log2 gene expression data

tag: tissue

value: Post-Menopausal

tag: tumor grade

value: No mets

value: Mesenchymal (MES)


title: 6H, biological rep2

tag: cultivar

tag: plant organ

value: seeds

tag: developmental stage

value: 6 hours imbibed seeds


title: Healthy Control with AA repl4

tag: cell type

value: dermal fibroblasts

tag: disease state

value: healthy control

tag: treatment

value: ascorbic acid


title: Healthy Control with AA repl2


title: S1-H22

description: log2 gene expression data

value: Breast cancer

tag: age (years)

tag: gender

value: Female

tag: race

value: Caucasian

tag: body mass index

tag: histology group

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set


title: TR, biological rep2

value: Testa rupture stage


title: Healthy Control with AA repl3


title: PMEC_3

tag: biological replicates

value: ANIMAL_1 III

value: E. coli

tag: time


title: PAM1316

status: Public on Dec 17 2015

type: genomic

city: Philadelphia

first: Daniel

middle: J

last: Rader

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
raw data file: genotyping_raw_Phase_1.txt
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system

hyb_protocol: standard Illumina protocol

scan_protocol: Illumina HiScan scanner

data_processing: SNP calling was performed with GenomeStudio (2010.3). Processed data file contains Genotype call (Genotype: A, T, C or G).

label: Cy3, Cy5

molecule: genomic DNA

source_name: Blood, high HDLC

label_protocol: Illumina Infinium HD Assay Kit

extract_protocol: genomic DNA was extracted from peripheral blood according to standard procedures.

tag: tissue

value: Blood

tag: hdlc status

value: high

tag: phase


title: HHDL2312


title: PDHS2875


title: HHDL2541

description:
raw data file: genotyping_raw_Phase_2.txt
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system


title: SCOR0054


title: HHDL2526


title: HHDL2058


title: HHDL2089


title: HHDL1392


title: HHDL1047


title: HHDL1184


title: PMEC_2

value: ANIMAL_1 II


title: Healthy Control  repl2


title: DS, biological rep1

tag: cultivar

tag: plant organ

tag: developmental stage

value: Mature dry seeds


title: HSC-3 cultured on top of plastic

city: Oulu

first: Pirjo

last: Åström

address: Aapistie 5A

country: Finland

institute: University of Oulu

description: HSC-3 cell line is an aggressive human oral tongue squamous cell carcinoma cell line labeled with RFP by stable transduction with commercial lentiviral particles containing a non-coding control sequence.

hyb_protocol: The cRNA was fragmented to 35 to 200 nt prior to hybridization to Affymetrix Human Genome U133 Plus 2.0 arrays containing approximately 55 000 human transcripts. The array was washed and stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR). Finally, biotinylated anti-streptavidin (Vector Laboratories Inc., Burlingame, CA) was used to amplify the staining signal and a second staining was performed with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned on a GeneChip Scanner 3000.

data_processing: The expression data was analyzed using dChip software.

source_name: Human oral tongue squamous cell carcinoma cells (HSC-3) cultured on top of uncoated plastic.

label_protocol: Three RNA samples were pooled; the pools contained an equal amount of RNA from each sample. In total, 1 µg of total RNA was used as a template to synthesize biotinylated cRNA by means of the GeneChip 3’IVT Express kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.

growth_protocol: HSC-3 (Japan Health Sciences Foundation, Japan) cells were cultured in a 1:1 DMEM/F-12 medium supplemented with 100 U/ml penicillin, 100 µg/ml streptomycin, 250 ng/ml fungizone, 50 µg/ml ascorbic acid and 0.4 µg/ml hydrocortisone and 10% heat inactivated fetal bovine serum. HSC-3 cells were labeled with RFP by stable transduction with commercial lentiviral particles containing a non-coding control sequence and selected with puromycin.

extract_protocol: The cells were harvested for RNA extraction using a Qiagen RNA kit (Hilden, Germany).

treatment_protocol: The cells were seeded into uncoated 6-well plates (three wells each). The next day the cells were harvested for RNA extraction.

tag: cell line


title: HSC-3 cultured on top of myogel

source_name: Human oral tongue squamous cell carcinoma cells (HSC-3) cultured on top of myogel coating.


title: PMEC_1

value: ANIMAL_1 I

tag: treatment


title: Healthy Control  repl1

tag: cell type

tag: disease state


title: Healthy Control with AA repl1


title: DS, biological rep2


title: HHDL0217

description:
raw data file: genotyping_raw_Phase_3.txt
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system


title: HHDL2304


title: HHDL2334


title: HHDL0099


title: CCS2194


title: HHDL1066


title: ProgressionFollowUp_Patient15

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

hyb_protocol: 60°C for 30 mins followed by 16h at 45°C

scan_protocol: BeadArray Reader protocol for DASL Gene Expression from Illumina

data_processing: No change, regression and progression follow up and baseline groups were compared separately. Background was removed using the detection P value algorithm. Normalization was done with the cubic spline algorithm. Differential expression of genes was done separately by group using the baseline values as reference.

source_name: Gastric tissue RNA at FollowUp

label_protocol: Streptavidin labeled cDNA was obtained following protocols from Illumina for FFPE samples (Cancer Panel). Streptavidin-labeled cDNA was then ampified using Cy3 and Cy5 labeled primers

growth_protocol: FFPE tissues of individuals with different satges of gastritis were used in this study

extract_protocol: Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissues using the RecoverAll Total Nucleic Acid Isolation from Ambion (Austin, TX), in five 10-20µm-thick tissue sections, as recommended by the vendor. The RNA was resuspended in DEPC-water and quantified by NanoDrop (ThermoFisher Scientific, Waltham, MA).

value: gastric tissue

value: Progression FollowUp gastric lesion

tag: subject

value: Patient 15


title: WT mice non-infected_sample 2

hyb_protocol: Hybridization using standard hybridization protocols from Illumina for 14h at 58°C

scan_protocol: Standard Illumina protocols for MouseWG-6_v2 chips from Illumina using the Illumina BeadArray Reader

data_processing: Background signal was removed using the Detection P value algorithm. Signals were normalized using the cubic spline algorithm. Differential expression was determined using the Illumina Custom Algorithm. Ratios were determined as the fraction between the treatments and the Control group

organism: Mus musculus

label_protocol: cRNA was labeled with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX),

growth_protocol: 6 week-old wild type and CD44-/- mice were maintained at specific pathogen free conditions.

extract_protocol: Total RNA was extracted with TriZol

treatment_protocol: Peritoneal macrophages were collected by peritoneal lavage with PBS three days after the peritoneal injection of thioglycollate

tag: genotype

value: WT


title: HHDL0572


title: ProgressionFollowUp_Patient13

value: Patient 13


title: ProgressionFollowUp_Patient11

value: Patient 11


title: WT mice H. pylori infected_sample 1


title: WT mice H. pylori infected_sample 2


title: CD44-/- mice non-infected_Sample 1


title: CD44-/- mice non-infected_Sample 2


title: ProgressionFollowUp_Patient10

value: Patient 10


title: ProgressionFollowUp_Patient8

value: Patient 8


title: ProgressionBaseline_Patient16

source_name: Gastric tissue RNA at baseline

value: Progression Baseline gastric lesion

value: Patient 16


title: ProgressionFollowUp_Patient9

value: Patient 9


title: ProgressionFollowUp_Patient3

value: Patient 3


title: ProgressionFollowUp_Patient2

value: Patient 2


title: ProgressionFollowUp_Patient4

value: Patient 4


title: ProgressionFollowUp_Patient7

value: Patient 7


title: ProgressionFollowUp_Patient6

value: Patient 6


title: WT mice non-infected_sample 1


title: ProgressionBaseline_Patient14

value: Patient 14


title: ProgressionFollowUp_Patient5

value: gastric tissue

value: Patient 5


title: ProgressionBaseline_Patient15

value: Patient 15


title: ProgressionFollowUp_Patient16

value: Progression FollowUp gastric lesion


title: ProgressionFollowUp_Patient1

value: Patient 1


title: ProgressionFollowUp_Patient12

value: Patient 12


title: ProgressionFollowUp_Patient14


title: ProgressionBaseline_Patient13

value: Patient 13


title: ProgressionBaseline_Patient12


title: CD44-/- mice H. pylori infected_Sample 2


title: CD44-/- mice H. pylori infected_Sample 1


title: ProgressionBaseline_Patient10

value: Patient 10


title: ProgressionBaseline_Patient6

value: Progression Baseline gastric lesion


title: ProgressionBaseline_Patient9


title: ProgressionBaseline_Patient5


title: ProgressionBaseline_Patient8

value: Patient 8


title: ProgressionBaseline_Patient7


title: ProgressionBaseline_Patient2


title: ProgressionBaseline_Patient4


title: RegressionFollowUp_Patient6

value: Regression FollowUp gastric lesion


title: RegressionFollowUp_Patient5


title: ProgressionBaseline_Patient1


title: RegressionFollowUp_Patient12


title: RegressionFollowUp_Patient9

value: Patient 9


title: RegressionFollowUp_Patient8


title: RegressionFollowUp_Patient3

value: Patient 3


title: RegressionFollowUp_Patient1


title: RegressionFollowUp_Patient2

value: Patient 2


title: RegressionBaseline_Patient11

value: Regression Baseline gastric lesion

value: Patient 11


title: ProgressionBaseline_Patient11


title: RegressionBaseline_Patient8


title: RegressionBaseline_Patient9


title: RegressionBaseline_Patient10


title: RegressionFollowUp_Patient11


title: ProgressionBaseline_Patient3


title: RegressionBaseline_Patient7

value: Patient 7


title: RegressionBaseline_Patient6

value: gastric tissue

value: Patient 6


title: RegressionBaseline_Patient5

value: Patient 5


title: RegressionBaseline_Patient2


title: RegressionFollowUp_Patient4

value: Patient 4


title: RegressionFollowUp_Patient10


title: RegressionBaseline_Patient4


title: RegressionFollowUp_Patient7


title: RegressionBaseline_Patient1

value: Patient 1


title: RegressionBaseline_Patient3


title: RegressionBaseline_Patient12

value: Patient 12


title: NoChangeFollowUp_Patient11

value: No Change FollowUp gastric lesion


title: NoChangeFollowUp_Patient9


title: NoChangeFollowUp_Patient10

value: Patient 10


title: NoChangeFollowUp_Patient7


title: NoChangeFollowUp_Patient6


title: NoChangeFollowUp_Patient4


title: NoChangeFollowUp_Patient5


title: NoChangeFollowUp_Patient3


title: NoChangeBaseline_Patient11

value: No Change Baseline gastric lesion


title: NoChangeFollowUp_Patient1


title: NoChangeBaseline_Patient9


title: NoChangeBaseline_Patient8

value: Patient 8


title: NoChangeBaseline_Patient10


title: NoChangeBaseline_Patient7


title: NoChangeFollowUp_Patient8


title: NoChangeBaseline_Patient6


title: NoChangeFollowUp_Patient2


title: NoChangeBaseline_Patient4


title: NoChangeBaseline_Patient3


title: NoChangeBaseline_Patient5


title: Term_CBLe_sample_8_female_39_weeks

city: Medford

first: Heather

middle: C

last: Wick

state: MA

address: 161 College Ave

department: Department of Computer Science

institute: Tufts University

description: Term CB Lean Sample 8 female 39 weeks

hyb_protocol: Arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method.  To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.

source_name: RNA from term umbilical cord blood

label_protocol: Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)

extract_protocol: RNA was extracted from 2.5-5 mL of umbilical cord blood preserved in PAXgene tubes. All samples were extracted using the Preanalytix PAXgene blood RNA kit. The RNA was then purified and eluted in RNasefree water. RNA was converted to cDNA and amplified using the NuGEN Ovation RNA Amplification System V2 with Ovation Whole Blood reagent, and then purified with the QIAquick PCR Purification kit.

tag: baby gender

value: female

tag: maternal weight

value: lean

value: term umbilical cord blood


title: NoChangeBaseline_Patient2

value: Patient 2


title: NoChangeBaseline_Patient1


title: Term_CBLe_sample_6_female_39_weeks

description: Term CB Lean Sample 6 female 39 weeks


title: Term_CBLe_sample_3_male_39_weeks

description: Term CB Lean Sample 3 male 39 weeks

value: male


title: Term_CBLe_sample_7_male_39_weeks

description: Term CB Lean Sample 7 male 39 weeks


title: Term_CBLe_sample_5_female_39_weeks

description: Term CB Lean Sample 5 female 39 weeks


title: Term_CBLe_sample_1_female_39_weeks

description: Term CB Lean Sample 1 female 39 weeks


title: Term_CBLe_sample_4_male_39_weeks

description: Term CB Lean Sample 4 male 39 weeks


title: Term_CBOB_sample__male_40_weeks

description: Term CB OB Sample 8 female 39 weeks

value: obese


title: Term_CBLe_sample_2_male_39_weeks

description: Term CB Lean Sample 2 male 39 weeks


title: H99_HiFe

city: Lynchburg

first: Michael

middle: S

last: Price

state: VA

address: 1971 University Blvd.

department: Biology & Chemistry

institute: Liberty University

description:
Raw data files:
3160_10464_v2_168_CNWash_7_10.gpr
3160_10465_v2_169_CNWash_1_7.gpr
3160_10466_v2_170_CNWash_8_2.gpr
3160_10467_v2_171_CNWash_11_8.gpr
3160_10471_v2_175_CNWash_9_12.gpr
3160_10472_v2_176_CNWash_6_9.gpr
Lsmean Treatment*Iron WT hi

hyb_protocol: Hybridization was performed at the Duke University Microarray Facility following the Hybridization protocol (http://www.genome.duke.edu/cores/microarray/).

scan_protocol: Slides were scanned at the Duke University Microarray Facility using an Axon Genepix 4000B scanner (http://www.genome.duke.edu/cores/microarray/).

data_processing: Data was analyzed using JMP genomics (SAS institute, Cary NC) and initial background subtraction was performed. Data were normalized using the Array Normalization process in JMP.

organism: Cryptococcus neoformans

source_name: yeast culture

label_protocol: Labeling was performed at the Duke University Microarray Facility following the 1 Round Amp Labeling protocol for spotted arrays (http://www.genome.duke.edu/cores/microarray/).

growth_protocol: The WT strain and the mig1Δ::NAT mutant were used for expression analysis using microarrays. Three biological replicates for each strain were grown in 10 ml of YPD overnight at 30°C. Cells were washed three times with low iron water and counted. Cells were inoculated in 5 ml of LIM or LIM + 100µM FeCl3 at 5X107 cells/ml, grown at 30°C for an additional 6 h and harvested for RNA extraction.

extract_protocol: Cells were broken by bead beating using a Retsch MM301 mixer mill and RNA was extracted with RNeasy kit (Qiagen) and treated with DNase (Qiagen) according to the manufacturer’s recommendations. The quality of RNA was analyzed with an Agilent 2100 Bioanalyzer and cDNA was synthesized using a Verso cDNA kit (Thermo Scientific).

tag: background strain

tag: genotype/variation

value: WT

value: LIM + 100mM FeCl3


title: Term_CBOB_sample_6_female_39_weeks

description: Term CB OB Sample 6 female 39 weeks


title: Term_CBOB_sample_7_male_40_weeks

description: Term CB OB Sample 7 male 40 weeks


title: Term_CBOB_sample_5_female_39_weeks

description: Term CB OB Sample 5 female 39 weeks


title: Term_CBOB_sample_1_female_39_weeks

description: Term CB OB Sample 1 female 39 weeks


title: mig1_HiFe

description:
Raw data files:
3160_10463_v2_88up_CNWash_10_4.gpr
3160_10464_v2_168_CNWash_7_10.gpr
3160_10467_v2_171_CNWash_11_8.gpr
3160_10468_v2_172_CNWash_5_11.gpr
3160_10470_v2_174_CNWash_12_3.gpr
3160_10471_v2_175_CNWash_9_12.gpr
Lsmean Treatment*Iron mig1 hi

value: mig1 deletion mutant


title: mig1_LoFe

description:
Raw data files:
3160_10462_v2_74_CNWash_4_1.gpr
3160_10463_v2_88up_CNWash_10_4.gpr
3160_10468_v2_172_CNWash_5_11.gpr
3160_10469_v2_173_CNWash_2_5.gpr
3160_10472_v2_176_CNWash_6_9.gpr
3160_10473_v2_178_CNWash_3_6.gpr
Lsmean Treatment*Iron mig1 lo

value: LIM


title: H99_LoFe

description:
Raw data files:
3160_10462_v2_74_CNWash_4_1.gpr
3160_10465_v2_169_CNWash_1_7.gpr
3160_10466_v2_170_CNWash_8_2.gpr
3160_10469_v2_173_CNWash_2_5.gpr
3160_10470_v2_174_CNWash_12_3.gpr
3160_10473_v2_178_CNWash_3_6.gpr
Lsmean Treatment*Iron WT lo


title: Kit+ progenitor cells sample 2

city: St Louis

first: John

last: Welch

state: MO

address: 660 South Euclid Ave

institute: Washington University

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module,5.0 ug of cDNA were hybridized into the GeneChip Hybridization Oven 640 for 18 hr at 45C on Exon 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were QC’d using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotations were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

source_name: Kit+ progenitor cells

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen WT-Ovation Pico RNA Amplification system from 500pg-50 ng total RNA

growth_protocol: Kit+ cells: Femurs, tibias, and pelvises were isolated from 6-8 weeks old UAS-GFP mice. Bone marrow cells were collected by centrifuging bones at 6000rpm for 2 minutes. Red blood cells were lysed by ACK Buffer (NH4Cl 150mM, KHCO3 10mM, Na2EDTA 0.1mM) on ice for 5 minutes.  Kit+ cells were isolated by magnetic-activated cell sorting (MACS) using an Automacs Pro (Miltenyl Biotec, San Diego, CA) per manufacture’s protocol. 1.5 million Kit+ cells per well were plated in 12-well-plate in progenitor cell expansion medium (RPMI 1640 +15% FBS + 50 ng/ml Scf + 25 ng/ml Flt3 + 10 ng/ml IL3 + 10 ng/ml Tpo + 50 µM β-Mercaptoethanol) for 4 days. Bone marrow-derived macrophages (BMMφ): Mouse bone marrow Kit- cells were isolated as above and grown in macrophage differentiation media (α-MEM + 10% FBS + 50 ng/ml MCSF) for 4 days.

extract_protocol: RNA was collected using Trizol per protocol.

tag: strain background

value: UAS-GFP mice

tag: age

value: 6-8 weeks old

value: Kit+ progenitor cells


title: Kit+ progenitor cells sample 3


title: Term_CBOB_sample_2_male_39_weeks

description: Term CB OB Sample 2 male 39 weeks

tag: tissue


title: Term_CBOB_sample_4_male_39_weeks

description: Term CB OB Sample 4 male 39 weeks


title: Term_CBOB_sample_3_male_39_weeks

description: Term CB OB Sample 3 male 39 weeks


title: mouse bone marrow-derived macrophages sample 3

source_name: bone marrow-derived macrophage

value: bone marrow-derived macrophage


title: Kit+ progenitor cells sample 1


title: mouse bone marrow-derived macrophages sample 1


title: mouse bone marrow-derived macrophages sample 2


title: t2-4b: human expression

city: Cleveland

last: Barnard

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic Foundation

description: human expression

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Bead averaged per probe on log2 scale, background-corrected using normal-gamma deconvolution model, log2 transformed with offset, quantile normalized

source_name: tumor escape BR 4 TR b

label_protocol: Three hundred nanograms of RNA was amplified and biotinylated for hybridization to Illumina Human Beadchips (HumanHT-12 v.4, Illumina, Inc., San Diego, CA) and also to Murine Beadchips (mouseRef-8 v2.0) using Illumina TotalPrep RNA Amplification Kit (AMIL1791, Applied Biosystem) according to the manufacturer’s protocol.

growth_protocol: The Ren-02 primary human RCC cell line was established from a patient-derived primary clear cell renal carcinoma.  This 42-year old male patient had metastatic clear cell RCC with disease progression after bevacizumab-based systemic therapy. A subcutaneous tumor nodule was biopsied, dissociated using the GentleMACS system (Miltenyi, San Diego, CA) and a continuous cell line established. For xenograft establishment, cells were expanded in vitro and  6 week old male NOD-scid-IL2r-/- (NSG) mice (Jackson Laboratories) were inoculated subcutaneously in the flanks with 2x106 Ren-02 cells (passage 3).

extract_protocol: Total RNA from individual tumors was prepared using the RNeasy Mini kit (Qiagen, Valencia, CA) with on-column DNase treatment (Qiagen # 79254) per manufacturer’s protocol. RNA was quantified by Nanodrop (ND-1000, Thermo Fisher Scientific, Wilmington, DE) and RNA integrity was assessed by agarose gel electrophoresis.

treatment_protocol: Treatment with sunitinib 40 mg/kg/d by gavage (Pfizer) was started 14d after tumor inoculation

value: RCC PDX tumor

tag: group

value: escape

tag: biological replicate

tag: technical replicate

value: b

tag: mouse


title: t2-2a: human expression

description: human expression

source_name: tumor escape BR 2 TR a

value: a


title: Lm+1722 HepG2_4/Lm HepG2_3

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

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

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

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: Lm HepG2_3

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

extract_protocol: Total RNA was isolated from HepG2 samples using miRNeasy kit (QIAGEN).

treatment_protocol: HepG2 cells were treated with 50 ng/ml IL-17A and 10 ng/ml IL-22 before L. monocytogenes in vitro infection at MOI 10. Reference cells were not treated with the cytokines before the infection. Two independe experiments were carried out.

tag: cell line

value: HepG2 human hepatocellular carcinoma line

tag: infection

value: L. monocytogenes

value: IL-17A and IL-22 before L. monocytogenes infection


title: Lm+1722 HepG2/Lm HepG2

source_name: Lm HepG2

source_name: Lm+1722 HepG2

tag: treatment


title: t2-3a: human expression

description: human expression

source_name: tumor escape BR 3 TR a


title: t2-1a: human expression

description: human expression

source_name: tumor escape BR 1 TR a


title: t2-1b: human expression

description: human expression

source_name: tumor escape BR 1 TR b


title: t2-2b: human expression

description: human expression

source_name: tumor escape BR 2 TR b


title: t2-3b: human expression

description: human expression

source_name: tumor escape BR 3 TR b


title: t1-4b: human expression

description: human expression

source_name: tumor response BR 4 TR b

value: response


title: t1-3b: human expression

description: human expression

source_name: tumor response BR 3 TR b


title: t1-1a: human expression

description: human expression

source_name: tumor response BR 1 TR a


title: t1-2b: human expression

description: human expression

source_name: tumor response BR 2 TR b


title: t1-1b: human expression

description: human expression

source_name: tumor response BR 1 TR b


title: t2-4a: human expression

description: human expression

source_name: tumor escape BR 4 TR a


title: pre3b: human expression

description: human expression

source_name: tumor pre-treatment BR 3 TR b

value: pre-treatment


title: THP-1 p21-3 CRISPR KLF4 virus

city: Seattle

first: Vivian

middle: G.

last: Oehler

state: Washington

address: 1100 Fairview Ave N. D5-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

data_processing: Signal intensities were quantile normalized using the Bioconductor package “lumi”

source_name: THP-1 cells

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

extract_protocol: Total RNA was extracted using Trizol and the Qiagen miRNEasy isolation kit.

treatment_protocol: Total RNA isolated from THP1 cells infected with KLF4 or empty control (ECV) lentivirus 5 days post infection (dpi), CRISPR cells were 17 days post selection.

value: 5 dpi KLF4, p21-targeting CRISPR


title: t1-4a: human expression

description: human expression

source_name: tumor response BR 4 TR a


title: pre3a: human expression

description: human expression

source_name: tumor pre-treatment BR 3 TR a


title: t1-3a: human expression

description: human expression

source_name: tumor response BR 3 TR a


title: pre1a: human expression

description: human expression

source_name: tumor pre-treatment BR 1 TR a


title: pre4a: human expression

description: human expression

source_name: tumor pre-treatment BR 4 TR a


title: THP-1 p21-3 CRISPR empty control virus

value: 5 dpi ECV, p21-targeting CRISPR


title: pre2a: human expression

description: human expression

source_name: tumor pre-treatment BR 2 TR a


title: THP-1 p21-2 CRISPR KLF4 virus


title: pre4b: human expression

description: human expression

source_name: tumor pre-treatment BR 4 TR b


title: THP-1 p21-2 CRISPR empty control virus


title: THP-1 150-4 CRISPR KLF4 virus

value: 5 dpi KLF4, miR-150-targeting CRISPR


title: t1-2a: human expression

description: human expression

source_name: tumor response BR 2 TR a


title: misfoldingGFP_minusUra_log

city: Japan

first: Hisao

last: Moriya

state: Okayama

address: 3-1-1 Tsushima-Naka

department: RCIS

institute: Okayama University

hyb_protocol: Gene expression hybridization kit

scan_protocol: Agilent Technologies Scanner G2505C US85000255

data_processing: Agilent feature extraction

organism: Saccharomyces cerevisiae

source_name: PYK1promoter-misfoldingGFP, SC–Ura medium, log phase cells

label_protocol: Low input quick amp labeling kit

growth_protocol: Yeast cells were grown in SC-Ura medium to the mid log-phase

extract_protocol: Hot-phenol method

treatment_protocol: Cells were collected by centrifugation

tag: strain


title: ssGFP_minusUra_log

source_name: PYK1promoter-ssGFP, SC–Ura medium, log phase cells


title: pre2b: human expression

description: human expression

source_name: tumor pre-treatment BR 2 TR b


title: pre1b: human expression

description: human expression

source_name: tumor pre-treatment BR 1 TR b


title: NES-GFP_minusUra_log

source_name: HXT7promoter-NES-GFP, SC–Ura medium, log phase cells


title: MTS-GFP_minusUra_log

source_name: PYK1promoter-MTS-GFP, SC–Ura medium, log phase cells


title: GFPdeg_minusUra_log

source_name: TDH3promoter-GFPdeg, SC–Ura medium, log phase cells


title: THP-1  NT-3 CRISPR empty control virus

value: 5 dpi ECV, non-targeting CRISPR


title: THP-1 150-3 CRISPR KLF4 virus


title: GFP_minusUra_log

source_name: TDH3promoter-GFP, SC–Ura medium, log phase cells


title: THP-1  NT-2 CRISPR KLF4 virus

source_name: THP-1 cells

value: 5 dpi KLF4, non-targeting CRISPR


title: THP-1  NT-2 CRISPR empty control virus


title: t2-4: mouse expression

description: mouse expression

source_name: tumor escape BR 4 TR a


title: t2-3: mouse expression

description: mouse expression

source_name: tumor escape BR 3 TR a


title: THP-1 150-3 CRISPR empty control virus

value: 5 dpi ECV, miR-150-targeting CRISPR


title: Vector_minusUra_log

source_name: Empty vector, SC–Ura medium, log phase cells


title: t2-2: mouse expression

description: mouse expression

source_name: tumor escape BR 2 TR a


title: t1-4b: mouse expression

description: mouse expression

source_name: tumor response BR 4 TR b


title: T47D_PRB_R5020_2

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description:
T47D_PRB_R_2
Replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were filtered and any probes with a detection P value less than 0.05 were removed from the normalized dataset. The data was then normalized using log2 transformation and quantile normalization with R using the lumi bioconductor package.

label: Biotin

source_name: Breast T47D cell line, progesterone receptor isoform B expressing, R5020 treated 24 hr

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

growth_protocol: Samples grown in complete medium (MEM, 5% FBS, 1% NEAA, 1% pen/strep, 6ng/ml insulin, 200 ug/ml G418) before 1 day starvation in IMEM medium plus 5% DCC, then treated in IMEM medium plus 5% DCC for 24 hr.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Samples treated in IMEM medium plus 5% DCC, with or without 10e-8 M R5020 for 24 hr.

tag: parental cell line

tag: parental cell type

value: breast cancer cell line

tag: stable vector integration

tag: time point

value: 24 hr


title: T47D_PRB_R5020_1

description:
T47D_PRB_R_1
Replicate 1


title: t2-1: mouse expression

description: mouse expression

source_name: tumor escape BR 1 TR a

value: RCC PDX tumor


title: t1-3a: mouse expression

description: mouse expression

source_name: tumor response BR 3 TR a


title: T47D_PRB_vehicle_3

description:
T47D_PRB_V_3
Replicate 3

source_name: Breast T47D cell line, progesterone receptor isoform B expressing, vehicle treated 24 hr

value: ethanol vehicle


title: t1-4a: mouse expression

description: mouse expression

source_name: tumor response BR 4 TR a


title: T47D_PRB_vehicle_2

description:
T47D_PRB_V_2
Replicate 2


title: T47D_PRB_R5020_3

description:
T47D_PRB_R_3
Replicate 3


title: t1-3b: mouse expression

description: mouse expression

source_name: tumor response BR 3 TR b

value: b


title: T47D_PRA_R5020_3

description:
T47D_PRA_R_3
Replicate 3

source_name: Breast T47D cell line, progesterone receptor isoform A expressing, R5020 treated 24 hr


title: t1-1b: mouse expression

description: mouse expression

source_name: tumor response BR 1 TR b


title: T47D_PRA_R5020_1

description:
T47D_PRA_R_1
Replicate 1


title: THP-1  NT-3 CRISPR KLF4 virus


title: t1-2a: mouse expression

description: mouse expression

source_name: tumor response BR 2 TR a

value: a


title: pre4: mouse expression

description: mouse expression

source_name: tumor pre-treatment BR 4 TR a


title: t1-2b: mouse expression

description: mouse expression

source_name: tumor response BR 2 TR b


title: T47D_PRA_R5020_2

description:
T47D_PRA_R_2
Replicate 2


title: T47D_PRB_vehicle_1

description:
T47D_PRB_V_1
Replicate 1


title: pre2: mouse expression

description: mouse expression

source_name: tumor pre-treatment BR 2 TR a


title: T47D_PRA_vehicle_2

description:
T47D_PRA_V_2
Replicate 2

source_name: Breast T47D cell line, progesterone receptor isoform A expressing, vehicle treated 24 hr


title: T47D_PRA_vehicle_3

description:
T47D_PRA_V_3
Replicate 3


title: pre1: mouse expression

description: mouse expression

source_name: tumor pre-treatment BR 1 TR a


title: pre3: mouse expression

description: mouse expression

source_name: tumor pre-treatment BR 3 TR a


title: T47D_PRnull_R5020_2

description:
T47D_NULL_R_2
Replicate 2

source_name: Breast T47D cell line, progesterone receptor null, R5020 treated 24 hr


title: HK-1 treated with PBS

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110  Xiangya  Road

department: Cancer  Research Institute

country: China

institute: Central South University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix® Multispecies miRNA 2.0  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: nasopharyngeal carcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

growth_protocol: The human nasopharyngeal carcinoma cell lines HK1 Cells were cultured in both RPMI1640 medium supplemented with 10% fetal bovine serum, 100 units/m of penicillin and streptomycin. Cultures were incubated at 37°C in a humidified incubator at 5% CO2.

treatment_protocol: Cells were grown in serum-free medium for 12 hours, and then EGF (50 ng/mL) or TGF-β (10ng/ml) or Control (PBS) was added in RPMI-1640 medium (with 1% serum) for an additional 36 hours.

tag: agent

value: PBS


title: T47D_PRnull_R5020_3

description:
T47D_NULL_R_3
Replicate 3


title: T47D_PRA_vehicle_1

description:
T47D_PRA_V_1
Replicate 1


title: HK-1 treated with EGF (50 ng/mL) for 36 h

value: EGF (50 ng/mL)


title: mouse tongue tumor 5

city: Kwei-Shan Tao-Yuan

first: An

last: Hsu

address: 259 Wen-Hwa 1st Road

country: Taiwan

institute: Chang Gung University

description: tongue tumor 5

data_processing: The data were extracted from Illumina BeadStudio software followed by log2 transformed and normalised using shift median in Partek Genomics Suite (version 6.6).

source_name: tongue tumor

extract_protocol: Invitrogen TRIzol reagent was used for extraction of tissue total RNA. Total RNA was quantified by Thermo Scientific NanoDrop spectrophotometer. The quality of total RNA was determined by Agilent 2100 Bioanalyzer.

treatment_protocol: Carcinogen-induced mice were treated with 200 µg/mL 4NQO and 500 µg/mL of arecoline for 8 weeks while contol mice were treated with DMSO for 8 weeks. After a 20-week rest period, all mice were sacrificed and normal tongue and tumor samples were removed and collected.

value: 8 months

value: tongue tumor


title: mouse tongue tumor 6

description: tongue tumor 6


title: T47D_PRnull_R5020_1

description:
T47D_NULL_R_1
Replicate 1


title: T47D_PRnull_vehicle_3

description:
T47D_NULL_V_3
Replicate 3

source_name: Breast T47D cell line, progesterone receptor null, vehicle treated 24 hr


title: HK-1 treated with TGF-β (10ng/ml) for 36 h

value: TGF-β (10ng/ml)


title: Sample_ID_9

city: South San Francisco

first: Mark

last: McCreary

state: California

address: 1 DNA Way, MS 93

department: Bioinformatics

institute: Genentech

description:
ST2 Knockout mouse retina (Normal) at day 0 - SampleID: SAM11945664 - Inventory Sample: 9
SAM11945664

hyb_protocol: Cy-dye-labeled cRNA was fragmented and hybridized to the Agilent’s whole mouse genome array as described in Agilent’s In Situ Hybridization Kit Plus.

scan_protocol: Following hybridization, the arrays were washed, dried and scanned on Agilent’s DNA microarray scanner

data_processing: Array imaging data was analyzed using Agilent’s Feature Extraction software 8.5. Raw feature extracted data were processed as previously described (Vander Lugt et al., 2014). Microarray data were filtered to include only a single probe per gene, selecting the probe with the highest variance when multiple probes were present for a given gene (Bourgon et al., 2010). Differential expression analysis was performed using the limma software package (Smyth, 2004). To identify genes differentially regulated in the ST2-/- mice, we first identified probes up-regulated by constant light exposure in ST2+/+ mice, selecting probes that showed >1.5 fold change at a Benjamini-Hochberg (Hochberg and Benjamini, 1990) adjusted P value of <0.01. These probes were further filtered to those that showed >1.25-fold difference at a Benjamini-Hochberg adjusted P value of <0.05 between ST2+/+ and ST2-/- mice

source_name: ST2 KO d0

label_protocol: Total RNA was converted to double-stranded cDNA and then to Cy-dye labeled cRNA using an Agilent Fluorescent Linear Amplification kit. All samples were labeled with Cy5 dye and hybridized against Cy3 dye-labeled universal mouse reference

growth_protocol: ST2 knock-out (ST2-/-) BALB/c mice were kindly provided by Dr. Andrew McKenzie (MRC Laboratory of Molecular Biology, Cambridge, UK) (Townsend et al., 2000). ST2-/- mice were backcrossed to the C57Bl/6J background for ten generations to generate ST2-/- C57Bl/6J mice. IL33tm1/+ and IL33tm2/tm2 BALB/c mice were obtained from Dr. Antonio Iglesias (F. Hoffmann-La Roche Ltd, Basel, Switzerland) (Bessa et al., 2014). Due to significant morbidity and mortality of IL33tm1/+ mice, IL33tm1/+ mice were crossed with ST2-/- BALB/c mice and maintained on ST2-/- background. IL33tm1/tm1 ST2+/- mice were generated by breeding female IL33tm1/+ST2-/- mice with male IL33tm1/+ST2+/+ mice. IL-1R1-/- (Il1r1tm1Imx), IL-18R1-/- (Il18r1tm1Aki) and IL-18-/- (Il18tm1Aki) C57Bl/6 mice were purchased from The Jackson Laboratory. IL-1R1-/- and IL-18R1-/- mice were backcrossed to the BALB/c background by speed congenics to generate IL-1R1-/- and IL-18R1-/- BALB/c mice respectively. Sprague-Dawley rats were purchased from The Charles River Laboratories. All animals were housed in pathogen free animal facility at Genentech with 12/12 h of light/dark cycle. Animal experiments were conducted in accordance with protocols approved by the Genentech Institutional Animal Care and Use Committee.

extract_protocol: After removal of the cornea, the anterior chamber fluid was absorbed with a Sugi wedge-shaped absorbent swab (Kettenbach Medical). The lens with the vitreous body attached was carefully pulled out from the posterior chamber using an angled microsurgical forceps. The lens-vitreous tissue was placed into a filtered centrifugation tube (Costar) containing 20 µl of protease inhibitor cocktail (Roche) dissolved in PBS and centrifuged at 14,000 x G for 5 min at 4 C. The vitreous was collected as the eluent from the lower chamber. The retina was separated from the sclera and RPE/choroid and rinsed in PBS. The retina was either dissociated for FACS analysis or homogenized for ELISA and Western blotting. Retina and RPE/choroid were homogenized in the cell lysis buffer (Cell Signaling Technology) using a tissue homogenizer (IKA). The retina and RPE/choroid homogenate was centrifuged at 14, 000 x G for 10 min at 4 C and the supernatant was collected. The vitreous and retina tissue lysates were stored at -80 C until analysis

treatment_protocol: Male BALB/c mice aged 8-12 weeks were kept in normal housing with light intensity of <100 lux (used for baseline, d0). For light exposure, animals were housed singly in slightly modified normal cages covered with only a flat wire rack with no filter lid. To avoid disruption of light entering the cages, food pellets were placed on the bottom of cages and water was provided through a water bottle attached to the side of the cages. Retinal degeneration was induced by placing the cages on the shelves of a Metro rack outfitted with 48” fluorescent cool white lights above each shelf. The rack was also enclosed in hanging white panels to reflect light evenly back to shelves. Shelf height was adjusted in relation to light source so that light intensity on each shelf was ~1200 lux as measured by a light meter. Cages were rotated within each shelf and between shelves during CLE to ensure equal light exposure. Animals were exposed to light for various days as indicated before evaluation.

tag: primary tissue

value: Eye - retina

tag: tissue diagnosis

value: Normal

tag: genotype

value: ST2 KO

source_name: Universal mouse reference

tag: reference

value: Universal mouse reference


title: mouse tongue tumor 7

description: tongue tumor 7

tag: age

tag: tissue


title: mouse tongue tumor 1

description: tongue tumor 1


title: Sample_ID_19

description:
ST2 Knockout mouse retina (Degenerative) at day 3 - SampleID: SAM11945674 - Inventory Sample: 19
SAM11945674

source_name: ST2 KO d3

value: Degenerative


title: mouse tongue tumor 4

description: tongue tumor 4


title: mouse tongue tumor 3

description: tongue tumor 3


title: Sample_ID_21

description:
Wildtype mouse retina (Degenerative) at day 10 - SampleID: SAM11945676 - Inventory Sample: 21
SAM11945676

source_name: WT d10

value: WT


title: T47D_PRnull_vehicle_1

description:
T47D_NULL_V_1
Replicate 1

value: breast cancer cell line


title: mouse tongue tumor 2

description: tongue tumor 2


title: Sample_ID_12

description:
Wildtype mouse retina (Degenerative) at day 3 - SampleID: SAM11945667 - Inventory Sample: 12
SAM11945667

source_name: WT d3


title: ES2_PRB_R5020_2

description:
OV_PRB_R_2
Replicate 2

source_name: Ovarian ES-2 cell line, progesterone receptor isoform B expressing, R5020 treated 24 hr

growth_protocol: Samples grown in McCoy's 5A Modified medium supplemented with 10% charcoal-stripped fetal bovine serum (i.e., DCC), 100 units/mL penicillin, 100 μg/mL streptomycin, and 0.5 mg/mL of G418 sulfate before 1 day starvation in IMEM medium plus 5% DCC, then treated in IMEM medium plus 5% DCC for 24 hr.

value: ovarian cancer cell line

value: 24 hr


title: ES2_PRB_R5020_1

description:
OV_PRB_R_1
Replicate 1


title: Sample_ID_18

description:
ST2 Knockout mouse retina (Degenerative) at day 3 - SampleID: SAM11945673 - Inventory Sample: 18
SAM11945673


title: ES2_PRB_R5020_3

description:
OV_PRB_R_3
Replicate 3


title: Sample_ID_29

description:
ST2 Knockout mouse retina (Degenerative) at day 10 - SampleID: SAM11945684 - Inventory Sample: 29
SAM11945684

source_name: ST2 KO d10


title: mouse normal tongue 5

description: normal tongue 5

source_name: normal tongue

value: tongue


title: ES2_PRB_vehicle_2

description:
OV_PRB_V_2
Replicate 2

source_name: Ovarian ES-2 cell line, progesterone receptor isoform B expressing, vehicle treated 24 hr

value: ethanol vehicle


title: mouse normal tongue 4

description: normal tongue 4


title: ES2_PRB_vehicle_3

description:
OV_PRB_V_3
Replicate 3


title: THP-1 150-4 CRISPR empty control virus

source_name: THP-1 cells

value: 5 dpi ECV, miR-150-targeting CRISPR


title: Sample_ID_30

description:
ST2 Knockout mouse retina (Degenerative) at day 10 - SampleID: SAM11945685 - Inventory Sample: 30
SAM11945685


title: mouse normal tongue 3

description: normal tongue 3


title: mouse normal tongue 2

description: normal tongue 2


title: Sample_ID_23

description:
Wildtype mouse retina (Degenerative) at day 10 - SampleID: SAM11945678 - Inventory Sample: 23
SAM11945678


title: ES2_PRA_R5020_2

description:
OV_PRA_R_2
Replicate 2

source_name: Ovarian ES-2 cell line, progesterone receptor isoform A expressing, R5020 treated 24 hr


title: Sample_ID_13

description:
Wildtype mouse retina (Degenerative) at day 3 - SampleID: SAM11945668 - Inventory Sample: 13
SAM11945668


title: ES2_PRA_R5020_3

description:
OV_PRA_R_3
Replicate 3


title: ES2_PRB_vehicle_1

description:
OV_PRB_V_1
Replicate 1


title: Sample_ID_11

description:
Wildtype mouse retina (Degenerative) at day 3 - SampleID: SAM11945666 - Inventory Sample: 11
SAM11945666


title: Sample_ID_27

description:
ST2 Knockout mouse retina (Degenerative) at day 10 - SampleID: SAM11945682 - Inventory Sample: 27
SAM11945682


title: ES2_PRA_R5020_1

description:
OV_PRA_R_1
Replicate 1


title: ES2_PRA_vehicle_3

description:
OV_PRA_V_3
Replicate 3

source_name: Ovarian ES-2 cell line, progesterone receptor isoform A expressing, vehicle treated 24 hr


title: mouse normal tongue 1

description: normal tongue 1


title: Sample_ID_2

description:
Wildtype mouse retina (Normal) at day 0 - SampleID: SAM11945657 - Inventory Sample: 2
SAM11945657

source_name: WT d0


title: T47D_PRnull_vehicle_2

description:
T47D_NULL_V_2
Replicate 2


title: ES2_PRA_vehicle_2

description:
OV_PRA_V_2
Replicate 2


title: Sample_ID_15

description:
Wildtype mouse retina (Degenerative) at day 3 - SampleID: SAM11945670 - Inventory Sample: 15
SAM11945670


title: Sample_ID_5

description:
Wildtype mouse retina (Normal) at day 0 - SampleID: SAM11945660 - Inventory Sample: 5
SAM11945660


title: Sample_ID_24

description:
Wildtype mouse retina (Degenerative) at day 10 - SampleID: SAM11945679 - Inventory Sample: 24
SAM11945679


title: ES2_PRA_vehicle_1

description:
OV_PRA_V_1
Replicate 1


title: ES2_PRnull_R5020_1

description:
OV_NULL_R_1
Replicate 1

source_name: Ovarian ES-2 cell line, progesterone receptor null, R5020 treated 24 hr


title: Sample_ID_8

description:
ST2 Knockout mouse retina (Normal) at day 0 - SampleID: SAM11945663 - Inventory Sample: 8
SAM11945663


title: Sample_ID_4

description:
Wildtype mouse retina (Normal) at day 0 - SampleID: SAM11945659 - Inventory Sample: 4
SAM11945659


title: ES2_PRnull_vehicle_3

description:
OV_NULL_V_3
Replicate 3

source_name: Ovarian ES-2 cell line, progesterone receptor null, vehicle treated 24 hr


title: ES2_PRnull_R5020_3

description:
OV_NULL_R_3
Replicate 3


title: ES2_PRnull_R5020_2

description:
OV_NULL_R_2
Replicate 2


title: Sample_ID_6

description:
ST2 Knockout mouse retina (Normal) at day 0 - SampleID: SAM11945661 - Inventory Sample: 6
SAM11945661


title: Sample_ID_22

description:
Wildtype mouse retina (Degenerative) at day 10 - SampleID: SAM11945677 - Inventory Sample: 22
SAM11945677


title: ES2_PRnull_vehicle_1

description:
OV_NULL_V_1
Replicate 1


title: siRNF20_R3

city: London

first: Sharon

last: Tooze

state: London

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Francis Crick Institute / London Research Institute

description: Transfected with siRNA and maintained nutrient replete conditions

hyb_protocol: Hybridisation to Illumina HT12v4 Bead array chip was carried out as per manufacturer's instructions

scan_protocol: Bead Array was scanned using the protocol of the Genome Centre, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom, EC1M 6BQ

data_processing: Data was analysed using Biocondutor 2.12 running on R3.0.0. Raw data was transformed using variance-stabilizing transformation before quantile normalisation using the lumi package in R.

source_name: Human embryonic kidney cell line

label_protocol: The Ambion Total Prep kit was used to generate biotinylated cRNA for labelling with Cy3-Streptavidin.

growth_protocol: HEK293A cells were grown in DMEM + 10% FBS and supplmented with 4mM L-Glutamine. Incubation conditions were 37oC and 10% CO2

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen) as per the manufacturer's instructions. RNA quantification and integrity was assayed by Nanodrop and Agilent Bioanalyser

treatment_protocol: To knockdown: a suspension of 70,000 cells/well in growth medium were plated on poly-D-lysine coated 24-well plates containing an siRNA mixture. The siRNA was a Lipofectamine 2000:siRNA mix made up in optimum. The final siRNA concentration per well was 37.5nM and siRNA seqeunces are provided in the accompanying study. 48hrs after knockdown the media was exchanged for fresh growth media. 72hrs after knockdown RNA was extracted as specified. Separate wells from the same experiment were taken for each replicate.

value: HEK293A Cells


title: Sample_ID_25

description:
Wildtype mouse retina (Degenerative) at day 10 - SampleID: SAM11945680 - Inventory Sample: 25
SAM11945680


title: siRNF20_R1


title: t1-1a: mouse expression

description: mouse expression

source_name: tumor response BR 1 TR a

value: RCC PDX tumor

tag: group

value: response

tag: biological replicate

tag: technical replicate

value: a


title: ES2_PRnull_vehicle_2

description:
OV_NULL_V_2
Replicate 2


title: Sample_ID_26

description:
ST2 Knockout mouse retina (Degenerative) at day 10 - SampleID: SAM11945681 - Inventory Sample: 26
SAM11945681


title: Sample_ID_14

description:
Wildtype mouse retina (Degenerative) at day 3 - SampleID: SAM11945669 - Inventory Sample: 14
SAM11945669


title: siRNF20_R2

tag: cell line


title: Sample_ID_28

description:
ST2 Knockout mouse retina (Degenerative) at day 10 - SampleID: SAM11945683 - Inventory Sample: 28
SAM11945683


title: siRNF40_R2

tag: treatment


title: Sample_ID_3

description:
Wildtype mouse retina (Normal) at day 0 - SampleID: SAM11945658 - Inventory Sample: 3
SAM11945658


title: Sample_ID_17

description:
ST2 Knockout mouse retina (Degenerative) at day 3 - SampleID: SAM11945672 - Inventory Sample: 17
SAM11945672


title: Sample_ID_1

description:
Wildtype mouse retina (Normal) at day 0 - SampleID: SAM11945656 - Inventory Sample: 1
SAM11945656


title: siRNF40_R1


title: siWAC_R2

value: siWAC


title: Sample_ID_20

description:
ST2 Knockout mouse retina (Degenerative) at day 3 - SampleID: SAM11945675 - Inventory Sample: 20
SAM11945675

value: Eye - retina


title: siWAC_R3


title: Sample_ID_7

description:
ST2 Knockout mouse retina (Normal) at day 0 - SampleID: SAM11945662 - Inventory Sample: 7
SAM11945662

source_name: ST2 KO d0

value: Normal


title: siWAC_R1


title: Sample_ID_16

description:
ST2 Knockout mouse retina (Degenerative) at day 3 - SampleID: SAM11945671 - Inventory Sample: 16
SAM11945671

value: ST2 KO

source_name: Universal mouse reference


title: RISCfree_R3

value: control


title: BCPAP miR-146b-5p mimic transfected

city: Kaohsiung

first: Chen

middle: Kai

last: Chou

address: No.123, Dapi Rd., Niaosong Dist

institute: Chang Gung Memorial Hospital-Kaohsiung Medical Center

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to a Agilent SurePrint G3 Human GE  8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h. After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5.

scan_protocol: Scanned images are analyzed by Feature extraction 10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: BCPAP miR-146b-5p mimic transfected

label_protocol: RNA from BCPAP control was labeled by Cy3 and RNA from BCPAP miR-146b-5p mimic transfected was labeled by Cy5. 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 or Cy5 (CyDye, Agilent Technologies, USA) during the in vitro transcription process. 0.3 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

growth_protocol: The human PAPILLARY thyroid cancer cell line BCPAP was routinely cultured in RPMI 1640 containing 10% FBS, 100 U/mL penicillin, 100 g/mL streptomycin, and 2mML-glutamine(GIBCO,Rockville, MD) at 37°C in a humidified chamber containing 5% CO2.

extract_protocol: RNA was extracted from separated cell populations using Qiagen RNeasy Mini Kit (QIAGEN, Valencia, CA)

treatment_protocol: The cells were seeded (3 X 105 cells per well in 6-well plate) in antibiotic-free medium for 24 hours prior to transfection. DharmaFECT transfection reagent (Dharmacon RNA Technologies, Lafayette, CO) was used to transfect cells with mimic miR-146b (DharmaconRNATechnologies) for 24 hours at 50% confluence following the manufacturers instructions. The miRIDIAN miRNA mimic negative control (Dharmacon RNA Technologies) was used as control. Samples were collected after 24 hours of miRNA mimic transfections for quantification of miRNA.  in antibiotic-free medium for 24 hours prior to transfection.  DharmaFECT transfection reagent (Dharmacon RNA Technologies,  Lafayette, CO) was used to transfect cells with mimicmiR-  146b (DharmaconRNATechnologies) for 24 hours at50%  confluence following the manufacturer’s instructions. The  miRIDIAN miRNA mimic negative control (Dharmacon RNA  Technologies) was used as control. Samples were collected after  24 hours of miRNA mimic transfections for quantification of  miRNA.

value: Human Papillary thyroid cancer cell line, BCPAP

source_name: BCPAP control


title: MDM-4h-dex100nM-rep4

city: Easter Bush

first: Alasdair

middle: W

last: Jubb

state: Midlothian

address: The Roslin Institute

department: Roslin Institute

institute: University of Edinburgh

hyb_protocol: Standard affymetrix protocols using GeneTitan. Performed by Edinburgh Genomics.

data_processing: Raw data was processed using R/Bioconductor: arrayQualityMetrics for quality control and the rma algorithm in the affy package to generate expression values.

source_name: monocyte derived macrophage

label_protocol: Standard affymetrix protocols, Performed by Edinburgh Genomics.

growth_protocol: CD14+ monocytes were extracted from whole blood donated by healthy volunteers using MACS separation (Miltenyi). They were differentiated in culture for 1 week in the presence of recombinant human CSF1 (10000U/ml),penicillin/streptomycin, Glutamax and 10% fetal calf serum then replated in fresh medium, also supplemented as above, for the time series experiment.

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen) and quality assessed using an 2100 Bioanalyzer (Agilent )

treatment_protocol: Samples were treated with 100nM dexamethasone (Sigma) for the indicated duration

tag: source

value: fully anonymized volunteers

tag: cell type

value: monocyte derived macrophage

tag: time

value: dex 100nM


title: MDM-2h-dex100nM-rep4

scan_protocol: Standard affymetrix protocols using GeneTitan. Performed by Edinburgh Genomics.


title: MDM-10h-dex100nM-rep4


title: MDM-24h-dex100nM-rep4


title: RISCfree_R1


title: MDM-1h-dex100nM-rep4


title: MDM-24h-dex100nM-rep3


title: RISCfree_R2


title: BMDM-24h-dex100nM-rep3

description: 10week old

source_name: bone marrow derived macrophage

growth_protocol: Bone marrow from 3 10 week old male C57BL/6 was extracted and differentiated in culture with 10% fetal calf serum and recombinant human CSF1 (10,000U/ml) for 1 week. They were then replated, again with serum and rhCSF1, at 0.5M cells/ml frot he time series.

tag: gender

value: male

value: bone marrow derived macrophage


title: BMDM-4h-dex100nM-rep3

description: 10week old


title: BMDM-10h-dex100nM-rep3

description: 10week old


title: MDM-10h-dex100nM-rep3


title: MDM-4h-dex100nM-rep3


title: MDM-baseline-rep4

value: baseline


title: MDM-1h-dex100nM-rep3


title: BMDM-2h-dex100nM-rep3

description: 10week old


title: Alcohol-SIV3

description:
SAMPLE 8
Alcohol-SIV treated

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

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

data_processing: Data was analyzed on the GenomeStudio Software v2011.1

organism: Macaca mulatta

source_name: Alcohol-SIV

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from SKM (gastrocnemius) using standard methodologies from QIAGEN

value: Alcohol

tag: infection

value: SIV

value: Skeletal muscle (gastrocnemius)


title: BMDM-1h-dex100nM-rep3

description: 10week old


title: BMDM-baseline-rep3

description: 10week old


title: MDM-2h-dex100nM-rep3


title: Alcohol-SIV2

description:
SAMPLE 7
Alcohol-SIV treated

tag: agent


title: MDM-24h-dex100nM-rep2


title: MDM-baseline-rep3


title: Alcohol-SIV1

description:
SAMPLE 6
Alcohol-SIV treated


title: BMDM-24h-dex100nM-rep2

description: 10week old


title: BMDM-10h-dex100nM-rep2

description: 10week old


title: Sucrose-SIV3

description:
SAMPLE 5
SIV treated control

source_name: Sucrose-SIV

value: Vehicle (sucrose)


title: MDM-4h-dex100nM-rep2


title: MDM-10h-dex100nM-rep2


title: BMDM-2h-dex100nM-rep2

description: 10week old


title: Sucrose-SIV2

description:
SAMPLE 4
SIV treated control


title: BMDM-4h-dex100nM-rep2

description: 10week old


title: MDM-2h-dex100nM-rep2


title: Control2

description:
SAMPLE 2
non-treated control

source_name: Control

value: Untreated


title: BMDM-1h-dex100nM-rep2

description: 10week old


title: BMDM-24h-dex100nM-rep1

description: 10week old


title: MDM-1h-dex100nM-rep2


title: Control1

description:
SAMPLE 1
non-treated control


title: BMDM-baseline-rep2

description: 10week old


title: MDM-24h-dex100nM-rep1


title: MDM-baseline-rep2


title: MDM-4h-dex100nM-rep1


title: BMDM-10h-dex100nM-rep1

description: 10week old


title: MDM-2h-dex100nM-rep1


title: BMDM-2h-dex100nM-rep1

description: 10week old


title: whole blood omeprazole 30mg/kg replicate 4 (Group 5_4)

status: Public on Dec 16 2015

city: Bonn

first: Gudrun

last: Ulrich-Merzenich

address: Sigmund-Freudstr. 25

department: Medical Clinic III

institute: University Clinic Centre UKB, Bonn University

description: Gene expression omeprazole 30mg/kg

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Rat Genome Oligo Microarrays (8x60K, Design ID 028279) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

organism: Rattus norvegicus

source_name: Peripheral Blood

label_protocol: 100 ng of total RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

extract_protocol: RNA was extracted from tissue and blood samples by PAXGene tissue RNA kit and PaxGene blood RNA kit (Qiagen) according to the manufacturer's instruction.

treatment_protocol: Tissue was exiced, immediately transferred into RNA-later tubes (BD). Blood was directly draw into PAXgeneRNAlater tubes (BD). Both were kept at -80°C until further use.

tag: strain

value: Wistar

value: whole blood


title: BMDM-4h-dex100nM-rep1

description: 10week old


title: BMDM-1h-dex100nM-rep1

description: 10week old


title: whole blood omeprazole 30mg/kg replicate 1 (Group 5_1)

description: Gene expression omeprazole 30mg/kg


title: MDM-baseline-rep1


title: whole blood omeprazole 30mg/kg replicate 3 (Group 5_3)

description: Gene expression omeprazole 30mg/kg


title: MDM-1h-dex100nM-rep1


title: Sucrose-SIV1

description:
SAMPLE 3
SIV treated control


title: whole blood STW5 2ml/kg replicate 3 (Group 3_3)

description: Gene expression esophagitis STW52ml/kg


title: whole blood STW5 2ml/kg replicate 2 (Group 3_2)

description: Gene expression esophagitis STW52ml/kg


title: whole blood omeprazole 30mg/kg replicate 2 (Group 5_2)

description: Gene expression omeprazole 30mg/kg


title: MDM-10h-dex100nM-rep1


title: whole blood STW5 2ml/kg replicate 4 (Group 3_4)

description: Gene expression esophagitis STW52ml/kg


title: whole blood STW5 0.5ml/kg replicate 4 (Group 4_4)

description: Gene expression esophagitis STW50.5ml/kg


title: whole blood STW5 0.5ml/kg replicate 3 (Group 4_3)


title: BMDM-baseline-rep1

description: 10week old


title: Sample_ID_10

description:
ST2 Knockout mouse retina (Normal) at day 0 - SampleID: SAM11945665 - Inventory Sample: 10
SAM11945665

tag: primary tissue

value: Eye - retina

tag: tissue diagnosis

value: Normal

tag: time point

value: Universal mouse reference


title: whole blood untreated replicate 2 (Group 2_2)

description: Gene expression esophagitis


title: whole blood untreated replicate 1 (Group 2_1)

description: Gene expression esophagitis


title: whole blood untreated replicate 3 (Group 2_3)

description: Gene expression esophagitis


title: whole blood sham replicate 4 (Group 1_4)

description: Gene expression Sham


title: whole blood STW5 2ml/kg replicate 1 (Group 3_1)

description: Gene expression esophagitis STW52ml/kg


title: whole blood untreated replicate 4 (Group 2_4)

description: Gene expression esophagitis


title: whole blood STW5 0.5ml/kg replicate 2 (Group 4_2)


title: esophageal tissue omeprazole 30mg/kg replicate 4 (Group 5_4)

description: Gene expression omeprazole 30mg/kg

value: esophageal tissue


title: whole blood sham replicate 2 (Group 1_2)

description: Gene expression Sham


title: esophageal tissue omeprazole 30mg/kg replicate 1 (Group 5_1)

description: Gene expression omeprazole 30mg/kg


title: whole blood sham replicate 1 (Group 1_1)

description: Gene expression Sham


title: esophageal tissue STW5 2ml/kg replicate 4 (Group 3_4)

description: Gene expression esophagitis STW52ml/kg


title: esophageal tissue STW5 2ml/kg replicate 3 (Group 3_3)

description: Gene expression esophagitis STW52ml/kg


title: esophageal tissue omeprazole 30mg/kg replicate 2 (Group 5_2)

description: Gene expression omeprazole 30mg/kg


title: esophageal tissue STW5 2ml/kg replicate 2 (Group 3_2)

description: Gene expression esophagitis STW52ml/kg


title: whole blood sham replicate 3 (Group 1_3)

description: Gene expression Sham


title: esophageal tissue STW5 0.5ml/kg replicate 4 (Group 4_4)


title: esophageal tissue STW5 2ml/kg replicate 1 (Group 3_1)

description: Gene expression esophagitis STW52ml/kg


title: esophageal tissue STW5 0.5ml/kg replicate 3 (Group 4_3)


title: esophageal tissue untreated replicate 4 (Group 2_4)

description: Gene expression esophagitis

source_name: esophageal tissue untreated replicate 4


title: esophageal tissue STW5 0.5ml/kg replicate 1 (Group 4_1)


title: esophageal tissue untreated replicate 2 (Group 2_2)

description: Gene expression esophagitis

source_name: esophageal tissue untreated replicate 2


title: esophageal tissue sham replicate 3 (Group 1_3)

description: Gene expression Sham

source_name: esophageal tissue sham replicate 3


title: esophageal tissue untreated replicate 1 (Group 2_1)

description: Gene expression esophagitis

source_name: esophageal tissue untreated replicate 1


title: esophageal tissue untreated replicate 3 (Group 2_3)

description: Gene expression esophagitis

source_name: esophageal tissue untreated replicate 3


title: esophageal tissue STW5 0.5ml/kg replicate 2 (Group 4_2)


title: esophageal tissue omeprazole 30mg/kg replicate 3 (Group 5_3)

description: Gene expression omeprazole 30mg/kg


title: esophageal tissue sham replicate 2 (Group 1_2)

description: Gene expression Sham

source_name: esophageal tissue sham replicate 2


title: esophageal tissue sham replicate 1 (Group 1_1)

description: Gene expression Sham

source_name: esophageal tissue sham replicate 1


title: esophageal tissue sham replicate 4 (Group 1_4)

description: Gene expression Sham

source_name: esophageal tissue sham replicate 4


city: West Lafayette

first: Fuyou

last: Fu

state: INDIANA

address: 915 W. State Street

institute: Fuyou Fu

description:
Sample name: 10DPPH
Gene expression data from Macrosclereid cell development 10DPP biological rep4

hyb_protocol: Standard Affymetrix protocol.

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

data_processing: Twenty-three macrosclereid RNA samples were manipulated for microarray analysis using the GeneChip Medicago Genome Array. The Bioconductor R package was used for gene expression analysis. Briefly, raw microarray data in CEL files were imported into Bioconductor using the R package affy and background correction was performed using the RMA (Robust Multi-Array Average) method.

organism: Medicago truncatula

source_name: 10 days post pollination

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

growth_protocol: Plants (Medicago truncatula, ecotype A17) were grown in pots containing a mixture of sand and perlite (2:8) under controlled growth chamber conditions with an average temperature of 23ºC, 50% humidity, and a 16-h photoperiod. Plants were watered/fertilized using a solution containing one tablespoon of Scotts Miracle-Gro per gallon water

extract_protocol: RNA was extracted from frozen macrosclereid cells using the Spectrum™ Plant Total RNA Kit with on-column DNaseI digestion (Sigma-Aldrich).

treatment_protocol: Randomly selected flowers were tagged (using small different colored tags with different colored strings) on the day after pollination.

tag: ecotype

value: 10 days post pollination

value: macrosclereid cells


description:
Sample name: 27DPPA
Gene expression data from Macrosclereid cell development 27DPP biological rep1

source_name: 27 days post pollination

value: 27 days post pollination


description:
Sample name: 20DPPF
Gene expression data from Macrosclereid cell development 20DPP biological rep3

source_name: 20 days post pollination

value: 20 days post pollination


description:
Sample name: 16DPPC
Gene expression data from Macrosclereid cell development 16DPP biological rep3

source_name: 16 days post pollination

value: 16 days post pollination


description:
Sample name: 13DPPA
Gene expression data from Macrosclereid cell development 13DPP biological rep1

source_name: 13 days post pollination

value: 13 days post pollination


description:
Sample name: 16DPPD
Gene expression data from Macrosclereid cell development 16DPP biological rep4


description:
Sample name: 20DPPD
Gene expression data from Macrosclereid cell development 20DPP biological rep2


title: 43_127009

city: Boston

first: Rinath

last: Jeselsohn

state: MD

address: 450 Brookline Ave, D728

department: Medical Oncology

institute: DFCI

hyb_protocol: Samples were run on the Affymetrix Human Transcriptome Array ( HTA) 2.0.

scan_protocol: An Affymetrix Fluidics station 450 and Affymetrix GeneChip Scanner 3000 7G were used per manufactures' instructions.

data_processing: QC and normalization with RMA was conducted using Affymetrix expression console.

source_name: primary breast cancer from post menopausal patients that developed metastatic disease

label_protocol: CDNA was labeled using FL-Ovation cDNA Biotin Module V2 ( Nugen).

extract_protocol: RNA was extracted from FFPE tumor samples using Rneasy FFPE kits ( Qiagen) and amplified with WT-Ovation FFPE Sytem V2 ( NuGEN).

tag: tissue

value: primary breast cancer

tag: age

tag: er (allred score)

tag: pr (allred score)


description:
Sample name: 27DPPC
Gene expression data from Macrosclereid cell development 27DPP biological rep3


description:
Sample name: 6DPPB
Gene expression data from Macrosclereid cell development 6DPP biological rep2

source_name: 6 days post pollination

value: 6 days post pollination


description:
Sample name: 6DPPD
Gene expression data from Macrosclereid cell development 6DPP biological rep4


description:
Sample name: 6DPPC
Gene expression data from Macrosclereid cell development 6DPP biological rep3


description:
Sample name: 10DPPC
Gene expression data from Macrosclereid cell development 10DPP biological rep2


description:
Sample name: 16DPPA
Gene expression data from Macrosclereid cell development 16DPP biological rep1


title: 16_185002


description:
Sample name: 16DPPB
Gene expression data from Macrosclereid cell development 16DPP biological rep2


description:
Sample name: 10DPPB
Gene expression data from Macrosclereid cell development 10DPP biological rep1


description:
Sample name: 13DPPC
Gene expression data from Macrosclereid cell development 13DPP biological rep3


description:
Sample name: 13DPPB
Gene expression data from Macrosclereid cell development 13DPP biological rep2


description:
Sample name: 13DPPD
Gene expression data from Macrosclereid cell development 13DPP biological rep4


description:
Sample name: 20DPPC
Gene expression data from Macrosclereid cell development 20DPP biological rep1


description:
Sample name: 27DPPB
Gene expression data from Macrosclereid cell development 27DPP biological rep2


title: 2_103001


description:
Sample name: 10DPPD
Gene expression data from Macrosclereid cell development 10DPP biological rep3


title: 8_121007


title: 94_195004


title: 95_195009


description:
Sample name: 6DPPA
Gene expression data from Macrosclereid cell development 6DPP biological rep1


title: 93_195001


title: 89_242006


title: 91_160002


title: 82_126019


description:
Sample name: 27DPPD
Gene expression data from Macrosclereid cell development 27DPP biological rep4


title: 92_160003


title: 84_126022


title: 79_126015


title: 88_242005


title: 80_126016


title: 74_126008


title: 83_126020


title: 86_242001


title: 75_126012A


title: 73_126007


title: 87_242003


title: 70_126004


title: 71_126005


title: 64_145002A


title: 58_243018


title: 63_231001


title: 62_161003


title: 57_243016


title: 60_150002


title: 68_161009


title: 56_243014


title: 67_161004


title: whole blood STW5 0.5ml/kg replicate 1 (Group 4_1)

description: Gene expression esophagitis STW50.5ml/kg


title: 52_243008


title: 69_126003


title: 72_126006


title: 54_243010


title: 46_127015


title: 49_243003


title: 48_243002


title: 50_243007


title: 44_127012


title: 37_127001


title: 47_127016


title: 42_127008


title: 39_127005


title: 41_127007


title: 45_127013


title: 38_127009


title: 29_244008


title: 30_247001


title: 35_130004


title: 33_247004


title: 32_247003


title: 53_243009


title: 36_246002


title: 34_272001


title: 26_244001


title: 23_187003


title: 25_187009


title: 17_185007


title: 14_180008


title: 15_185001


title: 21_185025


title: 5_116005


title: 7_121005


title: 11_124003


title: 18_185008


title: 6_121001


title: 9_121008


title: 35_290002


title: 12_121002


title: 34_235003


title: 33_235002


title: 20_185023


title: 36_290003


title: 13_125001


title: 22_187001


title: 37_290007


title: 10_121009


title: 29_184051


title: 4_113001


title: 81_126018


title: 30_184052


title: 1_124001


title: 31_182006


title: 32_235001


title: 28_184048


title: 25_184042


title: 23_184039


title: 27_184046


title: 26_184045


title: 22_184038


title: 15_184022


title: 16_184025


title: 24_184041


title: 17_184027


title: 20_184035


title: 12_184014


title: 18_184030


title: 14_184021


title: 13_184015


title: 11_184012


title: 7_14004


title: 9_140006


title: 10_140003


title: 8_140005


title: 4_184006


title: 3_184004


title: 1_195011


title: 6_184010


title: 2_184003


title: 19_184034


title: 5_184009


title: 548532_A11_532

city: Basel

first: Tobias

last: Heckel

address: Grenzacherstr. 124

department: pRED

country: Switzerland

institute: Roche

description: total RNA recovered from fresh frozen tissue from untreated minipigs

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

scan_protocol: Scanning was performed on a NimbleGen MS200 Microarray Scanner at 2 μm pixel resolution following the standard operating protocol of NimbleGen Systems Inc., Madison, WI USA. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to background correction, quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.). In addition this RMA normalized data was GRSN normalized according to the method of Pelz et al. (Pelz C et al. BMC Bioinformatics 2008, 9:520).

source_name: Minipig  5_M_210690

label_protocol: Labeling was performed using 10 ng of total RNA as input following the standard operating protocol on a Biomek FXp workstation (Beckman Coulter Inc., Brea, CA, USA) with the NuGen Ovation Pico WTA System V2 (NuGEN Technologies, Inc., SanCarlos, CA, USA; see http://www.nugeninc.com). Cy3 labeling of cDNA was performed with  the Roche NimbleGen One Color DNA Labeling Kit according to manufacturer's instructions (NimbleGen Systems Inc., Madison, WI USA. (See www.nimblegen.com).

growth_protocol: the tissue samples were collected from drug-naive, untreated animals of GLP drug safety studies carried out in accordance with current animal protection standards. Tissues were stored at -80°C until RNA extraction.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) . DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA).

value: urinary bladder

value: male

value: 1 year old minipig

tag: weigth

value: circa 20 kg

tag: facility

value: Ellegaard, Denmark


title: 548532_A03_532

source_name: Minipig  M_208393


title: 548532_A05_532

source_name: Minipig  4_F_306227

value: female


title: 548527_A07_532

source_name: Minipig  6_M_210758

value: gall bladder


title: 548527_A11_532


title: 548532_A10_532

source_name: Minipig  2_F_306273


title: 548527_A04_532


title: 548532_A02_532

source_name: Minipig  M_208431


title: 548532_A09_532

source_name: Minipig  F_304342


title: 548532_A01_532

source_name: Minipig  1_F_306285


title: 548532_A04_532

source_name: Minipig  3_F_306298


title: 548527_A01_532

source_name: Minipig  7_M_210995


title: 548532_A06_532


title: 548532_A07_532


title: 548527_A02_532


title: 548527_A09_532


title: 548527_A10_532


title: 548527_A12_532_bad


title: 548532_A08_532

source_name: Minipig  F_304362


title: 546612_A01_532

value: Aorta


title: 546612_A11_532


title: 546612_A02_532


title: 548527_A08_532


title: 548527_A05_532


title: 546612_A03_532


title: 546612_A08_532


title: 546612_A07_532


title: 546612_A12_532


title: 546612_A09_532


title: 546797_A05_532

value: Ovary


title: 546612_A04_532


title: 546797_A11_532


title: 546797_A04_532


title: 546797_A09_532

value: Testis


title: 549173_A04_532

value: Thyroid


title: 549173_A06_532


title: 546797_A07_532


title: 546797_A03_532


title: 549173_A05_532


title: 546797_A06_532


title: 546797_A12_532


title: 549173_A01_532

source_name: Minipig  8_M_210733


title: 546797_A01_532


title: 546797_A10_532


title: 546797_A08_532


title: 546797_A02_532


title: 549173_A07_532


title: 549173_A03_532


title: 548526_A01_532

value: cerebellum


title: 548526_A10_532


title: 546596_A06_532


title: 548526_A05_532


title: 548526_A08_532


title: 548526_A11_532


title: 548526_A06_532


title: 549173_A08_532


title: 548526_A03_532


title: 548526_A04_532


title: 549173_A09_532


title: 548526_A09_532


title: 544482_A12_532

value: skeletal muscle


title: 548583_A10_532

value: cerebrum (cortex)


title: 548526_A07_532


title: 548583_A02_532


title: 548583_A06_532


title: 548583_A11_532


title: 548583_A03_532


title: 548583_A01_532


title: 548583_A05_532


title: 548526_A02_532


title: 548583_A07_532


title: 548583_A09_532


title: 544482_A09_532


title: 548583_A04_532


title: 548583_A08_532


title: 544482_A05_532


title: 544482_A06_532


title: 544482_A10_532


title: 544482_A02_532


title: 544482_A03_532


title: 546595_A04_532

value: colon


title: 546595_A11_532


title: 544482_A08_532


title: 544482_A07_532


title: 544482_A01_532


title: 544482_A11_532


title: 546595_A01_532


title: 546595_A08_532


title: 546595_A05_532


title: 546595_A06_532


title: 546595_A03_532


title: 546595_A09_532


title: 544999_A02_532

value: Jejunum


title: 544999_A12_532


title: 546595_A10_532


title: 546595_A07_532


title: 544999_A01_532


title: 544999_A09_532


title: 544999_A05_532


title: 544999_A08_532


title: 544999_A10_532


title: 544999_A04_532


title: 544999_A07_532


title: 544679_A01_532

value: Duodenum


title: 544999_A06_532


title: 544999_A03_532


title: 544999_A11_532


title: 544679_A09_532


title: 544679_A10_532


title: 544679_A02_532


title: 544679_A05_532


title: 544679_A07_532


title: 546595_A02_532


title: 545040_A06_532

value: Stomach(fundus)


title: 544679_A08_532

value: male


title: 545040_A05_532

value: 1 year old minipig


title: 544679_A11_532

value: circa 20 kg


title: 544679_A03_532

value: Ellegaard, Denmark


title: 545040_A02_532


title: 545040_A10_532


title: 545040_A01_532


title: 545040_A11_532

value: female


title: 545040_A08_532


title: 545040_A12_532


title: 545040_A03_532


title: 544069_A02_532

value: spleen


title: 544069_A12_532


title: 545040_A07_532


title: 544069_A11_532


title: 545040_A04_532


title: Labial salivary gland_SjS_rep1

city: Shanghai

first: Huan

last: Shi

address: No.639, ZhiZaoJu Road

department: Oral and maxillafacial surgery

institute: Shanghai JiaoTong University school of medicine, affiliated 9th people's hospital

description:
LncRNA expression in LSG of SjS patients
LSG_SjS001

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3‐labeled cRNA using Gene Expression Hybridization Kit (Cat#5188‐5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188‐5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: Labial salivary gland, SjS patient

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One‐Color (Cat#5190‐2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Samples were store at liquid nitrogen before extracted

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596‐018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase‐Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

tag: disease state

value: SjS

value: Labial salivary gland

value: Female


title: Labial salivary gland_Control_rep2

description:
LncRNA expression in LSG of healthy controls
LSG_Ctrl002

source_name: Labial salivary gland, control subject

value: control


title: 544069_A07_532


title: Labial salivary gland_Control_rep3

description:
LncRNA expression in LSG of healthy controls
LSG_Ctrl003


title: 544069_A03_532


title: 544069_A06_532


title: 544069_A05_532


title: 544069_A04_532


title: Labial salivary gland_SjS_rep4

description:
LncRNA expression in LSG of SjS patients
LSG_SjS004


title: 544069_A01_532


title: Labial salivary gland_SjS_rep3

description:
LncRNA expression in LSG of SjS patients
LSG_SjS003


title: Labial salivary gland_Control_rep1

description:
LncRNA expression in LSG of healthy controls
LSG_Ctrl001


title: Labial salivary gland_Control_rep4

description:
LncRNA expression in LSG of healthy controls
LSG_Ctrl004


title: Labial salivary gland_SjS_rep2

description:
LncRNA expression in LSG of SjS patients
LSG_SjS002


title: 544623_A05_532

value: lung


title: 544069_A10_532


title: 544069_A09_532


title: whole blood, MPLA treated, Animal 80

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Sheep Genome microarrays 8x15K Design ID 019921 (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 37° C for 1 min, and stained with Streptavidin-Alexa555.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2505C Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

organism: Ovis aries

source_name: Whole Blood_MPLA treated

label_protocol: Labeled cRNA was prepared from total RNA samples. Briefly, the Poly(A)+ RNA population within total RNA was amplified using Arcturus RiboAmp HS reagents (Molecular Devices, Sunnyvale, CA).  Alternatively, MessageAMP II (Applied Biosystems, Foster City, CA) was used.  After a second round of reverse transcription, second-strand cDNA synthesis, and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of Biotin-11-UTP.  The quantity and quality of the cRNA was assayed by spectrophotometry and on the Agilent Bioanalyzer.

extract_protocol: RNA was extracted and purified using Ribopure (Ambion) RNA isolation

treatment_protocol: Sheep whole blood was incubated with 1microg LPS or  10 microg MPLA for 90 minutes

value: Whole Blood


title: 544069_A08_532


title: whole blood, LPS treated, Animal 80

source_name: Whole Blood_LPS treated


title: whole blood, LPS treated, Animal 65Y


title: 544623_A03_532


title: whole blood, MPLA treated, Animal 65Y


title: whole blood, PBS treated, Animal 80

source_name: Whole Blood_PBS treated


title: whole blood, LPS treated, Animal 170


title: whole blood, PBS treated, Animal 65Y


title: 544623_A02_532

source_name: Minipig  5_M_210690


title: 11636 Primary

city: saint louis

first: chidananda

last: Mudalagiriyappa

state: Missouri

address: 4940 Parkview Pl.

department: Surgery

institute: washington university in saint louis

description: Gene expression data from primary tumor Breast cancer patients

hyb_protocol: Hybridization was done following NuGEN’s recommendations using Affymetrix fluidic stations and Affymetrix hybridization, wash and stain kit.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
Affymetrix CEL files were imported into Partek Genomics Suite v6.5 and processed using the RMA algorithm without probe filtering.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: Primary Tumor

label_protocol: lablelling was done using NuGEN Encore Biotin module.

extract_protocol: Total RNA was isolated from Breast tumor samples using Trizol reagent (Invitrogen) according to manufacturer’s protocol.  The extracted RNA was quantified and qualitatively assessed using an Agilent Bioanalyzer and RNA NanoChip assay. cDNA synthesis and amplification was performed using the Ovation Pico SL kit from NuGEN.

tag: phenotype

value: Primary Tumor

value: Breast Tissue

tag: reference id

tag: pre/post therapy

tag: date of randomisation (month/date/year)

tag: allocated treatment

tag: menopausal   status

tag: er

tag: pr

tag: dtc positive(ihc)

tag: date of   recurrence

tag: date of death or date patient last known to be alive (month/date/year)


title: 11635 Primary

tag: tissue


title: 11634 Primary

value: Post

value: no

value: neg

value: No


title: 544623_A08_532

source_name: Minipig  M_208393

tag: gender

value: male

tag: age

value: 1 year old minipig


title: 544623_A09_532

tag: weigth

value: circa 20 kg

value: Ellegaard, Denmark


title: 544623_A12_532

tag: facility


title: whole blood, MPLA treated, Animal 170


title: 11585 Primary

value: Pre


title: 11584 Primary

value: pos


title: 545040_A09_532

value: Stomach(fundus)


title: whole blood, PBS treated, Animal 170


title: 11633 Primary

value: zometa


title: 544623_A01_532

source_name: Minipig  4_F_306227

value: female


title: 11586 Primary


title: 11632 Primary


title: whole blood, MPLA treated, Animal 51Y


title: whole blood, PBS treated, Animal 20


title: whole blood, LPS treated, Animal 20


title: 544623_A04_532

value: lung


title: whole blood, PBS treated, Animal 51Y

value: Whole Blood


title: 11583 Primary

value: Primary Tumor


title: 11580 Primary

value: Breast Tissue

value: Yes


title: whole blood, LPS treated, Animal 51Y


title: whole blood, MPLA treated, Animal 71Y


title: 544623_A10_532


title: 544623_A11_532


title: 11582 Primary

value: Post


title: 548530_A12_532_bad

value: liver


title: 544623_A07_532

source_name: Minipig  2_F_306273


title: 548530_A05_532


title: 544679_A06_532

value: Duodenum


title: Bortezomib rep2

city: La Jolla

first: Roy

middle: M

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

description:
4482545065_H
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw probe expression values were log2 transformed and normalized with quantiles normalization functions as implemented in the GeneSpring GX12 package.

tag: tissue source

value: prostate

tag: cell line

value: LNCaP

tag: cell type

value: prostate adenocarcinoma cells

tag: treated with

value: 50 nM Bortezomib (positive control)


title: 11581 Primary

tag: phenotype

tag: reference id

tag: pre/post therapy

value: Pre

tag: date of randomisation (month/date/year)

value: no


title: whole blood, MPLA treated, Animal 20


title: whole blood, LPS treated, Animal 71Y


title: CPT rep2

description:
4482545065_F
replicate 2

value: 500nM Campthotecin (positive control)


title: 11579 Primary

tag: allocated treatment

value: zometa

tag: menopausal   status

tag: er

value: pos

tag: pr

value: neg