title: B-CLL sample 710, poor prognosis


title: A549 cell line – exposure 3 Cobalt 2mM – 24h - replicate3

status: Public on Sep 22 2006

type: RNA

city: bagnols sur ceze

first: Bérenguer

last: Frédéric

department: SBTN

country: France

institute: CEA/DSV

description: Control sample from A549 cells was labelled in Cy5 and hybridized against Cobalt sample labelled in Cy3

data_processing: Ratios (test/control) were normalized towards the mean ratio of the microarray then converted to base-2 logarithms

molecule: total RNA

organism: Homo sapiens

source_name: A549 cell line – 2mM Cobalt – 24h

tag: Cobalt sample from A549 cells

source_name: A549 cell line – 0mM Cobalt – 24h

tag: Control sample from A549 cells


title: B-CLL sample 623, good prognosis

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

description: Aim: to compare the transcriptosomes of good prognosis CLL cases (ZAP-70-CD38-) to poor prognosis cases (ZAP-70+CD38+). Methods: Immunomagnetic isolation was done using MidiMacs resulting in >95% purity of leukemic cells as detected by FACS analysis of CD19+CD5+ cells. The leukemic cells were freshly purified from untreated patients and RNA was directly isolated from fresh cells without further ex vivo treatment of the cells.Eight immunomagnetically purified peripheral blood derived  ZAP-70+CD38+ CLL cases were compared with eight ZAP-70-CD38- B-CLL cases.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on HG-U133A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

label: biotin

source_name: immunomagnetically purified fresh CD19+ peripheral blood CLL cells

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

growth_protocol: no in vitro culture

extract_protocol: Isolation of total RNA was performed with QIAGEN Rneasy columns according to the manufacturer's instructions.

treatment_protocol: no treatment

tag: immunomagnetically purified native B-CLL cells from the peripheral blood of untreated patients


title: B-CLL sample 813, good prognosis


title: B-CLL sample 653, good prognosis


title: B-CLL sample 658, good prognosis


title: A549 cell line – exposure 3 Cobalt 2mM – 24h - replicate2

description: Control sample from A549 cells was labelled in Cy3 and hybridized against Cobalt sample labelled in Cy5


title: B-CLL sample 708, good prognosis


title: A549 cell line – exposure 3 Cobalt 2mM – 24h


title: A549 cell line – exposure 2 Cobalt 2mM – 24h - replicate4


title: A549 cell line – exposure 2 Cobalt 2mM – 24h - replicate2


title: A549 cell line – exposure 2 Cobalt 2mM – 24h - replicate1


title: B-CLL sample 621, good prognosis


title: A549 cell line – exposure 2 Cobalt 2mM – 24h - replicate5


title: A549 cell line – exposure 2 Cobalt 2mM – 24h


title: A549 cell line – exposure 2 Cobalt 2mM – 24h - replicate3


title: A549 cell line – exposure 1 Cobalt 2mM – 24h - replicate1


title: A549 cell line – exposure 1 Cobalt 2mM – 24h - replicate3


title: A549 cell line – exposure 2 Cobalt 2mM – 4h - replicate1

source_name: A549 cell line – 2mM Cobalt – 4h

source_name: A549 cell line – 0mM Cobalt – 4h


title: A549 cell line – exposure 1 Cobalt 2mM – 24h - replicate2


title: A549 cell line – exposure 2 Cobalt 2mM – 2h - replicate3

source_name: A549 cell line – 2mM Cobalt – 2h

source_name: A549 cell line – 0mM Cobalt – 2h


title: A549 cell line – exposure 1 Cobalt 2mM – 4h - replicate1


title: A549 cell line – exposure 1 Cobalt 2mM – 4h


title: A549 cell line – exposure 2 Cobalt 2mM – 4h


title: Ral for 48h B

status: Public on Sep 25 2006

city: Urbana

first: Jonna

last: Frasor

state: IL

department: Molecular and Integrative Physiology

country: USA

institute: University of Illinois

description: 1uM Raloxifene-treated 48h sample, set B


title: A549 cell line – exposure 2 Cobalt 2mM – 2h - replicate2


title: Brain_nAChRbeta4SubunitDeficent_MiceNob4437

city: Tel Aviv

first: Avi

last: Orr-Urtreger

address: 6 Weizmann St

department: Genetic Institute

country: Israel

institute: Tel Aviv Sourasky Medical Center

description: whole brain from nicotinic acetylcholine receptor beta4 subunit null mutant mouse

hyb_protocol: According to Affymetrix GeneChip expression analysis technical manual

scan_protocol: scanned with an Affymetrix Gene-Array Scanner according to Affymetrix GeneChip expression analysis technical manual

data_processing: MAS5.0, scaled to 150

label: biotin-labeled nucleotides

organism: Mus musculus

source_name: whole brain, nicotinic acetylcholine receptor subunit mutant mice and littermate controls

label_protocol: Enzo BioArray High Yield Transcript labeling kit

extract_protocol: Total RNA was isolated from whole brains using TRI REAGENT (Sigma-Aldrich, St. Louis, MO) according to the manufacturer's instructions, and further purified on a Qiagen RNeasy mini kit (Qiagen Sciences, Germantown, MD)

treatment_protocol: untreated nAChR beta4 subunit deficient mice

tag: Strain

tag: Gender

value: female

tag: Age

value: 8 weeks

tag: Tissue

value: whole brain


title: Brain_nAChRbeta4SubunitDeficent_MiceNob4424


title: Brain_nAChRbeta4SubunitDeficent_MiceNob4398

value: 7 weeks


title: A549 cell line – exposure 1 Cobalt 2mM – 24h


title: A549 cell line – exposure 2 Cobalt 2mM – 2h - replicate1


title: A549 cell line – exposure 2 Cobalt 2mM – 2h


title: SUP fraction used for normalization of Mam1

type: genomic

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

country: Japan

institute: The University of Tokyo

description: SUP used for normalization of Mam1 (GSM108203).

data_processing: The protocol provided by Affymetrix (GCOS ver1.4) was used.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Sup fraction (equal to Whole cell extract DNA)

tag: Prepared from SK1.


title: A549 cell line – exposure 1 Cobalt 2mM – 2h - replicate1


title: Brain_nAChRbeta4SubunitDeficent_MiceNob4363

description: whole brain from nicotinic acetylcholine receptor beta 4 subunit null mutant mouse

value: male

value: 9 weeks


title: A549 cell line – exposure 1 Cobalt 2mM – 2h


title: Brain_nAChRbeta4SubunitDeficent_MiceNob4365


title: Brain_Wild-type_MiceNoLT345

description: whole brain from wild-type littermate of nicotinic acetylcholine receptor subunit mutant mice

extract_protocol: Total RNA was isolated from whole brains using TRI REAGENT (Sigma-Aldrich, St. Louis, MO) according to the manufacturer?s instructions, and further purified on a Qiagen RNeasy mini kit (Qiagen Sciences, Germantown, MD)

treatment_protocol: untreated wild-type mice

value: 6 weeks


title: Brain_Wild-type_MiceNoLT346


title: A549 cell line – exposure 2 Cobalt 2mM – 30 mn - replicate3

source_name: A549 cell line – 2mM Cobalt – 30mn

source_name: A549 cell line – 0mM Cobalt – 30mn


title: 4C_Rad23a-fetal_liver-B

city: Rotterdam

first: Wouter

last: de Laat

address: Dr. Molewaterplein 50

department: Cell Biology

country: Netherlands

institute: Erasmus MC

description: Unprocessed (not normalized) hybridization ratios were used for analysis. These ratios showed clusters of 20-50 positive 4C-signals along the chromosome template. To define the clusters, a running mean or running median was applied, using a window size of 29 probes (on average 60 kb). Obtained values were compared to the running mean/median performed across randomized data. This was done for each array separately. Consequently, all measurements were appreciated relative to the amplitude and noise of that specific array. The False Discovery Rate (FDR), defined as (no. false positives) / (no. of false positives + no. of true positives), was determined as follows: (number of positives in the randomised set) / (number of positives in the data). The threshold level was determined using a top down approach to establish the minimal value for which: FDR<0.05.

data_processing: The signal ratio 4C-sample/genomic DNA was calculated for each probe.

source_name: genomic DNA  digested with HindIII and DpnII

tag: genomic DNA FVB

source_name: 4C sample obtained from E14.5 liver, digested with HindIII and DpnII

tag: 4C sample containing DNA amplified by inverse PCR using primers specific for a HindIII restriction fragment encompassing Rad23a.


title: WS vs Columbia - 13365768

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

institute: INRA

description: Which genes are expressed in Arabidopsis Pollen.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: Col

label_protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: pollen - Media : soil,hygrometry : 60%,Temperature : 20 C,Light : 8 hours light/ 16 hours night

tag: ecotype:columbia - dev.stage (Boyes et al. Plant Cell 2001)

source_name: WS

tag: ecotype:wassilewskija - dev.stage (Boyes et al. Plant Cell 2001)


title: A549 cell line – exposure 2 Cobalt 2mM – 30 mn - replicate2


title: E14.5_fetal_liver_2

description: affymetrix one-cycle cDNA synthesis protocol was used

data_processing: data of 3 E14.5 fetal liver and 3 E14.5 fetal brain experiments were normalized using RMA (bioconductor)

tag: tissue

value: E14.5 fetal liver, strain:FVB


title: Columbia vs WS - 13368677


title: A549 cell line – exposure 2 Cobalt 2mM – 30 mn - replicate1


title: Microarray Design (slide 70): leaf vs. bud

city: Athens

first: Alan

middle: R

last: Gingle

state: GA

address: 111 Riverbend Rd.

department: Center for Applied Genetics Technologies

institute: University of Georgia

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs/2006-07/57914.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter RatioFormulations = W1/W2 (685 nm/595); Parameter StdDev = Type 1; Parameter BackgroundSubtraction = LocalFeature; Parameter PixelSize = 10; Parameter NormalizationFactors = 1 1; Parameter ImageOrigin = 0, 0; Parameter FeatureType = Circular; Parameter LinesAveraged = 1; Parameter JpegOrigin = 1960, 820; Parameter DateTime = 2006/06/07 08:07:48; Parameter ScanRegion = 0,0,2251,5797; Parameter NormalizationMethod = None; Parameter Wavelengths = 685 nm 595; Parameter Image Origin = 0, 0; Parameter Type = GenePix Results 3; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Joshua,,Udall Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Scan Time = 08:07:48; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 2006/06/07; Parameter Pixel Size = 10; Parameter Scanner Model = arrayWoRx; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Analysis Software; Performer: Joshua,,Udall Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scan Time = 08:07:48; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 2006/06/07; Parameter Pixel Size = 10; Parameter Scanner Model = arrayWoRx; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Analysis Software; Performer: Joshua,,Udall

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: Gossypium hirsutum

source_name: leaf with Cy5

label_protocol:
Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug (buds); Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 5/31/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug; Performer: Joshua,,Udall
Protocol Type = Labeling; Parameter Tube label = 1; Parameter Date performed = 6/5/2006; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 24 ug; Parameter Type of label = Cy3; Parameter Name = Ran; Performer: Joshua,,Udall

extract_protocol: Parameter Date performed = May-06; Parameter Extraction method reference = Wilkins and Smart, 1996; Parameter Channel 1 reference name = Buds; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = A bulk of buds from 4-5 plants; Parameter Extracted molecule = RNA; Parameter Name = Josh and Lex; Performer: Joshua,,Udall

treatment_protocol: Parameter Genome = AD; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse / Bessey Hall / Ames, IA; Performer: Joshua,,Udall

tag: leaf with Cy5

tag: Parameter Accession number or name = Maxxa; Parameter Species = Gossypium hirsutum; Parameter Genome = AD1; Parameter Polyploid level = 4x; Parameter Tissue type = buds; Parameter Transgenes = none; Performer

value: Joshua,,Udall

source_name: bud with Cy3

label_protocol:
Protocol Type = Amplification; Parameter Approx RNA yield = 24 ug (Leaves); Parameter Date performed = 5/31/2006; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug; Performer: Joshua,,Udall
Protocol Type = Labeling; Parameter Date performed = 6/5/2006; Parameter Tube label = 2; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 16 ug; Parameter Type of label = Cy5; Parameter Name = Ran; Performer: Joshua,,Udall

extract_protocol: Parameter Date performed = May-06; Parameter Extraction method reference = Wilkins and Smart, 1996; Parameter Channel 2 reference name = Leaves; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = A bulk of leaves from 4-5 plants; Parameter Name = Josh and Lex; Parameter Extracted molecule = RNA; Performer: Joshua,,Udall

tag: bud with Cy3

tag: Parameter Accession number or name = Maxxa; Parameter Species = Gossypium hirsutum; Parameter Genome = AD1; Parameter Tissue type = buds; Parameter Polyploid level = 4x; Parameter Transgenes = none; Performer


title: Brain_Wild-type_MiceNoLT340


title: E14.5_fetal_liver_1


title: Microarray Design (slide 69): leaf vs. bud'

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs/2006-07/57913.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter RatioFormulations = W1/W2 (685 nm/595); Parameter StdDev = Type 1; Parameter BackgroundSubtraction = LocalFeature; Parameter PixelSize = 10; Parameter NormalizationFactors = 1 1; Parameter ImageOrigin = 0, 0; Parameter FeatureType = Circular; Parameter LinesAveraged = 1; Parameter JpegOrigin = 1890, 880; Parameter DateTime = 2006/06/05 13:06:52; Parameter ScanRegion = 0,0,2251,5797; Parameter NormalizationMethod = None; Parameter Wavelengths = 685 nm 595; Parameter Image Origin = 0, 0; Parameter Type = GenePix Results 3; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Joshua,,Udall Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Scan Time = 13:06:52; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 2006/06/05; Parameter Pixel Size = 10; Parameter Scanner Model = arrayWoRx; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Analysis Software; Performer: Joshua,,Udall Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scan Time = 13:06:52; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 2006/06/05; Parameter Pixel Size = 10; Parameter Scanner Model = arrayWoRx; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Analysis Software; Performer: Joshua,,Udall

source_name: bud' with Cy5

label_protocol:
Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug (buds); Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 5/31/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug; Performer: Joshua,,Udall
Protocol Type = Labeling; Parameter Tube label = 1; Parameter Date performed = 6/5/2006; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 24 ug; Parameter Type of label = Cy5; Parameter Name = Ran; Performer: Joshua,,Udall

tag: bud' with Cy5

source_name: leaf with Cy3

label_protocol:
Protocol Type = Amplification; Parameter Approx RNA yield = 24 ug (Leaves); Parameter Date performed = 5/31/2006; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug; Performer: Joshua,,Udall
Protocol Type = Labeling; Parameter Date performed = 6/5/2006; Parameter Tube label = 2; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 16 ug; Parameter Type of label = Cy3; Parameter Name = Ran; Performer: Joshua,,Udall

tag: leaf with Cy3


title: E14.5_fetal_liver_3


title: Microarray Design (slide 71): leaf vs. bud'

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs/2006-07/57915.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter RatioFormulations = W1/W2 (685 nm/595); Parameter StdDev = Type 1; Parameter BackgroundSubtraction = LocalFeature; Parameter PixelSize = 10; Parameter NormalizationFactors = 1 1; Parameter ImageOrigin = 0, 0; Parameter FeatureType = Circular; Parameter LinesAveraged = 1; Parameter JpegOrigin = 2010, 840; Parameter DateTime = 2006/06/07 08:31:38; Parameter ScanRegion = 0,0,2251,5797; Parameter NormalizationMethod = None; Parameter Wavelengths = 685 nm 595; Parameter Image Origin = 0, 0; Parameter Type = GenePix Results 3; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Joshua,,Udall Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Scan Time = 08:31:38; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 2006/06/07; Parameter Pixel Size = 10; Parameter Scanner Model = arrayWoRx; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Analysis Software; Performer: Joshua,,Udall Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scan Time = 08:31:38; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 2006/06/07; Parameter Pixel Size = 10; Parameter Scanner Model = arrayWoRx; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Analysis Software; Performer: Joshua,,Udall


title: A549 cell line – exposure 2 Cobalt 2mM – 30 mn

tag: Control sample from A549 cells

tag: Cobalt sample from A549 cells


title: Brain_Wild-type_MiceNoB4395

tag: Strain

tag: Gender


title: 4C_HS2-fetal_brain-A

source_name: 4C sample obtained from E14.5 brain, digested with HindIII and DpnII

tag: 4C sample containing DNA amplified by inverse PCR using primers specific for a HindIII restriction fragment encompassing hypersensitive site 2 of the murine beta-globin locus control region.

tag: genomic DNA C57BL/6


title: 4C_Rad23a-fetal_liver-A

tag: genomic DNA FVB


title: Brain_Wild-type_MiceNoB4394

tag: Age

tag: Tissue


title: E14.5_fetal_brain_2

value: E14.5, fetal brain

tag: strain

value: FVB


title: A549 cell line – exposure 1 Cobalt 2mM – 30 mn - replicate1


title: 4C_Rad23a-fetal_brain-A

tag: 4C sample containing DNA amplified by inverse PCR using primers specific for a HindIII restriction fragment encompassing Rad23a.


title: 4C_HS2-fetal_brain-B

description: Unprocessed hybridization ratios showed clusters of 20-50 positive 4C-signals along the chromosome template. To define the clusters, a running mean or running median was applied, using a window size of 29 probes (on average 60 kb). Obtained values were compared to the running mean/median performed across randomized data. This was done for each array separately. Consequently, all measurements were appreciated relative to the amplitude and noise of that specific array. The False Discovery Rate (FDR), defined as (no. false positives) / (no. of false positives + no. of true positives), was determined as follows: (number of positives in the randomised set) / (number of positives in the data). The threshold level was determined using a top down approach to establish the minimal value for which: FDR<0.05.


title: E14.5_fetal_brain_3

tag: tissue

value: E14.5 fetal brain, strain:FVB


title: Brain_Wild-type_MiceNob4367

extract_protocol: Total RNA was isolated from whole brains using TRI REAGENT (Sigma-Aldrich, St. Louis, MO) according to the manufacturer’s instructions, and further purified on a Qiagen RNeasy mini kit (Qiagen Sciences, Germantown, MD)


title: A549 cell line – exposure 1 Cobalt 2mM – 30 mn


title: E14.5_fetal_brain_1


title: Microarray Design (slide 74): bud vs. bud'

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs/2006-07/57918.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter RatioFormulations = W1/W2 (685 nm/595); Parameter StdDev = Type 1; Parameter BackgroundSubtraction = LocalFeature; Parameter PixelSize = 10; Parameter NormalizationFactors = 1 1; Parameter ImageOrigin = 0, 0; Parameter FeatureType = Circular; Parameter LinesAveraged = 1; Parameter JpegOrigin = 2040, 910; Parameter DateTime = 2006/06/12 12:57:37; Parameter ScanRegion = 0,0,2251,5797; Parameter NormalizationMethod = None; Parameter Wavelengths = 685 nm 595; Parameter Image Origin = 0, 0; Parameter Type = GenePix Results 3; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Joshua,,Udall Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Scan Time = 12:57:37; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 2006/06/12; Parameter Pixel Size = 10; Parameter Scanner Model = arrayWoRx; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Analysis Software; Performer: Joshua,,Udall Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scan Time = 12:57:37; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 2006/06/12; Parameter Pixel Size = 10; Parameter Scanner Model = arrayWoRx; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Analysis Software; Performer: Joshua,,Udall

source_name: bud with Cy5

tag: bud with Cy5

tag: Parameter Accession number or name = Maxxa; Parameter Species = Gossypium hirsutum; Parameter Genome = AD1; Parameter Polyploid level = 4x; Parameter Tissue type = buds; Parameter Transgenes = none; Performer

source_name: bud' with Cy3

label_protocol:
Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug (buds); Parameter Date performed = 5/31/2006; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug; Performer: Joshua,,Udall
Protocol Type = Labeling; Parameter Date performed = 6/5/2006; Parameter Tube label = 2; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 24 ug; Parameter Type of label = Cy3; Parameter Name = Ran; Performer: Joshua,,Udall

extract_protocol: Parameter Date performed = May-06; Parameter Extraction method reference = Wilkins and Smart, 1996; Parameter Channel 2 reference name = Buds; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = A bulk of buds from 4-5 plants; Parameter Name = Josh and Lex; Parameter Extracted molecule = RNA; Performer: Joshua,,Udall

tag: bud' with Cy3


title: dotA moi10 8hpi rep3

status: Public on Sep 21 2006

city: Boston

first: Ralph

last: Isberg

state: MA

address: 150 Harrison Ave.

department: Molecular Biology and Microbiology

institute: Tufts University School of Medicine

description: see Losick VP and Isberg RR. NF-kB Translocation Prevents Host Cell Death After Low Dose Challenge by Legionella pneumophila. Journal Experimental Medicine. (In Press)

hyb_protocol: Reference-Cy3- and Cy5-labeled cDNAs were hybridized in 1x Amersham hybridization buffer and 10% formamide in a Corning hybridization chamber for 48 hours at 42^0C. Glass slides were washed with increasing stringency in 1 x SSC, 0.2% SDS, followed by 0.1 x SSC, 0.2% SDS, and 0.1 x SSC buffers. The glass microarrays were spun dry and scanned immediately.

scan_protocol: Packard ScanArray 4000

data_processing: log scale of normalized intensities (lowest intensity dependent on normalization)

source_name: cy3 reference

label_protocol: Total RNA was reverse transcribed with superscript II RT (Invitrogen, # 18064) to incorporate the modified nucleotide 5-(3-aminoallyl)-dUTP (Ambion, # 8439) into cDNA. The resulting reactions were purified on Cyscribe GFX columns (Amersham) and coupled with either Cy3 or Cy5 NHS-ester dye (Amersham) in 50mM NaHC03 (pH=9.0). Reference, cDNA isolated from uninfected, unsorted U937 cells were always labeled with Cy3. Cy-dye labeled cDNA was purified on Cyscribe GFX column and incorporation of cy-dye was quantitated spectrophotometrically to normalize each sample set.

growth_protocol: U937 cells were grown in RPMI 1640 (Irvine) supplemented with 10% heat-inactivated fetal bovine serum (Hyclone) and 1 mM glutamine (Invitrogen). 5 x 10^7 U937 cells were differentiated using 10 ng/ml 12-tetradecanoyl phorbol 13-acetate (TPA) for 48 hr in T175 tissue culture flask, after which cells were washed, replated with fresh media in the absence of TPA.

extract_protocol: Total RNA was isolated from U937 cells using Qiagen RNAeasy kit, following manufacturer's instructions.

tag: U937, TPA differentiated

source_name: 8 hr dotA moi10 infection in U937 cells

label_protocol: Total RNA was reverse transcribed with superscript II RT (Invitrogen, # 18064) to incorporate the modified nucleotide 5-(3-aminoallyl)-dUTP (Ambion, # 8439) into cDNA. The resulting reactions were purified on Cyscribe GFX columns (Amersham) and coupled with either Cy3 or Cy5 NHS-ester dye (Amersham) in 50mM NaHC03 (pH=9.0). Sorted, cDNA isolated from uninfected U937 cells were always labeled with Cy5. Cy-dye labeled cDNA was purified on Cyscribe GFX column and incorporation of cy-dye was quantitated spectrophotometrically to normalize each sample set.

treatment_protocol: U937 cells were infected with dotA mutant L. pneumophila at MOI=10. Bacteria were then pelleted onto the monolayers by 5 min. centrifugation at 1,000 rpm in a table top centrifuge, to synchronize infections, incubated at 37oC, 5% C02 for 1 hour, and then washed three times before adding fresh medium. 8 hours post centrifugation, L. pneumophila-infected U937 cells were lifted by washing the monolayer once with PBS + 0.1 mM EDTA and then treating with 0.05 % Trypsin- EDTA solution (Gibco) for 1 minute. Complete RPMI/10%FBS medium was added back immediately and cells were collected by centrifugation at 1,000 RPM.

tag: infected with dotA L. pneumophila at MOI =10


title: 4C_beta-major-fetal_brain-2

source_name: genomic DNA  digested with HindIII and NlaIII

source_name: 4C sample obtained from E14.5 brain, digested with HindIII and NlaIII

tag: 4C sample containing DNA amplified by inverse PCR using primers specific for a HindIII restriction fragment encompassing the beta-major gene (Hbb-b1).


title: dimB 8hpi rep2

source_name: sorted 8 hr dimB infection in U937 cells

treatment_protocol: U937 cells were infected with dimB mutant L. pneumophila at MOI=1. Bacteria were then pelleted onto the monolayers by 5 min. centrifugation at 1,000 rpm in a table top centrifuge, to synchronize infections, incubated at 37oC, 5% C02 for 1 hour, and then washed three times before adding fresh medium. 8 hours post centrifugation, L. pneumophila-infected U937 cells were lifted by washing the monolayer once with PBS + 0.1 mM EDTA and then treating with 0.05 % Trypsin- EDTA solution (Gibco) for 1 minute. Complete RPMI/10%FBS medium was added back immediately and cells were collected by centrifugation at 1,000 RPM. U937 cells were then resuspended in less than 1 ml of media to concentrate the suspension. Cells were sorted at Tufts Laser Cytometry facility (http://www.tufts.edu/med/research/TLC.html) using a MoFlo (DakoCytomation) fluorescence activated cell sorter (FACS), and appropriate gates were collected for further analysis.

tag: infected with dimB L. pneumophila at MOI =1

tag: sorted


title: Microarray Design (slide 75): leaf vs. bud

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs/2006-07/57919.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter RatioFormulations = W1/W2 (685 nm/595); Parameter StdDev = Type 1; Parameter BackgroundSubtraction = LocalFeature; Parameter PixelSize = 10; Parameter NormalizationFactors = 1 1; Parameter ImageOrigin = 0, 0; Parameter FeatureType = Circular; Parameter LinesAveraged = 1; Parameter JpegOrigin = 2030, 970; Parameter DateTime = 2006/06/12 13:20:24; Parameter ScanRegion = 0,0,2251,5797; Parameter NormalizationMethod = None; Parameter Wavelengths = 685 nm 595; Parameter Image Origin = 0, 0; Parameter Type = GenePix Results 3; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Joshua,,Udall Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Scan Time = 13:20:24; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 2006/06/12; Parameter Pixel Size = 10; Parameter Scanner Model = arrayWoRx; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Analysis Software; Performer: Joshua,,Udall Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scan Time = 13:20:24; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 2006/06/12; Parameter Pixel Size = 10; Parameter Scanner Model = arrayWoRx; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Analysis Software; Performer: Joshua,,Udall

tag: leaf with Cy5

tag: bud with Cy3

tag: Parameter Accession number or name = Maxxa; Parameter Species = Gossypium hirsutum; Parameter Genome = AD1; Parameter Tissue type = buds; Parameter Polyploid level = 4x; Parameter Transgenes = none; Performer


title: Microarray Design (slide 67): bud vs. bud'

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs/2006-07/57911.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter RatioFormulations = W1/W2 (685 nm/595); Parameter StdDev = Type 1; Parameter BackgroundSubtraction = LocalFeature; Parameter PixelSize = 10; Parameter NormalizationFactors = 1 1; Parameter ImageOrigin = 0, 0; Parameter FeatureType = Circular; Parameter LinesAveraged = 1; Parameter JpegOrigin = 2450, 740; Parameter DateTime = 2006/06/05 12:07:36; Parameter ScanRegion = 0,0,2251,5797; Parameter NormalizationMethod = None; Parameter Wavelengths = 685 nm 595; Parameter Image Origin = 0, 0; Parameter Type = GenePix Results 3; Parameter Datafile type = Gal file; Software: type: feature extraction; Performer: Joshua,,Udall Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 6/7/2006; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite; Performer: Joshua,,Udall Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 6/7/2006; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite; Performer: Joshua,,Udall


title: Microarray Design (slide 68): leaf vs. bud

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs/2006-07/57912.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter RatioFormulations = W1/W2 (685 nm/595); Parameter StdDev = Type 1; Parameter BackgroundSubtraction = LocalFeature; Parameter PixelSize = 10; Parameter NormalizationFactors = 1 1; Parameter ImageOrigin = 0, 0; Parameter FeatureType = Circular; Parameter LinesAveraged = 1; Parameter JpegOrigin = 1850, 920; Parameter DateTime = 2006/06/05 12:32:26; Parameter ScanRegion = 0,0,2251,5797; Parameter NormalizationMethod = None; Parameter Wavelengths = 685 nm 595; Parameter Image Origin = 0, 0; Parameter Type = GenePix Results 3; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Joshua,,Udall Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Scan Time = 12:32:26; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 2006/06/05; Parameter Pixel Size = 10; Parameter Scanner Model = arrayWoRx; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Analysis Software; Performer: Joshua,,Udall Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scan Time = 12:32:26; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 2006/06/05; Parameter Pixel Size = 10; Parameter Scanner Model = arrayWoRx; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Analysis Software; Performer: Joshua,,Udall


title: 4C_Rad23a-fetal_brain-B

tag: genomic DNA FVB


title: dotA moi10 1hpi rep3

source_name: 1 hr dotA moi10 infection in U937 cells

treatment_protocol: U937 cells were infected with dotA mutant L. pneumophila at MOI=10. Bacteria were then pelleted onto the monolayers by 5 min. centrifugation at 1,000 rpm in a table top centrifuge, to synchronize infections, incubated at 37oC, 5% C02 for 1 hour, and then washed three times before adding fresh medium. 1 hour post centrifugation, L. pneumophila-infected U937 cells were lifted by washing the monolayer once with PBS + 0.1 mM EDTA and then treating with 0.05 % Trypsin- EDTA solution (Gibco) for 1 minute. Complete RPMI/10%FBS medium was added back immediately and cells were collected by centrifugation at 1,000 RPM.


title: dotA moi10 8hpi rep2

treatment_protocol: U937 cells were lifted by washing the monolayer once with PBS + 0.1 mM EDTA and then treating with 0.05 % Trypsin- EDTA solution (Gibco) for 1 minute. Complete RPMI/10%FBS medium was added back immediately and cells were collected by centrifugation at 1,000 RPM.


title: dotA moi10 1hpi rep2


title: dotA moi10 1hpi rep1


title: dotA moi10 8hpi rep1


title: 4C_beta-major-fetal_brain-1

tag: genomic DNA C57BL/6


title: dotA 8hpi rep3

source_name: sorted 8 hr dotA infection in U937 cells

treatment_protocol: U937 cells were infected with dotA mutant L. pneumophila at MOI=1. Bacteria were then pelleted onto the monolayers by 5 min. centrifugation at 1,000 rpm in a table top centrifuge, to synchronize infections, incubated at 37oC, 5% C02 for 1 hour, and then washed three times before adding fresh medium. 8 hours post centrifugation, L. pneumophila-infected U937 cells were lifted by washing the monolayer once with PBS + 0.1 mM EDTA and then treating with 0.05 % Trypsin- EDTA solution (Gibco) for 1 minute. Complete RPMI/10%FBS medium was added back immediately and cells were collected by centrifugation at 1,000 RPM. U937 cells were then resuspended in less than 1 ml of media to concentrate the suspension. Cells were sorted at Tufts Laser Cytometry facility (http://www.tufts.edu/med/research/TLC.html) using a MoFlo (DakoCytomation) fluorescence activated cell sorter (FACS), and appropriate gates were collected for further analysis.

tag: infected with dotA L. pneumophila at MOI =1


title: 4C_beta-major-fetal_liver-1

source_name: 4C sample obtained from E14.5 liver, digested with HindIII and NlaIII


title: dotA 8hpi rep2


title: dimB 8hpi rep3


title: dotA 1hpi rep2

source_name: sorted 1 hr dotA infection in U937 cells

treatment_protocol: U937 cells were infected with dotA mutant L. pneumophila at MOI=1. Bacteria were then pelleted onto the monolayers by 5 min. centrifugation at 1,000 rpm in a table top centrifuge, to synchronize infections, incubated at 37oC, 5% C02 for 1 hour, and then washed three times before adding fresh medium. 1 hours post centrifugation, L. pneumophila-infected U937 cells were lifted by washing the monolayer once with PBS + 0.1 mM EDTA and then treating with 0.05 % Trypsin- EDTA solution (Gibco) for 1 minute. Complete RPMI/10%FBS medium was added back immediately and cells were collected by centrifugation at 1,000 RPM. U937 cells were then resuspended in less than 1 ml of media to concentrate the suspension. Cells were sorted at Tufts Laser Cytometry facility (http://www.tufts.edu/med/research/TLC.html) using a MoFlo (DakoCytomation) fluorescence activated cell sorter (FACS), and appropriate gates were collected for further analysis.


title: dotA 8hpi rep1


title: 4C_HS2-fetal_liver-A

source_name: 4C sample obtained from E14.5 liver, digested with HindIII and DpnII

tag: 4C sample containing DNA amplified by inverse PCR using primers specific for a HindIII restriction fragment encompassing hypersensitive site 2 of the murine beta-globin locus control region.

source_name: genomic DNA  digested with HindIII and DpnII


title: 4C_HS2-fetal_liver-B


title: 4C_beta-major-fetal_liver-2


title: dotA 1hpi rep3


title: dotA 1hpi rep1


title: dimB 1hpi rep3

source_name: sorted 1 hr dimB infection in U937 cells

treatment_protocol: U937 cells were infected with dimB mutant L. pneumophila at MOI=1. Bacteria were then pelleted onto the monolayers by 5 min. centrifugation at 1,000 rpm in a table top centrifuge, to synchronize infections, incubated at 37oC, 5% C02 for 1 hour, and then washed three times before adding fresh medium. 1 hours post centrifugation, L. pneumophila-infected U937 cells were lifted by washing the monolayer once with PBS + 0.1 mM EDTA and then treating with 0.05 % Trypsin- EDTA solution (Gibco) for 1 minute. Complete RPMI/10%FBS medium was added back immediately and cells were collected by centrifugation at 1,000 RPM. U937 cells were then resuspended in less than 1 ml of media to concentrate the suspension. Cells were sorted at Tufts Laser Cytometry facility (http://www.tufts.edu/med/research/TLC.html) using a MoFlo (DakoCytomation) fluorescence activated cell sorter (FACS), and appropriate gates were collected for further analysis.


title: dimB 1hpi rep1

treatment_protocol: U937 cells were infected with dimB mutant L. pneumophila at MOI=1. Bacteria were then pelleted onto the monolayers by 5 min. centrifugation at 1,000 rpm in a table top centrifuge, to synchronize infections, incubated at 37oC, 5% C02 for 1 hour, and then washed three times before adding fresh medium. 1 hour post centrifugation, L. pneumophila-infected U937 cells were lifted by washing the monolayer once with PBS + 0.1 mM EDTA and then treating with 0.05 % Trypsin- EDTA solution (Gibco) for 1 minute. Complete RPMI/10%FBS medium was added back immediately and cells were collected by centrifugation at 1,000 RPM. U937 cells were then resuspended in less than 1 ml of media to concentrate the suspension. Cells were sorted at Tufts Laser Cytometry facility (http://www.tufts.edu/med/research/TLC.html) using a MoFlo (DakoCytomation) fluorescence activated cell sorter (FACS), and appropriate gates were collected for further analysis.


title: WT 8hpi rep2

source_name: sorted 8 hr WT infection in U937 cells

treatment_protocol: U937 cells were infected with WT (Lp02) L. pneumophila at MOI=1. Bacteria were then pelleted onto the monolayers by 5 min. centrifugation at 1,000 rpm in a table top centrifuge, to synchronize infections, incubated at 37oC, 5% C02 for 1 hour, and then washed three times before adding fresh medium. 8 hours post centrifugation, L. pneumophila-infected U937 cells were lifted by washing the monolayer once with PBS + 0.1 mM EDTA and then treating with 0.05 % Trypsin- EDTA solution (Gibco) for 1 minute. Complete RPMI/10%FBS medium was added back immediately and cells were collected by centrifugation at 1,000 RPM. U937 cells were then resuspended in less than 1 ml of media to concentrate the suspension. Cells were sorted at Tufts Laser Cytometry facility (http://www.tufts.edu/med/research/TLC.html) using a MoFlo (DakoCytomation) fluorescence activated cell sorter (FACS), and appropriate gates were collected for further analysis.

tag: infected with WT L. pneumophila at MOI =1


title: WT 1hpi rep3

source_name: sorted 1 hr WT infection in U937 cells

treatment_protocol: U937 cells were infected with WT (Lp02) L. pneumophila at MOI=1. Bacteria were then pelleted onto the monolayers by 5 min. centrifugation at 1,000 rpm in a table top centrifuge, to synchronize infections, incubated at 37oC, 5% C02 for 1 hour, and then washed three times before adding fresh medium. 1 hour post centrifugation, L. pneumophila-infected U937 cells were lifted by washing the monolayer once with PBS + 0.1 mM EDTA and then treating with 0.05 % Trypsin- EDTA solution (Gibco) for 1 minute. Complete RPMI/10%FBS medium was added back immediately and cells were collected by centrifugation at 1,000 RPM. U937 cells were then resuspended in less than 1 ml of media to concentrate the suspension. Cells were sorted at Tufts Laser Cytometry facility (http://www.tufts.edu/med/research/TLC.html) using a MoFlo (DakoCytomation) fluorescence activated cell sorter (FACS), and appropriate gates were collected for further analysis.


title: WT 8hpi rep3


title: dimB 8hpi rep1


title: dimB 1hpi rep2


title: Microarray Design (slide 72): bud vs. bud'

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs/2006-07/57916.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter RatioFormulations = W1/W2 (685 nm/595); Parameter StdDev = Type 1; Parameter BackgroundSubtraction = LocalFeature; Parameter PixelSize = 10; Parameter NormalizationFactors = 1 1; Parameter ImageOrigin = 0, 0; Parameter FeatureType = Circular; Parameter LinesAveraged = 1; Parameter JpegOrigin = 2090, 890; Parameter DateTime = 2006/06/07 08:54:12; Parameter ScanRegion = 0,0,2251,5797; Parameter NormalizationMethod = None; Parameter Wavelengths = 685 nm 595; Parameter Image Origin = 0, 0; Parameter Type = GenePix Results 3; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Joshua,,Udall Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Scan Time = 08:54:12; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 2006/06/07; Parameter Pixel Size = 10; Parameter Scanner Model = arrayWoRx; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Analysis Software; Performer: Joshua,,Udall Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scan Time = 08:54:12; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 2006/06/07; Parameter Pixel Size = 10; Parameter Scanner Model = arrayWoRx; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Analysis Software; Performer: Joshua,,Udall


title: WT 8hpi rep1


title: mock rep2

source_name: cy3 mock rep2

source_name: cy5 mock rep2

treatment_protocol: U937 cells were lifted by washing the monolayer once with PBS + 0.1 mM EDTA and then treating with 0.05 % Trypsin- EDTA solution (Gibco) for 1 minute. Complete RPMI/10%FBS medium was added back immediately and cells were collected by centrifugation at 1,000 RPM. U937 cells were then resuspended in less than 1 ml of media to concentrate the suspension. Cells were sorted at Tufts Laser Cytometry facility (http://www.tufts.edu/med/research/TLC.html) using a MoFlo (DakoCytomation) fluorescence activated cell sorter (FACS), and appropriate gates were collected for further analysis.


title: mock rep1

source_name: cy3 mock rep1

source_name: cy5 mock rep1


title: WT 1hpi rep1

source_name: cy3 reference

treatment_protocol: U937 cells were infected with WT (Lp02) L. pneumophila at MOI=1. Bacteria were then pelleted onto the monolayers by 5 min. centrifugation at 1,000 rpm in a table top centrifuge, to synchronize infections, incubated at 37oC, 5% C02 for 1 hour, and then washed three times before adding fresh medium. 1 hours post centrifugation, L. pneumophila-infected U937 cells were lifted by washing the monolayer once with PBS + 0.1 mM EDTA and then treating with 0.05 % Trypsin- EDTA solution (Gibco) for 1 minute. Complete RPMI/10%FBS medium was added back immediately and cells were collected by centrifugation at 1,000 RPM. U937 cells were then resuspended in less than 1 ml of media to concentrate the suspension. Cells were sorted at Tufts Laser Cytometry facility (http://www.tufts.edu/med/research/TLC.html) using a MoFlo (DakoCytomation) fluorescence activated cell sorter (FACS), and appropriate gates were collected for further analysis.


title: WT 1hpi rep2


title: mock rep3

source_name: cy3 mock rep3

source_name: cy5 mock rep3


title: GOF_stage14_replicate3

status: Public on Sep 20 2006

city: Mainz

first: Angela

last: Becker

address: Becherweg 32

department: Institute of Genetics

institute: University of Mainz

description:
Cy5/Cy3 labeled RNA was co-hybridized onto a QMT Amino (Quantifoil) glass slide. For wt control we pooled mRNA from UAS-gcm stock B5446 and Gal4-line MZ1060 in equal amounts.
Sample collection:
Embryo samples from the MZ1060 x B5446, B5446 and MZ1060 were collected in parallel as one-hour egg lays at 25°C, which were allowed to develop to the desired stage at 29°C.
First total RNA was isolated from all samples using the Rneasy Kit and then mRNA was isolated using the Oligotex Kit (both Qiagen,Hilden,Germany)
Microarray hybridization:
At least four independent experiments were performed for each of the 8 different stages
(embryonic stage 9 to 16) in competitive hybridizations against the pooled wildtype control of the same stage.
At least one dye swap was included in each of the repetitions.
We used the indirect labeling method, with 4,5µg random hexamer primer and 0,75µg Poly-dT primer ( both Invitrogen, Karlsruhe, Germany) added to 1µg mRNA.
For hybridization, the labeled cDNAs were taken up in SlideHyb buffer #1 (Ambion, Woodward, USA), denatured at 95°C for 5min,
and applied to the array. Hybridization was performed in appropriate chambers (TeleChem) in a waterbath at 55°C over night.
The hybridized glass slides were scanned on a ScanArray 5000 (Perkin Elmer, Wellesley, USA) using the ScanArray software (Version 3.1).
The resulting images (TIFF format, 16-bit grayscale) for each channel - Cy5 (632nm) and Cy3 (532nm) - were analyzed
further with the GenePix software (Version 5.0; Axon Instruments, Union City, USA).
As each microarray contains two replicates for each gene, we used the standard deviation (SD)
of their dye-ratio (Cy5/Cy3) to filter for reproducible hybridizations. Only if at least 30% of all genes on the array
had a SD of log(632/532) of less than 1/3 between the replicates was the microarray included for further analysis.

data_processing: Genepix 5.0/MChips software

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: stage14 embryo ectopic expression

tag: ectopic expression of glial cells missing with the Gal4-driver MZ1060

source_name: stage14 embryo wt

tag: pooled wildtypcontrol from Bloomington stock B5446 and Gal4-driver MZ1060


title: GOF_stage14_replicate2

description: Cy5/Cy3 labeled RNA was co-hybridized onto a QMT Amino (Quantifoil) glass slide. For wt control we pooled mRNA from UAS-gcm stock B5446 and Gal4-line MZ1060 in equal amounts.


title: GOF_stage11_replicate2

source_name: stage11 embryo ectopic expression

source_name: stage11 embryo wt


title: Microarray Design (slide 73): leaf vs. bud'

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs/2006-07/57917.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter RatioFormulations = W1/W2 (685 nm/595); Parameter StdDev = Type 1; Parameter BackgroundSubtraction = LocalFeature; Parameter PixelSize = 10; Parameter NormalizationFactors = 1 1; Parameter ImageOrigin = 0, 0; Parameter FeatureType = Circular; Parameter LinesAveraged = 1; Parameter JpegOrigin = 2140, 900; Parameter DateTime = 2006/06/12 12:32:20; Parameter ScanRegion = 0,0,2251,5797; Parameter NormalizationMethod = None; Parameter Wavelengths = 685 nm 595; Parameter Image Origin = 0, 0; Parameter Type = GenePix Results 3; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Joshua,,Udall Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Scan Time = 12:32:20; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 2006/06/12; Parameter Pixel Size = 10; Parameter Scanner Model = arrayWoRx; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Analysis Software; Performer: Joshua,,Udall Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scan Time = 12:32:20; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 2006/06/12; Parameter Pixel Size = 10; Parameter Scanner Model = arrayWoRx; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Analysis Software; Performer: Joshua,,Udall

source_name: bud' with Cy5

tag: bud' with Cy5

tag: Parameter Accession number or name = Maxxa; Parameter Species = Gossypium hirsutum; Parameter Genome = AD1; Parameter Polyploid level = 4x; Parameter Tissue type = buds; Parameter Transgenes = none; Performer

source_name: leaf with Cy3

tag: leaf with Cy3


title: GOF_stage13_replicate3

data_processing: Genepix5.0/MChips software

source_name: stage13 embryo wt

source_name: stage13 embryo ectopic expression


title: GOF_stage16_replicate2

source_name: stage16 embryo ectopic expression

source_name: stage16 embryo wt


title: GOF_stage14_replicate4


title: GOF_stage9_replicate4

source_name: stage9 embryo wt

source_name: stage9 embryo ectopic expression


title: GOF_stage16_replicate4


title: GOF_stage11_replicate4


title: GOF_stage15_replicate4

source_name: stage15 embryo wt

source_name: stage15 embryo ectopic expression


title: GOF_stage13_replicate4


title: GOF_stage10_replicate4

source_name: stage10 embryo wt

source_name: stage10 embryo ectopic expression


title: GOF_stage10_replicate3


title: GOF_stage12_replicate4

source_name: stage12 embryo wt

source_name: stage12 embryo ectopic expression


title: GOF_stage14_replicate5

source_name: stage14 embryo wt

source_name: stage14 embryo ectopic expression


title: GOF_stage9_replicate2


title: GOF_stage13_replicate2


title: GOF_stage15_replicate1


title: GOF_stage12_replicate3


title: GOF_stage16_replicate1

source_name: Stage16 embryo ectopic expression

source_name: Stage 16 embryo wt


title: GOF_stage15_replicate3


title: GOF_stage11_replicate1

source_name: Stage11 embryo ectopic expression

source_name: Stage11 embryo wt


title: GOF_Stage12_replicate2


title: GOF_stage9_replicate3


title: GOF_stage11_replicate3

source_name: stage11 embryo ectopic expression


title: GOF_stage12_replicate1

source_name: Stage12 embryo ectopic expression

source_name: Stage 12 embryo wt


title: GOF_Stage16_replicate3

source_name: stage16 embryo wt

source_name: stage16 embryo ectopic expression


title: GOF_stage14_replicate1

source_name: Stage14 embryo ectopic expression

source_name: Stage 14 embryo wt


title: GOF_stage9_replicate1

data_processing: GenePix 5.0/MChips software

source_name: Stage 9 embryo GOF

label_protocol: indirect labeling method with aa-dNTPs

extract_protocol: Qiagen RNeasy and Oligotex Kit

tag: ectopic expression of glial cells missing with the Gal4 driver MZ1060

source_name: Stage 9 embryo wt

tag: pooled wildtype control of heterozygous Bloomington stock B5446 and heterozygous Gal4 driver MZ1060


title: GOF_stage10_replicate2

source_name: stage10 embryp ectopic expression

source_name: stage10 embryo wt

tag: pooled wildtype control from Bloomington stock B5446 and Gal4-driver MZ1060


title: LOF_stage12_replicate4

description: gcmN7-4 mutant flies were balanced with either Kr-GFP (for stages 10 to 13) or Ubi-GFP (for stages 14 to 16) balancer chromosomes. Eggs were collected as described above, transferred into PBS buffer supplemented with 0.3% Tween 20 and homozygous mutant embryos were automatically sorted with the CopasTM Select embryo sorter by their lack of GFP-expression. For wt control we used OregonR wildtype embryos that were treated the same way like the mutant embryos.Cy5/Cy3 labeled RNA was co-hybridized onto a QMT Amino (Quantifoil) glass slide

source_name: stage12 embryo wt

tag: Oregon R wildtype embryos

source_name: stage12 embryo mutant

tag: gcm mutant embryos automated sorted


title: GOF_stage10_replicate1

source_name: Stage10 embryo ectopic expression

source_name: Stage10 embryo wt

tag: stage 10 pooled wildtype control from Bloomington stock B5446 and Gal4-driver MZ1060


title: GOF_stage13_replicate1

data_processing: Genepix 5.0/Mchips software

source_name: Stage 13 embryo GOF

source_name: Stage 13 embryo wt


title: LOF_stage11_replicate4

source_name: stage11 embryo wt

source_name: stage11 embryo mutant


title: LOF_stage10_replicate3

description: gcmN7-4 mutant flies were balanced with either Kr-GFP (for stages 10 to 13) or Ubi-GFP (for stages 14 to 16) balancer chromosomes. Eggs were collected as described above, transferred into PBS buffer supplemented with 0.3% Tween 20 and homozygous mutant embryos were automatically sorted with the CopasTM Select embryo sorter by their lack of GFP-expression. For wt control we used OregonR wildtype embryos that were treated the same way like the mutant embryos.Cy5/Cy3 labeled RNA was co-hybridized onto a QMT Amino (Quantifoil) glass slide.

source_name: stage10 embryo mutant


title: LOF_stage14_replicate4

source_name: stage14 embryo wt

source_name: stage14 embryos mutant


title: LOF_stage16_replicate4

source_name: stage16 embryo wt

source_name: stage16 embryo mutant


title: HUVEC_TSA_rep3

city: Toronto

first: Philip

middle: A.

last: Marsden

state: Ontario

address: 1 King's College Circle

department: Department of Medicine

country: Canada

institute: University of Toronto

description:
Data in the VALUE column were computed using the MAS5.0 algorithm.
Data in the VALUE_RMA column were computed using the RMA algorithm.
Data in the VALUE_GCRMA column were computed using the GCRMA algorithm.

hyb_protocol: Affymetrix Technical Documentation

scan_protocol: GeneArray(R) 2500 scanner, Affymetrix Technical Documentation

data_processing: See 'Description' above. Data were processed using MAS5.0, RMA and GCRMA.

label: Biotin

source_name: Human Umbilical Vein Endothelial Cell, TSA (500nM, 24h, Sigma)

label_protocol: Affymetrix Technical Documentation

growth_protocol:
Isolation and culture as previously described.
Marsden PA et al.  Molecular cloning and characterization of human endothelial nitric oxide synthase.  FEBS Lett 1992, 307(3):287-293.

extract_protocol:
Total cellular RNA was isolated by guanidinium-isothiocyanate extraction followed by cesium chloride density gradient centrifugation.
Chirgwin JM et al.  Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease.  Biochemistry 1979, 18(24):5294-5299.
Glisin V et al.  Ribonucleic acid isolation by cesium chloride centrifugation.  Biochemistry 1974, 13(12):2633-2637.

treatment_protocol: Confluent monolayer of HUVEC was treated with trichostatin A (TSA, 500 nM, Sigma) for 24 hours

tag: Human Umbilical Vein Endothelial Cell, Single Donor, Passage_3


title: Rice suspension cells under suc starvation for 48 hours, replicate 3

city: Taipei

first: Huei-Jing

last: Wang

state: Taipei

address: Academia Road, 128, Sec.2, Nankang

department: Inst of plant and microbial biology

country: Taiwan

institute: Academia sinica

description: Rice suspension cells under suc starvation for 48 hours, replecate 3

scan_protocol: The hybridization signals for each DNA element were detected with the use of Axon GenePix 4000B and analyzed with use of GenePix 4.0 (Axon Instruments, Inc., Union City, CA, USA).

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were mean centered and linear transformed to obtain the log and linear values given in the data table.

organism: Oryza sativa

source_name: Oryza sativa suspension cells under suc starvation for 48 hours

label_protocol: Total RNA extraction and mRNA purified from Suc-starved cells and the labeling of fluorescent cDNA probes were performed by the methods described in http://www.botany.sinica.edu.tw/microarray/protocols.htm

growth_protocol: Oryza sativa suspension cells cultured in  Murashige and Skoog medium without sucrose for 48 hours.

extract_protocol: Total RNA was extracted by use of the TripureTM Kit according to the manufacturer's manual (Genesis Biotech, Taipei, Taiwan).  mRNA from control and Suc-starved cells were purified from the respective 200 ug total RNA by use of Oligotex mRNA Mini Kit (Qiagen, Valencia, CA, USA).

tag: Oryza sativa cv Tainung67 suspension cells culture in suc free medium for 48 hours

source_name: Oryza sativa suspension cells control treatment for 48 hours

label_protocol: Total RNA extraction and mRNA purified from control cells and the labeling of fluorescent cDNA probes were performed by the methods described in http://www.botany.sinica.edu.tw/microarray/protocols.htm

growth_protocol: Oryza sativa suspension cells cultured in  Murashige and Skoog medium within 3% sucrose for 48 hours.

tag: As a control RNA, Oryza sativa cv Tainung67 suspension cells culture in medium within 3% sucrose for 48 hours.


title: HUVEC_TSA_rep2


title: LOF_stage13_replicate4

source_name: stage13 embryo wt

source_name: stage13 embryo mutant


title: LOF_stage13_replicate2


title: LOF_stage16_replicate2


title: Rice suspension cells under suc starvation for 48 hours, replicate 2

description: Rice suspension cells under suc starvation for 48 hours, replecate 2


title: LOF_stage10_replicate5

source_name: stage10 embryo wt


title: LOF_stage16_replicate3


title: Rice suspension cells under suc starvation for 48 hours, replicate 1

description: Rice suspension cells under suc starvation for 48 hours, replecate 1


title: LOF_stage14_replicate3

source_name: stage14 embryo mutant


title: LOF_stage16_replicate1


title: LOF_stage11_replicate3


title: LOF_stage10_replicate4

source_name: stage10 embryos mutant


title: HUVEC_TSA_rep1


title: Rice suspension cells under suc starvation for 24 hours, replicate 3

description: Rice suspension cells under suc starvation for 24 hours, replecate 3

source_name: Oryza sativa suspension cells under suc starvation for 24 hours

growth_protocol: Oryza sativa suspension cells cultured in  Murashige and Skoog medium without sucrose for 24 hours.

tag: Oryza sativa cv Tainung67 suspension cells culture in suc free medium for 24 hours

source_name: Oryza sativa suspension cells control treatment for 24 hours

growth_protocol: Oryza sativa suspension cells cultured in  Murashige and Skoog medium within 3% sucrose for 24 hours.

tag: As a control RNA, Oryza sativa cv Tainung67 suspension cells culture in medium within 3% sucrose for 24 hours.


title: Rice suspension cells under suc starvation for 24 hours, replicate 2

description: Rice suspension cells under suc starvation for 24 hours, replecate 2


title: LOF_stage14_replicate2


title: LOF_stage13_replicate3


title: HUVEC_control_rep3

source_name: Human Umbilical Vein Endothelial Cell, Control, 0 hours

treatment_protocol: Confluent monolayer of HUVEC was treated with a vehicle-control for 24 hours


title: LOF_stage12_replicate2

source_name: stage12 embryo mutant

source_name: stage12 embryo wt


title: LOF_stage11_replicate1

source_name: stage11 embryo mutant

source_name: stage11 embryo wt


title: LOF_stage11_replicate2


title: HUVEC_control_rep2

tag: Human Umbilical Vein Endothelial Cell, Single Donor, Passage _3


title: LOF_stage12_replicate1


title: Rice suspension cells under suc starvation for 12 hours compared with sorbitol control, replicate 3

description: Rice suspension cells under suc starvation sorbitol control for 12 hours, replecate 3

source_name: Oryza sativa suspension cells under suc starvation for 12 hours

growth_protocol: Oryza sativa suspension cells cultured in  Murashige and Skoog medium without sucrose for 12 hours.

tag: Oryza sativa cv Tainung67 suspension cells culture in suc free medium for 12 hours

source_name: Oryza sativa suspension cells sorbitol treatment for 12 hours

label_protocol: Total RNA extraction and mRNA purified from Suc-starved cells treated with sorbitol and the labeling of fluorescent cDNA probes were performed by the methods described in http://www.botany.sinica.edu.tw/microarray/protocols.htm

growth_protocol: Oryza sativa suspension cells cultured in  Murashige and Skoog medium without sucrose but with 88mM sorbitol for 12 hours.

tag: As a control RNA, Oryza sativa cv Tainung67 suspension cells culture in suc free medium within sorbitol for 12 hours.


title: Rice suspension cells under suc starvation for 12 hours compared with sorbitol control, replicate 1

description: Rice suspension cells under suc starvation sorbitol control for 12 hours, replecate 1


title: sva53_ovary_1

city: Okazaki

first: Shuji

last: Shigenobu

state: Aichi

address: Nishigonaka 38, Myodaiji

institute: National Institute for Basic Biology

description: sva53 ovaries #1

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/6-screw Hyb Chamber). See manufacturer's manual (#G4140-90010).

scan_protocol: Scanned using Agilent microarray scanner (G2565BA).

data_processing: Data were extracted with Agilent Feature Extraction 7.1 Software.

source_name: Ovaries from sva53 mutant flies, pool 1.

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Protocol. 100ng total RNA was used.

extract_protocol: RNeasy Mini kit (QIAGEN).

treatment_protocol: Germline clones homozygous for sva53[M1] were generated by the FLP/FRT/DFS system. The pole cells formed in sva53 embryos were transplanted into host embryos derived from osk-homozygous females. The transplanted embryos were allowed to develop into adults. Two pairs of ovaries were isolated by dissection. The ovaries were directly collected into Buffer RLT, a lysis buffer included in the RNeasy Mini kit (QIAGEN).

tag: Tissue

value: ovary

tag: Sex

tag: Strain

value: sva53 mutant

tag: Age

value: about 7 days

source_name: Ovaries from sva53/+ flies.

treatment_protocol: The pole cells formed in sva53/+ embryos were transplanted into host embryos derived from osk-homozygous females. The transplanted embryos were allowed to develop into adults. Three pairs of ovaries were isolated by dissection. The ovaries were directly collected into Buffer RLT, a lysis buffer included in the RNeasy Mini kit (QIAGEN).


title: LOF_stage10_replicate2

source_name: stage10 embryo mutant


title: sva53_ovary_3

description: sva53 ovaries #3

source_name: Ovaries from sva53 mutant flies, pool 3.


title: sva53_ovary_2

description: sva53 ovaries #2

source_name: Ovaries from sva53 mutant flies, pool 2.


title: HUVEC_control_rep1

treatment_protocol: Confluent monolayer of HUVEC was treated with a vehicle-control for 24 hours.


title: Rice suspension cells under suc starvation for 12 hours, replicate 2

description: Rice suspension cells under suc starvation for 12 hours, replecate 2

tag: Oryza sativa cv Tainung67 suspension cells culture in suc free medium for 12 hours.

source_name: Oryza sativa suspension cells control treatment for 12 hours

growth_protocol: Oryza sativa suspension cells cultured in  Murashige and Skoog medium within 3% sucrose for 12 hours.

tag: As a control RNA, Oryza sativa cv Tainung67 suspension cells culture in medium within 3% sucrose for 12 hours.


title: Rice suspension cells under suc starvation for 12 hours, replicate 3

description: Rice suspension cells under suc starvation for 12 hours, replecate 3


title: Rice suspension cells under suc starvation for 12 hours, replicate 1

description: Rice suspension cells under suc starvation for 12 hours, replecate 1


title: Rice suspension cells under suc starvation for 12 hours compared with sorbitol control, replicate 2

description: Rice suspension cells under suc starvation sorbitol control for 12 hours, replecate 2


title: LOF_stage13_replicate1

source_name: stage13 embryo mutant

source_name: stage13 embryo wt

tag: Oregon R wildtype embryos


title: Rice suspension cells under suc starvation for 24 hours, replicate 1

description: Rice suspension cells under suc starvation for 24 hours, replecate 1

source_name: Oryza sativa suspension cells under suc starvation for 24 hours


title: 02-07-05_Deng_Mouse430_2_I442

status: Public on Sep 19 2006

city: Bethesda

first: Cuiying

last: Xiao

state: MD

address: 10 Center Dr.

department: NIDDK

institute: NIH

description: A. Genotypes of mice: 796 (Brca1 +/co/MMTV-Cre) & 801 (Brca1 co/co/MMTV-Cre); I442 (Brca1 D11/D11;p53+/-) & I443 (Brca1 D+/+;p53+/-);1548 (Brca1 D11/D11;p53+/-) & T744 (Brca1 D+/+;p53+/-):  B. Pregnant day 16.5 for 796 & 801; Lactation day 1 for 1548 & T744; Virgin for I442 &I443.

data_processing: Affymetrix Microarray Suite version 5.0

extract_protocol: RNA STAT-60 (TEL-TEST, Inc) to extract total RNA

value: mixed background of 129/FVB/Black Swiss;Gender:female;Age:796 & 801 (5 mon); I442 & I443 (6 mon); 1548 & T744 (2 mon); Tissue:Mammary glands


title: 05-24-04_Deng_Mouse430_2_T744


title: LOF_stage12_replicate3

tag: gcm mutant embryos automated sorted


title: 05-24-04_Deng_Mouse430_2_1548


title: 02-07-05_Deng_Mouse430_2_I443


title: 02-07-05_Deng_Mouse430_2_801


title: 02-07-05_Deng_Mouse430_2_796


title: Livers of mice fed an atherogenic with a high-fat diet for 24 weeks

city: Kanazawa

first: Naoto

last: Matsuzawa-Nagata

state: Ishikawa

address: 13-1 Takara-machi

department: Medicinal Infomation

institute: Kanazawa University Graduate School of Medical Science

description: RNA amplified before cDNA synthesis

data_processing: Lowess normalization (GeneSpring software)

source_name: Livers of mice fed a standard chow for 24 weeks

tag: Gender

value: Male.

tag: Livers of mice fed an atherogenic with a high-fat (Ath+HF) diet for 24 weeks. The Ath+HF contains (by weight) 60% fat, 1.25% cholesterol, and 0.5% sodium cholate.


title: LOF_stage14_replicate1

source_name: stage14 embryo mutant

source_name: stage14 embryo wt


title: GOF_stage15_replicate2

description: Cy5/Cy3 labeled RNA was co-hybridized onto a QMT Amino (Quantifoil) glass slide. For wt control we pooled mRNA from UAS-gcm stock B5446 and Gal4-line MZ1060 in equal amounts.

source_name: stage15 embryo ectopic expression

tag: ectopic expression of glial cells missing with the Gal4-driver MZ1060

source_name: stage15 embryo wt

tag: pooled wildtypcontrol from Bloomington stock B5446 and Gal4-driver MZ1060


title: LOF_stage10_replicate1

source_name: stage10 embryo wt


title: Livers of mice fed an atherogenic diet for 24 weeks

description: RNA amplified before cDNA synthesis

value: Male

tag: Livers of mice fed a standard chow for 24 weeks

tag: Livers of mice fed an atherogenic (Ath) diet for 24 weeks. The Ath diet contains (by weight) 14% fat, 1.25% cholesterol, and 0.5% sodium cholate.


title: Livers of mice fed an atherogenic with a high-fat diet for 6 weeks

description: RNA amplified before cDNA synthesis.

source_name: Livers of mice fed a standard chow for 6 weeks

tag: Livers of mice fed an atherogenic with a high-fat (Ath+HF) diet for 6 weeks. The Ath+HF contains (by weight) 60% fat, 1.25% cholesterol, and 0.5% sodium cholate.


description: RNA amplified before cDNA synthesis.

source_name: Livers of mice fed a standard chow

tag: Livers of mice fed a standard chow for 6 weeks

source_name: Livers of mice fed an atherogenic diet

tag: Livers of mice fed an atherogenic diet for 6 weeks.

tag: The atherogenic diet containes (by weight) 14% fat, 1.25% cholesterol, and 0.5% sodium cholate.


title: normal lamb at 10d, biological rep 1

city: West Lafayette

first: Christopher

middle: A

last: Bidwell

state: IN

address: 125 South Russell Street

department: Animal Sciences

institute: Purdue University

description: Gene expression data from callipyge and normal lambs during the onset of muscle hypertrophy phenotype.

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Images were interpreted with Microarray Suite version 5.0 (MAS 5.0) in GCOS with no scaling or normalization.

organism: Ovis aries

source_name: 10 day normal (wild-type) longissimus dorsi total RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: lambs were allowed to nurse dams until 30 minutes prior to euthanasia

extract_protocol: Tissue homogenized in 4 M guanidinium thiocyanate, 25 mM EDTA, 1% sodium-N-lauroyl-sarcosine. Homogenates ultracentrifuged on 5.7 M CsCL cushion. RNA purified and DNase treated with Nucleospin RNA II columns (Machery-Nagel Inc).

treatment_protocol: Animals were euthanized, longissimus dorsi tissue excised and fixed in RNAlater (Ambion).

tag: Genotype

value: normal wild-type +/+

value: 10 days of age


title: normal lamb at 20d, biological rep 2

source_name: 20 day normal (wild-type) longissimus dorsi total RNA

value: 20 days of age


title: callipyge lamb at 30d, biological rep 2

source_name: 30 day callipyge longissimus dorsi total RNA

value: callipyge +/CLPG

value: 30 days of age


title: normal lamb at 30d, biological rep 2

source_name: 30 day normal (wild-type) longissimus dorsi total RNA


title: normal lamb at 20d, biological rep 1


title: HDAC1_knock_out_embryonic_stem_cells_biological_rep1

city: Vienna

first: Gordin

last: Zupkovitz

address: Dr. Bohrgasse 9

department: Medical Biochemistry

country: Austria

institute: MFPL

description: Gene expression data from HDAC1 knock out mouse embryonic stem cells

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Mus musculus embryonic stem cells derived from HDAC1 knock out embryos

growth_protocol: Dulbecco’s modified Eagle’s medium - high glucose supplemented with antibiotics, 15% v/v fetal calf serum and either 103 U/ml of leukemia inhibitory factor (LIF) on gelatinized culture dishes or without LIF on feeder cell layers

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

treatment_protocol: no treatment

value: HDAC1 knock out

tag: not differentiated


title: callipyge lamb at 30d, biological rep 1

tag: Age


title: HDAC1_knock_out_embryonic_stem_cells_biological_rep3


title: callipyge lamb at 10d, biological rep 2

source_name: 10 day callipyge longissimus dorsi total RNA


title: wild_type_embryonic_stem cells_biological_rep2

description: Gene expression data from wild type mouse embryonic stem cells

source_name: Mus musculus embryonic stem cells derived from wild type embryos

value: wild type


title: callipyge lamb at 20d, biological rep 2

source_name: 20 day callipyge longissimus dorsi total RNA


title: normal lamb at 10d, biological rep 2


title: HDAC1_knock_out_embryonic_stem_cells_biological_rep2


title: wild_type_embryonic_stem cells_biological_rep1


title: normal lamb at 30d, biological rep 1


title: callipyge lamb at 20d, biological rep 1


title: SF t8-2

status: Public on Sep 15 2006

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: cDNA labelling using random decamers and 33P-dCTP. Hibridization on L1-24 filter

data_processing: raw image quantitation background substracted

source_name: 144h in syntetic medium with 66 mg/l of Nitrogen (SF: Sluggish Fermentation)

tag: Total RNA from PYCC 4072 yeast strain growing for 144h in syntetic grape-juice medium with 66 mg/l of Nitrogen (SF

value: Sluggish Fermentation)


title: SF t8-1

description: cDNA labelling using random decamers and 33P-dCTP. Hibridization on L2-24 filter


title: wild_type_embryonic_stem cells_biological_rep3


title: SF t7-1

source_name: 96h in syntetic medium with 66 mg/l of Nitrogen (SF: Sluggish Fermentation)

tag: Total RNA from PYCC 4072 yeast strain growing for 96h in syntetic grape-juice medium with 66 mg/l of Nitrogen (SF


title: SF t7-2


title: SF t7-3

description: cDNA labelling using random decamers and 33P-dCTP. Hibridization on L1-2 filter


title: SF t6-3

source_name: 80h in syntetic medium with 66 mg/l of Nitrogen (SF: Sluggish Fermentation)

tag: Total RNA from PYCC 4072 yeast strain growing for 80h in syntetic grape-juice medium with 66 mg/l of Nitrogen (SF


title: SF t5-2

description: cDNA labelling using random decamers and 33P-dCTP. Hibridization on L2-2 filter

source_name: 48h in syntetic medium with 66 mg/l of Nitrogen (SF: Sluggish Fermentation)

tag: Total RNA from PYCC 4072 yeast strain growing for 48h in syntetic grape-juice medium with 66 mg/l of Nitrogen (SF


title: SF t5-3


title: SF t6-2

description: cDNA labelling using random decamers and 33P-dCTP. Hibridization on L2-1 filter


title: SF t4-2

description: cDNA labelling using random decamers and 33P-dCTP. Hibridization on L1-1 filter

source_name: 24h in syntetic medium with 66 mg/l of Nitrogen (SF: Sluggish Fermentation)

tag: Total RNA from PYCC 4072 yeast strain growing for 24h in syntetic grape-juice medium with 66 mg/l of Nitrogen (SF


title: SF t6-1


title: SF t4-1


title: callipyge lamb at 10d, biological rep1


title: NF t3-3

source_name: 96h in syntetic medium with 267 g/l of Nitrogen (NF: Normal Fermentation)

tag: Total RNA from PYCC 4072 yeast strain growing for 96h in syntetic grape-juice medium with 267 g/l of Nitrogen (NF

value: Normal Fermentation)


title: wt vs 25G#2

status: Public on Sep 18 2006

city: Salt Lake CIty

first: Mark

last: Metzstein

state: UT

department: Human Genetics

institute: University of Utah

description:
Simple annotation: RNA decay, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54281.gif; format: GIF

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 240, 17960; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Stefan,,Luschnig 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 = 38.89; Parameter Scan Time = 10:41:12; Parameter PMT Volts = 660; Parameter Scan Date = 2004-07-22; Parameter Pixel Size = 10; Parameter Laser on time = 177604; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Stefan,,Luschnig 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 = 38.89; Parameter Scan Time = 10:41:12; Parameter PMT Volts = 670; Parameter Scan Date = 2004-07-22; Parameter Pixel Size = 10; Parameter Laser on time = 542408; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.96; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Stefan,,Luschnig

source_name: wild type y w FRT ; BG2/+

tag: wild type y w FRT ; BG2/+


title: 25G vs wt#1

description:
Simple annotation: RNA decay, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54280.gif; format: GIF

source_name: WILD TYPE y w FRT ; BG2/+

tag: WILD TYPE y w FRT ; BG2/+


title: SF t4-3


title: NF t2-2

source_name: 48h in syntetic medium with 267 g/l of Nitrogen (NF: Normal Fermentation)

tag: Total RNA from PYCC 4072 yeast strain growing for 48h in syntetic grape-juice medium with 267 g/l of Nitrogen (NF


title: NF t2-3


title: NF t3-2


title: NF t1-3

source_name: 24 h in syntetic medium with 267 g/l of Nitrogen (NF: Normal Fermentation)

tag: Total RNA from PYCC 4072 yeast strain growing for 24 h in syntetic grape-juice medium with 267 g/l of Nitrogen (NF


title: NF t1-2


title: NF t3-1


title: RF t11-3

source_name: 144h in syntetic medium with 66 mg/l of Nitrogen and with addition of 200 mg/l of Nitrogen at 72h (RF: Re-fed Fermentation). Sampling 72h after re-feeding

tag: Total RNA from PYCC 4072 yeast strain growing for 144h in syntetic grape-juice medium with 66 mg/l of Nitrogen and with addition of 200 mg/l of Nitrogen at 72h (RF


title: NF t1-1


title: RF t10-2

source_name: 96h in syntetic medium with 66 mg/l of Nitrogen and with addition of 200 mg/l of Nitrogen at 72h (RF: Re-fed Fermentation). Sampling 24h after re-feeding

tag: Total RNA from PYCC 4072 yeast strain growing for 96h in syntetic grape-juice medium with 66 mg/l of Nitrogen and with addition of 200 mg/l of Nitrogen at 72h (RF


title: RF t11-2

value: Re-fed Fermentation). Sampling 72h after re-feeding


title: C.albicans alpha2::13myc chIP chip replicate 3 (Slide 64914)

city: Urrbrae

first: Anthony

last: Borneman

state: South Australia

address: Paratoo Rd

country: Australia

institute: The Australian Wine Research Institute

hyb_protocol: Nimblegen

scan_protocol: Nimblegen

data_processing: Samples were scanned and with each channel (635 (ch1) and 532 (ch2)) normalized separately according to Nimblegen protocols. log(2) ratios were calculated from these normalized 635 and 532 signals, with Random control spots removed during processing.

organism: Candida albicans

label_protocol: Klenow random priming (Borneman et al Genes Dev 2006)

growth_protocol: Grown at 25C to OD600 = 1.0 in Lee's media.

extract_protocol: Chromatin immunoprecipitation (Borneman et al Genes Dev 2006)

tag: C.albicans strain containing alpha2 tagged with 13 myc

source_name: WT control

tag: Wild type C.albicans


title: RF t9-3

source_name: 80h in syntetic medium with 66 mg/l of Nitrogen and with addition of 200 mg/l of Nitrogen at 72h (RF: Re-fed Fermentation). Sampling 8h after re-feeding.

tag: Total RNA from PYCC 4072 yeast strain growing for 80h in syntetic grape-juice medium with 66 mg/l of Nitrogen and with addition of 200 mg/l of Nitrogen at 72h (RF


title: RF t10-1

value: Re-fed Fermentation). Sampling 24h after re-feeding


title: RF t9-2

value: Re-fed Fermentation). Sampling 8h after re-feeding.


title: SF t8-3


title: NF t2-1


title: RF t9-1


title: C.albicans a1::13myc chIP chip replicate 1 (Slide 64920)

tag: C.albicans strain containing a1 tagged with 13 myc


title: KOfurB_rep3

city: Padova

first: Elisa

last: Dainese

state: Veneto

address: Via Gabelli 63

department: Microbiology and virology

country: Italy

institute: Univerity of Padua

description: Synthesis of labelled samples was performed as described in protocols of the Center for Applied Genomics (www.cag.icph.org)

scan_protocol: Prepared slides were immediately scanned using a 428TMArray Scanner (Affimetrix). Fluorescence intensities of Cy3 and Cy5 dies at each spot were quantified using the ImaGene software 5.0 (BioDiscovery, Inc.)

data_processing: Data obtained from qualified spots on the chip were normalised using the print-tip lowes implementation included in GEPAS v1.1 (http://gepas.bioinfo.cnio.es/). The values are expressed as ratio Cy5/Cy3 spots intensity determined from the normalized fluorescence intensity.

organism: Mycobacterium tuberculosis

source_name: M. tuberculosis culture H37Rv

growth_protocol: Mid log phase culture was centrifuged and the pellet frozen with dry ice

extract_protocol: Manganelli et al. Mol Micro (1999) 31:715-724

treatment_protocol: Culture grew in physiological condition (7H9 ADC Middlebrook)

tag: Strain H37Rv

source_name: M. tuberculosis culture furB mutant


title: RF t11-1


title: C.albicans a1::13myc chIP chip replicate 3 (Slide 68040)


title: KOfurB_rep4


title: KOfurB_rep5


title: zap1 deletion mutant vs. WT, replicate 2

status: Public on Sep 14 2006

city: San Francisco

first: Esther

middle: T

last: Chan

state: California

address: 1500 Owens Street, Suite 500

institute: Celgene Corporation

data_processing: The microarray data was spatially-detrended and Lowess-smoothed, giving the normalized log ratio of intensity for each spot in the mutant strain versus the WT strain and the average log intensity for each spot in the two strains.

source_name: Mutant strain with zap1 deleted

tag: Mutant strain with zap1 deleted

source_name: Wild-type strain

tag: Wild-type control


title: KOfurB_rep6

source_name: M. tuberculisis culture furB mutant


title: RF t10-3


title: KOfurB_rep2


title: KOfurB_rep1

source_name: M.tuberculosis culture H37Rv

source_name: M.tuberculosis culture furB mutant


title: zap1 deletion mutant vs. WT, replicate 1


title: yrr1 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with yrr1 deleted

tag: Mutant strain with yrr1 deleted


title: yrr1 deletion mutant vs. WT, replicate 1


title: yhp1 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with yhp1 deleted

tag: Mutant strain with yhp1 deleted


title: ypr015c deletion mutant vs. WT, replicate 1

source_name: Mutant strain with ypr015c deleted

tag: Mutant strain with ypr015c deleted


title: yox1 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with yox1 deleted

tag: Mutant strain with yox1 deleted


title: C.albicans alpha2::13myc chIP chip replicate 2 (Slide 64860)


title: upc2 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with upc2 deleted

tag: Mutant strain with upc2 deleted


title: C.albicans a1::13myc chIP chip replicate 2 (Slide 64842)


title: C.albicans alpha2::13myc chIP chip replicate 1 (Slide 63423)


title: xbp1 deletion mutant vs. WT, replicate 1

source_name: Mutant strain with xbp1 deleted

tag: Mutant strain with xbp1 deleted


title: upc2 deletion mutant vs. WT, replicate 1


title: ypr015c deletion mutant vs. WT, replicate 2


title: tos8 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with tos8 deleted

tag: Mutant strain with tos8 deleted


title: yap1 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with yap1 deleted

tag: Mutant strain with yap1 deleted


title: yhp1 deletion mutant vs. WT, replicate 1


title: tos8 deletion mutant vs. WT, replicate 1


title: yox1 deletion mutant vs. WT, replicate 1


title: xbp1 deletion mutant vs. WT, replicate 2


title: yap1 deletion mutant vs. WT, replicate 1


title: swi4 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with swi4 deleted

tag: Mutant strain with swi4 deleted


title: swi4 deletion mutant vs. WT, replicate 1


title: stp3 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with stp3 deleted

tag: Mutant strain with stp3 deleted


title: stp2 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with stp2 deleted

tag: Mutant strain with stp2 deleted


title: stp3 deletion mutant vs. WT, replicate 1


title: sut1 deletion mutant vs. WT, replicate 1

source_name: Mutant strain with sut1 deleted

tag: Mutant strain with sut1 deleted


title: stp2 deletion mutant vs. WT, replicate 1


title: ste12 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with ste12 deleted

tag: Mutant strain with ste12 deleted


title: ste12 deletion mutant vs. WT, replicate 1

source_name: Wild-type strain


title: spt2 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with spt2 deleted

tag: Mutant strain with spt2 deleted


title: SF t5-1

source_name: 48h in syntetic medium with 66 mg/l of Nitrogen (SF: Sluggish Fermentation)

tag: Total RNA from PYCC 4072 yeast strain growing for 48h in syntetic grape-juice medium with 66 mg/l of Nitrogen (SF


title: sip4 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with sip4 deleted

tag: Mutant strain with sip4 deleted


title: sps18 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with sps18 deleted

tag: Mutant strain with sps18 deleted

tag: Wild-type control


title: sfp1 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with sfp1 deleted

tag: Mutant strain with sfp1 deleted


title: sip4 deletion mutant vs. WT, replicate 1


title: spt2 deletion mutant vs. WT, replicate 1


title: rme1 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with rme1 deleted

tag: Mutant strain with rme1 deleted


title: skn7 deletion mutant vs. WT, replicate 1

source_name: Mutant strain with skn7 deleted

tag: Mutant strain with skn7 deleted


title: sps18 deletion mutant vs. WT, replicate 1


title: rme1 deletion mutant vs. WT, replicate 1


title: sfp1 deletion mutant vs. WT, replicate 1


title: rox1 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with rox1 deleted

tag: Mutant strain with rox1 deleted


title: rsc30 deletion mutant vs. WT, replicate 1

source_name: Mutant strain with rsc30 deleted

tag: Mutant strain with rsc30 deleted


title: sok2 deletion mutant vs. WT, replicate 1

source_name: Mutant strain with sok2 deleted

tag: Mutant strain with sok2 deleted


title: skn7 deletion mutant vs. WT, replicate 2


title: sok2 deletion mutant vs. WT, replicate 2


title: rfx1 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with rfx1 deleted

tag: Mutant strain with rfx1 deleted


title: rsc30 deletion mutant vs. WT, replicate 2


title: rfx1 deletion mutant vs. WT, replicate 1


title: put3 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with put3 deleted

tag: Mutant strain with put3 deleted


title: rgm1 deletion mutant vs. WT, replicate 1

source_name: Mutant strain with rgm1 deleted

tag: Mutant strain with rgm1 deleted


title: rox1 deletion mutant vs. WT, replicate 1


title: rgm1 deletion mutant vs. WT, replicate 2


title: pho4 deletion mutant vs. WT, replicate 1

source_name: Mutant strain with pho4 deleted

tag: Mutant strain with pho4 deleted


title: pho4 deletion mutant vs. WT, replicate 2


title: msn4 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with msn4 deleted

tag: Mutant strain with msn4 deleted


title: put3 deletion mutant vs. WT, replicate 1


title: msn2 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with msn2 deleted

tag: Mutant strain with msn2 deleted


title: msn2 deletion mutant vs. WT, replicate 1

source_name: Wild-type strain


title: msn4 deletion mutant vs. WT, replicate 1


title: mot3 deletion mutant vs. WT, replicate 1

source_name: Mutant strain with mot3 deleted

tag: Mutant strain with mot3 deleted


title: mbp1 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with mbp1 deleted

tag: Mutant strain with mbp1 deleted


title: mga1 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with mga1 deleted

tag: Mutant strain with mga1 deleted


title: mig1 deletion mutant vs. WT, replicate 1

source_name: Mutant strain with mig1 deleted

tag: Mutant strain with mig1 deleted


title: mig1 deletion mutant vs. WT, replicate 2

tag: Wild-type control


title: mot3 deletion mutant vs. WT, replicate 2


title: hms1 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with hms1 deleted

tag: Mutant strain with hms1 deleted


title: met31 deletion mutant vs. WT, replicate 1

source_name: Mutant strain with met31 deleted

tag: Mutant strain with met31 deleted


title: met31 deletion mutant vs. WT, replicate 2


title: mga1 deletion mutant vs. WT, replicate 1


title: gzf3 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with gzf3 deleted

tag: Mutant strain with gzf3 deleted


title: hac1 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with hac1 deleted

tag: Mutant strain with hac1 deleted


title: ino2 deletion mutant vs. WT, replicate 1

source_name: Mutant strain with ino2 deleted

tag: Mutant strain with ino2 deleted


title: ino2 deletion mutant vs. WT, replicate 2


title: hac1 deletion mutant vs. WT, replicate 1


title: gzf3 deletion mutant vs. WT, replicate 1


title: gis2 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with gis2 deleted

tag: Mutant strain with gis2 deleted


title: hap4 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with hap4 deleted

tag: Mutant strain with hap4 deleted


title: hap4 deletion mutant vs. WT, replicate 1


title: gis2 deletion mutant vs. WT, replicate 1


title: gis1 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with gis1 deleted

tag: Mutant strain with gis1 deleted


title: mbp1 deletion mutant vs. WT, replicate 1


title: gis1 deletion mutant vs. WT, replicate 1


title: gcn4 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with gcn4 deleted

tag: Mutant strain with gcn4 deleted


title: hms1 deletion mutant vs. WT, replicate 1


title: gat4 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with gat4 deleted

tag: Mutant strain with gat4 deleted


title: gat4 deletion mutant vs. WT, replicate 1


title: gat3 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with gat3 deleted

tag: Mutant strain with gat3 deleted


title: sut1 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with sut1 deleted

tag: Mutant strain with sut1 deleted


title: ecm22 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with ecm22 deleted

tag: Mutant strain with ecm22 deleted

source_name: Wild-type strain


title: gat3 deletion mutant vs. WT, replicate 1


title: ecm22 deletion mutant vs. WT, replicate 1


title: cup2 deletion mutant vs. WT, replicate 1

source_name: Mutant strain with cup2 deleted

tag: Mutant strain with cup2 deleted


title: cat8 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with cat8 deleted

tag: Mutant strain with cat8 deleted


title: crz1 deletion mutant vs. WT, replicate 1

source_name: Mutant strain with crz1 deleted

tag: Mutant strain with crz1 deleted


title: gcn4 deletion mutant vs. WT, replicate 1

tag: Wild-type control


title: cst6 deletion mutant vs. WT, replicate 2

source_name: Mutant strain with cst6 deleted

tag: Mutant strain with cst6 deleted


title: cat8 deletion mutant vs. WT, replicate 1


title: 120_GCN4 overexpression mutant vs. Empty vector, replicate 1

source_name: Control strain with empty vector

tag: Control strain carrying an empty 2-micron plasmid with an inducible GAL1 promoter

source_name: Mutant strain overexpressing 120_GCN4

tag: Mutant strain carrying 120_GCN4 under an inducible GAL1 promoter


title: bye1 deletion mutant vs. WT, replicate 1

source_name: Mutant strain with bye1 deleted

tag: Mutant strain with bye1 deleted


title: adr1 deletion mutant vs. WT, replicate 1

source_name: Mutant strain with adr1 deleted

tag: Mutant strain with adr1 deleted


title: adr1 deletion mutant vs. WT, replicate 2


title: 120_GCN4 overexpression mutant vs. Empty vector, replicate 2


title: cst6 deletion mutant vs. WT, replicate 1


title: crz1 deletion mutant vs. WT, replicate 2


title: 60_GCN4 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing 60_GCN4

tag: Mutant strain carrying 60_GCN4 under an inducible GAL1 promoter


title: bye1 deletion mutant vs. WT, replicate 2


title: 300_GCN4 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing 300_GCN4

tag: Mutant strain carrying 300_GCN4 under an inducible GAL1 promoter


title: 180_GCN4 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing 180_GCN4

tag: Mutant strain carrying 180_GCN4 under an inducible GAL1 promoter


title: 60_GCN4 overexpression mutant vs. Empty vector, replicate 2


title: 45_GCN4 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing 45_GCN4

tag: Mutant strain carrying 45_GCN4 under an inducible GAL1 promoter


title: cup2 deletion mutant vs. WT, replicate 2


title: 300_GCN4 overexpression mutant vs. Empty vector, replicate 2


title: 45_GCN4 overexpression mutant vs. Empty vector, replicate 1


title: 30_GCN4 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing 30_GCN4

tag: Mutant strain carrying 30_GCN4 under an inducible GAL1 promoter


title: 180_GCN4 overexpression mutant vs. Empty vector, replicate 1


title: 30_GCN4 overexpression mutant vs. Empty vector, replicate 2