title: 4T1 siDdx5-17 and simacroH2A1.2 #2

city: New York

first: Etienne

last: Dardenne

address: 1300 York Avenue

department: Pathology

institute: Weill Cornell Medecine

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Gene-level analyses were obtained using the Affymetrix Power Tools software, the RMA-sketch algorithm, core probesets, and antigenomic probes for background correction.

source_name: 4T1 cells siDdx5-17 and simacroH2A1.2, 25 nM, 48h

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

growth_protocol: 4T1 cell were maintained in DMEM with 10% fetal bovine serum in a CO2 humidified chamber at 37°C

extract_protocol: Total RNA was isolated using Trizol total RNA isolation reagent (Invitrogen) according to the manufacturer's protocol.

treatment_protocol: Cell were transfected with lipofectamin RNAimax and 25 nM of siRNA targetting DDX5/DDX17 and macroH2A1.1 or macroH2A1.2

value: 4T1 cells

tag: genotype/variation

value: depleted for ddx5 and ddx17 RNA helicases and macroH2A1.2


title: 4T1 siDdx5-17 and simacroH2A1.2 #3

status: Public on Sep 11 2012

type: RNA

state: NY

country: USA

label: Biotin

molecule: total RNA

organism: Mus musculus

tag: cell line


title: 4T1 siDdx5-17 and simacroH2A1.2 #1


title: cancer preop 50

city: Buffalo

first: Santosh

middle: Kumar

last: Patnaik

address: Elm and Carlton Streets

department: Thoracic Surgery

institute: Roswell Park Comprehensive Cancer Center

description: files with prefix 1_ are for Hy3 (Cy3) signals and 2_ for Hy5

hyb_protocol: Hybridization of the mix of Hy3-labeled sample and Hy5-labeled reference RNAs to the arrays at 56 C for 16 hours followed by washing was performed by Exiqon (Vedbaek, Denmark) on an HS Pro instrument (Tecan, Männedorf, Switzerland). The seventh generation miRCURY LNA microRNA arrays (Exiqon, Vedbaek, Denmark) that were used have approx. 1892 locked nucleic acid oligonucleotide probes on quadruplicate 100 µM-sized probe-spots (185 µM inter-spot distance) to detect 20 human non-microRNA small RNAs (20 array probes), 25 Exion-proprietary human miRPlus microRNAs (25 probes) and 1916 human miRBase microRNA database microRNAs (1892 probes). Thirty of the 1892+25=1917 probes recognize a total of 72 multiple microRNAs (2-6 per probe). Some of the microRNAs recognized by the 30 are also recognized by other, one-microRNA-specific probes. The array also has probes for viral, mouse and rat microRNAs.

scan_protocol: Arrays were scanned, after hybridization and washing, using the G2505B scanning system (Agilent, Santa Clara, CA, USA) by Exiqon (Vedbaek, Denmark).

data_processing: Array data processing was done in R (version 2.14.1) using the limma (version 3.10.2) Bioconductor package. The 'normexp' method with offset=10 was used for background-correction, and followed with within-array global 'loess' normalization, with span=1/3 and values from probe-spots with flag-values >1 ignored, and then, between-array 'quantile' normalization. For probe-set summarization, the median of the values from multiple spots was used when the ratio of the maximum and minimum values was >1.5; else, the mean was used.

organism: Homo sapiens

source_name: blood, lung cancer, individual 50

label_protocol: RNA was labeled by Exiqon, Vedbaek, Denmark using the miRCURY LNA microRNA Power labeling kit. Five hundred ng of RNA, as quantified using Bioanalyzer (Agilent, Santa Clara, CA, USA), was used per labeling reaction with the Cy3-like Hy3 dye. A human universal reference RNA, made by pooling contents of FirstChoice total RNA panel (Ambion, Austin, TX, USA; catalog no. AM6000), was similarly labeled with the Cy5-like Hy5 dye. Sixty-two synthetic small RNAs were spiked-in to the RNA samples before labeling as per the kit protocol.

extract_protocol: Total RNA was isolated from blood collected and stored in PAXgene Blood RNA tubes using a PAXgene Blood miRNA kit at the Roswell Park Cancer Institute, Buffalo, NY, USA as per the protocol suggested by the manufacturer (Qiagen, Valencia, CA, USA). The human universal reference RNA was made by pooling contents of FirstChoice total RNA panel that is made of RNA from different tissues of multiple individuals (Ambion, Austin, TX, USA; catalog no. AM6000).

tag: tissue

value: blood

tag: time

value: preop

tag: gender

value: male

tag: age

tag: disease state

value: squamous cell carcinoma of lung

tag: lung disease

value: Lung cancer (before surgical resection of lung cancer)

tag: individual

source_name: Human universal reference RNA from Ambion

value: Multiple

value: Mixed

tag: sample type


title: 4T1 siDdx5-17 and simacroH2A1.1 #3

source_name: 4T1 cells siDdx5-17 and simacroH2A1.1, 25 nM, 48h

value: depleted for ddx5 and ddx17 RNA helicases and macroH2A1.1


title: 4T1 siDdx5-17 and simacroH2A1.1 #2


title: control highrisk 50

source_name: blood, no lung cancer or nodule, individual 153

value: lung without lung cancer or non-cancerous nodule

value: None (no current or past lung cancer or non-cancerous nodule)

value: Human universal reference RNA from Ambion


title: 4T1 siDdx5-17 #4

source_name: 4T1 cells siDdx5-17 25 nM 48h

treatment_protocol: Cell were transfected with lipofectamin RNAimax and 25 nM of siRNA targetting DDX5 and DDX17 or Control

value: depleted or for ddx5 and ddx17 RNA helicases


title: cancer preop 48

source_name: blood, lung cancer, individual 48


title: control highrisk 49

source_name: blood, no lung cancer or nodule, individual 152


title: cancer preop 47

source_name: blood, lung cancer, individual 47

value: female


title: cancer preop 49

source_name: blood, lung cancer, individual 49


title: 4T1 siDdx5-17 and simacroH2A1.1 #1


title: 4T1 siDdx5-17 #1


title: 4T1 siDdx5-17 #2


title: cancer preop 46

source_name: blood, lung cancer, individual 46


title: control highrisk 48

source_name: blood, no lung cancer or nodule, individual 151


title: 4T1 siDdx5-17 #3


title: DN3 rep3

city: Frederick

first: Jack

last: Chen

state: MD

address: SAIC-Frederick Miller Dr

institute: NIH

hyb_protocol: The biotinlated cRNA (1.5 g per sample) was applied to Illumina Mouse-6 Expression BeadChips and hybridized overnight at 58°C.

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

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

growth_protocol: Bone marrow cells were cultured in IMDM (Lonza) with 10% FCS, 1% penicillin/streptomycin, and 2mM L-glutamine (Life Technologies) supplemented with 50ng/ml IL-7, 50ng/ml Flt3L and 50ng/ml SCF for 10 days before extracting RNA

extract_protocol: RNA was extracted with Rneasy Plus Micro kit (QIAGE) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain background

value: 6-8 weeks

value: lymphocytes


title: PT1

city: Genova (GE)

first: Massimiliano

last: Monticone

address: Largo R. Benzi, 10

country: Italy

institute: IRCCS AOU San Martino – IST, Genova

description:
Gene expression data from GBM TICs.

GBM TICs were obtained from tumor samples of patients subjected to surgery at Neurosurgery Department of the San Martino Hospital in Genova. An informed consent was obtained from all patients before surgery as required by the Ethic Board.

Cells isolation was described in detail elsewhere (SOX2 Silencing in Glioblastoma Tumor Initiating Cells Causes Stop of Proliferation and Loss of Tumorigenicity. Gangemi RM, Griffero F, Marubbi D, Perera M, Capra MC, Malatesta P, Ravetti GL, Zona GL, Daga A, Corte G. Stem Cells. 2008 Nov 6).

hyb_protocol: Fragmented cRNA, run on the Bioanalyzer to verify the correct electropherogram, was hybridized in a hybridization oven (16 hours, 45°C) to a Human Gene 1.0 ST array (Affymetrix) representing whole-transcript coverage. The washing and staining of the arrays with phycoerythrin-conjugated streptavidin (Molecular Probes, Eugene, OR) was completed in Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were subsequently scanned using a confocal laser GeneChip Scanner 3000 7G and GeneChip Command Console (Affymetrix).

data_processing: Affymetrix raw data files (CEL files) are used as input files in expression console environment (Affymetrix, Inc., Santa Clara, CA). Briefly, Cel files were processed using Robust Multi-Array Analysis procedure (Irizarry et al., 2003). The RMA method was used, first, to convert the intensities from the multiple probes in a probeset into a single expression value with greater precision and reduced background noise, relying on the perfect match probes only (ignoring the mismatch probes) and, after, to normalize by sketch quantile normalization. Also quality assessement were performed in expression console environment.

source_name: Human glioblastoma (GBM) tumor-initiating cells (TICs) - class I, expansive

label_protocol: Briefly, accordingly to the recommendations of the manufacturer, 100 ng total RNA was used in the first-round synthesis of double-stranded cDNA. The RNA was reverse transcribed using a WT cDNA synthesis and amplification kit (Affymetrix). The resulting biotin-labeled cRNA was purified using an IVT clean-up kit (Affymetrix) and quantified using a UV spectrophotometer (A260/280; Beckman, Palo Alto, CA). An aliquot (15 µg) of cRNA was fragmented by heat and ion-mediated hydrolysis at 94°C for 35 minutes.

growth_protocol:
Proliferation medium was DMEM-F12/Neurobasal additioned with 1% v/v B27 supplement, (Gibco Ltd, Paisley, Scotland), 2 mM L-glutamine (Gibco Ltd), recombinant human fibroblast growth factor (FGF-2, 10 ng/ml Peprotech, London, UK), recombinant human epidermal growth factor (EGF, 20 ng/ml Peprotech). The medium was changed twice a week. Under these conditions, TICs were grown as a monolayer in flasks coated with Matrigel (BD Biosciences, San Jose, CA) express stem cell markers, maintained intact self-renewal capacity, partial multilineage differentiation ability and gave rise to tumor when injected orthotopically in nude mice (SOX2 Silencing in Glioblastoma Tumor Initiating Cells Causes Stop of Proliferation and Loss of Tumorigenicity.
Gangemi RM, Griffero F, Marubbi D, Perera M, Capra MC, Malatesta P, Ravetti GL, Zona GL, Daga A, Corte G. Stem Cells. 2008 Nov 6).

extract_protocol:
miRNeasy Mini Kit (Qiagen) with DNase treatment.
RNA concentration and purity were determined from measuring absorbance at 260 and 280 nm; 2 μg total RNA was run on a 1% denaturing gel and 100 ng were loaded on the 2100 Bioanalyzer (Agilent, Palo Alto, CA) to verify RNA integrity.

treatment_protocol: GBM TICs were kept in a humidified 5% CO2 atmosphere at 37°C.

value: glioblastoma

tag: cell type

value: tumor-initiating cells

tag: tic class

value: expansive


title: PT3


title: Bcl2-OHT rep3

source_name: Bcl2 overexpression wild type pro-B

value: mixed C57BL/6 and 129S5

value: Bcl2 overexpression wild type

value: bone marrow cells

value: bone marrow derived pro-B cells


title: 4T1 siCtrl #2

source_name: 4T1 cells siCtrl 25nM 48h

value: 4T1 cells

value: control (wild type)


title: PT5

source_name: Human glioblastoma (GBM) tumor-initiating cells (TICs) - class II, highly diffusive

value: highly diffusive


title: PT2


title: PT4


title: 4T1 siCtrl #3


title: DN3 rep2


title: control highrisk 47

source_name: blood, no lung cancer or nodule, individual 150

value: blood

value: lung without lung cancer or non-cancerous nodule

value: Multiple

value: Mixed


title: control highrisk 46

source_name: blood, no lung cancer or nodule, individual 149

value: male

value: None (no current or past lung cancer or non-cancerous nodule)

value: Human universal reference RNA from Ambion


title: control highrisk 45

source_name: blood, no lung cancer or nodule, individual 148

value: female


title: PT6

value: glioblastoma

value: tumor-initiating cells


title: 4T1 siCtrl #4


title: 4T1 siCtrl #1


title: control highrisk 44

source_name: blood, no lung cancer or nodule, individual 147

source_name: Human universal reference RNA from Ambion


title: Bcl2+OHT rep3

source_name: Bcl2-rescued Bcl11a-deficient Pro-B

value: mixed C57BL/6 and 129S5

value: 6-8 weeks

value: Bcl2-rescued Bcl11a-deficient


title: ISA71_Replicate 4

city: Beltsville

first: Duk Kyung

last: Kim

address: Bldg. 1043, BARC-East

institute: USDA, ARS

description: Biological replicate 2 of 2 for ISA71 (Dye-exchange of ISA71_rep3)

hyb_protocol: With the use of Agilent’s Gene Expression Hybridization Kit (Cat# 5188-5242), 825ng of cyanine 3-labeled and cyanine 5-labeled linearly amplified cRNA was added to individual hybridization cocktails and then fragmented. At hybridization each well contained one cy3 and one cy5 labeled sample and control per pair.  The hybridization cocktail is then dispensed into the wells of gasket slides (4 samples/slide: Cat# G2534-60012) on top of which a Chicken 4x44K Gene Expression Microarray, (Cat# G2519F, AMADID 015068) was placed.  This microarray “sandwich” was then sealed in a hybridization chamber.  The microarrays were hybridized at 65°C rotating at 10 RPMs for 17 hours.  Slides were washed in Agilent’s Gene Expression Wash Buffers according to manufacturer recommendations.

scan_protocol: The microarrays were scanned on the Agilent Microarray Scanner.  Scanner data extraction and analysis was performed using Feature Extraction software version 10.7.3.1.

data_processing: Scanner data extraction and analysis was performed using Feature Extraction software version 10.7.3.1.  Microarray data quality was evaluated by reviewing ten standard QC metrics generated by the Agilent Technologies Feature Extraction Software version 10.7.3.1.  To determine if there was a large hybridization, staining, or wash artifacts, a visual examination of each array was performed by loading the array image into Feature Extraction Software.  Microarrays were determined to be free of any large artifacts (™ 10% of total surface area) that could have affected the quality of the data.

organism: Gallus gallus

label_protocol: Using Agilent’s 2-Color Quick Amp Labeling Kit, (Cat# 5190-0444), 0.5 to 1 ug of RNA (Agilent suggested: total RNA input range 50 ng - 2 μg) and Spike-In (2-Color RNA Spike-In Kit Cat# 5188-5279) were denatured in the presence of a T7 promoter primer.  Reverse Transcriptase was used to reverse-transcribe the mRNA.  cDNA was used as a template for in vitro transcription where a T7 RNA polymerase simultaneously amplified target material and incorporated cyanine 3- or cyanine 5-labeled CTP.  Labeled cRNA was purified using spin columns from the Qiagen RNeasy Mini Kit and the quantity and quality of the cRNA was determined by Nanodrop ND-1000 UV-VIS spectrophotometer.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: strain

value: Broiler

value: day 14

value: Splenocyte


title: control highrisk 42

source_name: blood, no lung cancer or nodule, individual 145


title: ISA71_Replicate 2

description: Biological replicate 1 of 2 for ISA71 (Dye-exchange of ISA71_rep1)


title: ISA70_Replicate 3

description: Biological replicate 2 of 2 for ISA70


title: EAAE+OHT rep3

source_name: Bcl11a-deficient pro-B

value: bone marrow cells

value: bone marrow derived pro-B cells


title: EAAE-OHT rep3

source_name: wide type pro-B

value: wild type


title: ISA71_Replicate 3

description: Biological replicate 2 of 2 for ISA71


title: Bcl2+OHT rep2


title: DN3 rep1

value: lymphocytes


title: EAAE-OHT rep2


title: control highrisk 41

source_name: blood, no lung cancer or nodule, individual 144

value: blood

value: lung without lung cancer or non-cancerous nodule

value: Multiple

value: Mixed


title: control highrisk 43

source_name: blood, no lung cancer or nodule, individual 146

value: male

value: None (no current or past lung cancer or non-cancerous nodule)

value: Human universal reference RNA from Ambion


title: cancer preop 44

source_name: blood, lung cancer, individual 44

value: preop

value: female

value: adenocarcinoma of lung

value: Lung cancer (before surgical resection of lung cancer)


title: cancer preop 45

source_name: blood, lung cancer, individual 45


title: ISA70_Replicate 2

description: Biological replicate 1 of 2 for ISA70 (Dye-exchange of ISA70_rep1)

value: Broiler

value: day 14


title: ISA70_Replicate 4

description: Biological replicate 2 of 2 for ISA70 (Dye-exchange of ISA70_rep3)

value: Splenocyte


title: Bcl2-OHT rep2

value: mixed C57BL/6 and 129S5

value: 6-8 weeks

value: Bcl2 overexpression wild type

value: bone marrow cells

value: bone marrow derived pro-B cells


title: ISA71_Replicate 1

description: Biological replicate 1 of 2 for ISA71


title: cancer preop 42

source_name: blood, lung cancer, individual 42

value: blood

value: Multiple


title: cancer preop 41

source_name: blood, lung cancer, individual 41

value: Mixed


title: ISA70_Replicate 1

description: Biological replicate 1 of 2 for ISA70


title: EAAE+OHT rep2


title: EAAE+OHT rep1


title: Bcl2-OHT rep1

source_name: Bcl2 overexpression wild type pro-B


title: Bcl2+OHT rep1

value: Bcl2-rescued Bcl11a-deficient


title: EAAE-OHT rep1

value: wild type


title: cancer preop 43

source_name: blood, lung cancer, individual 43

value: preop

value: male

value: Human universal reference RNA from Ambion


title: cancer preop 38

source_name: blood, lung cancer, individual 38

value: female

value: adenocarcinoma of lung

value: Lung cancer (before surgical resection of lung cancer)


title: cancer preop 39

source_name: blood, lung cancer, individual 39


title: cancer preop 40

source_name: blood, lung cancer, individual 40


title: control highrisk 40

source_name: blood, no lung cancer or nodule, individual 143

value: lung without lung cancer or non-cancerous nodule

value: None (no current or past lung cancer or non-cancerous nodule)


title: control highrisk 38

source_name: blood, no lung cancer or nodule, individual 141

source_name: Human universal reference RNA from Ambion


title: control highrisk 39

source_name: blood, no lung cancer or nodule, individual 142


title: control highrisk 37

source_name: blood, no lung cancer or nodule, individual 140


title: control highrisk 36

source_name: blood, no lung cancer or nodule, individual 139


title: control highrisk 35

source_name: blood, no lung cancer or nodule, individual 138


title: X6752318096 F MYC negative#3394

city: Berlin

first: Dinis

middle: Pedro

last: Calado

state: Buch

address: Robert-Rössle-Str. 10

country: Germany

institute: Max-Delbrück-Centrum für Molekulare Medizin (MDC)

description: biological replicate_2_MYC negative

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation in R; quantile normalization in natural scale

source_name: Germinal center B-cells

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

value: MYC negative B-cell

tag: transgene

value: MycEGFP (a Myc reporter allele, in which a MYC-EGFP fusion protein (MYCEGFP) is expressed from the endogenous Myc locus)

tag: genetic background


title: X6752318096 E MYC positive#3394

description: biological replicate_2_MYC positive

value: MYC positive B-cell


title: control highrisk 34

source_name: blood, no lung cancer or nodule, individual 137


title: DFMO-treated, spermidine 600', biological replicate 3

city: Rehovot

first: Guy

last: Landau

address: Herzl 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: SAMPLE 24

hyb_protocol: 2ug ss cDNA in 80 ul total volume were hybridized to a Mouse Gene 1.0 ST array using Affymetrix hybridization kit materials and hybridized for 17 hours at 45° at 60rpm. Post-hyb washes were done with Affymetrix wash solutions on the FS450 station using FS450_0007 protocol.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The analysis was carried out using Partek Genome Suite software (Partek Inc., St. Louis, Missouri 63141, http://www.partek.com), using RMA.

label_protocol: 200ng Total RNA were used for labeling. cDNA samples were generated and labeled using Affymetrix WT-cDNA synthesis and labeling kit.

growth_protocol: NIH3T3 cells were grown in DMEM supplemented with 10% FCS and 1% Pen/Strep in humidified incubator with 5% CO2 at 37C. Cells were seeded in 9 cm tissue culture dishes at conc. of 200.000 cells/dish in 10ml medium.

extract_protocol: Total RNA was extracted using TriReagent solution (Molecular research center inc.) according to manufacturer's protocol.

treatment_protocol: DFMO at final conc. of 1mM was added 24 hours after seeding. Spermidine at final conc.of 10uM  was added to 96h DFMO-treated cells and total cells were collected at the indicated time points. (In all experiments Spermidine was added in presence of 1mM aminoguanidine to inhibit polyamine oxidation)

value: Fibroblast

tag: cells collected at

value: 600min after addition of spermidine


title: control highrisk 33

source_name: blood, no lung cancer or nodule, individual 136

value: blood

value: Multiple


title: X6752318020 E MYC positive#3397

description: biological replicate_1_MYC positive


title: DFMO-treated, spermidine 600', biological replicate 1

description: SAMPLE 22


title: DFMO-treated, spermidine 600', biological replicate 2

description: SAMPLE 23


title: X6752318020 F MYC negative#3397

description: biological replicate_1_MYC negative


title: control highrisk 32

source_name: blood, no lung cancer or nodule, individual 135

value: Mixed


title: DFMO-treated, spermidine 480', biological replicate 3

description: SAMPLE 21

value: 480min after addition of spermidine


title: DFMO-treated, spermidine 480', biological replicate 1

description: SAMPLE 19


title: DFMO-treated, spermidine 480', biological replicate 2

description: SAMPLE 20


title: control highrisk 31

source_name: blood, no lung cancer or nodule, individual 134


title: DFMO-treated, spermidine 360', biological replicate 3

description: SAMPLE 18

value: 360min after addition of spermidine


title: DFMO-treated, spermidine 360', biological replicate 2

description: SAMPLE 17


title: DFMO-treated, spermidine 360', biological replicate 1

description: SAMPLE 16


title: cancer preop 37

source_name: blood, lung cancer, individual 37

value: preop

value: male

value: squamous cell carcinoma of lung


title: cancer preop 36

source_name: blood, lung cancer, individual 36

value: Human universal reference RNA from Ambion


title: cancer preop 35

source_name: blood, lung cancer, individual 35

value: female

value: Lung cancer (before surgical resection of lung cancer)


title: DFMO-treated, spermidine 240', biological replicate 2

description: SAMPLE 14

value: 240min after addition of spermidine


title: DFMO-treated, spermidine 240', biological replicate 3

description: SAMPLE 15


title: DFMO-treated, spermidine 120', biological replicate 3

description: SAMPLE 12

value: 120min after addition of spermidine


title: 6983-10-DONOR

city: Boston

first: Joshua

middle: David

last: Campbell

state: MA

address: 72 East Concord St.

institute: Boston University

description: RNA was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained with RMA and the Affymetrix CDF using Expression Console Version 1.0 software.

hyb_protocol: cDNA was end-labeled with a biotinylated dideoxynucleotide using terminal transferase. Five and a half micrograms of biotinylated cDNA was added to a hybridization cocktail, loaded on a Human Exon 1.0 ST GeneChip and hybridized for 16 hours at 45 ºC and 60 rpm. Following hybridization, the array was washed and stained according to the standard Affymetrix protocol.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000. These scans were used to generate CEL files for each array.

data_processing:
Expression Console Version 1.1 (Affymetrix Inc.) was used to generate transcript-level gene expression estimates via the robust multichip average (RMA) algorithm using the Affymetrix CDF (Gene Level - Core: RMA Sketch).  Gene symbols of transcript ids were retrieved using DAVID (http://david.abcc.ncifcrf.gov/). No filtering of genes was performed before statistical testing.
Quantile sketch normalized transcript level expression using the RMA algorithm with the Affymetrix CDF

source_name: Whole lung tissue

label_protocol: Ribosomal RNA was first removed using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, Carlsbad, CA). This treated RNA was then converted to cDNA and subsequently processed and biotin-labeled.

extract_protocol: High molecular weight RNA was isolated from tissue cores using the miRNeasy Mini Kit (Qiagen). The RNA integrity was assessed using an Agilent 2100 Bioanalyzer and RNA purity was assessed using a NanoDrop spectrophotometer.  One ug of RNA was processed and used as starting material for the microarray studies.

tag: lm

tag: patient

tag: slice

tag: copd status

tag: Sex

value: Male

tag: pack years

tag: notes


title: DFMO-treated, spermidine 240', biological replicate 1

description: SAMPLE 13

tag: cell line


title: DFMO-treated, spermidine 120', biological replicate 2

description: SAMPLE 11


title: cancer preop 34

source_name: blood, lung cancer, individual 34

tag: tissue

tag: time

tag: gender

tag: age

tag: disease state

tag: lung disease

tag: individual


title: cancer preop 33

source_name: blood, lung cancer, individual 33

tag: sample type


title: 6983-07-DONOR


title: 6983-09-DONOR


title: DFMO-treated, spermidine 120', biological replicate 1

description: SAMPLE 10

tag: cell type

tag: cells collected at


title: DFMO-treated, spermidine 60', biological replicate 3

description: SAMPLE 9

value: 60min after addition of spermidine


title: cancer preop 32

source_name: blood, lung cancer, individual 32


title: DFMO-treated, spermidine 60', biological replicate 2

description: SAMPLE 8

value: Fibroblast


title: cancer preop 31

source_name: blood, lung cancer, individual 31

source_name: Human universal reference RNA from Ambion


title: cancer preop 30

source_name: blood, lung cancer, individual 30


title: DFMO-treated, spermidine 60', biological replicate 1

description: SAMPLE 7


title: 6983-05-DONOR

tag: lm

tag: patient


title: 6983-04-DONOR

tag: slice

tag: copd status


title: DFMO-treated, spermidine 30', biological replicate 3

description: SAMPLE 6

value: 30min after addition of spermidine


title: 6983-06-DONOR

tag: Sex

tag: pack years


title: control highrisk 30

source_name: blood, no lung cancer or nodule, individual 133

value: blood

value: lung without lung cancer or non-cancerous nodule

value: None (no current or past lung cancer or non-cancerous nodule)


title: PHEO_AG_HS_193

type: genomic

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

country: France

institute: Ligue Contre Le Cancer

hyb_protocol: Standard Illumina protocol.

scan_protocol: Standard Illumina protocol.

data_processing: Standard Illumina protocol using BeadStudio software.

label: C-Bio and A-DNP

molecule: genomic DNA

label_protocol: Standard Illumina protocol.

extract_protocol: Tumor DNA was extracted from frozen tissue samples using a QIAamp DNA mini kit or an AllPrep kit (Qiagen).

value: pheochromocytoma

value: RET

value: somatic

tag: malignancy

value: benign


title: 6983-02-DONOR

tag: notes


title: PHEO_AG_HS_192

tag: tissue


title: PHEO_AG_HS_175


title: PHEO_AG_HS_169


title: 6983-03-DONOR


title: PHEO_AG_HS_198


title: PHEO_AG_HS_199

value: male


title: PHEO_AG_HS_182


title: DFMO-treated, spermidine 30', biological replicate 2

description: SAMPLE 5

tag: cell line


title: PHEO_AG_HS_197


title: PHEO_AG_HS_187


title: control highrisk 29 replicate 1

source_name: blood, no lung cancer or nodule, individual 132

tag: gender

tag: age

value: Multiple

value: Mixed

value: Human universal reference RNA from Ambion


title: DFMO-treated, spermidine 30', biological replicate 1

description: SAMPLE 4


title: PHEO_AG_HS_180


title: control highrisk 27

source_name: blood, no lung cancer or nodule, individual 130

value: female

tag: disease state

tag: lung disease


title: PHEO_AG_HS_171

value: germline


title: 6982-12-DONOR

value: Male


title: control highrisk 26

source_name: blood, no lung cancer or nodule, individual 129

tag: individual

tag: sample type


title: 6982-11-DONOR


title: DFMO-treated, unstimulated, 0', biological replicate 3

description: SAMPLE 3

source_name: NIH3T3_1mM DFMO_96hr_unstimulated

tag: cell type

tag: cells collected at

value: 0 min (unstimulated)


title: DFMO-treated, unstimulated, 0', biological replicate 1

description: SAMPLE 1

value: Fibroblast


title: DFMO-treated, unstimulated, 0', biological replicate 2

description: SAMPLE 2


title: PHEO_AG_HS_174


title: 6982-09-DONOR

tag: lm

tag: patient


title: PHEO_AG_HS_162


title: PHEO_AG_HS_156


title: control highrisk 25

source_name: blood, no lung cancer or nodule, individual 128


title: control highrisk 28

source_name: blood, no lung cancer or nodule, individual 131

value: pleural plaque of lung


title: PHEO_AG_HS_161


title: PHEO_AG_HS_173


title: PHEO_AG_HS_152


title: control highrisk 24

source_name: blood, no lung cancer or nodule, individual 127

value: blood


title: PHEO_AG_HS_167


title: control highrisk 23

source_name: blood, no lung cancer or nodule, individual 126

value: lung without lung cancer or non-cancerous nodule


title: 6982-07-DONOR

tag: slice

tag: copd status


title: 6982-04-DONOR

tag: Sex

tag: pack years


title: 6982-03-DONOR

tag: notes


title: control highrisk 22

source_name: blood, no lung cancer or nodule, individual 125

tag: tissue

value: None (no current or past lung cancer or non-cancerous nodule)


title: PHEO_AG_HS_146

value: pheochromocytoma

tag: malignancy

value: malignant


title: DFMO-treated 96h, biological replicate 1

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 7G

label_protocol: 200ng TotalRNA were used. cDNA samples were generated and labeled using Affymetrix WT-cDNA synthesis and labeling kit

extract_protocol: Total RNA was extracted at the indicated time points using TriReagent solution (Molecular research center inc.) according to manufacturer's protocol.

treatment_protocol: DFMO at final conc. of 1mM was added 24 hours after seeding.

tag: cell line

value: NIH3T3 fibroblasts

tag: agent

value: DFMO-treated

tag: time


title: PHEO_AG_HS_154

value: somatic

value: benign


title: PHEO_AG_HS_147

value: male


title: DFMO-treated 48h, biological replicate 1


title: PHEO_AG_HS_151


title: control highrisk 21

source_name: blood, no lung cancer or nodule, individual 124

tag: gender

tag: age

tag: disease state

tag: lung disease

value: Multiple

value: Mixed

value: Human universal reference RNA from Ambion


title: 6982-02-DONOR

source_name: Whole lung tissue

value: Male


title: DFMO-treated 96h, biological replicate 2


title: DFMO-treated 24h, biological replicate 3


title: cancer preop 28

source_name: blood, lung cancer, individual 28

value: preop

value: female

value: adenocarcinoma of lung

value: Lung cancer (before surgical resection of lung cancer)

tag: individual

tag: sample type


title: DFMO-treated 48h, biological replicate 2


title: DFMO-treated 24h, biological replicate 2


title: 6971-08-COPD

tag: lm

tag: patient


title: PHEO_AG_HS_139


title: cancer preop 27

source_name: blood, lung cancer, individual 27

value: blood

value: squamous cell carcinoma of lung


title: DFMO-treated 24h, biological replicate 1


title: cancer preop 25

source_name: blood, lung cancer, individual 25


title: PHEO_AG_HS_136

value: pheochromocytoma

value: RET

value: germline


title: 6971-06-COPD

tag: slice

tag: copd status


title: cancer preop 26

source_name: blood, lung cancer, individual 26

source_name: Human universal reference RNA from Ambion


title: PHEO_AG_HS_148

tag: Sex

value: syndromic


title: DFMO-treated 12h, biological replicate 1

value: NIH3T3 fibroblasts

value: DFMO-treated


title: cancer preop 29

source_name: blood, lung cancer, individual 29

value: male


title: DFMO-treated 12h, biological replicate 2


title: 6982-06-DONOR

tag: pack years

tag: notes


title: 6971-07-COPD


title: Untreated, control,  biological replicate 3

value: Untreated

value: control


title: cancer preop 24

source_name: blood, lung cancer, individual 24

tag: tissue

value: Multiple

value: Mixed

value: Human universal reference RNA from Ambion


title: 6971-04-COPD

value: Male


title: PHEO_AG_HS_133

value: female

tag: malignancy

value: benign


title: cancer preop 23

source_name: blood, lung cancer, individual 23

value: blood

value: preop

value: Lung cancer (before surgical resection of lung cancer)


title: 6971-03-COPD


title: Untreated, control,  biological replicate 2

tag: cell line

tag: agent


title: cancer preop 22

source_name: blood, lung cancer, individual 22

tag: time

tag: gender

value: squamous cell carcinoma of lung


title: 6971-05-COPD

tag: age


title: cancer preop 21

source_name: blood, lung cancer, individual 21

tag: disease state

value: adenocarcinoma of lung

tag: lung disease


title: Untreated, control,  biological replicate 1


title: cancer preop 20

source_name: blood, lung cancer, individual 20

tag: individual

tag: sample type


title: 6971-02-COPD

tag: lm

tag: patient


title: U87_MGMT.3_Rep3

city: Edmonton

first: Kathryn

last: Graham

state: Alberta

address: 11560 University Ave

department: Oncology

country: Canada

institute: University of Alberta

description: gene expression in  glioblastoma cell lines

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities.  The data was them imported into GeneSpring 7.3.1 and default normalization procedures were used.

source_name: glioblastoma cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was isolated an Rneasy kit (Qiagen) according to the manufacturer's instructions.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell type

value: glioblastoma cell line

tag: genotype/variation

value: MGMT-transfected


title: PHEO_AG_HS_131

value: pheochromocytoma

tag: Sex


title: 6970-11-COPD

tag: slice

tag: copd status

tag: pack years

tag: notes

value: alpha1-antitrypsin deficiency


title: U87_MGMT.2_Rep2

tag: cell line


title: PHEO_AG_HS_115

tag: tissue

value: syndromic

tag: malignancy


title: 6971-11-COPD

tag: age


title: 6970-09-COPD


title: 6970-10-COPD


title: U87_MGMT.1_Rep1


title: 6970-07-COPD


title: control highrisk 18

source_name: blood, no lung cancer or nodule, individual 121

tag: gender

value: male

tag: disease state

value: lung without lung cancer or non-cancerous nodule

value: None (no current or past lung cancer or non-cancerous nodule)


title: PHEO_AG_HS_109

value: RET

value: germline


title: U87_EV.2_Rep2

value: empty vector control


title: control highrisk 19

source_name: blood, no lung cancer or nodule, individual 122

value: female

tag: lung disease

tag: individual

value: Multiple

value: Mixed

value: Human universal reference RNA from Ambion


title: control highrisk 17

source_name: blood, no lung cancer or nodule, individual 120

value: blood

tag: sample type


title: U87_EV.3_Rep3


title: PHEO_AG_HS_122

value: benign


title: U87_EV.1_Rep1

value: glioblastoma cell line


title: 6970-04-COPD

tag: lm

tag: patient

value: Male


title: 6970-06-COPD


title: control highrisk 16

source_name: blood, no lung cancer or nodule, individual 119


title: control highrisk 20

source_name: blood, no lung cancer or nodule, individual 123


title: 6970-03-COPD

source_name: Whole lung tissue


title: PHEO_AG_HS_095

value: pheochromocytoma

value: somatic


title: control highrisk 15

source_name: blood, no lung cancer or nodule, individual 118


title: patient 12, noncancerous normal tissue, LMD

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description:
Gene expression profile of surgically resected material
Sample name: N12

hyb_protocol: Hybridization of Human V4.0 OpArray (Operon Biotechnologies, Cologne, Germany) were performed as per manufacturer's instruction.

scan_protocol: The microarrays were scanned using GenePix 4000B scanner (Axon Instruments, Foster City, CA).

data_processing: The raw data was processed by Array-Pro Analyzer Ver.4.5 (Media cybernetics, Bethesda, MD). The net intensity level of each spot was calculated by subtracting the background intensity from the raw intensity. Prior to statistical analysis, the net intensity values lower than 1 were set to 1 and were log-2 transformed.

source_name: noncancerous normal tissue, LMD

label_protocol: Amplification and labeling of RNA were performed using TargetAmp 2-round Aminoallyl-aRNA Amplification Kit 1.0 (Epicentre, Madison, WI).

extract_protocol: Total RNA was extracted from each tissue using RNeasy Micro kit (Qiagen, Venlo, The Netherlands) according to manufacturer's instruction. The quality of the obtained RNA was examined by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Invasive tumor, adjacent dysplastic lesions and noncancerous normal tissues were extracted using laser-capture microdissection.

value: noncancerous normal tissue


title: patient 12, adjacent dysplastic lesions, LMD

description:
Gene expression profile of surgically resected material
Sample name: D12

source_name: adjacent dysplastic lesions, LMD

value: adjacent dysplastic lesions


title: 6970-02-COPD

value: alpha1-antitrypsin deficiency


title: PHEO_AG_HS_123


title: PHEO_AG_HS_107


title: 6969-11-COPD

value: Female

value: von Willebrand disease; Hypertension


title: control highrisk 14

source_name: blood, no lung cancer or nodule, individual 117

value: male

value: lung without lung cancer or non-cancerous nodule

value: None (no current or past lung cancer or non-cancerous nodule)

source_name: Human universal reference RNA from Ambion


title: PHEO_AG_HS_094

value: female

value: RET

value: germline


title: patient 12, invasive tumor tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: T12

source_name: invasive tumor tissue, LMD

value: invasive tumor tissue


title: PHEO_AG_HS_110

value: benign


title: control highrisk 13

source_name: blood, no lung cancer or nodule, individual 116

value: blood

value: Multiple

value: Mixed

value: Human universal reference RNA from Ambion


title: 6969-09-COPD


title: patient 11, invasive tumor tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: T11


title: control highrisk 12

source_name: blood, no lung cancer or nodule, individual 115


title: patient 11, adjacent dysplastic lesions, LMD

description:
Gene expression profile of surgically resected material
Sample name: D11


title: control highrisk 11

source_name: blood, no lung cancer or nodule, individual 114


title: patient 11, noncancerous normal tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: N11

value: noncancerous normal tissue


title: 6969-08-COPD


title: 6969-07-COPD


title: PHEO_AG_HS_092

value: pheochromocytoma


title: cancer preop 18

source_name: blood, lung cancer, individual 18

tag: time

value: preop

value: squamous cell carcinoma of lung

value: Lung cancer (before surgical resection of lung cancer)


title: 6969-05-COPD

tag: Sex

value: Female

value: von Willebrand disease; Hypertension


title: 6969-04-COPD

tag: slice


title: PHEO_AG_HS_080

value: syndromic


title: cancer preop 19

source_name: blood, lung cancer, individual 19

value: male


title: cancer preop 17

source_name: blood, lung cancer, individual 17


title: PHEO_AG_HS_077


title: patient 10, invasive tumor tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: T10


title: PHEO_AG_HS_076

value: female


title: patient 10, adjacent dysplastic lesions, LMD

description:
Gene expression profile of surgically resected material
Sample name: D10

value: adjacent dysplastic lesions


title: 6969-03-COPD

tag: copd status


title: cancer preop 15

source_name: blood, lung cancer, individual 15

value: adenocarcinoma of lung


title: patient 09, invasive tumor tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: T09

value: invasive tumor tissue


title: 6969-02-COPD

tag: pack years


title: patient 09, adjacent dysplastic lesions, LMD

description:
Gene expression profile of surgically resected material
Sample name: D09


title: 6968-12-COPD

tag: notes


title: PHEO_AG_HS_099

value: somatic

value: benign


title: PHEO_AG_HS_071

value: RET

value: germline


title: PHEO_AG_HS_072


title: cancer preop 14

description: files with prefix 1_ are for Hy3 (Cy3) signals and 2_ for Hy5

source_name: blood, lung cancer, individual 14

value: blood

value: large cell carcinoma of lung

value: Multiple

value: Mixed

value: Human universal reference RNA from Ambion


title: PHEO_AG_HS_070

value: pheochromocytoma


title: patient 09, noncancerous normal tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: N09

value: noncancerous normal tissue


title: PHEO_AG_HS_098


title: patient 10, noncancerous normal tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: N10


title: PHEO_AG_HS_060


title: cancer preop 13

source_name: blood, lung cancer, individual 13

value: preop

value: Lung cancer (before surgical resection of lung cancer)


title: 6968-11-COPD

value: Female


title: PHEO_AG_HS_120

value: female


title: PHEO_AG_HS_061

value: male


title: 6968-10-COPD


title: PHEO_AG_HS_068


title: 6968-08-COPD


title: patient 07, invasive tumor tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: T07

value: invasive tumor tissue


title: patient 08, adjacent dysplastic lesions, LMD

description:
Gene expression profile of surgically resected material
Sample name: D08

value: adjacent dysplastic lesions


title: cancer preop 16

source_name: blood, lung cancer, individual 16

value: neuroendocrine carcinoma of lung


title: patient 08, noncancerous normal tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: N08


title: PHEO_AG_HS_059

value: MAX

value: somatic

value: benign


title: cancer preop 12

source_name: blood, lung cancer, individual 12

value: blood

value: adenocarcinoma of lung


title: PHEO_AG_HS_057


title: cancer preop 11

source_name: blood, lung cancer, individual 11

value: Multiple

value: Mixed


title: cancer preop 10

source_name: blood, lung cancer, individual 10

value: squamous cell carcinoma of lung

value: Human universal reference RNA from Ambion


title: PHEO_AG_HS_053

value: pheochromocytoma


title: 6968-06-COPD

description: RNA was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained with RMA and the Affymetrix CDF using Expression Console Version 1.0 software.

source_name: Whole lung tissue


title: control highrisk 10

source_name: blood, no lung cancer or nodule, individual 113

value: lung without lung cancer or non-cancerous nodule

value: None (no current or past lung cancer or non-cancerous nodule)


title: 6968-09-COPD

value: Female


title: patient 07, adjacent dysplastic lesions, LMD

description:
Gene expression profile of surgically resected material
Sample name: D07

source_name: adjacent dysplastic lesions, LMD


title: patient 08, invasive tumor tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: T08

source_name: invasive tumor tissue, LMD


title: control highrisk 9

source_name: blood, no lung cancer or nodule, individual 112

value: female

source_name: Human universal reference RNA from Ambion


title: 6968-04-COPD


title: patient 07, noncancerous normal tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: N07

source_name: noncancerous normal tissue, LMD

value: noncancerous normal tissue


title: PHEO_AG_HS_056


title: patient 06, invasive tumor tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: T06

value: invasive tumor tissue


title: 6967-13-COPD


title: control highrisk 8

source_name: blood, no lung cancer or nodule, individual 111


title: control highrisk 7

source_name: blood, no lung cancer or nodule, individual 110

value: male


title: PHEO_AG_HS_051


title: 6968-02-COPD


title: control highrisk 6

source_name: blood, no lung cancer or nodule, individual 109


title: 6967-11-COPD


title: patient 06, noncancerous normal tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: N06


title: patient 06, adjacent dysplastic lesions, LMD

description:
Gene expression profile of surgically resected material
Sample name: D06

value: adjacent dysplastic lesions


title: 6967-10-COPD


title: control highrisk 5

source_name: blood, no lung cancer or nodule, individual 108


title: patient 05, adjacent dysplastic lesions, LMD

description:
Gene expression profile of surgically resected material
Sample name: D05


title: 6967-08-COPD


title: patient 05, invasive tumor tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: T05


title: PHEO_AG_HS_049

value: somatic

value: malignant


title: 6967-06-COPD


title: control highrisk 4

source_name: blood, no lung cancer or nodule, individual 107

value: blood


title: PHEO_AG_HS_045

value: benign


title: 6967-05-COPD


title: patient 05, noncancerous normal tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: N05


title: control highrisk 2

source_name: blood, no lung cancer or nodule, individual 105

value: Multiple


title: 6967-04-COPD


title: control highrisk 3

source_name: blood, no lung cancer or nodule, individual 106

value: Mixed


title: control highrisk 1

source_name: blood, no lung cancer or nodule, individual 104


title: PHEO_AG_HS_041

value: RET


title: patient 04, adjacent dysplastic lesions, LMD

description:
Gene expression profile of surgically resected material
Sample name: D04


title: cancer preop 9

description: files with prefix 1_ are for Hy3 (Cy3) signals and 2_ for Hy5

source_name: blood, lung cancer, individual 9

value: preop

value: adenocarcinoma of lung

value: Lung cancer (before surgical resection of lung cancer)

value: Human universal reference RNA from Ambion


title: PHEO_AG_HS_052

value: paraganglioma


title: patient 04, noncancerous normal tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: N04


title: 6965-10-COPD

value: Male


title: cancer preop 8

source_name: blood, lung cancer, individual 8

value: female

value: squamous cell carcinoma of lung


title: 6965-09-COPD

source_name: Whole lung tissue


title: cancer preop 7

source_name: blood, lung cancer, individual 7

value: neuroendocrine carcinoma of lung


title: patient 03, invasive tumor tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: T03

value: invasive tumor tissue


title: patient 03, adjacent dysplastic lesions, LMD

description:
Gene expression profile of surgically resected material
Sample name: D03

source_name: adjacent dysplastic lesions, LMD

value: adjacent dysplastic lesions


title: patient 03, noncancerous normal tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: N03

value: noncancerous normal tissue


title: 6967-02-COPD

value: Female


title: 6965-08-COPD


title: PHEO_AG_HS_040

value: pheochromocytoma

value: syndromic

value: benign


title: cancer preop 6

source_name: blood, lung cancer, individual 6

value: blood

value: Multiple

value: Mixed


title: patient 02, invasive tumor tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: T02

source_name: invasive tumor tissue, LMD


title: PHEO_AG_HS_044

value: RET

value: germline


title: 6965-07-COPD

description: RNA was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained with RMA and the Affymetrix CDF using Expression Console Version 1.0 software.


title: cancer preop 5

source_name: blood, lung cancer, individual 5

value: preop

value: male

value: poorly differentiated non-small cell cancer of lung

value: Lung cancer (before surgical resection of lung cancer)

source_name: Human universal reference RNA from Ambion


title: cancer preop 4

source_name: blood, lung cancer, individual 4

value: squamous cell carcinoma of lung

value: Human universal reference RNA from Ambion


title: 6965-06-COPD

value: Male


title: 6965-05-COPD


title: patient 02, adjacent dysplastic lesions, LMD

description:
Gene expression profile of surgically resected material
Sample name: D02

value: adjacent dysplastic lesions


title: PHEO_AG_HS_034

value: female


title: PHEO_AG_HS_033

value: pheochromocytoma

value: somatic


title: PHEO_AG_HS_036

value: benign


title: patient 02, noncancerous normal tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: N02

source_name: noncancerous normal tissue, LMD

value: noncancerous normal tissue


title: 6965-03-COPD


title: cancer preop 2

source_name: blood, lung cancer, individual 2

value: blood

value: adenocarcinoma of lung

value: Multiple


title: 6965-04-COPD


title: cancer preop 3

source_name: blood, lung cancer, individual 3

value: Mixed


title: patient 04, invasive tumor tissue, LMD

description:
Gene expression profile of surgically resected material
Sample name: T04

value: invasive tumor tissue


title: PHEO_AG_HS_037


title: cancer preop 1

source_name: blood, lung cancer, individual 1

value: preop


title: PHEO_AG_HS_030

value: male


title: PHEO_AG_HS_058


title: PHEO_AG_HS_020


title: PHEO_AG_HS_031


title: PHEO_AG_HS_017


title: PHEO_AG_HS_029


title: LIN28KD-hES hjay 2

status: Public on Sep 10 2012

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

hyb_protocol: Hybridization cocktails containing ~5.5 ug of fragmented and labeled DNA target were prepared and applied to GeneChip Human Splice Junction arrays. Hybridization was performed for 16 hours using the Fluidics 450 station.

scan_protocol: Arrays were scanned using the Affymetrix 3000 7G scanner and GeneChip Operating Software version 1.4 to produce .CEL intensity files.

data_processing:
Data processed using Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.
HJAY_r2.pgf

molecule: polyA RNA

source_name: H9 human ES cells

label_protocol: WT Terminal Labeling Kit, Affymetrix

growth_protocol: HEK293 cells containing an integrated Flp-In site (Flp-In-293; Life Technologies) were cultured in DMEM media supplemented with 10% FBS and 2mM L-glutamine and passaged using TrypLE (LifeTechnologies). Human ES cell-lines H9 and HUES6 were grown in feeder-free conditions with mTeSR media (Stemcell Technologies) and on Matrigel (BD Biosciences) for support. Cells were passaged manually or with Dispase (BD Biosciences) every 5-7 days.

extract_protocol: Trizol (Life Technologies) extraction of RNA was performed according to the manufacturer’s instructions.

treatment_protocol: To generate the LIN28-V5 293 stable cell line, pEF5/FRT/LIN28-V5 plasmid was co-transfected along with the FLP Recombinase expressing plasmid pOG44 into Flp-In-293 cells using Lipofectamine-2000 (Life Technologies) according to the manufacturer’s instructions. Recombination and insertion of LIN28-V5 at the Flp-In site confers stable integration and expression of the LIN28-V5 fusion protein and hygromycin resistance. Stably transected clones were selected and propagated in media supplemented with 75-100 μg/ml hygromycin B (Life Technologies). To achieve knockdown of LIN28 in hES cells, we utilized an shRNA construct targeting human LIN28A in the pLKO.1 vector (TRCN0000102579; Open Biosystems). As a control, a pLKO.1 vector containing an shRNA toward GFP was used (Open Biosystems). Lentivirus expressing these constructs was prepared in 293T cells, as previously described (Yeo et al., 2009). Human ES cells were treated with Accutase to generate single cell suspensions and infected with LIN28 or matched control GFP virus. The media was changed daily and cells were harvested 72 hours after infection. To acheive TDP-43 over expression, Flp-In-293 cells were grown to ~70% confluency in 6-well cell culture plates and transfected with 4μg of TDP-43-GFP (Liu-Yesucevitz et al., 2010) or control pEGFP-C2 (AddGene) plasmid using Lipofectamine-2000 (Life Technologies) according to manufacturer’s instructions.  After 48 hours cells were harvested

tag: cell line

tag: treatment

value: LIN28 shRNA treated H9 cells


title: 116 Wistar, p5, 4i

city: Manhattan

first: Mark

middle: L

last: Weiss

state: KS

address: Coles Hall, Room 115

department: Anatomy and Physiology

institute: Kansas State University

description:
This Sample represents 2 technical replicates.
SAMPLES 33 & 34

data_processing:
The duplicate samples (technical replicates) were averaged. Normalization and all the data analysis were performed according to the manufacturer's instructions using the RT-PCR profiler instruction manual.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)] and Ct_HKG = geometric mean of Gapdh and Ldha.
An Excel spreadsheet was used to calculate deltaCt, fold change, etc.
GSE30582_fold_change.txt': Fold Change file reports sample/control cell line. Specifically, average sample/MEF ratios for 2(-delta delta Ct) fold change. This file is linked to the GSE30582 record as a supplementary file.

label: SYBR Green

organism: Rattus norvegicus

source_name: rat embryonic stem cells, passage 5, 4i medium

label_protocol: RT-PCR assays using a customized RT-PCR Profiler array (SABiosciences - Qiagen, Frederick, MD) following the manufacturer's instructions. Reverse transcription was performed from 1000 ng total RNA using the RT2 First Strand Kit (SA Biosciences). The focused array was run using Qiagen's RT2 qPCR Mastermix for the BioRad iQ5 thermal cycler (loading control dye). Quantitative real-time PCR were performed on a BioRad iCQ5 iCycler using Biorad iCycler IQ software version 3.1.7050. PCR program: 950C for 10 min, 40 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds. Followed by melt point analysis.

extract_protocol: Total RNA was extracted with the Qiagen RNeasy Mini Kit using the manufacturer's protocol, followed by DNase I treatment. First-strand synthesis using the Qiagen's RT2 first strand kit. Samples were stored at -80C until use.

tag: strain

value: Wistar

tag: cell type

value: embryonic stem cells

tag: differentiation status

value: undifferentiated

tag: passage

tag: cdna id


title: PHEO_AG_HS_012

tag: tissue

value: germline

tag: malignancy


title: Control KD-hES hjay 2


title: PHEO_AG_HS_011

value: female


title: LIN28KD-hES hjay 3


title: DA 53.1, p10, GERMLINE

description:
This Sample represents 2 technical replicates.
SAMPLES 19 & 20

source_name: rat embryonic stem cells, passage 9, 2i + LIF medium

value: Dark Agouti

value: embryonic stem cells, transfected with CAG promoter driving GFP


title: Control KD-hES hjay 3


title: LIN28KD-hES hjay 1


title: Control OE-Flp-In-293 hjay 1

source_name: human Flp-In-293 cells

value: TDP43 Over Expression


title: TDP43OE-Flp-In-293 hjay 1


title: Control OE-Flp-In-293 hjay 2


title: Control KD-hES hjay 1


title: Control OE-Flp-In-293 hjay 3


title: TS

description:
This Sample represents 2 technical replicates.
SAMPLES 17 & 18

source_name: rat trophoblast stem cells

extract_protocol: Total RNA was extracted with TRIZOL using the manufacturer's protocol, followed by DNase I treatment. First-strand synthesis using the Qiagen's RT2 first strand kit. Samples were stored at -80C until use.

value: Holtzman Sprague-Dawley

value: trophoblast stem cells


title: 115 LEA, p6, 4i

description:
This Sample represents 2 technical replicates.
SAMPLES 31 & 32

source_name: rat embryonic stem cells, passage 6, 4i medium

value: Long Evans Agouti


title: DA 54.1 EB, 5 d

description:
This Sample represents 2 technical replicates.
SAMPLES 13 & 14

source_name: rat embryonic stem cells differentiated to embryoid body for 5 days

value: embryoid bodies derived from line DA line 1, differentiated to embryoid bodies 5 days

value: 5 days differentiation


title: PHEO_AG_HS_013

value: pheochromocytoma

value: benign


title: Fischer 344 38, GERMLINE

description:
This Sample represents 2 technical replicates.
SAMPLES 25 & 26

source_name: rat embryonic stem cells, 2i + LIF medium

value: Fischer 344


title: DA 52 p9, GERMLINE

description:
This Sample represents 2 technical replicates.
SAMPLES 9 & 10


title: Fischer 344 2.1.1 p24, chimera

description:
This Sample represents 2 technical replicates.
SAMPLES 7 & 8

source_name: rat embryonic stem cells, passage 24, 2i + LIF medium

value: transgenic Fischer 344 expressing beta-galactosidase under the Rosa26 promoter


title: PHEO_AG_HS_016

value: syndromic


title: DA 54.1 p9 CHIMERA

description:
This Sample represents 2 technical replicates.
SAMPLES 5 & 6


title: Flp-In-293 hjay 3

value: Untreated Flp-In-293


title: LIN28V5-293 hjay 2

source_name: human LIN28-V5 293 stable cells

value: LIN28 Flp-In-293


title: TDP43OE-Flp-In-293 hjay 2


title: XEN

description:
This Sample represents 2 technical replicates.
SAMPLES 1 & 2

source_name: extraembryonic endoderm

value: extraembryonic endoderm

value: undifferentiated


title: TDP43OE-Flp-In-293 hjay 3


title: PHEO_AG_HS_006

value: male


title: Flp-In-293 hjay 1


title: LIN28V5-293 hjay 1


title: DA 54.1 EB, 10d

description:
This Sample represents 2 technical replicates.
SAMPLES 15 & 16

source_name: rat embryonic stem cells differentiated to embryoid body for 10 days

value: Dark Agouti

value: embryoid bodies derived from line DA line 1, differentiated to embryoid bodies 10 days

value: 10 days differentiation


title: DAc8, p35, GERMLINE

description:
This Sample represents 2 technical replicates.
SAMPLES 11 & 12

value: embryonic stem cells


title: PHEO_AG_HS_003

value: somatic


title: Flp-In-293 hjay 2


title: LIN28V5-293 hjay 3


title: Tendril-FS_rep3

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

institute: University of Verona

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

organism: Vitis vinifera

source_name: mature tendril (pool of tendrls at fruit set), replicate 3

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol: Vitis vinifera cv. Corvina (clone 48) samples were collected from a 7-year-old vineyard (45° 27’ 17” N, 11° 03’ 14” E, Montorio, Verona province, Italy) during 2008/2009 growing seasons. The vineyard is at 130 m. above sea level (a.s.l.), planted on a soil with the following composition: 36% sand, 36% say and 28% silt. The replacement cane Guyot rows are north-south oriented and 41B in used as rootstock.

extract_protocol: Total RNA was extracted from ~100 mg of liquid-nitrogen-grinded tissue using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO) following the manufacturer’s protocol. For berry flesh, senescing leaf and woody stem, it was necessary to isolate RNA from ~400 mg of grinded material, while for berry pericarp and skin, seed, rachis, root, latent and winter bud, from ~200 mg.  Lithium Chloride precipitation treatment was applied to some of the total RNA samples (from winter bud, from seed and rachis at vèraison and mid-ripening, from woody stem) to remove 230wavelenght-absorbant contaminants. Briefly, LiCl solution was mixed with total RNA solution to a final concentration of 2.5 M; after over-night incubation at 4°C, a cold centrifugation and ethanol-70% washing step, total RNA was resuspended in water.

tag: cultivar

value: Corvina

value: Tendril

tag: developmental stage


title: PHEO_AG_HS_038

value: pheochromocytoma

value: female


title: Tendril-WD_rep3

source_name: well developed tendril (pool of tendrils from shoot of 12 leaves), replicate 3


title: Tendril-WD_rep1

source_name: well developed tendril (pool of tendrils from shoot of 12 leaves), replicate 1


title: Stem-W_rep3

source_name: woody stem, replicate 3

value: Stem

value: woody stem


title: Stem-W_rep2

source_name: woody stem, replicate 2


title: Stem-G_rep1

source_name: green stem, replicate 1

value: green stem


title: PHEO_AG_HS_001

value: benign


title: Tendril-Y_rep3

source_name: young tendril (pool of tendrils from shoot of 7 leaves), replicate 3


title: BerrySkin-PHWII_rep2

source_name: berry skin post-harvest withering II (2nd month), replicate 2

value: Berry Skin

value: post-harvest withering II (2nd month)


title: BerrySkin-PHWIII_rep1

source_name: berry skin post-harvest withering III (3rd month), replicate 1

value: post-harvest withering III (3rd month)


title: Stem-W_rep1

source_name: woody stem, replicate 1


title: Stem-G_rep2

source_name: green stem, replicate 2


title: BerrySkin-PHWIII_rep2

source_name: berry skin post-harvest withering III (3rd month), replicate 2


title: Tendril-FS_rep2

source_name: mature tendril (pool of tendrls at fruit set), replicate 2


title: BerrySkin-PHWI_rep3

source_name: berry skin post-harvest withering I (1st month), replicate 3

value: post-harvest withering I (1st month)


title: BerrySkin-PHWIII_rep3

source_name: berry skin post-harvest withering III (3rd month), replicate 3


title: Stem-G_rep3

source_name: green stem, replicate 3


title: BerrySkin-PHWII_rep3

source_name: berry skin post-harvest withering II (2nd month), replicate 3


title: Tendril-WD_rep2

source_name: well developed tendril (pool of tendrils from shoot of 12 leaves), replicate 2


title: BerrySkin-R_rep3

source_name: berry skin ripening, replicate 3

value: ripening


title: BerrySkin-PHWII_rep1

source_name: berry skin post-harvest withering II (2nd month), replicate 1


title: Tendril-Y_rep2

source_name: young tendril (pool of tendrils from shoot of 7 leaves), replicate 2


title: Tendril-Y_rep1

source_name: young tendril (pool of tendrils from shoot of 7 leaves), replicate 1


title: BerrySkin-PHWI_rep1

source_name: berry skin post-harvest withering I (1st month), replicate 1


title: BerrySkin-R_rep2

source_name: berry skin ripening, replicate 2


title: BerrySkin-R_rep1

source_name: berry skin ripening, replicate 1


title: BerrySkin-PHWI_rep2

source_name: berry skin post-harvest withering I (1st month), replicate 2


title: BerrySkin-MR_rep3

source_name: berry skin mid-ripening, replicate 3

value: mid-ripening


title: BerrySkin-MR_rep2

source_name: berry skin mid-ripening, replicate 2


title: BerrySkin-V_rep2

source_name: berry skin véraison, replicate 2

value: véraison


title: BerrySkin-V_rep3

source_name: berry skin véraison, replicate 3


title: BerrySkin-PFS_rep3

source_name: berry skin post-fruit set, replicate 3

value: post-fruit set


title: BerrySkin-PFS_rep2

source_name: berry skin post-fruit set, replicate 2


title: Tendril-FS_rep1

source_name: mature tendril (pool of tendrls at fruit set), replicate 1


title: BerrySkin-V_rep1

source_name: berry skin véraison, replicate 1


title: Seedling_rep2

source_name: seedling pool of 3 developmental stages, replicate 2

value: Seedling

value: pool of 3 developmental stages


title: BerrySkin-PFS_rep1

source_name: berry skin post-fruit set, replicate 1

value: Corvina


title: Seed-MR_rep2

source_name: seed mid-ripening, replicate 2

value: Seed


title: PHEO_AG_HS_002

value: pheochromocytoma

value: female

value: germline


title: Seed-V_rep2

source_name: seed véraison, replicate 2


title: Seed-MR_rep1

source_name: seed mid-ripening, replicate 1


title: Seed-PFS_rep1

source_name: seed post-fruit set, replicate 1


title: Rachis-R_rep3

source_name: rachis ripening, replicate 3

value: Rachis


title: Seed-FS_rep1

source_name: seed fruit set, replicate 1

value: fruit set


title: Seed-V_rep3

source_name: seed véraison, replicate 3


title: Seed-V_rep1

source_name: seed véraison, replicate 1


title: Seed-FS_rep3

source_name: seed fruit set, replicate 3


title: Seedling_rep3

source_name: seedling pool of 3 developmental stages, replicate 3


title: BerrySkin-MR_rep1

source_name: berry skin mid-ripening, replicate 1

value: Berry Skin


title: Rachis-MR_rep3

source_name: rachis mid-ripening, replicate 3


title: Seed-MR_rep3

source_name: seed mid-ripening, replicate 3


title: Seedling_rep1

source_name: seedling pool of 3 developmental stages, replicate 1


title: Seed-FS_rep2

source_name: seed fruit set, replicate 2


title: Rachis-MR_rep2

source_name: rachis mid-ripening, replicate 2


title: Rachis-R_rep1

source_name: rachis ripening, replicate 1


title: Rachis-V_rep3

source_name: rachis véraison, replicate 3


title: Rachis-MR_rep1

source_name: rachis mid-ripening, replicate 1


title: Rachis-R_rep2

source_name: rachis ripening, replicate 2


title: Rachis-V_rep2

source_name: rachis véraison, replicate 2


title: Rachis-V_rep1

source_name: rachis véraison, replicate 1


title: Seed-PFS_rep2

source_name: seed post-fruit set, replicate 2


title: Rachis-PFS_rep3

source_name: rachis post-fruit set, replicate 3


title: Rachis-FS_rep3

source_name: rachis fruit set, replicate 3


title: Rachis-FS_rep1

source_name: rachis fruit set, replicate 1


title: Rachis-FS_rep2

source_name: rachis fruit set, replicate 2


title: Rachis-PFS_rep1

source_name: rachis post-fruit set, replicate 1


title: Pollen_rep2

source_name: pollen from disclosed flowers at more than 50% open flowers, replicate 2

value: Pollen


title: Pollen_rep3

source_name: pollen from disclosed flowers at more than 50% open flowers, replicate 3


title: BerryPericarp-PHWII_rep2

source_name: berry pericarp post-harvest withering II (2nd month), replicate 2

value: Berry Pericarp

value: post-harvest withering II (2nd month)


title: BerryPericarp-PHWII_rep3

source_name: berry pericarp post-harvest withering II (2nd month), replicate 3


title: Pollen_rep1

source_name: pollen from disclosed flowers at more than 50% open flowers, replicate 1


title: BerryPericarp-PHWIII_rep1

source_name: berry pericarp post-harvest withering III (3rd month), replicate 1

value: post-harvest withering III (3rd month)


title: BerryPericarp-PHWIII_rep3

source_name: berry pericarp post-harvest withering III (3rd month), replicate 3


title: Petal_rep3

source_name: pool of petals from undisclosed flowers at 10% and 50% open flowers, replicate 3

value: Petal


title: BerryPericarp-PHWIII_rep2

source_name: berry pericarp post-harvest withering III (3rd month), replicate 2


title: Petal_rep1

source_name: pool of petals from undisclosed flowers at 10% and 50% open flowers, replicate 1


title: Leaf-FS_rep2

source_name: mature leaf (pool of leaves from shoot at fruit set), replicate 2

value: Leaf


title: Leaf-S_rep1

source_name: senescencing leaf (pool of leaves at the beginning of leaf fall), replicate 1


title: Rachis-PFS_rep2

source_name: rachis post-fruit set, replicate 2

value: post-fruit set


title: Carpel_rep3

source_name: pool of carpels from undisclosed flowers at 10% and 50% open flowers, replicate 3

value: Carpel


title: BerryPericarp-PHWII_rep1

source_name: berry pericarp post-harvest withering II (2nd month), replicate 1


title: Leaf-S_rep2

source_name: senescencing leaf (pool of leaves at the beginning of leaf fall), replicate 2


title: BerryPericarp-PHWI_rep2

source_name: berry pericarp post-harvest withering I (1st month), replicate 2

value: post-harvest withering I (1st month)


title: Leaf-S_rep3

source_name: senescencing leaf (pool of leaves at the beginning of leaf fall), replicate 3

value: Corvina


title: Seed-PFS_rep3

source_name: seed post-fruit set, replicate 3

value: Seed


title: Carpel_rep2

source_name: pool of carpels from undisclosed flowers at 10% and 50% open flowers, replicate 2


title: Petal_rep2

source_name: pool of petals from undisclosed flowers at 10% and 50% open flowers, replicate 2


title: Carpel_rep1

source_name: pool of carpels from undisclosed flowers at 10% and 50% open flowers, replicate 1


title: BerryPericarp-PHWI_rep1

source_name: berry pericarp post-harvest withering I (1st month), replicate 1


title: Leaf-Y_rep3

source_name: young leaf (pool of leaves from shoot of 5 leaves), replicate 3


title: Leaf-FS_rep1

source_name: mature leaf (pool of leaves from shoot at fruit set), replicate 1


title: BerryPericarp-PHWI_rep3

source_name: berry pericarp post-harvest withering I (1st month), replicate 3


title: Leaf-FS_rep3

source_name: mature leaf (pool of leaves from shoot at fruit set), replicate 3


title: Leaf-Y_rep2

source_name: young leaf (pool of leaves from shoot of 5 leaves), replicate 2


title: Root_rep3

source_name: root in vitro cultivation, replicate 3

value: Root

value: in vitro cultivation


title: Leaf-Y_rep1

source_name: young leaf (pool of leaves from shoot of 5 leaves), replicate 1


title: Flower-FB_rep1

source_name: flowering begins (10% caps off), replicate 1

value: Flower

value: flowering begins (10% caps off)


title: Root_rep1

source_name: root in vitro cultivation, replicate 1


title: Root_rep2

source_name: root in vitro cultivation, replicate 2


title: Flower-F_rep3

source_name: flowering (50% caps off), replicate 3

value: flowering (50% caps off)


title: Flower-FB_rep2

source_name: flowering begins (10% caps off), replicate 2


title: Inflorescence-WD_rep2

source_name: well developed inflorescence (single flower separated), replicate 2

value: Inflorescence


title: BerryFlesh-PHWII_rep1

source_name: berry flesh post-harvest withering II (2nd month), replicate 1

value: Berry Flesh


title: Flower-FB_rep3

source_name: flowering begins (10% caps off), replicate 3


title: Inflorescence-WD_rep1

source_name: well developed inflorescence (single flower separated), replicate 1


title: Flower-F_rep2

source_name: flowering (50% caps off), replicate 2


title: BerryFlesh-MR_rep3

source_name: berry flesh mid-ripening, replicate 3

value: mid-ripening


title: BerryFlesh-PHWI_rep3

source_name: berry flesh post-harvest withering I (1st month), replicate 3


title: BerryFlesh-PHWII_rep2

source_name: berry flesh post-harvest withering II (2nd month), replicate 2

value: post-harvest withering II (2nd month)


title: BerryFlesh-R_rep2

source_name: berry flesh ripening, replicate 2

value: ripening


title: BerryFlesh-PHWI_rep1

source_name: berry flesh post-harvest withering I (1st month), replicate 1


title: BerryFlesh-R_rep1

source_name: berry flesh ripening, replicate 1


title: Flower-F_rep1

source_name: flowering (50% caps off), replicate 1


title: Inflorescence-Y_rep3

source_name: young inflorescence (single flower in compact groups), replicate 3


title: BerryFlesh-PHWIII_rep3

source_name: berry flesh post-harvest withering III (3rd month), replicate 3

value: post-harvest withering III (3rd month)


title: BerryFlesh-V_rep2

source_name: berry flesh véraison, replicate 2

value: véraison


title: BerryFlesh-PHWIII_rep1

source_name: berry flesh post-harvest withering III (3rd month), replicate 1


title: BerryFlesh-R_rep3

source_name: berry flesh ripening, replicate 3


title: Inflorescence-Y_rep2

source_name: young inflorescence (single flower in compact groups), replicate 2


title: BerryFlesh-PHWIII_rep2

source_name: berry flesh post-harvest withering III (3rd month), replicate 2


title: BerryFlesh-MR_rep2

source_name: berry flesh mid-ripening, replicate 2


title: BerryFlesh-V_rep3

source_name: berry flesh véraison, replicate 3


title: Inflorescence-Y_rep1

source_name: young inflorescence (single flower in compact groups), replicate 1


title: testes_DicerGCKO_P18_miRNA_rep2

city: Bar Harbor

first: Timothy

middle: Michael

last: Stearns

state: ME

address: 600 Main Street

department: Computational Sciences

institute: The Jackson Laboratory

description:
M38_MUT
miRNA

hyb_protocol: Biotin-labeled miRNA were hybridized to the Mus musculus miRNA Geniom Biochip for 16 hours at 42 °C. The Biochip was washed automatically.

scan_protocol: Signals were detected with the GRTA and evaluated using the Geniom Wizard Software.

data_processing: The miRNA array data were derived from Febit microarrays after background subtraction (subtracting median negative control intensities from each array). The background-subtracted data were transformed by adding a constant of one to all intensities and applying a log2 transformation. Any probe which had a median value of zero (zero intensity in at least two arrays in each sample group) was removed from the dataset. These probes were deemed to have no expression in either sample group. Upon filtering the probe sets, the density and distribution of intensities were examined. Upon review, sample M36 (GCKO sample) was found to have a distribution of intensities similar to WT samples. Data from sample M36 were removed based upon these criteria. All intensity data were re-examined for the remaining five arrays. Probes which had a median of zero (zero intensity in at least two arrays) for the WT samples and a minimum intensity of zero in at least one array for the mutant samples were removed. These probes were deemed to have no expression in either sample group. Upon filtering such probe sets, the density and distribution of intensities within sample groups were relatively equal. Quantile normalization was performed within sample groups given the distinct difference in intensity distributions between sample types. The normalized data were used for microarray analysis in R/maanova. One pairwise comparison was used to statistically resolve miRNA expression differences between WT and GCKO groups using the R/maanova analysis package. Differentially expressed miRNAs 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 pair-wise comparisons were calculated by permutation analysis and adjusted for multiple testing using the false discovery rate (FDR) q-value method. Differentially expressed miRNAs were declared at an FDR q-value threshold of 0.05.

source_name: testes, Dicer1 germ cell knockout, P18

label_protocol: Sample labeling with biotin was carried out by microfluidic-based enzymatic on-chip labeling of miRNAs.

extract_protocol: WT and GCKO testis RNA samples were analyzed with a Geniom Realtime Analyzer (GRTA, Febit, GmbH, Heidelberg, Germany) using the Geniom Biochip miRNA Mus musculus.

value: FVB x 129S1

tag: genotype

value: Dicer1 germ cell knockout

value: testes

tag: gender

value: male


title: Inflorescence-WD_rep3

source_name: well developed inflorescence (single flower separated), replicate 3

value: Corvina


title: BerryFlesh-V_rep1

source_name: berry flesh véraison, replicate 1


title: BerryFlesh-MR_rep1

source_name: berry flesh mid-ripening, replicate 1


title: BerryFlesh-PHWI_rep2

source_name: berry flesh post-harvest withering I (1st month), replicate 2

value: post-harvest withering I (1st month)


title: testes_wildtype_P18_miRNA_rep2

description:
M34_WT
miRNA

source_name: testes, wild-type control, P18

value: wild-type


title: testes_wildtype_P18_miRNA_rep1

description:
M33_WT
miRNA


title: BerryFlesh-PFS_rep3

source_name: berry flesh post fruit set, replicate 3

value: post fruit set


title: BerryFlesh-PFS_rep2

source_name: berry flesh post fruit set, replicate 2


title: testes_DicerGCKO_P18_miRNA_rep1

description:
M37_MUT
miRNA


title: MicroRNA expression profile in the large intestine of control mouse

city: Asahikawa-city

first: Mikihiro

last: Fujiya

state: Hokkaido

address: 1-1-1, Higashi 2-jou, Midorigaoka

department: Department of Medicine

institute: Asahikawa Medical University

hyb_protocol: We followed the manufacturer's protocol of the mirVana(TM) miRNA bioarray.

scan_protocol: We followed the manufacturer's protocol, and used GenePix 4000B.

data_processing:
We used Array-Pro Analyzer Ver.4.5 (Media Cybernetics, Inc.) for quantification.
We performed global median normalization and probe summarization by average.

source_name: Large intestine, control

label_protocol: We used the mirVana(TM) miRNA Labeling kit (Ambion) following the manufacturer's protocol.

extract_protocol: We used the mirVana(TM) Isolation Kit and flashPAGE(TM) System (Ambion) following the manufacturer's protocol.

tag: strain/background

value: female

tag: age

value: 45 days

value: large intestine


title: testes_DicerGCKO_P18_rep2

hyb_protocol: 2.3µg of biotin-labeled and fragmented cDNA was hybridized to the GeneChip® Mouse Gene 1.0 ST Array (Affymetrix) for 16 hours at 45°C. Post-hybridization staining and washing were performed according to the manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).

scan_protocol: The arrays were scanned with a GeneChip® Scanner 3000 laser confocal slide scanner.

data_processing: For the gene array data, average signal intensities for each probe set within arrays were calculated by the RMA function provided within the Affymetrix package for R using a custom (Entrez Gene, v12.1.0) chip description file (http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp). The RMA method incorporates convolution background correction, sketch-quantile normalization, and summarization based on a multi-array model fit robustly using the median polish algorithm (all samples processed together). For this experiment, one pairwise comparison was used to statistically resolve gene expression differences between wild-type and GCKO sample groups using the R/maanova analysis package. Specifically, differentially expressed genes were detected by using Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/maanova package. Statistical significance levels of the pairwise comparison were calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method. Differentially expressed genes were declared at an FDR q-value threshold of 0.05.

label_protocol: Following reverse transcription with random T7 primers (Affymetrix, Santa Clara, CA), double-stranded cDNA was synthesized with the GeneChip® WT cDNA Synthesis and Amplification Kit (Affymetrix). In an in vitro transcription (IVT) reaction with T7 RNA polymerase, the cDNA was linearly amplified to generate cRNA. In the second cycle of cDNA synthesis, random primers were used to generate single-stranded DNA in the sense orientation. Incorporation of dUTP in the cDNA synthesis step allowed for the fragmentation of the cDNA strand utilizing uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognizes the dUTP and allows for breakage at these residues. Labeling occurred by terminal deoxynucleotidyl transferase (TdT) where biotin was added to the cDNA by an Affymetrix Labeling Reagent.

extract_protocol: Total RNA, including miRNAs, were purified from WT (n=3) and GCKO (n=3) testes on P18 using the mirVana™ miRNA Isolation Kit, followed by analysis on the Agilent 2100 Bioanalyzer to determine quality.


title: BerryFlesh-PHWII_rep3

source_name: berry flesh post-harvest withering II (2nd month), replicate 3

value: Berry Flesh


title: testes_DicerGCKO_P18_rep3


title: testes_DicerGCKO_P18_rep1


title: Bud-W_rep3

source_name: winter bud, replicate 3

value: Bud

value: winter bud


title: BerryFlesh-PFS_rep1

source_name: berry flesh post fruit set, replicate 1


title: MicroRNA expression profile in the large intestine of IL-10-deficient mouse

source_name: Large intestine, IL-10-deficient


title: testes_wildtype_P18_rep2


title: injured miRNA

city: Philadelphia

first: Richard

last: Assoian

state: PA

address: 421 Curie Blvd

department: Pharmacology

institute: University of Pennsylvania

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes. Transfer 200μl of hyb solution to each array. Hybridize 16 hours at 45° at 60rpm.

data_processing: Data was processed using Partek Genomics Suite. Using default RMA method data was background corrected, quantile normalized, log2 transformed and summarized.

source_name: injured

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

growth_protocol: Mouse femoral arteries from four male, 5-6 mo old SMA-GFP mice subjected to fine wire injury.  The left femoral artery of each mouse was injured, and the contralateral artery was used as an uninjured control.  The mice were allowed to recover from the injury procedure for 14 days, at which time they were sacrificed.

extract_protocol: The arteries were carefully opened longitudinally and immediately imaged for GFP.  GFP-negative regions of the arteries, representing sites of vascular injury were microdissected, quick-frozen on dry ice, and stored in liquid nitrogen. RNeasy Mini kit was used for extraction.

value: femoral arteries

tag: genotype/variation

value: SMA-GFP

value: 5-6 mo old

tag: Sex


title: Bud-W_rep1

source_name: winter bud, replicate 1


title: testes_wildtype_P18_rep3

value: FVB x 129S1


title: testes_wildtype_P18_rep1


title: Control Pt 2 Cere

city: Bethesda

middle: N

last: Ziats

state: Maryland

address: 49 Convent Drive, Bld 49, Room 2c08

institute: National Institute of Child Health and Human Development

description:
Gene and lncRNA expression
4848-Cerebellum

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

scan_protocol: The hybridized arrays were washed, fixed, and scanned using the Agilent DNA Microarray Scanner (G2505B)

data_processing: Agilent Feature Extraction software (version 10.5.1.1) was used to analyze acquired array images.  Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).  After quantile normalization of the raw data, lncRNAs and mRNAs that at least 4 out of 8 samples had flagged as “Present” or “Marginal” were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs were identified through fold change (FC) filtering.  Differentially expressed lncRNAs and mRNAs with statistical significance (as determined by two-tailed student’s t-test < 0.05) were identified through Volcano Plot filtering.  Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). *The Sample data table contains the quantile-normalized intensity from all probes that were detected in at least 4/8 samples prior to any  data processing (e.g. prior to fold-change filtering).  There was a considerable number of probes not detected in this experiment.

extract_protocol: post-mortem brain was immedietly frozen at -80degrees celcius until processed. Total RNA was extracted by homogenizing samples in TRIzol® Reagent (Invitrogen) according to the manufacturer’s protocol.  RNA quantity was measured by NanoDrop ND-1000.  Agilent Bioanalyzer 2100 was used to assess RNA integrity for each sample, each of which was > 8.8

tag: race

value: Caucasian

tag: diagnosis

value: Control (non-affected)

value: 16yrs 271 days

tag: tissue source

value: Post mortem human brain

value: cerebellum


title: Bud-W_rep2

source_name: winter bud, replicate 2

value: Corvina


title: Bud-L_rep2

source_name: latent bud, replicate 2

value: latent bud


title: Bud-L_rep3

source_name: latent bud, replicate 3


title: Bud-L_rep1

source_name: latent bud, replicate 1


title: Bud-AB_rep3

source_name: bud after-burst (rosette of leaf tips visible), replicate 3


title: Bud-AB_rep2

source_name: bud after-burst (rosette of leaf tips visible), replicate 2


title: Bud-AB_rep1

source_name: bud after-burst (rosette of leaf tips visible), replicate 1


title: Bud-B_rep3

source_name: bud burst (green tip), replicate 3

value: bud burst (green tip)


title: Control 2

first: Maria

middle: Isabel

last: Ramirez

address: 72 E. Concord St. E603

department: Medicine

institute: Boston University School of Medicine

description:
Non-silencing 2
Independent transduction

hyb_protocol: The labeled fragmented DNA was hybridized to the GeneChip Mouse Gene Array 1.0ST (Affymetrix) for 16-18 h in a GeneChip Hybridization oven 640 at 45°C with constant rotation (60 rpm). The hybridized samples were washed and stained using Affymetrix fluidics station 450. The first stain with streptavidin-R-phycoerythrin (SAPE) was followed by signal amplification using a biotinylated goat anti-streptavidin antibody and another SAPE staining (Hybridization, Washing and Staining Kit, Affymetrix).

scan_protocol: Affymetrix GeneArray Scanner 3000 7G Plus

data_processing: CEL files were summarized using Affymetrix Expression Console (current version 1.1). Expression estimates were derived from the probe level hybridization intensities using the Robust Multi-Array Analysis (RMA) algorithm.  Differential expression between experimental and control samples was examined using Welch's T-test and a False Discovery Rate correction.

source_name: Lung Epithelial Cell Line

label_protocol: The total RNA (300 ng) was reverse transcribed using Whole Transcript cDNA Synthesis kit (Affymetrix). The cDNA obtained was used as a template for in vitro transcription using a Whole Transcript cDNA Amplification Kit (Affymetrix). The antisense cRNA obtained was purified using GeneChip Sample Cleanup Module (Affymetrix) and used as a template for reverse transcription (Whole Transcript cDNA Synthesis kit, Affymetrix) to produce single-stranded DNA in the sense orientation. During this step, dUTP was incorporated. Then, the DNA was fragmented using uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1), labeled with DNA Labeling Reagent and covalently linked to biotin using terminal deoxynucleotidyl transferase (TdT, Whole Transcript Terminal Labeling kit, Affymetrix). IVT and cDNA fragmentation quality controls were performed by an mRNA Nano assay in the Agilent 2100 Bioanalyzer.

growth_protocol: MLE-15 cells (provided by Dr. J. Whitsett, Children’s Hospital Medical Center, Cincinnati, OH) are murine lung epithelial cells produced from tumors in transgenic mice expressing the SV40 large tumor antigen under transcriptional control of the human surfactant protein C promoter (SP-C) (34). Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Life Technologies, Inc.), 10% heat-inactivated fetal bovine serum (FBS) (Life Technologies, Inc.), 100 units/ml penicillin G, 100 mg/ml streptomycin sulfate.

extract_protocol: Total RNA was isolated using QIAGEN’s RNeasy kit (Qiagen) and the sample integrity was verified using RNA 6000 Nano Assay RNA chips run in Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: To knockdown Grhl2 gene expression, a replication incompetent, VSV-G pseudotyped lentiviral vector that contained a GFP tracking reporter gene along with either a non-targeting control shRNA (RHS4346) or the shRNA targeting Grhl2 (V2LMM_20130) was employed (Open Biosystems). Lentiviruses were packaged and concentrated as described previously (19). MLE-15 cell infections with lentiviral vectors were performed for 16 h in the presence of polybrene (5 μg/ml) at a multiplicity of infection of 50. Stable cell lines were generated by puromycin dihydrochloride (5 μg/ml, Sigma) selection for 6 days.

tag: cell line

value: Lung Epithelial Cell Line MLE15

value: control


title: Control Pt 2 Prefrontal

description:
Gene and lncRNA expression
4848-PFC

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

value: male

value: prefrontal cortex


title: Control 1

description:
Non-silencing 1
Independent transduction


title: Grhl2 downregulation in MLE 15 cells 2

description:
Grhl2-shRNA 2
Independent transduction

value: Grhl2 knockdown


title: Autism Pt 2 Prefrontal

description:
Gene and lncRNA expression
5302-PFC

value: Autism

value: 16yrs 119 days


title: inj-60

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was processed using Partek Genomics Suite. Using default RMA method data was background corrected, quantile normalized, log2 transformed and summarized.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: inj

value: femoral arteries

tag: strain

value: SMA-GFP

value: 5-6 mo old


title: inj-61


title: Control Pt 1 Cere

description:
Gene and lncRNA expression
4670-Cerebellum

value: Caucasian

value: Control (non-affected)

value: 4yrs 237 days


title: Autism Pt 2 Cere

description:
Gene and lncRNA expression
5302-Cerebellum

value: Post mortem human brain

value: cerebellum


title: Bud-B_rep2

source_name: bud burst (green tip), replicate 2

value: Corvina

value: Bud


title: Grhl2 downregulation in MLE 15 cells 3

description:
Grhl2-shRNA 3
Independent transduction

value: Lung Epithelial Cell Line MLE15


title: Bud-S_rep3

source_name: bud swell, replicate 3

value: bud swell


title: Bud-S_rep2

source_name: bud swell, replicate 2


title: Control Pt 1 Prefrontal

description:
Gene and lncRNA expression
4670-PFC

value: male


title: Bud-B_rep1

source_name: bud burst (green tip), replicate 1

value: bud burst (green tip)


title: inj-63


title: testes_wildtype_P18_miRNA_rep3

description:
M35_WT
miRNA

source_name: testes, wild-type control, P18

value: FVB x 129S1

value: wild-type

value: testes


title: Grhl2 downregulation in MLE 15 cells 1

description:
Grhl2-shRNA 1
Independent transduction

value: Grhl2 knockdown


title: Bud-S_rep1

source_name: bud swell, replicate 1


title: Autism Pt 1 Cere

description:
Gene and lncRNA expression
5308-Cerebellum

value: Autism

value: 4yrs 182 days


title: control-63

source_name: control

value: femoral arteries

value: SMA-GFP

value: 5-6 mo old


title: control-61


title: BerryPericarp-R_rep3

source_name: berry pericarp ripening, replicate 3

value: Berry Pericarp

value: ripening


title: inj-57


title: BerryPericarp-R_rep2

source_name: berry pericarp ripening, replicate 2

value: Corvina


title: KO4

city: Fukuoka

first: Tomoki

last: Takeda

address: 3-1-1 Maidashi, Higashi-ku

department: Pharmaceutical sciences

institute: Kyushu University

description: Replicate 3.

hyb_protocol: Cy3-labeled cRNA (1.5 µg) was fragmented at 60°C for 30 min in a reaction mixture (250 µl) containing 1x fragmentation buffer and 2x blocking agent obtained from Agilent. On completion of the fragmentation reaction, 250 µl 2x Agilent hybridization buffer was added to the mixture, and this mixture was then hybridized to Agilent Whole Mouse Genome Oligo Microarrays for 17 hours at 65°C in a rotating oven. After hybridization, the microarray slides were washed with GE Wash Buffer 1 (Agilent) for 1 min at room temperature, and with GE Wash buffer 2 (Agilent) for 1 min at 37°C. Immediately after the washing, the slides were dried by centrifugal evaporator.

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

data_processing: The scanned images were analyzed by Feature Extraction Software (Agilent) using default parameters to subtract background and to obtain processed signal intensities by the algorithm of Spatially Detrend in the software.

source_name: SeBP1 knockout

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 0.5 μg RNA using a One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by purification with an RNeasy column (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked by NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using the RNeasy kit (QIAGEN).

tag: background/strain

value: SeBP1 knockout

value: ovary

value: female

value: 20 weeks


title: KO2

description: Replicate 2.


title: Autism Pt 1 Prefrontal

description:
Gene and lncRNA expression
5308-PFC

value: male

value: Caucasian

value: Post mortem human brain

value: prefrontal cortex


title: control-60


title: BerryPericarp-R_rep1

source_name: berry pericarp ripening, replicate 1


title: W2

description: Replicate 1.

source_name: Wild type

value: wild type


title: KO1

description: Replicate 1.


title: Male 1.0 estradiol-9

city: Little Rock

first: Isabelle

last: Racine Miousse

address: 15 Children's Way

institute: UAMS

description: mammary gene expression

hyb_protocol: Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N = 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.

scan_protocol: The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.

data_processing: Cel files were generated using GCOS and utilized for analysis using GeneSpring GX 11.5.

source_name: postnatal day 33-rat mammary gland

label_protocol: First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA  reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions

extract_protocol: Mammary gland pairs were collected and fresh frozen in liquid nitrogen. Total mammary glands RNA was isolated from the rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion.

value: Sprague-Dawley

tag: diet

value: 1 µg/kg/day E2


title: control-57

tag: tissue

value: femoral arteries


title: BerryPericarp-MR_rep1

source_name: berry pericarp mid-ripening, replicate 1

value: mid-ripening


title: control miRNA

value: SMA-GFP

value: 5-6 mo old


title: W3

description: Replicate 2.


title: W5

description: Replicate 3.


title: Male 10 estradiol-11

description: mammary gene expression

value: 10 µg/kg/day E2


title: BerryPericarp-MR_rep3

source_name: berry pericarp mid-ripening, replicate 3

value: Corvina

value: Berry Pericarp


title: Male 10 estradiol-10

description: mammary gene expression


title: BerryPericarp-MR_rep2

source_name: berry pericarp mid-ripening, replicate 2


title: Male 10 estradiol-12

description: mammary gene expression


title: BerryPericarp-V_rep2

source_name: berry pericarp véraison, replicate 2

value: véraison


title: BerryPericarp-V_rep3

source_name: berry pericarp véraison, replicate 3


title: BerryPericarp-V_rep1

source_name: berry pericarp véraison, replicate 1


title: Male 1.0 estradiol-8

description: mammary gene expression


title: Male 0.1 estradiol-6

description: mammary gene expression

value: 0.1 µg/kg/day E2