title: Muscle PCOS 12

status: Public on Oct 20 2007

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

country: Denmark

institute: Roskilde Hospital

description: Vastus lateralis muscle

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The R statistical software was applied for data analysis. The RMA method was used for global background correction and qspline was used for normalization. Gene expression index calculation was done using model based index calculation (MBEI). Only perfect match probes were included in data analysis. Welch two sample t-test was used to calculate p-values.

source_name: Vastus lateralis muscle

label_protocol: One µg purified total RNA was converted to biotin-labeled aRNA using the MessageAmpTM II-Biotin single round aRNA amplification kit.

extract_protocol: Frozen muscle tissue was homogenized in Trizol with a Polytron Homogenizer and total RNA was purified using TRIzol Reagent including an extra step after phase separation with chloroform. Briefly, 1 volume of phenol-chloroform-isoamylalcohol (25-24-1) was added to the aqueous phase and spun at 10.000 x g for 10 minutes at 4˚C. Then, 1 volume of chloroform was added to the aqueous phase and spun at 12.000 x g for 20 minutes at 4˚C before RNA precipitation.

tag: Vastus lateralis muscle


title: Muscle PCOS 4

type: RNA

description: Vastus lateralis muscle

label: Biotin

molecule: total RNA

organism: Homo sapiens


title: Muscle control 11

description: Vastus lateralis muscle


title: Muscle PCOS 3

description: Vastus lateralis muscle


title: Muscle control 15

description: Vastus lateralis muscle


title: Muscle control 9

description: Vastus lateralis muscle


title: Muscle control 18

description: Vastus lateralis muscle


title: 7 day recovery rep 3

status: Public on Aug 15 2007

city: Indianapolis

first: David

last: Basile

state: IN

address: 635 Barnhill Drive

department: Cellular & Integrative Physiology

country: USA

institute: Indiana University

description: This data set corresponds to 1 sample kidney following acute renal failure compared with 1 sample from a sham-operated control.  A total of 4 comparisons from 4 different pairs of rats were carried out at 24 hours and 4 comparisons from 4 paris of rats carried out at 7 days following surgery. Raw data is expressed per spot. Data for each gene is derived by combining replicate spots corresponding to each gene. These values are found in the corresponding series files.

hyb_protocol: 100 ng of total RNA was labeled with Cy3 or Cy5. Labeled cDNAs were then concentrated using Microcon YM-30 filters (Millipore, Bedford, MA) and hybridized to a microarray at 65°C for 16 h in a hybridization solution containing mouse Cot-1 DNA, 1 µg/µl poly-dA, 1.14 µg/µl yeast tRNA, 3.4x SSC, and 0.3% SDS. Slides were washed twice in 2Xssc/0.2% SDS/1 mM DTT and once in 0.2X SSC/1 mM DTT; slides were dried completely in a 60 degree C oven and prepared for scanning.

scan_protocol: Slides were scanned using a GenePix 4100A gene scanner; signals were obtained at 635 nm for Cy5 and 532 nm for Cy3.

data_processing: Raw data were categorized, selected, and adjusted to yield log-transformed, normalized ratios following the systematic method that was described previously by Liang et al, Physiological Genomics 12:229,2003.  Log-transformed ratios were obtained from average signal intensities among replicates for each unique element on the array.  Hybridizations were carried using kidney RNA derived from 1-sham and 1 post-ischemic rat; ratios for each unique oligonucleotide element were then averaged across multiple 4 hybridizations at each time point post-surgery (ie., 1 day, 7 day).   Mathematical manipulation and averaging of microarray data was facilitated using Stata Intercooled 8.2 (Stata Corp, College Station, TX).  Determination of differential expression was based on 95 % C.I. of all ratios.

organism: Rattus norvegicus

source_name: rat kidney; 7 day I/R injury; rat = ARF_7

label_protocol: Ovation aminallyl labeling kit, manufactureres protocol

extract_protocol: qiagen RNA extraction kit; manufacturers protocol

tag: rat kidney ischemia 45 min with 7 days recovery.

source_name: sham rat kidney  rat = sham_7

label_protocol: ovation aminoallyl labeling kit; manufacturers protocol

extract_protocol: qiagen RNA extraction kit; manufactures protocol

tag: sprague dawley rat kidney 7 days following sham


title: Transgenic nr 614

status: Public on Nov 29 2007

city: Uppsala

first: Richard

last: Marsell

address: Sjukhusvägen

department: Dep. of Surgical Sciences

country: Sweden

institute: Uppsala University

description: Gene expression data from kidneys of 8 week FGF23 TG mice and WT littermates

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 GeneChip® Scanner GA 2500.

data_processing: Subsequent analysis of the gene expression data was carried out in the statistical computing language R using packages available from the Bioconductor project. The raw data was normalized using the GCRMA method.

label: biotin

organism: Mus musculus

source_name: Mus Musculus Kidney

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: Kidneys were collected at 8 weeks of age

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

treatment_protocol: Transgenic mice were produced with microinjection technique with construct of human WT FGF23 behind a 1 alpha col 1 promotor

tag: Genotype

value: FGF23 TG on C57Bl strain

tag: Age

value: 8 weeks


title: 7 day recovery rep 4

description:
scription
 This data set corresponds to 1 sample kidney following acute renal failure compared with 1 sample from a sham-operated control. A total of 4 comparisons from 4 different pairs of rats were carried out at 24 hours and 4 comparisons from 4 paris of rats carried out at 7 days following surgery. Raw data is expressed per spot. Data for each gene is derived by combining replicate spots corresponding to each gene. These values are found in the corresponding series files.

scan_protocol: Protocol Slides were scanned using a GenePix 4100A gene scanner; signals were obtained at 635 nm for Cy5 and 532 nm for Cy3.

data_processing: Raw data were categorized, selected, and adjusted to yield log-transformed, normalized ratios following the systematic method that was described previously by Liang et al, Physiological Genomics 12:229,2003. Log-transformed ratios were obtained from average signal intensities among replicates for each unique element on the array. Hybridizations were carried using kidney RNA derived from 1-sham and 1 post-ischemic rat; ratios for each unique oligonucleotide element were then averaged across multiple 4 hybridizations at each time point post-surgery (ie., 1 day, 7 day). Mathematical manipulation and averaging of microarray data was facilitated using Stata Intercooled 8.2 (Stata Corp, College Station, TX). Determination of differential expression was based on 95 % C.I. of all ratios.

source_name: sham kidney rat = sham_8

label_protocol: Ovation aminallyl labeling kit

extract_protocol: qiagen RNA extraction

tag: sprague dawley rat kidney following 7 days recovery

source_name: ischemic kidney 7 days recovery, rat = ARF_8

label_protocol: ovation aminoallyl labeling protocol

extract_protocol: qiagen RNA extraction; manufacturers protocol

tag: post-ischemic rat kidney, sprague dawley following 45 min of bilateral renal ischemia and 7 days of recovery


title: Muscle PCOS 10

description: Vastus lateralis muscle


title: Muscle PCOS 27

description: Vastus lateralis muscle


title: Muscle control 13

description: Vastus lateralis muscle


title: Muscle control 7

description: Vastus lateralis muscle


title: Muscle control 10

description: Vastus lateralis muscle


title: Muscle control 12

description: Vastus lateralis muscle


title: Muscle PCOS 25

description: Vastus lateralis muscle


title: Muscle control 6

description: Vastus lateralis muscle


title: Muscle PCOS 16

description: Vastus lateralis muscle


title: Muscle control 8

description: Vastus lateralis muscle


title: CAF_1

status: Public on Sep 01 2007

city: Seattle

first: Denise

last: Mauldin

state: WA

address: 1100 Fairview Ave N D4-100

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description: Human carcinoma associated fibroblasts CAF_1 from Human hybridized against NPF Control

hyb_protocol: Two NPF cyclin D1 and two CAF samples (labeled with Cy3) were hybridized head-to-head with an NPF control sample labeled with Cy5. Probes were hybridized competitively to microarrays under a coverslip for 16 h at 63oC.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 by using a GenePix 4000B fluorescent scanner, and image intensity data were gridded and extracted using GenePix Pro 4.1 software.

data_processing: Differences in gene expression between NPF cyclin D1/NPF and CAF/NPF groups were determined using a two-sample t-test with Significance Analysis of Microarrays (SAM) software (http://www-stat.stanford.edu/_tibs/SAM/) with a False Discovery Rate (FDR) of +/- 10% considered significant (Tusher, PNAS, 2001).  Similarities in gene expression between NPF cyclin D1/NPF and CAF/NPF groups were determined using a one-sample t-test in SAM with an FDR of +/- 0.1% considered significant. These results were reduced to unique genes by eliminating all but the highest scoring clones for each gene.  A Pearson correlation coefficient was calculated in Excel to assess the strength of the linear relationship between NPF cyclin D1/NPF and CAF/NPF average log2 ratios.

source_name: NPF Control

label_protocol: Total RNA was amplified through one round of linear amplification using the MessageAmp aRNA kit (Ambion, Austin, TX). Sample quality and quantification was assessed by agarose gel electrophoresis and absorbance at A260. Cy3 and Cy5 labeled cDNA probes were made from 4 µg of amplified RNA.

extract_protocol: RNA was isolated from NPFs, CAFs, and NPF cyclin D1 cells using total RNA isolation kit (Qiagen).

tag: NPF Control

tag: Human carcinoma associated fibroblasts CAF_1. prostate cancer status

value: Y; Specimen ID:CAF_1; origin:primary prostate stromal cells from prostate with carcinoma; Tissue:carcinoma associated fibroblasts;


title: Muscle control 17

description: Vastus lateralis muscle


title: Muscle control 3

description: Vastus lateralis muscle


title: 7 day recovery rep 1

source_name: rat sham kidney; rat = sham_5

tag: sprague dawley rat following sham-surgery for renal ischemia

source_name: rat ischemic kidney 7 days; rat = ARF_5

tag: sprague dawley rat following 45 min of ischemia/7days of reperfusion


title: Muscle control 2

description: Vastus lateralis muscle


title: D1 NPF_cyclin D1_2

description: Human normal prostate fibroblasts overexpressing cyclin D1 NPF_cyclin D1_2 from Human hybridized against NPF Control

tag: Human normal prostate fibroblasts overexpressing cyclin D1 NPF_cyclin D1_2. prostate cancer status

value: N; Specimen ID:NPF_cyclin D1_2; origin:primary prostate stromal cells from benign peripheral prostate from patient with bladder cancer; Tissue:normal prostate fibroblasts overexpressing cyclin D1;


title: D1 NPF_cyclin D1_1

description: Human normal prostate fibroblasts overexpressing cyclin D1 NPF_cyclin D1_1 from Human hybridized against NPF Control

tag: Human normal prostate fibroblasts overexpressing cyclin D1 NPF_cyclin D1_1. prostate cancer status

value: N; Specimen ID:NPF_cyclin D1_1; origin:primary prostate stromal cells from benign peripheral prostate from patient with bladder cancer; Tissue:normal prostate fibroblasts overexpressing cyclin D1;


title: CAF_2

description: Human carcinoma associated fibroblasts CAF_2 from Human hybridized against NPF Control

tag: Human carcinoma associated fibroblasts CAF_2. prostate cancer status

value: Y; Specimen ID:CAF_2; origin:primary prostate stromal cells from prostate with carcinoma; Tissue:carcinoma associated fibroblasts;


title: Grade 2 (10911-7_vs_11155-9_s37_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

status: Public on Dec 31 2007

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: protocols according to Snijders,A.M. et al. (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat.Genet., 29, 263-264.

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent (www.agilent.com).

data_processing: Global median normalized value of the log2ratio.

molecule: genomic DNA

source_name: 10911-7_mammary carcinoma

tag: 9 months, mammary carcinoma, female, Balb/c WAP-T1, G2 (moderately differentiated)

extract_protocol: Genomic DNA was isolated using Puregene Genomic DNA Purification Kit according to the manufacturer's instruction (Gentra).

tag: 9 months, liver, female, Balb/c WAP-T1, n.a.d.


title: 24 hours rep 1

source_name: ischemic kidney RNA

tag: sprague dawley rat kidney; rat subjected to 45 min of ischemia; followed by 24 hours of repferusion.

source_name: sham-operated kidney RNA

tag: Sprague-Dawley rat kidney following sham-surgery


title: NHF10-hTERT_M_C3_26595

status: Public on Aug 01 2007

city: Morrisville

first: Tong

last: Zhou

state: NC

address: 133 Southcenter Court, Suite 400

department: Clincial Genetics

institute: Gentris Corperation

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

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

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

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

source_name: Sample RNA

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

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

extract_protocol: Qiagen RNeasy kit

treatment_protocol: Colcemid at 100 ng/ml was added to G2 cells and cells were incubated an additional 4 h to collect cells in mitosis (M).

tag: Normal human  fibroblast

source_name: Reference RNA

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

extract_protocol: Stratagene protocol for preparation of reference RNA

tag: global reference RNA


title: 7 day recovery rep 2

source_name: post-ischemic rat kidney; rat = ARF_6

tag: sprague dawley rat following bilateral 45 min renal ischemia/ 7 days reperfusion

source_name: sham rat kidney 7 day; rat = sham_6

tag: sprague dawley rat kidney, 7 days following sham surgery


title: 24 hours rep 3

source_name: ischemic rat kidney 24 hours; rat = ARF_3

tag: iscemic rat kidney following 45 min of ischemia and 24 hours after reperfusion.

source_name: sham operated rat kidney; rat = sham_3

tag: rat kidney from rat 24 hours following sham-operation


title: 24 hours rep 4

source_name: rat kidney following ischemia reperfusion; rat = ARF_4

tag: sprague dawley rat following bilateral renal injury; 45 min ischemia/24 hours reperfusion.

source_name: sham rat kidney; rat = sham_4

tag: sprague dawley rat kidney following sham-surgery


title: NHF10-hTERT_S_C3_26578

treatment_protocol: Cells released from G0 were incubated with the DNA polymerase inhibitor, aphidicolin (APC), at a concentration of 2 µg/ml for 24 h to collect cells at the beginning of S. APC was washed out and cells incubated for 3 hr to allow accumulation to mid S phase.


title: NHF10-hTERT_G1_C5_26582

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

source_name: reference RNA

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

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

treatment_protocol: G0 phase arrested cells were released from dishes with trypsin, reseeded at 1.3 x 104/cm2 and then incubated for 8 h to allow them to reach mid G1.


title: NHF3-hTERT_G2_C3_26558

treatment_protocol: Cells that were released from APC treatment also were incubated for 8 h to accumulate in G2.


title: NHF10-hTERT_G1_C3_26583


title: NHF10-hTERT_M_C5_U26594


title: NHF10-hTERT_G2_C3_26593


title: NHF10-hTERT_G0_C3_26581

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


title: NHF10-hTERT_S_C5_26585


title: NHF10-hTERT_G2_C5_26579


title: NHF3-hTERT_M_C5_26559


title: NHF3-hTERT_S_C5_26555


title: 24 hours rep 2

source_name: rat kidney ischemic reperfusion ARF_2

tag: sprague dawley rat 45 min bilateral ischemia, 24 hours reperfusion, rat =ARF_2.

source_name: rat kidney sham surgery; sham_2

tag: sprague dawley rat; 24 hours after sham surgery; rat = sham_2


title: NHF3-hTERT_G1_C3_26554


title: NHF3-hTERT_G2_C5_26557


title: NHF3-hTERT_M_C3_26573


title: NHF3-hTERT_G1_C5_26553


title: NHF3-hTERT_G0_C5_26551


title: NHF3-hTERT_S_C3_26556


title: NHF3-hTERT_G0_C3_26552


title: NHF1-hTERT_G2_C3_16168


title: NHF1-hTERT_G2_C5_16167


title: NHF1-hTERT_M_C5_16180


title: NHF1-hTERT_G1_C3_16136


title: NHF1-hTERT_S_C5_16137


title: NHF1-hTERT_G1_C5_13865


title: NHF1-hTERT_G0_C5_16133


title: NHF1-hTERT_S_C3_16166


title: NHF10-hTERT_Basal_C5_53958

status: Public on Jul 01 2007

growth_protocol: Normal human fibroblasts were cultured in DMEM (Invitrogen) supplemented with 2 mM L-glutamine (Invitrogen) and 20% fetal bovine serum (Sigma). All cell lines were maintained at 37oC in a humidified atmosphere of 5% CO2.

treatment_protocol: Logarithmically growing cells without any treatment were harvested for RNA extraction

tag: Normal human fibroblast


title: AT2-hTERT_Basal_C3_53963

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

growth_protocol: AT2 fibroblasts were cultured in DMEM (Invitrogen) supplemented with 2 mM L-glutamine (Invitrogen) and 20% fetal bovine serum (Sigma). All cell lines were maintained at 37oC in a humidified atmosphere of 5% CO2.

tag: Human ataxia telangiectasia  fibroblast

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


title: NHF10-hTERT_Basal_C3_53959


title: NHF1-hTERT_M_C3_16181


title: AT2-hTERT_basal_C5_53962

growth_protocol: AT1 fibroblasts were cultured in DMEM (Invitrogen) supplemented with 2 mM L-glutamine (Invitrogen) and 20% fetal bovine serum (Sigma). All cell lines were maintained at 37oC in a humidified atmosphere of 5% CO2.


title: NHF1-hTERT_G0_C3_17661


title: AT3-hTERT_1.5Gy_2h_C5_27045

growth_protocol: AT3 fibroblasts were cultured in AmnioMAXTM-C100 medium (450 ml basal medium +15 ml supplement) (Invitrogen, Carlsbad, CA) with 10% FBS(Sigma). All cell lines were maintained at 37oC in a humidified atmosphere of 5% CO2.

treatment_protocol: Cells were harvested 2 hr after 1.5 Gy iozining radiation treatment


title: AT3-hTERT_sham_6h_C3_27042

treatment_protocol: Cells were harvested 6 hr after sham treatment


title: AT2-hTERT_sham_6h_C3_26742


title: AT1-hTERT_Basal_C5_53960


title: AT3-hTERT_1.5Gy_24h_C3_27020

treatment_protocol: Cells were harvested 24 hr after 1.5Gy ionizing radiation treatment


title: AT3-hTERT_1.5Gy_24h_C5_27021

treatment_protocol: Cells were harvested 24 hr after 1.5 Gy iozining radiation treatment


title: AT3-hTERT_1.5Gy_6h_C3_27046

treatment_protocol: Cells were harvested 6 hr after ionizing radiation treatment


title: NHF1-hTERT_Basal_C5_53956


title: AT1-hTERT_Basal_C3_53961


title: AT2-hTERT_1.5Gy_24h_C3_26772

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

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


title: AT2-hTERT_1.5Gy_6h_C5_26746

treatment_protocol: Cells were harvested 6 hr after 1.5 Gy iozining radiation treatment


title: AT2-hTERT_1.5Gy_24h_C5_26771


title: AT2-hTERT_sham_6h_C5_26743


title: AT3-hTERT_1.5Gy_6h_C5_27019


title: AT3-hTERT_sham_6h_C5_27043


title: NHF1-hTERT_Basal_C3_53957


title: HRPC269_hormone resistant prostate cancer early stage

city: Kassel

first: Oliver

middle: Christoph

last: Stoss

department: Molecular Pathology

country: Germany

institute: Targos GmbH

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

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

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

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

source_name: prostate cancer resistant against complete androgen blockade (CAB)

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

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

treatment_protocol: transurethral resection (TUR)

tag: 90 percent tumor content

tag: Age


title: HRPC120_hormone resistant prostate cancer late stage

source_name: hormone resistant prostate cancer under LHRH treatment after androgen withrawal

tag: 80 percent tumor content


title: HRPC125_hormone resistant prostate cancer late stage


title: HRPC126_hormone resistant prostate cancer early stage


title: AT3-hTERT_1.5Gy_2h_C3_27044


title: AT2-hTERT_1.5Gy_6h_C3_26770


title: AT2-hTERT_1.5Gy_2h_C5_26744


title: HRPC124_hormone resistant prostate cancer early stage


title: AT2-hTERT_1.5Gy_2h_C3_26745


title: HRPC122_hormone resistant prostate cancer late stage


title: PCA22_localized prostate cancer

source_name: human prostate cancer of untreated patient

treatment_protocol: radical prostatectomy


title: PCA58_Iocally advanced prostate cancer

source_name: human prostate cancer treated with complete androgen blockade (CAB)


title: BPH217_benign prostate hyperplasia

source_name: BPH of untreated patient

tag: no invasive tumor content


title: PCA193_Iocally advanced hormone sensitive PCA

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


title: PCA17_localized prostate cancer

tag: 70 percent tumor content


title: PCA132_localized prostate cancer and benign prostate hyperplasia

treatment_protocol: radical prostatectomy and in vitro TUR

tag: 95 percent tumor content


title: PCA47_localized prostate cancer


title: PCA11_localized prostate cancer


title: HRPC123_hormone resistant prostate cancer early stage

tag: 82 percent tumor content


title: PCA28_localized prostate cancer


title: BPH142_benign prostate hyperplasia

source_name: BPH of patient treated with LHRH


title: BPH138_benign prostate hyperplasia


title: PCA33_localized prostate cancer


title: Wild type 1 with array type maize from Affymetrix

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: The Brittle2 (Bt2) gene is one of three genes in the maize genome coding for the small subunit of ADP-glucose pyro-phosphorylase (AGPase), a key enzyme in starch synthesis. It is predominantly expressed in the developing endosperm. The bt2 mutant is characterised by collapsed, brittle kernels on mature ears. During kernel development a strong increase in soluble sugars (mainly sucrose) and a strong reduction in starch content has been observed. The goal of the present study was to compare the transcriptome between wildtype and bt2 kernels (bt2-H2328 allele) at mid-development (35 days after pollination). The main biological question was, whether the block in starch synthesis caused the transcriptional induction of other metabolic pathways to allow an alternative use of the excess sucrose.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Zea mays

label_protocol: labelling Biotin direct, amplification=yes, RNAa 20 ug.

growth_protocol: seed - Grown in green house in Grodent substrate with 16 h day light plus artificial lighting and 8 h night with a temperature of 24degreeC/17degreeC. Humidity was not controlled but was approximately 70%/80%.

treatment_protocol: no treatment

tag: Zea mays (f252)  - dev.stage (Boyes et al. Plant Cell 2001):35 days after pollinisation


title: Wild type 2 with array type maize from Affymetrix


title: AT1-hTERT_1.5Gy_6h_C3_21713

source_name: Sample RNA

source_name: Reference RNA

tag: global reference RNA


title: AT1-hTERT_1.5Gy_24h_C5_21393


title: AT1-hTERT_1.5Gy_2h_C3_21711


title: AT1-hTERT_1.5Gy_6h_C5_21712


title: AT1-hTERT_sham_6h_C3_23979


title: R. palustris hydrogen-producing mutant (CGA571) Replicate #2

status: Public on Jun 29 2007

first: Yasuhiro

last: Oda

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

department: Department of Microbiology

institute: University of Washington

description: cDNA synthesis, fragmentation, labeling, hybridization, and processing of GeneChips were carried out as recommended by the manufacture (Affymetrix).

hyb_protocol: As recommended by the manufacturer (Affymetrix)

data_processing: The Affymetrix Microarray Suite was used for initial data acquisition and processing.

label: Biotinylated GeneChip reagent

organism: Rhodopseudomonas palustris

source_name: Photosynthetic bacterium Rhodopseudomonas palustris

growth_protocol: Photosynthetically grown with acetate and ammonium.

extract_protocol: Rhodopseudomonas palustris cells were disrupted by treatment with by bead beating and RNA was purified with the RNeasy Mini kit (Qiagen) including DNase treatment on the column.


title: R. palustris hydrogen producing mutant(CGA572) Replicate #1

scan_protocol: As recommended by the manufacturer (Affymetrix)


title: R. palustris wild-type (CGA009) Replicate #1

label: Biotinylated GeneChip DNA labeling reagent

molecule: polyA RNA

source_name: Photosyntheic bacterium Rhodopseudomonas palustris

label_protocol: As recommended by the manufacturer (Affymetrix)


title: AT1-hTERT_sham_6h_C5_23978


title: AT1-hTERT_1.5Gy_24h_C3_21394


title: R. palustris hydrogen-producing mutant (CGA572) Replicate #2

tag: R. palustris hydrogen-producing mutant (CGACGA572) Replicate #2


title: R. palustris hydrogen producing mutant (CGA574) Replicate #1

tag: R. palustris hydrogen producing mutant (CGACGA574) Replicate #1


title: R. palustris hydrogen-producing mutant (CGA570) Replicate #2

tag: R. palustris hydrogen-producin mutant (CGA570) Replicate #2


title: R. palustris hydrogen-producing mutant (CGA571) Replicate #1


title: AT1-hTERT_1.5Gy_2h_C5_21710


title: Mutant 1 with array type maize from Affymetrix

tag: Zea mays (f252)  mutant (+/bt2-H2328) - dev.stage (Boyes et al. Plant Cell 2001):35 days after pollinisation


title: R. palustris wild-type (CGA009) Replicate #2


title: R. palustris hydrogen-producing mutant (CGA584) Replicate #2

description: A high-density oligonucleotide microarray (Affymetrix GeneChip) was custom designed and manufactured by Affymetrix based on the sequences of ORFs and intergenic regions. cDNA synthesis, fragmentation, labeling, hybridization, and processing of custom designed Rhodopseudomonas palustris GeneChips were carried out as recommended by the manufacturer. Experiments were performed in duplicate with independently prepared samples.

label: total RNA


title: R. palustris hydrogen-producing mutant (CGA584) Replicate #1

growth_protocol: Photosynthetically grown with acetate and with ammonium.


title: R. palustris hydrogen-producing mutant (CGA574) Replicate #2


title: Hepatopancreas of X-organ-extirpated, premolted vs. X-organ-extirpated, postmolted males

status: Public on Jun 01 2007

city: Haifa

first: Moshe

last: Tom

department: Marine Biology and Biotechnology

country: Israel

institute: Israel Oceanographic and Limnological Research

description: Evaluated Gene expression ratio between hepatopncreas tissues of XO-SG extirpated premolted and XO-SG extirpated postmolted males was part of a broader experiment which includes males in five experimental conditions. Individual variability was integrated into the hybridization design, by using RNA populations of 3 individual crayfish males for each of four experimental conditions: injected-premolted, injected-postmolted, extirpated-premolted and extirpated-postmolted males. Three pools of reference intermolt individuals were used: Ref pool 1 contained RNA from 6 individuals whereas each of Ref pools 2 and 3 contained 3 individuals. Three hybridization sets, each composed of 8 slides, were carried out. In each set, one individual from each treatment was compared to one of the Ref pools, and in addition the treated individuals were compared to each other, totaling 8 slides. The design was balanced with respect to the dye labeling of the RNA populations, such that each individual RNA population was labeled with one dye on one slide and with the other dye in two other slides. The data table of this sample, comparing hepatopncreas tissues of XO-SG extirpated premolted and XO-SG extirpated postmolted males, is part of an integrative analysis of the entire 24 slides set, resulting with eight binary comparisons among experimental conditions (see data processing below).

hyb_protocol: Microarray slides were incubated with pre-hybridization solution (1% BSA; 5x SSC; 0.1% SDS, 25% formamide) for 2h at 42oC to block non-specific DNA interactions, reducing background fluorescence, followed by two short rinses in water, one in ethanol and drying by mild centrifugation of vertical slides. Dual-labeled solutions, aimed at binary comparisons between two experimental conditions, were prepared by mixing the two compared labeled cDNA populations, followed by 1:1 dilution with hybridization solution containing 200 µg/ml salmon sperm DNA, 10x SSC, 0.2% SDS, 50% formamide. The heat denatured hybridization mixture (3' at 95oC) was layered onto the microarray, covered (Lifterslip, Erie Scientific; #25x60-2-4789) and incubated over night at 42°C in humidified hybridization chamber (Corning). Following incubation, slides were washed as follows: 5’ at 42°C in x2 SSC - 0.1% SDS, mild shaking for 10’ at room temperature in x0.1 SSC - 0.1% SDS; mild shaking 4x for 5’ at room temperature in x0.1 SSC, ending by two quick dips, one in water and one in ethanol. The slides were dried by centrifugation.

scan_protocol: The slides were scanned by Axon 4000B laser scanner in two wavelengths, corresponding to the Cy3 and Cy5 emissions. The TIF imaged dual fluorescence was quantified by the GENEPIX software (Axon), which provided also weight index of the quality for each hybridized spot.

data_processing: Data analysis was conducted under the R/BioConductor environment (Gentleman et al., 2005). Calculation and statistical analysis of log2 expression ratios (VALUE column of the sample data table) of each unique spot across a binary comparison was carried out using the LIMMA package (Linear Models for Microarray data Analysis; Smyth, 2004). GENEPIX quantified image files were imported into LIMMA, spots with quality flags < -49 were marked as unreliable, and the Cy5 and Cy3 intensities within each slide were normalized using the print-tip Loess method. No background correction was applied. LIMMA calculated for each spot on an individual slide an M-value [M=log2(Cy5)/Cy3); Cy5 / Cy3 are the normalized emission intensities of the spot] and an emission intensity A-value [A=(log2(Cy5)*Cy3))/2]. Subsequently, LIMMA fitted a linear model to the expression data followed by Empirical Bayes smoothing. Inter-duplicate correlation method was used at the linear modeling step. A meanA value, which is the average spot emission intensity across the analyzed experiment, was calculated for each unique spot and only spots with meanA > 8.5 were included in the analysis, avoiding faint emissions. The LIMMA summary statistics of each unique spot included an estimated average M-value across each binary comparison associated to two statistical parameters: B statistic, the log-odds that the spot is differentially expressed and p-value, derived from a moderated t-statistic after multiple testing correction according to Benjamini and Hochberg (1995). All these parameters are found in the sample data table.

label: Cy3 and Cy5 alternatively in different slides (see Description below)

organism: Cherax quadricarinatus

source_name: Hepatopancreas from X-organ-extirpated-premolted males

label_protocol: Messenger RNA was labeled by the fluorescent dyes Cy3 and Cy5, using the amino allyl indirect cDNA labeling method, as follows: 200-400 ng mRNA of the transcript population was incubated for 10’ at 70oC with 100 µg dT primer (T15VN) and was immediately chilled on ice. The resulting RNA-dT primer hybrid was reverse transcribed in a total volume of 30 µl for 1h at 42oC, in a solution containing: reverse transcriptase (ImProm II, Promega #A3802; 1.5 µl/reaction), 32 units of RNase inhibitor, 3.5 mM of MgCl2 solution and 0.5 mM dNTP mix in which the dTTP was replaced by Amino Allyl-dUTP / dTTP mixture (4:1). The reverse transcription was followed by mRNA hydrolysis for 15’ at 65oC in alkaline pH (0.2 M NaOH (fresh), and 0.1 M of EDTA). The alkaline solution was neutralized by 0.35 M HEPES (pH 7.0) followed by buffer replacement and cDNA concentration, accomplished by wash x3 of the solution by 450 µl of water through Microcon YM-30 filter (Amicon, #42410) ending with a volume of 50-100 µl. The cDNAs were coupled to an aliquot of the fluorescent dyes Cy3 or Cy5 mono-reactive succinimidyl ester-derivetized NHS-ester through the reactive Amino Allyl groups. Raw dye solution was prepared from a tube of dry dye (Amersham PA23001 / PA25001 for Cy3 and Cy5, respectively) dissolved in 72 µl DMSO, divided into 8 single labeling aliquots. The reaction was carried out for 1h at room temperature in 9 µl of 0.1M fresh Na-Bicarbonate Buffer pH 9.0. Hydroxylamine was added to the solution at a final concentration of 1.33M and was incubated for 15’ at room temperature. Finally the solution was neutralized by sodium acetate, pH=5.2 to a final concentration of 72 mM and purified by affinity column-based kit (Qiaquick, Qiagen). Labeling level was evaluated by spectrophotometry at both 260 nm for cDNA estimation and 550 nm (Cy3) and 650 nm (Cy5) for labeling intensity measurement.

growth_protocol: C. quadricarinatus males were maintained in captivity, before and during the experiment at 28oC, with a photoperiod of 14L:10D

extract_protocol: EZ-RNA II Kit (Biological Industries, Israel) was used for total RNA extraction. PolyTtract kit (Promega) was used for mRNA extraction from total RNA solutions

treatment_protocol: The XO-SG complex was extirpated from three adult males sacrificed at premolt. Molt stage was monitored by X-ray of gastrolith size and by evaluating ecdysteroid level in the hemolymph. The experiment was terminated by sacrifice of the males, dissecting their hepatopancreas and its immediate freezing in liquid nitrogen. Total RNA and mRNA were purified later starting from the frozen tissue.

tag: Hepatopancreas of X organ-sinus gland-extirpated C. quadricarinatus males were dissected at premolt and snap frozen in liquid nitrogen.

source_name: Hepatopancreas from X-organ-extirpated-postmolted males

treatment_protocol: The XO-SG complex was extirpated from three adult males sacrificed at postmolt. Molt stage was monitored by X-ray of gastrolith size and by evaluating ecdysteroid level in the hemolymph. The experiment was terminated by sacrifice of the males, dissecting their hepatopancreas and its immediate freezing in liquid nitrogen. Total RNA and mRNA were purified later starting from the frozen tissue.

tag: Hepatopancreas of X organ-sinus gland-extirpated C. quadricarinatus males were dissected at postmolt and snap frozen in liquid nitrogen


title: Mutant 2 with array type maize from Affymetrix


title: Hepatopancreas of X-organ-extirpated, postmolted vs. i20-OH-ecdysone injected, postmolted males

description: Evaluated Gene expression ratio between hepatopncreas tissues of XO-SG extirpated postmolted and 20-OH-ecdysone injected-postmolted males was part of a broader experiment which includes males in five experimental conditions. Individual variability was integrated into the hybridization design, by using RNA populations of 3 individual crayfish males for each of four experimental conditions: injected-premolted, injected-postmolted, extirpated-premolted and extirpated-postmolted males. Three pools of reference intermolt individuals were used: Ref pool 1 contained RNA from 6 individuals whereas each of Ref pools 2 and 3 contained 3 individuals. Three hybridization sets, each composed of 8 slides, were carried out. In each set, one individual from each treatment was compared to one of the Ref pools, and in addition the treated individuals were compared to each other, totaling 8 slides. The design was balanced with respect to the dye labeling of the RNA populations, such that each individual RNA population was labeled with one dye on one slide and with the other dye in two other slides. The data table of this sample, comparing hepatopncreas tissues of XO-SG extirpated postmolted and 20-OH-ecdysone injected-postmolted  males, is part of an integrative analysis of the entire 24 slides set, resulting with eight binary comparisons among experimental conditions (see data processing below).

tag: Hepatopancreas of X organ-sinus gland-extirpated C. quadricarinatus males were dissected at postmolt and snap frozen in liquid nitrogen.

source_name: Hepatopancreas from 20-OH-ecdysone injected-postmolted males

treatment_protocol: 20-OH-ecdysone of 1 μg/μl in a 10% ethanol saline solution was administered to intermolt males by repetitive injections to the sinus at the base of the fifth walking leg twice a day in a gradually increasing volume until reaching a presumable hormone level of 1000 pg/µl. Three adult males sacrificed at postmolt. Molt stage was monitored by X-ray of gastrolith size and by evaluating ecdysteroid level in the hemolymph.

tag: Hepatopancreas of 20-OH-ecdysone injected C. quadricarinatus males were dissected at postmolt and snap frozen in liquid nitrogen.


title: MSC_rep1

status: Public on May 31 2007

city: Cologne

first: Sebastian

last: Knoebel

address: Nattermannallee 1

institute: MiltenyiBiotec GmbH

description: RNA was prepared from 4 independent samples of cultivated human foreskin fibroblasts and human MSC, respectively using the Nucleospin-II-RNA-Extraction-Kit (Macherey&Nagel). Samples were quantified by spectrophotometry and RNA integrity was checked by gel electrophoresis (Bioanalyser 2001, Agilent). A RNA pool prepared from equal amounts of all RNA samples was used as common reference for all hybridizations.

hyb_protocol: Hybridization of microarrays was performed as described in detail (PMID: 12016146) using a GeneTacTM Hybridization Station.

scan_protocol: Image capture and signal quantification of hybridized PIQORTM microarrays were done with the ScanArrayLite4000 Microarray Scanner (PackardBiosciences) and ImaGene software Version 5.0 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification of the scanned PIQORTM microarrays was done using ImaGene software Version 5.0 (BioDiscovery, Los Angeles, CA, USA). Local background was subtracted from the signal to obtain the net signal intensity and the ratio of Cy5/Cy3. Subsequently, the mean of the ratios of 4 corresponding spots representing the same cDNA was computed. The mean ratios were normalised using the Median method. For normalisation only those spots were used for which the fluorescent intensity in one of the two channels was twice the mean background of all unflagged spots. Only genes displaying a net signal intensity 2-fold higher than the mean background were used for further analysis.

source_name: common refrence: pool of RNA containing equal amounts of RNA from all channel_2 samples of this experiment series (fibroblast sample replicates 1-4 and MSC sample replicates 1-4)

label_protocol: 1 µg T7-amplified RNA  was labelled by reverse transcription with Cy3-dCTPs as described elsewhere (PMID: 8800675).

tag: common refrence

value: pool of RNA containing equal amounts of RNA from all channel_2 samples of this experiment series (fibroblast sample replicates 1-4 and MSC sample replicates 1-4, prepared as indicated)

source_name: mesenchymal stem cells (MSC)

tag: Bone marrow samples were collected from healthy donors after informed consent. MSC were isolated via their plastic adherence. Briefly, mononuclear cells were isolated from bone marrow by a Ficoll/ Paque Plus (Amersham Biosciences AB, Uppsala, Sweden) gradient separation. The separated cells were cultured in DMEM (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany), 20% FCS (PAA, Brisbane, Australia), 2 mM L-Glutamine (Gibco, Paisley, Scotland, UK) and 1% Penicillin-Streptomycin (10,000U/ml, Gibco) at 37°C, 5% CO2. After one day the non-adherent cells were removed by replacing the medium.


title: R. palustris hydrogen-producing mutant (CGA570) Replicate #1


title: Hepatopancreas of X-organ-extirpated, premolted vs. 20-OH-ecdysone injected, premolted  males

description: Evaluated Gene expression ratio between hepatopncreas tissues of XO-SG extirpated premolted and 20-OH-ecdysone injected-premolted males was part of a broader experiment which includes males in five experimental conditions. Individual variability was integrated into the hybridization design, by using RNA populations of 3 individual crayfish males for each of four experimental conditions: injected-premolted, injected-postmolted, extirpated-premolted and extirpated-postmolted males. Three pools of reference intermolt individuals were used: Ref pool 1 contained RNA from 6 individuals whereas each of Ref pools 2 and 3 contained 3 individuals. Three hybridization sets, each composed of 8 slides, were carried out. In each set, one individual from each treatment was compared to one of the Ref pools, and in addition the treated individuals were compared to each other, totaling 8 slides. The design was balanced with respect to the dye labeling of the RNA populations, such that each individual RNA population was labeled with one dye on one slide and with the other dye in two other slides. The data table of this sample, comparing hepatopncreas tissues of XO-SG extirpated premolted and 20-OH-ecdysone injected-premolted  males, is part of an integrative analysis of the entire 24 slides set, resulting with eight binary comparisons among experimental conditions (see data processing below).

source_name: Hepatopancreas from 20-OH-ecdysone injected-premolted males

treatment_protocol: 20-OH-ecdysone of 1 μg/μl in a 10% ethanol saline solution was administered to intermolt males by repetitive injections to the sinus at the base of the fifth walking leg twice a day in a gradually increasing volume until reaching a presumable hormone level of 1000 pg/µl. Three adult males sacrificed at premolt. Molt stage was monitored by X-ray of gastrolith size and by evaluating ecdysteroid level in the hemolymph.

tag: Hepatopancreas of 20-OH-ecdysone injected C. quadricarinatus males were dissected at premolt and snap frozen in liquid nitrogen.


title: MSC_rep4


title: Fibroblasts_rep4

source_name: foreskin fibroblasts

tag: Fibroblasts were generated according to a protocol of Rodemann et al (1984) from foreskins deriving from voluntary circumcisions of children aged 3 to 12 years. After washing with PBS fat was removed carefully and the tissue was cut into 4-6 mm2 pieces. The skin pieces were put into cell culture dishes with the dermal side down and were left to adhere for 10-15 min before medium (DMEM, 10% FCS, 2 mM L-Glutamine, 1% Penicillin-Streptomycin (10,000U/ml)) was added and they were cultured at 37°C, 5% CO2. The tissue pieces should stay adhered to the cell culture dish. After 2-3 weeks fibroblasts start so migrate out of the tissue pieces and the skin pieces were removed. After confluence had been reached, MSC and fibroblasts were detached by incubation with 0,25% trypsin/ EDTA (Gibco) for 5 min at 37°C.


title: Fibroblasts_rep2


title: MSC_rep3


title: Fibroblasts_rep1


title: Fibroblasts_rep3


title: Hepatopancreas of 20-OH-ecdysone injected, premolted vs. 20-OH-ecdysone injected, postmolted males

description: Evaluated Gene expression ratio between hepatopncreas tissues of 20-OH-ecdysone injected,premolted and 20-OH-ecdysone injected, postmolted males was part of a broader experiment which includes males in five experimental conditions. Individual variability was integrated into the hybridization design, by using RNA populations of 3 individual crayfish males for each of four experimental conditions: injected-premolted, injected-postmolted, extirpated-premolted and extirpated-postmolted males. Three pools of reference intermolt individuals were used: Ref pool 1 contained RNA from 6 individuals whereas each of Ref pools 2 and 3 contained 3 individuals. Three hybridization sets, each composed of 8 slides, were carried out. In each set, one individual from each treatment was compared to one of the Ref pools, and in addition the treated individuals were compared to each other, totaling 8 slides. The design was balanced with respect to the dye labeling of the RNA populations, such that each individual RNA population was labeled with one dye on one slide and with the other dye in two other slides. The data table of this sample, comparing hepatopncreas tissues of 20-OH-ecdysone injected, premolted and 20-OH-ecdysone injected, postmolted males, is part of an integrative analysis of the entire 24 slides set, resulting with eight binary comparisons among experimental conditions (see data processing below).

treatment_protocol: 20-OH-ecdysone of 1 μg/μl in a 10% ethanol saline solution was administered to intermolt males by repetitive injections to the sinus at the base of the fifth walking leg twice a day in a gradually increasing volume until reaching a presumable hormone level of 1000 pg/µl. Three adult males sacrificed at postmolt. Molt stage was monitored by X-ray of gastrolith size and by evaluating ecdysteroid level in the hemolymph


title: MSC_rep2


title: Hepatopancreas of 20-OH-ecdysone injected, premolted vs. intermolted males

description: Evaluated Gene expression ratio between hepatopncreas tissues of XO-SG extirpated premolted and intact intermolt males was part of a broader experiment which includes males in five experimental conditions. Individual variability was integrated into the hybridization design, by using RNA populations of 3 individual crayfish males for each of four experimental conditions: injected-premolted, injected-postmolted, extirpated-premolted and extirpated-postmolted males. Three pools of reference intermolt individuals were used: Ref pool 1 contained RNA from 6 individuals whereas each of Ref pools 2 and 3 contained 3 individuals. Three hybridization sets, each composed of 8 slides, were carried out. In each set, one individual from each treatment was compared to one of the Ref pools, and in addition the treated individuals were compared to each other, totaling 8 slides. The design was balanced with respect to the dye labeling of the RNA populations, such that each individual RNA population was labeled with one dye on one slide and with the other dye in two other slides. The data table of this sample, comparing hepatopncreas tissues of XO-SG extirpated premolted and intact intermolt males, is part of an integrative analysis of the entire 24 slides set, resulting with eight binary comparisons among experimental conditions (see data processing below).

treatment_protocol: 20-OH-ecdysone of 1 μg/μl in a 10% ethanol saline solution was administered to intermolt males by repetitive injections to the sinus at the base of the fifth walking leg twice a day in a gradually increasing volume until reaching a presumable hormone level of 1000 pg/µl. Three adult males sacrificed at premolt. Molt stage was monitored by X-ray of gastrolith size and by evaluating ecdysteroid level in the hemolymph. The experiment was terminated by sacrifice of the males, dissecting their hepatopancreas and its immediate freezing in liquid nitrogen. Total RNA and mRNA were purified later starting from the frozen tissue.

tag: Hepatopancreas of 20-OH-ecdysone injected, C. quadricarinatus males were dissected at premolt and snap frozen in liquid nitrogen

source_name: Hepatopancreas from intermolt males

treatment_protocol: Molt stage was monitored by X-ray of gastrolith size and by evaluating ecdysteroid level in the hemolymph. Twelve intermolt males were sacrificed and their hepatopancreas was dissected and immediately frozen in liquid nitrogen. Total RNA and mRNA were purified later starting from the frozen tissue, pooled into three mRNA groups of 6, 3 and 3 males.

tag: Hepatopancreas of intact intermolt C. quadricarinatus males were dissected and snap frozen in liquid nitrogen.


title: Hepatopancreas of X-organ-extirpated, postmolted vs. intermolted males

tag: Hepatopancreas of intact intermolt C. quadricarinatus males were dissected and snap frozen in liquid nitrogen


title: Hepatopancreas of 20-OH-ecdysone injected, postmolted vs. intermolted males


title: Control_vs_Cold_CT6748_24H_R1_T2

city: Orono

first: Benildo

middle: G

last: de los Reyes

state: ME

address: 5735 Hitchner Hall

department: School of Biology and Ecology

institute: University of Maine

description: This experiment was performed with two independent biological replicates (R1 and R2). The specific hybridization experiment described here represents the second of the two technical replicates (T2) within biological replicate R1.

hyb_protocol: Equal amounts of Cy5- and Cy3-labeled samples were combined, dried by speed-vac centrifugation and then dissolved in 1x hybridization buffer (Amersham-GE Healthcare) with 50% formamide. Hybridization was performed by applying the labeled mixture of control and cold stress samples onto the area of the microarray slide corresponding to the spot matrix and then covered with cover slip (Corning Life Sciences). The hybridization assembly was mounted in a tightly sealed and humidified portable hybridization cassette (Telechem International). Hybridization cassetes were wrapped with aluminum foil and incubated in 42C water bath for 16 to 18 hours. Following hybridization, the cover slips were gently peeled-off and the slides were washed in three stringency buffer solutions (TeleChem International): Buffer 1, 2x SSC (3M sodium chloride, 0.3M sodium citrate) plus 1% sarcosyl; Buffer 2, 2x SSC; Buffer 3, 0.2x SSC. All washing steps were carried out at room temperature for 5 minutes with moderate agitation.

scan_protocol: Microarrays were scanned at 635nm and 532nm using the Axon 4000A scanner. Scan image was acquired and processed by the GenePix Pro 3.0.

data_processing: Quality flagging was performed on the microarray scans using GenePix Pro 3.0. A complex quality control query was used to identify and select high quality spots (features) from the entire microarray matrix. Separate analysis was performed on the duplicate panels (tecnical replicate). This query was formulated to exclude features that belong to any of the following filter criteria: 1) The feature intensity is near background level; 2) The feature is irregular or not uniform (spotting irregularity); and 3) The background around the feature is not uniform (hybridization irregularity). Only the features that passed these stringent filter criteria were included in subsequent bioinformatic analysis of the gene expression data. Gene expression data in each image was normalized globally prior to high level analysis. VALUES represent the log of the ratio between the background subtracted intensity values at Cy5 (635 nm) and Cy3 (532 nm) (635/532). All high level analysis was performed by Acuity bionformatics Suite (Axon Instruments).

organism: Oryza sativa

source_name: Rice (Oryza sativa) seedlings at 24 hours at control temperature (29C)

label_protocol: The target RNA sample was processed in a two-step procedure using the CyScribe post-cDNA labeling kit (Amersham-GE Healthcare). The cDNA synthesis reaction was primed with oligo-dT catalyzed by CyScript reverse transcriptase. Aminoallyl-dUTPs were incorporated into first strand cDNA with an optimized nucleotide mix supplied in the kit. In the second step, cDNA samples with aminoallyl modification were chemically labeled with Cy5 fluorescent dye.

growth_protocol: Seedlings were germinated in ample water and allowed to develop to S3-stage at ambient temperature (29C) in a growth chamber.

extract_protocol: Total RNA was isolated from control seedlings using the TriZol extraction method according to manufacturer's (Invitrogen) protocol.

treatment_protocol: Control samples (seedlings at S3 stage) were incubated at ambient temperature (29C) for  24 hrs.

tag: Rice whole seedlings (coleoptile, radicle, prophyl), CT6748-8-CA-17, S3-stage.

source_name: Rice (Oryza sativa) seedlings at 24 hours under cold stress (10C)

label_protocol: The target RNA sample was processed in a two-step procedure using the CyScribe post-cDNA labeling kit (Amersham-GE Healthcare). The cDNA synthesis reaction was primed with oligo-dT catalyzed by CyScript reverse transcriptase. Aminoallyl-dUTPs were incorporated into first strand cDNA with an optimized nucleotide mix supplied in the kit. In the second step, cDNA samples with aminoallyl modification were chemically labeled with Cy3 fluorescent dye.

extract_protocol: Total RNA was isolated from cold-treated seedlings using the TriZol extraction method according to manufacturer's (Invitrogen) protocol.

treatment_protocol: Treatment samples (seedlings at S3 stage) were incubated at low temperature (10C) for 24 hrs


title: Control_vs_Cold_CT6748_12H_R2_T2

description: This experiment was performed with two independent biological replicates (R1 and R2). The specific hybridization experiment described here represents the second of the two technical replicates (T2) within biological replicate R2.

source_name: Rice (Oryza sativa) seedlings at 12 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at S3 stage) were incubated at ambient temperature (29C) for 12 hrs.

source_name: Rice (Oryza sativa) seedlings at 12 hours under cold stress (10C)

treatment_protocol: Treatment samples (seedlings at S3 stage) were incubated at low temperature (10C) for 12 hrs


title: Control_vs_Cold_CT6748_24H_R2_T2


title: Control_vs_Cold_CT6748_24H_R1_T1

description: This experiment was performed with two independent biological replicates (R1 and R2). The specific hybridization experiment described here represents the first of the two technical replicates (T1) within biological replicate R1.

treatment_protocol: Control samples (seedlings at S3 stage) were incubated at ambient temperature (29C) for 24 hr

treatment_protocol: Treatment samples (seedlings at S3 stage) were incubated at low temperature (10C) for 24 hr


title: Control_vs_Cold_CT6748_24H_R2_T1

description: This experiment was performed with two independent biological replicates (R1 and R2). The specific hybridization experiment described here represents the first of the two technical replicates (T1) within biological replicate R2.


title: Control_vs_Cold_CT6748_12H_R1_T2


title: Control_vs_Cold_CT6748_12H_R2_T1

treatment_protocol: Control samples (seedlings at S3 stage) were incubated at ambient temperature (29C) for 12 hr

treatment_protocol: Treatment samples (seedlings at S3 stage) were incubated at low temperature (10C) for 12 hr


title: Primary white adipocytes 7 days in culture W_o_43

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

institute: Karolinska Institutet

description: Gene expression data from primary cell culture

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C

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: Primary WAT cells 7 days after isolation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix single round amplification protocol from 5 ug total RNA

growth_protocol: In vitro culture

treatment_protocol: Differentiated

tag: Primary white adipocytes

tag: 7 days in culture


title: Primary white adipocytes 7 days in culture W_o_40


title: Control_vs_Cold_CT6748_12H_R1_T1


title: Primary white adipocytes 7 days in culture W_o_44


title: Control_vs_Cold_CT6748_6H_R1_T1

source_name: Rice (Oryza sativa) seedlings at 6 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at S3 stage) were incubated at ambient temperature (29C) for 6 hr

source_name: Rice (Oryza sativa) seedlings at 6 hours under cold stress (10C)

treatment_protocol: Treatment samples (seedlings at S3 stage) were incubated at low temperature (10C) for 6 hr


title: Control_vs_Cold_CT6748_6H_R2_T1


title: Control_vs_Cold_CT6748_6H_R2_T2

treatment_protocol: Control samples (seedlings at S3 stage) were incubated at ambient temperature (29C) for 6 hrs.

source_name: Rice (Oryza sativa) seedlings at 0.5 hour under cold stress (10C)

treatment_protocol: Treatment samples (seedlings at S3 stage) were incubated at low temperature (10C) for 6 hrs


title: Control_vs_Cold_CT6748_2H_R1_T2

source_name: Rice (Oryza sativa) seedlings at 2 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at S3 stage) were incubated at ambient temperature (29C) for 2 hrs.

source_name: Rice (Oryza sativa) seedlings at 2 hours under cold stress (10C)

treatment_protocol: Treatment samples (seedlings at S3 stage) were incubated at low temperature (10C) for 2 hrs


title: Control_vs_Cold_CT6748_0.5H_R1_T1

source_name: Rice (Oryza sativa) seedlings at 0.5 hour at control temperature (29C)

treatment_protocol: Control samples (seedlings at S3 stage) were incubated at ambient temperature (29C) for 0.5 hr

treatment_protocol: Treatment samples  (seedlings at S3 stage) were incubated at low temperature (10C) for 0.5 hr


title: Primary white adipocytes 7 days in culture W_o_36


title: Control_vs_Cold_CT6748_6H_R1_T2


title: Control_vs_Cold_CT6748_0.5H_R2_T1

treatment_protocol: Treatment samples (seedlings at S3 stage) were incubated at low temperature (10C) for 0.5 hr


title: Primary white adipocytes 7 days in culture W_o_39


title: Control_vs_Cold_CT6748_2H_R1_T1

treatment_protocol: Control samples (seedlings at S3 stage) were incubated at ambient temperature (29C) for 2 hr

treatment_protocol: Treatment samples (seedlings at S3 stage) were incubated at low temperature (10C) for 2 hr


title: Primary white adipocytes 7 days in culture W_o_35


title: Control_vs_Cold_CT6748_2H_R2_T2


title: Primary white adipocytes 4 days in culture W_y_51

source_name: Primary WAT cells 4 days after isolation

treatment_protocol: Non differentiated

tag: 4 days in culture


title: Control_vs_Cold_CT6748_2H_R2_T1


title: Control_vs_Cold_CT6748_0.5H_R2_T2


title: Control_vs_Cold_CT6748_0.5H_R1_T2


title: Primary white adipocytes 4 days in culture W_y_37


title: Primary white adipocytes 4 days in culture W_y_45


title: Primary white adipocytes 4 days in culture W_y_34


title: brain at T96, PTU, biological rep3

status: Public on May 12 2007

city: Victoria

first: Caren

middle: C

last: Helbing

state: British Columbia

address: PO Box 3055 Stn CSC

department: Biochemistry and Microbiology

country: Canada

institute: University of Victoria

description: Gene expression data sets obtained from three biological replicate arrays for each treatment and time point were analyzed for consistency and absolute agreement using intra-class correlation with a 2-way random effects model (SPSS Version 12.0, Chicago, IL, USA). The averages of the intra-class correlation coefficients over the replicate sets was not less than 0.82 with most values greater than 0.9 (Supplementary Table 3). Fold change response to each treatment was determined for each gene relative to the control and genes exhibiting fold change values greater than or equal to two were identified. As an additional quality measure and to reduce the chance of making a type I error, we omitted genes which displayed large variability over the replicate sets.  For each gene/replicate set, variability was measured using the equation:  (maximum value-minimum value)/2 which is appropriate for samples up to 5 per group (Montgomery, 1991). If the variation estimate for the gene/replicate set was greater than 1.1-1.7 (depending on the data set), the gene was removed from the final list of genes affected following chemical treatment for that time point. If less than 4 observations were available for a given time point and treatment, that gene was also removed from the final list of genes.

hyb_protocol: Prehybridization, hybridization, and posthybridization washes were performed at 65°C. The radiolabeled cDNA targets from MMI-, PTU-, and PER-exposed animals and their time-matched experimental controls were each divided into 3 pools of (n=3, 3, and 4) for each treatment time point such that three arrays were probed per treatment and time point. The radiolabeled cDNA targets from T3 and T4-exposed animals with their respective time-matched control animals, were derived from 3 individual animals such that one array was used for each individual. Hybridizations were carried out in 20 ml of hybridization solution containing 4x SSC, 10% (w/v) dextran sulfate, 1.0% (w/v) SDS, and 0.5% (w/v) Blotto. Prewarmed hybridization solution was added to each hybridization tube (35 mm internal diameter x 150 mm length; Amersham) containing the array membrane and prehybridization was allowed to continue for 2 h. Radiolabeled cDNA samples were then added to a final concentration of 5 x 105 cpm/ml and allowed to hybridize overnight. After hybridization, the membranes were rinsed briefly with 50 ml 2x SSC, then washed twice with 50 ml 2x SSC/0.1% SDS for 15 min, once with 50 ml 0.1x SSC/1.0% SDS for 25 min, and rinsed with 50 ml 0.1x SSC. The arrays were placed on 3MM filter paper (Rose Scientific Ltd, Edmonton, AB, Canada) soaked with ddH20 and wrapped with plastic wrap. Each processed membrane was exposed to a phosphorimager screen (Molecular Dynamics Inc., Sunnyvale, CA, USA) for five days.

scan_protocol: Hybridization signals were collected using a Storm 820 Gel and Blot Imaging System (Amersham) at 50 µm resolution.

data_processing:
The resulting image data were converted to a standard 8-bit TIFF file using Photoshop V5.0 (Adobe Systems Inc, San Jose, CA, USA). Both non-auto- and auto-level images were prepared for analysis in order to account for signal saturation. Non-auto-leveled images provide a linear range of strong signal intensities (such as alpha-actin) while auto-leveled images allow for analysis of the remaining signals.
Relative expression for each gene target was collected from the image data using ImaGene Version 5.6.1 (BioDiscovery Inc, El Segundo, CA, USA). Signal intensities for each gene and blank position were determined from the median spot pixel intensities and corrected by subtracting the local median background pixel intensities. Signal intensities that were derived from areas of non-specific hybridization on the arrays were not included in the final analysis. A non-signal background was determined from the median intensity value plus one standard deviation of blank positions across the auto-leveled data set, and signal intensities for gene positions exhibiting values below the no signal were adjusted to this value. Saturated gene positions identified in auto-level data were replaced across all data sets by the corresponding values obtained in the non-auto-level analysis.
Data for the three sets were analyzed by time point. Both non-auto- and auto-leveled data for each array were normalized using a geometric mean derived from the median signal intensities from the following genes: ribosomal proteins L8 and S10, GAPDH, ferritin, ubiquitin, NM23/dinucleotide phosphate kinase, cytoplasmic alpha-actin, and elongation factor-1 ? chain. The choice of which of these transcripts were used for normalization within a time point was dictated by spot quality and consistency (see Statistics below). The gene transcripts used for normalization across a time point are indicated in Supplementary Table 1.

organism: Xenopus laevis

source_name: NF stage 54 tadpoles at 96 h of exposure

label_protocol: Amplified RNA (aRNA) was produced using the MessageAmp aRNA Kit as per the manufacturer’s protocol (Ambion) from one microgram brain total RNA isolated from an individual (for the T3 and T4 experimental sets) or from three separate pools of total RNA from individuals (for the inhibitor experimental set). This aRNA (500 ng) was annealed with 500 ng random hexamer oligonucleotide (Amersham Biosciences Inc, Baie d’Urfé, QC, Canada), and cDNA was prepared using MMLV RNase H- Superscript II reverse transcriptase as described by the manufacturer (Invitrogen) with the following modifications: the dNTP mix consisted of 500 µM each of dGTP, dTTP, and dCTP, 4 µM dATP, and 50 µCi [alpha-32P] dATP (PerkinElmer Life Sciences, Inc, Boston, MA, USA). RNA was removed from the radiolabeled cDNA by addition of 10 ul 1M NaOH and incubation at 70 °C for 10 min. Samples were cooled to room temperature and 10 ul of 1M HCl were added to neutralize the reactions. The radiolabeled cDNA was purified using a QIAquick PCR purification kit (Qiagen) and, immediately prior to hybridization, was heat denatured for 5 min at 95°C and then quickly cooled on ice for 5 min.

extract_protocol: Brain tissue was collected from each individual tadpole and total RNA was isolated using TRIzol reagent as described by the manufacturer (Invitrogen Canada Inc., Burlington, Ontario, Canada).

treatment_protocol:
Experiment 1 (T4 and T3)
Twenty-eight early prometamorphic (NF stage 54;(Nieuwkoop and Faber, 1956; Shi, 2000)) tadpoles were continuously exposed to three separate T4 concentrations (10, 20.1, and 40.3 nM), and a LSW control in one exposure set, or five different T3 concentrations (0.48, 0.97, 1.92, 3.84, and 7.68 nM), and a LSW control in the second exposure set as described in detail in Zhang et al (2006). Each chemical exposure concentration was replicated twice along with the associated LSW control. At 24 h, 48 h and 96 h two animals per exposure replicate (four animals total per each individual treatment) were randomly selected, euthanized in MS-222, and preserved in RNAlater (Ambion Inc., Austin, Texas, USA) for analysis of gene expression.  On exposure day 14, all remaining organisms were euthanized in MS-222, weighed, and developmentally staged in a blind evaluation. Animals exposed to either chemical showed an acceleration of metamorphosis which was published previously (Zhang et al., 2006).

Experiment 2 (MMI, PTU and PER)
NF stage 54 tadpoles were continuously exposed to a single concentration of PTU (20 mg/L), MMI (100 mg/L) or PER (4 mg/L).  We have previously shown that exposure to these concentrations resulted in an increase in thyroid gland size at day 8 and significantly delayed metamorphosis at 14 days (Degitz et al., 2005; Tietge et al., 2005). The exposure regimen details are recorded elsewhere (Zhang et al., 2006). Briefly, tadpoles were randomly placed into 24 tanks (20 tadpoles/tank) and exposed (six tanks/chemical) to a single concentration of each chemical. At 24 h, 48 h and 96 h 5 tadpoles from two of the 6 tanks (10 tadpoles per each individual treatment) were randomly selected, euthanized in MS-222, and preserved in RNAlater (Ambion Inc., Austin, Texas, USA) for analysis of gene expression.

tag: NF stage 54 tadpoles from US Environmental Protection Agency, Mid-Continent Ecology Division in house culture


title: Primary brown adipocytes 4 days in culture B_y_10

source_name: Primary BAT cells 4 days after isolation

tag: Primary brown adipocytes


title: brain at T24, PER, biological rep2

source_name: NF stage 54 tadpoles at 24 h of exposure


title: brain at T96, PER, biological rep2


title: brain at T96, PER, biological rep1


title: brain at T96, PER, biological rep3


title: brain at T24, PER, biological rep1


title: brain at T96, PTU, biological rep2


title: brain at T48, PER, biological rep2

source_name: NF stage 54 tadpoles at 48 h of exposure


title: brain at T48, PER, biological rep3


title: Primary white adipocytes 4 days in culture W_y_33


title: Primary brown adipocytes 7 days in culture B_o_12

source_name: Primary BAT cells 7 days after isolation


title: Primary white adipocytes 4 days in culture W_y_38


title: Primary brown adipocytes 4 days in culture B_y_19


title: brain at T48, PER, biological rep1


title: Primary brown adipocytes 4 days in culture B_y_09


title: Primary brown adipocytes 4 days in culture B_y_06


title: Primary brown adipocytes 7 days in culture B_o_11


title: Primary brown adipocytes 7 days in culture B_o_22


title: Primary brown adipocytes 4 days in culture B_y_05


title: Primary white adipocytes 4 days in culture W_y_42


title: Primary white adipocytes 4 days in culture W_y_41


title: Primary brown adipocytes 7 days in culture B_o_08


title: Primary brown adipocytes 7 days in culture B_o_07


title: brain at T48, PTU, biological rep2


title: brain at T48, PTU, biological rep3


title: brain at T24, PTU, biological rep1


title: brain at T24, PTU, biological rep2


title: brain at T96, MMI, biological rep3


title: brain at T96, PTU, biological rep1


title: brain at T48, MMI, biological rep3


title: brain at T24, PTU, biological rep3


title: brain at T48, PTU, biological rep1


title: brain at T96, control, biological rep1


title: brain at T96, MMI, biological rep1


title: brain at T24, control, biological rep3


title: brain at T24, MMI, biological rep3


title: brain at T48, control, biological rep3


title: brain at T96, control, biological rep2


title: brain at T48, control, biological rep2


title: brain at T96, MMI, biological rep2


title: brain at T24, MMI, biological rep2


title: brain at T48, MMI, biological rep2


title: brain at T48, control, biological rep1


title: brain at T96, control, biological rep3


title: brain at T24, control, biological rep1


title: brain at T24, control, biological rep2


title: brain at T24, MMI, biological rep1


title: E2 slide 35 day 1

status: Public on May 10 2007

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

description:
See Martyniuk et al. 2006 (PMID: 16954407) for details. Also please check the website about the goldfish microarraay project:
wwww.auratus.ca

hyb_protocol: Genisphere protocol (http://www.genisphere.com/array_detection_home.html) Cy5 Cy3 labelling 2ug RNA labelled See Martyniuk et al. 2006 (PMID: 16954407) for details.

scan_protocol: 10um scan red 633nm and green 543nm laser.

data_processing: Lowess Normalization

organism: Carassius auratus

source_name: E2 - control hypothalamus, slide 35

label_protocol: See Martyniuk et al. 2006 (PMID: 16954407) for details on microarray labelling.

extract_protocol:
Trizol reagent,
Quantarray scan

tag: adult male goldfish, 2-3 years of age, exposed to silastic implant, 1 day exposure

source_name: E2 - treatment hypothalamus, slide 35

tag: adult male goldfish, 2-3 years of age, exposed to silastic implant containing 17β-estradiol (E2) (100ug/g body mass), 1 day exposure


title: E2 slide 42 day 1

source_name: E2 - treatment hypothalamus, slide 42

source_name: E2 - control hypothalamus, slide 42


title: brain at T48, MMI, biological rep1


title: AML cDNA hybridization-ID73-L

status: Public on May 01 2007

city: Shimotsukeshi

first: Hiroyuki

last: Mano

state: Tochigi

address: 3311-1 Yakushiji

department: Division of Functional Genomics

country: Japan

institute: Jichi Medical University

description: Leukemic fractions of ID73 AML patient have been hybridized.

hyb_protocol: 2 ug of cDNA were hybridized for 18 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The mean value for the internal control probe sets (defined by Affymetrix) was set to be 500.

label_protocol: Biotinylated cDNA were prepared according to the Ovation Biotin RNA Amplification and Labeling System, NuGEN Technologies, Inc.

extract_protocol: Total RNA was extracted by RNeasy mini spin column (Qiagen, Inc).

tag: Leukemic fractions of ID73 AML patient


title: E2 slide 25 day 1

source_name: E2 - treatment hypothalamus, slide 25

source_name: E2 - control hypothalamus, slide 25


title: AML cDNA hybridization-ID47-L

description: Leukemic fractions of ID47 AML patient have been hybridized.

tag: Leukemic fractions of ID47 AML patient


title: AML cDNA hybridization-ID09-L

description: Leukemic fractions of ID09 AML patient have been hybridized.

tag: Leukemic fractions of ID09 AML patient


title: AML cDNA hybridization-ID10-L

description: Leukemic fractions of ID10 AML patient have been hybridized.

tag: Leukemic fractions of ID10 AML patient


title: AML cDNA hybridization-ID13-L

description: Leukemic fractions of ID13 AML patient have been hybridized.

tag: Leukemic fractions of ID13 AML patient


title: AML cDNA hybridization-ID36-L

description: Leukemic fractions of ID36 AML patient have been hybridized.

tag: Leukemic fractions of ID36 AML patient


title: AML cDNA hybridization-ID32-L

description: Leukemic fractions of ID32 AML patient have been hybridized.

tag: Leukemic fractions of ID32 AML patient


title: AML cDNA hybridization-ID28-L

description: Leukemic fractions of ID28 AML patient have been hybridized.

tag: Leukemic fractions of ID28 AML patient


title: AML cDNA hybridization-ID70-L

description: Leukemic fractions of ID70 AML patient have been hybridized.

tag: Leukemic fractions of ID70 AML patient


title: AML cDNA hybridization-ID49-L

description: Leukemic fractions of ID49 AML patient have been hybridized.

tag: Leukemic fractions of ID49 AML patient


title: AML cDNA hybridization-ID43-L

description: Leukemic fractions of ID43 AML patient have been hybridized.

tag: Leukemic fractions of ID43 AML patient


title: AML cDNA hybridization-ID60-L

description: Leukemic fractions of ID60 AML patient have been hybridized.

tag: Leukemic fractions of ID60 AML patient


title: AML cDNA hybridization-ID29-L

description: Leukemic fractions of ID29 AML patient have been hybridized.

tag: Leukemic fractions of ID29 AML patient


title: AML cDNA hybridization-ID71-L

description: Leukemic fractions of ID71 AML patient have been hybridized.

tag: Leukemic fractions of ID71 AML patient


title: AML cDNA hybridization-ID06-L

description: Leukemic fractions of ID06 AML patient have been hybridized.

tag: Leukemic fractions of ID06 AML patient


title: AML cDNA hybridization-ID07-L

description: Leukemic fractions of ID07 AML patient have been hybridized.

tag: Leukemic fractions of ID07 AML patient


title: AML cDNA hybridization-ID44-L

description: Leukemic fractions of ID44 AML patient have been hybridized.

tag: Leukemic fractions of ID44 AML patient


title: AML cDNA hybridization-ID48-L

description: Leukemic fractions of ID48 AML patient have been hybridized.

tag: Leukemic fractions of ID48 AML patient


title: AML cDNA hybridization-ID59-L

description: Leukemic fractions of ID59 AML patient have been hybridized.

tag: Leukemic fractions of ID59 AML patient


title: AML cDNA hybridization-ID05-L

description: Leukemic fractions of ID05 AML patient have been hybridized.

tag: Leukemic fractions of ID05 AML patient


title: AML cDNA hybridization-ID61-L

description: Leukemic fractions of ID61 AML patient have been hybridized.

tag: Leukemic fractions of ID61 AML patient


title: UCB-MSC_UCB1_8.0_hr_U133B

city: Tempe

first: Kenro

last: Kusumi

state: AZ

department: School of Life Sciences

institute: Arizona State University

hyb_protocol: Hybridization was carried out according to Affymetrix protocol.

scan_protocol: Scan was carried out according to Affymetrix protocol.

data_processing: RMA method normalization implemented in BioConductor

label_protocol: Microarray target was prepared following the Affymetrix protocol.  In brief, cDNA was synthesized from total RNA using the SuperScript II double-stranded cDNA synthesis kit (Invitrogen), followed by in vitro transcription, where labeled cRNA was generated (Enzo).

extract_protocol: Total RNA was isolated from cells in culture using the RNeasy Mini Kit (Qiagen), according to manufacturer's protocol

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 8.0 hr after low-serum synchronization


title: UCB-MSC_UCB1_7.5_hr_U133B

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 7.5 hr after low-serum synchronization


title: AML cDNA hybridization-ID04-L

description: Leukemic fractions of ID04 AML patient have been hybridized.

tag: Leukemic fractions of ID04 AML patient


title: E2 slide 18 day 1

description:
See Martyniuk et al. 2006 (PMID: 16954407) for details. Also please check the website about the goldfish microarraay project:
wwww.auratus.ca

source_name: E2 - control hypothalamus, slide 18

tag: adult male goldfish, 2-3 years of age, exposed to silastic implant, 1 day exposure

source_name: E2 - treatment hypothalamus, slide 18

extract_protocol:
Trizol reagent,
Quantarray scan.

tag: adult male goldfish, 2-3 years of age, exposed to silastic implant containing 17β-estradiol (E2) (100ug/g body mass), 1 day exposure


title: UCB-MSC_UCB1_7.0_hr_U133B

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 7.0 hr after low-serum synchronization


title: UCB-MSC_UCB1_5.5_hr_U133B

source_name: human umbilical cord blood-derived mesenchymal stem cell population 1


title: UCB-MSC_UCB1_0_hr_U133B

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 0 hr after low-serum synchronization


title: UCB-MSC_UCB1_5.0_hr_U133B

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 5.0 hr after low-serum synchronization


title: UCB-MSC_UCB1_2.5_hr_U133B

tag: human umbilical cord blood-derived mesenchymal stem cell population 1


title: UCB-MSC_UCB1_1.5_hr_U133B

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 1.5 hr after low-serum synchronization


title: UCB-MSC_UCB1_0.5_hr_U133B

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 0.5 hr after low-serum synchronization


title: UCB-MSC_UCB1_6.5_hr_U133B

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 6.5 hr after low-serum synchronization


title: UCB-MSC_UCB1_4.5_hr_U133B

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 4.5 hr after low-serum synchronization


title: UCB-MSC_UCB1_6.0_hr_U133B

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 6.0 hr after low-serum synchronization


title: UCB-MSC_UCB1_3.5_hr_U133B

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 3.5 hr after low-serum synchronization


title: UCB-MSC_UCB1_4.0_hr_U133B

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 4.0 hr after low-serum synchronization


title: UCB-MSC_UCB1_2.0_hr_U133B

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 2.0 hr after low-serum synchronization


title: UCB-MSC_UCB1_11.0_hr

scan_protocol: Scans were carried out according to Affymetrix protocol.

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 11.0 hr after low-serum synchronization


title: UCB-MSC_UCB1_9.0_hr

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 9.0 hr after low-serum synchronization


title: UCB-MSC_UCB1_7.5_hr

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 7.5 hr after low-serum synchronization


title: UCB-MSC_UCB1_8.0_hr

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 8.0 hr after low-serum synchronization


title: UCB-MSC_UCB1_3.0_hr_U133B

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 3.0 hr after low-serum synchronization


title: UCB-MSC_UCB1_1.0_hr_U133B

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 1.0 hr after low-serum synchronization


title: UCB-MSC_UCB1_5.0_hr


title: UCB-MSC_UCB1_12.0_hr

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 12.0 hr after low-serum synchronization


title: UCB-MSC_UCB1_10.0_hr

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 10.0 hr after low-serum synchronization


title: UCB-MSC_UCB1_6.0_hr


title: UCB-MSC_UCB1_6.5_hr


title: UCB-MSC_UCB1_7.0_hr

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 7.0 hr after low-serum synchronization


title: UCB-MSC_UCB1_5.5_hr

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 5.5 hr after low-serum synchronization


title: UCB-MSC_UCB1_4.0_hr


title: UCB-MSC_UCB1_1.5_hr

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 1.5 hr after low-serum synchronization


title: UCB-MSC_UCB1_4.5_hr


title: UCB-MSC_UCB1_2.5_hr

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 2.5 hr after low-serum synchronization


title: CS_control_rep2

status: Public on Apr 30 2007

city: Boston

first: Francesca

last: Pignoni

state: MA

address: 243 Charles Street

department: Department of Ophthalmology

institute: Harvard Medical School and Massachusetts Eye and Ear Infirmary

description: Canton S wild type 80 hr post pupa formation head tissue used in comparative global genome analysis of wild type and otd-uvi mutant heads to understand the function of Otd in fly

hyb_protocol: Biotin labeled probes, were generated from 10µg total RNA according to the Enzo BioArray HighYield RNA Transcript Labeling Kit (Affymetrix, P/N900182).  15µg of the synthesized biotin-labeled cRNA target was fragmented and hybridized to arrays according to the standard Affymetrix protocol.

data_processing: Normalization was done at probe level using Invariantset algorithm. All other preprocessing was done based on MAS 5.0 algorithm.

organism: Drosophila melanogaster

source_name: Head Tissue (80 hr post pupa formation)

extract_protocol: 15 to 20 heads were dissected 80 hours after puapa formation from Canton S (wild type) and immediately transferred to 600ul trizol (GIBCO/ BRL), and stored at -80ºC.  RNA extraction was performed according to manufacturer’s instructions.  Qualitative and quantitative analysis of the total RNA was carried out using capillary electrophoresis on a RNA 6000 Nano Assay chip,  with the Agilent 2100 Bioanalyzer (Agilent Technologies USA).

tag: Strain

value: Canton S


title: Otd_mutant_rep2

description: otd-uvi mutant 80 hr post pupa formation head tissue used in comparative global genome analysis of wild type and otd-uvi mutant heads to understand the function of Otd in fly

source_name: head tissue (80hrs post pupa formation)

extract_protocol: 15 to 20 heads were dissected 80 hours after puapa formation from otd-uvi (mutant) and immediately transferred to 600ul trizol (GIBCO/ BRL), and stored at -80ºC.  RNA extraction was performed according to manufacturer’s instructions.  Qualitative and quantitative analysis of the total RNA was carried out using capillary electrophoresis on a RNA 6000 Nano Assay chip,  with the Agilent 2100 Bioanalyzer (Agilent Technologies USA).

value: ‘eye-specific’ mutant allele, otduvi


title: UCB-MSC_UCB1_2.0_hr


title: lin-35(n745) worms at L4 stage, third replicate

status: Public on Apr 27 2007

city: Laramie

first: David

last: Fay

state: WY

address: 1000 E. University Dept. 3944

department: MOLB

institute: University of Wyoming

description: L4 stage lin-35(n745) hermaphrodites

hyb_protocol: according to Affymetrix protocol

scan_protocol: according to Affymetrix protocol

data_processing: expression values were generated using RMA

organism: Caenorhabditis elegans

source_name: RNA from synchronized at L4 stage C. elegans population

label_protocol: 2.5 ug total RNA were used for cDNA synthesis. cDNA synthesis, cRNA synthesis, fragmentation and labeling were performed according to Affymetrix protocol.

growth_protocol: Worms were grown on NGM plates spotted with OP50 at 20 oC.

extract_protocol: Total RNA was extracted with phenol, cleaned with phenol:chlorophorm:isoamyl alcohol (25:24:1), and then with chlorophorm:isoamyl alcohol (24:1). Total RNA was precipitated overnight at 4 oC with 4M lithium acetate and DNAseI treated before purification on RNEasy minicolumns from Qiagen.

tag: L4 stage lin-35(n745) hermaphrodites


title: UCB-MSC_UCB1_0.5_hr

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 0.5 hr after low-serum synchronization


title: UCB-MSC_UCB1_3.5_hr

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 3.5 hr after low-serum synchronization


title: UCB-MSC_UCB1_1.0_hr


title: lin-35(n745) worms at L4 stage, second replicate

description: L4 stage lin-35(n745) hermaphrodites


title: CS_control_rep1

source_name: head tissue (80 hours after pupa formation)


title: Otd_mutant_rep1

description: Otd-uvi mutant 80 hr post pupa formation head tissue used in comparative global genome analysis of wild type and otd-uvi mutant heads to understand the function of Otd in fly

source_name: Head Tissue (80hrs after pupa formation

value: ‘eye-specific’ mutant allele, otd-uvi


title: Otd_mutant_rep3

source_name: Head tissue (80hrs after pupa formation)


title: lin-35(n745) worms at embryonic stage, third replicate

description: lin-35(n745) embryos

source_name: RNA from embryonic C. elegans population

tag: lin-35(n745) embryos


title: N2 (wt) worms at embryonic stage, third replicate

description: N2 embryos

tag: N2 embryos


title: UCB-MSC_UCB1_0_hr

tag: human umbilical cord blood-derived mesenchymal stem cell population 1, 0 hr after low-serum synchronization


title: lin-35(n745) worms at embryonic stage, second replicate

description: lin-35(n745) embryos


title: N2 (wt) worms at L4 stage, third replicate

description: L4 stage N2 hermaphrodites

tag: L4 stage N2 hermaphrodites


title: N2 (wt) worms at embryonic stage, second replicate

description: N2 embryos


title: N2 (wt) worms at L4 stage, second replicate

description: L4 stage N2 hermaphrodites


title: lin-35(n745) worms at L4 stage, first replicate

description: L4 stage lin-35(n745) hermaphrodites


title: UCB-MSC_UCB1_3.0_hr


title: lin-35(n745) worms at L1 stage, first replicate

description: L1 stage lin-35 null hermaphrodites

source_name: RNA from synchronized at L1 stage C. elegans population

tag: L1 stage lin-35(n745) hermaphrodites


title: Control treated cells Rep2

status: Public on Apr 19 2007

first: Geoffrey

last: Girnun

address: One Jimmy Fund Way

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: Nothing more to add

hyb_protocol: The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The cRNA is purified from the fragmentation reaction using phenol/chloroform extraction and ethanol precipitation. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: Array normalization, expression value calculation and clustering analysis were performed using DNA-Chip Analyzer. The Invariant Set Normalization method was used to normalize arrays at probe cell level to make them comparable, and the model-based method was used for probe-selection and computing expression values.

label: biotinylated

source_name: NSCLC adenocarcinoma cell line

label_protocol:
RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.
The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.
The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).

extract_protocol: Samples were scraped into trizol and transfered to phaselock tubes.  RNA was extracted according to manufactures directions.

treatment_protocol: Cells were cultured overnight in DMEM 10% FBS (pen/strep).  Media was changed with cells receiving either control media, 1 micromolar rosiglitazone, 10 micromolar carboplatin or combination of carboplatin and rosiglitazone.

tag: A549 NSCLC cell line


title: N2 (wt) worms at L4 stage, first replicate

description: L4 stage N2 hermaphrodites


title: Rosiglitazone + carboplatin Rep1

description: Nothing more to add


title: N2 (wt) worms at embryonic stage, first replicate

description: N2 embryos


title: lin-35(n745) worms at L1 stage, third replicate

description: L1 stage lin-35 null hermaphrodites


title: Carboplatin treated cells Rep1

description: Nothing more to add


title: Rosiglitazone + carboplatin Rep2

description: Nothing more to add


title: Carboplatin treated cells Rep2

description: Nothing more to add


title: Rosiglitazone treated cells Rep2

description: Nothing more to add


title: Rosiglitazone treated cells Rep1

description: Nothing more to add


title: SHP-77

status: Public on Apr 15 2007

city: Abbott Park

first: Dimitri

last: Semizarov

state: IL

address: 100 Abbott Park Rd, bld AP10, dept R4CD

institute: Abbott Laboratories

description: gDNA from cell line profiled on Affymetrix 100K arrays using the standard protocol

hyb_protocol: Affymetrix 100K protocol

scan_protocol: Affymetrix 100K protocol

data_processing: Standard Affymetrix data generation protocol: CEL, CHP files generated by the GCOS and GTYPE programs.

source_name: cell line

label_protocol: Affymetrix 100K protocol

extract_protocol: Qiagen DNAeasy kit

tag: SCLC cell line


title: H1048

tag: SCLC cell line H1048


title: H196

tag: SCLC cell line H196


title: lin-35(n745) worms at embryonic stage, first replicate

description: lin-35(n745) embryos


title: SW 1271

tag: SCLC cell line SW1271


title: NCI-446

tag: SCLC cell line NCI-446


title: H69AR

tag: SCLC cell line H69AR


title: 40 Or5h Rice Osmotic(Or5h) Roots 5 hours

status: Public on Apr 10 2007

city: Milan

first: Stefano

last: Berri

address: via Celoria 26

department: biomolecular sciences and biotechnology

country: Italy

institute: University of Milan

hyb_protocol: For array hybridisation, Cy3 and Cy5 labelled cDNA probes were mixed with Calf thymus DNA (Sigma) and EGT hybridization buffer (Eurogentec) and hybridised to the microarray (Eurogentec) at 42°c in a humid chamber (Corning) for 16 hours. Arrays were washed 5min in a 0.2xSSC-0.1% sodium dodecyl sulfate solution then 5min in 0.2xSSC. The arrays were spin-dried.

scan_protocol: The arrays were scanned using the Axon 4100A Scanner. The hybridisation data were collected and normalization performed using the GenePix Pro 3.0 software.

data_processing: Data were normalized using Limma, a package of Bioconductor, using loess, but giving different weight do spots. Weight of each spot is reported in the data table.

organism: Oryza sativa Japonica Group

label_protocol: 10 µg of total RNAs were used for Cy3 or Cy5 labelling using the Cyscribe First-Strand cDNA Labelling kit (Amersham). The labelled cDNA samples were purified using the CyScribe GFX Purification Kit (Amersham) and concentrated using a microcon YM-30 filter (Millipore). 5 ng of Luciferase RNA (Promega) was added to each RNA samples prior labelling and used as spiking / normalization control.!Sample_label_protocol_ch2 = 10 µg of total RNAs were used for Cy3 or Cy5 labelling using the Cyscribe First-Strand cDNA Labelling kit (Amersham). The labelled cDNA samples were purified using the CyScribe GFX Purification Kit (Amersham) and concentrated using a microcon YM-30 filter (Millipore). 5 ng of Luciferase RNA (Promega) was added to each RNA samples prior labelling and used as spiking / normalization control.

growth_protocol:
Seeds of rice genotype Nipponbarre were obtained from the International Rice Research Institute (IRRI). Dehisced seeds were sterilized with 15% (v/v) sodium hypochlorite for 30 min and then rinsed with distilled water. Seeds were germinated in Petri dishes at 28oC on Whatman® paper soaked in deionized water. After 4 days, rice seedlings were transferred in pots containing pouzzolane and allowed to growth under controlled conditions with a 28°C/25°C day/night temperatures, 12 hr photoperiod and 55-65% humidity for 2 weeks in Yoshida’s modified solution (1981): 0.7 mM KNO3, 1.2 mM Ca(NO3)2, 1.6 mM MgSO4, 0.5 mM (NH4)2SO4, 0.8 mM KH2PO4, 60 µM FeEDTA, 20µM MnSO4, 0.32 µM(NH4)6Mo7O24, 1.4 µM ZnSO4, 1.6 µM CuSO4, 45.2 µM H3BO3. Medium pH was adjusted to 5.0 twice a day. Seedlings at the 5 leaves stage without any visible tiller were carefully selected for stress treatments.
Seeds of rice genotype Nipponbarre were obtained from the International Rice Research Institute (IRRI). Dehisced seeds were sterilized with 15% (v/v) sodium hypochlorite for 30 min and then rinsed with distilled water. Seeds were germinated in Petri dishes at 28oC on Whatman® paper soaked in deionized water. After 4 days, rice seedlings were transferred in pots containing pouzzolane and allowed to growth under controlled conditions with a 28°C/25°C day/night temperatures, 12 hr photoperiod and 55-65% humidity for 2 weeks in Yoshida’s modified solution (1981): 0.7 mM KNO3, 1.2 mM Ca(NO3)2, 1.6 mM MgSO4, 0.5 mM (NH4)2SO4, 0.8 mM KH2PO4, 60 µM FeEDTA, 20µM MnSO4, 0.32 µM(NH4)6Mo7O24, 1.4 µM ZnSO4, 1.6 µM CuSO4, 45.2 µM H3BO3. Medium pH was adjusted to 5.0 twice a day. Seedlings at the 5 leaves stage without any visible tiller were carefully selected for stress treatments.

extract_protocol: TRIZOL protocol (Invitrogen, Carlsbad, CA), as indicated by the manufacturer.

treatment_protocol: 100 mM of mannitol was added in the hydroponic solution. Root and shoot tissues were harvested 1 hr or 5 hr after the beginning of stress treatment

tag: Tissue

value: 2-weeks old rice seedling Roots. Treatment:Osmotic

treatment_protocol: Water was added in the hydroponic solution. Root and shoot tissues were harvested 1 hr or 5 hr after the beginning of stress treatment

value: 2-weeks old rice seedling Roots. Treatment:Mock treatment


title: lin-35(n745) worms at L1 stage, second replicate

description: L1 stage lin-35 null hermaphrodites


title: H82

tag: SCLC cell line H82


title: 37 Or5h Rice Osmotic(Or5h) Roots 5 hours


title: 38 Or5h Rice Osmotic(Or5h) Roots 5 hours


title: 39 Or5h Rice Osmotic(Or5h) Roots 5 hours