title: Global gene expression of NASH patients, P66

city: Buffalo

first: Susan

last: Baker

address: 3435 Main street, 422 BRB

department: Pediatrics

institute: SUNY at Buffalo

hyb_protocol: 1, Fragmentation of cRNA. 2, Denature cRNA at 90C for 5 min. 3, Hybridization was performed at 37 C, for 18-24 hours. 4, Detection with Cy5-streptavidin conjugate.

scan_protocol: Microarray scanning and data acquisition were done at the gene expression facility, Roswell Park Cancer Institute, following their routine standard procedure.

data_processing: Data were median-normalized for comparison. Medium normalization were done by our collaborators at Roswell Park cancer institute and verified using MS Excel2003.

source_name: Patient liver biopsy

label_protocol:
Complementary DNA was prepared from total RNA.
In vitro transcription was then performed with biotin labeled substrate to produce biotin labeled cRNA.

extract_protocol: Samples were stored in RNAlater at -80 freezer before total RNA extraction with Qiagen RNeasy kit.

value: non-alcoholic steatohepatitis (NASH)

value: liver


title: WT-Xylan 24h Replicate 2

status: Public on Oct 21 2010

type: RNA

city: Ribeirao Preto

first: Wagner

middle: Rodrigo

last: de Souza

state: Sao Paulo

address: Av do Cafe

department: Pharmaceutical Sciences

country: Brazil

institute: University of Sao Paulo

description: Biological replicate 2 of 2. WT A. niger strain treated with xylan for 24h in minimal medium, no additional carbon source.

hyb_protocol: For the hybridization, 825 ng of each labeled cRNA was mixed with Agilent™ Fragmentation Mix and incubated at 60°C for exactly 30 minutes to fragment RNA. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 100 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in an oven (Agilent G2545A Hybridization Oven) set to 65°C for 17 hours. After, microarray slides were washed according to Agilent’s instructions.

scan_protocol: Scanned using the GenePix® 4000B microarray scanner (Molecular Devices, USA).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. Then, data were processed using the TIGR platform. Data were visualized using TMeV from TIGR, and the same software was used for statistical analysis (t test).

molecule: total RNA

organism: Aspergillus niger

source_name: A. niger mycelia xylan-treated 24h

label_protocol: Prior to labeling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 (for untreated samples) or Cyanine-5 (for xylan-treated samples) for 2 hours at 40oC.

growth_protocol: The A. niger WT strain was initially grown on minimal medium with fructose for 24 hours at 30oC.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions, followed by DNAse treatment and purification using the RNeasy® Mini Kit  (Qiagen).

treatment_protocol: Mycelia from the WT strain was transferred to minimal medium containing xylan 1% (w/v) with no additional carbon source for 6, 12 and 24 h at 30oC.

tag: strain

tag: genotype

value: WT

tag: tissue

value: mycelia

tag: agent

value: xylan

tag: time point

value: 24 hours

source_name: WT strain treated with fructose for 24h

value: fructose


title: mCG-PR_KLS_13wks_rep2

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

country: USA

institute: Washington University in St.Louis

hyb_protocol: Labeled targets were hybridized to Mouse Exon 1.0ST arrays (Affymetrix, Santa Clara, CA).

scan_protocol: Gene chips were scanned using Affymetrix GeneArray scanner GS 3000.

data_processing:
Raw data were processed with the RMA algorithm in Affymetrix Expression ConsoleTM version1.1 (Affymetrix Inc., USA).
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

label: biotin

organism: Mus musculus

source_name: Bone marrow

label_protocol: Amplified cDNA was biotin labeled using the EncoreTM Biotin Module (NuGen Technologies, San Carlos, CA) according to the manufacturer’s instructions.

extract_protocol: Total cellular RNA was purified using Trizol reagent, quantified using UV spectroscopy (Nanodrop Technologies, Wilmington,DE) and qualitatively assessed using an Experian Bioanalyzer (Hercules,CA).Amplified cDNA was prepared from 20ng of total RNA using the whole transcript WT-Ovation TM RNA Amplification System.

value: Bl/6 Taconic

tag: genotype/variation

value: mCG-PR N17

value: Bone marrow

tag: cell type

value: KLS

tag: time of progression

value: 13 wks


title: WT-Xylan 12h Replicate 1

description: Biological replicate 1 of 2. WT A. niger strain treated with xylan for 12h in minimal medium, no additional carbon source.

source_name: A. niger mycelia xylan-treated 12h

value: 12 hours


title: Global gene expression of NASH patients, P62

state: NY

organism: Homo sapiens

source_name: patient liver biopsy

tag: disease state


title: WT-Xylan 12h Replicate 2

description: Biological replicate 2 of 2. WT A. niger strain treated with xylan for 12h in minimal medium, no additional carbon source.


title: Global gene expression of NASH patients, normal control A154

source_name: Total RNA purchased from ADMET Technologies (Durham, NC), extracted from healthy liver tissue.

value: normal (control)


title: Chow 3

city: Wallace Wurth Building, Sydney

first: Margaret

middle: J

last: Morris

state: NSW

address: University of New South Wales

department: School of Medical Sciences

country: Australia

institute: University of New South Wales

description: Gene expression from islet

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene ST 1.0 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 100. The data is then normalised using RMA in log 2 space and differentially expressed genes were selected based on ANOVA of chow (Control) vs high fat diet (HFD).

organism: Rattus norvegicus

source_name: islet from female offspring of fathers fed on chow

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

growth_protocol: At 15 weeks of age, fathers were mated with normal females consuming chow, to generate the F1 offspring.

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

treatment_protocol: Fathers fed on HFD vs control, mate with females on normal chow then the female offspring's islet transcriptomics were analysed through microarray analysis

tag: gender

value: Female

value: Sprague-Dawley


title: Chow 2

description: Gene expression from islet


title: Global gene expression of NASH patients, normal control A99


title: WT-Xylan 6h Replicate 2

description: Biological replicate 2 of 2. WT A. niger strain treated with xylan for 6h in minimal medium, no additional carbon source.

source_name: A. niger mycelia xylan-treated 6h

value: 6 hours


title: Chow 1

description: Gene expression from islet


title: Global gene expression of NASH patients, P64

value: non-alcoholic steatohepatitis (NASH)


title: Global gene expression of NASH patients, P51

value: liver


title: Global gene expression of NASH patients, normal control A107


title: WT_KLS_12-13wks_rep2

value: wild type


title: WT-Xylan 6h Replicate 1

description: Biological replicate 1 of 2. WT A. niger strain treated with xylan for 6h in minimal medium, no additional carbon source.

value: WT

value: mycelia


title: mCG-PR_SLAM_7wks_rep2

value: SLAM

value: 7 wks


title: mCG-PR_SLAM_7wks_rep1

value: Bl/6 Taconic


title: Knockout_F1177A_rep02

status: Public on Oct 20 2010

city: Chicago

first: Eva

last: Martinez-Garcia

state: IL

address: 303 E. Superior St.

institute: Northwestern University

description: F1177A mutant

hyb_protocol: cRNA was hybridized to the Illumina Human/Mouse/Rat Expression BeadChip using standard protocols (provided by Illumina), then washed and stained with Streptavidin-Cy3 (Amersham) using Illumina provided protocols.

scan_protocol: The arrays were scanned on an Illumina BeadArray Reader

data_processing: the data was processed using GenomeStudio version 1.5.4

label: Biotin-UTP

source_name: KMS11 multiple myeloma cells, Knockout_F1177A_rep02

label_protocol: Samples were biotin-UTP labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion)

extract_protocol: Total RNA was extracted using Rneasy Mini Kit from Qiagen (Cat. No. 74104) in accordance with the prescribed protocol provided with the kit. 250 ng of RNA was reverse transcribed into cRNA and . cRNA was quantified using a nanodrop spectrophotometer and the cRNA quality (size distribution) was further analyzed on a 1% agarose gel

tag: cell line

value: KMS11 multiple myeloma cell line

tag: system

value: repletion

tag: protocol

value: F1177A mutant (active) restoration


title: 5'shRNA_noDOX_rep02

description: 5' shRNA No DOX

source_name: KMS11 multiple myeloma cells, 5'shRNA_noDOX_rep02

value: inducible knock down

value: 5' shRNA-mediated inducible knock-down of MMSET, No DOX


title: Knockout_F1177A_rep01

description: F1177A mutant

source_name: KMS11 multiple myeloma cells, Knockout_F1177A_rep01


title: 5'shRNA_+DOX_rep01

description: 5' shRNA +DOX

source_name: KMS11 multiple myeloma cells, 5'shRNA_+DOX_rep01

value: 5' shRNA-mediated inducible knock-down of MMSET, +DOX


title: Knockout_MMSETII_rep01

description: MMSET II

source_name: KMS11 multiple myeloma cells, Knockout_MMSETII_rep01

value: MMSET II (wildtype) restoration


title: WT_KLS_12-13wks_rep1

value: Bone marrow

value: KLS

value: 13 wks


title: Knockout_Y1118A_rep03

description: Y1118A mutant

source_name: KMS11 multiple myeloma cells, Knockout_Y1118A_rep03

value: Y1118A mutant (inactive) restoration


title: Knockout_Y1118A_rep02

description: Y1118A mutant

source_name: KMS11 multiple myeloma cells, Knockout_Y1118A_rep02


title: Knockout_F1177A_rep03

description: F1177A mutant

source_name: KMS11 multiple myeloma cells, Knockout_F1177A_rep03


title: 5'shRNA_+DOX_rep03

description: 5' shRNA +DOX

source_name: KMS11 multiple myeloma cells, 5'shRNA_+DOX_rep03


title: Knockout_DSRed_rep02

description: DSRed

source_name: KMS11 multiple myeloma cells, Knockout_DSRed_rep02

value: DSRed knockout (infected with empty vector)

tag: sample type

value: control cells for Knock out_MMSETII, and mutants Knockout_F1177A,Knockout_Y1118A


title: 5'shRNA_noDOX_rep01

description: 5' shRNA No DOX

source_name: KMS11 multiple myeloma cells, 5'shRNA_noDOX_rep01


title: Knockout_DSRed_rep01

description: DSRed

source_name: KMS11 multiple myeloma cells, Knockout_DSRed_rep01


title: Knockout_Y1118A_rep01

description: Y1118A mutant

source_name: KMS11 multiple myeloma cells, Knockout_Y1118A_rep01


title: 5'shRNA_noDOX_rep03

description: 5' shRNA No DOX

source_name: KMS11 multiple myeloma cells, 5'shRNA_noDOX_rep03


title: Knockout_MMSETII_rep02

description: MMSET II

source_name: KMS11 multiple myeloma cells, Knockout_MMSETII_rep02


title: Knockout_MMSETII_rep03

description: MMSET II

source_name: KMS11 multiple myeloma cells, Knockout_MMSETII_rep03


title: Global gene expression of NASH patient, P34

source_name: Patient liver biopsy

value: non-alcoholic steatohepatitis (NASH)

value: liver


title: Knockout_DSRed_rep03

description: DSRed

source_name: KMS11 multiple myeloma cells, Knockout_DSRed_rep03


title: 5'shRNA_+DOX_rep02

description: 5' shRNA +DOX

source_name: KMS11 multiple myeloma cells, 5'shRNA_+DOX_rep02


title: DBA_8h vs. basal replicate 10

city: München

first: Benno

last: Pütz

address: Kraepelinstr. 2

department: Statistical Genetics

country: Germany

institute: MPI of Psychiatry

hyb_protocol: The labeled aRNA samples were hybridized on Max-Planck Institute 24 k mouse cDNA arrays (Max-Planck-Institute of Psychiatry, Munich, Germany) as described at Deussing at al., 2207,  J Cereb Blood Flow Metab., performing 3 technical replicates for each control/CRH treated dye coupling combination.

scan_protocol: Mircorarrays were scanned on a PerkinElmer Life Sciences ScanArray 4000 laser scanner.

data_processing: The microarray data analysis was accomplished by the fixed circle quantification method using QuantArray (PerkinElmer Life Sciences) and raw data was normalized using a nonlinear regression method (Yang et al., 2002).

source_name: brain

label_protocol: aRNA synthesis and aRNA labelling was performed with the Amino Allyl MessageAmp™ aRNA Kit (Ambion) following the manufacturer’s protocol using 3 µg of total RNA.

growth_protocol: C57BL/6J and DBA/2J male mice with an age of 3-5 months (supplied from Harlan Winkelman, Borchen) were single housed under a 06:00-18:00 light cycle, where food and water were available ad libitum.

extract_protocol: Total RNA of PVN micropunctured tissue was extracted using the TRIzol reagent (Invitrogen) according to manufacturer´s instruction. RNA qualitiy was analysed by gel electrophoresis.

treatment_protocol: Mice were subjected to forced swimming in a cylinder of 24cm height and a diameter of 11 cm filled with water at 22-25°C for 5 minutes. Afterwards, they were transferred to their own original cage (i.e. single housed again) until decapitation.

tag: stress

value: stressed

value: basal


title: DBA_8h vs. basal replicate 6


title: DBA_8h vs. basal replicate 9


title: DBA_8h vs. basal replicate 8


title: DBA_8h vs. basal replicate 7


title: DBA_8h vs. basal replicate 5


title: 48hr Genistein 15uM

city: Stanford

first: James

middle: D

last: Brooks

state: CA

address: 300 Pasteur Drive

department: Department of Urology, Room S287

institute: Stanford University Medical Center

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48716.gif

hyb_protocol: not provided

scan_protocol: Scanner make: Axon Instruments (V1.00); Scanner Model: GenePix 4000B

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)

source_name: dmso

label_protocol: not provided

extract_protocol: not provided

tag: treatment

value: DMSO

value: LNCaP

value: prostate cancer epithlial cell line

source_name: Genistein 15uM

tag: treatment time

value: 15 uM Genistein


title: DBA_8h vs. basal replicate 4

tag: strain


title: 18hr Genistein 15uM

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48723.gif


title: 8hr Genistein 2uM

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48702.gif

source_name: Genistein 2uM

value: 8 h

value: 2 uM Genistein


title: TM_UPEC_60min_bio1_tec2

city: Giessen

first: Andreas Christian

last: Geisler

address: Frankfurter Str. 107

department: Med. Mikrobiologie

institute: Justus Liebig Universität Giessen

hyb_protocol: Double stranded cDNA and biotin labeled cRNA were purified using the mini columns included in the kit. The eluted cRNA was quantified with a NanoDrop spectrophotometer (NanoDrop Technologies, Rockland DE, USA) and quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies). Portions of 20 µg cRNA were subjected to fragmentation in the presence of Mg2+. Subsequently, 10 µg fragmented cRNA (target) was loaded onto CodeLink Rat Whole Genome Microarray glass slides containing 35.129 probe sets (Applied Microarrays, Tempe AZ, USA) and hybridized for 18 h in a Minitron shaker incubator (Infors AG, Bottmingen, Germany) at 37°C/300rpm. Washing and dyeing with Cy-5 coupled streptavidin followed the original protocol for CodeLink arrays (Applied Microarrays)

scan_protocol: Arrays were scanned using a GenePix 4000 B scanner and GenePix Pro 4.0 Software (Axon Instruments, Arlington, USA). Each RNA sample was hybridized onto two microarrays (= 2 technical replicates). A total of 24 microarrays (4 per group) were subjected to data analyses.

data_processing: Spots with an intensity below a negative control threshold were removed. Outliers were detected by their distance to the median of the replicates. Threshold was 3*median and ⅓*median. The missing values were imputed using SeqKNN whereas arrays that contained more than 50% deleted values were discarded. Data was normalized by quantile normalization. Data was log2 transformed. Differentially expressed genes were detected using RankProducts, for each treatment being compared to the untreated control chips. The resulting gene list was subjected to Source for annotation and DAVID for over representation analysis of gene categories. Gene clustering was conducted using dChip and Avadis.

source_name: testicular macrophage

label_protocol: Sample preparation was performed using the MessageAmp II Kit (Ambion, Applied Biosystems) following the manufacturer’s original protocol. Briefly, 1 µg total RNA were used in cDNA synthesis reactions with a poly-A binding primer containing the T7-polymerase promoter. Resulting cDNA was transcribed into cRNA in one round amplification in the presence of 11-Bio-UTP

extract_protocol: Testicular macrophages (TM) and peritoneal macrophages (PM) were isolated as described previously [Bhushan S, Tchatalbachev S, Klug J, Fijak M, Pineau C, et al. (2008) Uropathogenic Escherichia coli block MyD88-dependent and activate MyD88-independent signaling pathways in rat testicular cells. J Immunol 180: 5537-5547.]. Purity of TM and PM was estimated 80-90% by double immunofluorescence staining using the rat macrophage specific antibodies directed against ED1 (CD68) and ED2 (CD163, Serotec, Oxford, UK, 1:50 dilution. respectively)

value: male

value: Wistar

tag: weight


title: TM_UPEC_60min_bio2_tec2


title: 18hr Genistein 2uM

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48709.gif


title: TM_UPEC_60min_bio2_tec1


title: 24hr Genistein 2uM

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48718.gif


title: 24hr Genistein 15uM

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48725.gif


title: 36hr Genistein 15uM

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48724.gif


title: DBA_8h vs. basal replicate 3


title: TM_UPEC_60min_bio1_tec1


title: B cells 3 hrs control HI No.2

city: Cleveland

first: Anette

middle: H.

last: van Boxel-Dezaire

state: OH

address: 9500 Euclid Avenue

department: Molecular Genetics

institute: Cleveland Clinic Foundation

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Expression data normalization and differential expression analysis was handled through the Illumina BeadStudio Gene Expresson module V3.2.  The data were first normalized by using the quantile normalization algorithm provided by Illumina Beadstudio and then the differential expression analyses were performed by using Illumina’s custom model.  Downstream data processing and reporting was handled in R packages (http://www.r-project.org).  Genes for downstream analyses were filtered to include only those with both differential expression analysis p values of less than 0.001 and fold changes greater than 2, over the unstimulated (control) stimulation.

source_name: human primary B cells

label_protocol: A single-round of in vitro transcription (IVT) amplification was carried out using the Illumina RNA Amplification Kit, manufactured by Ambion, Inc., to amplify mRNA and thus to obtain ample amounts of biotinylated cRNA to perform the whole human genome gene expression assay using the humanRef-8 v2 expression beadchips micro-array (Illumina, San Diego, CA).

extract_protocol: Total RNA was isolated from the isolated unstimulated (control) or IFN-beta-stimulated blood cell subset by dissolving the cells in TRIZOL following the protocol of the manufacturer.  Quality control of RNA was performed with Agilent Bioanalyser.

treatment_protocol: Whole blood of 2 healthy individuals (HI) was either stimulated with 2000 IU/ml IFN-beta or left untreated (control) for 3 hrs, and pure B cells and monocytes were isolated directly from whole blood using anti-CD14 and anti-CD19 antibodies coupled to magnetic beads and the AutoMACS Pro (Miltenyi Biotec).

tag: tissue source

value: human whole blood

value: human primary B cells

tag: person

value: healthy individual No. 2

value: untreated


title: 4hr Genistein 15uM

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48715.gif

value: 4 h


title: DBA_8h vs. basal replicate 1

tag: time point


title: DBA_8h vs. basal replicate 2


title: Monos 3 hrs IFN-beta HI No.1

source_name: human primary monocytes

value: human primary monocytes

value: healthy individual No. 1

value: IFN-beta


title: Monos 3 hrs control HI No.1


title: 12hr Genistein 2uM

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48704.gif


title: TM_UPEC_30min_bio2_tec2


title: 12hr Genistein 15uM

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48722.gif


title: 36hr Genistein 2uM

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48711.gif


title: B cells 3 hrs IFN-beta HI No.2


title: 4hr Genistein 2uM

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48713.gif


title: 48hr Genistein 2uM

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48721.gif


title: B cells 3 hrs control HI No.1


title: TM_UPEC_30min_bio2_tec1


title: BL6_8h vs. basal replicate 10

value: stressed

value: basal


title: B cells 3 hrs IFN-beta HI No.1


title: 8hr Genistein 15uM

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48726.gif

value: DMSO

value: LNCaP


title: 0hr MSA 10uM

description:
Simple annotation: prostate cancer, selenium
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28349.gif

source_name: 14.5 uM selenium LNCaP total RNA

value: 14.5 uM selenium

value: prostate cancer epithlial cell line

source_name: MSA 10 uM 0h LNCaP total RNA

growth_protocol: Culture Volume = 25 ml; Growth Temperature = 37 C; Growth Vessel Volume = 150 mm diameter; Media = "RPMI 1640, 5% defined FBS"

value: 0 h

value: 10 uM MSA


title: BL6_8h vs. basal replicate 9


title: PRDM14 shRNA_3 Days knockdown_rep3

city: SINGAPORE

first: NA-YU

last: CHIA

address: 30 Biopolis Way

department: STEM CELL 6

country: Singapore

institute: Genome Institute of Singapore

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using median (MeV) by performing log2 transformation, followed by median centering on samples and median centering of genes across the samples

source_name: H1 hESCs

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: H1 hESCs were grown at 37degress for 5 days before the cells were passaged. Cells were seeded from in a ratio of 1:6 for PRDM14 shRNA and Luciferase shRNA transfection. Samples were harvested 3 days after transfection.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: hESCs that were seeded one day before were transfected with 2ug of the PRDM14 or Luciferase shRNA using 6ul of Fugene in 100ul optimen. After 20mins, the transfection mix were added to the cells.

value: experimental sample

tag: transfection

value: PRDM14 shRNA_3 Days knockdown


title: PRDM14 shRNA_3 Days knockdown_rep2

description: replicate 2


title: TM_UPEC_30min_bio1_tec2

value: male

value: Wistar


title: BL6_8h vs. basal replicate 8


title: TM_UPEC_30min_bio1_tec1


title: BL6_8h vs. basal replicate 7


title: BL6_8h vs. basal replicate 5


title: PRDM14 shRNA_3 Days knockdown_rep1

description: replicate 1


title: BL6_8h vs. basal replicate 4


title: BL6_8h vs. basal replicate 6


title: H1 hESCs_rep2

description:
replicate 2
control

growth_protocol: H1, H9 hESCs and relevant human iPSCs were grown at 37degress for 6 days before RNA collection

value: control sample

value: H1 hESCs


title: H1 hESCs_rep1

description:
replicate 1
control


title: Luciferase shRNA_3 Days knockdown_rep1

description: replicate 1

value: negative control

value: Luciferase shRNA_3 Days knockdown


title: MRC5 fibroblasts _rep2

description:
replicate 2
control

source_name: human embryonic lung fibroblasts

tag: cell type

value: MRC5 fibroblasts


title: TM_control_bio2_tec2


title: TM_control_bio1_tec2


title: Luciferase shRNA_3 Days knockdown_rep2

description: replicate 2


title: Luciferase shRNA_3 Days knockdown_rep3

description: replicate 3


title: MRC5 fibroblasts _rep1

description:
replicate 1
control


title: TM_control_bio1_tec1


title: PM_UPEC_60min_bio2_tec2

source_name: peritoneal macrophage


title: TM_control_bio2_tec1


title: H9 hESCs_rep2

description:
replicate 2
control

source_name: H9 hESCs

value: H9 hESCs


title: H9 hESCs_rep1

description:
replicate 1
control


title: T1 0h Curcumin

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26975.gif

source_name: cells treated with DMSO

source_name: 10uM Curcumin

value: 10 uM Curcumin uM


title: OSKC+PRDM14 hiPSC_rep1

description:
replicate 1
Sample

source_name: human iPSCs

tag: condition

value: OSKC

value: PRDM14 hiPSC


title: BL6_8h vs. basal replicate 3

value: basal

value: stressed


title: PM_UPEC_60min_bio1_tec1


title: BL6_8h vs. basal replicate 2


title: PM_UPEC_30min_bio2_tec2


title: PM_UPEC_60min_bio2_tec1


title: PM_UPEC_60min_bio1_tec2


title: DBA-BL6 vs. basal replicate 9


title: OSKC+PRDM14 hiPSC_rep2

description:
replicate 2
Sample


title: OSK+PRDM14 hiPSC_rep2

description:
replicate 2
Sample

value: OSK


title: BL6_8h vs. basal replicate 1


title: OSKC+NFRKB hiPSC_rep2

description:
replicate 2
Sample

value: NFRKB hiPSC


title: PM_UPEC_30min_bio2_tec1


title: HSC-3 cells treated with heat stress at 44°C for 12 h

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

description: HSC-3 cells, a human oral squamous carcinoma cell line, were cultured at 37°C. The cells were treated with heat stress 44°C for 90 min and followed by incubation for 12 h at 37°C. Non-treated cells were served as control.

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: Standard Affymetrix protocol

source_name: Human oral squamous carcinoma cell line HSC-3

label_protocol: 5 μg of total RNA was used to synthesize double-strand cDNA with a GeneChip® Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix). Biotin-labeled cRNA was then synthesized from the cDNA using GeneChip® Expression 3’-Amplification Reagents for IVT Labeling (Affymetrix).

extract_protocol: Total RNA was extracted from the cells using an RNeasy Total RNA Extraction Kit (Qiagen K. K., Tokyo, Japan). Then, RNA samples were treated with RNase-free DNase.

tag: time


title: OSKC+NFRKB hiPSC_rep1

description:
replicate 1
Sample

value: experimental sample


title: OSK+PRDM14 hiPSC_rep1

description:
replicate 1
Sample


title: HSC-3 cells treated with heat stress at 44°C for 0 h

description: HSC-3 cells, a human oral squamous carcinoma cell line, were cultured at 37°C. The cells were treated with heat stress 44°C for 90 min and followed by incubation for 0 h at 37°C. Non-treated cells were served as control.


title: DBA-BL6 vs. basal replicate 8

source_name: brain


title: DBA-BL6 vs. basal replicate 10


title: OSK+NFRKB hiPSC_rep2

description:
replicate 2
Sample


title: HSC-3 cells treated with heat stress at 44°C for 6 h

description: HSC-3 cells, a human oral squamous carcinoma cell line, were cultured at 37°C. The cells were treated with heat stress 44°C for 90 min and followed by incubation for 6 h at 37°C. Non-treated cells were served as control.


title: fibroblast 2 input, methyl-depleted [hFib2]

type: genomic

city: Baltimore

first: Akiko

last: Doi

state: MD

address: 855 N Wolfe St, Rangos 580

department: Medicine

institute: Johns Hopkins University School of Medicine

description:
DNA methylation data from iPS cells (input channel)
DNA methylation data from iPS cells (methyl-depleted channel)

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

scan_protocol: Arrays were scanned on a GenePix 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 software (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

molecule: genomic DNA

source_name: Input fraction from hFib2

label_protocol: 2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers for the input (UT) fraction and Cy5 nonamers for the methyl-depleted (MD) fraction per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

growth_protocol: Fibroblasts were grown in alpha-MEM containing 10 % inactivated fetal serum (IFS), 50 U/ml penicillin, 50 mg/ml streptomycin, and 1 mM L-glutamine.

extract_protocol: Genomic DNA (gDNA) were isolated using DNeasy kit (Qiagen) according to the manufacturer’s protocol. For each sample, 5 µg of genomic DNA was sheared into 1.6-3kb DNA size fragments, digested with McrBC, and fractionated on a 1% agarose gel alongside the sheared input (UT) fraction to enrich for the methyl-depleted (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.

value: adult dermal fibroblast

source_name: Methyl-depleted fraction from hFib2


title: HSC-3 cells treated with heat stress at 42°C for 12 h

description: HSC-3 cells, a human oral squamous carcinoma cell line, were cultured at 37°C. The cells were treated with heat stress 42°C for 90 min and followed by incubation for 12 h at 37°C. Non-treated cells were served as control.


title: PM_UPEC_30min_bio1_tec2

tag: gender

value: male


title: HSC-3 cells treated with heat stress at 42°C for 6 h

description: HSC-3 cells, a human oral squamous carcinoma cell line, were cultured at 37°C. The cells were treated with heat stress 42°C for 90 min and followed by incubation for 6 h at 37°C. Non-treated cells were served as control.

tag: cell line


title: DBA-BL6 vs. basal replicate 7


title: OSK+NFRKB hiPSC_rep1

description:
replicate 1
Sample


title: ES 3 input, methyl-depleted [H9]

source_name: Input fraction from H9

growth_protocol: hES cells were cultured in hES medium (80% DMEM/F12, 20% KO Serum Replacement,10 ng/ml bFGF, 1 mM L-glutamine, 100 M nonessential amino acids, 100 M 2-mercaptoethanol, 50 U/ml penicillin, and 50 mg/ml streptomycin).

value: H9 ES cells

source_name: Methyl-depleted fraction from H9


title: ES 2 input, methyl-depleted [BGO3]

description:
DNA methylation data from fibroblasts (input channel)
DNA methylation data from fibroblasts (methyl-depleted channel)

source_name: Input fraction from BGO3

value: BGO3 ES cells

source_name: Methyl-depleted fraction from BGO3


title: ES 1 input, methyl-depleted [BGO1]

source_name: Input fraction from BGO1

value: BGO1 ES cells

source_name: Methyl-depleted fraction from BGO1


title: HSC-3 cells treated with heat stress at 42°C for 0 h

description: HSC-3 cells, a human oral squamous carcinoma cell line, were cultured at 37°C. The cells were treated with heat stress 42°C for 90 min and followed by incubation for 0 h at 37°C. Non-treated cells were served as control.


title: DBA-BL6 vs. basal replicate 6


title: iPS 3 input, methyl-depleted [hFib2-iPS5]

source_name: Input fraction from hFib2-iPS5

growth_protocol: iPS cells were cultured in hES medium (80% DMEM/F12, 20% KO Serum Replacement,10 ng/ml bFGF, 1 mM L-glutamine, 100 M nonessential amino acids, 100 M 2-mercaptoethanol, 50 U/ml penicillin, and 50 mg/ml streptomycin).

value: iPS cells derived from hFib2

source_name: Methyl-depleted fraction from hFib2-iPS5


title: PM_UPEC_30min_bio1_tec1

source_name: peritoneal macrophage

value: Wistar


title: DBA-BL6 vs. basal replicate 4


title: HSC-3 cells (control)

description: HSC-3 cells, a human oral squamous carcinoma cell line, were cultured at 37°C. Non-treated cells were served as control.

value: control


title: PM_control_bio1_tec1


title: DBA-BL6 vs. basal replicate 3


title: PM_control_bio2_tec1


title: U937 cells treated with shikonin-1

source_name: Human lymphoma U937 cells

value: shikonin


title: DBA-BL6 vs. basal replicate 2


title: 0.3uM egcg

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/48926.gif

source_name: cells treated with DMSO

value: DMSO

value: LNCaP

value: prostate cancer epithlial cell line

source_name: 0hr self

value: 0 h


title: U937 cells treated with DMSO (control-1)


title: PM_control_bio1_tec2


title: DBA-BL6 vs. basal replicate 5

value: basal


title: PM_control_bio2_tec2


title: U937 cells treated with DMSO (control-2)


title: U937 cells treated with shikonin-2


title: RPMI cell line, miR16 KO, rep1

city: Boston

first: Daniel

middle: Ruben

last: Carrasco

state: MA

address: 44 Binney St

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Gene Expression data from mutiple myoloma cell line RPMI826 treated with miR16 siRNA

hyb_protocol: The labeled cDNAs were dissolved in 200ul MES Hybridization Buffer and were hybridized with microarray for 16 h at 45°C.

scan_protocol: Then the microarrays were washed and scanned by an Affymetrix GeneChip Scanner 3000, 7G.

data_processing: The data were normalized with plier16 method, in log2 transformed scale.

source_name: lentiviruses harboing miR16 KO transduced RPMI826 Cell lines

label_protocol: 15ug total RNA was amplified by using Affymetrix GeneChip® Two-Cycle Target Labeling Reagents for 2 rounds of linear amplification and was labeled with biotin-conjugated nucleotides incorporated in the final in vitro transcription reaction.

growth_protocol: Stably transduced RPMI 8226 and MMS1 Cell lines were evenly counted and grown in parallel flasks for a week until confluent, lysed at the same time point and RNA extracted for analysis.

extract_protocol: RNA was extracted according to the manufacturer's protocol, purified using RNeasy kit (Qiagen)

treatment_protocol: Cells were previously transduced by lentiviruses harboing GFP and miR16 binding sponges (or control mock sponges), sorted by flow cytometry, and expanded.

tag: cancer type

value: multiple myeloma

value: miR16 knock down


title: RPMI cell line, control, rep2

description: Gene Expression data from mutiple myoloma cell line RPMI826

source_name: lentiviruses harboing GFP transduced RPMI826 Cell lines


title: RPMI cell line, miR16 KO, rep2


title: DBA-BL6 vs. basal replicate 1

source_name: brain


title: RPMI cell line, control, rep1


title: RPMI cell line, control, rep3


title: RPMI cell line, miR16 KO, rep3


title: DBA_4h vs. basal replicate 10

value: stressed


title: DBA_4h vs. basal replicate 9


title: DBA_4h vs. basal replicate 8


title: cdka;1 mutant and wild type_rep2

city: OSLO

first: Paul

middle: E.

last: Grini

address: Blindernveien 31

department: Department of Molecular Biosciences

country: Norway

institute: University of Oslo

description:
AG8-8
Each biological replicate consists of 35 siliques from 10 individual plants.

hyb_protocol: Hybridizations were performed in a Slide Booster Hybridization Station (Advalytix, Brunnthal, Germany), and the slides were washed according to the manufacturers’ descriptions (Genisphere and Advalytix).

scan_protocol: The slides were scanned at 10 mm resolution on a G2505B Agilent DNA microarray scanner (Agilent Technologies,Palo Alto, CA, USA). The resulting image files were processed using GenePix 5.1 software (Axon Instruments, Union City, CA, USA).

data_processing:
Spots identified as not found or which were manually flagged as bad were filtered out. Spots with more than 50% saturated pixels were also excluded. The data sets were log-transformed and normalized using the printtip-loess approach. Within-array replicated measurements for the same gene were merged by taking the average between the replicates. The data were then scaled so that all array data sets had the same median absolute deviation. The differentially expressed genes were identified using the Limma software package. The p-values were then used to compute the q-values (Storey 2002).
References: Smyth, G. K. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3 (2004); Storey J.D. A direct approach to false discovery rates. Journal of the Royal Statistical Society. Series B-Statistical Methodology 64, 479–498 (2002).

organism: Arabidopsis thaliana

source_name: Siliques from wt (Col ecotype)

label_protocol: Total RNA (15 ug) and Super-Script III reverse transcriptase (Invitrogen, Carlsbad, CA,USA) were used in a reverse transcription reaction.  Microarray slides were printed by the Norwegian Microarray Consortium (Trondheim, Norway). A 3DNA Array 350 kit with Cy3- and Cy5-labelled dendrimers (Genisphere,Inc., Hatfield, PA, USA) was used for labelling.

growth_protocol: Seeds were sown out on soil and grown under the following conditions; 18oC day and 18oC night, 16 hr day length with 30 min adjustment of light to on and off, and 85 μmol/m2/sek in light intensity. 10 Ler plants were emasculated and pollinated after 48 hours, either with individual WT Col or with individual cdka;1 mutant pollen.

extract_protocol:
Three days after pollination (3 DAP), the siliques were dissected with hypodermic needles to remove carpel walls, the pistil with pollen attached to it and the pedicel with abcsission zone. The remaining seeds attached to the middle lamella were harvested in bulk in liquid nitrogen at the same time of the day.

Total RNA was isolated with the Spectrum Plant Total RNA Kit (Sigma, St. Louis,MO,USA) and was quantified with NanodropND 1000 (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: Untreated.

tag: ecotype of pollen

value: Col

tag: genotype of pollen

value: wild-type

tag: tissue

value: silique

tag: biological replicate

source_name: Siliques from cdka;1 mutant

value: cdka;1 mutation


title: MMS1 cell line, miR16 KO, rep1

description: Gene Expression data from mutiple myoloma cell line MMS1 treated with miR16 siRNA

source_name: lentiviruses harboing miR16 KO transduced MMS1 Cell lines

tag: treatment


title: MMS1 cell line, miR16 KO, rep2


title: cdka;1 mutant and wild type_rep3

description:
AG8-9
Each biological replicate consists of 35 siliques from 10 individual plants.


title: MMS1 cell line, miR16 KO, rep3


title: MMS1 cell line, control, rep3

description: Gene Expression data from mutiple myoloma cell line MMS1

source_name: lentiviruses harboing GFP transduced MMS1 Cell lines


title: cdka;1 mutant and wild type_rep1

description:
AG8-6
Each biological replicate consists of 35 siliques from 10 individual plants.


title: DBA_4h vs. basal replicate 7

tag: stress

tag: strain


title: ΔXlnR-SESB 24h Replicate 1

description: Biological replicate 1 of 2. ΔXlnR A niger strain treated with SESB for 24h in minimal medium, no additional carbon source

hyb_protocol: For the hybridization, 825 ng of each labeled cRNA was mixed with Agilent™ Fragmentation Mix and incubated at 60 °C for exactly 30 minutes to fragment RNA. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 100 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in an oven (Agilent G2545A Hybridization Oven) set to 65 °C for 17 hours. After, microarray slides were washed according to Agilent’s instruction

scan_protocol: Scanned using GenePix® 4000B microarray scanner (Molecular Devices, USA).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. After data were processed using TIGR platform. Data were visualized using TMeV from TIGR, and the same software has been used for statistical analysis (t test).

source_name: A. niger mycelia SESB-treated 24h, labeled with Cyanine-5

label_protocol: Prior to labelling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 (for untreated samples) or Cyanine-5 (for SES-treated samples) for 2 hours at 40 oC.

growth_protocol: A. niger strains (WT or ΔXlnR) were initially grown on minimal medium with fructose for 24 hours at 30 oC.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions, followed by DNAse treatment and purification using RNeasy® Mini Kit  (Qiagen).

treatment_protocol: Mycelia from both strains were transferred to minimal medium containing steam-exploded sugarcane with no additional carboun source for 6, 12 and 24 h, at 30 oC.

tag: agent

value: SESB

tag: genotype/variation

value: ΔXlnR

source_name: total RNA from ΔXlnR strain treated with fructose for 24 h, labeled with Cyanine-3

value: fructose


title: DBA_4h vs. basal replicate 6

tag: time point


title: ΔXlnR-SESB 24h Replicate 2

description: Biological replicate 2 of 2. ΔXlnR A niger strain treated with SESB for 24h in minimal medium, no additional carbon source


title: ΔXlnR-SESB 12h Replicate 1

source_name: A. niger mycelia SESB-treated 12h, labeled with Cyanine-5


title: ΔXlnR-SESB 12h Replicate 2


title: MMS1 cell line, control, rep1

value: control


title: DBA_4h vs. basal replicate 4


title: MMS1 cell line, control, rep2


title: DBA_4h vs. basal replicate 5


title: DBA_4h vs. basal replicate 3


title: DBA_4h vs. basal replicate 2


title: ΔXlnR-SESB 6h Replicate 2

source_name: A. niger mycelia SESB-treated 6h, labeled with Cyanine-5


title: COL+tunicamycin slide 59

city: Normal

first: Arunachalam Muthaiyan

email: amuthai@gmail.com, bjwilkin@ilstu.edu

address: Julian Hall

department: Biological Sciences

institute: Illinois State University

description:
tunicamycin affect on methicillin resistant S. aureus (MRSA) COL
Sample 2, Replicate 2 (slide 59_CTL_Cy5_EXP_Cy3.txt)

hyb_protocol: Labelled cDNA hybridised in slides placed in water bath for 16 h at 42 °C. Arrays then washed in 1x SSC (+0.02 % SDS)at room temperature for 2 and 5 min, in 0.1x SSC+0.1%SDS for 5 min, and then in 0.1x SSC for 10 min 2 times prior to drying and scanning.

scan_protocol: Arrays scanned using an Gene pix Microarray scaner, Gene pix professional, 4200A, axon Instrument scanner and Imagene version Pro 6.0 software.

data_processing: Data analysis was carried out using Spotfinder, version 224 , MIDAS2_19, MadRalph_1.0_Final_011503 and SAM . The mean values from each channel were log2 transformed and normalized using the LOWESS algorithm to remove intensity dependent effects within the calculated values. Normalised values were used to calculate the Cy3/Cy5 fluorescence ratios from experimental and biological repeats (seperate chemostat runs)with all replicates combined. Data was compiled from two aerobic and two anaerobic cultures each with a dye-swap replicate, thus providing two biological repeats within four technical repeats. The log2 ratio and raw signal intensity data are provided as supplementary files.  Results of the Q-value statistical analysis, and merging of replicate hybridizations are provided in the results_files.tar file on the Series record.

organism: Staphylococcus aureus

source_name: S. aureus COL grown in the presence of 400ng/ml of tunicamycin

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.

growth_protocol: Overnight grown S. aureus COL was inoculated in TSB medium (20 ml) in a 50 ml Erlenmeyer flask containing 400 ng/ml tunicamycin and incubated at 30°C, with shaking at 200 rpm. Growth was measured at regular intervals at 625 nm until OD= ~0.5.

extract_protocol: Bacterial cultures flushed directly into QIAGEN RNA protect before total RNA isolation using QIAGEN RNEasy Midi kit with on column DNAse digestion.

treatment_protocol: S. aureus grown in the presence of 400 ng/ml of tunicamycin till OD reached ~0.4

value: COL

source_name: S. aureus COL grown without tunicamycin


title: BL6_4h vs. basal replicate 10


title: DBA_4h vs. basal replicate 1


title: COL+tunicamycin slide 64

description:
tunicamycin affect on methicillin resistant S. aureus (MRSA) COL
Sample 2, Replicate1 raw (slide 64_CTL_Cy3_EXP_Cy5.txt)


title: BL6_4h vs. basal replicate 9


title: COL+tunicamycin slide 65

description:
tunicamycin affect on methicillin resistant S. aureus (MRSA) COL
Sample 2, Replicate1 raw (slide 65_CTL_Cy3_EXP_Cy5.txt)


title: COL+tunicamycin slide 56

description:
tunicamycin affect on methicillin resistant S. aureus (MRSA) COL
Sample 2, Replicate 2 (slide 56_CTL_Cy5_EXP_Cy3.txt)


title: BL6_4h vs. basal replicate 8


title: ΔXlnR-SESB 6h Replicate 1


title: WT-SESB 24h Replicate 2

description: Biological replicate 2 of 2. WT A niger strain treated with SESB for 24h in minimal medium, no additional carbon source

value: WT N402

source_name: total RNA from WT strain treated with fructose for 24 h, labeled with Cyanine-3


title: BL6_4h vs. basal replicate 7


title: BL6_4h vs. basal replicate 6


title: WT-SESB 24h Replicate 1

description: Biological replicate 1 of 2. WT A niger strain treated with SESB for 24h in minimal medium, no additional carbon source


title: antimiR-122 administration on the heart miRNome, 6W-PM treatment

city: Heidelberg

first: Mirco

last: Castoldi

address: Im Neuenheimer Feld 156

department: Department of Pediatric Oncology, Hematology and Immunology

institute: University of Heidelberg

description: Evaluation of the effect of antimiR-122 administration on the liver, spleen and heart miRNome.

hyb_protocol: Detailed hybridization protocol has been described in before (Castoldi M et al., Nature Protocol, miChip: an array-based method for microRNA expression profiling using locked nucleic acid capture probes, 2008). In brief; for each sample a microarray chamber with a microarray gasket slide (Agilent technologies, cat. G2534-60005) was prepared and labeled samples are sandwiched between the microarray gasket slide and the printed arrays. The secured holders were placed into the hybridization oven (Agilent technologies, cat. G2545A), and hybridization is carried out for at least 16 h with a rotating speed of four using a hybridization temperature of 54 °C. After hybridization, arrays were washed. Microarray chambers are removed one by one from the hybridization oven. Microarray chambers are opened and the gasket slide-array sandwiches are submerged in washing buffer 1 (W1; 2 x SSC, 0.1%SDS, at room temperature), and separated using forceps. Subsequently, hybridized arrays were stored in W1 (room temperature) until all arrays have been removed from the oven and separated from the microarray gasket slides. Successively, arrays were transferred into fresh W1 (room temperature) and washed on a rocking shaker for 10 min. Then, arrays were washed once in washing buffer 2 (W2, 0.2 x SSC, at room temperature) and washing buffer 3 (W3, 0.1 x SSC, at room temperature), each time for 10 min, and once in W3 for 5 min (all washes are performed at room temperature on a shaker). Finally, arrays are rinsed in double-distilled water (room temperature) and dried by centrifugation at 1500 rpm for 2 min at room temperature.

scan_protocol: Slides were scanned using a GenePix 4200AL microarray scanner (Axon instruments). Microarray images are analyzed using Genepix Pro 6.0 software (Axon instruments).

data_processing: Array images were generated by using the Genepix 4200AL laser scanner (Auto Loader, Axon Instruments). For this purpose, miChip arrays are scanned in batches using the Genepix auto PMT (Photo Multiplayer) algorithm, with pixel saturation tolerance set to 1% following the supplier’s protocol. The tiff images generated by the Genepix 4200AL scanner were loaded into Genepix 6 microarray analysis software. Artifact-associated spots were removed by both software- and visual-guided flags. Genepix measures signal intensities according to the local background subtraction method as a function of the median of foreground pixels minus median of background pixels. miChip data analysis was performed by using Bioconductor running the miCHIP script for data normalization in combination with the TMeV tool for data clustering.

label: RNA samples were labeled by using Cy-3

source_name: RNA extracted from mouse livers, spleens and hearts

label_protocol:
Labeling of total RNA for miChip v11 (Mouse) hybridizations has been described in detail before (Castoldi M et al., Nature Protocol, miChip: an array-based method for microRNA expression profiling using locked nucleic acid capture probes, 2008).
In brief; 1 µg of total RNA was aliquot in a volume of 10 µl of RNase free water and placed on ice. To minimize variability a labeling master mix was prepared that contains 1 x T4 RNA ligase buffer (Ambion), ATP (1.3 mM, final concentration), RNase inhibitors (20 U, final amount), RNA ligase (10 U, final amount), Cy3 labeled RNA linker (5´-p-rUrUrUrU-Cy3-3´, Biospring; 6.67 M, final concentration) and PEG (15.5%, final concentration) per reaction. 20 µl of the labeling master mix was added to the 1 µg of total RNA to yield a final volume of 30 µl. The reaction mix was then incubated for 12–16 h at 4°C. T4 RNA ligase and RNase inhibitor were heat denatured for 5 min at 95 °C and the reaction is briefly spun to collect the condensate at the bottom of the tube. Samples were stored on ice until further use. 70 µl of precipitation master mix containing sodium acetate (300 mM, final concentration) and linear acrylamide (2.5 g, final amount) per reaction was added to each sample. To precipitate the RNA, 300 µl of 100% ethanol were added to each sample and then samples are incubated for at least one hour at -80 °C. Samples are spun for 30 min at 20,000g, 4 °C. The supernatant was discarded and pellets were washed with 1 ml of 75% ethanol and centrifuged for 5 min at 13,000 rpm at room temperature. Pellets are then briefly air-dried at room temperature. Subsequently, pellets were dissolved in 440 µl of hybridization buffer [5 x SSC, 0.1% SDS, 25% formamide and 100 µg/ml of herring sperm DNA (Promega, D181B)], denatured for 5 min at 95 °C, and centrifuged for 5 min at 13,000 rpm at room temperature.

growth_protocol: Non Applicable

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) associated to mechanical shearing. RNA quality was assessed using the Bioanalyzer 2100 RNA nano chip (Agilent Technologies) and quantified with a NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies).

treatment_protocol:
Female C57/Bl6 genetic background mice aged 10-12 weeks were administrated with 25 g/gr of body weight of antimiR oligos. Oligos were designed either to target the liver specific miR-122 (antimiR-122-PM) or to carry two mismatches in the miR-122 seed sequences (antimiR-122-2MM). A third group of mice was administrated with the vehicle only (0.9% NaCl; antimiR-122-SAL).
At the time of harvest (3 and 6 weeks after administration) mice were euthanized by using CO2, and tissues were collected. Freshly harvested tissues were cut in five fragments of similar size, and snap frozen in liquid nitrogen. Subsequently all the tissues were stored in the -80˚C. In order to extract high quality RNA eppendorf tubes were transferred from the storage facility into dry ice. Fragment fragments of the tissues of interest were placed into individual eppendorf tubes and stored in dry ice. Subsequently, samples were moved into ice and 1 ml of Trizol (Invitrogen) was added to the sample. Tissues were immediately disrupted by using mechanical shearing (Tissuelyzer, Quiagen).Total RNA containing small RNA was extracted from the homogenate as previously described (Castoldi M et al., Nature Protocol, miChip: an array-based method for microRNA expression profiling using locked nucleic acid capture probes, 2008). RNA concentration and RNA quality were assessed by NanoDrop ND100 (NanoDrop technologies) and Agilent 2100 Bioanalyzer (Agilent Technologies).

value: intraperitoneal antimiR-122-PM

tag: length of treatment

value: heart

value: Female

tag: age

value: 10-12 week at beginning of treatment


title: WT-SESB 12h Replicate 1

description: Biological replicate 1 of 2. WT A niger strain treated with SESB for 12h in minimal medium, no additional carbon source


title: WT-SESB 6h Replicate 2

description: Biological replicate 2 of 2. WT A niger strain treated with SESB for 6h in minimal medium, no additional carbon source


title: antimiR-122 administration on the heart miRNome, 6W-SAL treatment

value: vehicle


title: BL6_4h vs. basal replicate 5

value: basal


title: antimiR-122 administration on the heart miRNome, 3W-SAL treatment


title: WT-SESB 6h Replicate 1

description: Biological replicate 1 of 2. WT A niger strain treated with SESB for 6h in minimal medium, no additional carbon source


title: COL+methicillin+tunicamycin Vs COL+methicillin slide 20

description:
tunicamycin sensitizes methicillin resistant S aureus (MRS A) COL to b-lactam antibiotic
Sample 1, Replicate 2 (slide 20_CTL_Cy5_EXP_Cy3.txt)

source_name: S. aureus COL grown in the presence of methicillin and traeted with tunicamycin for 2 hrs

growth_protocol: Overnight grown S. aureus COL was inoculated in TSB medium (20 ml) in a 50 ml Erlenmeyer flask containing 500 ug/ml methicillin and incubated at 30°C, with shaking at 200 rpm. Growth was measured at regular intervals at 625 nm until OD= ~0.5.

treatment_protocol: S aureus grown in the presence of methicillin was challenged with 400 ng/ml of tunicamycin for 2 hrs.


title: antimiR-122 administration on the heart miRNome, 3W-2MM treatment

value: intraperitoneal antimiR-122-2MM


title: COL+methicillin+tunicamycin Vs COL+methicillin slide 19

description:
tunicamycin sensitizes methicillin resistant S aureus (MRS A) COL to b-lactam antibiotic
Sample 1, Replicate 2 (slide 19_CTL_Cy5_EXP_Cy3.txt)

source_name: S. aureus COL grown in the presence of methicillin


title: antimiR-122 administration on the liver miRNome, 3W-PM Pool2 treatment

value: intraperitoneal antimiR-122-PM Pool2

value: liver


title: COL+methicillin+tunicamycin Vs COL+methicillin slide 18

description:
tunicamycin sensitizes methicillin resistant S aureus (MRS A) COL to b-lactam antibiotic
Sample 1, Replicate1 raw (slide 18_CTL_Cy3_EXP_Cy5.txt)


title: antimiR-122 administration on the heart miRNome, 3W-PM treatment


title: antimiR-122 administration on the liver miRNome, 3W-PM Pool1 treatment

value: intraperitoneal antimiR-122-PM Pool1


title: WT-SESB 12h Replicate 2

description: Biological replicate 2 of 2. WT A niger strain treated with SESB for 12h in minimal medium, no additional carbon source


title: antimiR-122 administration on the heart miRNome, 6W-2MM treatment


title: BL6_4h vs. basal replicate 4

value: stressed


title: BL6_4h vs. basal replicate 3


title: BL6_4h vs. basal replicate 1


title: antimiR-122 administration on the liver miRNome, 3W-2MM Pool2 treatment

value: intraperitoneal antimiR-122-2MM Pool2


title: BL6_4h vs. basal replicate 2


title: COL+methicillin+tunicamycin Vs COL+methicillin slide 17

description:
tunicamycin sensitizes methicillin resistant S aureus (MRS A) COL to b-lactam antibiotic
Sample 1, Replicate1 raw (slide 17_CTL_Cy3_EXP_Cy5.txt)


title: antimiR-122 administration on the liver miRNome, 3W-2MM Pool1 treatment

value: intraperitoneal antimiR-122-2MM Pool1


title: antimiR-122 administration on the liver miRNome, 3W-SAL Pool1 treatment


title: antimiR-122 administration on the liver miRNome, 6W-PM Pool2 treatment


title: antimiR-122 administration on the liver miRNome, 6W-2MM Pool2 treatment


title: antimiR-122 administration on the spleen miRNome, 3W-PM treatment

value: spleen


title: antimiR-122 administration on the liver miRNome, 6W-SAL Pool1 treatment


title: antimiR-122 administration on the liver miRNome, 6W-2MM Pool1 treatment


title: antimiR-122 administration on the liver miRNome, 6W-PM Pool1 treatment


title: antimiR-122 administration on the liver miRNome, 6W-SAL Pool2 treatment


title: antimiR-122 administration on the spleen miRNome, 6W-SAL treatment


title: antimiR-122 administration on the spleen miRNome, 6W-2MM treatment


title: Adult_dermal_fibroblasts_replicate1

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

country: Canada

institute: McMaster Stem Cell and Cancer Research Institute (SCC-RI)

description: cell type: Adult dermal fibroblasts

hyb_protocol: Performed according to the manufacturer's (Affymetrix) recommendations

data_processing:
Raw intensities from the CEL files were analyzed using dChIP software for data normalization, extraction of signal intensities and probeset-level analysis (see Data table below).
Supplementary .chp file: The perfect match intensities for each probe set were corrected for background and quantile-normalized (affymetrix-algorithm-name = rma-gene-default and program-name = Expression Console).

label: Biotin

label_protocol: Ambion MessageAmp II-biotin enhanced kit (manufacturer's recommendations)

extract_protocol: Total RNA was isolated using Norgen RNA isolation kit (manufacturer's recommendations)

value: Breast

value: between 30-40 yrs

tag: cell type

value: Adult dermal fibroblasts


title: antimiR-122 administration on the spleen miRNome, 3W-2MM treatment


title: CD45+ve_fibs_cytokine_treated_replicate2

description: cell type: Oct-4 transduced CD45+ve Fibs at day 37, treated with hematopoietic cytokines

scan_protocol: Performed according to the manufacturer's (Affymetrix) recommendations

value: Oct-4 transduced CD45+ve Fibs

tag: time

value: day 37

value: hematopoietic cytokines


title: antimiR-122 administration on the spleen miRNome, 3W-SAL treatment

source_name: RNA extracted from mouse spleens

tag: gender

value: Female

value: 10-12 week at beginning of treatment


title: antimiR-122 administration on the spleen miRNome, 6W-PM treatment

value: intraperitoneal antimiR-122-PM


title: CD45+ve_fibs_cytokine_treated_replicate1

source_name: Oct-4 transduced CD45+ve Fibs at day 37, treated with hematopoietic cytokines


title: 0h sulforaphane 2

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30470.gif

source_name: cells treated with DMSO

value: DMSO

tag: cell line

value: LNCaP

value: prostate cancer epithlial cell line

source_name: 0h exp

tag: treatment time

value: 0 h

value: control


title: CD45+ve_fibs_replicate2

description: cell type: Oct-4 transduced CD45+ve Fibs at day 21

source_name: Oct-4 transduced CD45+ve Fibs at day 21

value: day 21


title: Adult_dermal_fibroblasts_replicate2

description: cell type: Adult dermal fibroblasts


title: 0h 75uM Resveratrol

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28904.gif

source_name: 0h 75uM Resveratrol

value: 75 uM Resveratrol


title: Fibroblasts_day4_OCT4_replicate2

description: cell type: Adult dermal fibroblasts transduced with OCT4 (4 days post transduction)

value: 4 days post transduction


title: YPS3395.T325

status: Public on Oct 19 2010

city: Philadelphia

middle: Francis

last: Simola

state: PA

address: 1041 BRB II/III

department: Cell and Developmental Biology

institute: University of Pennsylvania

description:
raw data files: 13660615.gpr, 13666842.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf

hyb_protocol: Hybridized slides were incubated for 24–65 hours at 42◦C. Samples were hybridized to 2 dye-swapped microarrays. Unsynchronized MA line transcriptomes were produced with the same design. Corning UltraGAPS glass slides, spotted with the Operon AROS for Saccharomyces cerevisiae, V1.1, were used for all hybridizations. Each microarray targets 6388 protein-coding genes using 2 replicate spots per oligo, yielding 4 technical expression measurements per gene, strain, and timepoint. Slides were prepared for scanning by serial incubation in wash buffers and dried using both a vacuum and high-purity, filtered N2 gas.

scan_protocol: Slides were scanned at 10 μM resolution, 100% power, using an Agilent GenePix 4000B scanning confocal laser microscope. Gain was adjusted manually to optimize signal–noise ratios and to balance channel intensity distributions.

data_processing:
GenePix v6.0 (Agilent) was used for feature identification and subsequent spot quantification per channel. Bad spots were flagged manually for removal from further analysis; otherwise all spots were treated equally in GenePix. Briefly, data were log transformed and normalized for within and between slide normalization, including lowess transformation. Missing data were imputed using a combination of cubic spline interpolation and K-nearest neighbors. Details for data normalization are described in Supplemental materials and methods in the associated manuscript.
Normalized log2 fluorescence intensity of a gene at a particular timepoint of the cell cycle for a particular strain, relative to fluorescence intensity of that gene in a YPD media batch culture of the laboratory strain YPS183 in log phase; values are the average of within-slide (different spots) and between-slide (dye-swap) technical replicate measurements. The complete matrix of normalized data, including imputed expression data for 7 additional Samples (YPS2060.T111, YPS2060.T152, YPS2060.T194, YPS2067.T87, YPS2067.T111, YPS3137.T63, YPS3137.T227) since the overall experiment involves comparison of time series across yeast strains is provided as a supplementary file on the Series record.

organism: Saccharomyces paradoxus

label_protocol: Invitrogen AlexaFluor 555 and 647 fluorophores were used to label each cDNA sample.

growth_protocol: Strains were inoculated from frozen stock and cultured overnight in SD (synthetic dextrose) minimal medium at 30◦C (225 rpm). The next day cultures were diluted into fresh SD.

extract_protocol: Total RNA was extracted from each frozen cell culture sample using Qiagen’s RNeasy Kit, following manufacturer’s instructions. cDNA was prepared from 15 μg of each RNA sample using SuperScript III reverse transcriptase (Invitrogen) and compared directly to unsynchronized S. cerevisiae cDNA (YPS183 cultured at 30◦C in YPD until reaching OD600 1.1) on 2-channel spotted-oligo glass microarrays in a common reference design.

treatment_protocol: Upon reaching a culture density of OD600 ≈ 0.25, α-factor mating pheromone was added to a final concentration of 4 μM. Cultures were then incubated ≈75 min. until arrested and synchronized in late G1. The state of synchronization was determined by the appearance of < 10% shmoos and < 10% budding cells, visualized by light microscopy (100×, oil). Cultures were released from arrest by removing α-factor: 2× wash with 4◦C S medium (SD without dextrose) and resuspension of cell pellets with fresh 18◦C SD medium. Approximately 25 ml aliquots of each culture were distributed into 18 flasks and incubated at 18◦C (225 rpm). Incubation of cultures at 18◦C in SD medium more than doubles the CDC-period, allowing a more accurate comparison of measurements across strains by reducing temporal sampling variation.

tag: time (min after alpha-factor release)

organism: Saccharomyces cerevisiae

tag: growth conditions

value: unsynchronized, log phase, YPD


title: Fibroblasts_day4_OCT4_replicate1

source_name: Adult dermal fibroblasts transduced with OCT4 (4 days post transduction)

tag: tissue

value: Breast

value: between 30-40 yrs


title: YPS3395.T260

description:
raw data files: 13660612.gpr, 13666839.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3395.T301

description:
raw data files: 13660614.gpr, 13666841.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: CD45+ve_fibs_replicate1

value: Oct-4 transduced CD45+ve Fibs


title: YPS3395.T284

description:
raw data files: 13660613.gpr, 13666840.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3395.T345

description:
raw data files: 13660616.gpr, 13666843.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3395.T251

description:
raw data files: 13660611.gpr, 13666838.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: 0hr DMSO

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46713.gif

source_name: DMSO 0hr

value: DMSO control


title: YPS3395.T227

description:
raw data files: 13660610.gpr, 13666837.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3395.T111

description:
raw data files: 13660603.gpr, 13660622.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3395.T218

description:
raw data files: 13660609.gpr
raw data file dye swap pattern: 0,X
raw data file platform pattern: J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3137.T325

description:
raw data files: MDUser_13468001.gpr, MDUser_13467768.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3395.T63

description:
raw data files: 13660599.gpr, 13660620.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3137.T345

description:
raw data files: MDUser_13615095.gpr, MDUser_13607931.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3395.T194

description:
raw data files: 13660608.gpr, 13666836.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3395.T24

description:
raw data files: 13660597.gpr, 13660618.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3395.T48

description:
raw data files: 13660598.gpr, 13660619.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3395.T152

description:
raw data files: 13660606.gpr, 13666834.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3395.T135

description:
raw data files: 13660604.gpr, 13666833.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3395.T176

description:
raw data files: 13660607.gpr, 13666835.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3137.T218

description:
raw data files: MDUser_13467995.gpr, MDUser_13467765.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3137.T301

description:
raw data files: MDUser_13615094.gpr, MDUser_13607934.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3395.T0

description:
raw data files: 13660596.gpr, 13660617.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3137.T251

description:
raw data files: MDUser_13467997.gpr, MDUser_13467766.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3137.T260

description:
raw data files: MDUser_13615097.gpr, MDUser_13607933.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3395.T87

description:
raw data files: 13660602.gpr, 13660621.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3137.T284

description:
raw data files: MDUser_13467998.gpr, MDUser_13467767.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3137.T194

description:
raw data files: MDUser_13615096.gpr, MDUser_13607936.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: 0hr sulforaphane

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35784.gif

source_name: 80ug total RNA untreated


title: YPS3137.T152

description:
raw data files: MDUser_13615099.gpr, MDUser_13607935.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3137.T135

description:
raw data files: MDUser_13468328.gpr, MDUser_13463052.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3137.T24

description:
raw data files: MDUser_13615101.gpr, MDUser_13607937.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3137.T111

description:
raw data files: MDUser_13615098.gpr, MDUser_13607938.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3137.T48

description:
raw data files: MDUser_13468324.gpr, MDUser_13463050.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3137.T0

description:
raw data files: MDUser_13468323.gpr, MDUser_13463049.gpr, MDUser_13607939.gpr, MDUser_13615100.gpr
raw data file dye swap pattern: 0,1,1,0
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2006, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3137.T176

description:
raw data files: MDUser_13468368.gpr, MDUser_13463054.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3060.T345

description:
raw data files: 13613768.gpr, 13613496.gpr, 13659925.gpr
raw data file dye swap pattern: 0,1,0
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3060.T325

description:
raw data files: FGC_13290725.gpr, MDUser_13463319.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3060.T301

description:
raw data files: 13613770.gpr, 13613495.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3060.T227

description:
raw data files: 13613772.gpr, 13613497.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3060.T260

description:
raw data files: 13613769.gpr, 13613498.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3060.T284

description:
raw data files: FGC_13290724.gpr, MDUser_13463237.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2005, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3060.T251

description:
raw data files: MDUser_13463028.gpr
raw data file dye swap pattern: X,1
raw data file platform pattern: J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3060.T63

description:
raw data files: 13613773.gpr, 13613760.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3060.T176

description:
raw data files: FGC_13290729.gpr, MDUser_13466865.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2005, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3060.T194

description:
raw data files: 13608164.gpr, 13613782.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3060.T152

description:
raw data files: 13608165.gpr, 13613500.gpr, 13607649.gpr
raw data file dye swap pattern: 0,1,0
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3137.T87

description:
raw data files: MDUser_13468325.gpr, MDUser_13463051.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3060.T218

description:
raw data files: FGC_13290726.gpr, MDUser_13466864.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2005, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3060.T87

description:
raw data files: 13613774.gpr, MDUser_13463029.gpr, 13613501.gpr
raw data file dye swap pattern: 0,1,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2006, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3060.T135

description:
raw data files: FGC_13290728.gpr, MDUser_13466866.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2005, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3060.T48

description:
raw data files: 13613776.gpr, MDUser_13463238.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3060.T24

description:
raw data files: 13613775.gpr, 13613762.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3060.T111

description:
raw data files: 13613771.gpr, 13613502.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2079.T301

description:
raw data files: MDUser_13609104.gpr, MDUser_13609092.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2079.T345

description:
raw data files: MDUser_13609101.gpr, MDUser_13609089.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2079.T260

description:
raw data files: MDUser_13609106.gpr, MDUser_13609091.gpr, 13659917.gpr
raw data file dye swap pattern: 0,1,0
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2079.T325

description:
raw data files: MDUser_13615268.gpr, MDUser_13615282.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2079.T284

description:
raw data files: MDUser_13615267.gpr, MDUser_13615254.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS3060.T0

description:
raw data files: MDUser_13463239.gpr, MDUser_13463031.gpr, 13613778.gpr, 13613761.gpr
raw data file dye swap pattern: 0,1,0,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2006, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2079.T227

description:
raw data files: MDUser_13609105.gpr, MDUser_13609095.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2079.T251

description:
raw data files: MDUser_13615270.gpr, MDUser_13615253.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2079.T218

description:
raw data files: MDUser_13615269.gpr, MDUser_13615255.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2079.T176

description:
raw data files: MDUser_13615274.gpr, MDUser_13615257.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2079.T194

description:
raw data files: MDUser_13609108.gpr, MDUser_13609094.gpr, 13659916.gpr
raw data file dye swap pattern: 0,1,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2079.T152

description:
raw data files: MDUser_13609107.gpr, MDUser_13609097.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2079.T24

description:
raw data files: MDUser_13609112.gpr, MDUser_13609098.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2073.T345

description:
raw data files: MDUser_13463370.gpr, MDUser_13467769.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2079.T0

description:
raw data files: MDUser_13615278.gpr, MDUser_13615265.gpr, 13659918.gpr, MDUser_13609102.gpr, MDUser_13609111
raw data file dye swap pattern: 0,1,1,1,0
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2073.T301

description:
raw data files: MDUser_13463369.gpr, MDUser_13463525.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2073.T325

description:
raw data files: MDUser_13463240.gpr, MDUser_13463230.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2079.T87

description:
raw data files: MDUser_13615276.gpr, MDUser_13615262.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2079.T111

description:
raw data files: MDUser_13609110.gpr, MDUser_13609096.gpr, 13659919.gpr
raw data file dye swap pattern: 0,1,0
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2073.T227

description:
raw data files: MDUser_13463365.gpr, MDUser_13463523.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2073.T260

description:
raw data files: MDUser_13463366.gpr, MDUser_13463524.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2073.T251

description:
raw data files: FGC_13291197.gpr, MDUser_13463233.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2005, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2079.T135

description:
raw data files: MDUser_13615273.gpr, MDUser_13615256.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2073.T218

description:
raw data files: FGC_13296345.gpr, MDUser_13463235.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2005, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2073.T176

description:
raw data files: FGC_13296344.gpr, MDUser_13463236.gpr, 13613777.gpr
raw data file dye swap pattern: 0,1,1
raw data file platform pattern: J.Kim Yeast 2005, J.Kim Yeast 2006, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2073.T111

description:
raw data files: MDUser_13463017.gpr, MDUser_13463315.gpr, 13608160.gpr
raw data file dye swap pattern: 0,1,0
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2006, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2073.T194

description:
raw data files: MDUser_13463364.gpr, MDUser_13463522.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2079.T48

description:
raw data files: MDUser_13615275.gpr, MDUser_13615266.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2067.T345

description:
raw data files: 13614966.gpr, 13607664.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2073.T48

description:
raw data files: FGC_13296335.gpr, MDUser_13466862.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2005, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2073.T87

description:
raw data files: 13608163.gpr, MDUser_13467608.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2073.T135

description:
raw data files: MDUser_13463241.gpr, 13613779.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2079.T63

description:
raw data files: MDUser_13609109.gpr, MDUser_13609099.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2073.T152

description:
raw data files: MDUser_13463018.gpr, 13613780.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2073.T0

description:
raw data files: FGC_13296334.gpr, 13613792.gpr, MDUser_13463014.gpr
raw data file dye swap pattern: 0,1,0
raw data file platform pattern: J.Kim Yeast 2005, J.Kim Yeast 2007, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2073.T24

description:
raw data files: MDUser_13463015.gpr, MDUser_13463317.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2073.T63

description:
raw data files: MDUser_13463016.gpr, 13613783.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2073.T284

description:
raw data files: FGC_13290703.gpr, MDUser_13463231.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2005, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2067.T325

description:
raw data files: 13614964.gpr, 13607665.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2067.T284

description:
raw data files: 13614959.gpr, 13607667.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2067.T301

description:
raw data files: 13614961.gpr, 13607666.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2067.T260

description:
raw data files: 13611621.gpr, 13607668.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2067.T227

description:
raw data files: 13611618.gpr, 13607678.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2067.T251

description:
raw data files: 13611620.gpr, 13607674.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2067.T218

description:
raw data files: 13611619.gpr, 13611593.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2067.T176

description:
raw data files: 13611614.gpr, 13611588.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2067.T0

description:
raw data files: 13614951.gpr, 13614965.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2067.T194

description:
raw data files: 13611616.gpr, 13611589.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2067.T63

description:
raw data files: 13614956.gpr, 13611595.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2067.T24

description:
raw data files: 13614954.gpr, 13611597.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2067.T135

description:
raw data files: 13614955.gpr, 13611590.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2066.T345

description:
raw data files: 13615241.gpr, 13615236.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2067.T48

description:
raw data files: 13614953.gpr, 13611594.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2067.T152

description:
raw data files: 13614958.gpr, 13611591.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2066.T325

description:
raw data files: 13615244.gpr, 13615234.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2066.T301

description:
raw data files: 13609235.gpr, 13615260.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2066.T87

description:
raw data files: 13615329.gpr, 13615318.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2066.T135

description:
raw data files: 13615314.gpr
raw data file dye swap pattern: X,1
raw data file platform pattern: J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2066.T111

description:
raw data files: 13615327.gpr, 13615317.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2066.T251

description:
raw data files: 13609229.gpr
raw data file dye swap pattern: 0,X
raw data file platform pattern: J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2066.T260

description:
raw data files: 13609231.gpr, 13609240.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf