title: xue_rice_seed_MPSS

type: MPSS

city: Shanghai

first: Hong-Wei

last: Xue

address: 300 Fenglin Road

country: China

institute: Institute of Plant Physiology and Ecology,Shanghai Institutes of Biological Sciences

description:
All MPSS was performed essentially as described by Brenner et al. (Nat Biotechnol. 2000 18:630).
The specific modifications to the method for the MPSS sequencing of small RNAs are described by by Mineno et al.(Nucleic Acids Res. 2006 1765:1771).

data_processing: Distinct signatures were summed to obtain an abundance value for each signature sequence and normalized in ‘transcripts per million (TPM)’ for seed library as described by by Mineno et al.(Nucleic Acids Res. 2006 1765:1771).

molecule: other

organism: Oryza sativa

source_name: rice seed small RNA

extract_protocol: Total RNA was isolated separately from rice seeds collected at 3, 6, 9 and 12 days after anthesis (DAA) using Trizol Reagent (Invitrogene, Nottingham, UK), then mixed into a library and separated on denatured polyacrylamide gel electrophoresis (PAGE). The fraction of 18-26 nt small RNA was recovered by small RNA gel extraction Kit (TaKaRa Bio, Otsu, Japan).

tag: Rice (Oryza sativa, japonica cultivar Zhonghua 11) seeds collected at 3, 6, 9 and 12 days after anthesis (DAA).


title: Sample 52 - Ovary exposed to 7 mg O2/L for 4 d

status: Public on Feb 02 2009

type: RNA

city: Duluth

first: Dalma

last: Martinovic

state: MN

address: 6201 Congdon Blvd

department: ORD-NHEERL

country: USA

institute: U.S. EPA

description: Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

hyb_protocol: All of the labeling and post labeling procedures were conducted in ozone-free enclosure to ensure the integrity of the label.  Labeled materials were set up for the fragmentation reaction according to Agilent protocol described in their processing manual, and hybridized overnight in the rotating oven at 65°C in an ozone-free room.  The Agilent Oligo Microarray Zebrafish slide, with approximately 21, 000 genes represented was used for the gene expression analyses (4 x 44K format, product 015064).  Labeled samples (825 ng) were co-hybridized using sureHyb chambers from Agilent.  Wash conditions used were as outlined in the Agilent processing manual (protocol version 4.0).

scan_protocol: The arrays were scanned using Agilent scanner (G2505B). Agilent feature extraction software was used for extracting array data; the initial data quality analyses were done using Rosetta Luminator software (Rosetta Biosoftware, Seattle, WA).

data_processing: To generate lists of differentially expressed genes, output from Agilent’s feature extraction software was imported using GeneSpring GX 7.3.1 software (Agilent Technologies). The enhanced Agilent FE Import function was used to flag low quality spots based on feature saturation, uniformity, pixel population consistency and signal-to-noise ratio using procedures described in the Agilent Technologies Training Manual (version 4.5, May 2006). The ratios of treatment and reference raw intensity data then were log transformed and normalized using locally weighted least squares regression (lowess) normalization, available in GeneSpring GX 7.3.1.

molecule: total RNA

organism: Danio rerio

label_protocol: RNA from each condition of interest (treatment) was labeled with a Cy5 dye and hybridized onto arrays together with Cy3 labeled RNA taken from a standard reference pool of RNA extracted from sexually mature male and female gonads and brains, and female livers. For the microarray analyses, total RNA was amplified using Agilent low input linear amplification kit according to the process outlined by the manufacturer (Agilent Technologies). Amplified target cRNA (1-5 µg) was labeled with either cyanine-5 or cyanine-3 using ULS aRNA Flurorescent Labeling Kits from Kreatech according to the manufacturers protocol (Kreatech Biotechnology, Amsterdam, The Netherlands). Concentrations of labeled cRNA and the label incorporation was determined using Nanodrop-1000 spectrophotometer.

growth_protocol: 25°C, 16:8 light:dark photoperiod, fed live Artemia

extract_protocol: Gonads were thawed, homogenized and total RNA extracted with TRI Reagent® (Sigma-Aldrich, St. Louis, MO) following the manufacturer’s protocol. Total RNA was quantified using a nanodrop ND-100 spectrophotometer (Nanodrop technologies, Wilmington, DE). Integrity and purity of RNA samples was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Paulo Alto, CA) and an RNA Pico Chip Kit (Agilent).

treatment_protocol: fish were humanely euthanized in buffered tricaine methanesulfonate (Finquel, Argent, Redmond, WA, USA).

tag: Gender

value: Female

tag: Age

value: 7 months

tag: Strain

value: ab wild-type strain

tag: Tissue

value: Gonad

tag: Sample

value: Total RNA

source_name: Reference - pool of gonads and brains from males and females, and livers from females

extract_protocol: Tissues were thawed, homogenized and total RNA extracted with TRI Reagent® (Sigma-Aldrich, St. Louis, MO) following the manufacturer’s protocol. Total RNA was quantified using a nanodrop ND-100 spectrophotometer (Nanodrop technologies, Wilmington, DE). Integrity and purity of RNA samples was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Paulo Alto, CA) and an RNA Pico Chip Kit (Agilent).

value: Females and Males

value: gonads and brains from males and females, livers from females


title: Sample 78 - Ovary exposed to 7 mg O2/L for 4 d


title: Sample 50 -Ovary exposed to 7 mg O2/L for 4 d


title: Sample 75 - Ovary exposed to 7 mg O2/L for 4 d


title: Kidney_1K_SBH1 (male)

status: Public on Feb 03 2009

city: Ashkelon

first: Yoram

last: Yagil

address: Hahistadrut

country: Israel

institute: Ben-Gurion University, Barzilai Medical Center Campus

description: Expression data from male rat kidney

hyb_protocol: Following fragmentation, we hybridized cRNA overnight at 450C on GeneChip 230 2.0 Array. We washed the GeneChips and stained them in an Affymetrix Fluidics Station.

scan_protocol: We scanned the GeneChips using the GenChip Scanner 3000Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with the GeneChip Operating Software (GCOS); the arrays were normalized by the log scale Robust Multiaray Analysis (RMA)

label: Biotin

organism: Rattus norvegicus

label_protocol: We used the Genechip Affymetrix labeling kit and the standard protocol recommended by Affymetrix

growth_protocol: We fed the animals standard rat chow and provided water ad libitum

extract_protocol: We extracted total RNA using the RNeasy mini-kit from QIAGEN (Cat #74104)

tag: Strain:SBH/y after right uninephrectomy Gender:Male Age:4 months Diet:Regular rat chow


title: Transient ERG expression in 293HEK cells duplicate

city: New York

first: Brett

middle: S

last: Carver

state: NY

address: 1275 York Ave

department: Surgery

institute: Memorial Sloan-Kettering Cancer Center

description: 293 HEK cells transiently transfected with ERG or vector control

hyb_protocol: Following fragmentation 12 ug of cRNA were hybridized to Affymetrix HG-U133A chip according to standard protocol

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray scanner

data_processing: The data were processed into CHP and CEL files and analyed using GeneSpring software.

label: biotin

organism: Homo sapiens

source_name: 293 HEK cells

label_protocol: Biotinylated cRNA were prepared from 2ug total RNA

extract_protocol: Cells were incubated with Trizol and RNA was harvested according to the standard Trizol protocol.  RNA was then treated with DNAse.

tag: 293 HEK cells expressing ERG duplicate


title: Sample 53 - Ovary exposed to 7 mg O2/L for 4 d


title: Sample 88 - Ovary exposed to 3 mg O2/L for 4 d


title: Control 2

city: Winston-Salem

first: Charles

last: Wood

state: NC

address: Medical Center Blvd

department: Pathology

institute: Wake Forest University School of Medicine

description: Data were extracted from scanned images using GeneChip Operating Software(Affymetrix, Inc., Santa Clara,CA.

hyb_protocol: Standard Affymetrix protocol for Eukaryotic samples.  For each sample, ten µg of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to a Rhesus Macaque Microarray for 16 hours at 45ºC.  Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.

scan_protocol: Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000.

data_processing: Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.  The samples were analyzed using the MAS5 algorithm in Affymetrix Expression Console.

label: Biotin dye

organism: Macaca fascicularis

source_name: postmenopausal endometrium, Control 2

label_protocol: Enzo Bioarray kit.  Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences).  After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences).  The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).

extract_protocol: Total RNA was extracted from frozen endometrial samples using Tri Reagent (Molecular Research Center, Cincinnati,OH); purified using RNeasy Mini Kit (Qiagen, Valencia,CA); and quantified using NanoDrop ND1000 UV-vis spectrophotometer(NanoDrop, Wilmington,DE). RNA intactness and quality was confirmed using an Agilent 2100 Bioanalyzer (Wilmington,DE).

tag: Adult female ovariectomized macaque

tag: normal endometrium


title: Sample 49 - Ovary exposed to 7 mg O2/L for 4 d


title: Control 1

source_name: postmenopausal endometrium, Control 1

tag: adult female ovariectomized macaque


title: Sample 86 - Ovary exposed to 3 mg O2/L for 4 d


title: Sample 92 - Ovary exposed to 1 mg O2/L for 4 d


title: Sample 90 - Ovary exposed to 1 mg O2/L for 4 d


title: Sample 69 - Ovary exposed to 1 mg O2/L for 4 d

label_protocol: RNA from each condition of interest (treatment) was labeled with a Cy5 dye and hybridized onto arrays together with Cy3 labeled RNA taken from a standard reference pool of RNA extracted from sexually mature male and female gonads and brains, and female livers. For the microarray analyses, total RNA was amplified using Agilent low input linear amplification kit according to the process outlined by the manufacturer (Agilent Technologies). Amplified target cRNA (1-5 µg) was labeled with either cyanine-5 or cyanine-3 using ULS aRNA Flurorescent Labeling Kits from Kreatech according to the manufacturers protocol (Kreatech Biotechnology, Amsterdam, The Netherlands). Concentrations of labeled cRNA and the label incorporation was determined using Nanodrop-1000 spectrophotometer


title: Sample 85 - Ovary exposed to 3 mg O2/L for 4 d


title: Sample 65 - Ovary exposed to 1 mg O2/L for 4 d


title: Sample 74 - Testis exposed to 7 mg O2/L for 4 d

value: Male


title: Sample 84 - Ovary exposed to 3 mg O2/L for 4 d


title: Sample 77 -Testis exposed to 7 mg O2/L for 4 d


title: Sample 79 - Testis exposed to 7 mg O2/L for 4 d


title: Sample 93 - Testis exposed to 1 mg O2/L for 4 d


title: Sample 54 - Testis exposed to 7 mg O2/L for 4 d


title: Sample 83 - Testis exposed to 3 mg O2/L for 4 d


title: Sample 81 - Testis exposed to 3 mg O2/L for 4 d


title: Sample 87 - Testis exposed to 3 mg O2/L for 4 d


title: Sample 51 - Testis exposed to 7 mg O2/L for 4 d


title: Sample 82 - Testis exposed to 3 mg O2/L for 4 d


title: Sample 127 - Testis exposed to 7 mg O2/L for 14 d


title: Sample 89 - Ovary exposed to 1 mg O2/L for 4 d


title: Sample 103 -Testis exposed to 7 mg O2/L for 14 d

treatment_protocol: Fish were humanely euthanized in buffered tricaine methanesulfonate (Finquel, Argent, Redmond, WA, USA).


title: Sample 112 -Testis exposed to 3 mg O2/L for 14 d


title: Sample 68 - Testis exposed to 1 mg O2/L for 4 d


title: Sample 124 - Testis exposed to 7 mg O2/L for 14 d


title: Sample 91 - Testis exposed to 1 mg O2/L for 4 d


title: Sample 66 - Ovary exposed to 1 mg O2/L for 4 d


title: Sample 126 - Testis exposed to 7 mg O2/L for 14 d


title: Sample 111 - Testis exposed to 3 mg O2/L for 14 d


title: Sample 122 - Testis exposed to 7 mg O2/L for 14 d


title: Sample 94 - Testis exposed to 1 mg O2/L for 4 d


title: Sample 130 - Testis exposed to 3 mg O2/L for 14 d


title: Sample 116 - Testis exposed to 1 mg O2/L for 14 d


title: Sample 115 - Ovary exposed to 1 mg O2/L for 14 d

description:
Sample 115 - Ovary exposed to 7 mg O2/L for 14 d
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

tag: Characteristics


title: Sample 105 - Ovary exposed to 3 mg O2/L for 14 d

description:
Sample 105 - Ovary exposed to 7 mg O2/L for 14 d
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: Sample 119 -Testis exposed to 1 mg O2/L for 14 d


title: Sample 108 - Ovary exposed to 3 mg O2/L for 14 d

description:
Sample 108 - Ovary exposed to 7 mg O2/L for 14 d
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: Sample 138 - Testis exposed to 1 mg O2/L for 14 d


title: Sample 113 - Ovary exposed to 1 mg O2/L for 14 d

description:
Sample 113 - Ovary exposed to 7 mg O2/L for 14 d
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: Sample 117-Ovary exposed to 1 mg O2/L for 14 d

description:
Sample 117 - Ovary exposed to 7 mg O2/L for 14 d
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: Sample 134 - Testis exposed to 3 mg O2/L for 14 d


description:
Sample 123 - Ovary exposed to 7 mg O2/L for 14 d
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: Sample 67 - Testis exposed to 1 mg O2/L for 4 d


title: Sample 140 - Ovary exposed to 1 mg O2/L for 14 d

description:
Sample 140 - Ovary exposed to 7 mg O2/L for 14 d
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: Sample 114 - Testis exposed to 1 mg O2/L for 14 d


title: Sample 141 - Testis exposed to 1 mg O2/L for 14 d


title: Sample 136 - Ovary exposed to 3 mg O2/L for 14 d

description:
Sample 136 - Ovary exposed to 7 mg O2/L for 14 d
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: Sample 135 - Testis exposed to 3 mg O2/L for 14 d


description:
Sample 128 - Ovary exposed to 7 mg O2/L for 14 d
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: Sample 139-Ovary exposed to 1 mg O2/L for 14 d

description:
Sample 139 - Ovary exposed to 7 mg O2/L for 14 d
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

source_name: Sample 139 - Ovary exposed to 1 mg O2/L for 14 d


title: Sample 107 - Ovary exposed to 3 mg O2/L for 14 d

description:
Sample 107 - Ovary exposed to 7 mg O2/L for 14 d
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: Sample 132 - Ovary exposed to 3 mg O2/L for 14 d

description:
Sample 132 - Ovary exposed to 7 mg O2/L for 14 d
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.


description:
Sample 101 - Ovary exposed to 7 mg O2/L for 14 d
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

source_name: Sample 101 - Ovary exposed 7 to mg O2/L for 14 d

source_name: Reference – pool of gonads and brains from males and females, and livers from females


title: Sample 121 - Ovary exposed to 7 mg O2/L for 14 d

tag: Reference – pool of gonads and brains from males and females, and livers from females


title: Sante_Compost_Water_rep4

city: Wageningen

first: Jeroen

last: van Dijk

address: Bornsesteeg 45

country: Netherlands

institute: RIKILT, institute of food safety

description: Biological replicate 4 of 4

hyb_protocol: 1 μl of luciferase RNA (Invitrogen) was added to each sample. Labeled cDNA was dissolved in 40 μl of hybridisation buffer containing 5xSSC, 0.2% SDS, 5xDenhardt’s, 50% (v/v) formamide and 0.2 mg/ml denatured herring sperm DNA. The hybridisation was performed in a hybridisation frame (Geneframe, Implen, Munich, Germany) in 80 μl of hybridisation buffer containing Cy5-labelled potato tuber RNA and Cy3-labelled universal control cDNA, in equal volumes. Slides were hybridised overnight at 42°C in a hybridisation chamber in darkness. After hybridisation the slides were washed twice with 1xSSC/0.1%SDS (5min), twice with 0.1xSSC/0.1%SDS (5 min), twice with 0.1xSSC (5min and 1 min) and dried by centrifugation (1 min, 800 g).

scan_protocol: Microarrays were scanned after excitation of Cy5 dye with 633 nm laser and Cy3 dye with 543 nm laser using scanner ScanArray® Express HT (Perkin Elmer, USA). The microarrays were scanned at constant laser power (90 %) and 10 μm resolution settings.Tiff images were imported into the ArrayVision software (Imaging Research, Waalwijk, The Netherlands) and the fluorescent intensity, background and signal-to-noise ratio were determined for each spot.

data_processing: Quality checked, Filtering of spots with singnal to noise ratio below 3, Median normalized, VALUE data obtained from log2 of processed Cy5 signal/processed Cy3 signal. R statistical software and Genemaths XT®s software (Applied Maths, St-Martens-Latem, Belgium) was used for analysis.

organism: Solanum tuberosum

source_name: treatment Sante_Compost_Water

label_protocol: 25 µg of total RNA was primed with 2 µl 21-mer oligo-dT primer (1ug/ml) at 25°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 150 U SuperScript II RTase (Invitrogen), and 500 µM each dATP, dTTP, dGTP, with 40 µM dCTP Cy5-labeled

growth_protocol: Potatoes were grown at Nafferton Experimental Farm (University of Newcastle) under organic farming practices in a completely randomised block design with 4 replicate blocks; with all combinations of variety, fertilisation and crop protection being established on one plot in each block (size of individual plots 15 x 6 m)

extract_protocol: Total RNA extraction following a protocol for extraction of RNA from polysaccharide rich tissues  (Chang et al.,2003,Plant Molecular Biology Reporter, 11: 113–116)

treatment_protocol: Potatoes were planted into soils to which either chicken manure pellets or dairy manure compost were applied at a rate equivalent to 170 kgN/ha. The foliage of developing potato crops was then sprayed with either (a) Cu-oxychloride (product Headland Copper, 2 applications of 7.5 l/ha, equivalent to 3 kg Cu/ha), (b) an extract of Lychnis viscaria L. (German catch fly) that contains brassinosteroids known to induce plant resistance (product COMCAT, 2 applications of 200 g/ha) (c) water (at the same volume as used for the Cu-fungicide and alternative treatment sprays) as a control treatment.

tag: Cultivar

value: Sante

tag: Input regime

value: organic

tag: Sample size

value: 4-5 tubers

value: tuber

tag: Fertilizer

value: dairy manure compost

tag: Plant protection

value: Water

source_name: Universal control

tag: mixture of PCR products spotted on the microarray in vitro transcribed to RNA


title: Sante_Compost_CopperOxychloride_rep4

description: Biological replicate 4 of 4

value: Copper oxychloride


title: Sante_Compost_Comcat_rep4

description: Biological replicate 4 of 4

source_name: treatment Sante_Compost_Comcat

value: Comcat


title: N-2

city: Princeton

first: Patrick

middle: H

last: Bradley

state: NJ

address: 119 Lewis Thomas Labs

department: Molecular Biology

institute: Princeton University

hyb_protocol: reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=48835

scan_protocol: Pixel Size : 10 Scan Date : 2006-01-21 Scan Time : 13:51:51 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : A.7.5.1
Datafile type : Agilent result file

organism: Saccharomyces cerevisiae

source_name: Pre-starvation

label_protocol:
Type of label : Cy3
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32636

growth_protocol: media : YNB with glucose and ammonium

extract_protocol: Extraction method : Qiagen Rneasy Kit

tag: Strain Name

source_name: Nitrogen-starved 2 hr

label_protocol:
Type of label : Cy5
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32636

growth_protocol: media : YNB/agarose with glucose and no ammonium

treatment_protocol: Time : 2h


title: Sante_ChickenPellets_Comcat_rep4

description: Biological replicate 4 of 4

source_name: treatment Sante_ChickenPellets_Comcat

value: chicken manure pellets


title: N-8

scan_protocol: Pixel Size : 10 Scan Date : 2006-01-21 Scan Time : 13:11:59 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Nitrogen-starved 8 hr

treatment_protocol: Time : 8h


title: N-0.16

scan_protocol: Pixel Size : 10 Scan Date : 2006-01-21 Scan Time : 13:19:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Nitrogen-starved 10 min


title: LadyBalfour_Compost_CopperOxychloride_rep4

description: Biological replicate 4 of 4

value: LadyBalfour


title: LadyBalfour_Compost_Water_rep4

description: Biological replicate 4 of 4

source_name: treatment LadyBalfour_Compost_Water


title: LadyBalfour_Compost_Comcat_rep4

description: Biological replicate 4 of 4

source_name: treatment LadyBalfour_Compost_Comcat


title: Sante_ChickenPellets_CopperOxychloride_rep4

description: Biological replicate 4 of 4


title: C-4

scan_protocol: Pixel Size : 10 Scan Date : 2006-01-21 Scan Time : 13:27:48 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Carbon-starved 4 hr

growth_protocol: media : YNB/agarose with ammonium and no glucose

treatment_protocol: Time : 4h


title: N-4

scan_protocol: Pixel Size : 10 Scan Date : 2006-01-21 Scan Time : 14:00:12 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Nitrogen-starved 4 hr


title: C-2

scan_protocol: Pixel Size : 10 Scan Date : 2006-01-21 Scan Time : 13:04:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Carbon-starved 2 hr


title: Sante_ChickenPellets_Water_rep4

description: Biological replicate 4 of 4

source_name: treatment Sante_ChickenPellets_Water


title: C-0.16

scan_protocol: Pixel Size : 10 Scan Date : 2006-01-21 Scan Time : 12:56:09 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Carbon-starved 10 min


title: N-0.5

scan_protocol: Pixel Size : 10 Scan Date : 2006-01-21 Scan Time : 12:48:05 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Nitrogen-starved 30 min

treatment_protocol: Time : 0.5h


title: C-1

scan_protocol: Pixel Size : 10 Scan Date : 2006-01-21 Scan Time : 13:43:42 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Carbon-starved 1 hr

treatment_protocol: Time : 1h


title: N-1

source_name: Nitrogen-starved 1 hr


title: C-0.5

source_name: Carbon-starved 30 min


title: C-8

scan_protocol: Pixel Size : 10 Scan Date : 2006-01-21 Scan Time : 14:16:10 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Carbon-starved 8 hr


title: LadyBalfour_ChickenPellets_Water_rep4

description: Biological replicate 4 of 4

source_name: Universal control


title: LadyBalfour_ChickenPellets_CopperOxychloride_rep4

description: Biological replicate 4 of 4


title: Sante_Compost_Comcat_rep3

description: Biological replicate 3 of 4

source_name: treatment Sante_Compost_Comcat


title: Sante_ChickenPellets_Water_rep3

description: Biological replicate 3 of 4


title: Sante_ChickenPellets_CopperOxychloride_rep3

description: Biological replicate 3 of 4


title: LadyBalfour_ChickenPellets_Water_rep3

description: Biological replicate 3 of 4


title: Sante_Compost_Water_rep3

description: Biological replicate 3 of 4

source_name: treatment Sante_Compost_Water


title: Sante_Compost_CopperOxychloride_rep3

description: Biological replicate 3 of 4


title: Sante_Compost_Comcat_rep2

description: Biological replicate 2 of 4


title: Sante_Compost_CopperOxychloride_rep2

description: Biological replicate 2 of 4


title: LadyBalfour_Compost_Comcat_rep3

description: Biological replicate 3 of 4


title: LadyBalfour_Compost_Water_rep3

description: Biological replicate 3 of 4


title: Sante_ChickenPellets_Comcat_rep3

description: Biological replicate 3 of 4

source_name: treatment Sante_ChickenPellets_Comcat


title: Sante_ChickenPellets_Water_rep2

description: Biological replicate 2 of 4


title: LadyBalfour_Compost_CopperOxychloride_rep3

description: Biological replicate 3 of 4


title: LadyBalfour_ChickenPellets_Comcat_rep4

description: Biological replicate 4 of 4


title: Sante_ChickenPellets_CopperOxychloride_rep2

description: Biological replicate 2 of 4


title: LadyBalfour_ChickenPellets_Comcat_rep3

description: Biological replicate 3 of 4


title: Sante_Compost_Water_rep2

description: Biological replicate 2 of 4


title: LadyBalfour_ChickenPellets_CopperOxychloride_rep3

description: Biological replicate 3 of 4


title: Sante_ChickenPellets_Comcat_rep2

description: Biological replicate 2 of 4


title: LadyBalfour_Compost_Water_rep2

description: Biological replicate 2 of 4


title: LadyBalfour_Compost_CopperOxychloride_rep2

description: Biological replicate 2 of 4


title: Sante_Compost_Water_rep1

description: Biological replicate 1 of 4


title: LadyBalfour_ChickenPellets_Water_rep2

description: Biological replicate 2 of 4


title: LadyBalfour_Compost_Comcat_rep2

description: Biological replicate 2 of 4


title: LadyBalfour_ChickenPellets_CopperOxychloride_rep2

description: Biological replicate 2 of 4


title: LadyBalfour_ChickenPellets_Comcat_rep2

description: Biological replicate 2 of 4


title: Sante_Compost_Comcat_rep1

description: Biological replicate 1 of 4


title: Sante_ChickenPellets_Water_rep1

description: Biological replicate 1 of 4


title: LadyBalfour_Compost_Comcat_rep1

description: Biological replicate 1 of 4


title: Sante_ChickenPellets_CopperOxychloride_rep1

description: Biological replicate 1 of 4


title: Sante_Compost_CopperOxychloride_rep1

description: Biological replicate 1 of 4


title: LadyBalfour_Compost_CopperOxychloride_rep1

description: Biological replicate 1 of 4


title: LadyBalfour_ChickenPellets_Water_rep1

description: Biological replicate 1 of 4


title: Sante_ChickenPellets_Comcat_rep1

description: Biological replicate 1 of 4


title: LadyBalfour_Compost_Water_rep1

description: Biological replicate 1 of 4


title: root_rep1

description: root of 7-day-old seedlings

hyb_protocol: Affymetrix® GeneChip® Operating Software Version 1.0 was used for washing, staining, and scanning as described in the supplier’s protocol.

scan_protocol: Scanning procedures of the arrays were carried out using Affymetrix GeneChip Scanner 3000 as described in the Affymetrix technical manual.

data_processing: The data was 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 500.

source_name: root

label_protocol: RNA was labeled for use with the Affymetrix GeneChip Rice Genome array according to the manufactures protocol. (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Rice (Oryza sativa, japonica cultivar Zhonghua 11), was cultivated at day/night temperatures (28/22 °C) in phytotron

extract_protocol: RNA was extracted using the TRIzol method (Invitrogen).

tag: root


title: root_rep2

description: root of 7-day-old seedlings


title: leaf_rep1

description: leaf of 7-day-old seedlings

source_name: leaf

tag: leaf


title: endo6D_rep2

description: endosperm of seed collected at 6 days after anthesis (DAA)

source_name: endosperm

tag: endosperm


title: seedling_rep2

description: 10-day-old seedling

source_name: seedling

tag: seedling


title: seedling_rep1

description: 10-day-old seedling


title: leaf_rep2

description: leaf of 7-day-old seedlings


title: LadyBalfour_ChickenPellets_Comcat_rep1

description: Biological replicate 1 of 4

tag: Tissue


title: emb6D_rep2

description: embryo of seed collected at 6 days after anthesis (DAA)

source_name: embryo

tag: embryo


title: endo6D_rep1


title: T174 (T-ALL_#9)

status: Public on Jan 15 2009

type: genomic

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167.

molecule: genomic DNA

source_name: T-ALL blasts

label_protocol: Random 9-mers pre-labeled with either Cy3 or Cy5

extract_protocol: Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)

tag: Male, 23 years, CD7++, CD2+-, CD5+-, CD1a+, cyCD3++, CD4+, CD8 +-, cyTdT+, CD45 dim

tag: MspI representation of genomic DNA

tag: HpaII representation of genomic DNA


title: T163 (T-ALL_#8)

tag: Male, 18 years, CD7+, CD2+, CD5+, CD1a+, cyCD3+, CD4+, CD8 +-, cyTdT+, CD45 dim


title: T069 (T-ALL_#4)

tag: Male, 29 years, TCRab+ CD7+, CD2+, CD5+-, CD1a+-, cyCD3+, CD3+, CD4+, CD10+-, cyTdT+, CD45 dim


title: emb6D_rep1


title: T059 (T-ALL_#3)

tag: Male, 35 years, CD7+, CD2+, CD5+, CD1a+, cyCD3+, CD4+, CD8 +-, CD10+, cyTdT+, CD45 dim


title: T162 (T-ALL_#7)

tag: Male, 39 years, TCRgd+-, TCRab+-, CD7+, CD2+, CD5+, CD1a+, cyCD3+, CD3+ CD4+, CD8 +-, CD10+ cyTdT+, CD45 dim


title: T140 (T-ALL_#5)

tag: Male, 29 years, TCRab+, CD7+, CD2+, CD5+, cyCD3+, CD3+, CD4+, CD8 +-, cyTdT+, CD45 dim


title: T034 (T-ALL_#1)


title: T057 (T-ALL_#2)

tag: Male, 31 years, CD7+, CD2+, CD5+, cyCD3+, cyTdT+, CD45 dim


title: CD34+_Normal_#8

source_name: Bone marrow CD34+ cells

tag: CD34+ cells from bone marrow of healthy donor


title: CD34+_Normal_#6


title: CD34+_Normal_#5


title: CD34+_Normal_#4


title: CD34+_Normal_#7


title: CD34+_Normal_#3


title: CD34+_Normal_#1


title: LadyBalfour_ChickenPellets_CopperOxychloride_rep1

description: Biological replicate 1 of 4

tag: Cultivar

tag: Input regime

tag: Sample size

tag: Fertilizer

tag: Plant protection

tag: mixture of PCR products spotted on the microarray in vitro transcribed to RNA


title: CD34+_Normal_#2


title: 3327 (CEBPAmutantAML_#8)

source_name: AML blasts, CEBPA mutant

tag: Female, 59 years, FAB M1, Normal cytogenetics, CEBPA mut +


title: 2242 (CEBPAmutantAML_#4)

tag: Female, 54 years, FAB M1, Cytogenetics

value: del9q, CEBPA mut +


title: 2545 (CEBPAmutantAML_#6)

tag: Male, 24 years, FAB M1, Normal cytogenetics, CEBPA mut +

tag: MspI representation of genomic DNA


title: 2192 (CEBPAmutantAML_#2)

tag: Male, 45 years, FAB M1, Normal cytogenetics, CEBPA mut +

tag: HpaII representation of genomic DNA


title: 2218 (CEBPAmutantAML_#3)

tag: Male, 40 years, FAB M1, Normal cytogenetic, CEBPA mut +


title: 3491 (CEBPAsilencedAML_#6)

source_name: AML blasts, CEBPA silenced

tag: Male, 72 years, FAB M1, CEBPA silenced, Normal cytogenetics


title: 6947 (CEBPAsilencedAML_#7)

tag: Male, 21 years, FAB M1, CEBPA silenced, 47,XY,+19[22]


title: 2273 (CEBPAmutantAML_#5)

tag: Male, 16 years, FAB M1, Normal cytogenetics, CEBPA mut +


title: 7076 (CEBPAsilencedAML_#8)

tag: Female, 40 years, FAB M0, CEBPA silenced,  46,XX,del(6)(q13q23)[16];46,XX[4].nuc ish(MLLx2)[200]


title: 1316 (CEBPAmutantAML_#1)

tag: Male, 19 years, FAB M1, CEBPA mut +, normal cytogenetics


title: 2753 (CEBPAmutantAML_#7)

tag: Male 34 years, FAB M1, Cytogenetics


title: 3314 (CEBPAsilencedAML_#4)

tag: Male, 31 years, Complex karyotype, CEBPA silenced


title: 2668 (CEBPAsilencedAML_#2)

tag: Female, 41 years, CEBPA silenced, FAB M0, Complex karyotype


title: 2238 (CEBPAsilencedAML_#1)

tag: Male, 21 years, CEBPA silenced, FAB M1, Normal cytogenetics


title: 3483 (CEBPAsilencedAML_#5)

tag: Male, 45 years, FAB M1, 46,XY,add(2)(q35)[13]/46,XY[19], CEBPA silenced


title: Oviduct_from_Unmated_sample1

status: Public on Nov 24 2008

city: Rehovot

first: Yael

last: Heifetz

address: POB 12

institute: The Hebrew university of Jerusalem

description: Three-day-old mated and unmated females were dissected to remove the oviduct. Mated females were dissected at 3 hrs following the termination of mating. Tracts of 400-500 females of unmated and mated were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Department of Biological Services, Weizmann Institute. Arrays from mated females were compared to unmated females.

hyb_protocol: According to Affymetrix protocols.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 6G System

data_processing: RMA (Irizarry 2003), probe-based linear model (Chu et al 2002)

organism: Drosophila melanogaster

source_name: oviduct from 3-day-old unmated female

label_protocol: Enzo RNA transcript Labeling Kit, According to Affymetrix protocols.

growth_protocol: All flies were kept in a 12hr light/dark cycle at 23±2 Celsius degrees.

extract_protocol: TRIzol - chloroform

treatment_protocol: Females were all same age (3-day-old) and either mated or not. Mated females were dissected at 3 hrs postmating. Unmated (control) females were dissected at parallel times.

tag: oviduct from 3-day-old unmated female


title: Invasive Mammary carcinoma 2

status: Public on Oct 28 2008

city: sakuragaoka

first: souda

last: masakazu

state: kagoshima/kagoshima

department: tumor pathology, field of oncology

country: Japan

institute: kagoshima university graduate school of medical and dental sciences

description: Mammary glands and visible tumors were quickly excised with sharp scissors. For histological examination, left abdominal mammary glands and tumors were fixed in 10% phosphate-buffered formalin, dehydrated, embedded in paraffin, and stained with a hematoxylin and eosin (H.E.) solution. To detect DCIS by microscopic examination of whole mount specimens, the right mammary glands were fixed with 10% phosphate-buffered formalin for 24 hours, stained with alum carmine for 24 hours, and stored in cedar oil.

hyb_protocol: The hybridization solution was prepared using the gene expression hybridization kit (Agilent). The Agilent 60-mer array (G4130B) contains 20600 rat probe sequence. 1.5 µg of labeled cRNA and 10 µl of 25×fragmentation buffer were incubated at 60℃ for 30 minutes. Hybridization was carried out in 490 µl of a hybridization mixture at 60℃ for 17 hours in Agilent’s microarray hybridization chambers according to the Agilent protocol. The microarray slides were washed for approximately 1 minute each in gene expression wash buffer 1, wash buffer 2 and Acetonitrile according to the Agilent protocol. The Cy3 fluorescence intensities were determined by an Agilent DNA Microarray Scanner and then were analyzed by Feature Extraction software 9.1 (Agilent).

scan_protocol: Essential experimental and data processing protocols scanning protocol of raw data (one-color ) by Agilent microarray scanner 1. scan area : 61×21.6mm 2. scan resolution : 10µm 3. dye channel : green 4. green PMT : 100%  2) Image analysis and digitalization 1. software : Agilent’s Feature Extraction Ver. 9.1 2. File for spot finding using the Agilent scanner and Agilent’s Feature Extraction software : File name 013328_D_20060331.xml.zip 3. Grid : 013328_D_20060331 Image : US22502707_SLOT Protocol : GE1-v1_91

data_processing: Gene expression data 1.Normalization After subtracting the local and global background signals. The data flagged as being of poor quality according to the Agilent data extraction software were removed from the analysis. All data calculated by Feature Extraction software were imported to the GeneSpring GX 7.3.1 (Agilent). All the intensity data were then normalized by standard one-color normalization (Data transformation: set measurements less than 0.01 to 0.01, per chip: normalize to 50 percentile, per gene: normalize to specific sample).

source_name: mammary carcinoma

label_protocol: Equal quantities of total RNA from each sample were labeled using Agilent low RNA input linear amplification kit, and hybridized to Agilent oligonucleotide probe sequence. Briefly, total RNA (<100ng) was reverse transcribed into cDNA, using Moloney murine leukemia virus reverse transcriptase with T7 promoter primer, and incubated at 40℃ for 2 hours. Fluorescent cRNA were synthesized by in vitro transcription using T7 RNA polymerase and labeled with cyanine 3 (Cy3). Labeled cRNA were further purified using RNase mini purification columns (Qiagen) to remove unlabeled products. 1.5 µg of the fluorescently labeled cRNA were used for each of the microarray hybridization. The purity and concentration of amplified RNA were determined by Agilent 2100 Bioanalyzer.

extract_protocol: For frozen sampling, the abdominal mammary glands (numbers 4-6) and mammary tumors in the rat were quickly excised with a sharp scissor and were immediately embedded in a Tissue Tek OTC compound medium (Sakura, Tokyo, Japan) containing RNase-free water (1:1) and stored at－80℃ until LMD.   For LMD, the Application Solutions Laser Microdissection System (Leica Microsystems, Wetzlar, Germany) were used. Serial 6 µm-thick sections were prepared with a cryostat and were mounted onto a foil-coated glass slide (Matsunami Glass Ind., Ltd., Osaka, Japan). The section were then fixed in 5% acetic acid/ethanol for 3 minutes and stained with 0.05% to toluidine blue O (Merck KGaA, Darmstadt, Germany) for 10 second to maintain the morphologic quality required for accurate microdissection. The section was then washed, dehydrated, cleared in xylene. After careful drying, the sections were laser microdissected according to the manufacture’s instructions (Leica Microsystems).   Total RNA were extracted from each sample of laser microdissected cells into 350 µL of buffer RLT (Qiagen, Hilden, Germany) added β-mercaptoethanol to a concentration of 1%. Next, total RNA were purified with the RNeasy Mini kit (Qiagen) following by DNase treatment according to the manufacture’s protocol. The integrity of intact total RNA was verified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: The animals were female inbred Sprague-Dawley rats, maintained in a filtered air laminar flow at the Division of Laboratory Animal Science, Research Center for Life Science Resources, Kagoshima University. They were given a commercial diet (CE-2, CLEA Inc., Tokyo, Japan) and tap water ad libitum. The use of animals in this research complied with all relevant guidelines set by the Japanese government and Kagoshima University. At 50 days after birth, rats were given 1ml of sesame oil (control) or 20 mg of DMBA (Nacalai tesque, Inc. Kyoto Japan) dissolved in 1ml of sesame oil, by gastric intubation. Animals in the control group and DMBA-treated group were euthanized after 2 weeks (W) (n=20, n=22), 6W (n=17, n=20) and 8W (n=18, n=20), respectively.  We used by for each 1 for microarrays analysis

tag: characteristics

value: inbred Sprague-Dawley female rats.    Age:64 days (each 2 sample, control and DMBA-TEB), 92 (1 sample, DCIS), 106 days(1 sample, MC).

tag: 8 weeks of age

tag: disease


title: hESC-2

status: Public on Dec 06 2008

city: Stanford

first: Kitchener

middle: D.

last: Wilson

state: CA

address: S140 Grant Bldg

institute: Stanford University

hyb_protocol: 825 ng of Cy3- and Cy5- labeled and amplified cRNA was mixed and fragmented according to the Agilent technology protocol. cRNA was hybridized to 4x44K whole human genome microarray slides from Agilent (Part G4112F) according to the manufacturer’s instructions. The hybridization was carried in a rotating hybridization chamber in the dark at 65°C for 17 h.

scan_protocol: The array was scanned using Agilent G2505B DNA microarray scanner.

data_processing: The image files were extracted using Agilent Feature Extraction software version 9.5.1 applying LOWESS background subtraction and dye-normalization.

label_protocol: Using Low RNA Input Fluorescent Linear Amplification Kits (Agilent Technologies, Santa Clara, CA, USA), cDNA was reverse transcribed from each RNA sample, and cRNA was then transcribed and fluorescently labeled from each cDNA sample.

extract_protocol: Total RNA was isolated as described previously in Trizol (Invitrogen) followed by purification over a Qiagen RNeasy column (Qiagen).

tag: Undifferentiated human embryonic stem cells

source_name: Pooled Reference

tag: Pooled RNA from undifferentiated and differentiated hESCs


title: M. sedula grown on yeast extract + elemental sulfur (YS) vs. yeast extract (Y)

status: Public on Oct 22 2008

city: Raleigh

first: Kathryne

middle: Sherlock

last: Auernik

address: Partners II, rm 3309, 849 Main Campus Drive

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

description: Scatterplots of signal intensities are reviewed to check for balance between channels.

hyb_protocol: Sample preparation steps for microarray hybridization: Prepare Prehyb buffer: 225mL water, 75mL 20X SSC, 0.3g SDS, 0.3g BSA. Preheat Prehyb buffer 45 min 42 degree C. Prehybidize slides at 42 degree C for 45 min. Wash slides by dipping 5 time in sterile dH2O at RT. Dip twice in isopropanol at RT. Dry slide in slide spinner. Add 1 ul COT1-DNA (20mg/ml) to samples. Heat probe mixture to 95oC in heat block for 2 min to denature DNA, do a quick spin. Add 30 ul of 2x hyb. buffer that has been preheated to 42oC to each tube. Hybridization buffer: 27.2uL water, 20uL 20X SSC, 8uL 50X Denhardts solution, 24uL formamide, 0.8uL 10% SDS. Apply hyb. mix to slide and cover with a 20x60 mm polyethylene hydrophobic coverslip. Place slide in water proof container, cover well with foil and place in 42 degree C bath for 18-20 hours. The following is a standard hybridization method that seems to work well for this procedure: 1 wash cycle at 42 degree C with 2X SSC w/ 0.2% SDS. 1 wash cycle at RT with 0.5X SSC w/ 0.2% SDS. 3 wash cycles at RT with 0.5X SSC

scan_protocol: Images were aquired with a Perkin Elmer ScanArray Lite scanner containing 2 lasers. Channels were balanced using the line scan feature and by balancing the overall signals without the use of external standards

data_processing: Signals for each channel were obtained using ScanArray® Express 2.1 software using histogram quantitation and total normalization options to produce raw data, followed by manual verification of spot identification. Once all slides were quantitated, data from the experimental loop were analyzed with JMP Genomics 3.1 (SAS, NC), using a mixed effects ANOVA model [Wolfinger et al. J Comput Biol 8 625-637 (2001)].

label: Cy™3 dye (GE Healthcare)

organism: Metallosphaera sedula

label_protocol: Purified RNA was reverse transcribed using Superscript III (Invitrogen), re-purified, labeled with Cy3 dye (GE Healthcare), and hybridized to an Mse microarray slide (Corning).

growth_protocol:
Cells (DSMZ 5348) were grown aerobically at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2), supplemented with 0.1% yeast extract (Y). An initial density of mid 10^6 cells/mL was used in [two] 1 L bottles containing 300 mL volume of the same medium.
Mse was subcultured at least 3 times in Y-supplemented DSMZ 88 media.

extract_protocol: At harvest, cells were quickly chilled and then centrifuged at 9510 x g for 15 minutes at 4C. RNA was extracted and purified using an RNAqueous kit (Ambion).

treatment_protocol: Harvest of final passage occurred at mid-10^7 cells/mL (~24hrs post-inoculation).

tag: whole cells

label: Cy™5dye (GE Healthcare)

label_protocol: Purified RNA was reverse transcribed using Superscript III (Invitrogen), re-purified, labeled with Cy5 dye (GE Healthcare), and hybridized to an Mse microarray slide (Corning).

growth_protocol:
Cells (DSMZ 5348) were grown aerobically at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2), supplemented with 0.1% yeast extract + 20g/L elemental sulfur(YS). An initial density of mid 10^6 cells/mL was used in [two] 1 L bottles containing 300 mL volume of the same medium.
Mse was subcultured at least 3 times in YS-supplemented DSMZ 88 media.


title: TEBs(DMBA-treated) 2

source_name: TEBs(DMBA-treated)

tag: 2 weeks of age


title: M. sedula growth on yeast extract+potassium sulfate(YKS) vs. yeast extract + potassium tetrathionate (YKT)

data_processing: Signals for each channel were obtained using ScanArray® Express 2.1 software using histogram quantitation and total normalization options to produce raw data, followed by manual verification of spot identification. Once all slides were quantitated, data from the experimental loop were analyzed with JMP Genomics 3.1 (SAS, NC), using a mixed effects ANOVA model [Wolfinger et al. J Comput Biol 8 625-637 (2001).

growth_protocol:
Cells (DSMZ 5348) were grown aerobically at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2), supplemented with 0.1% yeast extract + 10g/L potassium tetrathionate(YKT). An initial density of mid 10^6 cells/mL was used in [two] 1 L bottles containing 300 mL volume of the same medium.
Mse was subcultured at least 3 times in YKT-supplemented DSMZ 88 media.

growth_protocol:
Cells (DSMZ 5348) were grown aerobically at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2), supplemented with 0.1% yeast extract + 6g/L potassium sulfate(YKS). An initial density of mid 10^6 cells/mL was used in [two] 1 L bottles containing 300 mL volume of the same medium.
Mse was subcultured at least 3 times in YKS-supplemented DSMZ 88 media.


title: M. sedula grown on yeast extract+potassium tetrathionate (YKT) vs. yeast extract+elemental sulfur (YS)


title: TEBs(control) 2

source_name: TEBs(control)

tag: normal


title: Ductal carcinoma in situ 1

source_name: Atypical ductal hyperplasia nodule

tag: 6 weeks of age


title: TEBs(DMBA-treated) 1


title: M. sedula grown on yeast extract + ferrous sulfate (YFS) vs yeast extract + potassium sulfate (YKS)

growth_protocol:
Cells (DSMZ 5348) were grown aerobically at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2), supplemented with 0.1% yeast extract + 10g/L FeSO4∙7H2O (YFS). An initial density of mid 10^6 cells/mL was used in [four] 1 L bottles containing 300 mL volume of the same medium.
Mse was subcultured at least 3 times in YFS-supplemented DSMZ 88 media.


title: Invasive Mammary carcinoma 1


title: TEBs(control) 1


title: 2686 (CEBPAsilencedAML_#3)

tag: Female, 31 years, FAB M1, Normal cytogenetics

tag: MspI representation of genomic DNA

tag: HpaII representation of genomic DNA


title: Ductal carcinoma in situ 2


title: Mse grown on yeast extract (Y) vs yeast extract + ferrous sulfate (YFS)

growth_protocol:
Cells (DSMZ 5348) were grown aerobically at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2), supplemented with 0.1% yeast extract+ 10g/L FeSO4∙7H2O(= YFS supplement). An initial density of mid 10^6 cells/mL was used in [four] 1 L bottles containing 300 mL volume of the same medium.
Mse was subcultured at least 3 times in this YFS-supplemented DSMZ 88 media.

label: Cy™5 dye (GE Healthcare)

growth_protocol:
Cells (DSMZ 5348) were grown aerobically at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2), supplemented with 0.1% yeast extract (Y). An initial density of mid 10^6 cells/mL was used in [two] 1 L bottles containing 300 mL volume of the same medium.
Mse was subcultured at least 3 times in 0.1%Y-supplemented DSMZ 88 media.


title: hESC-1

source_name: Human embryonic stem cells

tag: Undifferentiated hESCs

tag: Pooled RNA taken from undifferentiated and differentiated hESCs


title: Lethal Yellow mice pioglitazone treated #4

status: Public on Jul 08 2008

city: Vermillion

first: Kathleen

middle: M

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

institute: University of South Dakota

description: IACUC approval was obtained for all animal treatments.

hyb_protocol: CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection (080075-00/Rev. AA/2004-04)

scan_protocol: Scanning CodeLink Bioarrays on Agilent G2565 microarray scanner (63-0050-80/Rev.AC/2004-08)

data_processing: global median normalization, CodeLink Expression Analysis 4.1.0.4163

organism: Mus musculus

source_name: ovary

label_protocol: see CodeLink Gene Expression System: Manual Labelled cRNA Target Preparation (0080074-00/Rev. AA/2004-04)

extract_protocol: The ovaries were placed in RNAlater (Ambion) in the surgical suite.  The ovaries were homogenized in TRI reagent (MRC) using a Polytron (Brinkmann).  The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity was evaluated with the RNA 6000 NanoLabChip in an Agilent Bioanalyzer.

tag: Ovary from pioglitazone-treated obese Lethal Yellow female mouse (C57BL/6J Ay/a), 180 days of age, treated by gavage with pioglitazone (0.1 mg/day) from 120 to 180 days of age.


title: Lethal Yellow mice pioglitazone treated #3


title: T145 (T-ALL_#6)

tag: Male, 51 years, TCRab+, CD7+, CD2+, CD5+, CD1a+, cyCD3+, CD3+, CD4+, CD8 +-, CD10+ cyTdT+, CD45 dim


title: Lethal Yellow mice pioglitazone treated #2


title: T8AB

status: Public on Sep 30 2007

description: Samples T8AA and T8AB are technical replicates derived from the same cRNA.  Mesenteric arteries were dissected free from surrounding fat, connective tissue, and veins while submerged under RNAlater.

hyb_protocol: see CodeLink application notes and manuals

scan_protocol: CodeLink Bioarrays scanned on Agilent G2565 microarray scanner

data_processing: global median normalization

source_name: mesenteric arteries

extract_protocol: The mesenteric vasculature was dissected free from the gastrointestinal tract and placed in RNAlater (Ambion).  The mesenteric arteries were dissected free from the surrounding fat and connective tissues while immersed in RNAlater (Rodrigo et al., J Pharm Tox Meth 47(2):87-92, 2002).  The mesenteric arteries were homogenized in TRI reagent (MRC) using a Polytron (Brinkmann).  The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity was evaluated by spectrophotometry and agarose gel electrophoresis.

tag: Female ovariectomized Sprague-Dawley rat, 5.5 weeks of age, treated for 4 days with testosterone (1 mg/kg/day)


title: T2AB

description: Samples T2AA and T2AB are technical replicates derived from the same cRNA.  Mesenteric arteries were dissected free from surrounding fat, connective tissue, and veins while submerged under RNAlater.

label_protocol: see CodeLink application notes and manuals


title: Lethal Yellow mice control #3

tag: Ovary from control obese Lethal Yellow female mouse (C57BL/6J Ay/a), 180 days of age, treated by gavage with vehicle (0.1 ml 100% DMSO) from 120 to 180 days of age.


title: T4AB

description: Samples T4AA and T4AB are technical replicates derived from the same cRNA.  Mesenteric arteries were dissected free from surrounding fat, connective tissue, and veins while submerged under RNAlater.


title: T2AA


title: T4AA


title: T8AA


title: Lethal Yellow mice control #4


title: T6AB

description: Samples T6AA and T6AB are technical replicates derived from the same cRNA.  Mesenteric arteries were dissected free from surrounding fat, connective tissue, and veins while submerged under RNAlater.


title: Seminoma-18

status: Public on May 19 2008

city: Cambridge

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

description: no additional information

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Zebrafish Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (A4 samples) or 450 (A5 and A7 samples).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner (A4 samples) or Affymetrix 7G scanner (A5 and A7 samples).

data_processing: Bioconductor Affy package and gcRMA

source_name: Seminoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA according to the Affymetrix Expression Analysis Technical Manual.

growth_protocol: Zebrafish raised according to standard protocols

extract_protocol: Trizol according to the manufacturer's protocol

treatment_protocol: Tumors were dissected from zebrafish anaesthetized with 0.03% MESAB

tag: Seminoma from fish 36 months old


title: E8AB

description: Samples E8AA and E8AB are technical replicates derived from the same cRNA.  Mesenteric arteries were dissected free from surrounding fat, connective tissue, and veins while submerged under RNAlater.

tag: Female ovariectomized Sprague-Dawley rat, 5.5 weeks of age treated for 4 days with estradiol benzoate (0.15 mg/kg/day)


title: E8AA


title: E5AB

description: Samples E5AA and E5AB are technical replicates derived from the same cRNA.  Mesenteric arteries were dissected free from surrounding fat, connective tissue, and veins while submerged under RNAlater.


title: T6AA


title: Lethal Yellow mice control #2


title: E5AA


title: Lethal Yellow mice pioglitazone treated #1


title: Lethal Yellow mice control #1


title: E3AA

description: Samples E3AA and E3AB are technical replicates derived from the same cRNA.  Mesenteric arteries were dissected free from surrounding fat, connective tissue, and veins while submerged under RNAlater.


title: P.stutzeri A1501 treated with 20mM ammonia and 0.5% Oxygen tension-3

status: Public on Apr 20 2007

type: mixed

city: Beijing

first: yongliang

last: yan

address: zhongguancun south 12th

institute: CAAS

hyb_protocol: Labeled cDNA/DNA was purified using QIAquick columns and mixed with 50× Denharts; 20× SSC; yeast tRNA 24 μg; 1 mM HEPES, 10% SDS, the mixture was heated at 100 °C for 2 min and cooled to room temperature and applied to the array slides under glass coverslips. Hybridization was performed at 65°C overnight in a Micro hybridization incubator (Robbins Scientific; Sunnyvale, CA).

scan_protocol: GenePix 6.0 software (Axon Instruments, Inc.) was used for image analysis and data visualization.

data_processing:
First, the signals were normalized using with the GenePix 6.0 software and then with a locally weighted scatterplot smoothing regression (LOWESS) algorithm in the MIDAS software package.
Genes were considered to be differentially expressed if (i) average expression changed by at least 2-fold in three independent experiments performed with triplicate RNA samples or (ii) the change in gene expression was in the same direction (“increased” or “decreased”) in three experiments.

organism: Stutzerimonas stutzeri A1501

source_name: Genomic DNA of P. stutzeri A1501

label_protocol: The genomic DNA were then fluorescently labeled using BioPrime DNA Labeling System (Life Technologies/Invitrogen; Carlsbad, CA) following the manufacturer’s instructions. The genomic DNA was added to 2.5× random primers solution (50 mM Tris-HCl, pH6.8; 5 mM MgCl2; 10 mM 2-mercaptoethanol; 300 μg/ml oligodeoxyribonucleotide primer), boiled at 100 °C for 5 min and then chilled on ice. 10× dNTP Mix for DNA labelling (0.12 mM dATP, dGTP,dTTP; 0.06 mM dCTP; 1 mM Tris-HCl, pH 8.0; 0.1 mM EDTA); Cy3-dCTP (0.06 mM); Klenow fragment (40 U) were added. The mixture was briefly centrifugated and was incubated at 37°C overnight away from light. 5μl 0.5 M EDTA (pH 8.0) was used to stop reaction.

extract_protocol: The genomic DNA was extracted as the Protocol from the TIANamp Bacteria DNA kit from TIANGEN BIOTECH (BEIJING) CO., LTD

treatment_protocol: The genomic DNA of P.stutzeri A1501 without any treatments.

tag: strain

source_name: The cDNA of P. stutzeri A1501 - treated

label_protocol: The cDNA were then fluorescently labeled using BioPrime DNA Labeling System (Life Technologies/Invitrogen; Carlsbad, CA) following the manufacturer’s instructions. The cDNA was added to 2.5× random primers solution (50 mM Tris-HCl, pH6.8; 5 mM MgCl2; 10 mM 2-mercaptoethanol; 300 μg/ml oligodeoxyribonucleotide primer), boiled at 100 °C for 5 min and then chilled on ice. 10× dNTP Mix for DNA labelling (0.12 mM dATP, dGTP,dTTP; 0.06 mM dCTP; 1 mM Tris-HCl, pH 8.0; 0.1 mM EDTA); Cy5-dCTP (0.06 mM); Klenow fragment (40 U) were added. The mixture was briefly centrifugated and was incubated at 37°C overnight away from light. 5μl 0.5 M EDTA (pH 8.0) was used to stop reaction.

extract_protocol: The total RNA was extracted as the Protocol from the SV Total RNA Isolation System (Promega)

treatment_protocol: The bacterium was treated with 20mM ammonia and 0.5% Oxygen tension. The bacterium was collected simultaneous with bacterium treated with 0.1mM ammonia and 0.5% Oxygen when the nitrogenase activity was detectable, and then began the extraction process.


title: E2AA

description: Samples E2AA and E2AB are technical replicates derived from the same cRNA.  Mesenteric arteries were dissected free from surrounding fat, connective tissue and veins while submerged under RNAlater.


title: C5AB

description: Samples C5AA and C5AB are technical replicates derived from the same cRNA.  Mesenteric arteries were dissected free from surrounding fat, connective tissue, and veins while submerged under RNAlater.

tag: Female ovariectomized Sprague-Dawley rat, 5.5 weeks of age, treated for 4 days with vehicle (sesame oil)


title: chronic inflamed periodontal ligament cells

status: Public on Aug 01 2007

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: To monitor the relative abundance of mRNA for full-length human genes, the Affymetrix GeneChip HG_U133A was used, representing 22.283 probe sets (14.239 unique human genes). Labelled cRNA, fragmented to an average size of 100–150 bases, was hybridized to GeneChips. For each pool of cRNA, two GeneChips were hybridized. Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

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

source_name: human periodontal ligament

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

extract_protocol: RNeasy mini Kit (Qiagen, Hilden, Germany); The periodontal tissue was scraped off the roots of the teeth and treated with the RNeasy mini Kit (Qiagen, Hilden, Germany) to isolate total mRNA from chronic inflamed and healthy periodontal ligament cells. Quality control and quantitation of total mRNA samples were determined prior to the microarray experiments (Agilent 2100 Bioanalyzer, Agilent Technologies, Palo Alto, CA, USA). Prior to hybridizating the microarray, we tested each total RNA extracted from chronic inflamed and healthy periodontal ligament cells by real-time RT-PCR to validate the amount of NF?B, a key player during inflammation. Equal amounts of total mRNA were pooled into a control and an inflamed cell pool.

tag: genetic modification

value: no

tag: tissue

value: periodontal ligament cells


title: C8AA

description: Samples C8AA and C8AB are technical replicates derived from the same cRNA.  Mesenteric arteries were dissected free from surrounding fat, connective tissue, and veins while submerged under RNAlater.


title: C8AB


title: C5AA


title: P.stutzeri A1501 treated with 0.1mM ammonia and 0.5% Oxygen tension-2

treatment_protocol: The bacterium was treated with 0.1mM ammonia and 0.5% Oxygen tension till the nitrogenase activity was detectable. Then the bacterium was collected and extracted the total RNA.


title: C3AB

description: Samples C3AA and C3AB are technical replicates derived from the same cRNA.  Mesenteric arteries were dissected free from surrounding fat, connective tissue and veins while submerged under RNAlater.


title: C3AA


title: C4AA

description: Samples C4AA and C4AB are technical replicates derived from the same cRNA.  Mesenteric arteries were dissected free from surrounding fat, connective tissue and veins while submerged under RNAlater.


title: E3AB


title: C4AB


title: P.stutzeri A1501 treated with 20mM ammonia and 0.5% Oxygen tension-2


title: E2AB


title: P.stutzeri A1501 treated with 20mM ammonia and 0.5% Oxygen tension-1

hyb_protocol: Labeled cDNA was purified using QIAquick columns and mixed with 50× Denharts; 20× SSC; yeast tRNA 24 μg; 1 mM HEPES, 10% SDS, the mixture was heated at 100 °C for 2 min and cooled to room temperature and applied to the array slides under glass coverslips. Hybridization was performed at 65°C overnight in a Micro hybridization incubator (Robbins Scientific; Sunnyvale, CA).

treatment_protocol: the total DNA of the P.stutzeri A1501 without any treatment.

extract_protocol: The total RNA was extracted as the Protocol from the SV Total RNA Isolation System (Promega).

treatment_protocol: The bacterium was treated with 20mM ammonia and 0.5% Oxygen tension. The bacterium was collected simultaneous with the bacterium treated with 0.1mM ammonia and 0.5% Oxygen tension when the nitrogenase activity was detectable.Then the bacterium was collected and extracted the total RNA.


title: healthy periodontal ligament cells

description: healthy periodontal ligament cells


title: P.stutzeri A1501 treated with 0.1mM ammonia and 0.5% Oxygen tension-1


title: P.stutzeri A1501 treated with 0.1mM ammonia and 0.5% Oxygen tension-3


title: Endometriosis 11 WG

status: Public on Feb 15 2007

description: Each patient served as her own control; the eutopic endometrial biopsies were obtained from the patients at the same surgery in which the endometriotic explants were excised.  IRB approval and informed consent were obtained for all sample collection.

scan_protocol: see CodeLink application notes and manuals

source_name: endometriosis

extract_protocol: The eutopic and ectopic endometrial samples were placed in RNAlater (Ambion) in the surgical suite.  The endometrial samples were homogenized in TRI reagent (MRC) using a Polytron (Brinkmann).  The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity was evaluated with the RNA 6000 NanoLabChip in an Agilent Bioanalyzer.

tag: Human, female, of reproductive age, severe endometriosis, endometrioma


title: Endometriosis 10 WG

tag: Human, female, of reproductive age, mild endometriosis, peritoneal endometriosis


title: Endometriosis 9 WG

tag: Human, female, of reproductive age, minimal endometriosis, peritoneal endometriosis


title: Endometrium 10 WG

source_name: endometrium

tag: Human, female, of reproductive age, endometrial biopsy of eutopic endometrium, proliferative phase


title: Endometrium 11 WG


title: Endometriosis 4 WG


title: Endometrium 5 WG

tag: Human, female, of reproductive age, endometrial biopsy of eutopic endometrium,


title: 129X1/SvJ 119905_SOM01GFG

status: Public on Mar 12 2008

city: Baltimore

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

description: 129X1/SvJ 119905_SOM01GFG

data_processing: normalization: qspline

extract_protocol: Phenol chloroform. DNA pooled from 2-6 animals.

tag: sex

value: male

value: kidney

extract_protocol: Phenol chloroform


title: Endometrium 4 WG

tag: Human, female, of reproductive age, endometrial biopsy of eutopic endometrium, early secretory phase


title: Endometriosis 5B WG

tag: Human, female, of reproductive age, severe endometriosis


title: Endometriosis 6B WG

tag: Human, female, of reproductive age, moderate endometriosis, endometrioma


title: Endometrium 6B WG


title: Endometrium 9 WG


title: Endometrium 8 WG


title: Endometrium 7 WG


title: Endometriosis 8 WG

tag: Human, female, of reproductive age, severe endometriosis, peritoneal endometriosis


title: Endometriosis 2 WG


title: Endometriosis 7 WG

tag: Human, female, of reproductive age, mild endometriosis


title: Endometrium 2 WG


title: Endometriosis 3 WG


title: Endometrium 3 WG


title: D8-canine Control

status: Public on Oct 13 2006

city: Valhalla

first: Caroline

last: Ojaimi

institute: New York Medical College

description: heart samples are removed from control dogs

data_processing: MAS 5.0

organism: Canis lupus familiaris

source_name: Cardiac Tissues

tag: gender

tag: weight

value: total cardiac cells


title: D7-canine Control


title: Endometriosis 1 WG


title: D6-canine Control

source_name: Cardiac tissues


title: D5-canine Control


title: Endometrium 1 WG

tag: Human, female, of reproductive age, endometrial biopsy of eutopic endometrium, late proliferative phase


title: 60048_tumour_ovary

status: Public on Feb 17 2009

city: East Melbourne

first: Dariush

last: Etemadmoghadam

address: St Andrew's Place

country: Australia

institute: Peter MacCallum Cancer Centre

description: Hybridized to Affymetrix GeneChip Mapping 100K Set Array (50K_Xba240_SNP).

hyb_protocol: DNA was XbaI restriction digested, adapter ligated, PCR amplified, fragmented, labelled and hybridized to a 50K SNP XbaI array according to the manufacturer's instructions.

scan_protocol: Arrays were washed using an Affymetrix fluidics stations and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files and TXT files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Copy number normalization, batch correction and smoothing steps were performed using GISTIC as described in Beroukhim et al., 2007 (PMID 18077431) and Etemadmoghadam et al., in press.
Copy number ratio was generated by normalizing each tumor sample to the mean of normal reference samples with similar baseline signal intensity profiles to minimize systematic noise resulting from undetermined experimental factors. We used the 5 closest references, measured by Euclidean distance between each normal and tumor signal profile. Additional normal (diploid) data (which supplement the 16 reference samples available from the current submission) were obtained from the Broad Institute, Boston (Beroukhim et al., 2007; GSE9635) and from the Affymetrix 100K HapMap Trio Dataset (available from https://www.affymetrix.com/support/technical/sample_data/hapmap_trio_data.affx).

source_name: Tumor, ovary

label_protocol: The mapping array assays were performed according to the manufacturer’s protocol (Affymetrix, Santa Clara, CA).

growth_protocol: Fresh-frozen (LN2) tissue collected at surgery.

extract_protocol: Genomic DNA was extracted using a DNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.

treatment_protocol: DNA was extracted from whole tumor tissue for samples with ≥ 80% neoplastic cells. For samples with < 80% overall tumor cells, needle dissection of serial tumor sections was performed to enrich for the epithelial fraction prior to DNA extraction. Needle-dissected samples were stained with cresyl-violet to facilitate morphological distinction between tumor and stromal elements.

tag: Primary tumour

tag: Gender

value: F

tag: Stage

value: IIIC

tag: Histology

value: Ser/PapSer

tag: Grade


title: cr_yw273-2_12_Tumor_FF

status: Public on Feb 18 2009

city: Santa Clara

first: Yuker

last: Wang

address: 3380 Central Expressway

institute: Affymetrix

hyb_protocol: George Karlin-Neumann, Marina Sedova, Ronald Sapolsky, Jonathan Forman, Yuker Wang, Martin Moorhead, and Malek Faham Molecular Inversion Probes and Universal Tag Arrays: Application to Highplex Targeted SNP Genotyping p. 199-211; Cold Spring Harbor Lab "Genetic Variation: A Laboratory Manual", edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007).

data_processing:
George Karlin-Neumann, Marina Sedova, Ronald Sapolsky, Steven Lin,
Yuker Wang, Martin Moorhead, and Malek Faham
Molecular Inversion Probe Targeted Genotyping: Application to Copy Number Determination
p. 249-252; Cold Spring Harbor Lab "Genetic Variation: A Laboratory Manual", edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007).

Briefly, we used two chips per sample. For SNP A/B, one (xxxA.CEL) chip give signal / copy number of A allele, the other chip (xxxC.CEL) give that of B allele.  Copy number assessment of a given SNP is the sum of allele A and B.  We use normals as the reference for the test samples.  The copy number is a relative value between the test and normal references.

For more details, see Wang Y, Moorhead M, Karlin-Neumann G, Wang NJ, Ireland J, Lin S, Chen C, Heiser LM, Chin K, Esserman L, Gray JW, Spellman PT, Faham M.:    Analysis of molecular inversion probe performance for allele copy number determination.  Genome Biol. 2007;8(11):R246
Wang YK, Moorhead M, Karlin-Neumann G, Falkowski M, Chen C, Siddiqui F, Davis RW, Willis TD, Faham M.: Allele quantification using Molecular Inversion Probes (MIP). Nucleic Acids Res. 21:2528, 2005.

source_name: primary tumor in fresh frozen form

label_protocol:
George Karlin-Neumann, Marina Sedova, Ronald Sapolsky, Jonathan
Forman, Yuker Wang, Martin Moorhead, and Malek Faham
Molecular Inversion Probes and Universal Tag Arrays: Application to Highplex Targeted SNP Genotyping
p. 199-211; Cold Spring Harbor Lab "Genetic Variation: A Laboratory Manual",edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007).

extract_protocol: genomic DNA extracted from a fresh frozen block. It's a customer sample

tag: disease state

value: primary tumor

tag: sample

value: fresh frozen form

tag: tissue

value: Colorectal


title: Post BR soleus muscle biopsy: Nu_L2Spost_2

status: Public on Feb 12 2009

city: OTTAWA

first: Angele

last: CHOPARD

state: ONTARIO

address: 451 Smyth road

department: Faculty of Medicine

country: Canada

institute: University of Ottawa

description: Post BR soleus muscle biopsy

hyb_protocol: Each individual cRNA sample was Cy3-labeled and mixed with an equal amount of Cy5-labeled reference sample (pool of equal quantities of cRNA from 18 Pre-BR Soleus or 23 Pre-BR Vastus Lateralis biopsies). The mixture was pre-incubated with human Cot-I DNA (Gibco-BRL), yeast tRNA, and polyA RNA, and hybridized onto duplicate microarrays.

scan_protocol: All hybridized arrays were scanned by fluorescence confocal microscopy (Scan array 4000XL, GSI-Lumonics) anda images were quantified using Genepix Pro 5.1.0.19 Extraction Software

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal. Home made (MADSCAN) software was used.

source_name: Post BR soleus muscle biopsy

label_protocol: 500 ng total RNA was prepared for hybridization using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion). According to the manufacturer, total RNA was reverse transcribed with an oligo-dT primer containing a T7 RNA polymerase promoter, and then converted into double-stranded cDNA. cDNA was used in an in vitro transcription (IVT) reaction in presence of amino-allyl nucleotides. After column purification, the IVT reaction yielded 30-100 µg aminoallyl cRNA. IVT products were labeled either with cyanine 3 or cyanine 5, and fragmented with RNA Fragmentation Reagents (Ambion) into lengths around 100 bases before hybridization.

extract_protocol: Total RNA was extracted from frozen samples with a polytron homogeneizer and the RNeasy Fibrous Tissue Mini kit (Qiagen).

value: soleus muscle biopsy

source_name: reference


title: Post BR vastus lateralis muscle biopsy: Ex_D1Vpost_1

description: Post BR vastus lateralis muscle biopsy

source_name: Post BR vastus lateralis muscle biopsy

value: vastus lateralis muscle biopsy

tag: pool of equal quantities of cRNA from 18 Pre-BR Soleus or 23 Pre-BR Vastus Lateralis biopsies


title: tud progeny male 48 hr APF - replicate 1

status: Public on Feb 11 2009

city: Los Angeles

first: Matthew

last: Lebo

address: 1040 Child's Way

department: Molecular and Copmutational Biology

institute: University of Southern California

hyb_protocol: cDNA samples were then dried and resuspended in formamide (56%), sodium citrate buffer (SSC, 3.37×), SDS (1.12%), Denhardts (5.62×), and Polyadenylic acid potassium salt (0.9 mg/ml; Sigma-Aldrich, St. Louis, MO). Samples were boiled for 2 minutes and then applied to microarray slides underneath a LifterSlip (Erie Scientific, Portsmouth, PA). Microarrays were hybridized at 42◦C for 14-18 hours, then washed in a solution of 1.5% SDS and 1X SSC for 5 minutes, a solution of 0.20X SSC for 5 minutes, and two solutions of 0.05X SSC for 10 minutes each.

scan_protocol: All arrays were scanned using the GenePix 4100A scanner and GenePix Pro 5.0 software from Axon Instruments (Molecular Diagnostics, Sunnyvale, CA).

data_processing: Visual inspection of the microarray images filtered out florescence most likely not due to labeled cDNA binding; the data from these array elements was discarded. Array elements were only considered for further analysis if at least one channel (Cy3 or Cy5) had greater than 75% of the pixels with intensity values one standard deviation above background levels. All microarray normalization and statistical analyses were performed using the limma package of BioConductor in the program R.

source_name: tud progeny male 48 hr APF

label_protocol: cDNAs were directly labeled with Cy5 or Cy3 during the reverse transcription reaction; 30µg of total RNA was used as a starting template. The reverse transcription reaction was performed for two hours at 42◦C using the following reagents (values in parentheses are final molarity or final concentration): oligo dT primer (Operon, 3.75 μM), dithiothreitol (Invitrogen, 10 mM), First Strand Buffer (Invitrogen, 1×), dNTPs minus dTTP (Invitrogen, 0.5 mM), dTTP (Invitrogen, 50 μM), Cy-labeled dUTP (Perkin-Elmer, 0.625 nM), and Superscript II reverse transcriptase (Invitrogen, 10 U/μL). The reaction was stopped and RNA was hydrolyzed by a 20 minute incubation at 65◦C with NaOH (167 mM) and EDTA (83 mM). After neutralizing by adding HEPES buffer (pH8.0; 294 mM) and sodium acetate (pH5.2; 228 mM), cDNA samples were purified (Gel-Purification Kit, Qiagen, Valencia, CA).

extract_protocol: RNA was isolated from ~30 pupae by homogenization and extraction using the TRIzol® protocol (Invitrogen, Carlsbad, CA) and resuspended in 20µL diethylpyrocarbonate (DEPC)-treated H2O.

treatment_protocol: Male tud progeny were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 48 hours and then snap frozen in liquid nitrogen.

tag: Strain

value: tud Progeny

value: Male

tag: Age

value: 48 hr APF

tag: Tissue

value: Whole Body

source_name: Reference

extract_protocol: RNA was isolated from the entire batch by homogenization and extraction using the TRIzol(R) protocol (Invitrogen, Carlsbad, CA) and 30 ug were resuspended in 20µL diethylpyrocarbonate (DEPC)-treated H2O.

treatment_protocol: Male and female flies of all pupal stages were collected and snap frozen in liquid nitrogen.

value: Canton S

value: Male and Female

value: All pupal stages


title: tud progeny female 96 hr APF - replicate 1

source_name: tud progeny female 96 hr APF

treatment_protocol: Female tud progeny were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 96 hours and then snap frozen in liquid nitrogen.

value: Female

value: 96 hr APF


title: 131-NSS

status: Public on Feb 04 2009

city: San Diego

first: Xiao-Jun

last: Ma

address: 11025 Roselle St, Suite 200

institute: bioTheranostics, Inc.

description: breast cancer

hyb_protocol: Hybridization, washing and staining performed per manufacturer's instructions (Affymetrix)

scan_protocol: GeneChips were scannned using GeneChip Scanner 3000.

data_processing: Expression measures were extracted using the RMA algorithm with default parameters for background subtraction and quantile normalization.

source_name: breast cancer biopsy

label_protocol: Biotinylated cRNA were prepared after two-rounds of T7-based amplification using the RiboAmp kit (Arcturus BioScience)

growth_protocol: fresh frozen primary breast cancer biopsy

extract_protocol: Picopure RNA extraction kit (Arcturus BioScience, Inc.)

treatment_protocol: laser capture microdissected

tag: normal stroma


title: RSPA16 untreated replicate 2

city: Durham

first: John

middle: W.

last: Schmidt

department: Chemistry

institute: Duke University

description: See above.

hyb_protocol: According to Affymetrix recommendations for antisense prokaryotic arrays.

data_processing: For each GeneChip values corresponding to the level of expression (abundance of transcript) were calculated using the Affymetrix GeneChip Operating System (GCOS) software.  Different experiments were normalized to each other using RMAExpress, using background adjustment and quantile normalization (Version 1.0) (http://rmaexpress.bmbolstad.com).  The median normalized signal intensities from three biological replicates for each condition were calculated.  Genes determined to increase or decrease in expression 2-fold or more between data sets and were significantly different (two tailed Student’s t-test; P cut-off value of 0.10) were considered to be regulated.  In cases where a gene corresponded to more than one Affymetrix probe set, the median normalized signal intensities for theses probe sets were averaged.  Additionally, for each GeneChip the GCOS software determined if the signal for each probe was distinguishable from background variability, the “GCOS Call”.  If a signal was distinguishable from background it was declared “Present”, otherwise it was declared “Marginal” or “Absent”.  Genes were also considered upregulated and labeled as “Up” if the signal was “Absent” or “Marginal” for more than one untreated sample for a particular probe set and the signals for all ramoplanin treated samples were “Present” for that probe set.  Genes were considered downregulated and was labeled as “Down” if the signal was “Absent” or “Marginal” for more than one sample treated with ramoplanin for a particular probe set and the signals for the untreated samples were all “Present” for that probe set.

organism: Staphylococcus aureus

source_name: Staphylococcus aureus RSPA16

label_protocol: Labeled according to Affymetrix recommendations for antisense prokaryotic arrays.

growth_protocol:
Ramoplanin resistant S. aureus was isolated by step pressure.  Isolated colonies of S. aureus NCTC 8325-4 were inoculated into 5 mL aliquots of Cation Adjusted Muller Hinton Broth II (Becton, Dickinson and Company) supplemented with 0.02% BSA (CAMHB2+BSA) containing ramoplanin at concentrations of 0.1 to 10 μg/mL.  The cultures were incubated at 37 °C with aeration for 48 hours.  At 48 hours growth was observed in the culture containing 0.1 μg/mL ramoplanin.  This culture was used to inoculate 5 mL CAMHB2+BSA containing ramoplanin at concentrations of 0.1 to 5 μg/mL at a final conc of approx 1e6 CFU/mL.  These cultures were incubated for 24 to 72 hours at 37 °C with aeration.  The culture with growth in the highest concentration of ramoplanin was used to inoculate another series.  Passage of the culture in this fashion was continued.  Following the 16th series growth was observed in a culture containing 5 μg/mL ramoplanin.  A sample from this culture struck on Trptic Soy Agar (TSA, Becton, Dickinson and Company) with no antibiotic and incubated at 37 °C overnight.  An isolated colony was selected and restruck onto TSA and grown overnight at 37 °C twice.  An isolated colony was then selected and named RSPA16 for “Reduced Susceptibility to Peptide Antimicrobials 16th series.”
A 100 mL tryptic soy broth culture in a 250 mL flask was inoculated a small amount of overnight culture.  Incubated at 37C shaking at 200 rpm until OD620 = 0.4

extract_protocol: Cultures were combined with an equal volume ice cold ethanol:acetone (1:1) and flash frozen in liquid nitrogen.  Frozen cultures were thawed on wet ice and pelleted by centrifugation at 5,000 × g at 4 oC for 10 min. Total RNA was isolated using a RiboPure-Bacteria kit (Ambion) according to the manufacturer’s instructions.  Each RNA sample was electrophoresed to assess RNA integrity. Reverse transcription, cDNA fragmentation and terminal labeling of cDNA fragments with biotin were prepared and processed according to Affymetrix recommendations for antisense prokaryotic arrays.

treatment_protocol:
No Treatment, Control.
A culture at OD620 = 0.4 was incubated at 37C shaking at 200 rpm for 30 minutes.

tag: Staphylococcus aureus RSPA16 ("Reduced Susceptibility to Peptide Antimicrobials 16th series")


title: ASP cy5 - 3 days - low pmt - repeat 3 - mAdbID:78041

status: Public on Feb 03 2009

city: Bethesda

first: Vincent

last: Hearing

address: Bldg 37  Rm 2132

department: National Cancer Institute

institute: National Institutes of Health

description: mAdb experiment ID: 78041

hyb_protocol: Hybridization Protocol Other: For pre-hybrization, apply 45 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42 °C at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 µl COT-1 DNA (8-10 ug/ul) and 1 µl poly A (8-10 ug/ul). Denature target at 100°C 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C before adding to samples. Add 25 µl of 2X F-hyb buffer to samples, warm at 70 °C. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C water bath. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), for 1 minute in 0.05X SSC, and spin for 3 minutes at 650 rpm to dry. (Refer to NCI Microarray Manual)

scan_protocol: Creator: GenePix Pro 5.0.1.24 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.35;; 1.66 Temperature: 38.17

data_processing:
mAdb Data Processing Protocol (v. 1)
Calculation Method: After background correction, ratios were median centered based on signals greater than 100 in both channels and linear transformed to obtain the log and linear values given in the data table.

source_name: Untreated melanocytes - Cy3

label_protocol:
Cy3 Sample Labeling Protocol
Other: Sample was labeled with cy3 (Amersham Pharmacia Biotech, Piscataway, NJ) in an indirect mannerusing manufacturer's instructions.

extract_protocol:
Sample Extraction Protocol
Other: Used an RNeasy mini kit (Qiagen, Valencia, CA.

tag: Cell line

value: Melan-a

tag: Cell type

value: melanocytes

source_name: ASP - 3 days - Cy5

label_protocol:
Cy5 Sample Labeling Protocol
Other: Sample was labeled with cy5 (Amersham Pharmacia Biotech, Piscataway, NJ) in an indirect manner using manufacturer's instructions.

treatment_protocol:
Treatment type: compound
Agent: recombinant murine Agouti signaling protein (ASP)
Treatment dose: 10 nM
Treatment time: 3 days
Treatment temperature: 37 C