title: Melanoma tumor sample from patient 95

description:
replicate 1
LuM95

value: Male

value: Local


title: Melanoma tumor sample from patient 94

status: Public on Apr 01 2015

type: RNA

city: Lund

first: Göran

last: Jönsson

address: Scheelevägen 8

country: Sweden

institute: Lund University

description:
replicate 1
LuM94

hyb_protocol: Standard protocol for Whole-Genome Expression Direct Hybridization Assay was used (Illumina).

scan_protocol: Arrays were scanned using the iScan Reader (Illumina).

data_processing: The data was normalized using the cubic spline method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Malignant melanoma

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

extract_protocol: Total RNA was extracted using the Allprep kit (DNA/RNA mini kit) from Qiagen in accordance with the prescribed protocol provided with the kit. Quality control was performed using a Bioanalyser (Agilent).

tag: gender

tag: age

tag: tumor stage

value: General

tag: tissue

value: Subcutaneous

tag: distant metastasis free survival in days

tag: distant metastasis free survival (1=death, 0=alive)

tag: disease specific survival in days

tag: disease specific survival (1=death, 0=alive)


title: SCC-15+AzC 4d rep 1

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

description:
replicate 2
SCC-15 + AzC (1)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data analysis was performed with GeneSpring GX software (Agilent Technologies). Quantile normalization was performed. Differentially expressed gene lists were generated by using Fold Change analysis tool.

source_name: oral tumor

label_protocol: 500ng total RNA was converted into cDNA using biotinylated random nonamers, oligodeoxythymidine 18 primers and Illumina-supplied reagents, according to Illumina manufacturer's instructions.

growth_protocol: Oral cancer cell lines, such as OC3, SAS, SCC-15, and HSC3, were cultured with or without 10 uM of 5-aza-2’-deoxycytidine (AzC) for 4 days.

extract_protocol: Total RNA was isolated using an RNeasy mini kit (Qiagen) according to the manufacturer's instruction.

value: male

tag: cell line

value: epithelia

tag: treatment

value: AzC


title: Sample11

type: genomic

city: Cleveland

first: Bartlomiej

last: Przychodzen

state: Ohio

address: 9600 Euclid Avenue

department: THOR

country: USA

institute: Cleveland Clinic

description: Hybridized to GenomeWideSNP_6

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: not provided

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) and Affymetrix Genotyping Console Software (GCOS 4.0.0).

label: Biotin

molecule: genomic DNA

source_name: AML

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Standard protocol

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, Qubit and 2% agarose gel electrophoresis.

tag: diagnosis

value: acute myeloid leukemia (AML)


title: Untreated-Mdr2/KO Liver vs Tumor (Spon6F)

city: Jerusalem

first: Daniel

last: Goldenberg

address: Ein Kerem

department: Gene therapy

country: Israel

institute: Hadassah medical center

hyb_protocol: According to manufacturer protocol (Affymetrix)

data_processing:
The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities and ratios (including background subtraction and normalization), rejects outliers, and calculates statistical confidences (p-values).   Further analysis and visualization of the hybridization results was performed with the Agilent CGH Analytics software (V 3.5). Here, the following aberration filter settings have been used:  (i) Minimum number of probes present in an aberrant region = 2 (ii) Minimum absolute average log2 ratio for region = 0.3 corresponds to a fold change of 1.23.  (iii) The statistical analysis of aberrant regions was based on the aberrations detection method ADM-2
We used ADM-2 algorithm, the score represents the deviation of the weighted average of the normalized log ratios from its expected value of zero and incorporates quality information about each probe measurement.

organism: Mus musculus

source_name: Liver, Non Tumor, Untreated

growth_protocol: Regular growth on normal diet

extract_protocol: Tri-reagent

treatment_protocol: 70% PHx of both male and female Mdr2-KO mice at the age of either 3 or 6 months

value: Female

value: Untreated

tag: genotype

value: liver, non-tumor

source_name: Mdr2/KO-Untreated, Tumor

value: liver, tumor


title: Untreated-Mdr2/KO Liver vs Tumor (Spon5F)

scan_protocol: According to manufacturer protocol (Affymetrix)


title: Untreated-Mdr2/KO Liver vs Tumor (Spon2M)

label_protocol: According to manufacturer protocol (Affymetrix)


title: Melanoma tumor sample from patient 92

description:
replicate 1
LuM92

value: Regional

value: Lymph node


title: Untreated-Mdr2/KO Liver vs Tumor (Spon1M)


title: Post-PHx-Mdr2/KO Liver vs Tumor (PHx4M)

source_name: Liver, Non Tumor,  PHx

value: Partial hepatectomy

source_name: Mdr2/KO-PHx, Tumor


title: SCC-15 rep 1

description:
replicate 1
SCC-15 (1)

value: mock


title: SAS+AzC 4d rep 1

description:
replicate 2
SAS + AzC (1)

value: SAS


title: SCC-15+AzC 4d rep 2

description:
replicate 2
SCC-15 + AzC(2)


title: Melanoma tumor sample from patient 93

description:
replicate 1
LuM93

value: Male


title: SAS+AzC 4d rep 2

description:
replicate 2
SAS + AzC(2)


title: leukemia patient sample 8

city: Seoul

first: Kee-Beom

last: Kim

address: Heusokdong

country: South Korea

institute: Chung-Ang University

description: leukemia patient sample

hyb_protocol: hybridazation on Infinium HumanMethylation27 BeadChip array was performed according to manufacturer's protocol given in Infinium Assay Mehtylation Protocol Guide (Illumina, Inc.)

scan_protocol: Standard Illumina procedures using Illumina BeadStation 500G array scanner

data_processing: Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles. Background intensity computed from a set of negative controls was subtracted from each analytical data point. The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100). The ß-value reflects the methylation level of each CpG site.   A  ß-value of 0–1.0 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.

source_name: genomic DNA from leukemia patient sample

label_protocol: labeling was performed according to manufacturer's protocol given in Infinium Assay Methylation Protocol Guide (Illumina, Inc.)

growth_protocol: none, blood was drawn from leukemia patienta and normal control donors

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

treatment_protocol: Bisulfite treatment was performed as recommended for DNA methylation profiling with Illumina Infinium Beadchip arrays; Bisulfite conversion was performed using EZ DNA Methylation Kit (Zymo Research)

tag: disease status

value: leukemia

value: whole blood


title: Post-PHx-Mdr2/KO Liver vs Tumor (PHx6F)


title: Post-PHx-Mdr2/KO Liver vs Tumor (PHx3M)


title: Melanoma tumor sample from patient 91

description:
replicate 1
LuM91


title: Melanoma tumor sample from patient 89

description:
replicate 1
LuM89


title: Post-PHx-Mdr2/KO Liver vs Tumor (PHx5M)


title: SAS rep 1

description:
replicate 1
SAS (1)


title: leukemia patient sample 7

description: leukemia patient sample


title: OC3+AzC 4d rep 2

description:
replicate 2
OC3 + AzC(2)


title: V2/ C2

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: Vinclozolin sample two is compared to control sample two

hyb_protocol: The comparative MeDIP-Chip was performed with Roche Nimblegen’s custom whole genome array which contains 2 different array set, with 4,085,426 probes per sub-array.  Probe sizes range from 50-75 bp in length with the median probe spacing of approximately 300 bp. Two different comparative (MeDIP vs. MeDIP) hybridization experiments were performed for vinclozolin lineage versus control, with each array set encompassing DNA samples from 6 animals (3 each from vinclozolin and control).

scan_protocol: Scanning and image acquisition was performed in-house by Nimblegen Inc.

data_processing:
For the MeDIP-Chip and CNV experiments raw data from the Cy3 and Cy5 channels were imported into R (R Development Core Team (2010), R: A language for statistical computing, R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org), checked for quality and converted to MA values (M=Cy5-Cy3; A=(Cy5+Cy3)/2). Within array and between array normalizations were performed as follows: within each array, median normalization was performed. After each array was normalized within array, the arrays were then normalized between arrays using the A quantile normalization procedure. For the CGH, following normalization, the average value of each probe was calculated and two different copy number variation algorithms were used on each of these probes including CGHseg and cghFlasso.  These two algorithms were used with the default parameters.  The average values from the output of these algorithms were obtained. A threshold of 0.05 as a cut-off was used on the summary (average of the log-ratio from the three algorithms) where gains are probes above the positive threshold and losses are probes below the negative threshold. Consecutive probes (≥3) of gains and losses were used to identify separate CNV regions. A cut-off of 3-probe minimum was used and those regions were considered a valid CNV.  The statistically significant copy number variation regions (CNV) were identified. The chromosomal location of CNV and DMR clusters used an R-code developed to find chromosomal locations of clusters.  A 2 Mb sliding window with 50,000 base intervals was used to find the associated CNV and DMR in each window.  A Z-test statistical analysis with p<0.05 was used on these windows to find the ones with over-represented CNV and DMR were merged together to form clusters.  A typical cluster region averaged approximately 3-4 megabases in size.  The DMR and CNV association with specific rat genes and genome locations used the Gene NCBI database for rat gene locations and correlated the epimutations associated (overlapped) with the genes. The three adjacent probes constituted approximately a 200bp homology search. The KEGG pathway associations were identified using the KEGG website 'Search Pathway' tool. Statistically significant over-representation uses a Fisher’s exact analysis.
Nimblescan software-generated Cy3/Cy5 expression ratios are presented in the processed data files, but R-code data processing of raw data as described was used as the basis for conlusions in this study. Value definitions for processed data files: #meanM: are M values (rowMedians) for each probe. Where (M = Cy5–Cy3), #meanA: are A values (rowMedians) for each probe. Where (A = (Cy5 + Cy3)/2), and #meanP: is the calculated p-value showing statistical significance of each probe.

organism: Rattus norvegicus

source_name: DNA from F3 Vinclozolin lineage (V) sperm

label_protocol: MeDIP DNA samples from experimental lineages were labeled with Cy3 and MeDIP DNA samples from the control lineage were labeled with Cy5

growth_protocol: F0 generation time-pregnant females were exposed to daily intraperitoneal injections of vinclozolin (100 mg/kg BW/day) or dimethyl sulfoxide (vehicle) on days 8 through 14 of gestation. Treatment lineages are designated “control” or “vinclozolin” lineages. The offspring of the F0 generation rats were the F1 generation. Non-littermate females and males aged 70-90 days from F1 generation of control, or vinclozolin lineages were bred to obtain F2 generation offspring. The F2 generation rats were bred to obtain F3 generation offspring. The F1 - F3 generation offspring were not themselves treated directly with vinclozolin.

extract_protocol: The epididymis was dissected free of connective tissue, a small cut made to the cauda and placed in 5 ml of F12 culture medium containing 0.1% bovine serum albumin for 10 minutes at 37°C and then kept at 4ºC to immobilize the sperm.  The epididymal tissue was minced and the released sperm centrifuged at 13, 000 x g and stored in fresh nucleus isolation medium (NIM) buffer at -20ºC until processed further. Sperm heads were separated from tails through sonication preformed (without protease inhibitors) and then purified using a series of washes and centrifugations from a total of nine F3 generation rats per lineage (control or vinclozolin) that were 120 days of age. DNA extraction on the purified sperm heads was performed by phenol:chloroform:isoamyl alcohol extraction method, washed with 70% ethanol and resuspended . Equal concentrations of DNA from three individual sperm samples were used to produce three DNA pools per lineage and employed for chromatin immunoprecipitation of methylated DNA fragments (MeDIP). MeDIP was performed as follows: 6 ug of genomic DNA was subjected to series of three 20 pulse sonications at 20% amplitude and the fragment size verified through 2% agarose gels with approximately a 500 kb size; the sonicated genomic DNA was resuspended in 350 ul TE and denaturated for 10 min at 95°C and then immediately placed on ice for 5 min; 100 ul of 5X IP buffer (50 mM Na-phosphate pH7, 700 mM NaCl, 0.25% Triton X-100) was added to the sonicated and denatured DNA. An overnight incubation of the DNA was performed with 5 ug of antibody anti-5-methylCytidine monoclonal from Diagenode S.A at 4°C on a rotating platform. Protein A/G beads from Santa Cruz were prewashed on PBS-BSA 0.1% and resuspended in 40 ul 1X IP buffer. Beads were then added to the DNA-antibody complex and incubated 2 h at 4°C on a rotating platform. Beads bound to DNA-antibody complex were washed 3 times with 1 ml 1X IP buffer; washes included incubation for 5 min at 4°C on a rotating platform and then centrifugation at 6000 rpm for 2 min. Beads-DNA-antibody complex were then resuspended in 250 ul digestion buffer (50 mM Tris HCl pH 8, 10 mM EDTA, 0.5% SDS) and 3.5 ul of proteinase-k (20 mg/ml) was added to each sample and then incubated overnight at 55°C on a rotating platform. DNA purification was performed first with phenol and then with chloroform:isoamyl alcohol. Two washes were then performed with 70% ethanol, 1 M NaCl and glycogen. ChIP selected DNA was then resuspended in 30 ul TE buffer.

treatment_protocol: Vinclozolin

tag: generation

source_name: DNA from F3 Control lineage (C) sperm

treatment_protocol: Control


title: PBS LY6C- : PBS injected LY6C- monocytes [G32_LY6Cpool]

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building

department: Cancer Institute

country: United Kingdom

institute: UCL

description: Gene expression data from primary monocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mogene 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were preprocessed and normalised initially using the Bioconductor oligo package (RMA algorithm). (In Publication data were further merged with other public datasets and renormalised)

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

growth_protocol: Not applicable

extract_protocol: Extraction of total RNA was performedusing the RNAeasy Microkit (Qiagen, UK)

treatment_protocol: Monocytes populations were purified fromCD11c-DTR mice which were injected with PBS or diphtheria toxin 48 hours previously. Common monocyte progenitors (cMoP) were isolated from untreated C57BL/6 mice.

value: spleen

tag: cell type

value: monocyte

tag: strain

value: 8-12 weeks


title: Melanoma tumor sample from patient 88

description:
replicate 1
LuM88


title: V1/ C1

description: Vinclozolin sample one is compared to control sample one


title: leukemia patient sample 6

description: leukemia patient sample


title: F3-V3/F3-C3

description:
Normalized_F3_CNV_data_for_GEO.csv
Generation F3 vinclozolin sample three is compared to generation F3 control sample three

hyb_protocol: The array used for the copy number variation analysis was a chromosomal genomic hybridization (CGH) custom design by Roche Nimblegen that consisted of a whole genome tiling array of the rat genome with 385,102 probes per array. The probe size ranged from 50-75mer in length with median probe spacing of 1395bp. Three different comparative (CNV vs CNV) hybridization experiments were performed (2 array set) for each experiment vinclozolin versus control lineage, with each array including hybridizations from DNA pools from these different experiments. Equal concentrations of DNA from sperm samples from groups of three individuals were used to produce three different DNA pools per lineage and employed for the CNV analysis.

data_processing:
For the CNV and MeDIP-Chip experiments raw data from the Cy3 and Cy5 channels were imported into R (R Development Core Team (2010), R: A language for statistical computing, R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org), checked for quality and converted to MA values (M=Cy5-Cy3; A=(Cy5+Cy3)/2). Within array and between array normalizations were performed as follows: Within each array, probes were separated into groups by GC content and each group was separately normalized, between Cy3 and Cy5 using the loess normalization procedure. This allowed for GC groups to receive a normalization curve specific to that group. After each array was normalized within array, the arrays were then normalized between arrays using the A quantile normalization procedure. For the CGH, following normalization, the average value of each probe was calculated and two different copy number variation algorithms were used on each of these probes including CGHseg and cghFlasso.  These two algorithms were used with the default parameters.  The average values from the output of these algorithms were obtained. A threshold of 0.05 as a cut-off was used on the summary (average of the log-ratio from the three algorithms) where gains are probes above the positive threshold and losses are probes below the negative threshold. Consecutive probes (≥3) of gains and losses were used to identify separate CNV regions. A cut-off of 3-probe minimum was used and those regions were considered a valid CNV.  The statistically significant copy number variation regions (CNV) were identified. The chromosomal location of CNV and DMR clusters used an R-code developed to find chromosomal locations of clusters.  A 2 Mb sliding window with 50,000 base intervals was used to find the associated CNV and DMR in each window.  A Z-test statistical analysis with p<0.05 was used on these windows to find the ones with over-represented CNV and DMR were merged together to form clusters.  A typical cluster region averaged approximately 3-4 megabases in size.  The DMR and CNV association with specific rat genes and genome locations used the Gene NCBI database for rat gene locations and correlated the epimutations associated (overlapped) with the genes. The three adjacent probes constituted approximately a 200bp homology search. The KEGG pathway associations were identified using the KEGG website 'Search Pathway' tool. Statistically significant over-representation uses a Fisher’s exact analysis.
Nimblescan software-generated Cy3/Cy5 expression ratios are presented in the processed data files, but R-code data processing of raw data as described was used as the basis for conlusions in this study.

label_protocol: For each array DNA samples from the vinclozolin lineage were labeled with Cy3 and DNA samples from the control lineage were labeled with Cy5.


title: OC3 rep 1

description:
replicate 1
OC3 (1)

value: male

value: epithelia


title: Melanoma tumor sample from patient 87

description:
replicate 1
LuM87

value: Primary

value: Cutaneous


title: Post-PHx-Mdr2/KO Liver vs Tumor (PHx1M)

value: liver, non-tumor


title: SAS rep 2

description:
replicate 1
SAS (2)


title: OC3+AzC 4d rep 1

description:
replicate 2
OC3 + AzC (1)

value: AzC


title: Post-PHx-Mdr2/KO Liver vs Tumor (PHx2F)

value: Female

value: liver, tumor


title: leukemia patient sample 4

description: leukemia patient sample


title: Melanoma tumor sample from patient 90

description:
replicate 1
LuM90

value: General

value: Visceral


title: Melanoma tumor sample from patient 86

description:
replicate 1
LuM86


title: leukemia patient sample 2

description: leukemia patient sample


title: F3-V2/F3-C2

description:
Normalized_F3_CNV_data_for_GEO.csv
Generation F3 vinclozolin sample two is compared to generation F3 control sample two


title: leukemia patient sample 3

description: leukemia patient sample


title: leukemia patient sample 5

description: leukemia patient sample


title: normal sample 4

description: normal sample

source_name: genomic DNA from normal blood sample

value: normal


title: leukemia patient sample 1

description: leukemia patient sample


title: Melanoma tumor sample from patient 82

description:
replicate 1
LuM82

value: Male

value: Local


title: OC3 rep 2

description:
replicate 1
OC3 (2)

value: mock


title: F3-V1/F3-C1

description:
Normalized_F3_CNV_data_for_GEO.csv
Generation F3 vinclozolin sample one is compared to generation F3 control sample one


title: Melanoma tumor sample from patient 85

description:
replicate 1
LuM85

value: Regional

value: Lymph node


title: Melanoma tumor sample from patient 83

description:
replicate 1
LuM83


title: Melanoma tumor sample from patient 84

description:
replicate 1
LuM84

value: Subcutaneous


title: F1-V3/F1-C3

description:
Normalized_F1_CNV_data_for_GEO.csv
Generation F1 vinclozolin sample three is compared to generation F1 control sample three

source_name: DNA from F1 Vinclozolin lineage (V) sperm

source_name: DNA from F1 Control lineage (C) sperm


title: Melanoma tumor sample from patient 80

description:
replicate 1
LuM80


title: F1-V2/F1-C2

description:
Normalized_F1_CNV_data_for_GEO.csv
Generation F1 vinclozolin sample two is compared to generation F1 control sample two


title: F1-V1/F1-C1

description:
Normalized_F1_CNV_data_for_GEO.csv
Generation F1 vinclozolin sample one is compared to generation F1 control sample one


title: normal sample 2

description: normal sample

value: whole blood


title: Melanoma tumor sample from patient 76

description:
replicate 1
LuM76


title: normal sample 1

description: normal sample


title: Melanoma tumor sample from patient 78

description:
replicate 1
LuM78


title: Melanoma tumor sample from patient 81

description:
replicate 1
LuM81


title: Melanoma tumor sample from patient 79

description:
replicate 1
LuM79


title: OSCC T38 Methylation

description: OSCC

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software v1.1

label: Cy5 and Cy3

source_name: oral squamous cell carcinoma

label_protocol: Standard Illumina Protocol

extract_protocol: OSCC and non-OSCC pair-wise samples were prepared after cutting into 5μm-thick sections on a microtome with a disposable blade.Genomic DNA was extracted and purified using Qiagen DNeasy Kit  according to the manufacturer's instruction.

value: male

value: oral squamous cell carcinoma


title: Melanoma tumor sample from patient 77

description:
replicate 1
LuM77


title: OSCC T36 Methylation

description: OSCC


title: Melanoma tumor sample from patient 72

description:
replicate 1
LuM72


title: OSCC T40 Methylation

description: OSCC


title: OSCC T37 Methylation

description: OSCC


title: Airway epithelium, asthma sample 62

city: San Francisco

first: Stephanie

middle: A

last: Christenson

state: California

address: 513 PARNASSUS AVENUE, HSE1305

department: Pulmonary and Critical Care

institute: University of California, San Francisco

description:
MASTB-017
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

hyb_protocol: 2.75 µg of single-stranded DNA was hybridized to Affymetrix U133 Plus 2.0 arrays.

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent) as per manufacturer's protocol.

data_processing: Data underwent RMA normalization and Combat batch correction. Probeset IDs were defined using the Entrez Gene custom CDF v14 available for the Affymetrix U133 Plus 2.0 array available at brainarray.mbni.med.umich.edu.

source_name: airway epithelium, asthma, Th2 high

label_protocol: 25 ng of RNA was amplified using the NuGen RNA Ovation Amplification Kit.

extract_protocol: Total epithelial RNA was isolated using the miRNeasy Mini Kit (Qiagen).

value: airway epithelium

value: female

tag: disease state

value: asthma

tag: th2 group

value: high


title: Airway epithelium, asthma sample 60

description:
MASTB-012
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

source_name: airway epithelium, asthma, Th2 low

tag: age

tag: gender

value: low


title: Melanoma tumor sample from patient 75

description:
replicate 1
LuM75

value: Female

tag: tumor stage

tag: tissue


title: Airway epithelium, asthma sample 59

description:
MASTB-010
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, healthy sample 42

description:
MASTA-004
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

source_name: airway epithelium, healthy

value: healthy


title: Airway epithelium, asthma sample 61

description:
MASTB-015
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Melanoma tumor sample from patient 74

description:
replicate 1
LuM74

source_name: Malignant melanoma

tag: distant metastasis free survival in days

tag: distant metastasis free survival (1=death, 0=alive)


title: OSCC T33 Methylation

description: OSCC


title: OSCC T39 Methylation

description: OSCC


title: Airway epithelium, asthma sample 58

description:
MASTB-027
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Melanoma tumor sample from patient 73

description:
replicate 1
LuM73

tag: disease specific survival in days

tag: disease specific survival (1=death, 0=alive)


title: Melanoma tumor sample from patient 71

description:
replicate 1
LuM71


title: OSCC T32 Methylation

description: OSCC


title: Airway epithelium, healthy sample 43

description:
MASTA-017
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Melanoma tumor sample from patient 70

description:
replicate 1
LuM70


title: Melanoma tumor sample from patient 69

description:
replicate 1
LuM69

value: General


title: OSCC T35 Methylation

description: OSCC


title: OSCC T30 Methylation

description: OSCC


title: OSCC T34 Methylation

description: OSCC


title: Airway epithelium, asthma sample 56

description:
MASTB-023
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, asthma sample 55

description:
MASTB-021
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, asthma sample 57

description:
MASTB-025
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: OSCC T31 Methylation

description: OSCC


title: Airway epithelium, asthma sample 54

description:
MASTB-020
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, asthma sample 53

description:
MASTB-014
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: OSCC T29 Methylation

description: OSCC


title: Melanoma tumor sample from patient 68

description:
replicate 1
LuM68


title: Airway epithelium, healthy sample 40

description:
MASTA-003
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, healthy sample 41

description:
MASTA-016
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: OSCC T25 Methylation

description: OSCC


title: Melanoma tumor sample from patient 63

description:
replicate 1
LuM63


title: Airway epithelium, healthy sample 39

description:
MASTA-002
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: OSCC T27 Methylation

description: OSCC


title: Melanoma tumor sample from patient 61

description:
replicate 1
LuM61

value: Male


title: Melanoma tumor sample from patient 66

description:
replicate 1
LuM66


title: Melanoma tumor sample from patient 65

description:
replicate 1
LuM65


title: Airway epithelium, asthma sample 52

description:
MASTB-004
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Melanoma tumor sample from patient 67

description:
replicate 1
LuM67

value: Primary

value: Cutaneous


title: Melanoma tumor sample from patient 64

description:
replicate 1
LuM64

value: Regional


title: OSCC T24 Methylation

description: OSCC


title: OSCC T28 Methylation

description: OSCC


title: OSCC T26 Methylation

description: OSCC


title: Airway epithelium, healthy sample 38

description:
MASTA-012
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, asthma sample 51

description:
MASTB-003
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: OSCC T23 Methylation

description: OSCC


title: OSCC T22 Methylation

description: OSCC


title: Melanoma tumor sample from patient 59

description:
replicate 1
LuM59

value: In-transit


title: Melanoma tumor sample from patient 62

description:
replicate 1
LuM62


title: Melanoma tumor sample from patient 58

description:
replicate 1
LuM58

value: Lymph node


title: OSCC T20 Methylation

description: OSCC


title: Melanoma tumor sample from patient 60

description:
replicate 1
LuM60


title: Melanoma tumor sample from patient 57

description:
replicate 1
LuM57

value: Subcutaneous


title: OSCC T21 Methylation

description: OSCC

value: male


title: Airway epithelium, healthy sample 35

description:
MASTA-007
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, healthy sample 36

description:
MASTA-008
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, healthy sample 37

description:
MASTA-011
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, healthy sample 34

description:
MASTA-006
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: OSCC T19 Methylation

description: OSCC

value: oral squamous cell carcinoma


title: OSCC T18 Methylation

description: OSCC


title: OSCC T16 Methylation

description: OSCC


title: Airway epithelium, healthy sample 32

description:
MASTA-001
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: airway epithelium


title: normal sample 3

description: normal sample

value: normal

value: whole blood


title: Melanoma tumor sample from patient 54

description:
replicate 1
LuM54


title: Airway epithelium, asthma sample 49

description:
MASTB-041
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: female

value: asthma


title: OSCC T17 Methylation

description: OSCC


title: Airway epithelium, healthy sample 33

description:
MASTA-005
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Melanoma tumor sample from patient 52

description:
replicate 1
LuM52


title: OSCC T14 Methylation

description: OSCC


title: OSCC T13 Methylation

description: OSCC


title: OSCC T15 Methylation

description: OSCC


title: Airway epithelium, asthma sample 48

description:
MASTB-040
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: high


title: Melanoma tumor sample from patient 55

description:
replicate 1
LuM55


title: Airway epithelium, asthma sample 50

description:
MASTB-042
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: low


title: Melanoma tumor sample from patient 50

description:
replicate 1
LuM50


title: Melanoma tumor sample from patient 56

description:
replicate 1
LuM56


title: Melanoma tumor sample from patient 53

description:
replicate 1
LuM53


title: no sulfate fertilization, biological rep2

city: Harpenden

first: Astrid

last: Gruen

address: Rothamsted Research

department: Plant Biology and Crop Science

institute: Rothamsted Research

description: gene expression from field derived wheat material

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit was used for cRNA hybridization according to the user manual  P/N 702731 of GeneChip® Expression Wash, Stain and Scan protocol for Cartridge Arrays (P/N 702731 Rev.3). Gene chips were washed in the Affymetrix GeneChip fluidics station 450 (fluidics script  EukGE-WS2v5).

scan_protocol: Gene chips were scanned using the Affymetrix® GeneChip® Scanner 3000; default settings in GeneChip Command Console Software  (AGCC)  for 3' arrays.

data_processing: Probe cell intensity data are analysed in the Affymetrix GeneChip Expression Console  software using the MAS 5 algorithm and  Affymetrix default analysis settings and global scaling as normalization (3’ Expression Array Analysis: User Manual P/N 702387 Rev. 3). All probes were scaled to a target intensity (TGT) of 500.

organism: Triticum aestivum

source_name: Wheat exposed to limited S availiability

label_protocol: cDNA synthesis and biotin-modified cRNA were prepared from 500ng total RNA using the Affymetrix 3' IVT Express kit   (Affimetrix User Manual P/N 702646 rev.7)

growth_protocol: Winter wheat cv. Hereward sampled in May 2011 at booting stage; growing season 2010/11; common agricultural practices;

extract_protocol: Modified method by (Verwoerd et al. 1989) with an additional phenol-chloroform-isoamylalcohol extraction of the aqueous phase after the first centrifugation and RNAse-free DNAse treatment (Promega, Madison, USA). An additional silica-membrane purification kit was used (RNeasy Plant mini kit, Qiagen, Maryland, USA)

treatment_protocol: Fertilizer withdrawal leading to limited soil K, Mg, N P and P availability; N, P, K, Mg since 1843, S since 2000

tag: cultivar

value: Hereward

value: Root

tag: growth stage

value: booting


title: no sulfate fertilization, biological rep3


title: no phosphate fertilization, biological rep3

source_name: Wheat exposed to limited P availiability


title: no sulfate fertilization, biological rep1


title: Melanoma tumor sample from patient 51

description:
replicate 1
LuM51

value: Female


title: Melanoma tumor sample from patient 49

description:
replicate 1
LuM49

value: Male

value: Regional


title: Melanoma tumor sample from patient 45

description:
replicate 1
LuM45

value: In-transit


title: Airway epithelium, asthma sample 47

description:
MASTB-039
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, asthma sample 46

description:
MASTB-038
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, healthy sample 31

description:
MASTA-028
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: healthy


title: OSCC T7 Methylation

description: OSCC

value: male


title: OSCC T11 Methylation

description: OSCC

value: oral squamous cell carcinoma


title: OSCC T10 Methylation

description: OSCC


title: OSCC T12 Methylation

description: OSCC


title: OSCC T9 Methylation

description: OSCC


title: low nitrogen fertilization, biological rep3

source_name: Wheat exposed to limited N availiability


title: no phosphate fertilization, biological rep2


title: Airway epithelium, healthy sample 30

description:
MASTA-025
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: airway epithelium


title: Airway epithelium, asthma sample 44

description:
MASTB-037
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, asthma sample 45

description:
MASTB-006
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, asthma sample 43

description:
MASTB-036
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: OSCC T8 Methylation

description: OSCC


title: no magnesium fertilization, biological rep3

source_name: Wheat exposed to limited Mg availiability


title: Melanoma tumor sample from patient 44

description:
replicate 1
LuM44

value: Subcutaneous


title: OSCC T6 Methylation

description: OSCC


title: no phosphate fertilization, biological rep1


title: Melanoma tumor sample from patient 48

description:
replicate 1
LuM48

value: General

value: Visceral


title: no magnesium fertilization, biological rep2


title: low nitrogen fertilization, biological rep2


title: Melanoma tumor sample from patient 47

description:
replicate 1
LuM47


title: Melanoma tumor sample from patient 46

description:
replicate 1
LuM46

value: Lymph node


title: Melanoma tumor sample from patient 43

description:
replicate 1
LuM43


title: low nitrogen fertilization, biological rep1


title: Airway epithelium, asthma sample 42

description:
MASTB-035
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: asthma

value: high


title: Airway epithelium, healthy sample 29

description:
MASTA-023
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: female


title: Airway epithelium, healthy sample 28

description:
MASTA-022
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Melanoma tumor sample from patient 42

description:
replicate 1
LuM42


title: Melanoma tumor sample from patient 40

description:
replicate 1
LuM40


title: Airway epithelium, asthma sample 39

description:
MASTB-031
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: no potassium fertilization, biological rep1

source_name: Wheat exposed to limited K availiability

value: Hereward

value: Root


title: Melanoma tumor sample from patient 38

description:
replicate 1
LuM38


title: Melanoma tumor sample from patient 39

description:
replicate 1
LuM39

value: Female


title: OSCC T4 Methylation

description: OSCC


title: Airway epithelium, asthma sample 41

description:
MASTB-034
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: no magnesium fertilization, biological rep1

value: booting


title: Airway epithelium, asthma sample 40

description:
MASTB-032
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: control plot, biological rep3

source_name: Wheat exposed to optimal nutrient supply


title: non-OSCC N39 Methylation

description: non-OSCC

source_name: adjacent non-tumor epithelia

value: oral epithelia


title: no potassium fertilization, biological rep3


title: non-OSCC N38 Methylation

description: non-OSCC


title: Melanoma tumor sample from patient 36

description:
replicate 1
LuM36

value: Male

value: Local

value: Cutaneous


title: Melanoma tumor sample from patient 37

description:
replicate 1
LuM37

value: Regional


title: control plot, biological rep2


title: OSCC T2 Methylation

description: OSCC

value: male

value: oral squamous cell carcinoma


title: non-OSCC N40 Methylation

description: non-OSCC


title: OSCC T1 Methylation

description: OSCC


title: OSCC T5 Methylation

description: OSCC


title: no potassium fertilization, biological rep2


title: Airway epithelium, healthy sample 27

description:
MASTA-021
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: airway epithelium

value: healthy


title: control plot, biological rep1


title: non-OSCC N37 Methylation

description: non-OSCC


title: Airway epithelium, healthy sample 25

description:
MASTA-019
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, healthy sample 24

description:
SMOKE-064
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: non-OSCC N35 Methylation

description: non-OSCC


title: Airway epithelium, healthy sample 26

description:
MASTA-020
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: non-OSCC N33 Methylation

description: non-OSCC


title: Melanoma tumor sample from patient 34

description:
replicate 1
LuM34

value: Lymph node


title: Melanoma tumor sample from patient 35

description:
replicate 1
LuM35

value: Subcutaneous


title: Airway epithelium, healthy sample 23

description:
SMOKE-062
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: non-OSCC N36 Methylation

description: non-OSCC


title: Melanoma tumor sample from patient 33

description:
replicate 1
LuM33


title: non-OSCC N32 Methylation

description: non-OSCC


title: Airway epithelium, healthy sample 21

description:
SMOKE-057
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Melanoma tumor sample from patient 32

description:
replicate 1
LuM32


title: Melanoma tumor sample from patient 29

description:
replicate 1
LuM29

value: In-transit


title: Melanoma tumor sample from patient 30

description:
replicate 1
LuM30


title: Melanoma tumor sample from patient 31

description:
replicate 1
LuM31


title: non-OSCC N34 Methylation

description: non-OSCC


title: Airway epithelium, healthy sample 22

description:
SMOKE-061
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, healthy sample 20

description:
SMOKE-044
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: female


title: Melanoma tumor sample from patient 28

description:
replicate 1
LuM28


title: Airway epithelium, healthy sample 19

description:
SMOKE-043
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, healthy sample 17

description:
SMOKE-038
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, healthy sample 18

description:
SMOKE-040
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: non-OSCC N30 Methylation

description: non-OSCC


title: OSCC T3 Methylation

description: OSCC


title: Sample32

description: Hybridized to 250K_Nsp

source_name: AML

tag: diagnosis

value: acute myeloid leukemia (AML)


title: non-OSCC N31 Methylation

description: non-OSCC


title: Melanoma tumor sample from patient 27

description:
replicate 1
LuM27


title: Airway epithelium, healthy sample 16

description:
SMOKE-036
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: non-OSCC N28 Methylation

description: non-OSCC


title: Melanoma tumor sample from patient 41

description:
replicate 1
LuM41

value: General


title: Melanoma tumor sample from patient 24

description:
replicate 1
LuM24


title: non-OSCC N27 Methylation

description: non-OSCC


title: Sample29

description: Hybridized to 250K_Nsp


title: Melanoma tumor sample from patient 26

description:
replicate 1
LuM26

value: Female


title: Melanoma tumor sample from patient 25

description:
replicate 1
LuM25


title: Sample28

description: Hybridized to 250K_Nsp


title: non-OSCC N26 Methylation

description: non-OSCC


title: wild type rep6

city: Aviano

first: daniela

last: marconi

address: Via franco Gallini 2

country: Italy

institute: CRO AVIANO

description: Biological replicate 6 of 6

hyb_protocol: The Hybridization was performed acording to Ambion protocol

scan_protocol: Slides were analysed by Agilent Microarray Scanner G2565AA

data_processing: Background subtraction method: Marginal log-likelihood of foreground values for normal + exponential model and its derivatives.Whithin Normalization method: loess. Between Normalization method: quantile. Filtered by 20% of the IQR

source_name: wild type mice

label_protocol: cDNA synthesis, cDNA purification, in vitro transcription of amino-allyl RNA (aRNA), aRNA dye coupling, and purification of dye-labeled aRNA were performed using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, Austin, TX) following manufacturer's guidelines

extract_protocol: RNA has been extracted by using RNeasy Mini-Kit

treatment_protocol: Thymuses from 15-weeks old C57BL/6 mice (n=3 females and n=3 males) have been collected for all the genotypes. (Qiagen). All steps have been performed according to RNeasy Mini-Kit instructions.

value: thymus

value: 15 weeks

tag: genotype

value: wildtype

source_name: reference

tag: reference type

value: pool of RNAs derived from mouse fibroblasts of all the genotypes


title: Melanoma tumor sample from patient 23

description:
replicate 1
LuM23


title: Sample30

description: Hybridized to 250K_Nsp


title: Airway epithelium, healthy sample 14

description:
SMOKE-027
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: non-OSCC N24 Methylation

description: non-OSCC

value: oral epithelia


title: Melanoma tumor sample from patient 22

description:
replicate 1
LuM22

value: Regional


title: Airway epithelium, healthy sample 13

description:
SMOKE-025
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, healthy sample 15

description:
SMOKE-033
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Sample33

description: Hybridized to 250K_Nsp


title: non-OSCC N25 Methylation

description: non-OSCC

value: male


title: non-OSCC N29 Methylation

description: non-OSCC


title: Melanoma tumor sample from patient 21

description:
replicate 1
LuM21

value: Local


title: Sample31

description: Hybridized to 250K_Nsp


title: wild type rep4

description: Biological replicate 4 of 6


title: wild type rep5

description: Biological replicate 5 of 6


title: Airway epithelium, healthy sample 12

description:
SMOKE-020
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: airway epithelium


title: Melanoma tumor sample from patient 20

description:
replicate 1
LuM20

value: Male


title: Melanoma tumor sample from patient 19

description:
replicate 1
LuM19

value: Lymph node


title: non-OSCC N23 Methylation

description: non-OSCC


title: wild type rep3

description: Biological replicate 3 of 6


title: non-OSCC N22 Methylation

description: non-OSCC


title: Airway epithelium, asthma sample 38

description:
SAGE-057
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: asthma

value: high


title: Airway epithelium, asthma sample 37

description:
SAGE-050
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Sample6

description: Hybridized to 250K_Nsp


title: wild type rep2

description: Biological replicate 2 of 6


title: Sample5

description: Hybridized to 250K_Nsp


title: Sample27

description: Hybridized to 250K_Nsp


title: non-OSCC N21 Methylation

description: non-OSCC


title: Sample26

description: Hybridized to 250K_Nsp


title: Sample7

description: Hybridized to 250K_Nsp


title: wild type rep1

description: Biological replicate 1 of 6


title: statmin knock-out rep5

description: Biological replicate 5 of 6

source_name: stathmin knock-out mice

value: stathmin knockout


title: non-OSCC N20 Methylation

description: non-OSCC


title: Melanoma tumor sample from patient 18

description:
replicate 1
LuM18


title: Airway epithelium, asthma sample 34

description:
SAGE-041
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: statmin knock-out rep3

description: Biological replicate 3 of 6


title: Melanoma tumor sample from patient 17

description:
replicate 1
LuM17


title: non-OSCC N18 Methylation

description: non-OSCC


title: non-OSCC N19 Methylation

description: non-OSCC


title: non-OSCC N16 Methylation

description: non-OSCC


title: Airway epithelium, asthma sample 36

description:
SAGE-047
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: low


title: Airway epithelium, asthma sample 32

description:
SAGE-039
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, asthma sample 33

description:
SAGE-040
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: female


title: Airway epithelium, asthma sample 35

description:
SAGE-043
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Melanoma tumor sample from patient 15

description:
replicate 1
LuM15


title: Airway epithelium, asthma sample 31

description:
SAGE-038
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: statmin knock-out rep4

description: Biological replicate 4 of 6


title: Melanoma tumor sample from patient 13

description:
replicate 1
LuM13

value: In-transit

value: Subcutaneous


title: statmin knock-out rep6

description: Biological replicate 6 of 6

value: thymus

value: 15 weeks


title: Melanoma tumor sample from patient 16

description:
replicate 1
LuM16

value: Female


title: non-OSCC N17 Methylation

description: non-OSCC

value: oral epithelia


title: statmin knock-out rep2

description: Biological replicate 2 of 6

value: pool of RNAs derived from mouse fibroblasts of all the genotypes


title: Melanoma tumor sample from patient 14

description:
replicate 1
LuM14

value: Regional


title: Melanoma tumor sample from patient 12

description:
replicate 1
LuM12


title: Sample25

description: Hybridized to 250K_Nsp

value: acute myeloid leukemia (AML)


title: Airway epithelium, asthma sample 30

description:
SAGE-036
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: airway epithelium

value: male


title: Airway epithelium, asthma sample 29

description:
SAGE-034
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: non-OSCC N15 Methylation

description: non-OSCC


title: statmin and p27 knock-out rep5

description: Biological replicate 5 of 6

source_name: double knock-out mice

value: p27 and stathmin double knockout


title: Melanoma tumor sample from patient 11

description:
replicate 1
LuM11

value: Primary

value: Cutaneous


title: non-OSCC N12 Methylation

description: non-OSCC


title: Melanoma tumor sample from patient 9

description:
replicate 1
LuM9

value: Male

value: Lymph node


title: non-OSCC N13 Methylation

description: non-OSCC


title: non-OSCC N14 Methylation

description: non-OSCC


title: statmin knock-out rep1

description: Biological replicate 1 of 6

value: stathmin knockout


title: Airway epithelium, asthma sample 26

description:
SAGE-029
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: female

value: asthma

value: high


title: statmin and p27 knock-out rep3

description: Biological replicate 3 of 6

value: thymus

value: 15 weeks


title: Melanoma tumor sample from patient 8

description:
replicate 1
LuM8


title: Melanoma tumor sample from patient 6

description:
replicate 1
LuM6

value: Female


title: Melanoma tumor sample from patient 7

description:
replicate 1
LuM7


title: Airway epithelium, asthma sample 24

description:
SAGE-025
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: low


title: Airway epithelium, asthma sample 25

description:
SAGE-027
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: statmin and p27 knock-out rep1

description: Biological replicate 1 of 6

value: pool of RNAs derived from mouse fibroblasts of all the genotypes


title: non-OSCC N9 Methylation

description: non-OSCC

value: oral epithelia


title: Airway epithelium, asthma sample 27

description:
SAGE-031
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: airway epithelium


title: Melanoma tumor sample from patient 5

description:
replicate 1
LuM5

value: General

value: Visceral


title: Melanoma tumor sample from patient 10

description:
replicate 1
LuM10

value: Regional


title: p27 knock-out rep6

description: Biological replicate 6 of 6

source_name: p27 knock-out mice

value: p27 knockout


title: non-OSCC N10 Methylation

description: non-OSCC

value: male


title: non-OSCC N11 Methylation

description: non-OSCC


title: statmin and p27 knock-out rep4

description: Biological replicate 4 of 6

value: p27 and stathmin double knockout


title: non-OSCC N8 Methylation

description: non-OSCC


title: statmin and p27 knock-out rep2

description: Biological replicate 2 of 6


title: non-OSCC N7 Methylation

description: non-OSCC


title: Airway epithelium, asthma sample 22

description:
SAGE-020
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

source_name: airway epithelium, asthma, Th2 high


title: p27 knock-out rep3

description: Biological replicate 3 of 6


title: p27 knock-out rep4

description: Biological replicate 4 of 6


title: Melanoma tumor sample from patient 3

description:
replicate 1
LuM3

value: Primary

value: Cutaneous


title: Airway epithelium, asthma sample 28

description:
SAGE-032
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: asthma


title: non-OSCC N6 Methylation

description: non-OSCC


title: non-OSCC N3 Methylation

description: non-OSCC


title: Airway epithelium, asthma sample 23

description:
SAGE-022
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: high


title: statmin and p27 knock-out rep6

description: Biological replicate 6 of 6

value: thymus


title: Airway epithelium, asthma sample 17

description:
SAGE-011
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: p27 knock-out rep5

description: Biological replicate 5 of 6

value: 15 weeks


title: Airway epithelium, asthma sample 20

description:
SAGE-018
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: p27 knock-out rep1

description: Biological replicate 1 of 6


title: non-OSCC N5 Methylation

description: non-OSCC


title: non-OSCC N1 Methylation

description: non-OSCC


title: p27 knock-out rep2

description: Biological replicate 2 of 6


title: non-OSCC N2 Methylation

description: non-OSCC


title: Airway epithelium, asthma sample 21

description:
SAGE-019
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

source_name: airway epithelium, asthma, Th2 low

value: female


title: Melanoma tumor sample from patient 4

description:
replicate 1
LuM4

value: Male

value: Lymph node


title: Melanoma tumor sample from patient 2

description:
replicate 1
LuM2

value: Female


title: Airway epithelium, asthma sample 14

description:
SAGE-008
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: airway epithelium


title: Airway epithelium, asthma sample 15

description:
SAGE-009
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, asthma sample 13

description:
SAGE-006
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Patient-derived xenograft BCP-ALL-54

city: Randwick

first: Duohui

last: Jing

state: NSW

address: Lowy Cancer Research Centre, UNSW

department: Leukaemia Biology

country: Australia

institute: Children’s Cancer Institute Australia

description: patient-derived xenograft cells

data_processing: The data were log2-transformed and normalised using quantile normalisation in GenePattern

source_name: Patient-derived xenograft cells

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

extract_protocol: RNA was extracted with a combination of Trizol reagent and QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: BCP-ALL

tag: host organism

value: Mus musculus

tag: host strain

value: NOD/SCID

tag: mouse age

value: xenograft cells Injected at 6-10 weeks

value: Xenograft cells (>95% hCD45+ cells) from mouse spleens


title: Patient-derived xenograft BCP-ALL-56

description: patient-derived xenograft cells


title: Airway epithelium, asthma sample 19

description:
SAGE-016
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

tag: disease state

tag: th2 group

value: low


title: non-OSCC N4 Methylation

description: non-OSCC

tag: gender

value: male

value: oral epithelia


title: Patient-derived xenograft BCP-ALL-57

description: patient-derived xenograft cells


title: Airway epithelium, asthma sample 16

description:
SAGE-010
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

tag: age

value: asthma


title: Patient-derived xenograft BCP-ALL-55

description: patient-derived xenograft cells

tag: tissue


title: DON3G_pdr5_rep1

city: Tukuba

first: Tadahiro

last: Suzuki

state: Ibaraki

address: kan-nondai 2-1-12

department: Applied Microbiology Division

country: Japan

institute: National Food Rsearch Institute

description: Gene expression data from yeast

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: CEL file MAS5 normalized

organism: Saccharomyces cerevisiae

label_protocol: Approximately 500 ng of total RNA was processed to produce biotinylated aRNA targets using Affymetrix 3'IVT Express Kit.

growth_protocol: S. cerevisiae BY 4743 (BY4743; MATa/α his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 lys2Δ0) derivative pdr5 (PDR5 (YOR153W) knock-out strain) were grown in YPD medium at 25C for 2 days.

extract_protocol: Each sample of total RNA was extracted using FastRNA Pro Red kit (MP Biomedicals, US) according to the manufacturer’s instructions.

treatment_protocol: Yeast strain was grown in YPD medium with DMSO or 80 μM of deoxynivalenol-3-glucoside for 2 hours.

tag: strain

tag: treatment


title: DON3G_pdr5_rep3

description: Gene expression data from yeast


title: DON3G_pdr5_rep2

description: Gene expression data from yeast


title: Airway epithelium, asthma sample 18

description:
SAGE-015
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: high


title: Melanoma tumor sample from patient 1

description:
replicate 1
LuM1

source_name: Malignant melanoma

tag: tumor stage

value: Regional

tag: distant metastasis free survival in days

tag: distant metastasis free survival (1=death, 0=alive)

tag: disease specific survival in days


title: Patient-derived xenograft BCP-ALL-53

description: patient-derived xenograft cells

tag: diagnosis


title: Patient-derived xenograft BCP-ALL-51

description: patient-derived xenograft cells


title: Control_pdr5_rep2

description: Gene expression data from yeast

source_name: PDR5 mutant strain_control_dmso

tag: genotype

value: DMSO


title: Patient-derived xenograft BCP-ALL-52

description: patient-derived xenograft cells


title: Control_pdr5_rep1

description: Gene expression data from yeast


title: Control_pdr5_rep3

description: Gene expression data from yeast


title: Airway epithelium, asthma sample 12

description:
SAGE-005
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: female


title: M-3D04-UO126 48h

first: Wolfgang

middle: Michael

last: Korn

state: CA

address: 2340 Sutter Street

department: Medicine

institute: UCSF

description: gene expression data in MDAMB231 cells treated with EGF and the MEK inhibitor U0126 or controls

hyb_protocol: automated GeneChip® HT System (Affymetrix)

data_processing: probe set based gene expression measurements were generated from quantitated Affymetrix image files (“.CEL” files) with the RMA algorithm from the BioConductor tools suite.

source_name: MDA-MB-231 cells, 3D culture, UO126, 48h

growth_protocol: Cells were grown to 80% confluence in full serum containing medium. 24 hours prior to treatment, cells were transferred to low serum conditions

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen)

treatment_protocol: Cells were pre-treated the cells with U0126 (10uM) or DMSO (vehicle control) for 30 minutes (time -0.5h).  At time 0h, the cells were stimulated with EGF (10ng/ml).

tag: cell line

tag: cell type

value: Breast cancer

tag: culture

value: 3D culture


title: Airway epithelium, asthma sample 10

description:
SAGE-003
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, asthma sample 11

description:
SAGE-004
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Patient-derived xenograft BCP-ALL-26

description: patient-derived xenograft cells

tag: host organism

tag: host strain

tag: mouse age


title: Patient-derived xenograft BCP-ALL-50

description: patient-derived xenograft cells


title: Airway epithelium, asthma sample 09

description:
SAGE-002
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

tag: gender

tag: disease state

tag: th2 group


title: Patient-derived xenograft BCP-ALL-28

description: patient-derived xenograft cells

tag: tissue


title: Airway epithelium, asthma sample 08

description:
SAGE-001
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

tag: age


title: sh-G9a_rep 2

description: replicate 2

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina HumanHT-12   Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed sing Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4)

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep   RNA Amplification Kit (Ambion)

growth_protocol: K562 cells in RPMI1640 medium supplemented with 5 % fetal bovine serum (FBS) and 0.05 % antibiotics at 37 ℃ in a 5 % CO2 atmosphere

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

treatment_protocol: Stable cells were treated 1 ug/ml doxycycline for 48 h.

tag: genotype/variation

value: G9a knockdown


title: Patient-derived xenograft T-ALL-41

description: patient-derived xenograft cells

value: T-ALL


title: M-3D04-UO126 24h

scan_protocol: automated GeneChip® HT System (Affymetrix)

source_name: MDA-MB-231 cells, 3D culture, UO126, 24h

tag: treatment


title: Airway epithelium, asthma sample 07

description:
GBMC2-039
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: airway epithelium


title: M-3D04-DMSO-EGF 24h

source_name: MDA-MB-231 cells, 3D culture, DMSO-EGF, 24h

label_protocol: automated GeneChip® HT System (Affymetrix)

value: DMSO-EGF


title: M-3D04-EGF 48h

source_name: MDA-MB-231 cells, 3D culture, EGF, 48h

value: EGF


title: M-3D04-EGF 24h

source_name: MDA-MB-231 cells, 3D culture, EGF, 24h


title: M-3D04-control 48h

source_name: MDA-MB-231 cells, 3D culture, control, 48h


title: Airway epithelium, healthy sample 10

description:
GBMC2-034
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

source_name: airway epithelium, healthy

value: healthy


title: Airway epithelium, healthy sample 11

description:
GBMC2-038
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Jurkat, mock, total RNA, bio.rep #3

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

institute: University of Trento

description:
Total RNA sample extracted from Jurkat cells, mock
cytoplasmic RNA

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

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

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

source_name: Jurkat cells, mock, total RNA, biological replicate 3

growth_protocol: Jurkat cells were grown in RPMI supplemented with 10% FBS, antibiotics (100 units/ml penicillin-streptomycin) and 2mM L-Glutamine at 37° C under 5% CO2.

extract_protocol: Cells were treated with 100 μg/ml Cycloheximide for 5 min at 37°C in order to stabilize the polysomal complexes. After washing cells twice with cold PBS containing 10 μg/ml Cycloheximide, 1 ml of lysis buffer was added [10 mM NaCl, 10 mM MgCl2, 10 mM Tris–Cl pH 7.5, 1% Triton X-100, 1% sodium deoxycholate, 0.2 U/μl RNase inhibitor (Fermentas), 10 μg/ml Cycloheximide and 1 mM dithiothreitol]. Lysates were transferred to microcentrifuge tubes, incubated on ice for 2 min and centrifuged for 5 min at 12000 g at 4°C. The supernatant was loaded directly onto a 15–50% linear sucrose gradient prepared in a buffer containing 30 mM Tris–Cl pH 7.5, 100 mM NaCl, 10 mM MgCl2, and centrifuged at 4°C in a SW41 rotor (Sorvall) for 110 min at 180000 g. Sub-polysomal and polysomal fractions were collected using a Density Gradient System (Teledyne ISCO) with automated fraction collector (Foxy R1, Teledine ISCO) monitoring the absorbance at 254 nm. For RNA extraction, fractions were treated with proteinase K (100 μg/ml) in 1% SDS for 3 hr at 37°C. After phenol–chloroform separation and isopropanol precipitation, recovered RNA pellets were resuspended with 30 μl of RNase-free water. RNAs extracted from fractions were pooled (sub-polysomal RNA: fraction 2-7; polysomal RNA: fraction 8-11; total: fraction 2-11) for microarray analysis.

treatment_protocol: Jurkat cells were treated with DMSO for 48 hr (5*10^5 cells/ ml)

value: Jurkat

value: mock

tag: rna fraction

value: total RNA

tag: biological replicate


title: M-3D04-DMSO-EGF 48h

source_name: MDA-MB-231 cells, 3D culture, DMSO-EGF, 48h


title: M-3D04-control 24h

source_name: MDA-MB-231 cells, 3D culture, control, 24h


title: sh-CTL_rep 1

description: replicate 1

source_name: K562, sh-CTL

value: G9a wild type


title: sh-G9a_rep 1

description: replicate 1


title: NHK2

first: Matthew

last: Arno

state: LONDON

address: 150 Stamford Street

department: Genomics Centre

institute: King's College London

description:
SAMPLE 8.2
Primary skin keratinocytes (donor 2).

hyb_protocol: A total amount of 750 ng of biotin-labelled aRNA in a 5 µl volume was then used for HumanHT-12 V4.0 Expression BeadChip whole-genome gene expression direct hybridization assay system (Illumina) according to manufacturer's instruction.

scan_protocol: iScan system (Illumina).

data_processing: Data were processed using Genome Studio; no background correction has been applied; normalization: average; probe-level data.

source_name: keratinocytes from skin biopsy (donor 2)

label_protocol: In vitro transcription of biotin-labelled aRNA was performed with TargetAmp-Nano labelling kit (Epicentre) and purification with RNeasy Mini Kit (Qiagen). The quality and the quantity of the resultant biotin-labelled aRNAs were assessed using Bioanalyzer (Agilent) and Qubit Fluorometer (Life Technologies).

growth_protocol: Undifferentiated pluripotent cells were grown on Matrigel-coated dishes in mTeSR, keratinocytes in EpiLife medium and BJ fibroblasts in 10% FBS/DMEM.

extract_protocol: Total RNA were reverse transcribed into cDNA using SuperScript III Reverse Transcriptase (Life Technologies).

value: primary normal human keratinocytes (NHKs) from skin biopsy


title: Jurkat, mock, total RNA, bio.rep #4

source_name: Jurkat cells, mock, total RNA, biological replicate 4


title: Airway epithelium, healthy sample 09

description:
GBMC2-032
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Jurkat, FK866 treated, total RNA, bio.rep #4

description:
Total RNA sample extracted from Jurkat cells treated for 48h with FK866.
cytoplasmic RNA

source_name: Jurkat cells, FK866 treated, total RNA, biological replicate 4

treatment_protocol: Jurkat cells were treated with 5nM FK866 for 48 hr (5*10^5 cells/ ml)


title: M-3D04-DMSO-EGF 12h

source_name: MDA-MB-231 cells, 3D culture, DMSO-EGF, 12h


title: Jurkat, mock, total RNA, bio.rep #1

source_name: Jurkat cells, mock, total RNA, biological replicate 1


title: NHK1

description:
SAMPLE 8.1
Primary skin keratinocytes (donor 1).

source_name: keratinocytes from skin biopsy (donor 1)


title: Airway epithelium, asthma sample 05

description:
GBMC2-028
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

source_name: airway epithelium, asthma, Th2 low

value: asthma

value: low


title: Jurkat, mock, total RNA, bio.rep #2

source_name: Jurkat cells, mock, total RNA, biological replicate 2


title: Airway epithelium, asthma sample 06

description:
GBMC2-031
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

source_name: airway epithelium, asthma, Th2 high

value: high


title: M-3D04-EGF 12h

source_name: MDA-MB-231 cells, 3D culture, EGF, 12h


title: T3-KCL034-2

description:
SAMPLE 7.2
hESC line KCL034-derived keratinocytes replicate 2.

source_name: KCL034-derived keratinocytes

value: hESC-derived keratinocytes

tag: time point


title: M-3D04-U0126 12h

source_name: MDA-MB-231 cells, 3D culture, U0126, 12h

value: Breast cancer


title: Jurkat, FK866 treated, total RNA, bio.rep #3

source_name: Jurkat cells, FK866 treated, total RNA, biological replicate 3


title: T3-KCL034-3

description:
SAMPLE 7.3
hESC line KCL034-derived keratinocytes replicate 3.


title: Airway epithelium, healthy sample 07

description:
GBMC2-026
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

source_name: airway epithelium, healthy

value: male


title: T3-iKCL011-3

description:
SAMPLE 6.3
hiPSC line iKCL011-derived keratinocytes replicate 3.

source_name: iKCL011-derived keratinocytes

value: hiPSC-derived keratinocytes


title: T3-KCL034-1

description:
SAMPLE 7.1
hESC line KCL034-derived keratinocytes replicate 1.


title: Airway epithelium, healthy sample 08

description:
GBMC2-027
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: female


title: Jurkat, FK866 treated, total RNA, bio.rep #1

source_name: Jurkat cells, FK866 treated, total RNA, biological replicate 1


title: M-3D04-control 12h

description: gene expression data in MDAMB231 cells treated with EGF and the MEK inhibitor U0126 or controls

source_name: MDA-MB-231 cells, 3D culture, control, 12h

value: 3D culture


title: M-3D04-U0126 8h

source_name: MDA-MB-231 cells, 3D culture, U0126, 8h


title: Airway epithelium, healthy sample 05

description:
GBMC2-022
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: airway epithelium


title: Jurkat, mock, subpolysomal RNA, bio.rep #4

description:
Subpolysomal RNA sample extracted from Jurkat cells, mock
cytoplasmic RNA

source_name: Jurkat cells, mock, subpolysomal RNA, biological replicate 4

value: subpolysomal RNA


title: M-3D04-DMSO-EGF 8h

source_name: MDA-MB-231 cells, 3D culture, DMSO-EGF, 8h

value: DMSO-EGF


title: T3-iKCL011-2

description:
SAMPLE 6.2
hiPSC line iKCL011-derived keratinocytes replicate 2.


title: T3-iKCL011-1

description:
SAMPLE 6.1
hiPSC line iKCL011-derived keratinocytes replicate 1.


title: T3-iKCL004-3

description:
SAMPLE 5.3
hiPSC line iKCL004-derived keratinocytes replicate 3.

source_name: iKCL004-derived keratinocytes


title: Jurkat, mock, subpolysomal RNA, bio.rep #3

source_name: Jurkat cells, mock, subpolysomal RNA, biological replicate 3

value: Jurkat


title: M-3D04-U0126 4h

source_name: MDA-MB-231 cells, 3D culture, U0126, 4h


title: M-3D04-control 8h

source_name: MDA-MB-231 cells, 3D culture, control, 8h


title: Airway epithelium, asthma sample 04

description:
GBMC2-018
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Jurkat, FK866 treated, total RNA, bio.rep #2

description:
Total RNA sample extracted from Jurkat cells treated for 48h with FK866.
cytoplasmic RNA

source_name: Jurkat cells, FK866 treated, total RNA, biological replicate 2


title: Jurkat, mock, subpolysomal RNA, bio.rep #1

source_name: Jurkat cells, mock, subpolysomal RNA, biological replicate 1

value: mock


title: M-3D04-EGF 8h

source_name: MDA-MB-231 cells, 3D culture, EGF, 8h

value: EGF


title: Airway epithelium, healthy sample 02

description:
GBMC2-019
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

value: healthy


title: Airway epithelium, healthy sample 04

description:
GBMC2-021
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, healthy sample 06

description:
GBMC2-023
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, healthy sample 03

description:
GBMC2-020
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: Airway epithelium, healthy sample 01

description:
GBMC2-017
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: T3-iKCL004-2

description:
SAMPLE 5.2
hiPSC line iKCL004-derived keratinocytes replicate 2.


title: T0-KCL034-2

description:
SAMPLE 4.2
Undifferentiated hESC line KCL034 replicate 2.
Pluripotent.

source_name: undifferentiated hESC line KCL034

value: hESC cell line


title: T0-KCL034-3

description:
SAMPLE 4.3
Undifferentiated hESC line KCL034 replicate 3.
Pluripotent.


title: M-3D04-DMSO-EGF 4h

source_name: MDA-MB-231 cells, 3D culture, DMSO-EGF, 4h


title: Jurkat, FK866 treated, subpolysomal RNA, bio.rep #4

description:
Subpolysomal RNA sample extracted from Jurkat cells treated for 48h with FK866.
cytoplasmic RNA

source_name: Jurkat cells, FK866 treated, subpolysomal RNA, biological replicate 4


title: M-3D04-EGF 4h

description: gene expression data in MDAMB231 cells treated with EGF and the MEK inhibitor U0126 or controls

source_name: MDA-MB-231 cells, 3D culture, EGF, 4h


title: M-3D04-U0126 1h

source_name: MDA-MB-231 cells, 3D culture, U0126, 1h


title: Jurkat, mock, subpolysomal RNA, bio.rep #2

source_name: Jurkat cells, mock, subpolysomal RNA, biological replicate 2


title: T0-KCL034-1

description:
SAMPLE 4.1
Undifferentiated hESC line KCL034 replicate 1.
Pluripotent.


title: M-3D04-control 4h

source_name: MDA-MB-231 cells, 3D culture, control, 4h


title: T3-iKCL004-1

description:
SAMPLE 5.1
hiPSC line iKCL004-derived keratinocytes replicate 1.


title: Jurkat, FK866 treated, subpolysomal RNA, bio.rep #3

source_name: Jurkat cells, FK866 treated, subpolysomal RNA, biological replicate 3


title: M-3D04-EGF 1h

source_name: MDA-MB-231 cells, 3D culture, EGF, 1h


title: Airway epithelium, asthma sample 02

description:
GBMC2-013
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

source_name: airway epithelium, asthma, Th2 high

value: asthma


title: Airway epithelium, asthma sample 03

description:
GBMC2-016
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.

source_name: airway epithelium, asthma, Th2 low

value: low


title: M-3D04-DMSO-EGF 1h

source_name: MDA-MB-231 cells, 3D culture, DMSO-EGF, 1h


title: Jurkat, mock, polysomal RNA, bio.rep #4

description:
Polysomal RNA sample extracted from Jurkat cells, mock
cytoplasmic RNA

source_name: Jurkat cells, mock, polysomal RNA, biological replicate 4

value: polysomal RNA


title: M-3D04-U0126 05h

source_name: MDA-MB-231 cells, 3D culture, U0126, 05h


title: Jurkat, FK866 treated, subpolysomal RNA, bio.rep #1

source_name: Jurkat cells, FK866 treated, subpolysomal RNA, biological replicate 1


title: M-3D04-control 1h

source_name: MDA-MB-231 cells, 3D culture, control, 1h


title: Jurkat, FK866 treated, polysomal RNA, bio.rep #4

description:
Polysomal RNA sample extracted from Jurkat cells treated for 48h with FK866.
cytoplasmic RNA

source_name: Jurkat cells, FK866 treated, polysomal RNA, biological replicate 4


title: Jurkat, FK866 treated, subpolysomal RNA, bio.rep #2

source_name: Jurkat cells, FK866 treated, subpolysomal RNA, biological replicate 2


title: T0-iKCL011-3

description:
SAMPLE 3.3
Undifferentiated hiPSC line iKCL011 replicate 3.
Pluripotent.

source_name: undifferentiated hiPSC line iKCL011

value: hiPSC cell line


title: Jurkat, mock, polysomal RNA, bio.rep #2

source_name: Jurkat cells, mock, polysomal RNA, biological replicate 2


title: T0-iKCL011-1

description:
SAMPLE 3.1
Undifferentiated hiPSC line iKCL011 replicate 1.
Pluripotent.


title: Airway epithelium, asthma sample 01

description:
GBMC2-012
Airway epithelial gene expression data obtained from 3rd-4th generation bronchi at time of research bronchoscopy.


title: T0-iKCL011-2

description:
SAMPLE 3.2
Undifferentiated hiPSC line iKCL011 replicate 2.
Pluripotent.


title: Jurkat, mock, polysomal RNA, bio.rep #1

source_name: Jurkat cells, mock, polysomal RNA, biological replicate 1


title: Jurkat, mock, polysomal RNA, bio.rep #3

source_name: Jurkat cells, mock, polysomal RNA, biological replicate 3


title: T0-iKCL004-2

description:
SAMPLE 2.2
Undifferentiated hiPSC line iKCL004 replicate 2.
Pluripotent.

source_name: undifferentiated hiPSC line iKCL004


title: M-3D04-DMSO-EGF 05h

source_name: MDA-MB-231 cells, 3D culture, DMSO-EGF, 05h

value: Breast cancer


title: Jurkat, FK866 treated, polysomal RNA, bio.rep #2

source_name: Jurkat cells, FK866 treated, polysomal RNA, biological replicate 2


title: T0-iKCL004-1

description:
SAMPLE 2.1
Undifferentiated hiPSC line iKCL004 replicate 1.
Pluripotent.


title: Jurkat, FK866 treated, polysomal RNA, bio.rep #3

source_name: Jurkat cells, FK866 treated, polysomal RNA, biological replicate 3


title: T0-iKCL004-3

description:
SAMPLE 2.3
Undifferentiated hiPSC line iKCL004 replicate 3.
Pluripotent.


title: M-3D04-U0126 0h

source_name: MDA-MB-231 cells, 3D culture, U0126, 0h


title: Jurkat, FK866 treated, polysomal RNA, bio.rep #1

source_name: Jurkat cells, FK866 treated, polysomal RNA, biological replicate 1


title: Child's neonatal blood: 001-036-001-2007-A

city: Detroit

first: Douglas

last: Ruden

state: Michigan

address: 275 E. Hancock Ave., Room  291.1

department: Department of Obstetrics and Gynecology

institute: Wayne State University

hyb_protocol: Standard protocol defined by Illumina for HM450K

data_processing: Data normalization was performed using ChAMP in R (>3.0.3). Data was filtered for all possible SNPs from dbSNP database. Differential methylation analysis was done using A-clustering algorithm followed by estimation of methylation difference by Generalized estimation equation (GEE) from Sofer et al, 2012.

label: Cy3, Cy5

source_name: Dried blood spots

extract_protocol: DNA was isolated from dried blood spots with Qiagen EZ1 Advanced® using the DNA Investigator® reagents and protocol card. The “Stains on Fabric” preprocessing and Trace® (tip-dance) instrument protocol was used for isolation. The Quantifiler Human DNA Quantification Kit® (Applied Biosystems, Inc.) was used to determine the amount of amplifiable DNA.Approximately 3µg genomic DNA was diluted in 130µl of buffer TE (10mM Tris (pH 8.0), and 1mM EDTA (pH 8.0)) and sheared into ~200-600bp fragment using microcavitation (Covaris, Inc, setting: Duty Cycle = 5%, Intensity = 3, Cycles/burst = 200, Time = 75 seconds run at 6-8°C). 125µl of the sheared DNA samples were mixed with 330µl of buffer TE. The sheared DNA was denatured by boiling it in the Thermomixer at 95°C and 700rpm for ten minutes and left on ice for 10min.

tag: sample blood lead level

tag: mother's blood lead level

value: M

tag: age (months)

tag: mother's age (months)

tag: gestational age (months)

tag: smoking

value: Yes


title: Child's neonatal blood: 001-010-002-2009-A

scan_protocol: Standard protocol defined by Illumina for HM450K

value: F

value: No


title: Child's neonatal blood: 001-060-002-2010-A

label_protocol: Standard protocol defined by Illumina for HM450K


title: M-3D04-control 0h-2

source_name: MDA-MB-231 cells, 3D culture, control, 0h, repeat 2

tag: cell line

tag: cell type

tag: culture

value: 3D culture


title: M-3D04-DMSO 0h

source_name: MDA-MB-231 cells, 3D culture, DMSO, 0h

value: DMSO


title: Child's neonatal blood: 001-010-001-2012-A

tag: gender


title: BJ-2

description:
SAMPLE 1.2
Somatic donor fibroblasts line replicate 2.

source_name: neonatal foreskin fibroblast line BJ

value: BJ (ATCC, CRL-2522)

value: neonatal foreskin fibroblast cell line


title: BJ-1

description:
SAMPLE 1.1
Somatic donor fibroblasts line replicate 1.


title: M-3D04-EGF 05h

source_name: MDA-MB-231 cells, 3D culture, EGF, 05h


title: M-3D04-control 05h

source_name: MDA-MB-231 cells, 3D culture, control, 05h


title: SKBR3_+#hMADS-CM_rep3

city: Lyon

first: Minh Ngoc

last: Duong

address: 28 rue Laennec

department: Immunity, Microenvironment and Virus

country: France

institute: INSERM U1052 - CNRS 5286

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation with GeneSpring Version 1.9.0

source_name: breast cancer

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit

growth_protocol: BT474 and SKBR3 cells were grown in RPMI medium containing 10% FCS, 2 mM L-glutamine, 100 U/mL penicillin and 100 µg/mL streptomycin. Non-differentiated hMADS cells were cultured in 1 g/L DMEM medium supplemented with 10% FCS, 2 mM L-glutamine, 100 U/mL penicillin, 100 µg/mL streptomycin and 2.5 ng/mL FGF2.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN Qiamp RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with 2100 Bioanalyzer.

treatment_protocol:
differentiation protocol: hMADS cells were induced for differentiation in DMEM/F12 medium supplemented with insulin (5 µg/mL), transferrin (10 µg/mL), T3 (0.2 nM), rosiglitazone (1 µM), IBMX (100 µM), and dexamethasone (1 µM) (day 0). At day 3, the medium was changed without IBMX nor dexamethasone. At day 12, the medium was replaced and supplemented with 10% FCS. Conditioned medium from differentiated hMADS (#hMADS-CM) was taken at day 14.
exposure protocol: BT474 and SKBR3 cells were exposed to #hMADS-CM or the #hMADS control medium for 2 h

value: breast cancer

tag: medium

value: conditioned medium (CM) from differentiated hMADS

value: HER2 positive

tag: time exposure

value: 2 h


title: M-3D04-control 0h-1

source_name: MDA-MB-231 cells, 3D culture, control, 0h, repeat 1


title: HT-29 WT

city: Richmond

first: Bhaumik

middle: B

last: Patel

state: VA

address: 1201 Broad Rock Blvd

institute: Hunter Holmes McGuire VA Medical Center

description: Gene expression data from colon cancer cell line HT-29 in monolayer condition

hyb_protocol: The samples were hybridized with the GeneChip® Human Genome U133 Plus 2.0 Array for 16 hr. After hybridization, samples were washed and stained with the Affymetrix fluidics station 450.

scan_protocol: The arrays were scanned with the Affymetrix 3000 7G plus scanner.

data_processing: Dat and Cel files were obtained by the AGCC software, and the CHP files were generated with mas5 method by Affymetrix Expression Console. The data was imported into the Agilent GeneSpring GX software for further analysis.

label: Affymetrix 3'IVT labeling kit

source_name: colon cancer cell line HT-29

label_protocol: RNA intergrity was confirmed on the Nanodrop ND-1000 and analyzed with Agilent 2100 bioanalyzer. The samples were amplified and labeled using the Affymetrix 3'IVT labeling kit (Lot NO. 1010021).

growth_protocol: HT-29 human colon cancer cells obtained from ATCC, were maintained in 10cm tissue cultured treated plates as monolayer in Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12 (DMEM / F-12) supplemented with 10% fetal bovine serum, and 1X Antibiotic-Antimycotic liquid (AA). The cells were passaged using trypsin containing ethylenediaminetraacetic acid (EDTA) before they reached 70% confluence. Spheroids were formed by growing HT-29 monolayer cells in stem cell media (SCM: DMEM: F12, 1X AA, B27 supplement, epidermal growth factors and fibroblast growth factor) in 10cm non-treated, low adhesion plate. On day five the spheroids were harvested and used for extraction of total RNA.

extract_protocol: Total RNA was isolated using the mirVana™ miRNA Isolation Kit (Cat # AM1560, Life Technologies, Grand Island, NY) according to the manufacturer's protocol.

treatment_protocol: HT-29 human colon cancer cells were grown as monolayer in Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12 (DMEM / F-12) supplemented with 10% fetal bovine serum, and 1X Antibiotic-Antimycotic liquid (AA). HT-29 spheroids were grown in SCM.

tag: tissue

value: colon


title: HT-29 sphere

description: Gene expression data from colon cancer cell line HT-29 grown as spheroids

source_name: Spheroids made from colon cancer cell line HT-29


title: M-2D04-U0126 48h

description: gene expression data in MDAMB231 cells treated with EGF and the MEK inhibitor U0126 or controls

source_name: MDA-MB-231 cells, 2D culture, U0126, 48h, repeat 2

value: 2D culture

tag: treatment


title: Child's neonatal blood: 001-036-005-2009-A


title: SKBR3_+#hMADS-CM_rep2

description: replicate 2

scan_protocol: Standard Illumina scanning protocol


title: Child's neonatal blood: 001-036-002-2011-A


title: Child's neonatal blood: 001-036-003-2008-A


title: 5-8F

city: Changsha

first: Wei

last: Huang

address: Xiangya road no 110

country: China

institute: Central South University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

source_name: human nasopharynx cell line transfected with gene

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

extract_protocol: Total RNA of cell was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

tag: transfection

value: with gene


title: SuverV

source_name: human nasopharynx cell line transfected with empty vector

value: SuverV

value: empty vector


title: BJ-3

description:
SAMPLE 1.3
Somatic donor fibroblasts line replicate 3.


title: DICER_BrefA_C

city: Galway

first: Sharon

last: Glynn

address: Biosciences, NUI Galway

country: Ireland

institute: National University of Ireland Galway

description: Gene expression data from HCT116DICER treated with BrefA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data was collated and analyzed with BRBarraytools version 4.4 (MAS 5.0),

source_name: DICER , BrefA, 24hr

growth_protocol: Cells were grown in 10% Serum for 24 hours prior to treatment

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

treatment_protocol: HCT116 cells were treated with 0.5 mg/ml of BFA or 2 mg/ml of Tm for 24 h.

tag: genotype/variation

value: BREFELDIN A


title: M-2D04-DMSO-EGF 48h

source_name: MDA-MB-231 cells, 2D culture, DMSO-EGF, 48h, repeat 2

value: Breast cancer

value: DMSO-EGF


title: SKBR3_+#hMADS_control medium_rep3

description: replicate 3

value: control medium


title: M-2D04-EGF 48h

source_name: MDA-MB-231 cells, 2D culture, EGF, 48h, repeat 2

value: EGF


title: SKBR3_+#hMADS-CM_rep1

description: replicate 1


title: M-2D04-control 48h

source_name: MDA-MB-231 cells, 2D culture, control, 48h, repeat 2


title: Child's neonatal blood: 001-099-001-2011-A

source_name: Dried blood spots

value: M

value: No


title: SKBR3_+#hMADS_control medium_rep2

description: replicate 2


title: DICER_BrefA_A


title: Child's neonatal blood: 001-122-002-2011-A

value: F

value: Yes


title: Child's neonatal blood: 001-099-003-2007-A


title: M-2D04-EGF 24h

source_name: MDA-MB-231 cells, 2D culture, EGF, 24h, repeat 2


title: Child's neonatal blood: 001-122-001-2010-A


title: M-2D04-control 24h

source_name: MDA-MB-231 cells, 2D culture, control, 24h, repeat 2


title: M-2D04-U0126 24h

source_name: MDA-MB-231 cells, 2D culture, U0126, 24h, repeat 2


title: DICER_BrefA_B


title: DICER_Tm_C

description: Gene expression data from HCT116DICER, treated with Tm

source_name: DICER , Tm, 24hr

value: Tunicamycin


title: M-2D04-DMSO-EGF 24h

source_name: MDA-MB-231 cells, 2D culture, DMSO-EGF, 24h, repeat 2


title: BT474_#hMADS_control medium_rep3

description: replicate 3

source_name: breast cancer

value: breast cancer

value: HER2 positive


title: DICER_ctrl_C

description: Gene expression data from HCT116DICER

source_name: DICER ctrl

value: Control


title: BT474_+#hMADS-CM_rep3

description: replicate 3

value: conditioned medium (CM) from differentiated hMADS

value: 2 h


title: BT474_+#hMADS-CM_rep2

description: replicate 2


title: BT474_+#hMADS-CM_rep1

description: replicate 1


title: SKBR3_+#hMADS_control medium_rep1

description: replicate 1


title: DICER_Tm_B


title: DICER_ctrl_B

description: Gene expression data from HCT116DICER


title: BT474_#hMADS_control medium_rep2

description: replicate 2


title: Child's neonatal blood: 001-019-001-2006-A


title: Child's neonatal blood: 001-121-002-2007-A


title: DICER_Tm_A


title: Child's neonatal blood: 001-015-004-2008-A


title: M-2D04-DMSO-EGF 12h

source_name: MDA-MB-231 cells, 2D culture, DMSO-EGF, 12h, repeat 2

value: 2D culture


title: DICER_ctrl_A

description: Gene expression data from HCT116DICER


title: Child's neonatal blood: 001-015-002-2010-A


title: Child's neonatal blood: 001-019-003-2007-A


title: Child's neonatal blood: 001-015-006-2009-A


title: M-2D04-U0126 12h

source_name: MDA-MB-231 cells, 2D culture, U0126, 12h, repeat 2


title: p53KO_Tm_B

description: Gene expression data from HCT116p53KO, treated with Tm

source_name: p53KO , Tm, 24hr


title: M-2D04-EGF 12h

source_name: MDA-MB-231 cells, 2D culture, EGF, 12h, repeat 2


title: p53KO_Tm_A


title: M-2D04-DMSO-EGF 8h

source_name: MDA-MB-231 cells, 2D culture, DMSO-EGF, 8h, repeat 2


title: p53KO_BrefA_C

description: Gene expression data from HCT116p53KO treated with BrefA

source_name: p53KO , BrefA, 24hr


title: Child's neonatal blood: 001-027-002-2010-A


title: M-2D04-control 12h

source_name: MDA-MB-231 cells, 2D culture, control, 12h, repeat 2


title: p53KO_BrefA_B


title: M-2D04-U0126 8h

source_name: MDA-MB-231 cells, 2D culture, U0126, 8h, repeat 2


title: M-2D04-U0126 4h

source_name: MDA-MB-231 cells, 2D culture, U0126, 4h, repeat 2


title: BT474_#hMADS_control medium_rep1

description: replicate 1


title: p53KO_BrefA_A


title: M-2D04-control 8h

source_name: MDA-MB-231 cells, 2D culture, control, 8h, repeat 2


title: p53KO_Tm_C