title: slide13_adult: Pre- and postnatal hepatic expression profiles of two pig breeds

status: Public on Jul 27 2007

type: RNA

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: Total RNA was isolated using TRI Reagent (Sigma Aldrich) according to the manufacturer?s protocol. After DNAse treatment RNA was quantified and integrity checked by electrophoresis of 1 ?g RNA on 1% agarose gels containing formaldehyde stained with ethidium bromide. mRNA was isolated from total RNA using magnetic oligo-(dT)-bead (Dynabeads, Dynal). Pools of 1 ?g of mRNA of each group of animals were labelled with Cy3 or Cy5 using the CyScribe Post-Labeling Kit (GE Healthcare), which involves the use of oligo-(dT) primers and random nanomers for synthesis of amino allyl-labelled first-strand cDNA and coupling of cDNA with CyDye NHS ester. Cy3/Cy5 labelled cDNAs were purified used CyScribe GFX purify kit (GE Healthcare). Cy3- and Cy5-labelled cDNAs were hybridised to the set of 13297 pig-specific 70-mer oligonucleotides (Qiagen-NRSP8) at 42 ?C for 14?18 hours using the Pronto Universal Hybridization kit was used (Corning B.V. Life Science). Hybridized slides were washed once with 1נSSC, 0.2% (w/v) SDS for 10 minutes at 42 ?C and twice with 0.1נSSC, 0.2% (w/v) SDS. Finally, slides were dipped into distilled water and air-dried.

data_processing: Microarrays were scanned using the 428 Array Scanner (Affymetrix). Spots were quantified and quality filtering was applied using ImaGene5 software version 5.6 (BioDiscovery). Each spot had to pass a number of quality criteria including spot consistency, minimum intensity levels, and minimum signal-to-background ratio. The subtracted signal median of genes that passed filtering was analysed further with TIGR Microarray Data Analysis System (MIDAS) that allows performing normalisation steps: per spot, intensity dependent (lowess fit). Filtered and normalized expression data were analyzed using TIGR Multiexperiment Viewer (MEV). The t-test was conducted of each stage and the set of p-values for each stage was converted to a set of q values using the software program QVALUE. To compare all stages between DL and Pi, variance analysis (ANOVA, p < 0.05) was used and these subsequent analyses were compared using hierarchical clustering.

molecule: polyA RNA

organism: Sus scrofa

tag: 3rd pool of RNAs derived from liver of animals of the breed Pietrain (Pi) at adult 118 days

tag: 3rd pool of RNAs derived from liver of animals of the breed German Landrace (DL) at adult 118 days


title: slide12_adult: Pre- and postnatal hepatic expression profiles of two pig breeds

tag: 2nd pool of RNAs derived from liver of animals of the breed Pietrain (Pi) at adule 118 days

tag: 2nd pool of RNAs derived from liver of animals of the breed German Landrace (DL) at adult 118 days


title: slide7_91dpc: Pre- and postnatal hepatic expression profiles of two pig breeds

tag: 1st pool of RNAs derived from liver of animals of the breed Pietrain (Pi) at 91 dpc

tag: 1st pool of RNAs derived from liver of animals of the breed German Landrace (DL) at 91 dpc


title: ALC_cultured_s3ctrl-rep3

status: Public on Jul 20 2007

city: san francisco

first: Pamela

last: DenBesten

state: CA

address: 513 Parnassus Ave. Rm S-612

department: Orofacial sciences

country: USA

institute: UCSF

description: Comparison of in vitro cultured ameloblast-lineage cells with versus without 10uM NaF.

data_processing: The image file was inverted and spots were digitized using ScanAlyze software (Shareware, http://rana.lbl.gov/EisenSoftware.htm), and normalized by subtracting the background as the average intensity value of three spots containing plasmid DNA (PUC18). The average of two GAPDH spots were used as positive controls set as baseline values to which the signal intensity of other spots was compared. Using this normalized data, the signal intensity from the membranes was compared using the GEArray Analyzer program (Superarray Corp. http: //www.superarray.com).

molecule: total RNA

organism: Homo sapiens

source_name: human fetal teeth, digested, 60min

tag: Age

tag: Tissue

value: fetal tooth organ


title: ALC_cultured_s2F-rep2


title: slide9_91dpc: Pre- and postnatal hepatic expression profiles of two pig breeds

tag: 3rd pool of RNAs derived from liver of animals of the breed Pietrain (Pi) at 91 dpc

tag: 3rd pool of RNAs derived from liver of animals of the breed German Landrace (DL) at 91 dpc


title: slide3_35dpc: Pre- and postnatal hepatic expression profiles of two pig breeds

tag: 3rd pool of RNAs derived from liver of animals of the breed Pietrain (Pi) at 35 dpc

tag: 3rd pool of RNAs derived from liver of animals of the breed German Landrace (DL) at 35 dpc


title: Contralateral LGN layer 5 (non-deprived layer)

city: Cleveland

first: Henry

middle: J.

last: Kaminski

state: OH

address: 11100 Euclid Avenue

department: Neurology

institute: Case Western Reserve University

description:
Por319
Contralateral LGN Layer 5 (non-deprived) in Monocular Deprived Macaque Monkey

organism: Macaca mulatta

source_name: LGN in Monocular Deprived Macaque Monkey


title: slide10_91dpc: Pre- and postnatal hepatic expression profiles of two pig breeds

tag: 4th pool of RNAs derived from liver of animals of the breed Pietrain (Pi) at 91 dpc

tag: 4th pool of RNAs derived from liver of animals of the breed German Landrace (DL) at 91dpc


title: ALC_cultured_s3F-rep3


title: slide1_35dpc: Pre- and postnatal hepatic expression profiles of two pig breeds

tag: 1st pool of RNAs derived from liver of animals of the breed Pietrain (Pi) at 35 dpc

tag: 1st pool of RNAs derived from liver of animals of the breed German Landrace (DL) at 35 dpc


title: Contralateral LGN layer 6 (deprived layer)

description:
Por320
Contralateral LGN layer 6 (deprived) in Monocular Deprived Macaque Monkey


title: Contralateral LGN layer 3 (non-deprived layer)

description:
Por317
Contralateral LGN layer 3 (non-deprived) in Monocular Deprived Macaque Monkey


title: Contralateral LGN layer 4 (deprived layer)

description:
Por318
Contralateral LGN layer 4 (deprived) in Monocular Deprived Macaque Monkey


title: slide8_91dpc: Pre- and postnatal hepatic expression profiles of two pig breeds

tag: 2nd pool of RNAs derived from liver of animals of the breed Pietrain (Pi) at 91 dpc

tag: 2nd pool of RNAs derived from liver of animals of the breed German Landrace (DL) at 91 dpc


title: Contralateral LGN layer 1 (deprived layer)

description:
Por315
Contralateral LGN layer 1 (deprived) in Monocular Deprived Macaque Monkey


title: Ipsilateral LGN layer 3 (deprived layer)

description:
Por311
Ipsilateral LGN layer 3 (deprived) in Monocular Deprived Macaque Monkey


title: ALC_cultured_s2ctrl-rep2


title: Contralateral LGN layer 2 (non-deprived layer)

description:
Por316
Contralateral LGN layer 2 (non-deprived) in Monocular Deprived Macaque Monkey


title: 370 v 10R #3 Cy3Cy5

status: Public on Jul 19 2007

city: College Park

first: Kevin

middle: S

last: McIver

state: MD

address: 3124 Biociences Research Bldg. (413)

department: Cell Biology and Molecular Genetics

institute: University of Maryland, College Park

description: Details located in Ribardo et al 2006

hyb_protocol: 50C overnight

scan_protocol: GenePix 6.1

data_processing: ratio-based Pearson Centered normalization using Acuity 4.0

organism: Streptococcus pyogenes

label_protocol: Amersham CyScribe Post-Labelling Kit

growth_protocol: 37C in closed cap tubes to late exponential phase

extract_protocol: CsCl isolation with ultracentrifugation


title: 370 v 10R #1 Cy3Cy5

description: Details located in Ribardo et al 2006


title: 370 v 10R #2 Cy5Cy3

description: Details located in Ribardo et al 2006


title: Ipsilateral LGN layer 6 (non-deprived layer)

description:
Por314
Ipsilateral LGN layer 6 (non-deprived) in Monocular Deprived Macaque Monkey


title: slide11_adult: Pre- and postnatal hepatic expression profiles of two pig breeds

tag: 1st pool of RNAs derived from liver of animals of the breed Pietrain (Pi) at adult 118 days

tag: 1st pool of RNAs derived from liver of animals of the breed German Landrace (DL) at adult 118 days


title: Ipsilateral LGN layer 4 (non-deprived layer)

description:
Por312
Ipsilateral LGN layer 4 (non-deprived) in Monocular Deprived Macaque Monkey


title: Ipsilateral LGN layer 1 (non-deprived layer)

description:
Por309
Ipsilateral LGN layer 1 (non-deprived) in Monocular Deprived Macaque Monkey


title: 370 v 10R #2 Cy3Cy5

description: Details located in Ribardo et al 2006


title: Ipsilateral LGN layer 5 (deprived layer)

description:
Por313
Ipsilateral LGN layer 5 (deprived) in Monocular Deprived Macaque Monkey


title: ALC_cultured_s1F-rep1


title: ALC_cultured_s1ctrl


title: Ipsilateral LGN layer 2 (deprived layer)

description:
Por310
Ipsilateral LGN layer 2 (deprived) in Monocular Deprived Macaque Monkey


title: In_vivo_1-5mm_vs_Reference_2

status: Public on Jul 18 2007

city: Rockville

first: Jia

last: Liu

address: 9712 Medical Center Drive

institute: Plant Genomics

description: For in vitro tuber development expression analysis, RNA was isolated from in vitro microtubers at 2, 5, 10, 20 and 30 days following observed tuber induction.  Two microtuber populations were used as biological replicates for the developmental stages.  The RNA from all developmental stages was pooled to generate the reference samples.  Ten microarray hybridizations were performed.  For in vivo tuber development expression analysis, RNA was isolated from tubers growing in growth chamber conditions.  Tissues were divided into six group, according to developmental size: stolon (no tuber formation), 1-5 mm tubers, 6-10 mm tubers, 11-15 mm tubers, 16-25 mm tubers, and 26-35 mm tubers.  Two biological replicates of ten plants each were grown sequentially in the same growth chamber.  The RNA from all developmental stages was pooled to generate the reference samples.  Twelve microarray hybridizations were performed.  For all experiments, the RNA was labeled using the indirect labeling method with random hexamer primers.  Amplified cRNA was used as labeling template for stolons.  Total RNA was used as labeling template in all other labeling reactions.

data_processing: The TIFF images were quantified using Genepix 5.0. Local background was subtracted from the signal value and the data was normalized using the quantile method in the limma package of bioconductor.

organism: Solanum tuberosum

growth_protocol: Hormone-free tissue culture tuber-induction medium (0.5x MSMO, 8% sucrose, 0.5 mg/L nicotinic acid, 0.5 mg/L pyridoxide HCl, 0.2% Phytagel, pH 5.6); Continuous darkness at 20C

tag: Solanum tuberosum, In vivo tuber, Development


title: In_vivo_26-35mm_vs_Reference_2


title: 370 v 10R #1 Cy5Cy3

description: Details located in Ribardo et al 2006


title: In_vivo_11-15mm_vs_Reference_2


title: In_vivo_16-25mm_vs_Reference_2


title: In_vivo_16-25mm_vs_Reference_1


title: 370 v 10R #3 Cy5Cy3

description: Details located in Ribardo et al, 2006

label_protocol: Amersham CyScribe Post Labelling Kit


title: In_vitro_10Day_vs_Reference_2

tag: Solanum tuberosum, In vitro tuber, Development


title: In_vivo_26-35mm_vs_Reference_1


title: Mouse adult whole testis (XX/Sry)

status: Public on Jul 15 2007

city: bunkyo-ku

first: Anshin

last: Hoshino

state: tokyo

address: 1-1-1 yayoi

department: agriculture

country: Japan

institute: toukyo-univ.

description: Gene expression data from adult mouse testis(XX/Sry)

data_processing: MAS 5.0

label: biotin

organism: Mus musculus

source_name: Mouse adult whole testis (XX/Sry)

tag: Strain:B6/ Hsp-Sry

tag: Tissue:whole testis


title: Mouse adult seminiferous tubules of XX/Sry

description: Gene expression data from mouse adult seminiferous tubules  (XX/Sry)

tag: Strain:

tag: Tissue

value: seminiferous tubules


title: Mouse adult seminiferous tubules of W/Wv

description: Gene expression data from mouse adult seminiferous tubules  (W/Wv)

source_name: Mouse adult seminiferous tubules  (W/Wv) (WB x B6; purchased from SLC)

tag: Strain:(WB x B6; purchased from SLC)

tag: Tissue:seminiferous tubules


title: In_vitro_02Day_vs_Reference_2


title: In_vitro_30Day_vs_Reference_2


title: In_vitro_30Day_vs_Reference_1


title: In_vivo_6-10mm_vs_Reference_1


title: In_vivo_11-15mm_vs_Reference_1


title: In_vivo_Stolon_vs_Reference_2

tag: Solanum tuberosum, In vivo stolon, Development


title: In_vivo_1-5mm_vs_Reference_1


title: In_vivo_Stolon_vs_Reference_1


title: In_vitro_20Day_vs_Reference_2


title: In_vitro_05Day_vs_Reference_2


title: In_vitro_02Day_vs_Reference_1


title: In_vivo_6-10mm_vs_Reference_2


title: In_vitro_20Day_vs_Reference_1


title: In_vitro_05Day_vs_Reference_1


title: mouse adult whole testis (W/Wv)

description: Gene expression data from adult mouse testis(W/Wv)

source_name: mouse adult whole testis (W/Wv) (WB x B6; purchased from SLC)

tag: Strain:(W/Wv) (WB x B6; purchased from SLC)

tag: tissue:whole testis


title: In_vitro_10Day_vs_Reference_1


title: ALL53

status: Public on Jul 14 2007

city: Stanford

first: Dejan

last: Juric

address: 269 Campus Drive

department: Medicine, Oncology

institute: Stanford University School of Medicine

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64361.gif; format: GIF

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: universal common reference

tag: universal common reference


title: ALL36

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64344.gif; format: GIF


title: ALL39

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64347.gif; format: GIF


title: ALL52

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64360.gif; format: GIF


title: ALL38

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64346.gif; format: GIF


title: ALL35

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64343.gif; format: GIF


title: ALL16

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64324.gif; format: GIF


title: ALL14

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64322.gif; format: GIF


title: ALL13

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64321.gif; format: GIF


title: ZR75_1_Untreated_10%

city: Amsterdam

first: Dimitry

last: Nuyten

address: Plesmanlaan 121

department: Radiation Oncology

country: Netherlands

institute: The Netherlands Cancer Institute

description: Untreated versus treated (bortezomib) breast cancer cells.

data_processing: Fluorescent intensities were normalized and corrected for a variety of biases that affect the intensity measurements (e.g., color bias and print tip bias) according to Yang et al. (Nucleic Acids Res. 30, e15 (2002)). Weighted averages and confidence levels were computed according to the Rosetta Error Model (Hughes, T.R. et al., Cell 102, 109-126 (2000)).

growth_protocol: Breast cancer cells were grown in DMEM medium (Invitrogen) with 10% fetal bovine serum (FBS). Harvested at 70% confluence or 48h 0.1% serum starvation before harvesting

tag: Breast cancer cell lines; untreated

tag: NKI breast reference pool, 100 human breast tumors, early stage


title: ALL15

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64323.gif; format: GIF


title: T47D_Untreated_10%


title: T47D_Untreated_0.1%


title: ALL21

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64329.gif; format: GIF


title: ALL37

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64345.gif; format: GIF


title: ALL18

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64326.gif; format: GIF


title: ALL33

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64341.gif; format: GIF


title: MPL13E_untreated_10%


title: ALL20

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64328.gif; format: GIF


title: SKBR3_untreated_0.1%


title: MPL13E_untreated_0.1%


title: ALL19

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64327.gif; format: GIF


title: ALL34

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64342.gif; format: GIF


title: ALL51

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64359.gif; format: GIF


title: ALL40

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64348.gif; format: GIF


title: MCF7_Untreated_10%


title: MDA134_Untreated_0.1%


title: MCF7_Untreated_0.1%


title: ALL48

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64356.gif; format: GIF


title: ALL54

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64362.gif; format: GIF


title: ALL17

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64325.gif; format: GIF


title: ALL31

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64339.gif; format: GIF


title: ALL1

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64309.gif; format: GIF


title: ZR75_1_Untreated_0.1%


title: CAMA_1_Untreated_10%


title: ALL12

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64320.gif; format: GIF


title: ALL32

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64340.gif; format: GIF


title: ALL30

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64338.gif; format: GIF


title: SKBR3_untreated_10%

description: Untreated versus treated (bortezomib) breast cancer cells.


title: HBL100_Untreated_10%


title: T47D_Treated

description: Untreated versus treated (bortezomib), untranformed MCF10A and Transformed (see Adler et al, Nature Gen. 2006)

growth_protocol: Breast cancer cells were grown in DMEM medium (Invitrogen) with 10% fetal bovine serum (FBS).

treatment_protocol: 24h in 1uM bortezomib

tag: Breast cancer cell lines; treated


title: HBL100_Untreated_0.1%


title: MDA134_Treated


title: MDA134_Untreated_10%


title: ALL50

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64358.gif; format: GIF


title: CAMA_1_Untreated_0.1%


title: ALL49

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64357.gif; format: GIF


title: ALL44

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64352.gif; format: GIF


title: ALL47

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64355.gif; format: GIF


title: SKBR3_Treated


title: ALL45

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64353.gif; format: GIF


title: ALL11

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64319.gif; format: GIF


title: MCF10A_Treated_#6

growth_protocol: MCF10A cells were grown in DMEM/F12 (Invitrogen/Cambrex) with 5% fetal bovine serum, supplemented with EGF (20 ng/ml), insulin (10ug/ml) and hydrocortisone (0.5 ug/ml).

tag: breast epithelial cell line, transformed, treated


title: ALL10

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64318.gif; format: GIF


title: MCF10A_Treated_#3


title: MPL13E_Treated


title: ALL29

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64337.gif; format: GIF


title: ALL46

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64354.gif; format: GIF


title: ALL42

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64350.gif; format: GIF


title: ALL43

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64351.gif; format: GIF


title: ALL27

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64335.gif; format: GIF


title: MCF7_Treated


title: MCF10A_Untreated_#6

treatment_protocol: 48 hours @ 0.1% serum

tag: breast epithelial cell line, transformed, untreated


title: CAMA_1_Treated


title: HBL100_Treated


title: MCF10A_Treated_#4


title: MCF10A_Untreated_#5


title: MCF10A_Untreated_#4


title: smc deletion, replicate 4

status: Public on Jul 02 2007

city: Cambridge

first: Alan

middle: D.

last: Grossman

email: clee2@mit.edu, adg@mit.edu

state: MA

address: 31 Ames Street, 68-530

department: Biology

institute: MIT

description: See Britton RA et al. J Bacteriol. 2006 for protocol details.

data_processing: Cy3 and Cy5 signals for each spot were normalized to the total Cy3 and Cy5 signals of the array.  The total signal for each channel was calculated by summing the values of the total signals for each spot, which was calculated by multiplying the mean signal intensity (per pixel) by the number of pixels. Ratios were calculated only when the spot had a signal 1 standard deviation above background for 50% of pixels in each channel.

organism: Bacillus subtilis

source_name: smc deletion

tag: Strain

source_name: collective reference sample

tag: Mixture of wild-type RNA


title: MCF10A_Treated_#5


title: smc deletion, replicate 2


title: ALL28

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64336.gif; format: GIF


title: MCF10A_Untreated_#2

extract_protocol: see http://microarrays.nki.nl


title: MCF10A_Untreated_#3


title: smc disruption, replicate 3

source_name: smc disruption


title: smc disruption, replicate 4


title: MCF10A_Untreated_#1

growth_protocol: 48 hours @ 0.1% serum

tag: breast epithelial cell line, untransformed, untreated


title: ALL26

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64334.gif; format: GIF


title: smc deletion, replicate 3


title: ALL8

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64316.gif; format: GIF


title: ALL24

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64332.gif; format: GIF


title: ALL9

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64317.gif; format: GIF


title: ftsY disruption, replicate 4

source_name: ftsY disruption


title: smc disruption, replicate 1


title: smc deletion, replicate 1


title: ftsY disruption, replicate 3


title: smc disruption, replicate 2


title: ftsY disruption, replicate 2


title: Wild-type, replicate 3

source_name: Wild-type


title: Wild-type, replicate 2


title: ALL4

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64312.gif; format: GIF


title: wild-type vs. smc deletion, replicate 4


title: Wild-type, replicate 1

source_name: collective reference RNA


title: wild-type vs. smc deletion, replicate 3


title: ALL7

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64315.gif; format: GIF


title: ALL41

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64349.gif; format: GIF


title: ALL6

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64314.gif; format: GIF


title: ALL5

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64313.gif; format: GIF


title: Sprague-Dawley Male HighSalt OuterMedulla rat712 sd_medullar_k_712r_om_070302

status: Public on Jul 01 2007

city: West Point

first: David

middle: Lee

last: Gerhold

state: PA

address: Broad St & Sumneytown Pk

department: Mol Invest Toxicol

institute: Merck & Co.

description: Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks.

hyb_protocol: Five-microgram mRNA samples typically yielded between 30 and 150 mg purified cRNA. 15 microgram cRNA samples were fragmented at 95?C for 35 min in 10 mM MgCl2 to a mean size of ;50?100 nucleotides, added to hybridization buffer, and hybridized to the microarray for 16 h at 45?C. GeneChips were washed, stained with streptavidin-R-phycoerythrin, and scanned with a dedicated instrument to capture a fluorescence image (Molecular Dynamics).

scan_protocol: (per Affymetrix)

data_processing: SAFER: Proc American Stat Assoc. Holder 2002

label: streptavidin-phycoerythrin

organism: Rattus norvegicus

label_protocol:
(per Affymetrix technical manual P/N 700220) A primer encoding the T7 RNA polymerase promoter linked to oligo-dT17 was used to prime doublestranded
cDNA synthesis from each mRNA sample using Superscript II RNase H2 reverse transcriptase (Life Technologies, Rockville, MD). Each double-stranded cDNA sample
was purified by adsorption to silica (Qiaquick kit, Qiagen) according to manufacturer?s instructions, then in vitro transcribed using T7 RNA polymerase (MEGAscript T7 kit; Ambion,
Austin, TX), incorporating biotin-UTP and biotin-CTP (Enzo Biochemicals, New York, NY) into the resulting copy RNA (cRNA). These cRNA transcripts were purified using RNEasy (Qiagen).

extract_protocol:
Trizol(r) phenol-guanidinium extract
sup. to Qiaquick spin column

treatment_protocol: 14 weeks salt-controlled diet


title: wild-type vs. smc deletion, replicate 2


title: ALL22

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64330.gif; format: GIF


title: wild-type vs. smc deletion, replicate 1


title: Sprague-Dawley Male HighSalt OuterMedulla rat711 sd_medullar_k_711r_om_070302


title: ALL25

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64333.gif; format: GIF


title: Sprague-Dawley Male LowSalt OuterMedulla rat707 sd_medullar_k_707r_om_070302


title: Sprague-Dawley Male LowSalt OuterMedulla rat708 sd_medullar_k_708r_om_070302


title: ALL3

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64311.gif; format: GIF


title: ALL2

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64310.gif; format: GIF


title: ftsY disruption, replicate 1


title: Sprague-Dawley Female LowSalt OuterMedulla rat703 sd_medullar_k_703r_om_070302


title: Sprague-Dawley Female HighSalt OuterMedulla rat706 sd_medullar_k_706r_om_070302


title: Sprague-Dawley Female LowSalt OuterMedulla rat701 sd_medullar_k_701r_om_070302


title: Sprague-Dawley Female LowSalt OuterMedulla rat702 sd_medullar_k_702r_om_070302


title: Sprague-Dawley Female HighSalt OuterMedulla rat704 sd_medullar_k_704r_om_070302


title: Sprague-Dawley Male HighSalt Cortex rat711 sd_cortexr_k_711c_020802


title: Sprague-Dawley Male LowSalt Cortex rat708 sd_cortexr_k_708c_020802

scan_protocol: see manuscript (per Affymetrix)


title: Sprague-Dawley Male HighSalt Cortex rat712 sd_cortexr_k_712c_020802


title: Sprague-Dawley Male LowSalt Cortex rat709 sd_cortexr_k_709c_020802


title: Sprague-Dawley Female HighSalt Cortex rat705 sd_cortexr_k_705c_020802


title: Sprague-Dawley Female LowSalt Cortex rat701 sd_cortexr_k_701c_020802


title: Sprague-Dawley Female HighSalt Cortex rat706 sd_cortexr_k_706c_020802


title: Sprague-Dawley Female LowSalt Cortex rat703 sd_cortexr_k_703c_020802


title: Sprague-Dawley Male LowSalt Cortex rat707 sd_cortexr_k_707c_020802


title: Sprague-Dawley Female HighSalt Cortex rat704 sd_cortexr_k_704c_020802


title: Sprague-Dawley Female LowSalt Cortex rat702 sd_cortexr_k_702c_020802


title: ALL23

description:
Simple annotation: acute lymphoblastic leukemia, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64331.gif; format: GIF


title: Gonadectomized Dahl-Iwai Male HighSalt OuterMedulla rat12 gdahl_medullar_k_GX_12om_rh_051402


title: Gonadectomized Dahl-Iwai Male HighSalt OuterMedulla rat11 gdahl_medullar_k_GX_11om_rh_051402


title: Gonadectomized Dahl-Iwai Male HighSalt OuterMedulla rat10 gdahl_medullar_k_GX_10om_rh_051402


title: Gonadectomized Dahl-Iwai Female HighSalt OuterMedulla rat5 gdahl_medullar_k_GX_5om_050702


title: Gonadectomized Dahl-Iwai Male LowSalt OuterMedulla rat7 gdahl_medullar_k_GX_7om_rh_051402


title: Gonadectomized Dahl-Iwai Female HighSalt OuterMedulla rat6 gdahl_medullar_k_GX_6om_050702


title: Gonadectomized Dahl-Iwai Male LowSalt OuterMedulla rat9 gdahl_medullar_k_GX_9om_rh_051402


title: Gonadectomized Dahl-Iwai Female HighSalt OuterMedulla rat4 gdahl_medullar_k_GX_4om_050702


title: Gonadectomized Dahl-Iwai Male LowSalt OuterMedulla rat8 gdahl_medullar_k_GX_8om_rh_051402


title: Gonadectomized Dahl-Iwai Female LowSalt OuterMedulla rat3 gdahl_medullar_k_GX_3om_050702


title: Gonadectomized Dahl-Iwai Female LowSalt OuterMedulla rat2 gdahl_medullar_k_GX_2om_050702


title: Gonadectomized Dahl-Iwai Female LowSalt OuterMedulla rat1 gdahl_medullar_k_GX_1om_050702


title: Sprague-Dawley Male LowSalt OuterMedulla rat709 sd_medullar_k_709r_om_070302


title: Gonadectomized Dahl-Iwai Male LowSalt Cortex rat8 gdahl_cortexr_k_GX_8c_051702

scan_protocol: per Affymetrix

label: strpetavidin-phycoerythrin


title: Gonadectomized Dahl-Iwai Male LowSalt Cortex rat7 gdahl_cortexr_k_GX_7c_051702


title: Gonadectomized Dahl-Iwai Male HighSalt Cortex rat11 gdahl_cortexr_k_GX_11c_051702


title: Gonadectomized Dahl-Iwai Male HighSalt Cortex rat12 gdahl_cortexr_k_GX_12c_051702


title: Dahl-Iwai  Male HighSalt OuterMedulla rat114 dahl_medullar_114_1_OM_053001


title: Gonadectomized Dahl-Iwai Female HighSalt Cortex rat6 gdahl_cortexr_k_GX_6c_051702


title: Dahl-Iwai  Female HighSalt OuterMedulla rat106 dahl_medullar_106_1_OM_053001


title: Gonadectomized Dahl-Iwai Male HighSalt Cortex rat10 gdahl_cortexr_k_GX_10c_051702


title: Dahl-Iwai  Male LowSalt OuterMedulla rat110 dahl_medullar_110_1_OM_053001


title: Dahl-Iwai  Female HighSalt OuterMedulla rat107 dahl_medullar_107_1_OM_053001


title: Gonadectomized Dahl-Iwai Female HighSalt Cortex rat4 gdahl_cortexr_k_GX_4c_051702


title: Gonadectomized Dahl-Iwai Female LowSalt Cortex rat3 gdahl_cortexr_k_GX_3c_051702


title: Dahl-Iwai  Male LowSalt OuterMedulla rat109 dahl_medullar_109_1_OM_053001


title: Gonadectomized Dahl-Iwai Female LowSalt Cortex rat2 gdahl_cortexr_k_GX_2c_051702


title: Gonadectomized Dahl-Iwai Female LowSalt Cortex rat1 gdahl_cortexr_k_GX_1c_051702


title: Dahl-Iwai  Male HighSalt Cortex rat113 dahl_cortexr_k_113c_072001

source_name: Dahl-Iwai _Male_HighSalt_Cortex_rat113

tag: Dahl-Iwai _Male_HighSalt_Cortex_rat113


title: Dahl-Iwai  Female LowSalt OuterMedulla rat104 dahl_medullar_104_1_OM_053001


title: Dahl-Iwai  Female LowSalt OuterMedulla rat105 dahl_medullar_105_1_OM_053001


title: Gonadectomized Dahl-Iwai Female HighSalt Cortex rat5 gdahl_cortexr_k_GX_5c_051702


title: Dahl-Iwai  Male HighSalt Cortex rat112 dahl_cortexr_k_112c_072001

source_name: Dahl-Iwai _Male_HighSalt_Cortex_rat112

tag: Dahl-Iwai _Male_HighSalt_Cortex_rat112


title: Dahl-Iwai  Male HighSalt Cortex rat114 dahl_cortexr_k_114c_072001

source_name: Dahl-Iwai _Male_HighSalt_Cortex_rat114

tag: Dahl-Iwai _Male_HighSalt_Cortex_rat114


title: Dahl-Iwai  Male LowSalt Cortex rat109 dahl_cortexr_k_109c_072001

source_name: Dahl-Iwai _Male_LowSalt_Cortex_rat109

tag: Dahl-Iwai _Male_LowSalt_Cortex_rat109


title: Dahl-Iwai  Male LowSalt Cortex rat111 dahl_cortexr_k_111c_072001

source_name: Dahl-Iwai _Male_LowSalt_Cortex_rat111

tag: Dahl-Iwai _Male_LowSalt_Cortex_rat111


title: Dahl-Iwai  Male HighSalt OuterMedulla rat113 dahl_medullar_113_1_OM_053001


title: Dahl-Iwai  Female LowSalt OuterMedulla rat103 dahl_medullar_103_1_OM_053001


title: Dahl-Iwai  Male LowSalt OuterMedulla rat111 dahl_medullar_111_1_OM_053001


title: Dahl-Iwai  Female HighSalt Cortex rat107 dahl_cortexr_k_107c_072001


title: Dahl-Iwai  Female HighSalt Cortex rat106 dahl_cortexr_k_106c_072001


title: Dahl-Iwai  Female LowSalt Cortex rat105 dahl_cortexr_k_105c_072001

source_name: Dahl-Iwai _Female_LowSalt_Cortex_rat105


title: SFy_2

type: genomic

city: Beijing

first: Junping

last: Peng

address: No 6, Rongjing Eastern Street, BDA

country: China

institute: Chinese center for disease control and prevention

description: CGH

data_processing: Ratio of median

molecule: genomic DNA

organism: Shigella flexneri

source_name: genomic DNA

tag: Shigella flexneri variant y

organism: Escherichia coli


title: Dahl-Iwai  Female LowSalt Cortex rat104 dahl_cortexr_k_104c_072001

hyb_protocol: Five-microgram mRNA samples typically yielded between 30 and 150 mg purified cRNA. 15 microgram cRNA samples were fragmented at 95°C for 35 min in 10 mM MgCl2 to a mean size of ;50–100 nucleotides, added to hybridization buffer, and hybridized to the microarray for 16 h at 45°C. GeneChips were washed, stained with streptavidin-R-phycoerythrin, and scanned with a dedicated instrument to capture a fluorescence image (Molecular Dynamics).

source_name: dahl-Iwai _Female_LowSalt_Cortex_rat104

label_protocol:
(per Affymetrix technical manual P/N 700220) A primer encoding the T7 RNA polymerase promoter linked to oligo-dT17 was used to prime doublestranded
cDNA synthesis from each mRNA sample using Superscript II RNase H2 reverse transcriptase (Life Technologies, Rockville, MD). Each double-stranded cDNA sample
was purified by adsorption to silica (Qiaquick kit, Qiagen) according to manufacturer’s instructions, then in vitro transcribed using T7 RNA polymerase (MEGAscript T7 kit; Ambion,
Austin, TX), incorporating biotin-UTP and biotin-CTP (Enzo Biochemicals, New York, NY) into the resulting copy RNA (cRNA). These cRNA transcripts were purified using RNEasy (Qiagen).

extract_protocol: Trizol/Qiaquick

tag: dahl-Iwai _Female_LowSalt_Cortex_rat104


title: SF6_1

description: CGH

tag: Shigella flexneri 6


title: SFx_3

description: CGH

tag: Shigella flexneri variant x


title: SFy_3

description: CGH


title: SFx

description: CGH


title: Dahl-Iwai  Female LowSalt Cortex rat103 dahl_cortexr_k_103c_072001

source_name: Dahl-Iwai _Female_LowSalt_Cortex_rat103

tag: Dahl-Iwai _Female_LowSalt_Cortex_rat103


title: SF6_3

description: CGH


title: SFx_2

description: CGH


title: SF5_3

description: CGH

tag: Shigella flexneri 5


title: SD4_3

description: CGH

organism: Shigella dysenteriae

tag: Shigella dysenteriae 4


title: SFy_1

description: CGH


title: SF6_2

description: CGH


title: SF4a_1

description: CGH

tag: Shigella flexneri 4a


title: SF2b_3

description: CGH

tag: Shigella flexneri 2b


title: SF5

description: CGH


title: SF5_2

description: CGH


title: SF3_2

description: CGH

tag: Shigella flexneri 3


title: SF3_1

description: CGH


title: SF4b_2

description: CGH

tag: Shigella flexneri 4b


title: SF4b_3

description: CGH


title: SF4a_2

description: CGH


title: SF2b_1

description: CGH


title: SF2b_2

description: CGH


title: SF4b_1

description: CGH


title: SF4a_3

description: CGH


title: SF3_3

description: CGH


title: SF1b_2

description: CGH

tag: Shigella flexneri 1b


title: SF1a_3

description: CGH

tag: Shigella flexneri 1a


title: SF1b_1

description: CGH


title: SD13_1

description: CGH

tag: Shigella dysenteriae 13


title: SF1b_3

description: CGH


title: SD13_3

description: CGH


title: SD11_3

description: CGH

tag: Shigella dysenteriae 11


title: SD9_2

description: CGH

tag: Shigella dysenteriae 9


title: SD8_1

description: CGH

tag: Shigella dysenteriae 8


title: SD12_3

description: CGH

tag: Shigella dysenteriae 12


title: SD12_2

description: CGH


title: SF1a_2

description: CGH


title: SD9_1

description: CGH


title: SD11_1

description: CGH


title: SD13_2

description: CGH


title: SD9_3

description: CGH


title: SF1a_1

description: CGH


title: SD7_2

description: CGH

tag: Shigella dysenteriae 7


title: SD7_1

description: CGH


title: SD10_3

description: CGH

tag: Shigella dysenteriae 10


title: SD11_2

description: CGH


title: SD12_1

description: CGH


title: SD7_3

description: CGH


title: SD6_2

description: CGH

tag: Shigella dysenteriae 6


title: SD10_1

description: CGH


title: SD6_3

description: CGH


title: SD6_1

description: CGH


title: SD8_2

description: CGH


title: SD8_3

description: CGH


title: SD4_2

description: CGH


title: SD5_1

description: CGH

tag: Shigella dysenteriae 5


title: SD5_3

description: CGH


title: SD5_2

description: CGH


title: SD10_2

description: CGH


title: Sprague-Dawley Male HighSalt OuterMedulla rat710 sd_medullar_k_710r_om_070302


title: SD3_3

description: CGH

tag: Shigella dysenteriae 3


title: SD3_1

description: CGH


title: SD4_1

description: CGH

tag: Shigella dysenteriae 4


title: SD2_3

description: CGH

tag: Shigella dysenteriae 2


title: SD2_2

description: CGH


title: SB18_3

description: CGH

organism: Shigella boydii

tag: Shigella boydii 18


title: SB17_3

description: CGH

tag: Shigella boydii 17


title: SD2_1

description: CGH


title: SB18_2

description: CGH


title: SB15_3

description: CGH

tag: Shigella boydii 15


title: SB16_2

description: CGH

tag: Shigella boydii 16


title: SB15_2

description: CGH

tag: Shigella boydii  15


title: SD3_2

description: CGH


title: SB18_1

description: CGH


title: SB16_1

description: CGH


title: SB15_1

description: CGH


title: SB13_1

description: CGH

tag: Shigella boydii 13


title: SB16_3

description: CGH


title: SB12_2

description: CGH

tag: Shigella boydii serotype 12


title: SB14_2

description: CGH

tag: Shigella boydii 14


title: SB12_1

description: CGH


title: SB12_3

description: CGH


title: SB14_3

description: CGH


title: SB13_2

description: CGH

tag: Shigella boydii serotype 13


title: SB17_2

description: CGH


title: SB17_1

description: CGH


title: SB14_1

description: CGH


title: SB10_3

description: CGH

tag: Shigella boydii serotype 10


title: SB13_3

description: CGH


title: SB11_2

description: CGH

tag: Shigella boydii serotype 11


title: SB10_2

description: CGH


title: SB11_3

description: CGH


title: SB9_1

description: CGH

tag: Shigella boydii serotype 9


title: SB8_3

description: CGH

tag: Shigella boydii serotype 8


title: SB11_1

description: CGH


title: SB10_1

description: CGH


title: SB8_2

description: CGH


title: SB3_2

description: CGH

tag: Shigella boydii serotype 3


title: SB8_1

description: CGH


title: SB6_3

description: CGH

tag: Shigella boydii serotype 6


title: SB9_3

description: CGH


title: SB6_2

description: CGH


title: SB7_2

description: CGH

tag: Shigella boydii  serotype 7


title: SB9_2

description: CGH


title: SB5_1

description: CGH

tag: Shigella boydii serotype 5


title: SB3_1

description: CGH

tag: Shigella boydii serotype3


title: SB7_3

description: CGH

tag: Shigella boydii serotype 7


title: SB6_1

description: CGH


title: SB5_3

description: CGH


title: SB3_3

description: CGH


title: SB7_1

description: CGH


title: SB2_2

description: CGH

tag: Shigella boydii serotype 2


title: SB5_2

description: CGH


title: SB2_1

description: CGH

tag: Shigella boydii serogroup 2


title: SB1_2

description: CGH

data_processing: ration of median(635/532)

tag: Shigella boydii serotype 1


title: SB2_3

description: CGH

tag: Shigella boydii serotype2


title: SB1_1

description: CGH

source_name: SB1 genomic DNA

source_name: reference DNA


title: SB1_3

description: CGH

tag: Shigella boydii serogroup 1

source_name: genomic dna


title: Bovine_C22_cy5_C35_cy3

status: Public on Jun 30 2007

city: Columbia

first: Zhilin

state: MO

address: 920 East Campus Dr., ASRC S140

institute: University of Missouri-Columbia

description: The hybridization was carried out using the 3DNA Array 350 kit (Genisphere Inc., Hatfield, PA) according to the manufacture?s instructions. For each hybridization, 5?g of total RNA of each follicle sample were used. After hybridization, the slides were scanned using an Axon GenePix 4000B scanner (Axon Instruments Inc., Union City, CA) at 5?m resolution, and the image was analyzed using GenePix Pro 4.0.1.12 software (Axon Instruments Inc., Union City, CA). The result files and the image were linked together and stored in the local BioArray Software Environment (BASE) database (Saal et al., 2002).

data_processing: The result data were first filtered to remove all control spots, 3נSSC, and blank spots. Then the background-corrected-median-intensities were normalized using a pin-based-lowess-normalization within BASE. The log ratio of chanel 1 VS. chanel 2 were then outputed together with the raw data for each spot of all the arrays.

organism: Bos taurus

source_name: Bovine ovarian follicle C22

extract_protocol: RNAqueous-Midi kit, (Ambion Inc., Austin, Texas)

tag: ovarian follicle,  8mm, tube B, weight 0.0957g

source_name: Bovine ovarian follicle C35

tag: ovarian Follicle,  11X10mm, tube A, 0.0863g


title: Bovine_26_cy5_J980_cy3

hyb_protocol: 3DNA Array 350 kit (Genisphere Inc., Hatfield, PA)

source_name: Bovine ovarian follicle 26

tag: ovarian follicle,  8.5mm, tube A, weight 0.0511g

source_name: Bovine ovarian follicle J980

tag: ovarian follicle,  9X10mm, tube A, weight 0.0650g


title: Bovine_J980_cy5_27_cy3

label_protocol: 3DNA Array 350 kit (Genisphere Inc., Hatfield, PA)

source_name: Bovine ovarian follicle 27

tag: ovarian follicle,  9mm, tube A, weight 0.0589g


title: Bovine_J980_cy5_8_cy3

source_name: Bovine ovarian follicle 8

tag: ovarian follicle,  9mm, tube A, weight 0.0694g


title: Bovine_C26_cy5_33_cy3

source_name: Bovine ovarian follicle C26

tag: ovarian follicle, 12mm,  Tube A, Weight 0.0567g

source_name: Bovine ovarian follicle 33

tag: ovarian follicle,  8.5mm, tube A, weight 0.0660g


title: Bovine_26_cy5_C35_cy3


title: Bovine_8_cy5_C32_cy3

source_name: Bovine ovarian follicle C32

tag: ovarian follicle,  8.5mm, tube A, weight 0.0577g


title: Bovine_33_cy5_C13_cy3

source_name: Bovine ovarian follicle C13

tag: ovarian follicle,  10.5mm, tube A, weight 0.0836g


title: Bovine_8_cy5_C22_cy3


title: Bovine_C10_cy5_26_cy3

source_name: Bovine ovarian follicle C10

tag: ovarian follicle,  11.5mm, tube A, weight 0.1385g


title: Bovine_861_cy5_C10_cy3

description: The hybridization was carried out using the 3DNA Array 350 kit (Genisphere Inc., Hatfield, PA) according to the manufacture’s instructions. For each hybridization, 5µg of total RNA of each follicle sample were used. After hybridization, the slides were scanned using an Axon GenePix 4000B scanner (Axon Instruments Inc., Union City, CA) at 5µm resolution, and the image was analyzed using GenePix Pro 4.0.1.12 software (Axon Instruments Inc., Union City, CA). The result files and the image were linked together and stored in the local BioArray Software Environment (BASE) database (Saal et al., 2002).

data_processing: The result data were first filtered to remove all control spots, 3× SSC, and blank spots. Then the background-corrected-median-intensities were normalized using a pin-based-lowess-normalization within BASE. The log ratio of chanel 1 VS. chanel 2 were then outputed together with the raw data for each spot of all the arrays.

source_name: Bovine ovarian follicle 861

tag: ovarian follicle,  8.5mm, tube A, weight 0.0604g


title: Bovine_27_cy5_C32_cy3


title: Bovine_46_cy5_861_cy3

source_name: Bovine ovarian follicle 46

tag: ovarian follicle,  9mm, tube A, weight 0.043g


title: Bovine_C22_cy5_C26_cy3


title: Bovine_C12_cy5_46_cy3

source_name: Bovine ovarian follicle C12

tag: ovarian follicle,  10mm, tube A, 0.0805g


title: Bovine_31_Cy5_C10_cy3

source_name: Bovine ovarian follicle 31

tag: ovarian follicle,  11mm, tube B, weight 0.3062g


title: Bovine_33_cy5_C12_cy3


title: Bovine_C32_cy5_C26_cy3


title: 45r rna vs human ref rna - repeat 2 - mAdbID:43754

status: Public on Jun 01 2007

city: bethesda

first: binwu

last: tang

address: 9000 rockville pike

department: nci

institute: nih

description: mAdb experiment ID: 43754

hyb_protocol: FairPlay Microarray Labeling Kit Other: Use the FairPlay Microarray Labelling Kit instruction from Stratagen, CA.

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: Universal Human Reference RNA - Cy3

label_protocol: Cy3 Sample Labeling Protocol - generic

tag: Other

value: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

source_name: 45r DNR- Cy5

label_protocol: Cy5 Sample Labeling Protocol - generic

extract_protocol:
Sample Extraction Protocol
Extraction method: Trizol
Other: Total RNA was extracted using Trizol according to manufacturer's instructions (Invitrogen, Carlsbad, CA).

tag: Strain

value: athymic nude mouse

tag: Tissue

value: tumor

tag: Cell type

value: genetically modified (DNR expression) human breast cancer cell line xenografted into nude mice

tag: Disease state

value: breast cancer

tag: Genotype/Genetic variation

value: DNR expression


title: 42l rna vs. human ref rna - repeat 2 - mAdbID:43749

description: mAdb experiment ID: 43749

source_name: 42l Control - Cy5

value: human breast cancer cell line xenografted into nude mice


title: 44r rna vs human ref rna - repeat 2 - mAdbID:43751

description: mAdb experiment ID: 43751

source_name: 44r DNR- Cy5


title: 47l rna vs human ref. rna - repeat 2 - mAdbID:43627

description: mAdb experiment ID: 43627

source_name: 47l DNR- Cy5


title: 47r rna vs human ref. rna - repeat 2 - mAdbID:43757

description: mAdb experiment ID: 43757

source_name: 47r DNR- Cy5


title: 41r rna vs human ref rna - repeat 2 - mAdbID:43622

description: mAdb experiment ID: 43622

source_name: 41r Control - Cy5


title: 45l rna vs human ref rna - repeat 2 - mAdbID:43623

description: mAdb experiment ID: 43623

source_name: 45l DNR- Cy5


title: Bovine_C13_cy5_46_cy3


title: Bovine_C35_cy5_27_cy3

source_name: Bovine ovarian follicle C35

tag: ovarian Follicle,  11X10mm, tube A, 0.0863g

source_name: Bovine ovarian follicle 27

tag: ovarian follicle,  9mm, tube A, weight 0.0589g


title: 37l rna vs human ref.rna - repeat 2 - mAdbID:43619

description: mAdb experiment ID: 43619

source_name: 37l Control - Cy5


title: 36r rna vs human ref. rna - repeat 2 - mAdbID:43748

description: mAdb experiment ID: 43748

source_name: 36r Control - Cy5


title: 44l rna vs. human ref rna - repeat 2 - mAdbID:43422

description: mAdb experiment ID: 43422

source_name: 44l DNR- Cy5


title: 46r rna vs human ref rna - repeat 2 - mAdbID:43756

description: mAdb experiment ID: 43756

source_name: 46r DNR- Cy5


title: 38r rna vs. human ref rna - repeat 3 - mAdbID:43418

description: mAdb experiment ID: 43418

source_name: 38r Control - Cy5


title: 44r rna vs human ref rna - repeat 3 - mAdbID:43752

description: mAdb experiment ID: 43752


title: 39l rna vs human ref. rna - repeat 2 - mAdbID:43620

description: mAdb experiment ID: 43620

source_name: 39l Control - Cy5


title: 39r rna vs. human ref rna - repeat 2 - mAdbID:43419

description: mAdb experiment ID: 43419

source_name: 39r Control - Cy5


title: 43r rna vs human ref rna - repeat 2 - mAdbID:43421

description: mAdb experiment ID: 43421

source_name: Universal Human Reference RNA - Cy3

source_name: 43r DNR- Cy5


title: 43l rna vs. human ref rna - repeat 2 - mAdbID:43420

description: mAdb experiment ID: 43420

source_name: 43l DNR- Cy5


title: 45r rna vs human ref rna - repeat 1 - mAdbID:33397

description: mAdb experiment ID: 33397

source_name: Universal Human Reference RNA - Cy5

source_name: 45r DNR- Cy3


title: 36l rna vs human ref. rna - repeat 2 - mAdbID:43416

description: mAdb experiment ID: 43416

source_name: 36l Control - Cy5


title: Bovine_31_cy5_C13_cy3

source_name: Bovine ovarian follicle 31

source_name: Bovine ovarian follicle C13


title: 47r rna vs human ref. rna - repeat 1 - mAdbID:33600

description: mAdb experiment ID: 33600

source_name: 47r DNR- Cy3


title: 38r rna vs. human ref rna - repeat 2 - mAdbID:43417

description: mAdb experiment ID: 43417


title: 36r rna vs human ref. rna - repeat 1 - mAdbID:33599

description: mAdb experiment ID: 33599

source_name: 36r Control - Cy3


title: 46r rna vs human ref rna - repeat 1 - mAdbID:33398

description: mAdb experiment ID: 33398

source_name: 46r DNR- Cy3


title: 44r rna vs human ref rna - repeat 1 - mAdbID:33396

description: mAdb experiment ID: 33396

source_name: 44r DNR- Cy3


title: 37l rna vs human ref.rna - repeat 1 - mAdbID:33393

description: mAdb experiment ID: 33393

source_name: 37l Control - Cy3


title: 42l rna vs. human ref rna - repeat 1 - mAdbID:33395

description: mAdb experiment ID: 33395

source_name: 42l Control - Cy3


title: Series 3A: Hyp female mouse: control diet

status: Public on Jan 01 2007

city: Charlotte

first: Ralph

middle: A.

last: Meyer

state: NC

department: Orthopaedic Research Laboratory

institute: Carolinas Medical Center

description: Hyp is a mutation of the Phex gene on the X chromosome.  Mutation of this gene causes X-linked hypophosphatemia in mice and humans.

hyb_protocol: The standard Affymetrix protocol, Rev. 6, was followed for hybridization.

scan_protocol: The arrays were scanned once in an Affymetrix GeneArray Scanner 3000.

data_processing: Affymetrix GCOS 1.2 was used to scale all arrays to an average of 1200 with the mask files moe430a.msk and moe430b.msk from Affymetrix.  This balanced the two arrays so that the data could be combined into one spreadsheet.  The mask file had the effect of scaling all genes on the 430A array to an average of 500.

label: Biotin label of the cRNA with SAPE staining was used.

source_name: Mouse kidneys

label_protocol: Standard Affymetrix protocol, Affymetrix GeneChip Expression Analysis Technical Manual, Rev. 6, copyright 2004, was used to process these samples.

extract_protocol: TRIzol was used to extract total RNA from the kidney tissue.

treatment_protocol: The control (Teklad TD 86129) or low phosphorus (TD 86128) diet was fed for 3 days with deionized water ad libitum.  The mice were hemizygous Hyp (Hyp/Y) or heterozygous female (Hyp/+) mice or their normal littermate controls.  Mice were 10 weeks old when started on the diet protocol.

tag: C57BL/6J mice.


title: 43r rna vs human ref rna - repeat 1 - mAdbID:33368

description: mAdb experiment ID: 33368

source_name: 43r DNR- Cy3


title: Series 3A: Hyp female mouse: low phosphorus diet


title: Series 3A: Hyp male mouse: control diet


title: Series 3A: Normal female mouse: control diet


title: Series 3A: Hyp male mouse: low phosphorus diet


title: 47l rna vs human ref. rna - repeat 1 - mAdbID:33372

description: mAdb experiment ID: 33372

source_name: 47l DNR- Cy3


title: 39l rna vs human ref. rna - repeat 1 - mAdbID:33394

description: mAdb experiment ID: 33394

source_name: 39l Control - Cy3


title: 41r rna vs human ref rna - repeat 1 - mAdbID:33370

description: mAdb experiment ID: 33370

source_name: 41r Control - Cy3


title: Series 3A: Normal male mouse: control diet

tag: C57BL/6J mice


title: Series 3A: Normal male mouse: low phosphorus diet


title: 40r rna vs. human ref rna - repeat 2 - mAdbID:43621

description: mAdb experiment ID: 43621

source_name: Universal Human Reference RNA - Cy3

source_name: 40r Control - Cy5


title: Bovine_C12_Cy5_H893_Cy3

source_name: Bovine ovarian follicle C12

tag: ovarian follicle, 10mm, tube A, 0.0805g

source_name: Bovine ovarian follicle H893

tag: ovarian follicle, 9mm, tube A, weight 0.0469g


title: Series 3A: Normal female mouse: low phosphorus diet


title: 40r rna vs. human ref rna - repeat 1 - mAdbID:33369

description: mAdb experiment ID: 33369

source_name: Universal Human Reference RNA - Cy5

source_name: 40r Control - Cy3


title: 45l rna vs human ref rna - repeat 1 - mAdbID:33371

description: mAdb experiment ID: 33371

source_name: 45l DNR- Cy3


title: 39r rna vs. human ref rna - repeat 1 - mAdbID:33351

description: mAdb experiment ID: 33351

source_name: 39r Control - Cy3


title: 44l rna vs. human ref rna - repeat 1 - mAdbID:33353

description: mAdb experiment ID: 33353

source_name: 44l DNR- Cy3


title: Series 2A: Hyp female mouse: control diet

description: The Hyp mutation is generally thought to block the renal adaptation to low phosphorus diets.  In  contrast to this, we found many effects of diet not blocked by the Hyp mutation and many effects of the mutation not related to low phosphorus diet.  In addition, there were many genes differing between male and female mice.

data_processing: Affymetrix GCOS 1.2 was used to scale all arrays to an average of 1200 with mask files moe430a.msk and moe430b.msk from Affymetrix.  This balanced the two arrays so that the data could be combined into one spreadsheet.  The mask file had the effect of scaling all genes on the 430A array to an average of 500.

label: biotin label of the cRNA with SAPE staining

treatment_protocol: The control (Teklad TD86129) or low phosphorus (Teklad TD 86128) were fed for 3 days with deionized water ad libitum to mice at 10 weeks of age.  The mice were hemizygous (Hyp/Y) Hyp male or heterozygous (Hyp/+) Hyp female mice or their normal littermate controls.


title: Series 2A: Hyp female mouse: low phosphorus diet


title: 43l rna vs. human ref rna - repeat 1 - mAdbID:33352

description: mAdb experiment ID: 33352

source_name: 43l DNR- Cy3


title: Series 2A: Hyp male mouse: low phosphorus diet


title: 38r rna vs. human ref rna - repeat 1 - mAdbID:33350

description: mAdb experiment ID: 33350

source_name: 38r Control - Cy3


title: Series 2A: Normal female mouse: low phosphorus diet


title: 36l rna vs human ref. rna - repeat 1 - mAdbID:33367

description: mAdb experiment ID: 33367

source_name: 36l Control - Cy3


title: Series 2A: Normal male mouse: low phosphorus diet

source_name: Mouse kidneys

treatment_protocol: The control (Teklad TD86129) or low phosphorus (Teklad TD 86128) were fed for 3 days with deionized water ad libitum to mice at 10 weeks of age.


title: Series 2A: Hyp male mouse: control diet


title: Series 2A: Normal female mice: control diet

source_name: C57BL/6J mice


title: Bovine_H893_cy5_31_cy3

tag: ovarian follicle,  9mm, tube A, weight 0.0469g

source_name: Bovine ovarian follicle 31


title: Series 2A: Normal male mouse: control diet

treatment_protocol: The control (Teklad TD86129) or low phosphorus (Teklad TD 86128) were fed for 3 days with deionized water ad libitum.


title: Series 1A: normal female mouse: low phosphorus diet


title: Series 1A: Female Hyp mice: low phosphorus diet


title: Series 1A: normal male mouse: low phosphorus diet

source_name: mouse kidney


title: Series 3B: Hyp female mouse: low phosphorus diet

description: Hyp is a mutation of the Phex gene on the X chromosome.  Mutation of this gene causes X-linked hypophosphatemia in mice and humans.  A total of 24 samples were hybridized to both the Affymetrix MOE 430A and MOE 430B arrays.

data_processing: Affymetrix GCOS 1.2 was used to scale all arrays to an average of 1200 with the mask files moe430a.msk and moe430b.msk from Affymetrix.  This balanced the two arrays so that the data from the 430A and 430B arrays could be combined into one spreadsheet for each sample.  The mask file had the effect of scaling all genes on the 430A array to an average of 500.

source_name: mouse kidneys

treatment_protocol: The control (Teklad TD 86129) or low phosphorus (TD 86128) diet was fed for 3 days with deionized water ad libitum.  The mice were hemizygous Hyp male (Hyp/Y) or heterozygous female (Hyp/+) mice or their normal littermate controls.  Mice were 10 weeks old when started on the diet protocol.


title: Series 3B: Normal male mouse: low phosphorus diet


title: Series 1A: Normal female mouse: control diet


title: Series 1A: Normal male mouse: control diet

source_name: whole kidney

tag: Series 1, Normal male fed the control diet.  C57BL/6J mice, either normal or X-linked hypophosphatemic (Hyp), at 10 weeks of age fed control or low phosphorus diet for three days.  Hyp mice were hemizygous male (Hyp/Y) or heterozygous female (Hyp/+).  Littermate controls were used for normal mice.  Male and female mice were used.  Hyp is a mutation of the Phex gene.


title: Series 1A: Hyp female mouse: control diet


title: Series 2B: Hyp female mouse: low phosphorus diet


title: Series 3B: Hyp male mouse: low phosphorus diet


title: Series 3B: Normal female mouse: control diet


title: Series 1A: Hyp male mouse: low phosphorus diet

source_name: Mouse kidney


title: Series 1A: Hyp male mouse: control diet


title: Series 3B: Hyp male mouse: control diet


title: Series 2B: Normal female mouse: low phosphorus diet


title: Series 2B: Normal female mouse: control diet


title: Series 2B: Hyp male mouse: low phosphorus diet


title: Series 3B: Normal male mouse: control diet


title: Series 2B: Normal male mouse: control diet


title: Series 3B: Normal female mouse: low phosphorus diet


title: Series 3B: Hyp female mouse: control diet


title: Series 2B: Hyp male mouse: control diet


title: Series 2B: Hyp female mice: control diet


title: Series 2B: Normal male mouse: low phosphorus diet


title: Series 1B: Normal female mouse: low phosphorus diet


title: Series 1B: Hyp female mouse: low phosphorus diet


title: Series 1B: Hyp female mouse: control diet


title: Series 1B: Normal female mouse: control diet


title: Series 1B: Hyp male mouse: control diet


title: Series 1B: Normal male mouse: low phosphorus diet


title: Series 1B: Hyp male mouse: low phosphorus diet


title: slr0473_WT_2

city: Meguro

first: Mitsunori

last: Katayama

state: Tokyo

address: 3-8-1 Komaba

institute: University of Tokyo

description: 16S and 23S rRNA data was excluded from the analysis.

hyb_protocol: 65oC, overnight

scan_protocol: ScanArray 4000 (PerkinElmer, Inc., MA, USA)

data_processing: Signal of each individual spot was subtracted by background (average signal of corners of each spot) and divided by average value of all spot.

organism: Synechocystis sp. PCC 6803

source_name: slr1473 mutant

label_protocol: RNA Fluorescence labeling core kit, M-MLV version Ver.2.0 (Takara Bio Inc.)

growth_protocol: 0.5% CO2 at 30oC in BG-11

extract_protocol: RNeasy midi kit (Qiagen)

tag: slr0473 mutant

source_name: Wild type strain

tag: Wild type strain


title: Series 1B: Normal male mouse: control diet

treatment_protocol: The control (Teklad TD 86129) or low phosphorus (TD 86128) diet was fed for 3 days with deionized water ad libitum.  The mice were hemizygous male Hyp (Hyp/Y) or heterozygous female Hyp (Hyp/+) mice or their normal littermate controls.  Mice were 10 weeks old when started on the diet protocol.


title: slr1584_Light_Dark2

source_name: Light sample

extract_protocol: 0.5% CO2 at 30oC in BG-11

tag: Sample corrected from cells kept in darkness for 12 hours and subsequently illuminated for one hour

source_name: Dark sample


title: slr1584_WT_2

source_name: slr1584 mutant

tag: slr1584 mutant

treatment_protocol: Wild type strain


title: WT_Light_dark1

tag: Sample corrected from cells kept in darkness for 12 hours


title: sll1124_WT_2

source_name: sll1124 mutant

tag: sll1124 mutant


title: slr1393_WT_1

source_name: slr1393 mutant

tag: slr1393 mutant


title: slr1584_Light_Dark1


title: sll1473_Light_Dark2


title: slr1212_WT_1

source_name: slr1212 mutant

tag: slr1212 mutant


title: slr1584_WT_1

source_name: Wils type strain


title: sll1473_WT_2

source_name: sll1473 mutant

tag: sll1473 mutant


title: LNCaP_R1881_9h_rep2_R

city: São Paulo

first: Eduardo

middle: M

last: Reis

address: Av. professor Lineu Prestes, 748

department: Departamento de Bioquímica

country: Brazil

institute: Instituto de Química da Universidade de São Paulo

description: Hybridization included external mRNA spikes for quality control of the experiment (Lucidea Microarray ScoreCard) and a reference pool of RNA from 3 prostate carcinoma cell lines: LNCaP, DU145 and PC3 (cultured following ATCC suggested media), labeled using Cy3-dCTP. Raw images were analyzed using the ArrayVision software (Version 8.0, Imaging Research Inc.). An array template (or grid) was first automatically aligned to locate the position of each spot in the array, and subsequently manually adjusted to obtain the best possible alignment.

hyb_protocol: Labeled targets were ressuspended in 250 (l of 1 x hybridization buffer (25% formamide, 12.5% of proprietary Microarray Hybridization Buffer Version 2 from Amersham Biosciences cat. RPK0325) denatured for 2 min at 92 ºC and centrifuged at 13,000 rpm for 5 min. All slide processing steps (blocking, hybridization, washing) were carried out on an automated slide processor (ASP) from Amersham Biosciences. The slides were incubated for 16h at 42ºC and subsequently washed at room temperature in 1xSSC/0.2%SDS for 5min, 0.1xSSC/0.2%SDS for 5 min and in 0.1XSSC for 3 min. After the washing steps, slides were flushed with isopropanol and dried with an air flush at 42ºC.

scan_protocol: Images were obtained from each channel by laser scanning using GenePix 4000B microarray scanner (Axon Instruments). Slides were scanned with the following parameters: scanning resolution: 10-(m pixel;  excitation wave length: 633 nm (Cy5-labeled targets);  emission filter: 675 nm (Cy5-labeled targets); PMT voltage: 600 volts (Cy5-labeled targets).

data_processing: We employed in our analyses the Artifact-Removed density value (ARM) calculated for each spot by ArrayVision. The ARM value represents the average of all the pixels remaining in the spot, after first removing pixels with density values that exceed four median absolute deviations (MADs) from the median. The ARM density for each spot was subtracted by the median background surrounding the spot (distance of 2 pixels with 3 widths of pixels).The raw data of each spot was compared to the value of hibridization background using the Lucidea Microarray Scorecard to determine which spots have a signal above or below the detection limit of each hybridization, where the background was given by the signal measured on a negative control (plant cDNA). If their signal were at least 3 standard deviations above the average signal of the negative control, spots were considered expressed in LNCaP cells. We decided to use the mean intensity signal (40% trimmed) of each dataset for normalization between experiments, and to calculate the treatment to control sample ratios using only Cy5-labelled sample measurements.  A Cy3-labeled reference sample had been hybridized simultaneously with all time points (androgen-treated and ethanol control) and was used only as a quality control.

source_name: LNCaP/synthetic androgen (R1881)/9 hours.

label_protocol: Labeled targets for hybridizations were generated from total RNA in reverse transcription reactions using oligo dT as RT primer, following strictly the protocol accompanying the CyScribe First-Strand labeling kit (Amersham Biosciences, Piscataway, NJ). In short, 15 (g total RNA was combined with primers in a total volume of 11 (l, denatured at 70°C for 10 minutes, put on ice for 30 seconds, spin down and placed at room temperature for 10 minutes. Nine microliters of a premix solution was added containing 5X Superscript II reaction buffer (5X), 200 U Superscript II reverse transcriptase,  0.1 M DTT, dNTP mix (2 mM dATP, 2 mM dGTP, 2 mMdTTP ,1 mM dCTP) and 1 mM of Cy5-dCTP. After addition of the premix, the reaction was kept at room temperature for 10 minutes and then incubated at 42°C for 1.5 hr. RNA templates were removed by alkaline hydrolysis by adding 2 (l of 2.5 M sodium hydroxide and incubating the mixture at 37° C for 15 minutes.  The labeling reaction was neutralized with 10 (l 2 M MOPS free acid and labeled targets were purified using 96-well Millipore Multiscreen filter plates as follows: 5 volumes of 5.3 M Guanidine-HCl: 150 mM KOAc were added to labeling reactions. The mixture was applied on the plate and washed 4X with 80% EtOH by centrifugation at 3500 rpm for 5 min. Residual EtOH was spin out by an additional centrifugation at 3500 rpm for 5 minutes. Labeled targets were eluted in 50 (l 10mM Tris pH 8.5, by spinning at 3000 rpm for 5 minutes, dried on a SpeedVac and kept at -20°C, protected from light until use.

growth_protocol: Prostate carcinoma cell line LNCaP was maintained in RPMI 1640 medium supplemented with 10% (vol/vol) fetal calf serum (FCS), 3 mM L-glutamine, 100 µg/ml streptomicine and 100 U/ml peniciline.

extract_protocol: Total RNA was purified from cell extracts by CsCl gradient, after cell lysis (4M guanidine isotiocianate; 0.1M b-mercaptoethanol; 25 mM sodium citrate pH 7.0). Total RNA (100 µg sample) was treated with of RNAse-free DNAse (RNeasy - Qiagen) for 15min to minimize genomic DNA contaminants. Purity of the isolated RNA was estimated by measuring the ratio A 260/A 280. Integrity of total RNA was checked by electrophoresis using the Bio Sizing  total RNA Nano assay in the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: LNCaP cells were cultured for 24 hours in androgen-deprived medium, RPMI 1640 with 5% (wt/vol) charcoal-stripped FCS (Life Technologies). Synthetic androgen (R1881) was added to fresh RPMI 1640 medium, with 10% (wt/vol) charcoal-stripped FCS. Cells were harvested for RNA isolation after 9 hours.

tag: Designation

value: LNCaP clone FGC [LNCaP.FGC]; Tissue:prostate; Disease:carcinoma, derived from metastatic site, left supraclavicular lymph node; Age:50 years adult; Gender:male; Ethnicity:Caucasian; Isolation date:1977; Tumorigenic:Yes, in soft agar; Yes, the cells are tumorigenic in nude mice; ATCC Number:CRL-1740.


title: LNCaP_R1881_9h_rep2_L


title: sll0821_WT_1

source_name: sll0821 mutant

tag: sll0821 nutant


title: LNCaP_R1881_9h_rep1_L


title: LNCaP_R1881_9h_rep1_R


title: sll1124_WT_1


title: slr1969_WT_1

source_name: slr1969 mutant

tag: slr1969 mutant


title: LNCaP_R1881_6h_rep4_R

source_name: LNCaP/synthetic androgen (R1881)/6 hours.

treatment_protocol: LNCaP cells were cultured for 24 hours in androgen-deprived medium, RPMI 1640 with 5% (wt/vol) charcoal-stripped FCS (Life Technologies). Synthetic androgen (R1881) was added to fresh RPMI 1640 medium, with 10% (wt/vol) charcoal-stripped FCS. Cells were harvested for RNA isolation after 6 hours.


title: WT_Light_Dark2


title: slr1969_WT_2

source_name: sll1969 mutant

growth_protocol: 0.5% CO2 at 28dC in BG-11

tag: sll1969 mutant


title: LNCaP_R1881_6h_rep3_R


title: LNCaP_R1881_6h_rep4_L


title: LNCaP_R1881_6h_rep2_R


title: LNCaP_R1881_6h_rep3_L


title: slr1393_WT_2


title: sll0821_WT_2

tag: sll0821 mutant

tag: Wild type


title: LNCaP_R1881_6h_rep2_L


title: slr1805_WT_1

source_name: slr1805 mutant

tag: slr1805 mutant


title: sll1473_Light_Dark1


title: LNCaP_R1881_6h_rep1_R


title: LNCaP_R1881_6h_rep1_L


title: LNCaP_R1881_24h_rep2_R

source_name: LNCaP/synthetic androgen (R1881)/24 hours.

treatment_protocol: LNCaP cells were cultured for 24 hours in androgen-deprived medium, RPMI 1640 with 5% (wt/vol) charcoal-stripped FCS (Life Technologies). Synthetic androgen (R1881) was added to fresh RPMI 1640 medium, with 10% (wt/vol) charcoal-stripped FCS. Cells were harvested for RNA isolation after 24 hours.


title: LNCaP_R1881_24h_rep1_L


title: LNCaP_R1881_48h_rep1_R

source_name: LNCaP/synthetic androgen (R1881)/48 hours.

treatment_protocol: LNCaP cells were cultured for 24 hours in androgen-deprived medium, RPMI 1640 with 5% (wt/vol) charcoal-stripped FCS (Life Technologies). Synthetic androgen (R1881) was added to fresh RPMI 1640 medium, with 10% (wt/vol) charcoal-stripped FCS. Cells were harvested for RNA isolation after 48 hours.


title: LNCaP_R1881_48h_rep1_L


title: LNCaP_R1881_48h_rep2_R


title: LNCaP_R1881_48h_rep2_L


title: LNCaP_R1881_24h_rep1_R


title: LNCaP_R1881_18h_rep2_L

source_name: LNCaP/synthetic androgen (R1881)/18 hours.

treatment_protocol: LNCaP cells were cultured for 24 hours in androgen-deprived medium, RPMI 1640 with 5% (wt/vol) charcoal-stripped FCS (Life Technologies). Synthetic androgen (R1881) was added to fresh RPMI 1640 medium, with 10% (wt/vol) charcoal-stripped FCS. Cells were harvested for RNA isolation after 18 hours.


title: LNCaP_R1881_18h_rep1_R


title: LNCaP_R1881_18h_rep2_R


title: LNCaP_R1881_18h_rep1_L


title: LNCaP_R1881_12h_rep2_R

source_name: LNCaP/synthetic androgen (R1881)/12 hours.

treatment_protocol: LNCaP cells were cultured for 24 hours in androgen-deprived medium, RPMI 1640 with 5% (wt/vol) charcoal-stripped FCS (Life Technologies). Synthetic androgen (R1881) was added to fresh RPMI 1640 medium, with 10% (wt/vol) charcoal-stripped FCS. Cells were harvested for RNA isolation after 12 hours.


title: LNCaP_R1881_24h_rep2_L


title: LNCaP_R1881_12h_rep1_R


title: LNCaP_EtOH_9h_rep2_R

source_name: LNCaP/ethanol vehicle (control)/9 hours.

treatment_protocol: LNCaP cells were cultured for 24 hours in androgen-deprived medium, RPMI 1640 with 5% (wt/vol) charcoal-stripped FCS (Life Technologies). Ethanol vehicle (control) was added to fresh RPMI 1640 medium, with 10% (wt/vol) charcoal-stripped FCS. Cells were harvested for RNA isolation after 9 hours.


title: LNCaP_R1881_12h_rep1_L


title: LNCaP_R1881_12h_rep2_L


title: LNCaP_EtOH_9h_rep2_L


title: LNCaP_EtOH_6h_rep3_L

source_name: LNCaP/ethanol vehicle (control)/6 hours.

treatment_protocol: LNCaP cells were cultured for 24 hours in androgen-deprived medium, RPMI 1640 with 5% (wt/vol) charcoal-stripped FCS (Life Technologies). Ethanol vehicle (control) was added to fresh RPMI 1640 medium, with 10% (wt/vol) charcoal-stripped FCS. Cells were harvested for RNA isolation after 6 hours.


title: LNCaP_EtOH_9h_rep1_L


title: LNCaP_EtOH_6h_rep2_R


title: LNCaP_EtOH_6h_rep3_R


title: LNCaP_EtOH_6h_rep2_L


title: LNCaP_EtOH_9h_rep1_R


title: LNCaP_ETOH_6h_rep1_L


title: LNCaP_EtOH_48h_rep2_L

source_name: LNCaP/ethanol vehicle (control)/48 hours.

treatment_protocol: LNCaP cells were cultured for 24 hours in androgen-deprived medium, RPMI 1640 with 5% (wt/vol) charcoal-stripped FCS (Life Technologies). Ethanol vehicle (control) was added to fresh RPMI 1640 medium, with 10% (wt/vol) charcoal-stripped FCS. Cells were harvested for RNA isolation after 48 hours.


title: LNCaP_EtOH_48h_rep2_R


title: LNCaP_EtOH_48h_rep1_R


title: LNCaP_ETOH_6h_rep1_R


title: LNCaP_EtOH_24h_rep1_R

source_name: LNCaP/ethanol vehicle (control)/24 hours.

treatment_protocol: LNCaP cells were cultured for 24 hours in androgen-deprived medium, RPMI 1640 with 5% (wt/vol) charcoal-stripped FCS (Life Technologies). Ethanol vehicle (control) was added to fresh RPMI 1640 medium, with 10% (wt/vol) charcoal-stripped FCS. Cells were harvested for RNA isolation after 24 hours.


title: LNCaP_EtOH_24h_rep1_L


title: LNCaP_EtOH_24h_rep2_R


title: LNCaP_EtOH_12h_rep2_R

source_name: LNCaP/ethanol vehicle (control)/12 hours.

treatment_protocol: LNCaP cells were cultured for 24 hours in androgen-deprived medium, RPMI 1640 with 5% (wt/vol) charcoal-stripped FCS (Life Technologies). Ethanol vehicle (control) was added to fresh RPMI 1640 medium, with 10% (wt/vol) charcoal-stripped FCS. Cells were harvested for RNA isolation after 12 hours.


title: LNCaP_EtOH_48h_rep1_L


title: LNCaP_EtOH_18h_rep1_L

source_name: LNCaP/ethanol vehicle (control)/18 hours.

treatment_protocol: LNCaP cells were cultured for 24 hours in androgen-deprived medium, RPMI 1640 with 5% (wt/vol) charcoal-stripped FCS (Life Technologies). Ethanol vehicle (control) was added to fresh RPMI 1640 medium, with 10% (wt/vol) charcoal-stripped FCS. Cells were harvested for RNA isolation after 18 hours.


title: LNCaP_EtOH_18h_rep1_R


title: LNCaP_EtOH_18h_rep2_L


title: LNCaP_EtOH_24h_rep2_L


title: LNCaP_EtOH_12h_rep1_R


title: LNCaP_EtOH_18h_rep2_R


title: LNCaP_EtOH_12h_rep2_L


title: LNCaP_EtOH_12h_rep1_L


title: LNCaP_EtOH_0h_rep2_L

source_name: LNCaP/ethanol vehicle (control)/0 hours.

treatment_protocol: LNCaP cells were cultured for 24 hours in androgen-deprived medium, RPMI 1640 with 5% (wt/vol) charcoal-stripped FCS (Life Technologies). Ethanol vehicle (control) was added to fresh RPMI 1640 medium, with 10% (wt/vol) charcoal-stripped FCS. Cells were harvested for RNA isolation after 0 hours.


title: LNCaP_EtOH_0h_rep1_R


title: LNCaP_EtOH_0h_rep2_R


title: LNCaP_EtOH_0h_rep1_L


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_10_8_23_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

city: Research Triangle Park

first: James

middle: C

last: Bonner

address: 6 Davis Drive

department: Biological Sciences

institute: CIIT Centers for Health Research

description: JCB_10_8_23_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: affylmGUI, The Walter and Eliza Hall Institute of Medical Research

source_name: Sample Type: cells, Cell Line: ATCC 16Lu, Cell Type: human lung fibroblasts, Harvest Time Point: 8 hour

growth_protocol: Growth Media: DMEM 10%FBS,  Pen/Strep, Fungizone, Growth Conditions: 5% CO2, 37ïC

extract_protocol: Extraction Method: Qiagen

treatment_protocol: in vitro Treatment: V2O5, Treatment Time: 8, Units of Treatment Time: hour, Dose or Concentration: 10, Units of Dose or Concentration: ug/cm2

tag: Array Type

tag: Amount to Core

tag: Units of Amount

value: ul

tag: Ratio

tag: RNA Integrity Number

tag: Sample Preservation

value: snap frozen

tag: Pooled from Multiple Samples

value: Yes


title: sll1473_WT_1

source_name: sll1473 mutant

source_name: Wild type strain


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_10_24_40_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

description: JCB_10_24_40_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

source_name: Sample Type: cells, Cell Line: ATCC 16Lu, Cell Type: human lung fibroblasts, Harvest Time Point: 24 hour

treatment_protocol: in vitro Treatment: V2O5, Treatment Time: 24, Units of Treatment Time: hour, Dose or Concentration: 10, Units of Dose or Concentration: ug/cm2


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_10_4_37_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

description: JCB_10_4_37_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

source_name: Sample Type: cells, Cell Line: ATCC 16Lu, Cell Type: human lung fibroblasts, Harvest Time Point: 4 hour

treatment_protocol: in vitro Treatment: V2O5, Treatment Time: 4, Units of Treatment Time: hour, Dose or Concentration: 10, Units of Dose or Concentration: ug/cm2


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_10_8_8_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

description: JCB_10_8_8_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_10_1_6_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

description: JCB_10_1_6_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

source_name: Sample Type: cells, Cell Line: ATCC 16Lu, Cell Type: human lung fibroblasts, Harvest Time Point: 1 hour

treatment_protocol: in vitro Treatment: V2O5, Treatment Time: 1, Units of Treatment Time: hour, Dose or Concentration: 10, Units of Dose or Concentration: ug/cm2


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_10_24_10_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

description: JCB_10_24_10_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_10_24_25_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

description: JCB_10_24_25_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_10_4_7_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

description: JCB_10_4_7_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_10_8_38_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

description: JCB_10_8_38_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_10_4_22_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

description: JCB_10_4_22_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_10_1_36_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

description: JCB_10_1_36_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_10_1_21_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

description: JCB_10_1_21_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_10_12_24_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

description: JCB_10_12_24_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

source_name: Sample Type: cells, Cell Line: ATCC 16Lu, Cell Type: human lung fibroblasts, Harvest Time Point: 12 hour

treatment_protocol: in vitro Treatment: V2O5, Treatment Time: 12, Units of Treatment Time: hour, Dose or Concentration: 10, Units of Dose or Concentration: ug/cm2


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_0_8_18_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

description: JCB_0_8_18_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

treatment_protocol: in vitro Treatment: control, Treatment Time: 8, Units of Treatment Time: hour


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_0_4_32_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

description: JCB_0_4_32_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

treatment_protocol: in vitro Treatment: control, Treatment Time: 4, Units of Treatment Time: hour


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_10_12_9_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

description: JCB_10_12_9_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_0_4_2_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

description: JCB_0_4_2_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_0_8_3_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

description: JCB_0_8_3_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_0_1_16_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

description: JCB_0_1_16_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

treatment_protocol: in vitro Treatment: control, Treatment Time: 1, Units of Treatment Time: hour


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_10_12_39_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

description: JCB_10_12_39_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_0_1_31_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

description: JCB_0_1_31_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_0_4_17_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

description: JCB_0_4_17_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_0_24_20_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

description: JCB_0_24_20_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

treatment_protocol: in vitro Treatment: control, Treatment Time: 24, Units of Treatment Time: hour


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_0_8_33_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

description: JCB_0_8_33_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_0_24_35_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

description: JCB_0_24_35_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_0_12_34_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

description: JCB_0_12_34_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

treatment_protocol: in vitro Treatment: control, Treatment Time: 12, Units of Treatment Time: hour


title: 11 D Ptxl 0.01/Vehicle/6h/HG

status: Public on Dec 31 2006

city: Chapel Hill

first: Monte

last: Willis

address: 103 Mason Farm Road

department: Pathology & Laboratory Medicine

institute: UNC

description: Gene expression analysis was conducted using Agilent G4130A Rat 22K microarray slides.  Starting with 0.5 ug of total RNA, Cyanine-5 labeled cRNA was produced using the Agilent Low-Input RNA Amplification labeling kit according to manufacturer’s protocol.  2ug sample and 2ug reference amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Agilent Target Hybridization Controls and protocol.  Slides were  washed as indicated in the Agilent protocol.  Arrays were then scanned with an Axon GenePix 4000b.  Data was obtained using the GenePix Pro 6 software package.

data_processing: loess normalization, log2 transformation

source_name: RNA prepared from 1 day old whole rat pups

extract_protocol: GITC/Phenol/CHcl3 extraction CsCl2 banding

treatment_protocol: Untreated rat pups for reference RNA

tag: 1 day old whole rat pups

source_name: Rat aortic smooth muscle (tmt: Ptxl 0.01/Vehicle/6h/HG )

growth_protocol: The rat aortic smooth muscle cells were maintained at 37oC (5% CO2) in Dulbecco Minimal Essential Medium supplemented with 10% FBS, 2 mM L-glutamine, 100U/ml penicillin and 100 mg/ml streptomycin.

extract_protocol: The cell monolayer was rinsed twice in cold PBS, 5 ml each. Each plate of cells was then lysed in 0.6 ml of Buffer RLT (RNeasy Mini Kit, Qiagen) and total cellular RNA was prepared following the RNeasy protocol.

treatment_protocol: Cells were grown in 100 mm dishes in 10% FBS/DMEM to approximately 70-80 % confluence, and were washed once in serum-free DMEM, and then incubated for 16 h in DMEM containing 0.5 % (v/v) FBS.  The cells were then stimulated with drug/vehicle, insulin/vehicle in NG/HG for 6/24 hours and were extracted for RNA.

tag: Cell line

value: Rat aortic smooth muscle cells (RASMC)


title: 12 C Ptxl 0.01/Vehicle/24h/HG

hyb_protocol: 2ug sample and 2ug reference amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Agilent Target Hybridization Controls and protocol.

scan_protocol: Slides were  washed as indicated in the Agilent protocol.  Arrays were then scanned with an Axon GenePix 4000b.  Data was obtained using the GenePix Pro 6 software package.

label_protocol: Starting with 0.5 ug of total RNA, Cyanine-5 labeled cRNA was produced using the Agilent Low-Input RNA Amplification labeling kit according to manufacturer’s protocol.

source_name: Rat aortic smooth muscle (tmt: Ptxl 0.01/Vehicle/24h/HG)


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_0_24_5_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

description: JCB_0_24_5_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: 12 D Ptxl 0.01/Vehicle/24h/HG

source_name: Rat aortic smooth muscle (tmt: Ptxl 0.01/Vehicle/24h/HG


title: 12 A Ptxl 0.01/Vehicle/24h/HG


title: cells_ATCC 16 Lu _human lung fibroblasts_JCB_0_12_19_Lung_Fibroblast_Rcontrol_HG-U133A_2_IMFRT0014

description: JCB_0_12_19_Lung_Fibroblast_Rcontrol_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

source_name: Sample Type: cells, Cell Line: ATCC 16 Lu , Cell Type: human lung fibroblasts, Harvest Time Point: 12 hours

growth_protocol: Growth Media: DMEM 10%FBS,  Pen/Strep, Fungizone, Growth Conditions: 5% CO2, 37iC

treatment_protocol: in vitro Treatment: untreated, Treatment Time: 12, Units of Treatment Time: hours


title: 12 B Ptxl 0.01/Vehicle/24h/HG


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_0_12_4_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

description: JCB_0_12_4_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: cells_ATCC 16Lu_human lung fibroblasts_JCB_0_1_1_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

description: JCB_0_1_1_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts


title: 11 B Ptxl 0.01/Vehicle/6h/HG

source_name: Rat aortic smooth muscle (tmt: Ptxl 0.01/Vehicle/6h/HG)


title: 11 C Ptxl 0.01/Vehicle/6h/HG


title: 10 D Ptxl 0.01/Vehicle/24h/NG

source_name: Rat aortic smooth muscle (tmt: Ptxl 0.01/Vehicle/24h/NG)


title: 10 B Ptxl 0.01/Vehicle/24h/NG


title: 9 D Ptxl 0.01/Vehicle/6h/NG

source_name: Rat aortic smooth muscle (tmt: Ptxl 0.01/Vehicle/6h/NG)


title: 10 C Ptxl 0.01/Vehicle/24h/NG


title: 11 A Ptxl 0.01/Vehicle/6h/HG


title: 9 B Ptxl 0.01/Vehicle/6h/NG


title: 10 A Ptxl 0.01/Vehicle/24h/NG


title: 9 A Ptxl 0.01/Vehicle/6h/NG


title: 16 D Ptxl 0.01/Insulin/24h/HG

source_name: Rat aortic smooth muscle (tmt: Ptxl 0.01/Insulin/24h/HG)


title: 16 B Ptxl 0.01/Insulin/24h/HG


title: 15 C Ptxl 0.01/Insulin/6h/HG

source_name: Rat aortic smooth muscle (tmt: Ptxl 0.01/Insulin/6h/HG)


title: 15 B Ptxl 0.01/Insulin/6h/HG


title: 16 C Ptxl 0.01/Insulin/24h/HG


title: 15 D Ptxl 0.01/Insulin/6h/HG


title: 15 A Ptxl 0.01/Insulin/6h/HG


title: 16 A Ptxl 0.01/Insulin/24h/HG


title: 14 D Ptxl 0.01/Insulin/24h/NG

source_name: Rat aortic smooth muscle (tmt: Ptxl 0.01/Insulin/24h/NG)


title: 27 D Ptxl 1/Vehicle/6h/HG

source_name: Rat aortic smooth muscle (tmt: Ptxl 1/Vehicle/6h/HG)


title: 13 D Ptxl 0.01/Insulin/6h/NG

source_name: Rat aortic smooth muscle (tmt: Ptxl 0.01/Insulin/6h/NG)


title: 14 C Ptxl 0.01/Insulin/24h/NG


title: 28 A Ptxl 1/Vehicle/24h/HG

source_name: Rat aortic smooth muscle (tmt: Ptxl 1/Vehicle/24h/HG)


title: 27 A Ptxl 1/Vehicle/6h/HG


title: 14 B Ptxl 0.01/Insulin/24h/NG


title: 13 C Ptxl 0.01/Insulin/6h/NG


title: 28 C Ptxl 1/Vehicle/24h/HG


title: 26 D Ptxl 1/Vehicle/24h/NG

source_name: Rat aortic smooth muscle (tmt: Ptxl 1/Vehicle/24h/NG)


title: 27 B Ptxl 1/Vehicle/6h/HG


title: 28 D Ptxl 1/Vehicle/24h/HG


title: 25 D Ptxl 1/Vehicle/6h/NG

source_name: Rat aortic smooth muscle (tmt: Ptxl 1/Vehicle/6h/NG)


title: 26 C Ptxl 1/Vehicle/24h/NG


title: 14 A Ptxl 0.01/Insulin/24h/NG


title: 13 A Ptxl 0.01/Insulin/6h/NG


title: 13 B Ptxl 0.01/Insulin/6h/NG


title: 26 B Ptxl 1/Vehicle/24h/NG


title: 25 C Ptxl 1/Vehicle/6h/NG


title: 27 C Ptxl 1/Vehicle/6h/HG


title: 28 B Ptxl 1/Vehicle/24h/HG


title: 25 B Ptxl 1/Vehicle/6h/NG


title: 9 C Ptxl 0.01/Vehicle/6h/NG


title: 26 A Ptxl 1/Vehicle/24h/NG


title: 25 A Ptxl 1/Vehicle/6h/NG


title: 32 A Ptxl 1/Insulin/24h/HG

source_name: Rat aortic smooth muscle (tmt: Ptxl 1/Insulin/24h/HG)


title: 30 D Ptxl 1/Insulin/24h/NG

source_name: RNA prepared from 1 day old whole rat pups

source_name: Rat aortic smooth muscle (tmt: Ptxl 1/Insulin/24h/NG)


title: 32 B Ptxl 1/Insulin/24h/HG


title: 31 B Ptxl 1/Insulin/6h/HG

source_name: Rat aortic smooth muscle (tmt: Ptxl 1/Insulin/6h/HG)


title: 31 C Ptxl 1/Insulin/6h/HG


title: 44 C Ptxl 1000/Vehicle/24h/HG

source_name: Rat aortic smooth muscle (tmt: Ptxl 1000/Vehicle/24h/HG)


title: 43 D Ptxl 1000/Vehicle/6h/HG

source_name: Rat aortic smooth muscle (tmt: Ptxl 1000/Vehicle/6h/HG)


title: 29 A REP Ptxl 1/Insulin/6h/NG

source_name: Rat aortic smooth muscle (tmt: Ptxl 1/Insulin/6h/NG


title: 32 C Ptxl 1/Insulin/24h/HG


title: 44 D Ptxl 1000/Vehicle/24h/HG


title: 31 A Ptxl 1/Insulin/6h/HG


title: 31 D Ptxl 1/Insulin/6h/HG


title: 32 D Ptxl 1/Insulin/24h/HG


title: 43 C Ptxl 1000/Vehicle/6h/HG


title: 30 A Ptxl 1/Insulin/24h/NG


title: 44 B Ptxl 1000/Vehicle/24h/HG


title: 42 D Ptxl 1000/Vehicle/24h/NG

source_name: Rat aortic smooth muscle (tmt: Ptxl 1000/Vehicle/24h/NG)


title: 43 A Ptxl 1000/Vehicle/6h/HG


title: 29 B Ptxl 1/Insulin/6h/NG

source_name: Rat aortic smooth muscle (tmt: Ptxl 1/Insulin/6h/NG)


title: 30 C Ptxl 1/Insulin/24h/NG


title: 44 A Ptxl 1000/Vehicle/24h/HG


title: 42 C Ptxl 1000/Vehicle/24h/NG


title: 30 B Ptxl 1/Insulin/24h/NG


title: 29 D Ptxl 1/Insulin/6h/NG


title: 41 D Ptxl 1000/Vehicle/6h/NG

source_name: Rat aortic smooth muscle (tmt: Ptxl 1000/Vehicle/6h/NG)


title: 29 C Ptxl 1/Insulin/6h/NG


title: 43 B Ptxl 1000/Vehicle/6h/HG


title: 41 C Ptxl 1000/Vehicle/6h/NG


title: 41 B Ptxl 1000/Vehicle/6h/NG


title: 48 A Ptxl 1000/Insulin/24h/HG

source_name: Rat aortic smooth muscle (tmt: Ptxl 1000/Insulin/24h/HG)


title: 42 B Ptxl 1000/Vehicle/24h/NG


title: 46 C Ptxl 1000/Insulin/24h/NG

source_name: Rat aortic smooth muscle (tmt: Ptxl 1000/Insulin/24h/NG)


title: 47 D Ptxl 1000/Insulin/6h/HG

source_name: Rat aortic smooth muscle (tmt: Ptxl 1000/Insulin/6h/HG)


title: 42 A Ptxl 1000/Vehicle/24h/NG


title: 47 C Ptxl 1000/Insulin/6h/HG


title: 45 D Ptxl 1000/Insulin/6h/NG

source_name: Rat aortic smooth muscle (tmt: Ptxl 1000/Insulin/6h/NG)


title: 47 A Ptxl 1000/Insulin/6h/HG


title: 48 D Ptxl 1000/Insulin/24h/HG


title: 46 A Ptxl 1000/Insulin/24h/NG


title: 45 C Ptxl 1000/Insulin/6h/NG


title: 48 C Ptxl 1000/Insulin/24h/HG


title: 45 B Ptxl 1000/Insulin/6h/NG


title: 19 A Rapa 0.01/Vehicle/6h/HG

source_name: Rat aortic smooth muscle (tmt: Rapa 0.01/Vehicle/6h/HG)


title: 46 D Ptxl 1000/Insulin/24h/NG


title: 20 D Rapa 0.01/Vehicle/24h/HG

source_name: Rat aortic smooth muscle (tmt: Rapa 0.01/Vehicle/24h/HG)


title: 46 B Ptxl 1000/Insulin/24h/NG


title: 47 B Ptxl 1000/Insulin/6h/HG


title: 45 A Ptxl 1000/Insulin/6h/NG


title: 41 A Ptxl 1000/Vehicle/6h/NG


title: 20 C Rapa 0.01/Vehicle/24h/HG


title: 20 B Rapa 0.01/Vehicle/24h/HG


title: 19 B Rapa 0.01/Vehicle/6h/HG


title: 19 D Rapa 0.01/Vehicle/6h/HG


title: 48 B Ptxl 1000/Insulin/24h/HG


title: 20 A Rapa 0.01/Vehicle/24h/HG


title: 18 C Rapa 0.01/Vehicle/24h/NG

source_name: Rat aortic smooth muscle (tmt: Rapa 0.01/Vehicle/24h/NG)


title: 18 B Rapa 0.01/Vehicle/24h/NG


title: 17 C Rapa 0.01/Vehicle/6h/NG

source_name: Rat aortic smooth muscle (tmt: Rapa 0.01/Vehicle/6h/NG)


title: 18 D Rapa 0.01/Vehicle/24h/NG

source_name: RNA prepared from 1 day old whole rat pups


title: 23 D Rapa 0.01/Insulin/6h/HG

source_name: Rat aortic smooth muscle (tmt: Rapa 0.01/Insulin/6h/HG)


title: 24 C Rapa 0.01/Insulin/24h/HG

source_name: Rat aortic smooth muscle (tmt: Rapa 0.01/Insulin/24h/HG)


title: 17 A Rapa 0.01/Vehicle/6h/NG


title: 18 A Rapa 0.01/Vehicle/24h/NG


title: 17 B Rapa 0.01/Vehicle/6h/NG


title: 24 D Rapa 0.01/Insulin/24h/HG


title: 23 B Rapa 0.01/Insulin/6h/HG


title: 23 C Rapa 0.01/Insulin/6h/HG


title: 22 A Rapa 0.01/Insulin/24h/NG

source_name: Rat aortic smooth muscle (tmt: Rapa 0.01/Insulin/24h/NG)


title: 24 A Rapa 0.01/Insulin/24h/HG


title: 21 D Rapa 0.01/Insulin/6h/NG

source_name: Rat aortic smooth muscle (tmt: Rapa 0.01/Insulin/6h/NG)


title: 24 B Rapa 0.01/Insulin/24h/HG


title: 21 B Rapa 0.01/Insulin/6h/NG


title: 23 A Rapa 0.01/Insulin/6h/HG


title: 17 D Rapa 0.01/Vehicle/6h/NG


title: 36 D Rapa 1/Vehicle/24h/HG

source_name: Rat aortic smooth muscle (tmt: Rapa 1/Vehicle/24h/HG)


title: 36 B Rapa 1/Vehicle/24h/HG


title: 35 C Rapa 1/Vehicle/6h/HG

source_name: Rat aortic smooth muscle (tmt: Rapa 1/Vehicle/6h/HG)


title: 22 D Rapa 0.01/Insulin/24h/NG


title: 21 C Rapa 0.01/Insulin/6h/NG


title: 22 C Rapa 0.01/Insulin/24h/NG


title: 21 A Rapa 0.01/Insulin/6h/NG


title: 35 D Rapa 1/Vehicle/6h/HG


title: 35 A Rapa 1/Vehicle/6h/HG


title: 35 B Rapa 1/Vehicle/6h/HG


title: 22 B Rapa 0.01/Insulin/24h/NG


title: 36 A REP Rapa 1/Vehicle/24h/HG

source_name: Rat aortic smooth muscle (tmt: Rapa 1/Vehicle/24h/HG


title: 33 C Rapa 1/Vehicle/6h/NG

source_name: Rat aortic smooth muscle (tmt: Rapa 1/Vehicle/6h/NG)


title: 34 C Rapa 1/Vehicle/24h/NG

source_name: Rat aortic smooth muscle (tmt: Rapa 1/Vehicle/24h/NG)


title: 19 C Rapa 0.01/Vehicle/6h/HG


title: 34 B Rapa 1/Vehicle/24h/NG


title: 33 A Rapa 1/Vehicle/6h/NG


title: 39 C Rapa 1/Insulin/6h/HG

source_name: Rat aortic smooth muscle (tmt: Rapa 1/Insulin/6h/HG)


title: 34 A Rapa 1/Vehicle/24h/NG


title: 34 D Rapa 1/Vehicle/24h/NG


title: 40 B Rapa 1/Insulin/24h/HG

source_name: Rat aortic smooth muscle (tmt: Rapa 1/Insulin/24h/HG)


title: 39 A Rapa 1/Insulin/6h/HG


title: 33 B Rapa 1/Vehicle/6h/NG


title: 38 C Rapa 1/Insulin/24h/NG

source_name: Rat aortic smooth muscle (tmt: Rapa 1/Insulin/24h/NG)


title: 37 D Rapa 1/Insulin/6h/NG

source_name: Rat aortic smooth muscle (tmt: Rapa 1/Insulin/6h/NG)


title: 40 C Rapa 1/Insulin/24h/HG


title: 38 D Rapa 1/Insulin/24h/NG


title: 40 A Rapa 1/Insulin/24h/HG


title: 51 D Rapa 100/Vehicle/6h/HG

source_name: Rat aortic smooth muscle (tmt: Rapa 100/Vehicle/6h/HG)


title: 52 C Rapa 100/Vehicle/24h/HG

source_name: Rat aortic smooth muscle (tmt: Rapa 100/Vehicle/24h/HG)


title: 39 D Rapa 1/Insulin/6h/HG


title: 52 D Rapa 100/Vehicle/24h/HG


title: 51 C Rapa 100/Vehicle/6h/HG


title: 38 A Rapa 1/Insulin/24h/NG


title: 37 B Rapa 1/Insulin/6h/NG


title: 37 A Rapa 1/Insulin/6h/NG


title: 33 D Rapa 1/Vehicle/6h/NG


title: 38 B Rapa 1/Insulin/24h/NG


title: 37 C Rapa 1/Insulin/6h/NG


title: 51 A Rapa 100/Vehicle/6h/HG


title: 51 B Rapa 100/Vehicle/6h/HG


title: 52 B Rapa 100/Vehicle/24h/HG


title: 40 D Rapa 1/Insulin/24h/HG


title: 49 D Rapa 100/Vehicle/6h/NG

source_name: Rat aortic smooth muscle (tmt: Rapa 100/Vehicle/6h/NG)


title: 52 A Rapa 100/Vehicle/24h/HG

source_name: RNA prepared from 1 day old whole rat pups


title: 50 C Rapa 100/Vehicle/24h/NG

source_name: Rat aortic smooth muscle (tmt: Rapa 100/Vehicle/24h/NG)


title: 49 C Rapa 100/Vehicle/6h/NG


title: 50 B Rapa 100/Vehicle/24h/NG


title: 50 D Rapa 100/Vehicle/24h/NG


title: 55 D Rapa 100/Insulin/6h/HG

source_name: Rat aortic smooth muscle (tmt: Rapa 100/Insulin/6h/HG)


title: 56 D Rapa 100/Insulin/24h/HG

source_name: Rat aortic smooth muscle (tmt: Rapa 100/Insulin/24h/HG)


title: 50 A Rapa 100/Vehicle/24h/NG


title: 49 B Rapa 100/Vehicle/6h/NG


title: 55 A Rapa 100/Insulin/6h/HG


title: 49 A Rapa 100/Vehicle/6h/NG


title: 54 D Rapa 100/Insulin/24h/NG

source_name: Rat aortic smooth muscle (tmt: Rapa 100/Insulin/24h/NG)


title: 56 A Rapa 100/Insulin/24h/H

source_name: Rat aortic smooth muscle (tmt: Rapa 100/Insulin/24h/H)


title: 55 B Rapa 100/Insulin/6h/HG


title: 56 C Rapa 100/Insulin/24h/HG


title: 56 B Rapa 100/Insulin/24h/HG


title: 53 D Rapa 100/Insulin/6h/NG

source_name: Rat aortic smooth muscle (tmt: Rapa 100/Insulin/6h/NG)


title: 54 C Rapa 100/Insulin/24h/NG


title: 55 C Rapa 100/Insulin/6h/HG


title: 53 B Rapa 100/Insulin/6h/NG


title: 53 C Rapa 100/Insulin/6h/NG


title: 54 B Rapa 100/Insulin/24h/NG


title: 39 B Rapa 1/Insulin/6h/HG


title: 54 A Rapa 100/Insulin/24h/NG


title: 53 A Rapa 100/Insulin/6h/NG


title: 4 C DMSO/Vehicle/24h/HG

source_name: Rat aortic smooth muscle (tmt: DMSO/Vehicle/24h/HG )


title: 3 D DMSO/Vehicle/6h/HG

source_name: Rat aortic smooth muscle (tmt: DMSO/Vehicle/6h/HG )


title: 3 B DMSO/Vehicle/6h/HG


title: 4 D DMSO/Vehicle/24h/HG


title: 3 C DMSO/Vehicle/6h/HG


title: 4 B DMSO/Vehicle/24h/HG


title: 4 A DMSO/Vehicle/24h/HG


title: 2 B DMSO/Vehicle/24h/NG

source_name: Rat aortic smooth muscle (tmt: DMSO/Vehicle/24h/NG )


title: 2 C DMSO/Vehicle/24h/NG


title: 1 D DMSO/Vehicle/6h/NG

source_name: Rat aortic smooth muscle (tmt: DMSO/Vehicle/6h/NG )


title: 1 B DMSO/Vehicle/6h/NG


title: 3 A DMSO/Vehicle/6h/HG


title: 2 D DMSO/Vehicle/24h/NG