title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 7945

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-66


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBc, Halobacterium  GTF growth curve experiment, Array 7947

status: Public on Feb 23 2007

type: genomic

city: Seattle

first: Marc

last: Facciotti

state: WA

address: 1441 North 34th Street

country: USA

institute: Institute for Systems Biology

description: IP sample of Cmyc tagged TFBc expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBc grown to OD600 between 1.0 and 1.3 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-40

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See the ISB Microarray Facility website for microarray scanning details.

data_processing: AnalyzerDG software for spotfinding. see the ISB Microarray Pipeline webpage for more details.

label: Alexa 647

molecule: genomic DNA

organism: Halobacterium salinarum NRC-1

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TFBc

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-68

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBc grown to OD600 between 1.0-1.3 in standard growth media with 20microgram/ml mevinolin

extract_protocol: Cells were cross-linked with 1.2% formaldehyde and subsequently lysed via sonication.  DNA was sheared via sonication.  A small fraction of total DNA was kept for a whole cell extract (wce) background while the rest of the DNA was immunoprecipitated with antibody against the epitope tag in question.  Each DNA sample was treated with protease and RNAase and amplified by PCR utilizing ligated universal linkers as templates for amplification.  The resulting DNA was cleaned and quantified.

tag: IP sample of ChIP-Chip experiment of plasmid based expression of Cmyc tagged transcription factor TFBc grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3

label: Alexa 546

source_name: Halobacterium NRC1, whole cell extract (wce) from Cmyc tagged TFBc

tag: whole cell extract of CCmyc tagged transcription factor TFBc grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 7959

description: IP sample of Cmyc tagged TFBd expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBd grown to OD600 between 1.0 and 1.3 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TFBd

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-70

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBd grown to OD600 between 1.0-1.3 in standard growth media with 20microgram/ml mevinolin

tag: IP sample of ChIP-Chip experiment of plasmid based expression of Cmyc tagged transcription factor TFBd grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3

source_name: Halobacterium NRC1, whole cell extract (wce) from Cmyc tagged TFBd

tag: whole cell extract of CCmyc tagged transcription factor TFBd grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 7960

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-36

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-71


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBc, Halobacterium  GTF growth curve experiment, Array 7948

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-69

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-40


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBc, Halobacterium  GTF growth curve experiment, Array 7943

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-64

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-36


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBa, Halobacterium  GTF growth curve experiment, Array 7964

description: IP sample of Cmyc tagged TFBa expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBa grown to OD600 between 1.0 and 1.3 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TFBa

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-75

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBa grown to OD600 between 1.0-1.3 in standard growth media with 20microgram/ml mevinolin

tag: IP sample of ChIP-Chip experiment of plasmid based expression of Cmyc tagged transcription factor TFBa grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3

source_name: Halobacterium NRC1, whole cell extract (wce) from Cmyc tagged TFBa

tag: whole cell extract of CCmyc tagged transcription factor TFBa grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 7942

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-63

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 7961

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-37

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-72


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBa, Halobacterium  GTF growth curve experiment, Array 7966

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-77


title: Human IL-10 treated LPS-activated DCs, Donor E (E3)

status: Public on Feb 22 2007

type: RNA

city: Davis

first: William

last: Chang

state: CA

address: County Rd 98 and Hutchison Dr

department: Center for Comparative Medicine

institute: University of California, Davis

description: Monocyte-derived DCs from donor E were activated with LPS for 12 h.  An aliquot of cells were assayed by FACS to ensure the mature phenotype of the dendritic cells after LPS and IL-10 treatment.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hrs at 45C on the Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using wash protocol EukGE-WS2v5.

scan_protocol: Arrays were scanned on a GeneChip® Scanner 3000 7G

data_processing: Raw cel files were imported into ArrayAssist 3.3 software (Stratagene, La Jolla, CA) and processed using GC-RMA, including model-based normalization.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Monocyte-derived dendritic cells

label_protocol: Biotinylated cRNA were prepared from 10 micrograms of total RNA according to the standard Affymetrix protocol

growth_protocol: Isolated CD14+ monocytes were cultured with GM-CSF and IL-4 for 6 days to generate dendritic cells.

extract_protocol: Total RNA was extracted from cultured dendritic cells using the Qiagen RNeasy Mini Kit according the manufacturer’s instructions.

treatment_protocol: cells were concomitantly treated with LPS (10 ng/ml) and human IL-10 (50 ng/ml) for 12 hours.


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 7941

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-62


title: Viral IL-10 treated LPS-activated DCs, Donor E (E2)

treatment_protocol: cells were concomitantly treated with LPS (10 ng/ml) and cmv IL-10 (50 ng/ml) for 12 hours.


title: LPS-activated DCs, Donor E (E1)

description: Monocyte-derived DCs from donor E were activated with LPS for 12 h.  An aliquot of cells were assayed by FACS to ensure the mature phenotype of the dendritic cells after LPS treatment.

treatment_protocol: cells were treated with LPS (10 ng/ml) for 12 hours.

tag: LPS-activated DCs, Donor E


title: Untreated immature DCs, Donor D (D4)

description: Monocyte-derived DCs from donor D were left unstimulated.  An aliquot of cells were assayed by FACS to ensure the immature phenotype of the dendritic cells.

tag: Untreated immature DCs, Donor D


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBf, Halobacterium  GTF growth curve experiment, Array 8022

description: IP sample of Cmyc tagged TFBf expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBf grown to OD600 between 1.0 and 1.3 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TFBf

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-82

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBf grown to OD600 between 1.0-1.3 in standard growth media with 20microgram/ml mevinolin

tag: IP sample of ChIP-Chip experiment of plasmid based expression of Cmyc tagged transcription factor TFBf grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3

source_name: Halobacterium NRC1, whole cell extract (wce) from Cmyc tagged TFBf

tag: whole cell extract of CCmyc tagged transcription factor TFBf grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3


title: Human IL-10 treated LPS-activated DCs, Donor D (D3)

description: Monocyte-derived DCs from donor D were activated with LPS for 12 h.  An aliquot of cells were assayed by FACS to ensure the mature phenotype of the dendritic cells after LPS and IL-10 treatment.


title: LPS-activated DCs, Donor D (D1)

description: Monocyte-derived DCs from donor D were activated with LPS for 12 h.  An aliquot of cells were assayed by FACS to ensure the mature phenotype of the dendritic cells after LPS treatment.

tag: LPS-activated DCs, Donor D


title: Listeria_42oC vs 37oC

city: Ithaca

first: Patrick

last: Mc Gann

state: NY

address: 412 Stocking Hall

department: Food Science

institute: Cornell University

description: Due to the small number of targeted genes, two complete arrays were printed on each microarray slide. As two different probes, printed in duplicate, were used for each gene on a single array, the microarray design generated eight replicate spots for each gene per slide. Expression profiles were measured from three independent RNA extractions, resulting in twenty-four replicate spots per gene (twelve from each probe).

hyb_protocol: Before hybridization, microarray slides were treated for 10 min in a methyl pyrrilidone solution containing 0.18 M succinic anhydride, and 44 mM sodium borate (pH 8.0) and then washed in fresh methyl pyrrilidone for 10 min. Slides were successively washed for 1 min each in (i) nanopure H2O, (ii) 0.1% sodium dodecyl sulfate (SDS) (3 washes), (iii) nanopure water (5 washes), and (iv) 95% EtOH (1 wash). The slides were dried by centrifugation and immersed for 1 h in blocking solution (0.1% BSA, 5X SSC, 0.1% SDS) at 42oC. After blocking, the slides were washed for one minute each in nanopure H2O (5 washes) and in 95% EtOH (2 washes) and then dried by centrifugation. For the strains to be compared, labeled cDNA was resuspended in 50μl of hybridization buffer (5× SSC, 0.1% SDS, 0.1mM dithiothreitol (DTT), 0.5X formamide, 600μg/ml salmon sperm DNA ), denatured at 95oC for 5 min then applied to the slides using mSeries LifterSlips™ (Erie Scientific, Portsmouth, NH). Hybridization was conducted in a water bath at 42°C overnight. After hybridization, the slides were washed in 2X SSC+0.1% SDS (5 min at 42˚C), with subsequent washes at room temperature in 2X SSC+0.1% SDS (5 min), 2X SSC (5 min), 0.2X SSC (5 min), 0.05X SSC (1 min), followed by final rinse in nanopure H2O. The slides were dried by centrifugation.

scan_protocol: All images were scanned using a GenePix 4000b scanner (Axon Instruments Inc., Foster City, CA, USA). Acquired images were analyzed using GenePix 6.0 (Molecular Devices Corp., Sunnyvale, CA, USA).

data_processing:
Analyses of microarray data were performed in R (http://www.R-project.org) with Bioconductor (Gentleman et al., 2004) using LIMMA software (Wettenhall & Smyth, 2004). To correct for background noise, the background intensity was subtracted from the foreground intensity for each spot (Yang et al., 2001). For normalization within arrays, the data were weighted for the housekeeping genes and genomic DNA controls and normalized using a print-tip loess (Smyth & Speed, 2003). A linear model was fitted to the normalized log ratios and four B-statistics, t-statistics and P-values were generated for each gene

The VALUE column represents normalized log2 (CH1/CH2) ratios derived from 6 arrays (3 upper arrays & 3 lower arrays).  The 6 corresponding gpr files have been linked below as supplementary raw data files.

label: Alexa Flour 635

organism: Listeria monocytogenes 10403S

source_name: Listeria monocytogenes 10403S

label_protocol: cDNA was synthesized from 10 μg purified total RNA and labeled with Alexa Fluor dyes using the SuperScript Plus Indirect cDNA labeling system (Invitrogen Inc., Carlsbad, CA, USA).

extract_protocol: RNA was isolated from frozen bacterial pellets with the RNeasy kit (Qiagen) according to the manufacturer’s protocol for enzymatic and mechanical disruption, except that cells were sonicated twice on ice for three 30 s bursts at 18–21 W. Contaminating DNA was removed using Turbo DNase as per the manufacturers instructions (Ambion Inc., TX, USA). The final RNA pellet was resuspended in RNase-Free water (Qiagen).  Total nucleic acid concentration and purity were estimated using absorbance readings (260/280 nm) on a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).

tag: Listeria monocytogenes 10403S (serotype 1/2a) (Bishop & Henrichs, 1987) grown at 42oC

label: Alexa Flour 532

tag: Listeria monocytogenes 10403S (serotype 1/2a) (Bishop & Henrichs, 1987) grown at 37oC


title: Untreated immature DCs, Donor B (B4)

description: Monocyte-derived DCs from donor B were left unstimulated.  An aliquot of cells were assayed by FACS to ensure the immature phenotype of the dendritic cells.

tag: Untreated immature DCs, Donor B


title: Viral IL-10 treated LPS-activated DCs, Donor B (B2)

description: Monocyte-derived DCs from donor B were activated with LPS for 12 h.  An aliquot of cells were assayed by FACS to ensure the mature phenotype of the dendritic cells after LPS and IL-10 treatment.


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBc, Halobacterium  GTF growth curve experiment, Array 7944

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-65

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-37


title: LPS-activated DCs, Donor B (B1)

description: Monocyte-derived DCs from donor B were activated with LPS for 12 h.  An aliquot of cells were assayed by FACS to ensure the mature phenotype of the dendritic cells after LPS treatment.

tag: LPS-activated DCs, Donor B


title: Viral IL-10 treated LPS-activated DCs, Donor D (D2)


title: Renal saline 1week rep1

city: Toyoake

first: Ichino

last: Manabu

state: Aichi

address: Kutsukake-cho Denngakugakubo 1-98

department: Medical

country: Japan

institute: Fujita Health University

description: Kidney injected saline after 1week

hyb_protocol: Gene Expression Hybridization Kit (Agilent)

scan_protocol: Agilent microarray scanner system (Agilent)

data_processing: Data processed with FeatureExrtraction v7.1

organism: Rattus norvegicus

label_protocol:
Agilent In-situ oligo DNA microarray kit
Low RNA Input lilnear-amplify and labeling protocol

extract_protocol: RNeasy Mini Kit (QIAGEN)

tag: Strain

value: wister rat

tag: Gender

value: female

tag: Age

value: 4 weeks old

tag: Tissue

value: kidney


title: Listeria_30oC vs 37oC

tag: Listeria monocytogenes 10403S (serotype 1/2a) (Bishop & Henrichs, 1987) grown at 30oC


title: Renal saline 2week rep1

description: Kidney injected saline after 2week


title: Listeria_16oC vs 37oC

tag: Listeria monocytogenes 10403S (serotype 1/2a) (Bishop & Henrichs, 1987) grown at 16oC


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 7946

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-39

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-67

tag: IP sample of ChIP-Chip experiment of plasmid based expression of Cmyc tagged transcription factor TFBd grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3

tag: whole cell extract of CCmyc tagged transcription factor TFBd grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3


title: Renal saline 4week rep1

description: Kidney injected saline after 4week


title: Untreated immature DCs, Donor A (A4)

description: Monocyte-derived DCs from donor A were left unstimulated.  An aliquot of cells were assayed by FACS to ensure the immature phenotype of the dendritic cells.

tag: Untreated immature DCs, Donor A


title: IP fraction of ChIP-Chip sample from Cmyc tagged TBPb, Halobacterium  GTF growth curve experiment, Array 6973

description: IP sample of Cmyc tagged TBPb expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TBPb grown to OD600 between 1.0 and 1.3 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

label: Alexa 532

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TBPb

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-39

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TBPb grown to OD600 between 1.0-1.3 in standard growth media with 20microgram/ml mevinolin

tag: IP sample of ChIP-Chip experiment of plasmid based expression of Cmyc tagged transcription factor TBPb grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3

source_name: Halobacterium NRC1, whole cell extract (wce) from Cmyc tagged TBPb

tag: whole cell extract of CCmyc tagged transcription factor TBPb grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3


title: Renal scarring normal rep1

description: normal sample

label_protocol:
Agilent In-situ oligo DNA microarray kit
Low RNA Input lilnear-amplify and labeling protocol (Agilent)

tag: Data processing

value: Data processed with FeatureExrtraction v7.1


title: Viral IL-10 treated LPS-activated DCs, Donor A (A2)

description: Monocyte-derived DCs from donor A were activated with LPS for 12 h.  An aliquot of cells were assayed by FACS to ensure the mature phenotype of the dendritic cells after LPS and IL-10 treatment.


title: Renal scarring 6week rep1

description: Kidney injected E.coli strain DS 17 after 6week


title: Renal scarring 4week rep1

description: Kidney injected E.coli strain DS 17 after 4week


title: Renal scarring 1week rep1

description: Kidney injected E.coli strain DS 17 after 1week


title: Renal scarring 2week rep1

description: Kidney injected E.coli strain DS 17 after 2week


title: LPS-activated DCs, Donor A (A1)

description: Monocyte-derived DCs from donor A were activated with LPS for 12 h.  An aliquot of cells were assayed by FACS to ensure the mature phenotype of the dendritic cells after LPS treatment.

tag: LPS-activated DCs, Donor A


title: Medicago truncatula (A17)  12 hpi after 2.5 µM Al treatment, rep4

city: St Paul

first: Kathryn

middle: A

last: VandenBosch

state: MN

address: Room 250 BioSci 6022 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

description: Medicago truncatula (A17)  12 hpi after Al treatment rep4

hyb_protocol: Microarrays for each time point were hybridized to cDNAs from both Al- treated and control roots, with cDNAs from the two different treatments labeled with Cy5 and Cy3 dyes. Each hybridization was repeated at least six times to account for technical variability, with triplicates of each dye combination to control for dye effects. A modified two-step hybridization reaction was performed as described in the 3DNA Array 900 Expression Array Detection Kit (Genisphere).

scan_protocol: Microarray slides were scanned using an GenePix4000B (Axon) two-laser scanner and image analysis was performed using GenePix 5.0 (Axon) software

data_processing: Background-subtracted mean intensities for both tissues were log2 transformed and normalized using lowess and ANOVA

organism: Medicago truncatula

source_name: Medicago truncatula (A17)  12 hpi after control (-Al) treatment

label_protocol: 11 ug RNA from each of 3 biological replicates was pooled to make a total of 33 ug for cDNA synthesis with a RT Primer for labeling with either Cy3 or Cy5 dye molecules using a 3DNA Array 900 Expression Array Detection Kit for cDNA Microarrays (Genisphere, Inc., Hatfield, PA). cDNA was synthesized following instructions from 3DNA Array 900 Expression Array Detection Kit Appendix A (Genisphere Inc.).

growth_protocol: Medicago truncatula seeds were germinated as previously described (Penmetsa and Cook, 2000). Seedlings with radicles of about 1 cm in length were sown through the mesh bottoms of polypropylene cups. The cups were placed in precut holes of a plastic insert placed over a plastic tub that held 7.3 L of aerated nutrient solution. The nutrient solution contained: 1.2 mM KNO3, 0.8 mM Ca(NO3)2, 0.1 mM NH4H2PO4, 0.2 mM MgSO4, 10 µM FeNaEDTA, 50 µM KCl, 12.5 µM H3BO3, 1 µM MnSO4, 1 µM ZnSO4, 0.5 µM CuSO4, 0.1 µM Na2MoO4, and 0.1 µM NiCl2 (Pence et al., 2000). The pH of the nutrient solution was adjusted to 4.5 using 1 N HCl. Seedlings were grown for 72 h in a growth chamber (light/dark, 14/10 h) under a light intensity of 440 µmol photons m-2 s-1. Al treatment was initiated after 72 h by replacing the control growth solution with an identical solution that contained either 0 µM (control) or 2.5 µM Al added as AlK(SO4)3. The control and treatment solutions were adjusted to pH 4.5.  Root tips (approximately 0.5 cm in length) from control and 2.5 µM Al treated seedlings were harvested at 12 and 48 h after Al treatment immediately frozen in liquid nitrogen.

tag: Medicago truncatula; line - A17; tissue- root tips; age - 4 days; treatment - control (-Al) treatment

extract_protocol:
Root tip samples from 3 independent experimental replicates were collected for the experiment. RNA from frozen root tip samples was isolated using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) following the manufacturer's instructions.
Trifoliate leaf samples from 3 experimental replicates (9 plants total) were collected for the experiment. RNA from frozen leaf samples was isolated using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) was isolated using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) following the manufacturer's instructions.

tag: Medicago truncatula; line - A17; tissue- root tips; age - 4 days; treatment -  12 hpi after Al treatment


title: V2 Control, biological rep3

city: Knoxville

first: Dilip

middle: Raj

last: Panthee

state: TN

address: 2431 Joe Johnson Dr.

department: Plant Sciences

institute: University of Tennessee

description: Gene expression analysis in soybean in response to Phakopsora pachyrhizii.

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

scan_protocol: GeneChips were scanned using the Affymetrix 7G scanner.

data_processing: The image was scanned using GCOS software and the corresponding CEL file generated. Array Assist was used to summarize the signal values using the  GCRMA algorithm.

organism: Glycine max

source_name: Glycine max uninoculated leaf (Control)

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

growth_protocol: Three plants per pot were maintained and growing environment consisted of 28/20 degree celsius, 14/10 photoperiod with high humidity.

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

treatment_protocol: Under surface of the Asian soybean rust infected leaves were gently robbed on the upper surface of V2 stage plant leaves).

tag: 5601T unknown reaction to Asian soybean rust

tag: Leaf samples collected 72 hours after inoculation from V2 growth stage)


title: Medicago truncatula (A17)  12 hpi after 2.5 µM Al treatment, rep3

description: Medicago truncatula (A17)  12 hpi after Al treatment rep3

extract_protocol: Root tip samples from 3 independent experimental replicates were collected for the experiment. RNA from frozen root tip samples was isolated using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) following the manufacturer's instructions.

extract_protocol: Trifoliate leaf samples from 3 experimental replicates (9 plants total) were collected for the experiment. RNA from frozen leaf samples was isolated using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) was isolated using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) following the manufacturer's instructions.

tag: Medicago truncatula; line - A17; tissue- root tips; age - 4 days; treatment -  12 hpi after control (-Al) treatment


title: V2 Control, biological rep1

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


title: Medicago truncatula (A17)  12 hpi after 2.5 µM Al treatment, rep6

description: Medicago truncatula (A17)  12 hpi after Al treatment rep6


title: Rust Innoculated, biological rep3

source_name: Glycine max rust inoculated leaf (Treatment)

treatment_protocol: Control plants at V2 stage were not inoculated rather moved to an adjacent growth chamber with congruent growing environment).


title: V2 Control, biological rep2


title: Rust Innoculated, biological rep1


title: Medicago truncatula (A17)  12 hpi after 2.5 µM Al treatment, rep5

description: Medicago truncatula (A17)  12 hpi after Al treatment rep5


title: Rust Innoculated, biological rep2


title: Medicago truncatula (A17)  12 hpi after 2.5 µM Al treatment, rep1

description: Medicago truncatula (A17)  12 hpi after Al treatment rep1


title: FD vs Control_Comp6_1

status: Public on Feb 21 2007

city: St Genes-Champanelle

first: Christine

last: Leroux

address: Centre INRA de Theix

department: PHASE

country: France

institute: INRA

description: The signal and background mean intensities for the Cy3 and Cy5 channels from each spot were obtained using ImaGene 6.0 software (BioDiscovery, Inc).

hyb_protocol: 43 pmol of incorporated Cy3 and 43 pmol of incorporated Cy5 were co-hybridized at 42°C for 16 h on the oligoarray “URH-TALL _Bovine_Operon V1.1_1”. The pre-hybridization treatments, hybridization and washes were performed using the Pronto Plus Direct System (Promega and Corning B.V. Life Sciences) according to the manufacturer’s instructions.

scan_protocol: The slide was scanned for both dye channels at 532 and 635 nm with an Affymetrix 428 Array Scanner (MWG Biotech) at 10 µm resolution.

data_processing: After base-2 logarithm transformation, data were corrected for systematic dye bias by Lowess normalization using GeneSight 4.1 software (BioDiscovery, Inc).

organism: Capra hircus

label_protocol: 5 µg of purified total RNA was labeled with Cy5-dCTP (Amersham Biosciences Europe Gmbh) using the Pronto Plus Direct System (Promega and Corning B.V. Life Sciences) according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Invitrogen life technologies) according to the manufacturer’s instructions and further purified with the SV Total RNA Isolation System (Promega). RNA concentration and purity were determined by spectrophotometry at 260, 280 and 320 nm and RNA integrity was verified using a Bioanalyser 2100 (Agilent Technologies).

tag: Goat no.

value: lactating mammary gland

tag: Treatment

value: 48-h food-deprivation (FD)

label_protocol: 5 µg of purified total RNA was labeled with Cy3-dCTP (Amersham Biosciences Europe Gmbh) using the Pronto Plus Direct System (Promega and Corning B.V. Life Sciences) according to the manufacturer’s instructions.

value: control diet ad libitum


title: FD vs Control_Comp6_2

tag: Tissue


title: FD vs Control_Comp5_2


title: Small RNAs from Arabidopsis AGO1 complex

city: Cold Spring Harbor

first: Gregory

middle: J.

last: Hannon

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

description: Small RNAs that are associated with Arabidopsis AGO1 complex

data_processing: The small RNA sequences were mapped to the Arabidopsis genome provided by TIGR (release version 5) using Perl scripts

organism: Arabidopsis thaliana

source_name: Immunopurified Arabidopsis AGO1 complex

extract_protocol: Small RNAs were extracted from immunopurified AGO1 complex using Trizol reagent


title: Medicago truncatula (A17)  12 hpi after 2.5 µM Al treatment, rep2

description: Medicago truncatula (A17)  12 hpi after Al treatment rep2


title: FD vs Control_Comp5_1


title: FD vs Control_Comp4_2


title: Small RNAs from Arabidopsis whole extracts

description: Total small RNAs from Arabidopsis thaliana

source_name: whole plant extracts, Arabidopsis thaliana, wild-type Col-0

extract_protocol: Small RNAs were extracted by Trizol reagent and further purified by denaturing polyacrylamide gel


title: FD vs Control_Comp4_1


title: FD vs Control_Comp3_2


title: FD vs Control_Comp3_1


title: Tiling microarray OS16971 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 3

city: New Haven

first: Rajkumar

last: Sasidharan

state: CT

address: 266 Whitney Avenue

department: MB & B

institute: Yale University

hyb_protocol: Microarrays were hybridized with 4 ug abeled cDNA in 300 micro litre hybridization buffer (50 mM MES, 0.5 M NaCl, 10 mM EDTA, and 0.005% (v/v) Tween-20) for 16 hours at 50 deg C in disposable adhesive chambers (Grace BioLabs, Bend, OR) in a hybridization oven with constant agitation. Hybridized arrays were washed on an orbital Sample in non-stringent buffer (6x SSPE, 0.01% [v/v] Tween-20) for 10 minutes at room temperature, then in stringent buffer (100 mM MES, 0.1 M NaCl, 0.01% Tween-20) for 30 minutes at 45 deg C. This was followed by a 5-minute wash in non-stringent buffer and a 2-minute wash in 0.1X SSC.

scan_protocol: The arrays were dried with compressed nitrogen and scanned with an Axon 4000B laser scanner at 5 micro meter resolution.

data_processing: The fluorescence intensity data were extracted with the NimbleScan software (NimbleGen Systems, Madison, WI).

molecule: polyA RNA

organism: Oryza sativa

source_name: Poly(A)+ RNA population from japonica Rice seedling root, seedling shoot, panicle, and suspension cultured cells

label_protocol: The cDNAs were precipitated in ethanol:isopropanol (1:1 v/v) and resuspended in 0.1 M NaHCO3 to facilitate coupling of Alexa Fluor 555 NHS esters (Molecular Probes, Eugene, OR) to the reactive groups of the amino-allyl dUTPs and were purified with CyScribe GFX glass fiber spin columns (Amersham Bioscience, Piscataway, NJ).

extract_protocol: The four RNA population from seedling roots, seedling shoots, panicles, and suspension-cultured cells were pooled in equal amount and cDNAs were derived from the RNA mixture. Total RNA and mRNA were isolated using the RNeasy Plant Mini kit (Qiagen, Valencia, CA) and the Oligotex mRNA kit (Qiagen), respectively. First-strand cDNA was generated from 4 micro gram poly(A)+ RNA with SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA).

tag: The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA population (seedling root, seedling shoot, panicle, and suspension cultured cells).


title: Tiling microarray OS16951 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 3


title: Tiling microarray OS16948 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 2


title: Tiling microarray OS18799 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 3


title: Tiling microarray OS18732 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 2


title: Tiling microarray OS16969 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 10


title: Tiling microarray OS18742 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 11


title: Tiling microarray OS18918 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 12


title: Tiling microarray OS18755 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 6


title: Tiling microarray OS16974 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 8


title: FD vs Control_Comp2_2


title: Tiling microarray OS16979 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 8


title: EPA-treated cardiomyocytes (EPA-2)

city: Bologna

first: Annalisa

last: Astolfi

address: via massarenti 11

department: "Giorgio Prodi" Cancer Research center

country: Italy

institute: University of Bologna

description: Primary cardiomyocyte cultures were obtained from the ventricles of newborn Wistar rats by the method of Yagev et al.: some cells were grown in HAM F10 plus 10% fetal calf serum and 10% horse serum medium (controls), others in the same medium supplemented with 60 M Eicosapentaenoic acid (EPA) or docosahexaenoic acid (DHA). Media were changed every 48 hrs; cells were grown until complete confluence, then they were scraped off in ice cold PBS, and RNA isolation, labeling of complementary RNA (cRNA), hybridization to 22K-gene arrays (Rat oligo array G4130A) and assessment of expression ratios were performed. About one million cells treated with RNAlater were homogenized and total RNA was extracted by column technology (Rneasy Protect mini kit) and analyzed on both a spectrophotometer and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Only samples with 28S/18S ratio of >2.0 and no evidence of ribosomal peak degradation were included. The cRNA was generated by in vitro transcription with the use of T7 RNA polymerase (Low RNA input fluorescent linear amplification kit) and labeled with Cy3-CTP  or Cy5-CTP.

data_processing: Agilent FeatureExtraction software, Bioconductor packages

source_name: rat cardiomyocytes treated with EPA (swap)

source_name: rat cardiomyocytes (swap)


title: Tiling microarray OS18913 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 10


title: FD vs Control_Comp2_1


title: Tiling microarray OS18910 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 12


title: Tiling microarray OS16946 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 11


title: Tiling microarray OS18899 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 1


title: Tiling microarray OS16949 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 9


title: Tiling microarray OS16976 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 6


title: Tiling microarray OS18737 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 6


title: Tiling microarray OS18753 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 5


title: Tiling microarray OS18919 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 4


title: DHA-treated cardiomyocyte (DHA-1)

source_name: rat cardiomyocytes

source_name: rat cardiomyocytes treated with DHA


title: Tiling microarray OS16973 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 6


title: FD vs Control_Comp1_2


title: Tiling microarray OS18916 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 9


title: Tiling microarray OS16975 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 3


title: Tiling microarray OS18752 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 2


title: EPA-treated cardiomyocytes (EPA-1)

source_name: rat cardiomyocytes treated with EPA


title: 6827

status: Public on Feb 20 2007

city: Toronto

first: Christian

middle: R.

last: Marshall

state: ON

address: 101 College St.

department: Genetics & Genome Biology

country: Canada

institute: The Hospital for Sick Children

description: NAAR CP-B6-B10-8130-201

hyb_protocol: See Affymetrix GeneChip Mapping 10K 2.0 Assay. 1. Prepare the Hybridization Cocktail Master Mix (for multiple samples make 5% excess). 2. Transfer each of the labeled sample from the plate to a 1.5 mL Eppendorf tube. Aliquot 190 uL of the Hybridization Cocktail Master Mix into the 70 uL of labeled DNA samples. 3. Heat the 260 uL of hybridization mix and labeled DNA at 95°C in a heat block for 10 minutes to denature. 4. Cool down on crushed ice for 10 seconds. 5. Spin briefly at 2,000 rpm for 1 minute in a microfuge to collect any condensate. 6. Place the tubes at 48°C for 2 minutes. 7. Inject 80 uL denatured hybridization mix into the array. 8. Hybridize at 48°C for 16 to 18 hours at 60 rpm.

scan_protocol: See Affymetrix GeneChip Mapping 10K 2.0 Assay Manual. Fluidics Station 450/250 was used to automate the washing and staining of GeneChip® Mapping probe arrays. Arrays were scanned with the GeneChip® Scanner 3000 using GeneChip Operating Software (GCOS)

data_processing: Genotype calls were made using Affymetrix GeneChip Operating Software (GCOS) and Affymetrix GeneChip DNA Analysis Software (GDAS). Copy number variation was inferred using DNA Chip Analyzer (dCHIP).

label: Biotin Streptavidin Phycoerythin (SAPE)

source_name: blood or lymphoblast

label_protocol: See Affymetrix GeneChip Mapping 10K 2.0 Assay Manual, experiments were run in 96-well plate format 1. Prepare Labeling Mix as master mix ON ICE and vortex at medium speed for 2 seconds (for multiple samples, make 5% excess). 2. Aliquot 19.4 uL of Labeling Master Mix into the fragmentation plate containing 50.6 uL of fragmented DNA samples. 3. Seal the plate tightly with a plate cover. 4. Vortex the plate at medium speed for 2 seconds, and briefly spin the plate at 2,000 rpm for 1 minute. 5. Run the following program: 37ºC for 2 hours, 95ºC for 15 minutes, 4ºC Hold. 6. Briefly spin the plate at 2,000 rpm for 1 minute after the labeling reaction.

extract_protocol: standard phenol/chloroform method


title: 4667

description: NAAR CP-C6-B12-8131-101


title: 1092


title: 6672

description: NAAR CP-B5-B12-8104-111


title: 6019

description: NAAR CP-F2-C12-8170-101


title: 5403

description: NAAR CP-F3-F10-8116-201


title: Tiling microarray OS16978 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 4


title: Tiling microarray OS18920 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 7


title: FD vs Control_Comp1_1


title: 4317

description: NAAR CP-A4-A11-8101-201


title: DHA-treated cardiomyocytes (DHA-2)


title: 4310

description: NAAR CP-B2-G10-8094-201


title: 3818

description: NAAR CP-D5-D12-8110-111


title: Tiling microarray OS16618 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 12


title: Tiling microarray OS16972 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 5


title: 6982


title: 3703

description: NAAR CP-F4-F11-8116-203


title: 1746

description: NAAR CP-A5-A12-8101-202


title: Tiling microarray for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 12

extract_protocol:
The four RNA population from seedling roots, seedling shoots, panicles, and suspension-cultured cells were pooled in equal amount and cDNAs were derived from the RNA mixture.
Total RNA and mRNA were isolated using the RNeasy Plant Mini kit (Qiagen, Valencia, CA) and the Oligotex mRNA kit (Qiagen), respectively.
First-strand cDNA was generated from 4 micro gram poly(A)+ RNA with SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA).

tag: Four poly(A)+ RNA population from japonica Rice seedling root, seedling shoot, panicle, and suspension cultured cells


title: 3704

description: NAAR CP-E2-C11-8169-202


title: 4995


title: 4996


title: 4994


title: Tiling microarray OS18900 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 1


title: 4997


title: 4991


title: 4992


title: 4990


title: 579

description: NAAR CP-B8-D10-8231-203


title: 4987


title: 4983


title: 4988


title: 4985


title: 4989


title: Tiling microarray OS16606 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 2


title: 4984


title: 4982


title: 4986


title: 4981


title: 4993


title: 4979


title: 4975


title: 4976


title: 4977


title: 4974


title: 4973


title: 4972


title: 4970


title: 4969


title: Tiling microarray OS16945 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 7


title: 4964


title: 4971


title: 4962


title: 4961


title: 4965


title: 4966


title: 4968


title: 4959


title: 4960


title: 4978


title: 4958


title: 3082

description: NAAR CP-B3-B10-8103-201


title: 4957


title: 4954


title: 4952


title: 4956


title: 4953


title: 4950


title: 4955


title: 4951


title: 4949


title: 4945


title: 4946


title: 4941


title: 4942


title: 4947


title: 4944


title: 4948


title: 4980


title: 4963


title: 4938


title: 4940


title: 4937


title: 4998


title: 4939


title: 4935


title: 4929


title: 4934


title: 4932


title: 4927


title: 4931


title: 4922


title: 4925


title: 4926


title: 4924


title: 4933


title: 4928


title: 4930


title: 4920


title: 4919


title: 4921


title: 4918


title: 4916


title: 4923


title: 4917


title: 4915


title: 4914


title: 4943


title: 4913


title: 4911


title: 4909


title: 4910


title: 4905


title: 4902


title: 4903


title: 4900


title: 4907


title: 4898


title: 4894


title: 4906


title: 4908


title: 4893


title: 4912


title: 4904


title: 4895


title: 4892


title: 4890


title: 4897


title: 4889


title: 4891


title: 4888


title: 4936


title: 4887


title: 4884


title: 4882


title: 4877


title: 4872


title: 4883


title: 4878


title: 4873


title: 4885


title: 4880


title: 4870


title: 4875


title: 4869


title: 4886


title: 4879


title: 4899


title: 4876


title: 4871


title: 4881


title: 4868

description: NAAR CP-D2-H9-8123-202


title: 4901


title: 4867


title: 4866


title: 4863


title: 4864


title: 4865


title: 4862


title: 4860


title: 4861


title: 4859


title: 4857


title: 4855


title: 4856


title: 4853


title: 4852


title: 4858


title: 4854


title: 4848


title: 4847


title: 4850


title: 4844


title: 4843


title: 4845


title: 4851


title: 4846


title: 4838


title: 4837


title: 4839


title: 4835


title: 4833


title: 4834


title: 4841


title: 4831


title: 4842


title: 4832


title: 4836


title: 4826


title: 4824


title: 4829


title: 4827


title: 4825


title: 4828


title: 4823


title: 4830


title: 4822


title: 4821


title: 4820


title: 4818


title: 4815


title: 4819


title: 4817


title: 4811


title: 4840


title: 4814


title: 4813


title: 4812


title: 4874


title: 4896


title: 4805


title: 4809


title: 4810


title: 4808


title: 4804


title: 4803


title: 4802


title: 4798


title: 4800


title: 4799


title: 4801


title: 4849


title: 4794


title: 4795


title: 4797


title: 4790


title: 4789


title: 4796


title: 4791


title: 4792


title: 4788


title: 4793


title: 4787


title: 4786


title: 4784


title: 4783


title: 4778


title: 4777


title: 4785


title: 4782


title: 4781


title: 4775


title: 4776


title: 4779


title: 4774


title: 4773


title: 4772


title: 4767


title: 4769


title: 4762


title: 4766


title: 4761


title: 4771


title: 4760


title: 4770


title: 4759


title: 4763


title: 4765


title: 4768


title: 4754


title: 4757

description: NAAR CP-D1-B7-8079-111


title: 4755


title: 4756


title: 4806


title: 4758


title: 4752


title: 4753


title: 4764


title: CD8_0.5Gy_24h_5

status: Public on Feb 01 2008

city: Fontenay aux Roses Cedex

first: Gaetan

last: GRUEL

address: BP 17

department: Service de RadioBiologie et d'Epidemiologie

institute: Institut de Radioprotection et de Surete Nucleaire

description: The TIFF images were imported into GenePix Pro 6.0.1.00 (Axon, http://www.moleculardevices.com/pages/software/gn_genepix_pro.html). This program was used for image and grid alignment, spot detection and extraction of Cy5 (635 nm) and Cy3 (532 nm) intensities for all detected spots. Spots with little or no signal and obvious defects were flagged as non utilizable spots and labeled ‘not assigned’ (NA), to exclude them from further analysis.

hyb_protocol: The sample to be tested was first labeled with Cy3 and the reference pool, with Cy5. We then inversed fluorochrome labeling: Cy5 was used to label the test sample and Cy3, the reference pool (dye swap protocol). We added 10 µg of Cot-1 cDNA (Gibco-BRL Life Technologies), 10 µg of poly(A) (Amersham Pharmacia Biotech) and 10 µg of yeast tRNA (Gibco-BRL Life Technologies) to the labeled amplified RNA to prevent nonspecific hybridization. The nucleic acids were collected by centrifugation at 15,000 g for 1 hour at 4°C, and the resulting pellet was dissolved in 120 µl of 2x SSC (Sigma), 0.1% SDS (Sigma) and 0.1% salmon sperm DNA (Invitrogen), and denatured by heating for 2 min at 100°C. The glass microarray slides were placed in hybridization chambers (Corning) and incubated with the test sample and the reference pool overnight at 50°C. The microarray slides were washed at room temperature on an orbital shaker in 2x SSC, 0.1% SDS for 5min, in 1x SSC for 5min, 0.2x SSC for 5min and at last in 0.05x SSC for 5 min. The slides were dried by aerosol of pure compressed gas (AF France).

scan_protocol: slides were scanned with DNA Microarray Scanner (Agilent), with 10 µm resolution.

data_processing:
Data for each slide were imported into statistical data analysis system R (http://www.R-project.org). We then analyzed the log Cy5, log Cy3 and log ratio of non normalized probe signals, using the functions of the BioConductor marray package (http://www.bioconductor.org/) to check for the absence of abnormal bias during hybridization. Data were then normalized, using the Loess approach (window of 40%) implemented in the BioConductor marray package.

Sample data table VALUE column reports log base 2 ratio (test/ref).

source_name: CD8 cells irradiated 0.5Gy 24h

label_protocol: The amino-allyl amplified RNA samples were indirectly labeled by incubation with NH2-cyanin 5 (Cy5, Amersham) or NH2-cyanin 3 (Cy3, Amersham) as described in Amino Allyl MessageAmpTM II aRNA amplification kit protocol.

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen) according to manufacturer protocol. RNA were amplified and labelled with the Amino Allyl MessageAmpTM II aRNA amplification kit (Ambion), following the protocol supplied by the manufacturer.

tag: For each dose and at each time, CD4+, CD8+, B and NK cells were isolated using CD4 Negative Isolation Kit, CD8 Negative Isolation Kit, B cell Negative Isolation Kit and NK Cell Negative Isolation Kit (Dynal) respectively according to the manufacturer protocol.

source_name: Common reference amplified RNA

tag: The reference RNA for all hybridizations consisted of a mixture of total RNA from MNC obtained from 20 independent healthy donors.


title: 4751


title: 4750


title: 4748


title: 4740


title: 4746


title: 4745


title: 4741


title: 4747


title: 4742


title: 4744


title: 4728


title: 4732


title: 4737


title: 4729


title: 4730


title: 4743


title: 4738


title: 4733


title: 4736


title: 4739


title: 4731


title: 4726


title: 4749


title: 4735


title: 4734


title: 4727


title: 4816


title: 4725


title: 4724


title: 4720


title: 4723


title: 4721


title: 4722


title: 4712


title: 4706


title: 4701


title: 4716


title: 4780


title: 4717


title: 4703


title: 4718


title: 4711


title: 4714


title: 4709


title: 4715


title: 4707


title: 4702


title: 4719


title: 4713


title: 4710


title: 4708


title: 4705


title: 4700


title: 4699


title: 4697


title: 4698


title: 4695


title: 4696


title: 4686


title: 4689


title: 4691


title: 4690


title: 4687


title: 4684


title: 4685


title: 4682


title: 4694


title: 4693


title: 4683


title: 4679


title: 4688


title: 4676


title: 4680


title: 4678


title: 4692


title: 4677


title: 4671


title: 4675


title: 4670


title: 4674


title: 4672


title: 4666


title: 6995


title: 6994


title: 6985


title: 6998


title: 6997


title: 6996


title: 6986


title: 6989


title: 6988


title: 4669


title: 4668


title: 6990


title: 6993


title: 6992


title: 6987


title: 6983


title: 6984


title: 6981


title: 6978


title: 6991


title: 6979


title: 6980


title: 6977


title: 6976


title: 6971


title: 6972


title: 6966


title: 6975


title: 6974


title: 6973


title: 6967


title: 6969

description: NAAR CP-A7-E9-8208-201


title: 6968


title: 6964


title: 6959


title: 6962


title: 6960


title: 6970


title: 6963


title: 6965


title: 6961


title: 6957


title: 6958


title: 6956


title: 4681


title: 6950


title: 6951


title: 6937


title: 6939


title: 6955


title: 6940


title: 6946


title: 6952


title: 6949


title: 6942


title: 6947


title: 6945


title: 6944


title: 6934


title: 6941


title: 6936


title: 6953


title: 6935


title: 6948


title: 6938


title: 6933


title: 6943


title: 6932


title: 6931


title: 6924


title: 6929


title: 6928


title: 6916


title: 6919


title: 6926


title: 6930


title: 6922


title: 6918


title: 6925


title: 6920


title: 4704

description: NAAR CP-A1-C7-8031-101


title: 6913


title: 6914


title: 6912


title: 6909


title: 6915


title: 6923


title: 6907


title: 6921


title: 6910


title: 6911


title: 6908


title: 6927


title: 6905


title: 6906


title: 6894


title: 6903


title: 6895


title: 6897


title: 6900


title: 6890


title: 6889


title: 6898


title: 6917


title: 6888


title: 6893


title: 6901


title: 6885


title: 6899


title: 6904


title: 6884


title: 6902


title: 6883


title: 6886


title: 6896


title: 6892


title: 6887


title: 6882


title: 4673


title: 6881


title: 6880


title: 6879


title: 6874


title: 6875


title: 6859


title: 6863


title: 6870


title: 6860


title: 6891


title: 6866


title: 6877


title: 6872


title: 6878


title: 6862


title: 6864


title: 6871


title: 6869


title: 6873


title: 6876


title: 6867


title: 6868


title: 6857


title: 6865


title: 6855


title: 6856


title: 6837


title: 6853


title: 6850


title: 6840


title: 6836


title: 6845


title: 6848


title: 6854


title: 6851


title: 6843


title: 6834


title: 6846


title: 6849


title: 6842


title: 6847


title: 6841


title: 6835


title: 6839


title: 6852


title: 6831


title: 6832


title: 6844


title: 6858


title: 6838


title: 6833


title: 6823


title: 6820


title: 6813


title: 6822


title: 6825


title: 6829


title: 6826


title: 6816


title: 6821


title: 6811


title: 6824


title: 6819


title: 6814


title: 6808


title: 6810


title: 6817


title: 6812


title: 6830


title: 6809


title: 6828


title: 6815


title: 6818


title: 6807


title: 6805


title: 6800


title: 6795


title: 6782


title: 6787


title: 6801


title: 6804


title: 6791


title: 6785


title: 6798


title: 6796


title: 6799


title: 6790


title: 6781


title: 6788


title: 6797


title: 6786


title: 6803


title: 6793


title: 6784


title: 6792


title: 6794


title: 6789


title: 6802


title: 6783


title: 6806


title: NHF10-hTERT_G0_C5_26580

status: Public on Aug 01 2007

city: Morrisville

first: Tong

last: Zhou

state: NC

address: 133 Southcenter Court, Suite 400

department: Clincial Genetics

institute: Gentris Corperation

description: The gene expression level was presented as ratio of sample intensity against reference intensity.

hyb_protocol: 750ng of Cy3 and Cy5-labeled cRNA were used in the hybridization. The labeled cRNA from sham- or IR-treated samples was hybridized with the labeled global reference cRNA on an Agilent 22k human 1A array in a hybridization oven (Robbins Scientific Model 400, 1040-60-1AG) at 60oC for 17 h. Hybridization of sample RNA against reference RNA was done twice with dye swap.

scan_protocol: The arrays were scanned using the Agilent DNA Microarray Scanner with SureScan® Technology.

data_processing: Microarray images were analyzed using Agilent Feature Extraction Software (v7.1). Expression patterns and significant genes were extracted using "Extracting Microarray Gene Expression Patterns and Identifying Biologically Significant Genes” (EPIG)

source_name: reference RNA

label_protocol: 1 µg of global reference RNA (Stratagene) was converted to cDNA with reverse transcriptase then amplified using T7 RNA polymerase while labeling with Cy3-dUTP (Agilent’s Low RNA Input Linear Amplification Kit). The quality of each labeled cRNA was evaluated using an Agilent 2100 Bioanalyzer prior to hybridization.

extract_protocol: Stratagene protocol for preparation of reference RNA

tag: global reference RNA

source_name: Sample RNA

label_protocol: 1 µg of sample RNA was converted to cDNA with reverse transcriptase then amplified using T7 RNA polymerase while labeling with Cy5-dUTP (Agilent’s Low RNA Input Linear Amplification Kit). The quality of each labeled cRNA was evaluated using an Agilent 2100 Bioanalyzer prior to hybridization.

growth_protocol: Fibroblasts were cultured in DMEM high-glucose medium (Invitrogen, Carlsbad, CA, USA) supplemented with 2 mM L-glutamine (Invitrogen, Carlsbad, CA, USA) and 10% fetal bovine serum (FBS, Sigma Chemical Co, St. Louis, MO, USA)

extract_protocol: Qiagen RNeasy kit

treatment_protocol: Cells at a density of 1.3 x 104/cm2 and allowed to grow for 8 days to confluence-arrest in G0 phase

tag: Normal human  fibroblast


title: 6861


title: 6777


title: 6778


title: 6776


title: 6780


title: 6775


title: 6773


title: 6769


title: 6771


title: 6765


title: 6760


title: 6764


title: 6763


title: 6768


title: 6758


title: 6761


title: 6770


title: 6779


title: 6772


title: 6774


title: 6766

description: NAAR CP-C7-F10-8213-201


title: 6759


title: 6757


title: 6756


title: 6767


title: 6755


title: 6754


title: 6753


title: 6749


title: 6744


title: 6745


title: 6740


title: 6752


title: 6748


title: 6746


title: 6747


title: 6751


title: 6743


title: 6750


title: 6738


title: 6742


title: 6737


title: 6741


title: 6736


title: 6735


title: 6731


title: 6734


title: 6730


title: 6732


title: 6729


title: 6728


title: 6727


title: 6726


title: 6715


title: 6721


title: 6716


title: 6722


title: 6717


title: 6724


title: 6714


title: 6711


title: 6723


title: 6710


title: 6709


title: 6713


title: 6707


title: 6725


title: 6720


title: 6705


title: 6733


title: 6719


title: 6718


title: 6708


title: PCA121_Iocally advanced hormone sensitive PCA

status: Public on Jul 01 2007

city: Kassel

first: Oliver

middle: Christoph

last: Stoss

department: Molecular Pathology

country: Germany

institute: Targos GmbH

description: Gene expression data from human prostate tissue with 90 percent tumor content

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.

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

data_processing: The data were analyzed with the RMA algorithm in R using the quantile neromalization method

source_name: human prostate cancer of hormone sensitive patient treated with LHRH

label_protocol: Biotinylated cRNA were prepared according to the RiboAmp OA RNA 2 round amplification kit (Arcturus) starting from 1 ug RNA

extract_protocol: Trizol extraction of total RNA with subsequent purification via RNeasy Columns

treatment_protocol: transurethral resection (TUR)

tag: 90 percent tumor content

tag: Age


title: 6703


title: 6704


title: 6702


title: 6706


title: 6700


title: 6698


title: 6699


title: 6696


title: 6693


title: 6695


title: 6692


title: 6697


title: 6685


title: 6679


title: 6684


title: 6688


title: 6681


title: 6683


title: 6680


title: 6689


title: 6686


title: 6687


title: 6678


title: 6682


title: 6677


title: 6676


title: 6701


title: 6675


title: 6671


title: 6674


title: 6673


title: 6670


title: 6667


title: 6666


title: 6332


title: 6329


title: 6331


title: 6328


title: 6323


title: 6330


title: 6320


title: 6319


title: 6321


title: 6324


title: 6326


title: 6739


title: 6669


title: 6668


title: 6322


title: 6691


title: 6327


title: 6316


title: 6311


title: 6310


title: 6313


title: 6325


title: 6314


title: 6309


title: 6318


title: 6762


title: 6303


title: 6295


title: 6308


title: 6306


title: 6302


title: 6299


title: 6300


title: 6312


title: 6304


title: 6315


title: 6296


title: 6305


title: 6307


title: 6297


title: 6298


title: 6301


title: 6690


title: 6292


title: 6294


title: 6712


title: 6291


title: 6276


title: 6293


title: 6288


title: 6285


title: 6287


title: 6284


title: 6282


title: 6279


title: 6272


title: 6278


title: 6290


title: 6273


title: 6286


title: 6281


title: 6280


title: 6275


title: 6283


title: 6271

description: NAAR CP-F8-F9-8241-204


title: 6274


title: 6277


title: 6268


title: 6289


title: 6266


title: 6267


title: 6694


title: 6262


title: 6257


title: 6252


title: 6269


title: 6261


title: 6256


title: 6265


title: 6254


title: 6259


title: 6253


title: 6258


title: 6263


title: 6251


title: 6249


title: 6264


title: 6247


title: 6250


title: 6255


title: 6270


title: 6237


title: 6246


title: 6243


title: 6227


title: 6238


title: 6244


title: 6239


title: 6260


title: 6234


title: 6240


title: 6245


title: 6224


title: 6241


title: 6236


title: 6317


title: 6226


title: 6232


title: 6225


title: 6235


title: 6230


title: 6231


title: 6242


title: 6229


title: 6222


title: 6233


title: 6228


title: 6223


title: 6221


title: 6220


title: 6217


title: 6218


title: 6219


title: 6211


title: 6216


title: 6206


title: 6199


title: 6212


title: 6202


title: 6210


title: 6205

description: NAAR CP-C4-C11-8107-203


title: 6214


title: 6209


title: 6200


title: 6204


title: 6215


title: 6207


title: 6213


title: 6208


title: 6203


title: 6198


title: 6196


title: 6197


title: 6194


title: 6191

description: NAAR CP-C5-C12-8107-201


title: 6201


title: 6195


title: 6193


title: 6188


title: 6184


title: 6189


title: 6179


title: 6178


title: 6174


title: 6187


title: 6175


title: 6180


title: 6177


title: 6182


title: 6186


title: 6190


title: 6176


title: 6171


title: 6183


title: 6185


title: 6173


title: 6170


title: 6172


title: 6181


title: 6168


title: 6165


title: 6167


title: 6166


title: 6169


title: 6164


title: 6248


title: 6162


title: 6157


title: 6152


title: 6159


title: 6147


title: 6142

description: NAAR CP-A3-A10-8101-111


title: 6161


title: 6154


title: 6156


title: 6163


title: 6151


title: 6155


title: 6158


title: 6153


title: 6150


title: 6148


title: 6146


title: 6141


title: 6143


title: 6149


title: 6144


title: 6160


title: 6140


title: 6139


title: 6145


title: 6138


title: 6137


title: 6136


title: 6116


title: 6118


title: 6131


title: 6132


title: 6135


title: 6134


title: 6126


title: 6120


title: 6113


title: 6117


title: 6129


title: 6112


title: 6122


title: 6115


title: 6133


title: 6124


title: 6119


title: 6121


title: 6125


title: 6111


title: 6130


title: 6128


title: 6123


title: 6114


title: 6110


title: 6127


title: 6109


title: 6108


title: 6104


title: 6106


title: 6096


title: 6107


title: 6103


title: 6094


title: 6098


title: 6092


title: 6088


title: 6099


title: 6093


title: 6100


title: 6084


title: 6101


title: 6089


title: 6097


title: 6095


title: 6102


title: 6091


title: 6086


title: 6083


title: 6080


title: 6087


title: 6081


title: 6105


title: 6085


title: 6082


title: 6090


title: 6079


title: 6078


title: 6077


title: 6056


title: 6058


title: 6063


title: 6062


title: 6076


title: 6074


title: 6060


title: 6055


title: 6061


title: 6075


title: 6069


title: 6071


title: 6065


title: 6072


title: 6067


title: 6068


title: 6059


title: 6057


title: 6054


title: 6070


title: 6050


title: 6066


title: 6064


title: 6052


title: 6073


title: 6053


title: 6045


title: 6047


title: 6046


title: 6040


title: 6035


title: 6041


title: 6043


title: 6036


title: 6031


title: 6038


title: 6029


title: 6026


title: 6030


title: 6033


title: 6048


title: 6025


title: 6024


title: 6042


title: 6028


title: 6032


title: 6015


title: 6027


title: 6020


title: 6022


title: 6014


title: 6023


title: 6018


title: 6012


title: 6013


title: 6011


title: 6017


title: 6021


title: 6037


title: 6005


title: 6016


title: 6007


title: 6008


title: 6009


title: 5665


title: 6004


title: 6006


title: 6049


title: 6000


title: 5999


title: 5662


title: 5661


title: 6002


title: 6001


title: 5664


title: 5663


title: 5659


title: 5658


title: 5656


title: 5657


title: 5660


title: 5654


title: 5653


title: 5652


title: 6051


title: 5649


title: 5655


title: 6010


title: 5650


title: 5644


title: 5643


title: 5651


title: 5640


title: 5646


title: 5647


title: 5639


title: 5641


title: 5648


title: 5636


title: 5645


title: 5638


title: 5642


title: 5637


title: 5633


title: 5635


title: 5634


title: 6039


title: 5632


title: 5629


title: 5625


title: 5630


title: 5631


title: 6034


title: 5626


title: 5620


title: 5621


title: 5624


title: 5618


title: 5616


title: 5627


title: 5623


title: 5619


title: 5613


title: 5628


title: 5615


title: 5622


title: 5617


title: 5612


title: 6003


title: 5609


title: 5614


title: 5611


title: 5610


title: 5606


title: 5608


title: 5607


title: 5603


title: 5604


title: 5601


title: 5600


title: 5589


title: 5605


title: 5593


title: 5594


title: 5599


title: 5595


title: 5592


title: 5588


title: 5591


title: 5587


title: 5590


title: 5597


title: 5596


title: 5586


title: 5582


title: 5581


title: 5598


title: 5580


title: 5579


title: 5576


title: 5584


title: 5583


title: 5578


title: 5577


title: 5585


title: 5602


title: 5574


title: 5572


title: 5562


title: 5567


title: 5571


title: 5575


title: 5573


title: 5568


title: 5569


title: 5566


title: 5561


title: 5570


title: 5565


title: 5564


title: 5556


title: 5559


title: 5549


title: 5550


title: 5551


title: 5563


title: 5552


title: 5553


title: 5554


title: 5548


title: 5555


title: 5560


title: 5547


title: 5558


title: 5546


title: 5545


title: 5542


title: 5534


title: 5537


title: 5544


title: 5529


title: 5540


title: 5524


title: 5520


title: 5528


title: 5533


title: 5523


title: 5530


title: 5532


title: 5527


title: 5522


title: 5535


title: 5541


title: 5539


title: 5536


title: 5525


title: 5519


title: 5538


title: 5543


title: 5526


title: 5521


title: 5518


title: 5514


title: 5510


title: 5517


title: 5513


title: 5511


title: 5516


title: 5508


title: 5515


title: 5512


title: 5509


title: 5504


title: 5506


title: 5499


title: 5498


title: 5494


title: 5507


title: 5496


title: 5493


title: 5497


title: 5500


title: 5505


title: 5503


title: 5495


title: 5501


title: 5492


title: 5490


title: 5491


title: 5488


title: 5483


title: 5489


title: 5487


title: 5486


title: 5473


title: 5476


title: 5471


title: 5484


title: 5481


title: 5479


title: 5474


title: 5478


title: 5469


title: 5480


title: 5482


title: 5477


title: 5468


title: 5470


title: 5485


title: 5472


title: 5475


title: 5557


title: 5464


title: 5467


title: 5457


title: 5465


title: 5466


title: 5460


title: 5531


title: 5461


title: 5455


title: 5462


title: 5458


title: 5459


title: 5453


title: 5454


title: 5463


title: 5450


title: 5452


title: 5447


title: 5456


title: 5443


title: 5451


title: 5448


title: 5446


title: 5449


title: 5445


title: 5444


title: 5441


title: 5442


title: 5432

description: NAAR CP-C3-C10-8107-202


title: 5438


title: 5436


title: 5427


title: 5433


title: 5437


title: 5431


title: 5439


title: 5434


title: 5435


title: 5440


title: 5430


title: 5425


title: 5424


title: 5422


title: 5423


title: 5418


title: 5419


title: 5417


title: 5426


title: 5415


title: 5420


title: 5421


title: 5429


title: 5416


title: 5428


title: 5412


title: 5410

description: NAAR CP-C8-E9-8236-201


title: 5414


title: 5413


title: 5411


title: 5409


title: 5406


title: 5405


title: 5404


title: 5408


title: 5402


title: 5407


title: 5400


title: 5397


title: 5394


title: 5391


title: 5396


title: 5389


title: 5390


title: 5392


title: 5385


title: 5401


title: 5395


title: 5399


title: 5393


title: 5502


title: 5398


title: 5388


title: 5387


title: 5386


title: 5382


title: 5384


title: 5379


title: 5376


title: 5381


title: 5380


title: 5375


title: 5377


title: 5383


title: 5369


title: 5374


title: 5371


title: 5360


title: 5366


title: 5373


title: 5370


title: 5378


title: 5368


title: 5363


title: 5365


title: 5364


title: 5361


title: 5356


title: 5359


title: 5362


title: 5372


title: 5367


title: 5351


title: 5357


title: 5352


title: 5358


title: 5347


title: 5354


title: 5346


title: 5348


title: 5349


title: 5353


title: 5344


title: 5338


title: 5342


title: 5337


title: 5341


title: 5355


title: 5339


title: 6999


title: 7000


title: 5345


title: 5350


title: 5333


title: 5334


title: 5340


title: 6662


title: 5335


title: 5336


title: 6658


title: 6659


title: 6660


title: 6661


title: 6657


title: 6663


title: 6656


title: 6655


title: 6664


title: 6665


title: 6652


title: 6645


title: 6642


title: 6640


title: 6644


title: 6647


title: 6654


title: 6653


title: 6649


title: 6646


title: 6637


title: 6651


title: 6648


title: 6636


title: 6641


title: 6643


title: 6650


title: 6639


title: 6635


title: 6638


title: 6633


title: 6629


title: 6634


title: 6632


title: 6631


title: 6630


title: 6628


title: 6623


title: 6625


title: 6624


title: 6619


title: 6620


title: 6627


title: 6622


title: 5343


title: 6621


title: 6614


title: 6616


title: 6617


title: 6613


title: 6608


title: 6626


title: 6618


title: 6610


title: 6606


title: 6609


title: 6615


title: 6612


title: 6611


title: 6604


title: 6601


title: 6605


title: 6602


title: 6607


title: 6597


title: 6595


title: 6596


title: 6600


title: 6592


title: 6590


title: 6591


title: 6599


title: 6584


title: 6598


title: 6579


title: 6593


title: 6588


title: 6577


title: 6583


title: 6587


title: 6576


title: 6594


title: 6582


title: 6589


title: 6585


title: 6581


title: 6586


title: 6580


title: 6574


title: 6578


title: 6573


title: 6572


title: 6567


title: 6562


title: 6569


title: 6564


title: 6557


title: 6570


title: 6568


title: 6565


title: 6563


title: 6560


title: 6559


title: 6558


title: 6553


title: 6555


title: 6554


title: 6551


title: 6549


title: 6571


title: 6552


title: 6561


title: 6550


title: 6566


title: 6556


title: 6548


title: 6544


title: 6546


title: 6538


title: 6545


title: 6536


title: 6537


title: 6539


title: 6535


title: 6541


title: 6543


title: 6540


title: 6532


title: 6534


title: 6533


title: 6603


title: 6529


title: 6530


title: 6524


title: 6525


title: 6527


title: 6526


title: 6521


title: 6528


title: 6523


title: 6522


title: 6519


title: 6517


title: 6515


title: 6518


title: 6509


title: 6508


title: 6516


title: 6511


title: 6513


title: 6507


title: 6503


title: 6520


title: 6505


title: 6504


title: 6542


title: 6500


title: 6502


title: 6494


title: 6499


title: 6501


title: 6496


title: 6531


title: 6498


title: 6490


title: 6506


title: 6491


title: 6497


title: 6492


title: 6575


title: 6514


title: 6493


title: 6489


title: 6487


title: 6488


title: 6486


title: 6476


title: 6481


title: 6480


title: 6484


title: 6483


title: 6471


title: 6473


title: 6482


title: 6479


title: 6478


title: 6485


title: 6472


title: 6477


title: 6470


title: 6475


title: 6474


title: 6467


title: 6466


title: 6468


title: 6469


title: 6464


title: 6510


title: 6460


title: 6450


title: 6459


title: 6463


title: 6495


title: 6461


title: 6456


title: 6449


title: 6454


title: 6458


title: 6444


title: 6445


title: 6451


title: 6462


title: 6452


title: 6446


title: 6453


title: 6441


title: 6457


title: 6447


title: 6443


title: 6440


title: 6439


title: 6442


title: 6438


title: 6455


title: 6547


title: 6448


title: 6436


title: 6435


title: 6433


title: 6419


title: 6420


title: 6417


title: 6437


title: 6416


title: 6422


title: 6424


title: 6465


title: 6423


title: 6434


title: 6425


title: 6432


title: 6430


title: 6428


title: 6426


title: 6431


title: 6429


title: 6427


title: 6418


title: 6415


title: 6421


title: 6414


title: 6413


title: 6411


title: 6412


title: 6406


title: 6407


title: 6408


title: 6410


title: 6402


title: 6405


title: 6398


title: 6400


title: 6395


title: 6403


title: 6399


title: 6409


title: 6404


title: 6390


title: 6394


title: 6388


title: 6389


title: 6396


title: 6397


title: 6387


title: 6392


title: 6385


title: 6384


title: 6383


title: 6386


title: 6393


title: 6391


title: 6381


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title: 4175


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title: 4183


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title: 4167

description: NAAR CP-H1-E8-8089-202


title: 4189


title: 4168


title: 4166


title: 4165


title: Heat shock perturbation in a histidine-limited chemostat (4.88 hours)

status: Public on Feb 28 2007

city: Rehovot

first: sagi

last: levy

address: Hertzel

department: Molecular Genetics and Physics of Complex Systems

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: cDNA samples were labeled with Cy3 and Cy5 and combined with blockers: 5?g Herring sperm (Promega), 5?g tRNA (Gibco) and 17.5?g Poly A (Poly A oligos were synthesized with mixed length of 40, 50 and 60 Adenine residues). The labeled cDNAs were concentrated to 40?l using Microcon (Millipore) and 40?l of hybridization x2 solution (10x SSC, 50% formamide and 0.2% SDS) was added. Microarrays containing all yeast ORFs were pre-hybridized by incubating at 42C for 45 minutes in a solution containing 1% BSA, 25% formamide, 5x SSC and 0.1% SDS. The slides were washed in sterile water and dried by centrifugation (3 minutes, 2000 rpm). The labeled samples were boiled for 5 minutes, centrifuged for 1 minute, hybridized on the slide and placed in a hybridization chamber (Corning) for overnight incubation at 42C. The slides were then washed for 5 minutes at 42C with a solution containing 2x SSC and 0.1% SDS. Additional wash was performed at room temperature with a solution containing 0.1x SSC and 0.1% SDS, followed by three additional washes at room temperature in 0.1x SSC solution.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 using Aginlet DNA microarray scannerand image intensity data were extracted and analyzed with SpotReader (Niles Scientific) analysis software.

data_processing: Background intensity was removed by subtracting the mean array intensity and the ratios of the two dyes were log2-transformed. The two spots corresponding to each gene were then averaged, and genes with low intesity were excluded by manual inspection).

organism: Saccharomyces cerevisiae

source_name: Cells upon heat shock perturbation in a histidine-limited chemostat (4.88 hours)

label_protocol: cDNA was synthesized from total RNA using M-MLV Reverse TranscriptaseRNase H Minus (Promega) and labeled by the indirect amino-allyl method.

growth_protocol: Cells were grown in a histidine-limited chemostat (2 mg/l) and reached steady state at 30 degrees (C). The cells were then subjected to heat shock of 37 degrees for 5 hours

extract_protocol: Cells were collected, pelleted and immediately frozen.Total RNA was obtained using MasterPure yeast RNA purification kit (Epicenter).

tag: Strain

value: WT BY4741, haploid

source_name: Batch culture cells grown in a histidine-limited medium to late log phase

growth_protocol: Overnight cells (SD) were washed, transferred to histidine-limited medium (2 mg/l) and grown to late log phase at 30 degrees (C)


title: 4164


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title: 4012


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title: 5317

description: NAAR CP-F7-A8-8162-101


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title: 5084


title: 5078


title: 5073


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title: 5074


title: 5104


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title: 5027


title: 5026


title: 5033


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title: 4664


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title: 5000


title: 4662


title: 4661


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title: 4659


title: 4999


title: 5005


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title: 4632


title: 4631


title: 4642


title: 4649


title: 4650


title: 4643


title: 4635


title: 4640


title: 4636


title: 4648

description: NAAR CP-H6-H8-8154-111_2


title: 4630


title: 4646


title: 4629


title: 4628


title: 4624


title: 4625


title: 4623


title: 4627


title: 4620


title: 4615


title: 4610


title: 4604


title: 4613


title: 4626


title: 4616


title: 4609


title: 4605


title: 4608


title: 4611


title: 4617


title: 4621

description: NAAR CP-B4-B11-8104-101


title: 4602


title: 4614


title: 4619


title: 4607


title: 4612


title: 4606


title: 4601


title: 4622


title: 4603


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title: 4520


title: 4509


title: 4510


title: 4521


title: 4523


title: 4518


title: 4522


title: 4511

description: NAAR CP-E7-F12-8214-101


title: 4519


title: 4513


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title: 4506


title: 4503


title: 4504


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title: 4517


title: 4490


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title: 4479


title: 4475


title: 4480


title: 4508


title: 4505


title: 4471


title: 4466


title: 4470


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description: NAAR CP-F5-F12-8116-202


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