title: Medium treated replicate 1 - VAT

description: Biological replicate 1 of 5 for MT group (VAT)

source_name: visceral adipose tissue, under high fat diet with medium body weight treated with rimonabant


title: Medium treated replicate 2 - VAT

status: Public on Dec 15 2008

type: RNA

city: Lausanne

first: Carine

last: Poussin

address: Quartier UNIL-Sorge

country: Switzerland

institute: University of Lausanne

description: Biological replicate 2 of 5 for MT group (VAT)

hyb_protocol: Cy5-labeled RNA from adipose tissue and Cy3-labeled mouse universal reference of total RNA were hybridized on the M17K spotted array according published protocols (de Fourmestraux, J Biol Chem, 2004)

scan_protocol: Scanned on a Scanarray 4000 scanner. Tiff image analysis was done using the software ImaGene 4 (from BioDiscovery) in order to extract spot intensity signal for Cy3 and Cy5 channels.

data_processing: Print Tip Lowess normalized data obtained from log2 of processed Red signal/processed Green signal. The sma (Statistical Microarray Analysis) package from the statistical R software was used.

molecule: total RNA

organism: Mus musculus

label_protocol: Indirect labeling of amplified RNA with Cy3 or Cy5 fluorascent dye according to published protocols (de Fourmestraux, J Biol Chem, 2004)

growth_protocol: Six-week-old C57BL/6J male mice (Janvier, France) were fed a normal chow (NC; 12% fat, 28% protein, and 60% carbohydrate) or a high fat diet (HFD; 72% fat, 28% protein, and <1% carbohydrate) for 7 months. Their body weight and tolerance to intraperitoneal

extract_protocol: RNA from each sample was extracted as described in the protocol of peqGOLD TriFast (from peqLab). RNA quality was checked before and after amplification with a bioanalyzer 2100 (Agilent). RNA was amplified with MessageAmpTM kit (Ambion) according the manu

treatment_protocol: Each mouse was further treated with vehicle (0.1% Tween 80 (Fluka) in H2O) or rimonabant (10 mg.kg-1.day-1) administrated daily by gavage for 1 month. Vehicle or rimonabant treatments were randomly assigned in each group of NC and HFD mice. The body weigh

tag: C57Bl/6J mouse

source_name: Mouse universal reference total RNA (DB Biosciences, ref: 636657)

tag: Commercial RNA


title: High treated replicate 1 - VAT

description: Biological replicate 1 of 5 for HT group (VAT)

source_name: visceral adipose tissue, under high fat diet with high body weight treated with rimonabant


title: Medium treated replicate 4 - VAT

description: Biological replicate 4 of 5 for MT group (VAT)


title: Medium treated replicate 3 - VAT

description: Biological replicate 3 of 5 for MT group (VAT)


title: Normal chow treated replicate 2 - VAT

description: Biological replicate 2 of 5 for NCT group (VAT)

source_name: visceral adipose tissue of normal chow fed-mouse treated with rimonabant


title: Normal chow control replicate 4 - VAT

description: Biological replicate 4 of 4 for NCC group (VAT)

source_name: visceral adipose tissue of normal chow fed-mouse treated with the vehicle


title: Low treated replicate 3 - VAT

description: Biological replicate 3 of 4 for LT group (VAT)

source_name: visceral adipose tissue, under high fat diet with low body weight treated with rimonabant


title: Low treated replicate 4 - VAT

description: Biological replicate 4 of 4 for LT group (VAT)


title: Normal chow control replicate 1 - VAT

description: Biological replicate 1 of 4 for NCC group (VAT)


title: Low treated replicate 2 - VAT

description: Biological replicate 2 of 4 for LT group (VAT)


title: Normal chow control replicate 3 - VAT

description: Biological replicate 3 of 4 for NCC group (VAT)


title: High control replicate 5 - VAT

description: Biological replicate 5 of 5 for HC group (VAT)

source_name: visceral adipose tissue, under high fat diet with high body weight treated with the vehicle


title: N_3P aRNA-2 SHDD

status: Public on Dec 17 2008

city: Stockholm

first: Annika

last: Saaf

department: Department of Molecular Medicine & Surgery

country: Sweden

institute: Karolinska Institute, Karolinska University Hospital, Solna

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62223.gif
Disease State: Normal
Organism Part: back

hyb_protocol: not provided

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1920, 7880; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.49; Parameter Scan Time = 11:32:49; Parameter PMT Volts = 590; Parameter Scan Date = 2005-01-04; Parameter Pixel Size = 10; Parameter Laser on time = 211134; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.96; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.49; Parameter Scan Time = 11:32:49; Parameter PMT Volts = 740; Parameter Scan Date = 2005-01-04; Parameter Pixel Size = 10; Parameter Laser on time = 430137; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.51; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Homo sapiens

source_name: Stratagene Human Reference

label_protocol: not provided

extract_protocol: not provided

tag: Stratagene Human Reference Amplified 9/30/2002

source_name: Skin, Disease State: Normal, Organism Part: back


title: Normal chow control replicate 2 - VAT

description: Biological replicate 2 of 4 for NCC group (VAT)


title: Low treated replicate 1 - VAT

description: Biological replicate 1 of 4 for LT group (VAT)


title: High control replicate 1 - VAT

description: Biological replicate 1 of 5 for HC group (VAT)


title: High control replicate 3 - VAT

description: Biological replicate 3 of 5 for HC group (VAT)


title: Medium control replicate 4 - VAT

description: Biological replicate 4 of 5 for MC group (VAT)

source_name: visceral adipose tissue, under high fat diet with medium body weight treated with the vehicle


title: High control replicate 2 - VAT

description: Biological replicate 2 of 5 for HC group (VAT)


title: Medium control replicate 5 - VAT

description: Biological replicate 5 of 5 for MC group (VAT)


title: High control replicate 4 - VAT

description: Biological replicate 4 of 5 for HC group (VAT)


title: sdh3_delta_rep2

status: Public on Dec 16 2008

city: Kongens Lyngby

first: Kiran

middle: Raosaheb

last: Patil

address: Bulding 223, Søltofts Plads

country: Denmark

institute: Technical University of Denmark

description: Replicate 2 of 2.

hyb_protocol: cRNA was synthesized as described in the Affymetrix GeneChip Expression Analysis Manual, after which 15 micro-gram were hybridized to Yeast Genome S98 oligonucleotide arrays (Affymetrix).

scan_protocol: Microarrays were scanned in Agilent Gene Scanner (Affimetrix).

data_processing: Raw data processing was performed with the Microarray Suite software, version 5, with a global scaling factor for target intensity equal to 500. Average difference values, representing the absolute hybridization intensities were then calculated for each probe set.

label: biotin

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae sdh3 deletion mutant

label_protocol: As described in the Affymetrix GeneChip Expression Analysis Manual.

growth_protocol: Batch growth conditions with minimal medium

extract_protocol: Duplicate samples for microarray analysis were collected during the aerobic batch experiments with the sdh3Δ strain when the glucose concentration had reached 20±2 g/liter. Culture aliquots of 20 ml were transferred to falcon tubes already filled with 25ml of crushed ice and immediately centrifuged at 4000 rpm for 5 minutes. The pellets were rapidly frozen in liquid nitrogen and stored at -80ºC until further use. Total RNA was extracted by using the Fast Pro Red Kit (Obiogene, USA) according to the manufacture’s instructions with minor modifications.

tag: sdh3 deletion mutant in CEN.PK113-7D background


title: Medium control replicate 1 - VAT

description: Biological replicate 1 of 5 for MC group (VAT)


title: Medium control replicate 2 - VAT

description: Biological replicate 2 of 5 for MC group (VAT)


title: Medium control replicate 3 - VAT

description: Biological replicate 3 of 5 for MC group (VAT)


title: Low control replicate 4 - VAT

description: Biological replicate 4 of 5 for LC group (VAT)

source_name: visceral adipose tissue, under high fat diet with low body weight treated with the vehicle


title: Low control replicate 5 - VAT

description: Biological replicate 5 of 5 for LC group (VAT)


title: Low control replicate 2 - VAT

description: Biological replicate 2 of 5 for LC group (VAT)


title: Low control replicate 3 - VAT

description: Biological replicate 3 of 5 for LC group (VAT)


title: Medium treated replicate 5 - VAT

description: Biological replicate 5 of 5 for MT group (VAT)


title: Low control replicate 1 - VAT

description: Biological replicate 1 of 5 for LC group (VAT)


title: U2OS Dex 59th hour

city: Philadelphia

first: Michael

last: Hughes

state: PA

address: 421 Curie Bvd, Brb 835

country: USA

institute: UPenn

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99 degrees C for 5 min and hybridized for 16 h at 45 degrees C. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: signal calculated by RMA in Affymetrix Expression Console

source_name: U2OS osteosarcoma

label_protocol: Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

growth_protocol: U2OS cells (ATCC) were grown to confluence in DMEM supplimented with 10% FCS and P/S/G on 35mm dishes.

extract_protocol: Cells were washed briefly with 1X PBS.  1 mL Trizol (Invitrogen) was used to homogenize cells, and samples were frozen at -80 until total RNA was purified.

treatment_protocol: Cells were synchronized with Dexamethasone 24 hours before samples were collected.

tag: synchronized with dexamethasone


title: U2OS Dex 71st hour


title: U2OS Dex 67th hour


title: U2OS Dex 60th hour


title: U2OS Dex 69th hour


title: U2OS Dex 58th hour


title: U2OS Dex 64th hour


title: U2OS Dex 65th hour


title: U2OS Dex 62nd hour


title: U2OS Dex 66th hour


title: U2OS Dex 63rd hour


title: U2OS Dex 68th hour


title: N2-Cel-TORRNAi-fasting-biological rep3

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

country: Japan

institute: Graduate School of Biostudies, Kyoto University

description: Gene expression data from wild type worms at day 4 of adulthood.  Worms were grown on Cel-TOR RNAi plates and fasted for 48 h.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45 degrees C on C. elegans Genome array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with GCRMA algorithm

organism: Caenorhabditis elegans

source_name: Wild Type N2, N2-Cel-TORRNAi-fasting-biological rep3

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol (One-Cycle Target Labeling Assays) from 5 ug total RNA.

growth_protocol: All worms are grown at 20 degrees C.

extract_protocol: Total RNA was isolated and purified by following the manual of Sepasol(R)-RNA Ⅰ Super (nakalai tesque) and RNeasy mini kit (Qiagen), respectively.

treatment_protocol: Worms grown on RNAi plates (control RNAi or Cel-Rheb RNAi or Cel-TOR RNAi) were fed ad libitum or fasted for 48 h.

tag: Age

value: Day 4 of adulthood.


title: U2OS Dex 61st hour


title: U2OS Dex 57th hour


title: N2-Cel-TORRNAi-fasting-biological rep1

source_name: Wild Type N2, N2-Cel-TORRNAi-fasting-biological rep1


title: U2OS Dex 55th hour


title: N2-Cel-TORRNAi-fed-biological rep3

description: Gene expression data from wild type worms at day 4 of adulthood.  Worms were grown on Cel-TOR RNAi plates and fed ad libitum.

source_name: Wild Type N2, N2-Cel-TORRNAi-fed-biological rep3


title: N2-Cel-TORRNAi-fed-biological rep2

source_name: Wild Type N2, N2-Cel-TORRNAi-fed-biological rep2


title: U2OS Dex 54th hour


title: N2-Cel-TORRNAi-fed-biological rep1

source_name: Wild Type N2, N2-Cel-TORRNAi-fed-biological rep1


title: U2OS Dex 56th hour


title: U2OS Dex 52nd hour


title: U2OS Dex 48th hour


title: U2OS Dex 53rd hour


title: N2-Cel-RhebRNAi-fasting-biological rep3

description: Gene expression data from wild type worms at day 4 of adulthood.  Worms were grown on Cel-Rheb RNAi plates and fasted for 48 h.

source_name: Wild Type N2, N2-Cel-RhebRNAi-fasting-biological rep3


title: U2OS Dex 50th hour


title: N2-Cel-RhebRNAi-fasting-biological rep1

source_name: Wild Type N2, N2-Cel-RhebRNAi-fasting-biological rep1


title: N2-Cel-RhebRNAi-fasting-biological rep2

source_name: Wild Type N2, N2-Cel-RhebRNAi-fasting-biological rep2


title: U2OS Dex 49th hour


title: N2-controlRNAi-fasting-biological rep5

description: Gene expression data from wild type worms at day 4 of adulthood.  Worms were grown on control RNAi plates and fasted for 48 h.

source_name: Wild Type N2, N2-controlRNAi-fasting-biological rep5


title: U2OS Dex 51st hour


title: U2OS Dex 46th hour


title: N2-Cel-RhebRNAi-fed-biological rep3

description: Gene expression data from wild type worms at day 4 of adulthood.  Worms were grown on Cel-Rheb RNAi plates and fed ad libitum.

source_name: Wild Type N2, N2-Cel-RhebRNAi-fed-biological rep3


title: U2OS Dex 47th hour


title: N2-Cel-RhebRNAi-fed-biological rep2

source_name: Wild Type N2, N2-Cel-RhebRNAi-fed-biological rep2


title: N2-Cel-RhebRNAi-fed-biological rep1

source_name: Wild Type N2, N2-Cel-RhebRNAi-fed-biological rep1


title: U2OS Dex 70th hour


title: N2-Cel-RhebRNAi-fed-biological rep4

source_name: Wild Type N2, N2-Cel-RhebRNAi-fed-biological rep4


title: U2OS Dex 44th hour


title: N2-Cel-TORRNAi-fasting-biological rep2

source_name: Wild Type N2, N2-Cel-TORRNAi-fasting-biological rep2


title: U2OS Dex 43rd hour


title: U2OS Dex 45th hour


title: U2OS Dex 42nd hour


title: N2-controlRNAi-fasting-biological rep4

source_name: Wild Type N2, N2-controlRNAi-fasting-biological rep4


title: N2-controlRNAi-fed-biological rep4

description: Gene expression data from wild type worms at day 4 of adulthood.  Worms were grown on control RNAi plates and fed ad libitum.

source_name: Wild Type N2, N2-controlRNAi-fed-biological rep4


title: U2OS Dex 41st hour

source_name: U2OS osteosarcoma


title: U2OS Dex 39th hour


title: U2OS Dex 37th hour


title: N2-controlRNAi-fasting-biological rep2

source_name: Wild Type N2, N2-controlRNAi-fasting-biological rep2


title: U2OS Dex 35th hour


title: U2OS Dex 34th hour


title: N2-controlRNAi-fasting-biological rep3

source_name: Wild Type N2, N2-controlRNAi-fasting-biological rep3


title: N2-controlRNAi-fed-biological rep2

source_name: Wild Type N2, N2-controlRNAi-fed-biological rep2


title: U2OS Dex 30th hour


title: N2-controlRNAi-fasting-biological rep1

source_name: Wild Type N2, N2-controlRNAi-fasting-biological rep1


title: U2OS Dex 31st hour


title: U2OS Dex 38th hour


title: U2OS Dex 27th hour


title: N2-controlRNAi-fed-biological rep3

source_name: Wild Type N2, N2-controlRNAi-fed-biological rep3


title: U2OS Dex 36th hour


title: U2OS Dex 29th hour


title: N2-controlRNAi-fed-biological rep5

source_name: Wild Type N2, N2-controlRNAi-fed-biological rep5


title: U2OS Dex 40th hour


title: U2OS Dex 32nd hour


title: U2OS Dex 33rd hour


title: U2OS Dex 28th hour


title: N2-controlRNAi-fed-biological rep1

source_name: Wild Type N2, N2-controlRNAi-fed-biological rep1


title: U2OS Dex 26th hour


title: U2OS Dex 24th hour


title: U2OS Dex 25th hour


title: N2-Cel-RhebRNAi-fasting-biological rep4

source_name: Wild Type N2, N2-Cel-RhebRNAi-fasting-biological rep4


title: MSL1 low formaldehyde rnaiMOF SL2 cell line replicate 3

status: Public on Dec 14 2008

type: genomic

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

description: WGA amplified DNA was labeled, hybridized and scanned by imaGenes (www.imagenes-bio.de)

hyb_protocol: performed by imaGenes (www.imagenes-bio.de)

data_processing: raw signals of all channels in all replicate arrays were normalized and log2 transformed using the 'vsn' package in R/Bioconductor.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: IP DNA; MSL1 SL2 cell line after MOF RNAi

extract_protocol: ChIP DNA; cells were crosslinked in growth medium using 0.1% formaldehyde for 10 minutes at RT. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using the Bioruptor (Diagenode, Belgium) 8 times 30 seconds using the ‘high’ setting. Fragment size of the obtained chromatin was checked to be between 300 bp and 700 bp. Chromatin was precleared using a protein A/protein G-sepharose mixture for 1 hr at 4°C. 200 µl chromatin was incubated with appropriate amounts of antibodies in a total volume of 500 µl RIPA buffer at 4°C over night. After washing and crosslink revearsal, immunprecipitated nucleic acids were purified on GFX columns (GE Healthcare). IP DNA was amplified using the WGA kit (Sigma).

treatment_protocol: 1×10e6 SL2 cells were incubated with 10 µg dsRNA for 1 hour in serum-free medium. After addition of serum-containing medium, cells were incubated for 7 days at 26°C before chromatin preparation

tag: male cell line SL2

source_name: Input DNA; SL2 cell line after MOF RNAi

extract_protocol: Input DNA; cells were crosslinked in growth medium using 0.1% formaldehyde for 10 minutes at RT. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using the Bioruptor (Diagenode, Belgium) 8 times 30 seconds using the ‘high’ setting. Fragment size of the obtained chromatin was checked to be between 300 bp and 700 bp. After crosslink revearsal, nucleic acids were purified on GFX columns (GE Healthcare). Input DNA was amplified using the WGA kit (Sigma).


title: FH_RDE2_14028s_wt_MgMShock_3_7DS537

status: Public on Dec 13 2008

type: mixed

city: Irvine

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: biological replicate, Date of Scan Fri Feb 09 13:18:14 2007

hyb_protocol: overnight hyb on Corning UltraGAPS slides at 42°C in 25% formamide / 5xSSC / 0.1% BSA

scan_protocol: Perkin Elmer ScanArray 5000 scanner, image acquisition with ScanArray Express 3.0.1 software, spot quantification using Quantarray 3.0 software, adaptive quantification, protocol STv7S_01_051201

data_processing: normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: 14028s wt RNA MgMShock 060921

label_protocol: incorporation of Cy3-dCTP with Superscript RT and random hexamers

extract_protocol: RNeasy kit (QIAGEN)

tag: Salmonella typhimurium 14028s wt RNA harvested from LB stat culture that was transferred into MgM medium and grown for four more hours at 30°C

source_name: 14028s gDNA

label_protocol: incorporation of Cy5-dCTP using Klenow enzyme and random hexamers

extract_protocol: SIGMA GenElute bacterial genomic DNA extraction

tag: Salmonella typhimurium 14028s genomic DNA from stationary culture grown in LB at 37C with aeration


title: FH_RDE2_14028s_wt_MgMShock_1_7DS506

description: biological replicate, Date of Scan Tue Nov 07 14:09:48 2006

source_name: 14028s wt RNA MgMShock 060919


title: FH_RDE2_14028s_wt_MgMShock_2_7DS536

description: biological replicate, Date of Scan Thu Feb 01 14:50:33 2007

source_name: 14028s wt RNA MgMShock 060920


title: MSL2 high formaldehyde SL2 cell line replicate 2

scan_protocol: performed by imaGenes (www.imagenes-bio.de)

source_name: IP DNA; MSL2 SL2 cell line

extract_protocol: ChIP DNA; cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using the Bioruptor (Diagenode, Belgium) 8 times 30 seconds using the ‘high’ setting. Fragment size of the obtained chromatin was checked to be between 300 bp and 700 bp. Chromatin was precleared using a protein A/protein G-sepharose mixture for 1 hr at 4°C. 200 µl chromatin was incubated with appropriate amounts of antibodies in a total volume of 500 µl RIPA buffer at 4°C over night. After washing and crosslink revearsal, immunprecipitated nucleic acids were purified on GFX columns (GE Healthcare). IP DNA was amplified using the WGA kit (Sigma).

source_name: Input DNA; SL2 cell line

extract_protocol: Input DNA; cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using the Bioruptor (Diagenode, Belgium) 8 times 30 seconds using the ‘high’ setting. Fragment size of the obtained chromatin was checked to be between 300 bp and 700 bp. After crosslink revearsal, nucleic acids were purified on GFX columns (GE Healthcare). Input DNA was amplified using the WGA kit (Sigma).


title: MSL1 wt SL2 cell line replicate 1

source_name: IP DNA; MSL1 SL2 cell line

label_protocol: performed by imaGenes (www.imagenes-bio.de)


title: MSL1 rnaiGST SL2 cell line replicate 1

source_name: IP DNA; MSL1 SL2 cell line after GST RNAi

source_name: Input DNA; SL2 cell line after GST RNAi


title: MSL2 low formaldehyde SL2 cell line replicate 1


title: MSL1 wt SL2 cell line replicate 3


title: MSL1 rnaiMSL3 SL2 cell line replicate 2

source_name: IP DNA; MSL1 SL2 cell line after MSL3 RNAi

source_name: Input DNA; SL2 cell line after MSL3 RNAi


title: FH_RDE2_14028s_wt_MgMDil_1_7DS501

description: biological replicate, Date of Scan Wed Nov 01 11:29:42 2006

source_name: 14028s wt RNA MgMDil 060922

tag: Salmonella typhimurium 14028s wt RNA harvested from LB stat culture that had been diluted 100fold in MgM medium and grown to log phase


title: FH_RDE2_14028s_wt_MgMDil_2_7DS591

description: biological replicate, Date of Scan Fri Feb 16 14:58:15 2007

source_name: 14028s wt RNA MgMDil 060925


title: FH_RDE2_14028s_wt_MgMDil_3_7DS592

description: biological replicate, Date of Scan Fri Feb 16 15:19:44 2007

source_name: 14028s wt RNA MgMDil 060927


title: MSL1 wt SL2 cell line replicate 2


title: MSL1 rnaiGST SL2 cell line replicate 2


title: MSL1 low formaldehyde rnaiMOF SL2 cell line replicate 1


title: MSL1 low formaldehyde rnaiMOF SL2 cell line replicate 2


title: MSL1 rnaiMLE SL2 cell line replicate 1

source_name: IP DNA; MSL1 SL2 cell line after MLE RNAi

source_name: Input DNA; SL2 cell line after MLE RNAi


title: MSL1 low formaldehyde rnaiGST SL2 cell line replicate 3


title: FH_RDE2_14028s_wt_LBstat_2_7DS530

description: biological replicate, Date of Scan Fri Jan 26 10:06:05 2007

source_name: 14028s wt RNA LBstat 061019

tag: Salmonella typhimurium 14028s wt RNA harvested from LB stat culture


title: MSL2 low formaldehyde SL2 cell line replicate 2


title: MSL2 high formaldehyde SL2 cell line replicate 1


title: MSL1 low formaldehyde rnaiGST SL2 cell line replicate 2


title: FH_RDE2_14028s_wt_LBstat_3_7DS531

description: biological replicate, Date of Scan Fri Jan 26 10:41:50 2007

source_name: 14028s wt RNA LBstat 061020


title: MSL1 wt SL2 cell line replicate 4


title: MSL1 rnaiMLE SL2 cell line replicate 2


title: MSL1 low formaldehyde rnaiGST SL2 cell line replicate 1


title: MSL1 rnaiMSL3 SL2 cell line replicate 1


title: FH_RDE2_14028s_wt_LBstat_1_7DS508

description: biological replicate, Date of Scan Thu Nov 30 09:06:52 2006

source_name: 14028s wt RNA LBstat 061018

source_name: 14028s gDNA


title: FH_RDE2_14028s_wt_LBlog_2_7DS534

description: biological replicate, Date of Scan Thu Feb 01 12:06:31 2007

source_name: 14028s wt RNA LBlog 061019

tag: Salmonella typhimurium 14028s wt RNA harvested from LB log culture


title: FH_RDE2_14028s_smpB_MgMShock_2_7DS730

description: biological replicate, Date of Scan Tue Mar 20 09:03:08 2007

source_name: 14028s smpB RNA MgMShock 060920

tag: Salmonella typhimurium 14028s smpB RNA harvested from LB stat culture that was transferred into MgM medium and grown for four more hours at 30°C


title: FH_RDE2_14028s_smpB_MgMShock_3_7DS731

description: biological replicate, Date of Scan Tue Mar 20 09:31:52 2007

source_name: 14028s smpB RNA MgMShock 060921


title: WT(-MG)vsWT(+5.6 mM MG)_rep3

city: Ithaca

first: John

middle: D.

last: Helmann

state: NY

address: 372 Wing Hall

department: Microbiology

institute: Cornell University

hyb_protocol: Before hybridization of samples, the B. subtilis full genomic DNA microarray was pre-hybridized at 42oC for at least 45 min in 2x SSC, 0.05% SDS, 1% BSA, then the slide was washed six times with A. dest and were dried at 1500 rpm, RT for 5 min. Afterwards, the labelled cDNA mixture was denatured for 2 min at 95oC prior to hybridization, which was performed for at least 16h at 42oC. The hybridized slide was washed at RT for 5 min with 0.2x SSC, 0.1% SDS, 5 min with 0.2x SSC (two times) and was subsequently dried at RT at a speed of 1500 rpm for 5 min.

scan_protocol: Array was scanned with the ArrayWoRX scanner (GeneScan, Freiburg, Germany) and the ScanArray Express scanner (PerkinElmer Life and Analytical Sciences, Rodgau-Jügesheim, Germany). Spot finding and image analyses were done with Genespring software from Agilent Technologies (version 7.1).

data_processing: Data represents average of treated samples (Cy5) / average of untreated samples (Cy3). Ave represents the average of medians for duplicate spots (minus median of background).

organism: Bacillus subtilis

source_name: untreated

label_protocol: For the labelling of cDNA 25 µg total RNA with a B. subtilis gene specific primer mix (2.5 nM final concentration) (Eurogentec S.A., Seraing, Belgium) was used. For the external control 1 ng of Arabidopsis thaliana rbcL RNA (Stratagene, Amsterdam, Netherlands) was added and the reaction mix was incubated at 65oC for 10 min. The mixture was cooled down for 10 min at RT and following reagents were added and mixed: 10 µl 5x Superscript reaction buffer, 4 µl of a dNTP-master mix (5 mM dATP, 5 mM dGTP, 2 mM dTTP, 5 mM dCTP) (Roche Diagnostics, Penzberg, Germany), 0.1 mM Cy3 dUTP (for untreated sample) and 0.1 mM Cy5 dUTP (for the treated sample) (GE Healthcare, Freiburg, Germany), 0.01 M DTT, 1 µl Superscript reverse transcriptase (Invitrogen Life Technologies, Karlsruhe, Germany). The whole mixture was incubated at 42oC for 2h. Afterwards, 10 µm 1M NaOH was added for hydrolysis of RNA and incubated at 65oC for 10 min. 10 µm 1M HCl were added for neutralization and the reaction was filled up with 150 µl TE buffer  (pH 8.0). The labelled cDNA was purified using the CyScribe GFX Purification Kit (GE Healthcare, Freiburg, Germany) as described by the manufacturer. After purification both samples (untreated and treated) were combined in one Eppendorf tube and the volume was concentrated in a speed-vac. The labelled cDNA mix was re-suspended in 17 µl hybridization buffer (MWG AG Biotech, Ebersberg, Germany) and used for hybridization.

extract_protocol: B. subtilis wild type cells were grown in BMM medium to OD500 of 0.4 and harvested before and after 10 min exposure to 1 mM FA, 2.8 mM and 5.6 mM MG . Total RNA was isolated by the acid phenol method as described (Majumdar et al. 1991).

tag: WT

source_name: 5.6 mM MG


title: FH_RDE2_14028s_wt_LBlog_1_7DS500

description: biological replicate, Date of Scan Wed Nov 01 10:19:42 2006

source_name: 14028s wt RNA LBlog 061018


title: FH_RDE2_14028s_smpB_MgMShock_1_7DS511

description: biological replicate, Date of Scan Thu Nov 30 13:11:18 2006

source_name: 14028s smpB RNA MgMShock 060919


title: FH_RDE2_14028s_hfq_MgMShock_3_7DS539

description: biological replicate, Date of Scan Fri Feb 09 14:30:19 2007

source_name: 14028s hfq RNA MgMShock 060921

tag: Salmonella typhimurium 14028s hfq RNA harvested from LB stat culture that was transferred into MgM medium and grown for four more hours at 30°C


title: FH_RDE2_14028s_smpB_MgMDil_3_7DS770

description: biological replicate, Date of Scan Fri May 25 14:14:32 2007

source_name: 14028s smpB RNA MgMDil 060927

tag: Salmonella typhimurium 14028s smpB RNA harvested from LB stat culture that had been diluted 100fold in MgM medium and grown to log phase


title: FH_RDE2_14028s_smpB_LBstat_3_7DS675

description: biological replicate, Date of Scan Fri Mar 02 13:41:50 2007

source_name: 14028s smpB RNA LBstat 061020

tag: Salmonella typhimurium 14028s smpB mutant RNA harvested from LB stat culture


title: FH_RDE2_14028s_smpB_MgMDil_1_7DS502

description: biological replicate, Date of Scan Wed Nov 01 12:07:02 2006

source_name: 14028s smpB RNA MgMDil 060922


title: WT(-MG)vsWT(+5.6 mM MG)_rep2


title: FH_RDE2_14028s_smpB_LBstat_1_7DS509

description: biological replicate, Date of Scan Thu Nov 30 10:09:13 2006

source_name: 14028s smpB RNA LBstat 061018


title: FH_RDE2_14028s_smpB_LBstat_2_7DS672

description: biological replicate, Date of Scan Fri Mar 02 11:27:32 2007

source_name: 14028s smpB RNA LBstat 061019


title: FH_RDE2_14028s_smpB_MgMDil_2_7DS769

description: biological replicate, Date of Scan Fri May 25 13:47:40 2007

source_name: 14028s smpB RNA MgMDil 060925


title: FH_RDE2_14028s_hfq_MgMDil_3_7DS547

description: biological replicate, Date of Scan Fri Feb 16 14:05:47 2007

source_name: 14028s hfq RNA MgMDil 060927

tag: Salmonella typhimurium 14028s hfq RNA harvested from LB stat culture that had been diluted 100fold in MgM medium and grown to log phase


title: WT(-MG)vsWT(+2.8 mM MG)_rep3

source_name: 2.8 mM MG


title: WT(-MG)vsWT(+2.8 mM MG)_rep2


title: WT(-MG)vsWT(+5.6 mM MG)_rep1


title: FH_RDE2_14028s_hfq_MgMDil_2_7DS546

description: biological replicate, Date of Scan Fri Feb 16 13:25:12 2007

source_name: 14028s hfq RNA MgMDil 060925

source_name: 14028s gDNA


title: FH_RDE2_14028s_smpB_LBlog_1_7DS504

description: biological replicate, Date of Scan Tue Nov 07 11:22:04 2006

source_name: 14028s smpB RNA LBlog 061018

tag: Salmonella typhimurium 14028s smpB mutant RNA harvested from LB log culture


title: FH_RDE2_14028s_hfq_MgMDil_1_7DS503

description: biological replicate, Date of Scan Wed Nov 01 12:37:14 2006

source_name: 14028s hfq RNA MgMDil 060922


title: WT(-FA)vsWT(+1 mM FA)_rep3

source_name: untreated

source_name: 1 mM FA


title: WT(-MG)vsWT(+2.8 mM MG)_rep1


title: FH_RDE2_14028s_hfq_MgMShock_2_7DS538

description: biological replicate, Date of Scan Fri Feb 09 13:47:18 2007

source_name: 14028s hfq RNA MgMShock 060920


title: FH_RDE2_14028s_hfq_MgMShock_1_7DS507

description: biological replicate, Date of Scan Tue Nov 07 14:57:05 2006

source_name: 14028s hfq RNA MgMShock 060919


title: FH_RDE2_14028s_smpB_LBlog_3_7DS598

description: biological replicate, Date of Scan Tue Feb 27 14:25:35 2007

source_name: 14028s smpB RNA LBlog 061020


title: FH_RDE2_14028s_smpB_LBlog_2_7DS597

description: biological replicate, Date of Scan Tue Feb 27 13:46:46 2007

source_name: 14028s smpB RNA LBlog 061019


title: FH_RDE2_14028s_hfq_LBstat_3_7DS533

description: biological replicate, Date of Scan Fri Jan 26 11:26:45 2007

source_name: 14028s hfq RNA LBstat 061020

tag: Salmonella typhimurium 14028s hfq mutant RNA harvested from LB stat culture


title: FH_RDE2_14028s_hfq_LBstat_1_7DS510

description: biological replicate, Date of Scan Thu Nov 30 10:53:37 2006

source_name: 14028s hfq RNA LBstat 061018


title: WT(-FA)vsWT(+1 mM FA)_rep1


title: FH_RDE2_14028s_hfq_LBlog_3_7DS535

description: biological replicate, Date of Scan Thu Feb 01 12:47:45 2007

source_name: 14028s hfq RNA LBlog 061020

tag: Salmonella typhimurium 14028s hfq mutant RNA harvested from LB log culture


title: FH_RDE2_14028s_hfq_LBlog_1_7DS505

description: biological replicate, Date of Scan Tue Nov 07 12:02:47 2006

source_name: 14028s hfq RNA LBlog 061018


title: FH_RDE2_14028s_hfq_LBlog_2_7DS513

description: biological replicate, Date of Scan Fri Dec 08 10:16:50 2006

source_name: 14028s hfq RNA LBlog 061019


title: FH_RDE2_14028s_hfq_LBstat_2_7DS532

description: biological replicate, Date of Scan Fri Jan 26 11:05:51 2007

source_name: 14028s hfq RNA LBstat 061019


title: Flocculent strain HS 34 exponential growth phase vs powdery strain HS 37 exponential growth phase (Dye swap)

status: Public on Dec 12 2008

city: Leipzig

first: Franziska

last: Heine

address: Permoserstraße 15

department: Environmental Microbiology

institute: Helmholtz-Centre for Environmental Research - UFZ

description: Gene expression of cells of the flocculent strain HS 10 and the powdery strain HS 37 both harvested during exponential growth phase was analysed.

hyb_protocol: The differently labelled cDNAs (Fluorescein and Biotin) of both samples are hybridized (42°C over night) simultaneously in one experiment to the same array according to the slide manufacturer´s and Micromax TSA Kit recommendations.

scan_protocol: The microarrays were scanned by the Axon 4000B scanner; image intensity data were extracted and analysed with GenePix® Pro 6.0 software.

data_processing: Processed Data: Data from different scans of Dye-swap experiment were extracted by GenePix Pro 6.0 software, normalized and united. An outliertest has been applied in order to find outliers amongst the gene replicats. Subsequently, a t-test (1% and 5% probability of error) has been used in order to find regulated genes.

source_name: Cells from powdery strain HS 37

label_protocol:
The indirect labelling by the tyramide-signal-amplification method (MicromaxTM TSATM labelling and detection Kit from Perkin Elmer life sciences, MPS 522) was used to increase the Cy3/Cy5 signals of microarray detection.
6 µg of the total RNA were reverse transcribed and thereby the cDNA was labelled with Fluorescein-dCTP/ Biotin-dCTP.

extract_protocol: The isolation of RNA was done by disruption of the cells under liquid nitrogen using mortar and pistil and then the Qiagen RNeasy Midi Kit with some modifications within the manufacturers´ protocol and the Qiagen RNase-Free DNase Set were applied.

tag: Saccharomyces cerevisiae HS 37

source_name: Cells from flocculent strain HS 34

label_protocol: The indirect labelling by the tyramide-signal-amplification method (MicromaxTM TSATM labelling and detection Kit from Perkin Elmer life sciences, MPS 522) was used to increase the Cy5 signals of microarray detection. 6 µg of the total RNA were reverse transcribed and thereby the cDNA was labelled with Biotin-dCTP/ Fluorescein-dCTP.

tag: Saccharomyces cerevisiae HS 34


title: Flocculent strain HS 10 stationary growth phase vs powdery strain HS 37 stationary growth phase

source_name: Cells from flocculent strain HS 10 stationary growth phase

tag: Saccharomyces cerevisiae HS 10

source_name: Cells from powdery strain HS 37 stationary growth phase


title: Flocculent strain HS 10 stationary growth phase vs powdery strain HS 37 stationary growth phase (Dye swap)


title: Flocculent strain HS 34 exponential growth phase vs powdery strain HS 37 exponential growth phase


title: Flocculent strain HS 10 exponential growth phase vs powdery strain HS 12 exponential growth phase (Dye swap)

source_name: Cells from powdery strain HS 12

tag: Saccharomyces cerevisiae HS 12

source_name: Cells from flocculent strain HS 10


title: Flocculent strain HS 34 exponential growth phase vs powdery strain HS 12 exponential growth phase (Dye swap)


title: Flocculent strain HS 10 exponential growth phase vs powdery strain HS 12 exponential growth phase


title: Flocculent strain HS 34 exponential growth phase vs powdery strain HS 12 exponential growth phase


title: Flocculent strain HS 10 exponential growth phase vs powdery strain HS 37 exponential growth phase (Dye swap)


title: Flocculent strain HS 10 exponential growth phase vs powdery strain HS 37 exponential growth phase


title: FH_RDE2_14028s_wt_LBlog_3_7DS514

description: biological replicate, Date of Scan Fri Dec 08 09:24:18 2006

source_name: 14028s wt RNA LBlog 061020

source_name: 14028s gDNA

tag: Salmonella typhimurium 14028s genomic DNA from stationary culture grown in LB at 37C with aeration


title: Medicago truncatula seedlings, 2 wks hydroponics media, 200mM NaCl salt stress, 24 hour

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

description: Gene expression data of roots of Medicago truncatula seedlings grown two weeks in hydroponics media under salt stress

hyb_protocol: performed at 45℃ with rotation for 16h (Affymetrix GeneChip Hybridization Oven 640)

scan_protocol: using Affymetrix GeneChip Scanner 3000

data_processing: The hybridization data were analyzed using GeneChip Operating software (GCOS 1.4). The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of GCOS 1.4

organism: Medicago truncatula

source_name: Medicago truncatula seedlings, grown 2 wks in hydroponics media, 200mM NaCl salt stress, time point 24 hour

label_protocol: using the Custom MessageAmp™ II-Biotin by Ambion according to the manufacturer’s instruction

growth_protocol: grown two weeks in hydroponics media

extract_protocol: using TRIzol reagent performed according to the manufacturer’s instruction

treatment_protocol: 200mM NaCl salt stress

tag: Medicago truncatula seedlings

tag: grown two weeks in hydroponics media

tag: 200mM NaCl salt stress

tag: 2 ug of total RNA was used to synthesize doublestranded cDNA


title: Medicago truncatula seedlings, 2 wks hydroponics media, 200mM NaCl salt stress, 10 hour

source_name: Medicago truncatula seedlings, grown 2 wks in hydroponics media, 200mM NaCl salt stress, time point 10 hour


title: Medicago truncatula seedlings, 2 wks hydroponics media, 200mM NaCl salt stress, 2 hour

source_name: Medicago truncatula seedlings, grown 2 wks in hydroponics media, 200mM NaCl salt stress, time point 2 hour


title: Medicago truncatula seedlings, 2 wks hydroponics media, 200mM NaCl salt stress, 1 hour

source_name: Medicago truncatula seedlings, grown 2 wks in hydroponics media, 200mM NaCl salt stress, time point 1 hour


title: Medicago truncatula seedlings, 2 wks hydroponics media, 200mM NaCl salt stress, 5 hour

source_name: Medicago truncatula seedlings, grown 2 wks in hydroponics media, 200mM NaCl salt stress, time point 5 hour


title: Medicago truncatula seedlings, 2 wks hydroponics media, 200mM NaCl salt stress, 0 hour

data_processing: The hybridization data were analyzed using GeneChip Operating software (GCOS 1.4). The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of GCOS 1.4.

source_name: Medicago truncatula seedlings, grown 2 wks in hydroponics media, 200mM NaCl salt stress, time point 0 hour


title: Adult female time 24 insulin control replicate 2 of 2

city: Brisbane

first: Hong

last: You

state: QLD

address: 300 Herston Road

country: Australia

institute: Queensland Institute of Medical Reaseach

description: Adult female S. japonicum time 24

hyb_protocol: One-color Microarray-Based gene expression version 5.5 February 2007

scan_protocol: Microarrays were scanned using the Aglient DNA microarray scanner

data_processing: Agilent Feature Extraction software version 9.5.3.1

organism: Schistosoma japonicum

source_name: female, time 24, insulin control

label_protocol: Agilent Low RNA Input linear amplification kit

extract_protocol: Trizol / QIAGEN RNeasy isolated total RNA

tag: Adult

tag: time 24

tag: female


title: Adult male time 0.5 insulin control replicate 1 of 2

description: Adult male S. japonicum time 0.5

source_name: male, time 0.5, insulin control

tag: time 0.5

tag: male


title: Adult female time 24 insulin replicate 2 of 2

description: Adult female S. japonicum time 24

source_name: female, time 24, insulin


title: Adult male time 0.5 insulin control replicate 2 of 2

description: Adult male S. japonicum time 0.5


title: Adult female time 0.5 insulin control replicate 1 of 2

description: Adult female S. japonicum time 0.5

source_name: female, time 0.5, insulin control


title: Adult male time 3 insulin control replicate 2 of 2

description: Adult male S. japonicum time 3

source_name: male, time 3, insulin control

tag: time 3


title: Adult male time 24 insulin replicate 2 of 2

description: Adult male S. japonicum time 24

source_name: male, time 24, insulin


title: Adult male time 3 insulin control replicate 1 of 2

description: Adult male S. japonicum time 3


title: Adult male time 3 insulin replicate 2 of 2

description: Adult male S. japonicum time 3

source_name: male, time 3, insulin


title: Adult female time 3 insulin replicate 2 of 2

description: Adult female S. japonicum time 3

source_name: female, time 3, insulin


title: Adult male time 0.5 insulin replicate 2 of 2

description: Adult male S. japonicum time 0.5

source_name: male, time 0.5, insulin


title: Adult male time 0 insulin replicate 2 of 2

description: Adult male S. japonicum time 0

source_name: male, time 0, insulin

tag: time 0


title: Adult female time 3 insulin control replicate 1 of 2

description: Adult female S. japonicum time 3

source_name: female, time 3, insulin control


title: Adult female time 0.5 insulin control replicate 2 of 2

description: Adult female S. japonicum time 0.5


title: Adult female time 0 insulin replicate 2 of 2

description: Adult female S. japonicum time 0

source_name: female, time 0, insulin


title: Adult male time 24 insulin replicate 1 of 2

description: Adult male S. japonicum time 24


title: Adult male time 3 insulin replicate 1 of 2

description: Adult male S. japonicum time 3


title: Adult female time 0.5 insulin replicate 2 of 2

description: Adult female S. japonicum time 0.5

source_name: female, time 0.5, insulin


title: Adult female time 3 insulin control replicate 2 of 2

description: Adult female S. japonicum time 3


title: Adult female time 24 insulin control replicate 1 of 2

description: Adult female S. japonicum time 24


title: WT(-FA)vsWT(+1 mM FA)_rep2

source_name: untreated

tag: WT

source_name: 1 mM FA


title: Adult female time 24 insulin replicate 1 of 2

description: Adult female S. japonicum time 24


title: N-Tera2_infected_72hours_biologicalreplicate2_technical replicate4

status: Public on Dec 11 2008

city: Laval

first: Dominique

middle: Jean

last: Favreau

state: Quebec

address: 531 boul. des prairies, Bl.18

department: Neuroimmunovirology

country: Canada

institute: INRS-IAF

description: 72h - Infected(cy3) vs Mock(cy5)

hyb_protocol: Equimolar solution of cRNA from infected and mock-infected cells were hybridized for 17 hours at 65°C on the microarray chip human 1A oligo microarrays (V2), according to the Agilent 60-mer oligo microarray processing protocol

scan_protocol: Microarray fluorescence was revealed using the ProScanArray HT scanner (Perkin-Elmer) at a 5µm resolution and colometric intensity was quantified using the ProScanArray Express software (Perkin-Elmer).

data_processing: Raw data were analyzed with the opensource sofware Microarray Data Analysis System (MIDAS) from the TM4 microarray software suite. Data were subsequently subjected using to a background checking >2, a LOWESS normalization with a smooth parameter of 0.33, a standard deviation regularization and a slice analysis rejecting data with a p>0.05.

source_name: N-Tera2, HCoV-OC43 infected, 72hours

label_protocol: mRNA was linearly amplified using the Low RNA Input linear amplification kit (Agilent) according to the manufacturer’s protocol where CTP-Cy3 (Perkin-Elmer) and CTP-Cy5 (Perkin-Elmer) were incorporated into cRNA. Briefly, total RNA were reverse transcirbed using MMLV-RT and then linearly amplified using T7-polymerase with either Cy3 ou Cy5 labeled nucleotide

growth_protocol: N-Tera2 cells were differentiated into human neurons (NT2-N) as previously described(Pleasure et al 1992.). Briefly, 2x106 cells were seeded in a 75cm2 flask in DMEM with 10% FBS. The next day, medium was replaced by the same medium containing 10μM all-trans retinoic-acid (Sigma) and replaced every 3 days for 4 weeks. Cells were then trypsinized and plated into petri dishes or 24-well plates coated with poly-D-lysine (Sigma, P-1149) and matrigel (BD Bioscience) and cultured for 2 weeks with DMEM supplemented with 5% FBS, 1µM AraC, 10µM FudR and 10µM UriD (Sigma) with the medium replaced every 3 days.

extract_protocol: Total RNA was extracted at 24, 48 and 72 hours post-infection using the Agilent RNA extration kit (Agilent) following the manufacturer’s instructions, quantified using the spectrophotometer ND1000 (Nanodrop) and RNA integrity was assessed by microfluidic electrophoresis using the Agilent RNA 6000 Nano kit with the Agilent 2100 Bioanalyzer (Agilent)

treatment_protocol: Cells were infected at a MOI of 0.2 or mock-infected, then incubated at 37 °C for 2 hours, washed with PBS and incubated at 37°C with fresh medium. Cells were harvested at  24, 48 or 72 hours post-infection

tag: N-Tera2 differentiated human neuronal cells

tag: 72hours post-infection

tag: HCoV-OC43 Infected

source_name: N-Tera2, mock infected, 72hours

tag: Mock infected


title: Adult female time 3 insulin replicate 1 of 2

description: Adult female S. japonicum time 3


title: Adult female time 0 insulin replicate 1 of 2

description: Adult female S. japonicum time 0


title: Adult female time 0.5 insulin replicate 1 of 2

description: Adult female S. japonicum time 0.5


title: Adult male time 0 insulin replicate 1 of 2

description: Adult male S. japonicum time 0


title: Adult male time 24 insulin control replicate 2 of 2

description: Adult male S. japonicum time 24

source_name: male, time 24, insulin control


title: Adult male time 0.5 insulin replicate 1 of 2

description: Adult male S. japonicum time 0.5


title: N-Tera2_infected_72hours_biologicalreplicate2_technical replicate3

description: 72h - Infected(cy3) vs Mock(cy5)


title: gingival fibroblasts from subject 70_Ctrl3h_Ctrl6h

first: Johan

last: Lindberg

address: Roslagstullsbacken 21, Floor 3

institute: Royal Institute of Technology

description: In the normalized matrix the log-ratios are log2(ch2/ch1) which representes log2(cy5/cy3).

hyb_protocol: After prehybridizing of the slides for 30 minutes at 42°C in prehybridization buffer consisting of 1% BSA (Sigma-Aldrich), 5x SSC (where SSC consists of 0.15 M NaCl and 0.015 M sodium citrate) and 0.1% SDS, the arrays were washed, first in a trough containing water and then in a trough containing propan-2-ol, and centrifuged dry. After that the samples (one labeled with Cy5 and the other labeled with Cy3) were pooled and dried to a volume of 13.6 μl. Hybridization buffer consisting of 5x SSC, 50% formamide (Sigma-Aldrich), 0.1% SDS and 0.2 μg/μl Cot-1 DNA (Invitrogen) was added to the pooled samples to a final volume of 64.5 μl. The hybridization mixture was then denatured for 3 minutes at 95°C and cooled for 2 minutes on ice before being applied to the array. Lifterslips (Erie Scientific Company) were used to contain the hybridization mixture on the array during hybridization. The arrays were then placed, in hybridization chambers (Corning), in a water bath at 42°C for 14 to 18 hours. After hybridization the slides were washed once for 5 minutes at 42°C in wash buffer 1 (2x SSC, 0.1% SDS), once for 5 minutes in wash buffer 2 (0.1x SSC, 0.1% SDS) and five times, for 1 minute each, in wash buffer 3 (0.1x SSC). The slides were then centrifuged dry and scanned.

scan_protocol: An Agilent G2565BA scanner was used to scan the slides and acquire 50-megabyte TIFF images. The scanner resolution was set at 10 μm. GenePix 5.1.0.0 (Axon Instruments) was used to extract the raw signals from the TIFF images and to assign each spot an ID. Spots defined as 'not found' by GenePix were flagged with a negative flag (- 50) and removed downstream in the analysis. Spots with clearly abnormal morphology due to dust particles or other factors were manually flagged as bad (- 100) and were also removed in downstream analysis. No further processing of the slides was performed in GenePix.

data_processing: The data was analyzed using different packages in the software R (http://cran.r-project.org/). All packages except the KTH package (http://www.ktharray.se/) are available in the Bioconductor (http://www.bioconductor.org/) open source software project for analysis of genomic data. First, the raw data from GenePix was read into R. Thereafter, four filters were used to remove spots with abnormal physical properties, as previously described (PMID: 16507157). On average, 75% of all spots passed the filters for each slide. After filtering, the slides were normalized using print tip Lowess normalization (PMID: 11842121).

label_protocol: To prime cDNA synthesis, 1 μl of random hexamer primer (5 μg/μl; Operon) was added to 1 μg of amplified aRNA. The volume was adjusted to 18.4 μl with RNase-free water. The sample was mixed and incubated for 10 minutes at 70°C to denature the aRNA, then incubated for a further 5 minutes on ice and centrifuged briefly. A cDNA synthesis mixture (11.6 μl) consisting of 6 μl of 5x first-strand buffer, 3 μl of 0.1 M dithiothreitol, 2 μl of Superscript III (Invitrogen) and 0.6 μl of 50x aa-dUTP+dNTP mix (Sigma-Aldrich) was added to each sample. The whole mixture was gently mixed by pipetting and incubated at 25°C. After 10 minutes at this temperature the mixture was incubated at 46°C for a further 2 hours. To terminate the reaction and to hydrolyze the RNA strand, 3 μl of 0.2 M EDTA pH 8.0 and 4.5 μl of 1 M NaOH were added. The sample was vortex-mixed briefly, incubated for 15 minutes at 70°C, cooled to room temperature and centrifuged briefly. Then 4.5 μl of 1 M HCl was added to restore the pH to neutrality. The sample was vortex-mixed and centrifuged briefly. The cDNA was purified and eluted by the following procedure. First, 60 μl of water and 500 μl of PB buffer (MinElute Reaction Cleanup Kit) were added. The mixture was thoroughly mixed and transferred to a MinElute Reaction Cleanup Kit spin column and centrifuged for 30 seconds at 13,000 r.p.m. The flow-through was reapplied to the column and the centrifugation step was repeated. The flow-through was dis carded and 650 μl of 80% ethanol was added to the column. The column was centrifuged for 30 seconds at 13,000 r.p.m. and the flow-through was again discarded. The ethanol wash step was repeated and then the membrane was dried by centrifugation for 1 minute at 13,000 r.p.m. The column was transferred to a new tube, and 10 μl of 100 mM NaHCO3 pH 9.0 was added. The column was then incubated for 1 minute at room temperature; the sample was eluted by centrifugation for 30 seconds at 13,000 r.p.m. The elution step was repeated after a further addition of 10 μl of 100 mM NaHCO3 pH 9.0 to ensure high yield. To couple fluorophores, the eluate was mixed with a dried aliquot of either Cy3 or Cy5 mono-reactive esters (Amersham-Biosciences) and incubated for 30 minutes at room temperature in a dark container, after which 70 μl of water and 500 μl of PB buffer were added. The mixture was thoroughly mixed and transferred to a MinElute Reaction Cleanup Kit spin column, which was centrifuged for 30 seconds at 13,000 r.p.m. The flow-through was reapplied to the column and the centrifugation step was repeated. The flow-through was discarded and 650 μl of PE buffer (MinElute Reaction Cleanup Kit) was added. The column was centrifuged for 30 seconds at 13,000 r.p.m. and the flow-through was discarded. The wash step was repeated and then the membrane was washed by centrifugation for 1 minute at 13,000 r.p.m. The column was transferred to a new tube, 10 μl of EB buffer (MinElute Reaction Cleanup Kit) was added, and the column was incubated for 1 minute at room temperature. The sample was eluted by centrifugation for 30 seconds at 13,000 r.p.m. The elution step was repeated after a further addition of 10 μl of EB buffer, to ensure high yield. A Nanodrop instrument (Nanodrop Technologies) was used to confirm labeling success and to measure fluorophore concentrations. The fluorophore concentrations of the labeling reactions were used to balance the sample volumes. To obtain equal fluorophore amounts within each hybridization, a smaller volume of the sample with a higher fluorophore concentration was hybridized with the entire volume of the sample with a lower fluorophore concentration.

growth_protocol: Minced pieces of gingival tissue were explanted to 25 cm2 Falcon tissue culture flasks containing 5 ml of Dulbecco's Modified Eagle Medium (DMEM) supplemented with 50 units/ml penicillin, 50 μg/ml streptomycin (50 μg/ml) and 5% fetal calf serum (FCS, Invitrogen Life Technologies, Scotland, UK). Gingival fibroblasts were obtained by trypsinization of the primary outgrowth of cells. The cells were grown at 37°C with 5 % CO2 and routinely passaged using 0.025% trypsin in phosphate-buffered saline (PBS) containing 0.02% EDTA. Gingival fibroblasts were seeded in Petri dishes in DMEM supplemented with 5% FCS and cultured for 24 h at 37°C. The cell layers were then rinsed with serum-free DMEM followed by the addition of DMEM with or without the inflammatory mediator TNF and in the absence or presence of the inhibitors SP600125 (SP; Sigma-Aldrich, St. Louis, MO, USA) or Bay6 11-7082 (Bay, Sigma-Aldrich). After different incubation periods, as indicated in the figure legends, culture medium was removed and stored at -20°C for subsequent PGE2 determination. The cell monolayer was washed twice with ice-cold PBS and the cells were used for oligonucleotide microarray, flow cytometry or phosphorylation specific luminex analyses.

extract_protocol: For each of the three cell lines, two 100-mm Petri dishes were used for each treatment. After incubation for 1, 3 or 6 h with or without TNF (20 ng/ml), the cells were immediately frozen in liquid nitrogen and then stored at -70°C for subsequent isolation of total RNA. Total RNA was isolated from fibroblasts using the commercially available RNeasy kit (Qiagen Inc., CA, USA) and quantified spectrophotometrically at 260/280 nm. The RNA from each pair of dishes with identical cell line and treatment were pooled and treated as one sample throughout further analyses. The RNA quality was assessed using the RNA 6000 Nano LabChip kit of the Bioanalyzer system (Agilent).

treatment_protocol: See growth protocol for information.

tag: Human gingival fibroblasts were established from gingival biopsies obtained from a healthy individual with no clinical signs of periodontal disease.

source_name: gingival fibroblasts from subject 70_Ctrl6h


title: gingival fibroblasts from subject 70_TNF3h_TNF1h

source_name: gingival fibroblasts from subject 70_TNF1h


title: gingival fibroblasts from subject 69_TNF6h_Ctrl6h

source_name: gingival fibroblasts from subject 69_Ctrl6h


title: gingival fibroblasts from subject 69_TNF1h_Ctrl1h

source_name: gingival fibroblasts from subject 69_Ctrl1h


title: N-Tera2_infected_72hours_biologicalreplicate2_technical replicate1

description: 72h - Mock(cy3) vs Infected(cy5)

tag: HCoV-OC43 infected


title: N-Tera2_infected_72hours_biologicalreplicate2_technical replicate2

description: 72h - Mock(cy3) vs Infected(cy5)


title: Adult male time 24 insulin control replicate 1 of 2

description: Adult male S. japonicum time 24


title: N-Tera2_infected_72hours_biologicalreplicate1_technical replicate4

description: 72h - Infected(cy3) vs Mock(cy5)


title: gingival fibroblasts from subject 69_TNF3h_Ctrl3h

source_name: gingival fibroblasts from subject 69_Ctrl3h


title: gingival fibroblasts from subject 69_TNF6h_TNF3h

source_name: gingival fibroblasts from subject 69_TNF3h


title: 102_Pf_T_t27_repB_tech

city: Pretoria

first: Anna

middle: Catharina (Tharina)

last: van Brummelen

state: Gauteng

address: Lynwood Road

department: Biochemistry

country: South Africa

institute: University of Pretoria

description: Technical replicate

hyb_protocol: DeRisi style 70-mer oligonucleotide arrays were spotted in-house at the Princeton University Microarray Facility. The array design, post-processing, overnight hybridization at 65°C and washing were performed as described [Bozdech, Z., Zhu, J., Joachimiak, M., Cohen, F., Pulliam, B., and DeRisi, J. (2003) Genome Biol. 4(2), R9].

scan_protocol: Arrays were scanned with an Axon GenePix 4000A scanner and the images were analyzed with GenePix Pro 6.0 software (Axon Instruments).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. Raw data processing was performed with GenePix Pro 6.0 and data normalization and background subtraction occurred in the Princeton University Microarray database (PUMAdb, http://puma.princeton.edu).

organism: Plasmodium falciparum

source_name: P. falciparum, treated, 27 hpi

label_protocol: The cDNA obtained was divided into aliquots of 2 ug each and where possible two technical array replicates were performed. The 2 ug cDNA was coupled to either Cy3 (reference pool) or Cy5 (samples) at pH = 9.0 (Amersham Biosciences). Free dye was removed with DNA Clean and Concentrator-5 columns (Zymo Research).

growth_protocol: Parasite culturing and sampling for the transcriptomics, proteomics and metabolomics occurred independently, but perturbation conditions were replicated in terms of the parasite population, treatment and sampling times. 3D7 P. falciparum cultures were maintained in vitro in human A+ erythrocytes in RPMI 1640 medium (Sigma) with 0.5% (w/v) Albumax II (Gibco) according to established methods [Trager, W., and Jensen, J. (1976) Science 193(4254), 673-675].

extract_protocol: Total RNA was isolated from frozen PBS washed pellets from 15 ml culture samples with the Qiagen RNeasy kit, using a modified protocol including TRI-Reagent (Sigma) in the lysis step. Contaminating genomic DNA was removed with DNase I (Qiagen). A reference RNA pool was prepared from all three treated (T) and untreated (UT) time points, including both sets of biological replicates. First strand cDNA synthesis was initiated from 12 ug of total RNA with 775 pmol random primer 9 (New England Biolabs) and 250 pmol oligo-dT25 by incubation at 70°C for 10 min followed by cooling on ice for 10 min. Reverse transcription and amino-allyl incorporation were performed at 42°C as described [Bozdech, Z., Zhu, J., Joachimiak, M., Cohen, F., Pulliam, B., and DeRisi, J. (2003) Genome Biol. 4(2), R9], but the reaction was performed overnight using 480 U of SuperScript III (Invitrogen). Contaminating RNA was removed by hydrolysis with 0.5 M EDTA and 1 M NaOH at 65°C for 15 min and the reactions were purified with the Wizard SV Gel and PCR Clean-Up System (Promega).

treatment_protocol: Parasites were synchronized by consecutive sorbitol treatments for three generations and treated in the late schizont stage [42 hours post-invasion) hpi] with 5 mM DFMO (IC50 = 1 mM) and 5 uM 5’-{[(Z)-4-amino-2-butenyl]methylamino}-5’-deoxyadenosine (MDL73811, IC50 = 1 uM) to ensure complete parasite arrest in order to prevent parasites escaping cytostasis and causing asynchrony. At these dosages the combined drug effect is additive and cytostatic but complete enzyme inhibition was confirmed with radio-labelled substrate assays. Treatment was performed in duplicate (i.e. two biological replicates, A and B) alongside untreated controls. Drug treated (T) and untreated (UT) cultures at about 8-10% parasitaemia and 2-3% hematocrit, were harvested at three time points within the trophozoite stage [t1 = 19 hours post invasion (hpi), t2 = 27 hpi and t3 = 34 hpi], based on the morphology of untreated parasites after microscopic inspection of Giemsa-stained thin smears. Culture medium (with and without drug) was replaced halfway through the time course (18 hpi), but before the first sampling, to prevent metabolic stress of the parasites.

tag: Strain 3D7, asexual blood stage

source_name: RNA reference pool

tag: Strain 3D7, asexual blood stage, mixture of all samples included in experiment

tag: Total RNA mixture of all samples included in experiment


title: N-Tera2_infected_72hours_biologicalreplicate1_technical replicate2

description: 72h - Mock(cy3) vs Infected(cy5)


title: gingival fibroblasts from subject 70_TNF6h_TNF3h

source_name: gingival fibroblasts from subject 70_TNF3h


title: 094_Pf_T_t34_repB_tech

description: Technical replicate

source_name: P. falciparum, treated, 34 hpi


title: N-Tera2_infected_48hours_biologicalreplicate2_technical replicate4

description: 48h - Infected(cy3) vs Mock(cy5)

source_name: N-Tera2, HCoV-OC43 infected, 48hours

tag: 48hours post-infection

source_name: N-Tera2, mock infected, 48hours


title: gingival fibroblasts from subject 67_TNF3h_TNF1h

source_name: gingival fibroblasts from subject 67_TNF1h


title: gingival fibroblasts from subject 69_Ctrl6h_Ctrl1h


title: gingival fibroblasts from subject 69_TNF3h_TNF1h

source_name: gingival fibroblasts from subject 69_TNF1h


title: gingival fibroblasts from subject 70_TNF3h_Ctrl3h

source_name: gingival fibroblasts from subject 70_Ctrl3h


title: gingival fibroblasts from subject 70_Ctrl1h_TNF1h


title: 129_Pf_T_t34_repB

description: Biological replicate B


title: N-Tera2_infected_72hours_biologicalreplicate1_technical replicate1

description: 72h - Mock(cy3) vs Infected(cy5)

source_name: N-Tera2, mock infected, 72hours

source_name: N-Tera2, HCoV-OC43 infected, 72hours


title: 128_Pf_T_t27_repB

description: Biological replicate B


title: 127_Pf_T_t19_repB

description: Biological replicate B

source_name: P. falciparum, treated,19 hpi


title: 089_Pf_UT_t34_repB_tech

description: Technical replicate

source_name: P. falciparum, untreated, 34 hpi


title: 126_Pf_UT_t34_repB

description: Biological replicate B


title: 116_Pf_T_t19_repB_tech

description: Technical replicate


title: 090_Pf_T_t34_repA_tech

description: Technical replicate


title: 125_Pf_UT_t27_repB

description: Biological replicate B

source_name: P. falciparum, untreated, 27 hpi


title: 124_Pf_UT_t19_repB

description: Biological replicate B

source_name: P. falciparum, untreated,19 hpi


title: gingival fibroblasts from subject 67_TNF6h_Ctrl6h

source_name: gingival fibroblasts from subject 67_Ctrl6h


title: gingival fibroblasts from subject 67_Ctrl1h_Ctrl3h

source_name: gingival fibroblasts from subject 67_Ctrl3h


title: N-Tera2_infected_48hours_biologicalreplicate2_technical replicate3

description: 48h - Infected(cy3) vs Mock(cy5)


title: N-Tera2_infected_48hours_biologicalreplicate2_technical replicate1

description: 48h - Mock(cy3) vs Infected(cy5)


title: 097_Pf_UT_t34_repA_tech

description: Technical replicate


title: 111_Pf_T_t27_repA

description: Biological replicate A

source_name: P. falciparum, treated, 27 hpi


title: N-Tera2_infected_48hours_biologicalreplicate2_technical replicate2

description: 48h - Mock(cy3) vs Infected(cy5)


title: gingival fibroblasts from subject 69_Ctrl3h_Ctrl6h

source_name: gingival fibroblasts from subject 69_Ctrl6h


title: 112_Pf_T_t34_repA

description: Biological replicate A

source_name: RNA reference pool


title: 098_Pf_T_t27_repA_tech

description: Technical replicate


title: N-Tera2_infected_72hours_biologicalreplicate1_technical replicate3

description: 72h - Infected(cy3) vs Mock(cy5)


title: gingival fibroblasts from subject 70_TNF1h_Ctrl1h

source_name: gingival fibroblasts from subject 70_Ctrl1h


title: 109_Pf_UT_t34_repA

description: Biological replicate A


title: N-Tera2_infected_48hours_biologicalreplicate1_technical replicate2

description: 48h - Mock(cy3) vs Infected(cy5)

source_name: N-Tera2, HCoV-OC43 infected, 48hours


title: gingival fibroblasts from subject 69_Ctrl6h_TNF6h

source_name: gingival fibroblasts from subject 69_TNF6h


title: N-Tera2_infected_48hours_biologicalreplicate1_technical replicate4

description: 48h - Infected(cy3) vs Mock(cy5)

source_name: N-Tera2, mock infected, 48hours


title: gingival fibroblasts from subject 70_Ctrl6h_Ctrl1h


title: N-Tera2_infected_48hours_biologicalreplicate1_technical replicate3

description: 48h - Infected(cy3) vs Mock(cy5)


title: 107_Pf_UT_t19_repA

description: Biological replicate A


title: 108_Pf_UT_t27_repA

description: Biological replicate A


title: 095_Pf_UT_t19_repA_tech

description: Technical replicate


title: N-Tera2_infected_48hours_biologicalreplicate1_technical replicate1

description: 48h - Mock(cy3) vs Infected(cy5)


title: gingival fibroblasts from subject 70_Ctrl3h_TNF3h

source_name: gingival fibroblasts from subject 70_TNF3h


title: N-Tera2_infected_24hours_biologicalreplicate2_technical replicate4

description: 24h - Infected(cy3) vs Mock(cy5)

source_name: N-Tera2, HCoV-OC43 infected, 24hours

tag: 24hours post-infection

source_name: N-Tera2, mock infected, 24hours


title: N-Tera2_infected_24hours_biologicalreplicate2_technical replicate1

description: 24h - Mock(cy3) vs Infected(cy5)


title: N-Tera2_infected_24hours_biologicalreplicate2_technical replicate2

description: 24h - Mock(cy3) vs Infected(cy5)


title: N-Tera2_infected_24hours_biologicalreplicate2_technical replicate3

description: 24h - Infected(cy3) vs Mock(cy5)


title: gingival fibroblasts from subject 67_TNF1h_Ctrl1h

source_name: gingival fibroblasts from subject 67_Ctrl1h


title: gingival fibroblasts from subject 67_Ctrl6h_TNF6h

source_name: gingival fibroblasts from subject 67_TNF6h


title: N-Tera2_infected_24hours_biologicalreplicate1_technical replicate4

description: 24h - Infected(cy3) vs Mock(cy5)


title: N-Tera2_infected_24hours_biologicalreplicate1_technical replicate3

description: 24h - Infected(cy3) vs Mock(cy5)


title: gingival fibroblasts from subject 69_TNF1h_TNF6h


title: gingival fibroblasts from subject 67_TNF1h_TNF6h


title: ChIP-seq 2rounds_IgG

city: Bethesda

first: Dustin

middle: E

last: Schones

state: MD

address: Building 10, Room 7B20A, 9000 Rockville Pike

institute: NHLBI/NIH

description: IgG control

data_processing: Sequence reads were obtained and mapped to the mouse (February, 2006) and human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.  Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: CD4+ T cells

growth_protocol: Growth protocol as described in Liao et al., 2008

extract_protocol: Treatment protocol as described in Liao et al., 2008

tag: 2 rounds

tag: IgG control


title: gingival fibroblasts from subject 70_TNF6h_Ctrl6h

source_name: gingival fibroblasts from subject 70_Ctrl6h


title: ChIP-seq 2rounds_Stat5b

description: Chromatin IP against Stat5b antibody

treatment_protocol: Treatment protocol as described in Liao et al., 2008

tag: Stat5b antibody


title: ChIP-seq 2rounds_Stat5a

description: Chromatin IP against Stat5a antibody

tag: Stat5a antibody


title: gingival fibroblasts from subject 69_Ctrl1h_Ctrl3h

source_name: gingival fibroblasts from subject 69_Ctrl3h


title: ChIP-seq 13hr_IgG

description: IgG control

tag: 13 hour


title: N-Tera2_infected_24hours_biologicalreplicate1_technical replicate2

description: 24h - Mock(cy3) vs Infected(cy5)


title: SW48 p53 WT HETEROZYGOUS Colorectal cancer cells_12 Gy gamma radiation

city: Cambridge

first: Raymond

middle: Anthony

last: Pagliarini

state: MA

address: 250 Massachusetts Ave. Room 3C-292

department: Oncology

institute: NIBRI

description: colorectal cancer cell lines that differ only with respect to their endogenous TP53 status

hyb_protocol: Samples from the same cell line with and without gamma irradiation were hybridized to the same slide.  Labeled cRNA samples were used for hybridization to Agilent 4x44K microarrays and scanned as directed by the manufacurer.

scan_protocol: Agilent microarray scanner,as according to manufacturer

data_processing: Data were extracted using Feature Extraction software v8.1 (Agilent Technologies) under default settings for normalization.  Microarrays with higher than 5 percent feature of local background region outliers were excluded.  Distributions of signal and background intensity of both red and green channels were examined with boxplot and maPlot using the Bioconductor package.  The ratios of each feature were calculated after background subtraction and normalization.  Features exhibiting signifcant changes of gene expression were selected based on PValueLogRatio calculated from the feature extraction software.

source_name: SW48 Colorectal cancer cell line, exposed to 12Gy gamma radiation and incubated 24 hours before sample collection

label_protocol: cDNA was used as a template for in vitro transcription using T7 RNA polymerase and Cy-3 and Cy-5 labeled CTP

growth_protocol: Cells grown to 70% confluence in T75 flasks

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

treatment_protocol: Exposure to 12 Gy gamma radiation

tag: Cell Line

value: SW48, p53 status:+/-, Treatment:12 Gy gamma radiation

source_name: SW48 Colorectal cancer cell line, nonirradiated and incubated for same time as irradiated samples

value: SW48, p53 status:+/-, Treatment:No radiation


title: N-Tera2_infected_24hours_biologicalreplicate1_technical replicate1

description: 24h - Mock(cy3) vs Infected(cy5)

tag: N-Tera2 differentiated human neuronal cells


title: SW48 p53 NULL Colorectal cancer cells_12 Gy gamma radiation

value: SW48, p53 status:-/-, Treatment:12 Gy gamma radiation

value: SW48, p53 status:-/-, Treatment:No radiation


title: gingival fibroblasts from subject 70_Ctrl6h_TNF6h

source_name: gingival fibroblasts from subject 70_TNF6h


title: SW48 p53 WT Colorectal cancer cells_12 Gy gamma radiation

value: SW48, p53 status:+/+, Treatment:12 Gy gamma radiation

value: SW48, p53 status:+/+, Treatment:No radiation


title: DLD-1 p53 WT Colorectal cancer cells_12 Gy gamma radiation

source_name: DLD-1 Colorectal cancer cell line, exposed to 12Gy gamma radiation and incubated 24 hours before sample collection

value: DLD-1, p53 status:+/SIL, Treatment:12 Gy gamma radiation

source_name: DLD-1 Colorectal cancer cell line, nonirradiated and incubated for same time as irradiated samples

value: DLD-1, p53 status:+/SIL, Treatment:No radiation


title: DLD-1 p53 MUT Colorectal cancer cells_12 Gy gamma radiation

value: DLD-1, p53 status:S24F/SIL, Treatment:12 Gy gamma radiation

value: DLD-1, p53 status:S24F/SIL, Treatment:No radiation


title: gingival fibroblasts from subject 67_Ctrl3h_Ctrl6h

source_name: gingival fibroblasts from subject 67_Ctrl6h


title: ChIP-seq 13hr_Stat5b

description: Chromatin IP against Stat5b antibody


title: RKO p53 NULL Colorectal cancer cells_12 Gy gamma radiation

source_name: RKO Colorectal cancer cell line, exposed to 12Gy gamma radiation and incubated 24 hours before sample collection

value: RKO, p53 status:-/-, Treatment:12 Gy gamma radiation

source_name: RKO Colorectal cancer cell line, nonirradiated and incubated for same time as irradiated samples

value: RKO, p53 status:-/-, Treatment:No radiation


title: RKO p53 WT Colorectal cancer cells_12 Gy gamma radiation

value: RKO, p53 status:+/+, Treatment:12 Gy gamma radiation

value: RKO, p53 status:+/+, Treatment:No radiation


title: gingival fibroblasts from subject 70_Ctrl1h_Ctrl3h

source_name: gingival fibroblasts from subject 70_Ctrl3h


title: RKO p53 WT HETEROZYGOUS Colorectal cancer cells_12 Gy gamma radiation

value: RKO, p53 status:+/-, Treatment:12 Gy gamma radiation

value: RKO, p53 status:+/-, Treatment:No radiation


title: gingival fibroblasts from subject 67_TNF6h_TNF3h

source_name: gingival fibroblasts from subject 67_TNF3h


title: gingival fibroblasts from subject 69_Ctrl3h_TNF3h

source_name: gingival fibroblasts from subject 69_TNF3h


title: gingival fibroblasts from subject 67_Ctrl6h_Ctrl1h


title: ChIP-seq 13hr_Stat5a

description: Chromatin IP against Stat5a antibody


title: ChIP-seq 8hr_IgG

description: IgG control

tag: 8 hour


title: ChIP-seq 8hr_Stat5b

description: Chromatin IP against Stat5b antibody


title: ChIP-seq 8hr_Stat5a

description: Chromatin IP against Stat5a antibody


title: gingival fibroblasts from subject 67_Ctrl1h_TNF1h

source_name: gingival fibroblasts from subject 67_TNF1h


title: HCT116 p53 MUT HETEROZYGOUS Colorectal cancer cells_12 Gy gamma radiation

source_name: HCT116 Colorectal cancer cell line, exposed to 12Gy gamma radiation and incubated 24 hours before sample collection

value: HCT116, p53 status:R248W/+, Treatment:12 Gy gamma radiation

source_name: HCT116 Colorectal cancer cell line, nonirradiated and incubated for same time as irradiated samples

value: HCT116, p53 status:R248W/+, Treatment:No radiation


title: HCT116 p53 MUT Colorectal cancer cells_12 Gy gamma radiation

value: HCT116, p53 status:R248W/-, Treatment:12 Gy gamma radiation

value: HCT116, p53 status:R248W/-, Treatment:No radiation


title: HCT116 p53 NULL Colorectal cancer cells_12 Gy gamma radiation

value: HCT116, p53 status:-/-, Treatment:12 Gy gamma radiation

value: HCT116, p53 status:-/-, Treatment:No radiation


title: gingival fibroblasts from subject 69_Ctrl1h_TNF1h

source_name: gingival fibroblasts from subject 69_TNF1h


title: gingival fibroblasts from subject 67_Ctrl3h_TNF3h


title: 091_Pf_UT_t27_repA_tech

description: Technical replicate

source_name: P. falciparum, untreated, 27 hpi

source_name: RNA reference pool


title: gingival fibroblasts from subject 70_TNF1h_TNF6h


title: HCT116 p53 WT colorectal cancer cells_12 Gy gamma radiation

value: HCT116, p53 status:+/+, Treatment:12 Gy gamma radiation

value: HCT116, p53 status:+/+, Treatment:No radiation


title: gingival fibroblasts from subject 67_TNF3h_Ctrl3h

source_name: gingival fibroblasts from subject 67_Ctrl3h


title: HCT116 p53 WT HETEROZYGOUS colorectal cancer cells_12 Gy gamma radiation

value: HCT116, p53 status:+/-, Treatment:12 Gy gamma radiation

value: HCT116, p53 status:+/-, Treatment:No radiation


title: wildtype_glucose depletion_rep2

status: Public on Dec 10 2008

city: Geneva

first: Martine

last: Collart

address: Rue Michel-Servet 1, Centre Médical Universitaire

department: Microbiology and Molecular Medicine

institute: University of Geneva

description: wildtype, glucose depletion, rep2

hyb_protocol: standard Affymetrix procedure

scan_protocol: standard Affymetrix procedure

data_processing: scan analyzed by Affymetrix MicroArraySuite, MicroDB and DataMiningTool

source_name: wild-type strain, 30 min after glucose depletion

label_protocol: standard Affymetrix procedure

growth_protocol: Cells were grown in glucose rich medium to exponential phase and collected, or in glucose rich medium to glucose depletion and collected 30 min after glucose depletion.

extract_protocol: acid phenol method

tag: MATa gcn4Δ ura3-52 trp1Δ1 leu2::PET56 gal2


title: not2_glucose depletion_rep2

description: not2, glucose depletion, rep2

source_name: not2 null strain, 30 min after glucose depletion

tag: MATa gcn4Δ ura3-52 trp1Δ1 leu2::PET56 gal2 not2::KanMX4


title: not4_glucose depletion_rep1

description: not4, glucose depletion, rep1

source_name: not4 null strain, 30 min after glucose depletion

tag: MATa gcn4Δ ura3-52 trp1Δ1 leu2::PET56 gal2 not4::KanMX4


title: not2_glucose depletion_rep1

description: not2, glucose depletion, rep1


title: wildtype_glucose depletion_rep1

description: wildtype, glucose depletion, rep1


title: not4_glucose depletion_rep2

description: not4, glucose depletion, rep2


title: caf130_glucose depletion_rep2

description: caf130, glucosedeplection, rep2

source_name: caf130 null strain, 30 min after glucose depletion

tag: MATa gcn4Δ ura3-52 trp1Δ1 leu2::PET56 gal2 caf130::TRP1


title: ccr4_glucose depletion_rep1

description: ccr4, glucose depletion, rep1

source_name: ccr4 null strain, 30 min after glucose depletion

tag: MATa gcn4Δ ura3-52 trp1Δ1 leu2::PET56 gal2 ccr4::TRP1


title: caf130_glucose depletion_rep1

description: caf130, glucosedeplection, rep1


title: caf1_glucose depletion

description: caf1, glucose depletion

source_name: caf1 null strain, 30 min after glucose depletion

tag: MATa gcn4Δ ura3-52 trp1Δ1 leu2::PET56 gal2 caf1::TRP1


title: wildtype_exponential phase_rep1

description: wildtype, exponential phase, rep1

source_name: wild-type strain, exponential phase


title: not4_exponential phase

description: not4, exponential phase

source_name: not4 null strain, exponential phase


title: wildtype_exponential phase_rep2

description: wildtype, exponential phase, rep2


title: not3_exponential phase_rep1

description: not3, exponential phase, rep1

source_name: not3 null strain, exponential phase

tag: MATa gcn4Δ ura3-52 trp1Δ1 leu2::PET56 gal2 not3::KanMX4


title: not5_exponential phase

description: not5, exponential phase

source_name: not5 null strain, exponential phase

tag: MATa gcn4Δ ura3-52 trp1Δ1 leu2::PET56 gal2 not5::LEU2


title: not2_exponential phase_rep1

description: not2, exponential phase, rep1

source_name: not2 null strain, exponential phase


title: not2_exponential phase_rep2

description: not2, exponential phase, rep2


title: 3_Affymetrix

city: Uppsala

first: Richard

last: Rosenquist Brandell

address: Rudbeck Laboratory

department: Genetics and Pathology

institute: Uppsala University

description: Array experiments were performed according to the standard protocols for Affymetrix GeneChip® Mapping 250K arrays (Gene Chip Mapping 500K Assay Manual (P/N 701930 Rev2.), Affymetrix Inc., Santa Clara, CA).

hyb_protocol: Hybridized probes were captured by streptavidin-phycoerythrin conjugates using Fluidics Station 450

scan_protocol: GeneChip® Scanner 3000 7G (Affymetrix Inc., Santa Clara, CA)

data_processing: QC, genotype calling and log2 ratios were produced in the Affymetrix GeneChip® Genotyping Analysis Software (GTYPE) 4.1. The Dynamic Model (DM) algorithm was used to perform single sample QC. The QC specification for 250K is a Call Rate > 93% using the algorithm defaults. Genotype calls were made using the BRLMM algorithm. Parameter settings(CNAT 4.0.1): Transition decay 5 Mb, Median normalization and 0Mb smoothing factor. The reference set used consisted of 96 CEU samples from the HapMap project (www.hapmap.org/downloads/raw_data/affy500k/).

label: Total genomic DNA was digested with a restriction enzyme (Nsp1), ligated to an appropriate adapter for the enzyme, and subjected to PCR amplification using a single primer

source_name: Blood

label_protocol: After digestion with DNase I, the PCR products were labeled with a biotinylated nucleotide analogue using terminal deoxynucleotidyl transferase and hybridized to the microarray

extract_protocol: Extraction of genomic DNA was performed using QIAamp DNA Mini kit (Qiagen) according to the manufacturer's instructions.

tag: Gender

value: Male, Tumor content:97%


title: 5_Affymetrix

value: Female, Tumor content:96%


title: ccr4_exponential phase_rep1

description: ccr4, exponential phase, rep1

source_name: ccr4 null strain, exponential phase


title: 1_Affymetrix

value: Male, Tumor content:79%


title: 6_Affymetrix

value: Female, Tumor content:69%


title: 2_Affymetrix

value: Male, Tumor content:93%


title: 10_Affymetrix

value: Female, Tumor content:86%


title: 9_Affymetrix

value: Male, Tumor content:90%


title: ccr4_exponential phase_rep2

description: ccr4, exponential phase, rep2


title: ccr4_glucose depletion_rep2

description: ccr4, glucose depletion, rep2


title: 4_Affymetrix

value: Male, Tumor Content:93%


title: caf130_exponential phase_rep2

description: caf130, exponential phase, rep2

source_name: caf130 null strain, exponential phase


title: 8_Affymetrix

value: Female, Tumor content:87%


title: 7_Affymetrix

value: Female, Tumor content:92%


title: caf1_exponential phase_rep1

description: caf1, exponential phase, rep1

source_name: caf1 null strain, exponential phase


title: caf130_exponential phase_rep1

description: caf130, exponential phase, rep1


title: caf1_exponential phase_rep2

description: caf1, exponential phase, rep2


title: StrainBALB_M_HF_Rep1

city: Bar Harbor

first: Keith

last: Shockley

state: ME

address: 600 Main Street

department: Computational and Systems Biology

institute: The Jackson Laboratory

description: One group of mice was fed an atherogenic high-fat (30% fat) diet containing cholic acid to increase fat uptake and another was fed a low-fat (6% fat) regular chow diet.  Males and females from both diets were studied for mouse strains 129S1/SvImJ, A/J, BALB/cJ, C3H/HeJ, C57BL/6J, CAST/EiJ, DBA/2J, I/LnJ, MRL/MpJ-Tnfrsf6lpr/J, NZB/BINJ, PERA/Ei, and SM/J. All strains were sacrificed between 11- and 13 weeks of age except for CAST and PERA, which were harvested after 50 weeks of age. CAST and PERA were subsequently removed from our analysis based on discrepant harvest age, but can be found in our database (see below). Three replicate animals were used for each combination of diet, strain, and sex, resulting in a total of 120 mice surveyed for gene expression.

hyb_protocol: Fifteen micrograms of biotin-labeled and fragmented cRNA was then hybridized onto MOE430v2.0 GeneChip® arrays for 16 hours at 45°C. Post-hybridization staining and washing were performed according to the manufacturer’s protocols using the Fluidics Station 450 instrument (Affymetrix, Santa Clara, CA).

scan_protocol: Arrays were scanned with a GeneChip® Scanner 3000 laser confocal slide scanner. Images were quantified using GeneChip Operating Software (GCOS) v1.2 (Affymetrix).

data_processing: RMA values are in the VALUE column here. Briefly, the RMA method was used to adjust the background of perfect match (PM) probes, apply a quantile normalization of the corrected PM values and calculate final expression measures using the Tukey median polish algorithm.

source_name: Strain BALB, Males, HF Diet

label_protocol: The cDNA was linearly amplified with biotinylated nucleotides (Enzo Diagnostics, Farmingdale, NY) through an in vitro transcription reaction with T7 RNA polymerase.

extract_protocol: Liver samples were extracted from each mouse as described previously (Shockley and Churchill, 2006). Total RNA was reverse transcribed with oligo(dT)-T7 primers. before double-stranded cDNA was generated with the Superscript double-stranded cDNA synthesis custom kit (Invitrogen).

tag: Strain

value: BALB

tag: Sex

value: Male

tag: Diet

value: 30% fat

tag: Biological Replicate


title: 9_BAC

description: Genomic DNA extracted from CLL patients was analyzed using tiling 32K BAC microarrays.

hyb_protocol: Samples were hybridized and washed as previously described (PMID:17334996).

scan_protocol: Arrays were scanned on a Agilent microarray scanner (Agilent Technologies).

data_processing: Image data was analyzed using Genepix Pro 4.0 (Axon Instruments). Result files were loaded into BASE (http://base.thep.lu.se) where they were filtered, lowess normalized and segmented using Circular Binary Segmentation (CBS, DNAcopy package).

label: Cy3 (sample)

label_protocol: Copy number profiling was performed using tiling 32K BAC as previously described (PMID:17334996). Samples were labelled with Cy3, and male reference DNA (Promega) with Cy5.

extract_protocol: Extraction of genomic DNA was performed using QIAamp DNA Mini kit (Qiagen) according to the manufacturer's instructions. An additional purification step was performed using Phase Lock Gel Heavy (Eppendorf).

label: Cy5 (reference)

source_name: male reference DNA (Promega)

extract_protocol: see Promega's website

tag: male reference DNA (Promega)


title: 293-tet-On-EWS/NOR1 with doxycycline

city: Tokyo

first: Naganari

last: Ohkura

address: 5-1-1, Tsukiji, Chuo-ku

department: Tumor Endocrinology Project

institute: National Cancer Center Research Institute

description: To identify genes affected by EWS/NOR1 overexpression, we compared expression profiles between EWS/NOR1-induced 293-tet-On cells and its control cells.

hyb_protocol: Labeled cRNA was hybridized with the array in the hybridization buffer for 16 hours.

scan_protocol: GCOS (GeneChip operating software)

data_processing: GCOS (GeneChip operating software)

source_name: 293-tet-On-EWS/NOR1 cells, doxycycline treated

label_protocol: in vitro transcription, Affymetrix protocol

growth_protocol: DMEM supplemented with 10% FCS

extract_protocol: Qiagen RNeasy mini column

treatment_protocol: with doxycycline

tag: 293-tet-On-EWS/NOR1 cells were cultured with doxycycline for 24 hours.


title: 2_Agilent

description: Genomic DNA extracted from CLL patients was analyzed using Agilent 185K 60-mer oligonucleotide CGH microarrays.

hyb_protocol: Samples were hybridized and washed according to manufacturer's protocol (Ver 4.0, June 2006).

data_processing: Image data was analyzed using Feature Extraction ver 9.1 (Agilent Technologies). Result files were loaded into BASE (http://base.thep.lu.se) where they were filtered, lowess normalized and segmented using Circular Binary Segmentation (CBS, DNAcopy package).

label: Cy3-dUTP (sample)

label_protocol: Copy number profiling was performed using Agilent 185K 60-mer oligonucleotide CGH microarrays. Samples were labelled with Cy3-dUTP, and male reference DNA (Promega) with Cy5-dUTP.

label: Cy5-dUTP (reference)

source_name: Promega male reference DNA


title: 5_Agilent

value: Female


title: 10_Agilent


title: 6_Agilent


title: 7_Agilent


title: 9_Agilent


title: 1_Agilent


title: 3_Agilent


title: 4_Agilent


title: 8_Agilent


title: 2_BAC


title: 6_BAC


title: 3_BAC


title: 1_BAC


title: 7_BAC


title: 4_BAC


title: 10_BAC


title: TPA_NODOX_MKL_REP2

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

description: MKL1/HEL cells under 24 hr TPA-stimulated differentiation without dox induced MKL1 overexpression

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: The data was output from Beadstudio 3.1 that was log2 transformed and quantile normalized.

label_protocol: standard Illumina protocol

extract_protocol: RNeasy Mini Kit (Qiagen)

tag: MKL1/HEL cells under-TPA stimulated differentiation without dox induced MKL1 overexpression


title: 8_BAC


title: 5_BAC


title: TPA_NODOX_MKL_REP1


title: TPA_DOX_MKL_REP2

description: MKL1/HEL cells under 24 hr TPA-stimulated differentiation with dox induced MKL1 overexpression

tag: MKL1/HEL cells under-TPA stimulated differentiation with dox induced MKL1 overexpression


title: TPA_DOX_MKL_REP1


title: 6_Illumina

description: Genomic DNA extracted from CLL patients was genotyped using Infinium HumanHap300 Duo-v2 Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Beadstudio 3.1 with GT module 3.1.12 (Illumina).

label: C-Bio and A-DNP

label_protocol: Genotyping was performed using Illumina Infinium HumanHap300 Genotyping BeadChips according to the manufacturerÕs protocol (Illumina Inc., San Diego, CA, www.illumina.com). 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).


title: Onne06 muscle_SV_replicate 5a

status: Public on Dec 09 2008

city: Nanaimo

first: Shaorong

state: British Columbia

address: 3190 Hammond Bay Road

department: Salmon and Freshwater Ecosystems Division

institute: Fisheries and Oceans Canada

description:
White muscle tissue from a single fish compared to a major reference pool of muscle from all collected samples (n=79).
Technical replicate 1 of 2.

hyb_protocol: The array hybridization was performed on Tecan-HS4800 Pro Hybridization Station (Tecan Trading AG, Switzerland). Two ul of poly dA was added to the targets, which were then denatured for 10min at 80oC, followed by the addition of 125 ul of pre-warmed SlideHybe3 buffer (Ambion, TX, USA) before loading into the hybridization chamber. Hybridizations were performed in batches of 12-24 samples and conducted over a two-week period to minimize technical variance. Slide processing steps within the Tecan HS were conducted as follows: two 30 s slide wash steps (0.1% SDS followed by water) at 23oC, 3 min slide denaturation at 85oC with agitation, 1 min wash (5x SSC, 0.01% SDS, 1% BSA) at 43oC with a 30 s soak time, 1 h prehybridization at 43oC with medium agitation, two 1 min washes (water followed by 8x SSC, 0.1% SDS, 4X Denhardt’s) at 43oC, sample injection at 43oC with agitation, hybridization for 16 h at 43oC with low frequency agitation, two 30 s wash steps, one at 43oC (2x SSC, 0.01% SDS) followed by one at 23oC (0.25x SSC), slide drying at 23oC for 2.5 min.

scan_protocol: All arrays were scanned using a Perkin Elmer ScanArray Express (Perkin Elmer, Boston, MA), adjusting the PMT gain for optimized visualization of each image.

data_processing: The images were quantified using Imagene (BioDiscovery, El Segundo, CA, www.biodiscovery.com) and processed to GeneSight (version 4.1, BioDiscovery, Inc. El Segundo, CA, www.biodiscovery.com).  Data was prepared in GeneSight according to the following steps: correct for background intensity using local background correction; omit multiple spots with flags (1,2,3,4,5,6,7); raise all values below a specified value to the minimum threshold (20.0); replace missing values by the experimental means for each gene; LOWESS normalization is done locally with smoothing parameter of 0.2 and linear degree of fitness; finally, calculate the log base 2 and the difference of the log2 of 2 channels. This pairMean log difference (VALUE) was used for all subsequent data analysis.

label: Alexa 555

organism: Oncorhynchus nerka

source_name: Muscle tissue from a wild fish non-destructively sampled at Savonna

label_protocol: Five ug of aRNA were reverse transcribed into cDNA and labelled with Alexa dyes using the Invitrogen Indirect Labelling Kit, with modifications from the manufacturer’s instructions. Briefly, the cDNA was purified using Zymo-25 clean-up columns (Zymo Research, Orange, CA) and eluted using the 2X coupling buffer, supplied by Invitrogen. During dye labelling, samples were processed individually by first adding DMSO, then cDNA to the Alexa dye tube and incubating for 1h at room temperature. Then labeled sample were cleaned up by adding 50 ul of DNA binding buffer (Zymo) to each Alexa tube and then combining the sample and references for each slide into Zymo-25 clean-up columns. The unbound portion of the labelled cDNA was removed by centrifugation at 13,000 rpm/min. The labelled cDNA was washed three times with DNA wash buffer (Zymo) and eluted in 9 ul of 1X TE buffer.

extract_protocol: Total RNA was purified from white muscle tissue using Magmax™-96 for Microarrays Kits (Ambion Inc, Austin, TX, USA) with a Biomek NXP (Beckman Coulter, Mississauga, ON, Canada) automated liquid-handling instrument. Approximately 10 mg of frozen tissue was homogenized with stainless steel beads in TRI-reagent (Ambion Inc, Austin, TX, USA) on a MM301 mixer mill (Retsch Inc., Newtown, PA, USA). One hundred microlitre aliquots of homogenate were pipetted into 96-well plates and extractions were carried out according to the manufacturer's instructions using the No-Spin Procedure for frozen tissues, on the Biomek FXP. In the final step, RNA was eluted with RNAase-, DNAase-free water and RNA yield was determined by measuring the A260 of the eluate. Purity was assessed by measuring the A260/A280 ratio of the eluate. 500 ng to 5 ug of total RNA was amplified using a MessageAmpTMII-96 kit (Ambion, TX, USA), performed manually according to manufacturer’s instructions. Amplification steps were performed on a single 96-well plate for all samples at once.

tag: Number of individuals

tag: Mean weight

tag: Tissue

value: white muscle

label: Alexa 647

source_name: Pooled reference sample from all individuals collected

extract_protocol: Muscle tissue from each individual was extracted and amplified separately as described for the channel 1 sample. Equal quantities of aRNA from each sample were mixed for the pooled sample.


title: 5_Illumina


title: 9_Illumina


title: 3_Illumina


title: 2_Illumina


title: Onne06 muscle_Wspt_replicate 1

description: White muscle tissue from a single fish compared to a major reference pool of muscle from all collected samples (n=79).

source_name: Muscle tissue from a wild fish non-destructively sampled at Whonnock September


title: Onne06 muscle_Waug_replicate 10

source_name: Muscle tissue from a wild fish non-destructively sampled at Whonnock August


title: Onne06 muscle_Wspt_replicate 5


title: Onne06 muscle_Waug_replicate 9


title: Onne06 muscle_Waug_replicate 8


title: Onne06 muscle_Waug_replicate 7


title: Onne06 muscle_Wspt_replicate 6


title: Onne06 muscle_Waug_replicate 6


title: Onne06 muscle_Wspt_replicate 3


title: Onne06 muscle_Wspt_replicate 4


title: Onne06 muscle_Wspt_replicate 2


title: Onne06 muscle_Waug_replicate 4


title: 4_Illumina


title: Onne06 muscle_Waug_replicate 2


title: Onne06 muscle_Waug_replicate 5


title: Onne06 muscle_Waug_replicate 1


title: 10_Illumina


title: Onne06 muscle_Waug_replicate 3


title: 8_Illumina


title: Onne06 muscle_SV_replicate 2


title: Onne06 muscle_SOG_replicate 5

source_name: Muscle tissue from a wild fish non-destructively sampled at Strait of Georgia


title: Onne06 muscle_SV_replicate 4


title: Onne06 muscle_SOG_replicate 7


title: Onne06 muscle_SV_replicate 1


title: Onne06 muscle_SV_replicate 5b

description:
White muscle tissue from a single fish compared to a major reference pool of muscle from all collected samples (n=79).
Technical replicate 2 of 2.


title: Onne06 muscle_SV_replicate 3


title: Onne06 muscle_SV_replicate 6


title: Onne06 muscle_QCI_replicate 7

source_name: Muscle tissue from a wild fish non-destructively sampled at Queen Charlotte Islands


title: Onne06 muscle_SOG_replicate 4


title: Onne06 muscle_SOG_replicate 2


title: Onne06 muscle_SOG_replicate 1


title: Onne06 muscle_QCI_replicate 8


title: Onne06 muscle_SOG_replicate 3


title: Onne06 muscle_SOG_replicate 6


title: 7_Illumina


title: Onne06 muscle_QCI_replicate 4


title: Onne06 muscle_QCI_replicate 3


title: Onne06 muscle_LA_replicate 8

source_name: Muscle tissue from a wild fish non-destructively sampled at Lower Adams


title: Onne06 muscle_QCI_replicate 6


title: Onne06 muscle_QCI_replicate 1


title: Onne06 muscle_QCI_replicate 5


title: Onne06 muscle_LA_replicate 6


title: Onne06 muscle_QCI_replicate 2


title: Onne06 muscle_JS_replicate 18

source_name: Muscle tissue from a wild fish non-destructively sampled at Johnson Straight


title: Onne06 muscle_JS_replicate 15


title: Onne06 muscle_JS_replicate 17


title: Onne06 muscle_JS_replicate 14


title: Onne06 muscle_LA_replicate 3


title: Onne06 muscle_LA_replicate 2


title: Onne06 muscle_LA_replicate 5


title: Onne06 muscle_LA_replicate 1


title: Onne06 muscle_JS_replicate 13


title: Onne06 muscle_LA_replicate 4


title: Onne06 muscle_JS_replicate 11


title: Onne06 muscle_JS_replicate 7


title: Onne06 muscle_JS_replicate 5


title: Onne06 muscle_JS_replicate 6


title: 1_Illumina


title: Onne06 muscle_JS_replicate 3


title: Onne06 muscle_JS_replicate 16


title: Onne06 muscle_JDFS_replicate 13

source_name: Muscle tissue from a wild fish non-destructively sampled at Juan De Fuca


title: Onne06 muscle_JS_replicate 8


title: Onne06 muscle_LA_replicate 7


title: Onne06 muscle_JS_replicate 4


title: Onne06 muscle_JDFS_replicate 11


title: Onne06 muscle_JDFS_replicate 10


title: Onne06 muscle_JS_replicate 10


title: Onne06 muscle_JS_replicate 9


title: Onne06 muscle_JS_replicate 1


title: Onne06 muscle_JDFS_replicate 14