title: ALL30

status: Public on Sep 27 2007

city: RENNES

first: virginie

last: gandemer

address: 2 av du Pr Léon Bernard

department: génétique et developpement

institute: CNRS UMR6061/Université Rennes1

description: The Feature Extraction Software v7.5 (Agilent technologies, Palo Alto, CA, USA) was used to extract and analyse the signals.

hyb_protocol: Hybridization was carried out using the Agilent oligonucleotide microarray in situ hybridization plus kit (p/n 5184-3568), following the manufacturer’s instructions. Briefly, 750 ng of test sample cRNA was mixed with 750 ng of reference sample cRNA in the presence of target controls. This solution was subjected to fragmentation (30 min at 60°C) and then hybridization on 44K Human Whole-Genome 60-mer oligo-chips (G4112A, Agilent Technologies) in a rotary oven (4000 rpm, 60°C, 17h). Slides were disassembled and washed in solutions I and II according to the manufacturer’s instructions, and dried using a nitrogen-filled air gun before scanning.

scan_protocol: Microarrays were scanned with a dynamic autofocus microarray scanner (Agilent dual laser DNA microarray scanner -G2566AA, Agilent technologies, Palo Alto, CA, USA), using Agilent-provided parameters (Red and Green PMT were each set at 100%, and scan resolution was set to 10 μm).

data_processing: Agilent-provided settings were used except for subtraction of the local background and adjustment of the global background. Poor quality features that were either saturated in the two channels (50% of pixels > saturation threshold) or non-uniform were flagged. Only those features with a signal-to-noise ratio (SNR) of up to 2.6 in at least one channel and significantly different from the local background (two sided Student's t-test <0.01) were used for further analysis. The mean signal ratio of the two fluorescent intensities (Cy-5 cRNA test /Cy-3 pooled cRNA) is expressed as a logarithm (base 2), providing a relative quantitative gene expression measurement between two samples. For subsequent analysis, we used mean-centered log2 of the normalized (linear & lowess method) sample:reference ratio.

source_name: bone marrow lymphoblasts of patient 30

label_protocol: RNA samples were labeled using the Agilent low RNA input fluorescent linear amplification Kit (p/n 5184-3523) according to the manufacturer’s instructions. To avoid confounding by extraneous factors, all the experiments were performed with a single batch and processed by one technician on the same day for each step. Briefly, 500 ng of total RNA was reverse transcribed. Amplification and labeling were performed by T7-polymerase in vitro transcription, to give fluorescent-labeled cRNA. Test cRNAs were labeled with Cyanine-5 dyes (10 mM, PerkinElmer, Norwalk, CT). The dye incorporation rate was assessed with a Nanodrop® ND-1000 spectrophotometer and was found to be between 1.2 and 1.4 pmol/μl.

extract_protocol: Total RNA was recovered using a Qiagen RNeasy column (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. In-column DNase treatment was carried out before eluting the RNA to ensure the absence of genomic DNA. Recovered RNA was quantified using a Nanodrop 1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using a 2100 Bioanalyser (Agilent, Palo Alto, CA,USA). RNA samples with an RNA integrity number (RIN) greater than 9 were used for further analysis.

treatment_protocol: Mononuclear cells were isolated from bone marrow (2 ml samples, i.e. 5 million cells) by successive centrifugations through MLS medium (Eurobio, Courtabeuf, France). Isolated leukocytes were immediately stored at –80°C in 1 ml of RNA-PLUS solution (Qbiogene, Strasbourg, France).

tag: Patient 30 set B Female 2 years 2.2 WBC at diagnosis no recurrent rearrangement standard risk group

source_name: pool

label_protocol: RNA samples were labeled using the Agilent low RNA input fluorescent linear amplification Kit (p/n 5184-3523) according to the manufacturer’s instructions. To avoid confounding by extraneous factors, all the experiments were performed with a single batch and processed by one technician on the same day for each step. Briefly, 500 ng of total RNA was reverse transcribed. Amplification and labeling were performed by T7-polymerase in vitro transcription, to give fluorescent-labeled cRNA. Reference cRNAs were labeled with Cyanine-3 dyes (10 mM, PerkinElmer, Norwalk, CT). The dye incorporation rate was assessed with a Nanodrop® ND-1000 spectrophotometer and was found to be between 1.2 and 1.4 pmol/μl.

tag: equimolar-pooled mixture of each test RNA sample for the reference RNA


title: Human Ntera2 cells, Kap1 WG Array, 83319_ratio.gff

status: Public on Sep 29 2007

type: genomic

city: Davis

first: Kimberly

middle: Rose

last: Blahnik

state: CA

address: GBSF 1 Shields Ave

department: Genome and Biomedical Sciences

country: USA

institute: University of California Davis

description: A complete genomic analysis of KAP1 binding in human Ntera2 testicular carcinoma cells using a 38 array tiling set, identifying ~7000 KAP1 binding sites.

hyb_protocol: The hybridization of DNA samples for ChIP-ChIP analysis was performed by NimbleGen Systems, Inc. Briefly, 13ug of the Cy5-labeled ChIP sample and 13ug of the Cy3-labeled total sample were mixed, dried down, and resuspended in 40 ul of NimbleGen Hybridization Buffer (NimbleGen Systems) plus 1.5 ug of human COT1 DNA. After denaturation, hybridization was carried out in a MAUI Hybridization System (BioMicro Systems) for 18 h at 42°C. The arrays were washed using NimbleGen Wash Buffer System (NimbleGen Systems), dried by centrifugation.

scan_protocol: The arrays were scanned at 5-um resolution using the GenePix 4000B scanner (Axon Instruments).

data_processing: log base 2 ratios; specifically, fluorescence intensity raw data were obtained from scanned images of the oligonucleotide tiling arrays using NIMBLESCAN 2.0 extraction software (NimbleGen Systems). For each spot on the array, log2-ratios of the Cy5-labeled test sample versus the Cy3-labeled reference sample were calculated. Then, the biweight mean of this log2 ratio was subtracted from each point; this procedure is approximately equivalent to mean-normalization of each channel.

molecule: genomic DNA

organism: Homo sapiens

source_name: Ntera2 cells

label_protocol: The labeling of DNA samples for ChIP-ChIP analysis was performed by NimbleGen Systems, Inc. Briefly, each DNA sample (1 ug) was denatured in the presence of 5'-Cy3- or Cy5-labeled random nonamers (TriLink Biotechnologies) and incubated with 100 units (exo-) Klenow fragment (NEB) and dNTP mix [6 mM each in TE buffer (10 mM Tris/1 mM EDTA, pH 7.4; Invitrogen)] for 2 h at 37°C. Reactions were terminated by addition of 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water.

extract_protocol: Performed following the 'Chromatin Immunoprecipitation Assay (ChIPs)' protocol provided at http://genomics.ucdavis.edu/farnham

tag: KAP1 antibody immunoprecipitated DNA

label_protocol: see labeling protocol for channel 1

extract_protocol: see extract protocol for channel 1

tag: control total input


title: ALL28

type: RNA

country: France

molecule: total RNA

source_name: bone marrow lymphoblasts of patient 28

tag: Patient 28 set B Male 6 years 26.2 WBC at diagnosis no recurrent rearrangement standard risk group


title: ALL33

source_name: bone marrow lymphoblasts of patient 33

tag: Patient 33 set B Male 2.5 years 1.3 WBC at diagnosis TEL/AML1 rearrangement standard risk group


title: Human Ntera2 cells, Kap1 WG Array, 71235_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 73434_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 63784_ratio.gff


title: ALL31

source_name: bone marrow lymphoblasts of patient 31

tag: patient 31 set B Female 3 years 22.6 WBC at diagnosis no recurrent rearrangement standard risk group


title: ALL32

source_name: bone marrow lymphoblasts of patient 32

tag: Patient 32 set B Male 2 years 130 WBC at diagnosis TEL/AML1 rearrangement high risk group


title: Wildtype cocaine, technical replicate 2

city: Boston

first: Will

last: Renthal

state: MA

address: 60 Fenwood Rd.

institute: Brigham and Women's Hospital

description: Nucleus Accumbens, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg).

hyb_protocol: 16hrs at 55degress C using Illumina reagents

scan_protocol: Standard scan factor using Illumina Scanner

data_processing: The Raw data was extracted using MS5, and median-normalized.

label: biotin

organism: Mus musculus

source_name: Mouse Nucleus Accumbens from wildtype cocaine treated mice

label_protocol: linear amplification kit Ambion #IL1791.  Input amount: 200ng of total

extract_protocol: RNA was extracted with TriZol and purified with RNAeasy Micro kit.

tag: bilateral, 1mm-thick, 15gauge punches, pooled together from four mice


title: CGH WG-set_8of8 NA18505 vs. NA15510

status: Public on Sep 28 2007

city: New Haven

first: Jan

middle: Oliver

last: Korbel

state: CT

address: 266 Whitney Avenue

institute: Yale University

description: hybridized at Nimblegen facilities in Iceland

hyb_protocol: Nimblegen kit

scan_protocol: Nimblegen protocol

data_processing: Qspline normalization (Bioconductor)

label_protocol: Nimblegen kit

growth_protocol: Nimblegen kit

extract_protocol: Nimblegen kit

treatment_protocol: Nimblegen kit

tag: female


title: CGH WG-set_6of8 NA18505 vs. NA15510


title: Knockout cocaine, biological replicate 5

source_name: Mouse Nucleus Accumbens from knockout cocaine treated mice


title: CGH WG-set_7of8 NA18505 vs. NA15510

description: Nimblegen protocol (experiment carried out by Nimblegen)

data_processing: Qspline-normalization, note that data column gives Cy3/Cy5

extract_protocol: genomic DNA obtained from Coriell

label_protocol: see channel 1

extract_protocol: see channel 1


title: ALL25

source_name: bone marrow lymphoblasts of patient 25

tag: Patient 25 Male 3 years 5.4 WBC at diagnosis no recurrent rearrangement standard risk grouo


title: CGH WG-set_2of8 NA18505 vs. NA15510


title: ALL29

source_name: bone marrow lymphoblasts of patient 29

tag: Patient 29 set B Male 15 years 4.2 WBC no recurrent rearrangement high risk group


title: Human Ntera2 cells, Kap1 WG Array, 62802_ratio.gff_GPL5190


title: Wildtype saline, biological replicate 5

source_name: Mouse Nucleus Accumbens from wildtype saline treated mice


title: ALL27

source_name: bone marrow lymphoblasts of patient 27

tag: patient 27 set B Female 7.5 years 4 WBC at diagnosis no recurrent rearrangement standard risk group


title: Wildtype saline, biological replicate 4


title: Knockout cocaine, biological replicate 6


title: Knockout saline, biological replicate 4

source_name: Mouse Nucleus Accumbens from knockout saline treated mice


title: Knockout cocaine, biological replicate 4


title: Knockout cocaine, technical replicate 2


title: Knockout saline, biological replicate 6


title: Knockout saline, biological replicate 3


title: Wildtype cocaine, biological replicate 5


title: ALL16

scan_protocol: Microarrays were scanned with a dynamic autofocus microarray scanner (Agilent dual laser DNA microarray scanner -G2566AA, Agilent technologies, Palo Alto, CA, USA), using Agilent-provided parameters (Red and Green PMT were each set at 100%, and scan resolution was set to 10 m).

data_processing: Agilent-provided settings were used except for subtraction of the local background and adjustment of the global background. Poor quality features that were either saturated in the two channels (50% of pixels  saturation threshold) or non-uniform were flagged. Only those features with a signal-to-noise ratio (SNR) of up to 2.6 in at least one channel and significantly different from the local background (two sided Student's t-test <0.01) were used for further analysis. The mean signal ratio of the two fluorescent intensities (Cy-5 cRNA test /Cy-3 pooled cRNA) is expressed as a logarithm (base 2), providing a relative quantitative gene expression measurement between two samples. For subsequent analysis, we used mean-centered log2 of the normalized (linear & lowess method) sample:reference ratio.

source_name: bone marrow lymphoblasts of patient 16

label_protocol: RNA samples were labeled using the Agilent low RNA input fluorescent linear amplification Kit (p/n 5184-3523) according to the manufacturer’s instructions. To avoid confounding by extraneous factors, all the experiments were performed with a single batch and processed by one technician on the same day for each step. Briefly, 500 ng of total RNA was reverse transcribed. Amplification and labeling were performed by T7-polymerase in vitro transcription, to give fluorescent-labeled cRNA. Test cRNAs were labeled with Cyanine-5 dyes (10 mM, PerkinElmer, Norwalk, CT). The dye incorporation rate was assessed with a Nanodrop® ND-1000 spectrophotometer and was found to be between 1.2 and 1.4 pmol/l.

tag: Patient 16 set A 2 years 3.6 WBC at diagnosis no recurrent rearrangement standard risk roup

label_protocol: RNA samples were labeled using the Agilent low RNA input fluorescent linear amplification Kit (p/n 5184-3523) according to the manufacturer’s instructions. To avoid confounding by extraneous factors, all the experiments were performed with a single batch and processed by one technician on the same day for each step. Briefly, 500 ng of total RNA was reverse transcribed. Amplification and labeling were performed by T7-polymerase in vitro transcription, to give fluorescent-labeled cRNA. Reference cRNAs were labeled with Cyanine-3 dyes (10 mM, PerkinElmer, Norwalk, CT). The dye incorporation rate was assessed with a Nanodrop® ND-1000 spectrophotometer and was found to be between 1.2 and 1.4 pmol/l.


title: Human Ntera2 cells, Kap1 WG Array, 83310_ratio.gff


title: ALL23

source_name: bone marrow lymphoblasts of patient 23

tag: Patient 23 set A Male 2 years 15.4 WBC at diagnosis TEL/AML1 rearrangement standard risk group


title: Knockout cocaine, biological replicate 3


title: Wildtype cocaine, biological replicate 3


title: Knockout saline, biological replicate 5


title: Wildtype cocaine, biological replicate 6


title: Wildtype saline, biological replicate 3


title: Wildtype cocaine, biological replicate 4


title: Knockout saline, technical replicate 1

description: Nucleus Accumbends, Male 8-12 week old HDAC5 WT or KO mice treated with chronic (7 daily injections) saline or cocaine (20mg/kg).


title: Wildtype saline, biological replicate 6


title: CGH WG-set_1of8 NA18505 vs. NA15510


title: ALL20

source_name: bone marrow lymphoblasts of patient 20

tag: patient 20 set A Female 14 years 82 WBC at diagnosis no recurrent rearrangement high risk group


title: ALL17

source_name: bone marrow lymphoblasts of patient 17

tag: patient 17  Set A Male 4 years 47 WBC at diagnosis TEL/AML1 rearrangement standard risk group


title: ALL24

source_name: bone marrow lymphoblasts of patient 24

tag: Patient 24 set A Male 3 years 2.9 WBC at diagnosis no recurrent rearrangement standard risk group

source_name: pool


title: Wildtype saline, technical replicate 1


title: ALL21

source_name: bone marrow lymphoblasts of patient 21

tag: Patient 21 Male 6 years 68 WBC at diagnosis no recurrent rearrangement high risk group

tag: equimolar-pooled mixture of each test RNA sample for the reference RNA


title: CGH WG-set_4of8 NA18505 vs. NA15510

data_processing: Qspline normalization (Bioconductor); note that data column gives Cy3 / Cy5


title: Wildtype cocaine, biological replicate 1


title: ALL14

source_name: bone marrow lymphblasts of atient 14

tag: Patient 14 set A Female 5 years 4.5 WBC at diagnosis no recurrent rerrangement standard risk group


title: ALL13

source_name: bone marrow lymphoblasts of patient 13

tag: patient 13 Set A Female 4 years 24.3 WBC at diagnosis TEL/AML1 rearrangement standard risk group


title: ALL15

source_name: bone marrow lymphoblasts of patient 15

tag: Patient 15 set A Male 13 years 3.9 WBC at diagnosis no recurrent rearrangement high risk group


title: ALL18

source_name: bone marrow lymphoblasts of patient 18

tag: Patient 18 set A Male 10 years 35.8 WBC at diagnosis TEL/AML1 rearrangement high risk group


title: ALL12

source_name: bone marrow lymphoblasts of patient 12

tag: Patient 12 set A Female 6 years 18.4 WBC at diagnosis TEL/AML1 rearrangement standard risk group


title: Knockout saline, biological replicate 1

tag: bilateral, 1mm-thick, 15gauge punches, pooled together from four mice


title: ALL22

source_name: bone marrow lymphoblasts of patient 22

tag: Patient 22 set A Female 10 years 150 WBC at diagnosis no recurrent rearrangement high risk group


title: ALL26

source_name: bone marrow lymphoblasts of patient 26

tag: Patient 26 set A female 3 years 41 WBC at diagnosis no recurrent rearrangement standard risk group


title: CGH WG-set_5of8 NA18505 vs. NA15510

tag: female


title: ALL11

description: The Feature Extraction Software v7.5 (Agilent technologies, Palo Alto, CA, USA) was used to extract and analyse the signals

source_name: bone marrow lymphoblasts of patient 11

tag: Patien 11 set A Female 2 years 7.2 WBC at diagnosis no recurrent rearrangement standard risk group


title: ALL10

source_name: bone marrow blasts of patient 10

tag: Paient 10 set A Male 3 years 5.4 WBC at diagnosis no recurrent rearrangement standard risk group


title: ALL9

source_name: bone marrow lymphoblasts of patient 9

tag: Patient 9 set A Male 3 years 7.8 WBC at diagnosis no recurrent rearrangement standard risk group


title: Wildtype cocaine, technical replicate 1

source_name: Mouse Nucleus Accumbens from wildtype cocaine treated mice


title: Wildtype saline, biological replicate 1

source_name: Mouse Nucleus Accumbens from wildtype saline treated mice


title: Knockout cocaine, biological replicate 1

source_name: Mouse Nucleus Accumbens from knockout cocaine treated mice


title: Knockout cocaine, technical replicate 1


title: ALL19

source_name: bone marrow lymphoblasts of patient 19

tag: patient 19 set A Female 3 years 14.9 WBC at diagnosis no recurrent rearrangement standard risk group


title: CGH WG-set_3of8 NA18505 vs. NA15510

data_processing: Qspline normalization (Bioconductor), note that data column gives Cy3 / Cy5


title: Wildtype cocaine, biological replicate 2


title: ALL5

source_name: bone marrow lympoblasts of patient 5

tag: patient 5 set A male 4 years 18.5 WBC at diagnosis TEL/AML1 rearrangement standard risk group


title: Knockout cocaine, biological replicate 2


title: Knockout saline, biological replicate 2

source_name: Mouse Nucleus Accumbens from knockout saline treated mice

label_protocol: linear amplification kit Ambion #IL1791.  Input amount: 200ng of total RNA, IVT 2hrs.


title: ALL8

source_name: bone marrow lymphoblats of patient 8

tag: patient 8 set A Female 8 years 0.9 WBC at diagnosis no recurrent rearrangement standard risk group

source_name: pool


title: ALL6

source_name: bone marrow lymphoblasts of patient 6

tag: Patient 6 set A Female .5 years 52.5 WBC at diagnosis no recurrent rearrangement high risk group


title: Wildtype saline, biological replicate 2


title: ALL7

source_name: bone marrow lymphoblasts of patient 7

tag: Patient 7 set A Female 2 years 5.4 WBC at diagnosis no recurrent rearrangement standard risk group

tag: equimolar-pooled mixture of each test RNA sample for the reference RNA


title: ALL4

source_name: bone marrow lymphoblasts of patient 4

label_protocol: RNA samples were labeled using the Agilent low RNA input fluorescent linear amplification Kit (p/n 5184-3523) according to the manufacturer’s instructions. To avoid confounding by extraneous factors, all the experiments were performed with a single batch and processed by one technician on the same day for each step. Briefly, 500 ng of total RNA was reverse transcribed. Amplification and labeling were performed by T7-polymerase in vitro transcription, to give fluorescent-labeled cRNA. Test cRNAs were labeled with Cyanine-5 CTP dyes,  (10 mM, PerkinElmer, Norwalk, CT). The dye incorporation rate was assessed with a Nanodrop® ND-1000 spectrophotometer and was found to be between 1.2 and 1.4 pmol/l.

tag: Patient 4 set A female 1.5 years 1.2 WBC at diagnosis no recuurent rearrangement standard risk group

label_protocol: RNA samples were labeled using the Agilent low RNA input fluorescent linear amplification Kit (p/n 5184-3523) according to the manufacturer’s instructions. To avoid confounding by extraneous factors, all the experiments were performed with a single batch and processed by one technician on the same day for each step. Briefly, 500 ng of total RNA was reverse transcribed. Amplification and labeling were performed by T7-polymerase in vitro transcription, to give fluorescent-labeled cRNA. Reference cRNAs were labeled with Cyanine-3 CTP dyes,  (10 mM, PerkinElmer, Norwalk, CT). The dye incorporation rate was assessed with a Nanodrop® ND-1000 spectrophotometer and was found to be between 1.2 and 1.4 pmol/l.


title: ALL3

source_name: bone marrow lymphoblasts of patient 3

tag: Patient 3 male 2.5 years 4.5 WBC at diagnosis TEL/AML1 rearrangement standar risk group

label_protocol: RNA samples were labeled using the Agilent low RNA input fluorescent linear amplification Kit (p/n 5184-3523) according to the manufacturer’s instructions. To avoid confounding by extraneous factors, all the experiments were performed with a single batch and processed by one technician on the same day for each step. Briefly, 500 ng of total RNA was reverse transcribed. Amplification and labeling were performed by T7-polymerase in vitro transcription, to give fluorescent-labeled cRNA. reference cRNAs were labeled with Cyanine-3 dyes (10 mM, PerkinElmer, Norwalk, CT). The dye incorporation rate was assessed with a Nanodrop® ND-1000 spectrophotometer and was found to be between 1.2 and 1.4 pmol/l.


title: ALL2

hyb_protocol: Hybridization was carried out using the Agilent oligonucleotide microarray in situ hybridization plus kit (p/n 5184-3568), following the manufacturers instructions. Briefly, 750 ng of test sample cRNA was mixed with 750 ng of reference sample cRNA in the presence of target controls. This solution was subjected to fragmentation (30 min at 60C) and then hybridization on 44K Human Whole-Genome 60-mer oligo-chips (G4112A, Agilent Technologies) in a rotary oven (4000 rpm, 60C, 17h). Slides were disassembled and washed in solutions I and II according to the manufacturers instructions, and dried using a nitrogen-filled air gun before scanning.

scan_protocol: Microarrays were scanned with a dynamic autofocus microarray scanner (Agilent dual laser DNA microarray scanner -G2566AA, Agilent technologies, Palo Alto, CA, USA), using Agilent-provided parameters (Red and Green PMT were each set at 100%, and scan resolution was set to 10 ?m).

source_name: bone marrow lymphoblasts of patient 2

label_protocol: RNA samples were labeled using the Agilent low RNA input fluorescent linear amplification Kit (p/n 5184-3523) according to the manufacturers instructions. To avoid confounding by extraneous factors, all the experiments were performed with a single batch and processed by one technician on the same day for each step. Briefly, 500 ng of total RNA was reverse transcribed. Amplification and labeling were performed by T7-polymerase in vitro transcription, to give fluorescent-labeled cRNA. Test cRNAs were labeled with Cyanine-5 dyes (10 mM, PerkinElmer, Norwalk, CT). The dye incorporation rate was assessed with a Nanodrop ND-1000 spectrophotometer and was found to be between 1.2 and 1.4 pmol/?l.

extract_protocol: Total RNA was recovered using a Qiagen RNeasy column (Qiagen, Hilden, Germany) according to the manufacturers instructions. In-column DNase treatment was carried out before eluting the RNA to ensure the absence of genomic DNA. Recovered RNA was quantified using a Nanodrop 1000 spectrophotometer (Nanodrop Technology, Cambridge, UK) and RNA integrity was assessed using a 2100 Bioanalyser (Agilent, Palo Alto, CA,USA). RNA samples with an RNA integrity number (RIN) greater than 9 were used for further analysis.

treatment_protocol: Mononuclear cells were isolated from bone marrow (2 ml samples, i.e. 5 million cells) by successive centrifugations through MLS medium (Eurobio, Courtabeuf, France). Isolated leukocytes were immediately stored at 80C in 1 ml of RNA-PLUS solution (Qbiogene, Strasbourg, France)

tag: Patient 2 set A Female 7 years 21.6 WBC at diagnosis (count x 109/l) no recurrent rearrangement Standard risk group

label_protocol: RNA samples  were labeled using the Agilent low RNA input fluorescent linear amplification Kit (p/n 5184-3523) according to the manufacturers instructions. To avoid confounding by extraneous factors, all the experiments were performed with a single batch and processed by one technician on the same day for each step. Briefly, 500 ng of total RNA was reverse transcribed. Amplification and labeling were performed by T7-polymerase in vitro transcription, to give fluorescent-labeled cRNA. Reference cRNAs were labeled with Cyanine-3 CTP dyes (10 mM, PerkinElmer, Norwalk, CT). The dye incorporation rate was assessed with a Nanodrop ND-1000 spectrophotometer and was found to be between 1.2 and 1.4 pmol/?l.


title: Shoot WT ABA (100 uM) 4 hr rep1

status: Public on Sep 26 2007

city: Hayward

first: Don

middle: R

last: Maszle

address: 3935 Point Eden Way

institute: Mendel Biotechnology, Inc.

hyb_protocol: Affymetrix Eukaryotic Target Hybridization Protocol

scan_protocol: Affymetrix Scan Protocol using MAS5 and Agilent G2500A Scanner

data_processing: Rosetta Resolver v5.x  default Affymetrix pipeline

organism: Arabidopsis thaliana

source_name: Shoot WT ABA (100 uM) 4 hr

label_protocol: Ambion MessageAmp RNA Amplification for Array Analysis Catalog \#1750

growth_protocol: Plants were grown in a 24 hr chamber. 14-day old, plate-grown seedlings were harvested. Pools of ~24 seedlings were used per replicate.

extract_protocol: RNeasy Mini Protocol for Isolation of Total RNA from Plant Cells and Tissues and Filamentous Fungi, Qiagen RNeasy Mini Handbook 06/2001 page 75

tag: Treated sample


title: Shoot WT ABA (100 uM) 4 hr rep2


title: SHDL111

city: Paris

first: Corneliu

last: Henegar

state: Ile de France

address: 15 Rue de l'Ecole de Medecine

institute: Institut national de la santé et de la recherche médicale

description: We analyzed the gene expression profiles of subcutaneous white adipose tissue from 29 obese subjects during very low calorie diet (VLCD) using cDNA microarray. The patterns of expression were compared with that of 17 non-obese subjects.

hyb_protocol: The labeled cDNA mixtures were hybridized according to the protocol described at http://cmgm.stanford.edu/pbrown/protocols/index

scan_protocol: The arrays were immediately scanned using a GenePix 4000A confocal Scanner (Axon Instruments). Images were analyzed using GenePix pro 3 software.

data_processing: After scanning the arrays, the images were analyzed and ratio intensities were filtered and normalized using Stanford Microarray Database Online resources (http://genome-www5.stanford.edu/).The VALUE field represents the log(base2) of the print-tip loess normalized R/G ratio (mean).

source_name: Pool

label_protocol: One microgram of total RNA from each sample preparation was amplified using the MessageAmp RNA kit (Ambion, Austin, TX), and 3 µg aRNA was Cy-dye labeled using the CyScribe first-strand cDNA labeling kit (Amersham Biosciences, Orsay, France) (available at http://cmgm.stanford.edu/pbrown/protocols/index).

extract_protocol: Total RNA from scWAT was prepared using the RNeasy RNA Mini Kit (Qiagen, Courtaboeuf, France).

tag: Pool of human subcutaneous adipose tissue

source_name: Obese

tag: Obese subcutaneous adipose tissue (V)


title: Shoot WT rep3

source_name: Shoot WT

tag: Control sample


title: 12789585

source_name: Lean

tag: Lean subcutaneous adipose tissue (H)


title: 12794826

tag: Lean subcutaneous adipose tissue (F)


title: Shoot 35s::CBF4 19 rep1

source_name: Shoot 35s::CBF4_19

tag: Trangenic overexpression line


title: Shoot WT Mock (MS-Tween) 4 hr rep1

source_name: Shoot WT Mock (MS-Tween) 4 hr


title: SHDL156

tag: Obese subcutaneous adipose tissue (DEC)


title: Shoot WT Mock (MS-Tween) 4 hr rep2


title: Shoot 35s::AtNF-YB 3 rep2

source_name: Shoot 35s::AtNF-YB_3


title: 12789586

tag: Lean subcutaneous adipose tissue (D)


title: Shoot 35s::CBF4 10 rep1

source_name: Shoot 35s::CBF4_10


title: Shoot 35s::CBF4 10 rep2


title: SHDL113

tag: Obese subcutaneous adipose tissue (I)


title: Shoot 35s::CBF4 19 rep2


title: ALL1

source_name: bone marrow lymphoblasts of patient 1

label_protocol: RNA samples were labeled using the Agilent low RNA input fluorescent linear amplification Kit (p/n 5184-3523) according to the manufacturer’s instructions. To avoid confounding by extraneous factors, all the experiments were performed with a single batch and processed by one technician on the same day for each step. Briefly, 500 ng of total RNA was reverse transcribed. Amplification and labeling were performed by T7-polymerase in vitro transcription, to give fluorescent-labeled cRNA. Test cRNAs were labeled with Cyanine-5 dyes (10 mM, PerkinElmer, Norwalk, CT). The dye incorporation rate was assessed with a Nanodrop® ND-1000 spectrophotometer and was found to be between 1.2 and 1.4 pmol/μl.

treatment_protocol: Mononuclear cells were isolated from bone marrow (2 ml samples, i.e. 5 million cells) by successive centrifugations through MLS medium (Eurobio, Courtabeuf, France). Isolated leukocytes were immediately stored at –80°C in 1 ml of RNA-PLUS solution (Qbiogene, Strasbourg, France)

tag: Patient	1

tag: Set A	Female	5 years

tag: High risk group

label_protocol: RNA samples  were labeled using the Agilent low RNA input fluorescent linear amplification Kit (p/n 5184-3523) according to the manufacturer’s instructions. To avoid confounding by extraneous factors, all the experiments were performed with a single batch and processed by one technician on the same day for each step. Briefly, 500 ng of total RNA was reverse transcribed. Amplification and labeling were performed by T7-polymerase in vitro transcription, to give fluorescent-labeled cRNA. Reference cRNAs were labeled with Cyanine-3 CTP dyes (10 mM, PerkinElmer, Norwalk, CT). The dye incorporation rate was assessed with a Nanodrop® ND-1000 spectrophotometer and was found to be between 1.2 and 1.4 pmol/μl.


title: 12789727

tag: Lean subcutaneous adipose tissue (B)


title: Shoot WT rep2


title: SHDL157

tag: Obese subcutaneous adipose tissue (CAL)


title: Shoot WT rep1


title: Shoot 35s::AtNF-YB 6 rep2

source_name: Shoot 35s::AtNF-YB_6


title: SHDL159

tag: Obese subcutaneous adipose tissue (DOR)


title: 12789723

tag: Lean subcutaneous adipose tissue (A)


title: SHCV219

tag: Obese subcutaneous adipose tissue (PX)


title: SHDR225

tag: Pool of human subcutaneous adipose tissue

tag: Lean subcutaneous adipose tissue (omega8)


title: Animal 4 hepatectomy sham surgery 1h

city: Philadelphia

first: Egle

last: Juskeviciute

state: PA

address: 1020 Locust st. JAH 527

department: Pathology

institute: Thomas Jefferson University

description: To analyze the effects of surgical stress on gene expression levels in rat liver by performing sham surgery on the liver of rats and comparing the livers to reference RNA.

hyb_protocol: Reference and experimental probes were combined and competitively hybridized to microarrays for 18 hours at 37C.

scan_protocol: Slides were scanned using ScanArray 5000 fluorescent scanner (GSI Lumonics, Billerica, MA). The resulting images were quantified using ScanArray Express v2.2 software with the Adaptive Threshold segmentation (GSI Lumonics, Billerica, MA).

data_processing: Raw quantitated array data was normalized using the print-tip lowess and scale normalization algorithms

organism: synthetic construct

source_name: Reference RNA

label_protocol: indirect labeling protocol

extract_protocol: RT on empty pT7T3Pac vector

tag: Vector RNA. Hybridizes to all spots evenly

organism: Rattus norvegicus

source_name: Animal 4 hepatectomy sham surgery 1h

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.

tag: Strain:Sprague-Dawley, Gender:Male

tag: Liver removed 1 h after hepatectomy sham surgery.


title: SHDR206

tag: Lean subcutaneous adipose tissue (omega1)


title: SHDL120

tag: Obese subcutaneous adipose tissue (II)


title: SHCV220

tag: Obese subcutaneous adipose tissue (PC)


title: SHDO064

tag: Obese subcutaneous adipose tissue (DCH)


title: SHCV218

tag: Obese subcutaneous adipose tissue (PN)


title: SHDO066

tag: Obese subcutaneous adipose tissue (DI)


title: Shoot 35s::AtNF-YB 6 rep1

tag: Trangenic overexpression line


title: SHDR043

tag: Lean subcutaneous adipose tissue (omega9)


title: SHDR208

tag: Lean subcutaneous adipose tissue (omega3)


title: Desiccation vs hydration (72 hrs), replication 2

status: Public on Sep 25 2007

city: St. Paul

first: Eddie

middle: J

last: Cytryn

state: MN

address: 1991 Upper Buford Circle

department: Soil Water and Climate

institute: University of Minnesota

description: Transcriptional profiling of B. japonicum was compared between cells grown under desiccating (27%) and hydrating (100%) conditions

hyb_protocol: Both cy3 and cy5 labeled cDNAs to be compared were mixed, dried to completion, and then resuspended in 70 ul of preheated hybridization buffer (nuclease free water:formamide:20X SSC:1% SDS = 4:2.5:2.5:1) at 42 C. After adding 0.7 ul salmon sperm DNA (10 mg/ml) to prevent non-specific binding to the array, the mixture was hybridized at 42 C for 16 to 18 h. Hybridized arrays were washed with 1X SSC, 0.2% SDS at 42 C for 6 min, and, subsequently, with 0.1X SSC, 0.2% SDS at room temperature for 6 min, and twice with 0.1X SSC at room temperature for 3 min.

scan_protocol: The arrays were scanned using an Axon GenePix 4000B scanner (Molecular Devices Corp., Sunnyvale, CA). Signal intensities were analyzed using GenePix Pro 6.0 software (Molecular Devices Corp., Sunnyvale, CA).

data_processing: Signal intensities were normalized for spot and slide abnormalities using spatial lowess. Lowess adjusted data were subsequently analyzed by mixed effect microarray analysis of variance (MAANOVA) (Kerr et al. 2000). The resulting variety-by-gene interaction (VG) values were combined with the residual noise from each spot to obtain the filtered and adjusted expression values (Kerr et al. 2000; Kerr and Churchill 2001). Both lowess and MAANOVA are part of the R/maanova microarray statistical analysis package (http://www.jax.org/staff/churchill/labsite/). Expression values from two technical replicates in each array were combined, averaged, and subsequently subjected to significance analysis of microarray (SAM) data using the SAM package (Tusher et al. 2001). Significant genes were selected based on a 1.5- or 2-fold cut off threshold with a false discovery rate lower than 5%.

organism: Bradyrhizobium diazoefficiens USDA 110

source_name: Hydrated cells

label_protocol: 20 ug of total RNA was used for cDNA synthesis with superscript III reverse transcriptase and random hexamers (Invitrogen Corp.). After digesting the remaining RNA by RNase H (Fermentas), cDNA was purified using a Microcon YM-30 column (Millipore) and concentration was determined. Four micrograms of cDNA were used for labeling with either cy3 or cy5 (Armersham) and unincorporated dyes were removed using a Qiaquick PCR purification Kit (Qiagen).

extract_protocol: Standard hot-phenol method

tag: B. japonicum was grown in minimal medium supplemented with yeast extract and glycerol as a carbon source. At mid-log phase cells were filtered onto nitrocellulose membranes and incubated in desiccators for 4 h under full hydration (100%RH) conditions.

source_name: Desiccated cells

tag: B. japonicum was grown in minimal medium supplemented with yeast extract and glycerol as a carbon source. At mid-log phase cells were filtered onto nitrocellulose membranes and incubated in desiccators for 4 h under severe desiccation (27% RH).


title: Animal 2 hepatectomy sham surgery 1h

source_name: Animal 2 hepatectomy sham surgery 1h


title: SHCV230

tag: Obese subcutaneous adipose tissue (PO)


title: Animal 3 hepatectomy sham surgery 1h

source_name: Animal 3 hepatectomy sham surgery 1h


title: SHDO197

tag: Pool of human subcutaneous adipose tissue

tag: Obese subcutaneous adipose tissue (DG)


title: Desiccation vs hydration (24 hrs), replication 6


title: SHDR222

tag: Lean subcutaneous adipose tissue (omega6)


title: Desiccation vs hydration (72 hrs), replication 4


title: Shoot 35s::AtNF-YB 3 rep1


title: SHDO071

tag: Obese subcutaneous adipose tissue (DH)


title: Desiccation vs hydration (24 hrs), replication 4

label_protocol: 20 ug of total RNA was used for cDNA synthesis with superscript III reverse transcriptase and random hexamers (Invitrogen Corp.). After digesting the remaining RNA by RNase H (Fermentas), cDNA was purified using a Microcon YM-30 column (Millipore) and concentration was determined. Four micrograms of cDNA were used for labeling with either cy3 or cy5 (Armersham) and unincorporated dyes were removed using a Qiaquick PCR purification Kit (Qiagen)


title: Desiccation vs hydration (72 hrs), replication 3


title: Desiccation vs hydration (72 hrs), replication 6


title: Desiccation vs hydration (24 hrs), replication 2


title: Desiccation vs hydration (24 hrs), replication 1


title: SHDO195

tag: Obese subcutaneous adipose tissue (DA)


title: Desiccation vs hydration (4 hrs), replication 1


title: Animal 1 hepatectomy sham surgery 1h

tag: Vector RNA. Hybridizes to all spots evenly

source_name: Animal 1 hepatectomy sham surgery 1h

tag: Strain:Sprague-Dawley, Gender:Male

tag: Liver removed 1 h after hepatectomy sham surgery.


title: Desiccation vs hydration (4 hrs), replication 5

tag: B. japonicum was grown in minimal medium supplemented with yeast extract and glycerol as a carbon source. At mid-log phase cells were filtered onto nitrocellulose membranes and incubated in desiccators for 4 h under severe desiccation (27% RH)


title: Desiccation vs hydration (4 hrs), replication 2


title: Desiccation vs hydration (4 hrs), replication 6


title: Desiccation vs hydration (4 hrs), replication 4


title: Desiccation vs hydration (24 hrs), replication 3


title: Desiccation vs hydration (72 hrs), replication 5


title: Desiccation vs hydration (72 hrs), replication 1


title: Desiccation vs hydration (4 hrs), replication 3


title: Desiccation vs hydration (24 hrs), replication 5


title: 13137205

status: Public on Sep 24 2007

description:
Isolation of human preadipocytes:
Subcutaneous adipose tissues biopsies were obtained from non obese (BMI < 30 kg/m2) young female patients undergoing elective surgery. None of the patients had diabetes or metabolic disorders and taking medications. This study was approved by the Ethical Committees of Hôtel-Dieu (Paris, France). Minced adipose tissue was digested by collagenase treatment. The digested material was filtered and centrifuged. The resulting pellet (stroma-vascular fraction, SVF) was resuspended in erythrocyte lysis buffer (154 mM NH4Cl, 5.7 mM K2HPO4 and 0.1 mM EDTA, pH 7.0) at 250g for 10 min. After washing in PBS, the SVF cells were suspended in DMEM-10% FBS and used for cell culture at passage 2 in order to eliminate non preadipocyte cell contamination as confirmed by negative staining for macrophage markers (Ham 56 and Mac-1).
Preparation of human blood monocyte-derived macrophages and conditioned medium:
Blood from overweight (BMI > 25 kg/m2) female patients was immediately processed for plasma blood mononuclear cells (PBMC) isolation. Blood sample was layered on PBMC isolation medium (GE healthcare, little Chaford, UK). PBMCs were suspended in PBS/2% FBS/1mmol/L EDTA were incubated at room temperature for 15 min with CD14-positive selection cocktail, followed by 10 min incubation period with magnetic nanoparticles (Stemcell Technologies, Grenoble, France). The bead-coupled CD14+ cells were maintained for 24h in 2 ml of RPMI-10 % FBS at a cell density of 4x105 cells. After 8 days of differentiation, the cells were incubated in RPMI-1 % FBS for 24 h with 100 ng/ml lipopolysaccharides (LPS from E. Coli 0127:B8, Sigma St Louis, Mi, USA) prior collecting the medium (Ac CM). Control medium was RPMI-1 % FBS kept at 37°C for 24h in the absence of macrophages. The conditioned media of the macrophages obtained from 3-5 individuals were pooled and stored at –80°C until used. Distinct pools were used for each culture experiment.
Preparation of Adipose Tissue Macrophages (ATM) and conditioned medium:
Isolated human SVF cells were obtained from subcutaneous adipose tissue biopsies, as described above. SVF cells were suspended in PBS/2% FBS/1mmol/L EDTA were incubated at room temperature for 15 min with CD34-positive selection cocktail, followed by 10 min incubation period with magnetic nanoparticles (Stemcell Technologies, Grenoble, France). The CD34-negative cell fraction was incubated with CD14 positive selection cocktail. The bead-coupled CD14+ cells were maintained for 24h in 1 ml of RPMI-1 % FBS at cell density of 4x105 cells in 12-well plates to obtain macrophage conditioned media (ATM CM), which was stored at - 80°C before use.
Differentiation of human preadipocytes:
Preadipocytes were cultured for 24h in DMEM-10 % FBS at a cell density of 105 cells per well in 12-well plates. The preadipocytes were then incubated with control RPMI or Ac CM (corresponding to 1x105 activated macrophages) and DMEM/F12 induction medium (final concentration of 50 nM insulin, 100 nM dexamethasone, 0.25 mM IBMX and 100 nM rosiglitazone) for 4 days, as described in nous. Next, this medium was replaced by control RPMI or Ac CM and DMEM/F12 culture medium (final concentration of 50nM insulin and 100 nM rosiglitazone). The medium was changed every 2 days until 10-12 days. For ATM CM, the experimental conditions were as described above except that the proportion of ATM CM corresponds to 2x105 AT macrophages.

data_processing: After scanning the arrays, the images were analyzed and ratio intensities were filtered and normalized using the "limma" R package (http://bioinf.wehi.edu.au/limmaGUI/). The VALUE field represents the log(base2) of the print-tip loess normalized R/G ratio (mean).

source_name: Control medium

tag: Preadipocytes cultured with RPMI-1 % FBS control medium.

source_name: Activated monocytes

tag: Preadipocytes cultured with LPS activated human monocytes medium


title: 13134659


title: 13137264

tag: Preadipocytes cultured with RPMI-1 % FBS control medium


title: 13382089

description:
Isolation of human preadipocytes:
Subcutaneous adipose tissues biopsies were obtained from non obese (BMI < 30 kg/m2) young female patients undergoing elective surgery. None of the patients had diabetes or metabolic disorders and taking medications. This study was approved by the Ethical Committees of Hôtel-Dieu (Paris, France). Minced adipose tissue was digested by collagenase treatment. The digested material was filtered and centrifuged. The resulting pellet (stroma-vascular fraction, SVF) was resuspended in erythrocyte lysis buffer (154 mM NH4Cl, 5.7 mM K2HPO4 and 0.1 mM EDTA, pH 7.0) at 250g for 10 min. After washing in PBS, the SVF cells were suspended in DMEM-10% FBS and used for cell culture at passage 2 in order to eliminate non preadipocyte cell contamination as confirmed by negative staining for macrophage markers (Ham 56 and Mac-1).
Preparation of human blood monocyte-derived macrophages and conditioned medium:
Blood from overweight (BMI > 25 kg/m2) female patients was immediately processed for plasma blood mononuclear cells (PBMC) isolation. Blood sample was layered on PBMC isolation medium (GE healthcare, little Chaford, UK).  PBMCs were suspended in PBS/2% FBS/1mmol/L EDTA were incubated at room temperature for 15 min with CD14-positive selection cocktail, followed by 10 min incubation period with magnetic nanoparticles (Stemcell Technologies, Grenoble, France). The bead-coupled CD14+ cells were maintained for 24h in 2 ml of RPMI-10 % FBS at a cell density of 4x105 cells. After 8 days of differentiation, the cells were incubated in RPMI-1 % FBS for 24 h with 100 ng/ml lipopolysaccharides (LPS from E. Coli 0127:B8, Sigma St Louis, Mi, USA) prior collecting the medium (Ac CM). Control medium was RPMI-1 % FBS kept at 37°C for 24h in the absence of macrophages. The conditioned media of the macrophages obtained from 3-5 individuals were pooled and stored at –80°C until used. Distinct pools were used for each culture experiment.
Preparation of Adipose Tissue Macrophages (ATM) and conditioned medium:
Isolated human SVF cells were obtained from subcutaneous adipose tissue biopsies, as described above. SVF cells were suspended in PBS/2% FBS/1mmol/L EDTA were incubated at room temperature for 15 min with CD34-positive selection cocktail, followed by 10 min incubation period with magnetic nanoparticles (Stemcell Technologies, Grenoble, France). The CD34-negative cell fraction was incubated with CD14 positive selection cocktail. The bead-coupled CD14+ cells were maintained for 24h in 1 ml of RPMI-1 % FBS  at cell density of 4x105 cells in 12-well plates to obtain macrophage conditioned media (ATM CM), which was stored at - 80°C before use.
Differentiation of human preadipocytes:
Preadipocytes were cultured for 24h in DMEM-10 % FBS at a cell density of 105 cells per well in 12-well plates. The preadipocytes were then incubated with control RPMI or Ac CM (corresponding to 1x105 activated macrophages) and DMEM/F12 induction medium (final concentration of 50 nM insulin, 100 nM dexamethasone, 0.25 mM IBMX and 100 nM rosiglitazone) for 4 days, as described in nous. Next, this medium was replaced by control RPMI or Ac CM and DMEM/F12 culture medium (final concentration of 50nM insulin and 100 nM rosiglitazone). The medium was changed every 2 days until 10-12 days. For ATM CM, the experimental conditions were as described above except that the proportion of ATM CM corresponds to 2x105 AT macrophages.

hyb_protocol: The labeled cDNA mixtures were hybridized according to the protocol described at http://www.microarrays.ca/support/proto.html

label_protocol: One microgram of total RNA from each sample preparation was amplified using the MessageAmp RNA kit (Ambion, Austin, TX), and 3 µg aRNA was Cy-dye labeled using the CyScribe first-strand cDNA labeling kit (Amersham Biosciences, Orsay, France) (available at http://www.microarrays.ca/support/proto.html).


title: 13382091


title: adipocytes_vs_SVF_pool#2A

description: To compare adipocyte with SVF-overexpressed genes, we digested scWAT specimens of nine overweight female healthy patients (mean BMI 27.9 ± 6.8 kg/m2).

data_processing: After scanning the arrays, the images were analyzed and ratio intensities were filtered and normalized (ie, print-tip loess) using Stanford Microarray Database Online resources (http://genome-ww5.stanford.edu/MicroArray/SMD/).The VALUE field represents the log(base2) of R/G normalized ratio (mean).

source_name: SVF

tag: Adipose tissue stroma vascular fraction

source_name: Adipocyte

tag: Mature adipocytes extracted from human adipose tissue


title: 13377663


title: 13134610


title: adipocytes_vs_SVF_pool#2C


title: Human epidermal keratinocytes treated with IL-1 for 24 hr

status: Public on Sep 22 2007

city: New York

first: Miroslav

last: Blumenberg

state: NY

address: 455 First Ave #874

department: Dermatology

institute: NYU School of Medicine

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

label: Affymetrix standard

source_name: Cultured epidermal keratinocytes

label_protocol: Affymetrix standard

growth_protocol: Standard

extract_protocol: Affymetrix standard

treatment_protocol: Untreated control, 1hr

tag: Grown in Rheinwald medium, switched to KBM for 24 hrs, then with 25 ng/ml of human recombinant IL1 for 24 hrs


title: adipocytes_vs_SVF_pool#1A


title: 13382084


title: ICM pool 3 (n=4)

city: Rome

first: diego

last: arcelli

address: Via delle Messi d'Oro 156

country: Italy

institute: Regina Elena National Cancer Institute

description: Gene expression data from ICM NYHA III-IV CHF patients

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human GeneChip U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with was performed by using customized R language-based script using the Bioconductor packages for quality control analysis, data normalization, hierarchical clusters and identification of differentially expressed transcripts.

source_name: CHF NYHA III-IV pts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 11 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: Age (mean +- SE)


title: adipocytes_vs_SVF_pool#1B


title: Human epidermal keratinocytes control 24 h

tag: Grown in Rheinwald medium, switched to KBM for 24 hrs, then another 24 hrs


title: NICM pool 1 (n=2)

description: Gene expression data from NICM NYHA III-IV CHF patients


title: adipocytes_vs_SVF_pool#1C


title: Human epidermal keratinocytes controls 1 hr

tag: Grown in Rheinwald medium, switched to KBM for 24 hrs,


title: adipocytes_vs_SVF_pool#2B


title: ICM pool 2 (n=2)


title: NICM pool 4 (n=4)


title: Human epidermal keratinocytes control 4 hr

tag: Grown in Rheinwald medium, switched to KBM for 24 hrs


title: Human epidermal keratinocytes treated with IL-1 for 4 hr


title: Control pool 3 (n=5)

description: Gene expression data from controls

source_name: Healthy donors


title: 6h estrogen treatment

status: Public on Sep 21 2007

city: Kansas City

first: Dora

last: Agbas

state: KS

address: 3901 Rainbow blvd.

department: Physiology

institute: University of Kansas Medical Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Genechip Rat Genome U34A array. GeneChips were washed  at the Affymetrix Fluidics Station 400 and stained with SAPE.

scan_protocol: GeneChips were scanned using GeneArray2500 scanner

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 500.

source_name: myometrium

label_protocol: cDNA was prepared with Gibco BRL SuperScript Choice system, and biotinylated cRNA by in vitro transcription using Ambion MegaScript T7kit

extract_protocol: tissue was pulverized in liquid nitrogen and Trizol protocol was used for totalRNA extraction

treatment_protocol: 60 days old rats were ovariectomized a week prior of treatment, estradiol benzoate in 10ug/kg sc was given (or vehicle for control animals), 6 or 24 h after treatment uterine horns were collected, myometrium was quickly separated and flash frozen in liquid nitrogen. Tissues collected from 6 animals were pooled fro further analysis

tag: SD, female 70 days


title: NICM pool 3 (n=4)


title: ICM pool 4 (n=4)


title: Human epidermal keratinocytes treated with IL-1 1hr

treatment_protocol: IL-1 treated, 1hr

tag: Grown in Rheinwald medium, switched to KBM for 24 hrs then treated with 25 ng/ml human recombinant IL-1 for 1 hr


title: NICM pool 2 (n=2)


title: 6h control


title: ICM pool 1 (n=2)


title: 24h control


title: Control pool 2 (n=5)

description: Gene expression data from controls


title: 24h estrogen treatment


title: WM35, no treatment

city: Burlington

first: Viswanathan

last: Muthusamy

state: VT

address: 323A HSRF, 149 Beaumont Ave

institute: University of Vermont

description: Expression data with no treatment

hyb_protocol: Hybridizations were according to Affymetrix instructions

scan_protocol: The chips were scanned on a Hewlett Packard G2500A scanner

data_processing: Microarray Suite 5.0 (MAS 5.0; Affymetrix) software was used to analyze the HG-U133A arrays. All the arrays were normalized to a target signal intensity value of 500.

source_name: WM35 cell line

label_protocol: Biotinylated cRNA was prepared according to Affymetrix instructions

growth_protocol: Cells were grown in suitable growth media (Cascade Biologics Medium 254 for melanocytes and DMEM F12 with 5% serum for all cell lines)

extract_protocol: Total RNA was isolated using Qiagen Rneasy kit according to manufacturers' recommendations

treatment_protocol: Cells were treated with 5uM 5AzadC for 48 hours

tag: Melanoma cells


title: WM35, 48h treatment with 5 AzadC

description: Expression data after reversal of DNA methylation


title: Control pool 1 (n=2)

description: Gene expression data from controls


title: UACC903, 48h treatment with 5 AzadC

source_name: UACC903 cell line


title: Anaplastic Thyroid Carcinoma 3

city: Phoenix

first: Michael

last: Bittner

state: AZ

address: 445 N. 5th Street

department: Computational Biology

institute: Translational Genomics Research Institute

description: Anaplastic Thyroid Carcinoma 3 vs  Pooled Reference

hyb_protocol: Pool the Cy3 and Cy5 labeled cDNAs into a single 0.2 ml thinwall PCR tube and adjust the volume to 30 µl by either adding DEPC H2O, or removing water in a SpeedVac. Add 1 µl Poly d(A) (8 mg/ml), 1 µl of yeast tRNA (4 mg/ml), 1 µl of Human C0t-1 DNA (10 mg/ml), 6 µl of 20x SSC, and 1 µl of 50x Denhardt’s blocking solution. Mix the components well by pipetting, heat at 98°C for 2 minutes in a PCR cycler, cool quickly to 25°C and add 0.6ul of 10% SDS Centrifuge for 5 min at 14,000 x g. Apply the labeled cDNA to a 24 mm x 50 mm glass coverslip and then touch with the inverted microarray. Place the slide in a microarray hybridization chamber, add 5 µl of 3x SSC at the scribed end of the slide and seal the chamber. Submerge the chamber in a 65°C water bath and allow the slide to hybridize for 16-20 hours. Remove the hybridization chamber from the water bath, cool and carefully dry off.  Unseal the chamber and remove the slide. Place the slide, with the coverslip still affixed, into a Coplin jar filled with 0.5X SSC/0.01% SDS wash buffer. Allow the coverslip to fall from the slide and then remove the coverslip from the jar with a forceps.  Allow the slide to wash for 2-5 minutes. Transfer the slide to a fresh Coplin jar filled with 0.06X SSC. Allow the slide to wash for 2-5 minutes. Transfer the slide to a slide rack and centrifuge at low rpm (700-1000) for 3 minutes in a clinical centrifuge equipped with a horizontal rotor for microtiter plates

scan_protocol: Scan the washed slide in an Agilent 2505A microarray scanner with PMTs set to highest sensitivity, collecting a Cy3 and Cy5 Tiff image.

data_processing:
Procedures are explicitly detailed in papers in the Journal of Biomedical Optics. 1997 Oct; 2(4): 364–74, and Bioinformatics. 2002 Sep;18(9):1207-15.
A grid specifying the positions of spots in the various print areas is applied and manually adjusted.
A template mask for spot size, shape and location relative to the grid is produced by examining the brightest spots on the array and using a Mann-Whitney statistic to discern signal from local noise.
All positions in the grid are tested for the presence of signal using the template mask as a starting point and the Mann-Whitney statistic to define the signal containing area.
The mean and variance of the local background intensity and the signal intensity are calculated for each spot.
Quality parameters, signal to noise ratio, signal area size, background flatness, coefficients of variation of the signal, are collected and evaluated to assign a quality value to each measurement of the signals from both channels.
Estimate the ratio density distribution of a set of 88 housekeeping genes (printed in 5 replicates in these arrays) to obtain the mean and coefficient of variation (using a maximum-liklihood estimator).
Normalize the intensity values by iterative estimation of the multiplier (to be applied to intensities from one channel) to bring the ratio mean to 1.0, recalculating the coefficient of variation and ratio density distribution at each step.
Calculate the mean and standard deviation of the desired confidence interval limits as a function of the ratio coefficient of variation using a polynomial approximation.

label: Cy3 dUTP

source_name: Total RNA from ATC patient 3

label_protocol:
Add 150-200 micrograms of total RNA from tumor or 70 micrograms of total RNA from the Pooled Tumor Reference to a PCR tube in 16 microlters of water.
Add 1 microgram in 1 microliter of an anchored dT primer (5’-TTT TTT TTT TTT TTT TTT TTV N-3’) to each PCR tube.
Heat to 65°C for 10 minutes and cool on ice for 2 minutes.
Prepare a reaction mix of 1.74x first strand buffer (Stratagene), 87 µM dA,G,CTP, 35 µM dTTP, 174 µM Cy5 (or Cy3) dUTP, 17.4 mM DTT, 1.3 units/µl Rnasin, 17.4 units/µl Superscript II (Stratagene)
Add 23 µl of reaction mixture containing either Cy5-dUTP or Cy3-dUTP nucleotides, mix well by pipetting and use a brief centrifuge spin to concentrate in the bottom of the tube.
Incubate at 42°C for 30 min. then add 2 µl of 200 units/µl Superscript II, mix, and incpate at 42°C for a further 60 minutes.
Add 5 µl of 0.5M EDTA.
Add 10 µl 1N NaOH, incubate at 65Ο C for 60 minutes to hydrolyze residual RNA.  Cool to room temperature.
Neutralize by adding  25 µl of 1M Tris-HCl (pH 7.5).
Desalt the labeled cDNA by adding the neutralized reaction, 400 µl of TE pH 7.5 and 20 µg of human C0t-1 DNA to a MicroCon 100 cartridge.  Pipette to mix, spin for 10 minutes at 500 x g
Wash again by adding 200 µl TE pH 7.5 and concentrating to about 20-30 µl (approximately 8-10 min at 500 x g).
Recover by inverting the concentrator over a clean collection tube and spinning for 3 min at 500 x g.

growth_protocol:
Tumor and normal thyroid tissues were obtained from surgical biopsies.  Tissues were rapidly frozen and stored at -80°C until extracted.
The three tumor cell lines, TPC1 (papillary), BCPAP (papillary), ARO (anaplastic), used to construct the reference were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (GIBCO, Paisley, PA), 2 mM L-glutamine and 100units/ml penicillin-streptomycin (GIBCO).
Cells were freed from the plates for splitting  by using Tripsin/EDTA (GIBCO).
Cells were harvested at  80% confluency, washed twice in Dulbecco's Phosphate Buffered Saline and stored frozen until RNA was extracted.

extract_protocol:
The cell pellets from the three cell lines harvested from tissue culture, were washed twice in Dulbecco's Phosphate Buffered Saline and then 1ml of Trizol was added per 2X107 cells.
For tumor tissues, 100 mg of frozen tissue was added directly to 4 ml of Trizol, and dissociate by homogenization with a rotating blade tissue homogenizer.
A  2/10 volume of chloroform was added and shaken for 15 seconds.
Let stand for 3 minutes.  Centrifuge at 12,000 x g for 15 minutes at 4°C.
Take off the supernatant and add it to a polypropylene tube, recording the volume of the supernatant.
Add 0.53 volumes of ethanol to the supernatant slowly while vortexing, this will produce a final ethanol concentration of 35%.
Add the supernatant from an extraction of 2x107 to 1x108 cells to an RNeasy maxi column, which is seated in a 50 ml centrifuge tube.
Centrifuge at 2880 x g in a clinical centrifuge with a horizontal rotor at room temperature for 5 minutes.
Pour the flow-through back onto the top of the column and centrifuge again.
Discard the flow-through and add 15 ml of RW1 buffer to the column.
Centrifuge at 2880 x g for 5 minutes.
Discard flow-through then add 10 ml of RPE buffer.
Centrifuge at 2880 x g for 5 minutes.
Discard flow-through and add another 10 ml of RPE buffer.
Centrifuge at 2880 x g for 10 minutes.
Put the column in a fresh 50 ml tube and add 1 ml of DEPC treated water from the kit to the column.
Let stand for 1 minute.
Centrifuge at 2880 x g for 5 minutes.
Add another 1 ml of water to the column.
Let stand for 1 minute.
Centrifuge at 2880 x g for 10 minutes.
Aliquot out 400 µl portions of the column eluate to 1.5 ml Eppendorf tubes.
Add 1/10 volume of 3M sodium acetate (pH 5.2).
Add 1 ml of ethanol to each tube.
Let stand for 15 minutes.
Centrifuge at 12000 x g at 4C for 15 minutes.
Wash pellet 2 times in 75% EtOH then store at –80°C
Resuspend RNA at approximately 1 mg/ml in DEPC H2O.
Concentrate to greater than 7 mg/ml by centrifugation on a MicroCon 100 filter unit, centrifuge at 500 x g, checking as necessary to determine the rate of concentration.
Determine the concentration of RNA in the concentrated sample by spectrophotometry.

treatment_protocol: No treatments were applied to either the reference tumor cell lines or the resected normal thyroid or thyroid tumor samples.

tag: Anaplastic thyroid carcinoma

label: Cy5 dUTP

source_name: Pooled Tumor Reference

tag: Pool of equivalent amounts of total RNA from thyroid tumor cell lines TPC1 (papillary), BCPAP (papillary), ARO (anaplastic)


title: Neo6, 48h treatment with 5 AzadC

source_name: Neo6 cell line


title: C8161, 48h treatment with 5 AzadC

source_name: C8161 cell line


title: Anaplastic Thyroid Carcinoma 5

description: Anaplastic Thyroid Carcinoma 5 vs  Pooled Reference

source_name: Total RNA from ATC patient 5


title: Human epidermal keratinocytes treated controls 48 hr

tag: Grown in Rheinwald medium, switched to KBM for 24 hrs and another 48 hrs


title: UACC903, no treatment

description: Expression data with no treatment


title: Anaplastic Thyroid Carcinoma 4

description: Anaplastic Thyroid Carcinoma 4 vs  Pooled Reference

source_name: Total RNA from ATC patient 4


title: Papillary Thyroid Carcinoma 9

description: Papillary Thyroid Carcinoma 9 vs  Pooled Reference

source_name: Total RNA from PTC patient 9

tag: Papillary thyroid carcinoma


title: MelJuSo, 48h treatment with 5 AzadC

source_name: MelJuSo cell line


title: Papillary Thyroid Carcinoma 6

description: Papillary Thyroid Carcinoma 6 vs  Pooled Reference

source_name: Total RNA from PTC patient 6


title: Anaplastic Thyroid Carcinoma 1

description: Anaplastic Thyroid Carcinoma 1 vs  Pooled Reference

source_name: Total RNA from ATC patient 1


title: WM1205, no treatment

description: Expression data with no treatment

source_name: WM1205 cell line


title: Neo6, no treatment

description: Expression data with no treatment


title: WM1205, 48h treatment with 5 AzadC


title: Human epidermal keratinocytes treated with IL-1 for 48 hr

source_name: Cultured epidermal keratinocytes

treatment_protocol: IL1 treated 48hr

tag: Grown in Rheinwald medium, switched to KBM for 24 hrs, treated with 25 ng/ml IL1 for 48 hrs


title: C8161, no treatment

description: Expression data with no treatment


title: Papillary Thyroid Carcinoma 7

description: Papillary Thyroid Carcinoma 7 vs  Pooled Reference

source_name: Total RNA from PTC patient 7


title: Melanocytes, no treatment

description: Expression data with no treatment

source_name: Primary culture from normal cells

tag: Normal cells


title: MelJuSo, no treatment

description: Expression data with no treatment


title: Anaplastic Thyroid Carcinoma 2

description: Anaplastic Thyroid Carcinoma 2 vs  Pooled Reference

source_name: Total RNA from ATC patient 2


title: Papillary Thyroid Carcinoma 10

description: Papillary Thyroid Carcinoma 10 vs  Pooled Reference

source_name: Total RNA from PTC patient 10


title: Papillary Thyroid Carcinoma 3

description: Papillary Thyroid Carcinoma 3 vs  Pooled Reference

source_name: Total RNA from PTC patient 3


title: Papillary Thyroid Carcinoma 8

description: Papillary Thyroid Carcinoma 8 vs  Pooled Reference

source_name: Total RNA from PTC patient 8


title: Melanocytes, 48h treatment with 5 AzadC


title: Papillary Thyroid Carcinoma 5

description: Papillary Thyroid Carcinoma 5 vs  Pooled Reference

source_name: Total RNA from PTC patient 5

source_name: Pooled Tumor Reference


title: Papillary Thyroid Carcinoma 1

description: Papillary Thyroid Carcinoma 1 vs  Pooled Reference

source_name: Total RNA from PTC patient 1


title: N2 total RNA replicate 2

city: Boulder

first: liang

last: zhang

state: CO

address: University of Colorado at Boulder, Han lab, Department of MCD Biology, Campus box 0347

institute: university of colorado at boulder

description: Total RNA of Mixed staged N2 worms

hyb_protocol: SOP H2.0: Hybridization Application  1.0 PURPOSE: To provide a standard operating procedure for hybridization of  fluorocein labeled probes to cDNA or oligonucleotide elements on microarray glass  slides.  2.0 SPECIAL NOTES:  3.0 AUTHORS: Mike Heinz  4.0 RELATED DOCUMENTS: L3.0, L7.0, H4.0, H5.0, H6.0  5.0 REQUIRED MATERIALS AND EQUIPMENT:  Labeled probe Hybridization chamber apparatus  Hybridization oven Heat block  4xSSC Air gun/ canister  Timers Microcentrifuge  Hybridization buffer (check vendor) Forceps  Microarray(s) Pipettes  Coverslips (Erie Scientific)  6.0 DEFINITIONS:  7.0 PROCEDURE:  7.1 Set up  7.1.1 Using an air gun canister, blow off all hybridization chamber parts  to ensure they are clean, especially the microarray and the  coverslip.  7.1.2 Assemble microarray hybridization chamber/ microarray/ coverslip  apparatus. Make sure that the coverslip is appropriately placed  over the entire arrayed area.  7.1.3 Add 100ul of 4xSSC to the humidity well in each hybridization  chamber.  7.1.4 If frozen, remove probes from the 20C freezer and thaw at room  temperature in the dark if frozen. Ensure that each probe has  enough volume for the hybridization (ie. For a 25x25mm  coverslip, 20ul is needed to cover the array surface). Each probe  should have at least +2ul of probe in the tube compared to that of  the volume to be applied to the array. If a probe does not contain  the appropriate volume, add hybridization buffer (use appropriate  vendor) to reach desired volume. Make sure to mix the solution if  adding hyb buffer.  7.1.5 By checking the paperwork/ jobticket, make sure that the  appropriate probes have been thawed and that the appropriate  arrays have been placed in the chambers.  7.1.6 Heat the probes for 5 min. at 65C in the dark (or check for  appropriate denaturing temperatures and times).  7.1.7 Centrifuge the probes for 1 min. at max speed.  7.2 Application  7.2.1 Carefully pipette 20ul (or other amount) under the coverslip  covering the arrayed surface. Ensure that the array is completely  covered. If not completely covered, pipette additional probe under  the coverslip in increments of 2ul. Note any bubbles or  abnormalities.  7.2.2 Apply the coverglass and clamps. Using the torque wrench,  tighten the clamps. Make sure that the metal arms of the clamps  are not resting on the edge of the coverglass. Also, make certain  that the wrench is set at 46 lb/in.  7.2.3 Place the hybridization chambers in the hybrization box, then place  the hyb. box in the oven at 42C and hybridize overnight (minimum  of 12 hours). Make certain to place the chambers in the hyb. box  so that they are level and stable.

scan_protocol: Slides are scanned on a ScanArray Express HT Scanner to detect Cy3 and Cy5 fluorescence at 543 and 633nm, respectively. Laser power is kept constant for Cy3/Cy5 scans, and photomultiplier tube values were set for optimal intensity with minimal background. An additional scan is often done for each slide with the PMT set such that <1% of the elements are saturated in order to characterize spots which are saturated at the higher PMT setting. Gridding and analysis of images is performed with ScanArray software Express V3.0. Note that this Sample represents the data from 1 channel of a 'technically' dual channel hybridization.

data_processing: Signals from replicates of total worm lysates from wt and strains containing the ain-2::gfp or the ain-2 promoter::gfp  transgene were mean normalized and averaged respectively to generate standard profiles of gene expression in these worm  strains. We then calculated the ratio of signal of each gene from each IP sample to the standard gene expression profile  of the corresponding worm strain. Based on this ratio, a percentile rank of each gene relative to all genes in each IP  replicate was calculated. The percentile ranks in the three replicates of each IP were averaged. Student t test was  utilized to determine if the average percentile ranks of enrichment of individual genes were significantly higher (p  value) than the mean enrichment of all genes in the IP samples. To determine the AIN-1 or AIN-2 associated genes, we used  the following criteria: (1) average percentile ranks of enrichment is greater than the mean enrichment of all genes in  AIN-1 or AIN-2 IP with p<0.01; (2) average signal in AIN-1 or AIN-2 IP replicates is greater than the background signal  (including 2X standard deviation (SD)) (Background signal and SD were calculated based on signals from empty spots on  each microarray); (3) criteria 1 is not be satisfied for the same gene in the corresponding control IP.

organism: Caenorhabditis elegans

source_name: Total RNA of Mixed staged N2 worms

label_protocol: The samples were amplified once using the MessageAmp aRNA kit (Ambion) and labeled with cy3 or cy5 using the MicroMax ASAP kit (Perkin Elmer).

extract_protocol: RNAs were isolated from each immunocomplex after IP, or from total worm lysate, using the Trizol reagents (Invitrogen) according to vendor’s protocol.

tag: Total RNA of Mixed staged N2 worms


title: GFP IP replicate 1

description: GFP IP of mixed staged AIN-2 promoter:GFP injection line

tag: Immunoprecipitated RNA


title: Papillary Thyroid Carcinoma 2

description: Papillary Thyroid Carcinoma 2 vs  Pooled Reference

source_name: Total RNA from PTC patient 2


title: Normal Thyroid 3

description: Normal Thyroid 1 vs  Pooled Reference

source_name: Total RNA from normal thyroid 3

tag: normal tissue


title: AIN-2 promoter GFP replicate 1

description: Total RNA of mixed staged AIN-2 promoter:GFP injection line


title: AIN-2 promoter GFP replicate 2

source_name: Total RNA of mixed staged AIN-2 promoter:GFP injection line


title: Normal Thyroid 1

description: Normal Thyroid 1 vs  Pooled Reference

source_name: Total RNA from normal thyroid 1


title: AIN-2::GFP total RNA replicate 1

description: Total RNA of mixed staged AIN-2::GFP single copy integrated line A


title: Normal Thyroid 2

description: Normal Thyroid 1 vs  Pooled Reference

source_name: Total RNA from normal thyroid 2


title: Papillary Thyroid Carcinoma 4

description: Papillary Thyroid Carcinoma 4 vs  Pooled Reference

source_name: Total RNA from PTC patient 4


title: AIN-2 promoter GFP replicate 3

tag: Total RNA of mixed staged AIN-2 promoter:GFP injection line


title: AIN-2::GFP total RNA replicate 2

source_name: Total RNA of mixed staged AIN-2::GFP single copy integrated line A


title: AIN-2::GFP IP replicate 2

description: AIN-2::GFP IP of mixed staged AIN-2::GFP single copy integrated line A


title: VTA16 - case with substance abuse alcohol

city: Brisbane

first: Traute

last: Flatscher-Bader

state: Queensland

address: Queensland Biosciences Precinct, Level 5, CSIRO LI, 306 Carmody Road

department: Faculty of Natural Resources, Agriculture and Veterinary Science

country: Australia

institute: University of Queensland

hyb_protocol: Immediately after labelling, cDNA of each individual sample was hybridized together with the universal reference to one microarray slide: cDNA of sample and refernce were combined and purified though a QIAQuick PCR Purification column (Qiagen, Australia) according to manufacturer’s instructions. To the eluent 10 microl (10 microg) human Cot-1 DNA (GibcoBRL, Australia) was added and the volume was reduced to 22 microl with a Microcon YM-30 column. To the concentrated cDNA, 16 microl 20 X SSC, 40 microl deionized formamide and 2 microl 20% (w/v) SDS was added. Samples were incubated at 95C for 5 min, then at 45C for 60 min then chilled on ice. aRNA from the VTA was paired with a reference aRNA sample and hybridised on individual arrays. The microarray slides were incubated overnight for 18 h at 42C. Slides were washed in 1 X SSC/ 0.1 % (w/v) SDS; 0.5 X SSC; 0.2 X SSC sequentially at 50C for 10 min with gentle agitation, then centrifuged at 400 g for 5 min to remove residual wash solution.

scan_protocol: Slides were immediately scanned at 10 microm resolution on a Genetic Microsystems scanner using GMS Scan Array software (Genetic Microsystems, USA). Each pixel was assigned a value between 0-65,535 for each channel based on signal fluorescence.

data_processing:
Spots were detected in the scanned images by auto-segmentation using the standard default setting of the IMAGEne 6.1 (Biodiscovery, El Segundo, CA, USA) software, which are defined as follows: After overlaying the signals with a grid the software’s automated spot finding by auto-segmentation was employed. The following spot selection criteria were applied: Donut shapes were not allowed. Only elements with intensity three times above background, location with <60% offset from expected inter-spot distance, open perimeter of <20% and a shape regularity measured as area to perimeter ratio of at least 0.7 as well as <25% ignored pixels due to contamination or shape abnormality were selected.
(This was deleted for now: Data normalisation and analysis was completed with GeneSpring 6.2 software (Silicon Genetics, Redwood City, California, USA). A per-spot and per-chip intensity-dependent Lowess fit normalization was carried out. Genes other than those that were marked as ‘present’ in at least half of the hybridisations and not marked ‘absent’ in at least half the samples were filtered out. The cross-gene error model was used to quantify the average constant error across the spots for each pathology group and genes with a raw control signal less than this were removed from analysis. Arrays performed on cases with identical pathology were then treated as biological replicates. Using all reliably expressed data elements the arrays were subjected to two analyses of different stringency level in the applied criteria. Analysis A: no multiple testing correction. Genes were filtered for ‘confidence of expression’ (Genespring 6.2; Student’s t test, P<0.05 in one of the two case groups). This step served to reduce false positive genes. Within the resulting gene list a Student’s t-test was employed to detect differentially expressed elements (P≤0.05) by comparing the mean expression of each gene from alcoholic cases (n=6) with that of controls (n=6). Then, genes with a log transformed fold change of ≤ -0.30 or ≥ 0.18 were filtered out. Analysis B: Benjamini Hochberg Multiple Testing Correction was included at both filter stages. This reduced the false positives to ≤5% at each stage. )

molecule: polyA RNA

source_name: VTA tissue, postmortem

label_protocol: Microarray hybridization was performed on human single-spotted 19k (version 6) cDNA arrays (University Health Network Microarray Centre, Ontario Cancer Institute). To 10 microg aRNA, 5 microg random primers were added in 20 microl with RNase free H2O. Samples were incubated at 70C for 10 min then chilled on ice. To each sample, 1.5 microl (300 U) Superscript II, 8 microl 5 X 1st strand buffer, 4 microl 100 mM DTT, 1 microl RNase inhibitor, 1 microl 25 mM d(GAT)TP, 2 microl 2.5 mM dCTP, and 2 microl FluoroLink Cy3-dCTP (Amersham Biosciences, Australia) was added. Samples were incubated at 42C for 1 h. RNA was hydrolysed by the addition of 1 microl 0.5 M EDTA (pH 8) and 2 microl 2M NaOH followed by incubation at 65C for 10 min. Solutions were neutralised by the addition of 4 microl 1 M HCl, 4 microl 1M Tris/HCl (pH 8) and 100 mM sodium acetate.

extract_protocol: Total RNA was extracted from 50 mg of frozen tissue with 1 mL of TRIzol® (Invitrogen, Australia) following the manufacturer’s instruction. Samples were suspended in RNAse/DNAse-free water, maintaining concentrations above 1 microg/microL, then frozen at – 80°C. Anti-sense RNA (aRNA) was synthesised by linear amplification (Eberwine et al. 1992). Briefly, 1 microg total RNA with 1 microg T7-oligo dT21 primer (5’-TCT AGT CGA CGG CCA GTG AAT TGT AAT ACG ACT CAC TAT AGG GCG T21-3’) in 5 microl was incubated at 70C for 4 min then chilled on ice. 1 microl SuperScript II (200 U, GibcoBRL, Melbourne, Australia), 2 microl 100 mM dithiothreitol (DTT), 4 microl SuperScript II 1st Strand Buffer, 1 microl RNase inhibitor (40 U, GibcoBRL, Australia), 1 microl 10 mM dNTPs (Sigma, Sydney, Australia), and 1 microl H2O were added. Samples were incubated at 42C for 1 h then 65C for 15 min. To this, 1 microl ribonuclease H (2 U, Promega, Australia), 1 microl E. coli DNA ligase (5 U, New England Biolab, Australia), 5 microl E. coli DNA polymerase I (40 U, GeneWorks, Australia), 3 microl 10 mM dNTPs, 15 microl 2nd Strand Buffer [200mM Tris pH 6.9, 46mM MgCl2, 900mM KCl, 100mM (NH4)2SO4, 1.5mM NAD] and 105 microl H2O were added. After incubation at 16C for 2 h, 2 microl T4 DNA polymerase (10 U, New England Biolab, Australia) was added and samples were incubated at 16C for 15 min and heat inactivated at l phenol:chloroform70C for 10 min. Double stranded cDNA was extracted with 150  (1:1) and washed 3 times with 500 microl RNase free H2O in a Microcon YM-30 (Millipore, Australia) filter. The cDNA was recovered and the volume adjusted to 8 microl. To the concentrated cDNA, 2 microl each of ATP, GTP, CTP, UTP (75mM), 10X transcription buffer and MEGAscript T7 enzyme mix (Ambion, Australia) was added and the solution incubated at 37C for 4-16 h to allow in vitro transcription. The aRNA was extracted with TRIzol according to the manufacturer's instruction. Integrity of total RNA and amplified RNA (aRNA) was monitored with the Agilent Bioanalyser (Agilent, Forest Hill, Australia). Only cases that produced RNA samples with distinct 18S and 28S absorbance peaks and amplified RNA (aRNA) with consistent size profiles were allowed to proceed. Moreover, northern hybridisation was performed on each aRNA sample using a P32 labelled GAPDH probe. Only samples with a single, non-diffused GADPH signal were selected for further study. Northern blot verification of aRNA integrity: Formaldehyde gel electrophoresis: Agarose (1.1g) was dissolved in 68.4mL of boiling DEPC-treated water and 22.0mL 5 x MOPS (pH 7.0) and 19.6mL 37% (v/v) formaldehyde (12.3M, pH>4.0) were added to achieve final concentrations of 1 x MOPS and 2.2M formaldehyde in a volume of 30mL. The solution was poured into a gel casting mould and allowed to set for at least 20min followed by equilibration in 1 x MOPS, pH 7.0 for 30min. RNase/DNase free water was added to 10microg RNA to adjust the volume to 8microL. Then 2microL 5xsample buffer [5 x MOPS, 5mM EDTA pH8.0, 3.2% (v/v) formamide, 2.7% (v/v) formaldehyde, 20% (v/v) glycerol, 5microg/mL bromophenol blue] was added. The sample was denatured at 95C for 3min, snap cooled on ice and loaded onto the prepared formaldehyde gel. RNA species were separated electrophoretically at 100 V using 1 x MOPS, pH 7.0 as running buffer. The gel was incubated in 1 x MOPS, pH 7.0, 0.01% (v/v) Sybr® Gold (Molecular Probes, Mount Waverley, Australia) for 10min in the dark and RNA was visualized under a UV transluminator. RNA transfer and hybridisation: The RNA was transferred to Hybond-N membranes (Osmonics, Kent, United Kingdom) via an upward capillary method. Briefly, a wick was made from Whatman filter papers (Whatman, Kent, United Kingdom), soaked in 10 x standard saline citrate (SSC), and placed on the platform of the transfer apparatus. The formaldehyde gel was placed on the saturated filter paper and a pre-wetted Osmonics membrane paced on the upper surface of the gel. Wet filter paper was then placed above this followed by a large stack of paper towels and a small weight. aRNA transfer to the membrane was complete after 18-24h at room temperature with 10 x SSC as the blotting buffer. The efficiency of the transfer was estimated by re-visualizing the remaining RNA in the formaldehyde gel under UV light. Membranes were dried at 65C, UV cross-linked (125mJ/cm2) and pre-hybridized using 5mL Rapid-hyb buffer (Amersham Biosciences, Castle Hill, Australia) for 30min at 65C according to the manufacturers’ protocol. 33P-radiolabeled glyceraldehyde-3-phosphate dehydrogenase cDNA (0.1–0.2microCi/mL) was added and the membrane was hybridised at 65C for 2h. After hybridisation, the membrane was washed for 15min with 1 x SSC/0.1% (w/v) sodium dodecyl sulfate (SDS) at 65C. Dependant upon the signal strength after the initial wash, further washes were carried out with increasing stringency [0.25 x SSC/0.1% (w/v) SDS, 0.1 x SSC/0.1% (w/v) SDS]. Membranes were sealed in a plastic bag and autoradiographed at -70C between 1 and 5 days depending on signal strength.

treatment_protocol: Tissue was kept at -80C until use. All alcoholic cases complied with the definition by the Diagnostic and Statistical Manual for Mental Disorders (DSM IV) of the American Psychiatric Association for ‘substance abuse alcohol’. They had a history of chronic excessive drinking (≥80g of ethanol/day or diagnosed as long-term heavy drinker) and in most instances this behaviour persisted throughout adult live (>10 years). There was no evidence of any degenerative changes to the cellebellar granule cells and no confounding neurological or psychiatric disorders were diagnosed in any of the cases used for this study.

tag: case with substance abuse alcohol

tag: age

value: 73 years

tag: postmortem interval

value: 24 hours

tag: Cause of Death

value: Consequences of Cirrhosis

source_name: reference sample, brain tissue, postmortem

label_protocol: Microarray hybridization was performed on human single-spotted 19k (version 6) cDNA arrays (University Health Network Microarray Centre, Ontario Cancer Institute). To 10 microg aRNA, 5 microg random primers were added in 20 microl with RNase free H2O. Samples were incubated at 70C for 10 min then chilled on ice. To each sample, 1.5 microl (300 U) Superscript II, 8 microl 5 X 1st strand buffer, 4 microl 100 mM DTT, 1 microl RNase inhibitor, 1 microl 25 mM d(GAT)TP, 2 microl 2.5 mM dCTP, and 2 microl FluoroLink Cy5-dCTP (Amersham Biosciences, Australia) was added. Samples were incubated at 42C for 1 h. RNA was hydrolysed by the addition of 1 microl 0.5 M EDTA (pH 8) and 2 microl 2M NaOH followed by incubation at 65C for 10 min. Solutions were neutralised by the addition of 4 microl 1 M HCl, 4 microl 1M Tris/HCl (pH 8) and 100 mM sodium acetate.

tag: aRNA pooled from various brain regions was used as a reference sample.


title: N2 total RNA replicate 1

description: Total RNA of Mixed staged N2 worms


title: AIN-2::GFP total RNA replicate 3

tag: Total RNA of mixed staged AIN-2::GFP single copy integrated line A


title: Normal Thyroid 4

description: Normal Thyroid 1 vs  Pooled Reference

source_name: Total RNA from normal thyroid 4


title: AIN-2::GFP IP replicate 3

source_name: AIN-2::GFP IP of mixed staged AIN-2::GFP single copy integrated line A


title: VTA8 - case with substance abuse alcohol

label: FluoroLink Cy3-dCTP (Amersham Biosciences, Australia)

value: 37 years

value: 17 hours

tag: cause of death

value: Acute alcohol poisoning

label: FluoroLink Cy5-dCTP (Amersham Biosciences, Australia)


title: AIN-2::GFP IP replicate 1

tag: AIN-2::GFP IP of mixed staged AIN-2::GFP single copy integrated line A


title: GFP IP replicate 2

source_name: GFP IP of mixed staged AIN-2 promoter:GFP injection line


title: VTA15 - case with substance abuse alcohol

value: 50 years

tag: Cause of death

value: Ischaemic heart disease


title: Preimmune IP replicate 3

description: Preimmune IP of Mixed staged N2 worms

source_name: Preimmune IP of Mixed staged N2 worms

tag: Preimmune IP of Mixed staged N2 worms


title: Preimmune IP replicate 2

description: Preimmune IP of Mixed staged N2 worms


title: VTA13 - control case

description: VTA13 - control case

tag: control case age

value: 53 years

tag: postmortem inteval

value: 16 hours

value: Dilated cardiomyopathy


title: VTA14 - case with substance abuse alcohol

value: 46 years

value: Alcohol Toxicity


title: AIN-1 IP replicate 1

description: AIN-1 IP of Mixed staged N2 worms

source_name: AIN-1 IP of Mixed staged N2 worms

tag: AIN-1 IP of Mixed staged N2 worms


title: VTA1 control case

description: VTA1 control case

tag: control case

value: 68 years

value: 22 hours

value: Suicide by hanging. Asphyxia


title: AIN-1 IP replicate 2

description: AIN-1 IP of Mixed staged N2 worms

tag: Immunoprecipitated RNA


title: VTA10 - case with substance abuse alcohol

value: 59 years

value: 18 hours

value: Cardiomyopathy


title: AIN-1 IP replicate 3

description: AIN-1 IP of Mixed staged N2 worms


title: VTA6 - control case

description: VTA6 - control case

value: 58 years

tag: Casue of death


title: VTA2 - control case

description: VTA2 - control case

data_processing: Spots were detected in the scanned images by auto-segmentation using the standard default setting of the IMAGEne 6.1 (Biodiscovery, El Segundo, CA, USA) software, which are defined as follows: After overlaying the signals with a grid the software’s automated spot finding by auto-segmentation was employed. The following spot selection criteria were applied: Donut shapes were not allowed. Only elements with intensity three times above background, location with <60% offset from expected inter-spot distance, open perimeter of <20% and a shape regularity measured as area to perimeter ratio of at least 0.7 as well as <25% ignored pixels due to contamination or shape abnormality were selected.

source_name: aRNA, VTA, control case

treatment_protocol: All alcoholic cases complied with the definition by the Diagnostic and Statistical Manual for Mental Disorders (DSM IV) of the American Psychiatric Association for ‘substance abuse alcohol’. They had a history of chronic excessive drinking (≥80g of ethanol/day or diagnosed as long-term heavy drinker) and in most instances this behaviour persisted throughout adult live (>10 years). There was no evidence of any degenerative changes to the cellebellar granule cells and no confounding neurological or psychiatric disorders were diagnosed in any of the cases used for this study.

tag: Control case

tag: post mortem interval

value: 11 hrs

value: Pulmonary embolism

source_name: reference sample


title: VTA3 - control case

description: VTA3 - control case

value: 56 years

value: 24 hours

value: Cardiac coronary artery atheroma


title: Preimmune IP replicate 1

description: Preimmune IP of Mixed staged N2 worms


title: VTA 9 - case with substance abuse alcohol

tag: case with substance abuse alcohol

tag: age

value: 26 hours

value: Bleeding oesophagial varices


title: VTA4 - control case

description: VTA4 - control case

tag: Control case age

value: 20 hours

value: Coronary thrombosis


title: B. pertussis Tohama I vs. PRCB13

status: Public on Sep 20 2007

city: Turku

first: Teemu

last: Kallonen

address: Kiinamyllynkatu 13

department: Derpartment of Infectious Disease Surveillance and Control

country: Finland

institute: National Institute for Health and Welfare

description: CGH

hyb_protocol: The labeled DNA was purified with the purification kit of the same manufacturer and then combined. The volume of labeled DNA was reduced below 15.7 µl in vacuum centrifuge, and 2.5 µl of yeast tRNA (10mg/ml, Invitrogen Life Technologies, Carlsbad, USA), 4.3 µl of 20 x SSC (1 x SSC was 8.8g/l NaCl and 4.4 g/ trisodiumcitrate) and 0.8 µl of 10% SDS were added. After denaturation at 100°C for 3 min, 1.7 µl of 10 x digoxigenin was added. The final volume for hybridization was adjusted with water to 25 µl. Before hybridization, slides were fixed by UV-cross linking with 90 mJ cm-2, washed for 1 min in 0.1% of SDS and 2 min in water to remove residual salt, and incubated at 50ºC for 30 min in BSA solution containing 1% of BSA fraction V, 2 x SSC and 0.1% of SDS to block nonspecific binding. The slides were further washed in 2 x SSC for 3 min and then in 0.2 x SSC for 3 min. Hybridization was conducted under 22 x 25mm LifterSlip ™ coverslip (Erie Scientific Company, Portsmouth, USA) in hybridization chamber at 65°C for 16 h. To control humidity inside the hybridization chamber, a strip of thin paper, humidified with approximately 100 µl of 3.4 x SSC, was placed under the slide. After hybridization slides were washed at 65°C for 10 min with 1 x SSC and 0.1% of SDS. The following washes were conducted at room temperature for 10 min with 0.5 x SSC and 0.01% SDS, and for 3 min and 1 min with 0.1 x SSC. Slides were dried in slide centrifuge.

scan_protocol: scanned with ScanArray ®5000 (PerkinElmer, Waltham, USA).

data_processing:
We concentrated on finding the "clear absent" genes in each studied strain, which were clearly separated from the "present" genes by their logratio; no normalization and no averaging were required. Specifically, using our own r-script, log-transformed CH2/CH1-ratio is calculated. For defining the lost genes, logratio is plotted against average of channel intensities (MA-plot) and a cutoff logratio is selected based on the MA-plot to separate absent genes from present genes. Fuller description provided in the related manuscript.
The VALUE column reports log2 (test/Tohama I) ratio data.

organism: Bordetella pertussis

source_name: Tohama I

label_protocol: The 4 µg of digested DNA was labelled with the dye (Amershham Biosciences UK Limited, Buckinghamshire, England) according to the protocol of BioPrime®Array CGH Genomic Labeling System (Invitrogen Life Technologies, Carlsbad, USA). The labeled DNA was purified with the purification kit of the same manufacturer.

growth_protocol: Bacteria stored in -70°C were recultured on Charcoal agar (Oxoid Ltd, Basingstoke, England) with 10% defibrinated sheep blood. The plates were incubated at 35-36°C for 3 days. Bacteria were harvested and suspended in distilled water. Prior to DNA isolation, the concentration of bacterial suspension was adjusted to 2 x 109 cells/ml.

extract_protocol: B. pertussis DNA was isolated with GenElute™ Bacterial Genomic DNA Kit (Sigma-Aldrich Inc., St. Louis, USA) and then digested with Sma I (10 U/µg DNA, New England Biolabs, Ipswich, USA) according to the protocol of BioPrime®Array CGH Genomic Labeling System (Invitrogen Life Technologies, Carlsbad, USA).

tag: strain Tohama I; year of isolation

tag: strain PRCB13; year of isolation


title: S10_Muscle_Insulin_240min

city: San Antonio

first: Dawn

middle: K

last: Coletta

state: TX

address: 7703 Floyd Curl Drive

department: Medicine

institute: UTHSCSA

description: Gene expression data from skeletal muscle following 240 minutes of a insulin infusion (80 mU clamp)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 using protocol EukGE-ES2.

scan_protocol: The intensity of bound dye was measured with an argon laser confocal scanner (GeneArray scanner G2500A; Agilent).

data_processing: The Affymetrix data acquisition programs in GCOS automatically generate a cell intensity file (CEL) from the stored images that contain a single intensity value for each probe cell on the array.  The CEL files were imported into the R software package (http://www.r-project.org) and the probe level data were converted to expression measures using the Affy package from Bioconductor. Expression values for each mRNA were obtained by GC-Robust Multi-Array Analysis (GCRMA).  CEL files were normalized together and the expression values obtained were submitted to analysis with linear models of microarray data (LIMMA) to identify genes that were significantly increased or decreased with a false discovery rate (FDR) of less than 5%, and a fold change of greater than 1.5.

label: Biotin

source_name: Vastus Lateralis Muscle at 240 min

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).  A description of the protocol has been described previously (Richardson 2005)

extract_protocol: Muscle biopsies from each subject were homogenized in RNAStat solution (Tel-Test Inc., Friendswood, TX), using a Polytron homogenizer (Brinkmann Instruments Westbury, NY).  Total RNA was purified with RNeasy and DNase I treatment (Qiagen, Chatsworth, CA).

treatment_protocol: All subjects received a vastus lateralis muscle biopsy followed by a 180-min euglycemic, hyperinsulinemic (80 mU/m2.min) clamp, which was performed with infusion of 3-3H-glucose (prime=25 Ci, continuous infusion=0.25 Ci/min) to determine rates of glucose appearance and disposal, as previously described (DeFronzo, 1979). Biopsies of the vastus lateralis muscle were taken basally and at 30 and 240 minutes after the start of the insulin infusion, as previously described (Cusi 2000)

tag: Gender

value: Male

tag: Diabetes Status

value: Family History Negative

tag: Ethnicity

value: Mexican American


title: S11_Muscle_Insulin_240min

value: Female


title: B. pertussis Tohama I vs. PRCB291

description: CGH

tag: strain PRCB291; year of isolation


title: S12_Muscle_Baseline_0min

description: Gene expression data from skeletal muscle at baseline

source_name: Vastus Lateralis Muscle at 0 min

value: Caucasian


title: S11_Muscle_Insulin_30min

description: Gene expression data from skeletal muscle following 30 minutes of a insulin infusion (80 mU clamp)

source_name: Vastus Lateralis Muscle at 30 min


title: S12_Muscle_Insulin_240min


title: S9_Muscle_Insulin_30min


title: S11_Muscle_Baseline_0min


title: S10_Muscle_Baseline_0min


title: S9_Muscle_Baseline_0min


title: B. pertussis Tohama I vs. PRCB305

description: CGH

tag: strain PRCB305; year of isolation


title: S8_Muscle_Insulin_240min


title: Tohama I vs. PRCB41

description: CGH

tag: Strain PRCB41; year of isolation


title: S7_Muscle_Insulin_240min


title: S9_Muscle_Insulin_240min


title: Tohama I vs. PRCB20S

description: CGH

tag: Strain PRCB20S; year of isolation


title: S7_Muscle_Insulin_30min


title: B. pertussis Tohama I vs. PRCB374

description: CGH

tag: strain PRCB374; year of isolation


title: S8_Muscle_Insulin_30min


title: S12_Muscle_Insulin_30min


title: S10_Muscle_Insulin_30min


title: S8_Muscle_Baseline_0min


title: Tohama I vs. 1772

description: CGH

tag: Strain 1772; strain added to the whole cell vaccine in 1976.


title: Tohama I vs. 1977/7

description: CGH

tag: Strain 1977/7; year of isolation


title: S6_Muscle_Insulin_240min


title: S7_Muscle_Baseline_0min


title: Tohama I vs. PRCB223

description: CGH

tag: Strain PRCB223; year of isolation


title: B. pertussis Tohama I vs. PRCB382

description: CGH

tag: strain PRCB382; year of isolation


title: S6_Muscle_Insulin_30min


title: S6_Muscle_Baseline_0min


title: Tohama I vs. 18530

description: CGH

tag: Strain 18530; strain used for the production of whole cell vaccine in Finland since 1962.


title: Tohama I vs. PRCB179

description: CGH

tag: Strain PRCB179; year of isolation


title: B. pertussis Tohama I vs. 1977/3

description: CGH

tag: strain 1977/3; year of isolation


title: Tohama I vs. 18323

description: CGH

tag: strain Tohama I; year of isolation

tag: Strain 18323; year of isolation

value: 1946; PFGE-reference strain


title: S4_Muscle_Insulin_240min

tag: Gender


title: Tohama I vs. KKK22

description: CGH

tag: Strain Tohama I ; year of isolation

tag: Strain KKK22; year of isolation


title: Gr1-_2h LM infected_3_peritoneal lavage

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

country: Germany

institute: Miltenyi Biotec GmbH

hyb_protocol: Cy3 labeled cDNA in hybridization buffer was hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (44K) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with 6x SSPE buffer containing 0.005% N-lauroylsarcosine for 1 min followed by a second wash with 0.06x SSPE containing 0.005% N-lauroylsarcosine for 1 min and a final wash step with acetonitrile for 30 sec. All washing steps were performed at room temperature.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files

source_name: infected peritoneal cells, timepoint 2h

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: Mice were intraperitonealy infected with 104 L. monocytogenes (EGDe strain) in exponential growth phase (bacteria were grown in BHI at 108/ml, and diluted 10.000x in PBS immediately before injection).

extract_protocol: SuperAmplification was performed according to Miltenyi Biotec’s undisclosed protocol. Briefly, the amplification is based on a global PCR protocol of mRNA-derived cDNA. mRNA was isolated via magnetic bead technology.

treatment_protocol: Cells were directly sorted in the SuperAmp Lysis Buffer (Miltenyi Biotec, Bergisch Gladbach, Germany) using a FACS Aria cell-sorter (BD biosciences). Cell samples (1.103 cells per experimental point) were lysed using SuperAmp Lysis Buffer following manufacturer’s instructions

tag: Six-weeks old (C57Bl6, Cx3cr1gfp/+) mice

tag: infected with 1x104 of L. monocytogenes (EGDe strain) in exponential growth phase

tag: Gr1- monocytes purified as NK1.1- CD3- B220- CD11b+ F4/80low Gr1-, gfphigh


title: B. pertussis Tohama I vs. PRCB272

description: CGH

tag: strain PRCB272; year of isolation


title: B. pertussis Tohama I vs. KKK1330

description: CGH

tag: strain KKK1330; year of isolation


title: B. pertussis PRCB474 vs, Tohama I

description: CGH, dye swap

tag: strain PRCB474; year of isolation


title: Tohama I vs. KKK1330

description: CGH

tag: Strain KKK1330; year of isolation


title: S2_Muscle_Insulin_240min

tag: Diabetes Status

tag: Ethnicity


title: Gr1-_8h LM infected_3_peritoneal lavage

description: Cells were directly sorted in the SuperAmp Lysis Buffer (Miltenyi Biotec, Bergisch Gladbach, Germany) using a FACS Aria cell-sorter (BD biosciences).

source_name: infected peritoneal cells, timepoint 8h


title: S4_Muscle_Insulin_30min


title: Gr1-_8h LM infected_2_peritoneal lavage


title: B. pertussis Tohama I vs. PRCB461

description: CGH

tag: strain PRCB461; year of isolation


title: S5_Muscle_Baseline_0min


title: Gr1-_8h LM infected_1_peritoneal lavage


title: S4_Muscle_Baseline_0min