title: Blood_Control_52

description: Human whole blood DNA methylation sample; SAMPLE 52

tag: cortisol stress response area under the curve (auc) with respect to the increase

tag: total score on the childhood trauma questionnaire


title: skin-control d14-rep3

status: Public on Mar 16 2016

type: RNA

city: Gaithersburg

first: Tracy

middle: Anne

last: Delaney

state: MD

address: One Medimmune Way

department: Research

country: USA

institute: MedImmune LLC

description: RAG2 KO grafted with Balb/c splenocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HGU133 Plus 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

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

data_processing: The data was analyzed in R.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: skin, syngeneic graft, d14

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Qiagen Rneasy Fibrous Tissue Mini Kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Shaved dorsal scapular skin was snap frozen in liquid nitrogen and stored at -80C

tag: gender

value: female

tag: genotype/variation


title: skin-control d14-rep4

description: RAG2 KO grafted with Balb/c splenocytes


title: skin-isotype d14-rep1

description: RAG2 KO grafted with B10.D2 splenocytes

source_name: skin, GVH-SSc, isotype, d14


title: Myotubes Healthy C25 Primary rep2

city: Londonderry

first: William

middle: John

last: Duddy

address: C-TRIC building, Altnagelvin Hospital Campus

department: Northern Ireland Centre for Stratified Medicine

country: United Kingdom

institute: Ulster University

description: Myotubes Healthy C25 Primary rep2

hyb_protocol: 750ng of the biotin-labeled IVT product (cRNA) was hybridized to HumanHT-12v4_BeadChip for 16 hours, followed by washing, blocking, and streptavidin-Cy3 staining according to the WholeGenome Gene Expression Direct Hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScanSQ System

data_processing: Raw intensity values (Illumina idat files) of 94 samples were passed to the R lumidat library to create an EListRaw class object compatible with further downstream analyses in R/Bioconductor. Two samples were excluded at this stage due to having zero proportion of expressed probes (all other samples had more than 40% of probes expressed). The limma library was then used to carry out neqc normalization – this involves background correction followed by quantile normalization, using negative control probes for background correction and both negative and positive controls for normalization. Probes were excluded if: (1) they had low bead numbers in at least one sample; (2) they were not expressed (expression p-value < 0.01) in at least 16 arrays; (3) they were annotated as ‘no match’ or ‘bad’ quality according to the Bioconductor illuminaHumanv4.db library. This gave a total of 15,342 probes for further analysis.

organism: Homo sapiens

source_name: Cultured cells

label_protocol: An aliquot of 150 ng of high-quality total RNA from each sample was used for mRNA expression profiling. Reverse Transcription for synthesis of the cDNA strand, followed by a single in vitro transcription (IVT) amplification, that incorporates biotin-labeled nucleotides, were performed with Illumina® TotalPrep™ -96 RNA Amplification Kit (Ambion, Austin, TX).

extract_protocol: Cells were scraped and collected in PBS (100 uL). Cells were centrifuged at 13,000 rpm for 10 minutes, and PBS supernatant removed. Each pellet was dissolved in TRIzol (1 mL). The RNA was subsequently isolated (PureLink RNA Mini Kit, ‘Using TRIzol® Reagent with the PureLink® RNA Mini Kit’ section of the standard protocol) with the RNA eluted in 30 µL H2O.

tag: differentiation state

value: Myotube

tag: clonal state

value: Primary

tag: disease state

value: Healthy


title: Capan-1

city: Daejeon

first: Yang

last: Suk-Jin

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: KRIBB (Korea Research Institute of Bioscience and Biotechnology)

hyb_protocol: Labeled cRNA (750ng) was hybridized to HumanHT-12 v3 or v4 chips at 58℃ for 16 hours.

scan_protocol: After hybridizing procedures, chips were scanned using a BeadArray Reader and BeadScan software (Illumina).

data_processing: Data extraction and normalization were elevated by BeadStudio software (Illumina).

label: Biotin

source_name: Capan-1 cells

label_protocol: Illumina TotalPrep RNA Amplification kit (Applied Biosystem/Ambion, Austin, TX, USA) was used to generate biotin-UTP labeled cRNA according to manufacturer’s instructions

growth_protocol: ATCC (ATCC, Manassas, VA) and SNU (KCLB, Seoul, Korea) were maintained in Dulbecco’s modified Eagle medium (DMEM; Gibco BRL, Grand Island, NY) or Roswell Park Memorial Institute 1640 medium (RPMI1640; GIBCO BRL). JHH cell lines obtained from JCRB were maintained in William’s E medium (GIBCO BRL). All media was supplemented with heat-inactivated 10% fetal bovine serum (GIBCO BRL) and 1× Antibiotic-Antimycotic (GIBCO BRL). Cells were cultured at 37℃ in a humidified incubator under 5% CO2.

extract_protocol: Total RNA extraction was perforemd using QIAGEN RNeasy mini kit according to manufacturer's instruction. Total RNA integrity was determined with ExperionTM RNA StdSens (BIO-RAD).

treatment_protocol: None.

tag: cell line

tag: cell type

value: Human pancreas cancer cells


title: Blood_Control_51

type: genomic

city: Utrecht

first: Marco

last: Boks

state: Nederland

address: Heidelberglaan 100, PO box 85500, Huispostnr A01.146

department: Department of Psychiatry

country: Netherlands

institute: University Medical Center Utrecht

description: Human whole blood DNA methylation sample; SAMPLE 51

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

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

data_processing: Intensity read outs, quality control parameters and methylation measures were obtained from the genome studio software. X chromosome, Y chromosome, and non-specific binding probes were removed. Failed probes were excluded based on a detection p-value larger than 0.001 and bead count lower than 5. In addition, probes with SNPs of Minor Allele Frequency(MAF) larger than 5 percent within 10 base pairs of the primer were excluded after constructing ancestry estimates based on their principal components as proposed by Barfield et al (lists of CpG sites available at http://genetics.emory.edu/research/conneely/annotation-r-code.html). DNA methylation analysis was performed in R, using wateRmelon (providing routines to handle Illumina BeadStudio data and normalization), sva(batch effect removal)  and limma (for statistical routines). The data was normalized to remove systematic differences in overall signal distribution due to probe design bias using the Beta MIxture Quantile dilation (BMIQ) normalization as implemented in the watermelon package. After removing batch effects of sentrix array and position with the Combat procedure from the sva package.

molecule: genomic DNA

source_name: Whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from whole blood with the Gentra Puregene Kit (Qiagen, Valencia, CA, USA) following manufacturer's protocol. DNA concentration and integrity was assessed using riboGreen and BioAnalyser.

treatment_protocol: Bisulphite conversion was conducted with Zimo kits (ZYMO Research, Orange, CA, USA) using standard procedures.

tag: race

value: Caucasian

value: Female

tag: age

tag: total score on the life stressor checklist- revised

tag: cd8 t cell proportion

tag: monocytes cell proportion

tag: natural killer cell proportion

tag: cd4 t cell proportion

tag: bcell proportion

tag: granulocytes cell proportion

tag: sentrix

tag: position


title: skin-control d14-rep2

description: RAG2 KO grafted with Balb/c splenocytes

tag: gender

tag: genotype/variation


title: Myotubes Healthy C25 Primary rep1

description: Myotubes Healthy C25 Primary rep1

tag: differentiation state

tag: clonal state


title: skin-control d14-rep1

description: RAG2 KO grafted with Balb/c splenocytes


title: Myotubes Healthy C25 Clone rep4

description: Myotubes Healthy C25 Clone rep4

value: Clone

tag: disease state


title: Capan-2

source_name: Capan-2 cells

tag: cell line

tag: cell type


title: BxPC-3

source_name: BxPC-3 cells


title: skin-isotype d14-rep3

description: RAG2 KO grafted with B10.D2 splenocytes


title: Myotubes Healthy C25 Clone rep3

description: Myotubes Healthy C25 Clone rep3


title: AsPC-1

source_name: AsPC-1 cells


title: MIA-PaCa-2

source_name: MIA-PaCa-2 cells


title: Blood_Control_48

description: Human whole blood DNA methylation sample; SAMPLE 48

tag: race

tag: age

tag: cortisol stress response area under the curve (auc) with respect to the increase

tag: total score on the childhood trauma questionnaire


title: Blood_Control_47

description: Human whole blood DNA methylation sample; SAMPLE 47

tag: total score on the life stressor checklist- revised

tag: cd8 t cell proportion

tag: monocytes cell proportion

tag: natural killer cell proportion


title: Myotubes Healthy C25 Clone rep1

description: Myotubes Healthy C25 Clone rep1


title: Myotubes Healthy C25 Clone rep2

description: Myotubes Healthy C25 Clone rep2


title: Calu-1

source_name: Calu-1 cells

value: Human lung cancer cells


title: Myoblasts DMD 8036 Primary rep4

description: Myoblasts DMD 8036 Primary rep4

value: Myoblast

value: Duchenne muscular dystrophy


title: Blood_Control_49

description: Human whole blood DNA methylation sample; SAMPLE 49

tag: cd4 t cell proportion

tag: bcell proportion

tag: granulocytes cell proportion

tag: sentrix


title: Malme-3M

source_name: Malme-3M cells


title: NCI-H1299

source_name: NCI-H1299 cells


title: Calu-3

source_name: Calu-3 cells


title: NCI-H596

source_name: NCI-H596 cells


title: Myoblasts DMD 8036 Primary rep1

description: Myoblasts DMD 8036 Primary rep1

tag: differentiation state


title: Blood_Control_46

description: Human whole blood DNA methylation sample; SAMPLE 46

tag: gender

tag: position


title: Myoblasts DMD 8036 Clone rep3

description: Myoblasts DMD 8036 Clone rep3

tag: clonal state

tag: disease state


title: Myoblasts DMD 8036 Primary rep2

description: Myoblasts DMD 8036 Primary rep2


title: Blood_Control_44

description: Human whole blood DNA methylation sample; SAMPLE 44

tag: race


title: Blood_Control_54

description: Human whole blood DNA methylation sample; SAMPLE 54

value: Male

tag: age


title: Myoblasts DMD 8036 Clone rep1

description: Myoblasts DMD 8036 Clone rep1


title: Blood_Control_45

description: Human whole blood DNA methylation sample; SAMPLE 45

tag: cortisol stress response area under the curve (auc) with respect to the increase


title: Myoblasts DMD 6594 Primary rep4

description: Myoblasts DMD 6594 Primary rep4


title: Myoblasts DMD 8036 Primary rep3

description: Myoblasts DMD 8036 Primary rep3


title: Blood_Control_50

description: Human whole blood DNA methylation sample; SAMPLE 50

tag: total score on the childhood trauma questionnaire


title: Myoblasts DMD 8036 Clone rep2

description: Myoblasts DMD 8036 Clone rep2


title: LIMM-36

city: LEEDS

first: Milene

last: Volpato

address: St James University Hospital

department: LIRM

institute: University of Leeds

description: Gene expression data from colorectal liver metastasis tissue

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit, hybridasation performed by Gen-PROBE

scan_protocol: GeneChip® Command Console® Software (AGCC)

data_processing: Whole genome expression profiles were generated using the Affymetrix GeneChip® Human Transcriptome Array 2.0 (>6 million probes). Gene expression data were pre-processed using proprietary Affymetrix® Expression Console™ v1.3 software. The raw gene expression data (CEL files) were processed using the Robust Multichip Analysis (RMA) algorithm [32] which fits a linear model at probe level allowing the effect of differences in probe-specific affinity to be minimized and providing increased sensitivity to detect small changes between experimental and control samples. The RMA algorithm performs global background adjustment of the data from each chip prior to inter-array quantile normalization. Probe level expression values were then summarized to give gene-level expression values

source_name: colorectal liver metastasis patient with decreased systemic CCL2 levels following EPA-FFA treatment

label_protocol: 250ng of RNA was sent ot Affymetrix for  labelling with GeneChip® Human Transcriptome Array 2.0 and SensationPlusTM FFPE Sufficient for 12 reactions Amplification and WT Labeling Kit

growth_protocol: Tumour samples from obtaned from FFPE block, needle core sampling was used to extract tumour tissues from the blocks.

extract_protocol: RNA was extracted usinf the Qiagen FFPE kit

treatment_protocol: Patients were treated with 2g daily of EPA free fatty acid, 2g per day for a median duration of 30 [range 12-65] days

tag: tissue

value: colorectal liver metastasis

tag: treatment

value: EPA-FFA 2g/day


title: Myoblasts DMD 8036 Clone rep4

description: Myoblasts DMD 8036 Clone rep4


title: Blood_Control_42

description: Human whole blood DNA methylation sample; SAMPLE 42

tag: total score on the life stressor checklist- revised

tag: cd8 t cell proportion

tag: monocytes cell proportion


title: Blood_Control_41

description: Human whole blood DNA methylation sample; SAMPLE 41

tag: natural killer cell proportion

tag: cd4 t cell proportion

tag: bcell proportion


title: LIMM-32


title: LIMM-30


title: Myoblasts DMD 6594 Primary rep1

description: Myoblasts DMD 6594 Primary rep1

tag: differentiation state


title: Myoblasts DMD 6594 Primary rep3

description: Myoblasts DMD 6594 Primary rep3


title: LIMM-26

source_name: colorectal liver metastasis patient with increased systemic CCL2 levels following EPA-FFA treatment


title: Blood_Control_43

description: Human whole blood DNA methylation sample; SAMPLE 43

tag: gender

tag: granulocytes cell proportion

tag: sentrix


title: Blood_Control_40

description: Human whole blood DNA methylation sample; SAMPLE 40

tag: position


title: Myoblasts DMD 6594 Clone rep4

description: Myoblasts DMD 6594 Clone rep4

tag: clonal state

tag: disease state


title: Blood_Control_35

description: Human whole blood DNA methylation sample; SAMPLE 35

tag: race

tag: age

tag: cortisol stress response area under the curve (auc) with respect to the increase


title: Blood_Control_38

description: Human whole blood DNA methylation sample; SAMPLE 38

tag: total score on the childhood trauma questionnaire


title: Blood_Control_33

description: Human whole blood DNA methylation sample; SAMPLE 33

tag: total score on the life stressor checklist- revised


title: Myoblasts DMD 6594 Clone rep2

description: Myoblasts DMD 6594 Clone rep2


title: Myoblasts DMD 6594 Clone rep1

description: Myoblasts DMD 6594 Clone rep1


title: Myoblasts DMD 6311 Primary rep3

description: Myoblasts DMD 6311 Primary rep3


title: Myoblasts DMD 6311 Primary rep2

description: Myoblasts DMD 6311 Primary rep2


title: LIMM-20

tag: tissue

tag: treatment


title: LIMM-21


title: Blood_Control_32

description: Human whole blood DNA methylation sample; SAMPLE 32

tag: cd8 t cell proportion

tag: monocytes cell proportion

tag: natural killer cell proportion


title: Myoblasts DMD 6311 Primary rep4

description: Myoblasts DMD 6311 Primary rep4

tag: differentiation state


title: LIMM-24


title: LIMM-19


title: LIMM-17


title: Myoblasts DMD 6311 Primary rep1

description: Myoblasts DMD 6311 Primary rep1


title: Myoblasts DMD 6311 Clone rep4

description: Myoblasts DMD 6311 Clone rep4


title: LIMM-15


title: Blood_Control_31

description: Human whole blood DNA methylation sample; SAMPLE 31

tag: gender

tag: cd4 t cell proportion

tag: bcell proportion


title: Blood_Control_39

description: Human whole blood DNA methylation sample; SAMPLE 39

tag: granulocytes cell proportion

tag: sentrix

tag: position


title: Myoblasts DMD 6311 Clone rep3

description: Myoblasts DMD 6311 Clone rep3

tag: clonal state

tag: disease state


title: Blood_Control_30

description: Human whole blood DNA methylation sample; SAMPLE 30

tag: race

tag: age

tag: cortisol stress response area under the curve (auc) with respect to the increase


title: Blood_Control_36

description: Human whole blood DNA methylation sample; SAMPLE 36

tag: total score on the childhood trauma questionnaire

tag: total score on the life stressor checklist- revised


title: Blood_Control_29

description: Human whole blood DNA methylation sample; SAMPLE 29

tag: cd8 t cell proportion


title: LIMM-7

tag: tissue

tag: treatment


title: Blood_Control_22

description: Human whole blood DNA methylation sample; SAMPLE 22

tag: monocytes cell proportion

tag: natural killer cell proportion


title: LIMM-9


title: LIMM-4


title: Blood_Control_23

description: Human whole blood DNA methylation sample; SAMPLE 23

tag: gender

tag: cd4 t cell proportion


title: Blood_Control_28

description: Human whole blood DNA methylation sample; SAMPLE 28

tag: bcell proportion

tag: granulocytes cell proportion


title: Blood_Control_26

description: Human whole blood DNA methylation sample; SAMPLE 26

tag: sentrix

tag: position


title: Blood_Control_25

description: Human whole blood DNA methylation sample; SAMPLE 25


title: LIMM-3

description: Gene expression data from colorectal liver metastasis tissue


title: Myoblasts Healthy CHQ Primary rep3

description: Myoblasts Healthy CHQ Primary rep3

tag: differentiation state

tag: clonal state

tag: disease state

value: healthy


title: Blood_Control_24

description: Human whole blood DNA methylation sample; SAMPLE 24

tag: race

tag: age

tag: cortisol stress response area under the curve (auc) with respect to the increase


title: Blood_Control_27

description: Human whole blood DNA methylation sample; SAMPLE 27

tag: total score on the childhood trauma questionnaire

tag: total score on the life stressor checklist- revised

tag: cd8 t cell proportion


title: Myoblasts DMD 6311 Clone rep1

description: Myoblasts DMD 6311 Clone rep1


title: Blood_Control_37

description: Human whole blood DNA methylation sample; SAMPLE 37

tag: monocytes cell proportion


title: Blood_Control_34

description: Human whole blood DNA methylation sample; SAMPLE 34

tag: natural killer cell proportion


title: Myoblasts Healthy CHQ Primary rep2

description: Myoblasts Healthy CHQ Primary rep2


title: Myoblasts Healthy CHQ Primary rep4

description: Myoblasts Healthy CHQ Primary rep4


title: Myoblasts DMD 6311 Clone rep2

description: Myoblasts DMD 6311 Clone rep2


title: Myoblasts Healthy CHQ Primary rep1

description: Myoblasts Healthy CHQ Primary rep1


title: Myoblasts Healthy CHQ Clone rep1

description: Myoblasts Healthy CHQ Clone rep1


title: LIMM-10

tag: tissue

tag: treatment


title: Myoblasts Healthy CHQ Clone rep2

description: Myoblasts Healthy CHQ Clone rep2


title: Myoblasts Healthy CHQ Clone rep3

description: Myoblasts Healthy CHQ Clone rep3


title: Myoblasts Healthy CHQ Clone rep4

description: Myoblasts Healthy CHQ Clone rep4


title: Myoblasts Healthy C25 Primary rep4

description: Myoblasts Healthy C25 Primary rep4


title: Blood_Control_21

description: Human whole blood DNA methylation sample; SAMPLE 21

tag: gender

tag: cd4 t cell proportion

tag: bcell proportion


title: Myoblasts Healthy C25 Primary rep3

description: Myoblasts Healthy C25 Primary rep3


title: Myoblasts Healthy C25 Primary rep1

description: Myoblasts Healthy C25 Primary rep1


title: Myoblasts Healthy C25 Clone rep4

description: Myoblasts Healthy C25 Clone rep4


title: Myoblasts Healthy C25 Primary rep2

description: Myoblasts Healthy C25 Primary rep2


title: Myoblasts Healthy C25 Clone rep2

description: Myoblasts Healthy C25 Clone rep2


title: Blood_Control_20

description: Human whole blood DNA methylation sample; SAMPLE 20

tag: granulocytes cell proportion

tag: sentrix

tag: position


title: Blood_Control_18

description: Human whole blood DNA methylation sample; SAMPLE 18


title: Myoblasts Healthy C25 Clone rep3

description: Myoblasts Healthy C25 Clone rep3

tag: differentiation state

tag: clonal state

tag: disease state


title: Blood_Control_17

description: Human whole blood DNA methylation sample; SAMPLE 17

tag: race

tag: age

tag: cortisol stress response area under the curve (auc) with respect to the increase


title: Myoblasts Healthy C25 Clone rep1

description: Myoblasts Healthy C25 Clone rep1


title: Blood_Control_14

description: Human whole blood DNA methylation sample; SAMPLE 14

tag: total score on the childhood trauma questionnaire

tag: total score on the life stressor checklist- revised

tag: cd8 t cell proportion


title: Blood_Control_19

description: Human whole blood DNA methylation sample; SAMPLE 19

tag: monocytes cell proportion

tag: natural killer cell proportion


title: Blood_Control_15

description: Human whole blood DNA methylation sample; SAMPLE 15

tag: gender


title: Blood_Control_12

description: Human whole blood DNA methylation sample; SAMPLE 12

tag: cd4 t cell proportion


title: PC3_PGC1A__P_DOX_2

city: Derio

first: Verónica

last: Torrano Moya

address: 801 Building. Technology Park of Vizcaya

country: Spain

institute: CICbioGUNE

description: cells with doxycycline

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: PC3 cell line

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System (Epicentre)

extract_protocol: NucleoSpin® RNA isolation kit (Macherey-Nagel)

tag: cell line


title: PC3_PGC1A__P_DOX_3

description: cells with doxycycline


title: Blood_Control_16

description: Human whole blood DNA methylation sample; SAMPLE 16

tag: bcell proportion

tag: granulocytes cell proportion


title: PC3_PGC1A__P_DOX_1

description: cells with doxycycline


title: Blood_Control_6

description: Human whole blood DNA methylation sample; SAMPLE 06

tag: sentrix

tag: position


title: Blood_Control_9

description: Human whole blood DNA methylation sample; SAMPLE 09


title: Blood_Control_5

description: Human whole blood DNA methylation sample; SAMPLE 05


title: Blood_Control_11

description: Human whole blood DNA methylation sample; SAMPLE 11


title: PC3_PGC1A__M_DOX_2

description: cells without doxycycline


title: PC3_PGC1A__M_DOX_3

description: cells without doxycycline


title: Blood_Control_7

description: Human whole blood DNA methylation sample; SAMPLE 07


title: Blood_Control_13

description: Human whole blood DNA methylation sample; SAMPLE 13


title: Blood_Control_4

description: Human whole blood DNA methylation sample; SAMPLE 04


title: Blood_Control_10

description: Human whole blood DNA methylation sample; SAMPLE 10


title: Blood_Control_3

description: Human whole blood DNA methylation sample; SAMPLE 03


title: PC3_PGC1A__M_DOX_1

description: cells without doxycycline


title: pES10 d-G1 [expression]

city: Jerusalem

first: Ido

last: Sagi

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

description: Diploid ES cells in G1 (2c)

hyb_protocol: Affymetrix protocol, 11 µg cRNA

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

data_processing: Affymetrix Expression Console (RMA)

source_name: Diploid pES10 cells in G1 (2c)

label_protocol: 200 ng total RNA, Affymetrix protocol

extract_protocol: RNA was isolated using the RNeasy Micro Kit (Qiagen)

tag: cell type

value: diploid human parthenogenetic embryonic stem cells

tag: cell cycle phase

tag: passage

tag: differentiation status

value: undifferentiated


title: pES10 h-G1 [expression]

description: Haploid ES cells in G1 (1c), 3rd sort

source_name: Haploid pES10 cells in G1 (1c)

value: haploid human parthenogenetic embryonic stem cells

value: G1 (1c), 3rd sort


title: HEK293T_untreated

city: Aarhus

first: Tue

last: Fryland

state: Aarhus

address: Bartholins Allé 6

department: Biomedicine

country: Denmark

institute: Aarhus University

description: Untreated cells

hyb_protocol: Affymetrix GeneChip® Hybridization, Wash, and Stain Kit

scan_protocol: standard Affymetrix protocol

data_processing: rma

source_name: Cell line culture, Untreated

growth_protocol: HEK293T cells (controls and stable BRD1-S-V5 and BRD1-L-V5 cell lines) were grown in DMEM medium (Invitrogen, San Diego, CA, USA) supplemented with 5% fetal calf serum (FCS), 175 mg/L glutamine, 36 mg/L penicillin and 60 mg/L streptomycine at 37 oC in 5% CO2

extract_protocol: Qiagen Rneasy + Qiagen shredder columns (performed according to the supplied protocol)


title: HEK293T_stableexpression_BRD1-L (NM_001304808.1  refseq)

description: Stable/episomal expression of His6/V5 tagged BRD1-L (refseq NM_001304808.1  )

source_name: Cell line culture, stable/episomal expression BRD1-L

label_protocol: Affymetrix GeneChip® Hybridization, Wash, and Stain Kit


title: HEK293T_mock(dharmacon)BRD1_2

description: Mock treatment targeted against the BRD1 mRNA transcript (Dharmacon) rep2

source_name: Cell line culture, mock method 2


title: pre BI, DKO, rep.3

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

hyb_protocol: Affymetrix GeneChip arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.

data_processing: Probesets were summarized and probeset-level values normalized with the following functions vsn2() and rma() from R (version 2.10.0) / Bioconductor (version 2.5) packages vsn and affy respectively as well as the CDF environment MoGene-1_0-st-v1.r3.cdf (as provided by Bioconductor) and the annotation package mogene10sttranscriptcluster.

source_name: ex-vivo, FACS-sorted pre BI

label_protocol: 100 ng total RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix (GeneChip Whole Transcription Sense Target Labeling technical manual, Rev. 2).

growth_protocol: ex-vivo, FACS-sorted with markers  B220+, CD25-, C-kit+,IgM-, CD19+

extract_protocol: total RNA was isolated using the Qiagen Micro RNA kit according to the manufacturer's instructions

tag: genotype/variation

value: DKO

value: female

tag: age

value: 8 weeks


title: HuES64

hyb_protocol: Standard Illumina protocol

scan_protocol: HumanMethylation450 BeadChips were scanned with Illumina's iScan System

data_processing: IDAT files were processed and normalized by subset-quantile within array normalization (SWAN) and adjusted for batch effects using the R package ChAMP (version 1.4.0)

label: Cy5 and Cy3

source_name: Diploid ES cell line

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was isolated (NucleoSpin Tissue Kit, MACHEREY-NAGEL) and bisulfite converted (EZ DNA Methylation Kit, Zymo Research) according to the manufacturer's protocol

value: diploid ES cell line


title: Blood_Control_2

description: Human whole blood DNA methylation sample; SAMPLE 02

source_name: Whole blood

tag: race

value: Caucasian

tag: cortisol stress response area under the curve (auc) with respect to the increase

tag: total score on the childhood trauma questionnaire

tag: total score on the life stressor checklist- revised


title: HEK293T_stableexpression_BRD1-S (NM_001304809.1 )

description: Stable/episomal expression of His6/V5 tagged BRD1-S (refseq NM_001304809.1 )

source_name: Cell line culture, stable/episomal expression BRD1-S


title: Blood_Control_1

description: Human whole blood DNA methylation sample; SAMPLE 01

tag: gender

tag: cd8 t cell proportion

tag: monocytes cell proportion

tag: natural killer cell proportion


title: Blood_Control_8

description: Human whole blood DNA methylation sample; SAMPLE 08

tag: cd4 t cell proportion

tag: bcell proportion

tag: granulocytes cell proportion


title: pES12 h-G1 rep1

source_name: Haploid pES12 cells in G1 (1c) rep1

tag: cell line

tag: cell type

value: Haploid pES12 cells

value: Undifferentiated


title: pre BI, DKO, rep.2


title: HuES53

tag: passage


title: pre BI, WT, rep.3

value: wildtype


title: h-pES10 d-G2/M

source_name: Diploid pES10 cells in G2/M from a mixed haploid-diploid culture (4c)

value: Diploid pES10 cells

tag: cell cycle phase

tag: differentiation status


title: NYSCF2


title: pES12 d-G1 rep1

source_name: Diploid pES12 cells in G1 (2c) rep1

value: Diploid pES12 cells


title: pES10 d-G1 rep2

source_name: Diploid pES10 cells in G1 (2c) rep2


title: pES12 d-G1 rep2

source_name: Diploid pES12 cells in G1 (2c) rep2


title: HEK293T_siRNA(dharmacon)BRD1_2

description: siRNA treatment targeted against the BRD1 mRNA transcript (Dharmacon) rep2

source_name: Cell line culture, siRNA agianst BRD1 method 2


title: HEK293T_mock(dharmacon)BRD1_1

description: Mock treatment targeted against the BRD1 mRNA transcript (Dharmacon) rep1


title: pES10 h-G1 rep2

source_name: Haploid pES10 cells in G1 (1c) rep2

value: Haploid pES10 cells


title: pES10 d-G1 rep1

source_name: Diploid pES10 cells in G1 (2c) rep1


title: pre BI, DKO, rep.1

tag: genotype/variation

tag: age


title: pre BI, WT, rep.2


title: pre BI, WT, rep.1


title: HOB_batch3_rep2

status: Public on Mar 15 2016

city: Toronto

first: Jeff

middle: W

last: Martin

state: ON

address: 555 University Avenue

country: Canada

institute: Hospital for Sick Children

description:
SAMPLE X
Replicate 2

hyb_protocol: See Geiss GK, Bumgarner RE, Birditt B, et al. Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol 2008;26:317-25.

data_processing: Followed standard nCounter™ Data Analysis Guidelines (linked as supplementary PDF file)

source_name: Human osteoblast cell line

extract_protocol: Total RNA was extracted using the TRIzol Reagent method according to the manufacturer’s protocol (Invitrogen) and quantified using Bioanalyzer (Agilent Technologies). Total RNA from normal human osteoblasts was retrieved as described previously (Sadikovic B, Yoshimoto M, Chilton-MacNeill S, et al. Identification of interactive networks of gene expression associated with osteosarcoma oncogenesis by integrated molecular profiling. Hum Mol Genet 2009;18:1962-75).

value: Normal human osteoblast

value: HOB

value: not applicable

tag: sample type

tag: histologic subtype

tag: tumour location

tag: storage method

value: frozen


title: HOB_batch3_rep1

description:
SAMPLE W
Replicate 1

scan_protocol: See Geiss GK, Bumgarner RE, Birditt B, et al. Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol 2008;26:317-25.

tag: gender


title: MG63_batch3_rep1

description:
SAMPLE Y
Replicate 1

source_name: Osteosarcoma cell line

label_protocol: See Geiss GK, Bumgarner RE, Birditt B, et al. Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol 2008;26:317-25.

value: Osteosarcoma


title: SAOS_batch3_rep2

description:
SAMPLE V
Replicate 2

value: SAOS

value: FFPE


title: SAOS_batch3_rep1

description:
SAMPLE U
Replicate 1


title: MG63_batch3_rep2

description:
SAMPLE Z
Replicate 2


title: HEK293T_mock(Qiagen kit)BRD1

description: Mock treatment targeted against the BRD1 mRNA transcript (Qiagen kit)

source_name: Cell line culture, mock method 1


title: pES12 h-G1 rep2

source_name: Haploid pES12 cells in G1 (1c) rep2


title: U2OS_batch2_rep2

description:
SAMPLE T
Replicate 2


title: HEK293T_siRNA(dharmacon)BRD1_1

description: siRNA treatment targeted against the BRD1 mRNA transcript (Dharmacon) rep1


title: U2OS_batch2_rep1

description:
SAMPLE S
Replicate 1


title: pES10 h-G1 rep1

source_name: Haploid pES10 cells in G1 (1c) rep1


title: HEK293T_siRNA(Qiagen kit)BRD1

description: siRNA treatment targeted against the BRD1 mRNA transcript (Qiagen kit)

source_name: Cell line culture, siRNA agianst BRD1 method 1


title: MG63_batch2_rep2

description:
SAMPLE R
Replicate 2


title: HOB_batch2_rep2

description:
SAMPLE P
Replicate 2


title: MG63_batch2_rep1

description:
SAMPLE Q
Replicate 1


title: HOB_batch2_rep1

description:
SAMPLE O
Replicate 1


title: SAOS_batch2_rep2

description:
SAMPLE N
Replicate 2


title: SAOS_batch2_rep1

description:
SAMPLE M
Replicate 1


title: U2OS_batch1_rep3

description:
SAMPLE L
Replicate 3


title: U2OS_batch3_rep1

description:
SAMPLE AA
Replicate 1


title: U2OS_batch1_rep2

description:
SAMPLE K
Replicate 2


title: MG63_batch1_rep3

description:
SAMPLE I
Replicate 3


title: MG63_batch1_rep2

description:
SAMPLE H
Replicate 2


title: SAOS_batch1_rep3

description:
SAMPLE C
Replicate 3


title: HOB_batch1_rep1

description:
SAMPLE D
Replicate 1


title: SAOS_batch1_rep2

description:
SAMPLE B
Replicate 2


title: AZ_rep2

description:
SAMPLE 116
Replicate 2

source_name: Pediatric osteosarcoma

value: Pediatric osteosarcoma

value: F

value: Resection

value: mixed

value: femur


title: SAOS_batch1_rep1

description:
SAMPLE A
Replicate 1


title: AZ_rep1

description:
SAMPLE 115
Replicate 1


title: U2OS_batch1_rep1

description:
SAMPLE J
Replicate 1


title: AY_rep1

description:
SAMPLE 113
Replicate 1

value: osteoblastic


title: AX_rep1

description:
SAMPLE 111
Replicate 1


title: AX_rep2

description:
SAMPLE 112
Replicate 2


title: MG63_batch1_rep1

description:
SAMPLE G
Replicate 1


title: HOB_batch1_rep3

description:
SAMPLE F
Replicate 3


title: AW_rep1

description:
SAMPLE 109
Replicate 1

value: M

value: humerus


title: HOB_batch1_rep2

description:
SAMPLE E
Replicate 2


title: AV_rep1

description:
SAMPLE 107
Replicate 1

value: fibroblastic


title: AV_rep2

description:
SAMPLE 108
Replicate 2


title: AU_rep2

description:
SAMPLE 106
Replicate 2


title: AY_rep2

description:
SAMPLE 114
Replicate 2


title: cartilage, OA, pat2

first: Akihiro

last: Nakamura

address: 60 Leonard Avenue

department: Genetics and Development

institute: University Health Network

description:
Facet cartilage was extracted from medial aspect of the facet joint for both facet osteoarthritis and control samples
The 1_Exiqon_*_S01.txt raw files represent Hy3 data and the 0_Exiqon_*_S01.txt raw files represent Hy5 data.

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 7th gen (Exiqon, Denmark). The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria).

scan_protocol: microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA)

data_processing:
The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
Expression is reported as log2(Hy3/Hy5) ratios

source_name: facet joint cartilage

label_protocol: 400 ng total RNA from both facet osteoarthritis cartilage and control cartilage was labeled with Hy fluorescent labels, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: There was no growth protocol. Fresh facet cartilage was immediately homogenized using liquid nitrogen and extracted RNA.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: No treatment was performed for facet cartilage from patients with OA and lumbar disc herniation (control).

tag: disease state

value: OA

tag: tissue

value: facet cartilage (pooled from 3 facet OA cartilage samples)

source_name: reference RNA

value: reference RNA


title: cartilage, OA, pat1


title: AW_rep2

description:
SAMPLE 110
Replicate 2

value: not applicable


title: AT_rep2

description:
SAMPLE 104
Replicate 2

value: chondroblastic

value: frozen


title: AU_rep1

description:
SAMPLE 105
Replicate 1


title: AS_rep1

description:
SAMPLE 101
Replicate 1


title: cartilage, LDH, pat2

value: Lumbar disc herniation

tag: individual

value: patient 2

value: facet cartilage


title: AT_rep1

description:
SAMPLE 103
Replicate 1

value: Pediatric osteosarcoma


title: AS_rep2

description:
SAMPLE 102
Replicate 2

value: F

value: Resection


title: cartilage, LDH, pat1

value: patient 1


title: Tumor No.3

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description:
2555 miRNAs were spotted on each array.
Location of tumors: liver

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: HEH tumor tissues

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: no culture performed

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

treatment_protocol: no treatment performed

value: Liver

tag: disease status


title: Tumor No.1


title: Tumor No.2


title: AR_rep1

description:
SAMPLE 99
Replicate 1

value: M

value: Biopsy

value: osteoblastic

value: unknown

value: femur


title: AQ_rep2

description:
SAMPLE 98
Replicate 2

value: tibia


title: Normal No.2

description: 2555 miRNAs were spotted on each array.

source_name: normal tissues

value: healthy


title: AP_rep2

description:
SAMPLE 96
Replicate 2

value: not applicable


title: AQ_rep1

description:
SAMPLE 97
Replicate 1

value: frozen


title: Normal No.3

description: 2555 miRNAs were spotted on each array.


title: AR_rep2

description:
SAMPLE 100
Replicate 2


title: AP_rep1

description:
SAMPLE 95
Replicate 1


title: Normal No.1

description: 2555 miRNAs were spotted on each array.


title: AO_rep1

description:
SAMPLE 93
Replicate 1


title: AO_rep2

description:
SAMPLE 94
Replicate 2


title: AN_rep1

description:
SAMPLE 91
Replicate 1


title: AN_rep2

description:
SAMPLE 92
Replicate 2


title: AM_rep1

description:
SAMPLE 89
Replicate 1

value: nasal


title: AM_rep2

description:
SAMPLE 90
Replicate 2


title: pES12 h-G1

scan_protocol: BeadChips were scanned with Illumina's iScan System

data_processing:
IDAT files were processed using Genome Studio Genotyping Module (Illumina)
GC Score, B Allele Frequency and Log R Ratio values obtained from Genome Studio Genotyping Module (Illumina)

source_name: Haploid pES12 cells in G1 (1c)

extract_protocol: Genomic DNA was isolated using the NucleoSpin Tissue Kit (MACHEREY-NAGEL)

value: Undifferentiated


title: AL_rep2

description:
SAMPLE 88
Replicate 2

value: mixed


title: AI_rep2

description:
SAMPLE 82
Replicate 2

value: Pediatric osteosarcoma


title: AH_rep2

description:
SAMPLE 80
Replicate 2


title: AI_rep1

description:
SAMPLE 81
Replicate 1


title: pES12 d-G1

source_name: Diploid pES12 cells in G1 (2c)


title: AE_rep2

description:
SAMPLE 74
Replicate 2

value: Osteoblastic


title: AG_rep2

description:
SAMPLE 78
Replicate 2

value: F

value: Resection

value: humerus


title: AF_rep2

description:
SAMPLE 76
Replicate 2

value: chondroblastic

value: rib


title: AF_rep1

description:
SAMPLE 75
Replicate 1

value: Biopsy


title: AK_rep1

description:
SAMPLE 85
Replicate 1

value: M

value: osteoblastic

value: unknown


title: AG_rep1

description:
SAMPLE 77
Replicate 1


title: AE_rep1

description:
SAMPLE 73
Replicate 1

value: tibia


title: AC_rep2

description:
SAMPLE 70
Replicate 2

value: not applicable

value: femur


title: AK_rep2

description:
SAMPLE 86
Replicate 2

value: frozen


title: AD_rep2

description:
SAMPLE 72
Replicate 2


title: AD_rep1

description:
SAMPLE 71
Replicate 1


title: AC_rep1

description:
SAMPLE 69
Replicate 1


title: AA_rep2

description:
SAMPLE 66
Replicate 2

value: fibula


title: AJ_rep1

description:
SAMPLE 83
Replicate 1


title: AJ_rep2

description:
SAMPLE 84
Replicate 2


title: AB_rep1

description:
SAMPLE 67
Replicate 1


title: AB_rep2

description:
SAMPLE 68
Replicate 2


title: U2OS_batch3_rep2

description:
SAMPLE AB
Replicate 2

value: Osteosarcoma


title: Z_rep2

description:
SAMPLE 64
Replicate 2

value: Pediatric osteosarcoma


title: AA_rep1

description:
SAMPLE 65
Replicate 1


title: Z_rep1

description:
SAMPLE 63
Replicate 1

value: Osteoblastic


title: pES10 h-G1

source_name: Haploid pES10 cells in G1 (1c)

value: Undifferentiated


title: Y_rep1

description:
SAMPLE 61
Replicate 1

value: Resection

value: mixed

value: radius


title: pES10 d-G1

source_name: Diploid pES10 cells in G1 (2c)


title: W_rep2

description:
SAMPLE 58
Replicate 2


title: V_rep2

description:
SAMPLE 56
Replicate 2

value: F

value: Mixed


title: X_rep1

description:
SAMPLE 59
Replicate 1


title: AL_rep1

description:
SAMPLE 87
Replicate 1

value: M

value: Biopsy

value: nasal


title: U_rep2

description:
SAMPLE 54
Replicate 2

value: humerus


title: T_rep2

description:
SAMPLE 52
Replicate 2

value: not applicable


title: V_rep1

description:
SAMPLE 55
Replicate 1

value: femur


title: T_rep1

description:
SAMPLE 51
Replicate 1

value: frozen


title: U_rep1

description:
SAMPLE 53
Replicate 1


title: R_rep2

description:
SAMPLE 48
Replicate 2

value: fibroblastic


title: X_rep2

description:
SAMPLE 60
Replicate 2


title: R_rep1

description:
SAMPLE 47
Replicate 1


title: W_rep1

description:
SAMPLE 57
Replicate 1


title: Y_rep2

description:
SAMPLE 62
Replicate 2


title: P_rep2

description:
SAMPLE 44
Replicate 2

value: unknown


title: Q_rep1

description:
SAMPLE 45
Replicate 1

value: Pediatric osteosarcoma

value: tibia


title: S_rep1

description:
SAMPLE 49
Replicate 1

value: Osteoblastic


title: P_rep1

description:
SAMPLE 43
Replicate 1


title: S_rep2

description:
SAMPLE 50
Replicate 2

value: Resection


title: Q_rep2

description:
SAMPLE 46
Replicate 2


title: AH_rep1

description:
SAMPLE 79
Replicate 1

value: mixed


title: tomato-transgenic SlWRKY3-WT-MS medium-4 weeks replicat 2

city: Louvain-La-Neuve

first: IMENE

last: HICHRI

address: 5 (Bte 7.07.13) Place Croix du Sud

country: Belgium

institute: UCL

description: biological replicate 2 of 2, dye swap

hyb_protocol: Hybridization of the labeled cDNA (0.3 microg per sample) were added to hybridization buffer (Agilent In Situ Hybridization Kit Plus) and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially according to Agilent instructions.

scan_protocol: Scanned on an Agilent Scanner G2565B, Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Agilent Feature Extraction Software (v 9.1) was used for background subtraction and LOWESS normalization.

label: Alexa Fluor 555

organism: Solanum lycopersicum

source_name: tomato - transgenic SlWRKY3-control MS medium-4 weeks

label_protocol:
First strand cDNA was synthetized from 10 micrograms RNA. Synthesized cDNA were purified and labeled with Alexa Fluor 555 and Alexa Fluor 647. Experiments were carried out according to instructions of the Superscript Plus Indirect cDNA Labeling system (Invitrogen).
The quality of the labeled cDNA and its concentration were respectively measured with the 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA) and ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE).

growth_protocol: Tomato plants were grown for 4 weeks on MS (Murashige and Skoog) in vitro under 24°C/22°C and a 16h day/8h night photoperiod.

extract_protocol: Total RNA were extracted as described in Hichri et al. (2010)

treatment_protocol: No stress treatment was applied. Plants were grown under control conditions.

tag: plant age

value: 4 weeks-old plants

tag: treatment

value: MS (Murashige and Skoog) control medium for 4 weeks, in vitro

tag: genotype

tag: cultivar

value: Ailsa Craig

label: Alexa Fluor 647

source_name: tomato-WT-control MS medium-4 weeks

value: WT


title: O_rep1

description:
SAMPLE 41
Replicate 1

tag: cell type

tag: cell line

value: M

value: Biopsy


title: N_rep2

description:
SAMPLE 40
Replicate 2

value: biopsy

value: humerus


title: pgaI mutant + TDA(4) vs WT(4)

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

hyb_protocol: Hybridization was performerd according to the Agilent two-color microarray protocol

scan_protocol: Microarays were scanned using the Agilent DNA microarray scanner. Raw data was collected using the Agilent feature extraction software v10.7.3.1.

data_processing: Median values of Cy3 and Cy5 channel were processed in the R environment using the limma package. Backround correction was performed using the normexp method, Cy3 and Cy5 channels were loess normalized, quantile-normalization was used for separate microarrays.

organism: Phaeobacter inhibens

source_name: pgaI (AHL molecule mutant) supplemented with TDA

label_protocol: total RNA was labelled using the Universal Linker System (Kreatech) according to the manufacturers  protocol

growth_protocol: Strains were routinely grown in 500 ml baffeled Erlenmeyer flasks at 100 rpm at 28°C in 100 ml MB medium

extract_protocol: RNA was isolated and purified with the RNAprotect kit (QIAGEN) and the RNeasy kit (QIAGEN)

treatment_protocol: samples of four biological replicates of each strain were harvested in the late exponential growth phase

tag: genotype/variation

value: pgaI

value: supplemented with TDA

source_name: wild type

value: wild type


title: M_rep2

description:
SAMPLE 38
Replicate 2

value: not applicable

value: F

tag: age

value: osteoblastic

value: unknown

value: frozen


title: M_rep1

description:
SAMPLE 37
Replicate 1

value: Pediatric osteosarcoma

tag: sample type


title: Vehicle 48h 2

city: Houston

first: Leif

middle: E

last: Peterson

state: TX

address: 6565 Fannin, Suite MGJ6-031

department: Center for Biostatistics

institute: HMRI

hyb_protocol: 15.0 μg of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and fragmented labeled cRNA was loaded onto a GeneChip® array. The array was hybridized overnight at 45°C with rotation at 60 rpm then washed and stained with a streptavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated antistreptavidin.

scan_protocol: The stained array was scanned on the Affymetrix GeneChip® Scanner 3000.

data_processing: The images were analyzed and quality control metrics recorded using Affymetrix GCOS software version 1.1.2, standard settings.

source_name: RPMI + 10% css + ethanol 48 hours

label_protocol: Samples were labeled using the standard Affymetrix T7 oligo(dT) primer protocol (GeneChip Expression Analysis Technical Manual, Rev 2, Eukaryotic One-Cycle target preparation). Five ug of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for the vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was qualified using the Agilent Bioanalyer.

growth_protocol: LNCaP cells were grown in RPMI medium supplemented with 10% charcoal stripped FBS and treated as described with either ethanol vehicle or 10 nM DHT for 24 or 48 hours

extract_protocol: RNeasy Plus Mini Kit (Quiagen)

treatment_protocol: 10^6 LNCaP cells were plated in RPMI medium supplemented with 10% charcoal stripped serum (css). 24 hours later cells were treated with 10 nM DHT or ethanol vehicle. Cells were harvested 24 or 48 hours after treatment.

value: LNCaP

value: prostate cancer


title: N_rep1

description:
SAMPLE 39
Replicate 1

tag: histologic subtype

value: mixed


title: L_rep3

description:
SAMPLE 36
Replicate 3

value: Resection

value: Osteoblastic

tag: tumour location

value: femur


title: Vehicle 24h 1

source_name: RPMI + 10% css + ethanol 24 hours


title: tomato-WT-transgenic SlWRK3-MS medium-4 weeks replicat 1

description: biological replicate 1 of 2

value: 4 weeks-old plants

value: MS (Murashige and Skoog) control medium for 4 weeks, in vitro

value: WT

value: Ailsa Craig


title: pgaI mutant + TDA(2) vs WT(2)

value: pgaI

value: supplemented with TDA

value: wild type


title: Vehicle 24h 2


title: O_rep2

description:
SAMPLE 42
Replicate 2

value: not applicable

value: M

value: Biopsy

value: tibia

tag: storage method


title: L_rep2

description:
SAMPLE 35
Replicate 2

value: Pediatric osteosarcoma

tag: gender

value: F

value: frozen


title: DHT 48h 2

source_name: RPMI + 10% css + 10 nM DHT, 48 hours

value: LNCaP

value: prostate cancer


title: pgaI mutant(4) vs pgaR mutant(3)

source_name: pgaI (AHL molecule mutant)

source_name: pgaR (AHL regulator mutant)

value: pgaR


title: WT(3) vs pgaI mutant(3)


title: pgaR mutant(2) vs pgaI mutant + TDA(1)


title: Vehicle 48h 1


title: pgaR mutant(4) vs pgaI mutant + TDA(3)


title: DHT 48h 1


title: WT(1) vs pgaI mutant(1)


title: pgaI mutant(2) vs pgaR mutant(1)


title: DHT 24h 2

source_name: RPMI + 10% css + 10 nM DHT, 24 hours


title: DHT 24h 1


title: L_rep1

description:
SAMPLE 34
Replicate 1

source_name: Pediatric osteosarcoma

value: Resection

value: Osteoblastic

value: femur


title: Male_Placenta_WT_1

city: Jouy-en-Josas

first: Helene

last: Bierne

address: Domaine de Vilvert, bat 442, INRA Micalis

department: Micalis Institute

country: France

institute: INRAE - University PARIS SACLAY

description: Gene expression data

hyb_protocol: Hybridization cocktail and post-hybridization processing was performed according to the “Target Preparation for Affymetrix GeneChip® Eukaryotic Array Analysis” protocol found in the appendix of the Nugen protocol of the fragmentation kit.

scan_protocol: scanned with an Affymetrix Genechip Scanner 3000, generating CEL files for each array.

data_processing: Data were normalized with RMA, analysed with LPE with three FDR methods; the z real value is indicated in the matrix.

source_name: male mouse placenta (E16.5)

label_protocol: RNA was amplified with Ovation Pico WTA System v2  (Nugen Technologies, Inc.  #3302-12),  fragmented and biotin labeled using the Encore Biotin Module, (Nugen Technologies, Inc. #4200-12), according to the manufacturer's

growth_protocol: Placenta and embryonic livers of pregnant mice at embryonic day E16.5 were removed immediately after sacrifice, flash frozen in liquid nitrogen and stored at −80°C until further analysis.

extract_protocol: Total RNA was extracted with TRIzol reagent from biological replicates according to the manufacturer's instructions. RNA was treated with DNase I to remove residual DNA and then cleaned with DNase Inactivation Reagent (Ambion® Inc.) RNA was quality checked an then store at -80°C.

treatment_protocol: Total ablation of the BAHD1 gene.

value: wild-type


title: K_rep3

description:
SAMPLE 33
Replicate 3

value: chondroblastic

value: rib


title: Male_Placenta_WT_2

description: Gene expression data


title: Male_Placenta_WT_3

description: Gene expression data


title: Male_Placenta_Ko_3

description: Gene expression data

value: BAHD1 knockout


title: K_rep1

description:
SAMPLE 31
Replicate 1

value: not applicable


title: J_rep3

description:
SAMPLE 30
Replicate 3

value: fibula


title: J_rep2

description:
SAMPLE 29
Replicate 2

value: Biopsy


title: J_rep1

description:
SAMPLE 28
Replicate 1


title: Male_Placenta_Ko_1

description: Gene expression data


title: I_rep2

description:
SAMPLE 26
Replicate 2

value: tibia


title: I_rep1

description:
SAMPLE 25
Replicate 1

value: Pediatric osteosarcoma


title: I_rep3

description:
SAMPLE 27
Replicate 3

value: F


title: Female_Placenta_WT_3

description: Gene expression data

source_name: female mouse placenta (E16.5)


title: H_rep2

description:
SAMPLE 23
Replicate 2

value: Mixed

value: frozen


title: H_rep1

description:
SAMPLE 22
Replicate 1


title: H_rep3

description:
SAMPLE 24
Replicate 3


title: K_rep2

description:
SAMPLE 32
Replicate 2


title: Female_Placenta_WT_1

description: Gene expression data


title: G_rep3

description:
SAMPLE 21
Replicate 3

value: biopsy

value: fibroblastic


title: G_rep2

description:
SAMPLE 20
Replicate 2


title: Female_Placenta_Ko_2

description: Gene expression data


title: Female_Placenta_Ko_3

description: Gene expression data


title: Male_Liver_WT_2

description: Gene expression data

source_name: male mouse embryonic (E16.5) liver


title: F_rep3

description:
SAMPLE 18
Replicate 3

value: M

value: resection


title: G_rep1

description:
SAMPLE 19
Replicate 1

value: femur


title: Male_Placenta_Ko_2

description: Gene expression data


title: F_rep2

description:
SAMPLE 17
Replicate 2


title: Male_Liver_WT_3

description: Gene expression data

value: wild-type


title: Male_Liver_WT_1

description: Gene expression data


title: Female_Placenta_Ko_1

description: Gene expression data


title: F_rep1

description:
SAMPLE 16
Replicate 1


title: Female_Placenta_WT_2

description: Gene expression data


title: Female_Liver_WT_3

description: Gene expression data

source_name: female mouse embryonic (E16.5) liver


title: Male_Liver_Ko_3

description: Gene expression data


title: Male_Liver_Ko_2

description: Gene expression data


title: E_rep2

description:
SAMPLE 14
Replicate 2


title: Male_Liver_Ko_1

description: Gene expression data


title: E_rep1

description:
SAMPLE 13
Replicate 1


title: Female_Liver_Ko_1

description: Gene expression data


title: D_rep2

description:
SAMPLE 11
Replicate 2

value: Resection

value: Osteoblastic


title: D_rep3

description:
SAMPLE 12
Replicate 3


title: WT_A_MEF_3

description: gene-level expression

hyb_protocol: Labeled cDNA was hybridized wiht GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix) as described by the manufacturer.

scan_protocol: Affymetrix Mouse Exon 1.0 ST Array was scanned with the Affymetrix GeneChip Scanner 7G and the FS450_0007 protocol , as recommended in the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix)

data_processing: Data were normalized with RMA, analysed with LPE with three FDR methods. The file Matrix-Gene Core-RMA_LPE.KO_A.WT_A.xlsx is available on the series record and contains fold-changes and z values.

source_name: mouse embryonic fibroblasts_BAHD1_WT

label_protocol: RNA was amplified with GeneChip® WT cDNA Synthesis and Amplification Kit (Affymetrix) and biotin labeld with GeneChip® WT Terminal Labeling Kit (Affymetrix) according to the manufacturer's

growth_protocol: Mouse embryonic fibroblasts were generated as follows: Bahd1+/- mice were crossed. Embryos at E13.5 were beheaded and each scissor-minced carcass was digested with trypsin (GibCO/Invitrogen 25200072) diluted half into PBS during 8 minutes at 37 C under agitation. Every embryo was processed independently. The supernatant was then filtered on 70um filter (BD Falcon), and digested again with trypsin diluted ¼ to obtain a single cell suspension. About 10 millions of cells were plated per 14 cm plates in fibroblast medium (DMEM 4.5 g glucose/L, 10% FCS, gentamicin). Medium was then renewed every 2 to 3 days. Just before cells reach confluency, cells were trypsinised and frozen in FCS 10% DMSO.  flash frozen in liquid nitrogen and stored at −80°C until further analysis.

extract_protocol: Total RNA was extracted with TRIzol reagent from  biological replicates according to the manufacturer's instructions. RNA was treated with DNase I to remove residual DNA and then cleaned with DNase Inactivation Reagent (Ambion® Inc.) RNA was quality checked an then store at -80°C.

tag: strain

tag: developmental stage

value: embryonic fibroblasts


title: E_rep3

description:
SAMPLE 15
Replicate 3

value: not applicable


title: Female_Liver_Ko_2

description: Gene expression data

value: BAHD1 knockout


title: D_rep1

description:
SAMPLE 10
Replicate 1


title: C_rep3

description:
SAMPLE 9
Replicate 3

value: Biopsy


title: C_rep2

description:
SAMPLE 8
Replicate 2


title: WT_A_MEF_2

description: gene-level expression


title: B_rep3

description:
SAMPLE 6
Replicate 3

value: unknown


title: KO_A_MEF_2

description: gene-level expression

source_name: mouse embryonic fibroblasts_BAHD1_KO


title: C_rep1

description:
SAMPLE 7
Replicate 1

value: Pediatric osteosarcoma


title: Female_Liver_WT_1

description: Gene expression data


title: B_rep1

description:
SAMPLE 4
Replicate 1


title: WT_A_MEF_1

description: gene-level expression


title: KO_A_MEF_3

description: gene-level expression


title: B_rep2

description:
SAMPLE 5
Replicate 2


title: A_rep3

description:
SAMPLE 3
Replicate 3

value: F

value: tibia


title: siSOX4-1

city: Cambridge

first: Myriam

last: Heiman

state: Massachusetts

address: 43 Vassar St

institute: Massachusetts Institute of Technology

description: replicate 1

hyb_protocol: Per manufacturer's instruction

scan_protocol: Per manufacturer's instruction

data_processing: Non-normalized values indicate the average probe hybrydization signal. Normalized values are median-normalized. Final processed values  are fold-change siControl relative to siSOX4.

source_name: MDA-LM2 cells_siSOX4

label_protocol: Samples were biotin-labeled using the TargetAmp-Nano Labeling Kit for Ilumina Expression BeadChip

growth_protocol: Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep

extract_protocol: 48hr post-transfection, total RNA was extracted using Ambion MiRVana total RNA extraction kit (per manufacturer instructions).

treatment_protocol: Cells were transfected with siSOX4 and siControl using Lipofectamin 2000 per manufacturer guidelines.

value: siRNA


title: siControl-1

description: replicate 1

source_name: MDA-LM2 cells_siControl

value: siControl


title: siSOX4-2

description: replicate 2


title: KO_A_MEF_1

description: gene-level expression


title: siControl-2

description: replicate 2


title: WT_C_PLAC_1

scan_protocol: Affymetrix Mouse Exon 1.0 ST Array was scanned with the Affymetrix GeneChip Scanner 3000

data_processing: Only “Core” probes were used for the analysis. Data were normalized with RMA, analysed with LPE with three FDR methods; the zreal value is indicated in the matrix.

source_name: mouse placenta

growth_protocol: Placentas of pregnant mice at embryonic day E18.5 were removed immediately after sacrifice, flash frozen in liquid nitrogen and stored at −80°C until further analysis.

tag: genotype/variaton

value: embryonic day E18.5


title: KO_B_PLAC_3


title: KO_B_PLAC_2


title: KO_B_PLAC_1


title: WT_C_PLAC_3


title: cell line cisplatin3

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

source_name: human hepatocellular carcinoma

growth_protocol: Cell line:Cells were grown in MEM supplemented with 10% fetal bovine serum in a humidified atmosphere of 5% CO2 at 37℃.

treatment_protocol: Cell line:HuH7 cells were treated with 1 µg/ml cisplatin or without cisplatin for 24h.


title: cell line control3


title: A_rep1

description:
SAMPLE 1
Replicate 1

value: Mixed

value: frozen


title: cell line cisplatin2


title: WT_C_PLAC_2


title: cell line control2


title: cell line control1


title: cell line cisplatin1


title: NCOR & Vehicle 2 (48h)

source_name: NCOR1 siRNA, ethanol 48 hours

growth_protocol: LNCaP cells were grown in RPMI medium supplemented with 10%FBS and treated as described with either ethanol vehicle or 1μM casodex for 48 hours

extract_protocol: RNA was prepared with Trizol (Life Technologies) as recommended by the manufacturer and additional reprecipitations with isopropanol and ethanol were performed.

treatment_protocol: 2x10^6 LNCaP cells were electroporated with 800 pmoles of noncoding control siRNA or NCOR1 specific smart pool siRNA (Thermo Fisher Scientific) using R Buffer (Lonza) and Nucleofector Device (Lonza). Cells were plated in 10 cm dishes in RPMI + 10%FBS medium. 24 hours later cells were treated with 1μM casodex or ethanol vehicle. Cells were harvested 48 hours after treatment.

value: LNCaP

value: prostate cancer


title: NCOR & Vehicle 3 (48h)


title: Control Vehicle 3 (48h)

source_name: Control siRNA, ethanol 48 hours


title: Control Vehicle 2 (48h)


title: NCOR & Vehicle 1 (48h)


title: Control Vehicle 1 (48h)


title: NCOR & Casodex 3 (48h)

source_name: NCOR1 siRNA, 1μM casodex 48 hours


title: A_rep2

description:
SAMPLE 2
Replicate 2

value: Resection


title: Control Casodex 2 (48h)

source_name: Control siRNA, 1μM casodex 48 hours


title: NCOR & Casodex 1 (48h)


title: Control Casodex 3 (48h)


title: NCOR & Casodex 2 (48h)


title: Control Casodex 1 (48h)


title: Liver_Irradiated_Sake_mouse489

city: Fontenay-aux-Roses

first: Guillaume

last: Vares

institute: IRSN

description: Irradiated, Sake

hyb_protocol: RNA hybridized to miRCURY LNA microRNA arrays 7th generation (Exiqon, Vedbaek, Denmark).

scan_protocol: Slides were scanned using a SureScan Microarray Scanner (Agilent, Santa Clara, CA, USA) and the resulting images were analyzed using ImaGene 9 software with Nexus Expression analysis module (BioDiscovery, El Segundo, CA, USA).

data_processing:
Following background correction, quantile normalization was applied.
ImaGene9 computed normalized signal intensity

source_name: Liver

label_protocol: RNA was labeled with Hy3.

extract_protocol: Total RNA containing miRNAs was extracted from mouse livers (n = 3 per experimental condition) using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and a protocol slightly modified from the manufacturer’s instructions, as previously described (Vares et al, 2014). The quality of total RNA was checked using a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).

treatment_protocol: junmai-shu (Japanese sake) was administered to C3H/He mice every morning for one month using a feeding needle (0.6 mL per 23g body weight, corresponding to 0.026 ml/g body weight).

tag: irradiation

tag: alcohol consumption

value: Sake 0.6 mL


title: Liver_Irradiated_Sake_mouse486

description: Irradiated, Sake


title: Liver_Sake_mouse500

description: Sake

value: 0 Gy


title: Liver_Irradiated_Sake_mouse491

description: Irradiated, Sake


title: Liver_Sake_mouse485

description: Sake


title: Liver_Sake_mouse497

description: Sake


title: Liver_Irradiated_mouse479

description: Irradiated

value: 0 mL


title: HeLa tet off β-globin let7 doxycycline-treated vs tet off β-globin let7 wt control

description: Cells were transfected with β-globin let7 wt constructs.

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: HeLa tet off β-globin let7 wt control

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: HeLa tet off cells maintained in Dulbecco’s modified Eagle medium,supplemented with 10% fetal bovine serum

extract_protocol: Total RNA extraction of  cell lines was performed according to the manufacturer’s instructions by ISOGEN 2

treatment_protocol: HeLa tet off cells were treated with 1 μg/ml doxycycline for six hours or Phosphate buffered saline

value: HeLa

tag: construct

value: tet off β-globin let7 wt

source_name: HeLa tet off β-globin let7 wt  treated with Doxcycline 6h


title: Liver_Irradiated_mouse478

description: Irradiated


title: Liver_Irradiated_mouse467

description: Irradiated


title: MDAMB231_siZEB2pool

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.

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

data_processing: RMA-normalized expression values as obtained with the affy package of BioConductor. The reported values are on log2-scale.

source_name: MDAMB231 breast cancer cells, siRNA pool, knockdown ZEB2 gene

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: The human MDAMB231 breast carcinoma cell line was obtained from the American Type Tissue Collection. Cells were maintained in Leibovitz-15 with 10% FCS, 200 nM L-glutamine, 100 µg/ml penicillin, and 100 µg/ml streptomycin.

extract_protocol: Qiagen RNeasy Mini kit for total RNA purification according to manufacturers instructions.

treatment_protocol: MDAMB231 cells were transfected with 20 nM siRNA using the Dharmafect transfection reagent following the manufacturer's instructions (Dharmacon). Twenty-four hours later, the cells were extensively washed with PBS, incubated for 48 hours in culture medium and then total RNA was harvested.

tag: organism

value: Homo sapiens

value: MDA-MB231 (ATCC)

value: breast carcinoma cells

tag: knockdown

value: transient


title: Liver_Control_mouse462

description: Control


title: MDAMB231_shZEB2

source_name: MDAMB231 breast cancer cells, shZEB2,  knockdown ZEB2 gene

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 microg total RNA.

treatment_protocol: MDAMB231 cells stably transduced with control (pLVTH) or ZEB2 shRNA were established. Total RNA was harvested of each.

tag: cell type

value: stable


title: Liver_Control_mouse464

description: Control


title: MDAMB231_shRNA_ctrl

source_name: MDAMB231 breast cancer cells, shRNA, control knockdown

tag: cell line


title: Liver_Control_mouse466

description: Control


title: MDAMB231_siLUC_ctrl

source_name: MDAMB231 breast cancer cells, siRNA pool, knockdown luciferase


title: Patient 6 Normal Kidney Tissue No Enzyme Treatment

city: Los Angeles

first: Gangning

last: Liang

state: CA

address: 1441 Eastlake Ave, NOR 7344

department: Urology

institute: University of Southern California

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: BeadStudio software v3.2

label: Cy3, Cy5

source_name: CCTUO11787, Patient 6 Normal Kidney Tissue

label_protocol: Standard Illumina Protocol

growth_protocol: N/A, tissue was harvested directly from patients during nephrectomy

extract_protocol: Phenol/chloroform extraction with ethanol precipitation

treatment_protocol: Tissue was homoegenized and nuclei extracted, then treated as in Pandiyan, et al (2013), Nucleic Acids Research, PMID: 23408854

tag: diagnosis

value: Clear cell renal cell carcinoma (CCRCC)

tag: tissue type

value: adjacent normal tissue


title: Patient 6 ccRCC Tumor Tissue No Enzyme Treatment

source_name: CCTUO11787, Patient 6 ccRCC Tumor Tissue

value: ccRCC tumor


title: non-treatment

city: Niigata

first: yoshikazu

last: mikami

address: 1-757 Asahimatidori, Chuo-ku

department: Division of Microscopic Anatomy

institute: Niigata University Graduate School of Medical and Dental Sciences

description: Control

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 24 μl containing 1μl of 25x Agilent fragmentation buffer and 5μl of 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the microarray (SuperPrint G3 Rat 8x60k ver. 1.0, Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Microarray Scanner.

data_processing: The scanned images were analyzed with Agrent Feature Extention 10.7.3.1 using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Rattus norvegicus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng totalRNA using the Low Input Quick Amp Labeling kit (Agilent Techologies) according to the manufacturer's instructions.

growth_protocol: Cells were maintained in the growth medium [αMEM containing 10% fetal bovine serum (Japan Bioserum Co., Ltd., Tokyo, Japan) and 1% penicillin-streptomycin (Gibco, Grand Island, NY)].

extract_protocol: Total RNA was isolated using RNAiso Plus (Takara Bio, Shiga, Japan) according to the manufacturer’s instructions.

treatment_protocol: Confluent cells in 12-well plates were cultured in mineralization medium [growth media supplemented with 50 mg/mL L-ascorbate phosphate (Sigma Chemical Co., St. Louis, MO) and 1 mM β-glycerophosphate (Sigma)] in the presence or absence of the indicated concentrations of Poly(P).

value: osteoblast

tag: treated with

value: none (control)


title: Patient 4 Normal Kidney Tissue +M.SssI Treatment

source_name: CCTUO11750, Patient 4 Normal Kidney Tissue


title: Patient 4 Normal Kidney Tissue No Enzyme Treatment


title: Patient 5 Normal Kidney Tissue +M.SssI Treatment

source_name: CCTUO11753, Patient 5 Normal Kidney Tissue


title: Patient 6 ccRCC Tumor Tissue +M.SssI Treatment


title: Patient 5 ccRCC Tumor Tissue No Enzyme Treatment

source_name: CCTUO11753, Patient 5 ccRCC Tumor Tissue


title: treatment with high (1mg/ml) concentration of Poly(P)

source_name: ROS17/2.8_high polyphosphates

value: high (1mg/ml) concentration of polyphosphates


title: Patient 6 Normal Kidney Tissue +M.SssI Treatment


title: ANK vs Ø

status: Public on Mar 14 2016

city: Madrid

first: Susana

last: Guerra

address: Calle del Arzobispo Morcillo, 4

department: Department of Preventive Medicine

institute: Universidad Autónoma de Madrid

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol (version 6.5).

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

source_name: Primary human macrophages infected with poxvirus

label_protocol: Two-color microarray-based LowInput QuickAmp Labeling (Agilent)

growth_protocol: Human macrophage were insolated from Buffy coat from donors

extract_protocol: Ultraspect_II RNA (Biotecx, Houston, TX) was used to isolate total RNA

treatment_protocol: Purified human macrophages infected with MVA, ANK, WR, NYBH, NYVAC or CopV (3x10^6 cells/time postinfection; 5 PFU/cell), or mock-infected (MOCK).

tag: poxvirus strain

value: ANK

tag: biological replicate

value: macrophages

value: none (uninfected)

value: macrophage


title: Patient 5 Normal Kidney Tissue No Enzyme Treatment


title: Patient 5 ccRCC Tumor Tissue +M.SssI Treatment


title: Patient 2 ccRCC Tumor Tissue +M.SssI Treatment

source_name: CCTUO11275, Patient 2 ccRCC Tumor Tissue


title: treatment with low (0.01mg/ml) concentration of Poly(P)

source_name: ROS17/2.8_low polyphosphates

value: low (0.01mg/ml) concentration of polyphosphates


title: Patient 3 ccRCC Tumor Tissue +M.SssI Treatment

source_name: CCTUO11685, Patient 3 ccRCC Tumor Tissue


title: Patient 3 Normal Kidney Tissue No Enzyme Treatment

source_name: CCTUO11685, Patient 3 Normal Kidney Tissue


title: Patient 3 ccRCC Tumor Tissue No Enzyme Treatment


title: Patient 2 Normal Kidney Tissue No Enzyme Treatment

source_name: CCTUO11275, Patient 2 Normal Kidney Tissue


title: Patient 4 ccRCC Tumor Tissue +M.SssI Treatment

source_name: CCTUO11750, Patient 4 ccRCC Tumor Tissue


title: Patient 2 ccRCC Tumor Tissue No Enzyme Treatment


title: Patient 3 Normal Kidney Tissue +M.SssI Treatment


title: NYVAC vs Ø

value: NYVAC


title: Patient 1 ccRCC Tumor Tissue +M.SssI Treatment

source_name: CCTUO11024, Patient 1 ccRCC Tumor Tissue


title: Patient 4 ccRCC Tumor Tissue No Enzyme Treatment


title: Patient 1 ccRCC Tumor Tissue No Enzyme Treatment


title: Patient 2 Normal Kidney Tissue +M.SssI Treatment


title: Medulloblastoma_tumor_BID_MK4101_treated_80mpk_36h_rep4

city: Roma

first: Gessica

last: Filocamo

address: Via Savona 6

country: Italy

institute: Exiris s.r.l.

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
BID_80mpk_36h_4

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260). Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin. After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency. The labeled molecules are biotinylated-cRNA.

growth_protocol: Allograft of medulloblastoma into CD1 nude mice

extract_protocol: Total RNA was extracted in Eppendorf tubes using the Qiagen Rneasy mini kit.

treatment_protocol: subministration of the indicated amount of MK4101 or vehicle treatment

tag: host strain

value: nude CD1

value: allograft of medulloblastoma from Ptch1+/- mice

value: multiple dose (BID)

tag: tissue

value: Medulloblastoma


title: WR vs Ø

value: WR


title: Medulloblastoma_tumor_BID_MK4101_treated_80mpk_36h_rep2

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
BID_80mpk_36h_2


title: Medulloblastoma_tumor_BID_MK4101_treated_80mpk_36h_rep3

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
BID_80mpk_36h_3


title: WR vs CoV

value: CoV


title: MVA vs Ø

value: MVA


title: NYVAC vs WR


title: Patient 1 Normal Kidney Tissue +M.SssI Treatment

source_name: CCTUO11024, Patient 1 Normal Kidney Tissue

value: Clear cell renal cell carcinoma (CCRCC)

value: adjacent normal tissue


title: Medulloblastoma_tumor_BID_vehicle_treated_36h_rep5

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
BID_vehicle_36h_5

value: vehicle 36h


title: MVA vs NYVAC


title: Medulloblastoma_tumor_BID_vehicle_treated_24h_rep4

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
BID_vehicle_24h_4

value: vehicle 24h


title: CoV vs BH

value: BH


title: Medulloblastoma_tumor_BID_vehicle_treated_36h_rep2

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
BID_vehicle_36h_2


title: Medulloblastoma_tumor_BID_vehicle_treated_36h_rep1

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
BID_vehicle_36h_1


title: BH vs Ø

value: macrophages


title: Medulloblastoma_tumor_BID_vehicle_treated_36h_rep3

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
BID_vehicle_36h_3


title: Medulloblastoma_tumor_BID_vehicle_treated_36h_rep4

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
BID_vehicle_36h_4


title: BH vs ANK

value: ANK


title: Patient 1 Normal Kidney Tissue No Enzyme Treatment


title: Medulloblastoma_tumor_BID_vehicle_treated_24h_rep2

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
BID_vehicle_24h_2


title: Medulloblastoma_tumor_BID_MK4101_treated_80mpk_36h_rep1

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
BID_80mpk_36h_1


title: CoV vs Ø

value: none (uninfected)

value: macrophage


title: Medulloblastoma_tumor_BID_MK4101_treated_80mpk_24h_rep1

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
BID_80mpk_24h


title: Medulloblastoma_tumor_BID_vehicle_treated_24h_rep1

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
BID_vehicle_24h_1


title: Medulloblastoma_tumor_BID_vehicle_treated_24h_rep3

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
BID_vehicle_24h_3


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_36h_rep4

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_36h_4

value: single dose (QD)


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_36h_rep3

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_36h_3

value: nude CD1


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_36h_rep2

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_36h_2

value: allograft of medulloblastoma from Ptch1+/- mice


title: Medulloblastoma_tumor_QD_vehicle_treated_36h_rep3

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_36h_3


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_24h_rep3

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_24h_3


title: ANK vs MVA


title: Medulloblastoma_tumor_QD_MK4101_treated_40mpk_24h_rep1

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_40mpk_24h_1


title: Medulloblastoma_tumor_QD_MK4101_treated_40mpk_24h_rep4

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_40mpk_24h_4


title: Medulloblastoma_tumor_QD_MK4101_treated_40mpk_36h_rep3

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_40mpk_36h_3


title: Medulloblastoma_tumor_QD_vehicle_treated_24h_rep5

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_24h_5


title: Medulloblastoma_tumor_QD_MK4101_treated_40mpk_36h_rep2

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_40mpk_36h_2


title: Medulloblastoma_tumor_QD_vehicle_treated_24h_rep4

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_24h_4


title: Medulloblastoma_tumor_QD_MK4101_treated_40mpk_24h_rep3

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_40mpk_24h_3


title: Medulloblastoma_tumor_QD_vehicle_treated_24h_rep1

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_24h_1


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_24h_rep1

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_24h_1


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_36h_rep1

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_36h_1


title: Medulloblastoma_tumor_QD_vehicle_treated_36h_rep2

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_36h_2


title: Medulloblastoma_tumor_QD_MK4101_treated_40mpk_36h_rep1

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_40mpk_36h_1


title: Medulloblastoma_tumor_QD_MK4101_treated_40mpk_24h_rep2

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_40mpk_24h_2


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_24h_rep2

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_24h_2


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_12h_rep3

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_12h_3


title: Medulloblastoma_tumor_QD_vehicle_treated_24h_rep2

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_24h_2


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_12h_rep1

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_12h_1


title: Medulloblastoma_tumor_QD_vehicle_treated_36h_rep1

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_36h_1


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_12h_rep4

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_12h_4


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_12h_rep2

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_12h_2


title: Medulloblastoma_tumor_QD_MK4101_treated_40mpk_12h_rep2

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_40mpk_12h_2


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_24h_rep4

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_24h_4


title: Medulloblastoma_tumor_QD_MK4101_treated_40mpk_12h_rep3

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_40mpk_12h_3


title: Medulloblastoma_tumor_QD_vehicle_treated_24h_rep3

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_24h_3


title: Medulloblastoma_tumor_QD_MK4101_treated_40mpk_12h_rep1

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_40mpk_12h_1


title: Medulloblastoma_tumor_QD_vehicle_treated_6h_rep5

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_6h_5

value: vehicle for 6hrs


title: Medulloblastoma_tumor_QD_vehicle_treated_12h_rep2

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_12h_2

value: vehicle 12h

value: Medulloblastoma


title: Medulloblastoma_tumor_QD_vehicle_treated_12h_rep1

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_12h_1


title: Medulloblastoma_tumor_QD_vehicle_treated_12h_rep4

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_12h_4


title: Medulloblastoma_tumor_QD_MK4101_treated_40mpk_6h_rep5

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_40mpk_6h_5

value: MK4101 40mpk for 6hrs


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_6h_rep3

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_6h_3

value: MK4101 80mpk for 6hrs


title: Medulloblastoma_tumor_QD_vehicle_treated_6h_rep3

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_6h_3


title: Medulloblastoma_tumor_QD_vehicle_treated_6h_rep4

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_6h_4


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_1h_rep5

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_1h_5

value: MK4101 80mpk for 1hr


title: Medulloblastoma_tumor_QD_MK4101_treated_40mpk_1h_rep4

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_40mpk_1h_4

value: MK4101 40mpk for 1hr


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_1h_rep3

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_1h_3


title: Medulloblastoma_tumor_QD_MK4101_treated_40mpk_6h_rep3

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_40mpk_6h_3


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_1h_rep4

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_1h_4


title: Medulloblastoma_tumor_QD_MK4101_treated_40mpk_6h_rep1

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_40mpk_6h_1


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_6h_rep1

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_6h_1


title: Medulloblastoma_tumor_QD_vehicle_treated_6h_rep2

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_6h_2


title: Medulloblastoma_tumor_QD_MK4101_treated_40mpk_6h_rep4

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_40mpk_6h_4


title: Medulloblastoma_tumor_QD_vehicle_treated_6h_rep1

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_6h_1


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_1h_rep2

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_1h_2


title: Medulloblastoma_tumor_QD_vehicle_treated_12h_rep3

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_12h_3


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_6h_rep2

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_6h_2


title: Medulloblastoma_tumor_QD_MK4101_treated_40mpk_1h_rep3

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_40mpk_1h_3


title: Medulloblastoma_tumor_QD_MK4101_treated_40mpk_6h_rep2

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_40mpk_6h_2


title: Medulloblastoma_tumor_QD_MK4101_treated_80mpk_1h_rep1

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_80mpk_1h_1


title: Medulloblastoma_tumor_QD_MK4101_treated_40mpk_1h_rep1

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_40mpk_1h_1


title: Medulloblastoma_tumor_QD_MK4101_treated_40mpk_1h_rep2

description:
gene expression data of medulloblastoma allografts following treatment with a SHH inhibitor at the indicated time
QD_40mpk_1h_2


title: Medulloblastoma_tumor_QD_vehicle_treated_1h_rep5

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_1h_5

value: vehicle for 1hr


title: Medulloblastoma_tumor_QD_vehicle_treated_1h_rep4

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_1h_4


title: Medulloblastoma_tumor_QD_vehicle_treated_1h_rep3

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_1h_3


title: LungTumorNodule_mouse732_Kras37bpMarkerGenotype_A_homozygous_rep1

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

description: sample name: 732

hyb_protocol: Fluorescent dye-labeled cRNA was hybridized to SurePrint G3 Mouse Exon 4x180K arrays (Agilent); hybridization and washing were performed on Agilent’s microarray platform, according to standard protocols.

scan_protocol: Microarray images were acquired using an Agilent DNA microarray scanner.

data_processing: Raw data were generated using Agilent Feature Extraction software. Raw median probe intensities were pre-processed using the limma (Ritchie, 2015) package of the R/Bioconductor project. A batch effect was present as samples had been assayed in two different experiments (95 samples in batch 1 and 48 samples in batch 2). Thus, raw data from each batch of arrays were log2-transformed and normalized independently using quantile normalization. The ComBat method (Johnson, 2007), implemented in the sva R package (Leek, 2012), was then applied to remove the batch effect from normalized data. After ComBat correction expression data from replicated probes were summarized calculating the mean expression.

label_protocol: Total RNA was amplified using the Low Input Quick Amp WT Labeling kit, according to the manufacturer’s instructions (Agilent Technologies, Santa Clara, USA). 100 ng of total RNA was reverse-transcribed into double-stranded cDNA, which was translated into cRNA in the presence of Cy3-dCTP and amplified by T7 RNA polymerase.

growth_protocol: Mice were maintained at the animal facility of Fondazione IRCCS Istituto Nazionale dei Tumori. Animal experiments were authorized by the Institute Animal Experimentation Ethical Committee (CESA) in March 2012, according to the Italian law DL116/92), and performed in accordance to institutional guidelines

extract_protocol: Total RNA was extracted from lung tumor specimens using RNeasy Midi Kit (Qiagen), purified with RNeasy MinElute Cleanup (Qiagen), and quantified by spectrophotometry (ND-1000 spectrophotometer, NanoDrop, Wilmington, DE, USA). RNA integrity was verified using the RNA 6000 Nano Assay Kit (Agilent Technologies, Palo Alto, CA, USA); the mean RIN value was 8.9 (SD = 0.8; range, 6.7 to 9.9).

treatment_protocol: At 4 weeks of age, 143 male ABF4 mice were treated with a single intraperitoneal injection of urethane (1 g/kg body weight) according to a standard procedure for inducing the development of lung tumors (Shimkin, 1975).

tag: strain background

value: A/J X C57BL/6

tag: strain

value: offspring bred to the 4th generation (ABF4)

tag: gender

value: male

tag: age

value: 40 wks

tag: number of lung tumors

tag: kras37bp marker genotype

value: lung tumor nodule

tag: batch


title: LungTumorNodule_mouse654_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 654


title: LungTumorNodule_mouse823_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 823


title: LungTumorNodule_mouse694_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 694


title: LungTumorNodule_mouse974_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 974


title: PBMC_s021_24hr

city: Bethesda

first: Yuri

last: Kotliarov

address: 4 Memorial Dr., room 134

department: CHI

institute: NHLBI

description: Gene expression data from PBMC extracted from individual s021 at 24 hours after 250 mg of steroid administration

hyb_protocol: Labeled cDNA were hybridized to Human 1.0 ST GeneChip arrays (Affymetrix) and stained on a Genechip Fluidics Station 450 (Affymetrix), according to the respective manufacturers' instructions.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The raw intensities of gene probesets in the CEL files were processed using Affymetrix Power Tools. The apt-probeset_summarize script was used for background correction and normalization (RMA with sketch, quantile normalization). The Bioconductor package arrayQualityMetrics was used to assess the quality of the microarray data.

source_name: Individual s021 at 24 hours

label_protocol: Fragmented single-stranded sense cDNA were terminally labeled with biotin according to the standard Affymetrix protocol.

growth_protocol: Blood specimens were collected in heparinized syringes and peripheral blood mononuclear cells (PBMC) were isolated using Leucosep tubes with Ficoll-Paque Plus density gradient media and centrifugation. Fresh isolated PBMC were directly lysed in 700ul of Qiazol and stored at -80oC till isolation.

extract_protocol: Total RNA was isolated from freshly isolated PBMC using miRNeasy kit (Qiagen) according to the manufacturer’s instructions and eluted in 40ul of elution buffer with the addition of 1ul of RNase inhibitor (Invitrogen).

treatment_protocol: Eligible subjects were admitted to the NIH Clinical Center, a heparin lock was placed in the arm, and a minimum of one hour elapsed before the first blood draw to minimize any effect of a cortisol response due to I.V. insertion. Immediately after baseline phlebotomy the subjects were administered a single dose of intravenous (IV) hydrocortisone at either 50 mg or 250 mg concentrations.

value: PBMC

tag: dose

value: 250 mg hydrocortisone

tag: time

tag: individual

value: female

tag: ethnicity

value: Asian


title: PBMC_s021_12hr

description: Gene expression data from PBMC extracted from individual s021 at 12 hours after 250 mg of steroid administration

source_name: Individual s021 at 12 hours


title: PBMC_s021_1hr

description: Gene expression data from PBMC extracted from individual s021 at 1 hour after 250 mg of steroid administration

source_name: Individual s021 at 1 hour


title: LungTumorNodule_mouse661_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 661


title: PBMC_s021_8hr

description: Gene expression data from PBMC extracted from individual s021 at 8 hours after 250 mg of steroid administration

source_name: Individual s021 at 8 hours


title: Medulloblastoma_tumor_QD_vehicle_treated_1h_rep2

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_1h_2

value: nude CD1

tag: tissue type

value: allograft of medulloblastoma from Ptch1+/- mice

value: single dose (QD)


title: LungTumorNodule_mouse628_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 628


title: LungTumorNodule_mouse767_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 767


title: PBMC_s021_4hr

description: Gene expression data from PBMC extracted from individual s021 at 4 hours after 250 mg of steroid administration

source_name: Individual s021 at 4 hours


title: LungTumorNodule_mouse714_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 714


title: LungTumorNodule_mouse671_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 671


title: LungTumorNodule_mouse789_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 789


title: LungTumorNodule_mouse638_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 638


title: LungTumorNodule_mouse1077_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 1077


title: LungTumorNodule_mouse644_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 644


title: LungTumorNodule_mouse545_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 545