title: WM-266 cells that underwent transfection without addition of oligonucleotides - Replica 2

city: Milan

first: Myriam

last: Alcalay

address: Via Adamello 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology

description:
WM-266 cells that underwent the transfection procedure without the addition of any oligonucleotides.
NO_B

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were  hybridized with each biotin-labeled target.

scan_protocol: Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.

data_processing: The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: WM 266.4 metastatic melanoma cell line, NO

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA  The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.

growth_protocol: WM-266 cells were grown in MEM medium with Glutamax supplemented with 10% FCS, 0,1mM sodium pyruvate, 0,1mM non-essential amino acids.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each sample, an RNA pool was obtained by mixing equal quantities of total RNA from each of the three independent RNA extractions.

treatment_protocol: WM-266 cells were seeded in 6-well plates 24 hours prior to siRNA transfection. 200 pmol of siRNA oligos were transfected with Oligofectamine (Invitrogen, Carlsbad, CA) in serum-free medium. 72 hours later,  cells were harvested for RNA extraction.

tag: pir knock-down

value: no


title: WM-266 cells that underwent transfection without addition of oligonucleotides - Replica 1

status: Public on Aug 04 2010

type: RNA

description:
WM-266 cells that underwent the transfection procedure without the addition of any oligonucleotides.
NO_A

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: cell line


title: WM-266 cells transfected with CONTROL siRNA - Replica 2

description:
WM-266 cells transfected with on-target plus siCONTROL siRNA (Dharmacon) for control.
siCTR_B

source_name: WM 266.4 metastatic melanoma cell line, siCTR


title: PMBC_highIL6_24weeks_volunteer44

status: Public on Aug 03 2010

city: Sharnbrook

first: Fei Ling

last: Lim

state: Bedfordshire

address: Colworth Science Park

country: United Kingdom

institute: Unilever

description: This study looks at the effects of physical activity on mRNA expression profiles of the Peripheral Blood Mononuclear cells at several time points and after several weeks of physical activity.

hyb_protocol: The Agilent Hybridisation Kit (catalogue number 5188-5242) was used in conjunction with Agilent Mouse Oligo Arrays (catalogue number G4122F).  2μg of the labelled sample RNA were used for hybridisation according to the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol The hybridisation was performed for 17 h at 65 ºC at 10 rpm. Slides were them washed for 1 min at 22 ºC in Wash Solution 1 (catalogue number 5188-5325) and 1 min at 22 ºC in Wash Solution 2, pre-warmed to 37 ºC (catalogue number 5188-5326). Slides were incubated for 30s in Agilent Stabilisation and Drying Solution (catalogue number 5185-5979).

scan_protocol: Microarrays were scanned using the Agilent Technologies Scanner G2505B US45102871 (ChipScan software version A.7.0.1), scan region 61 X 21.6mm, scan resolution 5 micron single pass, extended dynamic range selected (XDR Hi 100%; XDR Lo 10%).

data_processing: Data was extracted from the scanned image using the Agilent Feature Extraction Software version. 9.1.3.1 (protocol GE1-v5_91_0806). The VALUE column came from the gProcessedSignal column of the result table.

source_name: PMBC, high IL6, post-exercise, volunteer 44

label_protocol: 400 ng RNA and 4 µl (1 : 5000 dilution) Agilent One-Color RNA Spike-In RNA were labelled with the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color according to Manufacture’s instructions as follows:  1.2 µl T7 Promoter Primer was added to 400 ng RNA and 4 µl spike in control and denatured at 65 ºC. First Strand Buffer, DTT, dNTP MMLV and RNaseOut was added. The cDNA was synthesised during the following incubation step (2h at 40 ºC). After 10 min denaturation at 65 ºC and the addition of Cy-labelled CTP, Transcription Buffer, DTT, NTP, PEG, RNaseOUT, Inorganic Phosphatase, and T7 RNA Polymerase the synthesis of the fluorescent labelled cRNA was performed during the second incubation step (2 h at 40 ºC).  The labelled cRNA was purified with the Qiagen RNeasy Mini Kit according to Manufacturer’s protocol.

growth_protocol:
Twenty sedentary male volunteers were recruited from the local community (primarily though newspaper advertisement) for this 24 week study. Subjects were interviewed by telephone and individuals who had known disease (e.g. heart disease, diabetes, arthritis) or who engaged in structured physical activity on more than two occasions per week were excluded. In addition, volunteers who smoked, had a BMI ≥ 35, or took regular medication were excluded from taking part. Participants who passed the initial screening were invited to attend an information session during which they completed a health questionnaire and were fitted with a physical activity monitor (Actiheart, Cambridge Neurotech Ltd., UK). Subjects were blinded to the purpose of this measurement and the data were used to objectively establish that they were inactive and not meeting current physical activity guidelines. Each volunteer provided written informed consent prior to participating in this investigation which was approved by the local ethics committee.
Maximal oxygen uptake (V.O2max) of each subject was determined using a submaximal speed test followed by an incremental incline test on a treadmill ergometer (Woodway, ELG 70 Weiss, Germany). The submaximal running protocol consisted of four steady-state exercise stages, each lasting four min, with speed increasing by 0.8 km.h-1 with each stage. One-minute expired air samples were collected at the end of each stage of exercise using Douglas bags. Measures of heart rate (HR) (Vantage NV, Polar Electro OY, Finland) and rate of perceived exertion (RPE) using a 6-20 scale were taken during the gas collection. Following adequate recovery subjects completed the incremental incline test, consisting of three-minute exercise stages with the incline increasing by 3% at the end of each stage. The test was performed to volitional fatigue to measure V.O2max and maximal heart rate. Expired gas samples were collected in the final min of each stage and during the final minute of exercise along with HR and RPE. Participants were required to meet two out of four standard criteria for having achieved V.O2max: heart rate ≥ than age-predicted maximum heart rate, respiratory exchange ratio ≥ 1.10, rating of perceived exertion ≥19 or reaching a plateau in V.O2.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit Qiagen.  The integrity of the RNA was confirmed with analysis by the Agilent 2100 bioanalyser using the RNA 6000 LabChip kit.

treatment_protocol:
Individuals completed a 24 week exercise training programme. For the first two weeks, individuals completed three exercise sessions per week and from week three onwards, this increased to four sessions per week. Intensity and duration were increased in a progressive manner across the 24 week programme. Subjects completed their exercise sessions in the Fitness Suite at the University of Bath. Their attendance, exercise duration and heart rate for each exercise were recorded using an electronic web-based monitoring system (Fitronics, Bath, UK). Once every fortnight, volunteers reported to the laboratory to complete one of four weekly exercise sessions so that intensity and heart rate response could be monitored and the prescription altered accordingly. For each exercise session, two-thirds of the total duration was spent on a treadmill with the remainder being selected from a choice of a semi-recumbent cycle ergometer, upright cycle ergometer or cross-trainer. Adherence to exercise training during the entire six-month period was calculated for each individual by dividing the total number of sessions performed during the exercise programme by the number of sessions prescribed for the training period x 100%.
Venous blood samples were collected after subjects had been in a supine position for 15 min. Prior to blood sample collection all volunteers were asked to refrain from strenuous activity and consuming alcohol for 24 h. Additionally, individuals were asked to refrain from taking medication (e.g. aspirin, paracetamol, ibuprofen) 48 h prior to the blood sample. Sixty ml of whole blood was collected by venepuncture in the ante-cubital vein. Ten ml was dispensed into tubes and left to clot at room temperature for 15 min in order to collect serum with the remainder dispensed into EDTA-coated tubes (Sarstedt Ltd., Leicester, UK). Peripheral blood mononuclear cells (PBMCs) were isolated from EDTA-treated blood using a one-step centrifugation technique (Lymphoprep, Nycomed, Norway). Harvested cells were washed twice in 20 ml PBS and then counted using an automated haematology analyser (SF-3000, Sysmex UK Ltd., UK). PBMCs were lysed in Trizol (Invitrogen, Paisley, UK), with the volume added dependent on cell concentration (1 ml per 5 106 cells), and then frozen at -70°C until subsequent analysis. Serum was analysed for interleukin-6 (IL-6) using a commercially available solid phase high-sensitivity ELISA (Quantikine, R and D Systems Inc., Abingdon, UK).

tag: Gender

value: Male

tag: Age (years)

tag: Height (m)

tag: Weight (kg)

tag: BMI

tag: VO2 max

tag: IL-6 (pg/ml)


title: WM-266 knock-down of Pirin by siRNA - Replica 2

description:
WM-266 cells transfected with siGENOME siRNA Smartpool Reagent (Dharmacon) for knock-down of Pirin.
siPIR_B

source_name: WM 266.4 metastatic melanoma cell line, siPIR

value: yes


title: WM-266 cells transfected with CONTROL siRNA - Replica 1

description:
WM-266 cells transfected with on-target plus siCONTROL siRNA (Dharmacon) for control.
siCTR_A


title: PMBC_highIL6_basal_volunteer44

source_name: PMBC, high IL6, pre-exercise, volunteer 44


title: WM-266 knock-down of Pirin by siRNA - Replica 1

description:
WM-266 cells transfected with siGENOME siRNA Smartpool Reagent (Dharmacon) for knock-down of Pirin.
siPIR_A


title: PMBC_lowIL6_basal_volunteer54

source_name: PMBC, low IL6, pre-exercise, volunteer 54


title: PMBC_lowIL6_basal_volunteer43

source_name: PMBC, low IL6, pre-exercise, volunteer 43


title: PMBC_lowIL6_24weeks_volunteer43

source_name: PMBC, low IL6, post-exercise, volunteer 43


title: PMBC_lowIL6_26weeks_volunteer42

source_name: PMBC, low IL6, 2 weeks post-exercise, volunteer 42


title: PMBC_lowIL6_26weeks_volunteer39

source_name: PMBC, low IL6, 2 weeks post-exercise, volunteer 39


title: PMBC_lowIL6_26weeks_volunteer54

source_name: PMBC, low IL6, 2 weeks post-exercise, volunteer 54


title: PMBC_lowIL6_24weeks_volunteer39

source_name: PMBC, low IL6, post-exercise, volunteer 39


title: PMBC_highIL6_26weeks_volunteer31

source_name: PMBC, high IL6, 2 weeks post-exercise, volunteer 31


title: PMBC_lowIL6_basal_volunteer39

source_name: PMBC, low IL6, pre-exercise, volunteer 39


title: PMBC_lowIL6_24weeks_volunteer54

source_name: PMBC, low IL6, post-exercise, volunteer 54


title: PMBC_lowIL6_24weeks_volunteer42

source_name: PMBC, low IL6, post-exercise, volunteer 42


title: PMBC_highIL6_24weeks_volunteer31

source_name: PMBC, high IL6, post-exercise, volunteer 31


title: PMBC_lowIL6_basal_volunteer42

source_name: PMBC, low IL6, pre-exercise, volunteer 42


title: PMBC_highIL6_26weeks_volunteer29

source_name: PMBC, high IL6, 2 weeks post-exercise, volunteer 29


title: PMBC_highIL6_basal_volunteer31

source_name: PMBC, high IL6, pre-exercise, volunteer 31


title: PMBC_highIL6_basal_volunteer29

source_name: PMBC, high IL6, pre-exercise, volunteer 29


title: PMBC_highIL6_basal_volunteer25

source_name: PMBC, high IL6, pre-exercise, volunteer 25


title: PMBC_highIL6_24weeks_volunteer25

source_name: PMBC, high IL6, post-exercise, volunteer 25


title: PMBC_lowIL6_26weeks_volunteer21

source_name: PMBC, low IL6, 2 weeks post-exercise, volunteer 21


title: PMBC_highIL6_24weeks_volunteer16

source_name: PMBC, high IL6, post-exercise, volunteer 16


title: PMBC_highIL6_24weeks_volunteer18

source_name: PMBC, high IL6, post-exercise, volunteer 18


title: PMBC_lowIL6_basal_volunteer21

source_name: PMBC, low IL6, pre-exercise, volunteer 21


title: PMBC_lowIL6_26weeks_volunteer1

source_name: PMBC, low IL6, 2 weeks post-exercise, volunteer 1


title: PMBC_lowIL6_24weeks_volunteer21

source_name: PMBC, low IL6, post-exercise, volunteer 21


title: PMBC_lowIL6_basal_volunteer1

source_name: PMBC, low IL6, pre-exercise, volunteer 1


title: PMBC_highIL6_26weeks_volunteer18

source_name: PMBC, high IL6, 2 weeks post-exercise, volunteer 18


title: PMBC_highIL6_basal_volunteer16

source_name: PMBC, high IL6, pre-exercise, volunteer 16


title: PMBC_highIL6_26weeks_volunteer16

source_name: PMBC, high IL6, 2 weeks post-exercise, volunteer 16


title: PMBC_highIL6_26weeks_volunteer44

source_name: PMBC, high IL6, 2 weeks post-exercise, volunteer 44


title: D. simulans (female) x D. sechellia (male) F1 hybrid male adult replicate 2

city: Hamilton

first: Rama

middle: S.

last: Singh

state: Ontario

address: 1280 Main Street West

department: Biology Department

country: Canada

institute: McMaster University

description: All information is provided above.

hyb_protocol: 80 μL of hybridization buffer (75 μl of DIG Easy Hyb [Roche], 4 μl of 10 mg/ml yeast tRNA [Invitrogen], and 4 μl of 10 mg/ml salmon sperm DNA [Sigma]) was added to each resuspended probe, followed by incubation at 65°C for 10 min. Both sample and reference probes were placed on the array, which was then placed in a sealed chamber in a 37°C water bath for 16-18 hours. The array was then washed for 3 × 15 min in pre-warmed 1 × SSC, 0.1% SDS. The array was then washed with room temperature 1 × SSC for ≤1min, followed by room temperature 0.1 × SSC for ≤ 15 sec.

scan_protocol: Array was scanned using a ScanArray 4000 XL (GSI Lumonics/Packard Biochips); images were preprocessed and quantified using QuantArray v3.0 (PerkinElmer).

data_processing:
While the CH1_SIG_MEAN, CH1_BKD_MEAN, CH2_SIG_MEAN, and CH2_BKD_MEAN columns are derived from the raw data, the VALUE column was derived as follows:
Data from the scanned microarrays were uploaded into GeneTraffic™ DUO version 3.0 (Iobion Informatics) and replicate spots were filtered such that any element showing greater than 200% covariance or a 2-fold greater difference among the highest and lowest measured replicate spot (including all elements within an array or between replicate arrays) was flagged. All elements flagged according to these criteria as well as those flagged by the internal quality control standards of the software were then manually inspected for the presence of unacceptable spots (e.g., incorrectly printed, contained visible surface scratches or matter interfering with the scanning, etc.). Such spots were removed, and if less than 6 usable replicates (i.e., 2 replicate spots per array) remained, the entire element was discarded. Furthermore, an element was discarded if a subset of the within-array replicate spots showed consistently different hybridization intensities; these spots likely represent clones that were incorrectly annotated as belonging to the same element in the CDMC’s Drosophila 12kv2 microarray annotation file (http://142.150.8.217/GT_annot.zip). The filtered raw data was then downloaded from GeneTraffic™ DUO version 3.0 and subjected to a second round of quality control, where spots were removed if they did not show an expression intensity of at least 100, as well as a two-fold expression intensity above either the local or global average background. All genes that did not have usable data from both replicate spots on all three microarrays in all four stages within a species were then removed from further analysis. The CDMC’s Drosophila 12kv2 microarray annotation file was then manually inspected in order to identify all spots for which a single Flybase gene number (FBgn) (FB2008_10 Dmel Release 5.13; http://flybase.org/) could unambiguously be identified. All control spots as well ambiguous clone spots were removed from further analysis, leaving only genes that were detectably expressed in all 4 stages in at least one of the 3 species or the hybrid.
	The data remaining after quality control were normalized using the ‘rlowess’ procedure (spatial-intensity joint loess) as implemented in the ‘maanova’ package in the R statistical software (http://research.jax.org/faculty/churchill/software/Rmaanova/index.html), using default values and a ‘TwoColor’ array type. The output for each spot on each array from maanova was then transformed into its log2(sample/reference) ratio, which is reported in the 'VALUE' column.

organism: Drosophila sechellia x Drosophila simulans

source_name: D. simulans (female) x D. sechellia (male) F1 hybrid male whole-body adult 2x amplified mRNA

label_protocol:
RNase-free water was added to 5 μg of total RNA from each sample to bring the final volume to 14.5 μl. 4 μl of random primer was added followed by incubation at 70°C for 10 min, then 42°C for 5 min. 19.5 μl of modified Indirect RT master mix was added to each tube, along with 2.0 μl of Superscript II RT and the reaction was incubated at 42°C for 3 hours.
The cDNA product was cleaned and precipitated by adding 8 μl of 1N NaOH to each reaction with mixing by pipetting followed by a quick spin and immediate incubation at 65°C for 10 min. 8 μl of 1N HCl was then added, followed by 4 μL of 1M Tris (pH 7.5), mixing by pipetting after each addition. 38 μl of water was added to bring the total volume to 100 μl, and the amino allyl-cDNA was purified using either the Qiagen PCR clean up or Invitrogen Purelink purification kit (using 80% EtOH for the wash buffer and eluting with 2 × 50 μl of water). After purification, 10 μl of 3M NaOAc, 1 μl of glycogen (20 μg/μl) and 120 μl of ice-cold isopropanol were added, and the cDNA was allowed to precipitate at –20°C for at least 75 min or overnight. The precipitated cDNA was then spun at >12,000 g for 30 min and the pellet was washed with 200 μl of 75% EtOH, followed by another spin at >12,000 g for 5 min. All EtOH was carefully pipetted from the tube and the probe pellet was allowed to dry for ≤ 1 min before resuspension in 5 μl of water.
Samples were then dye conjugated by addition of 3 μl of 0.3 M NaHCO3 to the resuspended amino allyl-cDNA, followed by 2 μl of reactive dye and subsequent incubation at room temperature in the dark for 1 hour. 90 μl of ddH2O was added to each sample, followed by purification using either the Qiagen PCR clean up or Invitrogen Purelink purification kit, washing with 80% EtOH 3 × and eluting with 3 × 50 μl of water. 15 μl of 3M NaOAc, 1.5 μl of glycogen (20 μg/μl) and 170 μl of ice-cold isopropanol were added to the labeled probe, and the DNA was allowed to precipitate at –20°C for at least 30 min. The precipitated probe was then spun at >12,000 g for 30 min and the pellet was washed with 200 μl of 75% EtOH, and spun at >12,000 g for 5 min. All EtOH was carefully pipetted from the tube and the probe pellet was allowed to dry for ≤ 1 min before resuspension in 5 μl of water.

extract_protocol: mRNA was extracted from a pool of 25 males using the RNeasy Mini kit (Qiagen). Samples were then amplified twice using the MessageAmp II aRNA kit (Ambion).

treatment_protocol: Flies were grown on standard cornmeal-molasses medium on 10 cm culture plates, painted with a small amount of water-diluted yeast. No more than 30 individuals were on a single  plate to prevent growth-dependent density effects. When flies reached the appropriate stage, they were collected in RNAlater (Ambion) on ice and placed immediately at -80 degrees centigrade.

tag: f1 hybrid

tag: strain

value: D.simulans (14021-0251.2) and D. sechellia (Cousin Island, Jean R. David, Centre National de la Recherche Scientific, Gif sur Yvette, France)

tag: gender

tag: stage

value: 1.5h post pupal eclosion

organism: Drosophila melanogaster

source_name: D. melanogaster male mixed-stage whole-body mRNA reference

label_protocol:
RNase-free water was added to 60 μg of total RNA from each sample, to bring the final volume to 19 μl. 21 μl of Indirect RT master mix was added into each tube and the reaction was incubated at 65°C for 5 min, then 42°C for 5 min. 2 μl of Superscript II RT was added to the sample, followed by incubation at 42°C for 3 hours.
The cDNA product was cleaned and precipitated by adding 8 μl of 1N NaOH to each reaction with mixing by pipetting followed by a quick spin and immediate incubation at 65°C for 10 min. 8 μl of 1N HCl was then added, followed by 4 μL of 1M Tris (pH 7.5), mixing by pipetting after each addition. 38 μl of water was added to bring the total volume to 100 μl, and the amino allyl-cDNA was purified using either the Qiagen PCR clean up or Invitrogen Purelink purification kit (using 80% EtOH for the wash buffer and eluting with 2 × 50 μl of water). After purification, 10 μl of 3M NaOAc, 1 μl of glycogen (20 μg/μl) and 120 μl of ice-cold isopropanol were added, and the cDNA was allowed to precipitate at –20°C for at least 75 min or overnight. The precipitated cDNA was then spun at >12,000 g for 30 min and the pellet was washed with 200 μl of 75% EtOH, followed by another spin at >12,000 g for 5 min. All EtOH was carefully pipetted from the tube and the probe pellet was allowed to dry for ≤ 1 min before resuspension in 5 μl of water.
	Samples were then dye conjugated by addition of 3 μl of 0.3 M NaHCO3 to the resuspended amino allyl-cDNA, followed by 2 μl of reactive dye and subsequent incubation at room temperature in the dark for 1 hour. 90 μl of ddH2O was added to each sample, followed by purification using either the Qiagen PCR clean up or Invitrogen Purelink purification kit, washing with 80% EtOH 3 × and eluting with 3 × 50 μl of water. 15 μl of 3M NaOAc, 1.5 μl of glycogen (20 μg/μl) and 170 μl of ice-cold isopropanol were added to the labeled probe, and the DNA was allowed to precipitate at –20°C for at least 30 min. The precipitated probe was then spun at >12,000 g for 30 min and the pellet was washed with 200 μl of 75% EtOH, and spun at >12,000 g for 5 min. All EtOH was carefully pipetted from the tube and the probe pellet was allowed to dry for ≤ 1 min before resuspension in 5 μl of water.

extract_protocol: mRNA was extracted from pools of 25 males at each stage listed above individually  using the RNeasy Mini kit (Qiagen). A large number of extracts were performed for each stage. Within-stage extracts were pooled, quantified, and the four stages were mixed together in equal concentration in order to produce the reference sample.

treatment_protocol: Flies were grown on standard cornmeal-molasses medium on 10 cm culture plates, painted with a small amount of water-diluted yeast. No more than 30 individuals were on a single  plate to prevent growth-dependent density effects. When flies reached the appropriate stage (synchronized to a 2h window), they were collected in RNAlater (Ambion) on ice and placed immediately at -80 degrees centigrade.

value: Equal concentration mix of 96h post larval emergence, 4h post puparium formation, 72h post puparium formation, and 1.5h post eclosion individuals.


title: PMBC_highIL6_basal_volunteer18

source_name: PMBC, high IL6, pre-exercise, volunteer 18


title: Slow vs. Fast Replicate 2

status: Public on Aug 05 2010

city: Bronx

first: Michael

last: Berney

state: NY

address: 1301 Morris Park Avenue

department: Department of Microbiology and Immunology

country: USA

institute: Albert Einstein College of Medicine

description: Biological replicate 2 of 5.

hyb_protocol: Hybrization performed according to SOP M008 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)

scan_protocol: Scanned Genepix 4000A scanner . Images were quantified using Spotfinder (TIGR).

data_processing: Total normalization and LOWESS normalization with MIDAS software (TIGR)

organism: Mycolicibacterium smegmatis MC2 155

source_name: Chemostat culture fast 50% air saturation

label_protocol: 10 µg of total RNA were reverse transcribed and labelled in a two step protocol according to SOP M007 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)

growth_protocol: Prior to each experiment bacteria were loop inoculated from a cryo-culture (-80°C) onto a LBT plate and incubated for 3 days at 37°C.  A colony was picked from the plate and inoculated into the 5 ml batch medium in a 30 ml glass universal and incubacted at 37°C on a rotary shaker at 200 rpm. At an OD between 0.3 - 0.5 a sample was withdrawn to inoculate the bioreactor (700 ml) to a starting OD600 of 0.005. The culture was then left in batch mode under oxystatic condition (maintaining an air saturation of 50% i.e. 10% dissolved oxygen concentration) until OD600 reached around 80% of maximum OD600 and then turned in to chemostat mode either at a dilution rate of 4.6 h-1 or 69 h-1. The chemostat was then left running for at least two volume changes before harvest.

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

tag: culture doubling time

value: 4.6 hours

source_name: Chemostat culture slow 50% air saturation

value: 69 hours


title: D. simulans (female) x D. sechellia (male) F1 hybrid male late pupal replicate 2

description: All information is provided above.

source_name: D. simulans (female) x D. sechellia (male) F1 hybrid male whole-body late pupal 2x amplified mRNA

value: 72h post puparium formation


title: D. simulans (female) x D. sechellia (male) F1 hybrid male late pupal replicate 3

description: All information is provided above.


title: D. simulans (female) x D. sechellia (male) F1 hybrid male early pupal replicate 1

description: All information is provided above.

source_name: D. simulans (female) x D. sechellia (male) F1 hybrid male whole-body early pupal 2x amplified mRNA

value: 4h post puparium formation


title: D. simulans (female) x D. sechellia (male) F1 hybrid male late pupal replicate 1

description: All information is provided above.


title: D. simulans (female) x D. sechellia (male) F1 hybrid male adult replicate 3

description: All information is provided above.


title: D. simulans (female) x D. sechellia (male) F1 hybrid male adult replicate 1

description: All information is provided above.


title: PMBC_lowIL6_24weeks_volunteer1

source_name: PMBC, low IL6, post-exercise, volunteer 1


title: D. simulans (female) x D. sechellia (male) F1 hybrid male early pupal replicate 3

description: All information is provided above.


title: Hs primary aortic endothelial cells grown on 30 nm nanotubes for 24 hrs_rep1

status: Public on Aug 14 2010

city: San Francisco

first: Andrea

middle: J

last: Barczak

state: CA

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

description: no additional information

hyb_protocol: Labeled cRNA was assessed using the Nandrop ND-100 , and equal amounts of Cy3 labeled target were hybridized to Agilent whole genome human arrays (platform acc# GPL6480) Hybridizations were performed for 14 hrs, according to the manufacturers protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner

data_processing: Raw signal intensities were extracted with Feature Extraction v10.1 software (Agilent). The dataset was normalized using the quantile normalization method. The median feature pixel intensity was used as the raw signal before normalization and no background subtraction was performed.

source_name: Human Aortic Endothelial Cells (HAEC)

label_protocol: 400ng of RNA was amplified and labeled using the One-Color Agilent Low RNA  Input Linear Amplification Kit

growth_protocol: Cells from Lonza were cultured according to manufacturer’s instructions using Lonza’s HAEC and HAoSMC complete media in a humidified 95% air/5% CO2 incubator at 37°C.  Cells were passaged less than 15 times.

extract_protocol: Total RNA was extracted using Qiagen's RNA easy kit

treatment_protocol: Cells were seeded onto surfaces with nanotube pore diameters of 30 nm, 100 nm, or flat surfaces at a density of 5 x 10^4 cells/cm^2 for 24 hours.

tag: cell type

value: Human Aortic Endothelial Cells (HAEC)

tag: protocol

value: 30 nm nanotubes


title: PMBC_lowIL6_26weeks_volunteer43

source_name: PMBC, low IL6, 2 weeks post-exercise, volunteer 43


title: D. simulans (female) x D. sechellia (male) F1 hybrid male early pupal replicate 2

description: All information is provided above.


title: ES_preblastocyst_KDMEM_rep2_Cy5labeled

city: Storrs

first: Mark

middle: Gerald

last: Carter

state: CT

address: 1392 Storrs Road

department: Center for Regenerative Biology

institute: University of Connecticut

description: ES cells, preblastocyst-derived in KnockOut DMEM, replicate 2, HyperCy5-labeled

hyb_protocol: Slides were plunged into 0.2% SDS 10 times, incubated 2-3 minutes with gentle shaking, and rinsed in a series of 5 milli-Q water baths. Slides were dried by immersion in isopropanol for 10-15 sec. followed by centrifugation at 1,000 rpm in a hanging bucket rotor. Slides were prehybridized in 5X SSC, 0.1% SDS, 1% bovine serum albumin at 42°C for 1 hour, washed and dried as before. Combined C3/Cy5 target mixes were hybridized in 50% Formamide, 10X SSC, 0.2% SDS for 40 hours at 42°C. Hybridized slides were sequentially washed in (1X SSC, 0.2% SDS), (0.1X SSC, 0.2% SDS), and 0.1X SSC for 4 minutes each, dried by centrifugation, and stored in argon gas until scanned.

scan_protocol: Washed slides were scanned using GenePix Pro 6.1 software on an MD Axon 4000B scanner, at 33% laser power, and 10 μm resolution. Automatic PMT adjustment was used, set at 0.05% saturated features. Images were saved as two-channel TIFF files.

data_processing: Two-channel TIFF scan images were overlayed with GAL file spot grids in GenePix Pro 6.1, irregular blocks and spots were manually adjusted when necessary, and unflagged bad features were manually flagged. Normalized, background-subtracted intensity data was exported to GPR files.

organism: Mus musculus

source_name: Stratagene Universal Mouse Reference

label_protocol: following stratagene's instructions

extract_protocol: following stratagene's instructions

tag: passage number

value: unknown

value: mixed

source_name: ES cells derived from preblastocyst in KnockOut DMEM

label_protocol: Ten micrograms of each total RNA sample was reverse transcribed, and remaining RNA was removed by adding 10 μl 1M NaOH, incubation at 65 °C for 15 min, followed by addition of 10 μl 1M HCl for pH neutralization. cDNA was purified using a modified QIAquick PCR purification kit protocol, spectrophotometer quantitated, then dried completely in a speed-vac and stored at -80°C until use. Cy dyes were conjugated to aminoallyl-labeled cDNA by resuspending each cDNA in 4.5 μl 0.1 M sodium carbonate buffer, combining with 4.5 μl of Cy3 or Hyper-Cy5 NHS-ester monoreactive dye in Dimethyl Sulphoxide (DMSO) and incubated in the dark at room temperature for approximately 1 hr, and then purified with a QIAquick PCR purification kit. Labeled cDNA target mixes were quantitated with a NanoDrop 1000 spectrophotometer (Thermo Scientific), combined in Cy-3/HyperCy-5 pairs and dried to 40 μl total volume in a Speed-vac.

growth_protocol: ES Cell lines, which were derived from blastocysts and preblastocysts in three different media, KDMEM, LG-MEMα, and HG-MEMα, were cultured to passage 8 on feeders, then lysed in TriZol (Invitrogen) and stored at -80 until RNA extraction.

extract_protocol: Total RNA was extracted as described in TriZol manufacturer's protocol. Approximately 100 ug of each total RNA preparation was further purified for microarray analysis using RNeasy Mini columns (Qiagen) as indicated by the manufacturer for total RNA purification, spectrophotometer-quantitated, and stored at -80 oC in 10 ug aliquots (1 ug/ul).

value: ES cells derived from preblastocyst

value: (CBS/CaJ X C57BL/6J) X (C57BL/6XDBA/2)F1


title: D. simulans (female) x D. sechellia (male) F1 hybrid male larval replicate 2

description: All information is provided above.

source_name: D. simulans (female) x D. sechellia (male) F1 hybrid male whole-body larval 2x amplified mRNA

value: 96h post larval emergence


title: D. sechellia male late pupal replicate 2

description: All information is provided above.

organism: Drosophila sechellia

source_name: D. sechellia male whole-body late pupal 2x amplified mRNA

value: Cousin Island (Jean R. David, Centre National de la Recherche Scientific, Gif sur Yvette, France)


title: D. simulans (female) x D. sechellia (male) F1 hybrid male larval replicate 1

description: All information is provided above.

value: Male


title: D. sechellia male early pupal replicate 3

description: All information is provided above.

source_name: D. sechellia male whole-body early pupal 2x amplified mRNA


title: D. sechellia male adult replicate 1

description: All information is provided above.

source_name: D. sechellia male whole-body adult 2x amplified mRNA


title: D. sechellia male late pupal replicate 3

description: All information is provided above.


title: D. simulans (female) x D. sechellia (male) F1 hybrid male larval replicate 3

description: All information is provided above.


title: D. sechellia male adult replicate 2

description: All information is provided above.


title: D. sechellia male adult replicate 3

description: All information is provided above.


title: D. sechellia male early pupal replicate 1

description: All information is provided above.


title: PMBC_highIL6_26weeks_volunteer25

source_name: PMBC, high IL6, 2 weeks post-exercise, volunteer 25


title: D. sechellia male larval replicate 1

description: All information is provided above.

source_name: D. sechellia male whole-body larval 2x amplified mRNA


title: D. sechellia male early pupal replicate 2

description: All information is provided above.

source_name: D. melanogaster male mixed-stage whole-body mRNA reference


title: D. sechellia male larval replicate 3

description: All information is provided above.


title: D. sechellia male larval replicate 2

description: All information is provided above.


title: D. simulans male adult replicate 1

description: All information is provided above.

organism: Drosophila simulans

source_name: D. simulans male whole-body adult 2x amplified mRNA


title: D. simulans male late pupal replicate 3

description: All information is provided above.

source_name: D. simulans male whole-body late pupal 2x amplified mRNA


title: D. simulans male adult replicate 3

description: All information is provided above.


title: D. simulans male early pupal replicate 1

description: All information is provided above.

source_name: D. simulans male whole-body early pupal 2x amplified mRNA


title: D. simulans male early pupal replicate 2

description: All information is provided above.


title: D. simulans male late pupal replicate 1

description: All information is provided above.


title: D. simulans male larval replicate 3

description: All information is provided above.

source_name: D. simulans male whole-body larval 2x amplified mRNA


title: PMBC_highIL6_24weeks_volunteer29

source_name: PMBC, high IL6, post-exercise, volunteer 29


title: D. simulans male early pupal replicate 3

description: All information is provided above.


title: D. simulans male late pupal replicate 2

description: All information is provided above.


title: D. melanogaster male adult replicate 1

description: All information is provided above.

source_name: D. melanogaster male whole-body adult 2x amplified mRNA


title: D. simulans male adult replicate 2

description: All information is provided above.


title: D. simulans male larval replicate 1

description: All information is provided above.


title: D. melanogaster male adult replicate 3

description: All information is provided above.


title: D. simulans male larval replicate 2

description: All information is provided above.


title: D. melanogaster male late pupal replicate 1

description: All information is provided above.

source_name: D. melanogaster male whole-body late pupal 2x amplified mRNA


title: D. melanogaster male late pupal replicate 3

description: All information is provided above.


title: D. melanogaster male late pupal replicate 2

description: All information is provided above.


title: D. melanogaster male early pupal replicate 3

description: All information is provided above.

source_name: D. melanogaster male whole-body early pupal 2x amplified mRNA


title: WT - 42 h - Cy5 - repeat 4 - mAdbID:79927

status: Public on Aug 01 2010

city: Bethesda

first: Snorri

middle: S

last: Thorgeirsson

state: MD

address: 37 Convent Dr. # 4146

department: Laboratory of Experimental Carcinogenesis

institute: National Cancer institute/NIH

description: mAdb experiment ID: 79927

hyb_protocol: Briefly, RNA samples were denaturated with 4 ug (d)T20 primer at 70degrees C for 5 minutes, chilled on ice, and incubated for 1 hour at 42degrees C in a 50-ul reaction mix containing 10 ul 10x First-Strand buffer (Invitrogen), 2.5 ul 20x deoxynucleotide triphosphate (dNTP) mix (10 mM dATP, dGTP, and CTP; 4 mM dTTP; and 6 mM aminoallyl-dUTP; Sigma-Aldrich), 5 ul of 0.1 M DTT, 2 ul SuperScript II (Invitrogen) reverse transcriptase, and 1 ul SUPERaseIn (Ambion ). After digestion with 4 U RNase H (Ambion Inc.) at 37degrees C for 20 minutes, the samples were cleaned up with a MinElute PCR Purification Kit (Qiagen). The eluted cDNA samples were concentrated by Speed Vac (Global Medical Instrumentation Inc.) and resolved in 20 ul 0.1 M NaHCO3 solution. The Cy3 and Cy5 dyes (Amersham Biosciences) were also dissolved in 20 ul of water. For the coupling reaction, 2 ul of dye was added to each sample, and the mix was left in a dark box for an hour. Labeled cDNA was purified again with a MinElute kit (Qiagen), and Cy3- and Cy5-labeled target and reference samples were combined. Before the hybridization, oligonucleotide microarrays were pretreated with a 5xSSC, 1% BSA, 0.1% SDS blocking solution. The samples were applied on the microarray slides in a hybridization mix containing 25% formamide, 0.1% SDS, and 5xSSC in 28 ul final volume. After overnight incubation, the slides were washed in a 1xSSC 0.1% SDS solution for 2 minutes and then consecutively in 1xSSC and 0.2xSSC solutions.

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.45;; 1.33 Temperature: 36.45

data_processing:
Data Processing Protocol
Calculation Method: Image spots with diameter less than 10 um or more than 300 um, signal intensity below background intensity, or signal intensity less than 2 x SD of background intensity for any of the 2 fluorescent channels were excluded. Only genes with at least 3 data points in each treatment were selected for further data analysis. Gene expression values were normalized by Loess and quantile normalization method across all primary hepatocyte samples. For each spot, log2 transformed intensity value was used for further data analysis.

source_name: Pooled Normal Mouse Liver (cy3)

label_protocol:
Cy3 Labeling Protocol
Other: Total RNA (20 ug) was used to synthesize fluorescently labeled (Amersham Biosciences) cDNA probes.

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was extracted from the frozen liver sections using TRIZOL (Invitrogen) following the manufacturer’s protocol.

tag: tissue

value: liver

source_name: WT - 42 h - Cy5

label_protocol:
Cy5 Labeling Protocol
Other: Total RNA (20 ug) was used to synthesize fluorescently labeled (Amersham Biosciences) cDNA probes.

treatment_protocol:
Treatment time: 42 hours
In-vivo treatment: Two-thirds partial hepatectomy (PH).

value: c-Metwt/wt/Albcre+/-


title: KO - 42h - Cy3 - repeat 4 - mAdbID:79926

description: mAdb experiment ID: 79926

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.63;; 1.37 Temperature: 43.01

source_name: Pooled Normal Mouse Liver (cy5)

source_name: KO - 42 h - Cy3

value: c-Metflox/flox/Albcre+/-


title: D. melanogaster male larval replicate 3

description: All information is provided above.

source_name: D. melanogaster male whole-body larval 2x amplified mRNA

value: Equal concentration mix of 96h post larval emergence, 4h post puparium formation, 72h post puparium formation, and 1.5h post eclosion individuals.


title: D. melanogaster male early pupal replicate 1

description: All information is provided above.


title: D. melanogaster male early pupal replicate 2

description: All information is provided above.


title: D. melanogaster male larval replicate 2

description: All information is provided above.


title: D. sechellia male late pupal replicate 1

description: All information is provided above.

source_name: D. sechellia male whole-body late pupal 2x amplified mRNA


title: KO - 42 h - Cy5 - repeat 2 - mAdbID:79919

description: mAdb experiment ID: 79919

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.47;; 1.25 Temperature: 37.96

source_name: KO - 42 h - Cy5


title: WT - 42h - Cy3 - repeat 1 - mAdbID:79921

description: mAdb experiment ID: 79921

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.53;; 1.3 Temperature: 41.78

source_name: WT - 42 h - Cy3


title: KO - 42h - Cy3 - repeat 3 - mAdbID:79925

description: mAdb experiment ID: 79925

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.6;; 1.35 Temperature: 42.76


title: WT - 42 h - Cy5 - repeat 6 - mAdbID:79917

description: mAdb experiment ID: 79917

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.43;; 1.25 Temperature: 37.18


title: WT - 24 h - Cy3 - repeat 4 - mAdbID:79463

description: mAdb experiment ID: 79463

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.39;; 1.44 Temperature: 35.83

source_name: WT - 24 h - Cy3

treatment_protocol:
Treatment time: 24 hours
In-vivo treatment: Two-thirds partial hepatectomy (PH).


title: WT - 42h - Cy3 - repeat 5 - mAdbID:79923

description: mAdb experiment ID: 79923

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.57;; 1.32 Temperature: 42.26


title: WT - 42h - Cy3 - repeat 3 - mAdbID:79922

description: mAdb experiment ID: 79922

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.58;; 1.31 Temperature: 42.01


title: WT - 0.5 h - Cy3 - repeat 4 - mAdbID:79462

description: mAdb experiment ID: 79462

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.43;; 1.42 Temperature: 35.16

treatment_protocol:
Treatment time: 0.5 hours
In-vivo treatment: Two-thirds partial hepatectomy (PH).


title: WT - 24 h - Cy5 - repeat 5 - mAdbID:79459

description: mAdb experiment ID: 79459

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.43;; 1.41 Temperature: 33.12

source_name: WT - 24 h - Cy5


title: KO - 48 h - Cy5 - repeat 2 - mAdbID:79461

description: mAdb experiment ID: 79461

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.42;; 1.42 Temperature: 34.51

source_name: KO - 48 h - Cy5

treatment_protocol:
Treatment time: 48 hours
In-vivo treatment: Two-thirds partial hepatectomy (PH).


title: KO - 42h - Cy3 - repeat 1 - mAdbID:79924

description: mAdb experiment ID: 79924

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.57;; 1.34 Temperature: 42.55


title: WT - 48h - Cy3 - repeat 5 - mAdbID:79455

description: mAdb experiment ID: 79455

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.45;; 1.46 Temperature: 36.62

source_name: WT - 48 h - Cy3


title: WT - 0.5 h - Cy5 - repeat 5 - mAdbID:79458

description: mAdb experiment ID: 79458

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.47;; 1.62 Temperature: 32.44


title: KO - 0.5 h - Cy3 - repeat 5 - mAdbID:79456

description: mAdb experiment ID: 79456

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.4;; 1.44 Temperature: 37.11


title: KO - 42 h - Cy5 - repeat 5 - mAdbID:79920

description: mAdb experiment ID: 79920

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.56;; 1.29 Temperature: 41


title: WT - 2 h - Cy3 - repeat 5 - mAdbID:79454

description: mAdb experiment ID: 79454

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.38;; 1.45 Temperature: 36.11

source_name: WT - 2 h - Cy3

treatment_protocol:
Treatment time: 2 hours
In-vivo treatment: Two-thirds partial hepatectomy (PH).


title: KO - 24 h - Cy3 - repeat 1 - mAdbID:79457

description: mAdb experiment ID: 79457

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.44;; 1.27 Temperature: 37.76

source_name: KO - 24 h - Cy3


title: KO - 0.5 h - Cy5 - repeat 6 - mAdbID:79452

description: mAdb experiment ID: 79452

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.4;; 1.45 Temperature: 34.67


title: WT - 2 h - Cy5 - repeat 6 - mAdbID:79450

description: mAdb experiment ID: 79450

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.43;; 1.65 Temperature: 33.16

source_name: WT - 2 h - Cy5


title: WT - 48 h - Cy5 - repeat 6 - mAdbID:79451

description: mAdb experiment ID: 79451

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.44;; 1.47 Temperature: 33.89

source_name: WT - 48 h - Cy5


title: KO - 48h - Cy3 - repeat 1 - mAdbID:79465

description: mAdb experiment ID: 79465

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.46;; 1.28 Temperature: 37.89

source_name: KO - 48 h - Cy3


title: HeLa_ERKvsC_rep6

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description:
- RNA quality control with Agilent Bioanalyzer 2100
- Dye incorporation with NanoDrop ND-1000
Keywords = mitochondria, MAP kinase

hyb_protocol: 2 micro gram labeled DNA per channel were mixed

scan_protocol: - scanned with a G2505B Microarray Scanner (Agilent Technologies) - quantification software: Feature Extraction 9.5 (GE2-v5_95, Agilent Technologies)

data_processing:
- Normalization of the log2(cy3/cy5)-ratios with pinwise non-linear loess regression
- variance homogenisation by division of each value with the standard deviation
  of the normalized log2-ratios
- statistical software: 'R' (http://cran.r-project.org)

source_name: HeLa MAP-kinase treated mitochondria

label_protocol:
-  totalRNA was transcribed, amplified and labeled according to BD Atlas SMART fluorescent probe amplification kit with following modifications:
-  RNA template was hydrolized after transcription (high pH, 30 min/70 degree celcius)
-  PCR amplification progress was monitored and stopped before reaching saturation

extract_protocol:
- Trizol (Invitrogen) isolation according to the manufactures standard protocol
- Subsequent DNase I treatment

tag: Subsequent DNase I treatment

source_name: HeLa untreated mitochondria

tag: mitochondria from HeLa cells


title: WT - 42 h - Cy5 - repeat 2 - mAdbID:79915

description: mAdb experiment ID: 79915

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.42;; 1.33 Temperature: 34.71

source_name: Pooled Normal Mouse Liver (cy3)

source_name: WT - 42 h - Cy5


title: KO - 48h - Cy3 - repeat 5 - mAdbID:78357

description: mAdb experiment ID: 78357

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.36;; 1.4 Temperature: 36.12

source_name: Pooled Normal Mouse Liver (cy5)


title: KO - 24 h - Cy5 - repeat 2 - mAdbID:79453

description: mAdb experiment ID: 79453

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [30] ScanPower: 100;; 100 LaserPower: 2.42;; 1.44 Temperature: 35.4

source_name: KO - 24 h - Cy5


title: KO - 48 h - Cy5 - repeat 6 - mAdbID:78356

description: mAdb experiment ID: 78356

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.44;; 1.42 Temperature: 35.38


title: HeLa_ERKvsC_rep5


title: WT - 48 h - Cy5 - repeat 4 - mAdbID:78352

description: mAdb experiment ID: 78352

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.46;; 1.39 Temperature: 32.48


title: KO - 48 h - Cy5 - repeat 4 - mAdbID:78354

description: mAdb experiment ID: 78354

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.4;; 1.51 Temperature: 33.18


title: WT - 48h - Cy3 - repeat 3 - mAdbID:78353

description: mAdb experiment ID: 78353

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.41;; 1.44 Temperature: 34.26


title: WT - 48h - Cy3 - repeat 1 - mAdbID:78351

description: mAdb experiment ID: 78351

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.31;; 1.31 Temperature: 36.64


title: WT - 48 h - Cy5 - repeat 2 - mAdbID:78350

description: mAdb experiment ID: 78350

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.39;; 1.31 Temperature: 35.86


title: WT - 12 h - Cy5 - repeat 6 - mAdbID:77880

description: mAdb experiment ID: 77880

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.44;; 1.35 Temperature: 31.78

source_name: WT - 12 h - Cy5

treatment_protocol:
Treatment time: 12 hours
In-vivo treatment: Two-thirds partial hepatectomy (PH).


title: HeLa_ERKvsC_rep4

tag: mitochondria from HeLa Cells


title: KO - 48h - Cy3 - repeat 3 - mAdbID:78355

description: mAdb experiment ID: 78355

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.38;; 1.42 Temperature: 34.88


title: HeLa_ERKvsC_rep3

description:
- RNA quality control with Agilent Bioanalyzer 2100
- Dye incorporation with NanoDrop ND-1000
Keywords = mitochondria, MAP-kinase

hyb_protocol: 0.8 micro gram labelled DNA per channel were mixed

label_protocol:
-  totalRNA was transcribed, amplified and labeled according to BD Atlas SMART fluorescent probe amplification kit with following modifications:
-  RNA template was hydrolized after transcription (high pH, 30 min/70 degree celcius)
-  PCR amplification progress was monitored and stopped before reaching saturatio


title: HeLa_ERKvsC_rep1


title: WT - 24 h - Cy5 - repeat 2 - mAdbID:77347

description: mAdb experiment ID: 77347

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.35;; 1.52 Temperature: 35.95


title: WT - 24 h - Cy3 - repeat 1 - mAdbID:77344

description: mAdb experiment ID: 77344

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.38;; 1.66 Temperature: 33.66


title: WT - 24 h - Cy3 - repeat 3 - mAdbID:77343

description: mAdb experiment ID: 77343

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.37;; 1.45 Temperature: 33.15


title: HeLa_ERKvsC_rep2


title: WT - 36 h - Cy5 - repeat 4 - mAdbID:77083

description: mAdb experiment ID: 77083

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.4;; 1.66 Temperature: 36.73

source_name: WT - 36 h - Cy5

treatment_protocol:
Treatment time: 36 hours
In-vivo treatment: Two-thirds partial hepatectomy (PH).


title: KO - 24 h - Cy3 - repeat 5 - mAdbID:77346

description: mAdb experiment ID: 77346

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.37;; 1.63 Temperature: 34.81


title: KO - 24 h - Cy3 - repeat 3 - mAdbID:77345

description: mAdb experiment ID: 77345

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.36;; 1.63 Temperature: 34.38


title: WT - 36h - Cy3 - repeat 1 - mAdbID:77078

description: mAdb experiment ID: 77078

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.42;; 1.61 Temperature: 33.74

source_name: WT - 36 h - Cy3


title: KO - 36 h - Cy5 - repeat 4 - mAdbID:77080

description: mAdb experiment ID: 77080

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.43;; 1.66 Temperature: 34.99

source_name: KO - 36 h - Cy5


title: WT - 12 h - Cy3 - repeat 5 - mAdbID:77342

description: mAdb experiment ID: 77342

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.44;; 1.65 Temperature: 32.6

source_name: WT - 12 h - Cy3


title: KO - 36h - Cy3 - repeat 1 - mAdbID:77077

description: mAdb experiment ID: 77077

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.4;; 1.62 Temperature: 33.13

source_name: KO - 36 h - Cy3


title: KO - 24 h - Cy5 - repeat 4 - mAdbID:77348

description: mAdb experiment ID: 77348

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.38;; 1.53 Temperature: 36.39


title: WT - 36 h - Cy5 - repeat 2 - mAdbID:77082

description: mAdb experiment ID: 77082

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.42;; 1.66 Temperature: 36.16


title: WT - 36h - Cy3 - repeat 3 - mAdbID:77079

description: mAdb experiment ID: 77079

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.4;; 1.66 Temperature: 34.29


title: KO - 36 h - Cy5 - repeat 2 - mAdbID:77081

description: mAdb experiment ID: 77081

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.4;; 1.66 Temperature: 35.56


title: KO - 36h - Cy3 - repeat 3 - mAdbID:77076

description: mAdb experiment ID: 77076

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.49;; 1.6 Temperature: 32.36


title: KO - 2 h - Cy5 - repeat 6 - mAdbID:76989

description: mAdb experiment ID: 76989

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.45;; 1.65 Temperature: 39.75

source_name: KO - 2 h - Cy5


title: KO - 2 h - Cy3 - repeat 5 - mAdbID:76995

description: mAdb experiment ID: 76995

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.51;; 1.62 Temperature: 41.49

source_name: KO - 2 h - Cy3


title: KO - 0.5 h - Cy3 - repeat 1 - mAdbID:76992

description: mAdb experiment ID: 76992

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.48;; 1.64 Temperature: 40.56


title: WT - 12 h - Cy3 - repeat 1 - mAdbID:76889

description: mAdb experiment ID: 76889

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.53;; 1.61 Temperature: 40.27


title: KO - 0.5 h - Cy3 - repeat 3 - mAdbID:76888

description: mAdb experiment ID: 76888

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.54;; 1.62 Temperature: 39.72


title: KO - 0.5 h - Cy5 - repeat 4 - mAdbID:76891

description: mAdb experiment ID: 76891

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.56;; 1.62 Temperature: 40.78


title: KO - 0.5 h - Cy5 - repeat 2 - mAdbID:76986

description: mAdb experiment ID: 76986

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.49;; 1.41 Temperature: 38.43


title: WT - 12 h - Cy5 - repeat 2 - mAdbID:76892

description: mAdb experiment ID: 76892

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.58;; 1.61 Temperature: 41.1


title: WT - 12 h - Cy5 - repeat 4 - mAdbID:76893

description: mAdb experiment ID: 76893

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.56;; 1.61 Temperature: 41.33


title: WT - 12 h - Cy3 - repeat 3 - mAdbID:76890

description: mAdb experiment ID: 76890

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.54;; 1.55 Temperature: 40.51


title: KO - 12 h - Cy3 - repeat 5 - mAdbID:76850

description: mAdb experiment ID: 76850

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.37;; 1.32 Temperature: 36.48

source_name: KO - 12 h - Cy3


title: KO - 2 h - Cy5 - repeat 8 - mAdbID:76844

description: mAdb experiment ID: 76844

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.49;; 1.61 Temperature: 36.79


title: KO - 12 h - Cy3 - repeat 1 - mAdbID:76854

description: mAdb experiment ID: 76854

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.45;; 1.67 Temperature: 39.47


title: KO - 12 h - Cy5 - repeat 6 - mAdbID:76853

description: mAdb experiment ID: 76853

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.4;; 1.67 Temperature: 38.08

source_name: KO - 12 h - Cy5


title: KO - 2 h - Cy5 - repeat 4 - mAdbID:76843

description: mAdb experiment ID: 76843

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.44;; 1.34 Temperature: 36.24


title: WT - 0.5 h - Cy5 - repeat 3 - mAdbID:76833

description: mAdb experiment ID: 76833

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.48;; 1.5 Temperature: 37.6


title: KO - 12 h - Cy5 - repeat 2 - mAdbID:76855

description: mAdb experiment ID: 76855

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.39;; 1.66 Temperature: 40.16


title: WT - 2 h - Cy5 - repeat 2 - mAdbID:76835

description: mAdb experiment ID: 76835

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.52;; 1.53 Temperature: 38.43

source_name: WT - 2 h - Cy5


title: KO - 12 h - Cy3 - repeat 3 - mAdbID:76849

description: mAdb experiment ID: 76849

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.36;; 1.29 Temperature: 34.5


title: KO - 2 h - Cy3 - repeat 7 - mAdbID:76839

description: mAdb experiment ID: 76839

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.45;; 1.25 Temperature: 34.18


title: KO - 12 h - Cy5 - repeat 4 - mAdbID:76852

description: mAdb experiment ID: 76852

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.42;; 1.67 Temperature: 37.54


title: KO - 2 h - Cy3 - repeat 3 - mAdbID:76838

description: mAdb experiment ID: 76838

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.46;; 1.17 Temperature: 33.54


title: KO - 2 h - Cy5 - repeat 2 - mAdbID:76837

description: mAdb experiment ID: 76837

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.51;; 1.32 Temperature: 39.72


title: KO - 2 h - Cy3 - repeat 1 - mAdbID:76832

description: mAdb experiment ID: 76832

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.5;; 1.53 Temperature: 36.89


title: WT - 2 h - Cy5 - repeat 4 - mAdbID:76836

description: mAdb experiment ID: 76836

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.49;; 1.41 Temperature: 38.75


title: WT - 0.5 h - Cy5 - repeat 1 - mAdbID:76834

description: mAdb experiment ID: 76834

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.49;; 1.5 Temperature: 38.04


title: WT - 2 h - Cy3 - repeat 3 - mAdbID:76831

description: mAdb experiment ID: 76831

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.48;; 1.53 Temperature: 36.35

source_name: WT - 2 h - Cy3


title: WT - 2 h - Cy3 - repeat 1 - mAdbID:76830

description: mAdb experiment ID: 76830

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.52;; 1.54 Temperature: 35.78


title: WT - 0.5 h - Cy3 - repeat 2 - mAdbID:76828

description: mAdb experiment ID: 76828

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.49;; 1.21 Temperature: 33.85


title: WT - 0 h - Cy3 - repeat 1 - mAdbID:75182

description: mAdb experiment ID: 75182

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.52;; 1.3 Temperature: 34.16

source_name: WT - 0 h - Cy3

treatment_protocol:
Treatment time: 0 hours
In-vivo treatment: Two-thirds partial hepatectomy (PH).


title: WT - 0 h - Cy3 - repeat 5 - mAdbID:75187

description: mAdb experiment ID: 75187

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.5;; 1.42 Temperature: 36.49


title: KO - 0 h - Cy3 - repeat 3 - mAdbID:75175

description: mAdb experiment ID: 75175

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.47;; 1.29 Temperature: 38.62

source_name: KO - 0 h - Cy3


title: KO - 0 h - Cy3 - repeat 4 - mAdbID:75176

description: mAdb experiment ID: 75176

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.5;; 1.39 Temperature: 39.19


title: KO - 0 h - Cy3 - repeat 2 - mAdbID:75174

description: mAdb experiment ID: 75174

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.49;; 1.47 Temperature: 38.1


title: KO - 0 h - Cy3 - repeat 1 - mAdbID:75173

description: mAdb experiment ID: 75173

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.44;; 1.27 Temperature: 37.41


title: KO - 0 h - Cy3 - repeat 5 - mAdbID:75177

description: mAdb experiment ID: 75177

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.45;; 1.39 Temperature: 39.64


title: Left atria shunt rep2 (set 2)

city: Ottawa

first: Adolfo

last: de Bold

state: ON

address: 40 Ruskin St.

department: Cardiovascular Endocrinology

institute: University of Ottawa Heart Institute

hyb_protocol: A total of 20 ug of fragmented cRNA was hybridized to each GeneChip® Rat Genome 230 2.0 array. After 16 hours of incubation at 45 C, the GeneChips® were washed and stained with Streptavidin- phycoerythrin biotinylated anti-streptavidin antibody in the Affymetrix GeneChip® Fluidics Station 400

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® 3000 Scanner

data_processing: The data was analyzed with Robust Multiple-Array Averaging (RMA) which uses a model based background correction, quantile normalization and robust averaging expression summary method.

label: Biotin

organism: Rattus norvegicus

source_name: Left atrial tissue following 28 days aorto-caval shunt operation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug of total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Total RNA was extracted using Qiagen mini columns according to the manufacturer's instructions.

treatment_protocol: Tissue was obtained from Sprague Dawley rats, sacrificed by decapitation. The tissue was snap-frozen in liquid nitrogen and stored at -80 ºC until RNA extraction

tag: Strain

value: Sprague-Dawley; Gender:male; Weight:225-275 g; Tissue:Heart atria and ventricles


title: Left atria sham rep2 (set 2)

source_name: Left atrial tissue following 28 days aorto-caval sham operation


title: Right atria sham rep3 (set 2)

source_name: Right atrial tissue following 28 days aorto-caval sham operation


title: WT - 0 h - Cy3 - repeat 3 - mAdbID:75183

description: mAdb experiment ID: 75183

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.53;; 1.42 Temperature: 35.68

source_name: Pooled Normal Mouse Liver (cy5)


title: Right atria sham rep1 (set 2)


title: Left atria shunt rep3 (set 2)


title: Left atria shunt rep1 (set 2)


title: Left atria sham rep3 (set 2)


title: Right atria shunt rep2 (set 2)

source_name: Right atrial tissue following 28 days aorto-caval shunt operation


title: WT - 0 h - Cy3 - repeat 4 - mAdbID:75186

description: mAdb experiment ID: 75186

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.46;; 1.45 Temperature: 35.83


title: Right atria shunt rep1 (set 2)


title: Right atria shunt rep3 (set 2)


title: Right atria sham rep2 (set 2)


title: PI vs PI

type: genomic

city: Bet-Dagan

first: Ron

last: Ophir

address: POB 6

department: Fruit Tree Sciences

country: Israel

institute: Agricultire Research Organization

description: Labeling, hybridization and scanning were done at the Weizmann Institute's DNA Microarray Facility (Rehovot, Israel).

hyb_protocol: Hybridization was performed according to standart protocols at the Weizmann Institute's DNA Microarray Facility (Rehovot, Israel).

scan_protocol: Scanning of the array was performed with the Agilent scanner at the Weizmann Institute's DNA Microarray Facility (Rehovot, Israel).

data_processing: Probe signal pre-processing and fitting were performed using the R-package for LIMMA. Following background subtraction, for within-array normalization we applied "lowess" method, and for between-array normalization "quantile" method was used. To select for statistical significance of signal ratios, two subsequent steps, fitting and empirical Bayesian correction for better variance estimation, were performed. The p-values were corrected using Benjamini and Hochberg method.

molecule: genomic DNA

organism: Cucumis melo subsp. melo

source_name: PI biological repeat 2

label_protocol: gDNA (2.5 μg) was digested with restriction enzymes AluI and RsaI (Promega). The digested DNA was used for labeling and hybridization following Agilent procedures for CGH.

extract_protocol: Genomic DNA was extracted using standard procedures from young leaves pooled from 10 plants of each of the different cultivars. Two separate pools were created for each cultivar. The DNA was treated with RNAseH (Sigma, USA) and re-purified using phenol/chloroform/isoamyl alcohol followed by ethanol precipitation.

tag: subspecies

value: agrestis

tag: cultivar

value: leaves

source_name: PI biological repeat 1


title: Left atria sham rep1 (set 2)


title: Left ventricles sham rep3 (set 1)

source_name: Left ventricular tissue following 28 days aorto-caval sham operation


title: Left ventricles shunt rep1 (set 1)

source_name: Left ventricular tissue following 28 days aorto-caval shunt operation


title: Left ventricles shunt rep3 (set 1)


title: Left ventricles shunt rep2 (set 1)


title: Left atria sham rep3 (set 1)


title: Left ventricles sham rep1 (set 1)


title: Dulce vs Dulce

source_name: Dulce biological repeat 1

value: melo

value: Dulce

source_name: Dulce biological repeat 2


title: PI vs Dulce


title: Left ventricles sham rep2 (set 1)


title: Left atria sham rep2 (set 1)


title: Dulce vs PI


title: Left atria shunt rep1 (set 1)


title: Left atria sham rep1 (set 1)


title: Left atria shunt rep2 (set 1)


title: Left atria shunt rep3 (set 1)


title: HCT116 p53KO cells untreated (replicate 10)

status: Public on Jul 31 2010

city: Singapore

first: Meng Ling

last: Choong

address: 31 Biopolis Way, #03-01 Nanos

department: Drug Discovery

country: Singapore

institute: Experimental Therapeutics Centre

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4235974020_G

hyb_protocol: Hybridization was performed according to Illumina 8-sample BeadChip IntelliHyb protocol

scan_protocol: Images were scanned using the Illumina BeadArray reader

data_processing: Data analysis performed with Illumina BeadStudio application. Data was normalized by cubic-spline method and background subtracted

source_name: HCT116 colon adenocarcinoma cell line, p53KO cells untreated (replicate 10)

label_protocol: Total RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion) according to the manufacturer's protocol

growth_protocol: Cells were grown in McCoy medium with 10% bovine serum supplemented with antibiotics and L-glutamine

extract_protocol: Total RNA extracted from cells using the Trizol method

treatment_protocol: Cells were first seeded overnight. Dosages for actinomycin D treatment was 1 nM, 10 nM, and 100 nM. Dosage for nutlin-3 was 4 uM. Dosages for leptomycin B was 2 nM and 20 nM. Cells were treated for 16 hours before RNA extraction.

tag: cell line

value: HCT116 p53KO


title: HCT116 p53KO cells untreated (replicate 7)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4235974020_A

source_name: HCT116 colon adenocarcinoma cell line, p53KO cells untreated (replicate 7)


title: HCT116 p53KO cells untreated (replicate 9)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4235974020_C

source_name: HCT116 colon adenocarcinoma cell line, p53KO cells untreated (replicate 9)


title: HCT116 p53KO cells treated with 2 nM leptomycin B (replicate 2)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4235974020_E

source_name: HCT116 colon adenocarcinoma cell line, p53KO, 2 nM leptomycin B (replicate 2)


title: HCT116 p53KO cells treated with 2 nM leptomycin B (replicate 3)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4235974020_F

source_name: HCT116 colon adenocarcinoma cell line, p53KO, 2 nM leptomycin B (replicate 3)


title: HCT116 p53KO cells treated with 2 nM leptomycin B (replicate 1)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4235974020_D

source_name: HCT116 colon adenocarcinoma cell line, p53KO, 2 nM leptomycin B (replicate 1)


title: HCT116 p53KO cells untreated (replicate 8)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4235974020_B

source_name: HCT116 colon adenocarcinoma cell line, p53KO cells untreated (replicate 8)


title: HCT116 wild type cells treated with 2 nM leptomycin B (replicate 2)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4235974011_E

source_name: HCT116 colon adenocarcinoma cell line, wild type, 2 nM leptomycin B (replicate 2)

value: HCT116 wild type


title: HCT116 wild type cells untreated (replicate 10)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4235974011_G

source_name: HCT116 colon adenocarcinoma cell line, wild type cells untreated (replicate 10)


title: HCT116 wild type cells treated with 2 nM leptomycin B (replicate 1)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4235974011_D

source_name: HCT116 colon adenocarcinoma cell line, wild type, 2 nM leptomycin B (replicate 1)


title: HCT116 wild type cells untreated (replicate 9)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4235974011_C

source_name: HCT116 colon adenocarcinoma cell line, wild type cells untreated (replicate 9)


title: HCT116 p53KO cells untreated (replicate 5)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190026_G

source_name: HCT116 colon adenocarcinoma cell line, p53KO cells untreated (replicate 5)


title: HCT116 wild type cells untreated (replicate 8)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4235974011_B

source_name: HCT116 colon adenocarcinoma cell line, wild type cells untreated (replicate 8)


title: HCT116 wild type cells untreated (replicate 7)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4235974011_A

source_name: HCT116 colon adenocarcinoma cell line, wild type cells untreated (replicate 7)


title: HCT116 wild type cells treated with 2 nM leptomycin B (replicate 3)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4235974011_F

source_name: HCT116 colon adenocarcinoma cell line, wild type, 2 nM leptomycin B (replicate 3)


title: HCT116 wild type cells untreated (replicate 4)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190011_E

source_name: HCT116 colon adenocarcinoma cell line, wild type cells untreated (replicate 4)


title: HCT116 p53KO cells untreated (replicate 4)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190011_F

source_name: HCT116 colon adenocarcinoma cell line, p53KO cells untreated (replicate 4)


title: HCT116 wild type cells untreated (replicate 5)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190011_G

source_name: HCT116 colon adenocarcinoma cell line, wild type cells untreated (replicate 5)


title: HCT116 p53KO cells untreated (replicate 6)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190026_H

source_name: HCT116 colon adenocarcinoma cell line, p53KO cells untreated (replicate 6)


title: HCT116 wild type cells treated with 20 nM leptomycin B (replicate 1)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190010_G

source_name: HCT116 colon adenocarcinoma cell line, wild type, 20 nM leptomycin B (replicate 1)


title: HCT116 wild type cells treated with 20 nM leptomycin B (replicate 2)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190010_H

source_name: HCT116 colon adenocarcinoma cell line, wild type, 20 nM leptomycin B (replicate 2)


title: HCT116 wild type cells treated with 20 nM leptomycin B (replicate 3)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190002_F

source_name: HCT116 colon adenocarcinoma cell line, wild type, 20 nM leptomycin B (replicate 3)


title: HCT116 p53KO cells treated with 20 nM leptomycin B (replicate 3)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190002_H

source_name: HCT116 colon adenocarcinoma cell line, p53KO, 20 nM leptomycin B (replicate 3)


title: GBM Spheroid culture 1 (microRNA)

status: Public on Jul 20 2010

city: Heidelberg

first: Aurelie

last: Ernst

address: Im Neuenheimer Feld 280

institute: DKFZ

description: untreated

hyb_protocol: Labeled material  was hybridized to the Illumina microRNA panel according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned on the BeadArray Reader, and automatic image registration and intensity extraction software was used to derive intensity data per bead type corresponding to each miRNA (Galinsky et al., 2003).

data_processing: The array intensity data were imported into Beadstudio ver. 2.0 (Illumina Inc., San Diego, CA) and quantile normalized.

source_name: Glioblastoma spheroid culture

label_protocol: Labeling was achieved by use of the incorporation of Cy3.

growth_protocol: Glioblastoma samples were enzymatically dissociated and resuspended in stem-cell medium made of DMEM/F-12 medium containing 20% BIT serum-free supplement, basic fibroblast growth factor (bFGF) and epidermal growth factor (EGF) at 20ng/ml each (all Provitro, Berlin, Germany)

extract_protocol: RNA  was isolated from the spheroid cultures using the MiRNeasy kit (Qiagen, Hilden, Germany). RNA quality and concentration were assessed with the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: ATRA + 10% FBS

tag: sample type

value: GBM Spheroid culture


title: GBM Spheroid culture 5 (microRNA)

description: untreated


title: 1.5 hour expression of synthetic protein DX in E. coli

status: Public on Jul 21 2010

city: Tempe

first: Joshua

last: Stomel

state: AZ

department: BON

institute: Biodesign Inst. at ASU

description:
GSE17568_raw_data.gpr.gz consists of 8 blocks of data, each of which was a separate data set on an 8 member array.
GSM437777 is associated with block 1 in the raw data file
GSM437780 is associated with block 2
GSM437782 is associated with block 3
GSM437783 is associated with block 4
GSM437785 is associated with block 6
GSM437786 is associated with block 7
GSM437787 is associated with block 8

hyb_protocol: According to the protocol contained in: Two-Color Microarray-Based E. Coli Model Organism Analysis FairPlay III Labeling Version 1, December 2008. 7th Draft Provided by Agilent

scan_protocol: Scanned by the ASU School of Life sciences DNA Laboratory on a 48 carousel Agilent 2564B using scanning software provided by agilent and extracted with GenePix 6.0 Pro.

data_processing: Data was processed by MATLAB to median normalize each channel and lowess normalize the sample set.

label: Alexa Fluor 647

organism: Escherichia coli

source_name: RNA from E. coli expressing synthetic protein DX for 1.5 hours

label_protocol: According to Alexa Fluor Reactive Dye Decapacks for Microarray Applications provided product information MP32755

extract_protocol: According to Invitrogen PureLink Micro-to-Midi Total RNA Purification System

treatment_protocol: E. coli cells containing a pBAD18 vector encoding synthetic protein DX exposed to arabinose inducer for 0.5h.  RNA extracted with Invitrogen PureLink kit.

tag: test

value: E. coli TOP10 containing pBAD18 vector exposed to arabinose inducer

label: Alexa Fluor 555

source_name: RNA from E. coli 1.5 hours after inoculation

treatment_protocol: Identical to Channel 1 with no arabinose added

tag: reference

value: E. coli TOP10 containing pBAD18 vector with no arabinose added


title: HCT116 wild type cells untreated (replicate 6)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190011_H

source_name: HCT116 colon adenocarcinoma cell line, wild type cells untreated (replicate 6)


title: HCT116 p53KO cells treated with 20 nM leptomycin B (replicate 2)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190001_H

source_name: HCT116 colon adenocarcinoma cell line, p53KO, 20 nM leptomycin B (replicate 2)


title: 4 hour expression of synthetic protein DX in E. coli

source_name: RNA from E. coli expressing synthetic protein DX for 4 hours

source_name: RNA from E. coli 4 hours after inoculation


title: 0.5 hour expression of synthetic protein DX in E. coli

description:
Raw data file consists of 8 blocks of data, each of which was a separate data set on an 8 member array.
GSM437777 is associated with block 1 in the raw data file
GSM437780 is associated with block 2
GSM437782 is associated with block 3
GSM437783 is associated with block 4
GSM437785 is associated with block 6
GSM437786 is associated with block 7
GSM437787 is associated with block 8

source_name: RNA from E. coli expressing synthetic protein DX for 0.5 hours

source_name: RNA from E. coli 0.5 hours after inoculation


title: GBM Spheroid culture 5 ATRA treated (microRNA)

description: ATRA treated


title: HCT116 p53KO cells treated with 20 nM leptomycin B (replicate 1)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190001_G

source_name: HCT116 colon adenocarcinoma cell line, p53KO, 20 nM leptomycin B (replicate 1)


title: 3 hour expression of synthetic protein DX in E. coli

source_name: RNA from E. coli expressing synthetic protein DX for 3 hours

source_name: RNA from E. coli 3 hours after inoculation


title: 3.5 hour expression of synthetic protein DX in E. coli

source_name: RNA from E. coli expressing synthetic protein DX for 3.5 hours

source_name: RNA from E. coli 3.5 hours after inoculation


title: 1 hour expression of synthetic protein DX in E. coli

source_name: RNA from E. coli expressing synthetic protein DX for 1 hours


title: 2 hour expression of synthetic protein DX in E. coli

source_name: RNA from E. coli expressing synthetic protein DX for 2 hours

source_name: RNA from E. coli 2 hours after inoculation


title: GBM Spheroid culture 4 ATRA treated (microRNA)

description: ATRA treated

source_name: Glioblastoma spheroid culture


title: GBM Spheroid culture 3 (microRNA)

description: untreated


title: GBM Spheroid culture 3 ATRA treated (microRNA)

description: ATRA treated


title: GBM Spheroid culture 2 (microRNA)

description: untreated


title: GBM Spheroid culture 4 (microRNA)

description: untreated


title: GBM Spheroid culture 2 ATRA treated (microRNA)

description: ATRA treated


title: GBM Spheroid culture 1 ATRA treated (microRNA)

description: ATRA treated


title: BW25113 log ethanol shock, biological rep3

city: Beijing

first: Ming

last: Chen

address: Zhongguancun Nandajie 12th,Haidian Zone

country: China

institute: Biotechnology Research Institute, Chinese academy of Agricultural Sciences

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

scan_protocol: The data were collected by using Affymetrix GeneChip Scanner 3000.

data_processing: Affymetrix GeneChip Operating Software (GCOS) Version 1.4

source_name: Escherichia coli BW25113

label_protocol: Affymetrix Technical Manual, Prokaryotic Sample and Array Processing

growth_protocol: E.coli cells grown with aeration in M9 media at 37º C until stationary phase (2.0) and were treated with 15%（v/v） ethanol shock for 15 min , after that the cells were harvested to extract RNA. M9 medium recipe is as follow: NH4Cl 0.5g Na2HPO4 3.0g KH2PO4 1.5g 2% (w/v)Dextrose per 1 liter.

extract_protocol: Total RNA was extracted using the commercial product TRIzol Reagent (Invitrogen, Carlsbad, CA).Disrupt about 107cells with a homogenizer with 1ml TRIzol Reafent on ice. Store the homogenate for 5 minutes at room temperature to permit the complete dissociation of nucleoprotein complexes. Next, supplement the homogenate with 0.2 ml chloroform per 1 ml of TRI Reagent, cover the samples tightly and shake vigorously for 15 seconds. Store the resulting mixture at room temperature for 2-15 minutes and centrifuge at 12,000 g for 15 minutes at 4 C. Following centrifugation, the mixture separates into a lower red phenol-chloroform phase, interphase and the colorless upper aqueous phase. Transfer the aqueous phase to a fresh tube. Precipitate RNA from the aqueous phase by mixing with isopropanol. Use 0.5 ml of isopropanol per 1 ml of TRI Reagent used for the initial homogenization. Store samples at room temperature for 5-10 minutes and centrifuge at 12,000 g for 8 minutes at 4 - 25 C. Remove the supernatant and wash the RNA pellet ( by vortexing) with 75% ethanol and subsequent centrifugation at 7,500 g for 5 minutes at 4 - 25 C. Add at least 1 ml of 75% ethanol per 1 ml TRI Reagent used for the initial homogenization. Remove the ethanol wash and briefly air-dry the RNA pellet for 3 - 5 min. Dissolve RNA in DEPC-treated water by passing solution a few times through a pipette tip. Using an on-column DNase digestion with RNase-free DNase I (Qiagen) to purify the total RNA.

treatment_protocol: E.coli cells grown in M9 media with at 37º C until stationary phase (2.0), then were treated with 15%（v/v） ethanol shock for 15 min after that the cells were harvested to extract RNA.

tag: genotype

value: wild type

tag: genetic background


title: BW25113 stationary ethanol shock, biological rep2


title: BW25113 stationary ethanol shock, biological rep3


title: BW25113 stationary ethanol shock, biological rep1


title: BW25113 log ethanol shock, biological rep2


title: BW25113 (rpoS-) stationary ethanol shock, biological rep1

source_name: Escherichia coli BW25113（rpoS-）

value: rpoS-


title: BW25113 (rpoS-) log ethanol shock, biological rep3


title: BW25113 log ethanol shock, biological rep1


title: BW25113 (rpoS-) stationary ethanol shock, biological rep3


title: BW25113 log, biological rep3

treatment_protocol: E.coli cells grown in M9 media with at 37º C until stationary phase (2.0), after that the cells were harvested to extract RNA.


title: BW25113 stationary, biological rep3


title: BW25113 (rpoS-) stationary ethanol shock, biological rep2


title: BW25113 (rpoS-) log ethanol shock, biological rep1


title: BW25113 stationary, biological rep1


title: BW25113 (rpoS-) log, biological rep3


title: BW25113 stationary, biological rep2


title: BW25113 log, biological rep1


title: BW25113 (rpoS-) stationary, biological rep2


title: BW25113 (rpoS-) log, biological rep1


title: BW25113 (rpoS-) log, biological rep2


title: BW25113 (rpoS-) stationary, biological rep1


title: BW25113 (rpoS-) stationary, biological rep3


title: BW25113 (rpoS-) log ethanol shock, biological rep2


title: BW25113 log, biological rep2


title: GBM Spheroid culture 5  (mRNA)

description: 2 raw text files: probes are spread on 2 different files (Stripes: _1 and _2) for each sample on the array

hyb_protocol: Labeled, amplified material (700 to 1250 ng per array) was hybridized to the Illumina Human whole genome Sentrix-6 V2 BeadChip® array according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Microarray scanning was done using a Beadstation array scanner, setting adjusted to a scaling factor of 1 and PMT settings at 430.

data_processing: Raw data extraction was done using the beadarray R package (svn release 1.7.0) from bioconductor.org. Bead outliers were removed when their expression value dropped below a threshold: the imaging system background, non-specific binding and cross hybridization signal. Individual bead types were flagged as filtered when their bead replicate count dropped below 17. All data was used for the mean expression value calculation within beadarray. Finally, we excluded a bead type when the bead type’s filter flag was set across all samples. Data analysis was done by variance stabilizing and spline normalizing the signals using the algorithms from the lumi R package (release 1.1.0) from bioconductor.org. 16,651 transcripts remained after filtering.

source_name: GBM Spheroid culture

label_protocol: Labeling was achieved by use of the incorporation of biotin-16-UTP.

extract_protocol: RNA  was isolated from the spheroid cultures using the RNeasy kit (Qiagen, Hilden, Germany). RNA quality and concentration were assessed with the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).


title: GBM Spheroid culture 5 ATRA treated (mRNA)


title: GBM Spheroid culture 4  (mRNA)


title: GBM Spheroid culture 3 (mRNA)


title: GBM Spheroid culture 1 (mRNA)


title: GBM Spheroid culture 4 ATRA treated (mRNA)


title: GBM Spheroid culture 3 ATRA treated (mRNA)


title: GBM Spheroid culture 1 ATRA treated (mRNA)


title: d20 In Vitro, Mmu22

status: Public on Jul 12 2010

city: Urbana

first: Rebecca

last: Krisher

state: IL

address: 1207 West Gregory Drive

institute: University of Illinois

description: Gene expression data of developmentally incompetent or immature oocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip 3000 7G

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.

molecule: polyA RNA

source_name: In vitro matured MII oocytes derived from d20 B6D2F1 female mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol following two-cycle amplification

growth_protocol: Germinal vesicle (GV) oocytes were isolated from mouse ovaries 48 hrs post-PMSG injection.  GV oocytes were matured in vitro for 16 hours in Gmat medium.  For collection of in vivo matured oocytes, mice were stimulated with hCG 48 hours post-PMSG.  Oocyte

extract_protocol: Poly A+ RNA extraction was performed using the DynaBeads mRNA Direct Kit from Invitrogen

treatment_protocol: GV, in vivo matured, and in vitro matured oocytes were exposed to 1% v/v (80-160 U/mL) hyaluronidase to remove the cumulus cells.

tag: Age

tag: Maturation

value: In vitro matured MII


title: GBM Spheroid culture 2 (mRNA)


title: 7-8 wk GV, Mmu18

source_name: Germinal vesicle stage oocytes derived from 7-8 wk old B6D2F1 female mice

value: Germinal vesicle


title: 7-8 wk In Vivo, Mmu08

source_name: In vivo matured MII oocytes derived from 7-8 wk old B6D2F1 female mice

value: In vivo matured MII


title: d26 In Vitro, Mmu05

source_name: In vitro matured MII oocytes derived from d26 B6D2F1 female mice


title: GBM Spheroid culture 2 ATRA treated (mRNA)


title: d26 In Vivo, Mmu12

source_name: In vivo matured MII oocytes derived from d26 B6D2F1 female mice


title: d26 In Vitro, Mmu16


title: d26 In Vitro, Mmu13


title: d20 In Vitro, Mmu24


title: d20 In Vitro, Mmu15


title: 7-8 wk In Vitro, Mmu19

source_name: In vitro matured MII oocytes derived from 7-8 wk old B6D2F1 female mice


title: 11006_TAM+_Carcinosarcoma, carcinosarcoma after >=2y prior tamoxifen treatment

status: Public on Jun 17 2010

city: Amsterdam

first: Petra

last: Nederlof

address: Plesmanlaan 121

department: Pathology

country: Netherlands

institute: The Netherlands Cancer Institute

hyb_protocol: hybridization as describe in Joosse SA, van Beers EH, Nederlof PM. Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. BMC Cancer 2007;7:43.

scan_protocol: ImaGene v6.0 software (BioDiscovery Inc) was used to translate the cy5/cy3 intensity ratios into average of the triplicates log2-ratio.

data_processing: average of triplicate Log2 ratios after Lowess pintip normalization

source_name: FFPE primary tumor material TAM+

label_protocol: Sample and reference DNA were labeled with the Cy5- or Cy3-conjugates from the Universal Linkages System (ULS; Kreatech biotechnology, Amsterdam, The Netherlands)

growth_protocol: FFPE tissue primary tumors used

extract_protocol: DNA isolation for arrayCGH was performed as described elsewhere. (20) In short, formalin-fixed paraffin-embedded FFPE tissue of uterine corpus cancer was used. Cases were discarded if the tumor cell percentage was below 70%.  Genomic DNA was isolated from 10*10µm thick paraffin slides. Slides were deparaffinized twice in xylene for 5 minutes, rehydrated in 100% (twice), 90%,70% ethanol and stained with hematoxylin. To remove formalin induced cross-links an overnight incubation in 1M NaSCN at 37°C was performed. Slides were subsequently washed in PBS twice for 10 minutes and air-dried. Tumor cells were collected by macro dissection by scraping from the slides and cells were transferred to a tube containing 200 µl ATL buffer (QIAamp® DNA Mini Kit cat 51304, Qiagen), 27 µl Proteinase-K was added and samples were incubated at 55°C while shaken at 450 rmp for at least 40 hours.  At intervals of 4, 16 and 24 hours additional 27 µl of Proteinase-K was added (Qiagen kit). Further isolation was done following the manufacturers instructions (Qiagen).

tag: gender

value: female

tag: tumor

value: endometrial

tag: histology

value: carcinosarcoma

source_name: genomic DNA from blood from 8 healthy females


title: Blood_statin myopathy_pool_HindIII

status: Public on Jul 09 2010

city: Buffalo

first: Paul

middle: J.

last: Isackson

address: 100 High St

department: Pediatrics

institute: University at Buffalo

description: data derived from two pools of 19 and 20 statin myopathy patients

hyb_protocol: DNA was digested with HindIII or XbaI, ligated, PCR amplified, fragmented, end-labeled and hybridized to the chip according the the manufacturers instructions.

scan_protocol: The arrays were then washed using Affymetrix fluidics station 450 and scanned using the GeneChip Scanner 3000 7G Plus.

data_processing: SNP intensity signals were obtained using CEL files generated by Affymetrix GTYPE using the DM algorithm.  A general linear regression model (Macgregor S, Visscher PM, Montgomery G, Analysis of pooled DNA samples on high density arrays without prior knowledge of differential hybridization rates. Nucleic Acids Res 2006; 34(7):e55) was used to identify differences between pools and calculate a z-score (the p-value of the z-test) for each SNP-pool comparison.  The data table linked to GSE17574 contains the calculated z-score for each SNP comparing case pools to control pools.

source_name: statin-induced myopathy patients

label_protocol: According to manufacturer (Affymetrix).

extract_protocol: Genomic DNA was prepared from whole blood collected in EDTA with a Puregene DNA isolation kit (Gentra Systems).

tag: tissue

value: whole blood


title: 7-8 wk In Vivo, Mmu01


title: 7-8 wk GV, Mmu11


title: 11003_TAM-_Carcinosarcoma, carcinosarcoma without prior tamoxifen treatment

source_name: FFPE primary tumor material TAM-

value: genomic DNA from blood from 8 healthy females


title: Blood_statin myopathy_pool_XbaI


title: 7-8 wk In Vitro, Mmu02


title: Blood_control_pool_HindIII

description: data derived from two pools of 20 statin-tolerant controls

source_name: statin-tolerant controls


title: 197T_TAM+_Carcinosarcoma, carcinosarcoma after >=2y prior tamoxifen treatment


title: Obl-MDA-PC-3-CM

status: Public on Jul 01 2010

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

description: conditioned medium of PC-3 cells

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software GCOS 1.4 (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 300.

source_name: conditioned medium of PC-3 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Osteoblasts were grown in alpha-MEM with 10 % fetal calf serum.  Cells were diffferentiated for 10 days in the presence of ascorbic acid (50 µg/ml) and ß-glycerophosphate (10 mM).

extract_protocol: Trizol extraction followed by Rneasy purification

treatment_protocol: After serum-starvation over night, cells were incubated for 6 hours with condtioned medium of MDA-PCa2b or PC-3 cells.

tag: cell type

value: primary osteoblast

tag: stage

value: day 10 of diffferentiation


title: 200T_TAM-_Carcinosarcoma, carcinosarcoma without prior tamoxifen treatment


title: Obl-MDA-PCa2b-CM

description: conditioned medium of MDA-PCa2b cells

source_name: conditioned medium of MDA-PCa2b cells


title: Blood_control_pool_XbaI


title: d26 In Vivo, Mmu07


title: 124T (V)_TAM+_Carcinosarcoma, carcinosarcoma after >=2y prior tamoxifen treatment

description: 124T (V)_TAM+_Carcinosarcoma


title: 028T (A)_TAM+_Carcinosarcoma, carcinosarcoma after >=2y prior tamoxifen treatment

description: 028T (A)_TAM+_Carcinosarcoma


title: 144T_TAM-_Carcinosarcoma, carcinosarcoma without prior tamoxifen treatment


title: 020T_TAM+_Carcinosarcoma, carcinosarcoma after >=2y prior tamoxifen treatment


title: Q455C8 8054_TAM+_Carcinosarcoma, carcinosarcoma after >=2y prior tamoxifen treatment

description: Q455C8 8054_TAM+_Carcinosarcoma


title: 077T_TAM-_Carcinosarcoma, carcinosarcoma without prior tamoxifen treatment