title: wild-type replicate three

description: See Auchtung et al. 2005. PNAS. 102(35):12554-9 for any additional details about protocols.

hyb_protocol: Samples were hybridized as described in Auchtung et al. 2005. PNAS. 102(35):12554-9.

scan_protocol: Arrays were scanned and analyzed with the program GENPIX 3.0 (Axon Instruments, Union City, CA).

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.

source_name: wild-type cells

label_protocol: Total RNA was labeled with Cy5 as described in Auchtung et al. 2005. PNAS. 102(35):12554-9.

growth_protocol: Cells were grown for several generations in S750 minimal medium to OD600~ 1 and collected for total RNA extraction.

extract_protocol: Cells were harvested and total RNA was extracted as described in Auchtung et al. 2005 PNA. 102(35):12554-9.

tag: Strain

source_name: collective reference sample

label_protocol: Total RNA was labeled with Cy3 as described in Auchtung et al. 2005. PNAS. 102(35):12554-9.

growth_protocol: Cells were grown for several generations in S750 minimal medium to OD600~ 1, when samples were removed for RNA extraction.  After additional time, cells exited exponential phase and transitioned to stationary phase (T0), at which point a second set of samples were collected for RNA extraction.

tag: Collective reference sample = Equal concentrations of RNA pooled from total RNA isolated from samples collected at OD600 ~ 1 and T0 (end of exponential phase) from three independently grown cultures of wt (JH642), phrC null (RSM121), phrF null (JMA163), and phrK (CAL7) cells.


title: 13130354

status: Public on Apr 20 2006

type: RNA

city: St-Hyacinthe

first: Vincent

last: Deslandes

state: Quebec

address: 3200 rue Sicotte

department: Groupe de Recherche sur les Maladies Infectieuses du Porc

country: Canada

institute: Université de Montréal - Faculté de Médecine Vétérinaire

description: Competitive hybridization of cDNA generated from A. pleuropneumoniae sero 1 strain s4074 RNA extracted in iron-rich or iron-restricted conditinos

data_processing: Image processing software: SpotFinder v.3.1.1.  Net median intensities were normalized using Lowess algorithm (MIDAS) and log2 ratios were generated

molecule: total RNA

organism: Actinobacillus pleuropneumoniae

tag: serotype 1, strain s4074

tag: iron-rich medium

tag: iron-restricted medium


title: Mdr2-KO heterozygous mouse, 12 month old mouse 3

status: Public on Apr 23 2006

city: Ramat-Gan

first: Mark

last: Katzenellenbogen

address: Ramat-Gan 52900, Israel

department: THE FACULTY OF LIFE SCIENCE, BIOINFORMATICS AND MICROARRAY UNIT

country: Israel

institute: Bar Ilan University

description: According to paper: Multiple adaptive mechanisms to chronic liver disease revealed at early stages of liver carcinogenesis in the Mdr2-knockout mice.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

label: biotin

organism: Mus musculus

source_name: Mdr2-KO heterozygous mouse, 12 month old mouse, liver sample

tag: Genotype

value: Mdr2-KO heterozygous mouse

tag: Age

value: 12 month


title: Mdr2-KO homozygous mouse, 12 month old mouse 1

source_name: Mdr2-KO homozygous mouse, 12 month old mouse, liver sample

value: Mdr2-KO homozygous mouse


title: PhrK deletion replicate two

status: Public on Apr 18 2006

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

country: USA

institute: MIT

organism: Bacillus subtilis

source_name: phrK null cells


title: PhrK deletion replicate one


title: wild-type replicate two


title: WDG16-81 yneAB HPUra treated repl 2

description: Hybridization of HPUra treated AIG105 and reference RNA

hyb_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.

data_processing: Ratio Cy5/Cy3 is normalized to total signal (log2 format, no background subtraction). Spots with >80% pixels above background were analyzed

source_name: HPUra treated cells

tag: AIG105 treated with HPUra for 60min. Replicate 2

source_name: reference RNA

tag: pooled RNA sample


title: WDG16-84 yneAB lexA untreated repl 2

description: Hybridization of untreated AIG266 and reference RNA

source_name: growing untreated cells

label_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.

tag: AIG266 growing in minimal medium. unteated replicate 2


title: WDG16-85 yneAB lexA untreated repl 3

growth_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.

tag: AIG266 growing in minimal medium untreated replicate 3

tag: pooled RNA


title: wild-type replicate one


title: PhrK deletion replicate three


title: WDG16-82 yneAB HPUra treated repl 3

extract_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.

tag: AIG105 treated with HPUra for 60min. Replicate 3


title: PhrF deletion replicate three

source_name: phrF null cells


title: PhrF deletion replicate one


title: PhrC deletion replicate three

source_name: phrC null cells


title: WDG16-80 yneAB HPUra treated repl 1

treatment_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.

tag: AIG105 treated with HPUra (38ug/ml) for 60min. Replicate 1


title: WDG16-78 yneAB untreated repl2

description: Hybridization of untreated AIG105 and reference RNA

tag: AIG 105 growing in minimal medium. replicate 2


title: WDG16-79 yneAB untreated repl3

source_name: untreated growing cells

tag: AIG105 growing in minimal medium. untreated. replicate 3


title: PhrF deletion replicate two


title: WDG12-66 recA sda HPUra treated repl3

description: Hybridization of HPUra treated AIG4 and reference sample

hyb_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7

data_processing: Ratio Cy5/Cy3 normalized to total signal (log2 format, no background subtraction). Spots with >80% pixels higher than background were analyzed

tag: AIG4 treated with HPUra for 60min. Replicate 3


title: WDG16-77 yneA untreated repl1

hyb_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7.

source_name: yneA growing untreated cells

tag: AIG105 (yneAB null) growing in minimal medium untreated. Replicte 1


title: WDG14-65 recA sda untreated replicate 2

description: Hybridization of untreated AIG4 and reference sample

source_name: untreated cells

label_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7

tag: AIG4 grown in minimal medium. Untreated replicate 2


title: WDG12-63 recA sda untreated repl 1

growth_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7

tag: AIG4 grown in minimal medium. Untreated replicate 1


title: WDG16-83 yneAB lexA untreated repl1

tag: AIG266 (yneAB, lexA) growing in minimal medium untereated. Replicate 1


title: WDG12-67 recA sda untreated repl 3

extract_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7

tag: AIG4 untreated replicate 3


title: PhrC deletion replicate one

tag: Strain

tag: Collective reference sample = Equal concentrations of RNA pooled from total RNA isolated from samples collected at OD600 ~ 1 and T0 (end of exponential phase) from three independently grown cultures of wt (JH642), phrC null (RSM121), phrF null (JMA163), and phrK (CAL7) cells.


title: WDG13-18 phage- recA UV treated repl 3

description: Hybridization of phage- recA UV treated sample with reference RNA

hyb_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7

source_name: UV treated cells

tag: YB3000 growing in minimal medium. treated with 25mJ/m2 UV. 60min after treatment. Replicate 3


title: WDG13-28 phage- recA UV treated repl2

label_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7

tag: YB3000 treated with UV 25mJ/m2. Samples taken 60min after treatment

tag: pooled RNA sample


title: WDG13-9 phage- recA untreated repl2

description: Hybridization of phage- recA untreated sample with reference RNA

extract_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7

tag: YB3000 grown in minimal medium. Replicate 2


title: WDG13-25 phage- recA untreated repl1

tag: YB3000 grown in minimal media. untreated replicate 1


title: WDG12-64 recA sda HPUra treated repl2

treatment_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7

tag: AIG4 treated with HPUra for 60min. Replicate 2

source_name: rference RNA


title: PhrC deletion replicate two


title: WDG13-16 phage- recA untreated repl 3

tag: YB3000 growing in minimal medium. untreated replicate 3

tag: pooled RNA sapmle


title: WDG13-24 phage- UV treated repl1

description: Hybridization of phage- UV treated sample with reference RNA

tag: YB886 treated with UV 25mJ/m2. 60min after treatment. Replicate 1


title: bso6-84 lexAind HPUra repl3

description: hybridization of HPUra treated AIG246 sample with reference RNA

data_processing: Ratio of Cy5/Cy3 is normalized to total signal (log2 format, no background subtraction). spots with >80% pixels above background were analyzed

tag: AIG246 treated with HPUra for 60min. Replicate 3


title: WDG12-23 WT untreated replicate 2

description: Hybridization of untreated WT and reference sample

tag: AG174 untreated replicate 2


title: WDG12-22 WT HPUra treated repl2

description: Hybridization of HPUra treated WT and reference sample

source_name: cell treated with HPUra

tag: AG174 treated with HPUra, 60min after treatment. replicate 2


title: bso6-83 lexAind HPUra repl2

tag: AIG246 treated with HPUra for 60min. Replicate 2


title: WDG13-8 phage- UV treated repl 2

tag: YB886 (phage-) treated with UV (25mJ/m2). 60min after treatment


title: WDG12-62 recA sda HPUra treated repl1

tag: AIG4 grown in minimal medium treated with HPUra (38ug/ml) for 60min. Replicate 1


title: WDG13-16 phage- UV treated repl 3

tag: YB886 treated with 25mJ/m2 UV. 60min after treatment. Replicate 3


title: WDG12-25 WT untreated repl 3

tag: AG174 untreated replicate 3


title: WDG12-21 WT untreated repl 1

tag: AG174 grown in minimal medium. Replicate 1

tag: pooled RNA samples


title: Rap K overexpression replicate three

hyb_protocol: Samples were hybridized as described in Auchtung et al. 2005. PNAS. 102(35):12554-9

source_name: Pspank-hy rapK uninduced cells

growth_protocol: Cells were grown for several generations in S750 minimal medium to OD600~ 0.8 (30 min after induction for treated cells grown in parallel) and collected for total RNA extraction.

tag: Strain

tag: Treated with IPTG

value: no

source_name: Pspank-hy rapK induced cells

growth_protocol: Cells were grown for several generations in S750 minimal medium to OD600~ 0.5 Cells were treated with IPTG and samples were collected for total RNA extraction ~30 min later.

treatment_protocol: Cells were treated with IPTG (1 mM final concentration) at OD600~ 0.5.  Samples were collected ~ 30 min. later.

value: yes


title: WDG13-23 phage- untreated repl1

description: Hybridization of phage- untreated sample with reference RNA

tag: YB886 untreated. grown in minimal medium. replicate 1

tag: pooled RNA sample


title: bso6-78 JJS39 HPUra treated repl 3

description: hybridization of HPUra treated JJS39 sample with reference RNA

tag: JJS treated with HPUra for 60min. replicate 3


title: WDG13-15 phage- untreated replicate 3

source_name: growing untreated cultures

tag: YB886 untreated growing in minimal medium. replicate 3


title: bso6-80 lexAind untreated repl 2

description: hybridization of untreated AIG246 sample with reference RNA

tag: AIG246 growing in minimal medium. untreated. replicate 2


title: bso6-81 lexAind untreated repl3

tag: AIG246 growing in minimal medium untreated. replicate 3


title: bso6-76 JJS39 HPUra repl1

tag: JJS39 treated with HPUra (38ug/ml) for 60min


title: WDG12-20 WT HPUra treated repl 1

source_name: HPUra treated wt cells

tag: AG174 grown in minimal medium HPUra treated (38ug/ml) Sample taken 60min after treatment. replicate 1


title: WDG12-24 WT HPUra treated repl3

source_name: HPUra treated sample 3

tag: AG174 treated with HPUra. 60min after treatment. Replicate 3


title: WDG13-7 phage- untreated repl2

tag: YB886 (phage-) growing in minimal medium. Untreated replicate 2


title: bso6-82 lexAind HPUra replicate 1

tag: AIG246 growing in minimal medium treated with HPUra for 60min. replicate 1


title: bso6-73 JJS39  unterated repl1

description: hybridization of untreated JJS39 sample with reference RNA

source_name: growing cultures

growth_protocol:
Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.
Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7.

tag: JJS39 (upp null) untreated growing in minimal medium. Repl 1


title: WDG14-18 phage- recA MMC 60min repl2

description: hybridization of RNA from MMC treated phage- recA  with reference RNA sample

data_processing: Ratio Cy5/Cy3 normalized to total signal (no background subtraction).Only spots with >80% pixels above background were analyzed

source_name: phage- recA MMC treated for 60min

growth_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7. Epub 2005 Aug 24.

treatment_protocol: Au et al. Genetic composition of the Bacillus subtilis SOS system.J Bacteriol. 2005 Nov;187(22):7655-66.

tag: YB3000 treated with MMC for 60min. replicate 2


title: Rap J overexpression replicate three

description: See Auchtung et al. 2005. PNAS. 102(35):12554-9 for any additional details about protocols.

source_name: Pspank-hy rapJ uninduced cells

source_name: Pspank-hy rapJ induced cells


title: Rap K overexpression replicate one


title: Rap J overexpression replicate two


title: WDG14-26 phage- recA MMC 60min repl3

hyb_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7.

tag: YB3000 treated with MMC. replicate 3

source_name: reference RNA


title: bso6-75 JJS39 untreated repl3

source_name: growing cells untreated

tag: JJS39 growing in minimal medium untreated. replicate 3


title: WDG14-36 phage- recA MMC 60 min repl1

source_name: phage- recA MMC fro 60min

label_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7.

tag: YB3000 treated with MMC for 60min replicate 1


title: NIH3T3 si-emp2

city: Suita

first: Rie

last: Nagaoka-Yasuda

state: Osaka

address: 1-3 Yamadaoka

department: Frontier Bioscience

country: Japan

institute: Osaka University

description: Basal gene expression in NIH3T3 cells

data_processing: GeneChip Operating Software

label: RNA probes labeled with biotin

source_name: NIH3T3 si-emp2

growth_protocol: 10% calf serum in DMEM

extract_protocol: Trizol LS

tag: NIH 3T3 cells infected with empty vector


title: Rap J overexpression replicate one

tag: Strain

tag: Treated with IPTG


title: NIH3T3 si-emp1

description: Basal gene expression in NIH3T3 cells

tag: NIH3T3 cells infected with empty psiRS.


title: Pc DamID, genomic tiling array, Embryonic Drosophila Kc167 cells, replicate 1

type: genomic

city: Amsterdam

first: Maarten

last: van Lohuizen

address: Plesmanlaan 121

department: Molecular Genetics

country: Netherlands

institute: NKI-AVL

description: Embryonic Drosophila cells, Kc167 cells

data_processing: The normalization factor of the log base 2-transformed data is given by the lowess function, the normalization factor is subtracted from the data

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Embryonic Drosophila Kc167 cells, expressing Pc-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Full length Pc were cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

extract_protocol: Sample extraction was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

tag: Pc-Dam (EXPERIMENTAL)

source_name: Embryonic Drosophila Kc167 cells, expressing Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

tag: Dam (REFERENCE)


title: WDG14-17 phage- recA untreated repl2

description: hybridization of phage- recA RNA with reference RNA sample

source_name: phage- recA untreated

extract_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7.

tag: YB3000 grown in minimal medium. replicate 2

tag: pooled RNA sample


title: WDG14-25 phage- recA untreated repl3

tag: YB3000 grown in minimal medium. replicate 3

growth_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7.


title: WDG14-33 phage- recA untreated repl1

tag: YB3000 grown in minimal medium. replicate 1

treatment_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7.


title: Rap H overexpression replicate three

source_name: Pspank-hy rapH uninduced cells

source_name: Pspank-hy rapH induced cells


title: Sample 10

city: Cincinnati

first: David

middle: F

last: Wieczorek

state: OH

address: 231 Albert Sabin Way

department: Molecular Genetics, Biochemistry and Microbiology

institute: University of Cincinnati

description: Samples used for hybridization consisted of pooled (P) and non-pooled (NP) RNA extracts from the three genotypic groups namely nontransgenic controls (NTG), alpha-TM175 and alpha-TM180. A total of ten hybridization experiments were performed in which each genotypic group was represented by two or more non-pooled (NP) individual RNA extracts and one pooled (P) sample that resulted from combining 20 individual heart extracts.

hyb_protocol: The protocol and conditions used during hybridization, blocking and washing:  Create a hybridization cocktail for a single probe array that contains 0.05 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 uL of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization Oven rotating at 60 rpm

scan_protocol: Images were scanned using a GeneArray scanner [Agilent Technologies, Palo Alto, CA]

data_processing:
Processed with Microarray suite (Affymetrix) to generate .CEL files that were subject to RMAExpress 0.1 (Irizarry et al 2003) normalization.
Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring 7.0 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering. The Raw CEL files were processed using the RMA (Robust Multichip Average). All the samples were then normalized to the mean of the pooled control.

source_name: ventricular tissue

label_protocol: Labeling involved use of Genechip Expression 3’ Amplification One-Cycle Target Labeling and Control Reagents Kit (Affymetrix) to prepare biotin-labeled fragmented cRNA.

extract_protocol:
Total RNA was extracted from the ventricular tissue using Trizol kit (Invitrogen) and then purified two times using RNeasy columns (Qiagen)
Quality control steps:   RNA quality was assessed by using the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA) and only those samples with 28S/18S ratios between 1.3 and 2 were subsequently used

tag: Sample

value: nontransgenic control (NTG)

tag: Replicate

tag: Pool

value: P


title: H3K4me3 ChIP-chip, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 1

description: Embryonic Drosophila cells, Kc167 cells

data_processing: After removal of low quality, redundant or ambiguous proves, hybridization data of 9,994 probes was used for analyses, all measured ratios were log base 2-transformed and normalized to the median value of the entire array

source_name: Embryonic Drosophila cells, Kc167 cells, ChIP histone H3K4me3

label_protocol: For the microarray analysis, immunoprecipitated DNA fragments were amplified using linker-modified PCR (LM-PCR). Randomly sheared DNA fragments were made blunt using T4 DNA polymerase for 15 min at 16�C in 10 mM Tris-HCl pH8.0, 50 mM NaCl, 10 mM MgCl2, 1 mM DTT, and 0.1 mM dNTPs. Adapter ligation, PCR amplification, labeling and hybridization were carried out according to the DamID protocol (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23degC

extract_protocol: The ChIP method was and adaptation of a previously published protocol (Rietveld, L.E., Caldenhoven, E. & Stunnenberg, H.G. In vivo repression of an erythroid-specific gene by distinct corepressor complexes. Embo J 21, 1389-97, 2002). Approximately 2x108 Kc cells were cross-linked by the addition of formaldehyde (1% final concentration). The reaction was quenched with 125 mM Glycine and the cells were washed twice with PBS. Subsequently, the cells were incubated 5� on ice in 1.5 ml lysis buffer (1% v/v SDS, 10 mM EDTA pH8.0, 50 mM Tris-HCl pH8.0, protease inhibitor cocktail - Roche). The cell lysates were sonicated and centrifuged to remove cell debris. We used the equivalent of 1 x 10E6 cells for one immunoprecipitation. Chromatin samples were diluted 10-fold in IP buffer (1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH8.0, 167 mM NaCl, protease inhibitor cocktail - Roche) and precleared with 10 ul 50% protein A Sepharose slurry containing 1mg/ml bovine serum albumine (BSA) for 1h agitation at 4degC. Precleared chromatin was incubated with 2 ug antibody overnight at 4degC. All subsequent ChIP steps were performed as described (Rietveld, L.E., Caldenhoven, E. & Stunnenberg, H.G. In vivo repression of an erythroid-specific gene by distinct corepressor complexes. Embo J 21, 1389-97, 2002). We used the following antibodies for ChIP analyses: anti-H3K27me3 - #07-449 from Upstate; anti-H3K4me3 - ab8580-50 from Abcam; and anti-IgG - 011-0000-003 from Jackson Immuno Research. The data were normalized to a parallel ChIP with anti-H3 antibody (ab1797-100 from Abcam), to correct for differences in nucleosome density.

tag: H3K4me3 ChIP-chip (EXPERIMENTAL)

source_name: Embryonic Drosophila cells, Kc167 cells, ChIP Histone H3

tag: H3 ChIP-chip (REFERENCE)


title: RapH overexpression replicate one


title: Pc DamID, genomic tiling array, Embryonic Drosophila Kc167 cells, replicate 2

description: Embryonic Drosophila cells, Kc167 cells


title: WDG14-16 phage- MMC 60min repl2

description: Comparison of phage- MMC treated RNA and reference RNA

hyb_protocol: Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.

data_processing: Ratio of Cy5/Cy3 normalized to total signal (log2 format). Spots with >80% pixels with signal intensity higher than background were analyzed

source_name: phage- MMC for 60min repl2

growth_protocol: Au et al. Genetic composition of the Bacillus subtilis SOS system.

tag: phage- (YB886) treated with 1ug/ml MMC for 60min. Replicate 2


title: Rap H overexpression replicate two


title: Sample 8

value: NP


title: WDG14-31 phage-  untreated repl1

description: Comparison of phage- untreated RNA and reference RNA

hyb_protocol: Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7. Epub 2005 Aug 24.

data_processing: Ratio of Cy5/Cy3 normalized to total signal. Spots with >80% pixels with signal intensity higher than background were analyzed

source_name: phage- untreated RNA

growth_protocol:
Au et al. Genetic composition of the Bacillus subtilis SOS system.
J Bacteriol. 2005 Nov;187(22):7655-66.

tag: phage- (YB886) grown in minimal medium. Replicate 1

tag: pooled RNA


title: WDG14-24 phage- MMC 60min repl3

source_name: phage- MMC for 60min

label_protocol: Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.

treatment_protocol: Au et al. Genetic composition of the Bacillus subtilis SOS system.

tag: YB886 treated with 1ug/ml MMC for 60 min

tag: replicate 3


title: Sample 9


title: WDG14-32 phage- MMC 60min repl1

source_name: phage- MMC 60min

extract_protocol: Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.

tag: phage- (YB886) treated with 1ug/ml MMC for 60min. Replicate 1


title: WDG14-15 phage- untreated repl2

source_name: phage-  untr repl2

tag: pahge- (YB886) grown in minimal medium. Replicate 2

growth_protocol: Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.


title: WDG14-23 phage- untreated repl3

tag: pahge- (YB886) untreated grown in minimal madium. Replicate 3

source_name: reference RNA

treatment_protocol: Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.


title: Rap F overexpression replicate three

source_name: Pspank-hy rapF uninduced cells

tag: Strain

tag: Treated with IPTG

source_name: Pspank-hy rapF induced cells


title: WDG14-14 recA MMC 60min rep 2

description: Comparison of RNA from MMC treated recA cells with reference RNA

data_processing: Ratio of Cy5/Cy3 normalized to total signal. Only spots with >80% pixesl above background were analyzed

source_name: recA mmc treated

growth_protocol: Au et al.

treatment_protocol: Au et al.

tag: recA (IRN444) treated with 1ug/ml MMC for 60min. repetition 2

tag: pooled RNA form cells growun under various conditions


title: WDG14-22 recA MMC 60min rep 3

source_name: recA treated with MMC

tag: recA (IRN444) treated with 1ug/ml MMC for 60min. replicate 3


title: Sample 6

tag: Sample

tag: Replicate


title: Rap F overexpression replicate two


title: Sample 7

tag: Pool


title: WDG14-13 recA untreated rep2

description: Comparison of RNA from untreated recA cells with reference RNA

source_name: RNA from recA untreated

tag: recA (IRN444) grown in minimal medium untreated. Repetition 2)

source_name: pooled reference RNA

tag: pooled RNA from cells grown under various conditions


title: WDG14-35 recA MMC 60min rep1

source_name: recA cells MMC treated

tag: recA (IRN444) treated with 1ug/ml MMC for 60min. Replicate 1


title: WDG14-21 recA untreated rep 3

source_name: recA untreated rep3

tag: recA (IRN444) untreated grown in minimal medium. repetition 3


title: WDG14-29 recA untr Rep1

source_name: recA untreated

tag: RNA from untreated recA cells. repetition1

tag: pooled RNA form cells grown under various conditions


title: Sample 5

source_name: ventricular tissue


title: WDG14-12 WT MMC 60min Rep2

description: Comperison of MMC treated sample with reference RNA

hyb_protocol: Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7. Epub 2005 Aug 24.

data_processing: Cy5/Cy3 ratio normalized to total signal from both channels. Spots with >80% pixels over bckgrnd were analyzed

source_name: WT MMC rep2

tag: WT (AG174) treated with 1ug/ml MMC for 60min. Repetition 2


title: WDG14-20 WT MMC 60min Rep3

description: Comparison of RNA from MMC treated cells with reference RNA

source_name: WT with MMC rep3

label_protocol:
Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.
Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7. Epub 2005 Aug 24.

growth_protocol:
Au et al.
Genetic composition of the Bacillus subtilis SOS system.
J Bacteriol. 2005 Nov;187(22):7655-66.

tag: WT (AG174) treated with 1ug/ml MMC for 60min. Repetition 3

source_name: Pooled reference RNA

tag: Pooled RNA from cells grown under various conditions


title: RapF overexpression replicate one

scan_protocol: Arrays were scanned and analyzed with the program GENEPIX 3.0 (Axon Instruments, Union City, CA)

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 above background for 50% of pixels in each channel.

label_protocol: Total RNA was labeled with Cy5 as described in Auchtung et al. 2005. PNAS. 102(35):12554-9

growth_protocol: Cells were grown for several generations in S750 minimal medium to OD600 ~ 0.8 (30 min. after induction for treated cells grown in parallel) and collected for total RNA extraction.

extract_protocol: Cells were harvested and total RNA was extracted as described in Auchtung et al. 2005. PNAS. 102(35):12554-9

tag: Strain

label: Cy 3

label_protocol: Total RNA was labeled with Cy3 as described in Auchtung et al. 2005. PNAS. 102(35):12554-9

growth_protocol: Cells were grown for at least four generations in S750 minimal medium to OD600 ~ 0.5.  Cells were treated with IPTG and samples were collected for total RNA extraction ~ 30 min later.

treatment_protocol: Cells were treated with IPTG (1 mM final concentration) at OD600 ~ 0.5.  Samples were collected ~ 30 min. later.


title: WDG14-27 WT 60min untreated rep1

description: Comperison of untreated sample with reference RNA

source_name: Unterated growing cells

label_protocol: Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD.

treatment_protocol: A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.

tag: exponentially frowing cells in minimal meduim

tag: Pooled RNA from growing cells under various conditions


title: WDG14-19 WT 60min U Rep3

source_name: WT untreated

treatment_protocol:
A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.
Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD.

tag: AG174 (WT)  exponentially growing

source_name: Pooled RNA

tag: Pooled Total RNA form frowing cells under various conditions


title: WDG14-28 WT MMC 60min Rep1

source_name: growing cells MMC replicate 1

growth_protocol: Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD.

tag: WT cells treated with 1ug/ml MMC for 60min


title: MCF7/BUS, hormone starvation, day 2, biological replication 2

status: Public on Apr 14 2006

city: Charlestown

first: Kathryn

last: Coser

address: Blg 149 13th St

department: DNA Microarray Core

institute: Mass General Hospital Cancer Center

description: Gene expression data from MCF7 (BUS stock) hormone starved for 2 day2.

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

organism: Homo sapiens

source_name: MCF7/BUS cells, human breast adenocarcinoma cell line, estrogen receptor-positive

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

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

treatment_protocol: MCF7/BUS cells were inoculated in a plastic dish in DMEM (phenol red-free, 5% stripped fetal calf serum) and cultured for the indicated period (0, 1, or 2 days).

tag: Hormone Starvation

value: Day 2


title: WDG14-11 WT untreated 60min rep2

source_name: wt total RNA 60min untreated

treatment_protocol:
A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.

Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD.
Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7. Epub 2005 Aug 24.

tag: AG174 exponentially growing

tag: pooled RNA from growing cells under variety of conditions


title: MCF7/BUS, hormone starvation, day 2, biological replication 3


title: MCF7/BUS, hormone starvation, day 2, biological replication 1


title: MCF7/BUS, hormone starvation, day 0, biological replication 3

description: Gene expression data from MCF7 (BUS stock) hormone starved for 0 day.

value: Day 0


title: MCF7/BUS, hormone starvation, day 1, biological replication 1

description: Gene expression data from MCF7 (BUS stock) hormone starved for 1 day.

value: Day 1


title: MCF7/BUS, hormone starvation, day 1, biological replication 2


title: Sample 1

tag: Sample

tag: Replicate

tag: Pool


title: MCF7/BUS, hormone starvation, day 1, biological replication 3


title: Sample 2


title: MCF7/BUS, 100 pM E2, 48 hours, biological replication 5

description: Gene expression data from MCF7 (BUS stock) exposed to 100 pM 17beta-estradiol for 48 hours.

treatment_protocol: MCF7/BUS cells were inoculated in a plastic dish in DMEM (phenol red-free, 5% stripped fetal calf serum) and incubated for 16 hours. Cells were then washed and cultued in DMEM supplemented with 17beta-estradiol (E2) at the indicated concentration. Total RNA was isolated 48 hours after E2 treatment.

tag: 17beta estradiol


title: Sample 3


title: Sample 4


title: MCF7/BUS, 100 pM E2, 48 hours, biological replication 4


title: MCF7/BUS, hormone starvation, day 0, biological replication 1


title: MCF7/BUS, hormone starvation, day 0, biological replication 2


title: NIH3T3 si-RetSat2

description: NIH3T3 cells highly resistant to t-BHP

tag: NIH3T3 cells expressing si-RSRNA


title: bso6-79 lexAind untreated repl1

description: hybridization of untreated AIG246 sample with reference RNA

source_name: growing cells

growth_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.

tag: AIG246 (lexAind) untreated growing in minimal medium. Replicate 1

source_name: reference RNA

tag: pooled RNA sample


title: MCF7/BUS, 100 pM E2, 48 hours, biological replication 2


title: MCF7/BUS, 60 pM E2, 48 hours, biological replication 2

description: Gene expression data from MCF7 (BUS stock) exposed to 60 pM 17beta-estradiol for 48 hours.

value: 60 pM


title: MCF7/BUS, 100 pM E2, 48 hours, biological replication 3


title: MCF7/BUS, 100 pM E2, 48 hours, biological replication 1


title: MCF7/BUS, 60 pM E2, 48 hours, biological replication 5


title: MCF7/BUS, 30 pM E2, 48 hours, biological replication 5

description: Gene expression data from MCF7 (BUS stock) exposed to 30 pM 17beta-estradiol for 48 hours.

value: 30 pM


title: MCF7/BUS, 60 pM E2, 48 hours, biological replication 3


title: MCF7/BUS, 60 pM E2, 48 hours, biological replication 1


title: MCF7/BUS, 30 pM E2, 48 hours, biological replication 4


title: MCF7/BUS, 10 pM E2, 48 hours, biological replication 4

description: Gene expression data from MCF7 (BUS stock) exposed to 10 pM 17beta-estradiol for 48 hours.

value: 10 pM


title: Rap K overexpression replicate two

description: See Auchtung et al. 2005. PNAS. 102(35):12554-9 for any additional details about protocols.

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.

source_name: Pspank-hy rapK uninduced cells

growth_protocol: Cells were grown for several generations in S750 minimal medium to OD600~ 0.8 (30 min after induction for treated cells grown in parallel) and collected for total RNA extraction.

tag: Treated with IPTG

source_name: Pspank-hy rapK induced cells

growth_protocol: Cells were grown for several generations in S750 minimal medium to OD600~ 0.5 Cells were treated with IPTG and samples were collected for total RNA extraction ~30 min later.


title: MCF7/BUS, 10 pM E2, 48 hours, biological replication 5


title: MCF7/BUS, 60 pM E2, 48 hours, biological replication 4


title: MCF7/BUS, 30 pM E2, 48 hours, biological replication 2


title: MCF7/BUS, 10 pM E2, 48 hours, biological replication 2


title: MCF7/BUS, 10 pM E2, 48 hours, biological replication 3


title: MCF7/BUS, 0 pM E2, 48 hours, biological replication 4

description: Gene expression data from MCF7 (BUS stock) exposed to 0 pM 17beta-estradiol for 48 hours.

value: 0 pM


title: MCF7/BUS, 30 pM E2, 48 hours, biological replication 3


title: bso6-77 JJS39 HPUra treated repl2

description: hybridization of HPUra treated JJS39 sample with reference RNA

source_name: HPUra treated cells

tag: JJS39 treated with HPUra for 60min. Rplicate 2


title: MCF7/BUS, 10 pM E2, 48 hours, biological replication 1


title: MCF7/BUS, 30 pM E2, 48 hours, biological replication 1


title: MCF7/BUS, 0 pM E2, 48 hours, biological replication 2


title: MCF7/BUS, 0 pM E2, 48 hours, biological replication 1


title: MCF7/BUS, 0 pM E2, 48 hours, biological replication 3


title: MCF7/BUS, 0 pM E2, 48 hours, biological replication 5


title: Subject 9 Gastrocnemius U133A

city: Boston

first: Peter

last: Kang

address: 300 Longwood Avenue

institute: Children's Hospital Boston

description: Affymetrix U133A

data_processing: MAS 5.0

source_name: Human skeletal muscles, autopsy

tag: geriatric


title: Subject 9 Tibilialis Anterior U133A

description: Affymetrix U133A


title: Subject 9 Deltoid U133A

description: Affymetrix U133A


title: Subject 8 Quadriceps U133A

description: Affymetrix U133A


title: WDG13-26 phage- recA UV treated repl 1

description: Hybridization of phage- recA UV treated sample with reference RNA

source_name: UV treated cells

tag: YB3000 treated with UV 25 mJ/m2. 60min after treatment. Replicate 1

tag: pooled RNA reference


title: Subject 9 Quadriceps U133A

description: Affymetrix U133A


title: Subject 8 Tibilialis Anterior U133A

description: Affymetrix U133A


title: Subject 8 Gastrocnemius U133A

description: Affymetrix U133A


title: Subject 8 Deltoid U133A

description: Affymetrix U133A


title: Subject 7 Quadriceps U133A

description: Affymetrix U133A


title: Subject 6 Gastrocnemius U133A

description: Affymetrix U133A


title: Subject 7 Gastrocnemius U133A

description: Affymetrix U133A


title: Subject 5 Deltoid U133A

description: Affymetrix U133A


title: Subject 6 Tibilialis Anterior U133A

description: Affymetrix U133A


title: Subject 7 Deltoid U133A

description: Affymetrix U133A


title: bso6-74 JJS39 untreated repl2

description: hybridization of untreated JJS39 sample with reference RNA

source_name: growing untreated cells

tag: JJS39 untreated growing in minimal medium. Replicate 2


title: Subject 6 Deltoid U133A

description: Affymetrix U133A


title: NIH3T3 si-RetSat1

description: NIH3T3 highly resistant to t-BHP

tag: NIH3T3 cells expressing si-RetSat


title: Subject 7 Tibilialis Anterior U133A

description: Affymetrix U133A


title: Subject 4 Gastrocnemius U133A

description: Affymetrix U133A

tag: pediatric


title: Subject 6 Quadriceps U133A

description: Affymetrix U133A


title: Subject 5 Gastrocnemius U133A

description: Affymetrix U133A


title: Subject 4 Tibilialis Anterior U133A

description: Affymetrix U133A


title: Subject 3 Quadriceps U133A

description: Affymetrix U133A


title: Subject 5 Tibilialis Anterior U133A

description: Affymetrix U133A


title: Subject 4 Quadriceps U133A

description: Affymetrix U133A


title: Subject 5 Quadriceps U133A

description: Affymetrix U133A


title: Subject 4 Deltoid U133A

description: Affymetrix U133A


title: Subject 3 Tibilialis Anterior U133A

description: Affymetrix U133A


title: Subject 3 Gastrocnemius U133A

description: Affymetrix U133A


title: Subject 2 Tibilialis Anterior U133A

description: Affymetrix U133A


title: Subject 3 Deltoid U133A

description: Affymetrix U133A


title: Subject 1 Quadriceps U133A

description: Affymetrix U133A


title: Subject 2 Quadriceps U133A

description: Affymetrix U133A


title: Subject 1 Deltoid U133A

description: Affymetrix U133A


title: Subject 2 Gastrocnemius U133A

description: Affymetrix U133A


title: 1EP11

city: Heidelberg

first: Frank

last: Mendrzyk

country: Germany

institute: German Cancer Research Center (DKFZ)

description: Comparison of normal versus tumor DNA (ependymoma). Whole-genome screening of DNA-copy number changes by array-based or matrix comparative genomic hybridization (matrix-CGH).

data_processing: Genepix result files

source_name: Pooled reference DNA from either 4 healthy males or females of the opposite sex compared to the sample.

source_name: Isolated tumor DNA, derived from ependymal tumors.


title: 1EP4


title: 1EP1


title: Subject 2 Deltoid U133A

description: Affymetrix U133A


title: 1EP5


title: 2EP36


title: 1EP7


title: 2EP35


title: 1EP12


title: 1EP10


title: 1EP2


title: 2EP26


title: 2EP29


title: 1EP3


title: 1EP9


title: 2EP30


title: 2EP32


title: 2EP33


title: 2EP34


title: 2EP24


title: 2EP27


title: 2EP31


title: 2EP28


title: 1EP8


title: 2EP23


title: 2EP22


title: 2EP21


title: Subject 9 Gastrocnemius U133B

description: Affymetrix U133B


title: 2EP18


title: Subject 9 Quadriceps U133B

description: Affymetrix U133B


title: 2EP20


title: Subject 9 Tibilialis Anterior U133B

description: Affymetrix U133B


title: Subject 8 Quadriceps U133B

description: Affymetrix U133B


title: 2EP15


title: 2EP14


title: Subject 8 Gastrocnemius U133B

description: Affymetrix U133B


title: Subject 9 Deltoid U133B

description: Affymetrix U133B


title: 2EP13


title: 2EP11


title: 2EP19


title: 2EP7


title: 2EP8


title: 2EP5


title: 2EP10


title: 2EP12


title: 2EP9


title: Subject 8 Deltoid U133B

description: Affymetrix U133B


title: Subject 7 Deltoid U133B

description: Affymetrix U133B


title: 2EP6


title: Subject 7 Quadriceps U133B

description: Affymetrix U133B


title: Subject 7 Tibilialis Anterior U133B

description: Affymetrix U133B


title: 2EP4


title: Subject 6 Gastrocnemius U133B

description: Affymetrix U133B


title: 2EP3


title: Subject 6 Quadriceps U133B

description: Affymetrix U133B


title: Subject 7 Gastrocnemius U133B

description: Affymetrix U133B


title: Subject 6 Tibilialis Anterior U133B

description: Affymetrix U133B


title: Subject 6 Deltoid U133B

description: Affymetrix U133B


title: 1EP39


title: Subject 5 Deltoid U133B

description: Affymetrix U133B


title: 1EP37


title: Subject 5 Tibilialis Anterior U133B

description: Affymetrix U133B


title: Wf9_BioRepII_TechRep2

city: Ames

first: Roger

last: Wise

state: IA

address: 411 Bessey Hall

institute: Iowa State University

description: Total RNA was extracted from 3rd, 4th, and 5th leaves, collected from six to ten greenhouse grown plants.

data_processing: GCOS (Affymetrix, CA) followed by signal intensity value determination using the MAS5 algorithm

organism: Zea mays

source_name: 3rd, 4th, and 5th leaves

tag: Maize line

tag: Tissue

value: 3rd, 4th, and 5th leaves

tag: Biological replication #

tag: Technical replication #


title: Mo17_BioRepIII_TechRep2


title: 1EP36


title: 1EP33


title: Subject 5 Quadriceps U133B

description: Affymetrix U133B


title: 1EP38


title: Wf9_BioRepIII_TechRep1


title: Wf9_BioRepII_TechRep1


title: Wf9_BioRepI_TechRep1


title: Subject 5 Gastrocnemius U133B

description: Affymetrix U133B


title: 1EP31


title: W23_BioRepIII_TechRep2


title: Subject 4 Gastrocnemius U133B

description: Affymetrix U133B


title: Wf9_BioRepI_TechRep2


title: W23_BioRepII_TechRep1


title: W23_BioRepII_TechRep2


title: Subject 4 Tibilialis Anterior U133B

description: Affymetrix U133B


title: Subject 8 Tibilialis Anterior U133B

description: Affymetrix U133B


title: W23_BioRepI_TechRep2


title: W23_BioRepIII_TechRep1


title: Mo17_BioRepIII_TechRep1


title: 1EP26


title: Subject 3 Tibilialis Anterior U133B

description: Affymetrix U133B


title: Subject 1 Gastrocnemius U133A

description: Affymetrix U133A


title: 1EP25


title: 2EP1


title: Wf9_BioRepIII_TechRep2


title: 1EP29


title: 1EP32


title: 1EP24


title: Subject 4 Quadriceps U133B

description: Affymetrix U133B


title: Subject 4 Deltoid U133B

description: Affymetrix U133B


title: 2EP16


title: Subject 3 Quadriceps U133B

description: Affymetrix U133B


title: Mo17_BioRepI_TechRep2


title: Mo17_BioRepI_TechRep1


title: Mo17_BioRepII_TechRep1


title: Subject 3 Gastrocnemius U133B

description: Affymetrix U133B


title: Mo17_BioRepII_TechRep2


title: B73_BioRepIII_TechRep1


title: B73_BioRepIII_TechRep2


title: B73_BioRepII_TechRep2


title: Subject 3 Deltoid U133B

description: Affymetrix U133B


title: B73_BioRepII_TechRep1


title: 1EP22


title: Subject 2 Tibilialis Anterior U133B

description: Affymetrix U133B


title: B73_BioRepI_TechRep2


title: B73_BioRepI_TechRep1


title: Subject 2 Gastrocnemius U133B

description: Affymetrix U133B


title: Subject 2 Quadriceps U133B

description: Affymetrix U133B


title: 2EP17


title: 2EP25


title: Subject 2 Deltoid U133B

description: Affymetrix U133B


title: 1EP23


title: 1EP20


title: 1EP19


title: 1EP21


title: 1EP15


title: 1EP17


title: 1EP16


title: 1EP14


title: Subject 1 Quadriceps U133B

description: Affymetrix U133B


title: Human 2091 fibroblasts, LY294002, Serum treatment, 4hr

status: Public on Apr 13 2006

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A/4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0/5.0 analysis software.

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

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. Serum (50ng/mL) was then added to cells and cells were collected at 4 hour after Serum treatment.

extract_protocol: RNA isolation was accomplished with TriZol (Invitrogen). The RNA (1 ?g) was amplified by in vitro transcription and reverse-transcribed into cDNA with Superscript II

source_name: Human 2091 fibroblasts, Serum starved for 48 hours

extract_protocol: The RNA (1 ?g) was amplified by in vitro transcription and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42?C.


title: Human 2091 fibroblasts, LY294002, Serum treatment, 8hr

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. Serum (50ng/mL) was then added to cells and cells were collected at 8 hour after Serum treatment.

extract_protocol: RNA isolation was accomplished with TriZol (Invitrogen). The RNA (1 ?g) was amplified by in vitro transcription and reverse-transcribed into cDNA with Superscript II.

tag: Human 2091 fibroblasts, Serum starved for 48 hours


title: 1EP13


title: Human 2091 fibroblasts, LY294002, Serum treatment, 2hr

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. Serum (50ng/mL) was then added to cells and cells were collected at 2 hour after Serum treatment.


title: Human 2091 fibroblasts, LY294002, Serum treatment, 1hr

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. Serum (50ng/mL) was then added to cells and cells were collected at 1 hour after Serum treatment.


title: Subject 1 Deltoid U133B

description: Affymetrix U133B


title: Human 2091 fibroblasts, LY294002, PDGF treatment, 4hr

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. PDGF (50ng/mL) was then added to cells and cells were collected at 4 hour after PDGF treatment.

source_name: Human 2091 fibroblasts, serum starved for 48 hours


title: Human 2091 fibroblasts, LY294002, Serum treatment, 0.5hr

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. Serum (50ng/mL) was then added to cells and cells were collected at 0.5 hour after Serum treatment.


title: Human 2091 fibroblasts, LY294002, PDGF treatment, 1hr

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. PDGF (50ng/mL) was then added to cells and cells were collected at 1 hour after PDGF treatment.

tag: Human 2091 fibroblasts, serum starved for 48 hours


title: Human 2091 fibroblasts, LY294002, PDGF treatment, 8hr

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. PDGF (50ng/mL) was then added to cells and cells were collected at 8 hour after PDGF treatment.


title: Human 2091 fibroblasts, LY294002, FGF treatment, 0.5hr

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. FGF (50ng/mL) was then added to cells and cells were collected at 0.5 hour after FGF treatment.


title: Human 2091 fibroblasts, LY294002, PDGF treatment, 0.5hr

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. PDGF (50ng/mL) was then added to cells and cells were collected at 0.5 hour after PDGF treatment.


title: Human 2091 fibroblasts, LY294002, EGF treatment, 8hr

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. EGF (50ng/mL) was then added to cells and cells were collected at 8 hour after EGF treatment.


title: Human 2091 fibroblasts, LY294002, FGF treatment, 4hr

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. FGF (50ng/mL) was then added to cells and cells were collected at 4 hour after FGF treatment.


title: Human 2091 fibroblasts, LY294002, PDGF treatment, 2hr

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. PDGF (50ng/mL) was then added to cells and cells were collected at 2 hour after PDGF treatment.


title: Human 2091 fibroblasts, LY294002, FGF treatment, 1hr

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. FGF (50ng/mL) was then added to cells and cells were collected at 1 hour after FGF treatment.


title: Human 2091 fibroblasts, LY294002, EGF treatment, 1hr

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. EGF (50ng/mL) was then added to cells and cells were collected at 1 hour after EGF treatment.


title: Human 2091 fibroblasts, LY294002, FGF treatment, 8hr

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. FGF (50ng/mL) was then added to cells and cells were collected at 8 hour after FGF treatment.


title: Human WI-38 fibroblasts, Serum treatment, 2hr, replicate 3

growth_protocol: WI-38 cells were serum starved for 48 hours . Serum (50ng/mL) was added to cells and cells were collected at 2 hour after Serum treatment.

source_name: Human WI-38 fibroblasts, Serum treatment, 0hr, replicate 3


title: 2EP2


title: Human 2091 fibroblasts, LY294002, EGF treatment, 4hr

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. EGF (50ng/mL) was then added to cells and cells were collected at 4 hour after EGF treatment.


title: Human WI-38 fibroblasts, Serum treatment, 4hr, replicate 3

growth_protocol: WI-38 cells were serum starved for 48 hours . Serum (50ng/mL) was added to cells and cells were collected at 4 hour after Serum treatment.

tag: Human WI-38 fibroblasts, Serum treatment, 0hr, replicate 3


title: Human 2091 fibroblasts, LY294002, FGF treatment, 2hr

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. FGF (50ng/mL) was then added to cells and cells were collected at 2 hour after FGF treatment.


title: Human WI-38 fibroblasts, Serum treatment, 8hr, replicate 3

growth_protocol: WI-38 cells were serum starved for 48 hours . Serum (50ng/mL) was added to cells and cells were collected at 8 hour after Serum treatment.


title: Human 2091 fibroblasts, LY294002, EGF treatment, 2hr

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. EGF (50ng/mL) was then added to cells and cells were collected at 2 hour after EGF treatment.


title: Human WI-38 fibroblasts, Serum treatment, 2hr, replicate 2

source_name: Human WI-38 fibroblasts, Serum treatment, 0hr, replicate 2


title: Human WI-38 fibroblasts, Serum treatment, 2hr, replicate 1

source_name: Human WI-38 fibroblasts, Serum treatment, 0hr, replicate 1


title: Human WI-38 fibroblasts, Serum treatment, 0.5hr, replicate 2

growth_protocol: WI-38 cells were serum starved for 48 hours . Serum (50ng/mL) was added to cells and cells were collected at 0.5 hour after Serum treatment.

tag: Human WI-38 fibroblasts, Serum treatment, 0hr, replicate 2


title: W23_BioRepI_TechRep1


title: Human WI-38 fibroblasts, Serum treatment, 0.5hr, replicate 3


title: Human 2091 fibroblasts, Serum treatment, 4hr, replicate 3

growth_protocol: 2091 cells were serum starved for 48 hours . Serum (50ng/mL) was added to cells and cells were collected at 4 hour after Serum treatment.

source_name: Human 2091 fibroblasts, Serum treatment, 0hr, replicate 3


title: Human WI-38 fibroblasts, Serum treatment, 8hr, replicate 2


title: Human WI-38 fibroblasts, Serum treatment, 0.5hr, replicate 1

tag: Human WI-38 fibroblasts, Serum treatment, 0hr, replicate 1


title: Human 2091 fibroblasts, Serum treatment, 4hr, replicate 2

source_name: Human 2091 fibroblasts, Serum treatment, 0hr, replicate 2


title: Human WI-38 fibroblasts, Serum treatment, 1hr, replicate 3

growth_protocol: WI-38 cells were serum starved for 48 hours . Serum (50ng/mL) was added to cells and cells were collected at 1 hour after Serum treatment.


title: Human WI-38 fibroblasts, Serum treatment, 4hr, replicate 2


title: Human WI-38 fibroblasts, Serum treatment, 8hr, replicate 1


title: Human WI-38 fibroblasts, Serum treatment, 4hr, replicate 1


title: Human 2091 fibroblasts, Serum treatment, 2hr, replicate 3

growth_protocol: 2091 cells were serum starved for 48 hours . Serum (50ng/mL) was added to cells and cells were collected at 2 hour after Serum treatment.

tag: Human 2091 fibroblasts, Serum treatment, 0hr, replicate 3


title: Human WI-38 fibroblasts, Serum treatment, 1hr, replicate 1


title: Human 2091 fibroblasts, Serum treatment, 8hr, replicate 1

growth_protocol: 2091 cells were serum starved for 48 hours . Serum (50ng/mL) was added to cells and cells were collected at 8 hour after Serum treatment.

source_name: Human 2091 fibroblasts, Serum treatment, 0hr, replicate 1


title: Human 2091 fibroblasts, Serum treatment, 0.5hr, replicate 3

growth_protocol: 2091 cells were serum starved for 48 hours . Serum (50ng/mL) was added to cells and cells were collected at 0.5 hour after Serum treatment.


title: Human 2091 fibroblasts, Serum treatment, 1hr, replicate 3

growth_protocol: 2091 cells were serum starved for 48 hours . Serum (50ng/mL) was added to cells and cells were collected at 1 hour after Serum treatment.


title: Human 2091 fibroblasts, Serum treatment, 8hr, replicate 2

tag: Human 2091 fibroblasts, Serum treatment, 0hr, replicate 2


title: Human 2091 fibroblasts, Serum treatment, 8hr, replicate 3


title: Human 2091 fibroblasts, Serum treatment, 2hr, replicate 2


title: Human 2091 fibroblasts, Serum treatment, 4hr, replicate 1

tag: Human 2091 fibroblasts, Serum treatment, 0hr, replicate 1


title: Human WI-38 fibroblasts, Serum treatment, 1hr, replicate 2


title: Human 2091 fibroblasts, Serum treatment, 1hr, replicate 2


title: Human 2091 fibroblasts, Serum treatment, 0.5hr, replicate 2


title: Human 2091 fibroblasts, Serum treatment, 1hr, replicate 1


title: Human 2091 fibroblasts, Serum treatment, 2hr, replicate 1


title: Human 2091 fibroblasts, Serum treatment, 0.5hr, replicate 1


title: Human WI-38 fibroblasts, PDGF treatment, 8hr, replicate 3

growth_protocol: WI-38 cells were serum starved for 48 hours . PDGF (50ng/mL) was added to cells and cells were collected at 8 hour after PDGF treatment.

source_name: Human WI-38 fibroblasts, PDGF treatment, 0hr, replicate 3


title: Human WI-38 fibroblasts, PDGF treatment, 2hr, replicate 3

growth_protocol: WI-38 cells were serum starved for 48 hours . PDGF (50ng/mL) was added to cells and cells were collected at 2 hour after PDGF treatment.

tag: Human WI-38 fibroblasts, PDGF treatment, 0hr, replicate 3


title: Human WI-38 fibroblasts, PDGF treatment, 4hr, replicate 2

growth_protocol: WI-38 cells were serum starved for 48 hours . PDGF (50ng/mL) was added to cells and cells were collected at 4 hour after PDGF treatment.

source_name: Human WI-38 fibroblasts, PDGF treatment, 0hr, replicate 2


title: Human WI-38 fibroblasts, PDGF treatment, 0.5hr, replicate 3

growth_protocol: WI-38 cells were serum starved for 48 hours . PDGF (50ng/mL) was added to cells and cells were collected at 0.5 hour after PDGF treatment.


title: Human WI-38 fibroblasts, PDGF treatment, 4hr, replicate 1

source_name: Human WI-38 fibroblasts, PDGF treatment, 0hr, replicate 1


title: Human WI-38 fibroblasts, PDGF treatment, 2hr, replicate 1

tag: Human WI-38 fibroblasts, PDGF treatment, 0hr, replicate 1


title: Human WI-38 fibroblasts, PDGF treatment, 8hr, replicate 2

tag: Human WI-38 fibroblasts, PDGF treatment, 0hr, replicate 2


title: Human WI-38 fibroblasts, PDGF treatment, 0.5hr, replicate 2


title: Human 2091 fibroblasts, PDGF treatment, 4hr, replicate 2

growth_protocol: 2091 cells were serum starved for 48 hours . PDGF (50ng/mL) was added to cells and cells were collected at 4 hour after PDGF treatment.

source_name: Human 2091 fibroblasts, PDGF treatment, 0hr, replicate 2


title: Human 2091 fibroblasts, PDGF treatment, 0.5hr, replicate 3

growth_protocol: 2091 cells were serum starved for 48 hours . PDGF (50ng/mL) was added to cells and cells were collected at 0.5 hour after PDGF treatment.

source_name: Human 2091 fibroblasts, PDGF treatment, 0hr, replicate 3


title: Human 2091 fibroblasts, PDGF treatment, 8hr, replicate 2

growth_protocol: 2091 cells were serum starved for 48 hours . PDGF (50ng/mL) was added to cells and cells were collected at 8 hour after PDGF treatment.

tag: Human 2091 fibroblasts, PDGF treatment, 0hr, replicate 2


title: Human 2091 fibroblasts, PDGF treatment, 2hr, replicate 3

growth_protocol: 2091 cells were serum starved for 48 hours . PDGF (50ng/mL) was added to cells and cells were collected at 2 hour after PDGF treatment.

tag: Human 2091 fibroblasts, PDGF treatment, 0hr, replicate 3


title: Human 2091 fibroblasts, PDGF treatment, 2hr, replicate 2


title: Human 2091 fibroblasts, PDGF treatment, 1hr, replicate 2

growth_protocol: 2091 cells were serum starved for 48 hours . PDGF (50ng/mL) was added to cells and cells were collected at 1 hour after PDGF treatment.


title: Human 2091 fibroblasts, PDGF treatment, 2hr, replicate 1

source_name: Human 2091 fibroblasts, PDGF treatment, 0hr, replicate 1


title: Human WI-38 fibroblasts, PDGF treatment, 2hr, replicate 2


title: Human WI-38 fibroblasts, PDGF treatment, 1hr, replicate 1

growth_protocol: WI-38 cells were serum starved for 48 hours . PDGF (50ng/mL) was added to cells and cells were collected at 1 hour after PDGF treatment.


title: Human 2091 fibroblasts, PDGF treatment, 8hr, replicate 3


title: Human 2091 fibroblasts, PDGF treatment, 1hr, replicate 3


title: Human 2091 fibroblasts, PDGF treatment, 0.5hr, replicate 2


title: Human WI-38 fibroblasts, PDGF treatment, 1hr, replicate 2


title: Human WI-38 fibroblasts, PDGF treatment, 0.5hr, replicate 1


title: Human 2091 fibroblasts, PDGF treatment, 8hr, replicate 1

tag: Human 2091 fibroblasts, PDGF treatment, 0hr, replicate 1


title: Human WI-38 fibroblasts, PDGF treatment, 1hr, replicate 3


title: Human 2091 fibroblasts, PDGF treatment, 4hr, replicate 3


title: Human 2091 fibroblasts, PDGF treatment, 4hr, replicate 1


title: Human 2091 fibroblasts, PDGF treatment, 1hr, replicate 1


title: Human WI-38 fibroblasts, FGF treatment, 4hr, replicate 3

growth_protocol: WI-38 cells were serum starved for 48 hours . FGF (50ng/mL) was added to cells and cells were collected at 4 hour after FGF treatment.

source_name: Human WI-38 fibroblasts, FGF treatment, 0hr, replicate 3


title: Subject 1 Gastrocnemius U133B

description: Affymetrix U133B

source_name: Human skeletal muscles, autopsy

tag: pediatric


title: Human 2091 fibroblasts, PDGF treatment, 0.5hr, replicate 1


title: Human WI-38 fibroblasts, FGF treatment, 0.5hr, replicate 3

growth_protocol: WI-38 cells were serum starved for 48 hours . FGF (50ng/mL) was added to cells and cells were collected at 0.5 hour after FGF treatment.

tag: Human WI-38 fibroblasts, FGF treatment, 0hr, replicate 3


title: Human WI-38 fibroblasts, PDGF treatment, 4hr, replicate 3


title: Human WI-38 fibroblasts, FGF treatment, 8hr, replicate 2

growth_protocol: WI-38 cells were serum starved for 48 hours . FGF (50ng/mL) was added to cells and cells were collected at 8 hour after FGF treatment.

source_name: Human WI-38 fibroblasts, FGF treatment, 0hr, replicate 2


title: Human WI-38 fibroblasts, FGF treatment, 1hr, replicate 2

growth_protocol: WI-38 cells were serum starved for 48 hours . FGF (50ng/mL) was added to cells and cells were collected at 1 hour after FGF treatment.

tag: Human WI-38 fibroblasts, FGF treatment, 0hr, replicate 2


title: Human WI-38 fibroblasts, FGF treatment, 0.5hr, replicate 1

source_name: Human WI-38 fibroblasts, FGF treatment, 0hr, replicate 1


title: Human 2091 fibroblasts, FGF treatment, 1hr, replicate 3

growth_protocol: 2091 cells were serum starved for 48 hours . FGF (50ng/mL) was added to cells and cells were collected at 1 hour after FGF treatment.

source_name: Human 2091 fibroblasts, FGF treatment, 0hr, replicate 3


title: Human 2091 fibroblasts, FGF treatment, 0.5hr, replicate 3

growth_protocol: 2091 cells were serum starved for 48 hours . FGF (50ng/mL) was added to cells and cells were collected at 0.5 hour after FGF treatment.

tag: Human 2091 fibroblasts, FGF treatment, 0hr, replicate 3


title: Human 2091 fibroblasts, FGF treatment, 8hr, replicate 3

growth_protocol: 2091 cells were serum starved for 48 hours . FGF (50ng/mL) was added to cells and cells were collected at 8 hour after FGF treatment.


title: Human WI-38 fibroblasts, FGF treatment, 2hr, replicate 3

growth_protocol: WI-38 cells were serum starved for 48 hours . FGF (50ng/mL) was added to cells and cells were collected at 2 hour after FGF treatment.


title: Human WI-38 fibroblasts, FGF treatment, 1hr, replicate 3


title: Human WI-38 fibroblasts, FGF treatment, 1hr, replicate 1

tag: Human WI-38 fibroblasts, FGF treatment, 0hr, replicate 1


title: Human WI-38 fibroblasts, FGF treatment, 0.5hr, replicate 2


title: Human WI-38 fibroblasts, FGF treatment, 2hr, replicate 2


title: Human WI-38 fibroblasts, FGF treatment, 2hr, replicate 1


title: Human WI-38 fibroblasts, FGF treatment, 8hr, replicate 3


title: Human 2091 fibroblasts, FGF treatment, 2hr, replicate 2

growth_protocol: 2091 cells were serum starved for 48 hours . FGF (50ng/mL) was added to cells and cells were collected at 2 hour after FGF treatment.

source_name: Human 2091 fibroblasts, FGF treatment, 0hr, replicate 2


title: Human 2091 fibroblasts, FGF treatment, 0.5hr, replicate 2

tag: Human 2091 fibroblasts, FGF treatment, 0hr, replicate 2


title: Human 2091 fibroblasts, FGF treatment, 1hr, replicate 2


title: Human 2091 fibroblasts, FGF treatment, 2hr, replicate 3


title: Human WI-38 fibroblasts, FGF treatment, 4hr, replicate 1


title: Human 2091 fibroblasts, FGF treatment, 4hr, replicate 2

growth_protocol: 2091 cells were serum starved for 48 hours . FGF (50ng/mL) was added to cells and cells were collected at 4 hour after FGF treatment.


title: Human WI-38 fibroblasts, FGF treatment, 8hr, replicate 1


title: Human 2091 fibroblasts, FGF treatment, 8hr, replicate 2


title: Human 2091 fibroblasts, FGF treatment, 4hr, replicate 3


title: Human 2091 fibroblasts, FGF treatment, 8hr, replicate 1

source_name: Human 2091 fibroblasts, FGF treatment, 0hr, replicate 1


title: Human WI-38 fibroblasts, FGF treatment, 4hr, replicate 2


title: Human 2091 fibroblasts, FGF treatment, 4hr, replicate 1

tag: Human 2091 fibroblasts, FGF treatment, 0hr, replicate 1


title: Human 2091 fibroblasts, LY294002, EGF treatment, 0.5hr

growth_protocol: 2091 cells were serum starved for 48 hours and  treated with LY294002 (30ng/mL) for 30 minutes. EGF (50ng/mL) was then added to cells and cells were collected at 0.5 hour after EGF treatment.

source_name: Human 2091 fibroblasts, serum starved for 48 hours


title: Human 2091 fibroblasts, FGF treatment, 1hr, replicate 1


title: Human 2091 fibroblasts, FGF treatment, 2hr, replicate 1


title: Human 2091 fibroblasts, EGF treatment, 0.5hr, replicate 3

growth_protocol: 2091 cells were serum starved for 48 hours . EGF (50ng/mL) was added to cells and cells were collected at 0.5 hour after EGF treatment.

source_name: Human 2091 fibroblasts, EGF treatment, 0hr, replicate 3


title: Human WI-38 fibroblasts, EGF treatment, 1hr, replicate 3

growth_protocol: WI-38 cells were serum starved for 48 hours . EGF (50ng/mL) was added to cells and cells were collected at 1 hour after EGF treatment.

source_name: Human WI-38 fibroblasts, EGF treatment, 0hr, replicate 3


title: Human 2091 fibroblasts, EGF treatment, 4hr, replicate 3

growth_protocol: 2091 cells were serum starved for 48 hours . EGF (50ng/mL) was added to cells and cells were collected at 4 hour after EGF treatment.

tag: Human 2091 fibroblasts, EGF treatment, 0hr, replicate 3


title: Human WI-38 fibroblasts, EGF treatment, 4hr, replicate 3

growth_protocol: WI-38 cells were serum starved for 48 hours . EGF (50ng/mL) was added to cells and cells were collected at 4 hour after EGF treatment.

tag: Human WI-38 fibroblasts, EGF treatment, 0hr, replicate 3


title: Human WI-38 fibroblasts, EGF treatment, 1hr, replicate 1

source_name: Human WI-38 fibroblasts, EGF treatment, 0hr, replicate 1


title: Human WI-38 fibroblasts, EGF treatment, 2hr, replicate 2

growth_protocol: WI-38 cells were serum starved for 48 hours . EGF (50ng/mL) was added to cells and cells were collected at 2 hour after EGF treatment.

source_name: Human WI-38 fibroblasts, EGF treatment, 0hr, replicate 2


title: Human 2091 fibroblasts, EGF treatment, 2hr, replicate 3

growth_protocol: 2091 cells were serum starved for 48 hours . EGF (50ng/mL) was added to cells and cells were collected at 2 hour after EGF treatment.


title: Human WI-38 fibroblasts, EGF treatment, 8hr, replicate 1

growth_protocol: WI-38 cells were serum starved for 48 hours . EGF (50ng/mL) was added to cells and cells were collected at 8 hour after EGF treatment.

tag: Human WI-38 fibroblasts, EGF treatment, 0hr, replicate 1


title: Human WI-38 fibroblasts, EGF treatment, 1hr, replicate 2

tag: Human WI-38 fibroblasts, EGF treatment, 0hr, replicate 2


title: Human WI-38 fibroblasts, EGF treatment, 0.5hr, replicate 2

growth_protocol: WI-38 cells were serum starved for 48 hours . EGF (50ng/mL) was added to cells and cells were collected at 0.5 hour after EGF treatment.


title: Human WI-38 fibroblasts, EGF treatment, 2hr, replicate 3


title: Human 2091 fibroblasts, EGF treatment, 2hr, replicate 2

source_name: Human 2091 fibroblasts, EGF treatment, 0hr, replicate 2


title: Human 2091 fibroblasts, EGF treatment, 1hr, replicate 2

growth_protocol: 2091 cells were serum starved for 48 hours . EGF (50ng/mL) was added to cells and cells were collected at 1 hour after EGF treatment.

tag: Human 2091 fibroblasts, EGF treatment, 0hr, replicate 2


title: Human WI-38 fibroblasts, EGF treatment, 0.5hr, replicate 3


title: Human WI-38 fibroblasts, EGF treatment, 0.5hr, replicate 1


title: Human WI-38 fibroblasts, EGF treatment, 4hr, replicate 2


title: Human WI-38 fibroblasts, EGF treatment, 8hr, replicate 3


title: Human WI-38 fibroblasts, EGF treatment, 2hr, replicate 1


title: Human WI-38 fibroblasts, EGF treatment, 4hr, replicate 1


title: Human 2091 fibroblasts, EGF treatment, 4hr, replicate 2


title: Human 2091 fibroblasts, EGF treatment, 0.5hr, replicate 2


title: Human 2091 fibroblasts, EGF treatment, 1hr, replicate 3


title: Human 2091 fibroblasts, EGF treatment, 8hr, replicate 2

growth_protocol: 2091 cells were serum starved for 48 hours . EGF (50ng/mL) was added to cells and cells were collected at 8 hour after EGF treatment.


title: Human 2091 fibroblasts, EGF treatment, 8hr, replicate 1

source_name: Human 2091 fibroblasts, EGF treatment, 0hr, replicate 1


title: Human 2091 fibroblasts, EGF treatment, 4hr, replicate 1

tag: Human 2091 fibroblasts, EGF treatment, 0hr, replicate 1


title: Human WI-38 fibroblasts, PDGF treatment, 8hr, replicate 1

growth_protocol: WI-38 cells were serum starved for 48 hours . PDGF (50ng/mL) was added to cells and cells were collected at 8 hour after PDGF treatment.

source_name: Human WI-38 fibroblasts, PDGF treatment, 0hr, replicate 1


title: Human 2091 fibroblasts, EGF treatment, 2hr, replicate 1


title: Human 2091 fibroblasts, EGF treatment, 1hr, replicate 1


title: Human 2091 fibroblasts, FGF treatment, 0.5hr, replicate 1

growth_protocol: 2091 cells were serum starved for 48 hours . FGF (50ng/mL) was added to cells and cells were collected at 0.5 hour after FGF treatment.


title: Human WI-38 fibroblasts, EGF treatment, 8hr, replicate 2


title: Comparison of 18-DPA li1 mutant with 18-DPA normal Fiber Repeat4

status: Public on Apr 12 2006

city: Shanghai

first: Xiao-Ya

last: Chen

address: No. 300, Fenglin Road

department: Institute of Plant Physiology and Ecology

country: China

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: RNAs from the 18-DPA li1 mutant fibers were compared to the 18-DPA normal fiber RNA. Probes were prepared by the Micromax TSA Labeling and Detection Kit (PerkinElmer, Wellesley, MA) using 10 μg total RNA. The probes were annealed to target cDNAs for 13 hr at 60 °C, and arrays were washed thrice for 20 min each: 60 °C in 2×SSC/0.2%SDS, room temperature in 2×SSC, and room temperature in 0.2×SSC.

data_processing: Images were acquired by scanning the slides with a ScanArray 4000 Scanner (Packard BioChip Technologies, Meriden, CT). Fluorescence signals were detected through ImaGene 5.6 (BioDiscovery, El Segundo, CA). For each signal, mean value of the four repeats was taken. Signals lower than 1000 were seen as low expression and omitted from further statistic analysis.

organism: Gossypium hirsutum

source_name: 18-DPA li1 mutant cotton fiber

tag: Total RNAs were prepared by a hot borate method (Wan and Wilkins,1994) from the 18-DPA li1 mutant fibers.

source_name: 18-DPA normal cotton fiber

tag: Total RNAs were prepared by a hot borate method (Wan and Wilkins,1994) from the 18-DPA normal fibers.


title: Human 2091 fibroblasts, EGF treatment, 8hr, replicate 3


title: TTE3 cells treated with BPA for 12 h-1

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

description: A mouse testicular Sertoli cell line, TTE3, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. TTE3 cells were treated with 0.2 mM bisphenol A (BPA) for 12 h.

data_processing: GeneChip Analysis Suite

label: phycoerythrin

source_name: Mouse testicular Sertoli cell line TTE3

tag: Mouse testicular Sertoli cell line TTE3


title: Mouse model of gastric cancer (control 72A)

city: New York

first: Shigeo

last: Takaishi

state: NY

address: 1130 St. Nicholas Avenue, ICRC 901A

department: Medicine (Division of Digestive and Liver Disease)

institute: Columbia University, College of Physicians and Surgeons

description: Total RNA was extracted from whole stomach of non-transgenic (FVB/N) mouse with H.felis for 6 months.

data_processing: data analyzed using MAS5.0

label: PE

tag: strain

value: FVB/N, gender:male, age:10 months, transgene:none, tissue:stomach, histology:intestinal metaplasia / gastric dysplasia . infection:H.felis (6 months)

tag: *Hypergastrinemic transgenic (INS-GAS) mice with Helicobacter felis infection for 6 months have an accelerated gastric cancer in stomach. (Wang TC et al, Gastroenterology, 2000, vol 118, p36-47)  This is one of the 3 control groups.


title: Mouse model of gastric cancer (control 78A)

description: Total RNA was extracted from whole stomach of non-transgenic (FVB/N) mouse without H.felis infection.

value: FVB/N, gender:male, age:10 months, transgene:none, tissue:stomach, histology:normal stomach. infection:none.


title: Comparison of 15-DPA li1 mutant with 15-DPA normal Fiber Repeat2

description: RNAs from the 15-DPA li1 mutant fibers were compared to the 15-DPA normal fiber RNA. Probes were prepared by the Micromax TSA Labeling and Detection Kit (PerkinElmer, Wellesley, MA) using 10 μg total RNA. The probes were annealed to target cDNAs for 13 hr at 60 °C, and arrays were washed thrice for 20 min each: 60 °C in 2×SSC/0.2%SDS, room temperature in 2×SSC, and room temperature in 0.2×SSC.

source_name: 15-DPA li1 mutant cotton fiber

tag: Total RNAs were prepared by a hot borate method (Wan and Wilkins,1994) from the 15-DPA li1 mutant fibers.

source_name: 15-DPA normal cotton fiber

tag: Total RNAs were prepared by a hot borate method (Wan and Wilkins,1994) from the 15-DPA normal fibers.


title: Comparison of 18-DPA li1 mutant with 18-DPA normal Fiber Repeat2


title: Comparison of 15-DPA li1 mutant with 15-DPA normal Fiber Repeat1


title: TTE3 cells treated with BPA for 6 h-2

description: A mouse testicular Sertoli cell line, TTE3, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. TTE3 cells were treated with 0.2 mM bisphenol A (BPA) for 6 h.


title: Mouse model of gastric cancer (control 68A)

description: Total RNA was extracted from whole stomach of INS-GAS mouse without H.felis.

source_name: INS-GAS mouse without Helicobacter felis

value: FVB/N, gender:male, age:10 months, transgene:human gastrin, tissue:stomach, histology:atrophic gastritis / intestinal metaplasia. infection:none

tag: *Hypergastrinemic transgenic (INS-GAS) mice with Helicobacter felis infection for 6 months have an accelerated gastric cancer in stomach. (Wang TC et al, Gastroenterology, 2000, vol 118, p36-47)

tag: This is one of the 3 control groups.


title: TTE3 cells treated with BPA for 6 h-1


title: Comparison of 18-DPA li1 mutant with 18-DPA normal Fiber Repeat3


title: Comparison of 15-DPA li1 mutant with 15-DPA normal Fiber Repeat3


title: Mouse model of gastric cancer (sample 63A)

description: Total RNA was extracted from whole stomach of H.felis infected INS-GAS mouse.

source_name: INS-GAS mouse with Helicobacter felis

value: FVB/N, gender:male, age:10 months, transgene:human gastrin, tissue:stomach, histology:gastric adenocarcinoma. infection:H.felis (6 months)


title: TTE3 cells treated with BPA for 3 h-1

description: A mouse testicular Sertoli cell line, TTE3, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. TTE3 cells were treated with 0.2 mM bisphenol A (BPA) for 3 h.


title: TTE3 cells treated with BPA for 12 h-2


title: Comparison of 15-DPA li1 mutant with 15-DPA normal Fiber Repeat4


title: Comparison of 18-DPA li1 mutant with 18-DPA normal Fiber Repeat1


title: Comparison of 12-DPA li1 mutant with 12-DPA normal Fiber Repeat3

description: RNAs from the 12-DPA li1 mutant fibers were compared to the 12-DPA normal fiber RNA. Probes were prepared by the Micromax TSA Labeling and Detection Kit (PerkinElmer, Wellesley, MA) using 10 μg total RNA. The probes were annealed to target cDNAs for 13 hr at 60 °C, and arrays were washed thrice for 20 min each: 60 °C in 2×SSC/0.2%SDS, room temperature in 2×SSC, and room temperature in 0.2×SSC.

source_name: 12-DPA li1 mutant cotton fiber

tag: Total RNAs were prepared by a hot borate method (Wan and Wilkins,1994) from the 12-DPA li1 mutant fibers.

source_name: 12-DPA normal cotton fiber

tag: Total RNAs were prepared by a hot borate method (Wan and Wilkins,1994) from the 12-DPA normal fibers.


title: TTE3 cells treated with BPA for 0 h-1

description: A mouse testicular Sertoli cell line, TTE3, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. TTE3 cells were treated with 0.2 mM bisphenol A (BPA) for 0 h.


title: Comparison of 12-DPA li1 mutant with 12-DPA normal Fiber Repeat1


title: Comparison of 12-DPA li1 mutant with 12-DPA normal Fiber Repeat4


title: Mouse model of gastric cancer (sample 59A)


title: Comparison of 12-DPA li1 mutant with 12-DPA normal Fiber Repeat2


title: TTE3 cells treated with BPA for 3 h-2


title: TTE3 cells treated with BPA for 0 h-2


title: Comparison of 9-DPA li1 mutant with 9-DPA normal Fiber Repeat4

description: RNAs from the 9-DPA li1 mutant fibers were compared to the 9-DPA normal fiber RNA. Probes were prepared by the Micromax TSA Labeling and Detection Kit (PerkinElmer, Wellesley, MA) using 10 μg total RNA. The probes were annealed to target cDNAs for 13 hr at 60 °C, and arrays were washed thrice for 20 min each: 60 °C in 2×SSC/0.2%SDS, room temperature in 2×SSC, and room temperature in 0.2×SSC.

source_name: 9-DPA li1 mutant cotton fiber

tag: Total RNAs were prepared by a hot borate method (Wan and Wilkins,1994) from the 9-DPA li1 mutant fibers.

source_name: 9-DPA normal cotton fiber

tag: Total RNAs were prepared by a hot borate method (Wan and Wilkins,1994) from the 9-DPA normal fibers.


title: Human 2091 fibroblasts, EGF treatment, 0.5hr, replicate 1


title: Comparison of 9-DPA li1 mutant with 9-DPA normal Fiber Repeat2


title: Comparison of 9-DPA li1 mutant with 9-DPA normal Fiber Repeat3


title: Comparison of 9-DPA li1 mutant with 9-DPA normal Fiber Repeat1


title: Comparison of 6-DPA li1 mutant with 6-DPA normal Fiber Repeat4

description: RNAs from the 6-DPA li1 mutant fibers were compared to the 6-DPA normal fiber RNA. Probes were prepared by the Micromax TSA Labeling and Detection Kit (PerkinElmer, Wellesley, MA) using 10 μg total RNA. The probes were annealed to target cDNAs for 13 hr at 60 °C, and arrays were washed thrice for 20 min each: 60 °C in 2×SSC/0.2%SDS, room temperature in 2×SSC, and room temperature in 0.2×SSC.

source_name: 6-DPA li1 mutant cotton fiber

tag: Total RNAs were prepared by a hot borate method (Wan and Wilkins,1994) from the 6-DPA li1 mutant fibers.

source_name: 6-DPA normal cotton fiber

tag: Total RNAs were prepared by a hot borate method (Wan and Wilkins,1994) from the 6-DPA normal fibers.


title: Comparison of 6-DPA li1 mutant with 6-DPA normal Fiber Repeat3


title: Comparison of 6-DPA li1 mutant with 6-DPA normal Fiber Repeat2


title: Comparison of 9-DPA Fiber with Ovule Repeat1

description: RNAs from the 9-DPA fiber-detached ovule were compared to the 9-DPA fiber RNA. Probes were prepared by the Micromax TSA Labeling and Detection Kit (PerkinElmer, Wellesley, MA) using 10 μg total RNA. The probes were annealed to target cDNAs for 13 hr at 60 °C, and arrays were washed thrice for 20 min each: 60 °C in 2×SSC/0.2%SDS, room temperature in 2×SSC, and room temperature in 0.2×SSC.

data_processing: Images were acquired by scanning the slides with a ScanArray 4000 Scanner (Packard BioChip Technologies, Meriden, CT). Fluorescence signals were detected through ImaGene 5.6 (BioDiscovery, El Segundo, CA). For each signal, mean value of the four repeats was taken. Signals lower than 2000 were seen as low expression and omitted from further statistic analysis.

source_name: 9-DPA cotton fiber

tag: Total RNAs were prepared by a hot borate method (Wan and Wilkins,1994) from the 9-DPA fibers.

source_name: 9-DPA cotton ovule (fiber-detached)

tag: Total RNAs were prepared by a hot borate method (Wan and Wilkins,1994) from the 9-DPA fiber-detached ovules.


title: Comparison of 9-DPA Fiber with Ovule Repeat2


title: Comparison of 9-DPA Fiber with Ovule Repeat4


title: Comparison of 6-DPA li1 mutant with 6-DPA normal Fiber Repeat1


title: Comparison of 9-DPA Fiber with Ovule Repeat3


title: Comparison of 18-DPA with 9-DPA Fiber Repeat4

description: RNAs from the 18-DPA fibers were compared to the 9-DPA fiber RNA. Probes were prepared by the Micromax TSA Labeling and Detection Kit (PerkinElmer, Wellesley, MA) using 10 μg total RNA. The probes were annealed to target cDNAs for 13 hr at 60 °C, and arrays were washed thrice for 20 min each: 60 °C in 2×SSC/0.2%SDS, room temperature in 2×SSC, and room temperature in 0.2×SSC.

source_name: 18-DPA cotton fiber

tag: Total RNAs were prepared by a hot borate method (Wan and Wilkins,1994) from the 18-DPA fibers.


title: Comparison of 18-DPA with 9-DPA Fiber Repeat3


title: Comparison of 18-DPA with 9-DPA Fiber Repeat2


title: Comparison of 15-DPA with 9-DPA Fiber Repeat1

description: RNAs from the 15-DPA fibers were compared to the 9-DPA fiber RNA. Probes were prepared by the Micromax TSA Labeling and Detection Kit (PerkinElmer, Wellesley, MA) using 10 μg total RNA. The probes were annealed to target cDNAs for 13 hr at 60 °C, and arrays were washed thrice for 20 min each: 60 °C in 2×SSC/0.2%SDS, room temperature in 2×SSC, and room temperature in 0.2×SSC.

source_name: 15-DPA cotton fiber

tag: Total RNAs were prepared by a hot borate method (Wan and Wilkins,1994) from the 15-DPA fibers.


title: Comparison of 18-DPA with 9-DPA Fiber Repeat1


title: Comparison of 15-DPA with 9-DPA Fiber Repeat4


title: Comparison of 9-DPA with 9-DPA Fiber Repeat4

description: RNAs from the 9-DPA fibers were compared to the 9-DPA fiber RNA. Probes were prepared by the Micromax TSA Labeling and Detection Kit (PerkinElmer, Wellesley, MA) using 10 μg total RNA. The probes were annealed to target cDNAs for 13 hr at 60 °C, and arrays were washed thrice for 20 min each: 60 °C in 2×SSC/0.2%SDS, room temperature in 2×SSC, and room temperature in 0.2×SSC.


title: Comparison of 12-DPA with 9-DPA Fiber Repeat4

description: RNAs from the 12-DPA fibers were compared to the 9-DPA fiber RNA. Probes were prepared by the Micromax TSA Labeling and Detection Kit (PerkinElmer, Wellesley, MA) using 10 μg total RNA. The probes were annealed to target cDNAs for 13 hr at 60 °C, and arrays were washed thrice for 20 min each: 60 °C in 2×SSC/0.2%SDS, room temperature in 2×SSC, and room temperature in 0.2×SSC.

source_name: 12-DPA cotton fiber

tag: Total RNAs were prepared by a hot borate method (Wan and Wilkins,1994) from the 12-DPA fibers.


title: Comparison of 12-DPA with 9-DPA Fiber Repeat1


title: Comparison of 9-DPA with 9-DPA Fiber Repeat3


title: Comparison of 15-DPA with 9-DPA Fiber Repeat2


title: Comparison of 12-DPA with 9-DPA Fiber Repeat2


title: Comparison of 6-DPA with 9-DPA Fiber Repeat2

description: RNAs from the 6-DPA fibers were compared to the 9-DPA fiber RNA. Probes were prepared by the Micromax TSA Labeling and Detection Kit (PerkinElmer, Wellesley, MA) using 10 μg total RNA. The probes were annealed to target cDNAs for 13 hr at 60 °C, and arrays were washed thrice for 20 min each: 60 °C in 2×SSC/0.2%SDS, room temperature in 2×SSC, and room temperature in 0.2×SSC.

source_name: 6-DPA cotton fiber

tag: Total RNAs were prepared by a hot borate method (Wan and Wilkins,1994) from the 6-DPA fibers.


title: Comparison of 12-DPA with 9-DPA Fiber Repeat3


title: Comparison of 15-DPA with 9-DPA Fiber Repeat3


title: Comparison of 6-DPA with 9-DPA Fiber Repeat1


title: Comparison of 6-DPA with 9-DPA Fiber Repeat3


title: Comparison of 3-DPA with 9-DPA Fiber Repeat2

description: RNAs from the 3-DPA fibers were compared to the 9-DPA fiber RNA. Probes were prepared by the Micromax TSA Labeling and Detection Kit (PerkinElmer, Wellesley, MA) using 10 μg total RNA. The probes were annealed to target cDNAs for 13 hr at 60 °C, and arrays were washed thrice for 20 min each: 60 °C in 2×SSC/0.2%SDS, room temperature in 2×SSC, and room temperature in 0.2×SSC.

source_name: 3-DPA cotton fiber

tag: Total RNAs were prepared by a hot borate method (Wan and Wilkins,1994) from the 3-DPA fibers.


title: Comparison of 3-DPA with 9-DPA Fiber Repeat3


title: Comparison of 3-DPA with 9-DPA Fiber Repeat1

description: RNAs from the 3-DPA fibers were compared to the 9-DPA fiber RNA.Probes were prepared by the Micromax TSA Labeling and Detection Kit (PerkinElmer, Wellesley, MA) using 10 μg total RNA. The probes were annealed to target cDNAs for 13 hr at 60 °C, and arrays were washed thrice for 20 min each: 60 °C in 2×SSC/0.2%SDS, room temperature in 2×SSC, and room temperature in 0.2×SSC.

source_name: 9 DPA cotton fiber


title: Comparison of 9-DPA with 9-DPA Fiber Repeat2


title: Comparison of 3-DPA with 9-DPA Fiber Repeat4


title: Comparison of 6-DPA with 9-DPA Fiber Repeat4


title: Comparison of 9-DPA with 9-DPA Fiber Repeat1


title: Treatment: DHT; time: 24 hrs; repeat: 3; chip B

status: Public on Apr 11 2006

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

description: A study of the SARM-regulated gene expression in LNCaP prostate carcinoma cells

data_processing: Standard Affymetrix scanning/normalization process

label: Biotin

source_name: LNCaP cells; Human, prostate carcinoma, metastasized to lymph node; Maintained in DMEM/8% charcoal-stripped serum for 3 days before treatment.

tag: In this experiment LNCaP cells

tag: were treated with Vehicle (ethanol),

tag: Treatment was done for 6 and 24 hrs.

tag: The entire experiment was repeated 3 times.


title: Treatment: 018; time: 24 hrs; repeat: 3; chip B


title: Treatment: vehicle; time 24 hrs; repeat: 2; chip B


title: Treatment: vehicle; time: 24 hrs; repeat: 3; chip B


title: Treatment: DHT; time: 24 hrs; repeat: 2; chip B


title: Treatment: vehicle; time: 6 hrs; repeat: 3

description:
A study of the SARM-regulated gene expression in LNCaP prostate carcinoma cells.
Treated with vehicle for 6 hrs

molecule: polyA RNA

source_name: LNCaP cells

treatment_protocol:
In this experiment LNCaP cells
were treated with Vehicle (ethanol),
DHT (10 nM) or RTI-6413-018 (100 nM).
Treatment was done for 6 and 24 hrs.
The entire experiment was repeated 3 times.

tag: LNCaP cells; Human, prostate carcinoma, metastasized to lymph node; Maintained in DMEM/8% charcoal-stripped serum for 3 days before treatment.


title: Treatment: DHT; time: 24 hrs; repeat: 3

description:
A study of the SARM-regulated gene expression in LNCaP prostate carcinoma cells.
Treated with DHT for 24 hrs


title: Treatment: 018; time: 24 hrs; repeat: 2; chip B


title: Treatment: DHT; time 6 hrs, repeat: 2, chip B

tag: The entire experiment was repeated 3 time


title: Treatment: RTI-6413-018; time: 24 hrs; repeat: 3

description:
A study of the SARM-regulated gene expression in LNCaP prostate carcinoma cells.
SARM-treated for 24 hrs.


title: A2 set #011 Ad AreaX Mix Type A

city: Durham

first: Osceola

last: Whitney

state: NC

address: Research Drive, Bryan Research Building, Room 401E

department: Neurobiology

institute: Duke University Medical Center

description: Animals were perfused with 4% paraformaldehyde, brains removed, processed further in fixative, 120um sagittal slices cut of the right hemisphere, and under a dissecting microscope, vocal nuclei dissected (HVC, RA, Area X, LMAN); the left hemisphere was used for in-situ hybridization verification of egr-1 induction. From the dissected vocal nuclei, total RNA was isolated, linearly amplified, converted to sense cDNA labeled with Cy3 or Cy5 dyes, and hybridized to the microarrays. For details see Wada et al., (in preparation).

data_processing: LOG ratio of median defined by 635/532 (not normalized).

organism: Taeniopygia guttata

source_name: Area X, Song behavior 60min

tag: A mix of Area X from brains of 3 singing adult male zebra finches. Cy-dye labeled probes were generated for vocal nuclei (HVC, RA, LMAN, and LAreaX) of silent (overnight) and singing birds (undirected, >30 bouts/h for 1hr).

source_name: Area X, quiet


title: Treatment: DHT; time: 6 hrs; repeat: 3

description:
A study of the SARM-regulated gene expression in LNCaP prostate carcinoma cells.
Treated with DHT for 6 hrs


title: Treatment: vehicle; time: 6 hrs; repeat: 2; chip B


title: Treatment: 018; time 6 hrs; repeat: 3; chip B


title: Treatment: RTI-6413-018; time: 6 hrs; repeat: 3

description:
A study of the SARM-regulated gene expression in LNCaP prostate carcinoma cells.
Treated with SARM for 6 hrs


title: Treatment: vehicle; time 24 hrs; repeat: 3

description:
A study of the SARM-regulated gene expression in LNCaP prostate carcinoma cells.
Treated with vehicle for 24 hrs


title: Treatment: RTI-6413-018; time: 24 hrs; repeat: 1; chip B

description:
A study of the SARM-regulated gene expression in LNCaP prostate carcinoma cells.
Treated with SARM for 24 hrs.


title: Treatment: RTI-6413-018; time: 24 hrs; repeat: 2


title: Treatment: 018; time: 6 hrs; repeat: 2; chip B


title: Treatment: DHT; time 6 hrs; repeat: 3; chip B


title: Treatment: vehicle; time: 6 hrs; repeat: 3; chip B


title: Human_macrophages_normoxia_repB

city: Göteborg

first: Per-Arne

last: Svensson

country: Sweden

institute: Internal Medicine

description: Total RNA was isolated with the RNeasy kit (Qiagen) from macrophages incubated at normoxia (21% oxygen) or hypoxia (0% oxygen) for 24 h. Two μg RNA from 4 donors incubated at normoxia and 4 donors at hypoxia was pooled respectively and these 2 pools were used for the target preparation and analyzed on duplicate DNA microarrays (Hu95A; Affymetrix).

data_processing: MAS 5, signal algorithm, global scaling (target intensity 500)

source_name: Human monocyte-derived macrophages

extract_protocol: Total RNA was isolated with the RNeasy kit (Qiagen).

tag: Human mononuclear cells were isolated by Ficoll-Paque centrifugation in a discontinuous gradient from buffy coats from healthy blood donors. Cells were differentiated in macrophage-SFM medium supplemented with 70 U/ml human granulocyte macrophage colony-stimulating factor. After 3 days, the medium was changed to macrophage-SFM without GM-CSF and cells were cultured up to 8 days


title: A2 set #024 Ad AreaX Single Type B

data_processing: LOG ratio of median defined by 532/635 (not normalized).

tag: Area X from brain of a quiet adult male zebra finch. Cy-dye labeled probes were generated for vocal nuclei (HVC, RA, LMAN, and LAreaX) of silent (overnight) and singing birds (undirected, >30 bouts/h for 1hr).

tag: Area X from brain of a singing adult male zebra finch. Cy-dye labeled probes were generated for vocal nuclei (HVC, RA, LMAN, and LAreaX) of silent (overnight) and singing birds (undirected, >30 bouts/h for 1hr).


title: Treatment: DHT; time: 24 hrs; repeat: 2

description:
A study of the SARM-regulated gene expression in LNCaP prostate carcinoma cells.
Treated with DHT for 24 hrs.


title: A2 set #006 Ad AreaX Mix Type B


title: A2 set#015 Ad AreaX Single Type A

source_name: Area-X, quiet


title: Treatment: DHT; time: 24 hrs; repeat: 1; chip B


title: A2 set#013 Ad MAN Single Type A

data_processing: LOG ratio of median defined by 635/532 (not normalized)

source_name: MAN, Song behavior 60min

tag: MAN brain of a singing adult male zebra finch. Cy-dye labeled probes were generated for vocal nuclei (HVC, RA, LMAN, and LAreaX) of silent (overnight) and singing birds (undirected, >30 bouts/h for 1hr).

source_name: MAN, quiet

tag: MAN brain of a quiet adult male zebra finch. Cy-dye labeled probes were generated for vocal nuclei (HVC, RA, LMAN, and LAreaX) of silent (overnight) and singing birds (undirected, >30 bouts/h for 1hr).


title: A2 set #010 Ad MAN Mix Type A

tag: A mix of RA from brains of 3 singing adult male zebra finches. Cy-dye labeled probes were generated for vocal nuclei (HVC, RA, LMAN, and LAreaX) of silent (overnight) and singing birds (undirected, >30 bouts/h for 1hr).

tag: A mix of MAN from brains of 3 singing adult male zebra finches. Cy-dye labeled probes were generated for vocal nuclei (HVC, RA, LMAN, and LAreaX) of silent (overnight) and singing birds (undirected, >30 bouts/h for 1hr).


title: Treatment: vehicle; time: 24 hrs; repeat: 2

description:
A study of the SARM-regulated gene expression in LNCaP prostate carcinoma cells.
Treated with ethanol vehicle for 24 hrs.


title: Human_macrophages_normoxia_repA


title: Human_macrophages_hypoxia_repA


title: Treatment: DHT; time: 6 hrs; repeat: 2


title: Treatment: RTI-6413-018; time: 6 hrs; repeat: 1; chip B


title: Treatment: vehicle; time: 6 hrs; repeat: 2

description:
A study of the SARM-regulated gene expression in LNCaP prostate carcinoma cells.
Vehicle treated for 6 hrs


title: A2 set #004 Ad RA Mix Type B

description: Animals were perfused with 4% paraformaldehyde, brains removed, processed further in fixative, 120um sagittal slices cut of the right hemisphere, and under a dissecting microscope, vocal nuclei dissected (HVC, RA, Area X, LMAN); the left hemisphere was used for in-situ hybridization verification of egr-1 induction. From the dissected vocal nuclei, total RNA was isolated, linearly amplified, converted to sense cDNA labeled with Cy3 or Cy5 dyes, and hybridized to the microarrays. For details see Wada et al., (in preparation)

source_name: RA, quiet

source_name: RA, Song behavior 60min