title: HOB replicate 1

description: gene expression data from HOB bioreplicate 1

hyb_protocol: Labeling, hybridization and scanning were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 4 (P/N 701880 Rev 4). (http://www.affymetrix.com/support/technical/byproduct.affx?product=hugene-1_0-st-v1).

data_processing: Data from RNA expression array experiments in the form of .cel files (GCOS 1.3 software) were imported into and analysed using the Partek Genomic Suite Software (PGS). The expression array .cel files for HOB, U2OS, and MG63 (2 arrays each) were imported using PGS Gene Expression Workflow tool (subject to RMA normalization and log2 transformation). The significantly over- and under-expressed genes in U2OS and in MG63 cell lines compared to HOB were detected using 1-way ANOVA tool at p<0.01 and +/- 2-fold enrichment. Significantly over- and under-expressed regions were annotated to the corresponding genes present on the Affymetrix Gene 1.0 Array using the HuGene-1_0-st-v1.na24.hg18.transcript.csv file.

label: TdT labeling kit

source_name: normal human osteoblasts

growth_protocol: The human OS cell lines U2OS (ATCC # HTB-96) and MG63 (ATCC # CRL-1427) were purchased from American Type Culture Collection ATCC (Rockville, MD) and maintained in alpha-Minimum Essential Medium (alpha-MEM) supplemented with 10% heat inactivated Fetal Bovine Serum and 2 mM L-Glutamine. Normal human osteoblasts (HOB) are primary osteoblasts from the hip bone of a normal male donor that were purchased from PromoCell (Heidelberg, Germany, Catalogue # C-12760) and maintained in medium provided by the manufacturer and used at culture passage 3. Three days after plating (~80% confluent), cells where harvested for DNA or RNA extractions.

extract_protocol: Total RNA from U2OS, MG63 cells and HOB was extracted using the TRIzol reagent method. Cells were washed 3 times by Phosphate Buffer Saline (PBS) and lysed in the culture vessel using TRizol (Invitrogen, Osaka, Japan). 1 ml of TRIzol was used for every 100 mm culture plates an RNase free environment. Chloroform was then added (200 µl for each 1 ml TRIzol) and the samples were centrifuged at high speed for 15 minutes at 4C. The aqueous layer was then transferred into a new tube and RNA was precipitated with iso-propanol followed by one wash using 70% ethanol. The RNA precipitate was then dissolved in 10-15 µl of RNAse free water

treatment_protocol: Cells were harvested with Tripsin (Invitrogen) as per manifacturers instructions

tag: Normal Human Osteoblast Cells from healthy male donor (Heidelberg, Germany, Catalogue # C-12760)


title: 323 ADH

status: Public on Sep 08 2009

type: RNA

city: Boston

first: Lyndsey

middle: A.

last: Emery

state: MA

address: 650 Albany Street - EBRC 4th Floor

department: Medicine - Hematology/Oncology

country: USA

institute: Boston University Medical Center

description: Gene expression data from case 323 ADH

hyb_protocol: 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)

scan_protocol: The stained arrays were scanned using a G2500 Scanner (Agilent)

data_processing: Images from the scanned chips were quantified and scaled using Affymetrix Microarray Suite 5.0 (Affymetrix), and the unnormalized data were then rescaled to a target of 100 to remove bias.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: atypical ductal hyperplasia epithelium

label_protocol:
To convert the RNA to cDNA, the purified total RNA was linearly amplified for two rounds using the MessageAMP aRNA Kit (Ambion, Austin, TX), in which the first round is based on an oligo-dT primer and T7 RNA polymerase.
For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).

extract_protocol: Following the manufacturer’s protocol, total RNA was extracted and purified using the Picopure RNA Isolation Kit (Arcturus Engineering).

treatment_protocol: Samples were microdissected from lightly H&E stained serial frozen tissue sections.

tag: tissue

value: laser capture microdissected human breast

tag: cell type

value: epithelial

tag: disease state

value: atypical ductal hyperplasia

tag: age range

value: 48-92 years old


title: norway 98_BC706A-BE

type: genomic

city: Stanford

first: Jonathan

last: Pollack

state: CA

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51810.gif

hyb_protocol: not provided

scan_protocol: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm), default computed normalization procedure, see SMD website

molecule: genomic DNA

source_name: Human female genomic DNA

label_protocol: not provided

extract_protocol: not provided

tag: Human female genomic DNA

source_name: Breast tumor genomic DNA

tag: Breast tumor genomic DNA


title: norway 26_BC123B-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51786.gif


title: ULLG_T-081

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39880.gif

source_name: NB

tag: NB


title: norway FU30_FU 30-AF

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38965.gif

source_name: Normal female genomic DNA

tag: Normal female genomic DNA

source_name: FUMI30 genomic DNA

tag: FUMI30 genomic DNA


title: ULLG_T-202

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39887.gif


title: 323 HN

description: Gene expression data from case 323 histologically normal breast epithelium

source_name: histologically normal breast epithelium

value: histologically normal


title: norway FU04_FU 04-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38942.gif

source_name: FUMI04 genomic DNA

tag: FUMI04 genomic DNA


title: norway 96_BC704B-AF

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51809.gif


title: Exiqon synthetic miRNA sample A #2

type: other

city: Kgs. Lyngby

first: Hanni

last: Willenbrock

address: Kemikalievej, bygning 208

department: Center for Biological Sequence Analysis

country: Denmark

institute: DTU

description: hybridization of synthetic RNA corresponding to human miRNA

hyb_protocol: Exiqon standard protocol for miRNAs

scan_protocol: Agilent DNA microarray scanner

data_processing: Feature extraction image analysis

molecule: other

source_name: Sample A

label_protocol: Exiqon standard end labelling protocol for miRNAs

tag: sample

value: synthetic miRNA


title: 228 DCIS

description: Gene expression data from case 228 DCIS

source_name: ductal carcinoma in situ epithelium

value: ductal carcinoma in situ


title: ULLG_T-011

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35173.gif


title: 275 DCIS

description: Gene expression data from case 275 DCIS


title: 228 ADH

description: Gene expression data from case 228 ADH


title: 228 HN

description: Gene expression data from case 228 histologically normal breast epithelium


title: HOB replicate 2

city: Toronto

first: Bekim

last: Sadikovic

state: Ontario

address: 555 University Avenue

country: Canada

institute: The SickKids Hospital and Princess Margaret Hospital

description: gene expression data from HOB bioreplicate 2

scan_protocol: Labeling, hybridization and scanning were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 4 (P/N 701880 Rev 4). (http://www.affymetrix.com/support/technical/byproduct.affx?product=hugene-1_0-st-v1).


title: ULLG_T-003

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34866.gif


title: 323 DCIS

description: Gene expression data from case 323 DCIS


title: norway FU17_FU 17-AF

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38953.gif

source_name: FUMI17 genomic DNA

tag: FUMI17 genomic DNA


title: 275 ADH

description: Gene expression data from case 275 ADH


title: 275 SH

description: Gene expression data from case 275 SH

source_name: simple ductal hyperplasia epithelium

value: simple ductal hyperplasia


title: 405 SH

description: Gene expression data from case 405 SH


title: 405 ADH

description: Gene expression data from case 405 ADH


title: 405 DCIS

description: Gene expression data from case 405 DCIS


title: 275 HN

description: Gene expression data from case 275 histologically normal breast epithelium


title: ULLG_T-007

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39884.gif

source_name: CO

tag: CO


title: 405 HN

description: Gene expression data from case 405 histologically normal breast epithelium


title: 258 DCIS

description: Gene expression data from case 258 DCIS


title: 258 ADH

description: Gene expression data from case 258 ADH


title: 226 HN

description: Gene expression data from case 226 histologically normal breast epithelium


title: 258 HN

description: Gene expression data from case 258 histologically normal breast epithelium


title: 232 DCIS

description: Gene expression data from case 232 DCIS


title: 226 DCIS

description: Gene expression data from case 226 DCIS (rehyb)


title: 232 HN

description: Gene expression data from case 232 histologically normal breast epithelium


title: 232 ADH

description: Gene expression data from case 232 ADH


title: norway FU05_FU 05-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38943.gif

source_name: FUMI05 genomic DNA

tag: FUMI05 genomic DNA


title: 237 DCIS

description: Gene expression data from case 237 DCIS


title: total small RNAs from C. remanei

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

description: Small RNA sequence data.

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: adapter sequences (ctCAGCgaccttggctgtcactca and polyA) were trimmed and inserts mapped to the C. remanei genome (WUSTL assembly version 15.0.1).

label: not applicable

organism: Caenorhabditis remanei

source_name: mixed stage animals

label_protocol: not applicable

extract_protocol: Total RNA extracted using miRVana miRNA isolation kit (Ambion). Small RNA fraction was isolated using PAGE. The RNAs were poly(A)-tailed using poly(A) polymerase followed by ligation of a RNA adapter to the 5'-phosphate of the small RNAs. First-strand cDNA synthesis was performed using an oligo(dT)-linker primer and M-MLV-RNase H- reverse transcriptase. The cDNA was PCR amplified and the 125 - 140 bp fraction of the cDNA pool was obtained by fractionation of the cDNA on a preparative 6% polyacrylamide gel. The eluted cDNA was purified using the Macherey & Nagel NucleoSpin Extract II kit and sequenced on 454 GS FLX system.

tag: strain

tag: developmental stage

value: mixed stages


title: total small RNAs from C. briggsae

description: Small RNA sequence data.

data_processing: adapter sequences (ctCACAgaccttggctgtcactca and polyA) were trimmed and inserts mapped to the C. briggsae genome (assembly version cb3).

organism: Caenorhabditis briggsae


title: 237 ADH

description: Gene expression data from case 237 ADH


title: 237 HN

description: Gene expression data from case 237 histologically normal breast epithelium


title: 380 DCIS

description: Gene expression data from case 380 DCIS


title: total small RNAs from C. elegans

description: Small RNA sequence data.

data_processing: adapter sequences (ctATCGgaccttggctgtcactca and polyA) were trimmed and inserts mapped to the C. elegans genome (assembly version WS190).

organism: Caenorhabditis elegans


title: ULLG_T-72

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40802.gif


title: norway FU10_FU 10-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38948.gif

source_name: FUMI10 genomic DNA

tag: FUMI10 genomic DNA


title: 380 SH

description: Gene expression data from case 380 SH

tag: tissue


title: 380 ADH

description: Gene expression data from case 380 ADH

tag: cell type


title: norway 06FU_FU 06-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38944.gif

source_name: FUMI06 genomic DNA

tag: FUMI06 genomic DNA


title: norway FU27_FU 27-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38963.gif

source_name: FUMI27 genomic DNA

tag: FUMI27 genomic DNA


title: ULLG_T-168

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39886.gif


title: 380 HN

description: Gene expression data from case 380 histologically normal breast epithelium

tag: disease state

tag: age range


title: norway FU08_FU 08-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38946.gif

source_name: FUMI08 genomic DNA

tag: FUMI08 genomic DNA


title: 274 DCIS

description: Gene expression data from case 274 DCIS


title: norway FU41_FU 41-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38975.gif

tag: Normal female genomic DNA

source_name: FUMI41 genomic DNA

tag: FUMI41 genomic DNA


title: norway FU07_FU 07-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38945.gif

source_name: FUMI07 genomic DNA

tag: FUMI07 genomic DNA


title: norway FU01_FU 01-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38940.gif

source_name: Normal female genomic DNA

source_name: FUMI01 genomic DNA

tag: FUMI01 genomic DNA


title: 274 ADH

description: Gene expression data from case 274 ADH

source_name: atypical ductal hyperplasia epithelium


title: norway FU15_FU 15-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38951.gif

source_name: FUMI15 genomic DNA

tag: FUMI15 genomic DNA


title: 274 HN

description: Gene expression data from case 274 histologically normal breast epithelium

source_name: histologically normal breast epithelium


title: ULLG_T-097

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35895.gif

source_name: NB

tag: NB


title: norway FU20_FU 20-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38957.gif

source_name: FUMI20 genomic DNA

tag: FUMI20 genomic DNA


title: norway FU24_FU 24-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38960.gif

source_name: FUMI24 genomic DNA

tag: FUMI24 genomic DNA


title: 248 DCIS

description: Gene expression data from case 248 DCIS

source_name: ductal carcinoma in situ epithelium


title: norway FU43_FU 43-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38970.gif

source_name: FUMI43 genomic DNA

tag: FUMI43 genomic DNA


title: ULLG_T-006

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34867.gif


title: 248 ADH

description: Gene expression data from case 248 ADH


title: ULLG_T-022

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41176.gif


title: 444 DCIS

description: Gene expression data from case 444 DCIS


title: OS2336 replicate 2

description: The Agilent Human Genome CGH microarray 244A (Agilent Technologies, Inc., Palo Alto, USA) were used for the array-CGH experiments. Three μg of Human Genomic DNA from multiple anonymous male donors (Promega Corporation, Madison, USA) and 3 μg of test genomic DNA sample were digested with AluI (5 units) and RsaI (5 units) (Promega) for a minimum of 2 hours at 37C. Digestion quality was assessed by the DNA 1000 LabChip Kit (Agilent 2100 Bioanalyzer, Agilent Technologies). Labelling reactions were performed using the Agilent Genomic DNA Labeling Kit PLUS (Agilent Technologies, Inc., Palo Alto, USA) according to the manufacturer’s directions. Briefly, the reference and sample DNA were labelled with 1.5 - 3 mM Cy3-dUTP or Cy5-dUTP (Agilent Technologies, Inc., Palo Alto, USA), and purified using a Centricon YM-30 filter (Millipore, Billerica, USA). Probe mixture of Cy3-labelled sample DNA, Cy5-labelled reference DNA, 50 μl of 1.0mg/ ml of human Cot-1 DNA (Invitrogen, USA), 52 μl of Agilent 10X Blocking Agent and 260 μl of Agilent 2X Hybridization Buffer (Agilent Technologies, Inc.) was denatured at 100C for 1 minute 30 seconds and incubated at 37C for 30 minutes. The probe was applied to the array using an Agilent microarray hybridization chamber, and hybridized for 40 hours at 65C in a rotating oven (Robbins Scientific, Sunnyvale, USA) at 20 rpm. Arrays were washed according to the manufacturer’s recommendations; air dried, and scanned using an Agilent 2565AA DNA microarray scanner (Agilent Technologies, Inc), and processed using Agilent’s Feature Extraction software. Dye-swapped duplicate experiments were carried out.

hyb_protocol: Probe mixture of Cy3-labelled sample DNA, Cy5-labelled reference DNA, 50 μl of 1.0mg/ ml of human Cot-1 DNA (Invitrogen, USA), 52 μl of Agilent 10X Blocking Agent and 260 μl of Agilent 2X Hybridization Buffer (Agilent Technologies, Inc.) was denatured at 100C for 1 minute 30 seconds and incubated at 37C for 30 minutes. The probe was applied to the array using an Agilent microarray hybridization chamber, and hybridized for 40 hours at 65C in a rotating oven (Robbins Scientific, Sunnyvale, USA) at 20 rpm. Arrays were washed according to the manufacturer’s recommendation and air dried.

scan_protocol: Arrays were scanned using an Agilent 2565AA DNA microarray scanner (Agilent Technologies, Inc).

data_processing: Data were processed using Agilent’s Feature Extraction software protocol for array-CGH data. To analyze genomic imbalance tumour samples (2 arrays each) the  processed R signal and processed G signal columns from the Agilent  Feature Extraction-generated a-CGH .txt files were imported into PGS.  The tumour-specific signal across all probes was normalized as a ratio  to baseline using Normalise to Baseline Tool in PGS, where baseline  data corresponded to the normal human DNA. The data was then log2  transformed using the PGS Normalization and Scaling Tool. In order to  detect regions of genomic gain and loss we applied the Genomic  Segmentation tool with segmentation parameters set at: min. probes:  10, p-value threshold: 0.01, and signal to noise: 0.1. Region report  was set at values bellow -.5/+.5 (log2) and p-value threshold of 0.05  for 2/2 (replicate) arrays in individual analysis or at 40% cut-off in  cumulative analysis (i.e. 4/10 tumour samples). Regions of significant  gain or loss were annotated to the corresponding genes present on the  Affymetrix Gene 1.0 Array using the  HuGene-1_0-st-v1.na24.hg18.transcript.csv file. Visualizations and  VENN analysis were performed in PGS.

source_name: Normal Human Genomic DNA

label_protocol: Labelling reactions were performed using the Agilent Genomic DNA Labeling Kit PLUS (Agilent Technologies, Inc., Palo Alto, USA) according to the manufacturer’s directions. Briefly, DNA was labelled with 1.5 - 3 mM Cy5-dUTP (Agilent Technologies, Inc., Palo Alto, USA), and purified using a Centricon YM-30 filter (Millipore, Billerica, USA).

extract_protocol: DNA was extracted after harvesting the cells by Trypsin (Invitrogen) followed by phenol-chloroform extraction and subsequent precipitation in 100% ethanol. DNA precipitate was washed with 70% ethanol then eluted in DNAse free water.

source_name: Osteosarcoma tumor sample 2336

label_protocol: Labelling reactions were performed using the Agilent Genomic DNA Labeling Kit PLUS (Agilent Technologies, Inc., Palo Alto, USA) according to the manufacturer’s directions. Briefly, DNA was labelled with 1.5 - 3 mM Cy3-dUTP (Agilent Technologies, Inc., Palo Alto, USA), and purified using a Centricon YM-30 filter (Millipore, Billerica, USA).

extract_protocol: Comercial DNA extracted as per manifacturers instructions - Human Genomic DNA from multiple anonymous male donors (Promega Corporation, Madison, USA)

tag: Paediatric Human Osteosarcoma Tissue Sample


title: OS2960 replicate 1

source_name: Osteosarcoma tumor sample 2960

tag: Human Genomic DNA from multiple anonymous male donors (Promega Corporation, Madison, USA)


title: OS2960 replicate 2


title: norway FU22_FU 22-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38958.gif

source_name: FUMI22 genomic DNA

tag: FUMI22 genomic DNA


title: 248 HN

description: Gene expression data from case 248 histologically normal breast epithelium

tag: tissue

tag: cell type


title: ULLG_T-014

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41174.gif


title: 444 SH

description: Gene expression data from case 444 SH

source_name: simple ductal hyperplasia epithelium

tag: disease state


title: 444 ADH

description: Gene expression data from case 444 ADH

tag: age range


title: OS182 replicate 2

source_name: Osteosarcoma tumor sample 182


title: OS183 replicate 1

source_name: Osteosarcoma tumor sample 183


title: ULLG_T-196

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37001.gif


title: ULLG_T-169

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39883.gif


title: OS2336 replicate 1


title: OS182 replicate 1


title: norway FU14_FU 14-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38974.gif

source_name: Normal female genomic DNA

source_name: FUMI14 genomic DNA

tag: FUMI14 genomic DNA


title: norway FU18_FU 18-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38955.gif

tag: Normal female genomic DNA

source_name: FUMI18 genomic DNA

tag: FUMI18 genomic DNA


title: 444 HN

description: Gene expression data from case 444 histologically normal breast epithelium


title: ULLG_T-122

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39885.gif


title: 13530281_23_34

city: Copenhagen

first: Kerstin

last: Skovgaard

address: Bülowsvej 27

department: Immunology and Parasitology

institute: National Veterinary Institute

hyb_protocol: 1. cDNA from two samples (2 x 25ul), 1ul salmon sperm DNA (10ug/ul) and 51ul 2xFormamide-Based Hybridization Buffer (Genisphere) were mixed. 70ul of this solution were applied under a 25x60mm LifterSlip (Erie Scientific). 2. Slides were incubated over-night in a Corning hybridization chamber at 44 degree Celcius in water bath 3. Slides were washed according to manufactures protecol with Wash buffer 1 pre-heated to 44 degree celcius, slides were dryed by centrifugation 4. 3DNA hybridization mix was prepared: 2.5ul of each capture reagent, Oyster 550 and Oyster 650 (3DNA Array900, Genisphere), 41ul SDS-based hybridization buffer (Genisphere), 35ul milliQ water and 1ul salmon sperm DNA (10ug/ul) were mixed. 5. 70ul 3DNA hybridization mix was applied to each slide and incubated in the dark for 4 hours at 62 degree in a water bath 6. Slides were washed according to manufactures protecol with Wash buffer 1 pre-heated to 64 degree celcius, slides were dryed by centrifugation

scan_protocol: Slides were scanned on a CCD-based ArrayWoRxe auto (Applied Precision)

data_processing:
1. Image processing and spot finding were performed using GenePixPro 6.0 (Molecular Devices Corp.)
2. Low intensity spots were flagged if they did not have at least 45% of their feature pixels more than 2 SD above background. Incorrectly placed spots were flagged manually.
3. Ratio based normalization using default options was performed in Acuity 4.0 (Molecular Devices Corp.)
4. Normalized background substracted medians for all spots were exported to Excel and used to calculate mean ln expression values for each gene in each pig.
5. Mean overall ln expression values was calculated for each gene across the 5 control pigs.
6. These values was respectively subtracted from the mean expression value for each gene in each of the infected pigs, and, there was finally calculated an overall mean ln difference across the 10 infected pigs as opposed to the control pigs.

label: Oyster 550

organism: Sus scrofa

source_name: Liver, Control

label_protocol: 7ug of RNA for each sample was labeled using Genisphere 3DNA Array900 labeling kit according to manufactures protecol for large-scale cDNA synthesis

growth_protocol:
15 pigs were used in this study, these were 8-10 weeks old castrates of the race Danish Landrace/Yorkshire/Duroc, from a specific pathogen free (SPF) herd, free of Actinobacillus pleuropneumoniae.
All animal procedures were approved by the Danish Animal Experiments Inspectorate.

extract_protocol: RNA was extracted using Qiagen RNeasy midi kit according to manufactures protecol with additional DNase treatment (RNase-free DNase, Qiagen) according to manufactures protecol. Quantity of the extracted total RNA was measured using Nanodrop ND-1000 and quality was measured using Agilent 2100 Bioanalyzer

treatment_protocol: 10 Pigs were inoculated with a total of 1ml McFarland suspension mixed 1:1 with Brain Heart infusion Broth + 0.5% NAD, containing approxemately 0.7 x 10E7 in both nostrils during inhalation, 5 pigs were not inoculated and used as controls, 14-18h post inoculation pigs were sacrificed, tissue samples of approximately 500mg were taken and snap frosen in liquid nitrogen and stored at -80 degrees until RNA extraction

tag: Pig no. 23, control, no. 4 of 5 replicates, not inoculated.

label: Oyster 650

source_name: Liver, Infected

tag: Pig no. 34, inoculated, no. 9 of 10 replicates, infected in 14-18h with Actinobacillus pleuropneumonia 5b (strain L20).


title: 13530280_36_24

tag: Pig no. 36, inoculated, no. 10 of 10 replicates, infected in 14-18h with Actinobacillus pleuropneumonia 5b (strain L20).

tag: Pig no. 24, control, no. 5 of 5 replicates, not inoculated.


title: OS180 replicate 1

source_name: Osteosarcoma tumor sample 180


title: 13536745_33_22

tag: Pig no. 33, inoculated, no. 8 of 10 replicates, infected in 14-18h with Actinobacillus pleuropneumonia 5b (strain L20).

tag: Pig no. 22, control, no. 3 of 5 replicates, not inoculated.


title: OS180 replicate 2


title: ULLG-T_088

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41147.gif

source_name: NB

tag: NB


title: OS179 replicate 1

source_name: Osteosarcoma tumor sample 179

tag: Paediatric Human Osteosarcoma Tissue Sample


title: norway FU25_FU 25-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38961.gif

source_name: FUMI25 genomic DNA

tag: FUMI25 genomic DNA


title: 13536749_21_32

tag: Pig no. 21, control, no. 2 of 5 replicates, not inoculated.

tag: Pig no. 32, inoculated, no. 7 of 10 replicates, infected in 14-18h with Actinobacillus pleuropneumonia 5b (strain L20).


title: 13530278_31_20

tag: Pig no. 31, inoculated, no. 6 of 10 replicates, infected in 14-18h with Actinobacillus pleuropneumonia 5b (strain L20).

tag: Pig no. 20, control, no. 1 of 5 replicates, not inoculated.


title: OS179 replicate 2

tag: Human Genomic DNA from multiple anonymous male donors (Promega Corporation, Madison, USA)


title: norway FU19_FU 19-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38956.gif

source_name: FUMI19 genomic DNA

tag: FUMI19 genomic DNA


title: 13536744_24_30

tag: Pig no. 30, inoculated, no. 5 of 10 replicates, infected in 14-18h with Actinobacillus pleuropneumonia 5b (strain L20).


title: 13536741_28_23

tag: Pig no. 28, inoculated, no. 4 of 10 replicates, infected in 14-18h with Actinobacillus pleuropneumonia 5b (strain L20).


title: norway FU11_FU 11-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38949.gif

tag: Normal female genomic DNA

source_name: FUMI11 genomic DNA

tag: FUMI11 genomic DNA


title: ULLG_T-201

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37011.gif


title: 13536770_26_21

tag: Pig no. 26, inoculated, no. 2 of 10 replicates, infected in 14-18h with Actinobacillus pleuropneumonia 5b (strain L20).


title: MIA.PACA2 AB1010

status: Public on Sep 05 2009

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

country: France

institute: Institut Paoli-Calmettes

description: Expression analysis of human pancreatic tumor cells treated with masitinib only.

hyb_protocol: Affymetrix standard protocols.

scan_protocol: Affymetrix standard protocols.

data_processing: RMA. Controls were removed, like all genes with low and poorly measured expression as defined by an expression value inferior to 100 units in all samples and an SD less than 0.1 on log2-transformed data. Thus, 8249 probe sets were selected and analysed.

source_name: human pancreatic tumour cell line, masitinib

label_protocol: Affymetrix standard protocols.

growth_protocol: Cells were maintained in RPMI (BxPC-3, Capan-2) or DMEM (MiaPaca2, Panc1) medium containing glutamax-1 (Lonza), supplemented with 100 U/ml penicillin/100 µg/ml streptomycin, and 10% foetal calf serum (AbCys, Lot S02823S1800).

extract_protocol: Qiagen RNeasy mini kits. On column, DNase digestion was used.

treatment_protocol: Masitinib (AB Science, Paris, France) was prepared from powder as a 10 or 20 mM stock solution in dimethyl sulfoxide and stored at −80°C. Gemcitabine (Gemzar, Lilly France) was obtained as a powder and dissolved in sterile 0.9% NaCl solution and stored as aliquots at -80°C. Fresh dilutions were prepared for each experiment.

tag: cell line

tag: cell type

value: pancreatic tumor cells

tag: treatment

value: masitinib


title: MIA.PACA2 GEM

description: Expression analysis of human pancreatic tumor cells treated with gemcitabine only.

source_name: human pancreatic tumour cell line, gemcitabine

value: gemcitabine


title: MIA.PACA2 both

description: Expression analysis of human pancreatic tumor cells treated with both masitinib and gemcitabine.

source_name: human pancreatic tumour cell line, masitinib and gemcitabine

value: masitinib and gemcitabine


title: norway FU39_FU 39-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38968.gif

source_name: FUMI39 genomic DNA

tag: FUMI39 genomic DNA


title: MIA.PACA2

description: Expression analysis of human pancreatic tumor cells with no treatment.

source_name: human pancreatic tumour cell line, none


title: OS178 replicate 2

description: The Agilent Human Genome CGH microarray 244A (Agilent Technologies, Inc., Palo Alto, USA) were used for the array-CGH experiments. Three μg of Human Genomic DNA from multiple anonymous male donors (Promega Corporation, Madison, USA) and 3 μg of test genomic DNA sample were digested with AluI (5 units) and RsaI (5 units) (Promega) for a minimum of 2 hours at 37C. Digestion quality was assessed by the DNA 1000 LabChip Kit (Agilent 2100 Bioanalyzer, Agilent Technologies). Labelling reactions were performed using the Agilent Genomic DNA Labeling Kit PLUS (Agilent Technologies, Inc., Palo Alto, USA) according to the manufacturer’s directions. Briefly, the reference and sample DNA were labelled with 1.5 - 3 mM Cy3-dUTP or Cy5-dUTP (Agilent Technologies, Inc., Palo Alto, USA), and purified using a Centricon YM-30 filter (Millipore, Billerica, USA). Probe mixture of Cy3-labelled sample DNA, Cy5-labelled reference DNA, 50 μl of 1.0mg/ ml of human Cot-1 DNA (Invitrogen, USA), 52 μl of Agilent 10X Blocking Agent and 260 μl of Agilent 2X Hybridization Buffer (Agilent Technologies, Inc.) was denatured at 100C for 1 minute 30 seconds and incubated at 37C for 30 minutes. The probe was applied to the array using an Agilent microarray hybridization chamber, and hybridized for 40 hours at 65C in a rotating oven (Robbins Scientific, Sunnyvale, USA) at 20 rpm. Arrays were washed according to the manufacturer’s recommendations; air dried, and scanned using an Agilent 2565AA DNA microarray scanner (Agilent Technologies, Inc), and processed using Agilent’s Feature Extraction software. Dye-swapped duplicate experiments were carried out.

source_name: Normal Human Genomic DNA

source_name: Osteosarcoma tumor sample 178

tag: Paediatric Human Osteosarcoma Tissue Sample


title: 13536747_20_25

tag: Pig no. 25, inoculated, no. 1 of 10 replicates, infected in 14-18h with Actinobacillus pleuropneumonia 5b (strain L20).


title: ULLG_T-056

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35892.gif

tag: NB


title: norway FU26_FU 26-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38962.gif

source_name: Normal female genomic DNA

source_name: FUMI26 genomic DNA

tag: FUMI26 genomic DNA


title: S160

city: San Diego

first: Yipeng

last: Wang

institute: Vaccine Research Institute of San Diego

description: prostate

hyb_protocol: Following Affymetrix protocol.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner.

data_processing: The data were analyzed and normalized with RMA.

source_name: prostate, S160

label_protocol: 50 microgram (10 microgram for biopsy tissue) of total RNA samples of each cases were amplified and labeled with biotin using Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 (NuGen Inc.).

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

tag: patient id

tag: sample type (t/tumor; biopsy; ctrl/autopsy sample)

value: Ctrl

tag: percentage of tumor


title: ULLG_T-111

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35894.gif


title: S163

description: prostate

source_name: prostate, S163


title: S162

description: prostate

source_name: prostate, S162


title: S161

description: prostate

source_name: prostate, S161


title: norway FU35_FU 35-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38966.gif

source_name: FUMI35 genomic DNA

tag: FUMI35 genomic DNA


title: S159

description: prostate

source_name: prostate, S159


title: norway FU09_FU 09-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38947.gif

source_name: FUMI09 genomic DNA

tag: FUMI09 genomic DNA


title: S156

description: prostate

source_name: prostate, S156

value: Biopsy

tag: percentage of tumor:


title: OS87B replicate 1

source_name: Osteosarcoma tumor sample 87B

tag: Human Genomic DNA from multiple anonymous male donors (Promega Corporation, Madison, USA)


title: S157

description: prostate

source_name: prostate, S157


title: 13536771_22_27

source_name: Liver, Control

tag: Pig no. 22, control, no. 3 of 5 replicates, not inoculated.

source_name: Liver, Infected

tag: Pig no. 27, inoculated, no. 3 of 10 replicates, infected in 14-18h with Actinobacillus pleuropneumonia 5b (strain L20).


title: norway FU29_FU 29-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38964.gif

tag: Normal female genomic DNA

source_name: FUMI29 genomic DNA

tag: FUMI29 genomic DNA


title: ULLG_T-080

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40803.gif

source_name: NB


title: S151

description: prostate

source_name: prostate, S151


title: S155

description: prostate

source_name: prostate, S155


title: S154

description: prostate

source_name: prostate, S154


title: S152

description: prostate

source_name: prostate, S152


title: S153

description: prostate

source_name: prostate, S153


title: S149

description: prostate

source_name: prostate, S149


title: S150

description: prostate

source_name: prostate, S150


title: S146

description: prostate

source_name: prostate, S146


title: S164

description: prostate

source_name: prostate, S164


title: S148

description: prostate

source_name: prostate, S148


title: S138

description: prostate

source_name: prostate, S138


title: norway FU16_FU 16-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38952.gif

source_name: Normal female genomic DNA

source_name: FUMI16 genomic DNA

tag: FUMI16 genomic DNA


title: S147

description: prostate

source_name: prostate, S147


title: S145

description: prostate

source_name: prostate, S145


title: S142

description: prostate

source_name: prostate, S142

value: T


title: S140

description: prostate

source_name: prostate, S140


title: S143

description: prostate

source_name: prostate, S143


title: S129

description: prostate

source_name: prostate, S129


title: S131

description: prostate

source_name: prostate, S131


title: S139

description: prostate

source_name: prostate, S139


title: S141

description: prostate

source_name: prostate, S141


title: S144

description: prostate

source_name: prostate, S144


title: S137

description: prostate

source_name: prostate, S137


title: S132

description: prostate

source_name: prostate, S132


title: norway FU02_FU 02-BE

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38941.gif

source_name: FUMI02 genomic DNA

tag: FUMI02 genomic DNA


title: S130

description: prostate

source_name: prostate, S130


title: S125

description: prostate

source_name: prostate, S125


title: S158

description: prostate

source_name: prostate, S158


title: S124

description: prostate

source_name: prostate, S124


title: S122

description: prostate

source_name: prostate, S122


title: S127

description: prostate

source_name: prostate, S127


title: S120

description: prostate

source_name: prostate, S120


title: S117

description: prostate

source_name: prostate, S117


title: S116

description: prostate

source_name: prostate, S116


title: S119

description: prostate

source_name: prostate, S119


title: S112

description: prostate

source_name: prostate, S112


title: S109

description: prostate

source_name: prostate, S109


title: S100

description: prostate

source_name: prostate, S100


title: S115

description: prostate

source_name: prostate, S115


title: S121

description: prostate

source_name: prostate, S121


title: S118

description: prostate

source_name: prostate, S118


title: S105

description: prostate

source_name: prostate, S105


title: S114

description: prostate

source_name: prostate, S114


title: S113

description: prostate

source_name: prostate, S113


title: S107

description: prostate

source_name: prostate, S107


title: S111

description: prostate

source_name: prostate, S111


title: S102

description: prostate

source_name: prostate, S102


title: S110

description: prostate

source_name: prostate, S110


title: S104

description: prostate

source_name: prostate, S104


title: S108

description: prostate

source_name: prostate, S108


title: S103

description: prostate

source_name: prostate, S103


title: S106

description: prostate

source_name: prostate, S106


title: S101

description: prostate

source_name: prostate, S101


title: S128

description: prostate

source_name: prostate, S128


title: S098

description: prostate

source_name: prostate, S098


title: S092

description: prostate

source_name: prostate, S092


title: S099

description: prostate

source_name: prostate, S099


title: S094

description: prostate

source_name: prostate, S094


title: S084

description: prostate

source_name: prostate, S084


title: S095

description: prostate

source_name: prostate, S095


title: S123

description: prostate

source_name: prostate, S123


title: S087

description: prostate

source_name: prostate, S087


title: S091

description: prostate

source_name: prostate, S091


title: S096

description: prostate

source_name: prostate, S096


title: S085

description: prostate

source_name: prostate, S085


title: S080

description: prostate

source_name: prostate, S080


title: S077

description: prostate

source_name: prostate, S077


title: S086

description: prostate

source_name: prostate, S086


title: S081

description: prostate

source_name: prostate, S081


title: S083

description: prostate

source_name: prostate, S083


title: S088

description: prostate

source_name: prostate, S088


title: S078

description: prostate

source_name: prostate, S078


title: S075

description: prostate

source_name: prostate, S075


title: S082

description: prostate

source_name: prostate, S082


title: S073

description: prostate

source_name: prostate, S073


title: S126

description: prostate

source_name: prostate, S126


title: S093

description: prostate

source_name: prostate, S093


title: S074

description: prostate

source_name: prostate, S074


title: S070

description: prostate

source_name: prostate, S070


title: S072

description: prostate

source_name: prostate, S072


title: S066

description: prostate

source_name: prostate, S066


title: S069

description: prostate

source_name: prostate, S069


title: S068

description: prostate

source_name: prostate, S068


title: S071

description: prostate

source_name: prostate, S071


title: S065

description: prostate

source_name: prostate, S065


title: S060

description: prostate

source_name: prostate, S060


title: S055

description: prostate

source_name: prostate, S055


title: S062

description: prostate

source_name: prostate, S062


title: S052

description: prostate

source_name: prostate, S052


title: S054

description: prostate

source_name: prostate, S054


title: S051

description: prostate

source_name: prostate, S051


title: S059

description: prostate

source_name: prostate, S059


title: S058

description: prostate

source_name: prostate, S058


title: S064

description: prostate

source_name: prostate, S064


title: S061

description: prostate

source_name: prostate, S061


title: S056

description: prostate

source_name: prostate, S056


title: S057

description: prostate

source_name: prostate, S057


title: S067

description: prostate

source_name: prostate, S067


title: S053

description: prostate

source_name: prostate, S053


title: S050

description: prostate

source_name: prostate, S050


title: S049

description: prostate

source_name: prostate, S049


title: S048

description: prostate

source_name: prostate, S048


title: S063

description: prostate

source_name: prostate, S063


title: S042

description: prostate

source_name: prostate, S042


title: S097

description: prostate

source_name: prostate, S097


title: S046

description: prostate

source_name: prostate, S046


title: S047

description: prostate

source_name: prostate, S047


title: S044

description: prostate

source_name: prostate, S044


title: S040

description: prostate

source_name: prostate, S040


title: S036

description: prostate

source_name: prostate, S036


title: S039

description: prostate

source_name: prostate, S039


title: S043

description: prostate

source_name: prostate, S043


title: S038

description: prostate

source_name: prostate, S038


title: S041

description: prostate

source_name: prostate, S041


title: S035

description: prostate

source_name: prostate, S035


title: S031

description: prostate

source_name: prostate, S031


title: S033

description: prostate

source_name: prostate, S033


title: Duodenum control diet rep2

city: Tampere

first: Alejandra

last: Rodriguez-Martinez

address: Biokatu 6

department: Institute of Biomedical Technology

country: Finland

institute: University of Tampere

description: no additional information

hyb_protocol: Standard Illumina hybridization protocol (18h at 55 degrees) was used).

scan_protocol: Standard scan factor in Illumina BeadArray reader was used.

data_processing: Array data were normalized with Chipster version 1.1.1 using the quantile normalization method.

organism: Mus musculus

source_name: Mouse duodenum

label_protocol: Illumina TotalPrep RNA Amplification kit (#IL1791, Ambion) was used following the manufacturer's protocol. Input amount was 300ng total RNA and duration of labeling reaction incubation was 14 hrs.

extract_protocol: RNA was extracted with RNeasy RNA isolation kit including RNase-free Dnase treatment (Qiagen) according to the manufacturer's protocol. Concentration and purity were measured with Nanodrop.

tag: gender

value: male

tag: strain

tag: tissue

value: duodenum

tag: age

value: 16-18 weeks


title: S037

description: prostate

source_name: prostate, S037

tag: patient id


title: S034

description: prostate

source_name: prostate, S034

tag: sample type (t/tumor; biopsy; ctrl/autopsy sample)


title: S030

description: prostate

source_name: prostate, S030

tag: percentage of tumor


title: S029

description: prostate

source_name: prostate, S029


title: Duodenum iron diet rep2

description: no additional information

source_name: Mouse duodenum, iron supplemented diet


title: Duodenum wt rep2

description: no additional information

value: 13 weeks


title: Duodenum control diet rep1

description: no additional information


title: S032

description: prostate

source_name: prostate, S032


title: Duodenum iron diet rep3

description: no additional information


title: Duodenum iron diet rep1

description: no additional information


title: S076

description: prostate

source_name: prostate, S076


title: S027

description: prostate

source_name: prostate, S027


title: Duodenum Hfeko rep2

description: no additional information

source_name: Mouse duodenum, Hfe knockout

value: 11 weeks


title: Duodenum wt rep1

description: no additional information

value: 12 weeks


title: Liver iron diet rep2

description: no additional information

source_name: Mouse liver, iron supplemented diet

value: liver


title: Liver control diet rep1

description: no additional information

source_name: Mouse liver


title: S022

description: prostate

source_name: prostate, S022


title: Duodenum Hfeko rep1

description: no additional information

value: 10 weeks


title: S023

description: prostate

source_name: prostate, S023


title: Liver control diet rep2

description: no additional information


title: S090

description: prostate

source_name: prostate, S090


title: S025

description: prostate

source_name: prostate, S025


title: Hippocampus-wildtype-rep1

first: Paul

middle: C

last: Boutros

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

hyb_protocol: Biotinylated and amplified cRNA was generated using Illumina® TotalPrep RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX). Labeled cRNA samples (750 ng) were then hybridized to MouseRef-8 v2.0 Expression BeadChips (Illumina, Inc., San Diego, CA) in accordance with Illumina’s standard protocols for hybridization, staining, and data acquisition.

scan_protocol: BeadChips were imaged using the Illumina BeadArray Reader (Infinium I FastScan scanner protocol), a two-channel 0.8 μm resolution confocal laser scanner. The BeadScan software was used for the identification of bead positions and the extraction of raw-data.

data_processing: Illumina data was pre-processed separately and identically for each tissue. All pre-processing was performed in the R statistical environment (v2.7.2) using the BioConductor open-source library (Gentleman RC et al. Genome Biol 2004). Raw array data (TIFF files) were first processed using the beadarray package (v1.8.0) (Dunning MJ et al. Bioinformatics 2007). The raw data was subsequently background-corrected using the non-linear Edwards model (Edwards D Bioinformatics 2003). Following careful quality assessment at the bead and gene level, no arrays were excluded. The background-corrected data was summarized in normal space using the standard Illumina method. The summarized data was transformed using the vst method as implemented in the lumi package (v1.6.2) (Lin SM et al. Nucleic Acids Res 2008), and then normalized using quantile splines (Workman C et al. Genome Biol 2002).

source_name: wildtype hippocampus

growth_protocol: All animal procedures were approved by the Animal Management Committee of Mount Sinai Hospital and complied with the requirements of the Province of Ontario Animals for Research Act 1971 and the Canadian Council on Animal Care.  Groups of 3-5 littermates were housed by sex in polycarbonate cages, and given ad libitum sterile food (Purina mouse chow) and water.  The vivarium was maintained under a controlled temperature (21ºC ± 1ºC), and humidity (50-60%), with a 12-h diurnal cycle (lights on: 0700-1900).  Animals with the SrrY269* mutation used in experiments contained >99.6% of the C57BL/6J genome.  The microarray study was conducted on experimentally naïve male mice that were 9 weeks of age.

extract_protocol: Dissected tissue from whole brain, hippocampus, frontal cortex, and cerebellum was homogenized in 1mL of Trizol (Invitrogen) using a Polytron homogenizer (PRO Scientific).  A 5-min incubation at room temperature preceded and followed the addition of 200 μL of chloroform (Sigma).  Samples were centrifuged at 12,000 × g for 15 min at 4°C and the aqueous phase was collected.  Total RNA was precipitated from the aqueous phase using 500 μL of isopropyl alcohol (Sigma), and samples were then incubated at room temperature for 10 min and centrifuged at 12,000 × g for 10 min at 4°C.  The RNA pellet was washed with 1 mL of 75% ethanol, centrifuged at 7,500 × g for 5 min at 4°C, and dissolved in 100 μL of DEPC-treated water (Applied Biosystems).  For the microarray experiment, additional purification of total RNA was completed with the Absolutely RNeasy RT-PCR Miniprep kit (Strategene).  RNA yield was quantified by UV spectrophotometry (NanoDrop ND-1000; Thermo Fisher Scientific) and RNA integrity was verified using the Agilent Bioanalyzer 2100 system (Agilent Technologies).

treatment_protocol: Animals were sacrificed by cervical dislocation and brain regions were immediately dissected while being kept cool with partially frozen ASCF (124 mM NaCl, 26 mM NaHCO3, 10 mM Glucose, 3.3 mM KCl, 1 mM NaHPO4, 2 mM CaCl2, 2 mM MgCl2).  Tissue was then frozen using liquid nitrogen (Praxair).

tag: Strain

value: C57BL/6, Gender:male, Age:9 weeks, Tissue:hippocampus, SRR-Genotype:wildtype


title: Hippocampus-wildtype-rep2

label_protocol: Biotinylated and amplified cRNA was generated using Illumina® TotalPrep RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX).


title: Liver iron diet rep3

description: no additional information


title: S024

description: prostate

source_name: prostate, S024


title: S021

description: prostate

source_name: prostate, S021


title: S026

description: prostate

source_name: prostate, S026


title: Hippocampus-wildtype-rep3


title: S020

description: prostate

source_name: prostate, S020


title: Hippocampus-SRRmutant-rep4

source_name: SRR mutant hippocampus

value: C57BL/6, Gender:male, Age:9 weeks, Tissue:hippocampus, SRR-Genotype:mutant


title: Hippocampus-SRRmutant-rep2


title: Hippocampus-wildtype-rep4


title: S019

description: prostate

source_name: prostate, S019


title: Liver wt rep1

description: no additional information


title: Liver wt rep2

description: no additional information

value: 14 weeks


title: Liver iron diet rep1

description: no additional information


title: Hippocampus-SRRmutant-rep3


title: Hippocampus-SRRmutant-rep1


title: FrontalCortex-wildtype-rep4

source_name: wildtype frontal cortex

value: C57BL/6, Gender:male, Age:9 weeks, Tissue:frontal cortex, SRR-Genotype:wildtype


title: FrontalCortex-wildtype-rep1


title: FrontalCortex-wildtype-rep3


title: S016

description: prostate

source_name: prostate, S016


title: S015

description: prostate

source_name: prostate, S015


title: Liver Hfeko rep2

description: no additional information

source_name: Mouse liver, Hfe knockout


title: FrontalCortex-wildtype-rep2


title: Liver Hfeko rep1

description: no additional information


title: S013

description: prostate

source_name: prostate, S013


title: S018

description: prostate

source_name: prostate, S018


title: S012

description: prostate

source_name: prostate, S012


title: Liver Hfeko rep3

description: no additional information


title: S010

description: prostate

source_name: prostate, S010


title: S009

description: prostate

source_name: prostate, S009


title: S011

description: prostate

source_name: prostate, S011


title: FrontalCortex-SRRmutant-rep2

source_name: SRR mutant frontal cortex

value: C57BL/6, Gender:male, Age:9 weeks, Tissue:frontal cortex, SRR-Genotype:mutant


title: FrontalCortex-SRRmutant-rep1


title: S017

description: prostate

source_name: prostate, S017


title: Cerebellum-wildtype-rep4

source_name: wildtype cerebellum

value: C57BL/6, Gender:male, Age:9 weeks, Tissue:cerebellum, SRR-Genotype:wildtype


title: Cerebellum-wildtype-rep2


title: S007

description: prostate

source_name: prostate, S007


title: Cerebellum-wildtype-rep3


title: Cerebellum-wildtype-rep1


title: S008

description: prostate

source_name: prostate, S008


title: S006

description: prostate

source_name: prostate, S006


title: FB2khd4Delta MM 2

status: Public on Sep 04 2009

city: Marburg

first: Michael

last: Feldbrügge

state: Hessen

address: Karl-von-Frisch-Strasse

department: Organismic Interactions

country: Germany

institute: MPI for Terrestrial Microbiology

description: experiment to measure changes in steady state mRNA levels after deletion of RNA-binding protein khd4

hyb_protocol: Affymetrix EukGE-WS2 on a GeneChip Fluidics Station 400

scan_protocol: Affymetrix GCS2500

data_processing: dChip

organism: Mycosarcoma maydis

source_name: deletion of khd4 (um03837) in FB2 background (lab strain UMa331k); hygromycin replacement

label_protocol: Target preparation was performed according to the standard Affymetrix protocol using the Enzo BioArray RNA transcript labeling kit.

growth_protocol: Strains were grown to an OD600 of 0.3 at 28°C in liquid minimal array medium containing glucose and glutamine.

extract_protocol: RNA isolation, sample preparation and hybridisation were performed as previously described (Scherer, M. et al. (2006) The Plant Cell; Zarnack, K. et al. (2008) Mol Microbiol)

tag: genotype

value: deletion of khd4

tag: genetic background


title: S005

description: prostate

source_name: prostate, S005


title: FB2 MM 2

description: control experiment

source_name: wildtype strain FB2

value: wildtype


title: Cerebellum-SRRmutant-rep4

source_name: SRR mutant cerebellum

value: C57BL/6, Gender:male, Age:9 weeks, Tissue:cerebellum, SRR-Genotype:mutant


title: Cerebellum-SRRmutant-rep3


title: Cerebellum-SRRmutant-rep2


title: FB2 MM 1

description: control experiment


title: Cerebellum-SRRmutant-rep1


title: S004

description: prostate

source_name: prostate, S004

value: T


title: S002

description: prostate

source_name: prostate, S002


title: S001

description: prostate

source_name: prostate, S001


title: MCAo biological rep4

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rattus norvegicus Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: affymetrix standard protocol

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

organism: Rattus norvegicus

source_name: Brain of rat subjected to MCAo

label_protocol: Biotinylated cRNA were prepared according to the Eukaryote Sample preparation as described in Expression Analysis Technical Manual, 2001, Affymetrix.

extract_protocol: Total RNA was isolated from brain tissues (frozen or fresh) by a single-step method using TRIzol® Reagent (Invitrogen, USA). The RNA samples were treated with RNase-free DNase at 37oC for 20 min and stored at -80oC until further use. Total RNA (20 –50μg) isolated from tissues was cleaned up using RNeasy spin columns (Qiagen, Germany) before cDNA synthesis.

value: Sprague Dawley


title: MCAo and treated with nPLA biological rep 2

source_name: Brain of rat subjected to MCAo and treated with nPLA


title: MCAo biological rep2


title: MCAo biological rep3


title: Sham operated biological rep2

source_name: Sham operated rat brain


title: YW 280

city: New York

first: Ashutosh

last: Chaudhry

state: NY

department: Immunology

institute: Memorial Sloan-Kettering Cancer Center

description: Gene expression data from regulatory T cells isolated from  Foxp3<Cre/wtS> Stat3<fl/fl> mice

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

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

data_processing: The data were analyzed with Bioconductor for the statistical software R (www.r-project.org). Expression values were background corrected, normalized and summarized by the default settings of the gcrma package.

source_name: Regulatory T cells isolated from  Foxp3<Cre/wtS> Stat3<fl/fl> mice

label_protocol: Biotinylated cRNA were prepared according to the manufacturer's protocol from total RNA (Ambion).

growth_protocol: Regulatory T cells were isolated from 6-8 week old female mice using FACS sorting

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

tag: cell type

value: T cells from spleen and lymph nodes

value: female

value: 6-8 weeks


title: FB2khd4Delta MM 1

source_name: deletion of khd4 (um03837) in FB2 background (lab strain UMa331g); hygromycin replacement


title: MCAo biological rep1


title: MCAo and treated with nPLA biological rep 3


title: nrg1 mutant vs. WT under carbon starvation

city: Lynchburg

middle: S

last: Price

state: VA

address: 1971 University Blvd.

department: Biology & Chemistry

institute: Liberty University

description:
Gene expression was compared between WT and nrg1∆ mutant strains of C. neoformans grown in Synthetic Complete medium with 0.1% glucose.

Ch1 Raw data files:
0319_3022_CU_383_CNWash_WT-NRG1_PooledRef.gpr
0319_3021_CU_382_CNWash_WT-NRG1_PooledRef_scan2.gpr
0362_4077_CU_342_CNWash_2-ref_1-H99.gpr

Ch2 Raw data files:
0319_3024_CU_242_CNWash_mut-nrg1_PooledRef.gpr
0319_3023_CU_385_CNWash_mut-nrg1_PooledRef.gpr
0362_4078_CU_343_CNWash_4-ref_3-nrg.gpr

hyb_protocol: Hybridization was performed at the Duke University Microarray Facility following the Hybridization protocol (http://microarray.genome.duke.edu/).

scan_protocol: Slides were scanned at the Duke University Microarray Facility using an Axon Genepix 4000B scanner (http://microarray.genome.duke.edu/).

data_processing: Extracted data were imported into a statistical software package (SAS v8, SAS Institute, Cary, NC), and initial background subtraction was performed.  Mixed model analysis of microarray data (Wolfinger, et al., 2001) was used to evaluate differential expression data using approaches presented elsewhere (Chhabra, et al., 2003; Pysz, et al., 2004; Price et al., 2005).  We calculated the statistical significance of each genomic element using least squared means estimates of gene-specific treatment effects across pairs of treatments obtained for each gene under each treatment condition.  Differences between treatment effects for pairs of inducing conditions were considered log2-transformed fold changes (Wolfinger, et al., 2001).  Genes were selected for further evaluation if they possessed a p-value <0.004 (corresponding to the significance of difference for SMG1).

label: For 0319_3022_CU_383_CNWash_WT-NRG1_PooledRef.gpr and 0319_3021_CU_382_CNWash_WT-NRG1_PooledRef_scan2.gpr TEST=Cy5 and reference=Cy3. Dyes were swapped for 0362_4077_CU_342_CNWash_2-ref_1-H99.gpr.

organism: Cryptococcus neoformans H99

source_name: Wild-type in carbon starvation

label_protocol: Labeling was performed at the Duke University Microarray Facility following the Direct Labeling protocol for spotted arrays (http://microarray.genome.duke.edu/).

growth_protocol: C. neoformans H99 was incubated in Synthetic Complete (SC) medium with 2% glucose overnight at 30C, pelleted, and resuspended in SC with 0.1% glucose for 30 minutes at 30C.

extract_protocol: Total RNA was extracted from lyophilized cells using Trizol Reagent (Invitrogen Life Technologies, Carlsbad, CA) following manufacturer's instructions.

tag: genome/variation

value: wild type

label: For 0319_3024_CU_242_CNWash_mut-nrg1_PooledRef.gpr and 0319_3023_CU_385_CNWash_mut-nrg1_PooledRef.gpr TEST=Cy5 and reference=Cy3. Dyes were swapped for 0362_4078_CU_343_CNWash_4-ref_3-nrg.gpr.

source_name: nrg1 mutant in carbon starvation

growth_protocol: C. neoformans H99 nrg1 mutant was incubated in Synthetic Complete (SC) medium with 2% glucose overnight at 30C, pelleted, and resuspended in SC with 0.1% glucose for 30 minutes at 30C.

value: nrg1∆ mutant


title: YW 265

description: Gene expression data from regulatory T cells isolated from  Foxp3<Cre/wtS> Stat3<fl/wt> mice

source_name: Regulatory T cells isolated from  Foxp3<Cre/wtS> Stat3<fl/wt> mice


title: Sham operated biological rep1


title: mRNA_human ES cell line

city: Los Angeles

first: Mark

middle: H.

last: Chin

address: 650 Charles E. Young Dr

department: Human Genetics

institute: UCLA

description: mRNA_human ES cell line

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on human expression arrays

scan_protocol: Gene chips were analyzed using GeneChip® Scanner 3000.

data_processing:
The raw data was processed using the RMA algorithm and was implemented using R (Bioconductor).
The data is presented as a summary of the highest confidence probesets for each given RefSeq identifier. (See Materials and Methods, Chin, et al. Cell Stem Cell, 2009)

label: Biotin

source_name: CSES4 (p37)

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

growth_protocol: Cell lines were cultured in ES cell media for ESC and iPS lines (Lowry, et al. PNAS, 2008) and DMEM for the fibroblast line.

treatment_protocol: Reprogrammed Cell lines were created as described in Lowry, et al. (PNAS, 2008)

tag: cell line

value: Human embryonic stem cell line (CSES4)

tag: passages


title: Donor6_24h_Wy

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description: no additional information

hyb_protocol: Hybridisation of 500ng cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described n the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.

source_name: Primary hepatocytes isolated from Donor 6 treated with Wy14643 for 24h

label_protocol: The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.

growth_protocol: Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.

extract_protocol: Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.

treatment_protocol: Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate.  The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.

value: Primary hepatocytes

tag: donor

tag: agent

tag: time

value: Male

value: 73 years old


title: 35 days, Nandrolone treatment 3

city: Bronx

first: Weiping

last: Qin

address: 130 West Kingsbridge Road, Room 1E-02

department: Center of Excellence for the Medical Consequences of SCI

institute: Bronx Veterans Affairs Medical Center

description: Gene expression data from Gastrocnemius muscles from the denervated hindlimb by administration of nandrolone for 7 days beginning 29 days after denervation

data_processing: MAS5 algorithm was first used on CEL files. Differentially expressed genes were identified using BRB Array Tools version 3.6.2, developed by Dr. Richard Simon and Amy Peng Lam with the following parameters for normalization and filtering:  data for each array were normalized using the median for the entire array; expression values were set to 10 if below this value, and excluded from further analysis if less than 20% of the values were at least 1.5-fold greater or smaller than the median for that probe set.  Significance of differences in expression among groups was determined using an F-test with significance set at p < 0.05 unless otherwise specified.

growth_protocol: The animal studies were reviewed and approved by the Institutional Animal Care and Use Committee of the James J. Peters VA Medical Center.

extract_protocol: RNA was extracted using phenol-chloroform , then further enriched using RNAeasy minicolumns (Qiagen, Valencia, CA). Verification of RNA integrity and microarray analysis were performed by the Microarray Core Facility at the Mount Sinai School of Medicine.  Samples selected for microarray analysis yielded RNA integrities greater than 8.0 using an Aligent Bioanalyzer.

treatment_protocol: Male Wistar-Hannover rats had undergone left sciatic nerve transaction followed by the administration of nandrolone or vehicle beginning either on the day of surgery or 29 days thereafter.

tag: gender

value: male

value: Wistar hannover


title: mRNA_Reprogrammed iPSC line 18 (p9)

description: mRNA_Reprogrammed iPSC line 18 (p9)

source_name: hiPSC line 18 (p9)

value: clone line 18


title: Donor6_6h_Wy

description: no additional information

source_name: Primary hepatocytes isolated from Donor 6 treated with Wy14643 for 6h


title: 35 days, Nandrolone treatment 1

source_name: Gastrocnemius muscles from the denervated hindlimb by administration of nandrolone for 7 days beginning 29 days after denervation

tag: strain


title: mRNA_Fibroblast cell line

description: mRNA_Fibroblast cell line

source_name: hiPSC line 1 (p61)

value: Fibroblast cell line (NHDF3535)


title: Donor6_24h_DMSO

description: no additional information

source_name: Primary hepatocytes isolated from Donor 6 treated with DMSO for 24h

value: control


title: FrontalCortex-SRRmutant-rep3

source_name: SRR mutant frontal cortex

value: C57BL/6, Gender:male, Age:9 weeks, Tissue:frontal cortex, SRR-Genotype:mutant


title: 35 days, Nandrolone treatment 2


title: Donor6_6h_DMSO

description: no additional information

source_name: Primary hepatocytes isolated from Donor 6 treated with DMSO for 6h


title: Donor5_24h_DMSO

description: no additional information

source_name: Primary hepatocytes isolated from Donor 5 treated with DMSO for 24h


title: 35 days, Vehicle treatment 3

description: Gene expression data from Gastrocnemius muscles from the denervated hindlimb by administration of Vehicle for 7 days beginning 29 days after denervation


title: 7 days, Nandrolone treatment 2

description: Gene expression data from Gastrocnemius muscles from the denervated hindlimb by administration of nandrolone for 7 days beginning concomitantly with denervation


title: 7 days, Nandrolone treatment 3

source_name: Gastrocnemius muscles from the denervated hindlimb by administration of nandrolone for 7 days beginning concomitantly with denervation


title: 35 days, Vehicle treatment 1

source_name: Gastrocnemius muscles from the denervated hindlimb by administration of Vehicle for 7 days beginning 29 days after denervation


title: Donor5_6h_Wy

description: no additional information

source_name: Primary hepatocytes isolated from Donor 5 treated with Wy14643 for 6h


title: Donor5_6h_DMSO

description: no additional information

source_name: Primary hepatocytes isolated from Donor 5 treated with DMSO for 6h


title: 7 days, Nandrolone treatment 1


title: Donor4_24h_DMSO

description: no additional information

source_name: Primary hepatocytes isolated from Donor 4 treated with DMSO for 24h

value: Female

value: 54 years old


title: 35 days, Vehicle treatment 2


title: Donor4_24h_Wy

description: no additional information

source_name: Primary hepatocytes isolated from Donor 4 treated with Wy14643 for 24h


title: Donor5_24h_Wy

description: no additional information

source_name: Primary hepatocytes isolated from Donor 5 treated with Wy14643 for 24h


title: 120' PDS 2

city: San Antonio

first: Deepak

last: Kaushal

state: TX

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

description: Biological replicate 2 , 120' post treatment

scan_protocol: scanned on an Axon 4000B scanner using GenePix 6.1

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal, using S+ ArrayAnalyzer/Spotfire

organism: Mycobacterium tuberculosis

source_name: M. tuberculosis delta-sigmaH mutant at log phase + 1 hr diamide 10 mM, then washed away + 120 min

growth_protocol: M. tuberculosis and its isogenic mutant were grown in Middlebrook's 7H9 supplemented media. Specific manipulations are mentioned in Mehra S & Kaushal D. J. Bacteriol. In Press.

extract_protocol: Total RNA extracted using Trizol/Beadbeater method using a Biospec Beadbeater and 0.1 mm silica/zirconia beads

tag: genotype/variation

value: delta-sigmaH mutant

tag: protocol

source_name: M. tuberculosis at log phase + 1 hr diamide 10 mM, then washed away + 120 min


title: 120' PDS 1

description: Biological replicate 1 , 120' post treatment

treatment_protocol: Mehra S & Kaushal D. J. Bacteriol. In Press.

value: log phase + 1 hr diamide 10 mM, then washed away + 120 min


title: 60' PDS 2

description: Biological replicate 2 , 60' post treatment

source_name: M. tuberculosis delta-sigmaH mutant at log phase + 1 hr diamide 10 mM, then washed away + 60 min

source_name: M. tuberculosis at log phase + 1 hr diamide 10 mM, then washed away + 60 min


title: 90' PDS 1

description: Biological replicate 1 , 90' post treatment

source_name: M. tuberculosis delta-sigmaH mutant at log phase + 1 hr diamide 10 mM, then washed away + 90 min

source_name: M. tuberculosis at log phase + 1 hr diamide 10 mM, then washed away + 90 min


title: Donor4_6h_DMSO

description: no additional information

source_name: Primary hepatocytes isolated from Donor 4 treated with DMSO for 6h

tag: age


title: 7 days, Vehicle treatment 1

description: Gene expression data from Gastrocnemius muscles from the denervated hindlimb by administration of Vehicle for 7 days beginning concomitantly with denervation


title: FrontalCortex-SRRmutant-rep4

source_name: SRR mutant frontal cortex


title: 7 days, Vehicle treatment 2

description: Gene expression data from Gastrocnemius muscles from the denervated hindlimb by administration of  Vehicle for 7 days beginning concomitantly with denervation


title: 30' PDS 2

description: Biological replicate 2 , 30' post treatment

source_name: M. tuberculosis delta-sigmaH mutant at log phase + 1 hr diamide 10 mM, then washed away + 30 min

source_name: M. tuberculosis at log phase + 1 hr diamide 10 mM, then washed away + 30 min


title: Donor3_6h_DMSO

description: no additional information

source_name: Primary hepatocytes isolated from Donor 3 treated with DMSO for 6h

value: 70 years old


title: 90' PDS 2

description: Biological replicate 2 , 90' post treatment

value: log phase + 1 hr diamide 10 mM, then washed away + 90 min

value: wild type


title: 7 days, Vehicle treatment 3

source_name: Gastrocnemius muscles from the denervated hindlimb by administration of  Vehicle for 7 days beginning concomitantly with denervation


title: Donor3_6h_Wy

description: no additional information

source_name: Primary hepatocytes isolated from Donor 3 treated with Wy14643 for 6h


title: 0' PDS 2

description: Biological replicate 2 , 0' post treatment

source_name: M. tuberculosis delta-sigmaH mutant at log phase + 1 hr diamide 10 mM, then washed away

source_name: M. tuberculosis at log phase + 1 hr diamide 10 mM, then washed away


title: 60' PDS 1

description: Biological replicate 1 , 60' post treatment

value: log phase + 1 hr diamide 10 mM, then washed away + 60 min


title: 30' PDS 1

description: Biological replicate 1 , 30' post treatment

value: log phase + 1 hr diamide 10 mM, then washed away + 30 min


title: Donor2_24h_DMSO

description: no additional information

source_name: Primary hepatocytes isolated from Donor 2 treated with DMSO for 24h

value: Primary hepatocytes

value: Male

value: 44 years old


title: Donor3_24h_Wy

description: no additional information

source_name: Primary hepatocytes isolated from Donor 3 treated with Wy14643 for 24h


title: Donor4_6h_Wy

description: no additional information

source_name: Primary hepatocytes isolated from Donor 4 treated with Wy14643 for 6h


title: Donor2_24h_Wy

description: no additional information

source_name: Primary hepatocytes isolated from Donor 2 treated with Wy14643 for 24h


title: Donor3_24h_DMSO

description: no additional information

source_name: Primary hepatocytes isolated from Donor 3 treated with DMSO for 24h


title: Donor1_24h_DMSO

description: no additional information

source_name: Primary hepatocytes isolated from Donor 1 treated with DMSO for 24h

value: 63 years old


title: Donor2_6h_DMSO

description: no additional information

source_name: Primary hepatocytes isolated from Donor 2 treated with DMSO for 6h


title: Donor2_6h_Wy

description: no additional information

source_name: Primary hepatocytes isolated from Donor 2 treated with Wy14643 for 6h


title: Donor1_24h_Wy

description: no additional information

source_name: Primary hepatocytes isolated from Donor 1 treated with Wy14643 for 24h


title: 0' PDS 1

description: Biological replicate 1 , 0' post treatment

value: log phase + 1 hr diamide 10 mM, then washed away


title: Donor1_6h_DMSO

description: no additional information

source_name: Primary hepatocytes isolated from Donor 1 treated with DMSO for 6h


title: Pre-diamide 2

description: Biological replicate 2 , pre treatment

source_name: M. tuberculosis delta-sigmaH mutant at log phase

value: log phase (control)

source_name: M. tuberculosis at log phase


title: Hom pool-15 generations 150 µM monomethylarsonous acid-replicate 1 Down

status: Public on Sep 03 2009

city: Berkeley

first: William

last: Jo

address: 119 Morgan Hall

institute: UC Berkeley

description: Down tag data processing

hyb_protocol: Reactions hybridized overnight to custom-built TAG4 microarrays (Affymetrix)

scan_protocol: After hybridization, arrays were stained and scanned at an emission wavelength of 560 nm using a GeneChip scanner (Affymetrix).

data_processing:
Robust mean Log2 intensity for replicate features calculated with S-plus/R function.
Up and down tags are processed separately and output reported as separate data sets.
Note: Platform GPL8633 contains the array design which will be helpful for users who do not want to use our preprocessing strategy.

organism: Saccharomyces cerevisiae

source_name: Homozygous pool-15 generations 150 µM monomethylarsonous acid-replicate 1

label_protocol: The strain-specific barcodes contained in the DNA were amplified by PCR using a set of biotinylated primers

growth_protocol: Growth in YPD (rich) media, 30 °C, 200 rpm. Measurements of optical density at 595 nm (OD595) to monitor growth

extract_protocol: Cells were collected and genomic DNA was extracted using the YDER kit (Pierce Biotechnology)

treatment_protocol: Chemical treatments incorporated into growth media, 3 concentrations with 3 biological replicates each, for 5 and 15 generations (g) of growth

tag: pool

value: Homozygous deletion mutants

tag: growth stage

value: 15 generations

value: monomethylarsonous acid

tag: concentration


title: Pre-diamide 1

description: Biological replicate 1 , pre treatment


title: Hom pool-15 generations 150 µM monomethylarsonous acid-replicate 2 Down

description: Down tag data processing

source_name: Homozygous pool-15 generations 150 µM monomethylarsonous acid-replicate 2


title: Hom pool-15 generations 75 µM monomethylarsonous acid-replicate 3 Down

description: Down tag data processing

source_name: Homozygous pool-15 generations 75 µM monomethylarsonous acid-replicate 3

value: 75 µM


title: Hom pool-15 generations 150 µM monomethylarsonous acid-replicate 2 Up

description: Up tag data processing


title: Hom pool-15 generations 150 µM monomethylarsonous acid-replicate 1 Up

description: Up tag data processing


title: Hom pool-15 generations 75 µM monomethylarsonous acid-replicate 3 Up

description: Up tag data processing


title: Hom pool-15 generations 75 µM monomethylarsonous acid-replicate 2 Up

description: Up tag data processing

source_name: Homozygous pool-15 generations 75 µM monomethylarsonous acid-replicate 2


title: Hom pool-15 generations 150 µM monomethylarsonous acid-replicate 3 Up

description: Up tag data processing

source_name: Homozygous pool-15 generations 150 µM monomethylarsonous acid-replicate 3


title: Hom pool-15 generations 75 µM monomethylarsonous acid-replicate 1 Down

description: Down tag data processing

source_name: Homozygous pool-15 generations 75 µM monomethylarsonous acid-replicate 1


title: Hom pool-15 generations 37.5 µM monomethylarsonous acid-replicate 3 Up

description: Up tag data processing

source_name: Homozygous pool-15 generations 37.5 µM monomethylarsonous acid-replicate 3


title: Hom pool-15 generations 37.5 µM monomethylarsonous acid-replicate 2 Down

description: Down tag data processing

source_name: Homozygous pool-15 generations 37.5 µM monomethylarsonous acid-replicate 2


title: Hom pool-15 generations 37.5 µM monomethylarsonous acid-replicate 3 Down

description: Down tag data processing


title: Donor1_6h_Wy

description: no additional information

source_name: Primary hepatocytes isolated from Donor 1 treated with Wy14643 for 6h


title: Hom pool-15 generations 150 µM monomethylarsonous acid-replicate 3 Down

description: Down tag data processing


title: Hom pool-15 generations 37.5 µM monomethylarsonous acid-replicate 1 Down

description: Down tag data processing

source_name: Homozygous pool-15 generations 37.5 µM monomethylarsonous acid-replicate 1


title: Hom pool-15 generations 300 µM sodium arsenite-replicate 3 Down

description: Down tag data processing

source_name: Homozygous pool-15 generations 300 µM sodium arsenite-replicate 3

value: arsenite


title: Hom pool-15 generations 300 µM sodium arsenite-replicate 1 Down

description: Down tag data processing

source_name: Homozygous pool-15 generations 300 µM sodium arsenite-replicate 1


title: Hom pool-15 generations 300 µM sodium arsenite-replicate 2 Down

description: Down tag data processing

source_name: Homozygous pool-15 generations 300 µM sodium arsenite-replicate 2


title: Hom pool-15 generations 75 µM monomethylarsonous acid-replicate 2 Down

description: Down tag data processing


title: Hom pool-15 generations 37.5 µM monomethylarsonous acid-replicate 1 Up

description: Up tag data processing


title: Hom pool-15 generations 300 µM sodium arsenite-replicate 2 Up

description: Up tag data processing


title: Hom pool-15 generations 300 µM sodium arsenite-replicate 3 Up

description: Up tag data processing


title: Hom pool-15 generations 75 µM monomethylarsonous acid-replicate 1 Up

description: Up tag data processing


title: Hom pool-15 generations 37.5 µM monomethylarsonous acid-replicate 2 Up

description: Up tag data processing


title: Hom pool-15 generations 300 µM sodium arsenite-replicate 1 Up

description: Up tag data processing


title: Hom pool-15 generations 150 µM sodium arsenite-replicate 3 Down

description: Down tag data processing

source_name: Homozygous pool-15 generations 150 µM sodium arsenite-replicate 3


title: Hom pool-15 generations 150 µM sodium arsenite-replicate 3 Up

description: Up tag data processing


title: Hom pool-15 generations 75 µM sodium arsenite-replicate 3 Up

description: Up tag data processing

source_name: Homozygous pool-15 generations 75 µM sodium arsenite-replicate 3


title: Hom pool-15 generations 150 µM sodium arsenite-replicate 2 Up

description: Up tag data processing

source_name: Homozygous pool-15 generations 150 µM sodium arsenite-replicate 2


title: Hom pool-15 generations 150 µM sodium arsenite-replicate 2 Down

description: Down tag data processing


title: Hom pool-15 generations 75 µM sodium arsenite-replicate 2 Up

description: Up tag data processing

source_name: Homozygous pool-15 generations 75 µM sodium arsenite-replicate 2


title: Hom pool-15 generations 75 µM sodium arsenite-replicate 1 Up

description: Up tag data processing

source_name: Homozygous pool-15 generations 75 µM sodium arsenite-replicate 1


title: Hom pool-15 generations 75 µM sodium arsenite-replicate 1 Down

description: Down tag data processing


title: Hom pool-15 generations 75 µM sodium arsenite-replicate 3 Down

description: Down tag data processing


title: Hom pool-5 generations 150 µM monomethylarsonous acid-replicate 2 Up

description: Up tag data processing

source_name: Homozygous pool-5 generations 150 µM monomethylarsonous acid-replicate 2

value: 5 generations


title: Hom pool-5 generations 150 µM monomethylarsonous acid-replicate 2 Down

description: Down tag data processing


title: Hom pool-5 generations 75 µM monomethylarsonous acid-replicate 3 Down

description: Down tag data processing

source_name: Homozygous pool-5 generations 75 µM monomethylarsonous acid-replicate 3


title: Hom pool-5 generations 150 µM monomethylarsonous acid-replicate 3 Up

description: Up tag data processing

source_name: Homozygous pool-5 generations 150 µM monomethylarsonous acid-replicate 3


title: Hom pool-15 generations 150 µM sodium arsenite-replicate 1 Down

description: Down tag data processing

source_name: Homozygous pool-15 generations 150 µM sodium arsenite-replicate 1


title: Hom pool-15 generations 75 µM sodium arsenite-replicate 2 Down

description: Down tag data processing


title: Hom pool-5 generations 75 µM monomethylarsonous acid-replicate 1 Up

description: Up tag data processing

source_name: Homozygous pool-5 generations 75 µM monomethylarsonous acid-replicate 1


title: Hom pool-5 generations 37.5 µM monomethylarsonous acid-replicate 3 Up

description: Up tag data processing

source_name: Homozygous pool-5 generations 37.5 µM monomethylarsonous acid-replicate 3


title: Hom pool-5 generations 150 µM monomethylarsonous acid-replicate 1 Down

description: Down tag data processing

source_name: Homozygous pool-5 generations 150 µM monomethylarsonous acid-replicate 1


title: Hom pool-5 generations 75 µM monomethylarsonous acid-replicate 2 Up

description: Up tag data processing

source_name: Homozygous pool-5 generations 75 µM monomethylarsonous acid-replicate 2


title: Hom pool-5 generations 75 µM monomethylarsonous acid-replicate 3 Up

description: Up tag data processing


title: Hom pool-5 generations 150 µM monomethylarsonous acid-replicate 1 Up

description: Up tag data processing


title: Hom pool-5 generations 75 µM monomethylarsonous acid-replicate 2 Down

description: Down tag data processing


title: Hom pool-5 generations 75 µM monomethylarsonous acid-replicate 1 Down

description: Down tag data processing


title: Hom pool-5 generations 37.5 µM monomethylarsonous acid-replicate 2 Down

description: Down tag data processing

source_name: Homozygous pool-5 generations 37.5 µM monomethylarsonous acid-replicate 2


title: Hom pool-5 generations 150 µM monomethylarsonous acid-replicate 3 Down

description: Down tag data processing


title: Hom pool-5 generations 37.5 µM monomethylarsonous acid-replicate 3 Down

description: Down tag data processing


title: Hom pool-15 generations 150 µM sodium arsenite-replicate 1 Up

description: Up tag data processing


title: Hom pool-5 generations 37.5 µM monomethylarsonous acid-replicate 2 Up

description: Up tag data processing


title: Hom pool-5 generations 37.5 µM monomethylarsonous acid-replicate 1 Up

description: Up tag data processing

source_name: Homozygous pool-5 generations 37.5 µM monomethylarsonous acid-replicate 1


title: Hom pool-5 generations 300 µM sodium arsenite-replicate 2 Up

description: Up tag data processing

source_name: Homozygous pool-5 generations 300 µM sodium arsenite-replicate 2


title: Hom pool-5 generations 37.5 µM monomethylarsonous acid-replicate 1 Down

description: Down tag data processing


title: Hom pool-5 generations 300 µM sodium arsenite-replicate 3 Down

description: Down tag data processing

source_name: Homozygous pool-5 generations 300 µM sodium arsenite-replicate 3


title: Hom pool-5 generations 300 µM sodium arsenite-replicate 1 Down

description: Down tag data processing

source_name: Homozygous pool-5 generations 300 µM sodium arsenite-replicate 1


title: Hom pool-5 generations 300 µM sodium arsenite-replicate 1 Up

description: Up tag data processing


title: Hom pool-5 generations 150 µM sodium arsenite-replicate 3 Down

description: Down tag data processing

source_name: Homozygous pool-5 generations 150 µM sodium arsenite-replicate 3


title: Hom pool-5 generations 75 µM sodium arsenite-replicate 3 Down

description: Down tag data processing

source_name: Homozygous pool-5 generations 75 µM sodium arsenite-replicate 3


title: Hom pool-5 generations 150 µM sodium arsenite-replicate 2 Down

description: Down tag data processing

source_name: Homozygous pool-5 generations 150 µM sodium arsenite-replicate 2


title: Hom pool-5 generations 150 µM sodium arsenite-replicate 1 Down

description: Down tag data processing

source_name: Homozygous pool-5 generations 150 µM sodium arsenite-replicate 1


title: Hom pool-15 generations rich media control-replicate 12 Up

description: Up tag data processing

source_name: Homozygous pool-15 generations rich media control-replicate 12

value: rich media (control)


title: Hom pool-5 generations 75 µM sodium arsenite-replicate 3 Up

description: Up tag data processing


title: Hom pool-5 generations 75 µM sodium arsenite-replicate 2 Up

description: Up tag data processing

source_name: Homozygous pool-5 generations 75 µM sodium arsenite-replicate 2


title: Hom pool-5 generations 300 µM sodium arsenite-replicate 3 Up

description: Up tag data processing


title: Hom pool-5 generations 75 µM sodium arsenite-replicate 1 Up

description: Up tag data processing

source_name: Homozygous pool-5 generations 75 µM sodium arsenite-replicate 1


title: Hom pool-15 generations rich media control-replicate 12 Down

description: Down tag data processing


title: Hom pool-5 generations 300 µM sodium arsenite-replicate 2 Down

description: Down tag data processing


title: Hom pool-5 generations 75 µM sodium arsenite-replicate 1 Down

description: Down tag data processing


title: Hom pool-15 generations rich media control-replicate 10 Up

description: Up tag data processing

source_name: Homozygous pool-15 generations rich media control-replicate 10


title: Hom pool-15 generations rich media control-replicate 10 Down

description: Down tag data processing


title: Hom pool-15 generations rich media control-replicate 11 Down

description: Down tag data processing

source_name: Homozygous pool-15 generations rich media control-replicate 11


title: Hom pool-5 generations 150 µM sodium arsenite-replicate 3 Up

description: Up tag data processing


title: Hom pool-15 generations rich media control-replicate 11 Up

description: Up tag data processing


title: Hom pool-5 generations 150 µM sodium arsenite-replicate 1 Up

description: Up tag data processing


title: Hom pool-15 generations rich media control-replicate 9 Down

description: Down tag data processing

source_name: Homozygous pool-15 generations rich media control-replicate 9


title: Hom pool-5 generations 150 µM sodium arsenite-replicate 2 Up

description: Up tag data processing


title: Hom pool-15 generations rich media control-replicate 7 Down

description: Down tag data processing

source_name: Homozygous pool-15 generations rich media control-replicate 7


title: Hom pool-15 generations rich media control-replicate 8 Down

description: Down tag data processing

source_name: Homozygous pool-15 generations rich media control-replicate 8


title: Hom pool-15 generations rich media control-replicate 7 Up

description: Up tag data processing


title: Hom pool-15 generations rich media control-replicate 6 Down

description: Down tag data processing

source_name: Homozygous pool-15 generations rich media control-replicate 6


title: Hom pool-15 generations rich media control-replicate 9 Up

description: Up tag data processing


title: Hom pool-15 generations rich media control-replicate 6 Up

description: Up tag data processing


title: Hom pool-5 generations 75 µM sodium arsenite-replicate 2 Down

description: Down tag data processing


title: Hom pool-15 generations rich media control-replicate 4 Up

description: Up tag data processing

source_name: Homozygous pool-15 generations rich media control-replicate 4


title: Hom pool-15 generations rich media control-replicate 3 Down

description: Down tag data processing

source_name: Homozygous pool-15 generations rich media control-replicate 3


title: Hom pool-15 generations rich media control-replicate 3 Up

description: Up tag data processing


title: Hom pool-15 generations rich media control-replicate 1 Up

description: Up tag data processing

source_name: Homozygous pool-15 generations rich media control-replicate 1


title: Hom pool-15 generations rich media control-replicate 4 Down

description: Down tag data processing


title: Hom pool-15 generations rich media control-replicate 2 Up

description: Up tag data processing

source_name: Homozygous pool-15 generations rich media control-replicate 2


title: Hom pool-15 generations rich media control-replicate 2 Down

description: Down tag data processing


title: Hom pool-5 generations rich media control-replicate 11 Up

description: Up tag data processing

source_name: Homozygous pool-5 generations rich media control-replicate 11


title: Hom pool-15 generations rich media control-replicate 5 Down

description: Down tag data processing

source_name: Homozygous pool-15 generations rich media control-replicate 5


title: Hom pool-15 generations rich media control-replicate 1 Down

description: Down tag data processing


title: Hom pool-5 generations rich media control-replicate 11 Down

description: Down tag data processing


title: Hom pool-15 generations rich media control-replicate 8 Up

description: Up tag data processing


title: Hom pool-5 generations rich media control-replicate 12 Down

description: Down tag data processing

source_name: Homozygous pool-5 generations rich media control-replicate 12


title: Hom pool-15 generations rich media control-replicate 5 Up

description: Up tag data processing


title: Hom pool-5 generations rich media control-replicate 12 Up

description: Up tag data processing


title: Hom pool-5 generations rich media control-replicate 10 Up

description: Up tag data processing

source_name: Homozygous pool-5 generations rich media control-replicate 10


title: Hom pool-5 generations rich media control-replicate 8 Down

description: Down tag data processing

source_name: Homozygous pool-5 generations rich media control-replicate 8


title: Hom pool-5 generations rich media control-replicate 9 Down

description: Down tag data processing

source_name: Homozygous pool-5 generations rich media control-replicate 9


title: Hom pool-5 generations rich media control-replicate 10 Down

description: Down tag data processing


title: Hom pool-5 generations rich media control-replicate 7 Up

description: Up tag data processing

source_name: Homozygous pool-5 generations rich media control-replicate 7


title: Hom pool-5 generations rich media control-replicate 6 Up

description: Up tag data processing

source_name: Homozygous pool-5 generations rich media control-replicate 6


title: Hom pool-5 generations rich media control-replicate 8 Up

description: Up tag data processing


title: Hom pool-5 generations rich media control-replicate 9 Up

description: Up tag data processing


title: Hom pool-5 generations rich media control-replicate 6 Down

description: Down tag data processing


title: Hom pool-5 generations rich media control-replicate 5 Down

description: Down tag data processing

source_name: Homozygous pool-5 generations rich media control-replicate 5


title: Hom pool-5 generations rich media control-replicate 5 Up

description: Up tag data processing


title: Hom pool-5 generations rich media control-replicate 4 Down

description: Down tag data processing

source_name: Homozygous pool-5 generations rich media control-replicate 4


title: Hom pool-5 generations rich media control-replicate 7 Down

description: Down tag data processing


title: Hom pool-5 generations rich media control-replicate 4 Up

description: Up tag data processing


title: Hom pool-5 generations rich media control-replicate 2 Down

description: Down tag data processing

source_name: Homozygous pool-5 generations rich media control-replicate 2


title: JLMy83-2L microarray

city: Durham

first: Jennifer

middle: Lynn

last: McCulley

state: NC

address: 374 CARL Building, Research Drive Box 3054

department: Molecular Genetics and Microbiology

institute: Duke University

description: JLMy83-2L microarray

hyb_protocol: Described in Lemoine, F. et al. Cell, Vol. 120, 587-598 (2005).

scan_protocol: Array scanned in Genepix 4000b scanner.

data_processing: The log2 R/G ratios for all probes in the array were collapsed to a single value in the case of repeated probes and normalized according to the median value for the entire array.

source_name: Chromosomal DNA from the experimental strain labeled with Cy5

label_protocol: Direct incorporation with klenow polymerase and random priming.

growth_protocol: All strains were grown at 30 degrees Celcius for the number of generations indicated.

extract_protocol: Genomic DNA was harvested with a standard yeast DNA extraction protocol.

treatment_protocol: Strains were not treated with exogenous chemicals, etc.

tag: ploidy

value: Diploid

tag: isogenicity

value: Isogenic to MS71

tag: generations subcultured

source_name: Chromosomal DNA from MS71 labeled with Cy3

value: Haploid


title: Hom pool-5 generations rich media control-replicate 3 Down

description: Down tag data processing

source_name: Homozygous pool-5 generations rich media control-replicate 3


title: Hom pool-5 generations rich media control-replicate 1 Down

description: Down tag data processing

source_name: Homozygous pool-5 generations rich media control-replicate 1


title: Hom pool-5 generations rich media control-replicate 1 Up

description: Up tag data processing


title: Control 3 microarray

description: Control 3 microarray

source_name: Chromosomal DNA from MS71 labeled with Cy5


title: JLMy83-3L microarray

description: JLMy83-3L microarray


title: JLMy83-1s microarray

description: JLMy83-1s microarray


title: Hom pool-5 generations rich media control-replicate 3 Up

description: Up tag data processing


title: JLMy82-4L microarray

description: JLMy82-4L microarray


title: JLMy82-5L microarray

description: JLMy82-5L microarray


title: Control 4 microarray

description: Control 4 microarray


title: JLMy83-5s microarray

description: JLMy83-5s microarray


title: JLMy83-4s microarray

description: JLMy83-4s microarray


title: Control 1 microarray

description: Control 1 microarray


title: Control 2 microarray

description: Control 2 microarray