title: wt5_mut3_1230

city: Riverside

first: Lisa

middle: Yael

last: Stein

address: Geology 2207, 900 Univ. Ave.

department: Environ. Sciences

institute: University of California

description: The aim of the experiment was to determine changes in global gene expression patterns in the absence of nitrite reductase (nirK) activity.  In particular, genes related to nitrosative stress in N. europaea were predicted to be up-regulated in nirK deficient cells.

hyb_protocol: Labeled cDNA libraries from wild-type and nirK-deficient cells were hybridized simultaneously to arrays under Hybrislips (Sigma-Alrich) and in a chamber (Corning) containing buffer (5x SSC, 0.1% SDS, 50% formamide, and 0.1 mg•ml-1 of salmon sperm DNA)  at 50 ˚C for 12 to 16 h. Following hybridization, arrays were washed with 2x SSC, 0.1% SDS for 5 min at 42 ˚C; 0.1x SSC, 0.1% SDS for 10 min at 42 ˚C; and 4 times with 0.1x SSC for 1 min at 26 °C.

scan_protocol: The arrays were completely dried by centrifugation and scanned using a Scan Array Express (Perkin Elmer).

data_processing: Scanned images were analyzed using ImaGene version 5.6 (Biodiscovery) for spot quality assessment and background subtraction.  Spot grids were manually fitted to microarray images and averaged florescence intensity and local background were calculated for each array element.  Spots with poor signal quality and/or high background were flagged and removed from the data set. Remaining data were transferred to Microsoft Access and GeneSpring version 6.0 (Silicon Genetics). Normalization for each array was accomplished by scaling total fluorescence measured for each dye to an equivalent averaged intensity for both Cy3 and Cy5 to directly compare ratios of signal at each spot.  Data exported to GeneSpring was also normalized by the spot and chip normalization algorithms. Ratios (VALUE) of hybridization between wild-type and nirK mutant N. europaea is reported for each gene.

organism: Nitrosomonas europaea

source_name: N. europaea late-log cells, wild-type

label_protocol: Fluorescently labeled cDNA was generated by incorporation of Cy3- or Cy5-dUTP (Amersham Biosciences) during a first-strand reverse transcription reaction of using total RNA as a template (Invitrogen). Labeled cDNA was treated with 1N NaOH at 65 ˚C for 20 min to degrade remaining RNA, purified using a PCR purification column (Qiagen), concentrated, and quantified by spectrophotometer.

extract_protocol: Total cellular RNA was extracted from late-log phase cultures of both wild-type and nirK-deficient N. europaea according to manufacturer’s instructions (AquaPure RNA Isolation, Biorad).  Residual chromosomal DNA was digested with DNase I and RNA was further purified using an RNeasy Mini kit (Qiagen).  Quantification and quality of RNA was assessed by agarose gel electrophoresis and spectrophotometer.

treatment_protocol: Cells were grown to late-log phase in mineral medium and harvested for total RNA extraction.

tag: strain ATCC 19718

source_name: N. europaea late-log cells, nirK mutant

tag: strain ATCC 19718 with kanamyacin resistance cassette integrated into nirK ORF


title: Aorta_untreated_20hr_rep2a

status: Public on Mar 23 2006

type: RNA

city: Seattle

first: Alfred

middle: C

last: Aplin

state: WA

address: Box 357470 HSB-UW

department: Pathology

country: USA

institute: University of Washington

description: RNA labeling, array hybridization, scanning, and initial data transformation done at the Center for Expression Arrays at the Univesity of Washington.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

label: Phycoerythrin

molecule: total RNA

organism: Rattus norvegicus

source_name: thoracic aorta, untreated, 20hr

label_protocol: Standard Affymetrix

growth_protocol: Thoracic aorta dissected, cut into 2mm rings, washed 12 times in serum free EBM (Cambrex BioScience) and cultured for 14 days in serum free-EBM, changing medium every third day.

extract_protocol: Four to Six individual rings combined, snap frozen in liquid nitrogen, crushed and extracted with Trizol reagent (Invitrogen) followed by RNAEasy Micro kit (Qiagen) purification with DNAse I treatment. Total RNA eluted into DEPC water.

tag: Strain

value: Fisher 344

tag: Gender

value: Male

tag: Age

value: 5 weeks

tag: Tissue

value: Thoracic aorta


title: wt3_mut5_1231

state: CA


title: wt3_mut5_3021


title: Aorta_Ang1_20hr_rep3b

source_name: thoracic aorta, Ang1 treated, 20hr

growth_protocol:
Thoracic aorta dissected, cut into 2mm rings, washed 12 times in serum free EBM (Cambrex BioScience) and cultured for 13 days in serum free-EBM, changing medium every third day.

On day 13 , recombinant human angiopoietin-1 protein (R&D Systems #923-AN) added to the culture at a final concentration of 100ng/ml in 0.5ml EBM containing 5ug/ml poly-His antibody (R&D Systems #MAB050).

extract_protocol: 20 hours after treatment with Ang-1, four to six individual rings were combined, snap frozen in liquid nitrogen, crushed, and extracted with Trizol reagent (Invitrogen) followed by RNAEasy Micro kit (Qiagen) purification with DNAse I treatment. Total RNA eluted into DEPC water.


title: Aorta_untreated_20hr_rep1a

label_protocol: Standard Affymetrix "two-cycle" target labeling

extract_protocol: Four to Six individual rings combined, snap frozen in liquid nitrogen, crushed and extracted with Trizol reagent (Invitrogen) followed by RNAEasy Micro kit (Qiagen) purification with DNAse I treatment.  Total RNA eluted into DEPC water.


title: wt3_mut5_7550


title: Aorta_untreated_20hr_rep3a


title: wt5_mut3_5590


title: Blood_Reverse

status: Public on Mar 24 2006

city: Urbana

first: Mark

middle: Robert

last: Band

state: IL

address: 1201 W. Gregory Dr

department: Biotechnology

institute: University of Illinois

description: Samples were labeled with an indirect labeling protocol using amino-allyl dUTP and hybridized overnight at 42C

data_processing: Value = log2 ratio of background corrected 632 median/background corrected 532 median

organism: Bos taurus

source_name: Universal Control 635

tag: Total RNA from bovine cell cultures of :

tag: Brain

tag: EBTR (tracheal cell line)

tag: MDBK (kidney cell line)

tag: BL-30 (lymphocyte line)

source_name: Blood 532

tag: Male, 2 week old Jersey calf


title: wt5_mut3_2540


title: DvH_untreated_240min_rep2_bp39:md33

status: Public on Mar 22 2006

type: mixed

city: Berkeley

first: Adam

middle: P.

last: Arkin

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM KCl.  This sample was not treated.  Time point = 240 min.

hyb_protocol: He, Z., Wu, L., Li, X., Fields, M., and Zhou, J. 2005.  Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

scan_protocol: ImaGene software

data_processing: The net median signal of each spot is calculated by subtracting the median background from the median signal and adding a pseudo-signal of 100 to enforce a positive value.  For resulting net signals less than 50, a value of 50 is used.  The RATIO and VALUE columns are left blank if either CH1_FLAG or CH2_FLAG is greater than 0, which indicates a bad spot.  The raw data corresponding to this sample are available at: http://vimss.lbl.gov/SaltStress/microarray-rawdata/ in the KCl folder.

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, untreated, 240 min.

growth_protocol: Cells were grown in LS4D medium using a batch culture method.

tag: str. Hildenborough

molecule: genomic DNA

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, genomic DNA.


title: DvH_250mM_KCl_120min_rep2_bp39:md33

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM KCl.  This sample was treated with 250 mM KCl.  Time point = 120 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, treated with 250 mM KCl, 120 min.

label_protocol: He, Z., Wu, L., Li, X., Fields, M., and Zhou, J.  2005. Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

treatment_protocol: Cells were treated with 250 mM KCl.


title: DvH_250mM_KCl_60min_rep1_bp39:md33

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM KCl.  This sample was treated with 250 mM KCl.  Time point = 60 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, treated with 250 mM KCl, 60 min.

extract_protocol: He, Z., Wu, L., Li, X., Fields, M., and Zhou, J.  2005. Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.


title: Polysomal redistribution of mRNAs during restimulation of primed Th2 cells (Exp 2)

city: San Francisco

first: Agnes

last: Paquet

address: 1550 Fourth Street, RM 545

institute: University of California, San Francisco

description: RNA from polysome associated fractions from primed and restimulated Th2 cells was extracted, reverse transcribed and labeled with Cy3 and Cy5, respectively. Samples were hybridized simultaneously to Microarray slides spotted with 70mer DNA oligonucleotides and fluorescence in the Cy3 and Cy5 channels was acquired using a microarray scanner.

hyb_protocol: http://www.arrays.ucsf.edu/protocols/cDNA Transcription, Labeling and Hybridization.pdf  Microarray slides spotted with 70mer DNA oligonucleotides representing ~16,500 unique murine mRNA transcripts (Array-Ready version 2.0, Qiagen) were washed in 0.02% SDS followed by distilled water, dried and prehybridized for 2 hours at 42C in 5X SSC/1% BSA/0.1% SDS.  After rinsing in water and drying, slides were hybridized for 40 hrs at 50C with the labeled cDNAs in HybBuffer (Genomic Solutions) and 30% formamide.  Hybridized slides were washed sequentially at room temperature for 1 min each in 1X SSC/0.03% SDS, 0.2X SSC, and 0.05X SSC before drying.

scan_protocol: http://www.arrays.ucsf.edu/protocols/genepix_protocol.pdf Fluorescence in the Cy3 and Cy5 channels was acquired using an Axon 4000B microarray scanner and GenePix software (Axon Instruments).

data_processing: Data were normalized using the R package Bioconductor software. Values indicate the difference in gene expression on a log2 scale. This value is calculated as M = log2(R/G), where R and G are the intensity for the Cy5 and Cy3 channels, erspectively (e.g.: M = 1 indicates 2-fold higher expression in the sample that was labeled with the Cy3 dye, and M = 0 indicates equal expression in both samples). “A” indicates the total signal intensity of a given spot on the microarray.  This value is calculated as A = ½*log2(R*G).

organism: Mus musculus

source_name: Th2 cells after 6 priming culture after 3h TCR restimulation

label_protocol:
http://www.arrays.ucsf.edu/protocols/cDNA Transcription, Labeling and Hybridization.pdf

RNA from polysome associated fractions 7-12 of the gradients described above were pooled and 30-100 ug of total RNA per sample were used to template a Superscript III reverse transcription reaction (Invitrogen) incorporating amino-allyl dUTP (Sigma).  cDNA samples were washed with distilled water on microcon-30 columns (Millipore), dried and labeled with Cy3 (primed samples) or Cy5 (restimulated samples) using CyDye reactive dye labeling kits (Amersham).  Unincorporated dye was removed using QiaQuick PCR purification columns (Qiagen), labeled cDNAs were eluted in 10mM Tris, pH 8, combined and dried.

treatment_protocol: DO11.10 x TCR-Ca-/- T cells were stimulated under Th2 conditions for 6 days. After removal of dead cells, primed cells were washed and rested for 20 min at 37C in complete media with 0.1 mg/ml cycloheximide added for the final 10 min; restimulated cells were activated with 10 ug/ml plate-bound I-Ad/ova complexes for 3 hrs.

tag: DO11.10 tcra-/- T cells

source_name: Th2 cells after 6 priming culture before 3h TCR restimulation

extract_protocol:
EXTRACT PROTOCOL:
Cells were washed with ice-cold PBS/CHX and resuspended in polysome extraction buffer (30 mM HEPES (pH 7.4), 15 mM MgCl2, 0.3 M NaCl, 1% Triton X-100, 0.1 mg/ml CHX, 1 mg/ml heparin, 500 U/ml SUPERase-In RNAse inhibitors, 1x Complete EDTA-free protease inhibitor cocktail).  After incubation on ice for 25 min, nuclei and debris were removed by centrifuging and the cleared supernatants transferred to fresh tubes.  1.5 ml of each extract (from 3 x 10exp8 T cells) were layered on a 37.5 ml 10-50% sucrose gradient prepared in SW28 ultraclear centrifuge tubes (Beckman Coulter) using the salts described above, but without detergent, RNAsin or protease inhibitors. After centrifugation for 220 min at 28,000 rpm (average RCF = 103,745), fractions were isolated using an ISCO density gradient fractionator by pumping 60% sucrose into the bottom of the tube and collecting the displaced volumes into acid phenol:chloroform, with constant monitoring of ultraviolet absorbance at 254 nm.  Extracted RNA was precipitated with isopropanol, washed and resuspended in distilled water.

treatment_protocol: DO11.10 x TCR-Ca-/- T cells were stimulated under Th2 conditions for 6 days. After removal of dead cells, primed cells were washed and rested for 20 min at 37C in complete media with 0.1 mg/ml cycloheximide added for the final 10 min.


title: Polysomal redistribution of mRNAs during restimulation of primed Th2 cells (Exp 1)

hyb_protocol: http://www.arrays.ucsf.edu/protocols/cDNA Transcription, Labeling and Hybridization.pdf

extract_protocol: Cells were washed with ice-cold PBS/CHX and resuspended in polysome extraction buffer (30 mM HEPES (pH 7.4), 15 mM MgCl2, 0.3 M NaCl, 1% Triton X-100, 0.1 mg/ml CHX, 1 mg/ml heparin, 500 U/ml SUPERase-In RNAse inhibitors, 1x Complete EDTA-free protease inhibitor cocktail).  After incubation on ice for 25 min, nuclei and debris were removed by centrifuging and the cleared supernatants transferred to fresh tubes.  1.5 ml of each extract (from 3 x 10exp8 T cells) were layered on a 37.5 ml 10-50% sucrose gradient prepared in SW28 ultraclear centrifuge tubes (Beckman Coulter) using the salts described above, but without detergent, RNAsin or protease inhibitors. After centrifugation for 220 min at 28,000 rpm (average RCF = 103,745), fractions were isolated using an ISCO density gradient fractionator by pumping 60% sucrose into the bottom of the tube and collecting the displaced volumes into acid phenol:chloroform, with constant monitoring of ultraviolet absorbance at 254 nm.  Extracted RNA was precipitated with isopropanol, washed and resuspended in distilled water.


title: DvH_250mM_KCl_240min_rep2_bp39:md33

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM KCl.  This sample was treated with 250 mM KCl.  Time point = 240 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, treated with 250 mM KCl, 240 min.


title: DvH_250mM_KCl_60min_rep2_bp39:md33


title: DvH_untreated_240min_rep1_bp39:md33


title: DvH_untreated_120min_rep3_bp39:md33

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM KCl.  This sample was not treated.  Time point = 120 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, untreated, 120 min.


title: DvH_untreated_120min_rep2_bp39:md33


title: DvH_250mM_KCl_120min_rep1_bp39:md33


title: DvH_250mM_KCl_60min_rep3_bp39:md33


title: DvH_250mM_KCl_240min_rep3_bp39:md33


title: DvH_250mM_KCl_120min_rep3_bp39:md33


title: DvH_untreated_60min_rep2_bp39:md33

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM KCl.  This sample was not treated.  Time point = 60 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, untreated, 60 min.


title: DvH_untreated_240min_rep3_bp39:md33


title: DvH_untreated_60min_rep3_bp39:md33


title: DvH_250mM_KCl_30min_rep2_bp39:md33

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM KCl.  This sample was treated with 250 mM KCl.  Time point = 30 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, treated with 250 mM KCl, 30 min.


title: DvH_250mM_KCl_240min_rep1_bp39:md33


title: DvH_untreated_60min_rep1_bp39:md33


title: DvH_untreated_30min_rep3_bp39:md33

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM KCl.  This sample was not treated.  Time point = 30 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, untreated, 30 min.


title: DvH_250mM_KCl_30min_rep1_bp39:md33


title: DvH_250mM_KCl_30min_rep3_bp39:md33


title: DvH_untreated_120min_rep1_bp39:md33


title: DvH_250mM_KCl_0min_rep1_bp39:md33

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM KCl.  This sample was treated with 250 mM KCl.  Time point = 0 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, treated with 250 mM KCl, 0 min.


title: DvH_untreated_30min_rep1_bp39:md33


title: DvH_250mM_KCl_0min_rep3_bp39:md33


title: DvH_untreated_0min_rep3_bp39:md33

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM KCl.  This sample was not treated.  Time point = 0 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, untreated, 0 min.


title: DvH_untreated_0min_rep1_bp31:md20

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM NaCl.  This sample was not treated.  Time point = 0 min.

data_processing: The net median signal of each spot is calculated by subtracting the median background from the median signal and adding a pseudo-signal of 100 to enforce a positive value.  For resulting net signals less than 50, a value of 50 is used.  The RATIO and VALUE columns are left blank if either CH1_FLAG or CH2_FLAG is greater than 0, which indicates a bad spot.  The raw data corresponding to this sample are available at: http://vimss.lbl.gov/SaltStress/microarray-rawdata/ in the NaCl-120min folder.


title: DvH_untreated_0min_rep1_bp39:md33


title: DvH_untreated_120min_rep2_bp31:md20

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM NaCl.  This sample was not treated.  Time point = 120 min.


title: DvH_untreated_120min_rep1_bp31:md20


title: DvH_untreated_0min_rep2_bp39:md33


title: DvH_250mM_NaCl_120min_rep1_bp31:md20

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM NaCl.  This sample was treated with 250 mM NaCl.  Time point = 120 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, treated with 250 mM NaCl, 120 min.

treatment_protocol: Cells were treated with 250 mM NaCl.


title: DvH_250mM_NaCl_0min_rep3_bp31:md20

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM NaCl.  This sample was treated with 250 mM NaCl.  Time point = 0 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, treated with 250 mM NaCl, 0 min.


title: DvH_untreated_240min_rep3_bp28:md14

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM NaCl.  This sample was not treated.  Time point = 240 min.

data_processing: The net median signal of each spot for each channel is calculated by subtracting the median background from the median signal and adding a pseudo-signal of 100 to enforce a positive value.  For resulting net signals less than 50, a value of 50 is used.  The RATIO and VALUE columns are left blank if either CH1_FLAG or CH2_FLAG is greater than 0, which indicates a bad spot.  The raw data corresponding to this sample are available at: http://vimss.lbl.gov/SaltStress/microarray-rawdata/ in the NaCl-timecourse folder.


title: DvH_250mM_NaCl_240min_rep1_bp28:md14

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM NaCl.  This sample was treated with 250 mM NaCl.  Time point = 240 min.

data_processing: The net median signal of each spot is calculated by subtracting the median background from the median signal and adding a pseudo-signal of 100 to enforce a positive value.  For resulting net signals less than 50, a value of 50 is used.  The RATIO and VALUE columns are left blank if either CH1_FLAG or CH2_FLAG is greater than 0, which indicates a bad spot.  The raw data corresponding to this sample are available at: http://vimss.lbl.gov/SaltStress/microarray-rawdata/ in the NaCl-timecourse folder.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, treated with 250 mM NaCl, 240 min.


title: DvH_untreated_120min_rep3_bp31:md20


title: DvH_250mM_NaCl_120min_rep2_bp31:md20


title: DvH_untreated_240min_rep2_bp28:md14


title: DvH_untreated_0min_rep3_bp31:md20


title: DvH_untreated_240min_rep1_bp28:md14


title: DvH_250mM_NaCl_120min_rep2_bp28:md14


title: DvH_250mM_NaCl_0min_rep2_bp31:md20


title: DvH_250mM_NaCl_240min_rep3_bp28:md14


title: DvH_250mM_NaCl_120min_rep1_bp28:md14


title: DvH_250mM_NaCl_0min_rep1_bp31:md20


title: DvH_250mM_NaCl_240min_rep2_bp28:md14


title: DvH_250mM_NaCl_120min_rep3_bp28:md14


title: DvH_untreated_120min_rep1_bp28:md14


title: DvH_untreated_30min_rep2_bp39:md33


title: DvH_untreated_0min_rep2_bp31:md20


title: DvH_untreated_120min_rep3_bp28:md14


title: DvH_untreated_120min_rep2_bp28:md14


title: DvH_250mM_NaCl_60min_rep2_bp28:md14

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM NaCl.  This sample was treated with 250 mM NaCl.  Time point = 60 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, treated with 250 mM NaCl, 60 min.


title: DvH_250mM_NaCl_30min_rep1_bp28:md14

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM NaCl.  This sample was treated with 250 mM NaCl.  Time point = 30 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, treated with 250 mM NaCl, 30 min.


title: DvH_untreated_60min_rep3_bp28:md14

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM NaCl.  This sample was not treated.  Time point = 60 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, genomic DNA.


title: DvH_250mM_NaCl_60min_rep3_bp28:md14


title: DvH_untreated_60min_rep2_bp28:md14


title: DvH_250mM_NaCl_0min_rep2_bp28:md14


title: DvH_250mM_NaCl_30min_rep3_bp28:md14


title: DvH_250mM_NaCl_30min_rep2_bp28:md14


title: DvH_untreated_60min_rep1_bp28:md14


title: DvH_untreated_0min_rep2_bp28:md14


title: DvH_untreated_30min_rep1_bp28:md14

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with 250 mM NaCl.  This sample was not treated.  Time point = 30 min.


title: Macaca mulatta spleen sample_SHIV control_rep1

city: Silver Spring

first: Rasha

last: Hammamieh

state: MD

address: 503 Robert Grant Ave

department: Molecular Pathology

institute: Walter Reed Army Institute of Research

description: Macaca mulatta blood sample_SHIV control

data_processing: Local background correction and intrachip LOWESS normalization was accomplished by Genespring® 7.0 (Agilent Tech., CA).

organism: Macaca mulatta

source_name: Macaca mulatta spleen tissue_332

tag: total RNA from SHIV treated Spleen Macaca mulatta

source_name: Macaca mulatta spleen tissue_ref

tag: Reference RNA prepared from a pool of 33 control Macaca mulatta tissue RNAs.


title: Macaca mulatta spleen sample exposed to SHIV 89.6 strain_rep1

description: Macaca mulatta blood sample exposed to SHIV 89.6 strain

source_name: Macaca mulatta spleen tissue_FEG


title: Macaca mulatta spleen sample_SHIV control_rep2

source_name: Macaca mulatta spleen tissue_331


title: Macaca mulatta spleen sample_SHIV control_rep3

source_name: Macaca mulatta spleen tissue_CJ2T


title: DvH_250mM_NaCl_0min_rep3_bp28:md14


title: Macaca mulatta spleen sample exposed to SHIV 89.6 strain_rep2

source_name: Macaca mulatta spleen tissue_TTH


title: TG+1C-3 vs NTG1C-5

city: Cincinnati

first: Bruce

middle: J

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

description: murine ASM cells

scan_protocol: Fluorescence intensity analyses and background subtraction were performed using an Axon Instruments scanner and GenePix software

data_processing: Lowess normalization and per-chip normalization using GeneSpring GX 7.3

source_name: cultured murine ASM (airway smooth muscle) cells from tracheal explants of NTG mice

label_protocol: The RNA samples are converted to cDNA using a SuperScript III based reverse transcription. Then the cDNA samples are labeled with Cy3 or Cy5 dyes and hybridized to pre-printed, pre-hybridized amine coated slides where a competitive hybridization occurs.

growth_protocol: Primary cultures of murine ASM cells were established from tracheal explants of NTG and  2AR-OE mice. Briefly, the trachea between the larynx and main stem bronchi was removed and placed in a sterile Petri dish containing Hanks' balanced saline solution supplemented with a 2x concentration of antibiotic-antimycotic solution. After additional surrounding tissue was removed with the aid of a dissecting microscope, the tracheal segment was split longitudinally and dissected into 2-3 mm squares. All of the segments from a single trachea were then placed intima side down in a sterile 60-mm dish. After allowing the explants to adhere, 2.5 ml of Dulbecco's modified Eagle's medium supplemented with 20% FCS and 2x antibiotic-antimycotic was added to cover the explants. Explanted trachea were subsequently removed when there was local confluency. Once the initial seed dish became confluent, cells were harvested by trypsinization and passed into 75-cm2 flasks. As previously described {}, >90% of these cells were smooth muscle cells, as determined by immunohistochemistry performed with an antibody raised against smooth muscle  -actin.

extract_protocol: Total RNA was prepared from cells between passages 8 and 10 using TRI Reagent (Molecular Research Center, Cincinnati, OH), and resuspended in DEPC-treated water. Each sample was visually inspected for degradation in agarose gels stained with ethidium bromide, and their quality was further checked for RNase degradation using an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

tag: murine ASM cells of NTG mice

source_name: cultured murine ASM (airway smooth muscle) cells of 2AR-OE mice

tag: murine ASM cells of 2AR-OE mice


title: DvH_untreated_0min_rep3_bp28:md14


title: DvH_untreated_30min_rep3_bp28:md14

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, untreated, 30 min.


title: Macaca mulatta spleen sample exposed to SHIV 89.6 strain_rep4

source_name: Macaca mulatta spleen tissue_PHB


title: DvH_untreated_30min_rep2_bp28:md14


title: Macaca mulatta spleen sample exposed to SHIV 89.6 strain_rep3

source_name: Macaca mulatta spleen tissue_JGH


title: DvH_250mM_NaCl_0min_rep1_bp28:md14


title: NTG2A-3 vs TG+2A-5

description: murine ASM cells

source_name: cultured murine ASM (airway smooth muscle) cells from tracheal explants of 2AR-OE mice


title: Macaca mulatta spleen sample_SHIV control_rep4

source_name: Macaca mulatta spleen tissue_DB47


title: DvH_250mM_NaCl_60min_rep1_bp28:md14


title: NTG2B-3 vs TG+2B-5

description: murine ASM cells


title: NTG1B-3 vs TG+1B-5

description: murine ASM cells


title: DvH_250mM_KCl_0min_rep2_bp39:md33

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, treated with 250 mM KCl, 0 min.


title: slide1_80min_15C

city: Hangzhou

first: haichun

last: gao

address: 388 Yuhangtang Rd.

country: China

institute: Zhejiang University

description: Global Transcriptome Analysis of the Cold Shock Response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold-shock proteins. AEM. 2006In press.

hyb_protocol: Global Transcriptome Analysis of the Heat Shock Response of Shewanella oneidensis J. Bacteriol. 2004 186: 7796-7803, PMID: 15516594, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=15516594

data_processing: Global Transcriptome Analysis of the Heat Shock Response of Shewanella oneidensis, PMID: 15516594, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=15516594

organism: Shewanella oneidensis MR-1

source_name: Total RNA of the sample at 15C 80 min after coldshock.

growth_protocol: Grown in LB medium to ~0.6 of OD600

treatment_protocol: Grown to mid-log phase then coldshock to 15C for 80min.

tag: strain

value: MR-1 (sample)

source_name: Total RNA of the sample before coldshock

treatment_protocol: Grown to mid-log phase just before applied to coldshock.

value: MR-1 (control)


title: slide4_40min_15C

scan_protocol: Global Transcriptome Analysis of the Heat Shock Response of Shewanella oneidensis J. Bacteriol. 2004 186: 7796-7803, PMID: 15516594, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=15516594

source_name: Total RNA of the sample at 15C 40 min after coldshock.

label_protocol: Global Transcriptome Analysis of the Cold Shock Response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold-shock proteins. AEM. 2006In press.

treatment_protocol: Grown to mid-log phase then coldshock to 15C for 40min.

tag: Strain


title: slide3_80min_15C

extract_protocol: Global Transcriptome Analysis of the Cold Shock Response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold-shock proteins. AEM. 2006In press.


title: TG+2C-3 vs NTG2C-5

description: murine ASM cells


title: NTG1A-3 vs TG+1A-5

description: murine ASM cells


title: slide4_80min_15C


title: DvH_untreated_0min_rep1_bp28:md14

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, untreated, 0 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, genomic DNA.


title: slide1_160min_15C

source_name: Total RNA of the sample at 15C 160 min after coldshock.

treatment_protocol: Grown to mid-log phase then coldshock to 15C for 160min.


title: slide3_40min_15C


title: slide5_80min_15C


title: slide5_80min_8C

source_name: Total RNA of the sample at 8C 80 min after coldshock.

treatment_protocol: Grown to mid-log phase then coldshock to 8C for 80min.


title: slide4_160min_15C


title: slide2_40min_15C


title: slide2_160min_15C


title: slide2_80min_15C


title: slide1_40min_15C


title: slide4_20min_15C

source_name: Total RNA of the sample at 15C 20 min after coldshock.

treatment_protocol: Grown to mid-log phase then coldshock to 15C for 20min.


title: slide3_160min_15C


title: slide5_160min_15C

source_name: Total RNA of the sample at 15C 160 min after coldshock


title: slide5_20min_15C


title: slide2_20min_15C


title: slide3_10min_15C

source_name: Total RNA of the sample at 15C 10 min after coldshock.

treatment_protocol: Grown to mid-log phase then coldshock to 15C for 10min.


title: slide3_20min_15C


title: slide1_20min_15C


title: slide5_40min_15C


title: slide2_10min_15C


title: slide5_5min_15C

source_name: Total RNA of the sample at 15C 5 min after coldshock.

treatment_protocol: Grown to mid-log phase then coldshock to 15C for 5min.


title: slide1_10min_15C


title: slide3_160min_8C

treatment_protocol: Grown to mid-log phase then coldshock to 8C for 40min.


title: slide1_5min_15C


title: slide5_160min_8C

source_name: Total RNA of the sample at 8C 160 min after coldshock.

treatment_protocol: Grown to mid-log phase then coldshock to 8C for 160min.


title: slide4_10min_15C


title: slide1_160min_8C


title: slide2_5min_15C


title: slide1_80min_8C


title: slide3_5min_15C


title: slide4_20min_8C

source_name: Total RNA of the sample at 8C 20 min after coldshock.

treatment_protocol: Grown to mid-log phase then coldshock to 8C for 5min.


title: slide2_160min_8C


title: slide2_80min_8C


title: slide5_40min_8C

source_name: Total RNA of the sample at 8C 40 min after coldshock.


title: slide2_40min_8C


title: slide4_5min_15C


title: slide4_80min_8C


title: slide4_40min_8C


title: slide4_160min_8C


title: slide3_40min_8C


title: slide3_80min_8C


title: slide2_20min_8C


title: slide1_40min_8C


title: slide5_10min_8C

source_name: Total RNA of the sample at 8C 10 min after coldshock.


title: slide5_20min_8C


title: slide3_20min_8C


title: slide4_10min_8C


title: slide3_10min_8C


title: slide5_10min_15C


title: slide2_10min_8C


title: slide1_10min_8C


title: slide4_5min_8C

source_name: Total RNA of the sample at 8C 5 min after coldshock.


title: slide2_5min_8C

hyb_protocol: Global Transcriptome Analysis of the Heat Shock Response of Shewanella oneidensis J. Bacteriol. 2004 186: 7796-7803, PMID: 15516594, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=15516594 Global Transcriptome Analysis of the Cold Shock Response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold-shock proteins. AEM. 2006In press.


title: Subcutaneous_adipose_cow_peak_lactation_Cy5

status: Public on Mar 21 2006

first: Juan

middle: J.

last: Loor

address: 1207 West Gregory Drive

department: Animal Sciences

description: Subcutaneous adipose RNA from cow at peak lactation

data_processing: loess normalization, log2 transformation

source_name: Subcutaneous adipose

tag: Subcutaneous adipose

source_name: reference standard RNA, labelled with Cy3

tag: Pool RNA from cattle tissues


title: ExptIII #148946 Sooty & Harosoy 63 biological rep 1

type: genomic

city: London

last: Gijzen

state: ON

address: 1391 Sandford St

department: Agriculture & AgriFood Canada

country: Canada

institute: SCPFRC London

description: Comparative genomic hybridization for HPS study, 2 soybean cultivars,Sooty & Harosoy 63

data_processing: Arrayvision LRGC scanner layout, background subtracted intensity

organism: Glycine max

source_name: Sooty biological rep 1

tag: soybean cultivar, bloom phenotype with trace surface HPS

source_name: Harosoy 63 biological rep 1

tag: soybean cultivar, dull-seeded phenotype with abundant surface HPS


title: Mesenteric_adipose_cow_peak_lactation_Cy3

description: Mesenteric adipose RNA from cow at peak lactation

source_name: Mesenteric adipose Cy3

tag: Mesenteric adipose RNA labelled with Cy3

source_name: reference standard RNA, labelled with Cy5

tag: Pool RNA form cattle tissues


title: Mammary_cow_peak_lactation_Cy5

description: Mammary RNA from cow at peak lactation

source_name: mammary Cy5

tag: Mammary RNA labelled with Cy5

tag: Pool of RNA from cattle tissues


title: slide3_5min_8C

source_name: Total RNA of the sample before coldshock

label_protocol: Global Transcriptome Analysis of the Cold Shock Response of Shewanella


title: ExptI #148932 Mukden & OX281 biological rep 1

description: Comparative genomic hybridization for HPS study, 2 soybean cultivars, Mukden & OX281

source_name: OX281 biological rep 1

source_name: Mukden biological rep 1

tag: soybean cultivar, shiny-seeded phenotype with trace surface HPS


title: slide5_5min_8C


title: #R56

status: Public on Mar 20 2006

city: New York

first: Deepa

last: Bhojwani

state: NY

address: Smilow Research Building 1206-B, 522 First Avenue

department: Pediatric Hematology Oncology

institute: New York University School of Medicine

description: Relapse sample

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

organism: Homo sapiens

source_name: bone marrow

label_protocol: 1µg of total RNA was used in a double amplification protocol using RiboAmp RNA amplification kits. 20 µg of labelled cRNA was fragmented for hybridization.

extract_protocol: Total RNA was extracted frpm cryopreserved cells using Qiagen Rneasy mini kits

tag: relapse sample


title: Liver_cow_peak_lactation_Cy5

description: Liver RNA from cow at peak lactation

source_name: liver, cow, labelled with Cy5

tag: Liver RNA labelled with Cy5


title: ExptI #148927 Mukden & OX281 biological rep 1


title: #R51

description: Relapse sample


title: ExptII #148944 Mukden & OX281 biological rep 2

source_name: OX281 biological rep 2

source_name: Mukden biological rep 2


title: #R53

description: Relapse sample


title: ExptIII #148945 Sooty & Harosoy 63 biological rep 1

description: Comparative genomic hybridization for HPS study, 2 soybean cultivars, Sooty & Harosoy 63


title: Mesenteric_adipose_cow_peak_lactation_Cy5

source_name: Mesenteric adipose Cy5

tag: Mesenteric adipose RNA


title: slide1_5min_8C


title: #R52

description: Relapse sample


title: Omental_adipose_cow_peak_lactation_Cy3

description: Omental adipose RNA from cow at peak lactation

source_name: Omental adipose

tag: Omental adipose RNA


title: #R55

description: Relapse sample


title: Omental_adipose_cow_peak_lactation_Cy5

tag: Omental adipose


title: Mammary_cow_peak_lactation_Cy3

description: Mammary RNA from cow at peak lactation

source_name: mammary Cy3

tag: Mammary RNA labelled with Cy3


title: ExptII #148943 Mukden & OX281 biological rep 2

data_processing: Arrayvision LRGC scanner layout

tag: soybean cultivar, shiny-seeded phenotype & trace surface HPS

tag: soybean cultivar, dull-seeded phenotype & abundant surface HPS


title: Liver_peak_lactation_cow

description: Liver from a cow at peak lactation.

source_name: liver, cow, labelled with Cy3

tag: Liver RNA from lactating cow at peak lactation

tag: Pool RNA from bovine tissues


title: #R54

description: Relapse sample


title: Subcutaneous_adipose_cow_peak_lactation_Cy3

source_name: Subcutaneous adipose

tag: Subcutaneous adipose

tag: Pool RNA from cattle tissues


title: #R49

description: Relapse sample


title: #R50

description: Relapse sample


title: #R48

description: Relapse sample


title: slide1_20min_8C

source_name: Total RNA of the sample at 8C 20 min after coldshock.

tag: strain

tag: Strain


title: #R41

description: Relapse sample


title: #R43

description: Relapse sample


title: #R45

description: Relapse sample


title: #R34

description: Relapse sample


title: #R40

description: Relapse sample


title: #R32

description: Relapse sample

source_name: blasts from peripheral blood


title: #R27

description: Relapse sample


title: #R42

description: Relapse sample


title: #R33

description: Relapse sample


title: #R24

description: Relapse sample


title: #R26

description: Relapse sample


title: #R22

description: Relapse sample


title: #R29

description: Relapse sample


title: #R31

description: Relapse sample


title: #R25

description: Relapse sample


title: #R18

description: Relapse sample


title: #R47

description: Relapse sample


title: #R13

description: Relapse sample


title: #R28

description: Relapse sample


title: #R17

description: Relapse sample


title: #R23

description: Relapse sample


title: #R8

description: Relapse sample


title: #R9

description: Relapse sample


title: #R19

description: Relapse sample


title: #R30

description: Relapse sample


title: #R14

description: Relapse sample


title: #R6

description: Relapse sample


title: #R7

description: Relapse sample


title: #R10

description: Relapse sample


title: #R5

description: Relapse sample


title: #D38

description: Diagnostic sample

tag: initial diagnosis sample of Pair 35


title: #R78

description: Relapse sample

tag: relapse sample of Pair 32


title: #D37

description: Diagnostic sample

tag: initial diagnosis sample of Pair 34


title: #D36

description: Diagnostic sample

tag: initial diagnosis sample of Pair 33


title: #R79

description: Relapse sample

tag: relapse sample of Pair 33


title: #R80

description: Relapse sample

tag: relapse sample of Pair 34


title: #R16

description: Relapse sample

tag: relapse sample


title: #R1

description: Relapse sample


title: #D35

description: Diagnostic sample

tag: initial diagnosis sample of Pair 32


title: #R81

description: Relapse sample

tag: relapse sample of Pair 35


title: #R77

description: Relapse sample

tag: relapse sample of Pair 31


title: #D33

description: Diagnostic sample

tag: initial diagnosis sample of Pair 30


title: #R76

description: Relapse sample

tag: relapse sample of Pair 30


title: #D31

description: Diagnostic sample

tag: initial diagnosis sample of Pair 28


title: #D32

description: Diagnostic sample

tag: initial diagnosis sample of Pair 29


title: #D30

description: Diagnostic sample

tag: initial diagnosis sample of Pair 27


title: #R72

description: Relapse sample

tag: relapse sample of Pair 26


title: #R75

description: Relapse sample

tag: relapse sample of Pair 29


title: #R70

description: Relapse sample

tag: relapse sample of Pair 25


title: #D21

description: Diagnostic sample

tag: initial diagnosis sample of Pair 20


title: #R73

description: Relapse sample

tag: relapse sample of Pair 27


title: #D27

description: Diagnostic sample

tag: initial diagnosis sample of Pair 125


title: #R74

description: Relapse sample

tag: relapse sample of Pair 28


title: #D34

description: Diagnostic sample

tag: initial diagnosis sample of Pair 31


title: #D23

description: Diagnostic sample

tag: initial diagnosis sample of Pair 22


title: #R64

description: Relapse sample

tag: relapse sample of Pair 20


title: #R61

description: Relapse sample

tag: relapse sample of Pair 17


title: #R66

description: Relapse sample

tag: relapse sample of Pair 22


title: #D24

description: Diagnostic sample

tag: initial diagnosis sample of Pair 23


title: #R67

description: Relapse sample

tag: relapse sample of Pair 23


title: #D26

description: Diagnostic sample

tag: initial diagnosis sample of Pair 24


title: #D18

description: Diagnostic sample

tag: initial diagnosis sample of Pair 17


title: #D29

description: Diagnostic sample

tag: initial diagnosis sample of Pair 26


title: #R69

description: Relapse sample

tag: relapse sample of Pair 24


title: #R63

description: Relapse sample

tag: relapse sample of Pair 19


title: #D19

description: Diagnostic sample

tag: initial diagnosis sample of Pair 18


title: #D22

description: Diagnostic sample

tag: initial diagnosis sample of Pair 21


title: #R62

description: Relapse sample

tag: relapse sample of Pair 18


title: #R15

description: Relapse sample

tag: relapse sample


title: #R60

description: Relapse sample

tag: relapse sample of Pair 16


title: #D20

description: Diagnostic sample

tag: initial diagnosis sample of Pair 19


title: #D16

description: Diagnostic sample

tag: initial diagnosis sample of Pair 15


title: #R44

description: Relapse sample

tag: relapse sample of Pair 15


title: #R46

description: Relapse sample

tag: relapse sample of Pair 14


title: #R2

description: Relapse sample

tag: relapse sample of Pair 12


title: #R65

description: Relapse sample

tag: relapse sample of Pair 21


title: #D15

description: Diagnostic sample

tag: initial diagnosis sample of Pair 14


title: #R38

description: Relapse sample

tag: relapse sample of Pair 8


title: #R59

description: Relapse sample

tag: relapse sample of Pair 10


title: #D11

description: Diagnostic sample

tag: initial diagnosis sample of Pair 10


title: #R39

description: Relapse sample

tag: relapse sample of Pair 4


title: #R20

description: Relapse sample

tag: relapse sample of Pair 3


title: #D14

description: Diagnostic sample

tag: initial diagnosis sample of Pair 13


title: #D13

description: Diagnostic sample

tag: initial diagnosis sample of Pair 12


title: #R37

description: Relapse sample

tag: relapse sample of Pair 5


title: #R36

description: Relapse sample

tag: relapse sample of Pair 6


title: #R12

description: Relapse sample

tag: relapse sample of Pair 9


title: #D9

description: Diagnostic sample

tag: initial diagnosis sample of Pair 9


title: #D5

description: Diagnostic sample

tag: initial diagnosis sample of Pair 5


title: #D8

description: Diagnostic sample

tag: initial diagnosis sample of Pair 8


title: #R21

description: Relapse sample

tag: relapse sample of Pair 13


title: #D12

description: Diagnostic sample

tag: initial diagnosis sample of Pair 11


title: #R35

description: Relapse sample

tag: relapse sample of Pair 7


title: #R58

description: Relapse sample

tag: relapse sample of Pair 11


title: #D4

description: Diagnostic sample

tag: initial diagnosis sample of Pair 4


title: #D7

description: Diagnostic sample

tag: initial diagnosis sample of Pair 7


title: Hsa32KO_shoot_heat shock_rep2

city: Taipei

first: Yee-yung

last: Charng

address: 128, Academia Rd. Sec. 2

department: Agric. Biotech. Res. Center

country: Taiwan

institute: Academia Sinica

data_processing: normalized by global scaling

organism: Arabidopsis thaliana

source_name: shoot, heat shock, 2h

tag: Ecotype

tag: Mutant allele

value: Hsa32 (At4g21320) T-DNA knockout, GABI-268A08

tag: Stage

value: 2 weeks old

tag: Tissue

value: shoot


title: #R4

description: Relapse sample

tag: relapse sample of Pair 2


title: #D3

description: Diagnostic sample

tag: initial diagnosis sample of Pair 3


title: #D17

description: Diagnostic sample

tag: initial diagnosis sample of Pair 16


title: Hsa32KO_shoot_heat shock_rep1

source_name: shoot, heat shock,  2h


title: NH 299141A

city: Philadelphia

first: Ted

last: Abel

state: PA

address: 415 S. University Ave

department: Biology

institute: University of Pennsylvania

description: processed in batch 2

hyb_protocol: standard

scan_protocol: standard

data_processing: RMA

source_name: Amygdala

label_protocol: Approximately 8 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: standard

tag: male C57bl6j, 12 weeks old


title: Hsa32KO_shoot_control_rep2

source_name: shoot, heat shock, control, 2h


title: #D2

description: Diagnostic sample

tag: initial diagnosis sample of Pair 2


title: #D1

description: Diagnostic sample

tag: initial diagnosis sample of Pair 1


title: Wt_shoot_heat shock_rep1

value: Col-0 wild type


title: NH 28892A

description: processed in batch 2


title: Wt_shoot_control_rep2


title: #R3

description: Relapse sample

tag: relapse sample of Pair 1


title: NH 17374A

description: processed in batch 1


title: NH 17172A

description: processed in batch 1


title: NH 29798A

description: processed in batch 2


title: FC 25589A

description: processed in batch 2


title: Hsa32KO_shoot_control_rep1


title: NH 16566A

description: processed in batch 1


title: NH 16364A

description: processed in batch 1


title: NH 3142153A

description: processed in batch 3


title: FC 3144146A

description: processed in batch 3


title: Wt_shoot_heat shock_rep2


title: #R11

description: Relapse sample

tag: relapse sample


title: FC 3148150A

description: processed in batch 3


title: NH 16768A

description: processed in batch 1


title: FC 23543A

description: processed in batch 2


title: NH 16970A

description: processed in batch 1


title: Wt_shoot_control_rep1


title: FC 21927A

description: processed in batch 2


title: FC 2103113A

description: processed in batch 2


title: CS 3143145A

description: processed in batch 3


title: CS 3151152A

description: processed in batch 3


title: CS 3147149A

description: processed in batch 3


title: CS 251101A

description: processed in batch 2


title: NH 78h

description: processed in batch 6

source_name: Hippocampus


title: NH 111h

description: processed in batch 4


title: NH 65h

description: processed in batch 7


title: CS 23139A

description: processed in batch 2


title: NH 66h

description: processed in batch 7


title: NH 64h

description: processed in batch 7


title: NH 82h

description: processed in batch 6


title: NH 67h

description: processed in batch 7


title: CS 21523A

description: processed in batch 2


title: NH 68h

description: processed in batch 7


title: NH 100h

description: processed in batch 4


title: NH 63h

description: processed in batch 7


title: FC 79h

description: processed in batch 6


title: CS 39h

description: processed in batch 5


title: FC 89h

description: processed in batch 4


title: FC 35h

description: processed in batch 5


title: CS 75h

description: processed in batch 6


title: FC 55h

description: processed in batch 6


title: CS 85h

description: processed in batch 4


title: FC 113h

description: processed in batch 4


title: FC 43h

description: processed in batch 5


title: FC 19h

description: processed in batch 5


title: CS 23h

description: processed in batch 5


title: CS 109h

description: processed in batch 4


title: CS 105h

description: processed in batch 4


title: CS 15h

description: processed in batch 5


title: CS 31h

description: processed in batch 5


title: Re-replication of S.cerevisae strain SB2023 after 3hrs - Replicate #1

city: Cambridge

first: Stephen

last: Bell

state: MA

address: 77 Massachusetts Ave

institute: MIT

description: SB2023: ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 lys2::hisG bar1::hisG orc6::HisMX6 MATa ORC6Rxl-PO4-,LEU2::ORC6 promoter, MCM7nls ORC2PO4-,GalCdc6dN::URA3 ARS418::iYDR310C

hyb_protocol: hybridized and washed according to Agilent's standard protocol.

scan_protocol: Scanned on an Agilent Scanner

data_processing: Cy3 and Cy5 levels were quantitated using Agilent’s Feature Extraction software. The resulting log ratios of experimental DNA/reference DNA for each spot on the array were then determined using the sma package for R (v2.1.0, http://www.r-project.org). We also performed scale normalization across the slides for each set of triplicate experiments so each experiment had the same median absolute deviation.

organism: Saccharomyces cerevisiae

source_name: SB2023 3hrs after induction of re-replication

label_protocol: 10 ug of DNA was labeled with 2 nmol of Cy3-dUTP (Amersham Biosciences, GE Healthcare) using 4 mg random nonamer oligo (IDT) and 0.25 l of high-concentration Klenow (NEB) at 37 degrees for one hour. Un-incorporated dye was removed using a microcon column (MW cutoff 30000, Millipore) by washing the sample three times with TE.

extract_protocol: DNA was isolated by bead beating. Briefly, whole cells were mixed with 200 mL of buffer (10 mM Tris pH 7.5, 1% SDS, 100 mM NaCl, 1 mM EDTA, 2% Triton X 100), 300 µL of glass beads, and 200 mL of phenol:chloroform:isoamyl-alcohol (25:24:1, GE Healthcare) and vortexed for 4 min. The DNA in the aqueous phase was precipitated and resuspended in 200 mL of TE. RNA was removed with RNAse (3 µg) treatment for 3 hr 37∞C. The DNA was then sheared to approximately 1 kb (Branson Sonicator 250), phenol:chloroform extracted, and EtOH precipitated.

treatment_protocol: Exponentially-growing cells were (OD600=0.4) were washed with water and moved to YP-RAF(2%) + 15 ug/ml nocodazole. When cells were >95% large-budded, galactose was added to a final concentration of 2%. Cells were collected 3 hours post galactose induction.

tag: Strain

source_name: G1 phase W303 (wild type)

label_protocol: 10 ug of DNA was labeled with 2 nmol of Cy5-dUTP (Amersham Biosciences, GE Healthcare) using 4 mg random nonamer oligo (IDT) and 0.25 l of high-concentration Klenow (NEB) at 37 degrees for one hour. Un-incorporated dye was removed using a microcon column (MW cutoff 30000, Millipore) by washing the sample three times with TE.

treatment_protocol: Exponentially-growing cells were arrested using 50ng/ml alpha-factor. Cells were collected when >95% were unbudded.


title: 5A-700700_WT A

city: University Park

first: Melissa

last: Durant

address: 452 N Frear

institute: Penn State University

description: no additional information needed

hyb_protocol: see above

data_processing: MeanFRG- MedianBCK>S.D. BCK, <26% saturation.  Ratio of Test/Ref.

molecule: polyA RNA

source_name: strain yMD13

growth_protocol: Cells were grown in CSM-HIS to OD600 of ~0.8.  Cultures were then rapidly shifted to 37ûC by adding warm media and placing in a 37ûC shaker incubator for 45 minutes before harvest at RT.

extract_protocol: Holstege et al.  1998.  Cell.  95:717-28

treatment_protocol: Heat shock (37C) of WT and mutant HAT strains, see below.

tag: strain yMD13 [WT]

label_protocol: [Chitikila et al.  2002. Mol Cell. 10:871-82

growth_protocol: see above

extract_protocol: see above

treatment_protocol: see above


title: Re-replication of S.cerevisae strain SB2023 after 3hrs - Replicate #3

tag: strain


title: 48B-700700_ts2 E

description: no additional information needed

scan_protocol: Chitikila et al.  2002. Mol Cell. 10:871-82

source_name: strain yMD14

tag: strain yMD14 [taf1-ts2]


title: 48A-700700_WT G

description: no additional information needed

label_protocol: Chitikila et al.  2002. Mol Cell. 10:871-82


title: 46A-700700_WT C

description: no additional information needed


title: 29A-700700_WT B

description: no additional information needed


title: 66A-700700_WT H

description: no additional information needed


title: 32B-700700_ts2 D

description: no additional information needed


title: 66B-700700_ts2 F

description: no additional information needed


title: Re-replication of S.cerevisae strain SB2125 after 3hrs - Replicate #1

description: SB2125: ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 lys2::hisG bar1::hisG orc6::HisMX6 MATa ORC6Rxl-PO4-,LEU2::ORC6 promoter, MCM7nls ORC2PO4-,GalCdc6dN::URA3 ARS_2_408039::iYDR310C

source_name: SB2125 3hrs after induction of re-replication

extract_protocol: DNA was isolated by bead beating. Briefly, whole cells were mixed with 200 mL of buffer (10 mM Tris pH 7.5, 1% SDS, 100 mM NaCl, 1 mM EDTA, 2% Triton X 100), 300 µL of glass beads, and 200 mL of phenol:chloroform:isoamyl-alcohol (25:24:1, GE Healthcare) and vortexed for 4 min. The DNA in the aqueous phase was precipitated and resuspended in 200 mL of TE. RNA was removed with RNAse (3 µg) treatment for 3 hr 37∞C. The DNA was then sheared to approximately 1 kb (Branson Sonicator 250), phenol:chloroform extracted, and EtOH precipitated


title: Re-replication of S.cerevisae strain SB2052 after 3hrs - Replicate #3

description: SB2052: orc6::HISMX6::LEU2::ORC6-ps,rxl ORC2-ps MCM7-NLS URA3::GAL-CDC6∆2-48-HA lys2::hisG bar1::hisG MA a iYDR309C::LYS2::ARS418mut

source_name: SB2052 3hrs after induction of re-replication


title: Re-replication of S.cerevisae strain SB2052 after 3hrs - Replicate #1


title: Re-replication of S.cerevisae strain SB2125 after 3hrs - Replicate #2


title: 7A-700690_WT E

description: no additional information needed


title: 70A-720720_WT D

description: no additional information needed


title: 32A-710710_WT F

description: no additional information needed


title: Re-replication of S.cerevisae strain SB2052 after 3hrs - Replicate #2


title: 46B-700700_ts2 B

description: no additional information needed


title: 70B-720720_ts2 C

description: no additional information needed


title: Re-replication of S.cerevisae strain SB2023 after 3hrs - Replicate #2


title: 29B-700700_ts2 A

description: no additional information needed


title: Re-replication of S.cerevisae strain SB2125 after 3hrs - Replicate #3


title: 69A-750700_sas3 B

description: no additional information needed

source_name: strain yMD11

tag: strain yMD11 [sas3 delete]


title: 73B-700700_sas3 ts2 A

description: no additional information needed

source_name: strain yMD12

tag: strain yMD12 [sas3 delete + taf1-ts2]


title: 73A-700700_sas3 A

description: no additional information needed


title: Genome-Wide Location Analysis of ORC during re-replication - Replicate #2

description: SB1507: orc6::HISMX6::LEU2::ORC6-ps,rxl ORC2-ps MCM7-NLS URA3::GAL-CDC6∆2-48-HA lys2::hisG bar1::hisG MA a in a W303 background.

source_name: ORC IP during re-replication

label_protocol: The total IP'd DNA was labeled with 2 nmol of Cy3-dUTP (Amersham Biosciences, GE Healthcare) using 4 mg random nonamer oligo (IDT) and 0.25 ul of high-concentration Klenow (NEB) at 37 degrees for one hour. Un-incorporated dye was removed using a microcon column (MW cutoff 30000, Millipore) by washing the sample three times with TE.

extract_protocol: Standard Chromatin Immunpreciptation assay was performed as previously described (Aparicio et al., 1997) using a polyclonal antibody against ORC (1:250 dilution).

treatment_protocol: Exponentially-growing cells were (OD600=0.4) were washed with water and moved to YP-RAF(2%) + 15 ug/ml nocodazole. When cells were >95% large-budded, galactose was added to a final concentration of 2%. Cells were collected 45 minutes post galactose induction.

source_name: ORC Input during re-replication

label_protocol: 1/10th of Input DNA was labeled with 2 nmol of Cy5-dUTP (Amersham Biosciences, GE Healthcare) using 4 mg random nonamer oligo (IDT) and 0.25 ul of high-concentration Klenow (NEB) at 37 degrees for one hour. Un-incorporated dye was removed using a microcon column (MW cutoff 30000, Millipore) by washing the sample three times with TE.

extract_protocol: Standard Chromatin Immunpreciptation assay was performed as previously described (Aparicio et al., 1997). Input DNA was removed before the addition of antibody.


title: Genome-Wide Location Analysis of ORC during re-replication - Replicate #3

label_protocol: The total IP'd DNA was labeled with 2 nmol of Cy5-dUTP (Amersham Biosciences, GE Healthcare) using 4 mg random nonamer oligo (IDT) and 0.25 ul of high-concentration Klenow (NEB) at 37 degrees for one hour. Un-incorporated dye was removed using a microcon column (MW cutoff 30000, Millipore) by washing the sample three times with TE.

label_protocol: 1/10th of Input DNA was labeled with 2 nmol of Cy3-dUTP (Amersham Biosciences, GE Healthcare) using 4 mg random nonamer oligo (IDT) and 0.25 ul of high-concentration Klenow (NEB) at 37 degrees for one hour. Un-incorporated dye was removed using a microcon column (MW cutoff 30000, Millipore) by washing the sample three times with TE.


title: Genome-Wide Location Analysis of ORC during re-replication - Replicate #1


title: 69B-700700_sas3 ts2 B

description: no additional information needed


title: 71A-720720_hat1 A

description: no additional information needed

source_name: strain yMD7

tag: strain yMD7 [hat1 delete]


title: 6B-690690_hpa2 ts2 A

description: no additional information needed

source_name: strain yMD5

tag: strain yMD10 [hpa2 delete + taf1-ts2]


title: Genome-Wide Location Analysis of Mcm2-7 during re-replication - Replicate #3

source_name: Mcm2-7 IP during re-replication

extract_protocol: Standard Chromatin Immunpreciptation assay was performed as previously described (Aparicio et al., 1997) using a polyclonal antibody against Mcm2-7, UM185, (1:250 dilution).

source_name: Mcm2-7 Input during re-replication


title: G1 phase Genome-Wide Location Analysis of Mcm2-7, wild type - Replicate #3

description: W303: ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 lys2::hisG bar1::hisG MATa

source_name: Mcm2-7 IP during G1 phase, wild type

extract_protocol: Standard Chromatin Immunpreciptation assay was performed as previously described (Aparicio et al., 1997) during G1 phase using a polyclonal antibody against Mcm2-7, UM185, (1:250 dilution).

source_name: Mcm2-7 Input during G1 phase, wild type


title: 68A-750700_hpa2 B

description: no additional information needed

source_name: strain yMD9

tag: strain yMD9 [hpa2 delete]


title: G1 phase Genome-Wide Location Analysis of Mcm2-7, wild type- Replicate #1


title: #D6

description: Diagnostic sample

source_name: bone marrow

tag: initial diagnosis sample of Pair 6


title: 67A-700700_hat1 B

description: no additional information needed


title: Genome-Wide Location Analysis of Mcm2-7 during re-replication - Replicate #1


title: Genome-Wide Location Analysis of Mcm2-7 during re-replication - Replicate #2


title: W303 (wild type) after 3hrs in re-replication conditions - Replicate #3

source_name: W303 after 3hrs in re-replication conditions

source_name: G1 phase W303 (wild type)


title: W303 (wild type) after 3hrs in re-replication conditions - Replicate #1


title: 8B-700720_hpa2 ts2 B

description: no additional information needed

source_name: strain yMD13

source_name: strain yMD10


title: Re-replication of S.cerevisae strain SB1507 after 3hrs - Replicate #1

description: SB1507: orc6::HISMX6::LEU2::ORC6-ps,rxl ORC2-ps MCM7-NLS URA3::GAL-CDC6∆2-48-HA lys2::hisG bar1::hisG MA a  in a W303 background.

data_processing: Cy3 and Cy5 levels were quantitated using Agilent’s Feature Extraction software. The resulting log ratios of experimental DNA/reference DNA for each spot on the array were then determined using the sma package [45] for R (v2.1.0, http://www.r-project.org). We also performed scale normalization across the slides for each set of triplicate experiments so each experiment had the same median absolute deviation.

source_name: SB1507 3hrs after induction of re-replication

treatment_protocol: exponentially-growing cells were (OD600=0.4) were washed with water and moved to YP-RAF(2%) + 15 ug/ml nocodazole. When cells were >95% large-budded, galactose was added to a final concentration of 2%. Cells were collected 3 hours post galactose induction.


title: W303 (wild type) after 3hrs in re-replication conditions - Replicate #2


title: 9B-700700_hpa2 A

description: no additional information needed


title: Re-replication of S.cerevisae strain SB1507 after 3hrs - Replicate #2


title: 33A-700700_gcn5 B

description: no additional information needed

source_name: strain yJS4

tag: strain yJS4 [gcn5 delete]


title: G1 phase Genome-Wide Location Analysis of Mcm2-7, wild type - Replicate #2


title: 71B-720720_hat1 ts2 A

description: no additional information needed

source_name: strain yMD8

tag: strain yMD8 [hat1 delete + taf1-ts2]


title: 30B-700700_gcn5 ts2 A

description: no additional information needed

source_name: strain yJS5

tag: strain yJS5 [gcn5 delete + taf1-ts2]


title: 51B-700700 esa1 ts2 B

description: no additional information needed

source_name: strain yMD28

tag: strain yMD28 [esa1-414 + taf1-ts2]


title: FC 27h

description: processed in batch 5

source_name: Hippocampus

tag: male C57bl6j, 12 weeks old


title: 67B-700700_hat1 ts2 B

description: no additional information needed


title: 47A-700700_esa1 A.gpr

description: no additional information needed

source_name: strain yMD27

tag: strain yMD27 [esa1-414]


title: 51A-720730_esa1 B.txt

description: no additional information needed


title: 33B-700700_gcn5 ts2 B

description: no additional information needed


title: 5B-700700_elp3 A

description: no additional information needed

source_name: strain yMD5

tag: strain yMD5 [elp3 delete]


title: 47B-700700_esa1 ts2 A

description: no additional information needed


title: i35B-700700 B

description: sample material is chip DNA

growth_protocol: Cells were grown in CSM-HIS to OD600 of ~0.8.  Cultures were then rapidly shifted to 37ûC by adding warm media and placing in a 37ûC shaker incubator for 45 minutes.  After HS, cells were crosslinked with 1% formaldehyde for 15minutes at RT and subsequently quenched with 0.125M glycine and harvested.

treatment_protocol: Heat shock (37C) of WT and mutant strains, see below.


title: 30A-725725_gcn5 A

description: no additional information needed


title: 9A-750700_elp3 B

description: no additional information needed


title: i15A-720720 A

description: sample material is chip DNA


title: i36B-700700 B

description: sample material is chip DNA

tag: strain yJS5 [gcn5 delete taf1-ts2]


title: 6A-700700_elp3 ts2 A

description: no additional information needed

source_name: strain yMD6

tag: strain yMD6 [elp3 delete + taf1-ts2]

tag: strain yMD13 [WT]


title: 1D clenbuterol, replicate 3

status: Public on Mar 18 2006

city: Ames

first: Diane

middle: Moody

last: Spurlock

state: IA

address: 239 Kildee Hall

department: Animal Science

institute: Iowa State University

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: raw signal data

label: Affymetrix standard protocol

source_name: gracillus muscle

label_protocol: Affymetrix standard protocol

growth_protocol: ad libitum access to feed and water

extract_protocol: Qiagen RNEasy Mini kit for muscle

treatment_protocol: vehicle control administered intraperitoneally for 9 days, followed by clenbuterol at 1 mg/kg body weight for 1 day

tag: C57BL/6J, 3-5 wk, male


title: 10D clenbuterol, replicate 1

treatment_protocol: clenbuterol administered intraperitoneally for 10 days at 1 mg/kg body weight


title: i33B-750750 B

description: sample material is chip DNA


title: i34A-750750 A

description: sample material is chip DNA

source_name: strain yMD14

tag: strain yMD14 [taf1-ts2]


title: i35A-700700 A

description: sample material is chip DNA


title: 8A-700700_elp3 ts2 B

description: no additional information needed


title: 10D clenbuterol, replicate 2


title: 10D clenbuterol, replicate 3


title: 1D clenbuterol, replicate 2


title: Control, replicate 3

treatment_protocol: vehicle control administered intraperitoneally for 10 days


title: 1D clenbuterol, replicate 1


title: i36A-700700 B

description: sample material is chip DNA


title: 10D clenbuterol, replicate 3, chip B

tag: C57BL/6J, 3-5 wk, males


title: 10D clenbuterol, replicate 2, chip B


title: Control, replicate 1

tag: C57BL/6J, 3 to 5 wk, male


title: 1D clenbuterol, replicate 1, chip B

treatment_protocol: vehicle control administered intraperitoneally for 9 days, then clenbuterol administered at 1 mg/kg body weight for 1 day


title: Control, replicate 3, chip B


title: Control, replicate 2


title: 10D clenbuterol, replicate 1, chip B


title: Control, replicate 2, chip B


title: Re-replication of S.cerevisae strain SB1507 after 3hrs - Replicate #3

tag: Strain


title: Control, replicate 1, chip B


title: 1D clenbuterol, replicate 2, chip B


title: 1D clenbuterol, replicate 3, chip B


title: OMC_G2_Rerep_UbP11_174_RME5-27_G2_Galp_vs_OMCrerepN2_70

status: Public on Mar 17 2006

first: Joachim

last: Li

address: 600 16th Street S376

department: Microbiology and Immunology

description: Data from Figure 2B of MBoC paper (citation coming soon)

hyb_protocol: Hybridization was performed in 3X SSC, 25mM HEPES pH7.0, 0.25% SDS at 63oC for 24 hours.

scan_protocol: Arrays were scanned with an Axon 3000B scanner using GenePix4.0.

data_processing: Data were filtered in GenePix to flag as bad features that had (1) obvious defects, (2) saturated pixels, (3) regression r^2 values less than 0.5 or (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background.  BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive.  Raw Cy5/Cy3 median of ratios values were normalized such that the average ratio was equal to the DNA content of the replicating cells as determined by flow cytometry.  The DNA content was 2.70C.

source_name: G2 phase re-replicating DNA OMC

label_protocol: amino-allyl-dUTP incorporation with Klenow.  Chemical coupling of dye to aa-dUTP labelled DNA.

tag: YJL3248 180 minutes after galactose induction while arrested at G2 phase

source_name: G2 phase non-re-replicating DNA OM

tag: YJL3244 180 minutes after galactose induction while arrested at G2 phase


title: OMC_G2_Rerep_LiUP1_093_RME7-2_G2_Galp_vs_OMCrerepN2_70

tag: YJL5493 180 minutes after galactose induction while arrested at G2 phase


title: OMC_G2_Rerep_UP11_188_RME6-20_G2_Galp_vs_OMCrerepN2_70


title: N-11D

city: Bethesda

first: Peter

last: Yuen

address: 10 Center Drive, Room 3N108

department: NIDDK

institute: NIH

description: Normal.  RNA from the N#11 rat was processed and hybridized to a separate array for a non-biological duplicate

data_processing: CodeLink Expression Analysis Software, then normalization by median centering

source_name: Normal #11, duplicate

label_protocol: CodeLink standard protocol

extract_protocol: half of each kidney was minced in > 20 volumes of RNAlater overnight; after removing RNAlater,kidneys were stored at -80 degrees C. Frozen kidneys were homogenized in TRIZOL, and crude RNA was isolated by the manufacturer's protocol. RNA was resuspended in DEPC water and further purified by RNeasy minikit (Qiagen). Crude RNA from each half kidney was purified on 5 minicolumns, which were serially eluted to keep the RNA concentration high without precipitation or evaporation.

tag: Strain:Sprague Dawley

tag: Gender

value: male

tag: Age

value: 6-8 weeks

tag: Tissue

value: kidney


title: S-2

description: Sham surgery is used here as a control for ischemia/reperfusion. Sham is expected to be similar to normal.

source_name: Sham #2

treatment_protocol: 40 min sham surgery, then harvest after 8 hours


title: MC2A_35_G2_Rerep_LiUP1_101_RME7-6_G2_MCrerep35N2_0

description: Data from Figure 7C of MBoC paper (citation coming soon)

data_processing: Data were filtered in GenePix to flag as bad features that had (1) obvious defects, (2) saturated pixels, (3) regression r^2 values less than 0.5 or (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background.  BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive.  Raw Cy5/Cy3 median of ratios values were normalized such that the average ratio was equal to the DNA content of the replicating cells as determined by flow cytometry.  The DNA content was 2.0C.

source_name: G2 phase re-replicating DNA MC2A

tag: YJL4489 240 minutes after galactose induction while arrested at G2 phase at 35 degrees C

source_name: G2 phase non-re-replicating DNA M

tag: YJL4486 240 minutes after galactose induction while arrested at G2 phase at 35 degrees C


title: MC2A_23_G2_Rerep_LiUP1_071_RME7-9_G2_MCrerep23N2_0

description: Data from Figure S13 of MBoC paper (citation coming soon)

tag: YJL4489 240 minutes after galactose induction while arrested at G2 phase at 23 degrees C

tag: YJL4486 240 minutes after galactose induction while arrested at G2 phase at 23 degrees C


title: C-1

description: Cisplatin causes acute renal failure. The 2h timepoint precedes leukocyte infiltration.

source_name: Cisplatin #1

treatment_protocol: inject 20 mg/kg cisplatin, i.p., harvest after 2h


title: MC2A_cdc7_23_G2_Rerep_LiUP1_073_RME7-9_G2_MC_cdc7-1_rerep23N2_0

source_name: G2 phase re-replicating DNA MC2A cdc7-1

tag: YJL5822 240 minutes after galactose induction while arrested at G2 phase at 23 degrees C

source_name: G2 phase non-re-replicating DNA M cdc7-1

tag: YJL5816 240 minutes after galactose induction while arrested at G2 phase at 23 degrees C


title: OMC_G2_Rerep_LiUP1_166_RME6-22_G2_Galp_vs_OMCrerepN2_70


title: C-3

description: Cisplatin causes acute renal failure.

source_name: Cisplatin #3


title: MC2A_35_G2_Rerep_LiUP1_074_RME7-9_G2_MCrerep35N2_0


title: MC2A_cdc7_35_G2_Rerep_LiUP1_102_RME7-6_G2_MC_rerep_cdc7-1_35N2_0

tag: YJL5822 240 minutes after galactose induction while arrested at G2 phase at 35 degrees C

tag: YJL5816 240 minutes after galactose induction while arrested at G2 phase at 35 degrees C


title: MC2A_23_G2_Rerep_LiUP1_099_RME7-6_G2_MCrerep23N2_0


title: MC2A_cdc7_23_G2_Rerep_LiUP1_072_RME7-9_G2_MC_cdc7-1_rerep23N2_0


title: MC2A_cdc7_35_G2_Rerep_LiUP1_076_RME7-9_G2_MC_cdc7-1_rerep35N2_0


title: Hg8-1

description: Mercuric chloride causes acute renal failure.

source_name: Mercuric chloride 8h #1

treatment_protocol: inject 4 mg/kg mercuric chloride, s.c., harvest after 8h


title: MC2A_G2_Rerep_LiU1_109_RME6-23_G2_Galp_vs_MCrerepN2_0

description: Data from Figure 6E of MBoC paper (citation coming soon)

tag: YJL4489 180 minutes after galactose induction while arrested at G2 phase

tag: YJL4486 180 minutes after galactose induction while arrested at G2 phase


title: Hg8-2

source_name: Mercuric chloride 8h #2


title: C-2

description: Cisplatin causes acute renal failure.  The 2h timepoint precedes leukocyte infiltration.

source_name: Cisplatin #2


title: MC2A_G2_Rerep_UbP11_172_RME5-27_G2_Galp_vs_MCrerepN2_0


title: MC2A_G2_Rerep_Uber_P7_233_BOE7_5_G2_GalpvsMCrerepN2_0


title: MC2A_ars317_G2_Rerep_LiUP1_107_RME7-8_G2_MCrerep_delARS317N2_0

description: Data from Figure 7B of MBoC paper (citation coming soon)

source_name: G2 phase re-replicating DNA MC2A ars317

tag: YJL5858 180 minutes after galactose induction while arrested at G2 phase


title: S-3

description: Sham surgery is used here as a control for ischemia/reperfusion.  Sham is expected to be similar to normal.

source_name: Sham #3


title: MC2A_G1_Release_LiU1_110_RME6-23_G1_Galp_vs_MCrerepN2_0

source_name: G1 release re-replicating DNA MC2A

tag: YJL4489 180 minutes after release from G1 (alpha factor) in the presence of galactose into a G2 phase arrest

source_name: G1 release non-re-replicating DNA M

tag: YJL4486 180 minutes after release from G1 (alpha factor) in the presence of galactose into a G2 phase arrest


title: MC2A_ars317_G2_Rerep_LiUP1_080_RME7-11_G2_MC_rerep_deARS317N2_0


title: S-1

source_name: Sham #1

tag: Strain:Sprague Dawley


title: MC2A_G1_Release_UP8_224_BOE7-10_G1_GalpvsMCrerepRGN2_0

description:
Data from Figure 6E of MBoC paper (citation coming soon)
This experiment was a dye swap so the Cy5 and Cy3 channels are reversed. The final normalized Value was calculated using the inverse of the median of the ratios.


title: MC2A_G2_Rerep_Uber_P7_232_BOE7_5_G2_GalpvsMCrerepN2_0


title: N-11

description: Normal

source_name: Normal #11

tag: Gender


title: IR8-2D

description: Ischemia/Repefusion causes acute renal failure. RNA from the IR8#2 rat was processed and hybridized to a separate array for a non-biological duplicate

source_name: Ischemia/Reperfusion 8h #2, duplicate

treatment_protocol: 40 min bilateral ischemia, 8 hours reperfusion, then harvest

tag: Age


title: MC2A_G1_Release_UbP11_175_RME5-28_G1_Galp_vs_MCrerepN2_0


title: Hg8-3

source_name: Mercuric chloride 8h #3

tag: Tissue


title: MC2A_G1_Release_UP8_223_BOE7-10_G1_GalpvsMCrerepRGN2_0


title: IR8-1D

description: Ischemia/Repefusion causes acute renal failure.  RNA from the IR8#1 rat was processed and hybridized to a separate array for a non-biological duplicate

source_name: Ischemia/Reperfusion 8h #1, duplicate


title: OC_G1_Release_UbP11_176_RME5-28_G1_Galp_vs_OCrerepN2_60

description: Data from Figure 5E of MBoC paper (citation coming soon)

data_processing: Data were filtered in GenePix to flag as bad features that had (1) obvious defects, (2) saturated pixels, (3) regression r^2 values less than 0.5 or (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background.  BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive.  Raw Cy5/Cy3 median of ratios values were normalized such that the average ratio was equal to the DNA content of the replicating cells as determined by flow cytometry.  The DNA content was 2.60C.

source_name: G1 release re-replicating DNA OC

tag: YJL3240 180 minutes after release from G1 (alpha factor) in the presence of galactose into a G2 phase arrest

source_name: G1 release non-re-replicating DNA O

tag: YJL4832 180 minutes after release from G1 (alpha factor) in the presence of galactose into a G2 phase arrest


title: OC_G1_Release_LiUP1_174_RME6-22_G1_Galp_vs_OCrerepN2_60


title: OC_G1_Release_LiUP1_112_RME6-23_G1_Galp_vs_OCrerepN2_60


title: IR2M-1

description: Ischemia/Repefusion causes acute renal failure. The 2h timepoint precedes leukocyte infiltration. Alpha melanocyte stimulating hormone has been shown to inhibit I/R-induced acute renal failure.

source_name: Ischemia/Reperfusion + alphaMSH 2h #1

treatment_protocol: 40 min bilateral ischemia, inject 50 micrograms alpha MSH per rat, i.v., 2 hours reperfusion, then harvest


title: IR8-2

description: Ischemia/Repefusion causes acute renal failure.

source_name: Ischemia/Reperfusion 8h #2


title: i15B-720720 A

description: sample material is chip DNA

source_name: strain yJS4

tag: strain yJS4 [gcn5 delete]

source_name: strain yMD13

tag: strain yMD13 [WT]


title: OC_G1_Release_LiUP1_111_RME6-23_G1_Galp_vs_OCrerepN2_60


title: OC_G2_Rerep_LiUP1_165_RME6-22_G2_Galp_vs_OCrerepN2_0

source_name: G2 phase re-replicating DNA OC

tag: YJL3240 180 minutes after galactose induction while arrested at G2 phase

source_name: G2 phase non-re-replicating DNA O

tag: YJL4832 180 minutes after galactose induction while arrested at G2 phase


title: OC_G2_Rerep_UbP11_173_RME5-27_G2_Galp_vs_OCrerepN2_0


title: OC_G2_Rerep_LiUP1_154_RME6-20_G2_Galp_vs_OCrerepN2_0


title: N-12

description: Normal

source_name: Normal #12


title: VD-4

description: Volume depletion is used here as a control for acute renal failure. VD is expected to be similar to normal.

source_name: Volume Depletion #4

treatment_protocol: Furosemide injection 20 mg/kg i.p. at 0 and 8 h, sodium-deficient diet then harvest at 24 h


title: VD-3

source_name: Volume Depletion #3


title: IR2-2

description: Ischemia/Repefusion causes acute renal failure. The 2h timepoint precedes leukocyte infiltration.

source_name: Ischemia/Reperfusion 2h #2

treatment_protocol: 40 min bilateral ischemia, 2 hours reperfusion, then harvest


title: OMC_G1_Release_UP8_177_BOE7-15_G1_GalpvsOMCrerepN3_20

description:
Data from Figure 4C of MBoC paper (citation coming soon)
This experiment was a dye swap so the Cy5 and Cy3 channels are reversed. The final normalized Value was calculated using the inverse of the median of the ratios.

data_processing: Data were filtered in GenePix to flag as bad features that had (1) obvious defects, (2) saturated pixels, (3) regression r^2 values less than 0.5 or (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background.  BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive.  Raw Cy5/Cy3 median of ratios values were normalized such that the average ratio was equal to the DNA content of the replicating cells as determined by flow cytometry.  The DNA content was 3.20C.

source_name: G1 release re-replicating DNA OMC

tag: YJL3248 180 minutes after release from G1 (alpha factor) in the presence of galactose into a G2 phase arrest

source_name: G1 release non-re-replicating DNA OM

tag: YJL3244 180 minutes after release from G1 (alpha factor) in the presence of galactose into a G2 phase arrest


title: OMC_G1_Release_UP8_176_BOE7-15_G1_GalpvsOMCrerepN3_20


title: N-2

description: Normal

source_name: Normal #2


title: N-2D

description: Normal.  RNA from the N#2 rat was processed and hybridized to a separate array for a non-biological duplicate

source_name: Normal #2, duplicate


title: IR2M-2

source_name: Ischemia/Reperfusion + alphaMSH 2h #2


title: OMC_G1_Release_UbP11_177_RME5-28_G1_Galp_vs_OMCrerepN3_20

description: Data from Figure 4C of MBoC paper (citation coming soon)


title: IR2-4

source_name: Ischemia/Reperfusion 2h #4


title: OC_G2_Rerep_LIU1_164_RME6-22_G2_Galp_vs_OCrerepN2_0


title: Hg2-2

description: Mercuric chloride causes acute renal failure. The 2h timepoint precedes leukocyte infiltration.

source_name: Mercuric chloride 2h #2

treatment_protocol: inject 4 mg/kg mercuric chloride, s.c., harvest after 2h


title: IR8-1

source_name: Ischemia/Reperfusion 8h #1


title: IR8-3

source_name: Ischemia/Reperfusion 8h #3


title: Hg2-1

source_name: Mercuric chloride 2h #1


title: OMC_S_Rerep_LiUP1_084_RME7-11_G1_vs_0_1MHU_OMC_rerepN1_40

description: Data from Figure 3B of MBoC paper (citation coming soon)

data_processing: Data were filtered in GenePix to flag as bad features that had (1) obvious defects, (2) saturated pixels, (3) regression r^2 values less than 0.5 or (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background.  BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive.  Raw Cy5/Cy3 median of ratios values were normalized such that the average ratio was equal to the DNA content of the replicating cells as determined by flow cytometry.  The DNA content was 1.40C.

source_name: S phase re-replicating DNA OMC

tag: YJL3249 240 minutes after release from G1 (alpha factor) into 0.1M hydroxyurea in the presence of galactose

source_name: G1 phase DNA OMC

tag: YJL3249 arrested in G1 (alpha factor)


title: OMC_S_Rerep_LiUP1_083_RME7-11_G1_vs_0_1MHU_OMC_rerepN1_40


title: OMC_S_Rerep_Li_UP1_138_RME6-16_G1_vs_0_1MHU_OMCrerepN1_40


title: OMC_S_phase_LiUP1_131_RME6-31_G1_vs_HU_OMCrep_3hrN1_40

description: Data from Figure 1D of MBoC paper (citation coming soon)

source_name: S phase DNA OMC

tag: YJL3248 180 minutes after release from G1 (alpha factor) into 0.1M hydroxyurea

tag: YJL3248 arrested in G1 (alpha factor)


title: OMC_S_Rerep_Li_UP1_139_RME6-16_G1_vs_0_1MHU_OMCrerepN1_40


title: OMC_S_phase_LiUP1_132_RME6-31_G1_vs_HU_OMCrep_300N1_40


title: N-3

description: Normal

source_name: Normal #3


title: OMC_G1_Release_LiU1_173_RME6-22_G1_Galp_vs_OMCrerepN3_20


title: VD-1

source_name: Volume Depletion #1


title: OMC_S_phase_LiUP1_120_RME6-27_G1_vs_0_1MHU_3hrN1_40


title: IR2-3

source_name: Ischemia/Reperfusion 2h #3

extract_protocol: half of each kidney was minced in > 20 volumes of RNAlater overnight; after removing RNAlater,kidneys were stored at -80 degrees C.  Frozen kidneys were homogenized in TRIZOL, and crude RNA was isolated by the manufacturer's protocol.  RNA was resuspended in DEPC water and further purified by RNeasy minikit (Qiagen).  Crude RNA from each half kidney was purified on 5 minicolumns, which were serially eluted to keep the RNA concentration high without precipitation or evaporation.


title: Hg2-3

description: Mercuric chloride causes acute renal failure.  The 2h timepoint precedes leukocyte infiltration.

source_name: Mercuric chloride 2h #3


title: VD-2

description: Volume depletion is used here as a control for acute renal failure.  VD is expected to be similar to normal.

source_name: Volume Depletion #2


title: A364a_S_phase_LiUP1_202_RME7-21_wtrerep_135mN1_35

data_processing: Data were filtered in GenePix to flag as bad features that had (1) obvious defects, (2) saturated pixels, (3) regression r^2 values less than 0.5 or (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background.  BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive.  Raw Cy5/Cy3 median of ratios values were normalized such that the average ratio was equal to the DNA content of the replicating cells as determined by flow cytometry.  The DNA content was 1.35C.

source_name: S phase DNA A364a

tag: YJL5834 135 minutes after release from G1 (alpha factor) into 0.1M hydroxyurea

source_name: G1 phase DNA A364a

tag: YJL5834 arrested in G1 (alpha factor)


title: N-1

description: Normal

source_name: Normal #1

tag: Strain:Sprague Dawley

tag: Gender


title: VD-1D

description:
Volume depletion is used here as a control for acute renal failure. VD is expected to be similar to normal.
RNA from the VD#1 rat was processed and hybridized to a separate array for a non-biological duplicate

source_name: Volume Depletion #1, duplicate

tag: Age

tag: Tissue


title: IR2-1

description: Ischemia/Repefusion causes acute renal failure.  The 2h timepoint precedes leukocyte infiltration.

source_name: Ischemia/Reperfusion 2h #1


title: TMD sample from patient with Down Syndrome_DSTMD148

status: Public on Mar 16 2006

city: Zurich

first: Jean-Pierre

last: Bourquin

address: Steinwiesstrasse 75

department: Pediatric Oncology

country: Switzerland

institute: University Children's Hospital Zurich

description: Transient myeloproliferative disease, Down Syndrome

source_name: bone marrow or peripheral blood

label_protocol: 2-10 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: mononuclear cells after Ficol gradient, RNA extract with TRIZOL and promega SV column

tag: diagnostic sample


title: IR2M-3

description: Ischemia/Repefusion causes acute renal failure. The 2h timepoint precedes leukocyte infiltration.  Alpha melanocyte stimulating hormone has been shown to inhibit I/R-induced acute renal failure.

source_name: Ischemia/Reperfusion + alphaMSH 2h #3


title: TMD sample from patient with Down Syndrome_DSTMD017


title: A364a_S_phase_LiUP1_057_RME7-22_wt_rep_135minN1_35


title: A364a_S_phase_LiUP1_062_RME7-26_wtrerep_135minN1_35


title: OMC_S_phase_LiUP1_127_RME6-31_G1_vs_HU_OMCrep_300N1_40


title: A364a_S_phase_LiUP1_066_RME7-27_wtrerep_135minN1_35


title: TMD sample from patient with Down Syndrome_DSTMD058


title: TMD sample from patient with Down Syndrome_DSTMD052


title: S288C_S_phase_LiUP1_200_RME7-21_wtS288c_120mN1_40

description: Data from Figure 1B of MBoC paper (citation coming soon)

source_name: S phase DNA S288c

tag: YJL5038 120 minutes after release from G1 (alpha factor) into 0.1M hydroxyurea

source_name: G1 phase DNA S288c

tag: YJL5038 arrested in G1 (alpha factor)


title: TMD sample from patient with Down Syndrome_DSTMD012


title: AMKL sample, Down-Syndrome_DSAMKL133

description: AMKL sample from patient with Down Syndrome


title: S288C_S_phase_LiUP1_059_RME7-24_wtS288c_120minN1_40


title: TMD sample from patient with Down Syndrome_DSTMD053


title: TMD sample from patient with Down Syndrome_DSTMD013


title: S288C_S_phase_LiUP1_86_RME7-16_wt-S288c_0_1M_HU_2hrN1_40


title: AMKL sample, Down-Syndrome_DSAMKL130


title: TMD sample from patient with Down Syndrome_DSTMD014


title: AMKL sample, Down-Syndrome_DSAMKL132


title: S288C_S_phase_LiUP1_058_RME7-24_wt_S288c_0_1M_HU_2hrN1_40


title: AMKL sample, Down-Syndrome_DSAMKL126


title: AMKL sample, Down-Syndrome_DSAMKL121


title: AMKL sample, Down-Syndrome_DSAMKL127


title: AMKL sample, Down-Syndrome_DSAMKL128


title: AMKL sample, Down-Syndrome_DSAMKL129


title: AMKL sample, Down-Syndrome_DSAMKL122


title: AMKL sample, Down-Syndrome_DSAMKL125


title: AMKL sample, Down-Syndrome_DSAMKL070


title: AMKL sample, Down-Syndrome_DSAMKL120


title: AMKL sample, Down-Syndrome_DSAMKL068


title: AMKL sample, Down-Syndrome_DSAMKL030


title: AMKL sample, Down-Syndrome_DSAMKL020


title: AMKL sample, Down-Syndrome_DSAMKL018


title: AMKL sample, Down-Syndrome_DSAMKL019


title: AML patient sample_AML008

description: AML diagnostic sample


title: AMKL sample, Down-Syndrome_DSAMKL016


title: AML patient sample_AML007

description: AML diagnostic sample


title: AMKL sample, Down-Syndrome_DSAMKL015


title: AML patient sample_AML006

description: AML diagnostic sample


title: AMKL sample, Down-Syndrome_DSAMKL011


title: AML patient sample_AML005

description: AML diagnostic sample


title: AMKL patient sample_AMKL097

description: AMKL diagnostic sample


title: AMKL sample, Down-Syndrome_DSAMKL124


title: AML patient sample_AML003

description: AML diagnostic sample


title: AML patient sample_AML009

description: AML diagnostic sample


title: AML patient sample_AML004

description: AML diagnostic sample


title: AML patient sample_AML001

description: AML diagnostic sample


title: AMKL patient sample_AMKL082

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL094

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL086

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL084

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL069

description: AMKL diagnostic sample


title: DS-AMKL patient sample_DS-AMKL057

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL041

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL049

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL047

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL096

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL083

description: AMKL diagnostic sample


title: DS-AML patient sample_DS-AML063

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL044

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL072

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL038

description: AMKL diagnostic sample


title: DS-AMKL patient sample_DS-AMKL070

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL036

description: AMKL diagnostic sample


title: DIV14 cortical neuron, KCl 2

city: Seoul

first: Hyun

last: Kim

country: South Korea

institute: College of Medicine, Korea university

description: Gene expression data from na?ve DIV 14 cortical neuron i.e. non activated state

hyb_protocol: Following fragmentation, MES buffer (2-[N-morpholino]ethansulfonic acid) containing 0.5mg biotinylated cRNA per 1ml actylated bovine serum albumin  were hybridized for 16 hr at 45C onto RN U34 Genechip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Genechip Operating Software version 1.3 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Rattus norvegicus embryonic day (E)17 cortex

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: cultured for 14days in Neurobasal media with B27 supplement at 37oC, 95% air, 5% CO2

extract_protocol: Total RNA was extracted using Qiagen RNA extraction kit according to the manufacturer's instructions.

treatment_protocol: Rat cortical neurons prepared on E17, cultured for 14 days were treated with 25mM KCl for 4hrs.

tag: age

value: days of in vitro culture(DIV)14


title: AMKL patient sample_AMKL085

description: AMKL diagnostic sample


title: DS-AML patient sample_DS-AML060

description: AMKL diagnostic sample


title: AML patient sample_AML002

description: AML diagnostic sample


title: DIV14 cortical neuron, control 2

treatment_protocol: Rat cortical neurons prepared on E17, cultured for 14 days were treated with PBS for 4hrs.


title: DIV14 cortical neuron, KCl 1


title: AMKL patient sample_AMKL029

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL054

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL048

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL042

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL074

description: AMKL diagnostic sample


title: DIV14 cortical neuron, control 1


title: HSVMC_HighK+_rep3

city: Burlington

first: Anjanette

middle: D

last: Watson

state: VT

address: 120A Marsh Life Science

department: Bioinformatics Core

institute: University of Vermont

description: each of three experiments cell cultures were split three ways; one of the resulting samples was left untreated (C), another was treated with thapsigargin (TG), and the third was treated with elevated K+ (K)

scan_protocol: The probe arrays were scanned (Hewlett-Packard GeneArray Scanner, Agilent Technologies, Inc.) to quantify the fluorescence intensity associated with each oligonucleotide probe.

label: biotin-labeled

source_name: cerebral artery

label_protocol: Double-stranded cDNA was then synthesized followed by an in vitro transcription reaction and fragmentation reaction to produce biotin-labeled cRNA fragments that were hybridized to the probe array at 45°C for 16 hr

growth_protocol: hcVSMCs and rat VSMCs (passages 2-4) were grown to approximately 60% confluence and serum starved in DMEM containing 0.1% FBS 24-48 hr prior to treatment

extract_protocol: Total RNA was extracted from treated hc VSMCs using TriZol reagent and chloroform.  RNA was precipitated using isoproponol and glycoblue, washed with 75% ethanol, dissolved in RNAse free water and quantified using the NanoDrop® spectrophotometer.

treatment_protocol: Early passage hcVSMCs (passage 2-4) were obtained from human cerebral artery explants. Briefly, 2 mm slices of human pial artery (IRB# CHRMS 01-195; informed consent) were applied to scored 60 mm culture dishes, cultured in SMGM2 media (Cambrex Bio Science, Hopkinton, MA), and passaged with trypsin/EDTA. For hypoxia exposure, cells were incubated at 2% O2 by N2 injection into a humidified CO2 incubator (Forma, Marietta, OH). NOC-18, Cu/Zn superoxide dismutase (SOD), catalase, xanthine, and xanthine oxidase were obtained from Calbiochem (San Diego, CA). S-nitroso-L-glutathione (GSNO) was obtained from Alexis

value: 45 years

value: human cerebral artery


title: AMKL patient sample_AMKL037

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL067

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL031

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL024

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL073

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL046

description: AMKL diagnostic sample


title: dy/dy dystrophic diaphragm 4, 8 week

city: Cleveland

first: Erik

last: van Lunteren

address: 10701 East Boulevard

department: Pulmonary 111J(W)

institute: Cleveland VA Medical Center

description: Standard Affymetrix

data_processing: Affymetrix MAS 5.0 software

label: Standard Affymetrix

source_name: dy/dy mouse

tag: 8 week old dy/dy dystrophic mouse diaphragm


title: dy/dy dystrophic diaphragm 3, 8 week

description: Standard Affymetrix

source_name: dy/dy mouse, 8 week


title: HVSMC_ Thapsigargin_treated_rep3

hyb_protocol: biotin-labeled cRNA fragments that were hybridized to the probe array at 45°C for 16 hr

source_name: human cerebral artery


title: AMKL patient sample_AMKL066

description: AMKL diagnostic sample

data_processing: Affymetrix Microarray Suite version 5.0


title: dy/dy dystrophic diaphragm 2, 8 week

description: Standard Affymetrix


title: HeLa normoxia batch 3

first: Sarah

last: Mense

address: 722 West 168th Street

department: Environmental Health Sciences

institute: Columbia University

description: astrocytes from second trimester (14-19 weeks) human fetal brains

source_name: HeLa

tag: Human cervical cancer cells


title: AMKL patient sample_AMKL032

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL045

description: AMKL diagnostic sample


title: HVSMC_ Thapsigargin_treated_rep1


title: HeLa normoxia batch 1


title: AMKL patient sample_AMKL050

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL039

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL033

description: AMKL diagnostic sample


title: HSVMC_HighK+_rep1


title: AMKL patient sample_AMKL026

description: AMKL diagnostic sample


title: HeLa normoxia batch 2


title: AMKL patient sample_AMKL040

description: AMKL diagnostic sample


title: HeLa hypoxia batch 2


title: AMKL patient sample_AMKL035

description: AMKL diagnostic sample


title: AMKL patient sample_AMKL028

description: AMKL diagnostic sample


title: Normal diaphragm 3, 8 week

description: Standard Affymetrix

source_name: Control mouse for dy/dy, 8 week

tag: 8 week old control mouse diaphragm


title: astrocytes normoxia batch 2

source_name: astrocyte

tag: astrocytes from second trimester human fetal brains


title: dy/dy dystrophic diaphragm 1, 8 week

description: Standard Affymetrix


title: AMKL patient sample_AMKL025

description: AMKL diagnostic sample


title: astrocytes hypoxia batch 2


title: HVSMC_Control_rep2


title: Normal diaphragm 1, 8 week

description: Standard Affymetrix