title: LNCaP EOS R

city: Tokyo

first: Shigeru

last: Saito

address: 2-34-17, Jingumae, Shibuya-ku

institute: INFOCOM CORPORATION

description: Gene expression data from EOS-selected cells 2 treated by ribavirin.

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The affy package in Bioconductor, R was used to generate the MAS5.0 data.

source_name: LNCaP, EOS 2 treated by ribavirin

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: We cultured EOS-transduced cancer cells in puromycin and enriched puromycin-resistant cancer cells with higher OCT4 expression after a-few-week culture period.

extract_protocol: Total RNA was isolated using an RNeasy Mini kit according to the manufacturer's protocol.

treatment_protocol: The EOS vector contains GFP and the puromycin-resistance gene driven by the OCT4 and SOX2 enhancers. We transduced an EOS vector into prostate cancer cells. As a control, we used a vector containing the ubiquitous PGK promoter driving GFP and a puromycin-resistance gene.

value: LNCaP

value: prostate cancer cells

tag: transduced vector

value: EOS

value: ribavirin


title: OVCA433-control-rep2

status: Public on Dec 31 2013

type: RNA

city: Houston

first: Tsz-Lun

last: Yeung

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gynecologic Oncology and Reproductive Medicine

country: USA

institute: University of Texas MD Anderson Cancer Center

description: Gene expression data from control OVCA433 cell line

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Ovarian cancer cell line OVCA433-Control sample

label_protocol: Biotinylated cRNA were prepared using the MessageAmp Premier RNA Amplification Kit (Ambion) according to the manufacturer's instruction from 100ng total RNA.

growth_protocol: OVCA433 ovarian cancer cell line was cultured in humidified incubator at 37C and 5% carbon dioxide. Culture medium RPMI1640 supplemented with 10% Fetal bovine serum was used as growth medium.

extract_protocol: Total RNA extraction was performed using the Purelink RNA mini kit (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: prior to treatment, cells were trypsinized, counted and seeded in 60mm cell culture dishes. 24 hours after cell seeding, the control group has cell culture medium replaced with fresh medium without versican, while the versican treatment group has cell culture medium replace with fresh medium containing versican. At 48 hours post transfection, transfected cells were harvested and total RNA was extracted.

tag: cell line

tag: treatment


title: LNCaP PGK 2

country: Japan

description: Gene expression data from control PGK2.

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

label: biotin

source_name: LNCaP, PGK 2 control

tag: cell type

value: PGK


title: LNCaP EOS 2

description: Gene expression data from EOS-selected cells 2.

source_name: LNCaP, EOS 2 selected


title: 8412 D ductus arteriosus SMC 21 days

city: Leiden

first: Regina

last: Bokenkamp

address: Albinusdreef 2

department: Dept of Pediatric Cardiology

country: Netherlands

institute: LUMC

hyb_protocol: Labeled RNA was hybridized to GeneChip Rat Genome 230 2.0 Array. Hybridization was performed using 12.5 μg of biotin-labeled RNA at 45°C for 16 hours under continuous rotation.

scan_protocol: Gene Chips were scanned using the Affymetrix Gene Chip Scanner 3000

data_processing: The Affymetrix probe level data were summarized using FARMS (Factor Analysis for Robust Microarray Summarization - http://www.bioinf.jku.at/software/farms/farms.html). Raw intensities were log2 transformed to get data normally distributed.

organism: Rattus norvegicus

source_name: ductus arteriosus SMC 21 days

label_protocol: Two rounds of linear mRNA amplification were performed (modified Eberwine protocol). The second round of amplification, starting from 100 ng of first round aRNA, was finalised during the IVT labelling.

growth_protocol: Pups from 6 timed–pregnant Wistar rats were delivered after respectively 18 and 21 days of gestation (spontaneous birth occurs at 22 days of gestation) by hysterotomy through a median abdominal incision

extract_protocol: RNA from microdissected cells was isolated using the RNeasy Minelute protocol.

treatment_protocol: Isolation of the fetal thorax was carefully performed in RNase free conditions, frozen in tissue tek, and stored at -80 C.

value: smooth muscle cell

tag: developmental stage

value: embryo 21 days

tag: tissue

value: ductus arteriosus

tag: strain

value: wistar


title: LNCaP EOS 1

description: Gene expression data from EOS-selected cells 1.

source_name: LNCaP, EOS 1 selected


title: 8 weeks wild type Mammary34

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

description: Gene expression data obtained from mouse whole mammary gland tissue

hyb_protocol: cDNA was fragmented and 10ug hybridized to an Affymetrix MG 430 2.0 array for 16 hours. Arrays were washed and stained using the Affy 450 Fluidics Station according to the manufacturer's protocol

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

data_processing: RMA

organism: Mus musculus

source_name: wild type FVB mouse whole mammary gland

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

growth_protocol: All animal experimental protocols were approved by the Institutional Animal Care and Use Committee of Children’s Hospital Boston

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

tag: age

value: 8 weeks

tag: genotype

value: wild type FVB mouse whole mammary gland

value: whole mammary gland tissue


title: 8 weeks wild type Mammary37


title: 8412 A Aorta endo 21 days

source_name: Aorta endo 21 days

value: endothelial cell

value: Aorta


title: 8469 F Aorta SMC 18.5 days

source_name: Aorta SMC 18.5 days

value: embryo 18.5 days


title: 8 weeks wild type Mammary33


title: 8399 F ductus arteriosus SMC 18.5 days

source_name: ductus arteriosus SMC 18.5 days


title: HepG2 NF2-LATS2-YAP-TAZ knockdown, rep1

city: Boston

first: Jianlong

last: Sun

state: MA

address: 1 Blackfan Street

department: Hematology/Oncology

institute: Boston Children's Hospital

description: gene expression data from HepG2 cell transfected with siRNA oligoes against NF2, LATS2, YAP, and TAZ

hyb_protocol: Samples are then hybridized onto arrays for approximately 18 hours in Affymetrix GeneChip Hybridization Oven 640. The arrays are then washed and stained with streptavidin phycoerythrin in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using theAffymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with the on-line GenePattern software suite with default analysis settings and RMA normalization.

label_protocol: Total RNA undergoes a reverse transcription reaction to generate double-stranded cDNA. The cDNA then undergoes an in-vitro transcription reaction in which biotin-labeled cRNA is created.

growth_protocol: All three cell lines were grown in DMEM medium supplied with 10% FBS and 1x Penicillin and Streptomycin.

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

treatment_protocol: 20-30% confluent cells were transfected with siRNA oligoes with a final concentration of 5nM per oligo.  Transfected cells were grown for 4 days before total RNA was extracted with Trizol.

value: cell line established from human hepatocellular carcinoma


title: HepG2 control, rep 1

description: gene expression data from HepG2 cell transfected with scramble oligo


title: HepG2 NF2-LATS2 knockdown, rep2

description: gene expression data from HepG2 cell transfected with siRNA oligoes against NF2 and LATS2


title: HepG2 NF2-LATS2-YAP-TAZ knockdown, rep2

source_name: HepG2 cell transfected with siRNA oligoes against NF2, LATS2, YAP, and TAZ


title: LNCaP PGK 1

description: Gene expression data from control PGK1.

source_name: LNCaP, PGK 1 control


title: 8412 A Aorta SMC 21 days

source_name: Aorta SMC 21 days


title: DU145 EOS R

source_name: DU145, EOS 2 treated by ribavirin


title: Tbr1-/-#3

city: Taipei

first: Yi-Ping

last: Hsueh

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

hyb_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array Following fragmentation, 15 ug of cRNA were hybridized for 17 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned witj Affymetrix GeneChip Scanner 3000  using the standard Affymetrix protocol,

data_processing: the initial DAT files were processed by Affymetrix GeneChip Operating Software (GCOS) to generate the raw signal intensity CEL files.

source_name: Tbr1-/- mouse embryo #3, E16.5

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

growth_protocol: Tbr mutant mice were maintained by backcross heterozygous Tbr1+/- mice with WT B6 mice for more than 10 generations. For experiment, Tbr1+/- female mated with Tbr1+/- male to generate all of +/+, +/- and -/- embryos. Only +/+ and -/- embryos were compared.

extract_protocol: Total RNA isolated from freshly dissected E16.5 mouse forebrains (4 WT and 4 Tbr1-/-) and purified by TRIzol reagent .

treatment_protocol: No special treatment. After disecting, forebrains were directly subjected to RNA purification.

value: embryonic day 16.5

tag: genotype/variation


title: 8469 D Aorta endo 18.5 days

source_name: Aorta endo 18.5 days


title: HepG2 NF2-LATS2 knockdown, rep 1

source_name: HepG2 cell transfected with siRNA oligoes against NF2 and LATS2


title: DU145 EOS 2

source_name: DU145, EOS 2 selected


title: Tbr1-/-#4

source_name: Tbr1-/- mouse embryo #4, E16.5


title: Tbr1-/-#1

source_name: Tbr1-/- mouse embryo #1, E16.5


title: WT#4

source_name: WT mouse embryo #4, E16.5

value: wild type


title: HaCaT NF2-LATS2-YAP-TAZ knockdown, rep2

description: gene expression data from HaCaT cell transfected with siRNA oligoes against NF2, LATS2, YAP, and TAZ

value: cell line established from human keratinocyte


title: HepG2 control, rep 2

source_name: HepG2 cell transfected with scramble oligo


title: Tbr1-/-#2

source_name: Tbr1-/- mouse embryo #2, E16.5


title: WT#3

source_name: WT mouse embryo #3, E16.5


title: 8399 F Aorta SMC 18.5 days


title: HaCaT NF2-LATS2-YAP-TAZ knockdown, rep1

source_name: HaCaT cell transfected with siRNA oligoes against NF2, LATS2, YAP, and TAZ


title: DU145 PGK 2

description: Gene expression data from control PGK2.

source_name: DU145, PGK 2 control

value: prostate cancer cells


title: 8462 C Aorta endo 21 days

source_name: Aorta endo 21 days


title: DU145 PGK 1

description: Gene expression data from control PGK1.

source_name: DU145, PGK 1 control


title: 8469 D Aorta SMC 18.5 days

source_name: Aorta SMC 18.5 days


title: WT #1

source_name: WT mouse embryo #1, E16.5


title: HaCaT control, rep 2

description: gene expression data from HaCaT cell transfected with scramble oligo


title: 8399 E Aorta endo 18.5 days


title: Pt 4

first: Frank

middle: H

last: Lau

address: 185 Cambridge St - CPZN 4500

institute: Center for Regenerative Medicine

description: Soft tissue from macrodactyly finger.

hyb_protocol: Hybridization to Affymetrix Human Genome U133 Plus 2.0 Arrays and subsequent array processing  was done by Asuragen.

scan_protocol: Scanning was performed by Asuragen.

data_processing: Raw expression values were analyzed with the Partek Genomics Suite (Partek).

source_name: Macrodactyly finger

label_protocol: 1.2 µg RNA was synthesized into complementary DNA (cDNA) with the Superscript III First Strand Synthesis Kit (Invitrogen).

growth_protocol: Fresh samples from surgical procedures.

extract_protocol: RNA was extracted via submersion in 1ml of Trizol, mechanical lysis using an RNase-free pestle (Kimble Chase Kontes), addition of 200 µl chloroform, and centrifugation (10,000g, 15 minutes, 4C). The supernatant was extracted and purified with RNeasy Mini Columns (Qiagen).

value: soft tissue from finger

tag: phenotype

value: macrodactyly


title: WT#2

source_name: WT mouse embryo #2, E16.5


title: HaCaT control, rep 1

source_name: HaCaT cell transfected with scramble oligo


title: 8469 F ductus arteriosus SMC 18.5 days

source_name: ductus arteriosus SMC 18.5 days

value: smooth muscle cell


title: Pt 2

description: Soft tissue from macrodactyly finger.


title: DU145 EOS 1

source_name: DU145, EOS 1 selected

value: EOS


title: HaCaT NF2-LATS2 knockdown, rep2

description: gene expression data from HaCaT cell transfected with siRNA oligoes against NF2 and LATS2


title: HaCaT NF2-LATS2 knockdown, rep 1

source_name: HaCaT cell transfected with siRNA oligoes against NF2 and LATS2


title: Pt 1

description: Soft tissue from macrodactyly finger.


title: HEK293T NF2-LATS2-YAP-TAZ knockdown, rep2

description: gene expression data from 293T cell transfected with siRNA oligoes against NF2, LATS2, YAP, and TAZ

value: cell line established from embryonic kidney


title: 8469 B Aorta endo 18.5 days

source_name: Aorta endo 18.5 days

value: wistar


title: Pt 3

description: Soft tissue from macrodactyly finger.


title: 8469 F Aorta endo 18.5 days


title: AR-siRNAi, biological rep3

city: San Diego

first: Zhou

last: Zhu

state: CA

address: 10646 Science Center Drive (CB4)

institute: Pfizer Worldwide Research & Development

description: Gene expression data from VCaP cells treated with AR-siRNA.

hyb_protocol: The labeled cRNA was fragmented as recommended by Affymetrix and 10 µg was added to a hybridization cocktail prior to loading onto individual GeneChip® Human Genome U133 Plus 2.0 Array.  The microarrays were hybridized at 45°C for 16 - 24 hours and washed and stained on an Affymetrix FS450 fluidics station according to manufacturer recommendations.

scan_protocol: The microarrays were scanned on a GeneChip® Scanner 3000.

data_processing: Expression profiling data were RMA normalized with affy package of Bioconductor (separately for compound and RNAi experiments).

source_name: Hormone refractory prostate cancer cells

label_protocol: cDNA was synthesized from 100 ng of high quality total RNA using the Affymetrix GeneChip® 3' IVT Express Kit (Cat# 901229).   First Strand Enzyme was used to reverse-transcribe the mRNA in the presence of a T7 containing oligo dT24 primer followed by second strand synthesis.  cDNA used as a template for in vitro transcription.  cRNA was purified using 3’ IVT Express magnetic beads and the quantity and purity of the cRNA was determined by absorbance at 260 nm and 260/280 absorbance ratio respectively.  The quality of the cRNA was evaluated by assessing the size distribution of the cRNA using a 1.25% MOPS gel.

growth_protocol: VCaP human prostate cell lines were obtained from ATCC and grown in DMEM (GIBCO Cat# 11995) 10% FBS (SIGMA Cat# 12103C-500ml).  Medium was supplemented with standard antibiotics (Penicillin-Streptomycin, GIBCO #15070-063).

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

tag: cells

value: VCaP

value: AR-siRNA


title: HEK293T NF2-LATS2-YAP-TAZ knockdown, rep1

source_name: 293T cell transfected with siRNA oligoes against NF2, LATS2, YAP, and TAZ


title: Pregnant-HighFat-rep4

city: Edinburgh

first: Donald

last: Dunbar

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Affymetrix overnight hybridisation at 45 degrees C

scan_protocol: Affymetrix HP GeneArray scanner

data_processing: CEL files imported into Affy package in Bioconductor. Normalisation with RMA (with background subtraction). Normalized gene expression values (RMA with background subtraction) were converted to linear scale from log2 scale. R v2.8.0, Biobase_2.2.2, and affy_1.20.2

source_name: Visceral fat,Pregnant, High fat

label_protocol: Affymetrix IVT biotin labelling

growth_protocol: Standard mouse cages in rodent facility.

extract_protocol: Trizol total RNA preparation

treatment_protocol: High 58% or control 10% fat feeding (see sample characteristics)

value: Visceral fat

tag: pregnancy status

value: Pregnant

tag: fat in diet

value: High fat (Research diets 12331)


title: Pregnant-HighFat-rep5


title: AR-siRNAi, biological rep2


title: HEK293T NF2-LATS2 knockdown, rep2

description: gene expression data from 293T cell transfected with siRNA oligoes against NF2 and LATS2


title: 8399 F Aorta endo 18.5 days

value: endothelial cell

value: embryo 18.5 days

value: Aorta


title: 8399 F ductus arteriosus endo 18.5 days

source_name: ductus arteriosus endo 18.5 days

value: ductus arteriosus


title: HEK293T NF2-LATS2 knockdown, rep 1

source_name: 293T cell transfected with siRNA oligoes against NF2 and LATS2


title: Pregnant-HighFat-rep3


title: AR-siRNA, biological rep1


title: Pregnant-HighFat-rep1


title: Pregnant-HighFat-rep2


title: 8469 B ductus arteriosus endo 18.5 days


title: HEK293T control, rep 2

description: gene expression data from 293T cell transfected with scramble oligo


title: 8399 H Aorta endo 18.5 days


title: 8412 I Aorta SMC 21 days

source_name: Aorta SMC 21 days

value: embryo 21 days


title: Scrambled siRNA, biological rep2

description: Gene expression data from VCaP cells treated with scrambled siRNA control.

value: Scrambled siRNA


title: 8412 I Aorta endo 21 days

source_name: Aorta endo 21 days


title: Pregnant-LowFat-rep3

source_name: Visceral fat,Pregnant, Low fat

value: Low fat (Research diets 12328)


title: Compound 30 (10uM), biological rep3

description: Gene expression data from VCaP cells treated with Compound 30 (10uM).

value: Compound 30 (10uM)


title: 8412 D ductus arteriosus endo 21 days

source_name: ductus arteriosus endo 21 days


title: HEK293T control, rep 1

source_name: 293T cell transfected with scramble oligo


title: Scrambled siRNA, biological rep1


title: 8469 D ductus arteriosus endo 18.5 days


title: Pregnant-LowFat-rep1


title: Pregnant-LowFat-rep4


title: Compound 30 (10uM), biological rep2


title: Pregnant-LowFat-rep5


title: Pregnant-LowFat-rep2


title: Vehicle, biological rep3

description: Gene expression data from VCaP cells treated with vehicle control.

value: Vehicle (0.1% DMSO)


title: Compound 30 (10uM), biological rep1


title: CD4+CD25high T cells in 2% O2 proband 4

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description: CD4+CD25high T cells cultivated for 4h in 2% O2 at 37°C, proband 4

hyb_protocol: Sense-strand DNA was hybridized on Affymetrix GeneChip Human Gene 1.0 ST Array.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 System.

data_processing: Microarray data were analyzed with Affymetrix GeneChip Command Console Software (Affymetrix). The advanced analysis was done with R (version 2.9) with package limma. Data preprocessing steps included RMA via usage of the R packages affy and probe summarization via the brainarray-cdf file version 12.1.0.

source_name: CD4+CD25high T cells

label_protocol: Biotinylated sense-strand DNA was generated from 100 ng of total RNA with WT Sense Target Labeling and Control Reagent (Affymetrix).

growth_protocol: CD4+CD25- or CD4+CD25high T cells were cultured in either 20% O2 (normoxia) or 2% O2 (hypoxia) in 200 microliter of X-VIVO 15, 200.000 cells/well in a 96-well round bottom plate without any further stimulation.

tag: proband age

value: 20-38 years

tag: proband sex

value: male

tag: bmi

value: body mass index < 26

value: peripheral blood

value: CD4+CD25high T cells

tag: subject

value: proband 4


title: Vehicle, biological rep2

value: VCaP


title: NonPregnant-HighFat-rep4

source_name: Visceral fat,Non pregnant, High fat

value: Visceral fat

value: Non pregnant

value: High fat (Research diets 12331)


title: 8412 I ductus arteriosus SMC 21 days

source_name: ductus arteriosus SMC 21 days

value: smooth muscle cell

value: wistar


title: NonPregnant-HighFat-rep5


title: Vehicle, biological rep1


title: 8462 A ductus arteriosus SMC 21 days

value: embryo 21 days

value: ductus arteriosus


title: NonPregnant-HighFat-rep1


title: CD4+CD25high T cells in 2% O2 proband 1

description: CD4+CD25high T cells cultivated for 4h in 2% O2 at 37°C, proband 1

treatment_protocol: CD4+CD25- or CD4+CD25high T cells were cultured in either 20% O2 (normoxia) or 2% O2 (hypoxia) in 200 microliter of X-VIVO 15, 200.000 cells/well in a 96-well round bottom plate without any further stimulation.

value: proband 1


title: NonPregnant-LowFat-rep5

source_name: Visceral fat,Non pregnant, Low fat

value: Low fat (Research diets 12328)


title: CD4+CD25- T cells in 2% O2 proband 4

description: CD4+CD25- T cells cultivated for 4h in 2% O2 at 37°C, proband 4

source_name: CD4+CD25- T cells

value: CD4+CD25- T cells


title: NonPregnant-HighFat-rep2


title: 8462 M Aorta endo 21 days

value: endothelial cell

value: Aorta


title: 8462 A ductus arteriosus endo 21 days


title: 8462 C ductus arteriosus SMC 21 days


title: 8462 M Aorta SMC 21 days


title: 8412 I ductus arteriosus endo 21 days


title: 8469 D ductus arteriosus SMC 18.5 days

source_name: ductus arteriosus SMC 18.5 days

value: embryo 18.5 days


title: CD4+CD25high T cells in 20% proband 4

description: CD4+CD25high T cells cultivated for 4h in 20% O2 at 37°C, proband 4

value: 20-38 years

value: male

value: body mass index < 26

value: peripheral blood


title: CD4+CD25high T cells in 20% O2 proband 3

description: CD4+CD25high T cells cultivated for 4h in 20% O2 at 37°C, proband 3

value: CD4+CD25high T cells

value: proband 3


title: NonPregnant-LowFat-rep3

value: Visceral fat

value: Non pregnant


title: NonPregnant-LowFat-rep1


title: CD4+CD25high T cells in 2% O2 proband 3

description: CD4+CD25high T cells cultivated for 4h in 2% O2 at 37°C, proband 3


title: 8469 B Aorta SMC 18.5 days

source_name: Aorta SMC 18.5 days

value: smooth muscle cell

value: wistar


title: CD4+CD25- T cells in 2% O2 proband 1

description: CD4+CD25- T cells cultivated for 4h in 2% O2 at 37°C, proband 1


title: NonPregnant-LowFat-rep2


title: CD4+CD25- T cells in 2% O2 proband 3

description: CD4+CD25- T cells cultivated for 4h in 2% O2 at 37°C, proband 3


title: Echinacea putative hybrid (E. paradoxa and E. pallida) PI631294, replicates 1 & 2

type: genomic

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Plenty Road

department: School of Science

country: Australia

institute: RMIT University

hyb_protocol: The SDA slides were pre-hybridized for 45 min at 42°C in a pre-warmed solution containing 5X standard saline citrate (SSC), 0.1% sodium dodecyl sulphate (SDS), 1% bovine serum albumin (BSA) and 25% formamide. The slides were rinsed twice with sterile MilliQ water and immediately dried with an air gun. The biotin-labelled targets (30 ng) were added to 17.5 μL of fresh 2X Hybridization buffer (250 μL of formamide, 250 μL of 10X SSC, 10 μL of 10% SDS), 0.5 µl of 1 mg/ml human Cot1 DNA (Invitrogen); 0.5 µl of 5 mg/ml PolyA (Sigma-Aldrich) and 0.5 µl of 10 mg/ml salmon sperm DNA (Sigma-Aldrich). The mixture (made up to 35 µl with sterile water) was denatured at 100°C for 2 min and immediately applied onto the array under a 22 × 22-mm lifter slip (Grale Scientific, Victoria, Australia). The slides were then placed in waterproof, humidified hybridization chambers (Corning Incorporated Life Sciences) and incubated overnight in a 47°C water bath. After hybridization, the coverslips were removed and the slides were washed once in 1X SSC and 0.1% SDS at 37°C for 8 min, once in 1X SSC and 0.1% SDS at 40°C for 5 min, once in 0.1X SSC and 0.1% SDS at 35°C for 5 min and once in 0.1X SSC at 35°C for 5 min. Subsequently, the slides were transferred to 500 mL of 6X SSPE-T buffer (0.9 M NaCl, 0.06 M NaH2PO4.H2O, 0.006 M EDTA, 0.005% Triton X-100, pH 7.4) without allowing them to dry. The biotinylated DNA targets bound on the array were then labelled with fluorescent FluoroLink™ streptavidin-labelled Cy3 dye (Amersham Pharmacia, UK) using a biotin-streptavidin system. Briefly, 200 μL of a Detection solution (0.5 µL of 0.8 µg/µL streptavidin-labelled Cy3, 0.8 µl of 25 µg/µL BSA, made to 200 µL with 6X SSPE-T) was applied directly onto the array surface and a 25x60-mm lifter slip was placed over it to evenly distribute the solution on the array. The slides were placed in hybridization chambers, wrapped in aluminum foil and incubated at 37 °C for 40 min in the dark. Finally, the slides were washed thrice in 6X SSPE-T for 5 min and rinsed with deionized water before being dried with an air gun. All hybridizations were performed with five technical replicates (subarrays) and two biological replicates, for a total of ten data points per array feature.

scan_protocol: Slides were scanned with a ScanArray Gx (PerkinElmer Life and Analytical Sciences, Downers Grove, IL) microarray scanner in conjunction with the supplied software. The slides were scanned with a resolution of 10 µm at 532 nm (Cy3, green laser) and at 50% photomultiplicator (PMT) gain whilst keeping background noise low. The scanned array was quantified using PerkinElmer ScanArray Express software v 2.0.

data_processing:
The ScanArray Express program individually quantified the signal intensity at each probe and normalized the data using the adaptive circle and LOWESS functions. Probes which did not hybridize were automatically flagged by the scanning software and labelled as 'bad'. Manual flagging was used to remove spots displaying inconsistent hybridization such as 'donut' spots. 'Good' probes were accepted as having a mean 'signal-to-noise ratio' (SNR) value of greater than 7 in more than half of the technical replications.
Data analysis included: Calculation of the mean signal-to-noise ratio for each feature between the five technical replicates. Normalization across the slides using the mean signal-to-noise ratio for all 283 spots in all hybridizations performed. Average of the biological replicates after normalization to produce a single value per feature.

molecule: genomic DNA

organism: Echinacea paradoxa x Echinacea pallida

source_name: Echinacea putative hybrid (E. paradoxa and E. pallida) leaves

label_protocol: The preparation of targets in all cases involved the double digestion of gDNA with AluI and HaeIII, and purification using the QIAquick® PCR Purification Kit (Qiagen, Inc.). Approximately 150 ng of purified digested DNA was labeled with Biotin-11-dUTP using the Biotin DecaLabelTM DNA Labeling Kit (Fermentas, ON, Canada). The reaction was incubated during 20 h and no further purification was performed.

growth_protocol: Fresh or preserved leaf samples were obtained.

extract_protocol: Total DNA was extracted from leaves using a modification of the standard CTAB procedure. Approximately 0.5 g of leaves was ground with liquid nitrogen to a fine powder. The powder was dissolved in 5 ml of CTAB Buffer (3% CTAB, 100 mM Tris-HCL pH 8.0, 20 mM EDTA pH 8.0, 1.4 M NaCl), 1 ml of 10% PVP and 1.2 ml of 10% CTAB. Subsequently, the mixture was incubated at 60 °C for 1 h and centrifuged at 13,000 rpm for 10 min. The supernatant obtained was further purified with a double chloroform extraction followed by precipitation with 7.5 M ammonium acetate and 100% ethanol. The precipitated DNA was resuspended in sterile water and subsequent cleanup was performed by using the DNeasy® column of the DNeasy® Plant Mini Kit (Qiagen) following the protocol in the user manual.

value: leaves

tag: family

value: Asteraceae

tag: order

value: Asterales


title: CD4+CD25high T cells in 20% O2 proband 1

description: CD4+CD25high T cells cultivated for 4h in 20% O2 at 37°C, proband 1

tag: cell type

tag: treatment

value: proband 1


title: mbAir16

city: Austin

first: Giorgio

last: Gorini

address: 2500 Speedway A4800

department: Waggoner Center for Alcohol and Addiction Research

institute: The University of Texas at Austin

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 40
A16

hyb_protocol: Standard Exiqon protocol.

scan_protocol: Images were analyzed using Imagene 8.0 (BioDiscovery, Hawthorne, CA).

data_processing: MiRNA microarray data analysis was implemented in R environment using the Linear Models for Microarray Data (LIMMA) package from Bioconductor (http://www.bioconductor.org). For each miRNA, a median was calculated from the intensity values of four replicates. Data were fitted into a linear model with an appropriate design matrix. Statistical differences between groups were calculated using an empirical Bayesian approach. False discovery rate (FDR) was assessed using the method of Benjamini and Hochberg

source_name: Midbrain, Air-2BC

label_protocol: Samples were labeled with Cy3, while the red channel was used for quality control and reference purposes

growth_protocol: Male C57BL/6J mice were acclimated to a reverse light cycle (6:00 am lights off, 6:00 pm lights on) for 21 days, food and water were available ad libitum throughout testing, and mice were group housed before the treatment.

extract_protocol: Total RNA was extracted from CTX and MB by using the mirVana PARIS kit (Life Technologies).

treatment_protocol: Mice subjected to a Chronic Intermittent Ethanol, and tested for Two-Bottle Choice drinking, as described by Finn et al. (2007) Alcoholism, clinical and experimental research 31: 939–949.

tag: tissue

value: Midbrain

tag: gender

value: Male

value: CIE-2BC air-exposed matched controls


title: CD4+CD25- T cells in 20% O2 proband 4

description: CD4+CD25- T cells cultivated for 4h in 20% O2 at 37°C, proband 4

value: 20-38 years

value: CD4+CD25- T cells

value: proband 4


title: CD4+CD25- T cells in 20% O2 proband 1

description: CD4+CD25- T cells cultivated for 4h in 20% O2 at 37°C, proband 1

value: male

value: body mass index < 26

value: peripheral blood


title: 8 OOX

city: Bar Harbor

first: Timothy

middle: Michael

last: Stearns

state: ME

address: 600 Main Street

department: Computational Sciences

institute: The Jackson Laboratory

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430v2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Average signal intensities for each probeset within arrays were calculated by and exported from Affymetrix's Expression Console (Version 1.1) software using the RMA method which incorporates convolution background correction, quantile normalization, and summarization based on a multi-array model fit robustly using the median polish algorithm. For this experiment, ten pairwise comparisons were used to statistically resolve gene expression differences between sample groups using the R/maanova analysis package. Specifically, differentially expressed genes were detected using Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/maanova package. Statistical significance levels of the pairwise comparisons were calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method.

source_name: mouse cumulus cells, OOX

label_protocol: Fragmented biotinylated aRNA were produced from 20ng Total RNA according to the standard protocol using the MessageAmp II aRNA Amplification Kit from Ambion for the first round of amplification and using the MessageAmp II Biotin Enhanced Kit from Ambion for the second round of amplification.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Micro kit according to the manufacturer's instructions.

value: female

value: antral follicles of ovaries

tag: complex type

value: OOX

value: culture

value: cumulus cells


title: mbAir15

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 39
A15

tag: strain


title: CD4+CD25- T cells in 20% O2 proband 3

description: CD4+CD25- T cells cultivated for 4h in 20% O2 at 37°C, proband 3

value: proband 3


title: 8399 E Aorta SMC 18.5 days

value: smooth muscle cell

tag: developmental stage

value: embryo 18.5 days

value: Aorta

value: wistar


title: 17 E2 OOX

source_name: mouse cumulus cells, OOX, E2

value: culture with estrogen


title: mbAir9

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 38
A09

value: Midbrain

value: Male

value: CIE-2BC air-exposed matched controls


title: Echinacea angustifolia plot 9, replicates 1 & 2

organism: Echinacea angustifolia

source_name: Echinacea angustifolia leaves

value: leaves

value: Asteraceae

value: Asterales


title: Echinacea pallida plot 5, replicates 1 & 2

organism: Echinacea pallida

source_name: Echinacea pallida leaves


title: H69M_3

city: BARCELONA

first: EDURNE

last: ARRIOLA

address: PASSEIG MARITIM 25-29

country: Spain

institute: HOSPITAL DEL MAR

description: Gene expression data from H69M cells

hyb_protocol: Sample was hybridized to Human Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 640

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 7G

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

label_protocol: 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labeling system and control reagents (Affymetrix)

extract_protocol: RNeasy Kit QIAGEN

tag: cell line

value: small cell lung cancer (SCLC)


title: mbAir26

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 41
A26


title: mbAir27

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 42
A27


title: Echinacea paradoxa var. neglecta PI631265, replicates 1 & 2

organism: Echinacea paradoxa var. neglecta

source_name: Echinacea paradoxa var. neglecta leaves


title: 2A OOX

value: female

value: antral follicles of ovaries


title: 9 OOX + Oocytes

source_name: mouse cumulus cells, OOX + oocytes

value: OOX

value: culture with oocytes


title: 14 OOX

value: culture

value: cumulus cells


title: mbAir6

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 37
A06


title: H69M_2

description: Gene expression data from H69M cells


title: Echinacea angustifolia PI631267, replicates 1 & 2


title: 15 OOX + Oocytes


title: Echinacea purpurea plot 10009, replicates 1 & 2

organism: Echinacea purpurea

source_name: Echinacea purpurea leaves


title: H69_3

description: Gene expression data from H69 cells


title: NonPregnant-LowFat-rep4

value: Visceral fat

value: Non pregnant

value: Low fat (Research diets 12328)

tag: age


title: mbEtOH31

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 35
E31

source_name: Midbrain, CIE-2BC

value: CIE-2BC EtOH vapor-exposed


title: 18 E2 OOX + Oocytes

source_name: mouse cumulus cells, OOX + oocytes, E2

value: culture with oocytes and estrogen


title: mbAir5

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 36
A05

value: Midbrain

value: Male


title: 13 COC

source_name: mouse cumulus cells, COC

value: COC


title: H69_2

description: Gene expression data from H69 cells


title: Echinacea purpurea cv. Purpurea, replicates 1 & 2

source_name: Echinacea purpurea cv. purpurea leaves

tag: cultivar

value: purpurea

value: leaves

value: Asteraceae


title: 16 E2 COC

source_name: mouse cumulus cells, COC, E2

value: female

value: culture with estrogen


title: Echinacea pallida PI631315, replicates 1 & 2

value: Asterales


title: H69M_1

description: Gene expression data from H69M cells

value: small cell lung cancer (SCLC)


title: mbEtOH30

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 34
E30


title: mbEtOH25

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 33
E25


title: 12 E2 OOX + Oocytes

value: antral follicles of ovaries

value: OOX


title: Echinacea pallida PI631296, replicates 1 & 2


title: 8462 M ductus arteriosus endo 21 days

source_name: ductus arteriosus endo 21 days

value: endothelial cell

value: embryo 21 days

value: ductus arteriosus

value: wistar


title: mbEtOH24

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 32
E24

value: CIE-2BC EtOH vapor-exposed


title: Echinacea angustifolia var. strigosa PI631266, replicates 1 & 2

organism: Echinacea angustifolia var. strigosa

source_name: Echinacea angustifolia var. strigosa leaves


title: mbEtOH20

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 31
E20

value: Midbrain


title: HepG2-PARP2 depleted-3

city: Debrecen

first: Peter

last: Bai

address: Nagyerdei krt. 98.

department: Department of Medical Chemistry

country: Hungary

institute: University of Debrecen, Medical and Health Science Center

hyb_protocol: Samples were hybridized at 45 degrees Celsius for 16 hours and then standard washing protocol was performed using GeneChip Fluidics Station 450. Core software Affymetrix GeneChip Command Console (AGCC).

scan_protocol: Arrays were scanned on GeneChip Scanner 7G (Affymetrix). Core software Affymetrix GeneChip Command Console (AGCC).

data_processing: Microarray data were analyzed by GeneSpring 10 GX software (Agilent BioTechnologies). Affymetrix CEL files were normalized Robust Multichip Analysis (RMA) algorithm and median normalization. Expressed genes were determined by filtering out the lowest 20th percentile of genes based on raw signal intensity. Then genes, which did not show at least 2-fold change difference from the median, were also filtered out, called non-changing genes. Statistical analysis was performed on the list of changing genes using T test, statistically significant difference was considered to p < 0.05 and fold change cut off value was 1.5.

source_name: HepG2 cells

label_protocol: Global expression pattern was analyzed on Affymetrix GeneChip Human Gene 1.0 ST arrays. Ambion WT Expression Kit (Life Technologies, Hungary) and GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labeling 250 ng of total RNA samples. Samples were hybridized at 45 oC for 16 hours and then standard washing protocol was performed using Affymetrix GeneChip Fluidics Station 450, the arrays were scanned on GeneChip Scanner 7G (Affymetrix). RNA labeling and hybridization was processed by UD-GenoMed Medical Genomic Technologies Ltd (Debrecen, Hungary).

growth_protocol: DMEM (1 g/L glucose, 10% FCS, 0.2 mg/mL G418).

extract_protocol: Total RNA was extracted from HepG2 cells using the RNeasy Mini Kit (Qiagen). RNA integrity was checked on Agilent Bioanalyser 2100 (Agilent Technologies), RNA samples with 9.0 RIN value were used in the further experiments. NanoDrop ND-1000 was used to determine RNA concentration.

treatment_protocol: PARP-2 silencing was performed employing shPARP-2 (small hairpin) and scPARP-2 (scrambled) shRNA by lentiviral delivery (Sigma) using 40 MOI lentiviruses coding shRNA sequence against PARP-2.

tag: transfection

value: shPARP-2 transfected


title: H69_1

description: Gene expression data from H69 cells


title: 7 COC

value: COC

value: culture

value: cumulus cells


title: Echinacea pallida PI631275, replicates 1 & 2

value: leaves

value: Asteraceae


title: Echinacea angustifolia var. angustifolia PI631272, replicates 1 & 2

source_name: Echinacea angustifolia var. angustifolia leaves


title: Echinacea angustifolia var. angustifolia PI631285, replicates 1 & 2


title: Echinacea pallida cv. Hula dancer, replicates 1 & 2

source_name: Echinacea pallida cv. Hula dancer leaves

value: Hula dancer


title: Echinacea paradoxa var. paradoxa PI631301, replicates 1 & 2

organism: Echinacea paradoxa var. paradoxa

source_name: Echinacea paradoxa var. paradoxa leaves

value: Asterales


title: 10 E2 COC

value: female

value: culture with estrogen


title: mbNaive46

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 26
N46

source_name: Midbrain, Ethanol Naïve

value: Male

value: EtOH-naive


title: mbNaive48

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 27
N48


title: mbEtOH2

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 30
E02


title: 8469 F ductus arteriosus endo 18.5 days

source_name: ductus arteriosus endo 18.5 days

value: endothelial cell

value: embryo 18.5 days


title: mbEtOH1

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 29
E01


title: mbNaive49

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 28
N49


title: HepG2-PARP2 depleted-1


title: 11 E2 OOX

source_name: mouse cumulus cells, OOX, E2

value: antral follicles of ovaries

value: OOX


title: 5 E2 OOX

source_name: mouse cumulus cells, OOX


title: HepG2-control-3

value: scrambled transfected


title: 3 OOX + Oocytes

source_name: mouse cumulus cells, OOX + oocytes

value: culture with oocytes


title: AZ-521_doxycycline_24h_rep2

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

hyb_protocol: Fluidics Station 450.

scan_protocol: Affymetrix GeneChip Scanner 3000.

data_processing: RMA normalization by apt-probeset-summarize.exe from Affymetrix.

source_name: AZ521 dnSox2 cells, induced, 24h

label_protocol: Affymetrix WT cDNA Synthesis and Amplification and Terminal labeling kits.

growth_protocol: Minimum Essential Medium containing glutamine (MEM-GlutaMAXTM-I) (Gibco, Darmstadt, Germany) supplemented with 10% tetracycline-negative fetal bovine serum (PAA, Pasching, Austria) and 1% penicillin/streptomycin (Invitrogen, Darmstadt, Germany). All cells were maintained at 37 °C and 5% CO2 in a 95% air-humidified incubator.

extract_protocol: Trizol

treatment_protocol: 1 µg/ml doxycycline was added to induce expression of dnSox2.

tag: genotype/variation

value: inducible dnSox2

value: gastric cancer cell line

value: doxycycline induced

tag: time point


title: AZ-521_doxycycline_24h_rep1


title: 4 E2 COC

value: COC

value: cumulus cells


title: AZ-521_doxycycline_24h_rep3


title: 1 COC

value: culture


title: HepG2-PARP2 depleted-2

value: shPARP-2 transfected


title: HepG2-control-1


title: Lymphoma-serum

city: New York

first: Bisen

last: Ding

state: NY

address: 1300 York Avenue

institute: Cornell Medical College

hyb_protocol: Fragmented cRNA was hybridized to the gene chips, washed, and stained with streptavidin phycoerythrin.

scan_protocol: The probe arrays were scanned with the Genechip System confocal scanner

data_processing: Affymetrix Microarray suite 5.0 as used to analyze the data

source_name: Lymphoma cells cultured in serum-containing medium

label_protocol: The Superscript choice kit (Invitrogen, Carlsbad,CA) was used to make cDNA with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. The biotin labeled cRNA was made by in vitro transcription (Enzo Diagnostics).

extract_protocol: The protocol used to extract RNA was according to Manufacturers specifications QIAGEN Rneasy kit

value: lymphoma cells


title: 6 E2 OOX + Oocytes

source_name: mouse cumulus cells, OOX + oocytes, E2

value: female

value: culture with oocytes and estrogen


title: Echinacea tennesseensis, replicates 1 & 2

organism: Echinacea tennesseensis

source_name: Echinacea tennesseensis leaves

value: leaves

value: Asteraceae

value: Asterales


title: NonPregnant-HighFat-rep3

source_name: Visceral fat,Non pregnant, High fat

value: Visceral fat

tag: pregnancy status

value: Non pregnant

tag: fat in diet

value: High fat (Research diets 12331)


title: Echinacea angustifolia var. strigosa PI631320, replicates 1 & 2

tag: family


title: Echinacea purpurea PI631313, replicates 1 & 2

source_name: Echinacea purpurea leaves

tag: order


title: AZ-521_doxycycline_18h_rep3

source_name: AZ521 dnSox2 cells, induced, 18h

tag: cell type


title: Lymphoma-EC-co-culture

source_name: Lymphoma cells co-cultured with endothelial cells

value: lymphoma cells co-cultured with endothelial cells


title: mbNaive41

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 22
N41

value: Midbrain

value: Male

tag: treatment

value: EtOH-naive


title: mbNaive42

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 23
N42

tag: tissue


title: mbNaive45

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 25
N45

tag: gender


title: HepG2-control-2

source_name: HepG2 cells

value: scrambled transfected


title: Echinacea purpurea PI631308, replicates 1 & 2


title: ctxAir27

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 21
A27

source_name: Cerebral Cortex, Air-2BC

value: Cerebral Cortex

value: CIE-2BC air-exposed matched controls


title: Echinacea pallida PI631290, replicates 1 & 2

source_name: Echinacea pallida leaves


title: AZ-521_doxycycline_12h_rep2

source_name: AZ521 dnSox2 cells, induced, 12h

value: inducible dnSox2

value: gastric cancer cell line

value: doxycycline induced


title: Echinacea paradoxa var. paradoxa PI631321, replicates 1 & 2

source_name: Echinacea paradoxa var. paradoxa leaves


title: Echinacea angustifolia var. angustifolia PI631318, replicates 1 & 2

source_name: Echinacea angustifolia var. angustifolia leaves


title: AZ-521_doxycycline_18h_rep1


title: sorted basal cells K5creL/L mice 3

city: Paris

first: charles

last: decraene

address: 26 rue d'ULM

country: France

institute: Institut Curie

description: gene expression of basal cells from K5creMycL/L mice

hyb_protocol: Mouse Genome 430 2.0 Arrays (Affymetrix) were hybridized, revealed and washed according the Affymetrix protocol.

scan_protocol: GeneChips were scanned using a 7 G scanner (Affymetrix) and images (DAT files) were converted to CEL files using GCOS software (Affymetrix)

data_processing: After MAS5 normalization done by Expression Console (Affymetrix), differentially expressed genes were identified by ANOVA. In addition, the modulations of gene expression were validated whenever, for each ratio, the higher median of gene expression value was up to 30 (corresponding to the estimated background cut-off, data not shown) and the corresponding fold-change greater than 1.5.

source_name: K5creMycL/L basal cells

label_protocol: cRNA synthesis was performed with total cellular RNA (3 µg) using the one-cycle Labelling kit from Affymetrix. With sorted cells, the WT-Ovation™ Pico RNA Amplification System and FL- Ovation™ cDNA Biotin Module V2 (Nugen) were applied on 1ng of total RNA to generate biotinylated cDNA  suitable for hybridization to Affymetrix Genechip® arrays.

growth_protocol: Experiments were conducted in accordance with French veterinary guidelines and those formulated by the Council of Europe for experimental animal use

extract_protocol: Total RNA was extracted from mammary tissues using Trizol Reagent (Invitrogen) followed by DNAse treatment and a clean-up step in miRNeasy Micro-columns (Qiagen).

tag: tumor stage

value: basal mammary cells

tag: label protocol

value: Nugen


title: ctxAir26

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 20
A26

tag: strain


title: ctxAir16

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 19
A16


title: Echinacea purpurea cv. white purpurea, replicates 1 & 2

source_name: Echinacea purpurea cv. white purpurea leaves

value: white purpurea

value: leaves

value: Asteraceae


title: AZ-521_doxycycline_12h_rep1

tag: cell line


title: AZ-521_doxycycline_8h_rep2

source_name: AZ521 dnSox2 cells, induced, 8h


title: Echinacea purpurea PI633669, replicates 1 & 2

value: Asterales


title: ctxAir15

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 18
A15


title: sorted basal cells K5creL/L mice 2


title: AZ-521_doxycycline_18h_rep2


title: CD31+CD133+

first: Adilia

last: Hormigo

address: 601 Elmwood Avenue, Box 645

institute: University of Rochester Medical Center

description: CD133+(Prom1+ ) CD31+ endothelial cells sorted from normal mouse brain vasculature

hyb_protocol: Standard Affymetrix protocol for Mouse 430 2.0 arrays.

data_processing: Affymetrix .cel and MAS5 normalized .chp files were imported into Genespring GX7 (Agilent) for analysis.

source_name: Normal vasculature

label_protocol: Nugen Ovation biotin labeling system using the standard protocol

extract_protocol: Total RNA was extracted using the Rneasy mini kit (Qiagen)

treatment_protocol: A population of CD31+CD133- and of CD31+CD133+ endothelial cells were obtained from mouse brain vasculature by Fluorescence Activated Cell Sorting.

value: brain vasculature

tag: sort population

tag: pathology

value: normal


title: AZ-521_doxycycline_8h_rep1


title: sorted basal cells Control mice 2

description: gene expression of basal cells from control mice

source_name: Control basal cells

value: control


title: Echinacea pallida PI631293, replicates 1 & 2


title: ctxAir9

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 17
A09

value: Male


title: Echinacea paradoxa var. neglecta PI631264, replicates 1 & 2

source_name: Echinacea paradoxa var. neglecta leaves


title: AZ-521_uninduced_24h_rep3

source_name: AZ521 dnSox2 cells, uninduced, 24h

value: uninduced


title: ctxAir6

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 16
A06


title: Echinacea paradoxa var. neglecta PI631263, replicates 1 & 2


title: ctxAir5

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 15
A05


title: sorted basal cells K5creL/L mice 1


title: ctxEtOH31

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 14
E31

source_name: Cerebral Cortex, CIE-2BC

value: CIE-2BC EtOH vapor-exposed


title: sorted basal cells Control mice 3


title: Control mice 4

description: gene expression from control mice

source_name: Control mice

value: control tissue

value: Affymetrix


title: AZ-521_uninduced_18h_rep3

source_name: AZ521 dnSox2 cells, uninduced, 18h

value: inducible dnSox2


title: AZ-521_uninduced_18h_rep2

value: gastric cancer cell line


title: sorted basal cells Control mice 1


title: AZ-521_uninduced_24h_rep1


title: AZ-521_uninduced_24h_rep2


title: ctxEtOH30

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 13
E30

value: Cerebral Cortex


title: AZ-521_uninduced_18h_rep1


title: ctxEtOH25

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 12
E25


title: AZ-521_uninduced_12h_rep2

source_name: AZ521 dnSox2 cells, uninduced, 12h


title: ctxEtOH24

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 11
E24


title: ctxEtOH20

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 10
E20


title: Control mice 2

description: gene expression from control mice


title: Control mice 1

description: gene expression from control mice


title: ctxEtOH2

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 9
E02


title: Control mice 3

description: gene expression from control mice


title: K5ΔNβcat Large hyperplasia 5

description: gene expression from large hyperplasia of K5ΔNβcat mice

source_name: K5ΔNβcat Large hyperplasia

value: large hyperplasia


title: AZ-521_uninduced_8h_rep1

source_name: AZ521 dnSox2 cells, uninduced, 8h


title: UA159 wild type control vs. UA159 nukacin ISK-1 treated, replicate2

city: Kagoshima

first: Kawada-matsuo

last: Miki

department: oral microbiology

institute: Kagoshima University

hyb_protocol: The Alexa Fluor® 555-labeled and Alexa Fluor® 647-labeled DNAs were mixed and hybridised on an array using a Hi-RPM Gene Expression Hybridization Kit (Agilent Technologies).

scan_protocol: The arrays were scanned using an Agilent scanner (Agilent Technologies).

data_processing: Data extraction, filtering and normalization were conducted using Feature Extraction Software (Agilent Technologies). Dye normalization of Linear and LOWESS were used for normalizing Agilent microarrays.

label: Alexa Fluor® 647

organism: Streptococcus mutans

source_name: UA159 wild type control

label_protocol: cDNA was synthesized from 10 μg of total RNA using a FairPlay III Microarray Labeling Kit (Agilent Technologies, Santa Clara, CA, USA), according to the manufacturer's instructions. The Agilent eArray platform was used to design a microarray; 14,028 probes (60-mers) were designed for the 2,012 protein-coding genes of S. mutans UA159 (up to seven probes per gene). For microarray analyses, test and control cDNAs were labeled with Alexa Fluor® 555 and Alexa Fluor® 647 (Molecular Probes Inc., OR, USA), respectively. The fluorescently labeled cDNA was purified using the QIAquick PCR Purification Kit (QIAGEN Inc., CA, USA).

growth_protocol: S. mutans UA159, D nsrRS and D lcrRS were grown in TSB at 37°C with 5% CO2 to OD660=0.3.

extract_protocol: Total RNA was extracted from bacterial cells using a FastRNA Pro Blue Kit (MP Biomedicals, Cleveland, OH, USA) according to the manufacturer's protocol.

treatment_protocol: Nisin A (2 μg/ml) or nukacin ISK-1 (4 μg/ml) was added to the medium.

tag: strain/background

tag: genotype

value: wild type

label: Alexa Fluor® 555

source_name: UA159 wild type, nukacin ISK-1 treated

value: nukacin ISK-1


title: K5ΔNβcat Large hyperplasia 3

tag: genotype/variation


title: AZ-521_uninduced_12h_rep1

tag: time point


title: K5ΔNβcat Large hyperplasia 4


title: K5ΔNβcat Large hyperplasia 2


title: CD31+CD133-

description: CD133-(Prom1- ) CD31+ endothelial cells sorted from normal mouse brain vasculature

scan_protocol: Standard Affymetrix protocol for Mouse 430 2.0 arrays.


title: UA159 nisin A treated vs. nsrRSKO in UA159 nisin A treated, replicate1

source_name: UA159 wild type, nisin A treated

value: nisin A

source_name: Delta-nsrRS, nisin A treated

value: delta-nsrRS


title: AZ-521_uninduced_8h_rep2


title: ctxNaive49

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 7
N49

source_name: Cerebral Cortex, Ethanol Naïve

value: EtOH-naive


title: UA159 wild type control vs. UA159 nukacin ISK-1 treated, replicate1


title: UA159 nisin A treated vs. nsrRSKO in UA159 nisin A treated, replicate2


title: UA159 wild type control vs. UA159 nisin A treated, replicate2


title: PC3 cells transfected with negative control, replicate 3

city: Lund

first: Yvonne

last: Ceder

address: Medicon Village

department: Laboratory Medicine

country: Sweden

institute: Lund University

hyb_protocol: GeneChip Human Gene 1.0 ST array, GeneChip Fluidics station 450

scan_protocol: GeneChip Scanner 3000, GeneChip Operating software, GenePix 4.0 (Axon instrument)

data_processing: Expression Console version 1.1.2 software; RMA normalization

source_name: PC3 cells

label_protocol: GeneChip WT terminal labelling kit

extract_protocol: acid phenol chloroform; RIP-ChIP was adapted from Easow et al. 2007, Peritz et al. 2006, and Hong et al. 2009.

value: androgen independent aggressive prostate cancer cell line

tag: transfection

value: negative control

tag: antibody

value: anti-Ago2 (11A9, IgG2a, rat, Ascenion, Munich, Germany)


title: ctxEtOH1

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 8
E01

value: Male


title: UA159 nukacin ISK-1 treated vs. lcrRSKO in UA159 nukacin ISK-1 treated, replicate1

source_name: Delta-lcrRS, nukacin ISK-1 treated

value: delta-lcrRS


title: ctxNaive48

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 6
N48


title: ctxNaive46

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 5
N46


title: UA159 wild type control vs. UA159 nisin A treated, replicate1


title: K5ΔNβcat Large hyperplasia 1


title: mbNaive44

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 24
N44

source_name: Midbrain, Ethanol Naïve

value: Midbrain


title: PC3 cells transfected with negative control, replicate 2


title: ctxNaive45

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 4
N45


title: ctxNaive44

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 3
N44


title: K5ΔNβcat small hyperplasia 4

description: gene expression from small hyperplasia of K5ΔNβcat mice

source_name: K5ΔNβcat small hyperplasia

value: small hyperplasia


title: PC3 cells transfected with miR-205, replicate 2


title: ctxNaive41

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 1
N41


title: 18.I.0

city: Vienna

first: Mariann

last: Gyongyosi

address: Wahringer Gurtel 18-20

country: Austria

institute: Medical University of Vienna

description: Gene expression 1 month after treatment

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.65 μg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Sus scrofa Genome Oligo Microarrays 4x44K V2 using hybridization chamber and oven. Finally, the microarrays were washed with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated (37 °C) Agilent Gene Expression Wash Buffer 2 for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies) and analyzed by the Agilent Feature Extraction Software (FES).

data_processing: Raw hybridization values were loaded into R (GNU R) using the R-package limma (v3.14.4), the values were background-corrected with method ‘normexp’ adding an offset of 1 and finally quantile normalized and log2-transformed.

organism: Sus scrofa

source_name: pig 18, infarcted core, not treated

label_protocol: 100 ng of each total RNA sample was used for the linear T7-based amplification step. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: Domestic pigs were pre-treated with per os 250 mg aspirin and 300 mg clopidogrel one day before induction of closed-chest reperfused myocardial infarction. After 1 month post-AMI, the pogs were randomized. During the follow-up, a daily dose of 100 mg aspirin and 75 mg clopidogrel were administered.

extract_protocol: Tissue-samples for RNA extraction were obtained directly after sacrification of the animals from myocardium in the remote border-(injection)-zone- and infarct core region, and stored in RNAlater (Qiagen, Germany) at -20°C. Total RNA was isolated from tissue samples with RNeasy Microarray Tissue Mini Kit (Qiagen, Germany) after manufacturer´s protocol. RNA quality was checked on RNA Nano chips via Agilent 2100 Bioanalyzer platform (Agilent Technologies), all RNA samples used for expression analysis had an RNA Integrity Number (RIN) higher than 6 indicating sufficient quality.

treatment_protocol: The pigs were randomized and received either secretome of apoptotic peripheral mononuclear cells or medium-placebo via percutaneous intramyocardial delivery. One month post treatment, cardiac magnet resonance with late enhancement protocol was performed, and the pigs were humanely euthanized.

value: domestic

tag: individual

value: Infarcted core

value: no


title: ctxNaive42

description:
Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes (Ambion Human Panel)
SAMPLE 2
N42

value: Cerebral Cortex


title: PC3 cells transfected with miR-205, replicate 1

tag: cell type


title: 18.N.0

description: Gene expression 1 month after treatment

source_name: pig 18, normal region, not treated

value: Normal region

tag: treatment


title: PC3 cells transfected with miR-205, replicate 3


title: 40.I.0

description: Gene expression 1 month after treatment

source_name: pig 40, infarcted core, not treated

tag: tissue


title: K5ΔNβcat mice tumor 11

description: gene expression from tumor of K5ΔNβcat mice

source_name: K5ΔNβcat mice tumor

value: tumor

value: Affymetrix


title: K5ΔNβcat small hyperplasia 1


title: Random melanoma patient 21

city: Budapest

first: Zoltan

last: Pos

address: 4 Nagyvarad ter

department: Dept. of Genetics, Cell- and Immunobiology

institute: Semmelweis University

description: Sporadic melanoma isolated from patient 21

hyb_protocol: Samples were prepared for hybridization using the GeneChip Hyb Wash and Stain Kit (Affymetrix); mixed with Control Oligonucleotide B2, Eukaryotic Hybridization Controls and Hybridization Mix from and loaded to Human Gene ST 1.0 Arrays (Affymetrix). Hybridization was done in a GeneChip Hybridization Oven 640 (Affymetrix) for 17 hours, at +45°C, 60 rpm. Arrays were washed and PE-labeled on a GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 7G with autoloader (Affymetrix). Raw data were generated with Affymetrix GeneChip Command Console

data_processing: Raw data from the generated .CEL files were imported into Partek Genomincs Suite using the RMA method. Sample batches scanned at different time points were adjusted by the Distance Weighted Discrimination method

source_name: Melanoma cells in culture

label_protocol: 250 ng total RNA per sample was amplified using a WT expression kit (Ambion).  Samples were subjected to reverse transcription for cDNA synthesis, subsequent in vitro transcription for cRNA synthesis, and magnetic bead-associated cRNA purification. The cRNA obtained was random primed, a second round of cDNA synthesis was carried out, and single stranded cDNA was isolated by RNase H treatment followed by magnetic bead isolation. Next, cDNA was labeled with help of a GeneChip WT Terminal Label and Control Reactions kit (Affymetrix). Samples were fragmented in the presence of Ung1 and Ape1, fragment length confirmed by E-Gel® Agarose Gel Electrophoresis (Invitrogen), fragments extended with TdT and thereby biotin-labeled.

growth_protocol: After surgical removal, stable cell cultures were established and maintained in IMDM (Gibco) supplemented by 10% Human Serum AB (Gemini)

extract_protocol: Total RNA was isolated using Qiagen’s RNEasy Mini Kit, following standard protocol. Sample purity and integrity was confirmed by A260/A280 spectrophotometry and capillary gel electrophoresis on a Nanodrop spectrophotometer (Nanodrop) and using RNA 6000 Nano Kits (Agilent) on a 2100 Bioanalyzer (Agilent), respectively.

value: melanoma cells

tag: sample type

value: Random

tag: patient id

tag: lesion id

tag: date of isolation

tag: origin

value: Surgery Branch, NIH, Bethesda, USA

tag: originator's sample label


title: K5ΔNβcat mice tumor 10

tag: strain

tag: tumor stage

tag: label protocol


title: 18.B.0

description: Gene expression 1 month after treatment

source_name: pig 18, border region, not treated

value: Border region


title: 16.N.1

description: Gene expression 1 month after treatment

source_name: pig 16, normal region, treated

value: yes


title: 40.B.0

description: Gene expression 1 month after treatment

source_name: pig 40, border region, not treated


title: Random melanoma patient 20

description: Sporadic melanoma isolated from patient 20


title: K5ΔNβcat small hyperplasia 5

tag: genotype/variation


title: K5ΔNβcat small hyperplasia 3


title: 16.I.1

description: Gene expression 1 month after treatment

source_name: pig 16, infarcted core, treated


title: PC3 cells transfected with negative control, replicate 1

tag: cell line

value: androgen independent aggressive prostate cancer cell line

value: negative control

value: anti-Ago2 (11A9, IgG2a, rat, Ascenion, Munich, Germany)


title: Random melanoma patient 19

description: Sporadic melanoma isolated from patient 19


title: K5ΔNβcat small hyperplasia 2


title: K5ΔNβcat mice tumor 8


title: Random melanoma patient 22

description: Sporadic melanoma isolated from patient 22


title: K5ΔNβcat mice tumor 9


title: Random melanoma patient 18

description: Sporadic melanoma isolated from patient 18


title: K5ΔNβcat mice tumor 7


title: Random melanoma patient 16

description: Sporadic melanoma isolated from patient 16


title: 15.I.1

description: Gene expression 1 month after treatment

source_name: pig 15, infarcted core, treated


title: K5ΔNβcat mice tumor 5


title: 15.B.1

description: Gene expression 1 month after treatment

source_name: pig 15, border region, treated


title: Random melanoma patient 17

description: Sporadic melanoma isolated from patient 17


title: 16.B.1

description: Gene expression 1 month after treatment

source_name: pig 16, border region, treated


title: 14.N.1

description: Gene expression 1 month after treatment

source_name: pig 14, normal region, treated


title: 15.N.1

description: Gene expression 1 month after treatment

source_name: pig 15, normal region, treated


title: K5ΔNβcat mice tumor 6


title: deciduous incisor tooth germ embryonic day 60  vs deciduous canine tooth germ embryonic day 50

city: xian

first: Ang

last: Li

address: Xi wu Road98#

country: China

institute: Stomatological Hospital of Xi’an Jiao-Tong University

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression). For two color experiments, the ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values.

source_name: 50 day deciduous canine tooth germ tissue

label_protocol: The assay started from 2 to 5 ug total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags (Cy3/Cy5) were used for the two RNA samples in dual-sample experiments.

extract_protocol: Total RNA was extracted using the Animal Tissue RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada), following the manufacturer's recommended protocol.

tag: tooth development

value: embryonic day 50

tag: types of teeth

value: deciduous canine (JY)

source_name: 50 day deciduous incisor tooth germ tissue

value: deciduous incisor (QY)


title: 14.B.1

description: Gene expression 1 month after treatment

source_name: pig 14, border region, treated

value: domestic

tag: individual


title: K5ΔNβcat mice tumor 4


title: deciduous premolar tooth germ embryonic day 60  vs deciduous incisor tooth germ embryonic day 60

source_name: 60 day deciduous incisor tooth germ tissue

value: embryonic day 60

source_name: 60 day deciduous premolar tooth germ tissue

value: deciduous premolar (QMY)


title: 14.I.1

description: Gene expression 1 month after treatment

source_name: pig 14, infarcted core, treated

value: Infarcted core


title: Random melanoma patient 12

description: Sporadic melanoma isolated from patient 12

tag: cell type


title: deciduous premolar tooth germ embryonic day 40  vs deciduous incisor tooth germ embryonic day 40

source_name: 40 day deciduous incisor tooth germ tissue

value: embryonic day 40

source_name: 40 day deciduous premolar tooth germ tissue


title: Random melanoma patient 14

description: Sporadic melanoma isolated from patient 14

source_name: Melanoma cells in culture


title: K5ΔNβcat mice tumor 2

source_name: K5ΔNβcat mice tumor

value: tumor

value: Affymetrix


title: K5ΔNβcat mice tumor 1


title: deciduous molar tooth germ embryonic day 50  vs deciduous molar tooth germ embryonic day 60

source_name: 60 day deciduous molar tooth germ tissue

value: deciduous molar (MY)

source_name: 50 day deciduous molar tooth germ tissue


title: K5ΔNβcat mice tumor 3


title: deciduous molar tooth germ embryonic day 40  vs deciduous canine tooth germ embryonic day 40

source_name: 40 day deciduous canine tooth germ tissue

source_name: 40 day deciduous molar tooth germ tissue


title: Random melanoma patient 15

description: Sporadic melanoma isolated from patient 15

value: melanoma cells

value: Random

value: Surgery Branch, NIH, Bethesda, USA


title: deciduous canine tooth germ embryonic day 60  vs deciduous premolar tooth germ embryonic day 50

source_name: 50 day deciduous premolar tooth germ tissue

source_name: 60 day deciduous canine tooth germ tissue


title: Random melanoma patient 13

description: Sporadic melanoma isolated from patient 13


title: Random melanoma patient 11

description: Sporadic melanoma isolated from patient 11


title: 13.I.1

description: Gene expression 1 month after treatment

source_name: pig 13, infarcted core, treated

tag: treatment

value: yes


title: 13.B.1

description: Gene expression 1 month after treatment

source_name: pig 13, border region, treated

tag: tissue

value: Border region


title: Random melanoma patient 10

description: Sporadic melanoma isolated from patient 10

tag: sample type


title: Random melanoma patient 8

description: Sporadic melanoma isolated from patient 8

tag: patient id


title: Random melanoma patient 9

description: Sporadic melanoma isolated from patient 9

tag: lesion id


title: 12.I.1

description: Gene expression 1 month after treatment

source_name: pig 12, infarcted core, treated


title: 11.N.1

description: Gene expression 1 month after treatment

source_name: pig 11, normal region, treated

value: Normal region


title: Random melanoma patient 7

description: Sporadic melanoma isolated from patient 7

tag: date of isolation


title: 11.I.1

description: Gene expression 1 month after treatment

source_name: pig 11, infarcted core, treated


title: 12.B.1

description: Gene expression 1 month after treatment

source_name: pig 12, border region, treated


title: 10.N.0

description: Gene expression 1 month after treatment

source_name: pig 10, normal region, not treated

value: no


title: Ventral Dentate Resistant #4

city: Philadelphia

first: mark

last: alter

state: PA

address: 125 S. 31st Street

department: Center for Neurobiology and Behvior

institute: University of Pennsylvania

description: Ventral Fluoxetine Resistant

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Robust Multiarray Analysis in Affymetrix Expression Console

source_name: Ventral dentate gyrus

label_protocol: standard Affymetrix protocol

value: Ventral dentate gyrus

tag: gender

value: male

tag: age

value: 7-8 wks

value: Fluoxetine

tag: response

value: Resistant


title: Random melanoma patient 4

description: Sporadic melanoma isolated from patient 4

tag: origin

tag: originator's sample label


title: Ventral Dentate Resistant #1

description: Ventral Fluoxetine Resistant

tag: strain


title: Random melanoma patient 6

description: Sporadic melanoma isolated from patient 6


title: Ventral Dentate Resistant #3

description: Ventral Fluoxetine Resistant


title: Ventral Dentate Resistant #2

description: Ventral Fluoxetine Resistant


title: Dorsal Dentate Resistant #4

description: Dorsal Fluoxetine Resistant

source_name: Dorsal dentate gyrus

value: Dorsal dentate gyrus


title: Dorsal Dentate Resistant #1

description: Dorsal Fluoxetine Resistant


title: 7420059_AOM d65

city: Liège

first: Claire

last: Josse

state: Liège

address: rue de l'hopital, 1

department: Medical Oncology

country: Belgium

institute: CHU Liege

description:
0007420059_raw
biological replicate 4 of 5. Second point of 2 time points

hyb_protocol: Hy3 and Hy5 labeled (sample_ch1 and sample_ch2) RNA were combined and hybridized overnight to miRXplore™ microarrays (Miltenyi Biotec GmbH) using the a-Hyb™ Hybridization Station (Miltenyi Biotec)

scan_protocol: Image capture and signal quantification of hybridized miRXplore™ microarrays microarrays were done with the Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA) and ImaGene software Version 8.0.1 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification was done using ImaGene software version 8.0.1 (BioDiscovery, Los Angeles, MA). Median normalization was performed using the calibration oligos

organism: synthetic construct

label_protocol: 2 µg of respective total RNA as well as 2 fmol of the Universal Reference (Miltenyi Biotec GmbH) were each mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labeled using a commercial kit (miRCury™ LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer. The total RNA and Universal Reference mix was hybridized in a dual colour approach to miRXplore™ microarrays (Miltenyi Biotec GmbH).

extract_protocol: RNA were extracted from the whole colon with 8 mL Tripur according to the manufacturer's instructions.

treatment_protocol: AOM 12 mg/kg in PBS, one intraperitoneal injection at day 1. DSS 2% in drinkable water, 3 cycles administration of 5 days followed by 16 days recovery. Fisrt day of first DSS cycle at day 7.

tag: reference

value: syntethic miRNA pool of 954 synthetic miRNAs in equimolar concentrations  from human, mouse, rat, and virus

source_name: AOM d65

value: Whole colonic tissue

value: AOM treated-mice for 65 days


title: 11.B.1

description: Gene expression 1 month after treatment

source_name: pig 11, border region, treated

value: domestic


title: Random melanoma patient 3

description: Sporadic melanoma isolated from patient 3

source_name: Melanoma cells in culture

value: melanoma cells


title: Dorsal Dentate Resistant #3

description: Dorsal Fluoxetine Resistant


title: Random melanoma patient 2

description: Sporadic melanoma isolated from patient 2

value: Random


title: Dorsal Dentate Resistant #2

description: Dorsal Fluoxetine Resistant


title: Recurrent melanoma patient H, 3rd recurrence

description: Recurrent melanoma isolated from patient H, 3rd recurrence

value: Recurrent

value: H

value: Surgery Branch, NIH, Bethesda, USA

value: barbaiotc 2297-1.2 p6 medi


title: Ventral Dentate Responder  #7

description: Ventral Fluoxetine Responder

value: Responder


title: Ventral Dentate Responder  #6

description: Ventral Fluoxetine Responder

value: Ventral dentate gyrus


title: Random melanoma patient 1

description: Sporadic melanoma isolated from patient 1


title: 10.B.0

description: Gene expression 1 month after treatment

source_name: pig 10, border region, not treated

value: Border region

value: no


title: Random melanoma patient 5

description: Sporadic melanoma isolated from patient 5


title: 7420032_AOM d65

description:
0007420032_raw
biological replicate 3 of 5. Second point of 2 time points

source_name: Universal Reference (Miltenyi Biotec GmbH)


title: 7420052_AOM d65

description:
0007420052_raw
biological replicate 5 of 5. Second point of 2 time points


title: Ventral Dentate Responder #8

description: Ventral Fluoxetine Responder

value: male

value: 7-8 wks

value: Fluoxetine


title: 7420031_AOM d15

description:
0007420031_raw
biological replicate 5 of 5. First point of 2 time points

value: syntethic miRNA pool of 954 synthetic miRNAs in equimolar concentrations  from human, mouse, rat, and virus

source_name: AOM d15

value: AOM treated-mice for 15 days


title: 7420029_AOM d65

description:
0007420029_raw
biological replicate 1 of 5. Second point of 2 time points

value: Whole colonic tissue

value: AOM treated-mice for 65 days


title: 7420030_AOM d65

description:
0007420030_raw
biological replicate 2 of 5. Second point of 2 time points


title: Ventral Dentate Responder #4

description: Ventral Fluoxetine Responder


title: Recurrent melanoma patient H, 2nd recurrence

description: Recurrent melanoma isolated from patient H, 2nd recurrence

value: melanoma cells

value: barbaiotc 2195 medi p7


title: 7420028_AOM d15

description:
0007420028_raw
biological replicate 4 of 5. First point of 2 time points


title: Recurrent melanoma patient H, 1st recurrence

description: Recurrent melanoma isolated from patient H, 1st recurrence

value: Recurrent

value: barbaiotc 2086 P9 frag


title: Ventral Dentate Responder #3

description: Ventral Fluoxetine Responder


title: Ventral Dentate Responder #5

description: Ventral Fluoxetine Responder


title: 7420027_AOM d15

description:
0007420027_raw
biological replicate 3 of 5. First point of 2 time points


title: 7420026_AOM d15

description:
0007420026_raw
biological replicate 2 of 5. First point of 2 time points


title: 7420025_AOM d15

description:
0007420025_raw
biological replicate 1 of 5. First point of 2 time points


title: Dorsal Dentate Responder #8

description: Dorsal Fluoxetine Responder

value: Dorsal dentate gyrus


title: Recurrent melanoma patient F, 3rd recurrence

description: Recurrent melanoma isolated from patient F, 3rd recurrence

value: F

value: Surgery Branch, NIH, Bethesda, USA

value: kilpatric 2139 frag P8


title: 7420078_DSS d65

description:
0007420078_raw
biological replicate 5 of 5. Second point of 2 time points

source_name: DSS d65

value: DSS treated-mice for 65 days


title: Recurrent melanoma patient G, 1st recurrence

description: Recurrent melanoma isolated from patient G, 1st recurrence

value: G

value: roman TC 1938 from sieve P7


title: Recurrent melanoma patient G, 3rd recurrence

description: Recurrent melanoma isolated from patient G, 3rd recurrence

value: roman TC 2108 medi p6


title: Neonates_Fx2.0-1_rep1

city: Okazaki

first: Kenji

last: Toyota

address: 5-1 Higashiyama

institute: National Institute for Basic Biology

description:
Gene expression after 48hr  in Fx2.0 treated neonate
Fx_2.0_1

hyb_protocol: 165 µg of Cyanine3-labeled cRNA were hybridized to the custom 4x44k D. magna microarray using the protocols of Agilent Technologies. After 17 h incubation with rotation, the microarrays were washed with Gene Expression Wash Buffer Kit (Agilent Technologies) according to the manufacturer’s protocols.

scan_protocol: DNA microarrays were scanned using a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA) at 5 µm resolution. The signal intensity of the spots was digitized using the microarray imager software (Combimatrix Molecular Diagnostics, Irvine, CA, USA).

data_processing: Data files generated by Agilent Feature Extraction Software were imported into Subio Platform (Subio Inc., Tokyo) for further data processing.

organism: Daphnia magna

source_name: Neonates, Fx-2.0-1, replicate 1

label_protocol: 500 ng of total RNA were prepared for microarray hybridization using the Quick Amp Labeling Kit and One-color RNA Spike-in kit (Agilent Technologies), and purified using the RNeasy Micro Kit (Qiagen) following the manufacturer’s protocol. The quality of Cyanine3-labeled complementary RNA (cRNA) was analyzed using the Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: At least 20 individuals were used for one set of samples for each chemical concentration and controls. Harvested daphnids were briefly washed and homogenized using the physcotron NS-310E (Nichion, Tokyo, Japan). Total RNA was purified with TRIZOL reagent (Invitrogen, Tokyo, Japan), and purified using the RNeasy Micro Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s protocols. The quality of total RNA was analyzed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Three experiments were conducted independently (biological triplicates).

tag: developmental stage

value: neonate

tag: agent

value: Fx

tag: dose (ppb)

value: whole body


title: Ventral Dentate Responder #2

description: Ventral Fluoxetine Responder

value: Ventral dentate gyrus

value: male

value: 7-8 wks

value: Fluoxetine

value: Responder


title: Recurrent melanoma patient G, 2nd recurrence

description: Recurrent melanoma isolated from patient G, 2nd recurrence

tag: cell type

value: melanoma cells

value: Recurrent

value: roman 2035 mel


title: Dorsal Dentate Responder  #6

description: Dorsal Fluoxetine Responder

value: Dorsal dentate gyrus

tag: treatment


title: Dorsal Dentate Responder  #7

description: Dorsal Fluoxetine Responder

tag: tissue


title: 7420054_DSS d65

description:
0007420054_raw
biological replicate 4 of 5. Second point of 2 time points

value: syntethic miRNA pool of 954 synthetic miRNAs in equimolar concentrations  from human, mouse, rat, and virus

value: Whole colonic tissue


title: 7420039_DSS d65

description:
0007420039_raw
biological replicate 3 of 5. Second point of 2 time points

value: DSS treated-mice for 65 days


title: Neonates_Fx1.0-3_rep1

description:
Gene expression after 48hr  in Fx1.0 treated neonate
Fx_1.0_3

source_name: Neonates, Fx-1.0-3, replicate 1


title: Recurrent melanoma patient E, 3rd recurrence

description: Recurrent melanoma isolated from patient E, 3rd recurrence

tag: sample type

value: E

value: CRO, Aviano, Italy


title: Neonates_Fx0.5-3_rep1

description:
Gene expression after 48hr  in Fx0.5 treated neonate
Fx_0.5_3

source_name: Neonates, Fx-0.5-3, replicate 1

value: neonate


title: Neonates_Fx0.5-2_rep1

description:
Gene expression after 48hr  in Fx0.5 treated neonate
Fx_0.5_2

source_name: Neonates, Fx-0.5-2, replicate 1

value: Fx


title: Recurrent melanoma patient F, 2nd recurrence

description: Recurrent melanoma isolated from patient F, 2nd recurrence

tag: patient id

value: F

value: Surgery Branch, NIH, Bethesda, USA

value: kilpatric 1937 frag P8


title: Neonates_Fx1.0-2_rep1

description:
Gene expression after 48hr  in Fx1.0 treated neonate
Fx_1.0_2

source_name: Neonates, Fx-1.0-2, replicate 1

value: whole body


title: Neonates_Fx1.0-1_rep1

description:
Gene expression after 48hr  in Fx1.0 treated neonate
Fx_1.0_1

source_name: Neonates, Fx-1.0-1, replicate 1


title: Dorsal Dentate Responder #4

description: Dorsal Fluoxetine Responder

value: male

value: 7-8 wks

value: Fluoxetine


title: Recurrent melanoma patient E, 2nd recurrence

description: Recurrent melanoma isolated from patient E, 2nd recurrence

value: melanoma cells

value: Recurrent

tag: lesion id


title: Recurrent melanoma patient F, 1st recurrence

description: Recurrent melanoma isolated from patient F, 1st recurrence

tag: date of isolation

value: kilpatric mel (1760)


title: 7420041_DSS d15

description:
0007420041_raw
biological replicate 5 of 5. First point of 2 time points

value: syntethic miRNA pool of 954 synthetic miRNAs in equimolar concentrations  from human, mouse, rat, and virus

source_name: DSS d15

value: DSS treated-mice for 15 days


title: 7420038_DSS d65

description:
0007420038_raw
biological replicate 1 of 5. Second point of 2 time points

value: Whole colonic tissue

value: DSS treated-mice for 65 days


title: Dorsal Dentate Responder #3

description: Dorsal Fluoxetine Responder

value: Dorsal dentate gyrus

tag: gender

value: Responder


title: 7420055_DSS d65

description:
0007420055_raw
biological replicate 2 of 5. Second point of 2 time points


title: 7420060_DSS d15

description:
0007420060_raw
biological replicate 4 of 5. First point of 2 time points


title: Dorsal Dentate Responder #5

description: Dorsal Fluoxetine Responder

tag: age


title: Recurrent melanoma patient D, 2nd recurrence

description: Recurrent melanoma isolated from patient D, 2nd recurrence

value: D

value: CRO, Aviano, Italy


title: Neonates_Mt500-3_rep1

description:
Gene expression after 48hr  in Mt500 treated neonate
Mt_500_3

source_name: Neonates, Mt500-3, replicate 1

value: neonate

value: Mt


title: Ventral Dentate Control #7

description: Ventral untreated

source_name: Ventral dentate gyrus

value: Ventral dentate gyrus

value: untreated

tag: response

value: control


title: Neonates_Fx0.5-1_rep1

description:
Gene expression after 48hr  in Fx0.5 treated neonate
Fx_0.5_1

source_name: Neonates, Fx-0.5-1, replicate 1

value: Fx

value: whole body


title: Neonates_Mt500-2_rep1

description:
Gene expression after 48hr  in Mt500 treated neonate
Mt_500_2

source_name: Neonates, Mt500-2, replicate 1


title: Recurrent melanoma patient D, 1st recurrence

description: Recurrent melanoma isolated from patient D, 1st recurrence

value: melanoma cells

value: Recurrent

tag: origin


title: Recurrent melanoma patient C, 2nd recurrence

description: Recurrent melanoma isolated from patient C, 2nd recurrence

value: C

tag: originator's sample label


title: 7420036_DSS d15

description:
0007420036_raw
biological replicate 3 of 5. First point of 2 time points

value: syntethic miRNA pool of 954 synthetic miRNAs in equimolar concentrations  from human, mouse, rat, and virus

tag: strain

value: DSS treated-mice for 15 days


title: Ventral Dentate Control #4

description: Ventral untreated

value: male

value: 7-8 wks


title: Recurrent melanoma patient C, 3rd recurrence

description: Recurrent melanoma isolated from patient C, 3rd recurrence

value: 146 III 6p


title: Ventral Dentate Control #6

description: Ventral untreated


title: Neonates_Mt250-2_rep1

description:
Gene expression after 48hr  in Mt250 treated neonate
Mt_250-2

source_name: Neonates, Mt250-2, replicate 1


title: Neonates_Mt250-3_rep1

description:
Gene expression after 48hr  in Mt250 treated neonate
Mt_250-3

source_name: Neonates, Mt250-3, replicate 1


title: Ventral Dentate Control #5

description: Ventral untreated


title: Ventral Dentate Control #8

description: Ventral untreated


title: Neonates_Mt250-1_rep1

description:
Gene expression after 48hr  in Mt250 treated neonate
Mt_250-1

source_name: Neonates, Mt250-1, replicate 1


title: Neonates_Mt500-1_rep1

description:
Gene expression after 48hr  in Mt500 treated neonate
Mt_500_1

source_name: Neonates, Mt500-1, replicate 1


title: Neonates_Mt125-3_rep1

description:
Gene expression after 48hr  in Mt125 treated neonate
Mt_125_3

source_name: Neonates, Mt125-3, replicate 1


title: Recurrent melanoma patient C, 1st recurrence

description: Recurrent melanoma isolated from patient C, 1st recurrence

source_name: Melanoma cells in culture


title: Ventral Dentate Control #3

description: Ventral untreated


title: Recurrent melanoma patient B, 2nd recurrence

description: Recurrent melanoma isolated from patient B, 2nd recurrence

value: B


title: 7420034_DSS d15

description:
0007420034_raw
biological replicate 1 of 5. First point of 2 time points

source_name: Universal Reference (Miltenyi Biotec GmbH)

tag: reference

value: Whole colonic tissue


title: 7420035_DSS d15

description:
0007420035_raw
biological replicate 2 of 5. First point of 2 time points


title: Neonates_Mt125-2_rep1

description:
Gene expression after 48hr  in Mt125 treated neonate
Mt_125_2

source_name: Neonates, Mt125-2, replicate 1

tag: developmental stage

value: neonate


title: 7420051_PBS d65

description:
0007420051_raw
biological replicate 5 of 5. Control mice. Second point of 2 time points

source_name: PBS d65

value: PBS treated-mice for 65 days


title: 7420048_PBS d65

description:
0007420048_raw
biological replicate 3 of 5. Control mice. Second point of 2 time points


title: Recurrent melanoma patient A, 4th recurrence

description: Recurrent melanoma isolated from patient A, 4th recurrence

value: A

value: Surgery Branch, NIH, Bethesda, USA


title: Ventral Dentate Control #1

description: Ventral untreated

value: Ventral dentate gyrus

value: untreated

value: control


title: Neonates_DMF-3_rep1

description:
Gene expression after 48hr  in DMF treated neonate
DMF-3

source_name: Neonates, DMF-3, replicate1

tag: agent

value: DMF (control)

value: whole body


title: Ventral Dentate Control #2

description: Ventral untreated


title: 7420047_PBS d65

description:
0007420047_raw
biological replicate 2 of 5. Control mice. Second point of 2 time points


title: Neonates_DMF-2_rep1

description:
Gene expression after 48hr  in DMF treated neonate
DMF-2

source_name: Neonates, DMF-2, replicate 1

tag: dose (ppb)


title: Neonates_Mt125-1_rep1

description:
Gene expression after 48hr  in Mt125 treated neonate
Mt_125_1

source_name: Neonates, Mt125-1, replicate 1

value: Mt


title: Dorsal Dentate Control #8

description: Dorsal untreated

source_name: Dorsal dentate gyrus

value: Dorsal dentate gyrus


title: Recurrent melanoma patient A, 3rd recurrence, 3rd synchronous lesion

description: Recurrent melanoma isolated from patient A, 3rd recurrence, 3rd synchronous lesion

tag: cell type

value: melanoma cells

value: Recurrent


title: Dorsal Dentate Control #7

description: Dorsal untreated

value: male

value: 7-8 wks

tag: treatment


title: 7420046_PBS d65

description:
0007420046_raw
biological replicate 1 of 5. Control mice. Second point of 2 time points

value: syntethic miRNA pool of 954 synthetic miRNAs in equimolar concentrations  from human, mouse, rat, and virus

tag: tissue


title: KP_MGH_capsule_delta_cps_rep3

city: Zhunan

first: Tzu-Wen

last: Huang

address: 35 Keyan Road

department: Institute of Molecular and Genomic Medicine

institute: National Health Research Institutes

description: This sample is of K. pneumoniae MGH 78578 capsule deletion mutant. The capsule gene cluster (KPN_02493 to KPN_02515) was entirely removed in the capsule deletion mutant. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.

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

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

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

organism: Klebsiella pneumoniae subsp. pneumoniae MGH 78578

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

growth_protocol:
K. pneumoniae MGH 78578 wild-type was grown to mid-log phase (O.D.600nm 0.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose.
K. pneumoniae MGH 78578 capsule deletion mutant was grown to mid-log phase (O.D.600nm 0.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose.

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA) and an Agilent 2100 bioanalyzer at the GeneChip Microarray Core (UCSD, San Diego, CA USA).

tag: genotype

value: Capsule deletion mutant

tag: phenotype

value: acapsular


title: Neonates_DMF-1_rep1

description:
Gene expression after 48hr  in DMF treated neonate
DMF-1

source_name: Neonates, DMF-1, replicate 1

value: neonate


title: Recurrent melanoma patient B, 1st recurrence

description: Recurrent melanoma isolated from patient B, 1st recurrence

tag: sample type

tag: patient id

value: B

tag: lesion id

value: CRO, Aviano, Italy


title: 7420050_PBS d65

description:
0007420050_raw
biological replicate 4 of 5. Control mice. Second point of 2 time points

value: Whole colonic tissue

value: PBS treated-mice for 65 days


title: 7420049_PBS d15

description:
0007420049_raw
biological replicate 5 of 5. Control mice. First point of 2 time points

source_name: PBS d15

value: PBS treated-mice for 15 days


title: Recurrent melanoma patient A, 2nd recurrence, 2nd synchronous lesion

description: Recurrent melanoma isolated from patient A, 2nd recurrence, 2nd synchronous lesion

value: A

tag: date of isolation

value: Surgery Branch, NIH, Bethesda, USA


title: 7420076_PBS d15

description:
0007420076_raw
biological replicate 4 of 5. Control mice. First point of 2 time points


title: Recurrent melanoma patient A, 3rd recurrence, 2nd synchronous lesion

description: Recurrent melanoma isolated from patient A, 3rd recurrence, 2nd synchronous lesion


title: KP_MGH_capsule_delta_cps_rep2

description: This sample is of K. pneumoniae MGH 78578 capsule deletion mutant. The capsule gene cluster (KPN_02493 to KPN_02515) was entirely removed in the capsule deletion mutant. It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: KP_MGH_capsule_WT_rep3

description: This sample is of wild-type K. pneumoniae MGH 78578. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: K. pneumoniae MGH 78578 wild-type

value: Wild-type

value: normal


title: 10.I.0

description: Gene expression 1 month after treatment

source_name: pig 10, infarcted core, not treated

value: domestic

tag: individual

value: Infarcted core

value: no


title: KP_MGH_capsule_delta_cps_rep1

description: This sample is of K. pneumoniae MGH 78578 capsule deletion mutant. The capsule gene cluster (KPN_02493 to KPN_02515) was entirely removed in the capsule deletion mutant. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.