title: Liver 15 days

source_name: Liver 15 days


title: H3K36me3_met1_rep2

status: Public on Jan 24 2012

type: genomic

city: Santa Cruz

first: Susan

last: Strome

state: CA

address: 1156 High St

department: MCD Biology

country: USA

institute: UC Santa Cruz

description: ChIP-chip of H3K36me3 in met-1 EEMB; channel ch1 is ChIP DNA; Antibody information: HK00001 H3K36me3:13C9;target name: H3K36me3;host: Mouse;antigen: KSAPATGGV(me3-K)KPHRYRPGTC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00001;short description: A protein G purified mouse monoclonal antibody to H3K36me3 (clone 13C9) obtained from Hiroshi Kimura. Used for ChIP; channel ch2 is Input DNA

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v1. Array scanning and raw data extraction were performed at Roche NimbleGen, according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays Users Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted and saved as .pair files by using NimbleScan software according to the NimbleScan v2.4 User?s Guide.

data_processing: ChIP-chip normalization standard nimblegen:JL:1 protocol.  The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value (results in linked .gff files). This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is WS180

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: H3K36me3 ChIP DNA for met-1 EEMB

label_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays Users Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

growth_protocol: Worm_embryo_growth_and_harvest_vSS3. Embryos were prepared by bleaching from gravid met-1 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85 % formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Pellets were frozen at -80C.

extract_protocol: Worm_embryo_extraction_vSS5. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated in ice water bath using a Diagenode Bioruptor at the highest setting for 14 pulses 30 seconds long with 1 minute pauses. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 um filter units (cat. UFC30HV0S) at 13,000 rpm, 4°C for 1 minute to remove lipids. Protein concentration was determined, and extracts were aliquoted and stored at -80ºC.   Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ul of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 uL elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo kit.   Worm_LM-PCR_Amplification_for_ChIP-chip_vSS2. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn: http://www.flychip.org.uk/protocols/chip/lm_pcr.php.  For more details see www.modencode.org

tag: strain

tag: developmental stage

value: Early Embryo

tag: genotype

tag: chip antibody

tag: Sex

value: population predominantly Hermaphrodites perhaps with some Males

source_name: Input DNA for met-1 EEMB

value: none, Input DNA


title: Liver 7 days

type: RNA

city: Lugo

first: Adrian

middle: Millan

last: Perez

state: Lugo

address: Facultad Veterinaria, Campus Universitario Pabellon IV 2 superior

department: Acuigen

country: Spain

institute: Universidad Santiago Compostela

description: Gene expression after challenging with Philasterides dicentrarchi

hyb_protocol: 0,6 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul adding 1ul 25x Agilent fragmentation buffer and 5 ul 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction 25 ul 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the turbot custom oligo-microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:016528_D_F_20070525) to obtain Processed Signal intensities.  Those microarrays having an average coefficient of variation (CV) across Spike-In and non-Spike-In probes below 10% were considered for further analysis. Secondly, the following features and/or genes which did not conform to the established quality criteria were filtered: i) non-uniform pixel distributed outliers and population replicate outliers according to the default Agilent feature extraction criteria; ii) features whose ratio between processed signal and its error was below 2; iii) spots not differentiated from background signal (as estimated for each spot); iv) features below the limit where the linear relationship between concentration and intensity was lost according to Spike-In information; v) genes which did not show at least 3 quality replicates out of 5 and/or a coefficient of variation (CV) across replicates >10%.

molecule: total RNA

organism: Scophthalmus maximus

source_name: Liver 7 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 150 individuals of ~ 30g from 20 equally represented families from a turbot company (Alrogal SA) were transported to CETGA (Centro Tecnológico Gallego de Acuicultura; NW Spain) facilities. Prior to challenge, fry were maintained during 10 days at standard culture conditions to cut down on transport stress and to check if they were free from diseases.

extract_protocol: Total RNA was extracted from pooled tissues of control and infected fish using TRIZOL Reagent (Life Technologies) according to manufacturer’s recommendations. All extractions were performed by the same researcher.

treatment_protocol: Fish were injected intracelomically (i.p.) with 0.1 ml of a parasite suspension of 2.5x10^6 parasites/mL. The presence of P. dicentrarchi in infected fish was checked by plating drops of the ascitic fluid and blood that were impregnated with ammoniacal pyridinated silver carbonate, and biometric measurements of taxonomically important characters were made under an optical microscope (Budiño et al., 2011b). The challenges were performed at the CETGA facilities in quarantine tanks. All fish used in the experiment were anaesthetized with benzocaine (50 mg/ml) and sacrificed by decapitation. Equal amounts of spleen, liver and head kidney were sampled from each fish, pooled per organ at each sampling point and immediately stored in liquid nitrogen.

tag: infection agent

value: 0.1 ml of 2.5x10^6 P. dicentrarchi/mL suspension

tag: time point

value: 7 day post-challenging

tag: tissue

value: liver


title: PVN_ECS_6h_rep1

city: Tokyo

first: Eri

last: Segi-Nishida

state: Tokyo

address: Niijuku 6-3-1

country: Japan

institute: Tokyo University of Science

description: Gene expression data from mouse PVN  at 6 h after ECS

hyb_protocol: Following fragmentation, 5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned by GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Mus musculus

label_protocol: RNA amplification reaction was carried out using 2 ng of total RNA by Ovation Pico WTA System (NuGEN Technologies, San Carlos, CA), and amplified cDNA products were fragmented and labeled to generate biotinylated cDNA targets by Ovation biotylation kit. Then 5 µg of labeled cDNA was used for subsequent microarray analysis.

extract_protocol: Cryocut sections (7 μm thickness) were placed non-coated glass slides (Jung CM3000 cryostat; Leica Microsystems, Wetzlar, Germany), fixed, stained and dehydrated using the following protocol: 75% of ethanol for 30 sec, RNase-free water for 30 sec, staining using Histogene (Applied Biosystems, Carlsbad, CA) for 20 sec, RNase-free water for 30 sec, 75% of ethanol for 30 sec, 95% of ethanol for 30 sec, 100% of ethanol for 30 sec twice, xylene for 5 min; then sections were vacuumed for 15 min to dry. Laser microdissection was carried out on the Pixell Ile Laser Capture Microdissection System (Applied Biosystems). Immediately after microdissection, samples were dissolved in denaturing buffer and total RNA was isolated using an RNeasy Micro Kit (Qiagen).

treatment_protocol: Bilateral ECS was administered via moistened spring-loaded ear clip electrodes to isoflurane-anesthetized mice using a pulse generator (ECT Unit; Ugo Basile, Comeria, Italy) (current, 25 mA; shock duration, 1 sec; frequency, 100 pulse/sec; pulse width, 0.5 msec). ECS-treated animals received one shock and tissue was collected at 2 or 6 h after shock. Sham-treated animals were handled the same fashion as ECS-treated animals, but no shock was delivered. Tissue of sham-treated animals was collected at 2 h after treatment. For microdissection from brain sections, the whole brains were quickly removed and rapidly frozen on dry ice, then stored at -20°C until microdissection.

value: paraventricular hypothalamus

tag: treatment

value: electroconvulsive seizure


title: MCF7-T

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

description: MicroRNA expression data directly after treatment with DAC

hyb_protocol: The labelled products were hybridized for 18 hr at 45C on Affymetrix GeneChip miRNA array (v1.0). GeneChips were washed and stained on GeneChip Fluidics 450 Workstations (Affymetrix Inc.).

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G (Affymetrix Inc.)

data_processing: The expression signals were acquired using the Affymetrix GeneChip Command Console Software (AGCC). The system was used to generate the numerical values of the probe intensity (Signal). The differentially expressed miRNAs were defined using Partek Genomics Suite software v6.5 (Partek Incorporated, Missouri, USA) and and RMA normalization.

organism: Homo sapiens

source_name: MCF7 Treated

label_protocol: Biotinylated microRNAs were prepared according to the FlashTag Biotin HSR RNA Labeling protocol (Genisphere) using 100ng RNA.

growth_protocol: HB2 cell line was cultured in DMEM, 10% FBS, Insulin (0.01 mg/ml, hydrocortisone (500 ng/ml). MDA-MB231, HS578T and MCF7 cell linee were cultured in DMEM, 10% FBS. SKBR3 cell line was cultured in McCoys 5A, 10% FBS. BT549 cell line was cultured in RPMI medium 1640, 10% FBS.

extract_protocol: Total RNA was extracted using AllPrep DNA/RNA/Protein Mini Kit (QIAGEN AG) according to the manufacturer's instructions. The RNeasy MinElute Cleanup Kit (QIAGEN AG) was used for isolation and purification of enriched miRNAs.

treatment_protocol: Cells were seeded (2 X l0^5 cells / T75 flasks) for 24h then media were removed and cells were freshly exposed to the 5-aza-2’-deoxycytidine (DAC) (Sigma Chemical Co.) at concentrations of l00nM in suspension culture every 24h until cultured cells reached 80-85 % confluence (~5 days). The cells were split for 10 follow-up passages at “drug holiday” condition.

value: treatment with DAC


title: MCF7-UT

description: MicroRNA expression data before treatment with DAC

source_name: MCF7 Un-treated


title: Liver control

source_name: Liver control

value: time 0; non-injected


title: BT549-UT

source_name: BT549 Un-treated


title: BT549-T

source_name: BT549 Treated


title: HS578T-UT

source_name: HS578T Un-treated


title: Spleen 7 days

source_name: Spleen 7 days

value: spleen


title: Spleen 15 days

source_name: Spleen 15 days

value: 15 day post-challenging


title: SKBR3-P10

description: MicroRNA expression data at passage 10 follow-up at “drug holiday” condition

source_name: SKBR3 Passage 10


title: Lung Metastasis Replicate 3

city: Shanghai

first: Wei-Zhong

last: Wu

address: Fenglin Rd 180, Xuhui district

department: Zhongshan Hospital

country: China

institute: Fudan University

hyb_protocol: Labeled RNA was precipitated with 0.3 M sodium acetate,2.5 volumes ethanol and resuspended in 20μl hybridization buffer containing 3xSSC,0.2% SDS and 15% formamide.The arrays were hybridized at 42°C overnight and washed with two consecutive solutions (0.2% SDS,2xSSC at 42°C for 4 min,and 0.2xSSC for 4 min at room temperature).

scan_protocol: Scanned on an CapitalBio LuxScan 10K/A dual channel scanner.

data_processing: Images were quantified using CapitalBio LuxScan Software (version 3.0). The raw miRNA expression data were quantile-normalized to correct for between-sample variations.

source_name: Lung metastasis of human liver carcinoma

label_protocol: 4 µg miRNA from each sample was labeled with 500 ng 5'-phosphatecytidyl-uridyl-cy3 with 2 units T4 ligase.The labeling reaction was performed at 4°C for 2 hours.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.Low-molecular-weight RNA (<200nt) was isolated from 20 µg total RNA using the PEG method (Thomson,J.M.,Perou,C.M.,Hammond,S.M.,2004,Nat Methods 1,47-53).

value: lung metastatic specimen of human hepatoma in HCCLM3 orthotopic xenograft mouse model

tag: histology

value: Hepatocellular carcinoma

tag: isolation

value: Micodessection

tag: storage

value: Liquid nitrogen

tag: mouse model strain

value: NOD BALb/c

tag: mouse model age

value: 4 weeks

tag: mouse model gender

value: male


title: Spleen 1 day

source_name: Spleen 1 day

value: 1 day post-challenging


title: Spleen 25 days

source_name: Spleen 25 days

value: 0.1 ml of 2.5x10^6 P. dicentrarchi/mL suspension

value: 25 day post-challenging


title: HS578T-T

source_name: HS578T Treated


title: Spleen control

source_name: Spleen control


title: 24hr_LPS_R1_vs_0hr_untreatedpool_252665510533_1_4.mev.refIsIA.out

city: Rockville

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

hyb_protocol: per Agilent GE protocol

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanner

data_processing: data extracted via Agilent Feature extraction

source_name: IA RAW2647 untreated

label_protocol: DNA probes for microarray experiments were generated by adding 2 ug of total RNA in a mixture containing 6 ug of random hexamers (Invitrogen), 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma), reaction buffer, and 400 units of SuperScript III reverse transcriptase (Invitrogen) at 42 C degree overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 70 C degree for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 (Amersham) was added at room temperature for 1h. Uncoupled label was removed using the Qiagen Minelute column (Valencia, CA).

extract_protocol: Total RNA was extracted using the Ambion mirVana RNA extraction protocol as described by the manufacturer.

tag: cell line

source_name: IB RAW2647 treated with LPS 24hr

label_protocol: DNA probes for microarray experiments were generated by adding 2 ug of total RNA in a mixture containing 6 ug of random hexamers (Invitrogen), 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma), reaction buffer, and 400 units of SuperScript III reverse transcriptase (Invitrogen) at 42 C degree overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 70 C degree for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy5 (Amersham) was added at room temperature for 1h. Uncoupled label was removed using the Qiagen Minelute column (Valencia, CA).


title: Liver 1 day

source_name: Liver 1 day

value: liver


title: 2hr_LPS_R2_vs_0hr_untreatedpool_252665510534_1_2.mev.refIsIA.out

source_name: IB RAW2647 treated with LPS 2hr


title: Pdx1-Cre;KrasLSL-G12D vs. Pdx1-Cre;KrasLSL-G12D;IKK2/betaF/F pancreatic tissues

city: Houston

first: Paul

middle: J

last: Chiao

state: Texas

address: 1515 Holcombe Blvd

department: Department of Molecular and Cellular Oncology

institute: The University of Texas M. D. Anderson Cancer Center

hyb_protocol: The Core Lab performed the hybridization using the protocol provided by Agilent. Microarray experiments were carried out using whole human genome oligo arrays with 44k 60-mer probes (Agilent Technologies, Palo Alto, CA) with 500 ng of total RNA starting material.

scan_protocol: The Core Lab performed image acquisition using the protocol provided by Agilent. The hybridized arrays were scanned with Agilent's dual laser-based scanner.

data_processing: Feature Extraction software version 8.0 (Agilent Technologies) was used to link a feature to a design file and to determine the relative fluorescence intensity between the two samples. The VALUEs in the Sample data table represent Lowess-normalized log10 ratios (Cy5/Cy3). The VALUES in the 'GSE27478_fold_change_data.txt' file (which is linked to the Series GSE27478 record as a supplementary file) are the fold changes of KrasD/+,PDX1-CRE:KrasD/+, PDX1-CRE,IKK2F/ MICE. The detailed statistical analysis was performed as described by Price et al. Proc Natl Acad Sci USA. 2007 Feb 27;104(9):3414-9 (PMID 17360660).

source_name: cDNA from Pdx1-Cre;KrasLSL-G12D pancreas

label_protocol: Performed by following the protocol provided by Agilent.

extract_protocol: Total RNA was extracted from mouse pancreata using the Trizol method. The integrity and purity of RNA was determined by the Agilent BioAnalyzer.

treatment_protocol: None.

value: pancreatic tumor

source_name: cDNA from Pdx1-Cre;KrasLSL-G12D;IKK2/betaF/F pancreas

label_protocol: The Core Lab performed probe labeling using the protocol provided by Agilent.

value: normal pancreas


title: 4hr_LPS_R2_vs_0hr_untreatedpool_252665510509_1_3.mev.refIsIA.out

source_name: IB RAW2647 treated with LPS 4hr


title: Lung Metastasis Replicate 2


title: 4hr_LPS_R1_vs_0hr_untreatedpool_252665510534_1_3.mev.refIsIA.out


title: 1hr_LPS_R2_vs_0hr_untreatedpool_252665510533_1_1.mev.refIsIA.out

source_name: IB RAW2647 treated with LPS 1hr


title: Spleen 3 days

source_name: Spleen 3 days

value: 3 day post-challenging


title: 24hr_LPS_R2_vs_0hr_untreatedpool_252665510510_1_4.mev.refIsIA.out


title: SKBR3-P7

description: MicroRNA expression data at passage 7 follow-up at “drug holiday” condition

source_name: SKBR3 Passage 7


title: SKBR3-P5

description: MicroRNA expression data at passage 5 follow-up at “drug holiday” condition

source_name: SKBR3 Passage 5


title: Lung Metastasis Replicate 1


title: Primary Tumor Replicate 2

source_name: Human primary liver carcinoma

value: hepatoma specimen in HCCLM3 orthotopic xenograft mouse model

value: Incisional biospy


title: Primary Tumor Replicate 3


title: SKBR3-P1

description: MicroRNA expression data at passage 1 follow-up at “drug holiday” condition

source_name: SKBR3 Passage 1


title: SKBR3-P3

description: MicroRNA expression data at passage 3 follow-up at “drug holiday” condition

source_name: SKBR3 Passage 3


title: Primary Tumor Replicate 1


title: SKBR3-T

source_name: SKBR3 Treated

value: treatment with DAC


title: 2hr_LPS_R1_vs_0hr_untreatedpool_252665510509_1_2.mev.refIsIA.out


title: Skin_7STWS_rep5

city: Faro

first: Florbela

middle: A.

last: Vieira

address: Campus de Gambelas

country: Portugal

institute: CCMAR - UALG

description: Gene expression of skin_scales of unfed fish and with scales removed (replicate 5) sampled at day 7 of the experiment

hyb_protocol: A total of 1650 ng of labelled cRNA was prepared for fragmentation adding 11 μl 10X Blocking Agent and 2.2 μl of 25X Fragmentation Buffer, heated at 60°C for 30 min, and finally diluted by addition with 55 μl 2X GE Hybridization buffer. A volume of 100 µl of hybridization solution was then dispensed in the gasket slide and assembled to the microarray slide (each slide containing four arrays). Slides were incubated for 17 h at 65°C in a Agilent Hybridization Oven, subsequently removed from the hybridization chamber, quickly submerged in GE Wash Buffer 1 to disassembly the slides and then washed in GE Wash Buffer 1 for approximately 1 minute followed by one additional wash in pre-warmed (37°C) GE Wash Buffer 2.

scan_protocol: After washing the arrays were scanned on a Agilent G2565BA DNA microarray scanner, at a resolution of 5 µm, modifying default settings to scan the same slide twice at two different sensitivity levels (XDR Hi 100% and XDR Lo 10%).

data_processing: The XDR Hi and XDR Lo images generated per array were analysed together and the data extracted. Background subtraction was performed using the standard procedure in the Agilent Feature Extraction Software 9.5.1. Spike-In Viral RNAs were used to control array hybridization intensities and ensure normalization gave a uniform signal across all microarray slides.

organism: Sparus aurata

source_name: Skin_Scales, Starved and scales removed day7, rep5

label_protocol: Samples from each treatment (5 replicates/group) were labelled with Cy3-dCTP and hybridizations were performed using the Agilent One-Colour Microarray-Based Gene Expression Analysis protocol. For each sample, 500 ng of total RNA were linearly amplified and labelled with Cy3-dCTP following the Agilent One-Color Microarray-Based Gene Expression Analysis protocol. A mixture of 10 different viral poly-adenilated RNAs (Agilent Spike-In Mix) was added to each RNA sample before amplification and labelling, to monitor the microarray analysis workflow. Labelled cRNA was purified with the Qiagen RNAeasy Mini Kit, and sample concentration and specific activity (pmol Cy3/µg cRNA) were measured in a NanoDrop® ND-1000 spectrophotometer.

extract_protocol: Total RNA was extracted from skin/scales of 5 individual fish using an RNeasy Mini kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions.  RNA quality and integrity were checked using an Agilent 2100 Bioanalyser (Agilent technologies, Palo Alto, CA) and only samples with an RNA integrity index number (RIN) >7.5 were processed for use in microarray analysis.

treatment_protocol: Sea bream were acclimatised for one week to the experimental circuit which consisted of 8 through-flow seawater tanks (500L), with water maintained at 19-21ºC, 36% salinity and a 12h light and 12h dark photoperiod. Food was withheld from the fasted experimental groups for 1 week (-7 days) prior to removal of the scales which was considered day 0 of the trial. The experiment had 3 treatment groups:  ST = fasted for duration of experiment; WS = scales removed at time 0; STWS = fasted for duration of the experiment with scales removed at time 0 and control group (N), no treatment. Duplicate tanks for each treatment were prepared and 5 fish were sampled from one tank 3 days after the scales had been removed and from the second tank 7 days after the scales had been removed. Two tanks contained the control fish and were sampled at the same time as the experimental groups at day 3 and 7. To remove the scales, fish were lightly anaesthetised in 2-phenoxyethanol (1:5000, Sigma-Aldrich, Madrid, Spain) and scales were removed (approximately 60-70%) from both sides of the fish by wiping fish . For sampling fish were anaesthetised in 2-phenoxyethanol, as described above, and fish were sacrificed by sectioning the spinal cord and skin was collected from below the dorsal fin and carefully dissected free of muscle and snap frozen in liquid nitrogen and stored at -80ºC.

value: Skin with scales

tag: time after scale removal

value: Day 7

tag: feeding

value: Unfed

tag: scales

value: Removed


title: Skin_7ST_rep3

description: Gene expression of skin_scales of unfed fish (replicate 3) sampled at day 7 of the experiment

source_name: Skin_Scales, Starved day7, rep3

value: Intact


title: SKBR3-UT

source_name: SKBR3 Un-treated


title: Skin_7STWS_rep2

description: Gene expression of skin_scales of unfed fish and with scales removed (replicate 2) sampled at day 7 of the experiment

source_name: Skin_Scales, Starved and scales removed day7, rep2


title: MDA-P10

source_name: MDA Passage 10

value: passage 10 follow-up at “drug holiday” condition


title: Skin_7STWS_rep4

description: Gene expression of skin_scales of unfed fish and with scales removed (replicate 4) sampled at day 7 of the experiment

source_name: Skin_Scales, Starved and scales removed day7, rep4


title: Skin_7ST_rep5

description: Gene expression of skin_scales of unfed fish (replicate 5) sampled at day 7 of the experiment

source_name: Skin_Scales, Starved day7, rep5


title: Skin_7STWS_rep3

description: Gene expression of skin_scales of unfed fish and with scales removed (replicate 3) sampled at day 7 of the experiment

source_name: Skin_Scales, Starved and scales removed day7, rep3


title: Skin_7ST_rep4

description: Gene expression of skin_scales of unfed fish (replicate 4) sampled at day 7 of the experiment

source_name: Skin_Scales, Starved day7, rep4


title: 1hr_LPS_R1_vs_0hr_untreatedpool_252665510510_1_1.mev.refIsIA.out

source_name: IA RAW2647 untreated

source_name: IB RAW2647 treated with LPS 1hr


title: Skin_7WS_rep4

description: Gene expression of skin_scales of fish with scales removed (replicate 4) sampled at day 7 of the experiment

source_name: Skin_Scales, Scales removed day7, rep4

value: Normal


title: Skin_7WS_rep5

description: Gene expression of skin_scales of fish with scales removed (replicate 5) sampled at day 7 of the experiment

source_name: Skin_Scales, Scales removed day7, rep5


title: 2_4 wt_60 (cy5) + lisR_t60 (cy3)

city: Groningen

first: Maarten

last: Mols

address: Nijenborgh 7

country: Netherlands

institute: University of Groningen

description:
Sample 16
exposed wildtype vs exposed lisR mutant
Agilent Feature Extraction file:
US22502548_251835910008_S01_GE2-v5_95_Feb07_2_4.txt

hyb_protocol: Total RNA extraction, cDNA synthesis, labelling, microarray hybridization and scanning was performed as previously described (Mols et al., 2010).

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Agilent Feature Extraction Software (v 8.1.1.1) was used for background subtraction and LOWESS normalization.

organism: Listeria monocytogenes

source_name: lisR_t60 (cy3)

growth_protocol: Wild type L. monocytogenes serotype 1/2c strain LO28 and mutant derivatives were grown at 37ºC, 180 rpm, in Brain Heart Infusion broth (BHI, Oxoid).

treatment_protocol: Cefuroxime was added to a final concentration of 4 µg ml-1. Prior to (t0) and after 1 hour after the addition (t60), 20 ml samples were pelleted at maximum speed at 4°C for 30 sec. After decanting the supernatant, pellets were dissolved in 1 ml of TRI-reagent (Ambion, UK) and stored at -80˚C until total RNA isolation.

tag: genotype/variation

value: lisR deletion mutant

tag: agent

value: cefuroxime

tag: exposure time

value: 60 min

value: wildtype LO28


title: Skin_7ST_rep2

description: Gene expression of skin_scales of unfed fish (replicate 2) sampled at day 7 of the experiment

source_name: Skin_Scales, Starved day7, rep2


title: Skin_7WS_rep3

description: Gene expression of skin_scales of fish with scales removed (replicate 3) sampled at day 7 of the experiment

source_name: Skin_Scales, Scales removed day7, rep3


title: Skin_7WS_rep2

description: Gene expression of skin_scales of fish with scales removed (replicate 2) sampled at day 7 of the experiment

source_name: Skin_Scales, Scales removed day7, rep2


title: Skin_7N_rep5

description: Gene expression of skin_scales of control fish (replicate 5) sampled at day 7 of the experiment

source_name: Skin_Scales, Control day7, rep5


title: Skin_7ST_rep1

description: Gene expression of skin_scales of unfed fish (replicate 1) sampled at day 7 of the experiment

source_name: Skin_Scales, Starved day7, rep1


title: MZL_052

city: Scottsdale

first: Esteban

last: Braggio

state: AZ

address: 13400 E. Shea Blvd, MCCRB-300

institute: Mayo Clinic Arizona

hyb_protocol: Aliquouts of agilent Oligo aCGH hybridization kit were added to the samples as recommended by the manafacture. Samples were heat at 95C for 3 minutes, then 37C for 30 minutes. Samples were dispense in the arrays and hybridized at 65C for 40 hours in a hybrization oven at 20rpm.

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

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: SMZL

label_protocol: 1ug of tumor and reference DNA were independently labeled with Bioprime labeling kit from Invitrogen with CY dyes from Amersham as recommended by the manafacture. Cy5 dye was used to label tumor DNA samples and Cy3 to label reference DNA samples. Next, labeled genomic reactions were cleaned-up with Microcon YM-30 columns

extract_protocol: Genomic DNA was obtained from frozen tumors using the Puregene Core A kit (Qiagen) according to manufacturer’s recommendations.

tag: pathology

value: SMZL

tag: gender

value: F

tag: organ

value: Spleen

source_name: Female reference DNA sample

tag: sample type

value: reference


title: Skin_7WS_rep1

description: Gene expression of skin_scales of fish with scales removed (replicate 1) sampled at day 7 of the experiment

source_name: Skin_Scales, Scales removed day7, rep1

tag: tissue


title: MDA-P5

description: MicroRNA expression data at passage 5 follow-up at “drug holiday” condition

source_name: MDA Passage 5

tag: treatment


title: MDA-P7

description: MicroRNA expression data at passage 7 follow-up at “drug holiday” condition

source_name: MDA Passage 7


title: MDA-P3

description: MicroRNA expression data at passage 3 follow-up at “drug holiday” condition

source_name: MDA Passage 3


title: 2_2 lisR_t0 (cy5) + lisR_t60 (cy3)

description:
Sample 14
unexposed lisR mutant vs exposed lisR mutant
Agilent Feature Extraction file:
US22502548_251835910008_S01_GE2-v5_95_Feb07_2_2.txt

label_protocol: Total RNA extraction, cDNA synthesis, labelling, microarray hybridization and scanning was performed as previously described (Mols et al., 2010).

source_name: lisR_t0 (cy5)

value: control

value: 0 min


title: 2_1 wt_t0 (cy3) + cesR_t0 (cy5)

description:
Sample 13
unexposed wildtype vs unexposed cesR mutant
Agilent Feature Extraction file:
US22502548_251835910008_S01_GE2-v5_95_Feb07_2_1.txt

source_name: wt_t0 (cy3)

extract_protocol: Total RNA extraction, cDNA synthesis, labelling, microarray hybridization and scanning was performed as previously described (Mols et al., 2010).

source_name: cesR_t0 (cy5)

value: cesR deletion mutant


title: 2_3 wt_t60 (cy5) + lisR_t60 (cy3)

description:
Sample 15
exposed wildtype vs exposed lisR mutant
Agilent Feature Extraction file:
US22502548_251835910008_S01_GE2-v5_95_Feb07_2_3.txt


title: Skin_7N_rep4

description: Gene expression of skin_scales of control fish (replicate 4) sampled at day 7 of the experiment

source_name: Skin_Scales, Control day7, rep4

value: Skin with scales

value: Day 7


title: 1_3 cesR_t0 (cy5) + cesR_t60 (cy3)

description:
Sample 11
unexposed cesR mutant vs exposed cesR mutant
Agilent Feature Extraction file:
US22502548_251835910008_S01_GE2-v5_95_Feb07_1_3.txt

source_name: cesR_t60 (cy3)


title: Skin_3STWS_rep4

description: Gene expression of skin_scales of unfed fish and with scales removed (replicate 4) sampled at day 3 of the experiment

source_name: Skin_Scales, Starved and scales removed day3, rep4

value: Day 3

value: Unfed

value: Removed


title: Skin_7STWS_rep1

description: Gene expression of skin_scales of unfed fish and with scales removed (replicate 1) sampled at day 7 of the experiment

source_name: Skin_Scales, Starved and scales removed day7, rep1


title: Skin_3STWS_rep2

description: Gene expression of skin_scales of unfed fish and with scales removed (replicate 2) sampled at day 3 of the experiment

source_name: Skin_Scales, Starved and scales removed day3, rep2


title: Skin_7N_rep2

description: Gene expression of skin_scales of control fish (replicate 2) sampled at day 7 of the experiment

source_name: Skin_Scales, Control day7, rep2

value: Normal

value: Intact


title: Skin_7N_rep3

description: Gene expression of skin_scales of control fish (replicate 3) sampled at day 7 of the experiment

source_name: Skin_Scales, Control day7, rep3


title: MDA-UT

description: MicroRNA expression data before treatment with DAC

source_name: MDA Un-treated


title: Skin_3STWS_rep1

description: Gene expression of skin_scales of unfed fish and with scales removed (replicate 1) sampled at day 3 of the experiment

source_name: Skin_Scales, Starved and scales removed day3, rep1


title: Skin_7N_rep1

description: Gene expression of skin_scales of control fish (replicate 1) sampled at day 7 of the experiment

source_name: Skin_Scales, Control day7, rep1


title: 1_1 wt_t0 (cy3) + lisR_t0 (cy5)

description:
Sample 9
unexposed wildtype vs unexposed lisR mutant
Agilent Feature Extraction file:
US22502548_251835910008_S01_GE2-v5_95_Feb07_1_1.txt

value: lisR deletion mutant


title: 1_4 wt_t60 (cy5) + cesR_t60 (cy3)

description:
Sample 12
exposed wildtype vs exposed cesR mutant
Agilent Feature Extraction file:
US22502548_251835910008_S01_GE2-v5_95_Feb07_1_4.txt

value: cefuroxime

value: 60 min


title: 1_2 wt_t0 (cy3) + wt_t60 (cy5)

description:
Sample 10
unexposed wildtype vs exposed wildtype
Agilent Feature Extraction file:
US22502548_251835910008_S01_GE2-v5_95_Feb07_1_2.txt

value: wildtype LO28


title: Skin_3STWS_rep3

description: Gene expression of skin_scales of unfed fish and with scales removed (replicate 3) sampled at day 3 of the experiment

source_name: Skin_Scales, Starved and scales removed day3, rep3


title: Skin_3ST_rep5

description: Gene expression of skin_scales of unfed fish (replicate 5) sampled at day 3 of the experiment

source_name: Skin_Scales, Starved day3, rep5


title: MDA-P1

description: MicroRNA expression data at passage 1 follow-up at “drug holiday” condition

source_name: MDA Passage 1


title: Skin_3ST_rep4

description: Gene expression of skin_scales of unfed fish (replicate 4) sampled at day 3 of the experiment

source_name: Skin_Scales, Starved day3, rep4


title: HB2-P10

description: MicroRNA expression data at passage 10 follow-up at “drug holiday” condition

source_name: HB2 Passage 10


title: MDA-T

description: MicroRNA expression data directly after treatment with DAC

source_name: MDA Treated

value: treatment with DAC


title: HB2-P7

description: MicroRNA expression data at passage 7 follow-up at “drug holiday” condition

source_name: HB2 Passage 7


title: HB2-P3

description: MicroRNA expression data at passage 3 follow-up at “drug holiday” condition

source_name: HB2 Passage 3


title: 2_3 wt_t60 (cy3) + lisR_t60 (cy5)

description:
Sample 7
exposed wildtype vs exposed lisR mutant
Agilent Feature Extraction file:
US22502548_251835910007_S01_GE2-v5_95_Feb07_2_3.txt

source_name: lisR_t60 (cy5)


title: Skin_3ST_rep1

description: Gene expression of skin_scales of unfed fish (replicate 1) sampled at day 3 of the experiment

source_name: Skin_Scales, Starved day3, rep1


title: 2_4 wt_60 (cy3) + lisR_t60 (cy5)

description:
Sample 8
exposed wildtype vs exposed lisR mutant
Agilent Feature Extraction file:
US22502548_251835910007_S01_GE2-v5_95_Feb07_2_4.txt


title: Skin_3WS_rep5

description: Gene expression of skin_scales of fish with scales removed (replicate 5) sampled at day 3 of the experiment

source_name: Skin_Scales, Scales removed day3, rep5


title: Skin_3ST_rep2

description: Gene expression of skin_scales of unfed fish (replicate 2) sampled at day 3 of the experiment

source_name: Skin_Scales, Starved day3, rep2


title: HB2-P1

source_name: HB2 Passage 1

value: passage 1 follow-up at “drug holiday” condition


title: HB2-P5

description: MicroRNA expression data at passage 5 follow-up at “drug holiday” condition

source_name: HB2 Passage 5


title: Skin_3STWS_rep5

description: Gene expression of skin_scales of unfed fish and with scales removed (replicate 5) sampled at day 3 of the experiment

source_name: Skin_Scales, Starved and scales removed day3, rep5


title: Skin_3ST_rep3

description: Gene expression of skin_scales of unfed fish (replicate 3) sampled at day 3 of the experiment

source_name: Skin_Scales, Starved day3, rep3


title: Skin_3WS_rep4

description: Gene expression of skin_scales of fish with scales removed (replicate 4) sampled at day 3 of the experiment

source_name: Skin_Scales, Scales removed day3, rep4


title: Skin_3WS_rep3

description: Gene expression of skin_scales of fish with scales removed (replicate 3) sampled at day 3 of the experiment

source_name: Skin_Scales, Scales removed day3, rep3


title: 2_2 lisR_t0 (cy3) + lisR_t60 (cy5)

description:
Sample 6
unexposed lisR mutant vs exposed lisR mutant
Agilent Feature Extraction file:
US22502548_251835910007_S01_GE2-v5_95_Feb07_2_2.txt

source_name: lisR_t0 (cy3)


title: Skin_3WS_rep1

description: Gene expression of skin_scales of fish with scales removed (replicate 1) sampled at day 3 of the experiment

source_name: Skin_Scales, Scales removed day3, rep1


title: HB2-UT

description: MicroRNA expression data before treatment with DAC

source_name: HB2 Un-treated


title: 1_4 wt_t60 (cy3) + cesR_t60 (cy5)

description:
Sample 4
exposed wildtype vs exposed cesR mutant
Agilent Feature Extraction file:
US22502548_251835910007_S01_GE2-v5_95_Feb07_1_4.txt

source_name: cesR_t60 (cy5)


title: Limb-bud-E15.5-N-L

status: Public on Jan 23 2012

city: Station 19

first: Denis

last: Duboule

state: Lausanne

address: SV 2843 (Bâtiment SV)

department: ISREC

institute: EPFL

hyb_protocol: standard Affymetrix protocol

scan_protocol: Tiling arrays were scanned using the Affymetrix GCS3000 7G scanner.

data_processing: In house software: Background subtraction followed by quantile normalization and RMA-style estimation by blocks based on UCSC Known Gene annotation for assembly ncbi3/mm9.

source_name: Mouse embryo stage E15.5 whole limb-bud

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Total RNA was extracted using RNeasy-mini columns (Qiagen), DNaseI digested on-column, treated with RNase free DNase I, (Roche) and further processed according to the Affymetrix GeneChip WT Double-Stranded Target Assay manual. Briefly, ribosomal RNAs were depleted and samples were reverse transcribed.

treatment_protocol: Embryonic forelimbs were cut along the body wall and kept in RNAlater

tag: developmental stage

value: Limb-bud


title: Limb-bud-E15.5-N-R


title: HB2-T

description: MicroRNA expression data directly after treatment with DAC

source_name: HB2 Treated


title: 1_3 cesR_t0 (cy3) + cesR_t60 (cy5)

description:
Sample 3
unexposed cesR mutant vs exposed cesR mutant
Agilent Feature Extraction file:
US22502548_251835910007_S01_GE2-v5_95_Feb07_1_3.txt

source_name: cesR_t0 (cy3)

value: control


title: Limb-bud-E15.5-L-L


title: Skin_3N_rep2

description: Gene expression of skin_scales of control fish (replicate 2) sampled at day 3 of the experiment

source_name: Skin_Scales, Control day3, rep2


title: Limb-bud-E13.5-N-2

source_name: Mouse embryo stage E13.5 whole limb-bud


title: Limb-bud-E15.5-L-R


title: Skin_3N_rep5

description: Gene expression of skin_scales of control fish (replicate 5) sampled at day 3 of the experiment

source_name: Skin_Scales, Control day3, rep5


title: 1_1 wt_t0 (cy5) + lisR_t0 (cy3)

description:
Sample 1
unexposed wildtype vs unexposed lisR mutant
Agilent Feature Extraction file:
US22502548_251835910007_S01_GE2-v5_95_Feb07_1_1.txt

value: 0 min

source_name: wt_t0 (cy5)


title: Limb-bud-E13.5-L-1


title: Limb-bud-E13.5-L-2


title: Limb-bud-E11.5-N-1

source_name: Mouse embryo stage E11.5 whole limb-bud


title: 2_1 wt_t0 (cy5) + cesR_t0 (cy3)

description:
Sample 5
unexposed wildtype vs unexposed cesR mutant
Agilent Feature Extraction file:
US22502548_251835910007_S01_GE2-v5_95_Feb07_2_1.txt

value: cesR deletion mutant


title: 1_2 wt_t0 (cy5) + wt_t60 (cy3)

description:
Sample 2
unexposed wildtype vs exposed wildtype
Agilent Feature Extraction file:
US22502548_251835910007_S01_GE2-v5_95_Feb07_1_2.txt


title: Skin_3N_rep4

description: Gene expression of skin_scales of control fish (replicate 4) sampled at day 3 of the experiment

source_name: Skin_Scales, Control day3, rep4

value: Skin with scales


title: Calu-3 18 hrs non-stretch

city: Aurora

first: Michael

last: Koeppen

institute: Univeristy of Colorado - Anschutz Medical Campus

description: Calu-3 human pulmonary epithelial cells without 18 hours of cyclic mechanical stretch

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

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

data_processing: The data were analyzed with dCHIP (Build 17. December 2010) using  default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Calu-3 cells without cylcic mechanical stretch

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

growth_protocol: Human bronchial epithelial cells (Calu-3 or A549) were cultured as described previously (Haeberle et al., 2008; Liedtke et al., 2005).

extract_protocol: Qiagen spin column protocol for total RNA extraction was performed according to manufacturer instruction

treatment_protocol: Calu-3 human bronchial epithelial cells were plated on BioFlex culture plates-collagen type I (BF-3001C; FlexCell International) and allowed to attach and grow to ~80% conﬂuence. The medium was changed to MEM plus 10% FBS. Plates were then placed on a FlexCell FX-4000T Tension Plus System and stretched at 20% stretch maximum, 0.7% stretch minimum, sine wave 2 s, on 2 s off.

tag: cell type

value: human pulmonary epithelial cells


title: Skin_3WS_rep2

description: Gene expression of skin_scales of fish with scales removed (replicate 2) sampled at day 3 of the experiment

source_name: Skin_Scales, Scales removed day3, rep2

value: Day 3


title: Skin_3N_rep3

description: Gene expression of skin_scales of control fish (replicate 3) sampled at day 3 of the experiment

source_name: Skin_Scales, Control day3, rep3


title: Calu-3 18 hrs stretch

description: Calu-3 human pulmonary epithelial cells with18 hours of cyclic mechanical stretch

source_name: Calu-3 cells with cylcic mechanical stretch


title: Skin_3N_rep1

description: Gene expression of skin_scales of control fish (replicate 1) sampled at day 3 of the experiment

source_name: Skin_Scales, Control day3, rep1


title: Limb-bud-E13.5-N-1


title: Limb-bud-E11.5-L-2


title: Limb-bud-E15.5-J-L


title: Limb-bud-E11.5-L-1


title: Limb-bud-E15.5-J-R


title: Limb-bud-E11.5-J-2


title: Limb-bud-E13.5-J-1


title: Limb-bud-E13.5-C-2


title: Limb-bud-E15.5-C-L


title: Limb-bud-E11.5-E-1


title: Limb-bud-E11.5-E-2


title: Limb-bud-E11.5-C-1


title: Limb-bud-E11.5-J-1


title: Limb-bud-E11.5-N-2


title: ipt1357, Salt-treated plants, biological rep3

city: Yokohama

first: Rie

last: Nishiyama

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi

department: Plant Science Center

institute: RIKEN

description: Gene expression data from salt-treated ipt1357 plants

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturer's instructions. Then Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 021169 Arabidopsis Ver.4 Oligo Microarray 4x44K G2519F for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed and dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with GeneSpring ver.11.5.1 (Agilent). Percentile normalization (75 percentile) was performed for each chip.

organism: Arabidopsis thaliana

source_name: Salt-treated Arabidopsis ipt1357 plants

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Arabidopsis thaliana WT and ipt1,3,5,7 mutant plants (Columbia ecotype) were grown on GM agar (0.8%) medium supplemented with 3% sucrose for 10 days (22ºC, 16-h-light/8-h-dark, 60 μmol m-2 sec-1 photon flux density).

extract_protocol: Total RNA was extracted from the salt-treated or untreated plants using TRIzol Reagent (Invitrogen) according to the manufacturer’s instruction.

treatment_protocol: The 10-d-old plants were transfered onto 1/2 MS agar plates without sucrose containing either 0 or 200 mM NaCl and then incubated for 24 hours.

tag: ecotype

value: Columbia

value: Whole plants

value: salt

tag: age

value: 11 day old seedlings


title: Limb-bud-E15.5-E-R


title: ipt1357, Salt-treated plants, biological rep2


title: Limb-bud-E15.5-E-L


title: Limb-bud-E13.5-E-2


title: Limb-bud-E13.5-E-1


title: Limb-bud-E13.5-C-1


title: Limb-bud-E15.5-C-R


title: Col-0, Salt-treated plants, biological rep2

description: Gene expression data from salt-treated Col-0 plants

source_name: Salt-treated Arabidopsis Col-0 plants

value: wildtype


title: Limb-bud-E11.5-C-2


title: Limb-bud-E13.5-J-2


title: ipt1357, Untreated plants, biological rep3

description: Gene expression data from untreated ipt1357 plants

source_name: Untreated Arabidopsis ipt1357 plants


title: ipt1357, Untreated plants, biological rep2


title: Col-0, Untreated plants, biological rep3

description: Gene expression data from untreated Col-0 plants

source_name: Untreated Arabidopsis Col-0 plants


title: Col-0, Untreated plants, biological rep2


title: Adenovirus EGFP transduced HUVEC

city: Vienna

first: Rainer

last: de Martin

address: Schwarzspanierstr. 17

department: Vascular Biology

country: Austria

institute: Medical University of Vienna

hyb_protocol: standard Affymetrix

scan_protocol: standard Affymetrix

data_processing: standard Affymetrix

source_name: human umbilical vein endothelial cells

label_protocol: standard Affymetrix

extract_protocol: Quiagen

tag: mRNA isolated 16 hours after transduction


title: Col-0, Salt-treated plants, biological rep3


title: non-transduced human umbilical vein endothelial cells

source_name: HUVEC

tag: non-transduced HUVEC


title: ipt1357, Salt-treated plants, biological rep1


title: ipt1357, Untreated plants, biological rep1


title: Neutrophils rep3 miRNA (HUG)

city: Nutley

first: Donavan

last: Cheng

state: NJ

address: 340 Kingsland Ave

department: Translational Research Sciences

institute: Hoffmann-LaRoche

description: Isolated at University Hospital of Geneva

hyb_protocol: Labeled RNA was hybridized to Affymetrix GeneChip miRNA microarrays according to manufacturer’s instructions.  Wash and stain protocol FS450_0003.

scan_protocol: GeneChips were scanned using the GC 30007G scanner.

data_processing: Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure.

label: Biotin

source_name: Neutrophils from healthy donors

label_protocol: Total RNA (300ng) was biotin labeled using the FlashTag™ HSR RNA labeling kit for Affymetrix miRNA arrays (Genisphere LLC., Hatfield, PA, USA) according to manufacturer’s instructions

extract_protocol: Total RNA, including small non-coding RNAs, was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.

value: Neutrophils


title: Col-0, Salt-treated plants, biological rep1


title: Col-0, Untreated plants, biological rep1


title: Adenovirus-Sox18-transduced HUVEC

description: HUVEC were transduced with a recombinant adenovirus (AdV) for expression of human SOX18 in an IRES-EGFP casette, or control AdV containing EGFP only. From these cells, as well as from non-transduced HUVEC, RNA was extracted 16 hours later using a Qiagen kit, and analyzed.

source_name: Human umbilical vein endothelial cells

extract_protocol: Qiagen

tag: mRNA prepared 16 hours after transduction


title: Neutrophils rep5 miRNA (HUG)


title: Neutrophils rep4 miRNA (HUG)


title: B cells rep3 miRNA (HUG)

source_name: B cells from healthy donors

value: B cells


title: Eosinophils rep1 miRNA (HUG)

source_name: Eosinophils from healthy donors

value: Eosinophils


title: B cells rep5 miRNA (HUG)


title: B cells rep1 miRNA (HUG)


title: Neutrophils rep2 miRNA (HUG)


title: NK cells rep3 miRNA (HUG)

source_name: NK cells from healthy donors

value: NK cells


title: Monocytes rep8 miRNA (HUG)

source_name: CD14+ Monocytes from healthy donors

value: CD14+ Monocytes


title: B cells rep4 miRNA (HUG)


title: Neutrophils rep1 miRNA (HUG)


title: Eosinophils rep3 miRNA (HUG)


title: Eosinophils rep2 miRNA (HUG)


title: NK cells rep5 miRNA (HUG)


title: B cells rep2 miRNA (HUG)


title: NK cells rep4 miRNA (HUG)


title: NK cells rep2 miRNA (HUG)


title: Monocytes rep9 miRNA (HUG)


title: NK cells rep1 miRNA (HUG)


title: CD8+ T cells rep5 miRNA (HUG)

source_name: CD8+ T cells from healthy donors

value: CD8+ T cells


title: Monocytes rep7 miRNA (HUG)


title: Monocytes rep6 miRNA (HUG)


title: Monocytes rep5 miRNA (HUG)


title: pDC rep5 miRNA (Roche)

description: CD123+ plasmacytoid dendritic cells (pDCs), CD11c+ myeloid dendritic cells (mDCs) and CD14+ monocytes were isolated using the EasySep®  Human pDCs Enrichment Kit, a custom EasySep®  Human mDCs Enrichment Kit (containing antibodies directed against CD3, CD19, CD14, CD16, CD19, CD25, CD34, CD56, CD66b, GlyA, CD85g, CD45RA, CD123 and dextran) and the Human CD14 positive Selection Kit (all from Stemcell Biotechnologies) respectively according to manufacturer’s instructions.

hyb_protocol: Labeled RNA was hybridized to Affymetrix GeneChip miRNA microarrays according to manufacturer’s instructions. Wash and stain protocol FS450_0003.

source_name: pDCs from healthy donor pool 17

value: pDCs


title: pDC rep3 miRNA (Roche)

source_name: pDCs from healthy donor pool 14


title: CD8+ T cells rep2 miRNA (HUG)


title: CD4+ T cells rep1 miRNA (HUG)

source_name: CD4+ T cells from healthy donors

value: CD4+ T cells


title: CD4+ T cells rep5 miRNA (HUG)


title: CD8+ T cells rep3 miRNA (HUG)


title: CD8+ T cells rep1 miRNA (HUG)


title: Saures_10min_Mupirocin_rep4

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

institute: Genomic Research Laboratory

description:
251486710012_rechts
Staphylococcus aureus COL control  vs Staphylococcus aureus COL 10 minutes mupirocin

hyb_protocol: Hybridizations were done in a total sample volume of 40 µl for 17 hours at 65°C at 10 rpm in a dedicated hybridization chamber (Agilent) and hybridisation oven (Robbins Scientific, Sunnyvale, CA, USA). After hybridization the slides were washed for one minute at room temperature in wash buffer 1 followed by a one minute washing step at 37°C with wash buffer 2. The slides were dried under nitrogen flow. Blocking reagents, hybridization buffer (Gene Expression Hybridization Kit) and washing solutions (Gene Expression Wash Buffer Kit) were purchased from Agilent.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.5.1.1).

data_processing: Agilent Feature Extraction Software (A 5.1.1) was used for background subtraction and LOWESS normalization.

organism: Staphylococcus aureus

source_name: Staphylococcus aureus control

label_protocol: Synthesis of Cy5-dCTP or Cy3-dCTP (Perkin-Elmer, Waltham, USA) labeled cDNA was done with 10 µg of total RNA as template by direct reverse-transcription using Superscript II (Invitrogen, Darmstadt, Germany) and random hexamers (Promega, Madison, USA) according to the manufacturer’s instructions. To degrade the RNA after cDNA synthesis the reaction mix was incubated for 30 min at room temperature with E. coli RNase H (Invitrogen, Darmstadt, Germany).Labeled cDNA was then purified with the QIAquick PCR Purification Kit (Qiagen, Mannheim Germany). The Cy-dye incorporation was analysed with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Rockland, USA). A sample volume corresponding to 30 pmol incorporated dye of the labeled cDNA was used for two-colour competitive hybridization experiments.

growth_protocol: The S. aureus strain COL was routinely grown aerobically in a defined synthetic medium (Gertz et al., 1999) with vigorous agitation at 37°C. For mupirocin experiments, pre-warmed medium was inoculated with cells from an exponentially growing over-night culture to an initial OD500nm of 0.1 At an OD500nm of 0.5. the culture was split and one part transferred to a pre-warmed Erlenmeyer-flask and treated with mupirocin while the remaining culture served as a control.

extract_protocol: Total RNA was isolated from S. aureus COL using the acid-phenol method (Gertz et al., 1999; Majumdar et al., 1991) with modifications described by Fuchs et al. (Fuchs et al., 2007)

treatment_protocol: The final mupirocin concentration used in all stress experiments was 0.03 µg/ml.

tag: strain

value: COL

value: control

source_name: Staphylococcus aureus 10 min mupirocin

value: 10 min mupirocin


title: CD4+ T cells rep4 miRNA (HUG)


title: CD8+ T cells rep4 miRNA (HUG)


title: pDC rep4 miRNA (Roche)

source_name: pDCs from healthy donor pool 16


title: CD4+ T cells rep3 miRNA (HUG)


title: Neutrophils rep1 miRNA (Roche)

description: Isolated using the EasySep® Human Neutrophil Enrichment Kit (Stem Cell Technologies, Grenoble, France)

source_name: Neutrophils from healthy donor pool 1


title: CD4+ T cells rep3 mRNA (HUG)

description: Isolated at University Hospital of Geneva (HUG)

hyb_protocol: Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.

data_processing: Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total 18,391 out of 54,675 probesets passed the QC and curation processes.

source_name: CD4+ T cells

label_protocol: Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).


title: mDC rep2 miRNA (Roche)

source_name: mDCs from healthy donor pool 15

value: mDCs


title: CD4+ T cells rep2 miRNA (HUG)


title: mDC rep1 miRNA (Roche)

source_name: mDCs from healthy donor pool 14


title: pDC rep2 miRNA (Roche)

source_name: pDCs from healthy donor pool 13


title: pDC rep1 miRNA (Roche)

source_name: pDCs from healthy donor pool 18


title: Neutrophils rep2 miRNA (Roche)

source_name: Neutrophils from healthy donor pool 2


title: Neutrophils rep4 miRNA (Roche)

source_name: Neutrophils from healthy donor pool 4


title: Neutrophils rep3 miRNA (Roche)

source_name: Neutrophils from healthy donor pool 3


title: Eosinophils rep4 miRNA (Roche)

description: Isolated using EasySep® Human Eosinophil Enrichment Kit (Stem Cell Technologies)

source_name: Eosinophils from healthy donor pool 8


title: Limb-bud-E13.5-I-2

source_name: Mouse embryo stage E13.5 whole limb-bud

value: Limb-bud


title: Saures_10min_Mupirocin_rep2

description:
251486710011_rechts
Staphylococcus aureus COL control  vs Staphylococcus aureus COL 10 minutes mupirocin


title: Limb-bud-E13.5-I-1


title: Limb-bud-E15.5-I-L

source_name: Mouse embryo stage E15.5 whole limb-bud


title: Limb-bud-E11.5-I-2

source_name: Mouse embryo stage E11.5 whole limb-bud


title: Limb-bud-E15.5-I-R


title: Saures_10min_Mupirocin_rep1

description:
251486710011_links
Staphylococcus aureus COL 10 minutes mupirocin vs Staphylococcus aureus COL control


title: Eosinophils rep2 miRNA (Roche)

source_name: Eosinophils from healthy donor pool 4


title: Limb-bud-E11.5-I-1


title: Eosinophils rep1 miRNA (Roche)

source_name: Eosinophils from healthy donor pool 1


title: Eosinophils rep3 miRNA (Roche)

source_name: Eosinophils from healthy donor pool 7


title: Limb-bud-E15.5-H-L


title: Saures_10min_Mupirocin_rep3

description:
251486710012_links
Staphylococcus aureus COL 10 minutes mupirocin vs Staphylococcus aureus COL wild type

source_name: Staphylococcus aureus 10 min mupirocin

source_name: Staphylococcus aureus control


title: CD8+ T cells rep5 miRNA (Roche)

description: CD14+ monocytes, CD8+ T cells, CD56+ NK cells and CD19 B cells were isolated using the Human CD14 positive Selection Kit, Human CD8+ T cells Enrichment Kit, EasySep® Human CD56+ NK cells Enrichment Kit, EasySep® Human CD19+ B cells Enrichment Kit (all from Stem Cell Technologies) respectively according to manufacturer’s instructions.

source_name: CD8+ T cells from healthy donor pool 4


title: CD8+ T cells rep4 miRNA (Roche)

source_name: CD8+ T cells from healthy donor pool 3


title: Limb-bud-E15.5-H-R


title: Limb-bud-E11.5-H-2


title: Limb-bud-E13.5-H-2


title: Limb-bud-E13.5-H-1


title: Limb-bud-E15.5-G-L


title: CD8+ T cells rep1 miRNA (Roche)

source_name: CD8+ T cells from healthy donor pool 10


title: CD8+ T cells rep3 miRNA (Roche)

source_name: CD8+ T cells from healthy donor pool 12


title: Limb-bud-E11.5-H-1


title: CD8+ T cells rep2 miRNA (Roche)

source_name: CD8+ T cells from healthy donor pool 11


title: CD4+ T cells rep3 mRNA (Roche)

description: CD4+ T cells were isolated from the monocytes-depleted fraction (obtained during the monocytes isolation) using the EasySep® Human CD4 Positive Selection Kit (Stemcell Technologies) according to manufacturer’s instructions.

data_processing: Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure.  Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release.  As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis.  A total of 20,367 out of 54,675 probesets passed the QC and curation processes, corresponding to 11,629 unique genes.

source_name: CD4+ T cells from healthy donor pool 4


title: NK cells rep5 miRNA (Roche)

source_name: NK cells from healthy donor pool 9


title: CD4+ T cells rep2 mRNA (Roche)

source_name: CD4+ T cells from healthy donor pool 3


title: CD4+ T cells rep5 mRNA (Roche)

source_name: CD4+ T cells from healthy donor pool 8


title: CD4+ T cells rep4 mRNA (Roche)

source_name: CD4+ T cells from healthy donor pool 7


title: NK cells rep4 miRNA (Roche)

source_name: NK cells from healthy donor pool 7


title: Limb-bud-E15.5-B-L

source_name: Mouse embryo stage E15.5 whole limb-bud


title: Limb-bud-E15.5-G-R


title: Limb-bud-E15.5-B-R


title: CD4+ T cells rep1 mRNA (Roche)

source_name: CD4+ T cells from healthy donor pool 2


title: CD4+ T cells rep2 miRNA (Roche)


title: NK cells rep1 miRNA (Roche)

source_name: NK cells from healthy donor pool 10


title: NK cells rep3 miRNA (Roche)

source_name: NK cells from healthy donor pool 6


title: Limb-bud-E13.5-G-2

source_name: Mouse embryo stage E13.5 whole limb-bud


title: Limb-bud-E13.5-G-1


title: CD4+ T cells rep1 miRNA (Roche)


title: Limb-bud-E13.5-B-2


title: Limb-bud-E13.5-B-1


title: Limb-bud-E11.5-G-1

source_name: Mouse embryo stage E11.5 whole limb-bud


title: CD4+ T cells rep4 miRNA (Roche)


title: CD4+ T cells rep3 miRNA (Roche)


title: Limb-bud-E11.5-B-2


title: NK cells rep2 miRNA (Roche)

source_name: NK cells from healthy donor pool 12


title: B cells rep5 miRNA (Roche)

source_name: CD19+ B cells from healthy donor pool 9


title: Limb-bud-E15.5-F-L


title: Limb-bud-E15.5-M-L


title: Limb-bud-E11.5-B-1


title: Limb-bud-E15.5-M-R


title: Limb-bud-E15.5-F-R


title: Limb-bud-E13.5-M-2


title: B cells rep4 miRNA (Roche)

source_name: CD19+ B cells from healthy donor pool 8


title: Limb-bud-E11.5-M-2


title: Limb-bud-E13.5-M-1


title: Limb-bud-E11.5-G-2


title: Limb-bud-E13.5-F-1


title: Limb-bud-E11.5-M-1


title: Limb-bud-E15.5-K-L


title: Limb-bud-E15.5-K-R


title: Limb-bud-E11.5-F-2


title: Limb-bud-E13.5-K-2


title: Limb-bud-E11.5-F-1


title: B cells rep3 miRNA (Roche)

source_name: CD19+ B cells from healthy donor pool 7


title: B cells rep2 miRNA (Roche)

source_name: CD19+ B cells from healthy donor pool 6


title: Monocytes rep9 miRNA (Roche)

source_name: CD14+ monocytes from healthy donor pool 8

value: Monocytes


title: Limb-bud-E11.5-K-2


title: B cells rep1 miRNA (Roche)

source_name: CD19+ B cells from healthy donor pool 11


title: Limb-bud-E11.5-K-1


title: Limb-bud-E15.5-A-L


title: Limb-bud-E15.5-D-L


title: Limb-bud-E13.5-F-2


title: Limb-bud-E15.5-A-R


title: Limb-bud-E15.5-D-R


title: Monocytes rep8 miRNA (Roche)

source_name: CD14+ monocytes from healthy donor pool 6


title: Limb-bud-E13.5-D-2


title: Limb-bud-E13.5-A-2


title: Limb-bud-E13.5-A-1


title: Limb-bud-E13.5-D-1


title: Limb-bud-E13.5-K-1


title: Monocytes rep7 miRNA (Roche)

source_name: CD14+ monocytes from healthy donor pool 2


title: Limb-bud-E11.5-A-2


title: Limb-bud-E11.5-D-1


title: Limb-bud-E11.5-D-2


title: Limb-bud-E11.5-A-1


title: Monocytes rep5 miRNA (Roche)

source_name: CD14+ monocytes from healthy donor pool 17


title: Monocytes rep4 miRNA (Roche)

source_name: CD14+ monocytes from healthy donor pool 16


title: Map3k7 (TAK1) knockout replicate 3

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: 5 micrograms of biotin-labeled cRNA was hybridized to an Affymetrix HT_MG-430_PM array using the Affymetrix GeneTitan system

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system

data_processing: Signals on arrays were summarized using the RMA method as implemented in the Affymetrix Expression Console software v1.1

source_name: splenic CD11c+ dendritic cells

label_protocol: 100 ng of total RNA was converted to biotin-labeled cRNA using the Affymetrix 3'-IVT Express protocol as per the manufacturer's recommendations

growth_protocol: Wild-type and Map3k7-CreER mice were treated with tamoxifen in vivo for 3 days to induce deletion of Map3k7 (TAK1).

extract_protocol: RNA was extracted using the Qiagen RNeasy micro kit according to the manufacturer's recommended protocol.

treatment_protocol: CD11c+ dendritic cells were purified from the spleen by flow cytometry and then lyzed in RNA extraction buffer.

value: splenic CD11c+ dendritic cells

tag: genotype/variation

value: tamoxifen


title: Monocytes rep6 miRNA (Roche)

source_name: CD14+ monocytes from healthy donor pool 18


title: Map3k7 (TAK1) knockout replicate 1


title: Map3k7 (TAK1) knockout replicate 2


title: wild-type replicate 1

value: WT


title: Monocytes rep3 miRNA (Roche)

source_name: CD14+ monocytes from healthy donor pool 15


title: Monocytes rep1 miRNA (Roche)

source_name: CD14+ monocytes from healthy donor pool 1


title: Monocytes rep2 miRNA (Roche)

source_name: CD14+ monocytes from healthy donor pool 13


title: wild-type replicate 2


title: G4 LSL-mTert PB-Pten/p53 11819PM mRNA

status: Public on Jan 21 2012

city: Boston

first: Zhihu

last: Ding

state: MA

address: 44 Binney Street

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 11819PM mRNA

hyb_protocol: The biotinylated cDNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C.

scan_protocol: Each cDNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: G4 LSL-mTert PB-Pten/p53

label_protocol: The fragmented product is labeled via enzymatic attachment of a biotin-labeled nucleotide to the 3’-hydroxyl end of the fragmented cDNA.

extract_protocol: Total RNA was extracted using TRIzol followed by RNeasy Mini kit (Qiagen) cleanup and RQ1 RNase-free DNase Set treatment (Promega) according to the manufacturer’s instructions

treatment_protocol: Prostate tumors were disected from G3 and G4 generations of LSL-mTert PB-Pten/p53 mouse model

tag: comment

value: Telomerase reactivation

tag: generations

tag: genotype

value: LSL-mTert PB-Pten/p53

value: prostate tumor

tag: genetic background


title: G3 LSL-mTert PB-Pten/p53 11756PT mRNA

description: G3 LSL-mTert PB-Pten/p53 G3 LSL-mTert PB-Pten/p53 11756PT mRNA

source_name: G3 LSL-mTert PB-Pten/p53


title: G4 LSL-mTert PB-Pten/p53 9493PT mRNA

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 9493PT mRNA


title: G4 LSL-mTert PB-Pten/p53 11959PT mRNA

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 11959PT mRNA


title: G4 LSL-mTert PB-Pten/p53 11649PT mRNA

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 11649PT mRNA


title: wild-type replicate 3


title: G4 LSL-mTert PB-Pten/p53 10118PT mRNA

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 10118PT mRNA


title: 45 Weeks b.2

city: Nedlands

first: Robert

middle: Jeffery

last: Marano

state: Western Australia

address: Sir Charles Gairdner Hospital, Hospital Avenue

department: School of Surgery

country: Australia

institute: Ear Science Institute Australia and the Ear Sciences Centre

description: Biological Replicate b, Technical Replicate 2

hyb_protocol: Standard Hybridising protocol

scan_protocol: Standard scanning protocol

data_processing: Data was normalised using Quantile normalisation plus Log2 Transformation

source_name: mouse cochlea

label_protocol: Biotinylated cRNA were created using the Ambion MessageAmp kit.

growth_protocol: Animals were aged in the laboratory under standard living conditions

extract_protocol: Total RNA, DNA and protein were extracted using the QIAGEN All Prep kit

treatment_protocol: Cochlea were removed immediately post mortem and placed into RNAlater. Total RNA was extracted the same day once material was taken to the laboratory.

value: 45 weeks

value: Cochlea (vestibular organs removed)


title: 45 Weeks a.2

description: Biological Replicate a, Technical Replicate 2


title: 45 Weeks b.1

description: Biological Replicate b, Technical Replicate 1


title: G4 LSL-mTert PB-Pten/p53 8781PT mRNA

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 8781PT mRNA


title: G4 LSL-mTert PB-Pten/p53 9492PT mRNA

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 9492PT mRNA


title: G3 LSL-mTert PB-Pten/p53 11563PT mRNA

description: G3 LSL-mTert PB-Pten/p53 G3 LSL-mTert PB-Pten/p53 11563PT mRNA


title: G4 LSL-mTert PB-Pten/p53 8589PT mRNA

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 8589PT mRNA


title: G4 LSL-mTert PB-Pten/p53 8591PT mRNA

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 8591PT mRNA


title: G4 LSL-mTert PB-Pten/p53 7106PT mRNA

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 7106PT mRNA


title: 45 Weeks a.1

description: Biological Replicate a, Technical Replicate 1


title: G3 LSL-mTert PB-Pten/p53 X11756PT4 aCGH

description: G3 LSL-mTert PB-Pten/p53 G3 LSL-mTert PB-Pten/p53 X11756PT4 aCGH

hyb_protocol: Hybridization was performed with the Tecan HS Pro hybridization station.

scan_protocol: Scanning was performed with Agilent scanner equipped Agilent Scanner Control software v7.0.

data_processing: Data were processed with the Feature Extraction (FE) software v9.5.

label_protocol: The fragmented product is labeled via exo-Klenow with Cyanine 3-dUTP.

extract_protocol: Total genomic DNA were extracted with Qiagen DNeasy Blood & Tissue Kit following according to the manufacturer's instructions.

value: Telomerase reactivation in the setting of telomere dysfunction

value: tail


title: G4 LSL-mTert PB-Pten/p53 X8781A4 aCGH

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 X8781A4 aCGH


title: 15 Weeks b.2

value: 15 weeks


title: G4 LSL-mTert PB-Pten/p53 X8591A4 aCGH

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 X8591A4 aCGH


title: G3 LSL-mTert PB-Pten/p53 X11563PT3 aCGH

description: G3 LSL-mTert PB-Pten/p53 G3 LSL-mTert PB-Pten/p53 X11563PT3 aCGH


title: G3 LSL-mTert PB-Pten/p53 8584PT mRNA

description: G3 LSL-mTert PB-Pten/p53 G3 LSL-mTert PB-Pten/p53 8584PT mRNA


title: G3 LSL-mTert PB-Pten/p53 7526PT mRNA

description: G3 LSL-mTert PB-Pten/p53 G3 LSL-mTert PB-Pten/p53 7526PT mRNA


title: G4 LSL-mTert PB-Pten/p53 X11923PT1 aCGH

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 X11923PT1 aCGH


title: G4 LSL-mTert PB-Pten/p53 X11959PT1 aCGH

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 X11959PT1 aCGH


title: G4 LSL-mTert PB-Pten/p53 X8589A4 aCGH

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 X8589A4 aCGH


title: G4 LSL-mTert PB-Pten/p53 X11960PT2 aCGH

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 X11960PT2 aCGH


title: G4 LSL-mTert PB-Pten/p53 X11649PT4 aCGH

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 X11649PT4 aCGH


title: 15 Weeks b.1

description: Biological Replicate b, Technical Replicate 1


title: G4 LSL-mTert PB-Pten/p53 X10118A4 aCGH

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 X10118A4 aCGH


title: G3 LSL-mTert PB-Pten/p53 7523PT mRNA

description: G3 LSL-mTert PB-Pten/p53 G3 LSL-mTert PB-Pten/p53 7523PT mRNA


title: G3 LSL-mTert PB-Pten/p53 X8584A3 aCGH

description: G3 LSL-mTert PB-Pten/p53 G3 LSL-mTert PB-Pten/p53 X8584A3 aCGH


title: G4 LSL-mTert PB-Pten/p53 X7106A4 aCGH

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 X7106A4 aCGH


title: 15 Weeks a.1

description: Biological Replicate a, Technical Replicate 1


title: Parkinson patient 2 with parkin mutations

city: Buffalo

first: Jian

last: Feng

state: NY

address: 955 Main Street, Room 3102

department: Department of Physiology and Biophysics

institute: State University of New York at Buffalo

hyb_protocol: Prior to hybridization, the test and reference probes were combined with 100 ug human fluorimetric Cot-1 (Invitrogen) and ethanol precipitated. Following centrifugation, the probes were resuspended in 110ul SlideHyb Buffer #3 (Ambion) containing 5ul of 100μg/ul Yeast tRNA (Invitrogen), heated to 95ºC for 5 minutes and incubated for 30 minutes at 37ºC to block repetitive elements on the probe. Hybridization was performed to RPCI 21K BAC array for 16 hours at 55ºC using a GeneMachine hybridization station (Genomic Solutions, Inc.) as described (Cowell, J. K. and N. J. Nowak. 2003. High-resolution analysis of genetic events in cancer cells using bacterial artificial chromosome arrays and comparative genome hybridization. Adv Cancer Res 90:91-125). After hybridization, the slides were automatically washed in the GeneMachines station with reducing concentrations of SSC and SDS. The final wash was 30 seconds in 0.1X SSC, followed by a two second 100 % ethanol dip. The slides were spun dry and scanned immediately at 5µm resolution using a GenePix 4200AL laser scanner (Molecular Devices Inc.)

scan_protocol: Slides were scanned on a GenePix 4200AL laser Scanner (Molecular Inc.) using GenePix Pro V5.0. Both lasers were set to 100% and the PMT was set to 500 for cy3 and 450 for cy5.

data_processing: Images were analyzed using Imagene 8.0 (BioDiscovery Inc.). The output of Image analysis was further processed by in-house developed programs. The log2 ratios of the test/control (values are not background subtracted) were normalized using a subgrid loess, with all flagged spots and clones on the sex chromosome are given a weight of zero. The mean of the replicate measures was taken and the final normalized log2 ratio was plotted against its genomic location.

source_name: Test Sample P002

label_protocol: 1μg of genomic DNA was fluorescently labeled using the BioArray CGH Labeling System (Enzo Life Sciences). Initially, the DNA was denatured in the presence of the random primer at 99ºC for 10 minutes in a thermalcycler, and then quickly cooled to 4ºC. The tubes were transferred to ice and labeling occurred with the addition of dNTP-cyanine 5 mix and Klenow. Incubation took place overnight at 37ºC in a thermalcycler. The unincorporated nucleotides were removed using a QIAquick PCR purification column (Qiagen) and the labeled probe was eluted with 2 x 25 ul washes.

growth_protocol: Prior to DNA extraction, induced pluripotent stem cells were grown on Matrigel coated 6-well plate in mTeSR medium (Stemcell technologies, Canada)

extract_protocol: Genomic DNA was isolated using QIAamp DNA Mini Kit according to the manufacturer instructions (QIAGEN)

treatment_protocol: Primary dermal fibroblast cells at passage 2 or 3 were infected for 16 hr with the following six kinds of lentiviruses (hOct4, hSox4, hKlf4 and hNanog each at MOI 15, c-Myc at MOI 6, and M2rtTA at MOI 30) in the presence of 4 µg/ml polybrene. One day later, infected fibroblasts were plated at 1×105 cells on MEF feeders in 10 cm dishes in DMEM containing 10% FBS, 2 mM L-Glutamine, 50 U/ml penicillin and 50 mg/ml streptomycin. Next day, the media were changed to hESC media and the transgenes were induced by the addition of doxycycline. Doxycycline (1 µg/ml) was added for at least 10 days and later at 0.5 µg/ml until hESC-like clones appeared. VPA (0.5 or 1 mM) was added for 7 days with DOX in the beginning. After initial appearance and death of transformed cells, clones with hESC morphology appeared between day 24 and 40. They were picked and expanded under hESC culture condition. These colonies were analyzed with immunocytochemistry, RT-PCR, in vivo and in vitro differentiation assay. The clones were used for genomic DNA extraction.

tag: subject

tag: gender

value: female

source_name: Normal control

value: male


title: 15 Weeks a.2

description: Biological Replicate a, Technical Replicate 2

tag: tissue


title: 4 weeks b.2

description: Biological Replicate b, Technical Replicate 2

value: 4 weeks


title: 4 weeks a.2


title: 4 weeks b.1


title: WT ARS305-Bait 4C 1

status: Public on Jan 20 2012

city: Cold Spring Harbor

first: Simon

middle: Robert Vincent

last: Knott

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

description:
Sample 27
ch1 raw data file: WT_4C_1_635.pair
ch2 raw data file: WT_4C_1_532.pair

hyb_protocol: Nimblegen standard protocol

scan_protocol: Genepix Personal 4100A Scanner (Axon Instruments).

data_processing: Samples 1-14 were within-array normalized as described in the supplemental mehods section of Knott et al. Cell 2011. Following normalization timepoints 2-7 were location normalized such that their 0.1 quantile was equal to that of their corrsponding strains first timpoint. Following this probes were median smoothed 2X with a smoothing window of 500 bps. Samples 15-30 were within-array normalized as described in Knott et al. 2009 (BMC Bioinformatics).  For Samples 15-26, following within array normalization probes were smoothed 2X with median smoothing (500 bp window).

organism: Saccharomyces cerevisiae

source_name: 4C amplified DNA

label_protocol: Nimblegen standard protocol

growth_protocol: Cells were grown in YEPD + α-factor for 4 hrs.

extract_protocol: 4C using ARS305 as bait as described in Knott et al. Cell 2011

tag: treatment protocol

tag: sample type

value: G1-arrested WT cells

source_name: WT G1-arrested genomic DNA

extract_protocol: Genomic DNA was extracted as described in as described in Viggiani, C.J., Knott, S.R., and Aparicio, O.M. (2010). Genome-wide analysis of DNA synthesis by BrdU immunoprecipitation on tiling microarrays (BrdU-IP-chip) in Saccharomyces cerevisiae. Cold Spring Harb Protoc 2010, pdb prot5385.

value: α-factor arrested

value: WT α-factor arrested genomic DNA


title: Normal subject 2

source_name: Test Sample C002

value: Normal subject 2


title: fkh1Δfkh2Δ2C ARS305-Bait 4C 2

description:
Sample 30
ch1 raw data file: Fkh_4C_2_635.pair
ch2 raw data file: Fkh_4C_2_532.pair

value: G1-arrested fkh1Δfkh2Δ2C cells

source_name: fkh1Δfkh2Δ2C G1-arrested genomic DNA

growth_protocol: Cells were grown in YEPD +  α-factor for 4 hrs.

value: fkh1Δfkh2Δ2C α-factor arrested genomic DNA


title: fkh1Δfkh2Δ2C ARS305-Bait 4C 1

description:
Sample 29
ch1 raw data file: Fkh_4C_1_635.pair
ch2 raw data file: Fkh_4C_1_532.pair


title: 4 weeks a.1


title: ORC_IP_fkh1Δfkh2Δ2C

description:
Sample 22
ch1 raw data file: Fkh_ORC_635.pair
ch2 raw data file: Fkh_ORC_532.pair

source_name: ORC-chIP-DNA

growth_protocol: Cells were grown in YEPD

extract_protocol: chIP-chip was performed as described in Viggiani, C.J., Aparicio, J.G., and Aparicio, O.M. (2009). ChIP-chip to analyze the binding of replication proteins to chromatin using oligonucleotide DNA microarrays. Methods Mol Biol 521, 255-278.

tag: ip antibody

value: anti-ORC [at 1:500 (Wyrick et al., 2001) ]

value: Asynchronous

value: Asynchronous fkh1Δfkh2Δ2C cells


title: MCM_IP_fkh1Δfkh2Δ2C

description:
Sample 24
ch1 raw data file: Fkh_MCM_635.pair
ch2 raw data file: Fkh_MCM_532.pair

source_name: MCM-chIP-DNA

value: anti-MCM2 [at 1:50 (Santa Cruz Biotech., SC-6680)] + anti-Mcm4 [at 1:50 (Santa Cruz Biotech., SC-33622)]


title: Cdc45_IP_fkh1Δfkh2Δ2C

description:
Sample 26
ch1 raw data file: Fkh_CDC45_635.pair
ch2 raw data file: Fkh_CDC45_532.pair

value: anti-Ha 16B12 [at 1:200 (Covance, MMS101R)]


title: Parkinson patient 1 with parkin mutations

source_name: Test Sample P001


title: ORC_IP_ARS305Δ_For_ARS305_Analysis

description:
Sample 20
ch1 raw data file: ARS305_ORC_635.pair
ch2 raw data file: ARS305_ORC_532.pair

value: ARS305 Mutant

value: Asynchronous ARS305 Mutant cells

source_name: ARS305 Mutant G1-arrested genomic DNA

value: ARS305 Mutant cells, α-factor arrested genomic DNA


title: ORC_IP_WT

description:
Sample 21
ch1 raw data file: WT_ORC_635.pair
ch2 raw data file: WT_ORC_532.pair

value: WT

value: Asynchronous WT cells


title: MCM_IP_WT

description:
Sample 23
ch1 raw data file: WT_MCM_635.pair
ch2 raw data file: WT_MCM_532.pair


title: BrdU_HU_IP_ARS305Δ_For_ARS305_Analysis

description:
Sample 16
ch1 raw data file: ARS305_BrdU_635.pair
ch2 raw data file: ARS305_BrdU_532.pair

source_name: BrdU-IP-DNA

growth_protocol: Cells were grown in YEPD + α-factor for 4 hrs. Cells were then released and pulsed with BrdU at the time indicated.

extract_protocol: BrdU-IP-chip was performed as described in Viggiani, C.J., Knott, S.R., and Aparicio, O.M. (2010). Genome-wide analysis of DNA synthesis by BrdU immunoprecipitation on tiling microarrays (BrdU-IP-chip) in Saccharomyces cerevisiae. Cold Spring Harb Protoc 2010, pdb prot5385.

value: anti-BrdU [at 1:1000 (GE Healthcare, RPN202)]

value: ARS305 Mutant cells α-factor arrested and released into HU and BrdU


title: WT ARS305-Bait 4C 2

description:
Sample 28
ch1 raw data file: WT_4C_2_635.pair
ch2 raw data file: WT_4C_2_532.pair

value: G1-arrested WT cells

value: α-factor arrested


title: BrdU_Pulse_fkh1Δfkh2Δ2C_Timepont_7

description:
Sample 14
ch1 raw data file: CVy139Clb2_tp7_635.pair
ch2 raw data file: CVy139Clb2_tp7_532.pair

value: pulsed with BrdU

tag: time

value: 48-60 minutes after α-factor release

value: fkh1Δfkh2Δ2C cells pulsed with BrdU (48-60 minutes after α-factor release)

source_name: fkh1Δfkh2Δ2CT G1-arrested genomic DNA

value: fkh1Δfkh2Δ2C genomic DNA from G1-arrested cells


title: ORC_IP_WT_For_ARS305_Analysis

description:
Sample 19
ch1 raw data file: WT_305_ORC_635.pair
ch2 raw data file: WT_305_ORC_532.pair

value: anti-ORC [at 1:500 (Wyrick et al., 2001) ]

value: Asynchronous

value: WT cells, α-factor arrested genomic DNA


title: G4 LSL-mTert PB-Pten/p53 X11819PM1 aCGH

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 X11819PM1 aCGH

value: Telomerase reactivation in the setting of telomere dysfunction

value: LSL-mTert PB-Pten/p53

value: prostate tumor

value: tail


title: Fkh1_IP_ARS305Δ_For_ARS305_Analysis

description:
Sample 18
ch1 raw data file: ARS305_Fkh1_Binding_635.pair
ch2 raw data file: ARS305_Fkh1_Binding_532.pair

value: anti-Fkh1 [at 1:200 (Casey et al., 2008)]

value: ARS305 Mutant

value: Asynchronous ARS305 Mutant cells

value: ARS305 Mutant cells, α-factor arrested genomic DNA


title: G4 LSL-mTert PB-Pten/p53 X9492PT2 aCGH

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 X9492PT2 aCGH


title: Normal subject 1

source_name: Test Sample C001

value: Normal subject 1

value: male

value: female


title: BrdU_Pulse_fkh1Δfkh2Δ2C_Timepont_6

description:
Sample 13
ch1 raw data file: CVy139Clb2_tp6_635.pair
ch2 raw data file: CVy139Clb2_tp6_532.pair

value: anti-BrdU [at 1:1000 (GE Healthcare, RPN202)]

value: pulsed with BrdU

value: 42-54 minutes after α-factor release

value: fkh1Δfkh2Δ2C cells pulsed with BrdU (42-54 minutes after α-factor release)


title: Fkh1_IP_WT_For_ARS305_Analysis

description:
Sample 17
ch1 raw data file: WT_305_Fkh1_Binding_635.pair
ch2 raw data file: WT_305_Fkh1_Binding_532.pair

value: WT

value: Asynchronous

value: Asynchronous WT cells

value: α-factor arrested


title: BrdU_Pulse_fkh1Δfkh2Δ2C_Timepont_4

description:
Sample 11
ch1 raw data file: CVy139Clb2_tp4_635.pair
ch2 raw data file: CVy139Clb2_tp4_532.pair

value: 30-42 minutes after α-factor release

value: fkh1Δfkh2Δ2C cells pulsed with BrdU (30-42 minutes after α-factor release)

value: fkh1Δfkh2Δ2C genomic DNA from G1-arrested cells


title: G4 LSL-mTert PB-Pten/p53 X10025PT2 aCGH

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 X10025PT2 aCGH

value: Telomerase reactivation in the setting of telomere dysfunction

value: LSL-mTert PB-Pten/p53

value: prostate tumor

value: tail


title: Cdc45_IP_WT

description:
Sample 25
ch1 raw data file: WT_CDC45_635.pair
ch2 raw data file: WT_CDC45_532.pair

value: anti-Ha 16B12 [at 1:200 (Covance, MMS101R)]

value: G1-arrested WT cells

value: WT α-factor arrested genomic DNA


title: G4 LSL-mTert PB-Pten/p53 X9493PT1 aCGH

description: G4 LSL-mTert PB-Pten/p53 G4 LSL-mTert PB-Pten/p53 X9493PT1 aCGH


title: BrdU_Pulse_fkh1Δfkh2Δ2C_Timepont_5

description:
Sample 12
ch1 raw data file: CVy139Clb2_tp5_635.pair
ch2 raw data file: CVy139Clb2_tp5_532.pair

value: anti-BrdU [at 1:1000 (GE Healthcare, RPN202)]

value: pulsed with BrdU

value: 36-48 minutes after α-factor release

value: fkh1Δfkh2Δ2C cells pulsed with BrdU (36-48 minutes after α-factor release)


title: BrdU_Pulse_fkh1Δfkh2Δ2C_Timepont_3

description:
Sample 10
ch1 raw data file: CVy139Clb2_tp3_635.pair
ch2 raw data file: CVy139Clb2_tp3_532.pair

value: 24-36 minutes after α-factor release

value: fkh1Δfkh2Δ2C cells pulsed with BrdU (24-36 minutes after α-factor release)


title: BrdU_Pulse_WT_Timepont_7

description:
Sample 7
ch1 raw data file: CVy43_tp7_635.pair
ch2 raw data file: CVy43_tp7_532.pair

value: WT

value: 48-60 minutes after α-factor release

value: WT cells pulsed with BrdU (48-60 minutes after α-factor release)

value: WT genomic DNA from G1-arrested cells


title: BrdU_Pulse_WT_Timepont_6

description:
Sample 6
ch1 raw data file: CVy43_tp6_635.pair
ch2 raw data file: CVy43_tp6_532.pair

value: 42-54 minutes after α-factor release

value: WT cells pulsed with BrdU (42-54 minutes after α-factor release)


title: BrdU_Pulse_WT_Timepont_3

description:
Sample 3
ch1 raw data file: CVy43_tp3_635.pair
ch2 raw data file: CVy43_tp3_532.pair

value: WT cells pulsed with BrdU (24-36 minutes after α-factor release)


title: BrdU_Pulse_WT_Timepont_1

description:
Sample 1
ch1 raw data file: CVy43_tp1_635.pair
ch2 raw data file: CVy43_tp1_532.pair

value: 12-24 minutes after α-factor release

value: WT cells pulsed with BrdU (12-24 minutes after α-factor release)


title: BrdU_Pulse_WT_Timepont_4

description:
Sample 4
ch1 raw data file: CVy43_tp4_635.pair
ch2 raw data file: CVy43_tp4_532.pair

value: 30-42 minutes after α-factor release

value: WT cells pulsed with BrdU (30-42 minutes after α-factor release)


title: BrdU_Pulse_WT_Timepont_2

description:
Sample 2
ch1 raw data file: CVy43_tp2_635.pair
ch2 raw data file: CVy43_tp2_532.pair

value: anti-BrdU [at 1:1000 (GE Healthcare, RPN202)]

value: 18-30 minutes after α-factor release

value: WT cells pulsed with BrdU (18-30 minutes after α-factor release)


title: SigF_chip_on_chip_2

city: Lausanne

first: Ruben

middle: C

last: Hartkoorn

state: Vaud

address: SV 3533 (Bâtiment SV) Station 19

department: GHI/SV

description: Comparison of Cy3 (test) to Cy5 (reference)

hyb_protocol: Labelled DNA  was hybridized to microarrays in an Agilent Technologies Microarray chamber at 55°C for 72 h in the following buffer: 1 M NaCl, 50 mM MES, 20% formamide, 20 mM EDTA, 1% Triton X-100.

scan_protocol: Arrays were scanned using an Agilent Technologies microarray scanner, following which results were extracted using the Genepix Pro 5.0 software

data_processing: Values were median normalised followed by log2 transformed

organism: Mycobacterium tuberculosis H37Rv

source_name: SigF chip DNA from H37Rv(ΔrsbW/sigF)::pMY769 with P-IA

label_protocol: DNA obtained from immunoprecipitation and total genomic DNA were labelled by Klenow random priming, with Cy3-dCTP or Cy5-dCTP (GE Healthcare), respectively, and purified with Qiagen MinElute kit, according to the manufacturer's protocol.

growth_protocol: Cultured 3 days in the pressence of pristinamiycin-IA

extract_protocol: Log phase cultures of H37Rv(ΔrsbW/sigF)::pMYsigF and H37Rv(ΔrsbW/sigF)::pMY769 were diluted to an OD600 of 0.05. After overnight incubation, P-IA (final concentration 2 μg/mL) was added to both cultures and these were incubated for 3 days at 37°C with shaking. Chromatin immunoprecipitation was performed as previously described (33), with some modifications. Briefly, protein/DNA complexes were cross-linked using formaldehyde (final concentration 1%, 10 min, 37°C) and quenched using glycine (final concentration 125 mM). Bacteria were pelleted and washed twice with Tris-buffered saline (20 mM Tris-HCl pH 7.5, 150 mM NaCl) and pellets stored at −80°C. Pellets were re-suspended in 600 μl immunoprecipitation buffer (50 mM Hepes-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, Roche Antiprotease mini) and disrupted by sonication at 4°C for 30 min (30 sec pulses with a Bioruptor, Diagenode) to shear DNA to an average size of 200–400 bp. Following centrifugation (2000 x g, 15 min), the supernatant was diluted to 1.1 mL in immunoprecipitation buffer and mixed overnight (4°C) with 20 μL of polyclonal rabbit anti-SigF antibody. In parallel, per sample, 100 μL of protein A/G UltraLink resin (Thermo Scientific) was washed in immunoprecipitation buffer and incubated overnight (4°C) in 1 mL of immunoprecipitation buffer with 1 mg/mL BSA and 0.1 mg/mL salmon sperm DNA. Following overnight blocking, protein A/G UltraLink resin was pelleted (2000 x g, 2 min) and mixed with the antibody, protein-DNA complex mixture (rotary mixer, 90 min, 4°C). The protein A/G UltraLink resin was pelleted (2000 x g, 2 min) and washed twice with immunoprecipitation buffer, once with immunoprecipitation buffer plus 500 mM NaCl, once with wash buffer III (10 mM Tris-HCl pH 8, 250 mM LiCl, 1 mM EDTA, 0.5% Nonidet-P40, 0.5% sodium deoxycholate), and once with Tris-EDTA buffer (pH 7.5). Immunoprecipitated complexes were eluted from the beads by treatment with 100 μl elution buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS) at 65°C for 20 min. Samples were then treated with RNase A and cross-links were reversed by incubation for 2 h at 56°C and 6 h at 65°C in 0.5× elution buffer plus 50 μg proteinase K. DNA was extracted twice with phenol-chloroform, precipitated and re-suspended in 20 μl of water.

tag: treatment

value: P-IA

tag: chip antibody

value: Polyclonal rabbit anti-SigF

source_name: SigF chip DNA from H37Rv(ΔrsbW/sigF)::pMYsigF with P-IA


title: G3 LSL-mTert PB-Pten/p53 X7523A3 aCGH

description: G3 LSL-mTert PB-Pten/p53 G3 LSL-mTert PB-Pten/p53 X7523A3 aCGH

source_name: G3 LSL-mTert PB-Pten/p53

value: Telomerase reactivation in the setting of telomere dysfunction

value: LSL-mTert PB-Pten/p53

value: prostate tumor

value: tail


title: SigF_chip_on_chip_3


title: SigF_chip_on_chip_4


title: BrdU_Pulse_fkh1Δfkh2Δ2C_Timepont_1

description:
Sample 8
ch1 raw data file: CVy139Clb2_tp1_635.pair
ch2 raw data file: CVy139Clb2_tp1_532.pair

value: pulsed with BrdU

value: fkh1Δfkh2Δ2C cells pulsed with BrdU (12-24 minutes after α-factor release)

value: fkh1Δfkh2Δ2C genomic DNA from G1-arrested cells


title: Tumor 4 from ApcD14/+ mouse 2

city: Montpellier

first: Caroline

last: Bonnans

address: 141 rue de la Cardonille

department: Oncology

country: France

institute: Functional Genomic Institute

hyb_protocol: The two labelled aRNA were mixed, fragmented and hybridized on one array of a Nimblegen 12-plex microarray according the manufacturer's instructions.

scan_protocol: Scanned on an Innopsys Innoscan900 scanner.

data_processing: Images were quantified using Nimblescan V2.5. The rawdata were normalized by Lowess and a quantile normalization was applied (Limma Package).

source_name: Tumor 4 from ApcD14/+ mouse 2

label_protocol: For the preparation of the labelled Cy3- and Cy5- aRNA target, one microgram of total RNA samples were amplified and labelled using Amino Allyl Message Amp II aRNA amplification kit (Ambion, Austin, TX, USA), according the manufacturer’s instructions.

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

tag: mouse

value: tumor

value: Test

source_name: Pool of equimolar RNA of each sample

value: Reference


title: Tumor 5 from ApcD14/+ mouse 2

source_name: Tumor 5 from ApcD14/+ mouse 2


title: G3 LSL-mTert PB-Pten/p53 X7526A3 aCGH

description: G3 LSL-mTert PB-Pten/p53 G3 LSL-mTert PB-Pten/p53 X7526A3 aCGH


title: Tumor from ApcD14/+:Arrb2-/- mouse 13

source_name: Tumor from ApcD14/+:Arrb2-/- mouse 13

growth_protocol: Tumors kept in RNA later at -80°C before RNA extraction

extract_protocol: Total RNA extracted by RNable according to manufacturer's instructions


title: Tumor 2 from ApcD14/+ mouse 2

source_name: Tumor 2 from ApcD14/+ mouse 2


title: Tumor 1 from ApcD14/+ mouse 2

source_name: Tumor 1 from ApcD14/+ mouse 2


title: BrdU_Pulse_fkh1Δfkh2Δ2C_Timepont_2

description:
Sample 9
ch1 raw data file: CVy139Clb2_tp2_635.pair
ch2 raw data file: CVy139Clb2_tp2_532.pair

value: fkh1Δfkh2Δ2C cells pulsed with BrdU (18-30 minutes after α-factor release)


title: Tumor from ApcD14/+:Arrb2-/- mouse 10

source_name: Tumor from ApcD14/+:Arrb2-/- mouse 10


title: Tumor 3 from ApcD14/+ mouse 1

source_name: Tumor 3 from ApcD14/+ mouse 1


title: Tumor 1 from ApcD14/+ mouse 1

source_name: Tumor 1 from ApcD14/+ mouse 1


title: BrdU_HU_IP_WT_For_ARS305_Analysis

description:
Sample 15
ch1 raw data file: WT_305_BrdU_635.pair
ch2 raw data file: WT_305_BrdU_532.pair

value: WT

value: WT cells α-factor arrested and released into HU and BrdU

source_name: WT G1-arrested genomic DNA

value: α-factor arrested

value: WT cells, α-factor arrested genomic DNA


title: Tumor from ApcD14/+:Arrb2-/- mouse 11

source_name: Tumor from ApcD14/+:Arrb2-/- mouse 11


title: Tumor 2 from ApcD14/+ mouse 1

source_name: Tumor 2 from ApcD14/+ mouse 1


title: Tumor from ApcD14/+:Arrb2-/- mouse 7

source_name: Tumor from ApcD14/+:Arrb2-/- mouse 7


title: Tumor from ApcD14/+:Arrb2-/- mouse 12

source_name: Tumor from ApcD14/+:Arrb2-/- mouse 12


title: Tumor from ApcD14/+:Arrb2-/- mouse 4

source_name: Tumor from ApcD14/+:Arrb2-/- mouse 4


title: Tumor 3 from ApcD14/+ mouse 2

source_name: Tumor 3 from ApcD14/+ mouse 2


title: BrdU_Pulse_WT_Timepont_5

description:
Sample 5
ch1 raw data file: CVy43_tp5_635.pair
ch2 raw data file: CVy43_tp5_532.pair

source_name: BrdU-IP-DNA

value: anti-BrdU [at 1:1000 (GE Healthcare, RPN202)]

value: 36-48 minutes after α-factor release

value: WT cells pulsed with BrdU (36-48 minutes after α-factor release)

value: WT genomic DNA from G1-arrested cells


title: Tumor from ApcD14/+:Arrb2-/- mouse 9

source_name: Tumor from ApcD14/+:Arrb2-/- mouse 9


title: Tumor from ApcD14/+:Arrb2-/- mouse 3

source_name: Tumor from ApcD14/+:Arrb2-/- mouse 3

source_name: Pool of equimolar RNA of each sample


title: Tumor from ApcD14/+:Arrb2-/- mouse 5

source_name: Tumor from ApcD14/+:Arrb2-/- mouse 5


title: Tumor from ApcD14/+:Arrb2-/- mouse 8

source_name: Tumor from ApcD14/+:Arrb2-/- mouse 8


title: Tumor 4 from ApcD14/+ mouse 1

source_name: Tumor 4 from ApcD14/+ mouse 1


title: Tumor from ApcD14/+:Arrb2-/- mouse 6

source_name: Tumor from ApcD14/+:Arrb2-/- mouse 6


title: Tumor from ApcD14/+:Arrb2-/- mouse 1

source_name: Tumor from ApcD14/+:Arrb2-/- mouse 1


title: SigF_chip_on_chip_1

source_name: SigF chip DNA from H37Rv(ΔrsbW/sigF)::pMY769 with P-IA

value: P-IA

value: Polyclonal rabbit anti-SigF

source_name: SigF chip DNA from H37Rv(ΔrsbW/sigF)::pMYsigF with P-IA


title: Tumor from ApcD14/+:Arrb2-/- mouse 2

source_name: Tumor from ApcD14/+:Arrb2-/- mouse 2