title: Whole Seed at the early maturation stage, biological replicate 2

description: Whole seeds containing early maturation-stage embryos were ground in liquid nitrogen using a mortar and pestle.

source_name: Soybean early maturation-stage seed

extract_protocol: Total RNA was extracted using Plant RNA Isolation Reagent (Invitrogen, Carlsbad, CA).


title: Whole Seed at the early maturation stage, biological replicate 1

status: Public on Jun 19 2007

type: RNA

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

country: USA

institute: University of California, Los Angeles

hyb_protocol: Following fragmentation, ten micrograms of cRNA were hybridized for 16 hr at 45?C with the GeneChip Soybean Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the Affymetrix GeneChip Operating System 1.3 (GCOS 1.3) using default analysis settings and global scaling as a normalization method. The trimmed mean target intensity of each array was set to 500.

label: biotin

molecule: total RNA

organism: Glycine max

label_protocol: Two nanograms of total RNA was amplified using the RiboAmp OA Amplification Kit (Molecular Devices, Sunnyvale, CA).  Biotinylated cRNAs were synthesized with the ENZO BioArray High Yield RNA Transcript Labeling Kit using all of the amplified RNA from the RiboAmp OA Kit.

growth_protocol: Soybean cv. Asgrow A3237 was grown in the UCLA Plant Growth Center using a 16:8 light-dark cycle at 22?C.

treatment_protocol: Seeds with length between 6.0 and 7.0 mm containing early maturation-stage embryos were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al.,  Plant Physiol.132. 27-35 (2003)).  Seed compartment was captured from eight-micron sections using a Leica LMD6000 system.

tag: Soybean cv. Asgrow A3237


title: Scoelicolor_M145 13h Replicate 1

type: mixed

city: Minneapolis

first: Salim

last: Charaniya

state: MN

address: 421 Washington Ave SE., 151 Amundson Hall

department: Chemical Engineering and Materials Science

institute: University of Minnesota

description: Comparison of wild type and mutant regulatory genes in a time course study with S. coelicolor

hyb_protocol: The labeled cDNA and gDNA were then mixed and co-hybridized to microarray slides in the presence of 50% formamide.  After 16 hours incubation at 50°C, slides were washed and scanned.

scan_protocol: Arrays were scanned using ScanArray5000 (Perkin Elmer, Wellesley, MA). Images were analyzed using GenePix (Axon Instruments, Union City, CA) to obtain raw intensity data for each spot.  The median fluorescence intensity from each spot was used for all subsequent analysis.

data_processing: A quantile normalization method was employed to normalize these log2 ratios from each hybridization (S Mehra, W Lian, KP Jayapal, SP Charaniya, DH Sherman, WS Hu: A framework to analyze multiple time series data: a case study with Streptomyces coelicolor. J Ind Microbiol Biotechnol 2006, 33:159-72).  The resulting log2 ratios were not only used to compare transcript levels of the same mRNA species in different biological samples, but also used as an estimate of the relative abundance of each mRNA species.

label: Alexa 647

organism: Streptomyces coelicolor

source_name: S. coelicolor RNA R5- medium 13h

label_protocol: The cDNA was then incubated with Alexa 647 (Invitrogen, Carlsbad, CA) for labeling as per manufacturer's instructions.

growth_protocol: S. coelicolor A3(2) strain M145 was maintained on R5 solid agar (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) for high density spores.  For liquid culture, spores were pre-germinated in 2xYT medium (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) and inoculated into R5- liquid medium (Huang, J., C. J. Lih, K. H. Pan, and S. N. Cohen. 2001. Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays. Genes Dev 15:3183-92) at a density of ~10exp7 spores/ml.  Baffled 2L flasks containing stainless steel coils with 350 ml working volume were used for liquid cultures.  Cultures were incubated at 30°C in an orbital shaker at 300 rpm.  For measuring cell growth, samples were collected at regular intervals and mixed with one-eighth volume of 2.5 M HCl and then subjected to sonication to break mycelial pellets (Brana, A. F., S. Wolfe, and A. L. Demain. 1986. Relationship between nitrogen assimilation and cephalosporin synthesis in Streptomyces clavuligerus. Arch Microbiol 146:46-51).  Absorbance of the resulting solution at 450 nm was then taken as a measure of growth.  Proper dilution was made to ensure an OD450 measurement below 1, which is in the linear range of detection.

extract_protocol: Immediately after culture samples were collected, one-fifth volume of an ice-cold stop solution (5% phenol in ethanol) (Bernstein, J. A., A. B. Khodursky, P. H. Lin, S. Lin-Chao, and S. N. Cohen. 2002. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci U S A 99:9697-702) was added to the sample volume to prevent RNA degradation.  The sample was quickly centrifuged at 4°C and the supernatant was discarded.  The remaining sample was then stored at -80°C.  To isolate RNA, the frozen pellets were transferred to a mortar and pestle and ground to fine powder in the presence of liquid nitrogen.  RLT solution from RNeasy Mini Kit (Qiagen Inc., Valencia, CA) was added before the ground pellets thawed.  The remaining steps for RNA isolation were carried out as per manufacturer's instructions.  RNA integrity was determined by gel electrophoresis while its quantity and purity were estimated by UV absorbance at OD260 and OD260/OD280, respectively.Total RNA was reverse transcribed to cDNA by SuperscriptII (Invitrogen, Carlsbad, CA) with random hexamers (IDT, Coralville, IA) incorporating aminoallyl-dUTP (Ambion, Austin, TX).

tag: Strain

tag: Sample

value: 13h Replicate 1

molecule: genomic DNA

source_name: S. coelicolor genomic DNA

label_protocol: The DNA was labeled with Label IT® Cy3 Labeling Kit (Mirus Bio Corp., Madison, WI) according to suppliers instructions.

growth_protocol: Spores for S. coelicolor M145 were generated on Mannitol-Soy flour or R5 agar  Cultures for genomic DNA preparation were performed in YEME medium with 0.5% glycine supplement at 30°C until early stationary phase (refer to T Kieser, MJ Bibb, MJ Buttner, KF Chater, DA Hopwood: Practical Streptomyces Genetics: The John Innes Foundation, Norwich, UK; 2000).

extract_protocol: Genomic DNA (gDNA) extraction was carried out using Kirby mix procedure as described elsewhere (T Kieser, MJ Bibb, MJ Buttner, KF Chater, DA Hopwood: Practical Streptomyces Genetics: The John Innes Foundation, Norwich, UK; 2000). About 500 µl of 20 µg/µl gDNA was sonicated briefly for 30-40 sec for shearing them to ~500 bp average size (confirmed by gel electrophoresis).


title: Laser capture microdissected (LCM) seed coat hourglass at the early maturation stage, biological replicate 2

description: Seed coat hourglass regions from early maturation-stage seeds were microdissected using the LEICA LMD6000 system.

source_name: Soybean early maturation-stage seed coat hourglass captured by LCM

extract_protocol: Total RNA was extracted using the PicoPure RNA Extraction Kit (Molecular Devices, Sunnyvale, CA).


title: Scoelicolor_R5_35h Replicate 2

description: Comparison of wild type and disruption mutants of regulatory genes in a time course study with S. coelicolor

source_name: S. coelicolor RNA R5- medium 35h

value: 35h Replicate 2


title: Laser capture microdissected (LCM) seed coat parenchyma at the early maturation stage, biological replicate 1

description: Seed coat parenchyma regions from early maturation-stage seeds were microdissected using the LEICA LMD6000 system.

source_name: Soybean early maturation-stage seed coat parenchyma captured by LCM


title: Scoelicolor_22h Replicate 2

source_name: S. coelicolor RNA R5- medium 22h

value: 22h Replicate 2


title: Scoelicolor_R5_37h Replicate 1

source_name: S. coelicolor RNA R5- medium 37h

value: 37h Replicate 1


title: Laser capture microdissected (LCM) seed coat palisade at the early maturation stage, biological replicate 1

description: Seed coat palisade regions from early maturation-stage seeds were microdissected using the LEICA LMD6000 system.

source_name: Soybean early maturation-stage seed coat palisade captured by LCM


title: Laser capture microdissected (LCM) seed coat hilum at the early maturation stage, biological replicate 1

description: Seed coat hilum regions from early maturation-stage seeds were microdissected using the LEICA LMD6000 system.

source_name: Soybean early maturation-stage seed coat hilum captured by LCM


title: Laser capture microdissected (LCM) seed coat hilum at the early maturation stage, biological replicate 2


title: Scoelicolor_22h Replicate 1

value: 22h Replicate 1


title: Scoelicolor_R5_31h Replicate 2

source_name: S. coelicolor RNA R5- medium 31h

value: 31h Replicate 2


title: Laser capture microdissected (LCM) seed coat parenchyma at the early maturation stage, biological replicate 2


title: Scoelicolor_R5_37h Replicate 2

value: 37h Replicate 2


title: Scoelicolor_R5_35h Replicate 1

value: 35h Replicate 1


title: Laser capture microdissected (LCM) seed coat aleurone at the early maturation stage, biological replicate 1

description: Seed coat aleurone regions from early maturation-stage seeds were microdissected using the LEICA LMD6000 system.

source_name: Soybean early maturation-stage seed coat aleurone captured by LCM


title: Laser capture microdissected (LCM) seed coat hourglass at the early maturation stage, biological replicate 1


title: Scoelicolor_R5_25h Replicate 2

source_name: S. coelicolor RNA R5- medium 25h

value: 25h Replicate 2


title: Laser capture microdissected (LCM) seed coat aleurone at the early maturation stage, biological replicate 2


title: Scoelicolor_R5_25h Replicate 1

value: 25h Replicate 1


title: Laser capture microdissected (LCM) cotyledon vascular bundle at the early maturation stage, biological replicate 2

description: Cotyledon vascular bundle regions from early maturation-stage seeds were microdissected using the LEICA LMD6000 system.

source_name: Soybean early maturation-stage cotyledon vascular bundle captured by LCM


title: Laser capture microdissected (LCM) cotyledon adaxial parenchyma at the early maturation stage, biological replicate 2

description: Cotyledon adaxial parenchyma regions from early maturation-stage seeds were microdissected using the LEICA LMD6000 system.

source_name: Soybean early maturation-stage cotyledon adaxial parenchyma captured by LCM


title: Laser capture microdissected (LCM) cotyledon vascular bundle at the early maturation stage, biological replicate 1


title: Scoelicolor_R5_19h Replicate 2

source_name: S. coelicolor RNA R5- medium 19h

value: 19h Replicate 2


title: Scoelicolor_R5_16h Replicate 3

source_name: S. coelicolor RNA R5- medium 16h

value: 16h Replicate 3


title: Laser capture microdissected (LCM) cotyledon adaxial parenchyma at the early maturation stage, biological replicate 1


title: Scoelicolor_R5_31h Replicate 1

value: 31h Replicate 1


title: Scoelicolor_R5_19h Replicate 1

value: 19h Replicate 1


title: Scoelicolor_R5_16h Replicate 2

value: 16h Replicate 2


title: Scoelicolor_R5_16h Replicate 1

value: 16h Replicate 1


title: Laser capture microdissected (LCM) cotyledon adaxial epidermis at the early maturation stage, biological replicate 1

description: Cotyledon adaxial epidermis regions from early maturation-stage seeds were microdissected using the LEICA LMD6000 system.

source_name: Soybean early maturation-stage cotyledon adaxial epidermis captured by LCM


title: Laser capture microdissected (LCM) cotyledon abaxial parenchyma at the early maturation stage, biological replicate 1

description: Cotyledon abaxial parenchyma regions from early maturation-stage seeds were microdissected using the LEICA LMD6000 system.

source_name: Soybean early maturation-stage cotyledon abaxial parenchyma captured by LCM


title: Laser capture microdissected (LCM) axis vascular bundle at the early maturation stage, biological replicate 1

description: Axis vascular bundle regions from early maturation-stage seeds were microdissected using the LEICA LMD6000 system.

source_name: Soybean early maturation-stage axis vascular bundle captured by LCM


title: Laser capture microdissected (LCM) cotyledon abaxial parenchyma at the early maturation stage, biological replicate 2


title: Laser capture microdissected (LCM) cotyledon adaxial epidermis at the early maturation stage, biological replicate 2


title: Laser capture microdissected (LCM) axis vascular bundle at the early maturation stage, biological replicate 2


title: Laser capture microdissected (LCM) cotyledon abaxial epidermis at the early maturation stage, biological replicate 2

description: Cotyledon abaxial epidermis regions from early maturation-stage seeds were microdissected using the LEICA LMD6000 system.

source_name: Soybean early maturation-stage cotyledon abaxial epidermis captured by LCM


title: Laser capture microdissected (LCM) cotyledon abaxial epidermis at the early maturation stage, biological replicate 1


title: Scoelicolor_R5_13h Replicate 1

source_name: S. coelicolor RNA R5- medium 13h

source_name: S. coelicolor genomic DNA


title: Scoelicolor_R5_13h Replicate 2

value: 13h Replicate 2


title: Scoelicolor_R5_10h Replicate 2

source_name: S. coelicolor RNA R5- medium 10h

value: 10h Replicate 2


title: Laser capture microdissected (LCM) axis shoot meristem at the early maturation stage, biological replicate 1

description: Axis shoot meristem regions from early maturation-stage seeds were microdissected using the LEICA LMD6000 system.

source_name: Soybean early maturation-stage axis shoot meristem captured by LCM


title: Scoelicolor_R5_35h

source_name: S. coelicolor RNA R5- medium 35h

growth_protocol: S. coelicolor A3(2) strain M145 was maintained on R5 solid agar (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) for high density spores.  For liquid culture, spores were pre-germinated in 2xYT medium (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) and inoculated into R5- liquid medium (Huang, J., C. J. Lih, K. H. Pan, and S. N. Cohen. 2001. Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays. Genes Dev 15:3183-92) at a density of ~10exp7 spores/ml.  Baffled 2L flasks containing stainless steel coils with 350 ml working volume were used for liquid cultures.  Cultures were incubated at 30°C in an orbital shaker at 300 rpm.  For measuring cell growth, samples were collected at regular intervals and mixed with one-eighth volume of 2.5 mM HCl and then subjected to sonication to break mycelial pellets (Brana, A. F., S. Wolfe, and A. L. Demain. 1986. Relationship between nitrogen assimilation and cephalosporin synthesis in Streptomyces clavuligerus. Arch Microbiol 146:46-51).  Absorbance of the resulting solution at 450 nm was then taken as a measure of growth.  Proper dilution was made to ensure an OD450 measurement below 1, which is in the linear range of detection.


title: Scoelicolor_R5_24h

source_name: S. coelicolor RNA R5- medium 24h


title: Scoelicolor_R5_22h Replicate 2

source_name: S. coelicolor RNA R5- medium 22h


title: Scoelicolor_R5_22h Replicate 1


title: Scoelicolor_R5_43h

source_name: S. coelicolor RNA R5- medium 43h


title: Scoelicolor_R5_26h

source_name: S. coelicolor RNA R5- medium 26h


title: Scoelicolor_R5_15h Replicate 2

source_name: S. coelicolor RNA R5- medium 15h

value: 15h Replicate 2


title: Scoelicolor_R5_15h Replicate 1

value: 15h Replicate 1


title: Scoelicolor_R5_10h Replicate 1

value: 10h Replicate 1


title: Laser capture microdissected (LCM) axis root meristem at the early maturation stage, biological replicate 2

description: Axis root meristem regions from early maturation-stage seeds were microdissected using the LEICA LMD6000 system.

source_name: Soybean early maturation-stage axis root meristem captured by LCM


title: Laser capture microdissected (LCM) axis root meristem at the early maturation stage, biological replicate 1


title: Laser capture microdissected (LCM) axis shoot meristem at the early maturation stage, biological replicate 2


title: Embryonic Reference, biological rep 3

status: Public on Jun 18 2007

city: Nashville

first: David

last: Miller

state: TN

address: 465 21st Avenue South

department: Cell and Developmental Biology

institute: Vanderbilt University

description:
N2 #3
Gene expression data from all wildtype embryonic nematode cells

hyb_protocol: Following fragmentation, 10-15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were normalized using Robust Multiarray analysis (RMA) in GeneTraffic (Stratagene). RMA normalized data were subjected to Significance Analysis of Microarray (SAM, Stanford) analysis. Enriched genes were obtained by finding genes with a 1.7x enriched at a False Discovery Rate (FDR) of less than or equal to 1%.

organism: Caenorhabditis elegans

source_name: All living C. elegans sorted cells

label_protocol: A 2-round IVT protocol (modified from the Affymetrix small-sample protocol) was used to convert 100 ng total RNA into biotinylated cRNA.

growth_protocol: Gravid adults expressing unc-4::GFP (A-class) were subjected to bleach/NaOH treatment to release embryos. Embryos were harvested and then treated with chitinase to degrade the eggshell. Cells were dissociated and plated on poly-L-lysine coated dishes for 24 hrs to allow differentiation. Cells were removed from the culture dish and sorted using the FACStar Plus (Becton Dickinson, San Jose, CA) that had been flushed with egg buffer. ~90% enrichment of GFP+ cells was obtained. For Reference dataset, wildtype (N2) animals were subjected to the same dissociation/cell culture treatment. FACS isolated all non-propidium iodide stained (i.e. living) cells.

extract_protocol: RNA was isolated from sorted cells using the micro-RNA isolation kit (Stratagene) using the recommended volumes for 1 million cells.

tag: cultured embryonic cells from wildtype (N2 isolate) nematodes


title: Laser capture microdissected (LCM) axis plumule at the early maturation stage, biological replicate 2

description: Axis plumule regions from early maturation embryos were microdissected using the LEICA LMD6000 system.

source_name: Soybean early maturation-stage axis plumule captured by LCM


title: Laser capture microdissected (LCM) axis parenchyma at the early maturation stage, biological replicate 1

description: Axis parenchyma regions from early maturation-stage seeds were microdissected using the LEICA LMD6000 system.

source_name: Soybean early maturation-stage axis parenchyma captured by LCM


title: Embryonic A-class, biological rep 3

description:
unc-4GFP#3
Gene expression data from embryonic A-class neurons

source_name: unc-4::GFP positive cells (A-class)

tag: cultured embryonic cells from unc-4::GFP transgenic animals


title: Laser capture microdissected (LCM) axis epidermis at the early maturation stage, biological replicate 1

description: Axis epidermis regions from early maturation embryos were microdissected using the LEICA LMD6000 system.

source_name: Soybean early maturation-stage axis epidermis captured by LCM


title: Embryonic A-class, biological rep 2

description:
unc-4GFP#2
Gene expression data from embryonic A-class neurons


title: Laser capture microdissected (LCM) axis parenchyma at the early maturation stage, biological replicate 2


title: Embryonic Reference, biological rep 1

description:
N2 #1
Gene expression data from all wildtype embryonic nematode cells


title: Embryonic Reference, biological rep 4

description:
N2 #4
Gene expression data from all wildtype embryonic nematode cells


title: Embryonic Reference, biological rep 2

description:
N2 #2
Gene expression data from all wildtype embryonic nematode cells


title: Staphylococcus aureus_control  45min_replicate3

status: Public on Jun 15 2007

city: Changchun

first: Xuming

last: Deng

address: Xi'an Street 5333#

country: China

institute: College of Animal Science and Veterinary Medicine, Jilin University

description: Control

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix GeneChip Opererating Software (GCOS) version 1.0

label: Biotin

organism: Staphylococcus aureus

source_name: Staphylococcus aureus_control

label_protocol: Conversion to cDNA and labeling was performed as described in Beenken et al., Journal of Bacteriology, 2004 July, 186(14):4665-4684

growth_protocol: (i) S. aureus strain ATCC25923 was grown overnight at 200 rpm in a rotary shaker at 37°C in 10 ml of MHB II, (ii) the culture were inoculated to an initial OD600 of 0.05 in 100 ml of MHB II in 250-ml Erlenmeyer flasks, the bacteria were grown at 37°C at 200 rpm to an OD600 of 0.3. and (iii) 1% (vol/vol) dimethyl sulfoxide (DMSO) was added to the culture, the bacterial suspensions were further incubated for 45 min at 37°C.

extract_protocol: Total bacterial RNA was isolated as described by Beenken et al., 2004 July, 186(14):4665-4684, PMID: 15231800, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=15231800

treatment_protocol: Dimethyl sulfoxide (DMSO, 1% (vol/vol))

tag: Standard strain ATCC25923


title: Staphylococcus aureus_control  45min_replicate1

description: Control

growth_protocol: (i) S. aureus strain ATCC25923 was grown overnight at 200 rpm in a rotary shaker at 37°C in 10 ml of MHB II, (ii) the culture were inoculated to an initial OD600 of 0.05 in 100 ml of MHB II in 250-ml Erlenmeyer flasks, the bacteria were grown at 37°C at 200 rpm to an OD600 of 0.3. and (iii) 1% (vol/vol) dimethyl sulfoxide (DMSO) was added to the culture, the bacterial suspensions were further incubated for 45 min at 37°C


title: Laser capture microdissected (LCM) axis epidermis at the early maturation stage, biological replicate 2

treatment_protocol: Seeds with length between 6.0 and 7.0 mm containing early maturation-stage embryos were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al.,  Plant Physiol.132. 27-35 (2003)).  Seed compartment was captured from eight-micron sections using a Leica LMD6000 system.	!Sample_treatment_protocol_ch1 = Seeds with length between 6.0 and 7.0 mm containing early maturation-stage embryos were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al.,  Plant Physiol.132. 27-35 (2003)).  Seed compartment was captured from eight-micron sections using a Leica LMD6000 system.


title: Scoelicolor_M145 18h Replicate 1

description: Comparison of wild type and mutant regulatory genes in a time course study with S. coelicolor

source_name: S. coelicolor RNA R5- medium 18h

value: 18h Replicate 1


title: Staphylococcus aureus_rhein 45min_replicate3

description: rhein treatment

source_name: Staphylococcus aureus_rhein

growth_protocol: (i) S. aureus strain ATCC25923 was grown overnight at 200 rpm in a rotary shaker at 37°C in 10 ml of MHB II, (ii) the culture were inoculated to an initial OD600 of 0.05 in 100 ml of MHB II in 250-ml Erlenmeyer flasks, the bacteria were grown at 37°C at 200 rpm to an OD600 of 0.3. (iii) 62.5 µl of a 12800 µg /ml rhein stock solution, prepared in dimethyl sulfoxide (DMSO), was added to the cultures, giving a final concentration of 1/2× MIC (8 µg/ml), and the final concentration of DMSO was 1% (vol/vol). Then, the bacterial suspensions were further incubated for 45 min at 37°C.

treatment_protocol: rhein (8 µg/ml)


title: Staphylococcus aureus_control  45min_replicate2

description: Control

growth_protocol: (i) S.aureus strain ATCC25923 was grown overnight at 200 rpm in a rotary shaker at 37°C in 10 ml of MHB II, (ii) the culture were inoculated to an initial OD600 of 0.05 in 100 ml of MHB II in 250-ml Erlenmeyer flasks, the bacteria were grown at 37°C at 200 rpm to an OD600 of 0.3. and (iii) 1% (vol/vol) dimethyl sulfoxide (DMSO) was added to the culture, the bacterial suspensions were further incubated for 45 min at 37°C.


title: Dahl Salt Sensitive Rat Lung- Hypoxia, SU-5416, and Sorafenib rep3

city: Chicago

first: Ankit

middle: A

last: Desai

state: IL

address: 929 East 57th Street, Room W403R

department: Medicine

institute: The University of Chicago

description: Gene expression data from rat lungs exposed to FiO2 of ~9.5%, SU5416, and Sorafenib (hypoxia-SU5416-Sorafenib).

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were again analyzed with GC Robust Multichip Average (RMA) module of Bioconductor package. In a separate subset analysis between hypoxia-SU5416 and hypoxia-SU5416-sorafenib groups, we normalized the same hypoxia-SU5416 (JG7-JG9) and the hypoxia-SU5416-sorafenib sample arrays against a total of seven arrays between the two groups (JG7-JG13) which produced the values diaplyed below compared against the GCRMA values derived for normoxia, hypoxia, and the first set of hypoxia-SU5416 values which which were normalized against all sample arrays including those of normoxia, hypoxia, and hypoxia-SU5416.

organism: Rattus norvegicus

source_name: Rat Lung

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

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

treatment_protocol: At the termination of each experiment, all animals were euthanized by exsanguination under anesthesia in accordance with institutional guidelines. The pulmonary vasculature was perfused via the pulmonary artery with sterile phosphate-buffered saline (PBS) and the right lung was clamped at the level of the mainstem bronchus, excised, and snap frozen in liquid nitrogen for subsequent RNA analysis/expression profiling. Right lung mRNA was isolated from 3 to 4 samples per strain and condition (as an example, we analyzed 4 SS rat strains exposed to control, and 3 SS rat strains exposed to hypoxia and sugen for expression profiling, etc.).

tag: Genotype

value: Dahl Salt Sensitive Rats with Hypoxia, SU-5416, and Sorafenib

tag: Weights


title: Embryonic A-class, biological rep 1

description:
unc-4GFP#1
Gene expression data from embryonic A-class neurons


title: Staphylococcus aureus_rhein 45min_replicate2

description: rhein treatment


title: Dahl Salt Sensitive Rat Lung- Hypoxia, SU-5416, and Sorafenib rep2


title: DLBCL SUDHL

type: genomic

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

description: DLBCL

hyb_protocol: standard Affymetrix procedures using Fluidics Station 400

scan_protocol: standard Affymetrix procedures using GeneChip Scanner 3000

data_processing: Affymetrix GeneChip GCOS 1.1, GTYPE (with CNAT 2.1beta)

organism: Homo sapiens

source_name: SUDHL-6 cell line

label_protocol: standard Affymetrix protocol starting from 250 ng of DNA.

extract_protocol: genomic DNA was extracted using the Puregen DNA Isolation kit (Gentra Systems, Minneapolis, MN, USA), dissolved in reduced EDTA TE buffer.

tag: human diffuse large B-cell lymphoma (DLBCL) cell line


title: DLBCL OZ

description: DLBCL

source_name: OZ cell line


title: DLBCL VAL

description: DLBCL

source_name: VAL cell line


title: Dahl Salt Sensitive Rat Lung- Hypoxia, SU-5416, and Sorafenib rep4


title: Dahl Salt Sensitive Rat Lung- Hypoxia with SU-5416 rep2b

description: Gene expression data from rat lungs exposed to FiO2 of ~9.5% and SU-5416 (hypoxia-SU-5416).

data_processing: The data were again analyzed with GC Robust Multichip Average (RMA) module of Bioconductor package. In a separate subset analysis between hypoxia-SU5416 and hypoxia-SU5416-sorafenib groups, we normalized the same hypoxia-SU5416 (JG7-JG9) sample arrays against a total of seven arrays between the two groups (JG7-JG13) which produced different GCRMA values compared to the previous hypoxia-SU5416 values displayed in columns J, K, and L (which were normalized against all sample arrays including those of normoxia, hypoxia, and hypoxia-SU5416).

value: Dahl Salt Sensitive Rats with Hypoxia and SU-5416


title: Dahl Salt Sensitive Rat Lung- Hypoxia with SU-5416 rep1b


title: Staphylococcus aureus_rhein 45min_replicate1

description: rhein treatment


title: DLBCL patient 05-139

description: DLBCL

source_name: DLBCL patient

extract_protocol: genomic DNA was extracted using the Qiagen DNA Mini kit (Qiagen, Hilden, Germany) dissolved in reduced EDTA TE buffer.

tag: human diffuse large B-cell lymphoma (DLBCL) clinical sample


title: DLBCL DOHH

description: DLBCL

source_name: DOHH-2 cell line


title: DLBCL patient 05-142

description: DLBCL


title: DLBCL patient 05-137

description: DLBCL


title: DLBCL patient 05-141

description: DLBCL


title: DLBCL K422

description: DLBCL

source_name: Karpas-422 cell line


title: DLBCL patient 05-136

description: DLBCL


title: DLBCL patient 05-134

description: DLBCL


title: DLBCL patient 05-138

description: DLBCL


title: DLBCL patient 05-131

description: DLBCL


title: DLBCL patient 05-133

description: DLBCL


title: Dahl Salt Sensitive Rat Lung- Hypoxia with SU-5416 rep3b


title: DLBCL patient 05-130

description: DLBCL


title: DLBCL patient 05-135

description: DLBCL


title: DLBCL patient 05-127

description: DLBCL


title: Dahl Salt Sensitive Rat Lung- Hypoxia, SU-5416, and Sorafenib rep1


title: DLBCL patient 05-124

description: DLBCL


title: DLBCL patient 05-126

description: DLBCL


title: DLBCL patient 05-128

description: DLBCL


title: DLBCL patient 05-122

description: DLBCL


title: DLBCL patient 05-132

description: DLBCL


title: DLBCL patient 05-129

description: DLBCL


title: DLBCL patient 05-123

description: DLBCL


title: Laser capture microdissected (LCM) axis plumule at the early maturation stage, biological replicate 1


title: PTLD patient 05-188

description: monoclonal B-cell PTLD from solid organ transplant recipient

source_name: PTLD patient

tag: human post-transplant lymphoproliferative disorder clinical sample (DLBCL)


title: DLBCL patient 05-125

description: DLBCL


title: PTLD patient 05-187

tag: human post-transplant lymphoproliferative disorder clinical sample (Burkitt/Burkitt-like)


title: PTLD patient 05-186


title: PTLD patient 05-183


title: PTLD patient 05-185


title: PTLD patient 05-184


title: PTLD patient 05-180


title: PTLD patient 05-176

tag: human post-transplant lymphoproliferative disorder clinical sample (polymorphic)


title: PTLD patient 05-177


title: PTLD patient 05-181


title: PTLD patient 05-175


title: PTLD patient 05-173


title: PTLD patient 05-189


title: PTLD patient 05-182


title: PTLD patient 05-174


title: PTLD patient 05-178


title: PTLD patient 05-172

tag: human post-transplant lymphoproliferative disorder clinical sample  (DLBCL)


title: PTLD patient 05-170


title: S. coelicolor YSK4425 40h (Culture#2)

status: Public on Jun 14 2007

first: Karthik

middle: P

last: Jayapal

address: 421 Washington Ave SE

description: No additional description

source_name: S. coelicolor RNA R5- medium 40h

growth_protocol: S. coelicolor A3(2) strain YSK4425 was maintained on R5 solid agar (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) for high density spores.  For liquid culture, spores were pre-germinated in 2xYT medium (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) and inoculated into R5- liquid medium (Huang, J., C. J. Lih, K. H. Pan, and S. N. Cohen. 2001. Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays. Genes Dev 15:3183-92) at a density of ~10exp7 spores/ml.  Baffled 2L flasks containing stainless steel coils with 350 ml working volume were used for liquid cultures.  Cultures were incubated at 30°C in an orbital shaker at 300 rpm.  For measuring cell growth, samples were collected at regular intervals and mixed with one-eighth volume of 2.5 M HCl and then subjected to sonication to break mycelial pellets (Brana, A. F., S. Wolfe, and A. L. Demain. 1986. Relationship between nitrogen assimilation and cephalosporin synthesis in Streptomyces clavuligerus. Arch Microbiol 146:46-51).  Absorbance of the resulting solution at 450 nm was then taken as a measure of growth.  Proper dilution was made to ensure an OD450 measurement below 1, which is in the linear range of detection.

extract_protocol: Immediately after culture samples were collected, one-fifth volume of an ice-cold stop solution (5% phenol in ethanol) (Bernstein, J. A., A. B. Khodursky, P. H. Lin, S. Lin-Chao, and S. N. Cohen. 2002. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci U S A 99:9697-702) was added to the sample volume to prevent RNA degradation.  The sample was quickly centrifuged at 4°C and the supernatant was discarded.  The remaining sample was then stored at -80°C.  To isolate RNA, the frozen pellets were transferred to a mortar and pestle and ground to fine powder in the presence of liquid nitrogen.  RLT solution from RNeasy Mini Kit (Qiagen Inc., Valencia, CA) was added before the ground pellets thawed.  The remaining steps for RNA isolation were carried out as per manufacturer's instructions.  RNA integrity was determined by gel electrophoresis while its quantity and purity were estimated by UV absorbance at OD260 and OD260/OD280, respectively. Total RNA was reverse transcribed to cDNA by SuperscriptII (Invitrogen, Carlsbad, CA) with random hexamers (IDT, Coralville, IA) incorporating aminoallyl-dUTP (Ambion, Austin, TX).

source_name: S. coelicolor genomic DNA


title: PTLD patient 05-179


title: S. coelicolor YSK4425 31h (Culture#2)

description: No additional description

source_name: S. coelicolor RNA R5- medium 31h


title: PTLD patient 05-171


title: S. coelicolor YSK3225 41h Replicate 2

description: No additional description

source_name: S. coelicolor RNA R5- medium 41h

growth_protocol: S. coelicolor A3(2) strain YSK3225 was maintained on R5 solid agar (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) for high density spores.  For liquid culture, spores were pre-germinated in 2xYT medium (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) and inoculated into R5- liquid medium (Huang, J., C. J. Lih, K. H. Pan, and S. N. Cohen. 2001. Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays. Genes Dev 15:3183-92) at a density of ~10exp7 spores/ml.  Baffled 2L flasks containing stainless steel coils with 350 ml working volume were used for liquid cultures.  Cultures were incubated at 30°C in an orbital shaker at 300 rpm.  For measuring cell growth, samples were collected at regular intervals and mixed with one-eighth volume of 2.5 M HCl and then subjected to sonication to break mycelial pellets (Brana, A. F., S. Wolfe, and A. L. Demain. 1986. Relationship between nitrogen assimilation and cephalosporin synthesis in Streptomyces clavuligerus. Arch Microbiol 146:46-51).  Absorbance of the resulting solution at 450 nm was then taken as a measure of growth.  Proper dilution was made to ensure an OD450 measurement below 1, which is in the linear range of detection.

value: 41h Replicate 2


title: S. coelicolor YSK4425 37h (Culture#2)

description: No additional description

source_name: S. coelicolor RNA R5- medium 37h


title: S. coelicolor YSK4425 22h (Culture#2)

description: No additional description

source_name: S. coelicolor RNA R5- medium 22h


title: S. coelicolor YSK4425 20h (Culture#2)

description: No additional description

source_name: S. coelicolor RNA R5- medium 20h


title: S. coelicolor YSK4425 24h (Culture#2)

description: No additional description

source_name: S. coelicolor RNA R5- medium 24h


title: S. coelicolor YSK4425 16h (Culture#2)

description: No additional description

source_name: S. coelicolor RNA R5- medium 16h


title: S. coelicolor YSK4425 26h (Culture#2)

description: No additional description

source_name: S. coelicolor RNA R5- medium 26h


title: S. coelicolor YSK3225 32h Replicate 2

description: No additional description

source_name: S. coelicolor RNA R5- medium 32h

value: 32h Replicate 2


title: S. coelicolor YSK3225 38h

description: No additional description

source_name: S. coelicolor RNA R5- medium 38h


title: S. coelicolor YSK3225 35h Replicate 1

description: No additional description

source_name: S. coelicolor RNA R5- medium 35h

value: 35h Replicate 1


title: S. coelicolor YSK3225 35h Replicate 2

description: No additional description

value: 35h Replicate 2


title: S. coelicolor YSK3225 41h Replicate 1

description: No additional description

value: 41h Replicate 1


title: S. coelicolor YSK3225 32h Replicate 1

description: No additional description

value: 32h Replicate 1


title: S. coelicolor YSK3225 37h Replicate 2

description: No additional description

value: 37h Replicate 2


title: S. coelicolor YSK3225 31h Replicate 2

description: No additional description

value: 31h Replicate 2


title: S. coelicolor YSK3225 28h Replicate 3

description: No additional description

source_name: S. coelicolor RNA R5- medium 28h

value: 28h Replicate 3


title: S. coelicolor YSK3225 28h Replicate 1

description: No additional description

value: 28h Replicate 1


title: S. coelicolor YSK3225 26h Replicate 2

description: No additional description

value: 26h Replicate 2


title: S. coelicolor YSK3225 24h Replicate 3 (Culture#1)

description: No additional description

value: 24h Replicate 3


title: S. coelicolor YSK3225 24h Replicate 4 (Culture#1)

description: No additional description

source_name: S. coelicolor RNA R5- medium 124h

value: 24h Replicate 4


title: S. coelicolor YSK3225 31h Replicate 1

description: No additional description

value: 31h Replicate 1


title: S. coelicolor YSK3225 24h Replicate 2 (Culture#1)

description: No additional description

value: 24h Replicate 2


title: S. coelicolor YSK3225 26h Replicate 1

description: No additional description

value: 26h Replicate 1


title: S. coelicolor YSK3225 24h Replicate 1 (Culture #1)

description: No additional description

value: 24h Replicate 1


title: S. coelicolor YSK3225 19h Replicate 1

description: No additional description

source_name: S. coelicolor RNA R5- medium 19h

value: 19h Replicate 1


title: S. coelicolor YSK3225 11h Replicate 1

description: No additional description

source_name: S. coelicolor RNA R5- medium 11h

value: 11h Replicate 1


title: S. coelicolor YSK3225 37h Replicate 1

description: No additional description

value: 37h Replicate 1


title: S. coelicolor YSK3225 22h Replicate 1

description: No additional description

value: 22h Replicate 1


title: S. coelicolor YSK3225 11h Replicate 2

description: No additional description

value: 11h Replicate 2


title: S. coelicolor YSK3225 19h Replicate 3

description: No additional description

value: 19h Replicate 3


title: S. coelicolor YSK3225 19h Replicate 2

description: No additional description

value: 19h Replicate 2


title: S. coelicolor YSK3225 19h Replicate 4

description: No additional description

value: 19h Replicate 4


title: S. coelicolor YSK3225 28h Replicate 2

description: No additional description

value: 28h Replicate 2


title: S. coelicolor YSK3225 24h Replicate 1

description: No additional description

source_name: S. coelicolor RNA R5- medium 24h Replicate 1


title: S. coelicolor YSK3225 18h

description: No additional description

source_name: S. coelicolor RNA R5- medium 18h

source_name: S. coelicolor genomic DNA


title: S. coelicolor YSK3225 26h

description: No additional description


title: S. coelicolor YSK3225 24h Replicate 2

description: No additional description

source_name: S. coelicolor RNA R5- medium 24h Replicate 2


title: S. coelicolor YSK3225 22h Replicate 2

description: No additional description

value: 22h Replicate 2


title: S. coelicolor YSK3225 42h

description: No additional description

source_name: S. coelicolor RNA R5- medium 42h


title: S. coelicolor YSK3225 32h

description: No additional description


title: S. coelicolor YSK3225 28h

description: No additional description


title: Bone marrow stromal cell (1773BMSC3F0664)

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

description: marrow stromal cells

hyb_protocol: Biotinylated cRNA was hybridized with a probe array for 16h at 45C, and the hybridized biotinylated cRNA was stained with streptavidin-PE.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner (Palo Alto).

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

source_name: human mesenchymal stem cells, cat no. PT-250, lot no. 3F0664 were purchased from Cambrex (East Rutherford, NJ, USA).

label_protocol: cDNA was subjected to in vitro transcription in the presence of biotinylated nucleoside triphosphates using the Enzo BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences), according to the manufacturer's protocol (One-Cycle Target Labeling and Control Reagent package).

extract_protocol: Total cellular RNA was isolated with the RNeasy Mini Kit (Qiagen), according to manufacture's instructions.). Genomic DNA was eliminated by DNase I (TAKARA BIO INC.) treatments.

tag: Human mesenchymal stem cells (1773BMSC3F0664)


title: Complex type germ cell tumor of human embryonic testis origin (1299NCR-G3NAd)

description: embryonal carcinoma cells

source_name: Complex type germ cell tumor

tag: Human embryonic testis (1299NCR-G3NAd)


title: Complex type germ cell tumor of human embryonic testis origin (1756NCR-G4Ad)

description: embryonal carcinoma cells

tag: Human embryonic testis (1756NCR-G4Ad)


title: 5-azacytidine-treatd POU5F1/Oct-4/3 overexpressing human cell

description: POU5F1/Oct-4/3 overexpressing human cells

source_name: Human cell line that was established from the pelvic tumor after treating with 5-azacytidine as a demethylating reagent

tag: Human female undifferentiated bone tumor of the pelvis (1806GST6-5Az)


title: MDA-MB-231 cells siLuc (control) transfected rep3 HG-U133A

status: Public on Jun 13 2007

city: Halle (Saale)

first: Juergen

last: Dittmer

department: Clinic of Gynecology

country: Germany

institute: University of Halle

description: following the instructions by Affymetrix

source_name: MDA-MB-231 cells_siLuc transfected_3 days post-tranfection

extract_protocol: RNA extraction kit “Nucleospin RNA II” (Macherey-Nagel, Dueren, Germany) was used

tag: MDA-MB-231 breast cancer cell line


title: MDA-MB-231 cells siLuc (ctrl) transfected rep2 HG-U133A

hyb_protocol: following the instructions by Affymetrix


title: MDA-MB-231 cells siLuc (control) transfected rep1 HG-U133A

scan_protocol: following the instructions by Affymetrix


title: MDA-MB-231 cells siRhoGDIbeta transfected rep2 HG-U133A

data_processing: following the instructions by Affymetrix

source_name: MDA-MB-231 cells_siRhoGDIbeta transfected_3 days post-tranfection


title: MDA-MB-231 cells siRhoGDIbeta transfected rep1 HG-U133A

label_protocol: following the instructions by Affymetrix


title: Bone marrow stromal cell (1112H4-1)

description: marrow stromal cells

source_name: bone marrow derived from human female

tag: Human mesenchymal stem cells (1112H4-1)


title: Human yolk sac tumor

description: yolk sac tumor cells

source_name: human yolk sac tumor

tag: Human embryonic testis (1842NCR-G1Ad)


title: MDA-MB-231 cells siRhoGDIbeta transfected rep3 HG-U133A


title: Complex type germ cell tumor of human embryonic testis origin (1754NCR-G2Ad)

description: embryonal carcinoma cells

tag: Human embryonic testis (1754NCR-G2Ad)


title: Bone marrow stromal cell (1838Yub610_10F)

description: marrow stromal cells

source_name: bone marrow derived from infant extra finger

tag: Human mesenchymal stem cells (1838Yub610_10F)


title: POU5F1/Oct-4/3 overexpressing human cell

source_name: Human cell line established from the pelvic tumor

tag: Human female undifferentiated bone tumor of the pelvis (1623GST6)


title: treated with Roziglitazone, 1000 mg/kg in Methylcellulose soln per orally, extracted 48h after treatment, biol. rep4

status: Public on Aug 12 2006

city: Lundtofte

first: Jeppe

middle: Skytte

last: Spicker

address: Building 208

department: CBS

country: Denmark

institute: Danish University of Technology

description: Gene expression data from rat liver 48 hours after treatment with compound.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 version 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned on GeneChip® Scanner 3000 7G 4C

data_processing: The data were analyzed with RMA. R was used with the affy package. Expresso with the following settings (bgcorrect.method=rma, normalize.method = quantiles.robust, pmcorrect.method=pmonly, summary.method=liwong) was used to normalize

source_name: Rat liver, left lateral lobe

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

extract_protocol: Frozen liver samples were homogenized in 2 ml TRIzol® reagent (Invitrogen ; Life Technologies, Scotland)  using an Ultra Turrax T25 basic homogenizer (IKA Labortechnik; IKA-Werke, Staufen, Germany). Chloroform (400 ?l) was added and homogenized samples were shaken vigorously by hand for 15 seconds. Phase separation was achieved by centrifugation for 15 min at 10,000 × g at 4°C. Total RNA from the aqueous phase was purified using the RNeasy 96 Qiagen vacuum system following the “Clean-up” procedure.

treatment_protocol: The animals were sacrificed 48 hours after treatment and organs were frozen for later analysis. Tissue samples of the left lateral lobe of the liver were snap frozen in liquid nitrogen, transferred to dry ice and stored at approximately -80?C

tag: Male Sprague-Dawley (Crl:CD(SD)IGS Br

tag: Age

value: between 5 and 6 weeks old


title: Rat liver, treated with NMF, 1000 mg/kg in saline i.p., extrated 48 hours after treatment, biological rep3


title: Rat liver, treated with NMF, 1000 mg/kg in saline i.p., extrated 48 hours after treatment, biological rep2


title: treated with Roziglitazone, 1000 mg/kg in Methylcellulose soln per orally, extracted 48h after treatment, biol. rep3


title: Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep4


title: Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep2


title: treated with Roziglitazone, 1000 mg/kg in Methylcellulose soln per orally, extracted 48h after treatment, biol. rep2


title: Rat liver, treated with NMF, 1000 mg/kg in saline i.p., extrated 48 hours after treatment, biological rep1


title: treated with Roziglitazone, 1000 mg/kg in Methylcellulose soln per orally, extracted 48h after treatment, biol. rep5


title: Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep9


title: Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep3


title: Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep1


title: Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep7


title: Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep6


title: Rat liver, treated with NMF, 1000 mg/kg in saline i.p., extrated 48 hours after treatment, biological rep4


title: Rat liver, treated with DMN, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep5


title: Rat liver, treated with DMN, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep4


title: Rat liver, treated with NMF, 1000 mg/kg in saline i.p., extrated 48 hours after treatment, biological rep5


title: Rat liver, treated with DNP, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep2


title: Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep8


title: Rat liver, treated with DMN, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep3


title: Rat liver, treated with DNP, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep4


title: Rat liver, treated with DNP, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep5


title: Rat liver, treated with DNP, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep3


title: Rat liver, treated with DMN, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep2


title: Rat liver, treated with Caerulein, 50 µg/kg in saline i.p., extrated 48 hours after treatment, biological rep5


title: Rat liver, treated with DNP, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep1


title: Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep5


title: Rat liver, treated with DMN, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep1


title: Rat liver, treated with Caerulein, 50 µg/kg in saline i.p., extrated 48 hours after treatment, biological rep4


title: Rat liver, treated with Caerulein, 50 µg/kg in saline i.p., extrated 48 hours after treatment, biological rep2


title: Rat liver, treated with ANIT, 125 mg/kg in corn oil per orally, extrated 48 hours after treatment, biological rep4


title: Rat liver, treated with ANIT, 125 mg/kg in corn oil per orally, extrated 48 hours after treatment, biological rep1


title: Rat liver, treated with Caerulein, 50 µg/kg in saline i.p., extrated 48 hours after treatment, biological rep1


title: Rat liver, treated with Caerulein, 50 µg/kg in saline i.p., extrated 48 hours after treatment, biological rep3


title: treated with Roziglitazone, 1000 mg/kg in Methylcellulose soln per orally, extracted 48h after treatment, biol. rep1


title: Rat liver, treated with ANIT, 125 mg/kg in corn oil per orally, extrated 48 hours after treatment, biological rep3


title: Rat liver, treated with ANIT, 125 mg/kg in corn oil per orally, extrated 48 hours after treatment, biological rep5


title: Rat liver, treated with ANIT, 125 mg/kg in corn oil per orally, extrated 48 hours after treatment, biological rep2