title: 2B1_Dlx5_replicate1

city: Chicago

first: Samin

last: Sajan

state: IL

address: 920 E. 58th Street, CLSC 317

institute: University of Chicago

description: 2B1 Otic vesicle cell line transiently transfected with Dlx5 and GFP expression vector and differentiated for 4 days at 37oC without gamma-interferon, replicate1

hyb_protocol: Fragmentation of cRNA was carried out following the standard Affymetrix procedure, and 10ug of fragmented cRNA from each sample was hybridized to the Mouse Genome 430 2.0 gene chips for 16-18 hours at 45oC.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: Analysis was carried out in Expression Console software (Affymetrix) by employing the Robust Multichip Analysis (RMA) algorithm. All normalized (log-base-2) expression values below 5.5 were considered ‘Absent’. For cell line microarray data the cut-off for making ‘Present’ calls was set to 4.8 since this was the expression of Dlx5 in Dlx5-transfected cells.

source_name: 2B1 Otic vesicle cell line over-expressing Dlx5 and GFP

label_protocol: To synthesize biotin-labeled target (cRNA) for hybridization to Affymetrix arrays, 22ul of the purified cDNA were used as template in in-vitro transcription reactions using the BioArray HighYield RNA Transcript Labeling Kit (ENZO Life Sciences, NY). Besides the template cDNA, all other components were added following the instructions provided by the manufacturer, and reactions were incubated at 37oC for 10 hours on the PCR machine mentioned above under 'extract protocol'. Labeled cRNA was purified using an RNA purification kit (Qiagen) following the manufacturer’s instructions and eluted in 50ul of water.

growth_protocol: Otic vesicles from wild-type and Dlx5-null embryos were microdissected from mouse developmental stages E10 and E10.5 in ice-cold PBS (calcium and magnesium free). These were timed-pregnancies determined by a vaginal plug, and each embryo was staged independently in a litter by the number of somites. Once the vesicles were isolated as cleanly as possible from the embryos, they were placed in 1mg/ml solution of dispase dissolved in PBS (calcium and magnesium free) for 10-15 minutes on ice to facilitate the removal of closely attached mesenchyme. For each stage and genotype two biological replicates were collected, each comprising between 4 and 8 otic vesicles. For the 2B1 cell line, two independent cultures were used for both the empty vector-transfected and the Dlx5- transfected samples. Cells were grown in chick embryo fibroblast medium at 32oC to a confluency of 70-80% in the presence of gamma-interferon, then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.

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

treatment_protocol: Otic vesicles were directly transferred into 1ml of TRIZOL. The 2B1 cell line was allowed to proliferate at 32oC in the presence of gamma-interferon to a confluency of 70-80% and then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.

tag: tissue

value: 2B1 cell line

tag: genotype/variation

value: 4 days post-differentiation in-vitro


title: WT_Col_24h_1

status: Public on Jul 01 2011

type: RNA

city: Cambridge

first: Suzanne

last: Szak

state: MA

address: 14 Cambridge Ctr

department: Drug Discovery

country: USA

institute: BiogenIdec, Inc.

hyb_protocol: The Mouse 430_2 GeneChip probe arrays were pre-hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol. 15 ug of labeled cRNA was fragmented in 30 uL 1X fragmentation buffer 100 mM KOAc, 30 mM MgOAc at 95°C for 35 minutes. The fragmented labeled cRNA was resuspended in 300 ?L 1X hybridization buffer containing 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20, 0.5 mg/mL Aceylated BSA, 0.1 mg/mL herring sperm DNA, control oligo B2, and control transcripts bioB 1.5 pM, bioC 5 pM, bioD 25 pM, and cre 100 pM, and hybridized to Genechip probe arrays according to manufacturer’s protocol (Affymetrix, Santa Clara, CA).

scan_protocol: The GeneChip probe arrays were scanned using GeneArray Scanner (Hewlett Packard, Corvallis, OR).

data_processing: CEL files were subjected to GC-content-based Robust Multi-array Average (GCRMA) normalization. Colon and Jejunum tissue data were processed separately. Expression levels were log (base 2) transformed. All calculations and analyses were carried out using R and Bioconductor computational tools. Analyses were applied to discover genes that were differentially expressed between specific sets of tissue. First, to identify differentially expressed genes between groups of samples, we applied the linear modeling approach (MANOVA) to fit gene expression levels (log2 transformed) according to the defined groups of samples and Bayesian posterior error analysis. Genes that exhibited a log-odds score greater than zero and fold change greater then 1.5 were considered significantly different.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Colon

label_protocol: Five ug of purified total RNA was used in a 20 uL first strand reaction with 200U SuperScript II (Invitrogen, Carlsbad,CA) and 0.5ug (dT) T7primer[5’GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG(T)24] in 1X first strand buffer (Invitrogen Life Technologies, Carlsbad, CA) with a 42°C incubation for 1 hour. Second strand synthesis was carried out by the addition of 40 U E. coli DNA Polymerase, 2 U E. coli RNase H, 10 U E. coli DNA Ligase in 1X second strand buffer (Invitrogen Life Technologies, Carlsbad, CA) followed by incubation at 16°C for 2 hrs. The second strand synthesis reaction was purified using the Genechip Sample Cleanup Module according to the manufacturer’s protocol (Affymetrix, Santa Clara, CA). The purified cDNA was amplified using BioArray high yield RNA transcription labeling kit (Enzo Life Sciences, Inc., Parmingdale, NY) according to manufacturer’s protocol to produce 70-120 ug of biotin labeled cRNA (compliment RNA).

extract_protocol: At 6h and 24h post-ionizing radiation mice were sacrificed, and whole colon and jejunum were harvested, and total RNA was isolated from these  tissues. Samples were homogenized using an Ultra-Turrax T8 (IKA-Werke, Staufen, Germany) in TRIzol reagent (Invitrogen Life Technologies, Carlsbad, CA) according to manufacturer's protocol. 100 ìg of total RNA was further purified using an RNeasy Mini column (QIAGEN, Valencia, CA) according to manufacturer's protocol.

treatment_protocol: Mice were treated with 3 Gy of ionizing radiation.

tag: strain

value: BALB/C

value: Colon

tag: genotype

value: WT

tag: treatment

value: 3 Gy ionizing radiation 24h


title: Fresh-frozen tissue 5M9

city: Toronto

first: Marc

last: Remke

address: 555 University Ave. Rm 1504

department: Laboratory Medicine and Pathobiology

country: Canada

institute: The Hospital for Sick Children

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485043832_S01_GE2-v5_95_Feb07_1_4.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485043832_S01_GE2-v5_95_Feb07_1_4.txt

hyb_protocol: Agilent hybridization protocol following the manufacturer’s instructions. Dye-swap design.

scan_protocol: Scanned on Agilent Scanner G25505B.

data_processing: Array raw data were generated using Feature Extraction 9.1 Software. Feature signals had to fulfill the following criteria to be considered for further analysis: a minimal signal to background ratio ≥ 1.5 in at least one channel; a minimal raw signal of 200; a mean to median spot intensity ≤ the 75% quantile + 3 times the interquartile range of all features on the array; and a feature replicate standard deviation ≤ 0.25 per array. Normalization of raw signals was performed using vsn (Huber et al., 2002). Dye-swap experiments were averaged. Probes with more than 80% missing values across all samples were removed. Based on BLASTing the probes sequence information against the genome, biological annotations were retrieved from EnsEMBL (version 54, NCBI Build 36 of the human genome reference sequence).

organism: Homo sapiens

source_name: tumoral tissue (medulloblastoma), SHH

label_protocol: Agilent labeling protocol following the manufacturer’s instructions.

growth_protocol: Fresh frozen material was milled in a Micro-Dismembrator S (B. Braun, Melsungen, Germany). Total RNA derived from human cerebellums from a pool of 24 donors (Clontech, LOT No.6060073) was used as reference.

extract_protocol: RNA was extracted from biopsy samples using Trizol and RNeasy mini columns following the manufacturer’s instructions.

value: medulloblastoma

tag: gender

value: male

tag: age (years)

tag: subtype

value: SHH

tag: histology

value: MBEN/desmoplastic

tag: ctnnb1 mutation

value: wildtype

source_name: normal cerebellum

value: cerebellum

tag: disease status

value: normal

tag: sample type

value: reference


title: 2B1_Dlx5_replicate2

description: 2B1 Otic vesicle cell line transiently transfected with Dlx5 and GFP expression vector and differentiated for 4 days at 37oC without gamma-interferon, replicate2

tag: age


title: WT_Col_6h_2

value: 3 Gy ionizing radiation 6h


title: Fresh-frozen tissue 5M4

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485043231_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485043231_S01_GE2-v5_95_Feb07_1_3.txt

source_name: tumoral tissue (medulloblastoma), group D

value: group D

value: classic


title: Fresh-frozen tissue 5M6

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485043832_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485043832_S01_GE2-v5_95_Feb07_1_1.txt


title: Fresh-frozen tissue 5M8

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485043832_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485043832_S01_GE2-v5_95_Feb07_1_3.txt

value: female


title: 2B1_empty_vector_replicate1

description: 2B1 Otic vesicle cell line transiently transfected with an empty vector only containing GFP and differentiated for 4 days at 37oC without gamma-interferon, replicate1

source_name: 2B1 Otic vesicle cell line over-expressing GFP only

value: 2B1 cell line

value: 4 days post-differentiation in-vitro


title: Control HCT15 colon cancer cells

city: Pamplona

first: Raquel

last: Malumbres

state: Navarra

address: Avenida Pio XII 55

department: Hemato-Oncology

country: Spain

institute: University of Navarra/ Clínica Universidad de Navarra

hyb_protocol: The microarrays used in our study were the Human 19K Oligo Array from Center for Applied Genomics (University of Medicine of New Jersey). Microarray slides were prehybridized in buffer containing 5x SSC, 25% formamide and 0.1% SDS at 42 °C for 45min and washed by dipping in isopropanol. The slides were then dipped in distilled water and dried with compressed air.  The Final Hybridization Mix was added to the prehybridized slide. A 22 x 60 mm coverslip was cleaned with compressed air and then gradually placed on the slide to form a thin layer of labeled targets. To maintain humidity inside the chamber, 20 ul 2x SSC was added to the two reservoir wells. The chamber was then tightly sealed and incubated at 55°C water bath overnight for 16-20 h. Slide was then removed from the chamber, washed for 10 min sequentially at 42C in 2x SSC/0.2% SDS buffer, at room temperature in 2x SSC buffer and at room temperature in 0.2x SSC buffer, rinsed in distilled water for 5 s, and dried by compressed air.  Then, we prepare the 3DNA Array 350 Capture Reagent (Vial 1) by thawing the vial in the dark at room temperature for 20 minutes, vortexing at the maximum setting for 3 seconds and microfuge briefly and incubating at 50-55°C for 10 minutes. Simultaneously we resuspended the 2X Hybridization Buffer (Vial 6) by heating to 70°C for at least 10 minutes. For each array, we prepare a 3DNA Hybridization Mix containing 2.5ul of 3DNA Array 350 Capture Reagent-1 (Vial 1),  2.5ul of 3DNA Array 350 Capture Reagent-2 (Vial 1) , 25ul of 2X Hybridization Buffer (Vial 6) and 20 ul of water. Gently vortex and briefly microfuge the 3DNA Hybridization Mix. We incubate the 3DNA Hybridization Mix first at 75-80°C for 10 minutes, and then we add the 3DNA Hybridization Mix to a prewarmed microarray, taking care to leave behind any precipitate at the bottom of the tube. To maintain humidity inside the chamber, 20ul 2x SSC was added to the two reservoir wells. The chamber was then tightly sealed and incubated at 60 °C water bath for 4 h.   Slide was then removed from the chamber, washed for 10 min sequentially at 65C in 2x SSC/0.2% SDS buffer, at room temperature in 2x SSC buffer and at room temperature in 0.2x SSC buffer, rinsed in distilled water for 5 s, and dried by compressed air.

scan_protocol: All slides were scanned immediately with an Affymetrix GMS 418 Array Scanner using appropriate gains on the photomultiplier tube to obtain the highest intensity without saturation. A 16 bit TIFF image was generated for each channel, Cy3 and Cy5. The image analysis was performed with Imagene 4.1 software (BioDiscovery) to quantify the signal intensities. Data from spots not recognized by the Imagene analysis software were excluded from further considerations (empty, poor and negative spots). Data from the spots visually identified as flawed (<15% in all arrays) were also removed. Only the spots with flag value equal to 0 were included in the analysis.

data_processing: The data sets were imported into Microsoft Excel in order to analyze the quality for each feature. Two parameters were used to asses the data filtration: difference between median and mean under 20% for each feature and intensity feature median greater than background mean plus 2 standard deviation. Normalization data was performed with ArrayNorm 1.7.2 software by using Lowess and Dye Swap Sim Fix Filter methods. Visualization of results was performed with the normalized data using average linkage and Euclidean distance as a measurement of similarity using GENESIS 1.5.0 Software (Alexander Sturn, Institute for Genomics and Bioinformatics, Graz University of Technology). ANOVA was used as statistical function to determine gene expression differences between resistant (cluster R) and sensitive (cluster S) cell groups. The differences were considered statistically significant when two-sided p-values were less than 0.01.

label: Cy5, Cy3

source_name: Total RNA from human HCT15 colorectal cancer cells

label_protocol: Labeling of total RNA was performed using 3DNA Array-350 Detection kit according to manufacturer's protocol (Genisphere, Hatfield, PA). Total RNA was reverse transcribed using reverse transcription (RT) primers. Briefly, 5 µg of total RNA and 1 µl of Cy3 or Cy5 capture sequence were brought to 11 µl with RNase free water and incubated for 10 min at 80°C. In a separate microtube 4 µl of 5x RT buffer, 1 µl dNTP mix, 2 µl 0.1M DTT, 1 ul of Superase In TM Rnase inhibitor and 1µl of Superscript II reverse transcriptase were combined and the reaction was incubated 2 h at 42°C. The reaction was terminated by adding 3.5 µl of 0.5 M NaOH/50 mM EDTA and incubating it at 65°C for 10 min. The reaction was neutralized with 5 µl 1 M Tris-Cl, pH 7.5. The Cy3 and Cy5 reactions were then combined and precipitated with 15 µg of linear acrylamide, 250 µl 3 M ammonium acetate, and 875 µl 100% ethanol at -20 °C for 1 hour. Following precipitation the pellet was dried with speed-vac. In preparation for hybridization the cDNA pellet was resuspended in 29 µl RNase free water deionized distilled water. Then, 29 µl hybridization buffer (vial 12) were added to the mix and incubated at 80 °C for 10 min, followed by 55 °C for 45 min. This is the Final Hybridization Mix for loading on the array.

growth_protocol: Cell lines were grown as monolayer in RPMI-1640 (Invitrogen) medium (DLD1, LS513, HCT116, HCT15, LS411N, SW1417 and SW48) and DMEM (Invitrogen) medium (HT29, CACO2, LS174T, SW1116, SW480 and SW948) supplemented with 10% of heat-inactivated fetal calf serum (Biological Industries), 400 U/ml of penicillin, 40 ug/ml of gemtamicine, 2 mM of L-glutamine (Sigma) and 10 mM of Hepes (Sigma). LoVo was grown in HAM’S F12 (Invitrogen) with 20% of FBS, 200 U/ml of penicillin and 20ug/ml of gemtamicine. All cell lines were cultured at 37C in a humidified atmosphere of 5% CO2.

extract_protocol: All cell lines were grown in P60 dishes and total RNA from each sample isolated by using the RNeasy Mini kit (Qiagen) and were exhaustively treated with RNase-free DNAse I. RNA quantification were performed using NanoDrop spectophotometer (Nucliber).

treatment_protocol: For assessment of OXA sensitivity, we treated the cells with different concetrations of OXA during 24 hours and analyzed them by MTT colorimetric assay to determine the IC50 for each cell line. We considered OXA highly sensitive cells those with IC50 under 1 microM. All cell lines were grown in P60 dishes, one aliquot treated with IC50 OXA and another for untreated control.

tag: cell type

value: colorectal cancer cells

tag: oxa sensitivity

source_name: Reference RNA (Human Reference RNA, Stratagene)

value: Human Reference RNA from Stratagene


title: Fresh-frozen tissue 5M3

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485043231_S01_GE2-v5_95_Feb07_1_2.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485043231_S01_GE2-v5_95_Feb07_1_2.txt

source_name: tumoral tissue (medulloblastoma), WNT

value: WNT


title: Control SW480 colon cancer cells

source_name: Total RNA from human SW480 colorectal cancer cells


title: Control SW1116 colon cancer cells

source_name: Total RNA from human SW1116 colorectal cancer cells


title: Fresh-frozen tissue 5M7

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485043832_S01_GE2-v5_95_Feb07_1_2.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485043832_S01_GE2-v5_95_Feb07_1_2.txt

value: medulloblastoma

value: mutated


title: Fresh-frozen tissue 5M15

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485047902_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485047902_S01_GE2-v5_95_Feb07_1_1.txt

value: male


title: Fresh-frozen tissue 5M19

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_repeat251485047987_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_repeat251485047987_S01_GE2-v5_95_Feb07_1_1.txt

source_name: tumoral tissue (medulloblastoma), group C

value: group C


title: E10.5_otic_vesicle_mut_replicate1

description: Otic vesicle at E10.5, replicate1

source_name: Mouse otic vesicle at E10.5 mut

value: inner ear


title: E10.5_otic_vesicle_mut_replicate2

description: Otic vesicle at E10.5, replicate1


title: KO_Col_0h_4

value: BALB/C

value: Colon

value: 3 Gy ionizing radiation 0h


title: Fresh-frozen tissue 5M17

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485047902_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485047902_S01_GE2-v5_95_Feb07_1_3.txt

value: SHH

value: wildtype

value: cerebellum

value: normal

value: reference


title: Fresh-frozen tissue 5M16

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485047902_S01_GE2-v5_95_Feb07_1_2.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485047902_S01_GE2-v5_95_Feb07_1_2.txt

value: female

value: classic


title: KO_Col_6h_3

value: 3 Gy ionizing radiation 6h


title: E10.5_otic_vesicle_wt_replicate2

description: Otic vesicle at E10.5, replicate1

source_name: Mouse otic vesicle at E10.5 wt

value: Wild-type


title: Fresh-frozen tissue 5M2

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485043231_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485043231_S01_GE2-v5_95_Feb07_1_1.txt

value: medulloblastoma

value: WNT


title: 2B1_empty_vector_replicate2

description: 2B1 Otic vesicle cell line transiently transfected with an empty vector only containing GFP and differentiated for 4 days at 37oC without gamma-interferon, replicate2

value: 2B1 cell line

value: 4 days post-differentiation in-vitro


title: Control SW48 colon cancer cells

source_name: Total RNA from human SW48 colorectal cancer cells

value: colorectal cancer cells

value: Human Reference RNA from Stratagene


title: Control SW1417 colon cancer cells

source_name: Total RNA from human SW1417 colorectal cancer cells


title: Fresh-frozen tissue 5M14

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485043844_S01_GE2-v5_95_Feb07_1_4.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485043844_S01_GE2-v5_95_Feb07_1_4.txt

value: mutated


title: E10.5_otic_vesicle_wt_replicate1

description: Otic vesicle at E10.5, replicate1

value: inner ear


title: Fresh-frozen tissue 5M18

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485047902_S01_GE2-v5_95_Feb07_1_4.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485047902_S01_GE2-v5_95_Feb07_1_4.txt

value: male

value: SHH


title: Control LS411N colon cancer cells

source_name: Total RNA from human LS411N colorectal cancer cells


title: Control LS174T colon cancer cells

source_name: Total RNA from human LS174T colorectal cancer cells


title: Fresh-frozen tissue 5M13

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485043844_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485043844_S01_GE2-v5_95_Feb07_1_3.txt

value: wildtype

value: cerebellum


title: Control LS513 colon cancer cells

source_name: Total RNA from human LS513 colorectal cancer cells


title: Control LoVo colon cancer cells

source_name: Total RNA from human LoVo colorectal cancer cells


title: Fresh-frozen tissue 4M58

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485031084_S01_GE2-v5_95_Feb07_1_2.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485031084_S01_GE2-v5_95_Feb07_1_2.txt

value: group C

value: large cell / anaplastic

source_name: normal cerebellum

value: normal

value: reference


title: E10_otic_vesicle_mut_replicate1

description: Otic vesicle at E10, replicate1

source_name: Mouse otic vesicle at E10 mut


title: Control DLD11 colon cancer cells

source_name: Total RNA from human DLD11 colorectal cancer cells


title: 6605-anti-miR-NC (negative control)

city: Rehovot

first: Einat

last: Sitbon

address: 10 Plaut St

country: Israel

institute: Rosetta Genomics

hyb_protocol: Labeled RNA was mixed with 33 hybridization buffer (Ambion), heated to 95 C for 3 min, and incubated with the miRdicator array for 12–16 hr

scan_protocol: Arrays were scanned using Agilent DNA Microarray Scanner Bundle (Agilent Technologies, Santa Clara, CA) at a resolution of 10 mm at 100% power. Array images were analyzed using SpotReader software (Niles Scientific, Portola Valley, CA).

data_processing: Triplicate spots were combined to produce one signal for each probe by taking the logarithmic mean of reliable spots. All data were log-transformed (base 2) and the analysis was performed in log-space. A reference data vector for normalization R was calculated by taking the median expression level of a subset of all probes (all miRs in mirbase 10) across samples. For each sample data vector S, a 2nd degree polynomial F was found so as to provide the best fit between the sample data and the reference data, such that R≈F(S). For each probe in the sample (element Si in the vector S), the normalized value (in log-space) Mi was calculated from the initial value Si by transforming it with the polynomial function F, so that Mi=F(Si). P-values were calculated using a two-sided t-test on the log-transformed normalized fluorescence signal. The fold-difference (ratio of the median normalized fluorescence) was calculated for each microRNA.

source_name: Hepatocellular carcinoma, Hep3B2.1-7

label_protocol: Fifteen micrograms of total RNA was labeled by ligation of an RNAlinker p-rCrU-Cy-dye

growth_protocol: Cells were grown in MEM–Eagle (+Earl's BBS), w/NEAA and 10% FBS with additions of sodium bicarbonate and sodium pyruvate.

extract_protocol: EZ-RNA II kit from Biological Industries, Israel, was used for total RNA extraction from cell lines

treatment_protocol: Cells were transfected with Oligofectamine (Invitrogen, Cat# 12252011) according to manufacturer instructions

tag: cell line

value: Hepatocellular carcinoma, Hep3B2.1-7

value: anti-miR-NC (negative control)


title: 6604-anti-miR-191


title: Fresh-frozen tissue 4M8

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485031082_S01_GE2-v5_95_Feb07_1_2.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485031082_S01_GE2-v5_95_Feb07_1_2.txt

value: medulloblastoma

value: WNT

value: classic


title: Fresh-frozen tissue 5M1

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485043230_S01_GE2-v5_95_Feb07_1_4.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485043230_S01_GE2-v5_95_Feb07_1_4.txt

source_name: tumoral tissue (medulloblastoma), group D

value: group D


title: Control HT29 colon cancer cells

source_name: Total RNA from human HT29 colorectal cancer cells

value: colorectal cancer cells

source_name: Reference RNA (Human Reference RNA, Stratagene)

value: Human Reference RNA from Stratagene


title: E10_otic_vesicle_wt_replicate2

description: Otic vesicle at E10, replicate2

source_name: Mouse otic vesicle at E10 wt

value: inner ear

value: Wild-type


title: Fresh-frozen tissue 5M10

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485043844_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485043844_S01_GE2-v5_95_Feb07_1_1.txt

value: female


title: Fresh-frozen tissue 5M12

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485043844_S01_GE2-v5_95_Feb07_1_2.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485043844_S01_GE2-v5_95_Feb07_1_2.txt

value: male

value: wildtype


title: Fresh-frozen tissue 4M43

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485031083_S01_GE2-v5_95_Feb07_1_2.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485031083_S01_GE2-v5_95_Feb07_1_2.txt

value: mutated

value: cerebellum


title: Fresh-frozen tissue 4M28

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485031082_S01_GE2-v5_95_Feb07_1_4.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485031082_S01_GE2-v5_95_Feb07_1_4.txt

source_name: tumoral tissue (medulloblastoma), WNT

value: normal


title: Fresh-frozen tissue 2M7

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485021032_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485021032_S01_GE2-v5_95_Feb07_1_3.txt

value: reference


title: Fresh-frozen tissue 4M55

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485031083_S01_GE2-v5_95_Feb07_1_4.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485031083_S01_GE2-v5_95_Feb07_1_4.txt


title: Fresh-frozen tissue 3M2

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485027005_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485027005_S01_GE2-v5_95_Feb07_1_3.txt


title: E10_otic_vesicle_mut_replicate2

description: Otic vesicle at E10, replicate2


title: Fresh-frozen tissue 3M5

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485027005_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485027005_S01_GE2-v5_95_Feb07_1_1.txt


title: BreastTumorTissue_control_10

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: data were normalized with the quantile method in R/BioConductor

label: biotin

source_name: BreastTumorTissue

label_protocol: Standard Illumina labeling protocol

growth_protocol: Fresh frozen human mammary tumor samples stored in liquid nitrogen

extract_protocol: RNA was isolated using miRvana miRNA isolation kit (Applied Biosystems) according to manufacturers protocol.

treatment_protocol: samples were homogenized with Precellys MK28-R Kit (6800Rpm, 3 x 25 s)

value: breast tumor

value: PTEN promoter wt


title: BreastTumorTissue_control_9


title: Fresh-frozen tissue 2M8

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485027006_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485027006_S01_GE2-v5_95_Feb07_1_3.txt

source_name: tumoral tissue (medulloblastoma), SHH

value: medulloblastoma

value: SHH

value: MBEN/desmoplastic


title: BreastTumorTissue_control_8


title: Fresh-frozen tissue 2M6

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485021031_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485021031_S01_GE2-v5_95_Feb07_1_1.txt

value: classic


title: Fresh-frozen tissue 2M19

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485021034_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485021034_S01_GE2-v5_95_Feb07_1_1.txt

value: group D


title: BreastTumorTissue_control_7


title: Fresh-frozen tissue 2M9

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485021064_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485021064_S01_GE2-v5_95_Feb07_1_1.txt


title: Fresh-frozen tissue 2M20

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485020936_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485020936_S01_GE2-v5_95_Feb07_1_3.txt


title: Fresh-frozen tissue 2M21

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485034554_S01_GE2-v5_95_Feb07_1_2.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485034554_S01_GE2-v5_95_Feb07_1_2.txt


title: Fresh-frozen tissue 2M4

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485021031_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485021031_S01_GE2-v5_95_Feb07_1_3.txt


title: Fresh-frozen tissue 2M17

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485027006_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485027006_S01_GE2-v5_95_Feb07_1_1.txt


title: Fresh-frozen tissue 2M11

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485021032_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485021032_S01_GE2-v5_95_Feb07_1_1.txt


title: Fresh-frozen tissue 2M14

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485021066_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485021066_S01_GE2-v5_95_Feb07_1_1.txt

source_name: tumoral tissue (medulloblastoma), group C

value: group C


title: Fresh-frozen tissue 2M15

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485021033_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485021033_S01_GE2-v5_95_Feb07_1_3.txt


title: Fresh-frozen tissue 1M8

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485020938_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485020938_S01_GE2-v5_95_Feb07_1_3.txt


title: BreastTumorTissue_control_4


title: Fresh-frozen tissue 2M5

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485036740_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485036740_S01_GE2-v5_95_Feb07_1_3.txt


title: Fresh-frozen tissue 1M5

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485020937_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485020937_S01_GE2-v5_95_Feb07_1_1.txt


title: Fresh-frozen tissue 2M16

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485021033_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485021033_S01_GE2-v5_95_Feb07_1_1.txt


title: BreastTumorTissue_control_6


title: Fresh-frozen tissue 1M9

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485034553_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485034553_S01_GE2-v5_95_Feb07_1_3.txt


title: >=5% myeloblast bone marrow 129

type: genomic

city: Cleveland

first: Kwok Peng

last: Ng

state: OH

address: 9500 Euclid Avenue

department: Ophthalmic Research

institute: Cleveland Clinic

description:
genomic DNA from bone marrow aspirates
HIGH129

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Cancer Panel 1 Methylation Microarray using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

source_name: MDS or AML bone marrow aspirates

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from bone marrow aspirates samples using Qiagen DNeasy Kit according to standard instructions

tag: cells

value: bone marrow aspirates

tag: who diagnosis

value: sAML


title: >=5% myeloblast bone marrow 130

description:
genomic DNA from bone marrow aspirates
HIGH130


title: BreastTumorTissue_control_2

tag: tissue


title: Fresh-frozen tissue 1M4

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485020993_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485020993_S01_GE2-v5_95_Feb07_1_1.txt

value: female

value: WNT


title: BreastTumorTissue_control_3


title: >=5% myeloblast bone marrow 127

description:
genomic DNA from bone marrow aspirates
HIGH127


title: >=5% myeloblast bone marrow 128

description:
genomic DNA from bone marrow aspirates
HIGH128


title: BreastTumorTissue_control_5


title: >=5% myeloblast bone marrow 126

description:
genomic DNA from bone marrow aspirates
HIGH126


title: Fresh-frozen tissue 1M33

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485027004_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485027004_S01_GE2-v5_95_Feb07_1_3.txt

value: wildtype


title: >=5% myeloblast bone marrow 125

description:
genomic DNA from bone marrow aspirates
HIGH125


title: Trichoderma atroviride during overgrowth with plant pathogen Rhizoctonia solani

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

country: France

institute: École normale supérieure

hyb_protocol: 1.5µg of labelled cDNA is mixed with one volume of 2X GE buffer (Agilent) and 10% of blocking agent. The hybridization sample volume is dispense on the selected microarray and incubated overnight at 65°C in a hybridization oven (Agilent). The array slides are washed 1 minute in "wash 1 buffer" at room temperature and one minute in "wash 2 buffer" at 37°C. The array slides are then air dryed and ready for scaning.

scan_protocol: Slides were scanned on an Agilent G2505C DNA microarray scanner and the TIFF images extracted using the Agilent Feature Extraction software (version 10.5.1.1) using the 20 bit coding ability.

data_processing: Data pretreatment was applied on each result file to discard flagged spots by Feature Extraction software. The data were normalised without background subtraction by the global Lowess method performed with the Goulphar software (Lemoine, 2006).

organism: Trichoderma atroviride

source_name: Total RNA extracted from T atroviride after contact with Rhizoctonia solani.

label_protocol: 1.5 µg RNA are retro transcribed using Superscript III retro transcriptase. The cDNA are purified using QiaQuick column (Quiagen) and incubated 1 hour at room temperature in presence of 0,05M NaBicarbonate and NHS-ester Cy5.The coupling is stoped by addition of hydroxylamine to a final concentration of 0,6M. Labeled cDNA are purified using QiaQuick column.

extract_protocol: Peripheral hyphal zones from each confrontation stage were harvested and shock frozen in liquid nitrogen. Mycelia were ground to a fine powder under liquid nitrogen and total RNA was isolated using the guanidinium thiocyanate method (Sambrook, 2001).

treatment_protocol: For mycoparasitism confrontation assays T. atroviride was grown on potato dextrose agar plates (BD Dicfo, Franklin Lakes, NJ, USA), covered with cellophane, in constant light at 25°C and harvested after T. virens had overgrown the host fungus Rhizoctonia solani by ca. 5 mm.

tag: condition

value: after contact with Rhizoctonia solani

source_name: Total RNA extracted from T atroviride control.

treatment_protocol: As control T. atroviride was confronted with itself and harvested at contact.

value: Control


title: >=5% myeloblast bone marrow 124

description:
genomic DNA from bone marrow aspirates
HIGH124


title: BreastTumorTissue_control_1

tag: genotype


title: Fresh-frozen tissue 1M28

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485021069_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485021069_S01_GE2-v5_95_Feb07_1_1.txt

value: large cell / anaplastic

value: cerebellum

value: normal


title: Fresh-frozen tissue 1M3

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485020937_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485020937_S01_GE2-v5_95_Feb07_1_3.txt

value: male

value: mutated

value: reference


title: Fresh-frozen tissue 1M31

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485034555_S01_GE2-v5_95_Feb07_1_2.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485034555_S01_GE2-v5_95_Feb07_1_2.txt

value: medulloblastoma

value: SHH


title: Fresh-frozen tissue 1M32

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485034555_S01_GE2-v5_95_Feb07_1_4.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485034555_S01_GE2-v5_95_Feb07_1_4.txt

value: classic


title: BreastTumorTissue_PTEN_promoter_variant carrier_8

value: breast tumor

value: PTEN promoter -903GA


title: BreastTumorTissue_PTEN_promoter_variant carrier_10


title: Fresh-frozen tissue 1M29

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485034554_S01_GE2-v5_95_Feb07_1_4.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485034554_S01_GE2-v5_95_Feb07_1_4.txt

value: group D


title: Fresh-frozen tissue 1M25

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485020940_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485020940_S01_GE2-v5_95_Feb07_1_3.txt


title: BreastTumorTissue_PTEN_promoter_variant carrier_7

value: PTEN promoter -975GC


title: Fresh-frozen tissue 1M21

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485021026_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485021026_S01_GE2-v5_95_Feb07_1_3.txt

value: group C


title: >=5% myeloblast bone marrow 122

description:
genomic DNA from bone marrow aspirates
HIGH122

value: bone marrow aspirates

value: sAML


title: Trichoderma atroviride during overgrowth with plant pathogen Rhizoctonia solani dye switch

value: Control

value: after contact with Rhizoctonia solani


title: >=5% myeloblast bone marrow 123

description:
genomic DNA from bone marrow aspirates
HIGH123


title: Fresh-frozen tissue 1M24

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485020939_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485020939_S01_GE2-v5_95_Feb07_1_1.txt

value: large cell / anaplastic

value: wildtype

value: cerebellum


title: Fresh-frozen tissue 1M19

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485021025_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485021025_S01_GE2-v5_95_Feb07_1_3.txt

value: female

value: normal


title: Fresh-frozen tissue 1M2

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485020936_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485020936_S01_GE2-v5_95_Feb07_1_1.txt

value: medulloblastoma

value: male

value: reference


title: >=5% myeloblast bone marrow 121

description:
genomic DNA from bone marrow aspirates
HIGH121


title: BreastTumorTissue_PTEN_promoter_variant carrier_9

value: breast tumor


title: BreastTumorTissue_PTEN_promoter_variant carrier_6

value: PTEN promoter -903GA


title: Trichoderma atroviride during first physical contact with plant pathogen Rhizoctonia solani dye switch

source_name: Total RNA extracted from T atroviride during contact with Rhizoctonia solani.

treatment_protocol: For mycoparasitism confrontation assays T. atroviride was grown on potato dextrose agar plates (BD Dicfo, Franklin Lakes, NJ, USA), covered with cellophane, in constant light at 25°C and harvested when the mycelia were at contact of the mycelia of the host fungus Rhizoctonia solani.

value: during contact with Rhizoctonia solani


title: Trichoderma atroviride before confrontation with plant pathogen Rhizoctonia solani

source_name: Total RNA extracted from T atroviride before contact with Rhizoctonia solani.

treatment_protocol: For mycoparasitism confrontation assays T. atroviride was grown on potato dextrose agar plates (BD Dicfo, Franklin Lakes, NJ, USA), covered with cellophane, in constant light at 25°C and harvested when the mycelia were ca. 5 mm apart the host fungus Rhizoctonia solani.

value: before contact with Rhizoctonia solani


title: Fresh-frozen tissue 1M20

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485021025_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485021025_S01_GE2-v5_95_Feb07_1_1.txt

value: group C

source_name: normal cerebellum


title: >=5% myeloblast bone marrow 120

description:
genomic DNA from bone marrow aspirates
HIGH120

value: bone marrow aspirates


title: Trichoderma atroviride before confrontation with plant pathogen Rhizoctonia solani dye switch


title: BreastTumorTissue_PTEN_promoter_variant carrier_5


title: Trichoderma atroviride during first physical contact with plant pathogen Rhizoctonia solani


title: Fresh-frozen tissue 1M22

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485021026_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485021026_S01_GE2-v5_95_Feb07_1_1.txt

value: WNT

value: classic

value: mutated


title: >=5% myeloblast bone marrow 119

description:
genomic DNA from bone marrow aspirates
HIGH119

value: sAML


title: Fresh-frozen tissue 1M16

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485020996_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485020996_S01_GE2-v5_95_Feb07_1_1.txt


title: BreastTumorTissue_PTEN_promoter_variant carrier_4

value: PTEN promoter -975GC


title: >=5% myeloblast bone marrow 118

description:
genomic DNA from bone marrow aspirates
HIGH118


title: BreastTumorTissue_PTEN_promoter_variant carrier_2


title: Fresh-frozen tissue 1M15

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485020996_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485020996_S01_GE2-v5_95_Feb07_1_3.txt

value: cerebellum


title: >=5% myeloblast bone marrow 116

description:
genomic DNA from bone marrow aspirates
HIGH116


title: >=5% myeloblast bone marrow 117

description:
genomic DNA from bone marrow aspirates
HIGH117


title: Fresh-frozen tissue 1M12

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485031084_S01_GE2-v5_95_Feb07_1_4.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485031084_S01_GE2-v5_95_Feb07_1_4.txt

value: SHH

value: MBEN/desmoplastic

value: wildtype


title: Fresh-frozen tissue 1M17

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485020939_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485020939_S01_GE2-v5_95_Feb07_1_3.txt

value: medulloblastoma

value: female

value: group D

value: normal


title: Fresh-frozen tissue 1M10

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485020995_S01_GE2-v5_95_Feb07_1_3.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485020995_S01_GE2-v5_95_Feb07_1_3.txt

value: large cell / anaplastic

value: reference


title: Fresh-frozen tissue 1M14

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485020938_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485020938_S01_GE2-v5_95_Feb07_1_1.txt

value: male


title: >=5% myeloblast bone marrow 115

description:
genomic DNA from bone marrow aspirates
HIGH115

value: bone marrow aspirates


title: BreastTumorTissue_PTEN_promoter_variant carrier_3

value: breast tumor

value: PTEN promoter -903GA


title: Genomic DNA of B. breve UCC2003 vs B. breve 12L

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

hyb_protocol: Labelled gDNA was hybridized using the Agilent CGH kit (part number 5188-5220) as described in the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis (v6.0) manual (publication number G4410-90010).

scan_protocol: Following hybridization, microarrays were washed as described in the manuals and scanned using Agilent's DNA microarray scanner G2565A.

data_processing: The scanning results were converted to data files with Agilent's Feature Extraction software (version 9.5). DNA microarray data was processed as previously described (Zomer et al. 2009).

organism: Bifidobacterium breve UCC2003

source_name: genomic DNA of B. breve species

label_protocol: Genomic DNA (gDNA) labeling for comparative genome hybridizations (CGH) was undertaken according to the BµG@S standard protocols (Hinds et al. 2002). In brief 5 µg of bifidobacterial genomic DNA was labeled with dCTP Cy3 (UCC2003) or dCTP Cy5 (test strain) using random primers (Promega) and a DNA polymerase I large Klenow fragment (Invitrogen).

growth_protocol: An overnight culture of B. breve was used to inoculate (1 % inoculum) 50 ml of MRS broth. Cells were incubated at 37°C until an optical density at 600 nm (OD600) of 0.5 was reached.

extract_protocol: Methods for cell disruption, DNA isolation were performed as described previously (O'Riordan et al. 1998).

treatment_protocol: Cells were then harvested by centrifugation at 8,000 x g for 1 min at room temperature and immediately frozen at -80oC.

tag: strain

organism: Bifidobacterium breve


title: Genomic DNA of B. breve UCC2003 vs B. breve 461


title: Genomic DNA of B. breve UCC2003 vs B. breve 14L


title: Genomic DNA of B. breve UCC2003 vs B. breve 689


title: Fresh-frozen tissue 1M13

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485020995_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485020995_S01_GE2-v5_95_Feb07_1_1.txt

tag: gender

value: WNT

value: classic

value: mutated


title: >=5% myeloblast bone marrow 113

description:
genomic DNA from bone marrow aspirates
HIGH113

value: sAML


title: >=5% myeloblast bone marrow 112

description:
genomic DNA from bone marrow aspirates
HIGH112


title: >=5% myeloblast bone marrow 114

description:
genomic DNA from bone marrow aspirates
HIGH114


title: Genomic DNA of B. breve UCC2003 vs B. breve LMG13208


title: Fresh-frozen tissue 1M1

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485021035_S01_GE2-v5_95_Feb07_1_1.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485021035_S01_GE2-v5_95_Feb07_1_1.txt

tag: age (years)

value: cerebellum


title: Genomic DNA of B. breve UCC2003 vs B. breve 658


title: >=5% myeloblast bone marrow 111

description:
genomic DNA from bone marrow aspirates
HIGH111


title: Genomic DNA of B. breve UCC2003 vs B. breve 13L


title: BreastTumorTissue_PTEN_promoter_variant carrier_1

value: PTEN promoter -1026CA


title: >=5% myeloblast bone marrow 110

description:
genomic DNA from bone marrow aspirates
HIGH110


title: 24h_0R_3

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

institute: Columbia University

description: EPI200 24h control 3

hyb_protocol: Hybridization to Agilent Whole Human Genome Oligo Microarrays (G4112A) was carried out in an Agilent hybridization oven for 17 h at 65°C in Agilent GE buffer according to the manufacturer's protocol.

scan_protocol: Hybridized slides were washed following Agilent's recommendations and then dried by centrifugation (1,500 rpm; 10 min) and immediately scanned with the Agilent DNA Microarray Scanner (G2505B) at 5 μm resolution and 100% PMT.

data_processing: Scanned images were analyzed with default parameters using Feature Extraction Software 9.1 for background correction and flagging of non-uniform features.  Background corrected hybridization intensities were imported into BRB-ArrayTools, Version 3.7.1 (Simon et al., 2007. PMID:19455231) log2-transformed and median normalized.

source_name: EPI200 24h control

label_protocol: RNA (100 ng of each sample) was labeled and amplified with the one-color Quick Amp Labeling Kit. Briefly, the procedure included reverse transcription and synthesis of cRNA covalently labeled with Cy3. The cRNA was purified with RNeasy (Qiagen, Valencia, CA) following the Agilent protocol and checked to ensure incorporation of > 8.0 pmol of Cy3 per μg of cRNA prior to fragmentation and hybridization

growth_protocol: EPI-200 was purchased from MatTek (Ashland, MA). At arrival, tissue plates were allowed to equilibrate to room temperature for 1h and then tissues were transferred to 6-well tissue culture dishes filled with NMM-100 medium (0.9ml/well) and cultured according to the manufacturer's instructions as previously described (Curren et al., 2006. PMID: 16781186).

extract_protocol: Total RNA was isolated using the RNAqueous Kit (Applied Biosystems, Foster City, CA) according to the manufacturer's instructions and stored at -80°C. Briefly, the procedure included homogenization in a Potter homogenizer, binding to a spin column and on-column treatment with DNase I. The impurities were washed out and RNA was eluted with a commercial elution buffer preheated to 75°C. RNA yield and quality were assessed with the NanoDrop spectrophotometer (Thermo Scientific, Waltham, MA) and the Bioanalyzer 2100 (Agilent Technologies, Foster City, CA).

treatment_protocol: For irradiation, samples were installed on a carousel and exposed to 0, 0.1 or 2.5 Gy 4.5 MeV protons using the track segment irradiation facility of the 5.5-MV Singletron accelerator at the Radiological Research Accelerator Facility (RARAF) of Columbia University.  After irradiation, samples were returned to  plates filled with fresh culture medium and cultured for 4, 16 or 24h.

tag: cell model

value: Mat-Tek EPI-200 3-dimensional skin model


title: 24h_250R_1

description: EPI200 24h 2.5 Gy 1


title: 24h_250R_3

description: EPI200 24h 2.5 Gy 3


title: 24h_250R_2

description: EPI200 24h 2.5 Gy 2


title: >=5% myeloblast bone marrow 109

description:
genomic DNA from bone marrow aspirates
HIGH109


title: 24h_10R_2

description: EPI200 24h 10 cGy 2

source_name: EPI200 24h 10 cGy


title: T1+2

city: Berlin

first: christoph

last: Hanski

address: Hindenburgdamm 30

country: Germany

institute: Charité Campus Benjamin Franklin

description: Gene expression in treated mice

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized hybridized for 16 hours at 45°C to an Affymetrix mouse 430A 2.0 GeneChip array.

scan_protocol: Probe arrays were scanned at 3-μm resolution using the Affymetrix GeneChip System confocal scanner 3000.

data_processing: Raw data were analyzed with the Affymetrix GeneChip Operating Software (GCOS) version 1.4.

source_name: murine colon epithelium

label_protocol: Biotynylated cRNA were prepared according to standard Affymetrix protocol from 3 µg total RNA

extract_protocol: Trizol extraction of total RNA according to the manufacturers instructions.

treatment_protocol: Mice were fed a diet containing 0.4% UDCA.

value: colon epithelium


title: 24h_10R_1

description: EPI200 24h 10 cGy 1

source_name: EPI200 24h 10cGy


title: 24h_0R_2

description: EPI200 24h control 2


title: 24h_0R_1

description: EPI200 24h control 1

source_name: EPI200 24h  control


title: T5+6

description: Gene expression in treated mice


title: T3+4

description: Gene expression in treated mice


title: Genomic DNA of B. breve UCC2003 vs B. breve NCTC11815


title: 16h_250R_2

description: EPI200 16h 2.5 Gy 2


title: >=5% myeloblast bone marrow 107

description:
genomic DNA from bone marrow aspirates
HIGH107


title: 24h_10R_3

description: EPI200 24h 10 cGy 3


title: 16h_250R_3

description: EPI200 16h 2.5 Gy 3


title: Genomic DNA of B. breve UCC2003 vs B. breve UCC2005


title: Genomic DNA of B. breve UCC2003 vs B. breve NCIMB8815


title: 16h_250R_1

description: EPI200 16h 2.5 Gy 1


title: >=5% myeloblast bone marrow 105

description:
genomic DNA from bone marrow aspirates
HIGH105


title: N5+6

description: Gene expression in normal mice

treatment_protocol: Mice were fed a standard diet


title: Genomic DNA of B. breve UCC2003 vs B. breve NCFB2258


title: >=5% myeloblast bone marrow 104

description:
genomic DNA from bone marrow aspirates
HIGH104


title: N3+4

description: Gene expression in normal mice


title: Genomic DNA of B. breve UCC2003 vs B. breve JCM7017


title: Genomic DNA of B. breve UCC2003 vs B. breve PRL6


title: Genomic DNA of B. breve UCC2003 vs B. breve NCFB2257


title: EmbryonicSecondaryDuct_Age15 rep 6

city: Bethesda

first: Kurt

last: Musselmann

state: MD

address: 30 Convent Dr, Room 426

department: Laboratory of Cell and Developmental Biology

institute: NIDCR

description:
laser microdissected sample
E15SD_006

hyb_protocol: Standard Agilent hybridization protocol: 1.5 mg of labeled RNA were fractionated and hybridized overnight (17h) at 60C, followed by washing according to Agilent's instructions.

scan_protocol: Standard Agilent scan using Agilent Microarray Scanner.  Sensitivities used were 10 and 100%

data_processing: GeneSpring 11.0, Quantile normalization of microarray data

source_name: Salivary gland, replicate 6

label_protocol: MessageAMP 2 AA labeling protocol, however, ratio of aaUTP to UTP was reduced from 1:1 to 1:3 to reduce background signal.  The RNA was then labeles following the manufacturers instructions.

extract_protocol: The RNA from the isolated cell samples were extracted using either Trizol or Rneasy Micro (Qiagen), and the RNA precipitated using glycogen as a carrier.  The samples were then amplified using MessageAMP 2AA, and the spike ins incorporated at the start of the 2nd round.

treatment_protocol: No special treatment of pregnant mice.  Embryos were isolated from timed pregnancies, the salivary glands isolated and embedded in OCT on top of nucleopore filters.  The filters were removed, and the salivary glands sectioned at 10um.  The sections were stained, and specific locations isolated by laser microdissection.

value: ICR

tag: collection method

value: laser microdissection

value: Embryonic day E15

value: salivary gland

tag: salivary gland domain

value: Secondary Duct


title: >=5% myeloblast bone marrow 102

description:
genomic DNA from bone marrow aspirates
HIGH102


title: >=5% myeloblast bone marrow 103

description:
genomic DNA from bone marrow aspirates
HIGH103


title: N1+2

description: Gene expression in normal mice


title: Genomic DNA of B. breve UCC2003 vs B. breve PRL4


title: 16h_10R_3

description: EPI200 16h 10 cGy 3

source_name: EPI200 16h 10 cGy


title: EmbryonicSecondaryDuct_Age15 rep 7

description:
laser microdissected sample
E15SD_007

source_name: Salivary gland, replicate 7


title: 16h_0R_3

description: EPI200 16h control 3

source_name: EPI200 16h control


title: 16h_0R_2

description: EPI200 16h control 2


title: 16h_10R_1

description: EPI200 16h 10 cGy 1

source_name: EPI200 16h 10cGy


title: Genomic DNA of B. breve UCC2003 vs B. breve UCC2004


title: EmbryonicSecondaryDuct_Age15 rep 5

description:
laser microdissected sample
E15SD_005

source_name: Salivary gland, replicate 5


title: 4h250R_3

description: EPI200 4h 2.5 Gy 3


title: EmbryonicSecondaryDuct_Age15 rep 4

description:
laser microdissected sample
E15SD_004

source_name: Salivary gland, replicate 4


title: 16h_10R_2

description: EPI200 16h 10 cGy 2


title: >=5% myeloblast bone marrow 100

description:
genomic DNA from bone marrow aspirates
HIGH100

source_name: MDS or AML bone marrow aspirates


title: >=5% myeloblast bone marrow 101

description:
genomic DNA from bone marrow aspirates
HIGH101


title: Genomic DNA of B. breve UCC2003 vs B. breve PRL5


title: EmbryonicSecondaryDuct_Age15 rep 2

description:
laser microdissected sample
E15SD_002

source_name: Salivary gland, replicate 2


title: >=5% myeloblast bone marrow 98

description:
genomic DNA from bone marrow aspirates
HIGH98


title: >=5% myeloblast bone marrow 99

description:
genomic DNA from bone marrow aspirates
HIGH99


title: >=5% myeloblast bone marrow 97

description:
genomic DNA from bone marrow aspirates
HIGH97


title: 4h250R_2

description: EPI200 4h 2.5 Gy 2


title: EmbryonicSecondaryDuct_Age15 rep 3

description:
laser microdissected sample
E15SD_003

source_name: Salivary gland, replicate 3


title: 4h250R_1

description: EPI200 4h 2.5 Gy 1


title: lps_stimulation_3

city: Regensburg

first: Matthias

last: Maneck

address: Franz-Josef-Strauß-Allee 11

department: Department of Pathology

institute: University of Regensburg

hyb_protocol: Fragmentation and hybridization of labelled anti sense RNA on Human Genome U133A 2.0 Arrays (Affymetrix) was performed was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays by the group of M. Hummel, Charité Berlin, as part of the MMML project.

scan_protocol: Samples were scanned using an Affymetrix GeneChip scanner

data_processing: Raw probe intensities were normalized using the variance stabilization method (vsn2: implemented in the vsn package in R). Subsequently probe sets were summarized using median polish.

source_name: BL-2 cell line after 6h of LPS stimulation

label_protocol: RNA was labelled for microarray hybridization using Affymetrix GeneChip® IVT Labelling Kit (Affymetrix).

extract_protocol: RNAs were extracted using the Qiagen RNAeasy Kit.

value: Burkitt lymphoma

tag: treatment

value: LPS 6h


title: 16h_0R_1

description: EPI200 16h control 1


title: >=5% myeloblast bone marrow 106

description:
genomic DNA from bone marrow aspirates
HIGH106

value: bone marrow aspirates


title: >=5% myeloblast bone marrow 108

description:
genomic DNA from bone marrow aspirates
HIGH108


title: lps_stimulation_2


title: Genomic DNA of B. breve UCC2003 vs B. breve JCM7019

source_name: genomic DNA of B. breve species


title: EmbryonicMainDuct_Age15 rep 7

description:
laser microdissected sample
E15MD_007

value: Main Duct


title: 4h10R_2

description: EPI200 4h 10 cGy 2

source_name: EPI200 4h 10 cGy


title: EmbryonicSecondaryDuct_Age15 rep 1

description:
laser microdissected sample
E15SD_001

source_name: Salivary gland, replicate 1


title: EmbryonicMainDuct_Age15 rep 8

description:
laser microdissected sample
E15MD_008

source_name: Salivary gland, replicate 8


title: 4h10R_3

description: EPI200 4h 10 cGy 3


title: lps_stimulation_1


title: control_2

source_name: BL-2 cell line


title: control_3


title: 4h10R_1

description: EPI200 4h 10 cGy 1

source_name: EPI200 4h 10cGy


title: PBMC_epimutationpatientIII2_rep1

city: Sydney

first: Megan

middle: P

last: Hitchins

state: NSW

address: Randwick High Street

department: Lowy Cancer Research Centre

country: Australia

institute: University of New South Wales

description: III2 from Lynch syndrome family 16.

hyb_protocol: Affymetrix® Genome-Wide Human SNP Nsp/Sty 6.0 User Guide (P/N 702504, Rev 3).

scan_protocol: Affymetrix® Genome-Wide Human SNP Nsp/Sty 6.0 User Guide (P/N 702504, Rev 3), GCFS 450, GCS 3000 HR, AGCC v3.0.

data_processing: APT v.1.12.0 used for preprocessing. Genotypes determined with apt-probeset-genotype (v. 1.264.2.2) using birdseed-v2 and cn-probe-chrXY-ratio for gender estimation. Intensity probe values extracted using apt-probeset-summarize (v. 1.178) with quant-norm.sketch=0, pm-only, med-polish, expr.genotype=true. The target distributions used for quantile normalization were separately generated on 300 WTCCC control samples (150 58BC and 150 NBS). Data was processed with the PennCNV-Affy routines to yield the 'GSE30348_gw6.lrr_baf.txt' file, which is linked to the Series GSE30348 record as a supplementary file. CNV calling with QuantiSNP, PennCNV and COKGEN.

source_name: Peripheral blood lymphocytes, asymptomatic carrier

extract_protocol: Genomic DNA was extracted from peripheral blood lymphocytes (PBL) and lymphoblastoid cell lines (LCL) using the phenol-chloroform method.

value: female

tag: phenotype

value: asymptomatic carrier of constitutional MLH1 epimutation

tag: family member

value: peripheral blood lymphocytes


title: >=5% myeloblast bone marrow 92

description:
genomic DNA from bone marrow aspirates
HIGH92


title: >=5% myeloblast bone marrow 93

description:
genomic DNA from bone marrow aspirates
HIGH93


title: >=5% myeloblast bone marrow 95

description:
genomic DNA from bone marrow aspirates
HIGH95


title: >=5% myeloblast bone marrow 94

description:
genomic DNA from bone marrow aspirates
HIGH94


title: >=5% myeloblast bone marrow 96

description:
genomic DNA from bone marrow aspirates
HIGH96


title: EmbryonicMainDuct_Age15 rep 4

description:
laser microdissected sample
E15MD_004

tag: age


title: 4h0R_3

description: EPI200 4h control 3

source_name: EPI200 4h control


title: PBMC_epimutationpatientII2_rep1

description: II2 from Lynch syndrome family 16.

label_protocol: Affymetrix® Genome-Wide Human SNP Nsp/Sty 6.0 User Guide (P/N 702504, Rev 3).

tag: cell type


title: PBMC_epimutationpatientI1_rep1

description: I1 from Lynch syndrome family 16.

source_name: Peripheral blood lymphocytes, cancer-affected carrier

value: cancer-affected carrier of constitutional MLH1 epimutation

tag: family relationship

value: mother


title: >=5% myeloblast bone marrow 91

description:
genomic DNA from bone marrow aspirates
HIGH91

tag: cells


title: PBMC_epimutationpatientII5_rep1

description: II5 from Lynch syndrome family 16.

value: proband


title: >=5% myeloblast bone marrow 90

description:
genomic DNA from bone marrow aspirates
HIGH90

tag: who diagnosis


title: 4h0R_1

description: EPI200 4h control 1

value: Mat-Tek EPI-200 3-dimensional skin model


title: Control-SiPolII

city: Taipei

first: Ming-Ta

last: Hsu

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang Ming University

description: Expression data from MCF-7 cell line transfected with non-targeting knockdown control psuper vector

hyb_protocol: Affymetrix microarray was performed using Human U133 2.0 (Affymetrix). Details of the methods for RNA quality, sample labeling, hybridization and expression analysis are according to the manual of Affymetrix Microarray Kit and Affymetrix website.

data_processing: MAS5.0 calculated signal intensities. Using scaling factor. The default settings are "scaling all probe sets to target signal: 500" and "normalization by user defined in value: 1

growth_protocol: Cells were grown to 85 % confluence in 10 cm tissue culture dish.

extract_protocol: Each 10 cm dish was washed with 1x PBS for three times. Total RNA was extracted according to the RNeasy® Mini Kit Spin Protocol (QIAGEN). The integrity of the RNA extract was checked by 1.2 % (w/v) agarose gel electrophoresis and the concentration of RNA was estimated by ultraviolet spectrophotometry.

treatment_protocol: MCF-7 cell line was subjected to siRNA knockdown of either non-targeting, POLRMT, or PolII for 72 hours

tag: cell line

value: MCF-7 breast cancer cell line

tag: cell line source

value: 69 year old female

tag: genotype/variation

value: control


title: >=5% myeloblast bone marrow 89

description:
genomic DNA from bone marrow aspirates
HIGH89


title: EmbryonicMainDuct_Age15 rep 2

description:
laser microdissected sample
E15MD_002

tag: strain

value: ICR

value: laser microdissection

value: Embryonic day E15

tag: tissue


title: >=5% myeloblast bone marrow 88

description:
genomic DNA from bone marrow aspirates
HIGH88


title: control_1

value: Burkitt lymphoma


title: SiMT-MCF-7

description: Expression data from MCF-7 cell line transfected with targeting POLRMT psuper vector

scan_protocol: Affymetrix microarray was performed using Human U133 2.0 (Affymetrix). Details of the methods for RNA quality, sample labeling, hybridization and expression analysis are according to the manual of Affymetrix Microarray Kit and Affymetrix website.

value: POLRMT knockdown


title: EmbryonicMainDuct_Age15 rep 1

description:
laser microdissected sample
E15MD_001

value: salivary gland


title: EmbryonicMainDuct_Age15 rep 3

description:
laser microdissected sample
E15MD_003

value: Main Duct


title: EmbryonicMainDuct_Age15 rep 6

description:
laser microdissected sample
E15MD_006

source_name: Salivary gland, replicate 6


title: SiPolII-MCF-7

description: Expression data from MCF-7 cell line transfected with targeting PolII psuper vector

label_protocol: Affymetrix microarray was performed using Human U133 2.0 (Affymetrix). Details of the methods for RNA quality, sample labeling, hybridization and expression analysis are according to the manual of Affymetrix Microarray Kit and Affymetrix website.

value: PolII knockdown


title: >=5% myeloblast bone marrow 87

description:
genomic DNA from bone marrow aspirates
HIGH87

value: bone marrow aspirates


title: EmbryonicBud_Age15 rep 9

description:
laser microdissected sample
E15MB_009

source_name: Salivary gland, replicate 9

value: Bud


title: EmbryonicBud_Age15 rep 7

description:
laser microdissected sample
E15MB_007

source_name: Salivary gland, replicate 7


title: DLD1 untreated

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

description: miRNA expression in a human colorectal cancer cell line DLD1

hyb_protocol: Hybridization was performed using a miRNA Labeling Reagent & Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 9.5) was used for background subtraction.

source_name: DLD1, untreated

label_protocol: Total RNA (100 ng) was labeled using a miRNA Labeling Reagent & Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: HCT116 and DNMT double KO cells were cultured in McCoy 5A medium supplemented with 10% heat-inactivated fetal bovine serum.  DLD1 and RKO cells were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2. Nomal colon RNA was purchased from BioChain.

extract_protocol: Total RNA was extracted using a mirVana miRNA isolation kit (Ambion).

treatment_protocol: Cells were treated with 2 microM 5-aza-2’-deoxycytidine (aza) for 72 h, replacing the drug and medium every 24 h.  In the combined protocol, cells were treated first with 2 microM aza for 72 h, and then with 3 mM 4-phenylbutyrate (PBA) for an additional 72 h, replacing the drug and medium every 24 h.

tag: disease state

value: colorectal cancer

value: untreated


title: SMC-Triptolide

description: Expression data from HUVSMC cell line treated with 0.3 mM of Triptolide for 24 hours

source_name: HUVSMC cell line treated with  0.3μM of Triptolide for 24 hours

treatment_protocol: Cells were treated with 0.3μM of Triptolide for 24 hours.

value: Human umbilical vein smooth muscle cells (HUVSMCs)

tag: agent

value: Triptolide


title: >=5% myeloblast bone marrow 86

description:
genomic DNA from bone marrow aspirates
HIGH86

source_name: MDS or AML bone marrow aspirates

value: AML


title: RKO untreated

description: miRNA expression in a human colorectal cancer cell line RKO

source_name: RKO, untreated

value: RKO


title: DLD1 5-aza-dC

description: miRNA expression in a human colorectal cancer cell line DLD1 treated with 5-aza-2'-deoxycytidine

source_name: DLD1, 5-aza-dC


title: EmbryonicBud_Age15 rep 8

description:
laser microdissected sample
E15MB_008

tag: collection method


title: Triptolide

description: Expression data from MCF-7 cell line treated with 0.3 mM of Triptolide for 24 hours

data_processing: MAS5.0 calculated signal intensities.  Using scaling factor. The default settings are "scaling all probe sets to target signal: 500" and "normalization by user defined in value: 1

source_name: MCF-7 cell line treated with  0.3μM of Triptolide for 24 hours

value: MCF-7 breast cancer cell line

value: 69 year old female


title: RKO 5-aza-dC

description: miRNA expression in a human colorectal cancer cell line RKO treated with 5-aza-2'-deoxycytidine

source_name: RKO, 5-aza-dC


title: Control-SiMT

source_name: MCF-7 cell line transfected with non-targeting knockdown control psuper vector

value: control


title: SMC-Control-T

description: Expression data from untreated HUVSMC cell line

source_name: HUVSMC cell line control


title: EmbryonicBud_Age15 rep 6

description:
laser microdissected sample
E15MB_006

value: ICR

value: laser microdissection

value: Embryonic day E15

tag: salivary gland domain


title: RKO aza PBA

description: miRNA expression in a human colorectal cancer cell line RKO treated with 5-aza-2'-deoxycytidine plus 4-phenylbutyric acid

source_name: RKO, 5-aza-C and 4-PBA

tag: treatment


title: 4h0R_2

description: EPI200 4h control 2

tag: cell model

value: Mat-Tek EPI-200 3-dimensional skin model


title: >=5% myeloblast bone marrow 85

description:
genomic DNA from bone marrow aspirates
HIGH85


title: EmbryonicBud_Age15 rep 5

description:
laser microdissected sample
E15MB_005

source_name: Salivary gland, replicate 5

value: salivary gland


title: PBMC_epimutationpatientII4_rep1

description: II4 from Lynch syndrome family 16.

source_name: Peripheral blood lymphocytes, asymptomatic carrier

tag: gender

value: female

tag: phenotype

value: asymptomatic carrier of constitutional MLH1 epimutation

tag: family member

value: peripheral blood lymphocytes


title: HCT116 5-aza-dC

description: miRNA expression in a human colorectal cancer cell line HCT116 treated with 5-aza-2'-deoxycytidine

source_name: HCT116, 5-aza-dC

value: colorectal cancer


title: HCT116 aza PBA

description: miRNA expression in a human colorectal cancer cell line HCT116 treated with 5-aza-2'-deoxycytidine plus 4-phenylbutyric acid

source_name: HCT116, 5-aza-dC and 4-PBA


title: HCT116 DNMT1 3B KO

description: miRNA expression in a human colorectal cancer cell line HCT116 in which DNMT1 and DNMT3B are genetically disrupted

source_name: HCT116, DNMT1 and 3B double KO

value: untreated

tag: genotype

value: DNMT1 and DNMT3B KO


title: >=5% myeloblast bone marrow 83

description:
genomic DNA from bone marrow aspirates
HIGH83

tag: cells

value: bone marrow aspirates


title: >=5% myeloblast bone marrow 84

description:
genomic DNA from bone marrow aspirates
HIGH84

tag: who diagnosis

value: AML


title: >=5% myeloblast bone marrow 82

description:
genomic DNA from bone marrow aspirates
HIGH82


title: >=5% myeloblast bone marrow 81

description:
genomic DNA from bone marrow aspirates
HIGH81


title: P3, PRE, AL lesional

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: standard GeneChip Affymetrix protocol

scan_protocol: Hewlett–Packard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor). Each platform was preprocess separately, then merged. An extra quantile normalization was needed to normalized across platforms.

source_name: P3, PRE, AL

label_protocol: standard GeneChip Affymetrix protocol

extract_protocol: Qiagen RNeasy Kit protocol

value: NB-UVB

tag: patient

tag: time

value: pre-treatment

value: lesional skin

tag: scorad


title: P3, PRE, ANL non-lesional

source_name: P3, PRE, ANL

value: non-lesional skin


title: >=5% myeloblast bone marrow 80

description:
genomic DNA from bone marrow aspirates
HIGH80


title: EmbryonicBud_Age15 rep 4

description:
laser microdissected sample
E15MB_004

source_name: Salivary gland, replicate 4

tag: strain

value: ICR

tag: age

value: Bud


title: Control-T

description: Expression data from untreated MCF-7 cell line

source_name: MCF-7 cell line control

tag: cell line

value: MCF-7 breast cancer cell line

tag: cell line source

value: 69 year old female

value: Control


title: P5, PRE, ANL non-lesional

source_name: P5, PRE, ANL

tag: tissue


title: EmbryonicBud_Age15 rep 3

description:
laser microdissected sample
E15MB_003

source_name: Salivary gland, replicate 3

tag: collection method

value: laser microdissection

value: Embryonic day E15

value: salivary gland

tag: salivary gland domain


title: EmbryonicBud_Age15 rep 2

description:
laser microdissected sample
E15MB_002

source_name: Salivary gland, replicate 2


title: EmbryonicSecondaryDuct_Age14 rep 7

description:
laser microdissected sample
E14SD_007

source_name: Salivary gland, replicate 7

value: Embryonic day E14

value: Secondary Duct


title: >=5% myeloblast bone marrow 78

description:
genomic DNA from bone marrow aspirates
HIGH78

source_name: MDS or AML bone marrow aspirates


title: >=5% myeloblast bone marrow 79

description:
genomic DNA from bone marrow aspirates
HIGH79


title: P4, PRE, AL lesional

source_name: P4, PRE, AL

tag: treatment


title: EmbryonicSecondaryDuct_Age14 rep 8

description:
laser microdissected sample
E14SD_008

source_name: Salivary gland, replicate 8


title: Pik3cg-/-_C2

city: Hinxton

first: Dirk

middle: Stefan

last: Paul

address: Wellcome Trust Genome Campus

department: Human Genetics

country: United Kingdom

institute: Wellcome Trust Sanger Institute

description: Pik3cg-/-, biol. rep. C, tech. rep. 2

hyb_protocol: Standard Illumina BeadChip protocols were used to hybridize to MouseWG-6 v2 Expression BeadChips. All experimental procedures were carried out according to the manufacturer’s protocol.

scan_protocol: Arrays were washed, detected and scanned according to the manufacturer’s protocol.

data_processing: On the raw expression data, we performed background subtraction, variance-stabilizing transformation and quantile normalization across all samples with the R package ‘lumi’.

source_name: Whole blood

label_protocol: Standard Illumina BeadChip protocols were used to generate biotinylated cRNA. All experimental procedures were carried out according to the manufacturer’s protocol.

extract_protocol: We extracted total RNA using the Mouse RiboPure-Blood RNA Isolation Kit (Ambion). Total RNA was quantified using the NanoDrop (Labtech International) and quality-checked using the 2100 Bioanalyzer (Agilent Technologies).

tag: gender

value: female

value: 13-16 weeks

tag: genetic background

value: whole blood


title: Pik3cg-/-_C1

description: Pik3cg-/-, biol. rep. C, tech. rep. 1


title: >=5% myeloblast bone marrow 77

description:
genomic DNA from bone marrow aspirates
HIGH77

value: bone marrow aspirates

value: AML


title: EmbryonicSecondaryDuct_Age14 rep 4

description:
laser microdissected sample
E14SD_004


title: EmbryonicSecondaryDuct_Age14 rep 6

description:
laser microdissected sample
E14SD_006

source_name: Salivary gland, replicate 6


title: P4, PRE, ANL non-lesional

source_name: P4, PRE, ANL

value: NB-UVB

value: pre-treatment


title: P6, PRE, AL lesional

source_name: P6, PRE, AL

value: lesional skin


title: >=5% myeloblast bone marrow 76

description:
genomic DNA from bone marrow aspirates
HIGH76


title: P2, PRE, AL lesional

source_name: P2, PRE, AL


title: EmbryonicMainDuct_Age15 rep 5

description:
laser microdissected sample
E15MD_005

source_name: Salivary gland, replicate 5

value: ICR

value: Main Duct


title: EmbryonicSecondaryDuct_Age14 rep 3

description:
laser microdissected sample
E14SD_003


title: EmbryonicBud_Age15 rep 1

description:
laser microdissected sample
E15MB_001

source_name: Salivary gland, replicate 1

value: Bud


title: >=5% myeloblast bone marrow 75

description:
genomic DNA from bone marrow aspirates
HIGH75


title: Pik3cg-/-_A2

description: Pik3cg-/-, biol. rep. A, tech. rep. 2


title: P2, PRE, ANL non-lesional

source_name: P2, PRE, ANL

value: non-lesional skin


title: Pik3cg-/-_A1

description: Pik3cg-/-, biol. rep. A, tech. rep. 1


title: >=5% myeloblast bone marrow 74

description:
genomic DNA from bone marrow aspirates
HIGH74


title: Pik3cg-/-_B2

description: Pik3cg-/-, biol. rep. B, tech. rep. 2


title: EmbryonicSecondaryDuct_Age14 rep 5

description:
laser microdissected sample
E14SD_005

value: laser microdissection


title: Pik3cg-/-_B1

description: Pik3cg-/-, biol. rep. B, tech. rep. 1


title: P10, PRE, ANL non-lesional

source_name: P10, PRE, ANL


title: WT_C2

description: WT, biol. rep. C, tech. rep. 2

value: WT


title: WT_B2

description: WT, biol. rep. B, tech. rep. 2


title: EmbryonicSecondaryDuct_Age14 rep 2

description:
laser microdissected sample
E14SD_002

value: salivary gland


title: P10, PRE, AL lesional

source_name: P10, PRE, AL


title: EmbryonicSecondaryDuct_Age14 rep 1

description:
laser microdissected sample
E14SD_001

value: Embryonic day E14


title: normal colon

description: miRNA expression in a normal colon tissue

source_name: normal colon

tag: disease state

value: normal colon

value: untreated


title: P8, PRE, AL lesional

source_name: P8, PRE, AL


title: WT_C1

description: WT, biol. rep. C, tech. rep. 1

value: female

value: 13-16 weeks

tag: genotype


title: EmbryonicMainDuct_Age14 rep 4

description:
laser microdissected sample
E14MD_004

source_name: Salivary gland, replicate 4


title: WT_B1

description: WT, biol. rep. B, tech. rep. 1

value: whole blood


title: >=5% myeloblast bone marrow 70

description:
genomic DNA from bone marrow aspirates
HIGH70

tag: cells

value: bone marrow aspirates

value: AML


title: >=5% myeloblast bone marrow 73

description:
genomic DNA from bone marrow aspirates
HIGH73

tag: who diagnosis


title: >=5% myeloblast bone marrow 69

description:
genomic DNA from bone marrow aspirates
HIGH69


title: EmbryonicMainDuct_Age14 rep 3

description:
laser microdissected sample
E14MD_003

source_name: Salivary gland, replicate 3


title: >=5% myeloblast bone marrow 71

description:
genomic DNA from bone marrow aspirates
HIGH71

source_name: MDS or AML bone marrow aspirates


title: >=5% myeloblast bone marrow 68

description:
genomic DNA from bone marrow aspirates
HIGH68


title: >=5% myeloblast bone marrow 67

description:
genomic DNA from bone marrow aspirates
HIGH67


title: EmbryonicMainDuct_Age14 rep 2

description:
laser microdissected sample
E14MD_002

source_name: Salivary gland, replicate 2


title: P7, PRE, AL lesional

source_name: P7, PRE, AL

value: NB-UVB

tag: patient

value: pre-treatment


title: WT_A2

description: WT, biol. rep. A, tech. rep. 2

source_name: Whole blood


title: P7, PRE, ANL non-lesional

source_name: P7, PRE, ANL

tag: time


title: EmbryonicBud_Age14 rep 8

description:
laser microdissected sample
E14MB_008

source_name: Salivary gland, replicate 8

value: ICR


title: EmbryonicBud_Age14 rep 7

description:
laser microdissected sample
E14MB_007

source_name: Salivary gland, replicate 7


title: 42w old FHH molsidomine female (4256273084_J)

first: Sebastiaan

last: Wesseling

address: Heidelberglaan 100

department: Nephrology & Hypertension

institute: University Medical Center Utrecht

description: Adult-mols-female

hyb_protocol: Signal is developed with streptavidin-Cy3.

scan_protocol: The BeadChip is scanned with the Illumina BeadArray Reader, which is a two-channel, 0.8 μm resolution confocal laser scanner. During the scan process, the BeadChip barcode is scanned, ensuring effective data management.

data_processing: The raw bead files (each file contained about 1 million beads) was reorganized into non-normalized data files using T4Illumina (see www.nephrogenomics.net/UMCUtrecht/Tools/). The data were log2-transformed and quantile normalized using the program FlexArray (see gqinnovationcenter.com/services/bioinformatics/flexarray/index.aspx?l=e). The statistical program CyberT was used to signify change in gene expression between any two groups (e.g. Molsidomine-vs-Untreated FHH of 2 days old). P<0.05 was considered significant. In our analysis we use Array_Address_ID, instead of ID_Ref, as identities for the genes because they contain more unique probe codes.

organism: Rattus norvegicus

source_name: rat kidney

label_protocol: The samples amplified and labeled using Illumina TotalPrep RNA Amplification Kit (Ambion, cat. nr. IL1791).

growth_protocol: 42w old FHH molsidomine female

extract_protocol: Kidneys was homogenized in TRIzol using beadbeater. Then RNA was extracted from Trizol and purified using NucleoSpin® RNA II kit from Macherey-Nagel (cat. #: 740 955). The purified RNA was sent to ServiceXS.com who processed the samples as recommended by Illumina.

treatment_protocol: Fawn-Hooded Hypertensive (FHH) rats were bred. Pregnant female FHH was treated with NO donor molsidomine in drinking water (120 mg/L) two weeks before to four weeks after birth. The offspring were sacrificed at 2d, 2w and 36w/42w (male/female respectively) old. The kidneys were isolated from these rats and subjected to BeadChip Illumina RatRef-12. Molsidomine-treated rats were compared to age- and gender-matched untreated FHH rats.

value: Fawn-Hooded Hypertensive

value: 42 weeks

value: kidney

value: molsidomine


title: P1, PRE, ANL non-lesional

source_name: P1, PRE, ANL

value: non-lesional skin

tag: scorad


title: P9, PRE, ANL non-lesional

source_name: P9, PRE, ANL


title: P9, PRE, AL lesional

source_name: P9, PRE, AL

value: lesional skin


title: 42w old FHH molsidomine female (4256273083_I)

description: Adult-mols-female

tag: strain


title: P8, POST, AL lesional

source_name: P8, POST, AL

value: post-treatment


title: >=5% myeloblast bone marrow 66

description:
genomic DNA from bone marrow aspirates
HIGH66


title: P3, POST, AL lesional

source_name: P3, POST, AL


title: WT_A1

description: WT, biol. rep. A, tech. rep. 1

tag: age

value: WT


title: EmbryonicBud_Age14 rep 5

description:
laser microdissected sample
E14MB_005

source_name: Salivary gland, replicate 5

value: laser microdissection

value: Embryonic day E14

value: salivary gland

value: Bud


title: >=5% myeloblast bone marrow 65

description:
genomic DNA from bone marrow aspirates
HIGH65

value: bone marrow aspirates


title: EmbryonicBud_Age14 rep 6

description:
laser microdissected sample
E14MB_006

source_name: Salivary gland, replicate 6


title: 42w old FHH molsidomine female (4256273084_F)

description: Adult-mols-female

value: female


title: EmbryonicMainDuct_Age14 rep 1

description:
laser microdissected sample
E14MD_001

source_name: Salivary gland, replicate 1

value: Main Duct


title: EmbryonicBud_Age14 rep 4

description:
laser microdissected sample
E14MB_004

source_name: Salivary gland, replicate 4


title: P3, POST, ANL non-lesional

source_name: P3, POST, ANL

value: NB-UVB


title: 42w old FHH molsidomine female (4256273078_B)

description: Adult-mols-female


title: >=5% myeloblast bone marrow 63

description:
genomic DNA from bone marrow aspirates
HIGH63

source_name: MDS or AML bone marrow aspirates

value: SAML


title: P5, POST, AL lesional

source_name: P5, POST, AL


title: >=5% myeloblast bone marrow 62

description:
genomic DNA from bone marrow aspirates
HIGH62


title: 36w old FHH molsidomine male (4256273083_F)

description: Adult-mols-male

growth_protocol: 36w old FHH molsidomine male

value: Fawn-Hooded Hypertensive

value: 36 weeks

value: male


title: >=5% myeloblast bone marrow 61

description:
genomic DNA from bone marrow aspirates
HIGH61


title: 42w old FHH molsidomine female (4256273008_A)

description: Adult-mols-female

value: 42 weeks

value: kidney

value: molsidomine


title: 36w old FHH molsidomine male (4256273008_K)

description: Adult-mols-male


title: P5, POST, ANL non-lesional

source_name: P5, POST, ANL

value: post-treatment

value: non-lesional skin


title: 36w old FHH molsidomine male (4256273083_C)

description: Adult-mols-male


title: EmbryonicBud_Age14 rep 3

description:
laser microdissected sample
E14MB_003

source_name: Salivary gland, replicate 3

value: ICR

value: laser microdissection


title: 36w old FHH molsidomine male (4256273084_D)

description: Adult-mols-male


title: >=5% myeloblast bone marrow 59

description:
genomic DNA from bone marrow aspirates
HIGH59


title: >=5% myeloblast bone marrow 60

description:
genomic DNA from bone marrow aspirates
HIGH60

value: sAML


title: EmbryonicSecondaryDuct_Age13 rep 5

description:
laser microdissected sample
E13.5SD_005

value: Embryonic day E13

value: salivary gland

value: Secondary Duct


title: EmbryonicSecondaryDuct_Age13 rep 4

description:
laser microdissected sample
E13.5SD_004


title: P1, PRE, AL lesional

source_name: P1, PRE, AL

value: pre-treatment

value: lesional skin


title: EmbryonicBud_Age14 rep 1

description:
laser microdissected sample
E14MB_001

value: Embryonic day E14

value: Bud


title: 36w old FHH molsidomine male (4256273078_A)

description: Adult-mols-male

value: Fawn-Hooded Hypertensive

value: 36 weeks


title: HCT116 untreated

description: miRNA expression in a human colorectal cancer cell line HCT116

source_name: HCT116, untreated

value: colorectal cancer

tag: cell line

value: untreated


title: EmbryonicSecondaryDuct_Age13 rep 3

description:
laser microdissected sample
E13.5SD_003


title: P6, POST, AL lesional

source_name: P6, POST, AL

value: NB-UVB


title: >=5% myeloblast bone marrow 58

description:
genomic DNA from bone marrow aspirates
HIGH58

value: bone marrow aspirates

value: SAML


title: 42w old FHH untreated female (4256273008_J)

description: Adult-untreated-female

source_name: rat kidney

growth_protocol: 42w old FHH untreated female

value: 42 weeks

value: kidney

value: female

value: Untreated


title: >=5% myeloblast bone marrow 64

description:
genomic DNA from bone marrow aspirates
HIGH64


title: P4, POST, AL lesional

source_name: P4, POST, AL

value: post-treatment


title: P6, POST, ANL non-lesional

source_name: P6, POST, ANL

value: non-lesional skin


title: >=5% myeloblast bone marrow 57

description:
genomic DNA from bone marrow aspirates
HIGH57


title: P2, POST, AL lesional

source_name: P2, POST, AL


title: 42w old FHH untreated female (4256273008_I)

description: Adult-untreated-female


title: >=5% myeloblast bone marrow 56

description:
genomic DNA from bone marrow aspirates
HIGH56


title: >=5% myeloblast bone marrow 55

description:
genomic DNA from bone marrow aspirates
HIGH55


title: P4, POST, ANL non-lesional

source_name: P4, POST, ANL


title: EmbryonicSecondaryDuct_Age13 rep 2

description:
laser microdissected sample
E13.5SD_002

source_name: Salivary gland, replicate 2

value: ICR

value: laser microdissection

value: Embryonic day E13

value: salivary gland

value: Secondary Duct


title: P2, POST, ANL non-lesional

source_name: P2, POST, ANL


title: EmbryonicSecondaryDuct_Age13 rep 1

description:
laser microdissected sample
E13.5SD_001

source_name: Salivary gland, replicate 1


title: EmbryonicMainDuct_Age13 rep 6

description:
laser microdissected sample
E13.5MD_006

source_name: Salivary gland, replicate 6

value: Main Duct


title: >=5% myeloblast bone marrow 54

description:
genomic DNA from bone marrow aspirates
HIGH54


title: 42w old FHH untreated female (4256273083_G)

description: Adult-untreated-female

value: Fawn-Hooded Hypertensive


title: P10, POST, AL lesional

source_name: P10, POST, AL

value: lesional skin


title: >=5% myeloblast bone marrow 53

description:
genomic DNA from bone marrow aspirates
HIGH53

source_name: MDS or AML bone marrow aspirates


title: >=5% myeloblast bone marrow 52

description:
genomic DNA from bone marrow aspirates
HIGH52


title: 36w old FHH untreated male (4256273083_J)

description: Adult-untreated-male

growth_protocol: 36w old FHH untreated male

value: 36 weeks

value: male


title: EmbryonicMainDuct_Age13 rep 5

description:
laser microdissected sample
E13.5MD_005

source_name: Salivary gland, replicate 5


title: EmbryonicMainDuct_Age13 rep 3

description:
laser microdissected sample
E13.5MD_003


title: P10, POST, ANL non-lesional

source_name: P10, POST, ANL

value: NB-UVB


title: EmbryonicMainDuct_Age13 rep 2

description:
laser microdissected sample
E13.5MD_002


title: 36w old FHH untreated male (4256273008_D)

description: Adult-untreated-male


title: 42w old FHH untreated female (4256273078_L)

description: Adult-untreated-female

value: 42 weeks


title: >=5% myeloblast bone marrow 51

description:
genomic DNA from bone marrow aspirates
HIGH51

value: bone marrow aspirates

value: SAML


title: >=5% myeloblast bone marrow 49

description:
genomic DNA from bone marrow aspirates
HIGH49


title: P7, POST, ANL non-lesional

source_name: P7, POST, ANL


title: EmbryonicCleft_Age13 rep 4

description:
laser microdissected sample
E13.5Cl_004

source_name: Salivary gland, replicate 4

value: Cleft


title: >=5% myeloblast bone marrow 48

description:
genomic DNA from bone marrow aspirates
HIGH48


title: >=5% myeloblast bone marrow 47

description:
genomic DNA from bone marrow aspirates
HIGH47


title: >=5% myeloblast bone marrow 50

description:
genomic DNA from bone marrow aspirates
HIGH50


title: 36w old FHH untreated male (4256273078_F)

description: Adult-untreated-male

value: kidney

value: Untreated


title: P1, POST, ANL non-lesional

source_name: P1, POST, ANL

value: post-treatment

value: non-lesional skin


title: P1, POST, AL lesional

source_name: P1, POST, AL


title: EmbryonicCleft_Age13 rep 3

description:
laser microdissected sample
E13.5Cl_003

source_name: Salivary gland, replicate 3

value: ICR

value: laser microdissection

value: Embryonic day E13


title: 36w old FHH untreated male (4256273084_B)

description: Adult-untreated-male

source_name: rat kidney


title: P7, POST, AL lesional

source_name: P7, POST, AL


title: 2w old FHH molsidomine female (4160685015_A)

growth_protocol: 2w old FHH molsidomine female

value: 2 weeks

value: female

value: molsidomine


title: 2w old FHH molsidomine female (4160685018_F)

value: Fawn-Hooded Hypertensive


title: EmbryonicMainDuct_Age13 rep 4

description:
laser microdissected sample
E13.5MD_004

value: salivary gland

value: Main Duct


title: EmbryonicMainDuct_Age13 rep 1

description:
laser microdissected sample
E13.5MD_001


title: EmbryonicCleft_Age13 rep 1

description:
laser microdissected sample
E13.5Cl_001


title: EmbryonicCleft_Age13 rep 2

description:
laser microdissected sample
E13.5Cl_002


title: 36w old FHH untreated male (4256273084_H)

description: Adult-untreated-male

value: 36 weeks

value: male


title: 2w old FHH molsidomine female (4160685013_K)


title: P8, POST, ANL non-lesional

source_name: P8, POST, ANL

value: NB-UVB


title: >=5% myeloblast bone marrow 46

description:
genomic DNA from bone marrow aspirates
HIGH46

value: bone marrow aspirates

value: sAML


title: 2w old FHH molsidomine female (4160685010_J)

value: kidney


title: >=5% myeloblast bone marrow 72

description:
genomic DNA from bone marrow aspirates
HIGH72

value: AML


title: >=5% myeloblast bone marrow 44

description:
genomic DNA from bone marrow aspirates
HIGH44

value: RAEB


title: >=5% myeloblast bone marrow 45

description:
genomic DNA from bone marrow aspirates
HIGH45


title: EmbryonicBud_Age14 rep 2

description:
laser microdissected sample
E14MB_002

value: ICR

value: Embryonic day E14

value: Bud


title: >=5% myeloblast bone marrow 43

description:
genomic DNA from bone marrow aspirates
HIGH43


title: EmbryonicCentralBud_Age13 rep 5

description:
laser microdissected sample
E13.5CB_005

value: laser microdissection

value: Embryonic day E13

value: Central Bud


title: SMAD4 Stimulated mRNA rep 2

city: Columbus

first: Brian

middle: Alexander

last: Kennedy

state: Ohio

address: 278 Chittenden AVE

institute: The Ohio State University

description: SMAD4 Stimulated A2780 cells rep 2

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on HGU133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner7g.

data_processing: MAS5 from affy package in Bioconductor

source_name: A2780 cell line

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

growth_protocol: cells grown in RPMI 1640 supplemented with 10% FBS in 5% CO2 incubator at 37C. Cells were inspected daily and split at ~70% confluance.

extract_protocol: Standard trizol extraction

treatment_protocol: 80% confluant cells were stimulated with 10ng/ml recombinant TGFβ1 for 3 hours prior to RNA extraction.

value: TGF-beta


title: >=5% myeloblast bone marrow 42

description:
genomic DNA from bone marrow aspirates
HIGH42


title: EmbryonicCentralBud_Age13 rep 3

description:
laser microdissected sample
E13.5CB_003

value: salivary gland


title: SMAD4 Stimulated mRNA rep 1

description: SMAD4 Stimulated A2780 cells rep 1


title: 2w old FHH molsidomine female (4160685004_B)

value: Fawn-Hooded Hypertensive

value: 2 weeks

value: female

value: molsidomine


title: 2w old FHH molsidomine female (4160685006_E)


title: SMAD4 Unstimulated mRNA rep 2

description: SMAD4 Unstimulated A2780 cells rep 2

value: untreated


title: lung cancer tissue_LCA021

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

institute: University Tuebingen

description: lung cancer tissue

hyb_protocol: standard affymetrix hybridisation protocol

scan_protocol: standard affymetrix scanning protocol with affymetrix 3000 7G Scanner

data_processing: The data were analyzed with GCOS version 1.1.1.052 using Affymetrix default analysis settings. Scaling was performed using Mask Files provided by Affymetrix (HGU133Anorm.msk for U133A arrays, HGU133_plus_2norm.msk for U133 Plus 2.0 arrays). The mean target intensity was arbitrarily set to 1200 (U133A) or 850 (U133 Plus 2.0). All samples were normalized with RMA algorithm.

source_name: lung cancer tissue

label_protocol: standard affymetrix labeling protocol

extract_protocol: standard qiagen isolation protocol

tag: cell type

value: adenocarcinoma


title: 2w old FHH molsidomine male (4160685013_I)

growth_protocol: 2w old FHH molsidomine male

tag: tissue

value: kidney

value: male


title: SMAD4 Stimulated mRNA rep 3

description: SMAD4 Stimulated A2780 cells rep 3


title: >=5% myeloblast bone marrow 41

description:
genomic DNA from bone marrow aspirates
HIGH41

value: bone marrow aspirates

value: RAEB


title: SMAD4 Unstimulated mRNA rep 3

description: SMAD4 Unstimulated A2780 cells rep 3


title: normal kidney tissue U133Plus_NTk2

description: normal kidney tissue U133Plus

source_name: normal kidney tissue U133Plus

tag: tissue type

value: normal kidney tissue


title: 2w old FHH molsidomine male (4160685018_A)


title: EmbryonicCentralBud_Age13 rep 2

description:
laser microdissected sample
E13.5CB_002

source_name: Salivary gland, replicate 2

value: ICR

tag: collection method

tag: salivary gland domain


title: SMAD4 Unstimulated mRNA rep 1

description: SMAD4 Unstimulated A2780 cells rep 1

tag: treatment


title: EmbryonicCentralBud_Age13 rep 4

description:
laser microdissected sample
E13.5CB_004

value: laser microdissection


title: >=5% myeloblast bone marrow 40

description:
genomic DNA from bone marrow aspirates
HIGH40


title: EmbryonicCentralBud_Age13 rep 1

description:
laser microdissected sample
E13.5CB_001

source_name: Salivary gland, replicate 1

value: Embryonic day E13


title: 2w old FHH molsidomine male (4160685010_E)

tag: gender


title: lung cancer tissue_LCA018

description: lung cancer tissue


title: lung cancer tissue_LCA020

description: lung cancer tissue


title: 2w old FHH molsidomine male (4160685006_H)


title: 2w old FHH molsidomine male (4160685004_K)