title: KD570

description: Kawasaki disease sample from KD570

source_name: Genomic DNA from KD570

value: PBMC


title: Neg. Control (H2O) 42 days 135

status: Public on Dec 31 2016

type: RNA

city: Ottawa

first: Mainul

last: Husain

address: 50 Colombine Driveway

country: Canada

institute: Health Canada

description: Biological replicate Day 42, Control

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

molecule: total RNA

organism: Mus musculus

source_name: Lung

label_protocol: Complementary DNA (cDNA) and cyanine labelled complementary RNA (cRNA) were synthesized from 200 ng of total RNA from individual mice from each of the CBNP exposed experimental (N = 5) and control groups (N = 5), and universal reference total RNA (Agilent Technologies, Inc., Mississauga, ON, Canada), using Low Input Quick Amp Labeling Kit (Agilent Technologies Inc., Mississauga, ON, Canada) according to the manufacturer’s instruction. Cyanine-labelled cRNAs were synthesized using T7 RNA polymerase in vitro transcription kits (Agilent Technologies Inc., Mississauga, ON, Canada) and later purified using RNeasy Mini Kits (Qiagen, Mississauga, ON, Canada); experimental and control cRNAs were labelled with Cyanine 5-CTP, and reference RNAs were labelled with Cyanine 3-CTP. Each experimental or control Cy-5 labelled cRNA sample (300 ng) was mixed with equimolar amounts of Cy-3 labelled reference cRNA and hybridized to Agilent SurePrint G3 Mouse GE 8x60K oligonucleotide microarrays (Agilent Technologies Inc., Mississauga, ON, Canada) for 17 h in a hybridization chamber at 65°C with a rotation speed of 10 rpm. Microarray slides were washed twice according to the manufacturer’s instructions (1X with wash buffer 1 and 1X with wash buffer 2; Agilent Technologies Inc., Mississauga, ON, Canada), and were scanned on an Agilent G2505C scanner at 3 µm resolution. Data from the scanned images were extracted using Agilent Feature Extraction software version 11.0.1.1.

growth_protocol: Six-to-seven week old female C57BL/6BomTac mice were purchased from Taconic (Ry, Denmark) and were allowed 1-2 weeks to acclimate. A total of 112 mice were divided into 8 experimental (N = 8 per group) and 8 control groups (N = 6 per group), and were maintained in polypropylene cages with sawdust bedding and enrichment, at 20-22°C temperature and relative humidity of 40-60% with a 12 h light-to-dark cycle. All mice received food and water ad libitum during the period of the whole experiment. All animal experiments were approved by the Danish “Animal Experiments Inspectorate” and performed according to their guidelines for ethical conduct and care for animals in research (The Danish Ministry of Justice, Animal Experiments Inspectorate, permission 2010/561-1779).

extract_protocol: Total RNA was isolated from random sections of lung tissues from 80 mice in total (n = 5 per exposed and control group) using TRIzol (Invitrogen, Carlsbad, CA, USA) and purified using RNeasy Plus Mini Kit (Qiagen, Mississauga, ON, Canada) according to the manufacturer’s instructions. Total RNA concentration was measured using NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE, USA) and RNA quality and integrity were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Mississauga, ON, Canada) according to the manufacturer’s instruction. All RNA samples showed A260/280 ratios between 2.0 and 2.15, and RNA integrity numbers (RIN) of 7 and above, and were used to conduct microarray and real-time RT-qPCR experiments. Total RNA samples were stored at -80°C until analysed.

treatment_protocol: Briefly, printex 90 was suspended in 0.2 µm filtered, ɤ-irradiated Nanopure Diamond UV water (Pyrogens: ˂0,001 EU/ml, total organic carbon: ˂3.0 ppb), for 16 min without pause, using a Branson Sonifier S-450D (Branson Ultrasonics Corp., Danbury, CT, USA), and was subjected to sonication using a Branson Sonifier S-450D (Branson Ultrasonics Corp., Danbury, CT, USA) equipped with a disruptor horn (model number 101-147-037(Jackson et al., 2011a)). Total sonication time was 16 min without pause; samples were kept cool on ice during the sonication procedure. Vehicle control solutions contained only Nanopure Diamond UV water was also sonicated as described above. A total of 112 C57BL/6 mice were divided into 8 experimental (N = 8 per group) and 8 control (N = 6 per group) groups. Prior to intratracheal instillation, mice were anesthetized with 4% Isofluoran. Mice from the experimental groups received a single dose of 0.162 mg/50 µl (162 µg per mouse) of CBNP suspension following by 200 µl air by intratracheal instillation. Mice from matching control groups received the same volume of control vehicle. Mice were anesthetized with subcutaneous injection of Hypnorm® (fentanyl citrate 0.315 mg/ml and fluanisone 10 mg/ml from Janssen Pharma) and Dormicum® (Midazolam 5 mg/mL from Roche) at 3 hrs, 1, 2, 3, 4, 5, 14 and 42 d following CBNP or control vehicle exposure. Blood was collected by cardiac puncture and was stabilized in 36 µl of 0.17M potassium-EDTA and kept on ice until plasma was isolated by centrifugation at 2500 x g for 10 min at 4°C. Lungs were flushed twice with 0.8ml sterile 0.9% NaCl through the trachea to obtain BAL fluid. BAL fluids were stored on ice until centrifugation at 400 x g for 10 min at 4°C. The BAL cells were re-suspended in 100 µl medium (HAM F-12 with 1% penicillin/streptomycin and 10% fetal bovine serum). Acellular BAL fluid was recovered and stored at -80°C. The total number of living and dead cells in BAL was determined by NucleoCounter NC-200TM (Chemometec, Denmark) from diluted cell suspension following manufacturer’s protocol, the total cell counts were calculated for each mouse. Lung and liver were collected immediately, were snap frozen in liquid nitrogen and stored at -80°C until analyzed.

tag: tissue

value: lung

tag: strain

value: C57BL/6BomTac Mouse

tag: treatment

value: Neg. Control (H2O)

tag: sampleID

tag: time point

value: 42 days

tag: dose

source_name: Agilent Universal Mouse Reference RNA (UMRR)

tag: sample type

value: Reference

tag: cell type

value: 11 mouse cell lines


title: 12-05KM546

city: Ulm

first: Stephan

middle: Rainer

last: Bohl

address: Alber Einstein Allee 23

department: Internal Medicine III

country: Germany

institute: University Hospital of Ulm

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed

label: Biotin

organism: Homo sapiens

source_name: mononuclear cells from bone marrow

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.

extract_protocol: The total RNA was purified with a TRIzol-based protocol.

treatment_protocol: Primary AML samples were taken at the time of diagnosis prior to treatment with DAC. For the analysis patients were then grouped based on the response to DAC which was given later during the course of the disease. In this study, DAC was given three times daily on 3 consecutive days (total dose 135mg/m², repeated every 6 weeks).

tag: age

tag: gender

value: male

tag: genetic risk group

value: intermediate

tag: dnmt3a status

value: WT

tag: npm1 status

tag: response to dac

value: yes response


title: Printex90 14 days 117

description: Biological replicate Day 14, Treated

hyb_protocol: Each experimental or control Cy-5 labelled cRNA sample (300 ng) was mixed with equimolar amounts of Cy-3 labelled reference cRNA and hybridized to Agilent SurePrint G3 Mouse GE 8x60K oligonucleotide microarrays (Agilent Technologies Inc., Mississauga, ON, Canada) for 17 h in a hybridization chamber at 65°C with a rotation speed of 10 rpm. Microarray slides were washed twice according to the manufacturer’s instructions (1X with wash buffer 1 and 1X with wash buffer 2; Agilent Technologies Inc., Mississauga, ON, Canada), and were scanned on an Agilent G2505C scanner at 3 µm resolution. Data from the scanned images were extracted using Agilent Feature Extraction software version 11.0.1.1.

value: 14 days


title: Neg. Control (H2O) 4 days 75

description: Biological replicate Day 4, Control

value: 4 days


title: Neg. Control (H2O) 5 days 82

description: Biological replicate Day 5, Control

value: 5 days


title: KD542

type: genomic

city: Kaohsiung

first: Kuang-Den

last: Chen

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: Kawasaki disease sample from KD542

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

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

data_processing: GenomeStudio methylation module v.1.9.0

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Genomic DNA from KD542

label_protocol: Standard Illumina Protocol

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

tag: Sex

tag: disease

value: Kawasaki disease

tag: cal


title: KD546

description: Kawasaki disease sample from KD546

source_name: Genomic DNA from KD546

tag: tissue


title: KD601

description: Kawasaki disease sample from KD601

source_name: Genomic DNA from KD601


title: Neg. Control (H2O) 3hours 51

description: Biological replicate 3 hours, Control

tag: strain


title: KD534

description: Kawasaki disease sample from KD534

source_name: Genomic DNA from KD534


title: Printex90 3hours 2

description: Biological replicate 3 Hours, Treated

tag: treatment


title: KD537

description: Kawasaki disease sample from KD537

source_name: Genomic DNA from KD537


title: FC938

description: Normal control sample from FC938

source_name: Genomic DNA from FC938

value: Normal control


title: KD517

description: Kawasaki disease sample from KD517

source_name: Genomic DNA from KD517


title: Neg. Control (H2O) 3hours 50

description: Biological replicate 3 hours, Control

tag: sampleID


title: Printex90 5 days 45

description: Biological replicate Day 5, Treated

tag: time point


title: KD444

description: Kawasaki disease sample from KD444

source_name: Genomic DNA from KD444


title: KD527

description: Kawasaki disease sample from KD527

source_name: Genomic DNA from KD527


title: KD528

description: Kawasaki disease sample from KD528

source_name: Genomic DNA from KD528


title: KD505

description: Kawasaki disease sample from KD505

source_name: Genomic DNA from KD505


title: Neg. Control (H2O) 1 day 57

description: Biological replicate Day 1, Control

value: 1 day

tag: dose


title: Neg. Control (H2O) 3 days 69

description: Biological replicate Day 3, Control

value: 3 days

tag: sample type


title: KD456

description: Kawasaki disease sample from KD456

source_name: Genomic DNA from KD456

value: PBMC


title: Neg. Control (H2O) 5 days 83

description: Biological replicate Day 5, Control

value: lung

value: C57BL/6BomTac Mouse

tag: cell type


title: Printex90 3hours 5

description: Biological replicate 3 Hours, Treated


title: FC940

description: Normal control sample from FC940

source_name: Genomic DNA from FC940

tag: age


title: FC926

description: Normal control sample from FC926

source_name: Genomic DNA from FC926


title: FC939

description: Normal control sample from FC939

source_name: Genomic DNA from FC939


title: Printex90 3 days 31

description: Biological replicate Day 3, Treated

source_name: Lung

source_name: Agilent Universal Mouse Reference RNA (UMRR)


title: Printex90 42 days 122

description: Biological replicate Day 42, Treated

value: 42 days


title: Printex90 5 days 46

description: Biological replicate Day 5, Treated

value: Reference


title: Neg. Control (H2O) 4 days 76

description: Biological replicate Day 4, Control

value: Neg. Control (H2O)

value: 11 mouse cell lines


title: Neg. Control (H2O) 2 days 66

description: Biological replicate Day 2, Control

value: 2 days


title: Neg. Control (H2O) 1 day 60

description: Biological replicate Day 1, Control


title: FC915

description: Normal control sample from FC915

source_name: Genomic DNA from FC915


title: Printex90 2 days 19

description: Biological replicate Day 2, Treated


title: FC919

description: Normal control sample from FC919

source_name: Genomic DNA from FC919


title: Printex90 4 days 33

description: Biological replicate Day 4, Treated


title: FC922

description: Normal control sample from FC922

source_name: Genomic DNA from FC922


title: FC497

description: Normal control sample from FC497

source_name: Genomic DNA from FC497


title: FC921

description: Normal control sample from FC921

source_name: Genomic DNA from FC921


title: FC906

description: Normal control sample from FC906

source_name: Genomic DNA from FC906


title: FC910

description: Normal control sample from FC910

source_name: Genomic DNA from FC910


title: Printex90 1 day 15

description: Biological replicate Day 1, Treated


title: Caudal_4

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

description: genotype:  Pitx3(gfp/+)

hyb_protocol: 300 ng of each labeled test sample was combined with 300 ng labeled  common reference and hybridized to SurePrint G3 Mouse GE 8x60K microarrays (G4858A-  028005, Agilent Technologies) according to manufacturer’s instructions.

scan_protocol: After washing, arrays were  scanned in an ozone-free room with an Agilent DNA microarray scanner (G2565CA, Agilent  Technologies).

data_processing:
Data was extracted with Feature Extraction software version 10.7.3.1 (Agilent Technologies). All  arrays were subjected to a set of quality control checks, such as visual inspection of the scans,  checking for spatial effects through pseudo-color plots, and inspection of pre- and post-normalized  data with box plots, ratio-intensity plots and principal component analysis. Normalized expression values were calculated by applying the robust multi-array average (RMA) algorithm on the Cy3 data.
During the RMA normalization probes were collapsed based on accession numbers which are in the  SystematicName  column of the raw data files.

source_name: Caudal

label_protocol: Labeling was performed in 50 mM carbonate   buffer (pH 8.5) for 1 hour at room temperature. The reaction was quenched by adding  hydroxylamine (Sigma-Aldrich) to a final concentration of 1 M. Following purification using the  RNeasy MinElute Cleanup Kit (Qiagen), yield and dye incorporation were measured on a  NanoDrop ND-2000.

extract_protocol: A 1:1 mixture of RNA and Extraction  Buffer (XB) was combined with an equal volume of 70% EtOH and loaded on column and spun  down. Flowthrough was discarded, columns were washed and 40 ul of DNAse mix (35 ul RDD  buffer + 5ul DNAseI stock solution (Qiagen RNAse-free DNAse set #79254)) was applied. After  15' incubation at Room Temperature, columns were washed and RNA was eluted according to the  manufacturer's protocol. Integrity of the isolated total RNA was evaluated using a High Sensitivity  R6K ScreenTape on a 2200 TapeStation instrument (Agilent Technologies)

treatment_protocol: Freshly dissected E14.5 Pitx3(gfp/+) ventral midbrains were separated into a rostral and caudal part  and dissociated using the Papain Dissociation Kit (Worthington Biochemical Products, LK003150).  Dissociated cells were collected in colorless L15, and sorted on a Cytopeia Influx Cell Sorter or BD  FACS Aria III using previously described settings.

value: Brain

tag: developmental stage

value: embryonic E14.5

source_name: pool of Gfp-negative cells from the same   specimens


title: FC481

description: Normal control sample from FC481

source_name: Genomic DNA from FC481


title: FC902

description: Normal control sample from FC902

source_name: Genomic DNA from FC902


title: Printex90 14 days 115

description: Biological replicate Day 14, Treated

value: 14 days


title: FC923

description: Normal control sample from FC923

source_name: Genomic DNA from FC923


title: Neg. Control (H2O) 14 days 130

description: Biological replicate Day 14, Control


title: Rostral_3

description: genotype:  Pitx3(gfp/+)

source_name: Rostral


title: FC477

description: Normal control sample from FC477

source_name: Genomic DNA from FC477


title: Rostral_2

description: genotype:  Pitx3(gfp/+)


title: FC479

description: Normal control sample from FC479

source_name: Genomic DNA from FC479


title: FC473

description: Normal control sample from FC473

source_name: Genomic DNA from FC473


title: Caudal_3

description: genotype:  Pitx3(gfp/+)


title: Rostral_4

description: genotype:  Pitx3(gfp/+)


title: FC470

description: Normal control sample from FC470

source_name: Genomic DNA from FC470


title: FC472

description: Normal control sample from FC472

source_name: Genomic DNA from FC472


title: Caudal_1

description: genotype:  Pitx3(gfp/+)


title: FC456

description: Normal control sample from FC456

source_name: Genomic DNA from FC456


title: FC454

description: Normal control sample from FC454

source_name: Genomic DNA from FC454


title: Caudal_2

description: genotype:  Pitx3(gfp/+)


title: LL31.gpr

city: Boston

first: Alan

last: Branco

address: 665 Huntington Ave.

department: Environmental Health

country: USA

institute: Harvard School of Public Health

description: Biological replicate

hyb_protocol: 3DNA procedure

scan_protocol: Scanned on an Axon 400B scanner. Images were quantified using Genepix.

data_processing: LOESS normalized, VALUE data obtained from log of processed Red signal/processed Green signal.

organism: Drosophila melanogaster

source_name: Total RNA from 35-day-old mated Ycongo flies.

label_protocol: 3DNA procedure

growth_protocol: Molasses medium was cooked in house with 850 mL of distilled water, 5 g of agar, 27.5 g of torula yeast, 52 g of corn meal, 55 g of dextrose, and 40 mL of unsulfured molasses. All strains were reared on this food at 23oC and 14-hour light cycle. In order to generate a genetically homogeneous population, all strains were submitted to individual crosses of single male and female for at least 5 generations before any study. Flies were aged for 33 days and allowed to mate for 48 hours with virgin female flies before flash frozen.

extract_protocol: TriZol procedure

tag: genotype

value: male (XY)

value: 35 days old, mated

source_name: Total RNA from 2-day-old unmated Ycongo flies.

growth_protocol: Molasses medium was cooked in house with 850 mL of distilled water, 5 g of agar, 27.5 g of torula yeast, 52 g of corn meal, 55 g of dextrose, and 40 mL of unsulfured molasses. All strains were reared on this food at 23oC and 14-hour light cycle. In order to generate a genetically homogeneous population, all strains were submitted to individual crosses of single male and female for at least 5 generations before any study. Flies were aged for 2 days before flash frozen

extract_protocol: TriZol procedure.

value: 2 days old, unmated


title: LL30.gpr

description: Biological replicate

source_name: Total RNA from 2-day-old virgin Yohio flies.

growth_protocol: Molasses medium was cooked in house with 850 mL of distilled water, 5 g of agar, 27.5 g of torula yeast, 52 g of corn meal, 55 g of dextrose, and 40 mL of unsulfured molasses. All strains were reared on this food at 23oC and 14-hour light cycle. In order to generate a genetically homogeneous population, all strains were submitted to individual crosses of single male and female for at least 5 generations before any study. Flies were aged for 2 before flash frozen.

source_name: Total RNA from 35-day-old mated Yohio flies.

growth_protocol: Molasses medium was cooked in house with 850 mL of distilled water, 5 g of agar, 27.5 g of torula yeast, 52 g of corn meal, 55 g of dextrose, and 40 mL of unsulfured molasses. All strains were reared on this food at 23oC and 14-hour light cycle. In order to generate a genetically homogeneous population, all strains were submitted to individual crosses of single male and female for at least 5 generations before any study. Flies were aged for 33 days and allowed to mate for 48 hours with virgin female flies before flash frozen


title: FC460

description: Normal control sample from FC460

source_name: Genomic DNA from FC460

value: Normal control


title: LL33.gpr

description: Biological replicate

source_name: Total RNA from 35-day-old virgin Ycongo flies.

growth_protocol: Molasses medium was cooked in house with 850 mL of distilled water, 5 g of agar, 27.5 g of torula yeast, 52 g of corn meal, 55 g of dextrose, and 40 mL of unsulfured molasses. All strains were reared on this food at 23oC and 14-hour light cycle. In order to generate a genetically homogeneous population, all strains were submitted to individual crosses of single male and female for at least 5 generations before any study. Flies were aged for 35 days before flash frozen.

value: 35 days old, unmated

growth_protocol: Molasses medium was cooked in house with 850 mL of distilled water, 5 g of agar, 27.5 g of torula yeast, 52 g of corn meal, 55 g of dextrose, and 40 mL of unsulfured molasses. All strains were reared on this food at 23oC and 14-hour light cycle. In order to generate a genetically homogeneous population, all strains were submitted to individual crosses of single male and female for at least 5 generations before any study. Flies were aged for 33 days and allowed to mate with virgin female flies for 48 hours before flash frozen.


title: LL23.gpr

description: Biological replicate

growth_protocol: Molasses medium was cooked in house with 850 mL of distilled water, 5 g of agar, 27.5 g of torula yeast, 52 g of corn meal, 55 g of dextrose, and 40 mL of unsulfured molasses. All strains were reared on this food at 23oC and 14-hour light cycle. In order to generate a genetically homogeneous population, all strains were submitted to individual crosses of single male and female for at least 5 generations before any study. Flies were aged for 33 days and allowed to mate for 48 hours with young virgin female flies before flash frozen.


title: FC459

description: Normal control sample from FC459

source_name: Genomic DNA from FC459


title: Rostral_1

description: genotype:  Pitx3(gfp/+)

source_name: pool of Gfp-negative cells from the same   specimens


title: LL32.gpr

description: Biological replicate

source_name: Total RNA from 2-day-old virgin Ycongo flies.

growth_protocol: Molasses medium was cooked in house with 850 mL of distilled water, 5 g of agar, 27.5 g of torula yeast, 52 g of corn meal, 55 g of dextrose, and 40 mL of unsulfured molasses. All strains were reared on this food at 23oC and 14-hour light cycle. In order to generate a genetically homogeneous population, all strains were submitted to individual crosses of single male and female for at least 5 generations before any study. Flies were aged for 2 days before flash frozen.

source_name: Total RNA from 35-day-old unmated Ycongo flies.

growth_protocol: Molasses medium was cooked in house with 850 mL of distilled water, 5 g of agar, 27.5 g of torula yeast, 52 g of corn meal, 55 g of dextrose, and 40 mL of unsulfured molasses. All strains were reared on this food at 23oC and 14-hour light cycle. In order to generate a genetically homogeneous population, all strains were submitted to individual crosses of single male and female for at least 5 generations before any study. Flies were aged for 35 days before flash frozen


title: LL28.gpr

description: Biological replicate

source_name: Total RNA from 35-day-old virgin Yohio flies.


title: LL29.gpr

description: Biological replicate


title: FC466

description: Normal control sample from FC466

source_name: Genomic DNA from FC466


title: LL22.gpr

description: Biological replicate

growth_protocol: Molasses medium was cooked in house with 850 mL of distilled water, 5 g of agar, 27.5 g of torula yeast, 52 g of corn meal, 55 g of dextrose, and 40 mL of unsulfured molasses. All strains were reared on this food at 23oC and 14-hour light cycle. In order to generate a genetically homogeneous population, all strains were submitted to individual crosses of single male and female for at least 5 generations before any study. Virgin flies were aged for 35 days before flash frozen.


title: normal lung_Non-smoker (NS5N)

city: Tokushima city

first: Koichiro

last: Kajiura

department: Department of Thoraci,Endocrine Surgery and Oncology

country: Japan

institute: Institute of Biomedical Sciences, Tokushima University Graduate School

hyb_protocol: bisulfite convered DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illuminascanner setting

data_processing: GenomeStudio V2011.1. The non_normalized.txt contains unmethylated and methylated signal intensities.

source_name: normal lung_Non-smoker

extract_protocol: genomic DNA was extracted and purified from Lung tumor or paired normal Lung samples using QIAamp® DNA Mini kit according to standard instructions.

tag: age (yrs)

tag: gender

value: M

tag: smoking status

value: Non-smoker (NS5N)

tag: brinkman index

tag: tnm factor

tag: Stage

value: normal lung


title: normal lung_Non-smoker (NS549N)

value: Non-smoker (NS549N)

tag: tissue


title: LL21.gpr

description: Biological replicate

tag: Sex


title: normal lung_Non-smoker (NS6N)

value: Non-smoker (NS6N)


title: normal lung_Non-smoker (NS4N)

value: Non-smoker (NS4N)


title: normal lung_Non-smoker (NS3N)

value: Non-smoker (NS3N)


title: lung adenocarcinoma_Non-smoker (NS4T)

source_name: lung adenocarcinoma_Non-smoker

value: Non-smoker (NS4T)

value: lung adenocarcinoma


title: lung adenocarcinoma_Non-smoker (NS3T)

value: Non-smoker (NS3T)


title: normal lung_Non-smoker (NS1N)

value: Non-smoker (NS1N)


title: lung adenocarcinoma_Non-smoker (NS1T)

value: Non-smoker (NS1T)


title: normal lung_smoker (S6N)

source_name: normal lung_smoker

value: smoker (S6N)


title: lung adenocarcinoma_Non-smoker (NS6T)

value: Non-smoker (NS6T)


title: normal lung_smoker (S5N)

value: smoker (S5N)


title: lung adenocarcinoma_Non-smoker (NS549T)

value: Non-smoker (NS549T)


title: lung adenocarcinoma_smoker (S6T)

source_name: lung adenocarcinoma_smoker

value: smoker (S6T)


title: lung adenocarcinoma_smoker (S5T)

value: M

value: smoker (S5T)


title: normal lung_smoker (S4N)

value: smoker (S4N)

value: normal lung


title: lung adenocarcinoma_Non-smoker (NS5T)

value: Non-smoker (NS5T)


title: T_2

city: Taipei City

first: Yueji

last: Li

address: No.7, Zhongshan S. Rd., Zhongzheng District,

institute: National Taiwan University

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 500 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors from the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% median scaling normalization method. Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculated average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

growth_protocol: cells were incubated in DMEM with 10% FBS

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧8).

treatment_protocol: Establish stable transfectants of pLKO-sh-ATMIN in HCT116 cells and analyze the miRNA expression level of  by microRNA microarray. HCT116 transfected with pLKO-sh-scr was used as a control experiment.

tag: cell line

value: colon


title: C_2


title: normal lung_smoker (S3N)

value: smoker (S3N)


title: lung adenocarcinoma_smoker (S1T)

value: smoker (S1T)


title: normal lung_smoker (S2N)

value: smoker (S2N)


title: T_1


title: lung adenocarcinoma_smoker (S2T)

value: smoker (S2T)

value: lung adenocarcinoma


title: genomic DNA from A2780_KO1.36

city: Baltimore

first: Stephen

middle: B

last: Baylin

state: MD

address: 1650 Orleans Street

department: Oncology

institute: Johns Hopkins University SOM

description: SAMPLE 4

hyb_protocol: Bisulfite-converted DNA was analyzed using Illumina’s Infinium Human Methylation450 Beadchip Kit (WG-314-1001) by following manufacturer’s manual. Beadchip contains 485,577 CpG loci in human genome. Briefly, 4 ul of bisulfite-converted DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer at 37C for 20-24 hours. Samples were fragmented using kit-provided reagents and buffer at 37C for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95C for 20 minutes. 12 ul of each sample was loaded onto a 12-sample chip and the chips were assembled into hybridization chamber as instructed in the manual. After incubation at 48C for 16-20 hours, chips were briefly washed and then assembled and placed in a fluid flow-through station for primer-extension and staining procedures.

scan_protocol: Polymer-coated chips were image-processed in Illumina’s iScan scanner.

data_processing:
Data were extracted using Methylation Module of GenomeStudio v1.0 Software.
Unmethylated and methylated signal intensities in Series supplementary file

growth_protocol: A2780 cells were maintained in RPMI-1640 medium containing 10% FBS.

extract_protocol: Genomic DNA was extracted using Promega Genomic Purification Kit following manufacturer's instructions

treatment_protocol: A2780 cells were infected with either Control or LentiCRISPR virus against TET2 gene for 2 days, followed by puromycin selection. Single clones were selected and validated after ~8 weeks selection in puromycin.

tag: genotype/variation

value: Tet2 KO


title: lung adenocarcinoma_smoker (S3T)

value: smoker (S3T)


title: normal lung_smoker (S1N)

value: smoker (S1N)


title: genomic DNA from A2780_KO2.32

description: SAMPLE 5


title: C_1


title: 1.5mm-anther-ms32-fertilesib-Rep1-Cy5

city: Stanford

first: John

middle: F

last: Fernandes

state: CA

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

description:
raw data file: US84703594_251604710206_S01_GE2-v5_95_Feb07_2_JF_1_2.txt
compare 1.5 mm anthers from ms32-mutant versus ms32-fertilesib
Cy5_206_2

hyb_protocol: 825 ng of each labeled target cRNA were hybridized for 17 h at 60C.

scan_protocol: Slides were scanned on an Agilent DNA microarray scanner as indicated in the manual.  Images were processed with the Agilent Feature Extraction software.

data_processing:
After removal of spots flagged by Feature Extraction as below background or saturated or outliers, intensities for each channel from Feature Extraction were normalized using lowess.  Average intensities were then calculated for each sample type for comparison.
The limma package of R was used to normalize the median intensities for each channel as follows: within each array using loess and between arrays using quantile method.

organism: Zea mays

label_protocol: Total RNA (50 ng) was amplified & labeled with Cy3 or Cy5 using Agilent Low RNA Input Linear Amplification Kit.

growth_protocol: Plants were grown and dissected at the Stanford field; tissues were collected and frozen in liquid nitrogen immediately.

extract_protocol: Total RNA was extracted from 30 - 60 mg of frozen tissues with TRIzol, digested with DNase I, and cleaned up with Qiagen RNeasy Mini kit.

value: 1.5mm whole anther


title: oxBS_A2780_shTET2_H2O2

description: SAMPLE 6

hyb_protocol: BS and oxBS DNA samples were analyzed using Illumina’s Infinium Human Methylation450 Beadchip Kit (WG-314-1001) by following manufacturer’s manual. Beadchip contains 485,577 CpG loci in human genome. Briefly, 4 ul of bisulfite-converted DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer at 37C for 20-24 hours. Samples were fragmented using kit-provided reagents and buffer at 37C for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95C for 20 minutes. 12 ul of each sample was loaded onto a 12-sample chip and the chips were assembled into hybridization chamber as instructed in the manual. After incubation at 48C for 16-20 hours, chips were briefly washed and then assembled and placed in a fluid flow-through station for primer-extension and staining procedures.

treatment_protocol: A2780 cells were 1) infected with control virus, no H2O2 (Scr_mock), 2) infected with control virus with H2O2 treatment (30 min plus 2.5 h resting) (Scr_H2O2), and 3) infected with shTET2 virus, with H2O2 treatment  (30 min plus 2.5 h resting) (shTET2_H2O2).


title: genomic DNA from A2780_shTET2_H2O2#2

data_processing: Data were extracted using Methylation Module of GenomeStudio v1.0 Software.

treatment_protocol: A2780 cells were 1) infected with control virus, no H2O2 (Scr_mock), 2) infected with control virus with H2O2 treatment (30 min plus 2.5 h resting) (Scr_H2O2), 3) infected with shTET2 virus, no H2O2 (shTET2_mock), and 4) infected with shTET2 virus, with H2O2 treatment  (30 min plus 2.5 h resting) (shTET2_H2O2, two biological replicates).

tag: infected with

value: shTET2 virus


title: genomic DNA from A2780_Scr_1

description: SAMPLE 1

value: control


title: BS_A2780_Scr_H2O2

description: SAMPLE 2


title: oxBS_A2780_Scr_mock

description: SAMPLE 4


title: BS_A2780_shTET2_H2O2

description: SAMPLE 3


title: genomic DNA from A2780_KO1.1

description: SAMPLE 3


title: oxBS_A2780_Scr_H2O2

description: SAMPLE 5


title: genomic DNA from A2780_Scr_2

description: SAMPLE 2


title: 1.5mm-anther-ms32-mutant-Rep2-Cy5

description:
raw data file: US84703594_251604710205_S01_GE2-v5_95_Feb07_2_JF_1_4.txt
compare 1.5 mm anthers from ms23-mutant versus ms32-mutant
Cy5_205_4


title: BS_A2780_Scr_mock

description: SAMPLE 1


title: genomic DNA from A2780_shTET2_mock


title: 1.5mm-anther-ms23-mutant-Rep2-Cy5

description:
raw data file: US84703594_251604710205_S01_GE2-v5_95_Feb07_2_JF_1_3.txt
compare 1.5 mm anthers from ms32-mutant versus ms23-mutant
Cy5_205_3


title: 1.5mm-anther-ms23-mutant-Rep3-Cy5

description:
raw data file: US84703594_251604710206_S01_GE2-v5_95_Feb07_2_JF_1_3.txt
compare 1.5 mm anthers from ms23-fertilesib versus ms23-mutant
Cy5_206_3


title: genomic DNA from A2780_Scr_H2O2

value: control virus


title: genomic DNA from A2780_Scr_mock


title: MDA_48H_tdt8

city: Serdang

first: Noraini

last: Nordin

state: selangor

address: Animal Tissue Culture Lab

department: Cell Biology

country: Malaysia

institute: University Putra Malaysia

description: Gene expression of control

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 2x60k array slides

data_processing: The scan images were analyzed with the feature extraction sofware 13.1 using default parameters by the Agilent Inc.

source_name: MDA MB-231, 48H, NLC-Blank, replicate 2

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

growth_protocol: MDA MB-231 cells was purchased from ATCC and sub-cultured under under certain conditioned (37°C+5% CO2) in cell culture media with 10% fetal bovine serum.

extract_protocol: Total RNA of the cells was extracted by using RNAeasy mini prep kit (Qiagen, USA) by following the manufacturer's recommendations.

treatment_protocol: NLC-Citral, Citral and NLC-Blank were diluted in the fresh media before treated the cells for 48 hours. The cells were incubated in the incubator for 48 hours post treatment.

value: MDA MB-231

value: Breast cancer cells


title: MDA_48H_tdt9

description: Gene expression of control

source_name: MDA MB-231, 48H, NLC-Blank, replicate 3


title: genomic DNA from A2780 H2O2 30 min

description: A2780 H2O2 30 min

treatment_protocol: A2780 cells were either untreated (mock), treated with H2O2 for 30 min and harvested immediately (H2O2 30 min), or treated with H2O2 for 30 min, replace with fresh medium and rested fro an additional 2.5 hour ( H2O2 3h). Mock cells were harvested at 30 min time point.


title: 1.5mm-anther-ms23-mutant-Rep3-Cy3

description:
raw data file: US84703594_251604710206_S01_GE2-v5_95_Feb07_2_JF_1_4.txt
compare 1.5 mm anthers from ms23-mutant versus ms23-fertilesib
Cy3_206_4


title: MDA_48H_tdt7

description: Gene expression of control

source_name: MDA MB-231, 48H, NLC-Blank, replicate 1


title: 1.5mm-anther-ms23-mutant-Rep1-Cy5

description:
raw data file: US84703594_251604710205_S01_GE2-v5_95_Feb07_2_JF_1_1.txt
compare 1.5 mm anthers from ms32-mutant versus ms23-mutant
Cy5_205_1


title: genomic DNA from A2780 H2O2 3 h

description: A2780 H2O2 3 h


title: 1.5mm-anther-ms23-fertilesib-Rep1-Cy5

description:
raw data file: US84703594_251604710206_S01_GE2-v5_95_Feb07_2_JF_1_4.txt
compare 1.5 mm anthers from ms23-mutant versus ms23-fertilesib
Cy5_206_4


title: 1.5mm-anther-ms32-mutant-Rep3-Cy5

description:
raw data file: US84703594_251604710206_S01_GE2-v5_95_Feb07_2_JF_1_1.txt
compare 1.5 mm anthers from ms32-fertilesib versus ms32-mutant
Cy5_206_1


title: 1.5mm-anther-ms32-mutant-Rep3-Cy3

description:
raw data file: US84703594_251604710206_S01_GE2-v5_95_Feb07_2_JF_1_2.txt
compare 1.5 mm anthers from ms32-mutant versus ms32-fertilesib
Cy3_206_2


title: 1.5mm-anther-ms23-fertilesib-Rep1-Cy3

description:
raw data file: US84703594_251604710206_S01_GE2-v5_95_Feb07_2_JF_1_3.txt
compare 1.5 mm anthers from ms23-fertilesib versus ms23-mutant
Cy3_206_3


title: MDA_48H_tdt4

description: Gene expression of positive control

source_name: MDA MB-231, 48H, CITRAL, replicate 1


title: genomic DNA from A2780_shTET2_H2O2#1


title: genomic DNA from A2780 mock

description: A2780 mock

source_name: A2780 mock


title: MDA_48H_tdt5

description: Gene expression of positive control

source_name: MDA MB-231, 48H, CITRAL, replicate 2


title: 1.5mm-anther-ms32-fertilesib-Rep1-Cy3

description:
raw data file: US84703594_251604710206_S01_GE2-v5_95_Feb07_2_JF_1_1.txt
compare 1.5 mm anthers from ms32-fertilesib versus ms32-mutant
Cy3_206_1


title: 1.5mm-anther-ms23-mutant-Rep2-Cy3

description:
raw data file: US84703594_251604710205_S01_GE2-v5_95_Feb07_2_JF_1_4.txt
compare 1.5 mm anthers from ms23-mutant versus ms32-mutant
Cy3_205_4


title: C39 DNA from control individual 39

first: Julia

last: Kolarova

address: Albert-Einstein-Allee 11

department: Institute of Human Genetics

institute: University Hospital Ulm

description: DNA from control individual 39

scan_protocol: Arrays were scanned using the Illumina iScan

data_processing: GenomeStudio software (version 2011.1, Methylation module version 1.9.0)

source_name: peripheral blood

extract_protocol: various DNA extraction methods

tag: (mlid) or (slid) as diagnosed prior to the study


title: MDA_48H_tdt1

description: Gene expression after 48 hours of treatment

source_name: MDA MB-231, 48h, NLC-Citral, replicate 1


title: MDA_48H_tdt2

source_name: MDA MB-231, 48h, NLC-Citral, replicate 2


title: lung adenocarcinoma_smoker (S4T)

value: M

value: smoker (S4T)


title: C38 1 DNA from control individual 38

description: DNA from control individual 38


title: C37 2 DNA from control individual 37

description: DNA from control individual 37


title: 1.5mm-anther-ms32-mutant-Rep2-Cy3

description:
raw data file: US84703594_251604710205_S01_GE2-v5_95_Feb07_2_JF_1_3.txt
compare 1.5 mm anthers from ms32-mutant versus ms23-mutant
Cy3_205_3


title: 1.5mm-anther-ms23-mutant-Rep1-Cy3

description:
raw data file: US84703594_251604710205_S01_GE2-v5_95_Feb07_2_JF_1_2.txt
compare 1.5 mm anthers from ms23-mutant versus ms32-mutant
Cy3_205_2


title: MDA_48H_tdt3

source_name: MDA MB-231, 48h, NLC-Citral, replicate 3


title: 1.5mm-anther-ms32-mutant-Rep1-Cy3

description:
raw data file: US84703594_251604710205_S01_GE2-v5_95_Feb07_2_JF_1_1.txt
compare 1.5 mm anthers from ms32-mutant versus ms23-mutant
Cy3_205_1


title: MDA_48H,tdt6

description: Gene expression of positive control

source_name: MDA MB-231, 48H, CITRAL, replicate 3


title: C38 2 DNA from control individual 38

description: DNA from control individual 38


title: skin-PCFCL-9

city: Paris

first: Anne

last: Janin

address: 1 Av C Vellefaux

country: France

institute: University Paris 7, INSERM, APHP

hyb_protocol: Agilent gene expression hybridization kit

scan_protocol: Agilent microarray scanner system

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determined feature intensities (including background subtraction), rejects outliers and calculated statistical confidences. The signal intensities from the single-experiment raw data lists were normalized by dividing the intensity values by their median. For determination of differential gene expression, FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware). Using this software we compared intensity profiles in a ratio experiment (table 4). All samples were labeled with Cy3, here, the ratio experiments were designated as PCFCL (controls) versus (vs.) PCLBCL-LT (samples) experiments (automated data output of the Resolver system).The Ratios were calculated by dividing sample signal intensity through control signal intensity.

source_name: skin

label_protocol: Agilent low imput quick amp labeling kit

extract_protocol: Qiagen Rneasy kit

tag: cutaneous lymphoma type

value: PCFCL


title: skin-PCFCL-10


title: C36 2 DNA from control individual 36

description: DNA from control individual 36


title: sw_2

data_processing: The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.

source_name: SW620 cells

treatment_protocol: Establish stable transfectants of pLKO-sh-ATMIN in SW620 cells and analyze the miRNA expression level of  by microRNA microarray. SW620 transfected with pLKO-sh-scr was used as a control experiment.

tag: transfection

value: pLKO-sh-ATMIN


title: skin-PCFCL-7


title: skin-PCFCL-8


title: sw_1


title: Larval brain Replicate 2

city: Gurabo

first: Adrinel

last: Vázquez Montes

state: PR

address: 189 Road Km 3.3

department: Biology

country: Puerto Rico

institute: SUAGM

hyb_protocol: The hybridization and washing protocol were done as recommended by the manufacturer (Two-Color Microarray-Based Gene Expression Analysis Protocol, Version 6.5, May 2010, from Agilent Technologies). Briefly, 825 ng of Cy-3 and Cy5-labeled cRNAs were combined with 10 X Blocking Agent, and 25 X Fragmentation Buffer at 60˚C for 30 min. The reaction was stopped with 2 X GEx Hybridization Buffer HI-RPM and hybridized to the oligo microarray for 17 hrs at 60˚C with continuing rotation (10 rpm). The reagents used for this step were from the Gene Expression Hybridization Kit. After hybridization, slides were washed during 1 min at RT using the GE Wash Solution 1, and 1 min at 37˚C with GE Wash Solution 2. Next, slides were washed for 10 seconds with acetonitrile (Sigma). A final washing was done using a Stabilization and Drying Solution for 30 sec.

scan_protocol: Data images were obtained by laser-based scanning using the Microarray Scanner and the Feature Extraction Software (v8.1) both from Agilent. Scanning parameters were as recommended by the manufacturer. Briefly, the resolution settings for scanning were 5 micrometers using minimum (10%) and maximum (100%) Photo Multiplier Tube detection sensitivities. An initial assessment of the array was performed using the information from the Quality Report extracted from the Feature Extraction Software (v8.1).

data_processing: The analysis of the microarray data consisted of the following steps: 1) within-array and 2) between-array normalization. Normalization of the data was as previously described (Smyth and Speed 2003). Briefly, in the “within-array normalization” analyses the M-values were normalized for each array separately using a global loess method without background correction, whereas in the “between-array normalization” analyses log-ratios were normalized to be comparable across arrays using the Aquantile method. Normalization success was determined using MA plot graphical representations. These MA-plots depict the log-ratio of Red versus Green (the M value in the y axis) against the overall intensity of each spot (the A value in the x axis). The log-ratio is represented by the M-value, M = log2(R) _ log2(G), and the overall intensity by the A-value, A = (log2(R) +log2(G))/2. In this experiment, RNA sources from the brain of third instar larvae after Pb+2 exposure were included. Dye swapping was done to correct for differences in the incorporation of the dyes. The main comparisons were done for each time point against the control sample and the Tunicamycin treated sample.

source_name: Control brain larvae rep 2

label_protocol: Total RNA from  pooled brains from control or experimental samples (20 brains/sample) was linearly amplified and labeled using two different fluorescent dyes: cyanine 3-CTP (Cy-3), and cyanine 5-CTP (Cy-5, Amersham Biosciences) as described in the Agilent Low RNA Input Linear Amplification Kit, Version 6.5, May 2010. Briefly, in the first reaction, 20 ng  of total RNA was mixed with T7 promoter primers and the diluted Spike-in Mix (A or B), incubated at 65˚C during 10 min and placed on ice for 5 min. The denatured primers and total RNA were mixed with the following reagents: 5 X First Strand Buffer, 0.1 M DTT, 10 mM dNTP mix, and AffinityScript RNase Block Mix. This reaction mix was incubated at 40˚C for 2 hrs, then at 70˚C for 15 min, and finally placed on ice for 5 min. Next, synthesis and labeling of cRNA was performed simultaneously mixing the prepared reaction (containing the dscDNA) with a transcription Master Mix: (5 X Transcription Buffer, 0.1 M DTT, NTP mix, T7 RNA polymerase blend, and Cy-3 or Cy-5 (10 mM, each). The reaction was incubated at 40˚C for 2 hrs. Amplified fluorescent cRNA probes were purified using the Qiagen's RNeasy-mini spin columns. Finally, fluorescently labeled cRNA samples were analyzed for yield and dye incorporation using the ND-1000 Spectrophotometer (NanoDrop Technologies, Rockland, DE). Only samples that presented a concentration of more than 6 pmol/μg (a measure representing efficient dye incorporation) were used for hybridization as recommended by the manufacturer.

growth_protocol: Flies were crossed during five days  in corn-based  Pb+2-free (500 μM sodium acetate) or  Pb+2-contaminated  medium (500 µM Pb+2 acetate).  Third instar wandering larvae were removed and brains dissected.

extract_protocol: Total RNA was isolated from the brain of staged third instar larvae using the RNeasy Mini Kit (Qiagen) and on column dnase treatment.  Concentration and integrity were detected using the Agilent's 2100 Bioanalyzer with an RNA 6000 Nano LabChip® Kit. Confirmatory readings were performed using the ND-1000 Spectrophotometer (NanoDrop Technologies, Rockland, DE).

tag: age

value: third instar larvae

value: brain

value: Wild Type

source_name: Lead brain larvae rep 2


title: skin-PCLBCLLT-6

value: PCLBCL-LT


title: skin-PCLBCLLT-3


title: C37 1 DNA from control individual 37

description: DNA from control individual 37


title: Larval brain Swap 2

source_name: Control  brain larvae swap 2

source_name: Lead  brain larvae swap 2


title: Larval brain Replicate 1

source_name: Control brain larvae rep 1

source_name: Lead brain larvae rep 1


title: skin-PCLBCLLT-5


title: Larval brain Swap 1

source_name: Control  brain larvae swap 1

source_name: Lead  brain larvae swap 1


title: C35 1 DNA from control individual 35

description: DNA from control individual 35


title: C34 1 DNA from control individual 34

description: DNA from control individual 34


title: neo_2

value: pLKO-sh-scr


title: skin-PCLBCLLT-2


title: C34 2 DNA from control individual 34

description: DNA from control individual 34


title: neo_1


title: skin-PCLBCLLT-4


title: C35 2 DNA from control individual 35

description: DNA from control individual 35


title: 1.5mm-anther-ms32-mutant-Rep1-Cy5

description:
raw data file: US84703594_251604710205_S01_GE2-v5_95_Feb07_2_JF_1_2.txt
compare 1.5 mm anthers from ms23-mutant versus ms32-mutant
Cy5_205_2


title: skin-PCLBCLLT-1


title: PfAP2-I-GFP-msp5mut 45 hours post invasion_2

city: University Park

first: Manuel

last: Llinas

state: Pennsylvania

address: Millennium Science Complex, Pollock Rd

department: Biochemistry and Molecular Biology

institute: Penn State University

description: 3D7 gene PfAP2-I with C-terminalGFP. TGCA DNA motif in promoter msp5.

hyb_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

scan_protocol: Agilent G2600D Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 11.5.1.1).

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction.

organism: Plasmodium falciparum

source_name: PfAP2-I-GFP-msp5MUT RNA

growth_protocol: P. falciparum 3D7 with PfAP2-I C-terminal GFP tag and P. falciparum 3D7 with PfAP2-I C-terminal GFP tag and TGCA DNA motif mutated in msp5 promoter were grown under shaking conditions.

extract_protocol: Starting at 18 hours post-invasion, samples were harvested in Trizol for total RNA extraction every 6 hours until 36h post-invasion and then every 3h until the end of the IDC (48h post-invasion).

tag: strain

value: 3D7 PfAP2-I-GFP-msp5MUT

tag: hours post invasion

source_name: 3D7 Mixed Stage Reference Pool


title: PfAP2-I-GFP-msp5mut 48 hours post invasion_2

label_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).


title: C33 3 DNA from control individual 33

description: DNA from control individual 33

source_name: peripheral blood


title: PfAP2-I-GFP-msp5mut 42 hours post invasion_2


title: C33 2 DNA from control individual 33

description: DNA from control individual 33


title: MB1

city: Xi'an

first: Ting

last: Wang

address: Changlexilu Road

country: China

institute: the Fourth Military Medical University

description: From the transgenic mice express a constitutively active Smo in cerebellar granule cells.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing:
Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.
Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: Medulloblastoma

label_protocol: Sample labeling were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Three cases of paired MB and CGNP cells were prepared for the extraction of total RNA.RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: Medulloblastoma

tag: genotype

tag: background strain

value: 4 months


title: C36 1 DNA from control individual 36

description: DNA from control individual 36


title: MB2


title: PfAP2-I-GFP-msp5mut 39 hours post invasion_2


title: PfAP2-I-GFP-msp5mut 36 hours post invasion_2


title: Ambion normal colon cell line

city: Helsinki

first: Johanna

last: Lotsari-Salomaa

address: Haartmaninkatu 8

department: Department of Medical Genetics

country: Finland

institute: University of Helsinki

hyb_protocol: Labelled and fragmented cRNA was hybridized with Affymetrix microarrays for 16h at 45 ̊in a rotation oven (60 rpm).

scan_protocol: The arrays were washed and stained with streptavidin-phycoerythrin in Affymetrix GeneChip Fluidics station 450 and scanned with Affymetrix GeneChip Scanner 3000. The image was analyzed using the GeneChip operating software (GCOS,Affymetrix,Santa Clara,CA).

data_processing: Data was analyzed using GeneSpring GX software (version 12.0, Agilent Techologies) and processed using robust multiarray analysis (RMA) algorithm for background correction, normalization and log2-transformation.

label: biotin

source_name: Ambion

label_protocol: 5 βg of total RNA was reverse transcripted by the Superscript Double Stranded cDNA Synthesis kit (Invitrogen,Paisley,UK). The BioArray high-yeild RNA transcript labelling kit (T7,Enzo Life Sciences,Farmingdale,NY) which amplified linearly cDNA and produced in vitro transcription reactions was used to produce biotinylated CTP and UTP-labelled cRNA.

growth_protocol: All cell lines were purchased from different commercial collections and cultured according to the suppliers' protocol.

extract_protocol: Total RNA was extracted and purified using Qiagen Rneasy kit (Qiagen Inc., Valencia,CA,USA). RNA integrity and yield were assessed by Agilent Bioanalyzer 2100 (Agilent Technologies,CA,USA). Only samples with an RNA integrity number (RIN) higher than 7.0 were included in the analysis.

treatment_protocol: No specific treatment: standard short-term culturing according to manufacturers'/suppliers' instructions.

value: Ambion normal colon cell line

tag: cell line vendor


title: C32 2 DNA from control individual 32

description: DNA from control individual 32


title: GNPs3

description: CGNPs were isolated from newborn mice (4 to 6-day-old)

source_name: Granule neuron precursors

value: Granule neuron precursors

value: 4-6 days


title: MB915


title: KM12 adenocarcinoma

source_name: canSAR (Cancer Research UK)

value: Cosmic id 905989


title: C33 1 DNA from control individual 33

description: DNA from control individual 33


title: C30 DNA from control individual 30

description: DNA from control individual 30


title: Amsbio normal colon pool, pool of 5 donors

source_name: Amsbio


title: LIM1215 colon carcinoma cell line

source_name: Ludwig Institute for Cancer Research


title: PfAP2-I-GFP-msp5mut 24 hours post invasion_2


title: C31 DNA from control individual 31

description: DNA from control individual 31


title: PfAP2-I-GFP-msp5mut 30 hours post invasion_2


title: C29 DNA from control individual 29

description: DNA from control individual 29


title: PfAP2-I-GFP-msp5mut 18 hours post invasion_2


title: HCA7 adenocarcinoma cell line

source_name: Imperial College London


title: PfAP2-I-GFP 48 hours post invasion_2

description: 3D7 gene PfAP2-I with C-terminalGFP

source_name: PfAP2-I-GFP RNA

value: 3D7 PfAP2-I-GFP


title: GNPs1


title: LoVo colorectal adenocarcinoma cell line

source_name: American Type Culture Collection

value: LoVo

value: ATCC CCL-229


title: PfAP2-I-GFP 45 hours post invasion_2

description: 3D7 gene PfAP2-I with C-terminalGFP


title: C25 DNA from control individual 25

description: DNA from control individual 25


title: C26 DNA from control individual 26

description: DNA from control individual 26


title: C27 DNA from control individual 27

description: DNA from control individual 27


title: SW48 colon adenocarcinoma cell line

value: ATCC CCL-231


title: RKO-1 colon carcinoma cell line

value: ATCC CRL-2577


title: C32 1 DNA from control individual 32

description: DNA from control individual 32


title: C28 DNA from control individual 28

description: DNA from control individual 28


title: RKO-2 colon carcinoma cell line


title: PfAP2-I-GFP 36 hours post invasion_2

description: 3D7 gene PfAP2-I with C-terminalGFP


title: GNPs4


title: PfAP2-I-GFP 39 hours post invasion_2

description: 3D7 gene PfAP2-I with C-terminalGFP


title: C24 DNA from control individual 24

description: DNA from control individual 24


title: PfAP2-I-GFP 42 hours post invasion_2

description: 3D7 gene PfAP2-I with C-terminalGFP


title: HCT15 colon adenocarcinoma cell line

value: ATCC CCL-225


title: PfAP2-I-GFP 30 hours post invasion_2

description: 3D7 gene PfAP2-I with C-terminalGFP


title: HCT116 colon carcinoma cell line

value: ATCC CCL-247


title: C23 DNA from control individual 23

description: DNA from control individual 23


title: Amsbio Dr.P set normal colon cell line

value: Amsbio Dr.P set normal colon cell line


title: PfAP2-I-GFP 24 hours post invasion_2

description: 3D7 gene PfAP2-I with C-terminalGFP


title: PfAP2-I-GFP 18 hours post invasion_2

description: 3D7 gene PfAP2-I with C-terminalGFP


title: C22 DNA from control individual 22

description: DNA from control individual 22


title: C21 DNA from control individual 21

description: DNA from control individual 21


title: HumanTumor_FreshFrozen_PRI_DH126

city: Durham

first: David

last: Hsu

state: NC

address: 905 S. LaSalle St. Rm 3008

department: Medical Oncology

institute: Duke University

hyb_protocol: The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).

data_processing: The data were analyzed using the R statistical platform with the Bioconductor affymetrix package [R version 2.13.1 (2011-07-08) and Bioconductor version 2.9].

source_name: human tumor, colorectal primary, fresh frozen tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Human tumors were flash frozen in OCT at time of surgical resection. An initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca).

tag: primary tumor site

value: colorectal

tag: metastatic tumor site

tag: molecular subgroup

value: MSCC 6


title: HumanTumor_FreshFrozen_PRI_DH128

value: MSCC 3


title: C20 DNA from control individual 20

description: DNA from control individual 20


title: HumanTumor_FreshFrozen_PRI_DH121

value: MSCC 4


title: PfAP2-I-GFP-msp5mut 45 hours post invasion

description:
3D7 gene PfAP2-I with C-terminalGFP. TGCA DNA motif in promoter msp5.
45 hpi mut

value: 3D7 PfAP2-I-GFP-msp5MUT


title: PfAP2-I-GFP-msp5mut 48 hours post invasion

description:
3D7 gene PfAP2-I with C-terminalGFP. TGCA DNA motif in promoter msp5.
48 hpi mut


title: PfAP2-I-GFP-msp5mut 39 hours post invasion

description:
3D7 gene PfAP2-I with C-terminalGFP. TGCA DNA motif in promoter msp5.
39 hpi mut


title: PfAP2-I-GFP-msp5mut 42 hours post invasion

description:
3D7 gene PfAP2-I with C-terminalGFP. TGCA DNA motif in promoter msp5.
42 hpi mut


title: HumanTumor_FreshFrozen_PRI_DH119


title: HumanTumor_FreshFrozen_PRI_DH114


title: C19 DNA from control individual 19

description: DNA from control individual 19


title: C16 DNA from control individual 16

description: DNA from control individual 16


title: C17 DNA from control individual 17

description: DNA from control individual 17


title: PfAP2-I-GFP-msp5mut 18 hours post invasion

description:
3D7 gene PfAP2-I with C-terminalGFP. TGCA DNA motif in promoter msp5.
18 hpi mut


title: PfAP2-I-GFP 45 hours post invasion

description:
3D7 gene PfAP2-I with C-terminalGFP
45 hpi wt


title: PfAP2-I-GFP 48 hours post invasion

description:
3D7 gene PfAP2-I with C-terminalGFP
48 hpi wt


title: PfAP2-I-GFP-msp5mut 36 hours post invasion

description:
3D7 gene PfAP2-I with C-terminalGFP. TGCA DNA motif in promoter msp5.
36 hpi mut


title: PfAP2-I-GFP-msp5mut 30 hours post invasion

description:
3D7 gene PfAP2-I with C-terminalGFP. TGCA DNA motif in promoter msp5.
30 hpi mut


title: HumanTumor_FreshFrozen_PRI_DH111

value: MSCC 1


title: HumanTumor_FreshFrozen_PRI_DH083


title: HumanTumor_FreshFrozen_PRI_DH076


title: HumanTumor_FreshFrozen_PRI_DH081


title: HumanTumor_FreshFrozen_PRI_DH102


title: HumanTumor_FreshFrozen_PRI_DH078


title: HumanTumor_FreshFrozen_PRI_DH109


title: C14 DNA from control individual 14

description: DNA from control individual 14


title: C13 DNA from control individual 13

description: DNA from control individual 13


title: HumanTumor_FreshFrozen_PRI_DH058


title: C11 DNA from control individual 11

description: DNA from control individual 11


title: C12 DNA from control individual 12

description: DNA from control individual 12


title: C8 DNA from control individual 8

description: DNA from control individual 8


title: C15 DNA from control individual 15

description: DNA from control individual 15


title: C18 DNA from control individual 18

description: DNA from control individual 18


title: HumanTumor_FreshFrozen_PRI_DH057


title: PfAP2-I-GFP 36 hours post invasion

description:
3D7 gene PfAP2-I with C-terminalGFP
36 hpi wt


title: C9 DNA from control individual 9

description: DNA from control individual 9


title: PfAP2-I-GFP 30 hours post invasion

description:
3D7 gene PfAP2-I with C-terminalGFP
30 hpi wt


title: C10 DNA from control individual 10

description: DNA from control individual 10


title: PfAP2-I-GFP-msp5mut 24 hours post invasion

description:
3D7 gene PfAP2-I with C-terminalGFP. TGCA DNA motif in promoter msp5.
24 hpi mut


title: PfAP2-I-GFP 42 hours post invasion

description:
3D7 gene PfAP2-I with C-terminalGFP
42 hpi wt


title: PfAP2-I-GFP 39 hours post invasion

description:
3D7 gene PfAP2-I with C-terminalGFP
39 hpi wt


title: PfAP2-I-GFP 24 hours post invasion

description:
3D7 gene PfAP2-I with C-terminalGFP
24 hpi wt


title: HumanTumor_FreshFrozen_PRI_DH045


title: PfAP2-I-GFP 18 hours post invasion

description:
3D7 gene PfAP2-I with C-terminalGFP
18 hpi wt


title: HumanTumor_FreshFrozen_PRI_DH050


title: HumanTumor_FreshFrozen_PRI_DH054


title: C7 DNA from control individual 7

description: DNA from control individual 7


title: C5 DNA from control individual 5

description: DNA from control individual 5


title: C3 DNA from control individual 3

description: DNA from control individual 3


title: C6 DNA from control individual 6

description: DNA from control individual 6


title: C4 DNA from control individual 4

description: DNA from control individual 4


title: HumanTumor_FreshFrozen_PRI_DH021


title: HumanTumor_FreshFrozen_PRI_DH034


title: HumanTumor_FreshFrozen_PRI_DH017


title: HumanTumor_FreshFrozen_PRI_DH032


title: HumanTumor_FreshFrozen_PRI_DH008

value: MSCC 2


title: HumanTumor_FreshFrozen_PRI_DH015

value: MSCC 5


title: C2 DNA from control individual 2

description: DNA from control individual 2


title: HumanTumor_FreshFrozen_PRI_DH010


title: HumanTumor_FreshFrozen_PRI_DH007


title: HumanTumor_FreshFrozen_PRI_DH011


title: C1 DNA from control individual 1

description: DNA from control individual 1


title: HumanTumor_FreshFrozen_PRI_DH005


title: ID36 1 DNA from individual 36

description: DNA from individual 36

value: MLID


title: HumanTumor_FreshFrozen_PRI_DH001


title: ID37 2 DNA from individual 37

description: DNA from individual 37


title: ID37 1 DNA from individual 37

description: DNA from individual 37


title: ID35 2 DNA from individual 35

description: DNA from individual 35


title: HumanTumor_FreshFrozen_PRI_CRC222A


title: HumanTumor_FreshFrozen_PRI_CRC146


title: ID36 2 DNA from individual 36

description: DNA from individual 36


title: HumanTumor_FreshFrozen_PRI_CRC059A


title: HumanTumor_FreshFrozen_PRI_CRC139A


title: ID35 1 DNA from individual 35

description: DNA from individual 35


title: HumanTumor_FreshFrozen_PRI_CRC018A_1


title: HumanTumor_FreshFrozen_PRI_CRC025


title: HumanTumor_FreshFrozen_PRI_CRC034


title: HumanTumor_FreshFrozen_PRI_CRC018A_2


title: HumanTumor_FreshFrozen_PRI_DH025


title: ID34 1 DNA from individual 34

description: DNA from individual 34


title: ID30 DNA from individual 30

description: DNA from individual 30


title: ID31 DNA from individual 31

description: DNA from individual 31


title: ID32 DNA from individual 32

description: DNA from individual 32


title: HumanTumor_FreshFrozen_PRI_CRC017A


title: HumanTumor_FreshFrozen_PRI_CRC020


title: ID34 2 DNA from individual 34

description: DNA from individual 34


title: ID33 DNA from individual 33

description: DNA from individual 33


title: ID27 DNA from individual 27

description: DNA from individual 27


title: ID28 DNA from individual 28

description: DNA from individual 28

value: SLID


title: HumanTumor_FreshFrozen_MET_CRC262

source_name: human tumor, colorectal primary, metastasis, fresh frozen tissue

value: Lung


title: ID29 DNA from individual 29

description: DNA from individual 29


title: HumanTumor_FreshFrozen_MET_CRC253A

value: Liver


title: ID25 2 DNA from individual 25

description: DNA from individual 25


title: ID22 2 DNA from individual 22

description: DNA from individual 22


title: ID22 3 DNA from individual 22

description: DNA from individual 22


title: HumanTumor_FreshFrozen_MET_CRC261A


title: HumanTumor_FreshFrozen_MET_CRC249B


title: ID24 DNA from individual 24

description: DNA from individual 24


title: HumanTumor_FreshFrozen_MET_CRC251B

value: Omentum


title: HumanTumor_FreshFrozen_MET_CRC236B


title: ID22 1 DNA from individual 22

description: DNA from individual 22


title: HumanTumor_FreshFrozen_MET_CRC236A


title: HumanTumor_FreshFrozen_MET_CRC221D


title: ID21 DNA from individual 21

description: DNA from individual 21


title: ID23 DNA from individual 23

description: DNA from individual 23


title: ID25 1 DNA from individual 25

description: DNA from individual 25


title: HumanTumor_FreshFrozen_MET_CRC230A


title: ID14 DNA from individual 14

description: DNA from individual 14


title: ID18 DNA from individual 18

description: DNA from individual 18


title: GC_normal_c

city: Dummerstorf

first: Jens

last: Vanselow

address: Wilhelm-Stahl-Allee 2

department: Reproductive Biology

institute: Leibniz Institute for Farm Animal Biology

description: Granulosa cells cultured at normal density rep3

hyb_protocol: The RNA was hybridized overnight (45°C) in the GeneChipR Hybridization Oven (Affymetrix) to the Affymetrix Bovine Gene 1.0 ST arrays. Washing and staining were performed according to the Affymetrix standard protocol.

scan_protocol: The scanning of the microarray was done with the GeneChip Scanner 3000 HR (Affymetrix) and image processing was done with the software AGCC (Affymetrix).

data_processing: Data analysis was performed with the Expression Console (Version V1.3.1.187, Affymetrix) using the RMA method for normalization. Further comparative analysis was done with the Transcriptome Analysis Console 3.0 (Affymetrix).

organism: Bos taurus

source_name: Cultured granulosa cells, normal density

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol (GeneChip® Expression 3’Amplification One-Cycle Target Labeling and Control Reagents).

growth_protocol: Granulosa cells were cultured serum-free in alpha-MEM supplemented with FSH, IGF-1 and androstenedione for 9 days.

extract_protocol: Total RNA from cultured cells was prepared using the NucleoSpin RNA Kit including removal of genomic DNA with RNAse free rDNAse (Macherey-Nagel).

treatment_protocol: Different initial plating density of granulosa cells represent different culture conditions.

tag: cell type

value: primary granulosa cells


title: GC_high_a

description: Granulosa cells cultured at high density rep1

source_name: Cultured granulosa cells, high density


title: GC_high_c

description: Granulosa cells cultured at high density rep3


title: HumanTumor_FreshFrozen_MET_CRC241A


title: HumanTumor_FreshFrozen_MET_CRC221C


title: HumanTumor_FreshFrozen_MET_CRC249A


title: ID19 1 DNA from individual 19

description: DNA from individual 19


title: ID20 1 DNA from individual 20

description: DNA from individual 20


title: GC_high_b

description: Granulosa cells cultured at high density rep2


title: HumanTumor_FreshFrozen_MET_CRC221A


title: ID16 DNA from individual 16

description: DNA from individual 16


title: HumanTumor_FreshFrozen_MET_CRC180A


title: HumanTumor_FreshFrozen_MET_CRC174B


title: GC_normal_b

description: Granulosa cells cultured at normal density rep2


title: ID17 DNA from individual 17

description: DNA from individual 17


title: HumanTumor_FreshFrozen_MET_CRC172A


title: Gemcitabine-resistant PANC-1 cells#2 [G15002]

city: Miaoli County

first: Jen-Liang

last: Su

address: No.35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan.

institute: National Health Research Institutes

description: PANC-1 ATCC ® CRL-1469™

hyb_protocol: Labeled miRNA targets enriched by NanoSep 100K (Pall Corporation, USA) were hybridized to the  Mouse & Rat miRNA OneArray® with Phalanx hybridization buffer using OneArray® Hybridization Chamber.

scan_protocol: MiRNAs-Chips were scanned by an Axon 4000B scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing:
The signal intensity of each spot was process by R program.
Spots that passed the criteria were normalized by 75% media scaling normalization method. Normalized spot intensities were transformed to gene expression log2 ratios between the control and treatment groups.

source_name: PANC-1 Gem 1500

label_protocol: MiRNAs were prepared from 2.5 μg total RNA samples and labeled using miRNA ULSTM Labeling Kit (Kreatech Diagnostics, The Netherlands).

growth_protocol: PANC-1, PANC-1 Gem 100 and PANC-1 Gem 1500 cells were grown in high glucose of Dulbecco's modified Eagle's medium containing 10% fetal bovine serum in 37℃ with 5% CO2.

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

treatment_protocol: PANC-1 Gem 100 cells were cultured in complete medium (10% FBS/DMEM) with 100 ng/ml gemcitabine; and PANC-1 Gem 1500 cells were cultured complete medium (10% FBS/DMEM) with 1500 ng/ml gemcitabine.

tag: agent

value: 1500 ng/ml gemcitabine

source_name: PANC-1 control


title: ID19 2 DNA from individual 19

city: Ulm

description: DNA from individual 19

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


title: Gemcitabine-resistant PANC-1 cells#1 [G15001]

description: PANC-1 ATCC ® CRL-1469™

tag: cell line


title: Gemcitabine-resistant PANC-1 cells#2 [G1002]

description: PANC-1 ATCC ® CRL-1469™

source_name: PANC-1 Gem 100

value: 100 ng/ml gemcitabine


title: ID13 DNA from individual 13

description: DNA from individual 13

source_name: peripheral blood


title: ID15 DNA from individual 15

description: DNA from individual 15


title: ID8 DNA from individual 8

description: DNA from individual 8


title: Gemcitabine-resistant PANC-1 cells#1 [G1001]

description: PANC-1 ATCC ® CRL-1469™


title: ID26 DNA from individual 26

description: DNA from individual 26


title: ID20 2 DNA from individual 20

description: DNA from individual 20


title: ID9 DNA from individual 9

description: DNA from individual 9


title: GC_normal_a

description: Granulosa cells cultured at normal density rep1


title: parental PANC-1 cells [C2]

description: PANC-1 ATCC ® CRL-1469™


title: GW-induced exosomes

city: Miaoli

first: HUAJUNG

last: LI

address: 35 Keyan Road,

description: miRNA expression data from GW627368-derived exosomes

hyb_protocol: 21.5 μLof Biotin-labeled sample were hybridized for 16 hr at 48℃ on miRNA 3.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Affymetrix GeneChip Command Console software (version4.0, Affymetrix) was used to analyze array images to get raw data and then Affymetrix Expression Console 1.3.1. for RMA normalization; Partek Genomics Suite software for statistical analysis

source_name: exosomes isolated from GW627368X-treated non-adherent mammary epithelial cells

label_protocol: Biotinylated miRNA were prepared using FlashTag Biotin HSR RNA Labeling Kit.

growth_protocol: NAMECs were propagated in MEGM medium (Lonza) according to standard protocols.

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

treatment_protocol: NAMECs were treated with GW627368X (1μg/ml) and PGE2 (1μM) for 96 h. The GW and PGE2 derived exosomes were collected from cell culture medium and extracted total RNA (included miRNA) by Trizol reagent.

tag: gender

value: female

tag: tissue type

value: mammary

value: Human mammary epithelial cell lines (HMLE)


title: PGE2-induced exosomes

description: miRNA expression data from PGE2-derived exosomes

source_name: exosomes isolated from PGE2-treated non-adherent mammary epithelial cells


title: HumanTumor_FreshFrozen_MET_CRC162A

value: colorectal


title: HumanTumor_FreshFrozen_MET_CRC167

value: MSCC 3


title: HumanTumor_FreshFrozen_MET_CRC170


title: HumanTumor_FreshFrozen_MET_CRC165A


title: parental PANC-1 cells [C1]

description: PANC-1 ATCC ® CRL-1469™


title: HumanTumor_FreshFrozen_MET_CRC159


title: HumanTumor_FreshFrozen_MET_CRC160A


title: ID11 DNA from individual 11

description: DNA from individual 11

tag: (mlid) or (slid) as diagnosed prior to the study


title: ID12 DNA from individual 12

description: DNA from individual 12


title: ID10 DNA from individual 10

description: DNA from individual 10


title: HumanTumor_FreshFrozen_MET_CRC151A


title: HumanTumor_FreshFrozen_MET_CRC149A


title: HumanTumor_FreshFrozen_MET_CRC147A


title: ID5 2 DNA from individual 5

description: DNA from individual 5


title: ID4 DNA from individual 4

description: DNA from individual 4


title: ID7 DNA from individual 7

description: DNA from individual 7


title: Nfat1-/- CD4+  T cells, infected, rep 2

city: Bronx

first: Fernando

last: Macian

state: NY

address: 1300 Morris Park Av.

department: Pathology

institute: Albert Einstein College of Medicine

hyb_protocol: Following fragmentation, 5.5 ug of sscDNA were hybridized in the Affymetrix hybridization over 645  for 17 hrs at 45C on a GeneChip Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Genechip scanner 7G.

data_processing: RMA-Sketch normalization was carried out using the Affymetrix Expression Console.

source_name: splenic CD4+ CD49d+ CD11a-high T cells

label_protocol: Biotinylated sscDNA were prepared according to the standard Affymetrix protocol from total RNA.

growth_protocol: Nfat1+/+ and Nfat1-/- mice were bred in house in a barrier facility.

extract_protocol: CD4+ T cells were isolated using magnetic beads (Dynabeads (Invitrogen)) and from these, CD11a-high, CD49d+ cells were positively sorted on a FACSAria. Total RNA was then extracted from pure cells by manufacturer's instructions using the Qiagen Rneasy Kit.

treatment_protocol: Nfat1+/+ and Nfat1-/- mice were either infected with Plasmodium yoelii 17XNL (2 x 10^4 infected red blood cells, intravenously administered), or kept as controls, for 21 days

value: CD4+ T cells

tag: infection

value: Plasmodium yoelii 17XNL

tag: genotype/variation

tag: tissue

value: spleen

value: 8-12 weeks old


title: ID6 DNA from individual 6

description: DNA from individual 6


title: HumanTumor_FreshFrozen_MET_CRC135A


title: HumanTumor_FreshFrozen_MET_CRC148A

value: MSCC 6


title: HumanTumor_FreshFrozen_MET_CRC133A

value: MSCC 1


title: Nfat1-/- CD4+  T cells, infected, rep 3

tag: strain

tag: age


title: HumanTumor_FreshFrozen_MET_CRC134A


title: HumanTumor_FreshFrozen_MET_CRC128C


title: ID2 1 DNA from individual 2

description: DNA from individual 2

value: SLID


title: Nfat1-/- CD4+  T cells, infected, rep 1


title: Nfat1-/- CD4+  T cells, uninfected, rep 3


title: ID3 DNA from individual 3

description: DNA from individual 3


title: HumanTumor_FreshFrozen_MET_CRC131A

value: Abdominal Wall

value: MSCC 2


title: ID2 2 DNA from individual 2

description: DNA from individual 2


title: HumanTumor_FreshFrozen_MET_CRC145A

value: Liver


title: Nfat1-/- CD4+  T cells, uninfected, rep 2


title: Nfat1-/- CD4+  T cells, uninfected, rep 1


title: ID5 1 DNA from individual 5

description: DNA from individual 5


title: Nfat1+/+ CD4+ T cells, infected, rep 3


title: ID1 DNA from individual 1

description: DNA from individual 1


title: Nfat1+/+ CD4+ T cells, infected, rep 2


title: HumanTumor_FreshFrozen_MET_CRC120A

value: Omentum

value: MSCC 5


title: HumanTumor_FreshFrozen_MET_CRC125A


title: HumanTumor_FreshFrozen_MET_CRC128A


title: Nfat1+/+ CD4+ T cells, infected, rep 1

value: female


title: DNA from PB 46, SGA

value: peripheral blood

tag: diagnosis

value: born small for gestational age (SGA)

tag: treatment with growth hormone

value: no


title: DNA from PB 49, SGA


title: HumanTumor_FreshFrozen_MET_CRC119A

value: colorectal


title: DNA from PB 32, SGA


title: Nfat1+/+ CD4+ T cells, uninfected, rep 2

value: CD4+ T cells


title: HumanTumor_FreshFrozen_MET_CRC112

value: MSCC 3


title: DNA from PB 36, SGA


title: HumanTumor_FreshFrozen_MET_CRC109A


title: DNA from PB 22, SGA


title: DNA from PB 31, SGA


title: DNA from PB 42, SGA


title: HumanTumor_FreshFrozen_MET_CRC108B


title: Nfat1+/+ CD4+ T cells, uninfected, rep 1

value: spleen


title: Nfat1+/+ CD4+ T cells, uninfected, rep 3

value: 8-12 weeks old


title: HumanTumor_FreshFrozen_MET_CRC107A

value: MSCC 4


title: HumanTumor_FreshFrozen_MET_CRC103C


title: HumanTumor_FreshFrozen_MET_CRC102A


title: DNA from PB 44, SGA


title: HIF2a/Myosin-Cre 006

city: Munich

first: Michael

last: Koeppen

address: Marchioninistr. 15

institute: Ludwig-Maximilians-University

hyb_protocol: standard Agilent hyb protocol

scan_protocol: standard protocol on the Agilent scanner

source_name: myocardial tissue

label_protocol: 0.5-1.0 microgram of Total RNA was used as a template for synthesis of cDNA utilizing the One Color Low input Agilent Quick Amp Labeling Kit.

extract_protocol: Total RNA including was isolated from approximately 30 mg of snap-frozen lung tissue using the Rneasy kit (Qiagen, Austin TX).

treatment_protocol: Mice underwent temporary ligation of left coronary artery for 45 min, floowed by 120 min reperfusion. Then we harvested the area-at-risk and snap-froze the tissue for further processing

value: myocardial tissue

tag: genotype

value: Hif2aloxP/loxP Myosin Cre+

tag: treatment

value: 45 min I + 120 min RP

value: male


title: HIF2a/Myosin-Cre 008


title: HumanTumor_FreshFrozen_MET_CRC108

tag: primary tumor site

tag: metastatic tumor site

value: Liver

value: MSCC 6


title: HIF2a/Myosin-Cre 007


title: HumanTumor_FreshFrozen_MET_CRC105B

tag: molecular subgroup

value: MSCC 2


title: DNA from PB 30, SGA

label_protocol: Standard Illumina Protocol


title: HIF2a/Myosin-Cre 005


title: HIF2a/Myosin-Cre 003

value: Control


title: HIF2a/Myosin-Cre 004


title: HumanTumor_FreshFrozen_MET_CRC118A


title: HIF2a/Myosin-Cre 001


title: HIF2a/Myosin-Cre 002


title: HumanTumor_FreshFrozen_MET_CRC103


title: HumanTumor_FreshFrozen_MET_CRC098D


title: Myosin-Cre 007

value: Myosin Cre+


title: Myosin-Cre 008


title: HumanTumor_FreshFrozen_MET_CRC096


title: RRx-001-5uM-1

first: Hongjuan

last: Zhao

address: 300 Pasteur Dr

department: Urology

institute: Stanford

description: SCC VII/SF is a spontaneously arising squamous cell cancer of C3H mice.

hyb_protocol: according to Infinium HD Methylation Assay, Manual Protocol (https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/infinium_assays/infinium_hd_methylation/infinium-hd-methylation-experienced-user-card-manual-15019522-01.pdf)

data_processing: Data was normalized using GenomeStudio

label: Cy5, Cy3

source_name: SCC VII, RRx-001 5um, 72hr

growth_protocol: Murine SCC VII cells were grown in DMEM medium supplemented with 10% fetal calf serum, 100 units/ml penicillin, and 100 µg/ml streptomycin in a 37°C humidified incubator with a mixture of 95% air and 5% CO2.

extract_protocol: Genomic DNA was isolated using a Qiagen AllPrep DNA/RNA Mini Kit (Qiagen) from SCC VII cells treated with the following compounds for 72 hours

treatment_protocol: Exponentially growing cells were plated in 100-mm dishes with 5-10 x 105 cells per dish in DMEM culture media and grown overnight.  Cells were treated with RRx-001, 5-azacytidine or 0.025% DMSO as a vehicle control for one to three days.  Media containing RRx-001, 5-azacytidine, or DMSO were replaced daily over the 3-day period.


title: Myosin-Cre 002


title: HumanTumor_FreshFrozen_MET_CRC093A

value: Lung


title: HumanTumor_FreshFrozen_MET_CRC088A

value: Omentum


title: Myosin-Cre 003


title: HumanTumor_FreshFrozen_MET_CRC083A

value: colorectal

value: Periotneal


title: Myosin-Cre 004


title: HumanTumor_FreshFrozen_MET_CRC097


title: Myosin-Cre 005


title: HumanTumor_FreshFrozen_MET_CRC094


title: Myosin-Cre 001


title: HumanTumor_FreshFrozen_MET_CRC087A


title: HumanTumor_FreshFrozen_MET_CRC089A

value: MSCC 3


title: HumanTumor_FreshFrozen_MET_CRC092


title: Myosin-Cre 006


title: HumanTumor_FreshFrozen_MET_CRC094B


title: HumanTumor_FreshFrozen_MET_CRC078A


title: liver_1m-_ko_rep2

city: Shanghai

first: Ze Guang

last: Han

address: No. 197 Second Rui Jin Rd.

institute: Key Laboratory of Systems Biomedicine (Ministry of Education) of Rui-Jin Hospital

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

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

source_name: 1-month-old_hepatocyte Arid1a knockout

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

growth_protocol: Mice were cultured in SPF room.

extract_protocol: Postnatal 5-day-old, 2-week-old and 1-month-old pups were sacrificed by decapitation. Pup livers were rapidly dissected and flash frozen in liquid nitrogen. Total RNA was extracted from liver samples with TRIzol reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

tag: strain background

value: hepatocyte Arid1a knockout

value: postnatal 1-month-old

value: liver


title: RRx-001-0.5uM-2

scan_protocol: according to Infinium HD Methylation Assay, Manual Protocol (https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/infinium_assays/infinium_hd_methylation/infinium-hd-methylation-experienced-user-card-manual-15019522-01.pdf)

source_name: SCC VII, RRx-001 0.5um, 72hr


title: HumanTumor_FreshFrozen_MET_CRC075A


title: RRx-001-2uM-1

source_name: SCC VII, RRx-001 2um, 72hr

label_protocol: according to Infinium HD Methylation Assay, Manual Protocol (https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/infinium_assays/infinium_hd_methylation/infinium-hd-methylation-experienced-user-card-manual-15019522-01.pdf)


title: liver_1m-_ko_rep1


title: liver_2w-_ko

source_name: 2-week-old_hepatocyte Arid1a knockout

value: postnatal 2-week-old


title: HumanTumor_FreshFrozen_MET_CRC063


title: HumanTumor_FreshFrozen_MET_CRC077A


title: HumanTumor_FreshFrozen_MET_CRC066A

value: MSCC 4


title: liver_1m_wildtype

value: wildtype


title: liver_5d-_ko_rep1

source_name: 5-day-old_hepatocyte Arid1a knockout

value: male

value: postnatal 5-day-old


title: HumanTumor_FreshFrozen_MET_CRC074A

source_name: human tumor, colorectal primary, metastasis, fresh frozen tissue

value: Liver

value: MSCC 1


title: control1

city: beijing

first: zhang

last: suwei

address: changping

institute: capitalbio

description: RNA from tumor tissues from patients with  non-metastatic TSCC

hyb_protocol: The labled RNA were hybridized for 16 hr at 48C on Affymetrix miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with miRNA QCTool using Affymetrix default analysis settings and quantile as normalization method.

source_name: tumor tissues of patiens with non- metastatic TSCC

label_protocol: About 1ug total RNA were polyA tailed and labled with FlashTag™ Biotin HSR Labeling Kit. This kit can be used to label any RNA sample, including total RNA, severely degraded RNA, plant RNA, and low molecular weight RNA.

treatment_protocol: Paired primary tumor tissues were obtained from patients with metastatic and non-metastatic TSCC. The tumor tissues were obtained from surgical excision. All tissues were snap-frozen in liquid  nitrogenat at -80C until use.

value: non-metastatic tumor tissue


title: liver_5d-_ko_rep2


title: HumanTumor_FreshFrozen_MET_CRC060


title: HumanTumor_FreshFrozen_MET_CRC067A


title: liver_2w_wildtype


title: HumanTumor_FreshFrozen_MET_CRC062


title: liver_5d_wildtype


title: p120L/L -K5Cre+/+ mouse embryos backskin

city: Madrid

first: Mirna

middle: Alicia

last: Perez-Moreno

state: Madrid

address: 3rd Melchor Fernandez Almagro st

department: Epithelial Cell Biology

country: Spain

institute: CNIO

description: p120L/L -K5Cre+/+

hyb_protocol: Chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 825 ng. Volume: 100 uL. Temperature (ºC): 65. Duration: 17 hours.

scan_protocol: Scanned on an G2565C DNA microarray scanner (Agilent).

data_processing: Images were quantified using Agilent Feature Extraction Software (ver. 10.1.1). Data preprocessed using background subtraction and LOWESS normalization.

label_protocol: Amount of nucleic acid labeled: 1µg. Amplification: by RNA polymerases. Commercial Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) kit by following manufacturer instructions. Agilent manual G4140-90050 Ver. 5.7 March 2008. Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores. Labeled samples are purified with silica-based RNeasy spin columns (Qiagen).

growth_protocol: Total skin of E18.5 embryos were collected

value: total skin

tag: genetic background

source_name: Total embryo skin

value: Total embryo skin


title: control10


title: RRx-001-0.5uM-1

city: Stanford


title: RRx-001-2uM-2


title: p120Δ/Δ -K5Cre+/T mouse embryos backskin

description: p120Δ/Δ -K5Cre+/T

source_name: p120Δ/Δ -K5Cre+/T

value: p120Δ/Δ -K5Cre+/T


title: HumanTumor_FreshFrozen_MET_CRC061

value: colorectal


title: control9


title: DMSO2

source_name: SCC VII, DMSO control

value: DMSO


title: RRx-001-5uM-2


title: DMSO1


title: control3


title: HumanTumor_FreshFrozen_MET_CRC054

value: Lung

value: MSCC 5


title: HumanTumor_FreshFrozen_MET_CRC051


title: HumanTumor_FreshFrozen_MET_CRC057A


title: HumanTumor_FreshFrozen_MET_CRC056

value: MSCC 3


title: control2


title: shiyan8

description: RNA from tumor tissues of patients with  metastatic TSCC

value: metastatic tumor tissue


title: HumanTumor_FreshFrozen_MET_CRC049


title: HumanTumor_FreshFrozen_MET_CRC058


title: HumanTumor_FreshFrozen_MET_CRC041

value: MSCC 6


title: HumanTumor_FreshFrozen_MET_CRC050

value: MSCC 2


title: shiyan17

source_name: tumor tissues of patients with  metastatic TSCC


title: KO_2

city: Copenhagen

first: Aditya

last: Sankar

email: cnj376@ku.dk, aditya.sankar@embl.de

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: University of Copenhagen

hyb_protocol: Samples were hybridized to Agilent SurePrint G3 Mouse GE 8x60K arrays (Agilent G4852A) using Gene Expression Hybridization kit (Agilent #5188-5242) according to manufacturer’s instructions.

scan_protocol: Arrays were scanned according to manufacturers instructions.

data_processing: The raw data was processed in R using the 'limma' package. Raw data was imported using function 'read.maimages' (source=agilent,green.only=TRUE), background corrected using 'backgroundCorrect' (method=normexp,offset=50) and normalized using 'normalizeBetweenArrays' (method="quantile). The filtering is a quality filtering and is completely unbiased and does not inflate p-values for a specific test. The expression table have been quality filtered and normalised, and control probes are removed from the final expression matrix. We have filtered probes for quality, so that probes must be at least 10% brighter than the 95% percentile of the negative control probes, on at least half of the arrays.

label_protocol: Samples were labeled according to manufacturer’s instructions using LowInput QuickAmp Labeling Kit One Color (Agilent #5190-2305) and One-Color RNA Spike-In kit (Agilent #5188-5282).

extract_protocol: Pituitary RNA was obtained from three independent littermate controls and null females under conditions decribed above. Tissues were collected, flash frozen in liquid nitrogen and stored at -80 C. Tissues were homogenized using a Fisherbrand Disposable Pestle system in RLT+ buffer and RNA was extracted using RNeasy Plus Mini kit (Qiagen, #74136) RNA quality was measured using an Agilent 2100 Bioanalyzer system (Agilent, #G2940CA) and RNA 6000 Nano reagents (Agilent, #5067-1511). RIN scores were at least 9.9 for RNA used in the microarray.

treatment_protocol: Virgin mature littermate female mice were oestrus cycle activated by exposure to dirty bedding from cage of a stud male. The animals were sacrificed 24 hours later.

value: KO; Jmjd2a-/-

tag: gender

value: female

value: 8 weeks

tag: time point

value: 24hr after oestrus cycle activation

value: pituitary


title: HumanTumor_FreshFrozen_MET_CRC040

value: Liver

value: MSCC 4


title: HumanTumor_FreshFrozen_MET_CRC047


title: shiyan6


title: HumanTumor_FreshFrozen_MET_CRC043A


title: KO_3


title: het-nox-rep.4

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

hyb_protocol: Hybridization was performed at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) and analyzed with GenePix software V5.2 (MDS).

data_processing: Raw data was further processed using R (http://www.R-project.org)

source_name: lung homogenate

label_protocol: Purified total RNA was amplified and Cy-labeled using the single-color QuickAmp kit (Agilent Technologies, Palo Alto, CA) following the kit instructions.

growth_protocol: Mice were grown under standard conditions with unlimited supply of food and water.

extract_protocol: RNA was isolated by using miRNeasy Mini Kit (Qiagen, Cat. No. 217004), RNA was eluted with RNAse-free water at the last step of the protocol, concentration was measured by nanodrop, RNA was stored at -80°C.

treatment_protocol: WT vs Fgf10+/- pups of the hyperoxia group were treated from P0-P3 with 85% oxygen in a chamber


title: KO_1


title: Control_3

value: wild type; Jmjd2a+/+


title: HumanTumor_FreshFrozen_MET_CRC044

value: Liver,MSCC 3


title: wt-nox-rep.4

value: wild-type


title: HumanTumor_FreshFrozen_MET_CRC045

value: colorectal


title: HumanTumor_FreshFrozen_MET_CRC033


title: het-nox-rep.2


title: HumanTumor_FreshFrozen_MET_CRC022


title: Control_2


title: HumanTumor_FreshFrozen_MET_CRC021B


title: HumanTumor_FreshFrozen_MET_CRC024A


title: HumanTumor_FreshFrozen_MET_CRC019


title: wt-nox-rep.1


title: shiyan11


title: HumanTumor_FreshFrozen_MET_CRC037A

value: MSCC 1


title: het-nox-rep.3


title: Control_1


title: HumanTumor_FreshFrozen_MET_CRC039A


title: HumanTumor_FreshFrozen_MET_CRC011


title: wt-hyx-rep.4


title: HumanTumor_FreshFrozen_MET_CRC025B

value: Lung

value: MSCC 5


title: HumanTumor_FreshFrozen_MET_CRC030A


title: HumanTumor_FreshFrozen_MET_CRC028A


title: wt-nox-rep.2


title: wt-nox-rep.3


title: het-hyx-rep.4