title: Hemocytes of R. philippinarum injected (intramuscular infection) with V. alginolyticus at 72h after challenge, I4_72H

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

description:
I4_72H
Hemocytes RNA of Ruditapes philippinarum.

hyb_protocol: Hybridized according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

scan_protocol: Array was scanned according to the standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%).

data_processing: Data were processed with Feature Extraction v9.5 and normalized by percentile shift at the 75th percentile using GeneSpring GX version 11.0.2 software (Agilent Technologies).

organism: Ruditapes philippinarum

source_name: Hemocytes, injected with Vibrio alginolyticus, 72 hours after challenge

label_protocol: Amplified and labeled according to the Agilent Low Input One-Color Microarray-Based Gene Expression Analysis protocol.

growth_protocol: R. philippinarum clams were obtained from a commercial shellfish farm (Vigo, Galicia, Spain). Clams were maintained in open circuit filtered sea water tanks at 15°C with aeration and were fed daily with Phaeodactylum tricornutum and Isochrysis galbana. Prior to the experiments, clams were acclimatized to aquaria conditions for one week.

extract_protocol: Total RNA isolation was conducted following the manufacturer's specifications in combination with the RNeasy mini kit (Qiagen) for RNA purification after DNase I treatment.

treatment_protocol: Clams were notched in the shell next to the adductor muscles and injected with 100 µl of Vibrio alginolyticus, strain TA15, (10^8 UFC/ml in PBS) to mimic an intramuscular infection. After stimulation, clams were returned to the tanks and maintained at 15ºC until hemocytes sampling.

value: hemocytes

value: Vibrio alginolyticus

tag: time point

value: 72 hours


title: SFA, 114_W0

status: Public on Jul 01 2014

type: RNA

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

country: Sweden

institute: Karolinska

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary RNA to Gene 1.1 ST Arrays, and then washed, stained and scanned slides using standardized protocols (Affymetrix, Inc., Santa Clara, CA).

scan_protocol: We used standardized Affymetrix protocols (Affymetrix, Inc., Santa Clara, CA).

data_processing: Subsequent data analyses were performed using the Affymetrix GeneChip Operating Software (GCOS) Version 1.4. To allow comparisons of transcript levels between samples, all samples were subjected to an all-probe set scaling to target signal 100. # Summarization: PLIER, Background correction: PM-GCBG, Normalization method: Global Median.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: white adipose tissue, SFA, week 0

label_protocol: Total RNA were amplified and biotin labeled using the Whole Transcript (WT) Sense Target Labeling Protocol.

extract_protocol: RNA was extracted using the Nucleospin RNA11 kit (Macherey-Nagel, Duren, Germany). RNA samples were treated with RNase-free DNase (Macherey-Nagel).

treatment_protocol: Patients had been fasting over night. An abdominal subcutaneous adipose tissue needle biopsy was obtained under local anesthesia. The biopsy was rapidly rinsed in saline and snap frozen in liquid nitrogen.

tag: tissue

value: abdominal subcutaneous adipose tissue

tag: gender

value: female

tag: age

value: 36 yrs

tag: treatment

value: SFA diet

tag: time

value: week 0

tag: individual identifier


title: Hemocytes of R. philippinarum injected (intramuscular infection) with V. alginolyticus at 72h after challenge, I3_72H

description:
I3_72H
Hemocytes RNA of Ruditapes philippinarum.


title: Hemocytes of R. philippinarum injected (intramuscular infection) with V. alginolyticus at 72h after challenge, I2_72H

description:
I2_72H
Hemocytes RNA of Ruditapes philippinarum.


title: G901 rep 2

city: Boston

first: Svitlana

last: Tyekucheva

state: MA

address: 450 Brookline Ave

country: USA

institute: Dana-Farber Cancer Institute

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The data were RMA normalized using Bioconductor package 'oligo' version 1.24.2.

source_name: ovarian cancer

label_protocol: WT-Ovation FFPE System V2 (NuGEN Inc; San Carlos, CA)

extract_protocol: RNA was extracted from paraffin scrolls using the RNeasy FFPE kit (Qiagen) with modification.  In brief, 1 ml of xylene was first added to a 25 μm paraffin scroll, vortexed vigorously for 10 sec and centrifuged at full speed for 2 min.  Supernatant was then removed and 1 ml of ethanol (100%) was added to the pellet, mixed by vortexing and centrifuged at full speed for 2 min.  Supernatant was removed and the tube was incubated at room temperature from 10 min with lid opened.  Subsequently, RNA was extracted using reagents provided in the RNeasy FFPE extraction kit according to the manufacturer’s instruction.  Finally, purified RNA was eluted from the RNeasy MinElute spin column using 30 μl RNase-free water.

tag: block age

tag: diagnosis

value: clear cell carcinoma

tag: percent tumor

tag: percent necrosis


title: Hemocytes of R. philippinarum injected (intramuscular infection) with V. alginolyticus at 72h after challenge, I5_72H

description:
I5_72H
Hemocytes RNA of Ruditapes philippinarum.


title: PUFA, 113_W0

source_name: white adipose tissue, PUFA, week 0

value: male

value: 28 yrs

value: PUFA diet


title: Meningioma patient H1239

type: other

city: Homburg/Saar

first: Christian

middle: Clemens

last: Harz

state: Saarland

address: Kirrberger Strasse 100

department: Department of Human Genetics

country: Germany

institute: Saarland University

description: 163 peptides, representing TXNDC16, were spotted in duplicates to identify seroreaction of serum autoantibodies

hyb_protocol: Arrays were blocked o.N. at 4°C (Blocking solution: 50mM Tris, 150mM NaCl, pH 7.5, 5% dry milk powder). Arrays were then incubated with serum (1:1,000 diluted in blocking solution) o.N. at 4°C. Arrays were washed three times with TBS-T (50mM Tris, 150mM NaCl, pH 7.5, 0.05% Tween20) for 10 min at RT and then incubated with Cy5-conjugated AffiniPure Rabbit Anti-Human IgA + IgG + IgM (H + L) (Dianova) (1:1,000 diluted in blocking solution) for 2h at RT. After secondary antibody incubation, arrays were washed twice with TBS-T and twice with TBS for 10 min at RT.

scan_protocol: The arrays were then scanned at 20-µm resolution (PTM Voltages 40) with a PerkinElmer ScanArray Express, images of the peptide arrays were processed with ScanArray Express software and signal intensities quantified

data_processing:
Column Ch1 Mean was extracted from all raw data files. All values for empty and GRID spots were excluded, leaving 326 (163 in duplicates) data point for each sample. All spots were classified into three groups via their mean foreground intensity values (2 “strongly seropositive” if x >= quantile 0.95, 1 “weakly seropositive” if quantile 0.8 <= x < quantile 0.95 and 0 “seronegative” if x < quantile 0.8). For each peptide, both spot values were multiplied, resulting 4 - strongly seroreactive, 2 - moderatly seroreactive, 1 - weakly seroreactive, 0 - seronegative.
Please note that the non_normalized.txt contains  Ch1 Mean values for all samples (each sequence represented in duplicates) and the identifiers in the 'index' column corresponds to those in the 'index' column in raw gpr files; sample data table contains classification values (for each sequence) described above.

molecule: other

source_name: Meningioma patient serum

label_protocol: No label was performed on the serum sample.

extract_protocol: Blood samples were centrifuged immediatly after withdrawal at 3,000 x g for 10 min and sera were subsequently stored at -20°C.

tag: subject status

value: Meningioma patient

tag: age (yrs)

tag: tumor stage

value: WHO grade III

tag: molecule type

value: serum autoantibodies


title: SFA, 112_W0

value: 34 yrs


title: G765 rep

value: serous carcinoma


title: G319 rep


title: Meningioma patient H1193


title: Meningioma patient H1213

value: WHO grade I


title: Hemocytes of R. philippinarum injected (intramuscular infection) with V. alginolyticus at 72h after challenge, I1_72H

description:
I1_72H
Hemocytes RNA of Ruditapes philippinarum.

value: hemocytes

value: Vibrio alginolyticus


title: G800 rep


title: Meningioma patient H1129


title: G901


title: PUFA, 111_W0

value: abdominal subcutaneous adipose tissue

value: 33 yrs


title: Hemocytes of R. philippinarum injected (intramuscular infection) with V. alginolyticus at 24h after challenge, I4_24H

description:
I4_24H
Hemocytes RNA of Ruditapes philippinarum.

source_name: Hemocytes, injected with Vibrio alginolyticus, 24 hours after challenge

value: 24 hours


title: SFA, 108_W0

value: 24 yrs

value: SFA diet


title: SFA, 109_W0

value: 26 yrs

value: week 0


title: Hemocytes of R. philippinarum injected (intramuscular infection) with V. alginolyticus at 24h after challenge, I3_24H

description:
I3_24H
Hemocytes RNA of Ruditapes philippinarum.


title: G969


title: G794 rep

value: clear cell carcinoma


title: Meningioma patient H1119

value: female

value: unknown


title: Meningioma patient H1102

value: Meningioma patient


title: Meningioma patient H1093

value: serum autoantibodies


title: Hemocytes of R. philippinarum injected (intramuscular infection) with V. alginolyticus at 24h after challenge, I2_24H

description:
I2_24H
Hemocytes RNA of Ruditapes philippinarum.


title: Hemocytes of R. philippinarum injected (intramuscular infection) with V. alginolyticus at 8h after challenge, I5_8H

description:
I5_8H
Hemocytes RNA of Ruditapes philippinarum.

source_name: Hemocytes, injected with Vibrio alginolyticus, 8 hours after challenge

value: 8 hours


title: PUFA, 107_W0

value: 27 yrs

value: PUFA diet


title: G765

value: serous carcinoma


title: Meningioma patient H1003

value: male

value: WHO grade I


title: Meningioma patient H767

value: WHO grade III


title: Meningioma patient H537


title: Hemocytes of R. philippinarum injected (intramuscular infection) with V. alginolyticus at 8h after challenge, I4_8H

description:
I4_8H
Hemocytes RNA of Ruditapes philippinarum.

value: hemocytes

value: Vibrio alginolyticus


title: PUFA, 106_W0

value: abdominal subcutaneous adipose tissue

value: 35 yrs


title: G653


title: Meningioma patient H386


title: Hemocytes of R. philippinarum injected (intramuscular infection) with V. alginolyticus at 8h after challenge, I3_8H

description:
I3_8H
Hemocytes RNA of Ruditapes philippinarum.


title: PUFA, 102_W0

value: 28 yrs

value: week 0


title: G403

value: clear cell carcinoma


title: Meningioma patient H50

value: unknown


title: PUFA, 104_W0

value: 22 yrs


title: Meningioma patient H72

value: Meningioma patient

value: female

value: serum autoantibodies


title: Meningioma patient H365

value: WHO grade II


title: Meningioma patient H149


title: PUFA, 103_W0

value: 31 yrs

value: PUFA diet


title: G776


title: Hemocytes of R. philippinarum injected (intramuscular infection) with V. alginolyticus at 3h after challenge, I4_3H

description:
I4_3H
Hemocytes RNA of Ruditapes philippinarum.

source_name: Hemocytes, injected with Vibrio alginolyticus, 3 hours after challenge

value: 3 hours


title: G678

value: serous carcinoma


title: G794


title: Hemocytes of R. philippinarum injected (intramuscular infection) with V. alginolyticus at 3h after challenge, I1_3H

description:
I1_3H
Hemocytes RNA of Ruditapes philippinarum.

value: hemocytes


title: Hemocytes of R. philippinarum injected (intramuscular infection) with V. alginolyticus at 3h after challenge, I2_3H

description:
I2_3H
Hemocytes RNA of Ruditapes philippinarum.

value: Vibrio alginolyticus


title: Hemocytes of R. philippinarum injected (intramuscular infection) with V. alginolyticus at 3h after challenge, I5_3H

description:
I5_3H
Hemocytes RNA of Ruditapes philippinarum.


title: Hemocytes of R. philippinarum injected (intramuscular infection) with V. alginolyticus at 8h after challenge, I1_8H

description:
I1_8H
Hemocytes RNA of Ruditapes philippinarum.

value: 8 hours


title: Hemocytes of R. philippinarum injected (intramuscular infection) with V. alginolyticus at 8h after challenge, I2_8H

description:
I2_8H
Hemocytes RNA of Ruditapes philippinarum.


title: PUFA, 101_W0

value: abdominal subcutaneous adipose tissue


title: G366


title: Hemocytes of R. philippinarum injected (intramuscular infection) with V. alginolyticus at 3h after challenge, I3_3H

description:
I3_3H
Hemocytes RNA of Ruditapes philippinarum.


title: G366 rep


title: Hemocytes of R. philippinarum injected (intramuscular) with PBS at 72h after challenge, C4_72H

description:
C3_72H
Hemocytes RNA of Ruditapes philippinarum.

source_name: Hemocytes, injected with PBS, 72 hours after challenge

treatment_protocol: Clams were notched in the shell next to the adductor muscles and injected with 100 µl of PBS. After stimulation, clams were returned to the tanks and maintained at 15ºC until hemocytes sampling.

value: PBS

value: 72 hours


title: G319


title: G800

value: clear cell carcinoma


title: 90-8TL_LACZ_JQ1_3

first: Thomas

last: De Raedt

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Harvard Medical School -  Brigham Women's Hospital

description: Gene expression data from JQ1 treated cells

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: BRB array tools

source_name: MPNST cell line 90-8TL_LACZ_100nM_JQ1_24h

label_protocol: Nugen Applause WT-amp ST kit

growth_protocol: 10% FBS, DMEM

extract_protocol: Trizol followed by RNeasy cleanup

treatment_protocol: 24h DMSO or 100nM JQ1

tag: cell line

value: MPNST cell line 90-8TL


title: Hemocytes of R. philippinarum injected (intramuscular) with PBS at 72h after challenge, C5_72H

description:
C5_72H
Hemocytes RNA of Ruditapes philippinarum.


title: genomic DNA from normal colon biopsies 191A

type: genomic

city: Basel

first: Faiza

last: Noreen

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27k Beadchip using standard Illumina protocol.

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

data_processing: Mean non-background corrected signal intensities of the methylated (M) and unmethylated (U) for each CpG locus were extracted using the Illumina BeadStudio software v3.2. Beta values were calculated after performing smoothQuantileNrmalization for color balance adjustment followed by background level corection and quantile based probe level normalization. We masked data point as “NA” for the following conditions; 1) Probes containing single-nucleotide polymorphisms (SNPs), 2) those that overlap with a repetitive element that covers the targeted CpG dinucleotide, 3) those that overlap with regions of insertions and deletions in the human genome. Beta values with detection P value greater than 0.01 were also replaced as NA. Furthermore, probes containing at least one “NA” across the normal sample set were masked as “NA”. Beta value was calculated as M/(M+U).

label: Cy5 and Cy3

molecule: genomic DNA

source_name: normal colon

label_protocol: Standard Illumina protocol.

extract_protocol: Genomic DNA was extracted and purified from normal colon biopsies using Qiagen DNeasy Kit according to standard instructions.

tag: colonic location

value: proximal

tag: disease state

value: normal

tag: aspirin

value: user

tag: hrt

tag: bmi

value: high

tag: smoking


title: Hemocytes of R. philippinarum injected (intramuscular) with PBS at 72h after challenge, C3_72H

tag: tissue

tag: treatment

tag: time point


title: genomic DNA from normal colon biopsies 517A

tag: gender

value: female

tag: age

value: nonuser


title: Hemocytes of R. philippinarum injected (intramuscular) with PBS at 72h after challenge, C1_72H

description:
C1_72H
Hemocytes RNA of Ruditapes philippinarum.


title: genomic DNA from normal colon biopsies 48A


title: 90-8TL_LACZ_JQ1_2


title: Hemocytes of R. philippinarum injected (intramuscular) with PBS at 72h after challenge, C2_72H

description:
C2_72H
Hemocytes RNA of Ruditapes philippinarum.


title: 90-8TL_LACZ_JQ1_1


title: PUFA, 119_W0

value: male

value: 27 yrs

value: PUFA diet

tag: time

value: week 0

tag: individual identifier


title: IMR90 Apoptosis (GPL17964)

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

description: Regional preferences in apoptotic DNA degradation were determined by co-hybridizing high molecular (> 48 kb) and degraded apoptotic DNA (~4 kb), which we have extracted from 1% low melting agarose and amplified by means of the GenomePlex Whole Genome Amplification Kit .

scan_protocol: scanned on an Agilent DNA Microarray Scanner G2565BA, Scan resolution: 2µm, Scan region: 61 x 21.6 mm, Green PMT: 100%, Red PMT: 100%

data_processing: TIFF image processing with Agilent Feature Extraction v10.5.1.1, CGH_105_Dec08 protocol. Data visualization and further analysis was performed with GenomeCATPro 1.3.1 (Tebel et al., manuscript in preparation; http://www.molgen.mpg.de/~abt_rop/molecular_cytogenetics/CGHPRO.html) and the UCSC genome browser (https://genome.ucsc.edu/index.html).

source_name: fetal lung fibroblast

label_protocol: Agilent Genomic DNA Enzymatic Labeling Kit

growth_protocol: IMR90 cell line was cultured in Eagle´s minimum essential medium (EMEM) supplemented  with 10% fetal bovine serum, 2 mM UltraGlutamine 1, 1 mM sodium pyruvate and 100units/ml penicillin/streptomycin. The fibroblasts were maintained at 37°C with a humidified atmosphere of 5% CO2 and ambient oxygen.

extract_protocol: ChIP was done according to the Transcription Factor ChIP kit protocol (Diagenode, Liège, Belgium). In brief, lysed cells were sonicated  for 60 minutes using the Bioruptor UCD-200 device (Diagenode, Liège, Belgium), followed by overnight incubation of 1x106 cells with 5 µg of antibodies against unmodified histone H3 (ab1791; Abcam, Cambridge, UK) and histone H4 lysine 8 acetylation (pAb-103-050; Diagenode, Liège, Belgium), respectively. The subsequent chromatin reverse crosslinking, elution and purification of ChIP and input DNA were done employing the IPure Kit (Diagenode, Liège, Belgium). Analysis of apoptotic DNA: after treatment cells were washed once in PBS, detached by five minutes treatment with trypsin-EDTA and the cell pellets were stored at -80°. For DNA isolation cells were treated with lysis buffer (0.40 M Tris-HCl pH 8.0, 0.06 M Na-EDTA, 0.15 M NaCl, 1% SDS) and RNA was digested for 1 hour at 37°C using 15 µg/mL RNase A. 1 M sodium perchlorate and one volume chloroform were added to deproteinize cell lysates. After phase separation and collection of the aqueous phase DNA was precipitated. 3 µg of genomic DNA were loaded onto a 1% low melt agarose gel, electrophoresed for 90 minutes at 120 V and stained with ethidium bromide for 30 minutes. DNA bands responding to non-fragmented (> 48 kb) and fragmented DNA (approximately 4 kb) were cut with a scalpel and collected. For the extraction of DNA from the gel pieces β-Agarase I (New England Biolabs, Ipswich, USA) was used according to the manufacturer´s protocol.

treatment_protocol: Apoptosis  was induced by staurosporine (Cell Signaling Technology, Inc., Danvers, USA), which was dissolved in dimethyl sulfoxide (DMSO, Sigma, Saint Louis, USA) to a stock concentration of 1 mmol/L. About 2 x 10^6 cells were exposed to either 1 µmol/L staurosporine/0.1%DMSO or 0.1% DMSO alone as a control for 4 hours at 37°C.

tag: sample type

value: DNA fragment ~ 4 kb

value: DNA fragment > 48 kb


title: genomic DNA from normal colon biopsies 271A


title: 90-8TL_SUZ12_3

description: Gene expression data from SUZ12 re-expressed cells

source_name: MPNST cell line 90-8TL_SUZ12-reexpression_DMSO

value: SUZ12 overexpression


title: genomic DNA from normal colon biopsies M031A


title: S. clavuligerus ΔccaR_Stationary growth phase_rep4

type: mixed

city: León

first: Paloma

last: Liras

state: León, Spain

address: Facultad de Biología. Campus de Vegazana

department: Molecular Biology

country: Spain

institute: Universidad de León

description:
Biological replicate 4 of 4. Stationary phase
D2.ccaR_t2-rep4

hyb_protocol: Cy3-cDNA (300 ng) and Cy5-labeled gDNA (10 pmol) were mixed, vacuum dried, resuspended in 32 μl of hybridization solution (Agilent) and applied on the microarray surface. Hybridizations were carried out at 55ºC and extended to 60 h to improve the quality of the results.

scan_protocol: Scanned on an Agilent DNA Microarray Scanner G2565BA. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Microarray data were normalized with the Bioconductor package limma (Smyth and Speed, 2003; Smyth, 2004). Weigthed median was applied within arrays. Weights were assigned as follows: 1, probes corresponding to S. coelicolor genes showing a raw Cy3 intensity value higher than 2000; 0.25, probes corresponding to S. clavuligerus genes; 0, the rest of probes. The normalized log2 of Cy3/Cy5 intensities is referred as the Mg value, which is proportional to the abundance of transcripts for a particular gene (Mehra et al., 2006).

organism: Streptomyces clavuligerus

source_name: ΔccaR_Stationary growth phase_totalRNA

label_protocol: Labelling reactions were performed according to the recommendations described by BioPrime® Array CGH Genomic Labeling Systems (Life Technologies). Total RNA was labelled with Cy3-dCTP (Amersham) using random primers and SuperScript™ II reverse transcriptase (Invitrogen). gDNA was labelled with Cy5-dCTP (Amersham) from random primers extended with the Klenow fragment of DNA polymerase (Roche). The final products were purified with MinElute columns (Qiagen) and labelling efficiencies were quantified spectrophotometrically.

growth_protocol: Culture conditions were optimized using SA medium (Starch-Asparagine, Aido et al., 1994) and the samples to extract RNA were collected at the exponential phase and early stationary growth phase of the cultures.

extract_protocol: 1% β-mercaptoethanol was added to stabilized culture samples. After 10 min the samples, in a cryogenic bath, were sonicated with 6 pulses of 30 s in a XL2020 Sonifier, set at 3.5 volts. The preparation was extracted with one volume of phenol/chloroform-isoamilic alcohol and the aqueous-phase was applied to RNeasy Mini Kit Columns (Qiagen) according to the manufacturer’s instructions. RNA preparations were incubated with DNaseI (Qiagen) to eliminate DNA contamination. Sample quantification was done with a NanoDrop ND-1000 UV-Vis Spectrophotometer and the integrity of the RNA was determined in a Bioanalyzer 2100 (Agilent Technologies). Only RNAs with an RNA integrity value above 7.0 were used.

treatment_protocol: Samples from the Streptomyces cultures were stabilized with two volumes of RNA Protect Bacteria Reagent (Qiagen) for 5 min

tag: strain

value: ΔccaR

value: Stationary growth phase

source_name: ATCC 27064_Stationary growth phase_genomicDNA [reference]


title: S. clavuligerus ΔccaR_Stationary growth phase_rep3

description:
Biological replicate 3 of 4. Stationary phase
D2.ccaR_t2-rep3


title: 90-8TL_SUZ12_2


title: Hemocytes of R. philippinarum injected (intramuscular) with PBS at 24h after challenge, C2_24H

description:
C2_24H
Hemocytes RNA of Ruditapes philippinarum.

source_name: Hemocytes, injected with PBS, 24 hours after challenge

value: hemocytes

value: PBS

value: 24 hours


title: IMR90 H4K8ac (GPL17964)

value: IP DNA

tag: chip antibody

tag: chip antibody manufacturer

value: Diagenode

tag: chip antibody catalog #

value: Input DNA


title: Hemocytes of R. philippinarum injected (intramuscular) with PBS at 24h after challenge, C3_24H

description:
C3_24H
Hemocytes RNA of Ruditapes philippinarum.


title: Hemocytes of R. philippinarum injected (intramuscular) with PBS at 24h after challenge, C5_24H

description:
C5_24H
Hemocytes RNA of Ruditapes philippinarum.


title: genomic DNA from normal colon biopsies K051A

value: female

tag: colonic location

value: proximal

tag: disease state

value: normal

value: user

value: high


title: 90-8TL_SUZ12_1

tag: cell line

value: MPNST cell line 90-8TL


title: 90-8TL_LACZ_veh_3

description: Gene expression data from control

source_name: MPNST cell line 90-8TL_LACZcontrol_DMSO

value: control


title: genomic DNA from normal colon biopsies K063A

tag: aspirin

value: nonuser

tag: hrt

tag: bmi


title: 90-8TL_LACZ_veh_2

description: Gene expression data from control

tag: treatment


title: S. clavuligerus ΔccaR_Stationary growth phase_rep2

description:
Biological replicate 2 of 4. Stationary phase
D2.ccaR_t2-rep2


title: Hemocytes of R. philippinarum injected (intramuscular) with PBS at 24h after challenge, C1_24H

description:
C1_24H
Hemocytes RNA of Ruditapes philippinarum.

tag: tissue

tag: time point


title: 90-8TL_LACZ_veh_1

description: Gene expression data from control


title: S. clavuligerus ΔccaR_Stationary growth phase_rep1

description:
Biological replicate 1 of 4. Stationary phase
D2.ccaR_t2-rep1


title: Hemocytes of R. philippinarum injected (intramuscular) with PBS at 8h after challenge, C5_8H

description:
C5_8H
Hemocytes RNA of Ruditapes philippinarum.

source_name: Hemocytes, injected with PBS, 8 hours after challenge

value: 8 hours


title: Hemocytes of R. philippinarum injected (intramuscular) with PBS at 8h after challenge, C3_8H

description:
C3_8H
Hemocytes RNA of Ruditapes philippinarum.


title: genomic DNA from normal colon biopsies K123A

tag: gender

tag: age

tag: smoking


title: Hemocytes of R. philippinarum injected (intramuscular) with PBS at 3h after challenge, C5_3H

description:
C5_3H
Hemocytes RNA of Ruditapes philippinarum.

source_name: Hemocytes, injected with PBS, 3 hours after challenge

value: 3 hours


title: S. clavuligerus ΔccaR_Exponential growth phase_rep4

description:
Biological replicate 4 of 4. Exponential phase
D1.ccaR_t1-rep4

source_name: ΔccaR_Exponential growth phase_totalRNA

value: ΔccaR

tag: time

value: Exponential growth phase

value: Stationary growth phase


title: Hemocytes of R. philippinarum injected (intramuscular) with PBS at 8h after challenge, C1_8H

description:
C1_8H
Hemocytes RNA of Ruditapes philippinarum.

value: hemocytes

value: PBS


title: S. clavuligerus ΔccaR_Exponential growth phase_rep3

description:
Biological replicate 3 of 4. Exponential phase
D1.ccaR_t1-rep3

tag: strain


title: F344_14W_7

city: Münster

first: Mona

last: Riemenschneider

address: Domagkstraße 3

institute: Genetic Epidemiology, University of Muenster

hyb_protocol: direct hybridization of the generated cRNA was done according to the manufacturer´s instruction.

scan_protocol: hybridized arrays were scanned using the BeadArray Reader (Illumina).

data_processing: raw data pre-processing was executed with Genome Studio (Illumina, Version 1.9.0). The data were normalised using quantile normalisation in R with methods of package 'lumi' and log2 transformed.

organism: Rattus norvegicus

source_name: left ventricle without interventricular septum

label_protocol: Biotinylated, amplified cRNA was generated using the Illumina TotalPrep RNA Amplification Kit (Life Technologies) according to the manufacturer´s instruction.

extract_protocol: total RNA was isolated using a standard trizol assay (TRIzol, Invitrogen Life Technologies) according to the manufacturer´s instructions.

value: male

value: heart

tag: developmental stage

value: 14 weeks


title: S. clavuligerus ΔccaR_Exponential growth phase_rep2

description:
Biological replicate 2 of 4. Exponential phase
D1.ccaR_t1-rep2


title: genomic DNA from normal colon biopsies K017C

value: female

value: distal


title: genomic DNA from normal colon biopsies K077A

value: proximal

value: normal


title: S. clavuligerus ΔccaR_Exponential growth phase_rep1

description:
Biological replicate 1 of 4. Exponential phase
D1.ccaR_t1-rep1


title: F344_14W_3


title: S. clavuligerus oppA2::aph_Stationary growth phase_rep4

description:
Biological replicate 4 of 4. Stationary phase
B2.oppA2_t2-rep4


title: F344_14W_5


title: genomic DNA from normal colon biopsies M002C

value: user

value: high


title: genomic DNA from normal colon biopsies M032A

value: nonuser


title: S. clavuligerus oppA2::aph_Stationary growth phase_rep2

description:
Biological replicate 2 of 4. Stationary phase
B2.oppA2_t2-rep2


title: genomic DNA from normal colon biopsies K017A


title: F344_14W_8


title: genomic DNA from normal colon biopsies M002A


title: Hemocytes of R. philippinarum injected (intramuscular) with PBS at 8h after challenge, C2_8H

description:
C2_8H
Hemocytes RNA of Ruditapes philippinarum.

value: 8 hours


title: Hemocytes of R. philippinarum injected (intramuscular) with PBS at 3h after challenge, C3_3H

description:
C3_3H
Hemocytes RNA of Ruditapes philippinarum.

value: 3 hours


title: Hemocytes of R. philippinarum injected (intramuscular) with PBS at 3h after challenge, C4_3H

description:
C4_3H
Hemocytes RNA of Ruditapes philippinarum.


title: F344_14W_4


title: S. clavuligerus oppA2::aph_Stationary growth phase_rep3

description:
Biological replicate 3 of 4. Stationary phase
B2.oppA2_t2-rep3


title: F344_14W_6


title: F344_14W_2


title: genomic DNA from normal colon biopsies K018A


title: Hemocytes of R. philippinarum injected (intramuscular) with PBS at 3h after challenge, C2_3H

description:
C2_3H
Hemocytes RNA of Ruditapes philippinarum.


title: genomic DNA from normal colon biopsies K064C


title: genomic DNA from normal colon biopsies K124C


title: S. clavuligerus oppA2::aph_Exponential growth phase_rep3

description:
Biological replicate 3 of 4. Exponential phase
B1.oppA2_t1-rep3


title: SHRSP_E20_4

source_name: whole heart

value: SHRSP


title: F344_14W_1


title: genomic DNA from normal colon biopsies 359A


title: SHRSP_E20_3


title: S. clavuligerus oppA2::aph_Exponential growth phase_rep4

description:
Biological replicate 4 of 4. Exponential phase
B1.oppA2_t1-rep4

value: Exponential growth phase


title: S. clavuligerus oppA2::aph_Exponential growth phase_rep2

description:
Biological replicate 2 of 4. Exponential phase
B1.oppA2_t1-rep2

value: Stationary growth phase


title: Hemocytes of R. philippinarum injected (intramuscular) with PBS at 3h after challenge, C1_3H

description:
C1_3H
Hemocytes RNA of Ruditapes philippinarum.

value: hemocytes


title: genomic DNA from normal colon biopsies K124A


title: S. clavuligerus ATCC 27064_Stationary growth phase_rep2

description:
Biological replicate 2 of 4. Control strain. Stationary phase
A2.wt_t2-rep2

source_name: ATCC 27064_Stationary growth phase_totalRNA


title: SHRSP_E20_1


title: S. clavuligerus ATCC 27064_Stationary growth phase_rep4

description:
Biological replicate 4 of 4. Control strain. Stationary phase
A2.wt_t2-rep4


title: SHRSP_14W_7


title: genomic DNA from normal colon biopsies 516A


title: S. clavuligerus oppA2::aph_Stationary growth phase_rep1

description:
Biological replicate 1 of 4. Stationary phase
B2.oppA2_t2-rep1


title: S. clavuligerus ATCC 27064_Stationary growth phase_rep3

description:
Biological replicate 3 of 4. Control strain. Stationary phase
A2.wt_t2-rep3


title: genomic DNA from normal colon biopsies K064A


title: genomic DNA from normal colon biopsies 48C


title: Time0-B

city: Berkeley

first: Hugh

last: Salamon

state: CA

address: 725 Folger Avenue

institute: Knowledge Synthesis Inc.

description: THP-1 cells were cultured in 24-well flat bottom plates, pre-treated with 20ng/ml PMA for 24 h

hyb_protocol: The Affymetrix Genechip WT Terminal Labeling and Hybridization protocol was used

scan_protocol: Chips were scanned using the Affymetrix 7G Plus scanner and Command Console Software

data_processing: Probeset expression was summarized with the RMA method using APT 1.15.0 software.  Command options included -a rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish.expon=true and --qc-probesets.

source_name: THP-1 cells, 0 hr, uninfected, untreated

label_protocol: The Ambion WT Expression Kit with accompanying protocol was used to label the samples

growth_protocol: Cells cultured in 24-well flat bottom plates 5 X 105 cells per well were pre-treated with 20ng/ml PMA for 24 h, and incubated with M. tuberculosis H37Rv.After 4 hours of infection, the medium was removed, cells were washed  to remove extracellular bacteria, and fresh medium was added

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

treatment_protocol: Cells were treated with VITD 4 hours after infection. THP-1 cells were washed with PBS at 24h and  collected  for analysis

value: 0 hr

tag: infection

value: uninfected

value: untreated


title: S. clavuligerus oppA2::aph_Exponential growth phase_rep1

description:
Biological replicate 1 of 4. Exponential phase
B1.oppA2_t1-rep1


title: Time0-A

value: 100 nM of 1α,25-dihydroxyvitamin D3


title: SHRSP_E20_2

value: male

value: heart


title: SHRSP_14W_6

value: 14 weeks


title: Time0-C


title: SHRSP_14W_5


title: genomic DNA from normal colon biopsies 191C

value: female

value: distal

value: normal


title: genomic DNA from normal colon biopsies M029A

value: proximal

value: user

value: high

value: nonuser


title: Uninf-VitD-B

source_name: THP-1 cells, 24 hr, uninfected, Vit D-treated

value: 24 hr


title: Uninf-VitD-A


title: Uninf-C

source_name: THP-1 cells, 24 hr, uninfected, untreated


title: S. clavuligerus ATCC 27064_Exponential growth phase_rep4

description:
Biological replicate 4 of 4. Control strain. Exponential phase
A1.wt_t1-rep4

source_name: ATCC 27064_Exponential growth phase_totalRNA

value: Exponential growth phase

value: Stationary growth phase


title: SHRSP_14W_4

value: SHRSP


title: genomic DNA from normal colon biopsies K087A

source_name: normal colon


title: S. clavuligerus ATCC 27064_Exponential growth phase_rep1

description:
Biological replicate 1 of 4. Control strain. Exponential phase
A1.wt_t1-rep1


title: Uninf-B

value: uninfected


title: SHRSP_14W_3


title: S. clavuligerus ATCC 27064_Exponential growth phase_rep3

description:
Biological replicate 3 of 4. Control strain. Exponential phase
A1.wt_t1-rep3


title: genomic DNA from normal colon biopsies 173A


title: genomic DNA from normal colon biopsies K051C


title: S. clavuligerus ATCC 27064_Exponential growth phase_rep2

description:
Biological replicate 2 of 4. Control strain. Exponential phase
A1.wt_t1-rep2


title: Uninf-A

value: untreated


title: genomic DNA from normal colon biopsies 214C


title: S. clavuligerus ATCC 27064_Stationary growth phase_rep1

description:
Biological replicate 1 of 4. Control strain. Stationary phase
A2.wt_t2-rep1


title: genomic DNA from normal colon biopsies M031C


title: Inf-VidD-A

source_name: THP-1 cells, 24 hr, Mtb-infected, Vit D-treated

value: M. tuberculosis H37Rv

value: 100 nM of 1α,25-dihydroxyvitamin D3


title: SHRSP_14W_2

value: male

value: heart


title: Inf-VidD-B


title: SHRSP_14W_1

value: 14 weeks


title: F344_E20_7


title: Inf-VidD-C


title: F344_E20_6


title: Inf-C

source_name: THP-1 cells, 24 hr, Mtb-infected, untreated


title: genomic DNA from normal colon biopsies 10C

value: female

value: distal


title: Inf-A


title: genomic DNA from normal colon biopsies 135A

value: proximal

value: normal


title: Inf-B


title: F344_E20_5


title: genomic DNA from normal colon biopsies 517C

value: high

value: user


title: F344_E20_2


title: genomic DNA from normal colon biopsies 271C

value: nonuser


title: genomic DNA from normal colon biopsies K724A


title: F344_E20_3


title: genomic DNA from normal colon biopsies 373A


title: genomic DNA from normal colon biopsies 359C


title: genomic DNA from normal colon biopsies M020A


title: F344_E20_1


title: genomic DNA from normal colon biopsies 40A


title: genomic DNA from normal colon biopsies K077C


title: genomic DNA from normal colon biopsies 95A


title: genomic DNA from normal colon biopsies 44C


title: Lung_15mgSilica_12weekexposure_rep5

city: Morgantown

first: Christina

middle: M

last: Umbright

state: WV

address: 1095 Willowdale Road

department: HELD

institute: DHHS/PHS/CDC/NIOSH

description: The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

hyb_protocol: Employing materials and protocols provided by Illumina, Inc (San Diego, CA,), each labeled cRNA sample was hybridized to RatRef-12 v1.0 expression beadchip (Illumina, Inc,) for 20 hrs at 58oC. Following hybridization, microarrays were washed to remove unbound and non-specifically hybridized target molecules and stained with Cy3-streptavidin conjugate (Illumina, Inc.). This was followed by a non-stringent washing to remove unbound conjugate.

scan_protocol: The arrays were scanned with the Illumina BeadStation 500 platform, following the protocol provided by the manufacturer (Illumina, Inc).

data_processing: Array data were extracted using Illumina's BeadStudio software (Framework version 3.0.19.0). Normalization and statistical analysis of the expression data were carried out in R/Bioconducter using the ‘lumi’ and ‘limma’ packages. The ‘lumi’ Bioconductor package covered the data input, quality control, force positive background correction, variance stabilization, normalization and gene annotation (http://bioconductor.org/packagees/2.2/ bioc/vignettes/lumi/inst/doc/lumi.pdf). Robust spline normalization was used to generate the values in the matrix table. After normalization, Lumi code deletes genes undetected (detection p-value, >0.01) and resulting in a subset of genes detected (detection p-value, <0.01) on the array. A linear model analysis using ‘limma’ package in R was conducted to identify differentially expressed genes. p values were calculated and log fold changes were converted to standard fold changes.  Resulting raw p-values were corrected for false discovery rate using the Benjamini-Hochberg method.

label: Biotin, Cy3-streptavidin

label_protocol: Biotin-labeled cRNA was generated from 375 ng RNA samples each by employing the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc, Austin, TX).

extract_protocol: Total RNA was isolated from the lung samples using RNeasy Fibrous Tissue Mini Kit (Qiagen, Inc, Valencia, CA) with on-column DNA digestion following the manufacturer's instructions.

value: CDF Fisher 344

value: 3 months

value: lung

value: 15mg/m3 silica

value: 12 weeks


title: genomic DNA from normal colon biopsies K705A


title: genomic DNA from normal colon biopsies K063C


title: Lung_15mgSilica_12weekexposure_rep1


title: F344_E20_4


title: Lung_15mgSilica_12weekexposure_rep2


title: breast tumor [TAM_423]

city: Stuttgart

first: Hiltrud

last: Brauch

address: Auerbachstr. 112

institute: Dr. Margarete Fischer-Bosch - Institute of Clinical Pharmacology

description: matched to TAM_333

hyb_protocol: Hybridisation, washing  and staining of GeneChip miRNA 2.0 arrays on Fluidics station 450 (fluidics script FS450_0003) was done as described in the specifications from Affymetrix

scan_protocol: GeneChip scanning was performed on the Affymetrix GCS3000 Scanner with autoloader, default AGCC scan parametres have been used

data_processing: Affymetrix software miRNA QC Tool (version 1.1.1.0, Affymetrix, 2010) was used for quality control of microarrays. Pre-processing of expression data was performed by robust multichip average (RMA) over 43 breast tumor samples (the 12 TAM samples plus additional 31 tumour samples not selected by a specific therapy).

source_name: breast tumor, non-recurrence

label_protocol: 300 ng of total RNA were labeled with biotin according to the standard Affymetrix protocol (FlashTag Biotin HSR Labeling procedure)

extract_protocol: Total RNA was isolated using RecoverAll Total Nucleic Acid Isolation Kit for FFPE (Life Technologies, Inc.) according to the manufacturer's specifications

tag: state of recurrence

value: Non-recurrence


title: Lung_15mgSilica_12weekexposure_rep3


title: Lung_0mgSilica_12weekexposure_rep5

value: 0mg/m3 silica


title: genomic DNA from normal colon biopsies 56A

tag: colonic location


title: Lung_15mgSilica_12weekexposure_rep4

value: male


title: Lung_15mgSilica_12weekexposure_rep6


title: Lung_0mgSilica_12weekexposure_rep6


title: Lung_0mgSilica_12weekexposure_rep3


title: breast tumor [TAM_81]

description: matched to TAM_372


title: genomic DNA from normal colon biopsies K078C

tag: disease state


title: genomic DNA from normal colon biopsies K705C


title: Lung_0mgSilica_12weekexposure_rep1


title: breast tumor [TAM_251]

description: matched to TAM_51


title: breast tumor [TAM_239]

description: matched to TAM_473


title: Lung_0mgSilica_12weekexposure_rep4


title: genomic DNA from normal colon biopsies K078A


title: breast tumor [TAM_90]

description: matched to TAM_12


title: genomic DNA from normal colon biopsies M027C


title: HepG2 cells_epigallocatechin gallate _50mg/L_5h_rep2

city: Tarragona

first: Anna

last: Arola-Arnal

state: Tarragona

address: Campus Sescelades. C/Marcel.lí Domingo s/n

institute: Universitat Rovira i Virgili

description:
D2
total RNA was extracted together with small RNAs (microRNAs)

hyb_protocol: RNA was suspended in febit's proprietary miRNA Hybridization Buffer (25 μl per array). Hybridization was performed automatically for 16 h at 42ºC using a Geniom RT®-Analyzer. In the next step, the biochip underwent a stringent wash. Following the labeling procedure, febit ran a microfluidic-based primer extension assay. This assay utilizes the bound miRNAs as a primer for an enzymatic elongation with labeled nucleotides. The elongation was performed with Klenow Fragments and biotinylated nucleotides at 37ºC for 15 minutes. Finally, the biochip was washed automatically.

scan_protocol: For maximum sensitivity, febit used biotin, which was detected with streptavidin-phycoerythrin (SAPE), in combination with febit's consecutive Signal Enhancement (CSE) procedure. The feature recognition (using Cy3 filter set) and signal calculation were performed automatically within milliseconds

data_processing:
Spatial effects on the chip were investigated and corrected.
Intensity value distribution of the raw data was analyzed and, if required, normalized using variance stabilizing normalization (VSN).
Analysis and normalization were performed using R/Bioconductor packages including limma and VSN for normalization

source_name: Human hepatocellular liver carcinoma (HepG2) cell line

label_protocol: The probes were designed as the reverse complements of all major mature miRNAs and the mature sequences. Additional nucleotides were added to the 5' end of each capture oligonucleotide as necessary for the enzymatic extension in the labeling procedure. The probes were synthesized with intra-array replicates to increase the statistical confidence and to compensate for potential positional effects. As a result, the raw data files contained 7 data points for each miRNA. The intensities of blank probes, which consisted only of one single T nucleotide, were used for background corrections. Spike-in controls were also performed for the labeling efficiency

growth_protocol: The cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Lonza, BE12-614) supplemented with 10% fetal bovine serum (Lonza, BE-14-802-F), 0.1 mM nonessential amino acids (Sigma, M7145), 100 U/ml penicillin, 100 µg/ml streptomycin (Lonza, BE-17-602E), 2 mM glutamine (Lonza, BE-17-605E), and 25 mM 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid (HEPES, Sigma, H3375) in a humidified incubator with 5% CO2 at 37 °C.

extract_protocol: Total RNA was isolated using the miRNeasy Mini Kit (QIAGEN) following the manufacturer’s protocol.

treatment_protocol: HepG2 cells were treated with 50 mg/L of epigallocatechin gallate, 100 mg/L of grape seed proanthocyanidin extract or 100 mg/L of cacao proanthocyanidin extract dissolved in DMSO (final DMSO concentration in growth media, 0.1%) for 5 h.

tag: cell line source

value: American Type Culture Collection (ATCC, LGC Promochen, HB8065)

tag: treatment group

value: epigallocatechin gallate _50mg/L_5h


title: genomic DNA from normal colon biopsies M007C

value: female

tag: aspirin

tag: hrt


title: Lung_15mgSilica_06weekexposure_rep5

tag: treatment

value: 06 weeks


title: genomic DNA from normal colon biopsies 601C

value: distal

tag: bmi


title: genomic DNA from normal colon biopsies 249C

value: normal


title: HepG2 cells_grape seed proanthocyanidin extract_100mg/L_5h_rep2

description:
C2
total RNA was extracted together with small RNAs (microRNAs)


title: breast tumor [TAM_473]

description: matched to TAM_239

source_name: breast tumor, recurrence

value: Recurrence


title: Lung_15mgSilica_06weekexposure_rep3

tag: tissue


title: breast tumor [TAM_372]

description: matched to TAM_81


title: breast tumor [TAM_51]

description: matched to TAM_251


title: breast tumor [TAM_12]

description: matched to TAM_90


title: genomic DNA from normal colon biopsies K076C

tag: gender

value: user

value: high


title: Lung_15mgSilica_06weekexposure_rep4

value: CDF Fisher 344

tag: age


title: genomic DNA from normal colon biopsies M027A

value: proximal

value: nonuser

tag: smoking


title: Lung_15mgSilica_06weekexposure_rep2

value: 3 months

value: lung

value: 15mg/m3 silica

tag: time


title: breast tumor [TAM_333]

description: matched to TAM_423


title: breast tumor [TAM_308]

description: matched to TAM_386


title: breast tumor [TAM_386]

description: matched to TAM_308

value: Non-recurrence


title: Lung_15mgSilica_06weekexposure_rep1

tag: strain

value: male


title: HepG2 cells_epigallocatechin gallate _50mg/L_5h_rep1

description:
D1
total RNA was extracted together with small RNAs (microRNAs)

value: American Type Culture Collection (ATCC, LGC Promochen, HB8065)


title: HepG2 cells_grape seed proanthocyanidin extract_100mg/L_5h_rep1

description:
C1
total RNA was extracted together with small RNAs (microRNAs)


title: genomic DNA from normal colon biopsies K127C


title: genomic DNA from normal colon biopsies M005C


title: HepG2 cells_cacao proanthocyanidin extract_100mg/L_5h_rep2

description:
B2
total RNA was extracted together with small RNAs (microRNAs)


title: Control_HepG2 cells_untreated_rep1

description:
A1
total RNA was extracted together with small RNAs (microRNAs)

value: untreated


title: HepG2 cells_cacao proanthocyanidin extract_100mg/L_5h_rep1

description:
B1
total RNA was extracted together with small RNAs (microRNAs)


title: Control_HepG2 cells_untreated_rep 2

description:
A2
total RNA was extracted together with small RNAs (microRNAs)


title: GT, nitrogen depleted, rep2

city: Kawasaki

first: Takashi

last: Osanai

state: Kanagawa

address: 1-1-1, Higashimita, Tamaku

department: School of Agriculture

country: Japan

institute: Meiji University

description:
GT2
Glucose-tolerant Synechocystis strain.
Two cDNAs of a gene are spotted on a microarray; therefore, one microarray experiment gives two signal intensities for each gene.

hyb_protocol: Labeling cDNAs are spotted onto CyanoChip (slide glass), and covered by slide glass, followed by incubation at 60 degree for overnight.

scan_protocol: Hybridization signals were measured with a 428 Array scanner (Affymetrix) and a software Affymetrix 428 array scanner version 1.1. Cy3 or Cy5 signals were scanned with 532 nm or 635 nm laser. Resolution were 2200 x 5760 pixels. Scanned pictures were saved as 16-bit TIFF files.

data_processing: Normalization was performed for adjusting total signal intensities between Cy3 and Cy5 by Excel (Microsoft). Each signal intensity was divided by total signal intensities.

organism: Synechocystis sp. PCC 6803

source_name: cyanobacteria, wild-type, nitrogen-depleted conditions

label_protocol: cDNAs were synthesized from total RNA by RNA Fluorescence Labeling Core Kit (M-MLV Version) Ver.2.0 (Takara Bio).

growth_protocol: Cells were grown in modified BG-11 liquid medium (5 mM NH4Cl as nitrogen sources) and transferred to BG-11 medium without nitrogen sources. Cells were cultivated for 4 h after nitrogen depletion under 50-70 micromolphotons/m2s.

extract_protocol: Total RNAs were isolated by hot-phenol method.

tag: genotype/variation

value: wild-type

tag: condition

value: nitrogen depleted


title: NOX10, nitrogen depleted, rep2

description:
NOX10_2
ntcA-overexpression strain.
Two cDNAs of a gene are spotted on a microarray; therefore, one microarray experiment gives two signal intensities for each gene.

source_name: cyanobacteria, ntcA overexpressing, nitrogen-depleted conditions

value: ntcA overexpressing


title: NOX10, nitrogen depleted, rep1

description:
NOX10_1
ntcA-overexpression strain.
Two cDNAs of a gene are spotted on a microarray; therefore, one microarray experiment gives two signal intensities for each gene.


title: NOX10, nitrogen replete, rep3

description:
NOX10_3
ntcA-overexpression strain.
Two cDNAs of a gene are spotted on a microarray; therefore, one microarray experiment gives two signal intensities for each gene.

source_name: cyanobacteria, ntcA overexpressing, nitrogen-replete conditions

growth_protocol: Cells were grown in modified BG-11 liquid medium (5 mM NH4Cl as nitrogen sources) under 50-70 micromolphotons/m2s.

value: nitrogen replete


title: GT, nitrogen depleted, rep1

description:
GT1
Glucose-tolerant Synechocystis strain.
Two cDNAs of a gene are spotted on a microarray; therefore, one microarray experiment gives two signal intensities for each gene.


title: NOX10, nitrogen replete, rep2


title: GT, nitrogen replete, rep3

description:
GT3
Glucose-tolerant Synechocystis strain.
Two cDNAs of a gene are spotted on a microarray; therefore, one microarray experiment gives two signal intensities for each gene.

source_name: cyanobacteria, wild-type, nitrogen-replete conditions


title: genomic DNA from normal colon biopsies K127A

value: female

value: normal


title: genomic DNA from normal colon biopsies K015C

value: distal

value: user


title: genomic DNA from normal colon biopsies K123C

value: high


title: Lung_0mgSilica_06weekexposure_rep5

value: CDF Fisher 344

value: 0mg/m3 silica

value: 06 weeks


title: GT, nitrogen replete, rep2


title: Lung_0mgSilica_06weekexposure_rep6

value: 3 months

value: lung


title: Lung_0mgSilica_06weekexposure_rep3

value: male


title: genomic DNA from normal colon biopsies 237C

value: nonuser


title: genomic DNA from normal colon biopsies K076A

value: proximal


title: Lung_0mgSilica_06weekexposure_rep2


title: Lung_15mgSilica_03weekexposure_rep5

value: 15mg/m3 silica

value: 03 weeks


title: Lung_0mgSilica_06weekexposure_rep4


title: Lung_15mgSilica_03weekexposure_rep6


title: Lung_0mgSilica_06weekexposure_rep1


title: genomic DNA from normal colon biopsies 601A


title: genomic DNA from normal colon biopsies K097C


title: NOX10, nitrogen replete, rep1

value: ntcA overexpressing


title: GT, nitrogen replete, rep1

value: wild-type

value: nitrogen replete


title: genomic DNA from normal colon biopsies 152C

value: female

value: normal


title: Lung_15mgSilica_03weekexposure_rep4


title: genomic DNA from normal colon biopsies 249A

value: user


title: Lung_0mgSilica_03weekexposure_rep6


title: Lung_15mgSilica_03weekexposure_rep3


title: genomic DNA from normal colon biopsies K113C

value: distal

value: high


title: Lung_15mgSilica_03weekexposure_rep1

value: CDF Fisher 344


title: genomic DNA from normal colon biopsies M005A


title: genomic DNA from normal colon biopsies 49C


title: genomic DNA from normal colon biopsies 237A


title: E13.5 WT

city: Yokohama City

first: Yasuharu

last: Ueno

address: 3-9  Fuku-ura, Kanazawa-ku

department: Graduate School of Medicine

institute: Yokohama City University

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

scan_protocol: Slides were scanned immediately after washing on the Agilent High-Resolution Microarray Scanner using one color scan setting for 4x44k v2 array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Mus musculus

source_name: E13.5 Liver cell from WT

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Purification kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For conditional knockout of Ezh2, the Ezh2 f/f mice were crossed with Rosa26::CreER(T2) mice (TaconicArtemis, Cologne, Germany). Mice were intraperitoneally injected with 100 μl of tamoxifen (10 mg / ml, dissolved in corn oil) daily from E8.5 to E10.5 to induce Cre-ERT activity. Embryonic hepatic progenitors were collected at E13.5 as described above from Rosa26::CreER(T2)+/-Ezh2f/f and Rosa26::CreER(T2)-/-Ezh2f/f littermates.

value: CD45- Ter119- liver cells

value: pooled

value: wild type


title: Lung_15mgSilica_03weekexposure_rep2

value: male

value: 3 months

value: lung


title: Lung_0mgSilica_03weekexposure_rep3

value: 0mg/m3 silica


title: Lung_0mgSilica_03weekexposure_rep2

value: 03 weeks


title: genomic DNA from normal colon biopsies 18C

value: nonuser


title: E13.5 Ezh2 KO

source_name: E13.5 Liver cell from Ezh2KO

value: Ezh2 KO


title: Lung_0mgSilica_03weekexposure_rep1


title: genomic DNA from normal colon biopsies K071C


title: Lung_0mgSilica_03weekexposure_rep4


title: genomic DNA from normal colon biopsies K015A

value: proximal


title: Lung_15mgSilica_06weekexposure_rep6

value: 15mg/m3 silica

value: 06 weeks


title: genomic DNA from normal colon biopsies K097A

value: female

value: normal

value: user


title: Lung_0mgSilica_12weekexposure_rep2

value: CDF Fisher 344

value: 12 weeks


title: genomic DNA from normal colon biopsies K106C

value: distal

value: high


title: genomic DNA from normal colon biopsies 275C


title: Tumor 63

city: Groningen

first: Floris

last: Foijer

address: Antonius Deusinglaan 1

department: European Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

hyb_protocol: RNA was hybridyzed using Illumina standard protocols

scan_protocol: Slides were scanned using Illumina standard protocols

data_processing: Data were quantile normalized following scanning and analyzed using Bioconductor lumi and limma packages.

source_name: T-ALL sample 63

label_protocol: Biotinylated cRNA was hybridized to llumina Sentrix Bead Chips and next labeled with streptavidin-conjugated Cy3 (Amersham) according to manufacturer’s protocol.

growth_protocol: Mice were sacrificed in most cases because of T-ALL, see for details accompanying paper, Sup. Data 1 for details tumors' genotypes

extract_protocol: Tissue was homogenized using bead-homogenization in Qiagen RNA-easy buffer 1. RNA was then purified using RNA-easy columns using manufacturer's protocols

treatment_protocol: Thymus, tumor was dissected and tumor samples were stored at -80 in pieces for subsequent analysis

value: T-ALL

value: p53 null

value: tumor

tag: sample type

value: Experiment

value: B6-129Sv mixed


title: genomic DNA from normal colon biopsies 49A

tag: colonic location

value: nonuser


title: Tumor 50

source_name: T-ALL sample 50

tag: disease state

value: Mps1DK p53null


title: genomic DNA from normal colon biopsies 268C


title: 26BK

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

description: carcinoma

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
normalized with BMIQ, version 1.1 (PMID: 23175756), R 3.0.2

unmethylated/methylated signal intensities are unavailable because they were not supplied to submitter by the service provider that performed the measurements

source_name: prostate

label_protocol: Standard Illumina labeling protocol

extract_protocol: DNA was extracted with QIAamp DNA Mini Kit in accordance with the prescribed protocol provided with the kit.

tag: malignacy type

value: Prostate carcinoma

tag: carcinoma percentage

tag: paired sample status

value: carcinoma


title: genomic DNA from normal colon biopsies 152A

value: proximal

tag: aspirin

tag: hrt


title: Tumor 49

source_name: T-ALL sample 49


title: Tumor 52

source_name: T-ALL sample 52


title: Tumor 48

source_name: T-ALL sample 48


title: Tumor 46

source_name: T-ALL sample 46


title: genomic DNA from normal colon biopsies K071A

source_name: normal colon

value: female

tag: bmi


title: 25BK

description: carcinoma


title: Lung_0mgSilica_03weekexposure_rep5

value: male

value: 3 months

tag: tissue

value: lung

tag: treatment

value: 0mg/m3 silica

value: 03 weeks


title: genomic DNA from normal colon biopsies K052C

tag: gender

value: distal

value: normal

tag: age

value: user

value: high


title: ccRCC tumor 2.45

city: Umeå

first: Linda

last: Köhn

address: Building 6M

department: Medical Biosciences/pathology

institute: Umeå University

description: Genomic DNA extracted from clear cell renal cell carcinoma tumors was genotyped using Infinium HumanCytoSNP-12 v2.1 BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from clear cell renal cell carcinoma was genotyped using Infinium HumanCytoSNP-12 v2.1 BeadChips (Illumina).

label: A-DNP, C-Bio

source_name: clear cell renal cell carcinoma

label_protocol: 200 ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-MSM). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FMS), precipitated with isopropanol and precipitation mix (PM1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA was done using a BioRobot M48 Workstation with MagAttract technology (Qiagen)

tag: tumor stage

value: un-metastasized tumor

value: Male

value: Kidney


title: Tumor 47

source_name: T-ALL sample 47

value: T-ALL

value: Mps1DK p53null

value: tumor

value: Experiment

tag: strain

value: B6-129Sv mixed


title: genomic DNA from normal colon biopsies K113A

value: female

value: proximal

tag: smoking

value: nonuser


title: ccRCC tumor 3.28

value: carcinoma


title: ccRCC tumor 3.17

value: metastasized tumor


title: ccRCC tumor 3.25

value: Female


title: 26B

description: carcinoma

value: Prostate carcinoma

value: control


title: genomic DNA from normal colon biopsies K013C

value: distal

value: normal

value: user

value: high


title: Tumor 44

source_name: T-ALL sample 44

value: T-ALL

tag: genotype/variation


title: genomic DNA from normal colon biopsies 18A


title: Tumor 42

source_name: T-ALL sample 42

value: Mps1DK p53null

tag: sample type


title: 23B

description: carcinoma


title: genomic DNA from normal colon biopsies 599C

tag: colonic location


title: Tumor 36

source_name: T-ALL sample 36

tag: disease state

value: p53 null

value: tumor


title: Tumor 38

source_name: T-ALL sample 38

value: Experiment

value: B6-129Sv mixed


title: 20BK

description: carcinoma

tag: malignacy type


title: 23BK

description: carcinoma

tag: carcinoma percentage


title: genomic DNA from normal colon biopsies K106A

value: female

value: proximal


title: Tumor 23

source_name: T-ALL sample 23


title: 21B

description: carcinoma

tag: paired sample status


title: ccRCC tumor 8.09-1A

value: Male

value: Kidney

value: carcinoma


title: 21BK

description: carcinoma

value: Prostate carcinoma


title: genomic DNA from normal colon biopsies 254C

tag: aspirin


title: 25B

description: carcinoma

value: control


title: genomic DNA from normal colon biopsies 268A

tag: hrt

value: nonuser


title: genomic DNA from normal colon biopsies 600C

value: distal

value: normal

tag: bmi


title: ccRCC tumor 8.09-2A

value: metastasized tumor

tag: tissue


title: 20B

description: carcinoma


title: ccRCC tumor 8.09-2B


title: ccRCC tumor 7.41-2A

value: un-metastasized tumor


title: genomic DNA from normal colon biopsies 275A

value: user


title: 18BK

description: carcinoma


title: ccRCC tumor 7.41-2B


title: 19BK

description: carcinoma


title: Tumor 22

source_name: T-ALL sample 22

value: T-ALL

value: Mps1DK p53null


title: Tumor 19

source_name: T-ALL sample 19

value: tumor

value: Experiment


title: ccRCC tumor 7.41-2C


title: Tumor 45

source_name: T-ALL sample 45

value: B6-129Sv mixed


title: genomic DNA from normal colon biopsies 136C

value: female


title: Tumor 20

source_name: T-ALL sample 20


title: ccRCC tumor 7.34-3D

value: Male


title: genomic DNA from normal colon biopsies K052A

value: proximal

value: high


title: 19B

description: carcinoma

source_name: prostate

value: Prostate carcinoma


title: 18B

description: carcinoma

value: control


title: genomic DNA from normal colon biopsies K013A

value: nonuser


title: genomic DNA from normal colon biopsies K092C

value: distal


title: Tumor 11

source_name: T-ALL sample 11


title: Tumor 13

source_name: T-ALL sample 13


title: genomic DNA from normal colon biopsies K86C

value: normal


title: Tumor 10

source_name: T-ALL sample 10


title: Tumor 21

source_name: T-ALL sample 21


title: Tumor 7

source_name: T-ALL sample 7


title: 15B

description: carcinoma


title: ccRCC tumor 7.34-1B

source_name: clear cell renal cell carcinoma

value: Kidney

value: carcinoma


title: ccRCC tumor 7.38-1A

value: un-metastasized tumor


title: Tumor 18

source_name: T-ALL sample 18

value: T-ALL


title: genomic DNA from normal colon biopsies 599A

source_name: normal colon

value: user


title: 14BK

description: carcinoma


title: ccRCC tumor 7.34-1A


title: ccRCC tumor 7.38-2A


title: ccRCC tumor 7.22

value: Female


title: 15BK

description: carcinoma


title: ccRCC tumor 7.18


title: 13BK

description: carcinoma


title: ccRCC tumor 7.38-1D


title: 14B

description: carcinoma


title: Control 5

source_name: Control sample thymus 5

value: wild type

value: thymus

value: Control


title: Control 4

source_name: Control sample thymus 4

value: B6-129Sv mixed


title: genomic DNA from normal colon biopsies 254A

value: female

value: proximal


title: Control 3

source_name: Control sample thymus 3


title: genomic DNA from normal colon biopsies 241C


title: 8BK

description: carcinoma

value: Prostate carcinoma


title: Control 2

source_name: Control sample thymus 2

value: control


title: 13B

description: carcinoma


title: genomic DNA from normal colon biopsies 572C

value: high

value: nonuser


title: ccRCC tumor 7.15

value: Male


title: 8B

description: carcinoma


title: genomic DNA from normal colon biopsies 600A

value: normal


title: ccRCC tumor 7.06

value: Kidney

value: carcinoma


title: Control 1

source_name: Control sample thymus 1


title: mouse-IL15KO-CL diet-3

city: Montréal

first: Mathieu

last: Vernier

state: Quebec

address: 2900 Edouard Montpetit

department: Biochemistry

country: Canada

institute: Université de Montréal

description: Sample 12

data_processing: The data were normalised with the Flexarray program (Genome Quebec) using the RMA background correction and Robust spline normalisation settings

source_name: IL15KO_brown adipose tissue_CL 316243-enriched diet

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: IL15 KO

tag: diet

value: enriched with the beta3-adrenergic agonist CL 316243

value: brown adipose tissue


title: mouse-IL15KO-CL diet-2

description: Sample 11


title: genomic DNA from normal colon biopsies 136A

tag: gender

value: user


title: genomic DNA from normal colon biopsies M029C

value: distal

tag: age


title: 7B

description: carcinoma


title: ccRCC tumor 7.02

tag: tumor stage

value: un-metastasized tumor

value: Female


title: mouse-IL15KO-CL diet-1

description: Sample 10


title: 5BK

description: carcinoma


title: ccRCC tumor 7.03


title: genomic DNA from normal colon biopsies K092A

value: female


title: ccRCC tumor 7.09


title: 7BK

description: carcinoma


title: mouse-IL15KO-normal diet-3

description: Sample 9

source_name: IL15KO_brown adipose tissue_normal diet


title: genomic DNA from normal colon biopsies K087C


title: mouse-IL15KO-normal diet-2

description: Sample 8


title: genomic DNA from normal colon biopsies K86A

value: proximal


title: mouse-IL15KO-normal diet-1

description: Sample 7


title: genomic DNA from normal colon biopsies 173C


title: 27A2

description: carcinoma

value: Prostate carcinoma


title: ccRCC tumor 6.32


title: genomic DNA from normal colon biopsies 572A


title: ccRCC tumor 6.43


title: mouse-wt-CL diet-3

description: Sample 6

source_name: wt_brown adipose tissue_CL 316243-enriched diet

value: wt


title: 22A2

description: carcinoma

source_name: prostate

value: control


title: ccRCC tumor 6.24


title: ccRCC tumor 6.27


title: ccRCC tumor 6.23


title: genomic DNA from normal colon biopsies 135C

value: nonuser

value: high


title: 22A1

description: carcinoma


title: ccRCC tumor 7.12


title: 5B

description: carcinoma


title: mouse-wt-normal diet-3

description: Sample 3

source_name: wt_brown adipose tissue_normal diet

value: normal


title: 26-RP

description: control

value: Bladder carcinoma


title: ccRCC tumor 6.19

value: Kidney

value: carcinoma


title: ccRCC tumor 6.20


title: ccRCC tumor 7.11

value: Male


title: 18-RP

description: control


title: mouse-wt-CL diet-1

description: Sample 4

value: enriched with the beta3-adrenergic agonist CL 316243

value: brown adipose tissue


title: genomic DNA from normal colon biopsies 223A

value: user


title: 19A1

description: carcinoma


title: mouse-wt-normal diet-2

description: Sample 2


title: 28-RP

description: control


title: mouse-wt-CL diet-2

description: Sample 5


title: ccRCC tumor 6.22

value: un-metastasized tumor


title: genomic DNA from normal colon biopsies 62C

value: distal


title: genomic DNA from normal colon biopsies 5A

value: female


title: ccRCC tumor 6.08

value: metastasized tumor


title: ccRCC tumor 6.15

value: Female


title: ccRCC tumor 6.14


title: genomic DNA from normal colon biopsies 223C


title: genomic DNA from normal colon biopsies K714C


title: Kidneys from YapCM-/- (3)

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

institute: University Health Network

description: replicate 3

scan_protocol: Standard Illumina scanning protocol (Genome Studio Version 1.7.0)

data_processing: The data were normalised using quantile normalisation in Genespring (version 12.0) followed by median centered normalization

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep-96 RNA amplification kit (Ambion).

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser using RNA 6000 nano kit (Agilent).

tag: strain

value: Mixed background (C57BL/6 x 129S1/SvImJ)

value: YapCM-/-

value: Embryonic kidneys


title: Kidneys from YapCM-/- (1)

description: replicate 1


title: Kidneys from YapCM-/- (2)

description: replicate 2


title: 1-RP

description: control


title: ccRCC tumor 6.06


title: genomic DNA from normal colon biopsies 516C

value: high

tag: smoking


title: 27A1

description: carcinoma

value: Prostate carcinoma


title: ccRCC tumor 6.33


title: 2-RP

description: control

value: Bladder carcinoma


title: 17-RP

description: control


title: genomic DNA from normal colon biopsies 111C

value: normal

value: nonuser


title: genomic DNA from normal colon biopsies 62A

value: proximal


title: genomic DNA from normal colon biopsies K714A


title: ccRCC tumor 5.20

value: Kidney

value: carcinoma


title: 19A2

description: carcinoma

value: control


title: Kidneys from control (2)

description: replicate 2

source_name: Control (2)

tag: genotype/variation


title: genomic DNA from normal colon biopsies 111A

value: user


title: 31-h

description: control

value: benign prostatic hyperplasia


title: Kidneys from control (3)

description: replicate 3

source_name: Control (3)


title: STIM1KO sham

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

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

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0 (Axon Instruments).

data_processing: The raw data of each spot was normalized by substitution with the mean intensity of the background signal determined by all blank spots' signal intensities of 95% confidence intervals.

source_name: Left ventricles, STIM1 KO, sham

label_protocol: Amino Allyl aRNA was synthesized using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion #1753). Cye dye coupling and fragmentation were performed according to the protocol supplied by TORAY Industries, Inc.

growth_protocol: Standard breeding was performed until 4 weeks after the operation.

extract_protocol: Total RNA samples were extracted from the left ventricles using ISOGEN II reagent (Nippon Gene).

treatment_protocol: For the banding procedure, 10-week-old male mice were anesthetized with a mixture of ketamine (90 mg/kg) and xylazine (10 mg/kg). The aortic arch was carefully exposed, and a 7-0 silk suture was used to tightly constrict the aorta between the brachiocephalic trunk and the left carotid artery over a wire of 0.3mm in diameter is put on the aorta. It is banded with the aorta together and is removed. Sham-operated mice were subjected to the same procedure without aortic banding. The hearts were isolated 4 weeks after the operation. The heart weight/body weight (HW/BW) ratio and cross-sectional area of myocytes within the left ventricular wall accordantly showed a greater than 1.5-fold increase in WT TAC compared to WT sham. KO mice showed significantly less cardiac hypertrophy than WT TAC.

tag: genotype

value: STIM1 KO

value: left ventricles

value: male

value: 14 weeks

tag: treatment

value: sham surgery

tag: average hw/bw


title: genomic DNA from normal colon biopsies M032C

value: female

tag: colonic location

value: distal

tag: disease state


title: genomic DNA from normal colon biopsies K101C


title: 30-h

description: control

tag: malignacy type

tag: carcinoma percentage

tag: paired sample status


title: mouse-wt-normal diet-1

description: Sample 1

value: wt

value: brown adipose tissue


title: 25-h

description: control


title: genomic DNA from normal colon biopsies K101A

value: normal

tag: aspirin

tag: hrt

tag: bmi


title: Kidneys from control (1)

description: replicate 1

source_name: Control (1)

value: Mixed background (C57BL/6 x 129S1/SvImJ)

tag: tissue

value: Embryonic kidneys


title: ccRCC tumor 4.31

source_name: clear cell renal cell carcinoma

value: un-metastasized tumor

tag: gender

value: Male

value: Kidney


title: Estradiol_replicate_4

city: GAINESVILLE

first: Charles

middle: Evans

last: Wood

state: Florida

address: 1345 Center Drive/Room M552

department: Physiology and Functional Genomics

institute: University of Florida

description: Gene expression 1 hr after sham BCO in estradiol-treated fetuses

hyb_protocol: This was performed following protocols from Agilent. Briefly 600 ng of each labeled cRNA was fragmented and then mixed with hybridization buffer using the Agilent gene expression hybridization kit. These were applied to a sheep 8 X 15 K array slide (Agilent  019921), containing 8 arrays with 15,744  oligomers with a length of 60 bases corresponding to 15,208 ovine genetic sequences published in the NCBI data base plus 500+ quality control probes provided by Agilent and  hybridized at 65oC for 17 h at 10 rpm.

scan_protocol: The arrays were hybridized, washed, dried, stabilized, and scanned at 5 μm at both 10 and 100 PMT with an Agilent G2505B Microarray scanner at the Interdisciplinary Center for Biotechnology Research at the University of Florida. Features were extracted with Agilent Feature extraction 9.1 software. Features flagged as Feature Non-uniform outliers were excluded from further analysis.

data_processing: Transcript levels were normalized to the chip median and log-transformed, in order to obtain more power in discovering differences between groups and compensate for systematic differences between the arrays.  To identify the genes that were differentially regulated (DR) between the treated and control fetuses, the normalized and transformed intensities were analyzed by one-way ANOVA (p<0.01).   All the statistical procedures were carried out using JMP Genomics 5 software (SAS Institute Inc, Cary, NC, USA).

organism: Ovis aries

source_name: fetal hypothalamus_estradiol_rep4

label_protocol: Five hundred ng of the DNase-treated RNA was labeled with Cyanine 3 (Cy3) CTP with the Agilent Quick Amp kit (5190-0442, New Castle, DE) according to their methodology, purified with the Qiagen RNeasy kit (Valencia, CA) according to Agilent’s revision of the Qiagen protocol as shown in the Quick Amp kit protocol except that the microcentrifugation was performed at room temperature instead of 4oC. The resulting labeled cRNA was analyzed with the NanoDrop spectrophotometer, and the specific activities and the yields of the cRNAs were calculated; these ranged from 9.0 to 12.8 pmol Cy3/µg RNA and from 4.29 to 10.38 µg, respectively. The labeled cRNA was stored at -80oC until use.

extract_protocol: RNA was extracted from the hypothalamus using Trizol (Invitrogen, Carlsbad, CA) , followed by RNeasy+ kits with on-column DNase treatment (Qiazol, Valencia, CA).The RNA concentration was determined with a Nanodrop spectrophotometer (ND-1000, ThermoFisher, Wilmington DE) and the integrity of the RNA was measured using an Agilent Bioanalyzer, 2100 model.  RNA Integrity Number (RIN) values ranged from 7.4 to 8.4.

treatment_protocol: 8 chronically catheterized late gestation fetal sheep were subjected to transient (10 min) brachiocephalic artery occlusion (BCO) followed by 50 min recovery; 8 additional fetal sheep were subjected to a 10 min period of sham BCO.  Half of the fetuses were chronically (5 days) treated with estradiol (250 ug/day).  Hypothalami were collected at the end of the recovery period.  4 groups (n=4) allowed comparison of control, estradiol, BCO, and BCO+estradiol.

tag: agent

value: estradiol

value: fetal hypothalamus


title: ccRCC tumor 3.29

tag: tumor stage

value: carcinoma


title: ccRCC tumor 5.12

value: Female


title: STIM1KO TAC

source_name: Left ventricles, STIM1 KO, TAC

tag: strain

value: STIM1 KO

value: left ventricles

value: male

tag: age

value: transverse aortic constriction (TAC)


title: 24-h

description: control

value: benign prostatic hyperplasia


title: 10-h

description: control


title: Estradiol_replicate_3

source_name: fetal hypothalamus_estradiol_rep3


title: genomic DNA from normal colon biopsies 285C

city: Basel

first: Faiza

last: Noreen

institute: University of Basel

data_processing: Mean non-background corrected signal intensities of the methylated (M) and unmethylated (U) for each CpG locus were extracted using the Illumina BeadStudio software v3.2. Beta values were calculated after performing smoothQuantileNrmalization for color balance adjustment followed by background level corection and quantile based probe level normalization. We masked data point as “NA” for the following conditions; 1) Probes containing single-nucleotide polymorphisms (SNPs), 2) those that overlap with a repetitive element that covers the targeted CpG dinucleotide, 3) those that overlap with regions of insertions and deletions in the human genome. Beta values with detection P value greater than 0.01 were also replaced as NA. Furthermore, probes containing at least one “NA” across the normal sample set were masked as “NA”. Beta value was calculated as M/(M+U).

source_name: normal colon

label_protocol: Standard Illumina protocol.

extract_protocol: Genomic DNA was extracted and purified from normal colon biopsies using Qiagen DNeasy Kit according to standard instructions.

value: female

value: distal

value: nonuser

tag: smoking

value: user


title: ccRCC tumor 3.15

value: metastasized tumor


title: 12-h

description: control


title: Nod2-/- 3

city: New York

first: Deepshika

last: Ramanan

state: New York

address: 550 First Ave

department: Immunology

institute: New York University

description: Shika KO3

hyb_protocol: Following fragmentation and labeling, cDNA was hybridized using the GeneChip WT Terminal Labeling and Hybridization kit

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)

data_processing: The data were RMA-normalized with GeneSpring GX from Agilent technologies (included in sample data table) and further analyzed using differential expression cutoff of 1.33 fold (provided in the final_data.txt).

source_name: Nod2-/-_laser captured Paneth cells

label_protocol: Biotinylated cDNA were prepared according to the standard protocol from 100ng total RNA (Ambion WT expression kit)

growth_protocol: Mice were sac'ed at 8 weeks of age

extract_protocol: The Leica LMD6000 Laser Microdissection system was used to capture crypt base epithelial cells and total RNA was extracted using the Arcturus PicoPure RNA isolation kit.

treatment_protocol: Small intestinal ileal sections were fixed in methacarn and embedded in paraffin.

tag: strain background

tag: genotype/variation

value: 8 weeks

value: small intestine

tag: cell type

value: laser captured Paneth cells


title: 23-h

description: control


title: Estradiol_replicate_2

source_name: fetal hypothalamus_estradiol_rep2

value: estradiol


title: ccRCC tumor 3.26

value: un-metastasized tumor

value: Kidney

tag: disease state


title: ccRCC tumor 3.16

value: Female

value: carcinoma


title: Nod2-/- 2

description: Shika KO2


title: Estradiol_replicate_1

source_name: fetal hypothalamus_estradiol_rep1

value: fetal hypothalamus


title: ccRCC tumor 3.13


title: genomic DNA from normal colon biopsies K016A

address: Mattenstrasse 28

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

tag: colonic location

value: proximal

value: normal

value: high


title: Estradiol Plus Brachiocephalic Occlusion_replicate_4

description: Gene expression 1 hr after BCO in estradiol-treated fetuses

source_name: fetal hypothalamus_estradiol+BCO_rep4

value: estradiol+BCO


title: Nod2-/- 1

description: Shika KO1


title: 6-h

description: control

tag: malignacy type

value: benign prostatic hyperplasia

tag: carcinoma percentage


title: genomic DNA from normal colon biopsies 65C

value: female

value: distal

tag: aspirin

value: nonuser


title: WT sham

source_name: Left ventricles, WT, sham

tag: genotype

value: WT

value: left ventricles

value: male

value: 14 weeks

tag: treatment

value: sham surgery

tag: average hw/bw


title: genomic DNA from normal colon biopsies 603C

tag: gender

tag: hrt

tag: bmi

value: user


title: 7-h

description: control

tag: paired sample status


title: WT3

description: Shika WT3

source_name: WT_laser captured Paneth cells

tag: age

value: 8 weeks

tag: tissue

value: small intestine

value: laser captured Paneth cells


title: Estradiol Plus Brachiocephalic Occlusion_replicate_3

source_name: fetal hypothalamus_estradiol+BCO_rep3

tag: agent

value: fetal hypothalamus


title: 5-h

description: control

source_name: prostate


title: Estradiol Plus Brachiocephalic Occlusion_replicate_2

source_name: fetal hypothalamus_estradiol+BCO_rep2


title: WT TAC

source_name: Left ventricles, WT, TAC

tag: strain

value: transverse aortic constriction (TAC)


title: genomic DNA from normal colon biopsies 149C

value: normal

value: high

tag: smoking


title: genomic DNA from normal colon biopsies K053C

tag: disease state


title: ccRCC tumor 2.23

tag: tumor stage

value: un-metastasized tumor

value: Female

value: Kidney

value: carcinoma


title: Estradiol Plus Brachiocephalic Occlusion_replicate_1

source_name: fetal hypothalamus_estradiol+BCO_rep1

value: estradiol+BCO


title: ccRCC tumor 2.17

value: Male


title: ccRCC tumor 3.10


title: genomic DNA from normal colon biopsies 603A

value: female

tag: colonic location

value: proximal

value: nonuser


title: Brachiocephalic Occlusion_replicate_3

description: Gene expression 1 hr after BCO

source_name: fetal hypothalamus_BCO_rep3

value: BCO


title: genomic DNA from normal colon biopsies K016C

value: distal

value: user


title: MPNST_RapPD_2

city: Boston

first: Clare

last: Malone

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School -  Brigham Women's Hospital

description: Gene expression data from rapamycin/PD-0325901 treated tumor

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: BRB array tools

source_name: NPcis Mouse MPNST_Rapamycin_Pd-0325901

label_protocol: Nugen Applause WT-amp ST kit

extract_protocol: Trizol followed by RNeasy cleanup

treatment_protocol: 14h with vehicle, or 5mg/kg Rapamycin IP, or 1.5mg/kg PD-0325901 OG twice daily, or combination of 5mg/kg rapamycin IP and 1.5mg/kg PD-0325901 OG twice daily

value: Primary mouse mouse malignant peripheral nerve sheath tumor (MPNST)

tag: genetic model

value: NPcis


title: genomic DNA from normal colon biopsies K025C

tag: aspirin


title: WT1

description: Shika WT1

tag: strain background

tag: genotype/variation

value: WT

value: 8 weeks

value: small intestine

tag: cell type

value: laser captured Paneth cells


title: Brachiocephalic Occlusion_replicate_2

description: Gene expression 1 hr after BCO

source_name: fetal hypothalamus_BCO_rep2

value: fetal hypothalamus


title: MPNST_PD901_2

description: Gene expression data from PD-0325901 treated tumor

source_name: NPcis Mouse MPNST_PD-0325901


title: genomic DNA from normal colon biopsies K018C

tag: gender

value: normal


title: MPNST_RapPD_1

source_name: NPcis Mouse MPNST_Rapamycin_PD-0325901


title: ccRCC tumor 2.03

source_name: clear cell renal cell carcinoma

value: un-metastasized tumor

value: Kidney

value: carcinoma


title: MPNST_PD901_1


title: genomic DNA from normal colon biopsies 296C

source_name: normal colon

value: female

tag: hrt


title: ccRCC tumor 2.11

value: metastasized tumor

value: Female


title: ccRCC tumor 2.38

value: Male


title: Control_replicate_4

description: Gene expression 1 hr after sham BCO

source_name: fetal hypothalamus_control_rep4

value: control


title: Control_replicate_3

description: Gene expression 1 hr after sham BCO

source_name: fetal hypothalamus_control_rep3


title: WT2

description: Shika WT2


title: Brachiocephalic Occlusion_replicate_1

description: Gene expression 1 hr after BCO

source_name: fetal hypothalamus_BCO_rep1

value: BCO


title: genomic DNA from normal colon biopsies 285A

value: proximal

value: nonuser

tag: bmi

value: user


title: genomic DNA from normal colon biopsies 65A

value: high


title: Control_replicate_2

description: Gene expression 1 hr after sham BCO

source_name: fetal hypothalamus_control_rep2


title: MPNST_Rap_2

description: Gene expression data from rapamycin treated tumor

source_name: NPcis Mouse MPNST_Rapamycin

value: Primary mouse mouse malignant peripheral nerve sheath tumor (MPNST)

value: NPcis


title: genomic DNA from normal colon biopsies 407C

value: distal


title: MPNST_Rap_1


title: MPNST_Veh_2

description: Gene expression data from vehicle treated tumor

source_name: NPcis Mouse MPNST_vehicle


title: MPNST_Veh_1


title: genomic DNA from normal colon biopsies 238C

value: normal


title: ccRCC tumor 1.14

value: un-metastasized tumor


title: genomic DNA from normal colon biopsies 149A


title: Control_replicate_1

description: Gene expression 1 hr after sham BCO

source_name: fetal hypothalamus_control_rep1

value: fetal hypothalamus


title: Day 4 EB_Gem knockdown_rep3

city: Saint Louis

first: Kristen

middle: L

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

description: Day 4 EB, rep 3, GemKD

hyb_protocol: RNA was hybridized to Affymetrix Mouse Gene 1.0 ST microarrays and washed and stained with the GeneChip Fluidics Station 450 (Affymetrix) according to standard protocols.

scan_protocol: Array image acquisition was done with GeneChip Scanner 3000 7G (Affymetrix) and image processing with Affymetrix GeneChip Command Console (AGCC) software.

data_processing: Raw CEL and DAT files were analyzed with dChip software (http://biosun1.harvard.edu/complab/dchip/) after normalization to exclude probe sets that did not meet the following preliminary cutoff values: 1) expression, represented by model-based expression indices (MBEI), was changed more than 1.2-fold in treated versus untreated samples (E/B >1.2) groups; 2) MBEI differences were larger than 30 (E-B > 30); and 3) expression was claimed as present (P) in at least one sample in each experiment. For each sample type, the entire experiment was repeated three times. Probe sets were considered putatively Geminin-regulated if they met microarray cutoff values in at least 2 of the 3 experiments.

source_name: day 4 embryoid bodies, dox from day 0 Gem knockdown

label_protocol: 1 microgram of RNA was prepared by the Whole Transcript Sense Target Labeling (Affymetrix) standard protocol to add biotin label.

growth_protocol: ES cells were differentiated into embryoid bodies for 4 or 5 days. ES cells were maintained on irradiated MEFs in DMEM plus 15% fetal bovine serum (HyClone), 1mM sodium pyruvate, 0.1mM non-essential amino acids (Gibco), 2mM Glutamine, 1000U/mL LIF (Chemicon) and 100μM 2-mercaptoethanol (Sigma). For EB formation, ES cells were feeder subtracted and plated at 6,000/ml on 10 cm petri dishes treated with 5% polyheme to prevent cell adhesion and were differentiated in IMDM with 15% FCS, 1% L-glutamine, 50µg/ml ascorbic acid and 4.5X10-4 M MTG. Dox is added at 0.5 µg/ml to induce overexpression of Gem or miRNAs targeting endogenous Gem transcripts.

extract_protocol: RNA was prepped with the Qiagen RNeasy kit.

treatment_protocol: Embryoid bodies from the Gem knockdown line were collected on day 4. Embryoid bodies from the Gem overexpression line were collected on days 4 or 5.

tag: background/strain

tag: es cell line

tag: es cell line type

value: Geminin knockdown

value: embryoid bodies

tag: differentiation day

tag: dox addition

value: Dox added day 0


title: ccRCC tumor 2.09

tag: tissue

value: Kidney

value: carcinoma


title: ccRCC tumor 1.13

value: metastasized tumor

value: Female

tag: disease state


title: ccRCC tumor 2.01

tag: tumor stage


title: genomic DNA from normal colon biopsies 37C

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27k Beadchip using standard Illumina protocol.

value: female

tag: colonic location

tag: age

tag: smoking


title: ccRCC tumor 1.11

value: Male


title: Day 4 EB_GemOE_control_rep3

description: Day 4 EB, rep 3, GemOE control

source_name: day 4 embryoid bodies, GemOE, no dox control

value: Geminin overexpression

value: no Dox


title: ccRCC tumor 1.12


title: Day 4 EB_Gem overexpression_rep3

description: Day 4 EB, rep 3, GemOE

source_name: day 4 embryoid bodies, dox from day 3 Gem overexpression

value: Dox added day 3


title: genomic DNA from normal colon biopsies K025A

value: proximal

tag: aspirin

value: nonuser

value: high


title: ccRCC tumor 1.09


title: Day 4 EB_GemKD_control_rep3

description: Day 4 EB, rep 3, control

source_name: day 4 embryoid bodies, GemKD, no dox control


title: genomic DNA from normal colon biopsies 351C

value: distal

value: normal


title: ccRCC tumor 1.08


title: ccRCC tumor 6.21


title: ccRCC tumor 5.11


title: ccRCC tumor 4.20

value: un-metastasized tumor


title: ccRCC tumor 4.05


title: genomic DNA from normal colon biopsies 245C


title: genomic DNA from normal colon biopsies 296A


title: Brachiocephalic Occlusion_replicate_4

description: Gene expression 1 hr after BCO

source_name: fetal hypothalamus_BCO_rep4

tag: agent

value: BCO

value: fetal hypothalamus


title: Day 4 EB_GemKD_control_rep2

description: Day 4 EB, rep 2, control

value: Geminin knockdown

tag: cell type

value: embryoid bodies


title: genomic DNA from normal colon biopsies K095C

tag: gender


title: genomic DNA from normal colon biopsies K053A

tag: hrt


title: Day 5 EB_GemOE_control_rep2

description: Day 5 EB, rep 2, control

source_name: day 5 embryoid bodies, GemOE, no dox control


title: Day 4 EB_Gem knockdown_rep2

description: Day 4 EB, rep 2, GemKD

value: Dox added day 0


title: Day 5 EB_Gem overexpression_rep2

description: Day 5 EB, rep 2, GemOE

source_name: day 5 embryoid bodies, dox from day 3 Gem overexpression


title: ccRCC tumor 3.19

value: Kidney

value: carcinoma


title: genomic DNA from normal colon biopsies 407A

value: female

tag: bmi

value: user


title: Day 4 EB_Gem knockdown_rep1

description: Day 4 EB, rep1, GemKD

tag: background/strain


title: genomic DNA from normal colon biopsies 183C


title: ccRCC tumor 5.07

value: Male


title: genomic DNA from normal colon biopsies 238A


title: genomic DNA from normal colon biopsies 392C


title: Day 4 EB_GemKD_control_rep1

description: Day 4 EB, rep1, control

tag: es cell line

value: no Dox


title: ccRCC tumor 3.14

value: Female


title: ccRCC tumor 3.06

value: metastasized tumor


title: genomic DNA from normal colon biopsies 37A

value: proximal

value: nonuser


title: Day 5 EB_Gem overexpression_rep1

description: Day 5 EB, rep 1, GemOE

tag: es cell line type

value: Geminin overexpression

value: Dox added day 3


title: ccRCC tumor 3.12

value: un-metastasized tumor


title: kidney cortex 3.12

description: Genomic DNA extracted from normal kidney cortex was genotyped using Infinium HumanCytoSNP-12 v2.1 BeadChips (Illumina).

source_name: kidney cortex

value: not applicable


title: kidney cortex 3.06


title: T-ALL tumor 364 (non-aneuploid)

description:
63Th
non-aneuploid; genotype in Sup data 1 accompanying paper

hyb_protocol: Labeled DNA was hybridyzed to Agilent 244K oligo arrays (mm9 build, design 014695) using manufacturer's standard protocols

scan_protocol: Arrays were scanned on an Agilent 2565BA scanner

data_processing: Data was imported into Agilent Genomc Workbench, quantile normalized and log 2 Cy5/Cy3 ratios were exported to Excel.

source_name: control p53 null T-ALL sample

label_protocol: Tumor DNA and reference DNA were labeled with Cy3 and Cy5 dNTP respectively using Exo Klenow fragment and Agilent random primers using Agilent standard protocols

growth_protocol: Mice were sacrificed when gravely ill (in vast majority of cases because of T-ALL) See for details Supplementary info S1 accompanying paper

extract_protocol: Tissue was homogenized using bead-homogenization in Qiagen DNA-easy buffer 1. DNA was then purified using DNA-easy columns using Qiagen protocols

treatment_protocol: Thymus was dissected and stored at -80 in pieces for subsequent analysis

tag: strain

tag: chromosome instability

value: non-CIN

value: male

value: T-ALL

value: p53 f/f control tumor

source_name: sex-matched control liver

value: sex-matched liver (mix several litter mates)


title: T118_CTC

city: Santa Monica

first: Neal

middle: Percy

last: Kawas

address: 2200 Santa Monica Blvd

department: Molecular Oncology

institute: John Wayne Cancer Institute

description: SNP and copy number calls.

hyb_protocol: Following fragmentation, 3ug of gDNA was annealed for 16 hours at a temperature of 50C to Affymetrix Genomewide SNP Array 6.0 at a pH of 6.6.

scan_protocol: Scanned on 7G 3000 manufactured by Affymetrix.

data_processing: SNPs were called using the Birdseed v2 algorithm (.CHP files), and copy number variations were called using the CN5 algorithm (.CNCHP files) using Affymetrix Genotyping Console 4.0 under good laboratory practice (GLP) conditions. Sample table and .CNCHP data are based on genome build NCBI36 (hg18).

label: Biotin

source_name: Blood

label_protocol: Biotinylated gDNA was prepared according to the standard Affymetrix protocol from3 ug of gDNA.

growth_protocol: Cell lines were grown at 37C in a 5% CO2 humidified atmosphere, in RPMI 1640 supplemented with 10% fetal bovine serum.

extract_protocol: DNA extraction from frozen tumor tissues, and cell lines was carried out with the QIAamp DNA mini kit (QIAGEN, Valencia, CA). DNA extraction from CTCs was carried out using DNAzol (Molecular Research Center, Cincinnati, OH) according to the manufacturer's instructions.

treatment_protocol: No treatment.

value: metastatic melanoma

tag: cancer stage

value: III

tag: patient group

value: paired

tag: pair number

value: CTC (amplified)

tag: isolation method

value: GM3, GM2, GD5


title: T-ALL tumor 35 (non-aneuploid)

description:
35Th
non-aneuploid; genotype in Sup data 1 accompanying paper

value: female

tag: disease state

tag: tissue


title: Staphylococcus aureus  biofilm cells_Licochalcone A 60 min_replicate1

city: Changchun

first: lu

last: yu

state: Jilin

address: Xi’an Road 5333#

department: Institute of Zoonosis

country: China

institute: Jilin University

description: Gene expression data from Staphylococcus aureus  biofilm cells with Licochalcone A treatment at 60min

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix GeneChip Opererating Software (GCOS) version 1.0

organism: Staphylococcus aureus

label_protocol: Conversion to cDNA and labeling was performed as described in Hutter et al., Antimicrobial agents and chemotherapy, 2004, 48(8):2838-284

growth_protocol: S. aureus strain ATCC29213 was grown overnight at 200 rpm in a rotary shaker at 37°C in 10 ml of TSB, after 12 hours, the culture were inoculated to an initial OD600 of 0.05 in 100 ml of TSB in 250-ml Erlenmeyer flasks, the planktonic cells were grown at 37°C at 200 rpm to an OD600 of 0.3. Within biofilm, the overnight culture were inoculated to an initial OD600 and diluted in TSBg to obtain the final concentration of 1× 105cfu/ml, 30 ml bacterial suspension diluted in 2% glucose-supplemented TSB containing 1 × 105 cfu/ml into the culture dish, then incubated in air for 48 h at 37°C

extract_protocol: Total bacterial RNA was isolated as described by Hutter et al., 2004, 48(8):2838-2844

treatment_protocol: Licochalcone A stock solution, prepared in dimethyl sulfoxide (DMSO), was added to the cultures, giving a final concentration of 1/2× MIC (2 μg/ml), and the final concentration of DMSO was 0.1% (vol/vol) as control group. Biofilms washed once with PBS to remove any unbound bacteria, Licochalcone A stock solution, prepared in dimethyl sulfoxide (DMSO), was added to the cultures, giving a final concentration of 4× MIBC (64 μg/ml), and the final concentration of DMSO was 0.1% (vol/vol) as control group. Then, the bacterial planktonic and biofilm cells were further incubated for 60 min at 37°C

value: Standard strain ATCC29213

value: biofilm cells


title: Staphylococcus aureus  biofilm cells_Licochalcone A 60 min_replicate2


title: T119_CTC

description: SNP and copy number calls.

value: GM3, GM2, GD6


title: Staphylococcus aureus  biofilm cells_control 60min_replicate2

description: Gene expression data from Staphylococcus aureus  biofilm cells  at 60min


title: genomic DNA from normal colon biopsies K095A

department: Department of Biomedicine

source_name: normal colon

tag: colonic location

value: proximal

value: normal

tag: age

tag: aspirin

value: nonuser

tag: smoking


title: Staphylococcus aureus  biofilm cells_control 60min_replicate1

description: Gene expression data from Staphylococcus aureus  planktonic cells  at 60min

tag: cell type


title: genomic DNA from normal colon biopsies M033C

tag: gender

value: distal

tag: hrt

tag: bmi


title: genomic DNA from normal colon biopsies M026C

value: high


title: ccRCC tumor 3.01

source_name: clear cell renal cell carcinoma

tag: tumor stage

value: metastasized tumor

value: Female

value: Kidney

value: carcinoma


title: ccRCC tumor 2.44

value: Male