title: Hypoxic-seedlings, ate1 ate 2, rep 2

city: Riverside

first: Takeshi

last: Fukao

address: Department of Botany and Plant Sciences

institute: University of California, Riverside

description:
ate1 ate2 seedlings treated with hypoxic conditions for 2h
Hypoxia_ate1 ate2_2

hyb_protocol: Hybridization of 12 μg of biotin-labelled cRNA to each Arabidopsis ATH1 Genome Array (GeneChip System®, Affymetrix) chips were performed at 45 °C for 16 h, in the Affymetrix GeneChip Workstation (hybridization oven 640, Fluidics Station 450), using 10 µg of Biotin-labeled aRNA, according to the manufacturer's protocol.

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

data_processing: CEL files from the Affymetrix Chips were processed by use of the R program (http://cran.at.r-project.org/) and Bioconductor packages (http://www.bioconductor.org/). The Robust Multi-chip Average (RMA) normalization was performed using the default settings of the corresponding R function. Present, Marginal or Absent (P/M/A) calls were computed with the affy package.

organism: Arabidopsis thaliana

source_name: Hypoxic-seedlings, ate1 ate 2

label_protocol: Biotin-labelled cRNA was synthesized from 500 ng total RNA with the Affymetrix 3’ IVT Express Labelling kit (Santa Clara, CA).

growth_protocol: Seeds used for this analysis  were after-ripened seeds obtained from plants grown at the same time within the same tray within the same controlled environment chambers to minimize differences in pre-harvest history. For pre-germinated seeds samples, seeds were surface sterilized for 5 min in 5% (v/v) bleach and then washed twice in distilled water. The seeds were then plated on square plates containing 0.5×Murashige and Skoog (MS, Sigma-Aldrich) salt mixture in 1% (w/v) bacto-agar and stratified at 4˚C for 48 h. Plates were incubated vertically at 22°C in 150 μmol m−2 s−1 constant light for 24 h and then whole seeds were sampled for total RNA extraction. For hypoxia-treated seedling samples, seeds were surface sterilized with 95 % (v/v) ethanol for 5 min, followed by 10 min submergence in bleach solution (20 % (v/v) bleach and 0.1 % (v/v) Tween-20), and finally rinsed three times with sterile water. Seeds were stored at 4°C for 3 days, and then plated on solid MS plates (0.43 % (w/v) Murashigi Skoog (MS) salts (Sigma, St. Louis, MO), 0.4 % (w/v) phytage, pH 5.75l (Sigma), 1 % (w/v) sucrose, pH 5.7), and placed at a vertical orientation in a growth chamber (Percival Scientific, Inc., http://www.percival-scientific.com/; model CU36L5C8) under long day conditions (16 h light at ~80 µmol photons m-2 s-1/ 8 h darkness) at 23 °C for 7 days.

extract_protocol: Total RNA was extracted by using QIAGEN RNeasy Plant Mini kit according to the manufacture's protocol. RNase-Free DNase treatment was conducted during the column purification process.

treatment_protocol: Hypoxia treatment commenced at the end of the 16 h light cycle under 6.5 µmol s–1 m–2 light, in open or sealed chambers. For hypoxia, 99.995% argon gas was bubbled through water and into the chamber for 2 h. Control plants were exposed to the same light and temperature conditions but maintained in air. Whole seedlings were frozen under liquid nitrogen within 3 min of release from treatment and stored at -80 oC until use.

value: seedlings

tag: genotype

value: ate1 ate2

value: 7 d old

tag: treatment

value: hypoxic conditions


title: HCI-005 xenograft 1st passage [expression]

status: Public on Oct 23 2011

type: RNA

city: Salt Lake City

first: Alana

last: Welm

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

country: USA

institute: Huntsman Cancer Institute / University of Utah

description: ILC Stage 2B

hyb_protocol: Agilent one-color heterologous gene expression hybridization and wash protocol.

scan_protocol: Microarray slides were scanned on an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.

data_processing:
TIFF images from the scanned microarrays were processed using Agilent Feature Extraction software version 10.5.1.1.
gProcessedSignal values were filtered to remove control features,  non-uniform outliers and feature population outliers. Remaining values were average to yield a single value for each unique probe.
Probe intensities were log transformed (log base 2) and quantile normalized.

molecule: total RNA

organism: Homo sapiens

label_protocol: Agilent one-color quick-amp labeling protocol.

growth_protocol: Flash frozen tumor tissue from human subject or mouse xenograft

extract_protocol: Total RNA isolated using Trizol

tag: tumor type

value: metastatic

tag: er status

tag: pr status

tag: her2 status

tag: Stage

value: ILC Stage 2B

tag: tumor id

tag: sample type

value: xenograft 1st passage

tag: tissue

value: metastatic breast cancer tumor


title: HCI-004 xenograft 2nd passage [expression]

description: IDC Stage 2A

value: primary breast tumor

value: IDC Stage 2A

value: xenograft 2nd passage


title: HCI-003 xenograft 4th passage [expression]

description: IDC Stage 3A

value: IDC Stage 3A

value: xenograft 4th passage


title: HCI-005 original tumor [expression]

description: ILC Stage 2B

source_name: HCI-005 original tumor [expression]

value: original tumor


title: HCI-004 original tumor [expression]

description: IDC Stage 2A

source_name: HCI-004 original tumor [expression]


title: Aerobic-seedlings, prt6-1, rep 2

state: CA

description:
prt6-1 seedlings treated with aerobic (normal) conditions for 2h
Air_prt6_2

label: biotin

source_name: Aerobic-seedlings, prt6-1

tag: age

value: aerobic (normal) conditions


title: HCI-003 xenograft 1st passage [expression]

description: IDC Stage 3A


title: HCI-002 xenograft 1st passage [expression]

description: IDC Stage 3A


title: HCI-002 original tumor [expression]

description: IDC Stage 3A

source_name: HCI-002 original tumor [expression]


title: HCI-001 xenograft 5th passage [expression]

description: IDC Stage 4

value: IDC Stage 4

value: xenograft 5th passage


title: HCI-002 xenograft 5th passage [expression]

description: IDC Stage 3A


title: HCI-003 original tumor [expression]

description: IDC Stage 3A

source_name: HCI-003 original tumor [expression]


title: HCI-007 xenograft 1st passage [copy number]

type: genomic

description: ILC Stage 2B

hyb_protocol: Affymetrix 500K Mapping Hyb/Wash/Stain protocol

scan_protocol: Affymetrix GeneChips were scanned in an Affymetrix 3000 7G microarray scanner

data_processing:
Microarray images were processed using Affymetrix GeneChip Operating Software version 1.4.
Copy number calculated in Partek Genomics Suite software.

molecule: genomic DNA

label_protocol: Affymetrix Mapping 500K StyI labeling protocol

extract_protocol: Genomic DNA extracted with Qiagen DNEasy tissue kit

value: metastatic  breast cancer tumor


title: HCI-008 xenograft 1st passage [copy number]

description: Inflammatory breast cancer Stage 2B

value: Inflammatory breast cancer Stage 2B


title: HCI-005 xenograft 1st passage [copy number]

description: ILC Stage 2B


title: HCI-011 original tumor [copy number]

description: ILC Stage 3C

source_name: HCI-011_original_tumor_[copy number]

value: ILC Stage 3C


title: HCI-001 xenograft 2nd passage [expression]

description: IDS Stage 4

value: IDS Stage 4


title: HCI-012 xenograft 2nd passage [copy number]

description: IDC Stage 99

value: metastatic

value: IDC Stage 99


title: HCI-007 original tumor [copy number]

description: ILC Stage 2B

source_name: HCI-007_original_tumor_[copy number]

value: ILC Stage 2B


title: HCI-010 xenograft 2nd passage [copy number]

description: IDC Stage 2C

value: IDC Stage 2C


title: HCI-009 xenograft 2nd passage [copy number]

description: Poorly differentiated adenocarcinoma Stage 99


title: Leaf-Line4-20mM-10AMday2-rep2

status: Public on Oct 22 2011

city: Saint Louis

first: Jim

last: Morrell

state: Missouri

address: 800 North Lindbergh Blvd

department: Biotechnology

institute: Monsanto Co.

hyb_protocol: Affymetrix GeneChips, custom made for Monsanto Company, were allowed to equilibrate to RT and 1X hybridization buffer (0.10M MES, 0.96M NaCl, 0.02M EDTA and 0.01% Tween) was brought to 45C. Chips were loaded with 1X hybridization buffer and incubated at 45C for 10min with rotation of 60rpm in a Hybridization Oven 640 (Affymetrix). During this time samples were prepared as follows: 20X eukaryotic hybridization controls (Affymetrix) were heated at 65C for 5min. 7.5ug labeled DNA was brought to 100ul with molecular biology grade water and the following were added: 4.0ul of control oligo B2 (Affymetrix), 12ul 20X eukaryotic hybridization controls, 2.4ul 10mg/ml salmon sperm DNA (Invitrogen), 2.4ul 50mg/ml acetylated BSA (Invitrogen) and 120ul 2X hybridization buffer. Samples were then heated at 99C for 5min, followed by 45C for 5min. Samples were centrifuged at 14,000g for 5min at RT to pellet any particulate matter. During this centrifugation, chips were removed from the hybridization oven and drained of the 1X hybridization buffer; replacing it with the hybridization cocktail after centrifugation. Chips were then placed into the hybridization oven and incubated for 16h at 45C with a rotation of 60rpm.

scan_protocol: Hybridized GeneChips were washed, stained and scanned according to the manufacturer’s instructions using the GeneChip Fluidics Station 450 (Affymetrix), an Affymetrix GeneChip Scanner 3000 and the GeneChip Operating Software (GCOS) (Affymetrix).

data_processing: Data from Affymetrix GCOS system were normalized by RMA algorithm in Partek Genomics Suite software and then scaled to 75th percentile of 500 over all chips.

organism: Zea mays

source_name: Line4 grown with 20mM ammonium nitrate sampled at 10am_day2

label_protocol: For labeling, 500ng of purified total RNA was used as input. TargetAmp™ 1-Round Biotin-aRNA Amplification Kit 105 kit from Epicentre (TAB1R80524) was used in amplification and labeling process following the kit protocol. In the end, Biotin-labelind-aRNA probe was generated and QCed by OD reading (yield) and Agilent bioanalyzer (quality).

growth_protocol: The soil used for filling the pots is Hummert’s Metro Mix 200 (~120g/pot), without a starter fertilizer. The nutrients are dispensed in the form of full strength Hoagland nutrient solution containing precise amounts of N added (2mM NH4NO3 for low N screening and 20mM NH4NO3 for high N screening runs). The supplemented low N samples (N02T20) were dispensed a 20mM NH4NO3 solution 2 hours prior to first being sampled. Each pot is manually dispensed 100ml of nutrient solution three times a week on alternate days starting at 10 days after planting. The plants are harvested after 4 weeks for the low N treatment and 3 weeks for the sufficient N treatment.

extract_protocol: Mature leaf tissues are grounded using pestle and mortar with liquid nitrogen. 150mg-250mg grounded tissues were aliquoted to each Lysing Matix E tube (Qbiogen).  RNA extraction was done using modified CTAB (0.5% CTAB, 0.05M Tris-HCl, 0.8M Nacl, 10mM EDTA/PH8.0) method using Qbiogen Fast Prep instrument. 750 ul of CTAB solution and 400ul of Phenol (PH4, from Amersco) were added to ground tissue. Fasta Prep beat was performed for 45 sec at setting 6. Later contents were centrifuged at 10,000g/10min.Supernatant was extracted twice with Phenol:Chloroform:Isoamyl alcohol (24:24:1) mixture. RNA in the upper phase was precipitated with ethanol. Precipitated RNA pellet was suspended in RNase free water (85ul) and treated with 5ul DNase I (2u/ul, Ambion) for 30min at 37C. DNase treated RNA was purified using RNeasy pink column (Qiagen). Quality of the purified RNA was determined by using Beckman DU640 spectrophotometer and Agilent Bio-analyzer 2100. The A260/A280 O.D. ratio of RNA samples measured using Beckman DU640 spectrophotometer was between 1.8 and 2.3. The 28s/18s ratio determined by using Agilent Bioanalyzer was above 0.8.

treatment_protocol: The treatment is the growth condition (see growth protocol).

value: Monsanto Z. mays line 4

tag: developmental stage

value: Leaf tissue from 4 plants

tag: growth nutrient

value: 20mM NH4NO3

tag: nitrogen condition

value: N20:Sufficient Nitrogen

tag: sampletime

value: 10AM day2


title: HCI-011 xenograft 1st passage [copy number]

description: ILC Stage 3C

value: xenograft 1st passage


title: HCI-012 original tumor [copy number]

description: IDC Stage 99

source_name: HCI-012_original_tumor_[copy number]

value: original tumor


title: HCI-004 original tumor [copy number]

description: IDC Stage 2A

source_name: HCI-004_original_tumor_[copy number]

value: primary breast tumor

value: IDC Stage 2A


title: HCI-005 original tumor [copy number]

description: ILC Stage 2B

source_name: HCI-005_original_tumor_[copy number]

value: metastatic  breast cancer tumor


title: HCI-001 original tumor [expression]

description: IDC Stage 4

source_name: HCI-001 original tumor [expression]

value: IDC Stage 4


title: Leaf-Line4-20mM-10AMday2-rep1


title: Leaf-Line4-20mM-10AMday2-rep3


title: Leaf-Line4-20mM-11PMday1-rep2

source_name: Line4 grown with 20mM ammonium nitrate sampled at 11pm_day1

value: 11PM day1


title: HCI-002 xenograft 2nd passage [copy number]

description: IDC Stage 3A

value: IDC Stage 3A

value: xenograft 2nd passage


title: Leaf-Line4-20mM-11PMday1-rep3


title: HCI-010 original tumor [copy number]

description: IDC Stage 2C

source_name: HCI-010_original_tumor_[copy number]

value: metastatic


title: HCI-004 xenograft 2nd passage [copy number]

description: IDC Stage 2A


title: HCI-009 original tumor [copy number]

source_name: HCI-009_original_tumor_[copy number]

value: Poorly differentiated adenocarcinoma Stage 99


title: HCI-008 original tumor [copy number]

description: Inflammatory breast cancer Stage 2B

source_name: HCI-008_original_tumor_[copy number]

value: Inflammatory breast cancer Stage 2B


title: HCI-001 xenograft 5th passage [copy number]

description: IDC Stage 4

value: xenograft 5th passage


title: Leaf-Line4-20mM-10AMday1-rep2

source_name: Line4 grown with 20mM ammonium nitrate sampled at 10am_day1

value: Monsanto Z. mays line 4

value: Leaf tissue from 4 plants

value: 10AM day1


title: HCI-003 xenograft 1st passage [copy number]

description: IDC Stage 3A


title: Leaf-Line4-20mM-11PMday1-rep1

value: 20mM NH4NO3

value: N20:Sufficient Nitrogen


title: Leaf-Line4-20mM-10AMday1-rep1


title: HCI-002 original tumor [copy number]

description: IDC Stage 3A

source_name: HCI-002_original_tumor_[copy number]

value: original tumor


title: Leaf-Line4-2mMthen20mM-10AMday2-rep3

source_name: Line4 grown with 2mM and then 20mM ammonium nitrate sampled at 10am_day2

value: 2mM and then 20mM NH4NO3

value: N02T20:Limiting Nitrogen Supplemented

value: 10AM day2


title: HCI-003 original tumor [copy number]

description: IDC Stage 3A

source_name: HCI-003_original_tumor_[copy number]

value: primary breast tumor


title: Leaf-Line4-2mMthen20mM-10AMday2-rep1


title: HCI-002 xenograft 5th passage [copy number]

description: IDC Stage 3A


title: Leaf-Line4-2mMthen20mM-10AMday2-rep2


title: Leaf-Line4-20mM-10AMday1-rep3


title: Leaf-Line4-2mM-10AMday2-rep2

source_name: Line4 grown with 2mM ammonium nitrate sampled at 10am_day2

value: 2mM NH4NO3

value: N02 :limited nitrogen


title: Leaf-Line4-2mMthen20mM-11PMday1-rep1

source_name: Line4 grown with 2mM and then 20mM ammonium nitrate sampled at 11pm_day1

value: 11PM day1


title: HCI-001 xenograft 2nd passage [copy number]

description: IDS Stage 4

value: IDS Stage 4

value: xenograft 2nd passage


title: Leaf-Line4-2mMthen20mM-10AMday1-rep1

source_name: Line4 grown with 2mM and then 20mM ammonium nitrate sampled at 10am_day1


title: Leaf-Line4-2mM-10AMday2-rep3


title: Leaf-Line4-2mMthen20mM-11PMday1-rep2


title: Leaf-Line4-2mMthen20mM-11PMday1-rep3


title: Leaf-Line4-2mM-11PMday1-rep3

source_name: Line4 grown with 2mM ammonium nitrate sampled at 11pm_day1


title: Leaf-Line4-2mMthen20mM-10AMday1-rep2


title: Leaf-Line4-2mMthen20mM-10AMday1-rep3


title: Leaf-Line4-2mM-10AMday1-rep1

source_name: Line4 grown with 2mM ammonium nitrate sampled at 10am_day1


title: Leaf-Line4-2mM-10AMday1-rep3


title: Leaf-Line4-2mM-10AMday1-rep2


title: Leaf-Line4-2mM-10AMday2-rep1


title: Leaf-Line4-2mM-11PMday1-rep2


title: Leaf-Line3-20mM-11PMday1-rep2

source_name: Line3 grown with 20mM ammonium nitrate sampled at 11pm_day1

value: Monsanto Z. mays line 3


title: Leaf-Line3-20mM-11PMday1-rep1


title: HCI-001 original tumor [copy number]

description: IDC Stage 4

source_name: HCI-001_original_tumor_[copy number]

value: IDC Stage 4


title: Leaf-Line3-20mM-11PMday1-rep3


title: Leaf-Line3-20mM-10AMday1-rep2

source_name: Line3 grown with 20mM ammonium nitrate sampled at 10am_day1


title: Leaf-Line3-20mM-10AMday1-rep3


title: Leaf-Line3-20mM-10AMday1-rep1


title: Leaf-Line4-2mM-11PMday1-rep1

value: Monsanto Z. mays line 4


title: Leaf-Line3-2mMthen20mM-10AMday2-rep2

source_name: Line3 grown with 2mM and then 20mM ammonium nitrate sampled at 10am_day2

value: Leaf tissue from 4 plants


title: Leaf-Line3-2mMthen20mM-11PMday1-rep2

source_name: Line3 grown with 2mM and then 20mM ammonium nitrate sampled at 11pm_day1


title: Leaf-Line3-2mMthen20mM-10AMday2-rep1


title: Leaf-Line3-2mMthen20mM-10AMday2-rep3


title: primary human hepatocytes 4420061183_F

city: Basel

first: Guido

last: Steiner

address: Grenzacher Strasse

department: TRS/BEDA - Biostatistics

country: Switzerland

institute: Hoffmann La-Roche

hyb_protocol: After statistical randomization of sample order, labeled cRNA (1.5 µg/sample) was used  for array hybridization using the Whole-Genome Gene Expression Direct Hybridization Assay and Illumina Human-6  Expression BeadChips version 3 arrays (Illumina Inc., San Diego, CA, USA). Staining and washing steps were  performed as suggested by the manufacturer.

scan_protocol: BeadChips were scanned using an Illumina BeadArray® reader  (Illumina Inc.).

data_processing: Raw data were extracted using BeadStudio© software (version 3.1.3.0) with  Gene Expression Module 3.4.0 (Illumina Inc.).  For the non-normalized matrix, no signal preprocessing (like background subtraction or normalization) has  been performed, and values are on the natural (linear) scale.  Two types of files are given, as exported directly from the Illumina BeadStudio software:    -  *_Sample_Probe_Profile.txt containing actual expression values (AGV_Signal columns) and     5 additional parameters for each hybridization.    - *_ Sample_Table.txt containing quality parameters for each hybridization, as calculated by    the Illumina Beadstudio software    For the normalized matrix, data was quantile normalized and put on a log2 scale, without removal of background  signal.

source_name: primary human hepatocytes

label_protocol: Total RNA (1 µg/sample) was converted to complementary (c) DNA using the low-RNA input fluorescent linear  amplification kit (Agilent Technologies). cDNA was converted to cRNA and biotinylated using biotin-LC  vinyl CTP. Amplified and biotinylated cRNA was quantified and quality checked by formaldehyde agarose gel  electrophoresis.

growth_protocol: Primary human hepatocytes (Hepacult GmbH, Regensburg, Germany) were seeded at a density of  0.15 x 106/cm2 in six-well plates.

extract_protocol: Total RNA was extracted with TRI Reagent® (Molecular Research Center, Inc., Cincinnati, OH, USA) according  to the manufacturer’s instructions and RNA samples were stored at –80°C. Total RNA was quantified on a  NanoDrop™ spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and RNA integrity was determined  on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: They were then incubated for 6 hours at 37°C in a 5%  carbon-dioxide-humidified atmosphere in 1.5 ml of William’s Medium E + 2 mM L-glutamine  (Sigma-Aldrich Corp., St Louis, MO, USA) containing aleglitazar (0.013, 0.064 or 0.32 µM),  tesaglitazar (1.44, 7.2 or 36.0 µM), Pio/Feno (6.0/0.11, 30.0/0.56 or 150.0/2.8 µM) or vehicle  (0.1% dimethyl sulfoxide). The concentrations were chosen based on in vitro transactivation data  providing EC50-aligned, low, medium and high concentrations of each of the three treatments, such  that there was similar receptor activation across treatments at each concentration level.

tag: condition

value: Tesaglitazar

value: uM

tag: species

value: Human

tag: Sex

value: Female

value: Hepatocytes

value: Illumina TotalPrep RNA Amplification

tag: ivt_total [ug/ml]

tag: rna_total [ug/ml]

tag: doselevel

tag: chiptype

tag: chipexpirationdate

tag: hybdate

tag: scandate


title: primary human hepatocytes 4420061183_E

value: DMSO

value: percent


title: Leaf-Line3-2mMthen20mM-10AMday1-rep2

source_name: Line3 grown with 2mM and then 20mM ammonium nitrate sampled at 10am_day1

tag: genotype

value: 2mM and then 20mM NH4NO3

value: N02T20:Limiting Nitrogen Supplemented

value: 10AM day1


title: primary human hepatocytes 4420061183_A


title: Leaf-Line3-2mMthen20mM-11PMday1-rep1

tag: tissue

value: 11PM day1


title: Leaf-Line3-2mMthen20mM-11PMday1-rep3


title: Leaf-Line3-2mMthen20mM-10AMday1-rep3


title: Leaf-Line3-2mM-11PMday1-rep2

source_name: Line3 grown with 2mM ammonium nitrate sampled at 11pm_day1

value: 2mM NH4NO3

value: N02 :limited nitrogen


title: primary human hepatocytes 4420061183_B

value: pioglitazone

value: Fenofibrate


title: primary human hepatocytes 4420061183_D


title: primary human hepatocytes 4420061097_E

value: Aleglitazar


title: Leaf-Line3-2mM-11PMday1-rep3

value: Monsanto Z. mays line 3

value: Leaf tissue from 4 plants


title: Leaf-Line3-2mMthen20mM-10AMday1-rep1


title: primary human hepatocytes 4420061183_C

value: uM

value: Human


title: Leaf-Line3-2mM-10AMday1-rep1

source_name: Line3 grown with 2mM ammonium nitrate sampled at 10am_day1


title: Leaf-Line3-2mM-11PMday1-rep1


title: Leaf-Line3-2mM-10AMday1-rep3


title: primary human hepatocytes 4420061097_F

value: Female

value: Hepatocytes


title: primary human hepatocytes 4420061097_C

value: Tesaglitazar

value: Illumina TotalPrep RNA Amplification


title: Leaf-Line3-2mM-10AMday1-rep2


title: primary human hepatocytes 4420061097_D


title: primary human hepatocytes 4420061052_E


title: Leaf-Line2-20mM-11PMday1-rep2

source_name: Line2 grown with 20mM ammonium nitrate sampled at 11pm_day1

value: Monsanto Z. mays line 2

value: 20mM NH4NO3

value: N20:Sufficient Nitrogen


title: primary human hepatocytes 4420061097_B


title: Leaf-Line2-20mM-10AMday1-rep3

source_name: Line2 grown with 20mM ammonium nitrate sampled at 10am_day1

value: 10AM day1


title: Leaf-Line2-20mM-11PMday1-rep1

value: 11PM day1


title: Leaf-Line2-20mM-10AMday1-rep2


title: Leaf-Line2-20mM-11PMday1-rep3


title: Leaf-Line2-2mMthen20mM-10AMday2-rep3

source_name: Line2 grown with 2mM and then 20mM ammonium nitrate sampled at 10am_day2

value: 2mM and then 20mM NH4NO3

value: N02T20:Limiting Nitrogen Supplemented

value: 10AM day2


title: primary human hepatocytes 4420061097_A

value: DMSO

value: percent


title: primary human hepatocytes 4420061052_D


title: primary human hepatocytes 4420061052_A

value: Aleglitazar


title: Leaf-Line2-2mMthen20mM-10AMday2-rep1

value: Leaf tissue from 4 plants


title: primary human hepatocytes 4420061052_F

value: uM

value: Human


title: Leaf-Line2-2mMthen20mM-10AMday2-rep2


title: Leaf-Line2-2mMthen20mM-11PMday1-rep3

source_name: Line2 grown with 2mM and then 20mM ammonium nitrate sampled at 11pm_day1


title: primary human hepatocytes 4420061052_C

value: pioglitazone

value: Fenofibrate

value: Female

value: Hepatocytes


title: Leaf-Line2-20mM-10AMday1-rep1

value: Monsanto Z. mays line 2

value: 20mM NH4NO3


title: Leaf-Line2-2mMthen20mM-11PMday1-rep1


title: primary human hepatocytes 4420061052_B

value: Tesaglitazar

value: Illumina TotalPrep RNA Amplification


title: primary human hepatocytes 4420061041_F


title: Leaf-Line2-2mMthen20mM-11PMday1-rep2

value: 2mM and then 20mM NH4NO3

value: 11PM day1


title: primary human hepatocytes 4420061041_C


title: primary human hepatocytes 4420061041_E


title: Leaf-Line2-2mMthen20mM-10AMday1-rep2

source_name: Line2 grown with 2mM and then 20mM ammonium nitrate sampled at 10am_day1

value: N02T20:Limiting Nitrogen Supplemented

value: 10AM day1


title: Leaf-Line2-2mMthen20mM-10AMday1-rep3


title: Leaf-Line2-2mMthen20mM-10AMday1-rep1


title: primary human hepatocytes 4420061041_D


title: primary human hepatocytes 4420061041_B


title: primary human hepatocytes 4420061040_E

value: DMSO

value: percent


title: primary human hepatocytes 4420061040_F


title: primary human hepatocytes 4420061041_A

value: Aleglitazar


title: primary human hepatocytes 4420061040_D

value: uM


title: Leaf-Line2-2mM-11PMday1-rep1

source_name: Line2 grown with 2mM ammonium nitrate sampled at 11pm_day1

value: Leaf tissue from 4 plants

value: 2mM NH4NO3

value: N02 :limited nitrogen


title: Leaf-Line2-2mM-11PMday1-rep2


title: primary human hepatocytes 4420061040_B

value: Human

value: Female


title: primary human hepatocytes 4420061040_C

value: Hepatocytes


title: Leaf-Line2-2mM-11PMday1-rep3

value: Monsanto Z. mays line 2


title: Leaf-Line2-2mM-10AMday1-rep3

source_name: Line2 grown with 2mM ammonium nitrate sampled at 10am_day1


title: primary human hepatocytes 4420061040_A

value: pioglitazone

value: Fenofibrate


title: Leaf-Line1-20mM-11PMday1-rep3

source_name: Line1 grown with 20mM ammonium nitrate sampled at 11pm_day1

value: Monsanto Z. mays line 1

value: 20mM NH4NO3

value: N20:Sufficient Nitrogen


title: Leaf-Line1-20mM-11PMday1-rep1

value: 11PM day1


title: Leaf-Line1-20mM-10AMday1-rep2

source_name: Line1 grown with 20mM ammonium nitrate sampled at 10am_day1

value: 10AM day1


title: primary human hepatocytes 4420061038_B

value: Illumina TotalPrep RNA Amplification


title: primary human hepatocytes 4420061038_F


title: Leaf-Line2-2mM-10AMday1-rep1


title: primary human hepatocytes 4420061034_E


title: primary human hepatocytes 4420061038_D

value: Tesaglitazar


title: primary human hepatocytes 4420061038_C

value: DMSO

value: percent


title: primary human hepatocytes 4420061034_F

value: uM


title: Leaf-Line1-20mM-10AMday1-rep3

value: Leaf tissue from 4 plants


title: Leaf-Line2-2mM-10AMday1-rep2

value: 2mM NH4NO3

value: N02 :limited nitrogen


title: primary human hepatocytes 4420061038_A

value: Aleglitazar

value: Human

value: Female

value: Hepatocytes


title: primary human hepatocytes 4420061034_C

value: pioglitazone

value: Fenofibrate


title: primary human hepatocytes 4420061038_E


title: primary human hepatocytes 4420061034_D


title: Leaf-Line1-20mM-11PMday1-rep2

value: Monsanto Z. mays line 1

value: 20mM NH4NO3

value: N20:Sufficient Nitrogen


title: Leaf-Line1-2mMthen20mM-10AMday2-rep1

source_name: Line1 grown with 2mM and then 20mM ammonium nitrate sampled at 10am_day2

value: 2mM and then 20mM NH4NO3

value: N02T20:Limiting Nitrogen Supplemented

value: 10AM day2


title: Leaf-Line1-2mMthen20mM-10AMday2-rep2


title: primary human hepatocytes 4420061034_B

value: Illumina TotalPrep RNA Amplification


title: Leaf-Line1-2mMthen20mM-10AMday2-rep3


title: Leaf-Line1-2mMthen20mM-11PMday1-rep3

source_name: Line1 grown with 2mM and then 20mM ammonium nitrate sampled at 11pm_day1

value: 11PM day1


title: Leaf-Line1-20mM-10AMday1-rep1

value: Leaf tissue from 4 plants

value: 10AM day1


title: Leaf-Line1-2mMthen20mM-11PMday1-rep1


title: Leaf-Line1-2mMthen20mM-11PMday1-rep2


title: primary human hepatocytes 4420061001_F

value: uM


title: primary human hepatocytes 4420061034_A

value: DMSO

value: percent


title: primary human hepatocytes 4420061001_C

value: Human

value: Female


title: primary human hepatocytes 4420061001_D

value: Aleglitazar

value: Hepatocytes


title: primary human hepatocytes 4420061001_A

value: Tesaglitazar


title: primary human hepatocytes 4313143135_F


title: Leaf-Line1-2mMthen20mM-10AMday1-rep3

source_name: Line1 grown with 2mM and then 20mM ammonium nitrate sampled at 10am_day1

value: Monsanto Z. mays line 1


title: Leaf-Line1-2mM-11PMday1-rep3

source_name: Line1 grown with 2mM ammonium nitrate sampled at 11pm_day1

value: 2mM NH4NO3

value: N02 :limited nitrogen


title: Leaf-Line1-2mMthen20mM-10AMday1-rep1

value: 2mM and then 20mM NH4NO3

value: N02T20:Limiting Nitrogen Supplemented


title: Leaf-Line1-2mM-11PMday1-rep1


title: Leaf-Line1-2mMthen20mM-10AMday1-rep2


title: Leaf-Line1-2mM-11PMday1-rep2


title: primary human hepatocytes 4420061001_E

source_name: primary human hepatocytes

value: Illumina TotalPrep RNA Amplification


title: intermediate_mature_bone_marrowMCs_and_MMs_AO.B2

city: Copenhagen

first: Corinna

middle: Cavan

last: Pedersen

address: Juliane Mariesvej 20, 9322

country: Denmark

institute: Rigshospitalet

description:
US22502610_13638666_S01_Cropped_001.gpr
numbers = person; letters = cell population
Biological replicate 3b

hyb_protocol: Slides were placed in the hybridization chambers and primed by injecting hybridization buffer into each chamber. Finally, the target preparations were injected and incubated for 16 hours at 60ºC with medium agitation. After hybridization, slides were washed, soaked in wash buffers, and dried as recommended by the manufacturer (Exiqon). Slides were removed from the hybridization station and kept in the dark in a nitrogen sphere until scanning.

scan_protocol: Slides were scanned in an Agilent DNA microarray scanner (G2565BA). Image analysis was performed using the Genepix® Pro Software (version 6.1.2; Molecular Devices, Philadelphia, USA). A gene array list(GAL) file (www.exiqon.com. GAL file: 208000V8.1_208001V8.1_208002V8.1_lot_number_20278-20399_hsap.gal.  2-11-2007) with miRNA annotations according to miRBase (version 10) was applied to annotate features and generate a Genepix Results (GPR) File for each image, with median  foreground and mean background values for each spot.

data_processing: GPR files were loaded into the R (version 2.0.1) software environment (Gentleman R, Isaka R: R: A Language for Data Analysis and Graphics. Journal of Computational and Graphical Statistics 1996, 5: 299-314) using the Limma software package (Smyth, G. K. (2005). Limma: linear models for microarray data. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor, R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds.), Springer, New York, pages 397–420). Normalization of fluorescence signals between all samples was performed in R (version 2.0.1) using qspline (Workman C, Jensen LJ, Jarmer H, Berka R, Gautier L, Nielser HB et al.: A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol 2002, 3(9):research0048) prior to all statistical analysis.

source_name: Bone marrow neutrophil precursors

label_protocol: Total RNA extracted from BM and PB cell populations was labeled with the miRCURYTM Array Labeling kit (Exiqon, Vedbæk, Denmark) and hybridized to miRCURYTM LNA microRNA Arrays (Exiqon) in a Tecan HS400 hybridization station (Tecan Nordic AB, Brøndby, Denmark). Labeling with the fluorescent dyes Hy3 and Hy5 and preparation of wash buffers were done according to the manufacturer’s instructions (Exiqon)

extract_protocol: All cell populations were isolated on a PercollTM density gradient followed by immunomagnetic depletion as described in Bjerregaard MD, Jurlander J, Klausen P, Borregaard N, Cowland JB: The in vivo profile of transcription factors during neutrophil differentiation in human bone marrow. Blood 2003, 101: 4322-4332.

tag: maturation stage

value: myelocytes and metamyelocytes


title: Peripheral_blood_PMNs_SKP.PMN

description:
US22502610_13638669_S01_Cropped_001.gpr
numbers = person; letters = cell population
Biological replicate 1d

source_name: Peripheral blood neutrophils

value: neutrophil granulocytes


title: Peripheral_blood_PMNs_AO.PMN

description:
US22502610_13639013_S01_Cropped_001.gpr
numbers = person; letters = cell population
Biological replicate 3d


title: mature_bone_marrow_BCs_and_SCs_AO.B1

description:
US22502610_13639011_S01_Cropped_001.gpr
numbers = person; letters = cell population
Biological replicate 3c

value: band cells and segmented neutrophil cells


title: immature_bone_marrow_MBs_and_PMs_SKP.B3

description:
US22502610_13639013_S01_Cropped_001.gpr
numbers = person; letters = cell population
Biological replicate 1a

value: myeloblasts and promyelocytes


title: intermediate_mature_bone_marrowMCs_and_MMs_AJ.B2

description:
US22502610_13639010_S01_Cropped_001.gpr
numbers = person; letters = cell population
Biological replicate 2b


title: primary human hepatocytes 4313143135_D

value: uM


title: Leaf-Line1-2mM-10AMday1-rep3

source_name: Line1 grown with 2mM ammonium nitrate sampled at 10am_day1

tag: developmental stage

value: Leaf tissue from 4 plants

value: 10AM day1


title: primary human hepatocytes 4313143135_C

value: Human

value: Female


title: Peripheral_blood_PMNs_JO.PMN

description:
US22502610_13639009_S01_Cropped_001.gpr
numbers = person; letters = cell population
Biological replicate 4d


title: mature_bone_marrow_BCs_and_SCs_AJ.B1

description:
US22502610_13639007_S01_Cropped_001.gpr
numbers = person; letters = cell population
Biological replicate 2c


title: immature_bone_marrow_MBs_and_PMs_JO.B3

description:
US22502610_13639002_S01_Cropped_001.gpr
numbers = person; letters = cell population
Biological replicate 4a


title: primary human hepatocytes 4420061001_B

value: DMSO

value: percent

value: Hepatocytes


title: primary human hepatocytes 4313143135_E

value: Aleglitazar


title: intermediate_mature_bone_marrowMCs_and_MMs_SKP.B2

description:
US22502610_13639011_S01_Cropped_001.gpr
numbers = person; letters = cell population
Biological replicate 1b


title: immature_bone_marrow_MBs_and_PMs_AJ.B3

description:
US22502610_13639009_S01_Cropped_001.gpr
numbers = person; letters = cell population
Biological replicate 2a


title: Leaf-Line1-2mM-10AMday1-rep2

value: Monsanto Z. mays line 1

tag: growth nutrient

value: 2mM NH4NO3

value: N02 :limited nitrogen


title: Peripheral_blood_PMNs_AJ.PMN

description:
US22502610_13639002_S01_Cropped_001.gpr
numbers = person; letters = cell population
Biological replicate 2d


title: Leaf-Line1-2mM-10AMday1-rep1

tag: nitrogen condition


title: intermediate_mature_bone_marrowMCs_and_MMs_JO.B2

description:
US22502610_13639007_S01_Cropped_001.gpr
numbers = person; letters = cell population
Biological replicate 4b


title: Cortex_control_12-week,biological rep1

city: Shanghai

first: Chunxia

last: Li

state: Choose a State

address: 3663 Zhongshan Road

department: Key Laboratory of Brain Functional Genomics, Ministry of Education

country: China

institute: East China Normal University

description: Gene expression data from long-term control rats

hyb_protocol: Samples were hybridized using  GeneChip® WT Hybridization, Wash and Stain Kit following the manufacturer’s instructions

scan_protocol: Slides were scanned by GeneChip® Scanner 3000  and Command Console Software  with default settings.

data_processing: The primary data were generated by Expression Console. Raw data were normalized by RMA algorithm, Gene Spring Software (Agilent technologies, Santa Clara, CA, US). The values were log2 transformed.

organism: Rattus norvegicus

source_name: cortex, control, 12-week

label_protocol: Samples were enzymatically fragmented and biotinylated using the GeneChip® WT Terminal Labeling Kit following the manufacturer’s instructions

growth_protocol: The rats (n=6 per group) were decapitated rapidly and the cortices and hippocampi were dissected. The left and right hippocampus and cortices from each rat were taken apart, and stored at -70C before use.

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit  following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100

treatment_protocol: Half of the hippocampi and cortices from each rat were used for RNA extraction. The hippocampus and cortex of every three rats from one group were pooled together, respectively.

value: cortex

tag: treatment

value: control

tag: time point

tag: strain

value: Sprague-Dawley

tag: age

tag: gender

value: male


title: muscle_leucine_rep1

city: Calgary

first: Lindsay

middle: K

last: Eller

state: AB

address: 2500 University Dr. NW

department: Faculty of Kinesiology

country: Canada

institute: University of Calgary

hyb_protocol: As per Affymetrix protocol (Whole Transcript Sense Target Labeling Assay Manual for Rat Gene 1.0 ST Array available at www.affymetrix.com)

scan_protocol: The chip scanned as per Affymetrix protocol using an Affymetrix Fluidics 450 scan station.

data_processing: The data was analyzed using Affymetrix Expression Console (algorithm-name: rma-gene-default, algorithm-version: 1.0, algorithm-param-quantification-name:med-polish).

source_name: gastrocnemius from leucine fed rats

growth_protocol: 12 week old rats were provided one of 3 ad libitium diets for 8 weeks.  Diets were prepared with 10% (by kcal) of either casein, leucine, or dairy protein.

extract_protocol: Total RNA was extracted from liver using Trizol Reagent (Invitrogen, Carlsbad, CA) and purified using the Qiagen RNeasy Miniprep (Qiagen, Mississauga, ON, Canada).  RNA was quantified using Ribogreen and RT performed using the Omniscript RT Kit as per manufacturers directions (Qiagen, Mississauga, ON, Canada).

treatment_protocol: Rats were over-anaesthetized with isoflurane and killed via aortic cut.  Muscle was excised and submerged in liquid nitrogen immediately.  Liver was stored at -80˚C until analysis.

value: gastrocnemius muscle

tag: diet

value: leucine

value: 20 weeks


title: mature_bone_marrow_BCs_and_SCs_JO.B1

description:
US22502610_13639010_S01_Cropped_001.gpr
numbers = person; letters = cell population
Biological replicate 4c

value: band cells and segmented neutrophil cells


title: muscle_dairy_rep2

source_name: gastrocnemius from dairy fed rats

label_protocol: As per Affymetrix protocol (Whole Transcript Sense Target Labeling Assay Manual for Rat Gene 1.0 ST Array available at www.affymetrix.com)

value: dairy


title: Cortex_control_12-week,biological rep2


title: muscle_dairy_rep1


title: muscle_casein_rep1

source_name: gastrocnemius from casein fed rats

value: casein


title: Cortex_curcumin-treated_12-week,biological rep2

description: Gene expression data from rats after long-term curcumin treatment.

source_name: cortex, curcumin-treated, 12-week

value: curcumin


title: Hippocampus_control_12-week,biological rep2

source_name: hippocampus, control, 12-week

value: hippocampus


title: Hippocampus_curcumin-treated_12-week,biological rep2

source_name: hippocampus, curcumin-treated, 12-week


title: muscle_casein_rep2


title: Cortex_control_6-week,biological rep2

description: Gene expression data from short-term control rats

source_name: cortex, control, 6-week


title: muscle_leucine_rep2


title: mature_bone_marrow_BCs_and_SCs_SKP.B1

description:
US22502610_13638666_S01_Cropped_001.gpr
numbers = person; letters = cell population
Biological replicate 1c


title: immature_bone_marrow_MBs_and_PMs_AO.B3

description:
US22502610_13638669_S01_Cropped_001.gpr
numbers = person; letters = cell population
Biological replicate 3a

value: myeloblasts and promyelocytes


title: Hippocampus_curcumin-treated_12-week,biological rep1


title: CPT-11 and PHY-906 Treated Spleen - repeat 10 - mAdbID:105133

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 105133

hyb_protocol: Hybridization Protocol Other: Hybridization was carried out overnight at 42°C.

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.15;; 3.48 Temperature: 30.08 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).

data_processing:
BRBArray Tools Data Processing
Calculation Method: Raw data were background subtracted. The complete experimental data set including 111 samples from mouse tumor, liver and spleen was filtered retaining transcripts with at least 20% spot presence with spot size requirement >20 uM, and intensity in at least one channel > 200 and increasing to 200 the intensity of the lower channel. Intensity ratios above 64 were truncated. Data were normalized using median normalization for each gene.

organism: Mus musculus

source_name: Mixed Normal Mouse Tissues

label_protocol:
Cy5 Labeling Protocol
Other: RNA were labeled with Cy5 using ULS aRNA Fluorescent Labeling kit (Kreatech, Netherlands).

extract_protocol:
TRIzol Extraction Protocol
Other: Total RNA was extracted from tissues using TRIzol® (Invitrogen).

value: female

tag: other

value: Sample Pooling Protocol:Mouse reference RNA was prepared by homogenization and pooling of selected mouse tissues (lung, heart, muscle, kidneys, liver and spleen) from 3 female C57Bl/6 mice.

source_name: CPT-11 and PHY-906 Treated Spleen

label_protocol:
Cy3 Labeling Protocol
Other: RNA were labeled with Cy3 using ULS aRNA Fluorescent Labeling kit (Kreatech, Netherlands).

treatment_protocol:
Treatment type: compound
Agent: Irinotecan (CPT-11, Camptosar(TM)), PHY-906
Treatment dose: 360mg/kg (CPT-11), 500mg/kg (PHY-906)
Treatment time: 72 hours
In-vivo treatment: Murine Colon 38 cells were transplanted subcutaneously into four- to six-week-old female BDF-1 mice (Charles River Laboratories, Wilmington, MA). After 10 to 14 days, mice with tumor sizes of 150-300mm(3) were selected. On Day 0, ten mice were treated with CPT-11 and PHY-906 (n=10). PHY906 was given 30 minutes prior to CPT-11 administration. PHY906 was given orally for 72 hours (500mg/kg twice a day). CPT-11 (360mg/kg) was administered intra-peritoneally. Mice were terminated by cervical dislocation 72 hours after initiation of drug treatment. Tumor tissue was removed and divided and either frozen for total RNA isolation or placed in 10% neutral buffered formalin for histological analysis.

value: 4-6 weeks

value: Spleen

tag: disease state

value: subcutaneous murine colon 38 implanted tumor


title: Hippocampus_control_6-week,biological rep2

source_name: hippocampus, control, 6-week

value: control


title: Cortex_curcumin-treated_6-week,biological rep2

description: Gene expression data from rats after short-term curcumin treatment.

source_name: cortex, curcumin-treated, 6-week

value: cortex

value: Sprague-Dawley


title: Cortex_curcumin-treated_12-week,biological rep1

value: male


title: Hippocampus_control_12-week,biological rep1


title: primary human hepatocytes 4313143135_A

tag: condition

value: pioglitazone

value: Fenofibrate

value: uM

tag: species

value: Human

tag: Sex

value: Female

value: Hepatocytes

value: Illumina TotalPrep RNA Amplification

tag: ivt_total [ug/ml]

tag: rna_total [ug/ml]

tag: doselevel

tag: chiptype

tag: chipexpirationdate


title: CPT-11 and PHY-906 Treated Spleen - repeat 8 - mAdbID:105131

description: mAdb experiment ID: 105131

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.16;; 3.44 Temperature: 30.78 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).

tag: tissue

value: lung, heart, muscle, kidneys, liver and spleen


title: Cortex_control_6-week,biological rep1

tag: treatment


title: CPT-11 and PHY-906 Treated Spleen - repeat 9 - mAdbID:105132

description: mAdb experiment ID: 105132

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.1;; 3.75 Temperature: 26.57 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).

value: female


title: Cortex_curcumin-treated_6-week,biological rep1

value: curcumin

tag: time point


title: primary human hepatocytes 4313143135_B

value: Aleglitazar

tag: hybdate

tag: scandate


title: CPT-11 and PHY-906 Treated Spleen - repeat 6 - mAdbID:105129

description: mAdb experiment ID: 105129

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.16;; 3.44 Temperature: 30.6 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).

tag: strain

tag: gender

value: Sample Pooling Protocol:Mouse reference RNA was prepared by homogenization and pooling of selected mouse tissues (lung, heart, muscle, kidneys, liver and spleen) from 3 female C57Bl/6 mice.

tag: age

value: 4-6 weeks

value: Spleen


title: Hippocampus_curcumin-treated_6-week,biological rep1

source_name: hippocampus, curcumin-treated, 6-week

value: hippocampus


title: CPT-11 and PHY-906 Treated Spleen - repeat 7 - mAdbID:105130

description: mAdb experiment ID: 105130

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.14;; 3.44 Temperature: 31.21 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).

tag: other

tag: disease state

value: subcutaneous murine colon 38 implanted tumor


title: Wildtype grown on 2g/L glycerol, biological replicate 4

city: Richmond

first: Stephen

last: Fong

state: VA

address: 601 W. Main Street

institute: VCU

description: Gene expression data from wildtype strain on glycerol

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized per manufacturer protocols to Affymetrix E. coli Antisense Genome Arrays

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

data_processing: The data were analyzed with RMA using quartile normalization.  The output file is in logarithmic scale.

organism: Escherichia coli

source_name: wildtype strain on glycerol

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

growth_protocol: Overnight precultures were inoculated into fresh medium.  Cells were harvested during mid-exponential growth phase (A600 ~ 0.5) for RNA extraction.

extract_protocol: RNAprotect was added prior to RNA extraction using Qiagen RNeasy kits following the manufacturer protocol

treatment_protocol: Ecoli was evolved on either lactate supplemented minimal medium or glycerol supplemented minimal medium for 60 days or 44 days, respectively.

value: unevolved


title: Wildtype grown on 2g/L glycerol, biological replicate 5


title: CPT-11 and PHY-906 Treated Liver - repeat 7 - mAdbID:105122

description: mAdb experiment ID: 105122

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.14;; 3.48 Temperature: 31.42 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).

source_name: CPT-11 and PHY-906 Treated Liver

value: Liver


title: CPT-11 and PHY-906 Treated Liver - repeat 8 - mAdbID:105123

description: mAdb experiment ID: 105123

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.14;; 3.48 Temperature: 31.36 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 and PHY-906 Treated Spleen - repeat 4 - mAdbID:105127

description: mAdb experiment ID: 105127

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.16;; 3.45 Temperature: 30.39 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Hippocampus_curcumin-treated_6-week,biological rep2

value: Sprague-Dawley

value: male


title: CPT-11 and PHY-906 Treated Liver - repeat 1 - mAdbID:105116

description: mAdb experiment ID: 105116

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.12;; 3.62 Temperature: 29.65 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 and PHY-906 Treated Spleen - repeat 1 - mAdbID:105124

description: mAdb experiment ID: 105124

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.14;; 3.57 Temperature: 29.35 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 and PHY-906 Treated Spleen - repeat 2 - mAdbID:105125

description: mAdb experiment ID: 105125

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.14;; 3.55 Temperature: 29.59 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Hippocampus_control_6-week,biological rep1

value: control


title: CPT-11 and PHY-906 Treated Liver - repeat 4 - mAdbID:105119

description: mAdb experiment ID: 105119

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.13;; 3.5 Temperature: 30.69 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 and PHY-906 Treated Liver - repeat 3 - mAdbID:105118

description: mAdb experiment ID: 105118

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.15;; 3.49 Temperature: 31.3 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 and PHY-906 Treated Liver - repeat 2 - mAdbID:105117

description: mAdb experiment ID: 105117

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.11;; 3.53 Temperature: 30.32 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 Treated Liver - repeat 6 - mAdbID:105112

description: mAdb experiment ID: 105112

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.12;; 3.51 Temperature: 30.39 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).

source_name: CPT-11 Treated Liver

treatment_protocol:
Treatment type: compound
Agent: Irinotecan (CPT-11, Camptosar(TM))
Treatment dose: 360mg/kg (CPT-11)
Treatment time: 72 hours
In-vivo treatment: Murine Colon 38 cells were transplanted subcutaneously into four- to six-week-old female BDF-1 mice (Charles River Laboratories, Wilmington, MA). After 10 to 14 days, mice with tumor sizes of 150-300mm(3) were selected. On Day 0, ten mice were treated with CPT-11 (n=10). CPT-11 (360mg/kg) was administered intra-peritoneally. Mice were terminated by cervical dislocation 72 hours after initiation of drug treatment. Tumor tissue was removed and divided and either frozen for total RNA isolation or placed in 10% neutral buffered formalin for histological analysis.


title: Wildtype grown on 2g/L glycerol, biological replicate 3


title: CPT-11 and PHY-906 Treated Spleen - repeat 3 - mAdbID:105126

description: mAdb experiment ID: 105126

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.14;; 3.55 Temperature: 29.81 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 Treated Liver - repeat 5 - mAdbID:105111

description: mAdb experiment ID: 105111


title: CPT-11 Treated Liver - repeat 3 - mAdbID:105109

description: mAdb experiment ID: 105109

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.08;; 3.69 Temperature: 27.94 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain glycerolC day 20, biological rep2

description: Gene expression data from glycerol evolved strain

source_name: glycerol evolved strain

value: day 20


title: Strain glycerolC day 20, biological rep3


title: CPT-11 and PHY-906 Treated Liver - repeat 5 - mAdbID:105120

description: mAdb experiment ID: 105120

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.12;; 3.5 Temperature: 30.45 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 and PHY-906 Treated Spleen - repeat 5 - mAdbID:105128

description: mAdb experiment ID: 105128

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.15;; 3.44 Temperature: 31.03 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 Treated Liver - repeat 9 - mAdbID:105115

description: mAdb experiment ID: 105115

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.08;; 3.67 Temperature: 28.28 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Wildtype grown on 2g/L glycerol, biological replicate 2


title: CPT-11 Treated Liver - repeat 8 - mAdbID:105114

description: mAdb experiment ID: 105114

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.12;; 3.62 Temperature: 29.59 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 Treated Liver - repeat 7 - mAdbID:105113

description: mAdb experiment ID: 105113

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.12;; 3.62 Temperature: 29.32 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 and PHY-906 Treated Liver - repeat 6 - mAdbID:105121

description: mAdb experiment ID: 105121

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.1;; 3.67 Temperature: 28.89 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 Treated Liver - repeat 4 - mAdbID:105110

description: mAdb experiment ID: 105110

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.11;; 3.57 Temperature: 30.2 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 Treated Liver - repeat 2 - mAdbID:105108

description: mAdb experiment ID: 105108

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.04;; 3.68 Temperature: 26.63 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Wildtype grown on 2g/L glycerol, biological replicate 1

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


title: Strain glycerolE day 44, biological rep3

value: day 44


title: Strain glycerolE day 20, biological rep3


title: Strain glycerolE day 44, biological rep2


title: Strain glycerolE day 44, biological rep1


title: PHY-906 Treated Liver - repeat 8 - mAdbID:105106

description: mAdb experiment ID: 105106

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.15;; 3.5 Temperature: 31.3 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).

source_name: PHY-906 Treated Liver

treatment_protocol:
Treatment type: compound
Agent: PHY-906
Treatment dose: 500mg/kg (twice a day)
Treatment time: 72 hours
In-vivo treatment: Murine Colon 38 cells were transplanted subcutaneously into four- to six-week-old female BDF-1 mice (Charles River Laboratories, Wilmington, MA). After 10 to 14 days, mice with tumor sizes of 150-300mm(3) were selected. On Day 0, ten mice were treated with PHY-906 (n=10). PHY906 was given orally for 72 hours (500mg/kg twice a day). Mice were terminated by cervical dislocation 72 hours after initiation of drug treatment. Tumor tissue was removed and divided and either frozen for total RNA isolation or placed in 10% neutral buffered formalin for histological analysis.


title: CPT-11 Treated Liver - repeat 1 - mAdbID:105107

description: mAdb experiment ID: 105107

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.12;; 3.52 Temperature: 30.57 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PHY-906 Treated Liver - repeat 5 - mAdbID:105103

description: mAdb experiment ID: 105103

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.15;; 3.51 Temperature: 31.03 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PHY-906 Treated Liver - repeat 4 - mAdbID:105102

description: mAdb experiment ID: 105102

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.15;; 3.49 Temperature: 31.18 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PHY-906 Treated Liver - repeat 6 - mAdbID:105104

description: mAdb experiment ID: 105104

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.15;; 3.48 Temperature: 32.43 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PHY-906 Treated Liver - repeat 2 - mAdbID:105100

description: mAdb experiment ID: 105100

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.14;; 3.49 Temperature: 31.55 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain glycerolD day 20, biological rep3


title: Strain glycerolD day 44, biological rep1


title: PHY-906 Treated Liver - repeat 3 - mAdbID:105101

description: mAdb experiment ID: 105101

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.15;; 3.48 Temperature: 32.46 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PBS Treated Liver - repeat 8 - mAdbID:105041

description: mAdb experiment ID: 105041

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.11;; 3.61 Temperature: 29.2 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).

source_name: PBS Treated Liver

treatment_protocol:
Treatment type: compound
Agent: Phosphate Buffered Saline (PBS)
In-vivo treatment: Murine Colon 38 cells were transplanted subcutaneously into four- to six-week-old female BDF-1 mice (Charles River Laboratories, Wilmington, MA). After 10 to 14 days, mice with tumor sizes of 150-300mm(3) were selected. On Day 0, ten mice were treated with PBS (n=10). Mice were terminated by cervical dislocation 72 hours after initiation of drug treatment. Tumor tissue was removed and divided and either frozen for total RNA isolation or placed in 10% neutral buffered formalin for histological analysis.


title: Strain glycerolD day 44, biological rep3


title: Strain glycerolE day 20, biological rep1


title: Strain glycerolD day 20, biological rep1


title: PBS Treated Liver - repeat 9 - mAdbID:105042

description: mAdb experiment ID: 105042

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.12;; 3.6 Temperature: 29.9 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain glycerolD day 20, biological rep2


title: PBS Treated Liver - repeat 7 - mAdbID:105040

description: mAdb experiment ID: 105040

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.1;; 3.66 Temperature: 28.8 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PHY-906 Treated Liver - repeat 1 - mAdbID:105099

description: mAdb experiment ID: 105099

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.15;; 3.49 Temperature: 32.49 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain glycerolD day 44, biological rep2


title: PBS Treated Liver - repeat 10 - mAdbID:105043

description: mAdb experiment ID: 105043

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.13;; 3.53 Temperature: 30.57 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PHY-906 Treated Liver - repeat 7 - mAdbID:105105

description: mAdb experiment ID: 105105

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.08;; 3.78 Temperature: 27.97 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain glycerolC day 20, biological rep1


title: Strain glycerolC day 44, biological rep1


title: Strain glycerolC day 44, biological rep2


title: PBS Treated Liver - repeat 6 - mAdbID:105039

description: mAdb experiment ID: 105039

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.07;; 3.67 Temperature: 28.37 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PBS Treated Liver - repeat 3 - mAdbID:105036

description: mAdb experiment ID: 105036

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.12;; 3.59 Temperature: 30.11 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain glycerolC day 44, biological rep3


title: PBS Treated Liver - repeat 5 - mAdbID:105038

description: mAdb experiment ID: 105038

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.09;; 3.79 Temperature: 27.82 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain glycerolB day 20, biological rep1

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


title: Strain glycerolE day 20, biological rep2


title: Strain glycerolB day 20, biological rep2


title: CPT-11 Treated Spleen - repeat 8 - mAdbID:104787

description: mAdb experiment ID: 104787

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.11;; 3.72 Temperature: 28.25 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).

source_name: CPT-11 Treated Spleen


title: Strain glycerolB day 44, biological rep1


title: Strain glycerolA day 44, biological rep3


title: Strain glycerolA day 44, biological rep2


title: Strain glycerolB day 20, biological rep3


title: Strain glycerolB day 44, biological rep2


title: CPT-11 Treated Spleen - repeat 1 - mAdbID:104789

description: mAdb experiment ID: 104789

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.12;; 3.71 Temperature: 28.52 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain glycerolB day 44, biological rep3


title: PBS Treated Liver - repeat 1 - mAdbID:105034

description: mAdb experiment ID: 105034

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.07;; 3.8 Temperature: 26.69 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain glycerolA day 20, biological rep3


title: CPT-11 Treated Spleen - repeat 4 - mAdbID:104775

description: mAdb experiment ID: 104775

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.1;; 3.73 Temperature: 27.49 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain glycerolA day 44, biological rep1


title: PBS Treated Liver - repeat 2 - mAdbID:105035

description: mAdb experiment ID: 105035

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.12;; 3.62 Temperature: 29.47 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain glycerolA day 20, biological rep2


title: CPT-11 Treated Spleen - repeat 2 - mAdbID:104772

description: mAdb experiment ID: 104772

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.09;; 3.64 Temperature: 25.9 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 Treated Spleen - repeat 7 - mAdbID:104785

description: mAdb experiment ID: 104785

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.14;; 3.56 Temperature: 29.1 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PBS Treated Liver - repeat 4 - mAdbID:105037

description: mAdb experiment ID: 105037

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.14;; 3.54 Temperature: 30.84 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 Treated Spleen - repeat 5 - mAdbID:104776

description: mAdb experiment ID: 104776

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.11;; 3.73 Temperature: 27.94 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 Treated Spleen - repeat 6 - mAdbID:104783

description: mAdb experiment ID: 104783

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.13;; 3.7 Temperature: 28.8 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PHY-906 Treated Spleen - repeat 10 - mAdbID:104769

description: mAdb experiment ID: 104769

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.17;; 3.45 Temperature: 32.8 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).

source_name: PHY-906 Treated Spleen


title: CPT-11 Treated Spleen - repeat 3 - mAdbID:104773

description: mAdb experiment ID: 104773

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.11;; 3.73 Temperature: 27.06 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PHY-906 Treated Spleen - repeat 9 - mAdbID:104768

description: mAdb experiment ID: 104768

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.16;; 3.39 Temperature: 33.19 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain glycerol2 day 44, biological rep2


title: Strain glycerol1 day 44, biological rep3


title: Strain glycerol1 day 44, biological rep2


title: Strain glycerolA day 20, biological rep1


title: Strain glycerol2 day 44, biological rep1


title: Strain glycerol1 day 44, biological rep1


title: Strain glycerol1 day 20, biological rep3


title: Strain glycerol2 day 20, biological rep1


title: Strain glycerol2 day 44, biological rep3


title: PHY-906 Treated Spleen - repeat 8 - mAdbID:104767

description: mAdb experiment ID: 104767

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.18;; 3.47 Temperature: 33.1 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain glycerol1 day 20, biological rep2


title: PHY-906 Treated Spleen - repeat 4 - mAdbID:104763

description: mAdb experiment ID: 104763

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.17;; 3.47 Temperature: 32.71 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain glycerol2 day 20, biological rep3


title: PHY-906 Treated Spleen - repeat 2 - mAdbID:104761

description: mAdb experiment ID: 104761

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.17;; 3.44 Temperature: 32.58 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain glycerol2 day 20, biological rep2

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


title: PHY-906 Treated Spleen - repeat 5 - mAdbID:104764

description: mAdb experiment ID: 104764

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.16;; 3.42 Temperature: 32.4 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain glycerol1 day 20, biological rep1


title: PHY-906 Treated Spleen - repeat 3 - mAdbID:104762

description: mAdb experiment ID: 104762

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.17;; 3.44 Temperature: 32.49 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PBS Treated Spleen - repeat 9 - mAdbID:104758

description: mAdb experiment ID: 104758

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.15;; 3.43 Temperature: 31.67 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).

source_name: PBS Treated Spleen


title: PHY-906 Treated Spleen - repeat 7 - mAdbID:104766

description: mAdb experiment ID: 104766

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.17;; 3.46 Temperature: 32.95 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PBS Treated Spleen - repeat 7 - mAdbID:104756

description: mAdb experiment ID: 104756

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.16;; 3.44 Temperature: 31.85 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PBS Treated Spleen - repeat 6 - mAdbID:104755

description: mAdb experiment ID: 104755

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.14;; 3.43 Temperature: 31.27 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Wildtype grown on 2g/L lactate, biological replicate 2

description: Gene expression data from wildtype strain on lactate

source_name: wildtype strain on lactate


title: Wildtype grown on 2g/L lactate, biological replicate 5


title: Wildtype grown on 2g/L lactate, biological replicate 3


title: PBS Treated Spleen - repeat 8 - mAdbID:104757

description: mAdb experiment ID: 104757

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.15;; 3.43 Temperature: 31.58 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Wildtype grown on 2g/L lactate, biological replicate 6


title: PBS Treated Spleen - repeat 5 - mAdbID:104754

description: mAdb experiment ID: 104754

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.15;; 3.44 Temperature: 31.03 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PHY-906 Treated Spleen - repeat 1 - mAdbID:104760

description: mAdb experiment ID: 104760

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.18;; 3.43 Temperature: 32.19 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PBS Treated Spleen - repeat 3 - mAdbID:104752

description: mAdb experiment ID: 104752

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.16;; 3.45 Temperature: 30.32 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PHY-906 Treated Spleen - repeat 6 - mAdbID:104765

description: mAdb experiment ID: 104765

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.18;; 3.46 Temperature: 33.04 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PBS Treated Spleen - repeat 1 - mAdbID:104750

description: mAdb experiment ID: 104750

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.13;; 3.48 Temperature: 28.86 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PBS Treated Spleen - repeat 2 - mAdbID:104751

description: mAdb experiment ID: 104751

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.14;; 3.46 Temperature: 29.65 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PBS Treated Spleen - repeat 10 - mAdbID:104759

description: mAdb experiment ID: 104759

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.17;; 3.44 Temperature: 32 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactateE day 60, biological rep1

description: Gene expression data from lactate evolved strain

source_name: lactate evolved strain

value: day 60


title: PBS Treated Spleen - repeat 4 - mAdbID:104753

description: mAdb experiment ID: 104753

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.16;; 3.43 Temperature: 30.78 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).

value: lung, heart, muscle, kidneys, liver and spleen


title: Strain lactateE day 20, biological rep2


title: CPT-11 and PHY-906 Treated Tumor - repeat 9 - mAdbID:104244

description: mAdb experiment ID: 104244

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.44 Temperature: 31.42 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).

value: female

source_name: CPT-11 and PHY-906 Treated Tumor

value: Murine Colon 38 Tumor


title: Strain lactateE day 20, biological rep3

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


title: Strain lactateE day 60, biological rep3


title: Wildtype grown on 2g/L lactate, biological replicate 4


title: Strain lactateE day 20, biological rep1


title: CPT-11 and PHY-906 Treated Tumor - repeat 8 - mAdbID:104243

description: mAdb experiment ID: 104243

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.46 Temperature: 32.46 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).

source_name: Mixed Normal Mouse Tissues


title: Strain lactateE day 60, biological rep2


title: CPT-11 and PHY-906 Treated Tumor - repeat 4 - mAdbID:104239

description: mAdb experiment ID: 104239

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.44 Temperature: 31.67 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 and PHY-906 Treated Tumor - repeat 6 - mAdbID:104241

description: mAdb experiment ID: 104241

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.43 Temperature: 32.31 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 and PHY-906 Treated Tumor - repeat 5 - mAdbID:104240

description: mAdb experiment ID: 104240

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.48 Temperature: 32.28 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactateD day 60, biological rep2


title: CPT-11 and PHY-906 Treated Tumor - repeat 3 - mAdbID:104238

description: mAdb experiment ID: 104238

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.45 Temperature: 31.55 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactateD day 60, biological rep3


title: Strain lactateD day 20, biological rep3


title: Strain lactateD day 20, biological rep2


title: Wildtype grown on 2g/L lactate, biological replicate 1


title: CPT-11 and PHY-906 Treated Tumor - repeat 7 - mAdbID:104242

description: mAdb experiment ID: 104242

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.45 Temperature: 32.43 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactateC day 60, biological rep3


title: CPT-11 and PHY-906 Treated Tumor - repeat 2 - mAdbID:104237

description: mAdb experiment ID: 104237

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.2;; 3.42 Temperature: 31.27 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactateD day 60, biological rep1


title: CPT-11 and PHY-906 Treated Tumor - repeat 1 - mAdbID:104236

description: mAdb experiment ID: 104236

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.17;; 0.01 Temperature: 31.18 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactateC day 60, biological rep2


title: Strain lactateC day 20, biological rep2


title: Strain lactateD day 20, biological rep1


title: CPT-11 Treated Tumor - repeat 10 - mAdbID:104235

description: mAdb experiment ID: 104235

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.19;; 3.4 Temperature: 31.09 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).

source_name: CPT-11 Treated Tumor


title: CPT-11 Treated Tumor - repeat 4 - mAdbID:104229

description: mAdb experiment ID: 104229

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.16;; 3.43 Temperature: 28.62 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 Treated Tumor - repeat 9 - mAdbID:104234

description: mAdb experiment ID: 104234

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.18;; 3.39 Temperature: 30.87 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactateC day 20, biological rep1


title: CPT-11 Treated Tumor - repeat 5 - mAdbID:104230

description: mAdb experiment ID: 104230

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.17;; 3.61 Temperature: 29.1 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: CPT-11 Treated Tumor - repeat 7 - mAdbID:104232

description: mAdb experiment ID: 104232

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.19;; 3.44 Temperature: 29.96 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactateC day 20, biological rep3


title: CPT-11 Treated Tumor - repeat 6 - mAdbID:104231

description: mAdb experiment ID: 104231

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.17;; 3.57 Temperature: 29.47 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactateC day 60, biological rep1


title: Strain lactateB day 60, biological rep2


title: CPT-11 Treated Tumor - repeat 8 - mAdbID:104233

description: mAdb experiment ID: 104233

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.19;; 3.4 Temperature: 30.6 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactateB day 60, biological rep3


title: Strain lactateB day 60, biological rep1


title: CPT-11 Treated Tumor - repeat 3 - mAdbID:104228

description: mAdb experiment ID: 104228

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.15;; 3.68 Temperature: 28.13 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactateB day 20, biological rep3

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


title: PHY-906 Treated Tumor - repeat 9 - mAdbID:104225

description: mAdb experiment ID: 104225

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.22;; 3.49 Temperature: 32.83 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).

source_name: PHY-906 Treated Tumor


title: CPT-11 Treated Tumor - repeat 2 - mAdbID:104227

description: mAdb experiment ID: 104227

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.14;; 3.7 Temperature: 27.46 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactateB day 20, biological rep2


title: PHY-906 Treated Tumor - repeat 7 - mAdbID:104223

description: mAdb experiment ID: 104223

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.47 Temperature: 32.67 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactateA day 60, biological rep4


title: PHY-906 Treated Tumor - repeat 6 - mAdbID:104222

description: mAdb experiment ID: 104222

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.46 Temperature: 32.58 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactateA day 60, biological rep3


title: CPT-11 Treated Tumor - repeat 1 - mAdbID:104226

description: mAdb experiment ID: 104226

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 100;; 100 LaserPower: 3.23;; 3.85 Temperature: 26.82 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactateB day 20, biological rep1


title: PHY-906 Treated Tumor - repeat 8 - mAdbID:104224

description: mAdb experiment ID: 104224

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.48 Temperature: 32.77 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PBS Treated Tumor - repeat 10 - mAdbID:104216

description: mAdb experiment ID: 104216

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.43 Temperature: 31.82 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).

source_name: PBS Treated Tumor


title: PHY-906 Treated Tumor - repeat 3 - mAdbID:104219

description: mAdb experiment ID: 104219

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.47 Temperature: 32.22 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PHY-906 Treated Tumor - repeat 2 - mAdbID:104218

description: mAdb experiment ID: 104218

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.42 Temperature: 32.13 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PHY-906 Treated Tumor - repeat 4 - mAdbID:104220

description: mAdb experiment ID: 104220

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.47 Temperature: 32.37 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactateA day 60, biological rep2


title: PHY-906 Treated Tumor - repeat 1 - mAdbID:104217

description: mAdb experiment ID: 104217

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.44 Temperature: 32.06 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactateA day 60, biological rep1


title: Strain lactateA day 20, biological rep3


title: Strain lactate3 day 60, biological rep3


title: Strain lactate3 day 60, biological rep2


title: Strain lactate3 day 60, biological rep1


title: PBS Treated Tumor - repeat 9 - mAdbID:104215

description: mAdb experiment ID: 104215

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.45 Temperature: 31.55 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PBS Treated Tumor - repeat 7 - mAdbID:104213

description: mAdb experiment ID: 104213

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.2;; 3.43 Temperature: 31.3 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactateA day 20, biological rep1


title: Strain lactate3 day 20, biological rep3


title: Strain lactateA day 20, biological rep2


title: PBS Treated Tumor - repeat 8 - mAdbID:104214

description: mAdb experiment ID: 104214

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.41 Temperature: 31.39 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PHY-906 Treated Tumor - repeat 5 - mAdbID:104221

description: mAdb experiment ID: 104221

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.48 Temperature: 32.49 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactate2 day 60, biological rep2


title: PBS Treated Tumor - repeat 6 - mAdbID:104212

description: mAdb experiment ID: 104212

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.19;; 3.41 Temperature: 30.57 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactate2 day 60, biological rep3

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


title: Strain lactate3 day 20, biological rep2


title: Strain lactate3 day 20, biological rep1


title: PBS Treated Tumor - repeat 1 - mAdbID:103036

description: mAdb experiment ID: 103036

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.13;; 3.65 Temperature: 27.06 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactate2 day 60, biological rep1


title: PBS Treated Tumor - repeat 5 - mAdbID:104211

description: mAdb experiment ID: 104211

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.19;; 3.4 Temperature: 30.26 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Strain lactate2 day 20, biological rep2


title: PBS Treated Tumor - repeat 4 - mAdbID:103158

description: mAdb experiment ID: 103158

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.19;; 3.4 Temperature: 30.11 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: PBS Treated Tumor - repeat 2 - mAdbID:103037

description: mAdb experiment ID: 103037

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.15;; 3.57 Temperature: 28.19 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).


title: Sun leaves_2xozone_270606_rep3

status: Public on Oct 21 2011

city: Neuherberg

first: Maren

last: Olbrich

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz Zentrum München

description: A coefficient of variation about all microarrays of one time point was calculated using Acuity 4.0 microarray informatics software [Axon Instruments]. We used only those spots that had a coefficient of variation < 50 and were present on at least half of identical slides. We express the median values as log2 ratios.

hyb_protocol: Blocking: 1. 0.1 % SDS for 2 minutes shaking, 2. 0.1 % SDS for 2 minutes shaking, 3. H2Obidest. for 2 minutes shaking, 4. washing of slides in H2Obidest., 5. washing another time with water for 2 minutes, 6. for 2 minutes in cooking water, 7. for 5 minutes in fresh sodium-boric-solution (0.75 g NaBH4 in 200 ml PBS and 75 ml 100% Ethanol p.a.), 8. 1 minutes washing in 0.1 % SDS, 9. another time washing in 0.1 % SDS for 1 minute, 10. 1 minute washing in H2Obidest, 11. incubating in 100% EtOH for about 20 seconds. Hybridization for 16h up to 20h at 42°C in a hybridization furnace. Washing: in wash buffer (1x SSC/0.2% SDS) for 4 minutes at 42 °C, 4 minutes in wash buffer (0.1x SSC und 0.2% SDS), 2 minutes in wash buffer (0.1x SSC), 2 minutes in wash buffer (0.1x SSC), 2 minutes in Millipore water.

scan_protocol: Hardware: GenePix 4000A (Axon Instruments, Sunnyvale, USA), simultaneous scanning of both wavelengths (532nm, 635nm). Software: GenePix Pro 6.0 (Axon Instruments (Sunnyvale, USA) FLA 8000 Version 1.3.

data_processing:
Normalization via GenePix Pro 4.0.
For normalization, only spots were used which (1) were not marked with "bad", "absent", or "not found"; (2) spots that had for both wavelengths more than 55% of pixel above background one standard deviation; (3) spots with a pixel intensity for both wavelengths above 500; (4) coefficient of determination of actual regression of both wavelengths was above 0.5; (5) light saturation of pixel was under 3%. On the basis of these values, all genes of the array were normalized.

organism: Fagus sylvatica

label_protocol: Cy5 Mono-Reactive Dye Pack dissolved in 85 µl DMSO, dried cDNA dissolved in 4.5µl Na2CO3, 4.5µl dissolved Cy5 dye was added and incubated for about 2 hours at room temperature and in the dark. Precipitate with 35 µl 100 mM NaAc (pH 5,2), purified with QIAquick PCR Purification Kit, Qiagen, Hilden. Dried and dissolved in 62 µl hybridization buffer (50% formamide, 5-fach SSC, 0.1% SDS, 2% salmon sperm DNA (w/w), then for 3 minutes at 90°C, centrifuged and put on array.

extract_protocol: According to Kiefer et al. 2000.

value: about 60 years

value: five pooled sun leaves

tag: tree

tag: exposition

value: 2x ambient ozone, restricted to 150 ppm

tag: sampling

value: 27th of June 2006

label_protocol: Cy3 Mono-Reactive Dye Pack dissolved in 85 µl DMSO, dried cDNA dissolved in 4.5µl Na2CO3, 4.5µl dissolved Cy3 dye was added and incubated for about 2 hours at room temperature and in the dark. Precipitate with 35 µl 100 mM NaAc (pH 5,2), purified with QIAquick PCR Purification Kit, Qiagen, Hilden. Dried and dissolved in 62 µl hybridization buffer (50% formamide, 5-fach SSC, 0.1% SDS, 2% salmon sperm DNA (w/w), then for 3 minutes at 90°C, centrifuged and put on array.

value: 1x ambient ozone


title: PBS Treated Tumor - repeat 3 - mAdbID:103038

description: mAdb experiment ID: 103038

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.14;; 3.6 Temperature: 28.55 Scanning Protocol Other: Microarray slides were scanned by GenePix Pro 4.0 (Axon, Sunnyvale, CA).

value: Sample Pooling Protocol:Mouse reference RNA was prepared by homogenization and pooling of selected mouse tissues (lung, heart, muscle, kidneys, liver and spleen) from 3 female C57Bl/6 mice.

value: 4-6 weeks

value: subcutaneous murine colon 38 implanted tumor


title: Sun leaves_2xozone_270606_rep5

value: 1x ambient ozone, restricted to 150 ppm


title: Sun leaves_2xozone_270606_rep2

source_name: Sun leaves_1xozone_270606_rep.2

source_name: Sun leaves_2xozone_270606_rep.2


title: IDC57

city: Madrid

first: Gema

last: Moreno-Bueno

state: Madrid

address: Arturo Duperier

department: Biochemistry

country: Spain

institute: IIB

hyb_protocol: The arrays hybridization was performed using In Situ Hybridization Kit Plus (Agilent technologies) according to Peinado et al, Cancer Research 2008.

scan_protocol: After hybridization and washing, the slides were scanned in an Axon GenePix Scanner (Axon Instruments), according to manufacturer´s protocol.

data_processing: The slides were analyzed using Feature Extraction Software 10.0 (Agilent technologies), following manufacturer’s protocol. A hierarchical clustering method was applied to group the genes and samples on the basis of the similarities in expression and the unsupervised analyses were visualized using the SOTA and TreeView software assuming euclidean distances between genes (http://bioinfo.cnio.es/cgi-bin/tools/clustering/sotarray). Genes with potentially significant changes in expression were identified using the POMELO program (http://www.genoma.wi.mit.edu/MPR/software). We tested the null hypothesis of equal means among groups using T-test, computing p-values using a permutation test. To select differentially expressed genes, we adjusted for multiple testing using the False Discovery Rate (FDR) method (Chung et al, 2004)

source_name: Total RNA from breast tumor biopsies

label_protocol: 1mg from tRNA was labelled and array hybridized using the Low RNA Linear Amplification Kit (Agilent) following manufacturer’s protocol.

extract_protocol: 1mg of total RNA from each independent tumours were labelled with Cy5-dUTP and as control a pooled RNA obtained from equal concentration of each RNA tumor sample labelled with Cy3-dUTP was used. The amplification and labelling of mRNA were performed using   Low RNA Linear Amplification Kit (Agilent technologies),  following manufacturer’s protocol

value: Female

tag: cell type

value: infiltrative breast ductal carcinoma

source_name: Pool from the analysed samples


title: Sun leaves_2xozone_270606_rep4

source_name: Sun leaves_1xozone_270606_rep.4

source_name: Sun leaves_2xozone_270606_rep.4


title: IDC58


title: Strain lactate2 day 20, biological rep1

value: day 20


title: IDC55


title: Strain lactate2 day 20, biological rep3


title: IDC51


title: Sun leaves_2xozone_270606_rep1

source_name: Sun leaves_1xozone_270606_rep.1

source_name: Sun leaves_2xozone_270606_rep.1


title: Shade leaves_2xozone_270606_rep5

source_name: Shade leaves_1xozone_270606_rep.4

value: five pooled shade leaves

source_name: Shade leaves_2xozone_270606_rep.4


title: IDC54


title: Shade leaves_2xozone_270606_rep7


title: IDC52


title: IDC56


title: Shade leaves_2xozone_270606_rep4

source_name: Shade leaves_1xozone_270606_rep.3

source_name: Shade leaves_2xozone_270606_rep.3


title: IDC53


title: Sun leaves_2xozone_120906_rep9

source_name: Sun leaves_1xozone_120906_rep.5

value: 12th of September 2006

source_name: Sun leaves_2xozone_120906_rep.5


title: Shade leaves_2xozone_270606_rep6

source_name: Shade leaves_1xozone_270606_rep.5

source_name: Shade leaves_2xozone_270606_rep.5


title: Sun leaves_2xozone_120906_rep10


title: IDC50


title: IDC49


title: IDC48


title: Shade leaves_2xozone_270606_rep3


title: Shade leaves_2xozone_270606_rep1

source_name: Shade leaves_1xozone_270606_rep.1

source_name: Shade leaves_2xozone_270606_rep.1


title: IDC47


title: Sun leaves_2xozone_120906_rep8


title: Sun leaves_2xozone_120906_rep4


title: Sun leaves_2xozone_120906_rep7

source_name: Sun leaves_1xozone_120906_rep.4

source_name: Sun leaves_2xozone_120906_rep.4


title: IDC45

source_name: Total RNA from breast tumor biopsies

source_name: Pool from the analysed samples


title: IDC44


title: Sun leaves_2xozone_120906_rep5

source_name: Sun leaves_1xozone_120906_rep.3

source_name: Sun leaves_2xozone_120906_rep.3


title: IDC43


title: Shade leaves_2xozone_270606_rep2

source_name: Shade leaves_1xozone_270606_rep.2

source_name: Shade leaves_2xozone_270606_rep.2


title: Sun leaves_2xozone_120906_rep3

source_name: Sun leaves_1xozone_120906_rep.2

source_name: Sun leaves_2xozone_120906_rep.2


title: Sun leaves_2xozone_120906_rep6


title: IDC40


title: Sun leaves_2xozone_120906_rep2


title: IDC39


title: Sun leaves_2xozone_120906_rep1

source_name: Sun leaves_1xozone_120906_rep.1

source_name: Sun leaves_2xozone_120906_rep.1


title: IDC46


title: Shade leaves_2xozone_120906_rep4


title: IDC42


title: IDC37


title: Shade leaves_2xozone_120906_rep6


title: IDC41


title: IDC34


title: IDC36


title: Shade leaves_2xozone_120906_rep3

source_name: Shade leaves_1xozone_120906_rep.2

source_name: Shade leaves_2xozone_120906_rep.2


title: IDC33


title: IDC38


title: Sun leaves_2xozone_091006_rep10

value: 9th of October 2006


title: Shade leaves_2xozone_120906_rep2


title: IDC35


title: IDC32


title: Sun leaves_2xozone_091006_rep8


title: IDC28


title: Sun leaves_2xozone_091006_rep9

source_name: Sun leaves_1xozone_091006_rep.5

source_name: Sun leaves_2xozone_091006_rep.5