title: PancTuRef vs. BN1282


title: PancTuRef vs. HD1520

status: Public on Jun 01 2016

type: RNA

city: Santa Monica

first: Habib

last: Hamidi

state: CA

address: 2825 Santa Monica Blvd., Suite 200

country: USA

institute: UCLA

hyb_protocol: 825 ng each of labeled reference mix (cy3 label) and individual sample (cy5 label) were applied to Whole Human Genome 4X44 microarrays (Agilent G4112F) using the In Situ Hybridization Kit Plus (Agilent) protocol

scan_protocol: Slides were read on an Agilent G2505B scanner.  All  experiments were scanned with extended dynamic range enabled.

data_processing:
Agilent Feature Extraction Software (v9.5.1) was used with no background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, error model used to determine to determine significance and well-above-background = most conservation, dye normalization select method = Rank Consistent probes, no spatial detrend method applied.
Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1  (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.

molecule: total RNA

organism: Homo sapiens

source_name: 66 pooled pancreatic tumors

label_protocol: RNA were labeled with Cy3-CTP or Cy5-CTP using the Quick-Amp Labeling Kit (Agilent) following manufacturer's instructions

extract_protocol: Total RNA extracted using Qiagen RNeasy Kit following manufacturer's protocol.

tag: reference

value: 66 pooled pancreatic tumors

tag: morphology

value: Tumor

tag: pdac

value: N

tag: rin


title: PancTuRef2 vs. 25244A


title: PancTuRef vs. HD1521

value: Y


title: PancTuRef vs. 4462-97


title: PancTuRef2 vs. 25132A


title: PancTuRef2 vs. 26531A


title: PancTuRef2 vs. 22462A


title: PancTuRef vs. HD1519


title: PancTuRef vs. 12464A


title: PancTuRef vs. HD222-1


title: PancTuRef2 vs. 26836A


title: OVDM1 cell line at late passage, technical rep 2

city: BETHESDA

first: Anna

last: Roschke

address: 37 Center Dr

institute: NCI-NIH

description: Gene expression data from OVDM1 cell line at late passage

hyb_protocol: Hybridization was performed following Affymetrix GeneChip 3'IVT Express Manual P/N 702646 Rev 6. For washing and staining Affymetrix GenChip Fluidics Station 450/240 User's Guide P/N 08-0092 Rev. G was followed.

scan_protocol: Scanning was done using the Affymetrix GeneChip Scanner 3000

data_processing: The data were  analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Data analysis was also performed using BRB-ArrayTools Version 4.3.0-Beta_3. Genes showing minimal variation across the set of arrays were excluded from the analysis. Genes whose expression differed by at least 1.5 fold from the median in at least 20% of the arrays were retained.

label: biotin

source_name: OVDM1 cell line at late passage

label_protocol: RNA amplification, fragmentation and labeling were performed following the Affymetrix GeneChip 3'IVT Express Manual P/N 702646 Rev 6

growth_protocol: The OVDM1 cell line was cultured in a medium of equal volumes of MCDB 105 Medium and Medium 199 (both Sigma-Aldrich, St. Louis, MO), heat inactivated FBS, 50 ug/ml of Gentamicin and 100X Antibiotic/Antimycotic (all Invitrogen/Life Technologies) were added to a final concentration of 5%, 50 ug/ml and 1X respecitvely. When close to confluence, cell were subcultured in a split ratio of 1 to 4.

extract_protocol: Total RNA was extracted utilizing the Qiagen miRNeasy MiniKit (Qiagen, Valencia, CA)

tag: cell line


title: PancTuRef vs. HD287-1


title: PancTuRef vs. HD257-1


title: PancTuRef vs. HD204-2


title: PancTuRef vs. HD197-1


title: PancTuRef vs. HD176-1


title: PancTuRef vs. 5679A


title: PancTuRef vs. HD188-1


title: PancTuRef vs. HD167-1


title: PancTuRef vs. 11461A


title: PancTuRef vs. HD162-1


title: PancTuRef vs. 25019A


title: PancTuRef vs. HD45-1


title: PancTuRef vs. HD58


title: PancTuRef vs. HD27-1


title: PancTuRef vs. HD1348-1

value: Normal


title: PancTuRef vs. HD22


title: PancTuRef vs. HD24-1


title: PancTuRef2 vs. HD427


title: PancTuRef2 vs. HD164

value: Pancreatitis


title: PancTuRef2 vs. HD49-1

value: Panreatitis


title: PancTuRef vs. HD46-1


title: PancTuRef vs. HD59-1


title: PancTuRef vs. 10942A


title: PancTuRef2 vs. HD804


title: PancTuRef2 vs. HD28-1


title: PancTuRef2 vs. HD202


title: PancCLRefMixB (30CL) vs. Hs700T

source_name: reference_mix: The reference mix contained equal amounts of 30 pancreatic cancer cell line

value: 30 pooled pancreatic cancer cell lines

source_name: pancreatic cancer cell lines


title: PancCLRefMixB (30CL) vs. HUPT4


title: PancTuRef vs. HD25-1


title: PancCLRefMixB (30CL) vs. HPAC

value: HPAC


title: PancCLRefMixB (30CL) vs. Hs766T


title: PancCLRefMixB (30CL) vs. Panc05.04


title: PancCLRefMixB (30CL) vs. DAN G

value: DAN G


title: PancCLRefMixB (30CL) vs. Panc04.03


title: PancCLRefMixC(30CL) vs. Capan-1(updated)


title: PancCLRefMixB (30CL) vs. Panc02.03


title: PancCLRefMixB (30CL) vs. MUT J

value: MUT J


title: PancCLRefMixC(30CL) vs. HPAF-2(updated)


title: PancCLRefMixB (30CL) vs. Panc03.27


title: PancCLRefMixB (30CL) vs. MIA PaCa-2

value: MIA PaCa-2


title: PancCLRefMixB (30CL) vs. HUPT3


title: PancCLRefMixB (30CL) vs. Capan-2


title: PancCLRefMixC(30CL) vs. CF PAC-1(updated)

value: CF PAC-1


title: PancCLRefMixB (30CL) vs. BxPC-3


title: PancCLRefMixB (30CL) vs. PATU 8902

value: PATU 8902


title: PancCLRefMixB (30CL) vs. PSN-1


title: PancCLRefMixB (30CL) vs. YAP-C

value: YAP-C


title: PancCLRefMixB (30CL) vs. Panc08.13


title: PancCLRefMixB (30CL) vs. PL-45


title: PancCLRefMixB (30CL) vs. PATU 8988T

value: PATU 8988T


title: PancCLRefMixB (30CL) vs. SW1990


title: PancCLRefMixB (30CL) vs. PANC-1


title: PancCLRefMixB (30CL) vs. AsPC-1


title: PancCLRefMixB (30CL) vs. PATU 8988S

value: PATU 8988S


title: imWilms10_P7

city: Duesseldorf

first: Brigitte

last: Royer-Pokora

address: Universitätsstr. 1

country: Germany

institute: Institute of Human Genetics and Anthropology, Heinrich-Heine-University Duesseldorf

hyb_protocol: 1.65 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 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x GE hybridization buffer HI- RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (4x 44K) 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) and air dried.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Scans were quantified using Agilent Feature Extraction Software (batch A: V10.7.1.1; batch B: V11.5.1.1) applying default parameters. Control spots were removed, replicate oligos averaged. Arrays were quantile normalized between chips using R-software (Limma).

source_name: Wilms10 tumor 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.

growth_protocol: Cells were cultivated in MCSG-medium (Lonza) at 37 degree and 5% CO2.  Medium was changed every third day.

extract_protocol: RNA was prepared using the RNAeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations, with an included on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Batch B: The cell culture of Wilsm10 was immortalized with telomerase (pBABE-hygro hTERT- from Addgene) and a triple mutant SV40 large T antigen (U19 del89-97tsA58). Both construct were transduced into Wilms10 cells using a  retroviral virus. After transduction the cells were cultured in G418 (selection for T-antigene; 200µg/ml)  for a week, followed with hygromycin (selection for telomerase; 20 µg/ml). In addition single cell clones were isolated and cultivated initially at 33 degree for maintenance of the temperature sensitive T-Antigene.

tag: tissue

value: kidney

tag: gender

value: female

tag: batch

value: B

value: immortalized tumor cell line of patient Wilms10


title: PancCLRefMixB (30CL) vs. SU.86.86


title: CHP134, CPX treated 24h, total RNA, bio.rep #2

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

description:
Total RNA sample extracted from CHP134 cells treated with 5 µM CPX for 24 hours.
cpx24.tot.2

hyb_protocol: Hybridization, blocking and washing were performed according to Agilent protocol: “One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling)”: (https://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-Color_v6.0.pdf).

scan_protocol: Hybridized microarray slides were scanned with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies, Santa Clara, CA) at 5 micron resolution with the manufacturer’s software (Agilent ScanControl 8.1.3). The scanned TIFF images were analyzed numerically using the Agilent Feature Extraction Software version 10.7.7.1 according to the Agilent standard protocol GE1_107_Sep09.

data_processing: The scanned TIFF images were analyzed numerically and the background corrected using the Agilent Feature Extraction Software version 10.7.7.1 according to the Agilent standard protocol GE1_107_Sep09. The output of Feature Extraction was analyzed with the R software environment for statistical computing (http://www.r-project.org/) and the Bioconductor library of biostatistical packages (http://www.bioconductor.org/). Signal intensities across arrays were normalized with the quantile normalization algorithm.

source_name: CHP134 cells, CPX treated, total RNA, biological replicate 2

growth_protocol: CHP134 cells were purchased from ECACC (Cat. No. 06122002). The cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium 1640 medium supplemented with 10% fetal bovine serum (FBS) and 2 mM glutamine at 37 °C in a humidified atmosphere of 5 % CO2.

extract_protocol: Total RNA was extracted using RNeasy Plus Mini kit (Qiagen) following the instructions of the supplier and eluted in 50 μl of water.

treatment_protocol: CHP134 cells growing in 10 cm cell culture dishes were treated with 5 µM CPX for 24 hours.

tag: disease

value: neuroblastoma

tag: agent (compound)

value: CPX

tag: rna fraction

value: total RNA

tag: biological replicate


title: CHP134, CPX treated 24h, polysomal RNA, bio.rep #2

description:
Polysomal RNA sample extracted from CHP134 cells treated with 5 µM CPX for 24 hours.
cpx24.poly.2

molecule: cytoplasmic RNA

source_name: CHP134 cells, CPX treated, polysomal RNA, biological replicate 2

extract_protocol: To extract polysomal RNA, the following procedure was applied. CHP134 cells were incubated with 100 μg/ml cycloheximide for 4 minutes, rinsed with phosphate buffer saline and lysed directly in cell-culture vessels [10 mM NaCl, 10 mM MgCl2, 10 mM Tris–HCl, pH 7.5, 1 % Triton X-100, 1 % sodium deoxycholate, 100 μg/ml cycloheximide, 0.2 U/μl RNase inhibitor, 1 mM DTT]. The lysate was collected with a cell scraper, pipetted into a microcentrifuge tube and after 5 minutes incubation on ice centrifuged for 10 min at 12000 g at 4 °C. The supernatant was transferred into a new microcentrifuge tube and stored at –80 °C. The lysates were fractionated by ultracentrifugation (Sorvall rotor, 100 min at 180000 g) through 15–50 % linear sucrose gradient containing 30 mM Tris–HCl, pH 7.5, 100 mM NaCl, 10 mM MgCl2.  Polysomal fractions were collected monitoring the absorbance at 254 nm. Polysomal RNA was isolated after proteinase K treatment, phenol–chloroform extraction and isopropanol precipitation and finally resuspended in 50 μl of water. RNA quality was assessed using the Agilent 2100 Bioanalyzer platform.

value: polysomal RNA


title: CHP134, CPX treated 24h, polysomal RNA, bio.rep #1

description:
Polysomal RNA sample extracted from CHP134 cells treated with 5 µM CPX for 24 hours.
cpx24.poly.1

source_name: CHP134 cells, CPX treated, polysomal RNA, biological replicate 1


title: CHP134, CPX treated 24h, total RNA, bio.rep #3

description:
Total RNA sample extracted from CHP134 cells treated with 5 µM CPX for 24 hours.
cpx24.tot.3

source_name: CHP134 cells, CPX treated, total RNA, biological replicate 3


title: imWilms10_P6


title: CHP134, untreated, total RNA, bio.rep #3

description:
Total RNA sample extracted from untreated CHP134 cells.
ctrl24.tot.3

source_name: CHP134 cells, untreated, total RNA, biological replicate 3

treatment_protocol: CHP134 cells growing in 10 cm cell culture dishes were treated with vehicle for 24 hours.

value: vehicle


title: PancCLRefMixB (30CL) vs. Panc10.05

value: 30 pooled pancreatic cancer cell lines


title: CHP134, untreated, polysomal RNA, bio.rep #2

description:
Polysomal RNA sample extracted from untreated CHP134 cells.
ctrl24.poly.2

source_name: CHP134 cells, untreated, polysomal RNA, biological replicate 2


title: CHP134, CPX treated 24h, polysomal RNA, bio.rep #3

description:
Polysomal RNA sample extracted from CHP134 cells treated with 5 µM CPX for 24 hours.
cpx24.poly.3

source_name: CHP134 cells, CPX treated, polysomal RNA, biological replicate 3


title: CHP134, CPX treated 24h, total RNA, bio.rep #1

description:
Total RNA sample extracted from CHP134 cells treated with 5 µM CPX for 24 hours.
cpx24.tot.1

source_name: CHP134 cells, CPX treated, total RNA, biological replicate 1


title: CHP134, untreated, polysomal RNA, bio.rep #3

description:
Polysomal RNA sample extracted from untreated CHP134 cells.
ctrl24.poly.3

source_name: CHP134 cells, untreated, polysomal RNA, biological replicate 3


title: CHP134, untreated, total RNA, bio.rep #1

description:
Total RNA sample extracted from untreated CHP134 cells.
ctrl24.tot.1

source_name: CHP134 cells, untreated, total RNA, biological replicate 1


title: CHP134, untreated, total RNA, bio.rep #2

description:
Total RNA sample extracted from untreated CHP134 cells.
ctrl24.tot.2

source_name: CHP134 cells, untreated, total RNA, biological replicate 2


title: CHP134, untreated, polysomal RNA, bio.rep #1

description:
Polysomal RNA sample extracted from untreated CHP134 cells.
ctrl24.poly.1

source_name: CHP134 cells, untreated, polysomal RNA, biological replicate 1


title: M1_macrophage_LDL_loaded

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridisation of 5.5ug labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Washing and staining of the arrays was done on a Affymetrix 450 fluidics stations using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Arrays where then scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using the RMA algorithm in the Bioconductor library 'Oligo' (v1.12). Only probesets that had evidence 'core' were included. (http://www.affymetrix.com/support/help/exon_glossary/index.affx)

source_name: blood monocytes treated with GM-CSF to obtain 'classically' activated macrophages, oxLDL -loaded

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA; P/N 900652) was used for the preparation of labelled cDNA from 100 ng of total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

growth_protocol: Blood was obtained from healthy volunteers by venipuncture and collected in EDTA Vacutainer tubes. Mononuclear cells were isolated by Ficoll-Paque (Pharmacia Biotech AB, Uppsala, Sweden) density-gradient centrifugation. Monocytes were isolated from mononuclear cells by adherence to plastic in 12-well cell culture clusters (Corning, NY, USA). No restrictions on the diet of the volunteers were imposed.

extract_protocol: Total RNA was prepared from cells using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Monocytes were differentiated into M1 and M2 macrophages by incubation with granulocyte-macrophage colony-stimulating factor (GM-CSF) or macrophage colony-stimulating factor (M-CSF)(100 ng/ml, R&D Systems, Minneapolis, MN, USA), respectively, for 5 days in RPMI 1640 culture medium supplemented with glutamine, gentamycine, pyruvate, and 10% fetal calf serum. To induce cellular accumulation of LDL, macrophages were incubated with oxidized LDL (50 μg/ml) for 24 hours. Accumulation of LDL was quantified by Oil-Red-O staining according to routine procedures and by measuring apolipoprotein B (apoB) in cell lysates by ELISA.

tag: cell type

value: blood monocytes

tag: treatment

value: gm-csf (100 ng/ml) for 5 days

value: male.


title: Bmi1 overexpression_replicate 2

city: Darmstadt

first: Ulrike

last: Nuber

address: Schnittspahnstrasse 13

institute: TU Darmstadt

scan_protocol: Scanning was performed according to the Affymetrix standard protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay User manual, P/N 701880 Rev.5)

data_processing: Microarray data was normalized by the Robust Multi-array Average (RMA) method using the Expression Console software.

organism: Mus musculus

source_name: empty vector neurosphere culture

label_protocol: 300 ng of total RNA was used for the first strand cDNA synthesis. Sample preparation and hybridization to Affymetrix Mouse Gene ST 1.0 arrays, washing, and scanning were performed according to the Affymetrix standard protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay User manual, P/N 701880 Rev.5)

growth_protocol: Lateral ventricle wall tissue was dissected from 4-6 week-old CD1 mice (Charles River), cells were dissociated with Accutase (PAA) and filtrated (cell strainer 50 µm, BD Biosciences). Single cells were plated in untreated flasks at a density of approximately 1x105 cells/mL and cultured at 37°C and 5% CO2 in NSP medium, containing DMEM/F12 (1:1) + GlutaMax (Invitrogen), B27 (1x), penicillin (100 units/mL), streptomycin (100 µg/mL, all from Invitrogen), HEPES (10 mM), Partricin (0.5 µg/mL, Biochrom), insulin (20 µg/mL, Sigma-Aldrich), EGF and FGF (both 20 µg/mL, PAN Biotech). For passaging, NSPs were dissociated after 7-9 days with Accutase, cell numbers were determined with a cell counter (CASY technology) and replated at 1x105 cells/mL. Transduced neurosphere cells used for microarrays were cultured under clonal density conditions (2000 cells per well, i.e. 1 cell/µL or 1-2 cells/cm2) in standard 6-well plates).

extract_protocol: Total RNA was extracted according to the manufacturer’s instructions using the AllPrep DNA/RNA kit (Qiagen). Concentration, purity and integrity of the RNA were assessed with the Agilent 2100 bioanalyzer with the RNA 6000 Nano LabChip® (Agilent Technologies).

treatment_protocol: Cells were transduced with a pCMMP-Bmi1 retroviral vector (test samples), or empty vector (control samples) and sorted by FACS based on eGFP expression.

tag: strain

tag: age

value: 4-6 week-old

value: materal ventricle wall tissue

tag: protocol

value: neural stem/progenitor cells were isolated from the lateral ventricle wall of 4-6 week-old CD1 mice and grown as neurospheres

tag: transduction

value: neurosphere cells transduced with a pCMMP-Bmi1 retroviral vector

tag: genotype/variation


title: Bmi1 overexpression_replicate 1

hyb_protocol: Sample preparation and hybridization to Affymetrix Mouse Gene ST 1.0 arrays, washing, and scanning were performed according to the Affymetrix standard protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay User manual, P/N 701880 Rev.5)


title: Empty vector control_replicate 2

source_name: Bmi1-overexpressing neurosphere culture

value: neurosphere cells transduced with empty vector

value: control


title: Empty vector control_replicate 3


title: Empty vector control_replicate 1


title: M2_macrophage_LDL_loaded

source_name: blood monocytes treated with M-CSF to obtain 'alternatively' activated macrophages, oxLDL -loaded

value: m-csf (100 ng/ml) for 5 days


title: Bmi1 overexpression_replicate 3


title: Input_KO3

city: Illkirch

first: Herve

middle: M

last: Moine

address: 1 rue Laurent Fries

department: Translational medicine and neurogentics

country: France

institute: CNRS

hyb_protocol: Following fragmentation and end-labelling, 2.07 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix).

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: CEL files were processed with Affymetrix Expression Console software version 1.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

source_name: KO-Fmr1 Input mouse neuronal RNA

label_protocol: CLIP and Input RNAs were used to prepare biotinylated double strand cDNA targets with the NuGEN Ovation Pico WTA System V2 Kit followed by the NuGEN Encore Biotin Module Kit  using the Affymetrix Mouse Exon 1.0 ST platform.

growth_protocol: Cortical neurons from E17 mouse embryos (C57Bl6 genetic background) were grown for 8 DIV prior 254 nm UV treatment to induce crosslink prior collection and cell lysis.

extract_protocol: RNAs were extracted by phenol/chloroform (V/V) followed by chloroform/isoamyl alcohol (24:1) extraction and ethanol precipitated in presence of 0.3M Na acetate.

value: cortical primary neuron

tag: assayed molecule


title: Input_KO5


title: Input_WT4

source_name: WT Input mouse neuronal RNA


title: CLIP_Wt5

source_name: WT CLIP mouse neuronal RNA

value: CLIP RNA


title: Input_KO2


title: CLIP_KO4

source_name: KO-Fmr1 CLIP mouse neuronal RNA


title: Input_KO1


title: CLIP_Wt3


title: Input_WT3


title: CLIP_KO5


title: CLIP_Wt2


title: CLIP_Wt1


title: CLIP_KO3


title: Input_WT5


title: Input_WT1


title: CLIP_Wt4


title: Input_KO4


title: Input_WT2


title: CLIP_KO1


title: WT_P2_male_2

city: Geneva

first: Gianpaolo

last: Rando

state: GE

address: 30, quai Ernest-Ansermet

department: Molecular Biology

country: Switzerland

institute: University of Geneva

hyb_protocol: Affymetrix Mouse Gene 1.0 ST arrays were hybridized with 5 microgramme of labeled, amplified cDNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

source_name: whole liver from P2 suckling pups, PPARa +/+

label_protocol: 100 ng RNA was used to perform target preparation using the Whole Transcript Sense Target Labeling Protocol procedure (Affymetrix, High Wycombe, UK).

growth_protocol: Male and female PPARa (+/-) heterozygous mice were mated to obtain in the same litter PPARa (+/+) and (-/-) pups. This breeding scheme was chosen to have a similar uterine and lactation environment for WT and KO pups.

extract_protocol: RNA from whole livers was isolated with 500 microliters of TRIzol reagent (Invitrogen) following manufacturer's protocol and the acqueous phase was purified with silica columns (Qiagen RNeasy) following manufacturer's instructions.  RNA concentration and purity was measured by NanoDrop-ND-1000 spectrophotometer and the integrity of RNA was controlled on Aligent 2100 bioanalyzer chips. Only RNAs with RIN number >8 were used for labeling.

treatment_protocol: Suckling pups were killed two days after birth (P2). To control for milk access availability, only litters of 6-8 pups were used.

value: whole liver

tag: developmental stage

value: P2 suckling pups

value: PPARa +/+

tag: Sex

value: male


title: WT_P2_male_3

tag: tissue


title: WT_P2_male_1


title: WT_P2_female_9

value: female


title: KO_P2_male_5

source_name: whole liver from P2 suckling pups, PPARa -/-

value: PPARa -/-


title: KO_P2_male_6


title: WT_P2_female_7


title: WT_P2_female_8


title: WT_E19.5_mouse6

source_name: whole liver from E19.5 fetus, PPARa +/+

growth_protocol: One male and one female PPARa (+/-) heterozygous SV129 mice were mated to obtain in the same litter PPARa (+/+) and (-/-) fetuses. This breeding scheme was chosen to have a similar uterine environment for WT and KO fetuses.

treatment_protocol: Mouse fetuses were obtained from the mother at the last day of pregnancy (E19.5, cesarean section) or two days after birth (P2). To control for milk access availability, only litters of 6-8 pups were used.

value: E19.5 fetus


title: KO_P2_female_12


title: KO_P2_female_10


title: KO_P2_female_11


title: WT_E19.5_mouse4


title: WT_E19.5_mouse3


title: WT_E19.5_mouse2


title: WT_E19.5_mouse5


title: KO_E19.5_mouse5

source_name: whole liver from E19.5 fetus, PPARa -/-


title: KO_P2_male_4


title: KO_E19.5_mouse6


title: KO_E19.5_mouse4


title: WT_E19.5_mouse1


title: matUPD17_sample2

type: genomic

city: New York City

first: Ricky

middle: Shantilal

last: Joshi

state: NY

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner protocol

data_processing: The methylation value was set to null for probes with a detection p-value >0.01. Probe sequences (50-mer oligonucleotides) were uniquely mapped to the reference human genome hg18 (NCBI36) using BLAT, allowing up to 2 mismatches and 1 gap. Beta values from the autosomal probes were quantile normalized using lumi package in R.

label: Cy3, Cy5

molecule: genomic DNA

source_name: Maternal Uniparental Disomy for chromosome 17

label_protocol: Standard Illumina labelling protocol

extract_protocol: All samples were identified and obtained from collaborating clinical genetics laboratories. As these samples were provided by many different contributors, it is likely that the DNA extraction protocols varies among samples.

tag: disease status

value: Peripheral Blood

tag: gender

value: Male


title: CLIP_KO2


title: KO_E19.5_mouse3


title: patUPD8_sample2

source_name: Paternal Uniparental Disomy for chromosome 8

value: Female


title: CHM_sample3

source_name: Complete Hydatidiform Mole

value: Complete Hydatidiform Mole


title: KO_E19.5_mouse1


title: ki2

city: Singapore

last: Brichkina

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation

source_name: lung firbroblasts

label_protocol: Biotinylated cRNA were prepared with the Illumina totalPrep-96 RNA Amplification Kit

growth_protocol: fibroblasts were cultured in DMEM/F12 supplemented with 15% FCS, used for the array at passage 1

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: p38ki/ki (ki)

value: lung fibroblasts

value: 10 weeks


title: matUPD8_sample2

source_name: Maternal Uniparental Disomy for chromosome 8


title: CHM_sample4


title: wt2

description: replicate 2


title: OT_sample4

source_name: Ovarian Teratoma

value: Ovarian Teratoma


title: ki3

description: replicate 3


title: CHM_sample2


title: wt3

description: replicate 3


title: ki1

description: replicate 1


title: OT_sample2


title: KO_E19.5_mouse2


title: wt1

description: replicate 1


title: Monocytes from a premonopausal low BMD woman (L-GE-88M.CEL)

city: New Orleans

first: Yao-Zhong

last: Liu

state: LA

address: 1440 Canal Street, Suite 2001

department: Dept. of Biostatistics and Bioinformatics

institute: Tulane University School of Public Health

hyb_protocol: Preparation of cDNA, hybridization, and scanning of the Affymetrix HG-133A arrays was performed according to the manufacturer's protocol for the HG-133A arrays (Affymetrix, Santa Clara, CA).

data_processing: we used RMA (robust multiarray average) method to normalize the array signals and analyzed differential expression analysis through the Altanalyze software.

source_name: monocytes

extract_protocol: Total RNA from monocytes was extracted using Qiagen RNeasy Mini kit (Qiagen, Inc., Valencia, CA). We used Agilent Bioanalyzer (Agilent, Santa Clara, CA) to control the RNA quality before each array experimant, where RNA integrity number (RIN) should be no less than 7.0.

treatment_protocol: Monocyte isolation from whole blood was performed with a monocyte-negative isolation kit (Miltenyi Biotec Inc, Auburn, CA) following manufacturer's recommandation.

tag: bone mineral density

value: low BMD

tag: state

value: premenopausal

value: monocytes


title: patUPD2_sample3

source_name: Paternal Uniparental Disomy for chromosome 2


title: patUPD7_sample1

source_name: Paternal Uniparental Disomy for chromosome 7


title: matUPD7_sample2

source_name: Maternal Uniparental Disomy for chromosome 7


title: Monocytes from a premonopausal low BMD woman (L-GE-86M.CEL)

scan_protocol: Preparation of cDNA, hybridization, and scanning of the Affymetrix HG-133A arrays was performed according to the manufacturer's protocol for the HG-133A arrays (Affymetrix, Santa Clara, CA).


title: OT_sample3


title: matUPD15_sample4

source_name: Maternal Uniparental Disomy for chromosome 15


title: matUPD20_sample4

source_name: Maternal Uniparental Disomy for chromosome 20


title: Monocytes from a premonopausal low BMD woman (L-GE-84M.CEL)

label_protocol: Preparation of cDNA, hybridization, and scanning of the Affymetrix HG-133A arrays was performed according to the manufacturer's protocol for the HG-133A arrays (Affymetrix, Santa Clara, CA).


title: CHM_sample1


title: matUPD14_sample1

source_name: Maternal Uniparental Disomy for chromosome 14


title: matUPD16_sample4

source_name: Maternal Uniparental Disomy for chromosome 16


title: Monocytes from a premonopausal low BMD woman (L-GE-83M.CEL)


title: Monocytes from a premonopausal low BMD woman (L-GE-75M.CEL)


title: Monocytes from a premonopausal low BMD woman (L-GE-76M.CEL)


title: OT_sample1


title: Monocytes from a premonopausal low BMD woman (L-GE-89M.CEL)


title: Monocytes from a postmonopausal low BMD woman (L-GE-72M.CEL)

value: postmenopausal


title: Monocytes from a premonopausal low BMD woman (L-GE-70M.CEL)


title: patUPD7_sample2

value: Paternal Uniparental Disomy for chromosome 7


title: Monocytes from a postmonopausal low BMD woman (L-GE-67M.CEL)


title: matUPD15_sample3

value: Maternal Uniparental Disomy for chromosome 15


title: Monocytes from a postmonopausal low BMD woman (L-GE-66M.CEL)


title: matUPD15_sample2


title: Monocytes from a postmonopausal low BMD woman (L-GE-64M.CEL)


title: Monocytes from a postmonopausal low BMD woman (L-GE-63M.CEL)


title: Monocytes from a postmonopausal low BMD woman (L-GE-69M.CEL)


title: Monocytes from a premonopausal low BMD woman (L-GE-61M.CEL)


title: Monocytes from a postmonopausal low BMD woman (L-GE-62M.CEL)


title: matUPD20_sample3

value: Maternal Uniparental Disomy for chromosome 20


title: patUPD6_sample3

source_name: Paternal Uniparental Disomy for chromosome 6


title: matUPD22_sample1

source_name: Maternal Uniparental Disomy for chromosome 22


title: matUPD14_sample2

value: Maternal Uniparental Disomy for chromosome 14


title: Monocytes from a premonopausal low BMD woman (L-GE-58M.CEL)


title: matUPD7_sample1

value: Maternal Uniparental Disomy for chromosome 7


title: UPD3_sample2

source_name: Uniparental Disomy for chromosome 3

value: Uniparental Disomy for chromosome 3

value: Peripheral Blood


title: Monocytes from a premonopausal low BMD woman (L-GE-60M.CEL)

value: Female


title: matUPD12_sample1

source_name: Maternal Uniparental Disomy for chromosome 12


title: Monocytes from a premonopausal low BMD woman (L-GE-57M.CEL)


title: UPD9_sample2

source_name: Uniparental Disomy for chromosome 9

value: Uniparental Disomy for chromosome 9

value: Male


title: Monocytes from a postmonopausal low BMD woman (L-GE-56M.CEL)


title: patUPD9_sample1

source_name: Paternal Uniparental Disomy for chromosome 9


title: Monocytes from a postmonopausal low BMD woman (L-GE-52M.CEL)


title: Monocytes from a premonopausal low BMD woman (L-GE-54M.CEL)


title: Monocytes from a postmonopausal low BMD woman (L-GE-51M.CEL)


title: patUPD4_sample2

source_name: Paternal Uniparental Disomy for chromosome 4


title: Monocytes from a postmonopausal low BMD woman (L-GE-50M.CEL)


title: patUPD15_sample3

source_name: Paternal Uniparental Disomy for chromosome 15


title: Monocytes from a postmonopausal low BMD woman (L-GE-48M.CEL)


title: UPD3_sample3


title: patUPD6_sample2

value: Paternal Uniparental Disomy for chromosome 6


title: matUPD8_sample1

source_name: Maternal Uniparental Disomy for chromosome 8


title: patUPD15_sample4

value: Paternal Uniparental Disomy for chromosome 15


title: matUPD17_sample1

source_name: Maternal Uniparental Disomy for chromosome 17


title: Monocytes from a premonopausal low BMD woman (L-GE-46M.CEL)

source_name: monocytes


title: Monocytes from a premonopausal low BMD woman (L-GE-49M.CEL)


title: matUPD4_sample1

source_name: Maternal Uniparental Disomy for chromosome 4


title: Monocytes from a postmonopausal low BMD woman (L-GE-43M.CEL)


title: Monocytes from a premonopausal low BMD woman (L-GE-41M.CEL)


title: Monocytes from a premonopausal low BMD woman (L-GE-44M.CEL)


title: Monocytes from a postmonopausal low BMD woman (L-GE-40M.CEL)


title: Monocytes from a premonopausal low BMD woman (L-GE-39M.CEL)


title: patUPD13_sample1

source_name: Paternal Uniparental Disomy for chromosome 13


title: patUPD4_sample1

value: Paternal Uniparental Disomy for chromosome 4


title: patUPD5_sample1

source_name: Paternal Uniparental Disomy for chromosome 5


title: Monocytes from a postmonopausal low BMD woman (L-GE-37M.CEL)

value: low BMD


title: patUPD6_sample1


title: matUPD20_sample2

source_name: Maternal Uniparental Disomy for chromosome 20


title: Monocytes from a postmonopausal low BMD woman (L-GE-35M.CEL)


title: Monocytes from a postmonopausal low BMD woman (L-GE-32M.CEL)


title: Monocytes from a premonopausal low BMD woman (L-GE-36M.CEL)

value: premenopausal


title: Monocytes from a postmonopausal low BMD woman (L-GE-38M.CEL)

value: monocytes


title: matUPD2_sample1

source_name: Maternal Uniparental Disomy for chromosome 2


title: Monocytes from a postmonopausal low BMD woman (L-GE-31M.CEL)

value: postmenopausal


title: Monocytes from a postmonopausal low BMD woman (L-GE-25M.CEL)


title: matUPD13_sample1

source_name: Maternal Uniparental Disomy for chromosome 13


title: patUPD2_sample1

source_name: Paternal Uniparental Disomy for chromosome 2


title: Monocytes from a premonopausal low BMD woman (L-GE-21M.CEL)


title: Monocytes from a premonopausal high BMD woman (H-GE-85M.CEL)

value: high BMD


title: patUPD8_sample1

source_name: Paternal Uniparental Disomy for chromosome 8


title: patUPD2_sample2

value: Paternal Uniparental Disomy for chromosome 2


title: matUPD20_sample1

value: Maternal Uniparental Disomy for chromosome 20


title: matUPD16_sample2

source_name: Maternal Uniparental Disomy for chromosome 16


title: Monocytes from a premonopausal high BMD woman (H-GE-81M.CEL)


title: Monocytes from a premonopausal high BMD woman (H-GE-79M.CEL)


title: Monocytes from a postmonopausal high BMD woman (H-GE-80M.CEL)


title: patUPD1_sample2

source_name: Paternal Uniparental Disomy for chromosome 1


title: 45,X_mat_sample2

source_name: Turner syndrome 45,X (Maternal)

value: Turner syndrome 45,X (Maternal)


title: matUPD16_sample1

value: Maternal Uniparental Disomy for chromosome 16


title: Monocytes from a premonopausal high BMD woman (H-GE-78M.CEL)


title: 563351A02 - NF_NAA_RB4 vs NAA_RB4

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: We would like to know how symbiotic molecules such as Nod Factors (NF) influence lateral root (LR) development in M. truncatula. We have preliminary evidence that this action is through early stages of root development. Auxin is the major phytohormone controlling LR development and we also have evidence that NF interfere with auxin for the control of LR development. This transcriptomic study aims at finding new molecular targets that would be responsive to auxin and NF treatment, even at a higher level by the combination of both auxin and NF. Such targets could be involved in the control or early development stages of LR that would be controlled both by auxin and NF treatment.

hyb_protocol: NAA_RB4 Cy5 / NF_NAA_RB4 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Medicago truncatula

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: roots - Grown on M medium gelified with Phytagel (4 g/L) (as described in Olah et al., PJournal, 2005)), 21 °C with a 16h light/8h dark period.

treatment_protocol: Name:NAA - compound based treatment - compound addition,naa:quantity 1uM time 10hour . Sample_Treated name (name of the treatment to apply at this sample): 10-6M NAA Reference protocol or description Sample treatment protocol : -2 day old M. truncatula (accession A17) plantlets grown on M medium were transferred for 2 days on M medium+ 10-5M NPA (1-N-Naphthylphthalamic acid, auxin transport inhibitor) then transferred for 10 h on M medium containing 10-6M NAA

tag: cultivar

tag: harvest date

treatment_protocol: Name:NAA_NF - compound based treatment - compound addition,naa_nf:quantity 1.1uM time 10hour . Sample_Treated name (name of the treatment to apply at this sample): NF 10-7 M + NAA 10-6 M -2 day old M. truncatula (accession A17) plantlets grown on M medium were transferred for 2 days on M medium+ 10-5M NPA (1-N-Naphthylphthalamic acid, auxin transport inhibitor) then transferred for 10 h on M medium containing NF 10-7M + NAA 10-6M.


title: matUPD6_sample1

source_name: Maternal Uniparental Disomy for chromosome 6


title: 45,X_pat_sample1

source_name: Turner syndrome 45,X (Paternal)

value: Turner syndrome 45,X (Paternal)


title: Monocytes from a premonopausal high BMD woman (H-GE-77M.CEL)

tag: cell type


title: 557332A10 - NF_NAA_RB5 vs CTRL_RB5

hyb_protocol: CTRL_RB5 Cy5 / NF_NAA_RB5 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)

treatment_protocol: Name:SOLVENT - compound based treatment - compound addition,solvent:time 10hour . Sample_Treated name (name of the treatment to apply at this sample): solvent only ( 50% acetonitrile + NAA solvent) Reference protocol or description Sample treatment protocol : -2 day old M. truncatula (accession A17) plantlets grown on M medium were transferred for 2 days on M medium+ 10-5M NPA (1-N-Naphthylphthalamic acid, auxin transport inhibitor) then transferred for 10 h on M medium containing equivalent quantity of solvent for NF 10-7M + NAA 10-6M.

tag: treatment


title: patUPD15_patUPD21_sample1

source_name: Paternal Uniparental Disomy for chromosome 15 and 21

value: Peripheral Blood


title: matUPD9_sample1

source_name: Maternal Uniparental Disomy for chromosome 9

value: Female


title: matUPD3_sample1

source_name: Maternal Uniparental Disomy for chromosome 3


title: 563351A01 - NAA_RB4 vs NF_NAA_RB4

hyb_protocol: NF_NAA_RB4 Cy5 / NAA_RB4 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Monocytes from a premonopausal high BMD woman (H-GE-73M.CEL)

source_name: monocytes


title: Monocytes from a premonopausal high BMD woman (H-GE-82M.CEL)


title: Monocytes from a premonopausal high BMD woman (H-GE-71M.CEL)


title: Monocytes from a premonopausal high BMD woman (H-GE-74M.CEL)


title: 45,X_pat_sample2


title: 557332A09 - CTRL_RB5 vs NF_NAA_RB5

hyb_protocol: NF_NAA_RB5 Cy5 / CTRL_RB5 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 557332A07 - CTRL_RB5 vs NAA_RB5

hyb_protocol: NAA_RB5 Cy5 / CTRL_RB5 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 557332A08 - NAA_RB5 vs CTRL_RB5

hyb_protocol: CTRL_RB5 Cy5 / NAA_RB5 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 45,X_mat_sample1


title: Monocytes from a postmonopausal high BMD woman (H-GE-65M.CEL)


title: Monocytes from a postmonopausal high BMD woman (H-GE-59M.CEL)


title: patUPD14_sample2

source_name: Paternal Uniparental Disomy for chromosome 14


title: patUPD1_sample1

value: Paternal Uniparental Disomy for chromosome 1


title: Monocytes from a premonopausal high BMD woman (H-GE-68M.CEL)


title: matUPD15_sample1

source_name: Maternal Uniparental Disomy for chromosome 15

value: Male


title: Monocytes from a postmonopausal high BMD woman (H-GE-55M.CEL)


title: Monocytes from a postmonopausal high BMD woman (H-GE-53M.CEL)


title: Monocytes from a postmonopausal high BMD woman (H-GE-47M.CEL)


title: 557332A06 - NAA_RB3 vs CTRL_RB3

hyb_protocol: CTRL_RB3 Cy5 / NAA_RB3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 557332A03 - CTRL_RB4 vs NF_RB4

hyb_protocol: NF_RB4 Cy5 / CTRL_RB4 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)

treatment_protocol: Name:NF - compound based treatment - compound addition,nf:quantity 0.1uM time 10hour . Sample_Treated name (name of the treatment to apply at this sample): 10-7M NF -2 day old M. truncatula (accession A17) plantlets grown on M medium were transferred for 2 days on M medium+ 10-5M NPA (1-N-Naphthylphthalamic acid, auxin transport inhibitor) then transferred for 10 h on M medium containing 10-7M NF


title: 557332A01 - CTRL_RB3 vs NF_RB3

hyb_protocol: NF_RB3 Cy5 / CTRL_RB3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Monocytes from a postmonopausal high BMD woman (H-GE-45M.CEL)


title: 557332A04 - NF_RB4 vs CTRL_RB4

hyb_protocol: CTRL_RB4 Cy5 / NF_RB4 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Monocytes from a postmonopausal high BMD woman (H-GE-42M.CEL)


title: Monocytes from a postmonopausal high BMD woman (H-GE-34M.CEL)


title: matUPD16_sample3


title: patUPD14_sample1

value: Paternal Uniparental Disomy for chromosome 14


title: patUPD15_sample1

source_name: Paternal Uniparental Disomy for chromosome 15


title: 557269A12 - NF_NAA_RB5 vs NAA_RB5

hyb_protocol: NAA_RB5 Cy5 / NF_NAA_RB5 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 557332A02 - NF_RB3 vs CTRL_RB3

hyb_protocol: CTRL_RB3 Cy5 / NF_RB3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 557269A09 - CTRL_RB5 vs NF_RB5

hyb_protocol: NF_RB5 Cy5 / CTRL_RB5 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 557269A10 - NF_RB5 vs CTRL_RB5

hyb_protocol: CTRL_RB5 Cy5 / NF_RB5 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Monocytes from a premonopausal high BMD woman (H-GE-30M.CEL)


title: Monocytes from a premonopausal high BMD woman (H-GE-29M.CEL)


title: Monocytes from a premonopausal high BMD woman (H-GE-28M.CEL)


title: Monocytes from a postmonopausal high BMD woman (H-GE-26M.CEL)


title: Monocytes from a premonopausal high BMD woman (H-GE-27M.CEL)


title: Monocytes from a premonopausal high BMD woman (H-GE-33M.CEL)


title: Monocytes from a postmonopausal high BMD woman (H-GE-20M.CEL)


title: Monocytes from a premonopausal high BMD woman (H-GE-24M.CEL)


title: Monocytes from a premonopausal high BMD woman (H-GE-15M.CEL)


title: Monocytes from a postmonopausal high BMD woman (H-GE-23M.CEL)


title: Monocytes from a premonopausal high BMD woman (H-GE-17M.CEL)


title: Monocytes from a postmonopausal high BMD woman (H-GE-13M.CEL)


title: Monocytes from a premonopausal high BMD woman (H-GE-19M.CEL)


title: 557269A11 - NAA_RB5 vs NF_NAA_RB5

hyb_protocol: NF_NAA_RB5 Cy5 / NAA_RB5 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 557269A06 - NAA_RB4 vs CTRL_RB4

hyb_protocol: CTRL_RB4 Cy5 / NAA_RB4 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Monocytes from a postmonopausal high BMD woman (H-GE-11M.CEL)

hyb_protocol: Preparation of cDNA, hybridization, and scanning of the Affymetrix HG-133A arrays was performed according to the manufacturer's protocol for the HG-133A arrays (Affymetrix, Santa Clara, CA).


title: 557269A03 - NAA_RB3 vs NF_NAA_RB3

hyb_protocol: NF_NAA_RB3 Cy5 / NAA_RB3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 557269A04 - NF_NAA_RB3 vs NAA_RB3

hyb_protocol: NAA_RB3 Cy5 / NF_NAA_RB3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 557269A08 - NF_NAA_RB4 vs CTRL_RB4

hyb_protocol: CTRL_RB4 Cy5 / NF_NAA_RB4 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Monocytes from a postmonopausal high BMD woman (H-GE-10M.CEL)


title: 557269A01 - CTRL_RB3 vs NF_NAA_RB3

hyb_protocol: NF_NAA_RB3 Cy5 / CTRL_RB3 Cy3 : 30mmol. (Hyb_Scan_Nimb_GEO.doc)


title: Monocytes from a premonopausal high BMD woman (H-GE-22M.CEL)


title: 557269A07 - CTRL_RB4 vs NF_NAA_RB4

hyb_protocol: NF_NAA_RB4 Cy5 / CTRL_RB4 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 557269A05 - CTRL_RB4 vs NAA_RB4

hyb_protocol: NAA_RB4 Cy5 / CTRL_RB4 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Monocytes from a postmonopausal high BMD woman (H-GE-18M.CEL)


title: Monocytes from a postmonopausal high BMD woman (H-GE-07M.CEL)


title: Beas-P40, biological rep3

city: Beijing

first: Caixia

last: Guo

address: No.10 Xitoutiao, You An Men

country: China

institute: Capital Medical University

description: Gene expression data from Beas-P40 cells as control

hyb_protocol: Following labeling, 5.5 μg of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 2.0 in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

source_name: The passage-matched control Beas-2B cells without amorphous silica nanoparticles treatment

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion® WT Expression Kit. WT Expression Kit

growth_protocol: Human lung epithelial cells, Beas-2B were obtained from the Cell Resource Center, Shanghai Institutes for Biological Sciences, PRC. Cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) medium (Invitrogen, USA) supplemented with 10% fetal bovine serum (Invitrogen, USA) at 37°C in a 5% CO2 humidified incubator.

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

treatment_protocol: 1×106 Beas-2B cells were seeded into 10-cm (diameter) dishes for 24 hours and maintained in 5 μg/mL amorphous silica nanoparticles for 48 hours per passage. This process was continued for about 18 weeks (40 passages). Passage-matched cells without amorphous silica nanoparticles treatment were used as control.

tag: cell line


title: Monocytes from a postmonopausal high BMD woman (H-GE-01M.CEL)


title: 557269A02 - NF_NAA_RB3 vs CTRL_RB3

hyb_protocol: CTRL_RB3 Cy5 / NF_NAA_RB3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Monocytes from a postmonopausal high BMD woman (H-GE-06M.CEL)


title: Beas-P40, biological rep2


title: 557332A05 - CTRL_RB3 vs NAA_RB3

hyb_protocol: NAA_RB3 Cy5 / CTRL_RB3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Monocytes from a postmonopausal high BMD woman (H-GE-04M.CEL)


title: Cancer stem-like cells from CMT-U27 cacner cell line - single culture

city: Warsaw

first: Magdalena

last: Król

address: Nowoursynowska 159

department: Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

description: Biological replicate of CMT-U27-CSC

hyb_protocol: The hybridization was performed with custom AMADID microarrays (Agilent, USA) using the mRNA Complete Labeling and Hyb Kit (Agilent, USA) according to the manufacturer's protocol.

scan_protocol: Acquisition and analysis of hybridization intensities were performed using a DNA microarray scanner (Agilent).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Canis lupus familiaris

source_name: CMT-U27 - CSC

label_protocol: The miRNA Complete Labeling and Hyb Kit (Agilent, USA) was used according to the manufacturer's recommendations.

growth_protocol: Cells were cultured in optimal conditions: a medium (RPMI-1640) enriched with 10% (v/v) heat-inactivated fetal bovine serum (FBS), penicillin-streptomycin (50 iU mL-1), and fungizone (2.5 mg mL-1) (reagents obtained from Sigma Aldrich, USA) in an atmosphere of 5% CO2 and 95% humidified air at 37Â°C, and were routinely subcultured every second day.

extract_protocol: The total RNA from the samples was isolated using a Total RNA kit (A&A Biotechnology, Poland) according to the manufacturer's protocol.

treatment_protocol: Two canine mammary cancer cell lines (CMT-U27 and P114) were stained using  anti-Sca1 (stem cell antigen 1), anti-EpCAM (Epithelial cell adhesion molecule)  and anti-CD44 antibody. The FACS analysis showed 0,02-0,05% of Sca1+/EpCAM+/CD44+ in each of the cell line. Cancer stem-like cells were collected using FACS Aria II then  co-cultured with tumor associated macrophages and used for further analysis of gene expression.

tag: age

value: day 3

source_name: CMT-U27 - CSC - coculture with macrophages


title: BeasSiNPs-P40, biological rep1

description: Gene expression data from BeasSiNPs-P40 cells

source_name: Beas-2B cells treated with 5 μg/mL amorphous silica nanoparticles for 40 passages


title: BeasSiNPs-P40, biological rep3


title: BeasSiNPs-P40, biological rep2


title: Cancer stem-like cells from P114 cacner cell line - single culture

description: Biological replicate of P114-CSC

source_name: P114 - CSC

source_name: P114 - CSC - coculture with macrophages


title: SLE patient with lupus nephritis-12

city: Dallas

first: yun

last: lian

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description:
9703627076_J
replicate 12

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation with Genespring software

source_name: peripheral blood mononuclear cell

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

extract_protocol: Total RNA was isolated from PBMC by standard phenol–chloroform extraction using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA) according to the manufacturer's instructions.

value: blood


title: SLE patient with lupus nephritis-15

description:
9703627070_B
replicate 15


title: SLE patient with lupus nephritis-14

description:
9703627071_K
replicate 14


title: SLE patient with lupus nephritis-13

description:
9703627057_K
replicate 13


title: Coculture of cancer stem-like cells from CMT-U27 cacner cell line cocultured with macrophages

description: Biological replicate of CMT-U27-CSC


title: SLE patient with lupus nephritis-11

description:
9703627076_G
replicate 11


title: SLE patient with lupus nephritis-10

description:
9703627076_F
replicate 10


title: Coculture of cancer stem-like cells from P114 cacner cell line cocultured with macrophages

description: Biological replicate of P114-CSC


title: SLE patient with lupus nephritis-09

description:
9703627071_D
replicate 9


title: SLE patient with lupus nephritis-06

description:
9703627057_D
replicate 6


title: SLE patient with lupus nephritis-03

description:
9461595024_L
replicate 3


title: SLE patient with lupus nephritis-08

description:
9482861018_L
replicate 8


title: Lockd knockout, rep 4

city: Philadelphia

first: Vikram

last: Paralkar

state: PA

address: 3400 Civic Center Boulevard, Perelman Center, 7th Floor, South Pavilion Extension

institute: University of Pennsylvania

hyb_protocol: Samples were hybridized with GeneChip Mogene 2.0 ST Arrays (Affymetrix) and scanned at the University of Pennsylvania Molecular Profiling Facility

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Raw data were normalized useing RMA algorithm (rma-gene-full option). Data analysis and statistical evaluations were performed with customized Matlab scripts (R2012b)
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

source_name: G1E_Lockd deletion

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Cells were grown in G1E media as described previously (Weiss et al, MCB 1997)

extract_protocol: RNA was isolated from cultured cells using the Qiagen Rneasy kit

treatment_protocol: CRISPR/Cas9 was used to delete Lockd

tag: cell line background

value: erythroid cell line

value: Lockd deletion


title: SLE patient with lupus nephritis-05

description:
9703627076_D
replicate 5


title: SLE patient with lupus nephritis-07

description:
9482861018_K
replicate 7


title: SLE patient with lupus nephritis-04

description:
9703627076_A
replicate 4


title: Lockd knockout, rep 2


title: Lockd knockout, rep 1


title: SLE patient with lupus nephritis-02

description:
9461595024_I
replicate 2


title: Lockd Control, rep 3

source_name: G1E_Lockd control

value: Lockd WT


title: Lockd knockout, rep 3


title: SLE patient-15

description:
9703627070_C
replicate 15


title: Lockd Control, rep 1


title: Lockd Control, rep 2


title: SLE patient with lupus nephritis-01

description:
9461595024_G
replicate 1


title: SLE patient-13

description:
9703627071_H
replicate 13


title: Breast tumor tissue 38

city: Uppsala

first: Ananya

last: Roy

address: Dag Hammarskjöldsväg

country: Sweden

institute: Uppsala University

description: Mus 38

hyb_protocol: GeneChip® ST Arrays ( GeneChip® Mouse Gene 2.0 ST Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm as per Affymetrix GeneChip® WT Terminal Labeling and Hybridization User Manual (P/N 702808 Rev. 6, Affymetrix Inc., Santa Clara, CA).According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev 3, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G.

scan_protocol: GeneChip® Scanner 3000 7G

data_processing:
The raw data was normalized in the free software Expression Console provided by Affymetrix (http://www.affymetrix.com) using the robust multi-array average (RMA) method first suggested by Li and Wong in 2001. Subsequent analysis of the gene expression data was carried out in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project (www.bioconductor.org). In order to search for the differentially expressed genes between X and the Y groups an empirical Bayes moderated t-test was then applied, using the ‘limma’ package. To address the problem with multiple testing, the p-values were adjusted using the method of Benjamini and Hochberg.
MoGene-2_0-st.rma-gene-full.chp
Raw data was normalized in the free software Expression Console provided by Affymetrix (http://www.affymetrix.com) using the robust multi-array average (RMA) method first suggested by Li and Wong.To address the problem with multiple testing, the p-values were adjusted using the method of Benjamini and Hochberg .

source_name: PyMT+ SG-/-

label_protocol: 250 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the Ambion WT Expression Kit( P/N 4425209 Rev C 09/2009)

growth_protocol: Breast tumour tissue snap freezed in liquid nitrogen

extract_protocol: All samples were snap frozen in liquid N2 and genotyped. Trizol RNA extraction, RNA concentration was measured with ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and RNA quality was evaluated using the Agilent 2100 Bioanalyzer system (Agilent Technologies Inc, Palo Alto, CA).

value: Breast tumor

value: PyMT+ SG-/-


title: SLE patient-10

description:
9703627071_F
replicate 10


title: Breast tumor tissue 37

description: Mus 37

source_name: PyMT+ SG+/-

value: PyMT+ SG+/-


title: SLE patient-12

description:
9703627071_G
replicate 12


title: Breast tumor tissue 31

description: Mus 31


title: SLE patient-07

description:
9703627057_H
replicate 7


title: SLE patient-09

description:
9703627076_I
replicate 9


title: Breast tumor tissue 32

description: Mus 32


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter PiNN 49

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

institute: FBN

description: Gene expression data from skeletal muscle of adult pig breed (PiNN).

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

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

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

organism: Sus scrofa

source_name: skeletal muscle

label_protocol: biotin-labeled cRNAs were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: breed

value: Pietrain

value: adult

value: longissimus dorsi


title: Breast tumor tissue 39

description: Mus 39

tag: genotype/variation


title: SLE patient-08

description:
9703627076_H
replicate 8


title: Breast tumor tissue 30

description: Mus 30


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter PiNN 62


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter PiNN 47


title: SLE patient-11

description:
9703627057_L
replicate 11


title: SLE patient-05

description:
9482861018_I
replicate 5


title: SLE patient-06

description:
9703627076_B
replicate 6


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter PiNN 36


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter PiNN 41


title: SLE patient-04

description:
9703627071_C
replicate 4


title: normal control-25

description:
9703627057_B
replicate 25


title: SLE patient-03

description:
9703627076_E
replicate 3


title: SLE patient-14

description:
9703627057_G
replicate 14


title: SLE patient-01

description:
9461595024_H
replicate 1


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter PiNN 35


title: normal control-24

description:
9703627057_A
replicate 24


title: SLE patient-02

description:
9461595024_J
replicate 2


title: total RNA from adjacent normal tissue of OT8 [WG-DASL]

city: new delhi

first: binay

last: panda

address: 1649A vasant kunj

country: India

institute: ganit labs foundation

scan_protocol: HiScan, Illumina

data_processing: Analyzed with GenomeStudio V2011.1 Gene Expression module 1.9.0 (Illumina). Transformed and normalized using VST and LOESS methods, provided within R Bioconductor package, lumi. Batch correction was performed using ComBat

label_protocol: Standard Illumina protocol

extract_protocol: Total RNA was extracted using PureLink RNA mini kit (Invitrogen) and RNA quality was checked on the bioanalyzer using RNA Nano6000 chip (Agilent). RNA samples with poor RIN numbers (≤7) on the bioanalyzer chip, indicating partial degradation of RNA were processed using Illumina WGDASL assay and the ones with good RIN numbers (>7) were biotin-labelled using Illumina TotalPrep RNA Amplification kit (Ambion) as per the manufacturer’s recommendations.

tag: patient id

tag: disease

value: Oral tongue squamous cell carcinomas (OTSCC)

tag: tissue type

value: adjacent normal tissue

tag: patient age

tag: patient gender

value: M

tag: patient survival status

value: Dead

tag: patient overall survival (months)

tag: patient disease-free survival (months)


title: Beas-P40, biological rep1


title: normal control-23

description:
9703627050_K
replicate 23

tag: Sex

value: Female

tag: tissue


title: normal control-22

description:
9703627050_J
replicate 22

value: Male


title: total RNA from tumor tissue of OT6 [WG-DASL]

value: tumor tissue

tag: tumor grade

value: MDSCC

tag: tumor stage

tag: tumor nodal status

value: Alive


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter Duroc 59

description: Gene expression data from skeletal muscle of adult pig breed (Duroc).

value: Duroc

tag: age


title: total RNA from tumor tissue of OT8 [WG-DASL]


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter PiNN 19


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter PiNN 21


title: total RNA from adjacent normal tissue of OT6 [WG-DASL]


title: total RNA from tumor tissue of OT54 [WG-DASL]

value: F


title: normal control-21

description:
9703627050_I
replicate 21

value: blood


title: normal control-20

description:
9703627050_H
replicate 20


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter Duroc 42


title: normal control-18

description:
9703627067_J
replicate 18


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter Duroc 58


title: normal control-19

description:
9703627067_C
replicate 19


title: total RNA from tumor tissue of OT51 [WG-DASL]

value: WDSCC


title: normal control-17

description:
9703627067_I
replicate 17


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter PiNN 20


title: total RNA from adjacent normal tissue of OT54 [WG-DASL]


title: total RNA from tumor tissue of OT52 [WG-DASL]


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter Duroc 46


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter Duroc 43


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter Duroc 32


title: total RNA from adjacent normal tissue of OT51 [WG-DASL]


title: normal control-14

description:
9703627050_E
replicate 14


title: normal control-15

description:
9703627050_G
replicate 15


title: normal control-16

description:
9703627067_H
replicate 16


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter Duroc 38


title: total RNA from tumor tissue of OT5 [WG-DASL]


title: total RNA from adjacent normal tissue of OT5 [WG-DASL]


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter Duroc 31


title: total RNA from adjacent normal tissue of OT28 [WG-DASL]


title: normal control-12

description:
9703627050_B
replicate 12


title: normal control-13

description:
9703627050_D
replicate 13


title: total RNA from tumor tissue of OT28 [WG-DASL]


title: normal control-11

description:
9703627050_A
replicate 11


title: normal control-10

description:
9703627067_G
replicate 10


title: total RNA from tumor tissue of OT22 [WG-DASL]


title: total RNA from tumor tissue of OT26 [WG-DASL]


title: total RNA from adjacent normal tissue of OT22 [WG-DASL]


title: normal control-09

description:
9703627067_A
replicate 9


title: total RNA from adjacent normal tissue of OT26 [WG-DASL]


title: total RNA from tumor tissue of OT17 [WG-DASL]

value: PDSCC


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter Duroc 28


title: total RNA from adjacent normal tissue of OT19 [WG-DASL]


title: normal control-08

description:
9461595045_A
replicate 8


title: total RNA from tumor tissue of OT11 [WG-DASL]


title: normal control-07

description:
9461595034_D
replicate 7


title: total RNA from tumor tissue of OT12 [WG-DASL]


title: normal control-04

description:
9461595024_D
replicate 4


title: normal control-06

description:
9461595034_C
replicate 6


title: total RNA from adjacent normal tissue of OT17 [WG-DASL]


title: total RNA from tumor tissue of OT1 [WG-DASL]


title: total RNA from adjacent normal tissue of OT12 [WG-DASL]


title: normal control-01

description:
9461595024_A
replicate 1


title: normal control-05

description:
9461595034_A
replicate 5


title: total RNA from adjacent normal tissue of OT11 [WG-DASL]


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter Duroc 24


title: normal control-03

description:
9461595024_C
replicate 3


title: Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter PiNN 22

value: Pietrain


title: R1 TIC10 9286492007_G

city: Hershey

first: Penn State

last: COM

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

data_processing: The data were normalised using Quantile Normalization

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

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.

tag: treatment

tag: cell type

value: RKO


title: normal control-02

description:
9461595024_B
replicate 2


title: R1 TIC10 9286492007_H


title: total RNA from adjacent normal tissue of OT1 [WG-DASL]


title: R1 dmso 9286492007_F

value: DMSO-treated


title: par TIC10 9286492007_D

source_name: RKO


title: R1 dmso 9286492007_E


title: par dmso 9286492007_A


title: par TIC10 9286492007_C


title: 18 T 5655639024_F

tag: cell line


title: 9_DIV_rep3

city: Frankfurt am Main

first: Andreas

middle: G

last: Chiocchetti

address: Deutschordenstr 50

department: Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy

institute: JW Goethe University

data_processing: Raw average intensities of the beads per probe without background correction were log2 transformed and quantile normalized using the limma package in R

source_name: SH-SY5Y cell line_9 day_RA+BDNF-induced neuronal differentiation

growth_protocol: SH-SY5Y cells were proliferated using standard conditions (DMEM, 10% FBS, 1% Sodium Pyruvate and 1% Penicillin/Streptomycin at 37°C and 5% CO2.

extract_protocol: RNA was extracted using the GeneJet RNA purification kit according to the manufacturer’s protocol (Fermentas) including DNAse treatment.

treatment_protocol: For neuronal differentiation cells were grown in Neurobasal®-A medium with 1x GlutaMAX, 1x B-27 supplement, 10µM Retinoic acid, 2mM cAMP, 50ng/ml hBDNF, 1% Penicillin/Streptomycin and 20mM KCl over a time course of 11 days changing the medium every other day. The time-points for morphological and mRNA analysis were set 24h after changing the medium and were as follows 0 (undifferentiated cells), 1, 3, 5, 7, 9 and 11 days in vitro (DIV)

tag: gender

value: female

value: neuroblastoma

tag: days in vitro


title: total RNA from tumor tissue of OT19 [WG-DASL]

tag: patient id

tag: disease

value: Oral tongue squamous cell carcinomas (OTSCC)

tag: tissue type

value: M


title: 18 T 5655639024_E


title: 18 T 5655639024_D


title: 18 C 5655639024_B


title: 79333

city: Cambridge

first: Kerstin

last: Lindblad-Toh

state: MA

address: 715 Main Street

department: Vertebrate Genome Biology

institute: Broad Institute

hyb_protocol: Standard Illumina protocol for Infinium HD Beadchip

scan_protocol: Two iScans with dual autoloaders

data_processing: Illumina GenomeStudio Version 2011.1 with Genotyping Module 1.9.4

source_name: whole blood

label_protocol: Canine HD Whole-Genome Genotyping BeadChip using the Infinium HD Ultra Assay

extract_protocol: Qiagen QIAamp DNA blood midi kit

tag: breed

value: Pembroke Welsh corgi (PWC)

tag: status

value: DM-affected


title: 68622

value: DM-unaffected


title: 18 C 5655639024_A


title: 7_DIV_rep3

source_name: SH-SY5Y cell line_7 day_RA+BDNF-induced neuronal differentiation


title: 64718


title: 11_DIV_rep3

source_name: SH-SY5Y cell line_11 day_RA+BDNF-induced neuronal differentiation


title: 18 C 5655639024_C


title: 5_DIV_rep3

source_name: SH-SY5Y cell line_5 day_RA+BDNF-induced neuronal differentiation


title: 1_DIV_rep3

source_name: SH-SY5Y cell line_1 day_RA+BDNF-induced neuronal differentiation


title: 66404


title: total RNA from adjacent normal tissue of OT52 [WG-DASL]

value: adjacent normal tissue

tag: patient age

tag: patient gender

tag: patient survival status

tag: patient overall survival (months)

tag: patient disease-free survival (months)


title: 67122


title: 64368


title: 11_DIV_rep2


title: 65148


title: 76661


title: 61997


title: 3_DIV_rep3

source_name: SH-SY5Y cell line_3 day_RA+BDNF-induced neuronal differentiation


title: 63495


title: 62664


title: 0_DIV_rep3

source_name: SH-SY5Y cell line_undifferentiated


title: 62305


title: par dmso 9286492007_B


title: 61517


title: 9_DIV_rep2


title: 61827


title: 61519


title: 7_DIV_rep2


title: 61037


title: 5_DIV_rep2


title: 9_DIV_rep1


title: 0_DIV_rep2


title: 61063


title: 3_DIV_rep2


title: 5_DIV_rep1


title: 11_DIV_rep1


title: 7_DIV_rep1


title: 1_DIV_rep2


title: 3_DIV_rep1


title: 1_DIV_rep1


title: 61032


title: 60403


title: hTERT_p53_POSTN_3

city: Houston

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

label: Biotin

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

value: primary esophageal cells (EPC)

tag: genotype/variation

value: expressing hTERT, mutant P53, and POSTN


title: 0_DIV_rep1


title: 60156

tag: age


title: hTERT_p53_3

value: expressing hTERT and mutant P53


title: 60378


title: hTERT_p53_1


title: hTERT_p53_POSTN_1


title: hTERT_3

source_name: hTERT

value: immortalized by expression of hTERT


title: 35853


title: 60400


title: 47870


title: 60385


title: 60584


title: hTERT_1


title: 56798


title: hTERT_p53_2


title: hTERT_2


title: cher 1-5 P4

city: Erlangen

first: Uwe

last: Sonnewald

address: Staudtstr. 5

department: Biology, Biochemistry

institute: Friedrich-Alexander-University

description: Gene expression after 10 weeks under shortday conditions

hyb_protocol: following fragmentation, 1.65 µg of Cy3-labeled cRNA were hybridisied for 17h at 65°C on 4x44K Agilent Arabidopsis_v4 arrays. Arrays were washed according to the protocol (One-Color Microarray-based gene expression analysis v.5.5)

scan_protocol: Microarrays were scanned using Agilent G2565B Microarray Scanner. Data were extracted using Feature Extraction Version: FE Version 12.5.1 (Agilent Technologies Germany). Data extraction using protocol GE1_v5_95_Feb07

data_processing: After importing text files via feature extraction software (Version12.5.1; Agilent Technologies) into GeneSpring GX 11.0 (Silicon Genetics) microarray data were log2-transformed followed by normalization to the 75th percentile and corrected to the median of all samples. The identification of differentially regulated genes between cher1-4, cher1-5 and control plants with >2.0-fold change and P < 0.05 was achieved by using T-test unpaired and Benjamini–Hochberg multiple test correction (Benjamini and Hochberg, 1995).

organism: Arabidopsis thaliana

source_name: Arabidopsis, leaf, cher 1-5, replicate 4

label_protocol: Cy3-labeled cRNA were prepared according to the agilent protocol from 80mg  total RNA after the method published by Logemann et al. (1987) (One-Color Microarray-based gene expression analysis v.5.5)

growth_protocol: Arabidopsis thaliana seeds were sown on soil and stratificated at 4°C for 2 days to synchronize germination. Following stratification, plants were cultivated under short-day conditions (SD; 8 h light at 22°C, 16 h dark at 19°C), 10 weeks old plants

extract_protocol: RNA extraction after Logemann (1987)

treatment_protocol: no special treatment, 2 source leaves from 4 different plants formed 1 pool (P), quick frozen with liquid nitrogen

tag: genotype

value: cher1-5:Col-0 with GGA -->GAA at position 740 of cds

tag: tissue

value: leaves

value: 10 weeks


title: 55957


title: 28650


title: 61035


title: cher 1-5 P2

source_name: Arabidopsis, leaf, cher 1-5, replicate 2


title: cher 1-5 P3

source_name: Arabidopsis, leaf, cher 1-5, replicate 3


title: 29304


title: hTERT_p53_POSTN_2

tag: cell line


title: 31544


title: 25529


title: 25683


title: cher 1-5 P1

source_name: Arabidopsis, leaf, cher 1-5, replicate 1


title: cher 1-4 P4

source_name: Arabidopsis, leaf, cher 1-4, replicate 4

value: cher 1.4:T-DNA insertion line SALK-065853 (ecotype Col-0, kanamycin resistance)


title: cher 1-4 P3

source_name: Arabidopsis, leaf, cher 1-4, replicate 3


title: cher 1-4 P2

source_name: Arabidopsis, leaf, cher 1-4, replicate 2


title: 25324


title: 25396


title: PWC_BI_175649_JOHNSON_81977

value: older unaffected control


title: 28059


title: WT P4

source_name: Arabidopsis, leaf, control, replicate 4

value: wild type Col-0


title: 26531


title: WT P2

source_name: Arabidopsis, leaf, control, replicate 2


title: WT P1

source_name: Arabidopsis, leaf, control, replicate 1


title: PWC_BI_175648_JOHNSON_74844

source_name: whole blood


title: cher 1-4 P1

source_name: Arabidopsis, leaf, cher 1-4, replicate 1


title: PWC_BI_175647_JOHNSON_75816


title: 34779


title: BOXER_BI_5545_BROAD_5545

value: Boxer


title: BOXER_BI_89203_JOHNSON_71334


title: 60431


title: BOXER_BI_89202_JOHNSON_70247


title: BOXER_BI_89119_JOHNSON_59743


title: BOXER_BI_89189_JOHNSON_67030


title: PWC_BI_175646_JOHNSON_87150


title: BOXER_BI_89107_JOHNSON_58306


title: 59050


title: BOXER_BI_89109_JOHNSON_58966


title: BOXER_BI_89079_JOHNSON_55061


title: BOXER_BI_9282_BROAD_9282


title: BOXER_BI_89200_JOHNSON_68616


title: VCap_OBP-801

city: Nagoya

first: Keisuke

last: Katsushima

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku

department: Department of Epigenomics

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

description: miRNA expression after 48hr in induction of OBP-801

hyb_protocol: Labeled samples were purified with MicroBio-Spin 6 columns (Bio-Rad, Richmond, CA) and hybridized to microarray at 55 °C with rotation at 20 rpm for 20 hours.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol miRNA_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Prostate cancer cell, 48hr, OBP-801, replicate 1

label_protocol: One hundred ng of total RNA was labeled with pCp-Cy3 (Agilent Technologies) and 15 units of T4 RNA ligase (GE Healthcare, Little Chalfont, Buckinghamshire, UK) at 16°C for 2 hours.

growth_protocol: LNCap and VCap cell lines were purchased from ATCC (Manassas, VA, USA). These cells were cultured in RPMI 1640 (Life Technologies, Carlsbad, CA) supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was isolated using TRIzol (Life Technologies) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000.

treatment_protocol: LNCap and VCap cells were added 10nM OBP and incubated for 48 hours at 37 ºC in a humidified incubator with 5% CO2.

value: VCap

tag: gender

value: male


title: 54453

value: Pembroke Welsh corgi (PWC)


title: LNCap_OBP-801

value: LNCap


title: BOXER_BI_7291_BROAD_7291

value: DM-unaffected


title: cumulus cells of normal patient_rep5

city: Shanghai

first: Xin

last: Huang

state: Shanghai

address: No.2699 Gaoke east road

department: Reproductive Medicine Centre

institute: Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine

description: Gene expression of cumulus cells in normal women

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

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

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

source_name: cumulus cells isolated from normal patient

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.

treatment_protocol: All the PCOS participants included in the study were women undergoing in vitro fertilization.Ovarian stimulation and oocyte retrieval protocols were carried out as below.pituitary down-regulation was started with mid-luteal phase GnRH agonist (Diphereline 3.75mg, PharmaBiotech, Paris, France). Once adequate pituitary down-regulation was confirmed [absence of ovarian cysts>=18mm in diameter and serum estradiol (E2) levels of <50 pg/ml]. Controlled ovarian stimulation was conducted with recombinant FSH (Follitropin Alfa, Serono, London, UK). Human chorionic gonadotropin (hCG; 10,000 IU, Profasi; Serono Laboratories) was given in when two or more follicles were at least 18mm in diameter and the serum E2 levels were at least 300pg/ml per dominant follicle. Oocyte retrieval was performed 36h after hCG administration. Cumulus cells were separated from the oocyte with strippers mechanically and washed twice in cold phosphate buffer saline (Dubelcco’s medium) (Gibco, invitrogen, Paris, France) then centrifuged at 200g for 10 min. The supernatant was removed and the pellet was resuspended in RLT buffer of the Reasy Mini Kit.

tag: cell type

value: cumulus cells

tag: disease state

value: normal


title: BOXER_BI_89095_JOHNSON_55817

value: DM-affected


title: BOXER_BI_175632_JOHNSON_60182

value: 11 or older


title: BOXER_BI_175645_JOHNSON_63056


title: LNCap_DMSO

description: miRNA expression after 48hr in induction of DMSO

source_name: Prostate cancer cell, 48hr, DMSO, replicate 1


title: BOXER_BI_89077_JOHNSON_54758


title: BOXER_BI_175633_JOHNSON_67469


title: BOXER_BI_89068_JOHNSON_44368


title: cumulus cells of normal patient_rep4


title: cumulus cells of normal patient_rep3


title: cumulus cells of normal patient_rep2


title: cumulus cells of normal patient_rep1


title: cumulus cells of PCOS patient_rep5

description: Gene expression of cumulus cells in PCOS women

source_name: cumulus cells isolated from PCOS patient

value: PCOS


title: cumulus cells of PCOS patient_rep4


title: BOXER_BI_89070_JOHNSON_44786


title: cumulus cells of PCOS patient_rep3


title: cumulus cells of PCOS patient_rep2


title: BOXER_BI_175630_JOHNSON_43320


title: BOXER_BI_89207_JOHNSON_64026


title: BOXER_BI_175631_JOHNSON_52772


title: SporadicPRCC2_TumorTissue12

city: Singapore

first: Weng Khong

last: Lim

state: Singapore

address: 11 Hospital Drive

department: Department of Medical Sciences

institute: National Cancer Centre Singapore

description: Gene expression profiling of hereditary and sporadic Type 2 Papillary Renal Cell Carcinoma (PRCC2) and adjacent normal tissue from PRCC2 patients

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

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

data_processing: CEL files were loaded into R and then preprocessed and normalized using RMA. A custom CDF (GPL16311) was used to reannotate the probes.

source_name: Tumor tissue from sporadic PRCC2

label_protocol: Standard Affymetrix protocol, 10ug of RNAeasy-purified total RNA

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer's instructions, followed by purification using the Qiagen RNAeasy kit.

value: Cancer

tag: disease status

value: sporadic PRCC2


title: SporadicPRCC2_TumorTissue19

tag: tissue type


title: SporadicPRCC2_TumorTissue15


title: SporadicPRCC2_TumorTissue18


title: SporadicPRCC2_TumorTissue9


title: SporadicPRCC2_TumorTissue17


title: SporadicPRCC2_TumorTissue13


title: SporadicPRCC2_TumorTissue14


title: MCF7_shGFP

city: Seoul

first: Jiyeon

last: YUN

address: 317,Cancer research institute, Seoul Nat. Univ. Youngondong, Jongnogu, Seoul

country: South Korea

institute: Cancer research institute

description:
differentiated mammary epithelium
total RNA

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: The cells were cultured in 5% CO2  and 37C incubator.

extract_protocol: Total RNAs was harvested using Rneasy mini kit (Qiagen) and all processes were performed according to the manufacturer's instructions.

treatment_protocol: each cell was transduced with shGFP or shRAD21-lentivirus and selected by fresh medium containing puromycin.

value: shGFP transfection


title: SporadicPRCC2_TumorTissue10


title: SporadicPRCC2_TumorTissue5


title: SporadicPRCC2_TumorTissue3


title: SporadicPRCC2_TumorTissue8


title: SporadicPRCC2_TumorTissue11


title: SporadicPRCC2_TumorTissue4


title: SporadicPRCC2_TumorTissue6


title: MCF7_shRAD21

value: shRAD21 transfection


title: BOXER_BI_89204_JOHNSON_74434

tag: breed


title: BOXER_BI_6597_BROAD_6597

tag: status


title: BOXER_BI_89209_JOHNSON_55138


title: BOXER_BI_12683_BROAD_12683


title: SporadicPRCC2_TumorTissue16


title: SporadicPRCC2_TumorTissue2


title: E045-Tc7

city: Bethesda

first: Perwez

middle: S

last: Hussain

state: MD

address: 37 Convent Drive, Building 37, Room3044B

institute: National Cancer Institute

description: 20100816_Perwez2 miRNA 081310_E45-Tc7_03E045-Tc7

hyb_protocol: Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturer's instructions. Hybrdization reactions were performed according to the manufacturer's instructions (NanoString).

scan_protocol: For each assay, a high-density scan (600 fields of view) was performed.

data_processing:
The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using code count normalization according to manufacturer's protocol (Nanostring). Log2 normalized data was imported to Parkek Genomic Suite 6 and batch effect was removed before analysis.
NanoString Technologies v1.6.0
miRBase Identifier (miRBase 16)

source_name: pancreatic ductual adenocarcinoma_69

extract_protocol: Tissues were flash frozen immediately after surgery.RNA from frozen tissue samples was extracted using standard TRIZOL (Invitrogen) protocol. RNA quality was confirmed with the Agilent 2100 Bioanalyzer (Agilent Technologies) before the microarray gene expression profiling

value: Tumor

tag: surval months

tag: survival status

tag: mif status

value: High


title: E033-Tc7

description: 20100816_Perwez1 miRNA 081310_E33-Tc7_09E033-Tc7

source_name: pancreatic ductual adenocarcinoma_67


title: E203-Tp1

description: 20100817_Perwez6 miRNA 081310_E203-Tp1_09E203-Tp1

source_name: pancreatic ductual adenocarcinoma_65


title: E048-Tc7

description: 20100816_Perwez2 miRNA 081310_E48-Tc7_05E048-Tc7

source_name: pancreatic ductual adenocarcinoma_68


title: 14694T

description: 20100727_Perwez miRNA 072710_14694T_01

source_name: pancreatic ductual adenocarcinoma_1


title: SporadicPRCC2_TumorTissue1


title: E052-Tc7

description: 20100816_Perwez2 miRNA 081310_E52-Tc7_07E052-Tc7

source_name: pancreatic ductual adenocarcinoma_66


title: E082-Tp1

description: 20100818_Perwez3 miRNA 081310_E82-Tp1_03E082-Tp1

source_name: pancreatic ductual adenocarcinoma_64


title: SporadicPRCC2_NormalTissue_5

source_name: Normal tissue from sporadic PRCC2 patient

value: Normal


title: HereditaryPRCC2_TumorTissue_3

source_name: Tumor tissue from hereditary PRCC2

value: hereditary PRCC2


title: HereditaryPRCC2_TumorTissue_4


title: HereditaryPRCC2_TumorTissue_5


title: SporadicPRCC2_NormalTissue_6


title: SporadicPRCC2_NormalTissue_2


title: HereditaryPRCC2_NormalTissue_2

source_name: Normal tissue from hereditary PRCC2 patient


title: HereditaryPRCC2_TumorTissue_2


title: SporadicPRCC2_NormalTissue_1


title: HereditaryPRCC2_TumorTissue_1


title: VCap_DMSO

value: VCap

value: male


title: SporadicPRCC2_NormalTissue_3


title: WT P3

source_name: Arabidopsis, leaf, control, replicate 3

value: wild type Col-0

value: leaves

value: 10 weeks


title: SporadicPRCC2_NormalTissue_4


title: 34435T

description: 20100728_Perwez4 miRNA 072710_34435T_0434435T

source_name: pancreatic ductual adenocarcinoma_63

value: Low


title: 32018T

description: 20100728_Perwez3 miRNA 072710_ 32018T_1032018T

source_name: pancreatic ductual adenocarcinoma_62


title: E028-Tp1

description: 20100816_Perwez1 miRNA 081310_E28-Tp1_07E028-Tp1

source_name: pancreatic ductual adenocarcinoma_61


title: E250-Tp1

description: 20100817_Perwez7 miRNA 081310_E250-Tp1_11E250-Tp1

source_name: pancreatic ductual adenocarcinoma_60


title: E064-Tp3

description: 20100816_Perwez2 miRNA 081310_E64-Tp3_11E064-Tp3

source_name: pancreatic ductual adenocarcinoma_59


title: E229-Tp1

hyb_protocol: Hybrdization reactions were performed according to the manufacturer's instructions (NanoString).

scan_protocol: standard Nanostring protocol

source_name: pancreatic ductual adenocarcinoma_56

tag: survival months


title: E234-Tp1

source_name: pancreatic ductual adenocarcinoma_57


title: E220-Tp1

source_name: pancreatic ductual adenocarcinoma_55


title: E178-Tp1

source_name: pancreatic ductual adenocarcinoma_54


title: E165-Tp1

source_name: pancreatic ductual adenocarcinoma_53


title: E162-Tp1

source_name: pancreatic ductual adenocarcinoma_52


title: unknown_0002_1

city: San Francisco

first: David

last: Quigley

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

description: Gene expression from unknown dorsal skin exposed to TPA

hyb_protocol: 90 microliters of hybridization sample were incubated in the Affymetrix GeneTitan Hybridization Oven instrument for 16 hours at 48C

scan_protocol: Arrays were processed with the Affymetrix GeneTitan Fluidics Station instrument, using the MoGene-1_1-st-v1-96 fluidics script and GeneTitan Hybridization, Wash, and Stain Kit for WT Array Plates. Arrays were scanned in the Affymetrix GeneTitan Multi-Channel (MC) instrument with the AGCC GeneTitan Instrument Control.

data_processing: CEL files were background corrected and normalized with RMA using oligo in R and then log2 transformed

source_name: dorsal skin

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

growth_protocol: Mice were aged to 8 weeks, housed in standard conditions with standard chow and water ad libitum.

extract_protocol: Trizol followed by Qiagen RNEasy clean-up

treatment_protocol: For TPA treatment, the dorsal skins of FVB/N, Spret/Ei, and FVB/N x Spret/Ei mice were shaved and two days later treated with a single dose of TPA (200 ml of 10-4 M solution in acetone) or vehicle alone. Mice were sacrificed at 0, 2, 4, 6, 24, 48, and 72 hours, and after one week.

tag: hours

value: unknown

tag: batch

value: dorsal skin

tag: treatment

value: TPA


title: HereditaryPRCC2_NormalTissue_1


title: cumulus cells of PCOS patient_rep1

source_name: cumulus cells isolated from PCOS patient

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

value: cumulus cells

value: PCOS


title: unknown_unknown_1

tag: genotype


title: unknown_0006_1

tag: tissue


title: SPR_0024_2

description: Gene expression from Spretus dorsal skin exposed to TPA

value: SPR


title: E109Tp1

description: 20100818_Perwez3 miRNA 081310_E109Tp1_11E109Tp1

source_name: pancreatic ductual adenocarcinoma_58


title: SPR_0048_1


title: E152-Tc5

source_name: pancreatic ductual adenocarcinoma_51


title: E139-Tp1

source_name: pancreatic ductual adenocarcinoma_50


title: SPR_1008_2


title: SPR_1008_1


title: SPR_0048_2


title: E138-Tp1

source_name: pancreatic ductual adenocarcinoma_49


title: E136-Tp1

source_name: pancreatic ductual adenocarcinoma_48


title: E133-Tp4

source_name: pancreatic ductual adenocarcinoma_47


title: SPR_0024_1


title: SPR_0004_1


title: SPR_0012_2


title: E123-Tc7

source_name: pancreatic ductual adenocarcinoma_45


title: E130-Tp1

source_name: pancreatic ductual adenocarcinoma_46


title: SPR_0012_1


title: F1_1008_6

description: Gene expression from F1 dorsal skin exposed to TPA


title: SPR_0000_1

description: Gene expression data from untreated Spretus dorsal skin

value: untreated


title: F1_1008_5


title: SPR_0006_1


title: SPR_0004_2


title: E120-Tc7

source_name: pancreatic ductual adenocarcinoma_44

value: Tumor


title: E088-Tc7

source_name: pancreatic ductual adenocarcinoma_41


title: E119-Tc7

source_name: pancreatic ductual adenocarcinoma_43

value: High


title: E094-Tc7

source_name: pancreatic ductual adenocarcinoma_42


title: SPR_0002_1


title: SPR_0000_2


title: F1_1008_2


title: E086-Tc8

source_name: pancreatic ductual adenocarcinoma_40


title: F1_1008_1


title: F1_1008_3


title: F1_1008_4


title: E073-Tc7

source_name: pancreatic ductual adenocarcinoma_39