title: genomic DNA from whole blood of subject Sample29

source_name: Whole Blood

tag: tissue

value: female

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

value: Control

tag: family number

tag: relation to proband


title: genomic DNA from whole blood of subject Sample30

status: Public on May 28 2015

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

country: USA

institute: University of California, Los Angeles

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:
BeadStudio software v3.2.
Unmethylated and methylated signal intensities and detection p values in Series supplementary file

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from EDTA tubes using the RecoverEase DNA Isolation Kit.

value: whole blood

tag: Sex


title: HFC_Male_LKO_rep2

type: RNA

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

description: Gene expression data from a male LKO mouse X518 on a high-fat diet with cholesterol

hyb_protocol: 150 ng of total RNA was used for hybridization of Affymetrix Gene Chip Mouse 1.0 ST Arrays according to the manufacturer’s instructions (Genechip® Whole Transcript (wt) Sense Ttarget Labeling Assay Manual – P/N 701880 Rev 4). Labeled samples were injected into Affymetrix arrays and hybridized at 45°C and 60 rpm for 16 h in an Affymetrix Hybridization Oven. Arrays were stained and washed in the Affymetrix GeneChip Fluidic Station 450.

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

data_processing:
GeneChip data was processed and analyzed using R/Bioconductor packages. Data were summarized (w.r.t. core meta-probeset annotations and AFFX control probes, probes grouped to the level of transcripts) and quantile-normalized (background computed from antigenomic probes) using RMA algorithm from XPS package.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Male LKO mouse X518 on a high-fat diet with cholesterol

label_protocol: Total RNA was used to synthesize double-stranded cDNA with random hexamer primers tagged with a T7 promoter sequence. The double-stranded cDNA was subsequently used as a template and amplified by T7 RNA polymerase producing cRNA. In the second cycle of cDNA synthesis, random hexamers were used to prime reverse transcription of the cRNA and dUTP was incorporated to produce single-stranded DNA. This single-stranded DNA sample were then treated with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognized the unnatural dUTP residues and broke the DNA strand. DNA was labeled by terminal eoxynucleotidyl transferase (TdT) with the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Cyp51 KO (LKO) mice and their control littermates (LWT) were bred at the Medical Experimental Centre, Faculty of Medicine, University of Ljubljana, Slovenia and maintained in a temperature and humidity controlled environment under 12h light/dark cycle (lights were on from 7.00 am to 7.00 pm). Animals had ad libitum access to food and acidified tap water (pH = 3).

extract_protocol: Mice were euthanized after a 5 h fast with cervical dislocation at the same time of the light period (11.30 am – 3.00 pm) in order to avoid diurnal variability as much as possible. Liver was removed, weighed, cut to thin slices and snap-frozen in liquid nitrogen and stored at - 80° C for subsequent analysis. Liver samples were first pulverized and then isolated using QuickGene Tissue Kit S II and QuickGene-810 (Fujifilm, Singapore) according to the manufacturer’s instructions. RNA quantity and quality were assessed with NanoDrop and Agilent 2100 Bioanalyzer instruments. All samples isolated fulfilled the minimum requirements (OD260/280 and OD230/280 > 1.8) for microarray hybridization.

treatment_protocol: After the weaning period, 3-week LKO and LWT mice of both sexes were randomly assigned to one of the three diets: standard laboratory chow (1324, Altromin, Lage, Germany) regarded as a low-fat no-cholesterol diet (LFnC); high-fat diet without cholesterol (HFnC) (D12108C, Research Diets, Inc., New Brunswick, NJ, USA) and high-fat diet with 1.25% (w/w) of cholesterol (HFC) (D12106C, Research Diets, Inc., New Brunswick, NJ, USA). A total of 136 mice (9 to 13 animals per group) were fed the specified diets for 16 weeks.

tag: strain

value: liver

tag: diet

value: HFC

tag: genotype

value: Cyp51 KO LKO

value: M

tag: batch

tag: animal

tag: treatment

value: high-fat diet with cholesterol


title: 24hrs_NoxAB_WT_C

city: Ottawa

first: Thérèse

last: Ouellet

state: ON

address: 960 Carling Ave, room 2091

department: Eastern Cereal and Oilseed Research Centre

country: Canada

institute: Agriculture and Agri-Food Canada

description:
Roblin, 24 hrs after WT inoculation in spk 2, which followed NoxABΔ inoculation in spk 0, rep C
Gene expression data from Roblin spikelet 2, after inoculation of Fg NoxABΔ in spk 0 then Fg WT in spk 2, 24 hrs after inoculation 2

hyb_protocol: According to Affymetrix instructions for the GeneChip® 3' IVT Express Kit. All samples were processed in one experimental batch.

data_processing: The probe-level data for the whole profiling experiment were assembled into one dataset using the Just RMA protocol implemented in the software FlexArray 1.6.1 (Genome Quebec, Montreal, Canada) using the default parameters.

organism: Triticum aestivum

source_name: Roblin, spk 0 NoxABΔ, spk 2 WT for 24 hrs

growth_protocol: Plants were grown in growth cabinets at 20 C/16 hrs daylight; 16 C/8 hrs night until heads reached mid anthesis; then they were moved to the misting room.

extract_protocol: Total RNA from each sample was isolated using a modified version of the Trizol method (Invitrogen Life Technologh, ON, Canada).  The RNA samples were treated with an RNase-free DNase (Qiagen, Mississauga, Canada) and cleaned up using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Wheat heads at mid-anthesis were inoculated as follow: 10 µl of either water (mock inoculation) or a 100,000 spores/ml suspension of the Fusarium graminearum mutant strain NoxABΔ (DAOM 239571) or Tri6Δ (DAOM 237993) was point-inoculated into each of two basal florets of one developed spikelet (spk 0) of 16 wheat heads.  The inoculated plants were mist-irrigated for 10 second intervals every 15 minutes for 24 hours to maintain high humidity, at a temperature of 25 oC. After 24 hrs of misting, a spikelet (spk 2) close to spk 0 was inoculated in the same manner with either water or  a 100,000 spores/ml suspension of the pathogenic Fusarium graminearum strain DAOM 233423. Eight treated heads were used for each three biological replicates, and inoculated spikelets spk 2 were sampled at 8 and 24 hours after the second inoculation.  The sampled tissues were immediately frozen in liquid nitrogen and stored at -80 C until used.

value: spring wheat cv Roblin

value: inoculated spikelet spk 2

tag: tissue age

value: heads after mid-anthesis

tag: inoculation treatment 1 on spk 0

value: Fg NoxABΔ

tag: inoculation treatment 2 on spk 2

value: Fg WT

tag: hours after inoculation 2


title: Bladder tumor UC_0717_1

city: Lund

first: Mattias

last: Aine

address: Klinikgatan 28

department: Oncology

country: Sweden

institute: Lund University

hyb_protocol: According to manufacturers specifications at the Nimblegen genomics facility

data_processing: Control hybridization probes as well as all probes not mapping to hg18 autosomes were removed and raw intensities were log2 transformed, the resulting individual dye channels were lowess normalized with respect to probe GC content, ratios were formed by subtracting the Cy3 channel intensities from the Cy5 intensities and the resulting matrix was quantile normalized. Replicate probes were median merged and a PCA-based method for removal of technical variation was applied (Lauss et al. 2013, Cancer informatics).

source_name: Input DNA

growth_protocol: Primary tumor DNA

extract_protocol: Genomic DNA was extracted using DNeasy/Allprep (QIAGEN)  spin columns acording to manufacturers specifications, 1250ng genomic DNA was subjected to sonication followed by MeDIP (Diagenode), WGA whole genome amplification (Sigma-Aldrich) and WGA2 re-amplification (Sigma-Aldrich), yielding sufficient amounts of DNA for hybridization to Nimblegen arrays. All sample and input reactions were treated in parallel and (where possible) subjected to the same protocol steps.

treatment_protocol: MeDIP (WGA)

tag: hoglund lab uid

tag: tissue

value: Bladder tumor

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

value: AllPrep

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation

source_name: MeDIP DNA

treatment_protocol: Input Control (WGA)


title: Bladder tumor UC_0162_1

scan_protocol: According to manufacturers specifications at the Nimblegen genomics facility

value: DNeasy

value: Ta

tag: Sex


title: 24hrs_NoxAB_WT_B

description:
Roblin, 24 hrs after WT inoculation in spk 2, which followed NoxABΔ inoculation in spk 0, rep B
Gene expression data from Roblin spikelet 2, after inoculation of Fg NoxABΔ in spk 0 then Fg WT in spk 2, 24 hrs after inoculation 2

scan_protocol: According to Affymetrix instructions for the GeneChip® 3' IVT Express Kit. All samples were processed in one experimental batch.

tag: genotype

tag: tissue age

tag: inoculation treatment 1 on spk 0

tag: inoculation treatment 2 on spk 2


title: genomic DNA from whole blood of subject Sample28

tag: tissue

value: female

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: 24hrs_NoxAB_WT_A

description:
Roblin, 24 hrs after WT inoculation in spk 2, which followed NoxABΔ inoculation in spk 0, rep A
Gene expression data from Roblin spikelet 2, after inoculation of Fg NoxABΔ in spk 0 then Fg WT in spk 2, 24 hrs after inoculation 2

label_protocol: According to Affymetrix instructions for the GeneChip® 3' IVT Express Kit. All samples were processed in one experimental batch.

tag: hours after inoculation 2


title: Bladder tumor UC_0766_1

label_protocol: According to manufacturers specifications at the Nimblegen genomics facility

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation


title: HFnC_Male_LKO_rep2

institute: Faculty of Medicine, University of Ljubljana

description: Gene expression data from a male LKO mouse X335 on a high-fat no-cholesterol diet

source_name: Male LKO mouse X335 on a high-fat no-cholesterol diet

tag: strain

tag: tissue

tag: diet

value: HFnC

tag: genotype

tag: Sex

tag: batch

tag: animal

tag: treatment

value: high-fat no-cholesterol diet


title: HFC_Female_LWT_rep2

description: Gene expression data from a female LWT mouse X114 on a high-fat diet with cholesterol

source_name: Female LWT mouse X114 on a high-fat diet with cholesterol

value: liver

value: LWT

value: F


title: 24hrs_NoxAB_dH20_B

description:
Roblin, 24 hrs after water inoculation in spk 2, which followed NoxABΔ inoculation in spk 0, rep B
Gene expression data from Roblin spikelet 2, after inoculation of Fg NoxABΔ in spk 0 then water in spk 2, 24 hrs after inoculation 2

source_name: Roblin, spk 0 NoxABΔ, spk 2 water for 24 hrs

tag: tissue age

tag: inoculation treatment 1 on spk 0

tag: inoculation treatment 2 on spk 2

value: water

tag: hours after inoculation 2


title: Bladder tumor UC_0600_1

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: tp53 mutation


title: Bladder tumor UC_0704_1

tag: tissue

value: B

tag: who1999 stage simple

tag: who 1999 grade

tag: Sex

value: M

tag: fgfr3 mutation

tag: pik3ca mutation


title: HFC_Female_LKO_rep2

description: Gene expression data from a female LKO mouse X615 on a high-fat diet with cholesterol

source_name: Female LKO mouse X615 on a high-fat diet with cholesterol

tag: strain

tag: diet

value: HFC

tag: genotype

value: Cyp51 KO LKO

tag: batch

tag: animal

tag: treatment

value: high-fat diet with cholesterol


title: genomic DNA from whole blood of subject Sample25

value: whole blood

value: male

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

value: Control

tag: family number

tag: relation to proband


title: Bladder tumor UC_0523_1

tag: hoglund lab uid

tag: tissue

value: Bladder tumor

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

value: AllPrep

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

value: Tx

tag: who 1999 grade

tag: Sex

tag: tp53 mutation


title: 24hH20_WT-C

description:
Roblin, 24 hrs after WT inoculation in spk 2, which followed water inoculation in spk 0, rep C
Gene expression data from Roblin spikelet 2, after inoculation of water in spk 0 then Fg WT in spk 2, 24 hrs after inoculation 2

source_name: Roblin, spk 0 water, spk 2 WT for 24 hrs

tag: genotype

value: spring wheat cv Roblin

value: inoculated spikelet spk 2

tag: tissue age

value: heads after mid-anthesis

tag: inoculation treatment 1 on spk 0

tag: inoculation treatment 2 on spk 2

value: Fg WT

tag: hours after inoculation 2


title: genomic DNA from whole blood of subject Sample23

tag: tissue

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: HFnC_Male_LWT_rep2

description: Gene expression data from a male LWT mouse X231 on a high-fat no-cholesterol diet

source_name: Male LWT mouse X231 on a high-fat no-cholesterol diet

tag: strain

value: liver

tag: diet

value: HFnC

value: LWT

tag: batch

tag: animal

tag: treatment

value: high-fat no-cholesterol diet


title: Bladder tumor UC_0549_1

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: Sex

value: M

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: genomic DNA from whole blood of subject Sample26

tag: tissue

value: female

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: 24hH20_WT-B

description:
Roblin, 24 hrs after WT inoculation in spk 2, which followed water inoculation in spk 0, rep B
Gene expression data from Roblin spikelet 2, after inoculation of water in spk 0 then Fg WT in spk 2, 24 hrs after inoculation 2

tag: genotype

tag: tissue age

tag: inoculation treatment 1 on spk 0

value: water

tag: inoculation treatment 2 on spk 2

tag: hours after inoculation 2


title: 24hrs_NoxAB_dH20_C

description:
Roblin, 24 hrs after water inoculation in spk 2, which followed NoxABΔ inoculation in spk 0, rep C
Gene expression data from Roblin spikelet 2, after inoculation of Fg NoxABΔ in spk 0 then water in spk 2, 24 hrs after inoculation 2

value: Fg NoxABΔ


title: genomic DNA from whole blood of subject Sample27

value: whole blood

tag: Sex


title: LFnC_Male_LKO_rep2

description: Gene expression data from a male LKO mouse X207 on a low-fat no-cholesterol diet

source_name: Male LKO mouse X207 on a low-fat no-cholesterol diet

tag: strain

tag: diet

value: LFnC

value: Cyp51 KO LKO

tag: batch

tag: animal

tag: treatment

value: low-fat no-cholesterol diet


title: 24hrs_NoxAB_dH20_A

description:
Roblin, 24 hrs after water inoculation in spk 2, which followed NoxABΔ inoculation in spk 0, rep A
Gene expression data from Roblin spikelet 2, after inoculation of Fg NoxABΔ in spk 0 then water in spk 2, 24 hrs after inoculation 2

tag: tissue


title: 24hH20_WT-A

description:
Roblin, 24 hrs after WT inoculation in spk 2, which followed water inoculation in spk 0, rep A
Gene expression data from Roblin spikelet 2, after inoculation of water in spk 0 then Fg WT in spk 2, 24 hrs after inoculation 2


title: 24hH20_H20-C

description:
Roblin, 24 hrs after water inoculation in spk 2, which followed water inoculation in spk 0, rep C
Gene expression data from Roblin spikelet 2, after inoculation of water in spk 0 then water in spk 2, 24 hrs after inoculation 2

source_name: Roblin, spk 0 water, spk 2 water for 24 hrs


title: genomic DNA from whole blood of subject Sample22

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

value: Control


title: HFnC_Female_LKO_rep2

description: Gene expression data from a female LKO mouse X428 on a high-fat no-cholesterol diet

source_name: Female LKO mouse X428 on a high-fat no-cholesterol diet

value: F


title: HFnC_Female_LWT_rep2

description: Gene expression data from a female LWT mouse X534 on a high-fat no-cholesterol diet

source_name: Female LWT mouse X534 on a high-fat no-cholesterol diet


title: Bladder tumor UC_0115_1

tag: hoglund lab uid

value: Bladder tumor

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

value: DNeasy

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: LFnC_Female_LKO_rep2

description: Gene expression data from a female LKO mouse X401 on a low-fat no-cholesterol diet

source_name: Female LKO mouse X401 on a low-fat no-cholesterol diet

tag: strain

tag: tissue

tag: diet

tag: genotype

tag: Sex

tag: batch

tag: animal

tag: treatment


title: genomic DNA from whole blood of subject Sample20

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: 24hH20_H20-A

description:
Roblin, 24 hrs after water inoculation in spk 2, which followed water inoculation in spk 0, rep A
Gene expression data from Roblin spikelet 2, after inoculation of water in spk 0 then water in spk 2, 24 hrs after inoculation 2

value: spring wheat cv Roblin

value: inoculated spikelet spk 2

tag: tissue age

value: heads after mid-anthesis

tag: inoculation treatment 1 on spk 0

tag: inoculation treatment 2 on spk 2

tag: hours after inoculation 2


title: HFC_Male_LWT_rep2

description: Gene expression data from a male LWT mouse X420 on a high-fat diet with cholesterol

source_name: Male LWT mouse X420 on a high-fat diet with cholesterol

tag: strain

tag: tissue

value: liver

tag: diet

value: HFC

tag: genotype

value: LWT

value: high-fat diet with cholesterol


title: LFnC_Female_LWT_rep2

description: Gene expression data from a female LWT mouse X109 on a low-fat no-cholesterol diet

source_name: Female LWT mouse X109 on a low-fat no-cholesterol diet

tag: Sex

tag: batch

tag: animal

tag: treatment


title: 24hH20_H20-B

description:
Roblin, 24 hrs after water inoculation in spk 2, which followed water inoculation in spk 0, rep B
Gene expression data from Roblin spikelet 2, after inoculation of water in spk 0 then water in spk 2, 24 hrs after inoculation 2

value: water


title: LFnC_Male_LWT_rep2

description: Gene expression data from a male LWT mouse X510 on a low-fat no-cholesterol diet

source_name: Male LWT mouse X510 on a low-fat no-cholesterol diet

value: M


title: Bladder tumor UC_0211_2

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

value: Ta

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: genomic DNA from whole blood of subject Sample17

source_name: Whole Blood

tag: tissue

value: whole blood

tag: Sex

value: male

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: NIH3T3_adipo diff med 2 hours

city: Nagoya

first: Atsushi

last: Enomoto

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Pathology

country: Japan

institute: Nagoya University Graduate School of Medicine

description:
NIH-3T3 cells cultured to overconfluency, followed by stimulation by adipogenic differentiation medium for 2 hours
AR0088_06

hyb_protocol: Cy3-labelled cRNA fragmentation reaction ahd hybridization to Agilent Whole Mouse Genome Microarray 4 x 44K were performed by Dragon Genomics Center (Takara Bio, Yokkaichi, Japan).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with the Agilent Feature Extraction software ver. 9.5 (Agilent).

source_name: NIH-3T3 cells, overconfluency, followed by stimulation by adipogenic differentiation medium for 2 hours

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was prepared using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer's recommendations. RNA quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: cell line

value: NIH-3T3 fibroblasts

tag: confluency

value: Overconfluent

tag: treatment


title: NIH3T3_overconfluent (100% + 3 days)

description:
NIH-3T3 cells cultured to 100% confluency, followed by additional culture for 3 days
AR0088_05

source_name: NIH-3T3 cells, 100% confluency, followed by additional culture for 3 days

value: additional culture for 3 days


title: genomic DNA from whole blood of subject Sample21

value: female

value: Control


title: genomic DNA from whole blood of subject Sample19


title: HFC_Male_LKO_rep1

description: Gene expression data from a male LKO mouse X311 on a high-fat diet with cholesterol

source_name: Male LKO mouse X311 on a high-fat diet with cholesterol

tag: strain

tag: diet

tag: genotype

value: Cyp51 KO LKO

tag: batch

tag: animal


title: Bladder tumor UC_0582_1

source_name: Input DNA

tag: hoglund lab uid

tag: tissue

value: Bladder tumor

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

value: AllPrep

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: Sex

value: F

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation

source_name: MeDIP DNA


title: Bladder tumor UC_0615_1


title: NIH3T3_80%

description:
NIH-3T3 cells cultured to 80% confluency
AR0088_04

source_name: NIH-3T3 cells, 80% confluency

tag: cell line

tag: confluency


title: genomic DNA from whole blood of subject Sample16

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: 3T3-L1_adipo diff med 2 hours

description:
3T3-L1 cells cultured to overconfluency, followed by stimulation by adipogenic differentiation medium for 2 hours
AR0088_03

source_name: 3T3-L1 cells, overconfluency, followed by stimulation by adipogenic differentiation medium for 2 hours

value: 3T3-L1 fibroblasts

tag: treatment


title: Bladder tumor UC_0524_1

tag: hoglund lab uid

tag: tissue

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple


title: HFnC_Male_LKO_rep1

description: Gene expression data from a male LKO mouse X036 on a high-fat no-cholesterol diet

source_name: Male LKO mouse X036 on a high-fat no-cholesterol diet

tag: strain

value: liver

tag: diet

value: HFnC

tag: genotype

tag: Sex

tag: batch

tag: animal

value: high-fat no-cholesterol diet


title: genomic DNA from whole blood of subject Sample13

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: HFC_Female_LKO_rep1

description: Gene expression data from a female LKO mouse X122 on a high-fat diet with cholesterol

source_name: Female LKO mouse X122 on a high-fat diet with cholesterol

tag: tissue

value: HFC

tag: treatment

value: high-fat diet with cholesterol


title: HFC_Male_LWT_rep1

description: Gene expression data from a male LWT mouse X121 on a high-fat diet with cholesterol

source_name: Male LWT mouse X121 on a high-fat diet with cholesterol

value: LWT

value: M


title: HFC_Female_LWT_rep1

description: Gene expression data from a female LWT mouse X023 on a high-fat diet with cholesterol

source_name: Female LWT mouse X023 on a high-fat diet with cholesterol


title: Bladder tumor UC_0230_1

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

value: D

tag: dna extraction method

value: DNeasy

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: Bladder tumor UC_0544_1

value: B

value: Ta

tag: Sex


title: 3T3-L1_overconfluent (100% + 3 days)

description:
3T3-L1 cells cultured to 100% confluency, followed by additional culture for 3 days
AR0088_02

source_name: 3T3-L1 cells,100% confluency, followed by additional culture for 3 days

tag: cell line

tag: confluency

value: Overconfluent

value: additional culture for 3 days


title: 3T3-L1_80%

description:
3T3-L1 cells cultured to 80% confluency
AR0088_01

source_name: 3T3-L1 cells, 80% confluency


title: HFnC_Male_LWT_rep1

description: Gene expression data from a male LWT mouse X128 on a high-fat no-cholesterol diet

source_name: Male LWT mouse X128 on a high-fat no-cholesterol diet

tag: strain

tag: tissue

tag: diet

tag: genotype

tag: batch

tag: animal

tag: treatment


title: HFnC_Female_LKO_rep1

description: Gene expression data from a female LKO mouse X039 on a high-fat no-cholesterol diet

source_name: Female LKO mouse X039 on a high-fat no-cholesterol diet

value: Cyp51 KO LKO


title: LFnC_Male_LKO_rep1

description: Gene expression data from a male LKO mouse X008 on a low-fat no-cholesterol diet

source_name: Male LKO mouse X008 on a low-fat no-cholesterol diet

value: LFnC

value: low-fat no-cholesterol diet


title: HFnC_Female_LWT_rep1

description: Gene expression data from a female LWT mouse X041 on a high-fat no-cholesterol diet

source_name: Female LWT mouse X041 on a high-fat no-cholesterol diet

value: F


title: genomic DNA from whole blood of subject Sample14

source_name: Whole Blood

value: whole blood

value: male

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

value: Control

tag: family number

tag: relation to proband


title: genomic DNA from whole blood of subject Sample18

tag: Sex

value: female


title: genomic DNA from whole blood of subject Sample15


title: LFnC_Female_LKO_rep1

description: Gene expression data from a female LKO mouse X101 on a low-fat no-cholesterol diet

source_name: Female LKO mouse X101 on a low-fat no-cholesterol diet

value: liver


title: genomic DNA from whole blood of subject Sample11


title: genomic DNA from whole blood of subject Sample24


title: Bladder tumor UC_0414_1

tag: hoglund lab uid

value: Bladder tumor

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

value: AllPrep

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: DC, ns , biological rep 2

status: Public on May 27 2015

city: Tuebingen

first: Tica

last: Pichulik

address: Auf der Morgenstelle 15

country: Germany

institute: University of Tuebingen

hyb_protocol: Probes (15 μg) were hybridized for 16 h to Affymetrix Human Gene ST 1.0 array whole transcript coverage of approximately 29,000 genes from the human genome by 33,297 probe sets, processed using a GeneChip Fluidics Station 450 according to recommended protocols (EukGE-WS2v5; Affymetrix)

scan_protocol: Images were captured using the GeneChip Scanner 3000 (Affymetrix).

data_processing: Transcript levels were determined using GeneChip Operating Software (GCOS1.2; Affymetrix), and data were normalized by global scaling. Robust multi-array average (RMA) expression was measured by probe sequence information (GCRMA) in BioConductor R statistics and analyzed using Data Mining Tool (DMT 3.1; Affymetrix) and GeneSpring 7.2 (Silicon Genetics).

label: Biotin

source_name: Human MDDcs transfected with nonsense mimic for 24h, biological replicate 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA.

growth_protocol: Human monocytes were isolated from buffy coats using CD14 magnetic bead isolation and differentiated into dendritic cells by addition of GM-CSF for 5 days.

extract_protocol: Total RNA extraction was performed using the miRNeasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: 3 million DCs were transfected with Pre-miR-650 (PM11602) or nonsense control (AM17110) using Amaxa nucleofection.

tag: cell type

value: Human monocyte-derived dendritic cells


title: genomic DNA from whole blood of subject Sample12

tag: tissue

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number


title: genomic DNA from whole blood of subject Sample6

tag: Sex

tag: relation to proband


title: DC, ns , biological rep 1

source_name: Human MDDcs transfected with nonsense mimic for 24h, biological replicate 1


title: DC, miR-650, biological rep 2

source_name: Human MDDcs transfected with miR-650 mimic for 24h, biological replicate 2


title: genomic DNA from whole blood of subject Sample9


title: DC, miR-650, biological rep 1

source_name: Human MDDcs transfected with miR-650 mimic for 24h, biological replicate 1


title: DC, ns , biological rep 3

source_name: Human MDDcs transfected with nonsense mimic for 24h, biological replicate 3


title: DC, miR-650, biological rep 3

source_name: Human MDDcs transfected with miR-650 mimic for 24h, biological replicate 3


title: UC_colon_inactive_201

city: Leuven

first: Ingrid

last: Arijs

address: Herestraat 49

department: Clinical and Experimental Medicine

country: Belgium

institute: KULeuven

description: Biopsy from uninflamed colonic mucosa of inactive UC patient

hyb_protocol: After fragmentation of DNA, labeled DNA was hybridized for 16h at 45°C on Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: The arrays were washed and stained in a fluidics station using the GeneChip hybridization, Wash end Stain kit (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

data_processing: Probe level analysis was performed on the Affymetrix raw data (.cel files) with the robust multichip average (RMA) method implemented in the Bioconductor package 'aroma.affymetrix' to obtain a log2 expression value for each gene probe set

label_protocol: Biotin-labeled single-stranded DNA was synthesized using the Affymetrix GeneChip WT terminal Labeling kit (Affymetrix), according to manufacturer's instructions.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Benelux B.V.), according to the manufacturer’s instructions.

value: colon

tag: disease

value: ulcerative colitis

tag: disease activity

value: inactive


title: UC_colon_inactive_199

source_name: Biopsy from uninflamed colonic mucosa of inactive UC patient


title: LFnC_Male_LWT_rep1

description: Gene expression data from a male LWT mouse X304 on a low-fat no-cholesterol diet

source_name: Male LWT mouse X304 on a low-fat no-cholesterol diet

tag: strain

tag: diet

tag: genotype

value: LWT

value: M

tag: batch

tag: animal

tag: treatment


title: UC_colon_inactive_198

tag: tissue


title: UC_colon_inactive_197


title: genomic DNA from whole blood of subject Sample5

tag: age

tag: dna methylation age


title: UC_colon_inactive_200


title: genomic DNA from whole blood of subject Sample10

tag: age acceleration vs controls

tag: age acceleration vs controls in children


title: genomic DNA from whole blood of subject Sample8

tag: cor sample vs gold standard

tag: disease status


title: UC_colon_inactive_196


title: genomic DNA from whole blood of subject Sample7

tag: Sex

tag: family number


title: UC_colon_inactive_194

tag: disease


title: genomic DNA from whole blood of subject Sample3

tag: relation to proband


title: genomic DNA from whole blood of subject Sample2


title: UC_colon_inactive_193

tag: disease activity


title: UC_colon_inactive_186


title: UC_colon_inactive_192


title: UC_colon_inactive_191


title: UC_colon_inactive_189


title: UC_colon_inactive_190


title: DMSO_control (VLX60)

city: Uppsala

first: Mårten

last: Fryknäs

address: Akademiska sjh ingång 61

department: Medical sciencies

institute: Uppsala university

description: Gene expression data from MCF7 cells treated 0.1% DMSO for 6 hours.

hyb_protocol: Affymetrix GeneChip® expression arrays (Human Genome U133 Plus 2.0 Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm.

scan_protocol: According to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and using the robust multi-array average (RMA) available from the Bioconductor project in the free statistical computing language R.

source_name: Breast cancer cell line MCF7

label_protocol: 2 micrograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA).

extract_protocol: Extraction of total RNA was performed using Qiagen Rneasy minikit according to the manufacturer's instructions

treatment_protocol: MCF7 control cells treated with 0.1% DMSO for 6 hours.

tag: perturbagen

value: small molecule, type:control, name:DMSO control, concentration:0.1%, vehicle:DMSO, duration:6 h, cell:MCF7

tag: cell line

value: DMSO


title: genomic DNA from whole blood of subject Sample4


title: UC_colon_inactive_185


title: UC_colon_inactive_182


title: UC_colon_inactive_181


title: UC_colon_active_178

description: Biopsy from inflamed colonic mucosa of active UC patient

value: active


title: UC_colon_active_175

source_name: Biopsy from inflamed colonic mucosa of active UC patient


title: UC_colon_active_177


title: UC_colon_inactive_184


title: UC_colon_inactive_188


title: LFnC_Female_LWT_rep1

description: Gene expression data from a female LWT mouse X005 on a low-fat no-cholesterol diet

source_name: Female LWT mouse X005 on a low-fat no-cholesterol diet

tag: strain

tag: diet

value: LFnC

tag: genotype

value: F

tag: batch

value: low-fat no-cholesterol diet


title: UC_colon_inactive_180

tag: tissue


title: UC_colon_active_176


title: UC_colon_inactive_179


title: UC_colon_active_174


title: UC_colon_inactive_183


title: UC_colon_active_173


title: UC_colon_active_172


title: UC_colon_active_160


title: UC_colon_active_171


title: UC_colon_active_170


title: UC_colon_active_158


title: UC_colon_inactive_195


title: VLX60

description: Gene expression data from MCF7 cells treated with VLX60 for 6 hours.

extract_protocol: Extraction of total RNA was performed using Qiagen Rneasy minikit according to the manufacturer's instructions.

treatment_protocol: MCF7 cells treated with 10 microM VLX60 for 6 hours.

value: small molecule, type:treatment, name:VLX60, concentration:.00001 M, vehicle:DMSO, duration:6 h, cell:MCF7

tag: treatment


title: UC_colon_active_165


title: UC_colon_active_159


title: UC_colon_active_166


title: UC_colon_active_162


title: UC_colon_active_164


title: UC_colon_active_169


title: UC_colon_active_155


title: UC_colon_active_163


title: UC_colon_active_167


title: ESC_H1_R1

city: Tallahassee

first: David

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

description: House genomic data

hyb_protocol: Standard NimbleGen protocol. Briefly, Cy3 and Cy5 labeled DNA samples (31 ug each) were co-hybridized to Nimblegen CGH arrays containing oligonucleotide probes across the entire human genome.

scan_protocol: GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing: DEVA (Nimblegen) software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from independent biological replicates in which early and late replicating DNA were labeled reciprocally were loess-normalized to remove signal intensity-dependent bias (limma package, R/Bioconductor) and early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using basic functions in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

source_name: Early-replicating DNA

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

growth_protocol: Human embryonic stem cell (hESC) cultures were routinely maintained using defined media (DM) as previously described (Wang et al. 2007. Blood. 110:4111-9).

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as previously described (Ryba, T. et al., 2011. Nat Protoc 6: 870–895). Briefly, replication intermediates were prepared from cells pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245] and Ryba, T. et al [Nat Protoc (2011) 6: 870–895].

tag: differentiation stage

value: Embrionic stem cells

source_name: Late-replicating DNA


title: UC_colon_active_168


title: UC_colon_active_153


title: UC_colon_active_157


title: UC_colon_active_161


title: UC_colon_active_154


title: UC_colon_active_152


title: UC_colon_active_156


title: ESC_H1_R2

description: House genomic data


title: Ellermeier C difficile Iron fur rep2 tech2

city: Iowa City

first: Craig

middle: D.

last: Ellermeier

state: IA

address: 51 Newton Rd 3-630 BSB

department: Microbiology

institute: University of Iowa

description: This sample is of the Clostridium difficile CD630 JIR8094 fur::ltrB::erm mutant. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Inc., following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen, Inc., following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Clostridioides difficile 630

source_name: Clostridium difficile CD630 JIR8094 fur mutant

label_protocol: Labeling was performed by NimbleGen Inc., following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Clostridium difficile 630 erm wild type and fur mutant were grown to mid-log phase (O.D.600 nm 0.8) anerobically (80% N2, 10% CO2, 10% H2) at 37°C in tryptone-yeast extract medium containing 0.25 mM ferric chloride (Ho et al. Infect. Immun. ).

extract_protocol: Total RNA was extracted using trizol (Invitrogen) and contaminating DNA was removed by turbo DNase (Ambion) digestion. DNAseI was removed from the RNA samples using the RNeasy kit (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Genomics Division at the Iowa Institute of Human Genetics (University of Iowa, Iowa City, Iowa).

tag: phenotype

value: fur-


title: Ellermeier C difficile Iron fur rep3 tech2

description: This sample is of the Clostridium difficile CD630 JIR8094 fur::ltrB::erm mutant. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Ellermeier C difficile Iron fur rep3 tech1


title: Ellermeier C difficile Iron fur rep2 tech1


title: genomic DNA from whole blood of subject Sample1

value: whole blood

value: female

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

value: Control


title: UC_colon_active_146

value: colon

tag: disease


title: Ellermeier C difficile Iron fur rep1 tech2

description: This sample is of the Clostridium difficile CD630 JIR8094 fur::ltrB::erm mutant. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Ellermeier C difficile Iron wild type rep1 tech2

description: This sample is of wild type Clostridium difficile CD630 JIR8094. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Clostridium difficile CD630 JIR8094 wild type

value: Wild-type

value: normal


title: Ellermeier C difficile Iron wild type rep1 tech1

tag: accession


title: Ellermeier C difficile Iron wild type rep3 tech1

description: This sample is of wild type Clostridium difficile CD630 JIR8094. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: UC_colon_active_149

value: ulcerative colitis

tag: disease activity


title: UC_colon_active_144


title: UC_colon_active_148


title: UC_colon_active_147


title: Ellermeier C difficile Iron fur rep1 tech1


title: Ellermeier C difficile Iron wild type rep3 tech2


title: Ellermeier C difficile Iron wild type rep2 tech2

description: This sample is of wild type Clostridium difficile CD630 JIR8094. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: UC_colon_active_140


title: UC_colon_active_143


title: UC_colon_active_145


title: UC_colon_active_151


title: Ellermeier C difficile Iron wild type rep2 tech1


title: UC_colon_active_142


title: ProxFL_10.5_WT+RA [Affymetrix]

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

description:
proximal, WT E10.5 (+RA)
RSM10402

hyb_protocol: Heat the Hybridization Cocktail at 99°C for 5 minutes. Cool to 45°C for 5 minutes. Inject the appropriate amount of the specific sample into the Affymetrix Mouse Genome 430 2.0 array through one of the septa. Place array in 45°C hybridization oven, at 60 rpm, and incubate for 16 hours.

scan_protocol: GeneChip Scaner 3000 was used . The core software was used GCOS for image processing.

data_processing: The data were analzyed with Affymetrix MAS 5.0 algorithm using Bioconductor package.  Signal intensiy was normalized using quantilie normalization method.

source_name: Forelimb buds

label_protocol: The ds-cDNA derived from total RNA was incubated at 37℃ for 16hr with both IVT Labeling NTP mix and IVT Labeling Enzyme Mix to synthesize Biotin-Labeled cRNA.

extract_protocol: Total RNA was extracted using the Rneasy Micro Kit (QIAGEN) following the manufacturer's protocol.

treatment_protocol: Wild type embryos received all trans Retinoic acid (100 mg/kg) at E10.25 by maternal oral gavage.

tag: genotype/variation

value: WT

value: Proximal forelimb buds

tag: retinoic acid treatment


title: UC_colon_active_139


title: DisFL_10.5_WT+RA [Affymetrix]

description:
distal, WT E10.5 (+RA)
RSM10403

tag: strain

value: Distal forelimb buds


title: UC_colon_active_150

value: active


title: DisFL_10.5_Ring1A/B-dKO [Affymetrix]

description:
distal, Ring1A/B-dKO E10.5
RSM09168

value: Prx1-Cre; Ring1A-/-; Ring1Bfl/fl

value: No


title: UC_colon_active_141


title: ExVivo_pDCs_6hr_CpG1668_YFPpos_rep1

city: Duesseldorf

first: Stefanie

last: Scheu

state: Nordrhein-Westfalen

address: Universitaetsstr. 1

department: Institute of Medical Microbiology and Hospital Hygiene

institute: University of Duesseldorf

description: Gene expression after i.v. injection of CpG 1668 complexed to DOTAP for 6hr in IFNβ/YFPpos vs. IFNβ/YFPneg splenic pDCs

hyb_protocol: Cy3 labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (4x44K, Design ID 014868) using Agilent’s recommended hybridization chamber and oven. The microarrays were washed once with 6x SSPE buffer containing 0.005% N-lauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.5.1.1 ) was used to read out and process the microarray image files.

source_name: splenic pDCs, YFPpos, 6 hr CpG1668, rep1

label_protocol: SuperAmplification was performed according to Miltenyi Biotec’s undisclosed protocol. Briefly, the amplification is based on a global PCR protocol of mRNA-derived cDNA. mRNA was isolated via magnetic bead technology. 250 ng of each of the amplified cDNAs were used as template for Cy3 labeling

extract_protocol: RNA was isolated from ex vivo FACS-sorted pDCs using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 photometer.

treatment_protocol: Mice were i.v. injected with 1.5 nmol CpG 1668 complexed to DOTAP for 6 hr. Spleens were minced and digested with collagenase VIII (Roche) and DNase I (Sigma) for 30 min at 37 °C. Erythrocytes were lysed and FACS sorting for IFNβ/YFPpos and IFNβ/YFPneg pDCs was performed after MACS (Miltenyi Biotec) depletion of CD3ε+ and CD19+ cells using a FACS Aria cell sorter (BD).

value: spleen

tag: cell type

value: sorted pDCs

tag: ifnβ  status

value: positive


title: ExVivo_pDCs_6hr_CpG1668_YFPpos_rep2

source_name: splenic pDCs, YFPpos, 6 hr CpG1668, rep2

tag: tissue


title: UC_colon_active_136


title: ExVivo_pDCs_6hr_CpG1668_YFPneg_rep1

source_name: splenic pDCs, YFPneg, 6 hr CpG1668, rep1

value: negative


title: UC_colon_active_137


title: ProxFL_10.5_Ring1A/B-dKO [Affymetrix]

description:
proximal, Ring1A/B-dKO E10.5
RSM09167


title: UC_colon_active_130


title: UC_colon_active_132


title: UC_colon_active_135


title: UC_colon_active_128


title: UC_colon_active_131


title: PEN205 strain third repetition

city: Toulouse

first: Ceren

last: Alkim

address: 135 avenue de Rangueil

country: France

institute: LISBP-INSA

hyb_protocol: 0.6 µg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Yeast V2 Oligo Microarrays (G4813A-016322) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: The slides were scanned on a Tecan scanner MS200

data_processing: Data were analyzed by Feature Extraction V.11.5.1.1. RNA

organism: Escherichia coli

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 0.5 µg RNA using the One-color Low Input Quick Amp Kit (Agilent) according to the manufacturer's instructions, followed by Agilent Nano-prep RNA purification (Agilent, Santa Clara, CA). Dye incorporation and cRNA yield were checked with the NanoDrop-2000 spectrophotometer.

growth_protocol: M9 mineral medium containing (D)-xylose as the only carbon source (100 ml in 500 ml shake flasks) was inoculated from exponentially growing wild-type cells or synthetic cells (cultivated on xylose M9 medium) to adjust an OD of ~0.1. Cultures were incubated at 37°C under shaking until OD reached ~1. Then they were split into two 50 ml aliquots and further cultivated in 250 ml shake flasks in the presence or absence of 10 mM glycolaldehyde. After 30 min of incubation, 1 ml of the cell suspension was withdrawn and centrifuged at 1500 x g (Eppendorf 5415D) for 5 min. The supernatant was removed and the cell pellets were directly subject to RNA extraction. Experiment were repeated three times.

extract_protocol: The RNeasy Mini Kit (QIAGEN) was used to extract RNA. Quantity and quality of the samples were determined by NanoDrop (Thermo) and Bioanalyzer (Agilent Technologies), respectively

treatment_protocol: WT cells were treated with 10 mM Glycolaldehyde for 30 min whenever the culture OD600nm reached ~1.

tag: agent

value: control


title: UC_colon_active_133


title: UC_colon_active_138


title: UC_colon_active_129


title: WT strain treated with glycolaldehyde second repetition

source_name: wild-type MG1655 + glycolaldehyde 10 mM

value: glycolaldehyde


title: UC_colon_inactive_187

value: inactive


title: PEN205 strain second repetition


title: UC_colon_active_127

value: colon


title: ProxFL_10.5_control [Affymetrix]

description:
proximal, WT E10.5
RSM09165


title: WT strain without glycolaldehyde third repetition

source_name: wild-type MG1655


title: PEN205 strain first repetition


title: WT strain treated with glycolaldehyde first repetition


title: WT strain treated with glycolaldehyde third repetition


title: UC_colon_active_134


title: DisFL_10.5_control [Affymetrix]

description:
distal, WT E10.5
RSM09166


title: WT strain without glycolaldehyde second repetition


title: UC_colon_active_124


title: UC_colon_active_123


title: FL_10.5_RING1B 2/2 [Agilent]

description: forelimb 10.5E Ring1B

hyb_protocol: Agilent Mammalian ChIP-on-chip Version 9.0, August 2006

data_processing: Scanned images were quantified with Agilent Feature Extraction software.

source_name: Forelimb buds (ChIP fraction)

extract_protocol: Antibodies against Ring1B (clone #3) (Atsuta et al., 2001) and H3K27me3 (07-449, Millipore) were used for immunoprecipitation. Purified immunoprecipitated and whole cell extract (input) DNA were amplified using the double-round T7 RNA polymerase-based amplification method (van Bakel et al., 2008).

treatment_protocol: Whole forelimb buds at E10.5 from wild type embryos were fixed in 1% formaldehyde/PBS for 20 min at room temperature, washed three times with cold PBS containing protease inhibitors and stored at -80°C. Pools of forelimb buds were used for ChIP and it was performed as described previously (Endoh et al., 2012).

value: Whole forelimb buds

tag: chip antibody

tag: chip antibody info

source_name: Forelimb buds (whole cell extract (input) DNA))

value: none (input)


title: UC_colon_active_125

value: ulcerative colitis


title: FL_10.5_H3K27me3 2/2 [Agilent]

description: forelimb 10.5E H3K27me3

scan_protocol: Agilent Mammalian ChIP-on-chip Version 9.0, August 2006

value: WT

tag: age

value: Millipore #07-449


title: WT strain without glycolaldehyde first repetition


title: UC_colon_active_119


title: UC_colon_active_126


title: UC_colon_active_118


title: UC_colon_active_120


title: UC_colon_active_121


title: UC_colon_active_116


title: Data 275 Area3

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

description:
Array 3
Biological replicate 3 of 4.

hyb_protocol: The hybridization of Agilent-028298 microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics).

data_processing: Background subtracted, Loess and Quantile normalized data obtained from log2 of processed Red signal/processed Green signal. Flexarray software used.

organism: Bos taurus

source_name: granulosa cells, 2h pre-LH surge

label_protocol:
Amplification of RNA was performed using the RiboAmpPlus RNA Amplification kit (Life Technologies). This procedure may be required for microarray experiments with limited amounts of starting material. The RiboAmpPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from nanogram quantities of total cellular RNA. The RiboAmpPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a T7 RNA polymerase catalyzed amplification.
Labeling of aRNA was performed using the Universal Linkage System (ULS) by Kreatech. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: GCs were provided by Dr. S J Dieleman (Utrecht University, The Netherlands). The ovarian stimulation treatment and ovariectomy protocol were described in detail by Knijn et al. (2002, 2011). Briefly, normally cyclic Holstein Friesian cows (n=30) were presynchronized using an ear implant for 9 days (3 mg norgestomet, Crestar; Intervet International BV, Boxmeer, The Netherlands) and a single administration of 3 mg norgestomet and 5 mg estradiol valerate (Intervet International BV). Two days before implant removal, prostaglandin was administered (15 mg Prosolvin, Intervet International BV) to induce a new estrous cycle. Nine days after estrus, the animals received another Crestar implant for 5 days. From day 10 of the estrous cycle, cows were treated with oFSH (Ovagen ICP, Auckland, New Zealand) twice a day in decreasing doses over 4 days. Prostaglandin was administered with the fifth dose of FSH. The ear implant was removed 49-50 h later and a GNRH dose (Intervet International BV) was given to induce the LH surge. In the 2 h pre-LH group, cows were ovariectomized 2 h after removal of the ear implant. In the 6 and 22 h post-LH groups, ovariectomy was performed at 58 and 74 h after prostaglandin administration, which is 8 and 24 h after GNRH; the LH surge occurs on average 2.2 h after GNRH (Knijn et al. 2011) and ovulation 24 h after the LH surge (Dieleman et al. 1983). For the post-LH group, animals received GNRH at the time of removal of the implant and were ovariectomized 8 or 24 h after receiving GNRH, which itself occurs 6 and 22 h after the induced LH. After ovariectomy, ovaries were transported to the laboratory in 0.9% NaCl at 37 °C. After removal of the cumulus-oocyte complex by aspiration, the follicles were cut and turned inside out. GCs were scraped off in a small volume of PBS and centrifuged. This isolation procedure recovers mainly mural GCs but minor contamination by theca cells occurring during scraping was demonstrated by PCR amplification of the CYP17a1 gene (data not shown). The supernatant was removed and the GC pellet was frozen at -80 °C until RNA extraction. Cows were assigned randomly to the three experimental groups (2 h pre-LH surge, 6 h post-LH surge, and 22 h post-LH surge) and four pools of GC were prepared. For each group, pools 1, 2, and 3 were used for microarray hybridization and pools 1, 2, and 4 for real-time PCR validation.

extract_protocol: Total RNA extraction was done using the PicoPure RNA Isolation Kit (Arcturus) from Life Technologies. The PicoPure RNA Isolation Kit enables recovery of total cellular RNA from pico-scale samples.

tag: breed

value: Holstein Friesian

tag: Sex

value: female

value: granulosa cells

tag: follicular size

tag: time point

value: -2 hours luteinizing hormone surge

source_name: granulosa cells, 6h post-LH surge

value: >8 mm

value: 6 hours post-luteinizing-hormone surge


title: UC_colon_active_122

tag: disease

value: active


title: UC_colon_active_117


title: Data 276 Area4

description:
Array 8
Biological replicate 4 of 4.

source_name: granulosa cells, 22h post-LH surge

value: pre-ovulatory

value: 22 hours post-luteinizing-hormone surge


title: UC_colon_active_112

source_name: Biopsy from inflamed colonic mucosa of active UC patient


title: Data 275 Area2

description:
Array 2
Biological replicate 2 of 4.


title: Data 276 Area3

description:
Array 7
Biological replicate 3 of 4.


title: Data 275 Area1

description:
Array 1
Biological replicate 1 of 4.


title: Data 275 Area4

description:
Array 4
Biological replicate 4 of 4.


title: UC_colon_active_108


title: UC_colon_active_110


title: UC_colon_active_107


title: UC_colon_active_113


title: UC_colon_active_106


title: UC_colon_active_105


title: UC_colon_active_114


title: UC_colon_active_111


title: control_colon_86

description: Biopsy from normal colonic mucosa of control individual

value: control

value: normal


title: Data 276 Area1

description:
Array 5
Biological replicate 1 of 4.


title: Data 276 Area2

description:
Array 6
Biological replicate 2 of 4.


title: control_colon_80

source_name: Biopsy from normal colonic mucosa of control individual

value: colon


title: control_colon_85


title: control_colon_84


title: control_colon_82


title: UC_colon_active_109


title: UC_colon_active_115


title: control_colon_79


title: control_colon_76


title: control_colon_77


title: control_colon_78


title: CD_colon_active_6

description: Biopsy from inflamed colonic mucosa of active CD patient

value: Crohn's disease


title: CD_colon_active_4

source_name: Biopsy from inflamed colonic mucosa of active CD patient


title: control_colon_81


title: Esc2_Myc_HU_SUP (INPUT)

city: Milan

first: Madhusoodanan

last: Urulangodi

state: Milan

address: Via Adamello 16

country: Italy

institute: IFOM

description:
W303 Esc2-13Myc (FY1028) cells were arrested in G1 with alpha-factor (2μg/ml) and then released in media containing HU 0.2M for 60 minutes.
Processed data files: Esc2_Myc_HU_signal.bar, Esc2_Myc_HU_pvalue.bar, Esc2 Myc_HU_signal.bed, Esc2 Myc_HU_pvalue.bed

hyb_protocol: Labelled probes were hybridized to Affymetrix S. cerevisiae whole genome tiling R arrays.

scan_protocol: Arrays were scanned on an Affymetrix Scanner.

data_processing: BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

organism: Saccharomyces cerevisiae

source_name: W303 Esc2-13Myc yeast cells, no antibody

label_protocol: Synthesis of cDNA, IVT amplification, and labeling were carried out following the Affymetrix GeneChip Expression Analysis protocol.

growth_protocol: Cells were grown in 200 ml of YPD media at 25°C in 1L flask for a density of 1.2x10^7 cells/ml.

extract_protocol: Extraction was performed as described in Bermejo et al., 2009.

treatment_protocol: G1 synchronization was performed by α-factor treatment (2 μg/ml) for 150 minutes. Cells were pelleted and released in media containing 0.2 M HU at 25°C for 60 min and fixed with 1% formaldehyde for 120 min at room temperature. Pelleted cells were washed twice with ice-cold PBS buffer and resuspended in 0.8 ml of lysis buffer (50 mM HEPES, pH-7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton-X100,and 0.1% Na-deoxycholate) supplemented with 1X complete protease inhibitor cocktail (Roche) and glass beads. Cells were broken with multibeads shocker, 60 min total time with 1 min shaking and 1 min pause at 2500 rpm at 4°C. Recovered cell lysate was centrifuged and the pellet was then resuspended in 0.45 ml of protease inhibitor supplemented lysis buffer. Chromatin was sheared by applying 5 sonication cycles of 15 seconds at 1.5 tune while keeping the sample on ice. The supernatant recovered after centrifugation was then incubated with Myc antibody bound magnetic beads overnight at 4°C. Washing and the recovery of immunoprecipitated DNA was performed as described in Bermejo et al., 2009.

value: W303 Esc2-13Myc


title: CD_colon_active_7


title: CD_colon_active_1


title: Patient normal samples

type: SRA

city: Salt Lake City

first: Mumtahena

last: Rahman

state: UT

address: 20 South 2030 East, Rm 420

department: Biomedical Informatics

institute: University of Utah

description: Please note that the samples were sequenced using Illumina Genome Analyzer or Illumina HiSeq 2000 (https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2).

library_source: transcriptomic

data_processing:
Alignment and quantification with R open source package "Rsubread" v 1.14.2
FPKM normalization with R open source packages edgeR and limma
TPM normalization from the FPKM values.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Tab delimited text files containing integer based raw gene counts for 9264 tumor samples in TCGA_24.Illumina.tumor_Rsubread_FeatureCounts.txt, FPKM values in TCGA_24.Illumina.tumor_Rsubread_FPKM.txt and TPM values in PANCAN24.Illumina.tumor_Rsubread_TPM.txt. Tab delimited txt file containing all 548 clinical variables for 9264 samples in TCGA_24_548_Clinical_Variables_9264_Samples.txt. In addition, Tab delimited text file containing integer based raw gene counts, FPKM and TPM values for 741 normal samples in TCGA_24.Illumina.normal_Rsubread_FeatureCounts.txt, TCGA_24.Illumina.normal_Rsubread_FPKM.txt and TCGA_24.Illumina.normal_Rsubread_TPM.txt respectively.

source_name: All 741 normal samples have been combined to create the processed matrix files

extract_protocol: Please refer to TCGA Genome Characterization Center extraction and library contruction protocol.

tag: tissue type

value: Normal


title: M0505+PAX2+Cre cell line, biological replicate 1

first: Ensaf

last: Alhujaily

address: 501 Smyth road

institute: University of Ottawa

hyb_protocol: Labeled target cDNA was hybridized to the Affymetrix Genechip Mouse Gene 2.0 array at 45C for 17 hours.  GeneChips were washed and stained using the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with Gene Expression Console using Affymetrix default analysis settings for RMA processing.

source_name: Murine ovarian surface epithelial cell line established in May 2005_+PAX2+Cre

label_protocol: cDNA was prepared according to the standard Affymetrix protocol using the Ambion WT Expression kit (Life Technologies) from 300 ng total RNA.  cDNA was biotinilated and fragmented using the Affymetrix GeneChip Wt Terminal Labeling kit.

growth_protocol: all  cells were grown in murine OSE (MOSE) media (α-Minimal Essential Medium, 10% fetal calf serum, 0.002μg/mL EGF, 1μg/mL ITSS, 0.1μg/ml Gentamicin, 0.005mg/mL Streptomycin, 5U/mL Penicillin)

extract_protocol: RNA was extracted using the Qiagen RNAeasy Mini Kit according to the manufacterers directions.

treatment_protocol: M0505 cells were infected with GFP- lentiviral construct (WPI, as a vector control) or PAX2 and GFP-expressing constructs. Using FACS analysis, the infected cells were sorted for positive GFP. A subline of M0505+PAX2 were treated with AdCre to delete expression of both GFP and PAX2. Then, this subline was sorted for GFP-negative cells and named as M0505+PAX2+cre

tag: background strain

value: FVB/N

value: ovarian surface epithelium

tag: cell line


title: CD_colon_active_3

tag: disease activity


title: CD_colon_active_8


title: CD_colon_active_2


title: M0505+PAX2 cell line, biological replicate 2

source_name: Murine ovarian surface epithelial cell line established in May 2005_+PAX2


title: M0505+PAX2+Cre cell line, biological replicate 2

description: Murine ovarian surface epithelial cell line established in May 2005


title: M0505+WPI cell line, biological replicate 1

source_name: Murine ovarian surface epithelial cell line established in May 2005_+WPI


title: M0505+PAX2 cell line, biological replicate 1


title: Esc2_Myc_HU_IP

source_name: W303 Esc2-13Myc yeast cells, anti-Myc antibody

tag: strain

tag: genotype/variation

value: anti-Myc [C-Myc Antibody (9E10); Santa Cruz, sc-40]


title: control_colon_83


title: CD_colon_active_5


title: M0505+WPI cell line, biological replicate 2

tag: cell type


title: Human retina periphery 32 year old

city: New Haven

first: Hui

middle: Cong

last: Cai

state: CT

address: 300 George St, Suite 8100

institute: Yale University

hyb_protocol: Affymetrix standard protocol for "Target Hybridization" (Columbia University Core Facility provided service)

scan_protocol: Affymetrix standard protocol for "probe array scan" (Columbia University Core Facility provided service)

data_processing: Using Affymetrix Expression Console and GeneSifter Genetic Analysis system (Geospiza, Inc., Seattle, WA); selecting expression levels > 50 in densitometry, and there was at least 2.0-fold difference in expression level that was statistically significant (p < 0.05 with Benjamini and Hochberg adjusted student t-test)

source_name: Human retina periphery 32 year old

label_protocol: Affymetrix standard "ONe-Cyecle Target Labeling" kit (P/N 900493)

extract_protocol: total RNA was isolated and purified using a Qiagen RNeasy Mini Kit according to manufacturer’s instructions

tag: gender

value: male


title: Human retina periphery 75 year old

source_name: Human retina periphery 75 year old


title: Human retina periphery 43 year old

source_name: Human retina periphery 43 year old

value: female


title: Human retina periphery 74 year old

source_name: Human retina periphery 74 year old


title: Recovery24hr, biological rep3

first: Yasuhiro

last: Higashi

department: Center for Sustainable Resource Science

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: The obtained data was summarized by the method of MAS5, and normalized as baseline to median of all samples using GeneSpring version 12 (Agilent Technologies).

organism: Arabidopsis thaliana

source_name: leaf_Recovery24hr_20 days old

label_protocol: Standard Affymetrix procedures

growth_protocol: Arabidosis wild-type ecotype Columbia plants were grown on agar plates at 22 degree C under a 16-h-light/8-h-dark cycle.

extract_protocol: RNeasy plant mini kit (Qiagen)

treatment_protocol: Eighteen-day-old Arabidosis plants were subjected to heat stress at 38 degree C for a day (heat08hr, heat24hr), then continued to be grown at 22 degree C for a day (recovery08hr, recovery24hr).

tag: ecotype

value: wild-type

value: 20 days

tag: sample group

tag: tissue

value: leaf


title: FL_10.5_RING1B 1/2 [Agilent]

description: forelimb 10.5E Ring1B

source_name: Forelimb buds (ChIP fraction)

label_protocol: Agilent Mammalian ChIP-on-chip Version 9.0, August 2006

value: WT

value: Whole forelimb buds

tag: age

tag: chip antibody

tag: chip antibody info

source_name: Forelimb buds (whole cell extract (input) DNA))

value: none (input)


title: Recovery08hr, biological rep3

source_name: leaf_Recovery08hr_19 days old

value: 19 days


title: Human retina macula 32 year old

scan_protocol: Affymetrix standard protocol for "Probe Array Scan" uisng Genechip software (Columbia University Core Facility provided service)

source_name: human retinal macula 32 year old


title: Heat08hr, biological rep3

source_name: leaf_Heat08hr_18 days old

value: 18 days


title: Control24hr, 20 days old, biological rep3

source_name: leaf_Control24hr_20 days old


title: Control08hr, 19 days old, biological rep3

source_name: leaf_Control08hr_19 days old


title: Human retina periphery 32 year old sample2


title: Control24hr, 19 days old, biological rep3

source_name: leaf_Control24hr_19 days old


title: Human retina periphery 74 year old sample2


title: Heat24hr, biological rep3

source_name: leaf_Heat24hr_19 days old


title: Human retina macula 74 year old

source_name: Human retina macula 74 year old


title: Human retina macula 79 year old

source_name: Human retina macula 79 year old


title: Control24hr, 18 days old, biological rep3

source_name: leaf_Control24hr_18 days old


title: Human retina macula 18 year old

source_name: human retina macula 18 year old


title: Heat24hr, biological rep2


title: Human retina macula 75 year old

source_name: Human retina macula 75 year old


title: Heat08hr, biological rep2


title: Control24hr, 18 days old, biological rep2


title: Control08hr, 18 days old, biological rep3

source_name: leaf_Control08hr_18 days old


title: Human retina macula 21 year old

source_name: human retina macula, 21 year old


title: Control24hr, 20 days old, biological rep2


title: Control24hr, 19 days old, biological rep2


title: Recovery24hr, biological rep2

source_name: leaf_Recovery24hr_20 days old


title: Control08hr, 18 days old, biological rep2


title: FL_10.5_H3K27me3 1/2 [Agilent]

description: forelimb 10.5E H3K27me3

source_name: Forelimb buds (ChIP fraction)

value: Millipore #07-449


title: Control08hr, 19 days old, biological rep2


title: Recovery08hr, biological rep1


title: Heat24hr, biological rep1


title: Heat08hr, biological rep1


title: Control24hr, 18 days old, biological rep1


title: Control24hr, 19 days old, biological rep1


title: Control08hr, 19 days old, biological rep1


title: Control24hr, 20 days old, biological rep1


title: Liver_120hr_treated_8

status: Public on May 26 2015

city: Austin

first: Elizabeth

last: Osterndorff-Kahanek

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description: Replicate 8

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The R package Lumi was used to transform and normalize the data using variance stabilization transformation and quantile normalization. Only genes with a detection p value ≤ 0.05 and present on ≥ 80% of arrays are included in the normalized data.
Expression value outliers were identified with Grubbs' test and removed.

source_name: liver, ethanol vapor treated, 120 hr

label_protocol: Biotinylated cRNAs were prepared with the Illumina® TotalPrep-96™ RNA Amplification kit from Ambion according to manufacturer's instructions.

extract_protocol:
Whole brains were cryosectioned at 300um. Specific brain regions were isolated using a 1.25 mm (AMY) or 2.0 mm (NAC, PFC) micropunch. Eight, 6 and 5-8 micropunces were collected from AMY, NAC and PFC, respectively.
Total RNA was isolated using the MagMAX™-96 for Microarrays Total RNA Isolation Kit (Ambion, Austin, TX) using the manufacturer supplied modification to collect both mRNAs and small RNAs. Quality control was performed with the Agilent Tape Station.

value: adult (10-12 weeks)

value: liver


title: IMR90 + OSKM-B

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description: IMR90 cells infected with OSKM retroviruses, technical replicate 2

data_processing: The data were normalized using cubic spline in Illumina GenomeStudio and also using the VAMPIRE Bayesian model with a 2-sided Bonferroni-corrected threshold of 0.05.

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

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

value: human embryonic fibroblast

tag: time

value: Day 5 of reprogramming


title: Control08hr, 18 days old, biological rep1


title: Liver_120hr_treated_4

description: Replicate 4


title: Recovery24hr, biological rep1


title: IMR90 GFP-B

description: IMR90 cells infected with GFP retrovirus, technical replicate 2


title: IMR90 control-A

description: human embryonic fibroblast IMR90 cells, technical replicate 1

source_name: human embryonic fibroblast IMR90 cells


title: IMR90 + OSKM-A

description: IMR90 cells infected with OSKM retroviruses, technical replicate 1


title: Liver_120hr_treated_2

description: Replicate 2


title: Liver_120hr_treated_6

description: Replicate 6


title: Liver_120hr_treated_5

description: Replicate 5


title: Liver_120hr_treated_3

description: Replicate 3


title: Liver_120hr_treated_1

description: Replicate 1


title: Liver_120hr_control_8

description: Replicate 8

source_name: liver, saline control, 120 hr


title: Recovery08hr, biological rep2

source_name: leaf_Recovery08hr_19 days old


title: Liver_120hr_control_6

description: Replicate 6


title: Liver_120hr_treated_7

description: Replicate 7


title: IMR90 control-B

description: human embryonic fibroblast IMR90 cells, technical replicate 2


title: Liver_120hr_control_7

description: Replicate 7


title: Liver_120hr_control_5

description: Replicate 5


title: Liver_120hr_control_4

description: Replicate 4


title: Liver_120hr_control_3

description: Replicate 3


title: Liver_120hr_control_2

description: Replicate 2


title: Liver_8hr_treated_7

description: Replicate 7

source_name: liver, ethanol vapor treated, 8 hr


title: Liver_8hr_treated_8

description: Replicate 8


title: Liver_120hr_control_1

description: Replicate 1


title: Liver_8hr_treated_6

description: Replicate 6


title: Liver_8hr_treated_5

description: Replicate 5


title: Liver_8hr_treated_4

description: Replicate 4


title: IMR90 GFP-A

description: IMR90 cells infected with GFP retrovirus, technical replicate 1


title: Liver_8hr_control_3

description: Replicate 3

source_name: liver, saline control, 8 hr


title: Liver_8hr_treated_3

description: Replicate 3


title: Liver_8hr_control_8

description: Replicate 8


title: Liver_8hr_control_5

description: Replicate 5


title: Liver_8hr_control_4

description: Replicate 4


title: Liver_8hr_treated_1

description: Replicate 1


title: Liver_0hr_treated_6

description: Replicate 6

source_name: liver, ethanol vapor treated, 0 hr


title: Liver_0hr_treated_8

description: Replicate 8


title: Liver_8hr_treated_2

description: Replicate 2


title: Liver_0hr_treated_5

description: Replicate 5


title: Liver_8hr_control_6

description: Replicate 6


title: Liver_0hr_treated_7

description: Replicate 7


title: Liver_8hr_control_7

description: Replicate 7


title: Liver_8hr_control_1

description: Replicate 1


title: Liver_0hr_treated_3

description: Replicate 3


title: Liver_0hr_treated_4

description: Replicate 4


title: Liver_0hr_treated_2

description: Replicate 2


title: Liver_0hr_treated_1

description: Replicate 1


title: Liver_0hr_control_6

description: Replicate 7

source_name: liver, saline control, 0 hr


title: Liver_0hr_control_5

description: Replicate 6


title: Liver_0hr_control_4

description: Replicate 5


title: Liver_0hr_control_7

description: Replicate 8


title: Liver_0hr_control_2

description: Replicate 3


title: Liver_8hr_control_2

description: Replicate 2


title: Liver_0hr_control_1

description: Replicate 2


title: Liver_0hr_control_3

description: Replicate 4


title: PFC_0hr_control_6

description: Replicate 6

source_name: prefrontal cortex, saline control, 0 hr

value: prefrontal cortex


title: Colon_GG_repl5

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization, washing and scanning of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.22.0).

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) guar gum (at the expense of corn starch), replicate 5

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: C57BL/6J mice were purchased from Harlan (Horst, the Netherlands), and housed in a light and temperature-controlled animal facility of Wageningen University (12:12 h light/dark cycle, 20±2 °C). Mice had free access to feed and water.

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

treatment_protocol: Mice were fed a low fat control diet for 2 weeks. After this adaptation period, mice were stratified according to their body weight and allocated to the control diet group (n=5, low fat diet) or one of the dietary fiber groups (n=6 per fiber diet). The diets enriched in dietary fiber were identical to the control diet, except that 10% (w/w) of corn starch was replaced by each fiber (20% for RS, since according to the supplier, the RS was only 50% resistant to digestion in the small intestine, and was therefore included in the diet at a 20% (w/w) level, i.e. double the amount of the other fibers). The following fibers were used: inulin (brand name Frutafit IQ), oligofructose (brand name Frutalose OFP; FOS), arabinoxylan (brand name NAXUS; AXUS), guar gum (brand name Viscogum; GG) and resistant starch (brand name ActiStar; RS). After 10 days of dietary intervention, mice were fasted overnight and subsequently provided with 1 g of experimental diet. After 4 hours, mice were anesthetized using isoflurane and sacrificed by cervical dislocation. Colon was removed, mucosal scrapings were collected, snap-frozen in liquid nitrogen and stored at −80°C (scrapings).

tag: strain/background

value: 12 weeks

value: colonic mucosal scrapings


title: Colon_FOS_repl5

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) oligofructose (at the expense of corn starch), replicate 5

value: male


title: Index patient

city: London

first: Venu

middle: Madhav

last: Pullabhatla

address: Great Maze Pond

department: Guy's Hospital

country: United Kingdom

institute: Biomedical Research Centre

description: rep 1

data_processing: The background was subtracted and the data was quantile normalized using Illumina genome studio software version 2010.3. The negative values indicate that the observed signal intensity of the probe is not above background. Quantile normalized average signal intensity values across the samples and the intensity values was averaged across 4 biological replicates for Normal adult Control

source_name: Skin

label_protocol: Illumina array HumanHT-12 v4.0 Expression BeadChip kit used according to the maufacturers instructions.

extract_protocol: RNA was extracted using the Ambion mirVana miRNA Isolation kit in accordance with the manufacturers instructions. Quality control was performed with an Agilent Bioanalyser.

value: skin

tag: phenotype

value: multi-organ epithelial inflammation associated with an inherited loss-of-function mutation in EGFR

tag: Stage

value: Infant


title: Colon_RS_repl3

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 20% (w/w) resistant starch (at the expense of corn starch), replicate 3


title: Colon_RS_repl6

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 20% (w/w) resistant starch (at the expense of corn starch), replicate 6


title: Colon_RS_repl4

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 20% (w/w) resistant starch (at the expense of corn starch), replicate 4


title: Colon_AXUS_repl5

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) arabinoxylan (at the expense of corn starch), replicate 5


title: NAC_0hr_treated_2

description: Replicate 2

source_name: nucleus accumbens, ethanol vapor treated, 0 hr

value: nucleus accumbens


title: NAC_8hr_control_1

description: Replicate 1

source_name: nucleus accumbens, saline control, 8 hr


title: Colon_GG_repl3

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) guar gum (at the expense of corn starch), replicate 3


title: Colon_GG_repl4

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) guar gum (at the expense of corn starch), replicate 4


title: Colon_FOS_repl2

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) oligofructose (at the expense of corn starch), replicate 2


title: Colon_FOS_repl3

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) oligofructose (at the expense of corn starch), replicate 3


title: NAC_8hr_control_2

description: Replicate 2


title: Colon_GG_repl1

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) guar gum (at the expense of corn starch), replicate 1


title: Colon_RS_repl2

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 20% (w/w) resistant starch (at the expense of corn starch), replicate 2


title: Colon_RS_repl1

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 20% (w/w) resistant starch (at the expense of corn starch), replicate 1


title: Colon_GG_repl6

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) guar gum (at the expense of corn starch), replicate 6


title: Colon_AXUS_repl2

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) arabinoxylan (at the expense of corn starch), replicate 2


title: Colon_FOS_repl6

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) oligofructose (at the expense of corn starch), replicate 6


title: Colon_AXUS_repl6

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) arabinoxylan (at the expense of corn starch), replicate 6


title: Colon_AXUS_repl4

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) arabinoxylan (at the expense of corn starch), replicate 4


title: Colon_FOS_repl1

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) oligofructose (at the expense of corn starch), replicate 1


title: Colon_RS_repl5

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 20% (w/w) resistant starch (at the expense of corn starch), replicate 5


title: Colon_FOS_repl4

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) oligofructose (at the expense of corn starch), replicate 4


title: Colon_AXUS_repl3

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) arabinoxylan (at the expense of corn starch), replicate 3


title: Colon_GG_repl2

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) guar gum (at the expense of corn starch), replicate 2


title: Colon_AXUS_repl1

source_name: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) arabinoxylan (at the expense of corn starch), replicate 1


title: cell subpopulation, CD24 and SSEA-4 negative 2

city: Oslo

first: Nirma

last: Skrbo

address: Ullernchauseen 70

department: Dep of Genetics

country: Norway

institute: Oslo University Hospital

description: Gene expression from mouse xenograft of human breast cancer

hyb_protocol: Hybridization was performed according to the manufacturer’s protocol (Agilent One-Color Microarray-Based Gene Expression Analysis v6.0) using 1650 ng cy3-labeled cRNA per sample and hybridized onto Whole Human Genome Oligo Microarrays (4x44K, G4112F).

scan_protocol: The microarrays were scanned using Agilent Technologies Microarray Scanner (G2505C). Data were extracted from the scanned images using Feature Extraction software (Agilent Technologies), version 10.7 and protocol GE1-107-Sep09 for mRNA, using default settings and FULL text output.

data_processing: Microarray expression data were filtered for spot quality and quantile normalized using GeneSpring GX Software (Agilent). The final dataset was generated by additionally averaging the signal intensity of  multiple unique probes for each gene. This set, linked on the Series table, included data for 24210 unique genes on 15 microarrays from the four cell subpopulations.

source_name: Patient-derived breast cancer xenograft

label_protocol: 50-100 ng total RNA was amplified and labeled with cy3-CTP following Agilent Low Input Quick Amplification Labeling Kit protocol for One-Color Microarray-Based Gene Expression Analysis

extract_protocol: Total RNA from FACS sorted cell subpopulations was isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. Total RNA concentration was measured using NanoDrop (NanoDrop Technologies)

treatment_protocol: Single cell suspension from an luminal-like breast cancer was prepared by enzymatic disaggregation of tumours.  The cells were re-suspended in cold staining buffer (PBS containing 0.5 % FCS and 3 % human immune globulin (Gammaguard) (N.V Baxter S.A, Belgium)  and stained with fluorescently-labelled antibodies, diluted according to the manufacturers’s recommendation. Following 30 min incubation at 4oC, the stained cells were washed ones with PBS, then re-suspended in DMEM/F12 with 0.,5% human serum albumin, 2% Hepes, Penicillin and Streptomycin and further sorted by FACS DIVA flow cytometer (Becton Dickinson), equipped with a 488nm Argon laser (Coherent) and 633nm HeNe laser (Spectra Physics).The single cell suspensions were  stained with 1 µg/ml propidium iodide (PI) (Sigma) prior to  sorting to exclude the dead cells from the analysis.

tag: xenograft

value: Breast Cancer

tag: cancer subtype

value: Luminal

tag: subpopulation

value: CD24 and SSEA-4 negative


title: cell subpopulation, CD24 and SSEA-4 positive 2

value: CD24 and SSEA-4 positive


title: cell subpopulation, CD24 positive 4

value: CD24 positive


title: cell subpopulation, CD24 positive 2


title: cell subpopulation, CD24 and SSEA-4 positive 1


title: cell subpopulation, CD24 positive 3


title: cell subpopulation, CD24 and SSEA-4 negative 1


title: Cell subpopulation, SSEA4 positive 3

value: SSEA4 positive


title: cell subpopulation, CD24 and SSEA-4 positive 3


title: cell subpopulation, CD24 and SSEA-4 negative 4


title: cell subpopulation, CD24 positive 1


title: Cell subpopulation, SSEA4 positive 2


title: cell subpopulation, CD24 and SSEA-4 negative 3


title: Cell subpopulation, SSEA4 positive 4


title: Cell subpopulation, SSEA4 positive 1


title: genomic DNA from semen of male 40M07

city: Seoul

first: Hwan Young

last: Lee

address: 103 Daehak-ro, Jongno-gu

department: Forensic Medicine

country: South Korea

institute: Seoul National University College of Medicine

hyb_protocol: bisulfite converted DNA was amplified, fagmented 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: BeadStudio software v3.2; the non_normalized.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using QIAamp DNA Investigator Kit and Mini Kit

tag: age (years)

value: Male

tag: ethnicity

value: Korean-Asian

value: semen


title: XY Ctnnb1/Sox9 DKO_Rep4

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from E14.5 XY Ctnnb1/Sox9 DKO gonads

hyb_protocol: 4.6 μg of amplified biotin-aRNAs were fragmented and hybridized to each array for 18 hours at 45°C in a rotating hybridization. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0004.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files.

source_name: E14.5 XY Ctnnb1/Sox9 DKO gonads

label_protocol: Forty (40) nanograms of total RNA (due to varying concentrations among samples) was amplified as directed in the WT-Ovation Pico RNA Amplification System protocol, and labeling with biotin following the Encore Biotin Module.

extract_protocol: A single pair of gonads (14.5 dpc) was separated from the mesonephros and was used as one biological replicate (3 to 4 biological replicates were included for each genotype). Total RNA was isolated using Picopure extraction kit (Arcturus). RNA quality and concentration were determined using N Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, California)

treatment_protocol: All embryos used in this study resulted from the crossing between Ctnnb1f/f; Sox9f/f females with Sf1-cre+/Tg ; Ctnnb1+/f; Sox9+/f males. The genotype of the gonads used in this study is as follows: Sf1-cre+/Tg ; Ctnnb1+/f; Sox9+/f as control, Sf1-cre+/Tg; Ctnnb1f/f; Sox9+/f as Ctnnb1 KO, Sf1-cre+/Tg; Ctnnb1+/f; Sox9f/f as Sox9 KO, and Sf1-cre+/Tg ; Ctnnb1f/f; Sox9f/f as Ctnnb1/Sox9 DKO

tag: genotype

value: Sf1-cre+/Tg ; Ctnnb1f/f; Sox9f/f

value: gonads

tag: developmental stage

value: fetus

tag: embryonic stage

tag: chromosome composition

value: XY


title: XY Ctnnb1/Sox9 DKO_Rep2

tag: tissue


title: XY Ctnnb1/Sox9 DKO_Rep3


title: XY Sox9KO_Rep2

description: Gene expression from E14.5 XY Sox9KO gonads

source_name: E14.5 XY Sox9KO gonads

value: Sf1-cre+/Tg; Ctnnb1+/f; Sox9f/f


title: XY Sox9KO_Rep4


title: genomic DNA from saliva of male 30M08

tag: age (yrs)

tag: gender

value: saliva


title: XY Sox9KO_Rep3


title: XY Sox9KO_Rep1


title: genomic DNA from semen of male 40M10


title: XY Ctnnb1KO_Rep4

description: Gene expression from E14.5 XY Ctnnb1KO gonads

source_name: E14.5 XY Ctnnb1KO gonads

value: Sf1-cre+/Tg; Ctnnb1f/f; Sox9+/f


title: genomic DNA from semen of male 40M05


title: MKN45colonies_cisplatin

first: Kohei

last: Kume

address: 300 George St

department: Center of Molecular and Cellular Oncology

description: MeDIP-chip MKN45 DTCs

hyb_protocol: Cy-labeled MeDIP DNA samples (6 ug each) were incubated at 95°C for 5 minutes in a total volume of 18 ul containing 2x Hybridization buffer, Hybridization Component A, and Alignment Oligo following the manufacturers’ instructions. After the incubation, 16 ul of the sample was hybridized to Human Meth 385K Prom Plus CpG Array for 16 hours at 42°C on the Mixing Panel on the NimbleGen Hybridization System 4 (Roche NimbleGen). After hybridization, the microarray was washed with the NimbleGen Wash Buffer Kit and then dried.

scan_protocol: The array slide was scanned on the Agilent Microarray Scanner (Agilent Technologies) using a two-color scan setting for 385K array (Scan resolution, 5 um; Dye channels 1 and 2 were set to 532 and 635, respectively, and laser intensity 1 and 2 were set to 100%).

data_processing:
The scanned images were analyzed with NimbleScan v2.6 Software (NimbleGen) using default parameters.
The raw data was first normalized by Z score transformation, and then calculated as a Cy5/Cy3 log2 ratio.

source_name: MeDIP DNA from bulk MKN45 colonies

label_protocol: MeDIP DNA samples from untreated colonies and DTCs were labeled with Cy3 and Cy5, respectively.

growth_protocol: MKN45 cells were sparsely disseminated and cultured for 13 days.

extract_protocol: Genomic DNA was isolated from bulk of MKN45 colonies using the DNeasy Kit (QIAGEN).

value: male

tag: disease state

value: gastric cancer

tag: cell type

value: MKN45 colonies

tag: treatment

tag: medip antibody

value: Anti-5-methylcytosine (5-mC) antibody [33D3], Abcam, catalog# Ab10805

source_name: MeDIP DNA from bulk MKN45 DTCs, cisplatin-treated

growth_protocol: MKN45 cells were sparsely disseminated in the presence of 0.2 µM CIS and cultured for 13 days.

value: MKN45 DTCs

value: cisplatin


title: genomic DNA from whole blood of male 30M03

source_name: male_30s_whole blood

value: whole blood


title: genomic DNA from saliva of male 40M10

description:
fragmented genomic DNA
40M10SA

value: Male


title: genomic DNA from semen of male 30M05

value: Korean-Asian


title: AMY_120hr_control_7

description: Replicate 7

source_name: amygdala, saline control, 120 hr

tag: strain

tag: age

value: adult (10-12 weeks)

value: amygdala


title: XY Ctnnb1KO_Rep3

value: gonads


title: XY Ctnnb1KO_Rep1

value: fetus


title: XY Ctnnb1KO_Rep2

value: XY


title: genomic DNA from whole blood of male 40M05

source_name: male_40s_whole blood


title: genomic DNA from semen of male 30M08

value: semen


title: genomic DNA from saliva of male 20M02

value: saliva


title: genomic DNA from whole blood of male 40M10


title: genomic DNA from saliva of male 30M05

description:
fragmented genomic DNA
30M05SA


title: XY Ctr_Rep4

description: Gene expression from E14.5 XY gonads

source_name: E14.5 XY gonads

value: Sf1-cre+/Tg ; Ctnnb1+/f; Sox9+/f


title: genomic DNA from whole blood of male 40M07


title: genomic DNA from semen of male 30M04


title: genomic DNA from whole blood of male 30M05


title: genomic DNA from saliva of male 30M04

description:
fragmented genomic DNA
30M04SA


title: XY Ctr_Rep3

description: Gene expression from E14.5 XY gonads


title: genomic DNA from saliva of male 40M07

description:
fragmented genomic DNA
40M07SA


title: genomic DNA from whole blood of male 50M06

source_name: male_old_whole blood


title: XY Ctr_Rep1

description: Gene expression from E14.5 XY gonads


title: XX Ctnnb1/Sox9 DKO_Rep4

description: Gene expression from E14.5 XX Ctnnb1/Sox9 DKO gonads

source_name: E14.5 XX Ctnnb1/Sox9 DKO gonads

value: Sf1-cre+/Tg ; Ctnnb1f/f; Sox9f/f

value: XX


title: XY Ctr_Rep2

description: Gene expression from E14.5 XY gonads


title: genomic DNA from whole blood of male 20M06

source_name: male_young_whole blood