title: Subject 5 / lung subsegment instillated by LPS

city: Marcy L'Etoile

first: Frederic

last: Reynier

address: Chemin de l'Orme

country: France

institute: bioMerieux

hyb_protocol: Fragmented and labeled cDNA was hybridized for 18 h at 50°C in a hybridization solution containing 7% DMSO. Hybridization was performed using GeneChip Human Genome U133 Plus 2.0 arrays (Affymetrix). After washing, chips were stained with streptavidin-phycoerythrin according to Affymetrix EukGE-WS2v4 protocol using the Fluidic FS450 station.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000. Affymetrix GeneChip Operating Software version 1.4 (GCOS) was used to manage Affymetrix GeneChip array data and to automate the control of GeneChip fluidics stations and scanners.

data_processing: Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affy package of the Bioconductor microarray analysis environment.  Before the analysis of differentially expressed genes, a filter was applied to minimize the technical noise. In both groups, the genes with an expression level under a threshold value corresponding to the overall median value from all microarrays were removed. Linear model for microarray, as implemented in the LIMMA package available on the Bioconductor environment, was selected to identify differentially expressed genes

source_name: Macrophages obtained from a contralateral lung segment challenged with LPS

label_protocol: cDNA was synthesized from 50 ng of total RNA using the WT-OvationTM System (NuGEN, San Carlos, CA, USA) powered by Ribo-SPIATM technology. Fragmented cDNA was end labeled with a biotin-conjugated nucleotide analog (DLR-1a; Affymetrix, Santa Clara, CA, USA) using terminal transferase (Roche Diagnostics, Mannheim, Germany).

extract_protocol: BAL fluid (BALF) was immediately centrifuged for 10 min at 1200 rpm at 4°C. BALF cells were passed over a 40 µm nylon filter (BD Falcon, Bedford, MA) and resuspended in ice-cold sterile automated magnetic cell sorting and separation (autoMACS) buffer (PBS, 0.5% bovine serum albumin, 2 mM EDTA; pH = 7.4). Subsequently, cells were incubated for 15 min with CD71 microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) at 4°C. Cells were washed again in autoMACS buffer and purified by autoMACS (Miltenyi Biotec). Total and viable cell counts were determined before and after the isolation procedure using a Burker-Turk haemocytometer and trypan blue (Emergo, Landsmeer, the Netherlands). Additionally, cytospins were prepared before and after autoMACS and stained with Giemsa. Total and differential cell counts revealed a recovery of 35-40% macrophages and a purity of isolated macrophages of >95% in all groups. After isolation, alveolar macrophages were dissolved in RNAeasy lysis Buffer (buffer RLT, QIAGEN, Hilden, Germany) and stored at -80°C until used for RNA isolation with RNeasy Mini kit (QIAGEN, Hilden, Germany).  Hence, in each subject alveolar macrophages were harvested from a lung segment instilled with LPS and from a contralateral lung segment instilled with sterile saline.

treatment_protocol: Ten milliliters of sterile saline was instilled into a lung subsegment (either the right middle lobe or lingula) followed by instillation of LPS (in 10 ml saline) from Escherichia coli (United States Pharmacopeial Convention, Lot G, Bureau of Biologics, United States Food and Drug Administration, Rockville, MD) into the contralateral lung, using a flexible video bronchoscope. The subjects were randomized to left or right lungs for saline or LPS instillation. The subjects received LPS at a dose of 4 ng/kg body weight. A bilateral bronchoalveolar lavage (BAL) was performed 6 hours post-challenge; seven successive 20 ml aliquots of pre-warmed 0.9% saline were instilled in the saline-challenged subsegment of the lung and each aspirated immediately with low suction. This procedure was repeated in the LPS-challenged subsegment of the contralateral lung.

value: alveolar macrophage

value: LPS

tag: individual

value: Subject 5


title: Subject 7 / lung subsegment instillated by LPS

status: Public on Sep 15 2012

type: RNA

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: treatment

value: Subject 7

tag: gender

value: male


title: Subject 7 / lung subsegment instillated by Saline

source_name: Macrophages obtained from a contralateral lung segment challenged with saline

value: saline


title: Subject 5 / lung subsegment instillated by Saline


title: Subject 6 / lung subsegment instillated by Saline

value: Subject 6


title: RW-SS-7

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

country: USA

institute: Oregon State University

description: Gene expression data from regular weight mice exposed to sidestream smoke (SS)

hyb_protocol: Biotin-labeled cRNA (15 µg) was fragmented to a size range between 50-200 bases for array hybridization.  After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.

data_processing: Raw intensity data were quantile normalized by Robust Multi-Array Analysis (RMA) summarization and probes were subject to quality control to measure the efficiency of transcription, integrity of hybridization, and consistency of qualitative calls.

organism: Mus musculus

source_name: Regular weight mice exposed to sidestream smoke (SS), biological rep5

label_protocol: Complementary DNA was synthesized from 3 µg of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA from the cDNA template, according to manufacturer’s protocols (Affymetrix One-Cycle Target Labeling Kit).

growth_protocol: Control, i.e., nonobese or regular weight (RW) and diet-induced obese (DIO) male C57BL/6 mice at 13 weeks of age were purchased from the Jackson Laboratories (Bar Harbor, ME).  For this study, RW mice are defined as those mice fed a regular diet consisting of pelleted PMI® 5002 Certified Rodent Diet (PMI 5002 Rodent Diet®, Richmond, IN; ~5kcal% fat) throughout the study.  DIO mice were fed a high calorie/high fat diet consisting of pelleted D12492 Rodent Diet (Research Diets Inc., New Brunswick, NJ; 60kal% fat) throughout the study starting at six weeks of age for a total of nine weeks prior to the start of the 4-day LPS exposure study.

extract_protocol: Total RNA was collected using the RNeasy Kit (Qiagen, Valencia, CA).

treatment_protocol: Groups (N=8 biological replicates) of RW and DIO C57BL/6 mice (15-weeks old at start of exposures) were exposed to either filtered air (sham controls, SC), mainstream (MS) or sidestream (SS) cigarette smoke by nose-only inhalation exposure for 5 hr/day for a total of eight exposures over two weeks as follows: 5 consecutive days of exposure, followed by 2 days with no exposure, then three days of exposure, with necropsies occurring the day following the last exposure.

tag: strain

tag: tissue

value: lung

tag: body weight

value: regular weight

value: Sidestream smoke (SS)


title: Subject 4 / lung subsegment instillated by Saline

value: Subject 4


title: DIO-SS-3

description: Gene expression data from diet induced obese mice exposed to sidestream smoke (SS)

source_name: Diet induced obese mice exposed to sidestream smoke (SS), biological rep3

value: obese


title: Subject 4 / lung subsegment instillated by LPS


title: RW-SS-3

source_name: Regular weight mice exposed to sidestream smoke (SS), biological rep3


title: Subject 6 / lung subsegment instillated by LPS


title: RW-SS-8

source_name: Regular weight mice exposed to sidestream smoke (SS), biological rep6


title: RW-SS-6


title: RW-SS-4

source_name: Regular weight mice exposed to sidestream smoke (SS), biological rep4


title: RW-SS-2

source_name: Regular weight mice exposed to sidestream smoke (SS), biological rep2


title: DIO-SS-2

source_name: Diet induced obese mice exposed to sidestream smoke (SS), biological rep2


title: Subject 2 / lung subsegment instillated by Saline

value: Subject 2


title: Subject 3 / lung subsegment instillated by Saline

value: Subject 3


title: DIO-MS-8

description: Gene expression data from diet induced obese mice exposed to mainstream smoke (MS)

source_name: Diet induced obese mice exposed to mainstream smoke (MS), biological rep8

value: Mainstream smoke (MS)


title: Subject 2 / lung subsegment instillated by LPS


title: Subject 1 / lung subsegment instillated by Saline

value: Subject 1


title: DIO-MS-5

source_name: Diet induced obese mice exposed to mainstream smoke (MS), biological rep5


title: DIO-MS-7

source_name: Diet induced obese mice exposed to mainstream smoke (MS), biological rep7


title: DIO-MS-6

source_name: Diet induced obese mice exposed to mainstream smoke (MS), biological rep6


title: RW-SS-1

source_name: Regular weight mice exposed to sidestream smoke (SS), biological rep1


title: Subject 1 / lung subsegment instillated by LPS


title: DIO-MS-1

source_name: Diet induced obese mice exposed to mainstream smoke (MS), biological rep1


title: RW-MS-8

description: Gene expression data from regular weight mice exposed to mainstream smoke (MS)

source_name: Regular weight mice exposed to mainstream smoke (MS), biological rep6


title: Set2, MSC, biological rep4

city: Houston

first: LI

last: SHEN

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

hyb_protocol: Samples were amplified, labeled, and 10μg of cDNA was hybridized to the HG-U133 Plus 2.0 Affymetrix GeneChip array according the manufacturer’s protocol

scan_protocol: Gene Array Scanned using Microarray Suite software

data_processing: RMA (Robust Multichip Average) algorithm is used for quantification of the data - PEC & PCO samples are processed together, and MCO & MSC were processed together.

source_name: mesenchymal stem cells (cultured alone)

growth_protocol: MSCs cultured in MSC GM media (Lonza); PECs cultured in EGM-2MV media (Lonza); Co-cultures cultured in EGM-2MV media

extract_protocol: Total RNA was extracted using the TRIzol method (Invitrogen, Carlsbad, CA). RNA was purified using the RNeasy mini-kit (Qiagen, Alameda, CA) and the quality

treatment_protocol: All cells were subjected to sorting via magnetic bead selection using CD31 antibody (endothelial cell specific)

value: mesenchymal stem cells


title: Set2, MCO, biological rep4

source_name: mesenchymal stem cells (co-cultured with PECs then FACS purified)

label_protocol: Samples were amplified, labeled, and 10μg of cDNA was hybridized to the HG-U133 Plus 2.0 Affymetrix GeneChip array according the manufacturer’s protocol


title: DIO-MS-2

source_name: Diet induced obese mice exposed to mainstream smoke (MS), biological rep2


title: DIO-MS-4

source_name: Diet induced obese mice exposed to mainstream smoke (MS), biological rep4


title: Set2, MSC, biological rep1


title: Set2, MCO, biological rep1


title: RW-MS-6


title: RW-MS-5

source_name: Regular weight mice exposed to mainstream smoke (MS), biological rep5


title: Set2, MSC, biological rep2


title: Set2, MSC, biological rep3


title: RW-MS-7


title: RW-MS-4

source_name: Regular weight mice exposed to mainstream smoke (MS), biological rep4


title: Set2, MCO, biological rep2


title: Set1, PCO, biological rep4

source_name: pulmonary endothelial cells (co-cultured with MSCs then FACS purified)

value: pulmonary endothelial cells


title: Set1, PCO, biological rep1


title: RW-MS-3

source_name: Regular weight mice exposed to mainstream smoke (MS), biological rep3


title: RW-MS-2

source_name: Regular weight mice exposed to mainstream smoke (MS), biological rep2


title: Set1, PCO, biological rep2


title: RW-MS-1

source_name: Regular weight mice exposed to mainstream smoke (MS), biological rep1


title: DIO-SC-8

description: Gene expression data from diet induced obese mice exposed to filtered air (sham control, SC)

source_name: Diet induced obese mice exposed to filtered air (sham control, SC), biological rep8

value: control


title: Set1, PEC, biological rep3

source_name: pulmonary endothelial cells (cultured alone)


title: Set1, PEC, biological rep2


title: Set1, PEC, biological rep4


title: Set2, MCO, biological rep3


title: Set1, PCO, biological rep3


title: RW-SS-5

source_name: Regular weight mice exposed to sidestream smoke (SS), biological rep5


title: Set1, PEC, biological rep1


title: DIO-SC-7

source_name: Diet induced obese mice exposed to filtered air (sham control, SC), biological rep7


title: DIO-SC-2

source_name: Diet induced obese mice exposed to filtered air (sham control, SC), biological rep2


title: DIO-SC-4

source_name: Diet induced obese mice exposed to filtered air (sham control, SC), biological rep4


title: DIO-SC-1

source_name: Diet induced obese mice exposed to filtered air (sham control, SC), biological rep1


title: DIO-SC-3

source_name: Diet induced obese mice exposed to filtered air (sham control, SC), biological rep3


title: A549 siRNA SDS3 CNTRL 2

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description: Gene expression from A549 cells after transfection with non-targeting siRNA, replicate 2

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.

data_processing: Array intensities were processed using the RMA algorithm in R/bioconductor.

source_name: A549 lung cancer cells

label_protocol: Biotinylated cRNA was prepared according to the Ambion Biotin Enhanced MessageAmp II aRNA amplification kit (according to manual rev. C rev 5/16/2008) from 1 ug total RNA.

growth_protocol: 7.5x10^4 A549 cells were plated in each well of a 6-well plate.  Cells were plated in F-12K media (Cellgro) with 10% FBS in triplicate.

extract_protocol: Cells were lysed in Trizol (Invitrogen) three days after transfection, RNA was extracted and then processed through an RNeasy column (QIAGEN) using the RNA clean-up protocol.

treatment_protocol: A549 cells were transfected  one day after plating using 50 nM siRNAs (Ambion non-targeting siRNA (AM4637); FAM60A siRNA (s33909)) and Dharmafect 1 transfection reagent.

tag: cell line

value: human lung cancer

tag: sirna

value: non-targeting


title: A549 siRNA SDS3 CNTRL 1

description: Gene expression from A549 cells after transfection with non-targeting siRNA, replicate 1


title: A549 siRNA FAM60A 3

description: Gene expression from A549 cells after transfection with FAM60A targeting siRNA, replicate 3

value: FAM60A targeting


title: DIO-SC-5

source_name: Diet induced obese mice exposed to filtered air (sham control, SC), biological rep5


title: A549 siRNA SDS3 CNTRL 3

description: Gene expression from A549 cells after transfection with non-targeting siRNA, replicate 3


title: Human PBMC total RNA in baseline s12 [QPCR]

city: Kuopio

first: Otto

middle: Taavetti

last: Mykkänen

address: Yliopistonranta 1

department: Public Health and Clinical Nutrition

country: Finland

institute: University of Eastern Finland

data_processing:
Raw Ct values (non-normalized data) were quantified with a standard curve on each plate per transcript and the quantities were corrected by a calibrator (0.3 ng/µL cDNA). The last 12 columns of the non_normalized data contains calibration control sample data from plate specific calibrator used with the data normalization process.
Data was normalized to the endogenous control, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene to gain an average of the total RNA equivalents per sample and then log-transformed (ln). The equation in short from the amount of mRNA (ng) quantified: (target (ng)/calibrator(ng)) /(GADPH(ng) /calibrator(ng)) = relative expression to GADPH

label: FAM

source_name: Human PBMCs

label_protocol: FAM™ with ABI Prism 7500 SDS software (TaqMan Gene Expression Assays; Foster City, CA, USA)

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit according to the manufacturer’s instructions (Qiagen, Valencia, CA). The RNA concentration was measured using a NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE). RNA was reverse transcribed into cDNA for microarrays and quantitative PCR (QPCR) using the High-Capacity cDNA Archive Kit (Applied Biosystems, Foster City, CA).

treatment_protocol: PBMCs were available from all study participants at 0 and 8 weeks. The total RNA for microarrays were selected from 3 subject PBMCs isolated from overnight fasting blood samples collected in a BD Vacutainer CPT Cell Preparation Tube with Sodium Citrate (BD, Franklin Lakes, NJ) according to the manufacturer’s instructions.

value: female

tag: age (years)

tag: time point

value: 0 wk

tag: group

value: intervention (test)

tag: acute inflammation during the interventio (plasma hscrp >10mg/mlyes/no)

value: no


title: A549 siRNA SDS3 1

description: Gene expression from A549 cells after transfection with SDS3 targeting siRNA, replicate 1

value: SDS3 targeting


title: DIO-SC-6

source_name: Diet induced obese mice exposed to filtered air (sham control, SC), biological rep6

value: lung


title: A549 siRNA SDS3 2

description: Gene expression from A549 cells after transfection with SDS3 targeting siRNA, replicate 2


title: A549 siRNA FAM60A 1

description: Gene expression from A549 cells after transfection with FAM60A targeting siRNA, replicate 1


title: A549 siRNA SDS3 3

description: Gene expression from A549 cells after transfection with SDS3 targeting siRNA, replicate 3


title: RW-SC-7

description: Gene expression data from regular weight mice exposed to filtered air (sham control, SC)

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep7

value: regular weight


title: RW-SC-5

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep5


title: RW-SC-3

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep3


title: RW-SC-8

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep8


title: A549 siRNA FAM60A CNTRL 1


title: RW-SC-4

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep4


title: A549 siRNA FAM60A 2

description: Gene expression from A549 cells after transfection with FAM60A targeting siRNA, replicate 2


title: RW-SC-2

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep2


title: A549 siRNA FAM60A CNTRL 3


title: RW-SC-6

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep6


title: Colo205RC PLX4720 resistant cell line

first: Scott

last: Kopetz

address: 1515 Holcombe Blvd, Unit 426

hyb_protocol: hybridization to Affymetrix HGU133 plus2 according to the standard Affymetrix protocol

scan_protocol: imaging on GeneChip Scanner 3000 (Affymetrix)

data_processing: The data were first quantified using the MAS5 algorithm. The Robust Multiarray Analysis (RMA) algorithm was used to normalize and quantify the data.

source_name: Colo205RC PLX4720 resistant cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Culture dish + Media with 10%serum

extract_protocol: Total RNA was extracted cell lines using the Qiagen RNeasy Kit according to the manufacturer's protocol.

treatment_protocol: Resistant lines were grown in PLX4720-free media x 24 hours prior to harvesting

value: Colo205RC PLX4720 resistant cell line

value: colon cancer


title: HT29 parental cell line

source_name: HT29 parental cell line

value: HT29 parental cell line


title: A549 siRNA FAM60A CNTRL 2


title: DIO-LPS_8

description: Gene expression data from diet induce obese mice exposed to LPS

source_name: Diet induce obese mice exposed to LPS, biological rep8

treatment_protocol: Groups of RW and DIO C57BL/6 mice (15-weeks old at start of exposures) were exposed to either filtered air (sham controls, SC) or 0.5 µg/L LPS by nose-only inhalation exposure for 1 hr/day for 4 days over a 10-day period with necropsies occurring on the day following the last exposure (Day 11).

value: obese

tag: agent

value: LPS


title: HT29RC PLX4720 resistant cell line

source_name: HT29RC PLX4720 resistant cell line

value: HT29RC PLX4720 resistant cell line


title: DIO-LPS_5

source_name: Diet induce obese mice exposed to LPS, biological rep5


title: RW-SC-1

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep1

value: control


title: DIO-LPS_4

source_name: Diet induce obese mice exposed to LPS, biological rep4


title: Colo205 parental cell line

source_name: Colo205 parental cell line

value: Colo205 parental cell line


title: Human PBMC total RNA after bilberry enriched diet s3

hyb_protocol: Standard Illumina protocol with streptavidin-Cy3 detection (Amersham, Piscataway, NJ, USA).

scan_protocol: Standard protocol in Illumina Beadstation and BeadStudio (Illumina, Inc., version 3.0.14).

data_processing:
The data was quantile normalized and resulting gene specific bead-summary data was used as the basis for the gene expression analyses in the statistical programming language R, primarily using beadarray (Dunning et al. 2007) and limma (Smyth et al.2004) packages from the Bioconductor project (Gentleman et al. 2004).
Dunning MJ, Smith ML, Ritchie ME, Tavaré S. beadarray: R classes and methods for Illumina bead-based data. Bioinformatics. 2007 Aug 2007 Jun 22. PubMed PMID: 17586828.15;23(16):2183-4. Epub
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. PubMed PMID: 15461798; PubMed Central PMCID: PMC545600.
Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004;3:Article3. Epub 2004 Feb 12. PubMed PMID: 16646809.

label_protocol: The cDNA was in vitro transcribed to biotin-labeled complementary RNA (cRNA). Labeling, hybridizations and scanning were carried out in The Finnish Microarray and Sequencing Centre (Turku, Finland).

value: PBMC

tag: age

value: 44 years

value: 8 wk


title: DIO-LPS_6

source_name: Diet induce obese mice exposed to LPS, biological rep6


title: DIO-LPS_3

source_name: Diet induce obese mice exposed to LPS, biological rep3


title: DIO-LPS_2

source_name: Diet induce obese mice exposed to LPS, biological rep2


title: Small intestinal Lin-c-Kit-Sca-1- cells

city: Osaka

first: Youngae

last: Lee

address: 3-1 Yamadaoka, Suita

country: Japan

institute: Osaka University

description: Gene expression data from intestinal Lin-c-Kit-Sca-1- cells

hyb_protocol: Following fragmentation, 50 ul of cDNA was hybridized for 18 hr at 45°C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner (Affymetrix).

data_processing: The data were analyzed with Microarray Suite software (Version 5.0, Affymetrix) and GeneSpring software (Silicon Genetics) with RMA normalization and log2 transformation.

source_name: Lin-c-Kit-Sca-1- cells isolated from small intestinal LP

label_protocol: cDNA was synthesized according to the Ovation Pico WTA system protocol (NuGEN) from 20 ng total RNA and biotinylated cDNA was prepared according to the FL-Ovation cDNA Biotin Mudule V2 protocol (NuGEN) from 5 ug total cDNA .

growth_protocol: Small intestinal LP cells were isolated from BALB/C female mice and stained with the biotinylated anti-mouse lineage cocktail, anti-mouse c-Kit (CD117, clone 2B8), and anti-mouse Ly-6A/E (Sca-1, clone D7) antibodies, and then Lin-c-Kit+Sca-1- cells and Lin-c-Kit-Sca-1- cells were sorted by FACSAria.

extract_protocol: Total RNA was extracted withTrizol and was purified with RNeasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Normal BALB/c mice at 8 weeks old.

value: BALB/c

value: Female

value: 8 week-old

tag: number

value: 5 mice


title: DIO-LPS_7

source_name: Diet induce obese mice exposed to LPS, biological rep7

value: lung


title: Human PBMC total RNA after bilberry enriched diet s2

value: female


title: DIO-LPS_1

source_name: Diet induce obese mice exposed to LPS, biological rep1


title: Small intestinal Lin-c-Kit+Sca-1- cells

description: Gene expression data from intestinal Lin-c-Kit+Sca-1- cells

source_name: Lin-c-Kit+Sca-1- cells isolated from small intestinal LP


title: DIO-SC_8

description: Gene expression data from diet induce obese mice exposed to filtered air (sham control, SC)

source_name: Diet induce obese mice exposed to filtered air (sham control, SC), biological rep8


title: Human PBMC total RNA after bilberry enriched diet s1

value: 58 years


title: DIO-SC_7

source_name: Diet induce obese mice exposed to filtered air (sham control, SC), biological rep7


title: Human PBMC total RNA in baseline s3

source_name: Human PBMC total RNA in baseline s3

value: 0 wk


title: DIO-SC_4

source_name: Diet induce obese mice exposed to filtered air (sham control, SC), biological rep4


title: Mice SI Smooth Muscle_IL17+6-shogaol_rep2

city: Inashiki-gun

first: Mitsue

last: Nishiyama

state: Ibaraki

address: 3586 Yoshiwara, Ami-machi

department: Tsumura Research Laboratories

institute: Tsumura & Co.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx Hybridization buffer HI-RPM (Agilent) was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays 4x44k (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then rinsed with Acetonitrile for cleaning up and drying.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505A) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Mice small intestine, 24h culture with IL17 and 6-shogaol, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Smooth musle strips were carefully peeled off from mice small intestine in the saline. About 1cm of strips were incubated in the antibiotics added medium 199 with or without IL17 and 6-shogaol for 24hours.

extract_protocol: RNA was prepared using RNeasy Fibrous Tissue Mini Kit (QIAGEN K.K., Japan) following the manufacture's protocol.

value: Balb/c

value: small intestinal smooth muscle


title: DIO-SC_2

source_name: Diet induce obese mice exposed to filtered air (sham control, SC), biological rep2

value: obese


title: DIO-SC_3

source_name: Diet induce obese mice exposed to filtered air (sham control, SC), biological rep3


title: DIO-SC_5

source_name: Diet induce obese mice exposed to filtered air (sham control, SC), biological rep5


title: Mice SI Smooth Muscle_IL17+6-shogaol_rep1

source_name: Mice small intestine, 24h culture with IL17 and 6-shogaol, replicate 1


title: DIO-MS-3

description: Gene expression data from diet induced obese mice exposed to mainstream smoke (MS)

source_name: Diet induced obese mice exposed to mainstream smoke (MS), biological rep3

value: Mainstream smoke (MS)


title: Mice SI Smooth Muscle_IL17+6-shogaol_rep6

source_name: Mice small intestine, 24h culture with IL17 and 6-shogaol, replicate 6


title: Subject 3 / lung subsegment instillated by LPS

source_name: Macrophages obtained from a contralateral lung segment challenged with LPS

value: alveolar macrophage

value: LPS

value: Subject 3

value: male


title: Mice SI Smooth Muscle_IL17+6-shogaol_rep3

source_name: Mice small intestine, 24h culture with IL17 and 6-shogaol, replicate 3


title: Mice SI Smooth Muscle_IL17+6-shogaol_rep4

source_name: Mice small intestine, 24h culture with IL17 and 6-shogaol, replicate 4


title: DIO-SC_1

source_name: Diet induce obese mice exposed to filtered air (sham control, SC), biological rep1

value: control


title: DIO-SC_6

source_name: Diet induce obese mice exposed to filtered air (sham control, SC), biological rep6


title: RW-LPS_6

description: Gene expression data from regular weight mice exposed to LPS

source_name: Regular weight mice exposed to LPS, biological rep6

value: regular weight


title: Mice SI Smooth Muscle_IL17+6-shogaol_rep5

source_name: Mice small intestine, 24h culture with IL17 and 6-shogaol, replicate 5


title: RW-LPS_5

source_name: Regular weight mice exposed to LPS, biological rep5


title: RW-LPS_8

source_name: Regular weight mice exposed to LPS, biological rep8


title: Mice SI Smooth Muscle_IL17_rep5

source_name: Mice small intestine, 24h culture with IL17, replicate 5


title: RW-LPS_4

source_name: Regular weight mice exposed to LPS, biological rep4


title: Mice SI Smooth Muscle_IL17_rep4

source_name: Mice small intestine, 24h culture with IL17, replicate 4


title: RW-LPS_3

source_name: Regular weight mice exposed to LPS, biological rep3


title: RW-SC_6

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep6


title: partial responder clopidogrel and partial responder ASA WPM

city: Sao Paulo

first: Andre

middle: Ducati

last: Luchessi

address: Av. Prof Lineu Prestes, 580

country: Brazil

institute: University of Sao Paulo

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Exon 1.0 ST Array . GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the a GeneArray Scanner (Affymetrix).

data_processing:
Raw data were processed with the Expression Console (Affymetrix) with gene leval and for background correction and normalization. For the microarray data statystic analisis was performed using Partek® Genomic Suite (Partek inc, St. Louis USA) . We defined a probeset as present when it had a P value <0.01
HuEx-1_0-st-v2.r2.dt1.hg18.core.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: blood partial responder clopidogrel and partial responder ASA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: not applicable

extract_protocol: Total RNA extraction was performed using the commercially available kit PAXgene Blood RNA, and samples were automatically prepared using spin-column kits Qiacube.

treatment_protocol: All patients were treated crhonically with acetylsalicylic acid (ASA) (100 mg/day) and clopidogrel (75 mg/day).

tag: bmi

tag: aru value

tag: pru value

value: blood

value: clopidogrel and  ASA

tag: response


title: RW-SC_5

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep5


title: RW-SC_4

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep4


title: RW-LPS_2

source_name: Regular weight mice exposed to LPS, biological rep2


title: Mice SI Smooth Muscle_IL17_rep2

source_name: Mice small intestine, 24h culture with IL17, replicate 2


title: RW-SC_3

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep3


title: RW-LPS_1

source_name: Regular weight mice exposed to LPS, biological rep1


title: RW-LPS_7

source_name: Regular weight mice exposed to LPS, biological rep7


title: Mice SI Smooth Muscle_IL17_rep6

source_name: Mice small intestine, 24h culture with IL17, replicate 6


title: RW-SC_7

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep7


title: Human PBMC total RNA in baseline s2

source_name: Human PBMC total RNA in baseline s2

tag: cell type

value: PBMC

tag: gender

value: 48 years


title: partial responder clopidogrel and responder ASA SRR

source_name: blood partial responder clopidogrel and responder ASA

tag: tissue

tag: treatment


title: responder clopidogrel and responder ASA SQA

source_name: blood responder clopidogrel and responder ASA

value: responder clopidogrel and responder ASA


title: Human PBMC total RNA in baseline s1

source_name: Human PBMC total RNA in baseline s1

value: female


title: RW-SC_2

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep2

tag: strain

value: lung

tag: body weight


title: RW-SC_8

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep8


title: Mice SI Smooth Muscle_IL17_rep3

source_name: Mice small intestine, 24h culture with IL17, replicate 3

value: Balb/c


title: Mice SI Smooth Muscle_control_rep5

source_name: Mice small intestine, 24h culture, replicate 5

value: small intestinal smooth muscle


title: non responder clopidogrel and partial responder ASA RVP

source_name: blood non responder clopidogrel and partial responder ASA


title: RW-SC_1

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep1


title: Mice SI Smooth Muscle_control_rep6

source_name: Mice small intestine, 24h culture, replicate 6


title: partial responder clopidogrel and partial responder ASA SPA

source_name: blood partial responder clopidogrel and partial responder ASA


title: non responder clopidogrel and partial responder ASA RFG


title: Mice SI Smooth Muscle_control_rep4

source_name: Mice small intestine, 24h culture, replicate 4


title: hrp3Δ nucleosome mapping

type: genomic

city: Canberra

first: Tamas

last: Fischer

state: ACT

address: Building 131, Garran Rd

department: The John Curtin School of Medical Research

country: Australia

institute: The Australian National University

description:
hrp3Δ
used for the definition of the first and last nucleosomes according to the annotated transcriptional start and stop sites

hyb_protocol: Hybridization, blocking, and washing was performed following the Agilent instructions

scan_protocol: Scanning of arrays was eprformed using Agilent DNA Microarray Scanner and Agilent Scan control software (v A.8.4.1.)

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) Protocol: ChIP_107_Sep09 with modifications; Background Substraction Method - Local Background; Feature Set For Surface Fit - FeaturesInNegativeControlRange; Perform Filtering For Surface Fit - True; Adjust Background Globally - True; Adjust Background Globally to - 0; Normalization Correction Method - Lowess Only

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: cells in log phase

label_protocol: 1 μg of mononucleosomal and genomic DNA was labeled in two steps using Invitrogen Bioprime Array CGH kit followed by Cy5 and Cy3 labeling according to the manufacturer instructions (GE Healthcare).

growth_protocol: Yeast strains were grown in YEA rich medium (30°C, 150 rpm) up to log phase

extract_protocol: Phenol-Chloroform extraction followed by ethanol precipitation. Mononucleosomal DNA fractions of the different Mnase concentrations were purified from agarose gel and pooled.

treatment_protocol: Cells growing logarithmically were fixed in 0.5 % formaldehyde (30°C, 100 rpm) and spheroplasted. Spheroplasts were incubated with different concentraions of micrococcal nuclease (MNase, 2-28 U/mL). Genomic DNA was extracted from mock control (no MNase treatment), reaction was stopped by adding a stop buffer (5 % SDS, 100 mM EDTA pH8.0), followed by RNaseA and proteinaseK treatment and an overnight incubation at 65°C.

value: deletion strain hrp3Δ

tag: dna subtype

value: mononucleosomal DNA

value: genomic DNA


title: mit1Δ nucleosome mapping

description:
mit1Δ
used for the definition of the first and last nucleosomes according to the annotated transcriptional start and stop sites

value: deletion strain mit1Δ


title: non responder clopidogrel and non responder ASA ORJ

source_name: blood non responder clopidogrel and non responder ASA


title: set2Δ nucleosome mapping

description:
set2Δ
used for the definition of the first and last nucleosomes according to the annotated transcriptional start and stop sites

value: deletion strain set2Δ


title: pob3Δ 1 nucleosome mapping

description:
pob3Δ 1
used for the definition of the first and last nucleosomes according to the annotated transcriptional start and stop sites

value: deletion strain pob3Δ


title: non responder clopidogrel and non responder ASA MRM

value: male


title: Mice SI Smooth Muscle_IL17_rep1

source_name: Mice small intestine, 24h culture with IL17, replicate 1


title: hrp1Δhrp3Δ 1 nucleosome mapping

description:
hrp1Δhrp3Δ 1
used for the definition of the first and last nucleosomes according to the annotated transcriptional start and stop sites

value: deletion strain hrp1Δhrp3Δ


title: pob3Δ 2 nucleosome mapping

description:
pob3Δ 2
used for the definition of the first and last nucleosomes according to the annotated transcriptional start and stop sites


title: hrp1Δ nucleosome mapping

description:
hrp1Δ
used for the definition of the first and last nucleosomes according to the annotated transcriptional start and stop sites

value: deletion strain hrp1Δ


title: hrp1Δhrp3Δ 2 nucleosome mapping

description:
hrp1Δhrp3Δ 2
used for the definition of the first and last nucleosomes according to the annotated transcriptional start and stop sites


title: wildtype 2 nucleosome mapping

description:
wildtype 2
used for the definition of the first and last nucleosomes according to the annotated transcriptional start and stop sites

value: wildtype strain


title: Mice SI Smooth Muscle_control_rep1

source_name: Mice small intestine, 24h culture, replicate 1

value: control


title: alp13Δ nucleosome mapping

description:
alp13Δ
used for the definition of the first and last nucleosomes according to the annotated transcriptional start and stop sites

value: deletion strain alp13Δ


title: Mice SI Smooth Muscle_control_rep2

source_name: Mice small intestine, 24h culture, replicate 2


title: Mice SI Smooth Muscle_control_rep3

source_name: Mice small intestine, 24h culture, replicate 3


title: wildtype 3 nucleosome mapping

description:
wildtype 3
used for the definition of the first and last nucleosomes according to the annotated transcriptional start and stop sites


title: non responder clopidogrel and  partial responder ASA JSM

source_name: blood non responder clopidogrel and  partial responder ASA

value: blood

value: clopidogrel and  ASA


title: HeLaPARG2_t-RA_3

city: Illkirch

first: Frédéric

last: Coin

address: 1, rue laurent fries

department: Functional Genomics and Cancer

institute: IGBMC

description: Hela expressing an shRNA against PARG

hyb_protocol: Following fragmentation and end-labeling, 1.9 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Human Gene 1.0 ST arrays (Affymetrix) interrogating 28,853 genes represented by approximately 27 probes spread across the full length of the gene.

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.1. CEL files were further processed with Affymetrix Expression Console software version 1.1 to calculate probeset signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

source_name: HeLa, shRNA against PARG, t-RA

label_protocol: Biotinylated single strand cDNA targets were prepared, starting from 250 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671), according to Affymetrix recommendations.

extract_protocol: Total RNA from shPARG and shCTL cells were extracted before or 3 hours after t-RA treatment (10μM) using GenElute Mammalian Total RNA Miniprep kit (Sigma). Two independent experiments were performed and named Sample 1 or Sample 2. RNA quality was verified by analysis on the 2100 Bioanalyzer (Agilent).

treatment_protocol: t-RA treatment 10mM for 3h

tag: cell line

value: HeLa

tag: genotype/variation

value: shRNA against PARG


title: responder clopidogrel and non responder ASA MGA

source_name: blood responder clopidogrel and non responder ASA


title: responder clopidogrel and responder ASA MQM

source_name: blood responder clopidogrel and responder ASA

value: responder clopidogrel and responder ASA


title: wildtype 1 nucleosome mapping

description:
wildtype 1
used for the definition of the first and last nucleosomes according to the annotated transcriptional start and stop sites


title: Bacteria suspension heated to a core temperature of 71°C                - Replicate 5

city: QUEBEC

first: ANTHONY

last: GUERNEC

state: QUEBEC

address: 2425 RUE DE L'AGRICULTURE

department: ANIMAL SCIENCE

country: Canada

institute: UNIVERSITE LAVAL

description:
Biological replicate 5 of 5. Bacteria at 71°C compared to the common reference prepared from control bacteria at 37°C
Sample name: Treatment 4 - rep5

hyb_protocol: Hybridization was performed onto Agilent Escherichia coli gene expression microarray 8x15K according to the two-color microarray-based procaryote analysis protocol (Agilent technologies). Alexa fluor labelled cDNA obtained from the 5 replicates of control cultures at 37°C were pooled and used as a common reference for all hybridization. An aliquot of 300ng of this pooled control cDNA and 300ng of labelled cDNA from one of the experimental group were mixed together with blocking agent in the hybridization buffer (Gene expression hybridization kit, Agilent technologies) and loaded onto one of the eight microarray areas available on the slide. The biological replicates of the different treatment were randomly distributed on the slides. The microarray slides were incubated in the hybridization chamber at 65°C for 17h under constant vertical rotation. After hybridization, the slides were removed from the chambers and washed sequentially with GE washer buffers 1 and 2 (Agilent technologies).

scan_protocol: Microarray slides were scanned on a TECAN PowerScannerTM (TECAN group Ltd., Switzerland) and features extraction were processed with the Array-Pro 6.3 ANALYZER software (Media Cybernetics Inc., Bethesda, MD, USA).

data_processing: LOWESS normalized data obtained from log2 of processed Red signal (treated)/processed Green signal (control) are given in the data table below. All microarray data were analyzed using R software and Limma package (part of Bioconductor). All the probes encoding for positive and negative controls were not used and have been removed. Only raw data superior to background values and with homogeneous fluorescent signals were considered (H < 0.2). Red and green signal heterogeneity was estimated as followed: H = |(trimmed mean of raw intensity - median of raw intensity)|/|(0.5*(trimmed mean of raw intensity + median of raw intensity)). After LOWESS normalization, the differences between the four heat-treatments were tested by Analysis of Variance (ANOVA) followed by a priori tests (P-value < 0.0001 and P-value FDR after Benjamini Yekutieli adjustment < 0.01). Six contrasts (Contrast1:T1 vs T2, Contrast2:T1 vs T3, Contrast3: T1 vs T4, Contrast4: T2 vs T3, Contrast5: T2 vs T4, Contrast6: T3 vs T4) were performed. Normalized Log2 ratio between treatments and the results of the statistical analysis have been linked as a supplementary file on the Series record.

label: alexa fluor 555

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Control bacteria at 37°C (common reference).  Total RNA isolated from 5 indepedent cultures (pooled after cDNA labeling).

label_protocol: Indirect labelling of RNA templates was based on the initial protocol described by Seidel and modified by Schroeder, Snesrud and Yang for the TIGR standard operating procedure (see Hegde P et al, 2000, Biotechniques 29(3):548-562). An amount of 5μg of total RNA were reverse transcribed for 3h at 42°C using Superscript II enzyme and random hexamers in the presence of 0.5mM each dATP, dCTP, dGTP, 0.3mM dTTP (Invitrogen, Life technologies) and 0.2mM 5-(3-aminoallyl)-dUTP (Sigma Aldrich). After hydrolysis of the remaining RNAs and purification on Qiaquick columns (Qiaquick PCR purification kit; Qiagen Inc.), the amine-modified cDNA obtained from control and heated cells were coupled to the succinimidyl ester of Alexa fluor 555 and 647 reactive dyes, respectively (Molecular probes, Life technologies). Unincorporated dyes were removed by purification on Qiaquick PCR purification columns.

growth_protocol: For each biological replicate, frozen aliquots (500μl) of E. coli K12 stock cultures were subcultured in 10 ml of Brain Heart Infusion (BHI) and incubated overnight at 37°C. Cells were then sub-cultured (1% v/v) into 50ml BHI broth and incubated at 37°C for 24h under constant agitation (150 rpm). The bacterial suspensions were then inoculated (1% v/v) in 200ml BHI broth and grown in the same conditions to stationary phase (OD600nm of 0.9).

extract_protocol: Frozen cell pellets were lyzed with lysozyme (Sigma Aldrich) and proteinase K (Qiagen Inc.) at room temperature. Total RNA was isolated from cell lysates using RNeasy Midi Kit according to the manufacturer's instructions (Qiagen Inc.). All RNA samples were then treated with DNase I (Ambion, Life technologies) before a phenol/chloroform purification and an overnight precipitation at -20°C in absolute ethanol containing LiCl 8M. After centrifugation, RNA pellets were air-dried in a vacuum concentrator ( vacufuge plus; Eppendorf).

treatment_protocol: After reaching an OD600nm of 0.9, cell cultures were placed immediately in a shaking water bath along with another BHI flask carrying a type T thermocouple connected to a MultiPaq 21 datalogger (Datapaq Inc.) for temperature profile and the process lethality values monitoring in real time. Bacteria suspension were heated at 58°C to process lethality values of 2 and 3, at 60°C to a process lethality value of 3, or until a temperature of 71°C was reached. Just after heating, cell suspension was cooled in an iced water bath under constant agitation (150 rpm) until the temperature dropped back to no less than 37°C in order to avoid cold stress. Cell suspensions were then centrifuged and the remaining cell pellets were treated with RNA protect bacteria reagent (Qiagen Inc.) prior to freezing at -80°C.

value: strain K12 substrain MG1655

tag: growth protocol

value: Controls grown to an optimal temperature of 37°C

tag: growth phase

value: stationary phase (grown to an OD600nm of 0.9)

label: alexa fluor 647

source_name: Bacteria at 71°C

value: Treatment 4 (core temperature of 71°C)


title: HeLaPARG1_t-RA_3

description: Hela expressing an shRNA against PARG


title: Bacteria suspension heated to a core temperature of 71°C                - Replicate 2

description:
Biological replicate 2 of 5. Bacteria at 71°C compared to the common reference prepared from control bacteria at 37°C
Sample name: Treatment 4 - rep2


title: HeLaPARG2_t-RA_0

description: Hela expressing an shRNA against PARG

source_name: HeLa, shRNA against PARG, non-treated


title: Bacteria suspension heated to a core temperature of 71°C                - Replicate 3

description:
Biological replicate 3 of 5. Bacteria at 71°C compared to the common reference prepared from control bacteria at 37°C
Sample name: Treatment 4 - rep3


title: hrp3Δ gene expression

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) Protocol: GE2_107_Sep09 with modifications; Background Substraction Method - Local Background; Detrend on Replicates Only - False; Robust Neg Ctrl Stats? - True; Choose universal error, or the most conservative - Use Universal Error Model; Dye Normalization Probe Selection Method/Variable Rank Tolerance - True; Max Number Ranked Probes - -1; Normalization Correction Method - Lowess Only; Spikein Target Used - False

source_name: rRNA depleted RNA of hrp3Δ

label_protocol: Invitrogen SuperScript Indirect cDNA labeling system, labeled with Cy5(mutant) and Cy3(WT) according to the manufacturer instructions (GE Healthcare).

extract_protocol: Ribosomal RNA was depleted from total RNA extracts of all strains using a mixture of 5' biotinylated rRNA probes. rRNA depleted RNA was reverse transcribed using the Invitrogen SuperScript Indirect cDNA labeling system, primed with random hexamers

treatment_protocol: RNA was isolated from either wildtype strains or deletion mutants using TRI Reagent (Sigma Aldrich) following the manufacturers instructions

value: deletion strain hrp3Δ

tag: rna subtype

value: rRNA depleted RNA

source_name: rRNA depleted RNA of wiltype


title: Bacteria suspension heated to a core temperature of 71°C                - Replicate 4

description:
Biological replicate 4 of 5. Bacteria at 71°C compared to the common reference prepared from control bacteria at 37°C
Sample name: Treatment 4 - rep4


title: hrp1Δhrp3Δ gene expression

source_name: rRNA depleted RNA of hrp1Δhrp3Δ


title: hrp1Δ 1 gene expression

description: hrp1Δ 1

source_name: rRNA depleted RNA of hrp1Δ


title: HeLaCTL2_t-RA_3

description: Hela expressing an shRNA control

source_name: HeLa, shRNA control, t-RA

value: shRNA control


title: partial responder clopidogrel and responder ASA JBP

source_name: blood partial responder clopidogrel and responder ASA

value: male

tag: age


title: Bacteria suspension heated at 60°C to a process lethality value of 3 - Replicate 4

description:
Biological replicate 4 of 4. Bacteria at 60°C F = 3 compared to the common reference prepared from control bacteria at 37°C
Sample name: Treatment 3 - rep4

source_name: Bacteria at 60°C F = 3

value: Treatment 3 (60°C F = 3)


title: partial responder clopidogrel and partial responder ASA JCS

source_name: blood partial responder clopidogrel and partial responder ASA

tag: bmi


title: Bacteria suspension heated at 60°C to a process lethality value of 3 - Replicate 3

description:
Biological replicate 3 of 4. Bacteria at 60°C F = 3 compared to the common reference prepared from control bacteria at 37°C
Sample name: Treatment 3 - rep3


title: Bacteria suspension heated to a core temperature of 71°C                - Replicate 1

description:
Biological replicate 1 of 5. Bacteria at 71°C compared to the common reference prepared from control bacteria at 37°C
Sample name: Treatment 4 - rep1


title: hrp1Δ 2 gene expression

description: hrp1Δ 2

value: deletion strain hrp1Δ

value: wildtype strain


title: partial responder clopidogrel and partial responder ASA JMO

tag: aru value


title: HeLaCTL1_t-RA_3

description: Hela expressing an shRNA control


title: HeLaCTL1_t-RA_0

description: Hela expressing an shRNA control

source_name: HeLa, shRNA control, non-treated


title: responder clopidogrel and partial responder ASA FDCLAP

source_name: blood responder clopidogrel and partial responder ASA

tag: pru value


title: partial responder clopidogrel and non responder ASA FDRP

source_name: blood partial responder clopidogrel and non responder ASA

tag: response


title: Bacteria suspension heated at 60°C to a process lethality value of 3 - Replicate 2

description:
Biological replicate 2 of 4. Bacteria at 60°C F = 3 compared to the common reference prepared from control bacteria at 37°C
Sample name: Treatment 3 - rep2


title: Bacteria suspension heated at 58°C to a process lethality value of 3 - Replicate 4

description:
Biological replicate 4 of 4. Bacteria at 58°C F = 3 compared to the common reference prepared from control bacteria at 37°C
Sample name: Treatment 2 - rep4

source_name: Bacteria at 58°C F = 3

value: Treatment 2 (58°C F = 3)


title: responder clopidogrel and partial responder ASA JGG

value: blood


title: partial responder clopidogrel and partial responder ASA BRS

value: clopidogrel and  ASA


title: alp13Δ 1 ChIP

description: alp13Δ 1

source_name: cells in log phase

label_protocol: 1 μg of WGA amplified samples was labeled in two steps using Invitrogen Bioprime Array CGH kit followed by Cy5 and Cy3 labeling according to the manufacturer instructions (GE Healthcare).

extract_protocol: purification via Quiagen MinElute kit

treatment_protocol: Logarithmically growing cells were fixed with 3% pFA and afterwards with 0.1% DMA. Fixed samples were lysed and the DNA sonicated into DNA fragments of about 500-1000 bp. 10 uL of the supernatant were used for the whole cell extract (WCE). ChIP was performed using a H3K9/K14ac antibody (Diagenode) with binding overnight. The ChIP samples were bound to the beads for 1.5 h to magnetic protein A beads (millipore) followed by a series of extensive washing. Elution was performed twice at 65°C. WCE and ChIP samples were incubated with RNaseA for 2 h at 37°C, afterwards with proteinaseK at 37°C for 2h and de-crosslinked at 65°C overnight.

value: deletion strain alp13Δ

tag: sample

value: ChIP sample

value: WCE genomic DNA


title: non responder clopidogrel and responder ASA CRG

source_name: blood non responder clopidogrel and responder ASA

tag: gender


title: Bacteria suspension heated at 58°C to a process lethality value of 3 - Replicate 3

description:
Biological replicate 3 of 4. Bacteria at 58°C F = 3 compared to the common reference prepared from control bacteria at 37°C
Sample name: Treatment 2 - rep3

source_name: Control bacteria at 37°C (common reference).  Total RNA isolated from 5 indepedent cultures (pooled after cDNA labeling).

value: strain K12 substrain MG1655


title: HeLaCTL2_t-RA_0

description: Hela expressing an shRNA control

value: HeLa


title: Bacteria suspension heated at 60°C to a process lethality value of 3 - Replicate 1

description:
Biological replicate 1 of 4. Bacteria at 60°C F = 3 compared to the common reference prepared from control bacteria at 37°C
Sample name: Treatment 3 - rep1

value: Controls grown to an optimal temperature of 37°C

value: stationary phase (grown to an OD600nm of 0.9)


title: HeLaPARG1_t-RA_0

description: Hela expressing an shRNA against PARG

value: shRNA against PARG


title: set2Δ 2 ChIP

description: set2Δ 2

value: deletion strain set2Δ


title: Bacteria suspension heated at 58°C to a process lethality value of 3 - Replicate 2

description:
Biological replicate 2 of 4. Bacteria at 58°C F = 3 compared to the common reference prepared from control bacteria at 37°C
Sample name: Treatment 2 - rep2


title: partial responder clopidogrel and partial responder ASA CGG

tag: tissue


title: alp13Δ 2 ChIP

description: alp13Δ 2


title: partial responder clopidogrel and non responder ASA BMP

tag: treatment


title: partial responder clopidogrel and responder ASA ASPM


title: set2Δ 1 ChIP

description: set2Δ 1

tag: strain


title: PRDX4 KO, ERO1alpha and beta double mutant 2

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Hybridized using Affymetrix Hybridization, Wash and Stain Kit

scan_protocol: GCS3000 using AGCC 3

data_processing: RMA

label: Biotin

label_protocol: Labelled using Ambion WT Expression Kit and Affymetrix Hybridization, Wash and Stain Kit

growth_protocol: Cultured in DMEM with NEAA, Pencillin Streptomycin, Glutamax

extract_protocol: RNAs were extracted using Trizol (Invitrogen) according to manufacturer's instruction

tag: genetic background

tag: genotype

tag: cell type

value: Cultured T antigen transformed Mouse Embrionic Fibroblasts


title: ERO1alpha and beta double mutant 3

description: ERO1alpha and beta double mutant

source_name: ERO1alpha and beta double mutant

value: ERO1alpha and beta double mutant


title: hrp1Δhrp3Δ 1 ChIP

description: hrp1Δhrp3Δ 1

value: deletion strain hrp1Δhrp3Δ


title: PRDX4 KO, ERO1alpha and beta double mutant 3


title: wildtype 1 ChIP

description: wildtype 1


title: hrp1Δhrp3Δ 2 ChIP

description: hrp1Δhrp3Δ 2


title: PRDX4 KO, ERO1alpha and beta double mutant 1


title: Bacteria suspension heated at 58°C to a process lethality value of 2 - Replicate 5

description:
Biological replicate 5 of 5. Bacteria at 58°C F = 2 compared to the common reference prepared from control bacteria at 37°C
Sample name: Treatment 1 - rep5

source_name: Bacteria at 58°C F = 2

value: Treatment 1 (58°C F = 2)


title: Bacteria suspension heated at 58°C to a process lethality value of 3 - Replicate 1

description:
Biological replicate 1 of 4. Bacteria at 58°C F = 3 compared to the common reference prepared from control bacteria at 37°C
Sample name: Treatment 2 - rep1


title: non responder clopidogrel and partial responder ASA APL

source_name: blood non responder clopidogrel and partial responder ASA

value: male


title: ERO1alpha and beta double mutant 2

description: ERO1alpha and beta double mutant


title: wildtype 2 ChIP

description: wildtype 2

value: wildtype strain


title: Bacteria suspension heated at 58°C to a process lethality value of 2 - Replicate 4

description:
Biological replicate 4 of 5. Bacteria at 58°C F = 2 compared to the common reference prepared from control bacteria at 37°C
Sample name: Treatment 1 - rep4


title: responder clopidogrel and non responder ASA APF

source_name: blood responder clopidogrel and non responder ASA

value: blood


title: ERO1alpha and beta double mutant 1

description: ERO1alpha and beta double mutant


title: Bacteria suspension heated at 58°C to a process lethality value of 2 - Replicate 1

description:
Biological replicate 1 of 5. Bacteria at 58°C F = 2 compared to the common reference prepared from control bacteria at 37°C
Sample name: Treatment 1 - rep1


title: Bacteria suspension heated at 58°C to a process lethality value of 2 - Replicate 3

description:
Biological replicate 3 of 5. Bacteria at 58°C F = 2 compared to the common reference prepared from control bacteria at 37°C
Sample name: Treatment 1 - rep3


title: Bacteria suspension heated at 58°C to a process lethality value of 2 - Replicate 2

description:
Biological replicate 2 of 5. Bacteria at 58°C F = 2 compared to the common reference prepared from control bacteria at 37°C
Sample name: Treatment 1 - rep2


title: Wild-type MEFs 1

description: Wild-type MEFs

source_name: Wild-type MEFs

value: Wild-type


title: Dysferlinopathy DYS individual 25

status: Public on Sep 14 2012

city: rotterdam

first: Mario

last: Pescatori

address: Westplein 11

country: Netherlands

institute: Health e-genomics

hyb_protocol: Hybridization was performed on an illumina air hybridization owen. Slides were washed  and stained using reagents and protocols provided by Illumina.

scan_protocol: Slides were scanned on an Illumina Iscan BeadChip reader, following the protocol provided by illumina for the HumanHT-12_V3_0_R1  BeadChip.

data_processing: Data were extracted from the scan files using Illumina Genome Studio and exported both as raw and preprocessed expression data. Before analysis, the dataset was quantile normalized, local background was not subtracted, and the expression values for the missing bead were imputed using the GenomeStudio imputation algoritm

source_name: Muscle tissue

label_protocol: Biotin labelled cRNA was produced using the Ambion TotalPrep RNA amplification kit

extract_protocol: Total RNA was extracted from muscle biopsies using the Trizol reagent followed by an additional clean up step on Qiagen RNAeasy column, following protocols provided by the manufacturer

tag: individual

value: deltoid

value: M

tag: disease state

value: Dysferlinopathy DYS


title: set2Δ gene expression

source_name: rRNA depleted RNA of set2Δ

value: deletion strain hrp1Δ

value: rRNA depleted RNA

source_name: rRNA depleted RNA of wiltype


title: hrp1Δhrp3Δ gene expression

source_name: rRNA depleted RNA of hrp1Δhrp3Δ


title: partial responder clopidogrel and partial responder ASA AMP

source_name: blood partial responder clopidogrel and partial responder ASA

value: clopidogrel and  ASA


title: Wild-type MEFs 2

description: Wild-type MEFs


title: partial responder clopidogrel and partial responder ASA AMR


title: Inflammatory Myopathy individual 21

value: quadriceps

value: Inflammatory Myopathy


title: hrp3Δ gene expression

source_name: rRNA depleted RNA of hrp3Δ

value: deletion strain hrp3Δ


title: Dermatomyositis  DM individual 18

value: F

value: Dermatomyositis  DM


title: Dysferlinopathy DYS individual 23


title: alp13d 2 gene expression

description: alp13d 2

source_name: rRNA depleted RNA of alp13Δ


title: alp13Δ 1 gene expression

description: alp13Δ 1


title: Dysferlinopathy DYS individual 24


title: Dysferlinopathy DYS individual 22


title: Necrotizing Myopathy individual 19

value: Necrotizing Myopathy


title: Inflammatory Myopathy individual 20


title: FSHD T2-STIR + individual 13

value: FSHD T2-STIR +


title: Dermatomyositis  DM individual 17


title: Polymyositis  PM individual 16

value: Polymyositis  PM


title: FSHD T2-STIR - individual 9

value: FSHD T2-STIR -


title: Polymyositis  PM individual 15


title: Wheat_Biorep6_TIme2

city: Winnipeg

first: Sylvie

last: Cloutier

state: MB

address: 195 Dafoe Road

institute: Agriculture and Agri-Food Canada

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45◦C on GeneChip Wheat Genome Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix scanner 3000

data_processing: Data and statistical analyses for identification of differentially regulated genes were performed with the R-Bioconductor software package “affy” (Gentleman et al. 2004) using the following settings: background correction using robust multi-chip analysis and Lowess normalized and summarised using median Polish algorithm.   Student’s t-tests were performed to detect significant differences in expression between time points.   Benjamini-Hochberg correction was applied to the P-values to control false discovery rate (Benjamini and Hochberg, 1995).

organism: Triticum aestivum

source_name: 6 HPI Puccinia triticina

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using the GeneChip® 3' IVT express kit.

growth_protocol: The six transgenic lines were grown in growth room at 20◦C with a 16h photoperiod and a photon flux density of approximately 145 µmol m−2s−2.

extract_protocol: Total RNA was extracted independently for each individual leaf sample using the TRI Reagent according to manufacturer’s instructions (Ambion).

treatment_protocol: Plants were inoculated at the 4-5 leaf stage with urediniospores of P.  triticina avirulence genotype 96-14-1 CCDS mixed with a non-phytotoxic mineral oil (Bayol-Esso Canada). Twenty-five µl of a 16∙6 mg uredinispores/ml of mineral oil inoculum were sprayed onto the plants through an inoculator at about 3-5 psi until runoff of the spore suspensions. The inoculated plants were allowed to dry for at least 30 min to let the oil volatilize and then incubated overnight in a 100% humidity chamber (Percival model I-60D, Percival Scientific)

value: Leaves

tag: genotype/variation

value: Lr1 transgenic line


title: FSHD T2-STIR + individual 8

value: paravertebral


title: Wheat_Biorep6_TIme3

source_name: 24 HPI Puccinia triticina


title: FSHD T2-STIR + individual 14

value: biceps femoris


title: Wheat_Biorep4_TIme1

source_name: 0 h (prior to inoculation) Puccinia triticina


title: Wheat_Biorep5_TIme2


title: Wheat_Biorep5_TIme1


title: Wheat_Biorep2_TIme3


title: FSHD T2-STIR + individual 12

value: M


title: Wheat_Biorep4_TIme2


title: Wheat_Biorep1_TIme2


title: Wheat_Biorep5_TIme3


title: Wheat_Biorep1_TIme3


title: Wheat_Biorep3_TIme1


title: Wheat_Biorep6_TIme1


title: Wheat_Biorep2_TIme2


title: Wheat_Biorep2_TIme1


title: Wheat_Biorep3_TIme3


title: Wheat_Biorep4_TIme3


title: WT_C_4.CEL

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

description: SRA accession from the same sample: SRR453569

hyb_protocol: Samples were hybridized with GeneChip yeast2 Arrays (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) by A GeneChip Fluidics Station FS-400 and GeneChip Scanner 3000 7G

data_processing: Probe Logarithmic Intensity Error (PLIER)

organism: Saccharomyces cerevisiae CEN.PK113-7D

label_protocol: Labelling was done according to the Affymetrix GeneChip Expression Analysis Technical Manual.

growth_protocol: Batch and Chemostat cultivation on glucose

extract_protocol: Total RNA was isolated from frozen cell pellets using FastRNA® Pro RED kit (QBiogene, Inc, USA)

treatment_protocol: biomass samples were taken at steadystate, cooled down imeediately and centrifuged with cooling, The cell prllets were frozen in liquid nitrogen

tag: cultivation protocol

value: Chemostat


title: WT_B_3.CEL

description: SRA accession from the same sample: SRR453568

value: Batch


title: Wheat_Biorep1_TIme1


title: WT_B_1.CEL

description: SRA accession from the same sample: SRR453566


title: WT_B_2.CEL

description: SRA accession from the same sample: SRR453567


title: WT_C_8.CEL

description: SRA accession from the same sample: SRR453570


title: Wheat_Biorep3_TIme2


title: FSHD T2-STIR - individual 11


title: FSHD T2-STIR - individual 10


title: WT_C_9.CEL

description: SRA accession from the same sample: SRR453571


title: A549_3h_GPBP-1_v1

city: Valencia

first: Fernando

last: Revert

state: Valencia

address: Autopista del Saler 16

country: Spain

institute: Centro de Investigación Príncipe Felipe

description: Gene expression after 3 hours with GPBP-1

hyb_protocol: 1600 ng of labeled cRNA were hybridized with the Whole Human Genome Oligo Microarray Kit (Agilent) containing 41000+ unique human genes and transcripts following 'One-Color Microarray-Based Gene Expression Analysis' protocol Version 6.0 (Agilent).

scan_protocol: Arrays were scanned in an Agilent Microarray Scanner according to the manufacturer's instructions and data extracted using Agilent Feature Extraction Software 10.7.1 following the Agilent protocol GE1_107_Sep09, grid template 014850_D_F_20100430 and the QC Metric Set GE1_QCMT_Sep09.

data_processing: Raw data files were background corrected using supplier’s methodology (Agilent Feature Extraction Software) and intensity signal standardized across arrays via quantile normalization algorithm.

label_protocol: 150 ng of total RNA were used to produce Cyanine 3-CTP-labeled cRNA using the Low Input Quick Amp Labelling Kit One-Color (Agilent) according to the manufacturer’s instructions

growth_protocol: A549 cells were grown with Dulbecco's modified Eagle's medium + 10% Fetal Bovine Serum at 37 C and 5% CO2

extract_protocol: Cells were lysed and total RNA was extracted with RNeasy Protect mini kit (Qiagen) according to manufacturer's recommendations.

treatment_protocol: Human A549 cells were cultured with or without 200 ng/mL of rcGPBP-1 for 3 hours

tag: cell line

tag: tissue origin

value: lung

value: epithelial, adenocarcinoma


title: FSHD T2-STIR - individual 8

value: quadriceps


title: A549_3h_GPBP-1_v2


title: A549_3h_TBS_v1

description: Gene expression after 3 hours with TBS


title: URE-shControl-3

city: Bronx

first: Boris

last: Bartholdy

state: NY

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

description: sorted GFP+ URE cells infected with luciferase control shRNA

hyb_protocol: Hybridization kit; GeneChip Hybridization Wash and Stain Kit (Affymetrix). GeneChip; Affymetrix Mouse Gene 1.0ST microarrays (Affymetrix)

scan_protocol: GeneChip Scanner 3000 7G system (Affymetrix).

data_processing: Microarray data was normalized with the RMA algorithm of Affymetrix Power Tools  (v 1.178). Log2-transformed signals are listed. A t-test with Welch approximation for  unequal  group variances with p-values based on t-distribution was performed with a cutoff of p<0.1 in Multiple Experiment Viewer v.4 pilot2 (http://www.tm4.org/mev/) (PMID: 16939790). Subsequently, the probes with -log10(p) value <0.05 and a mean difference >  0.5 were considered differentially expressed and used for further analysis.

source_name: URE cell line

label_protocol: 10ng RNA was used for amplification of cDNA by Nugen Ovation pico WTA system following the manufacture’s protocol. labeling was performed by GeneChip WT terminal labeling kit (Affymetrix).

growth_protocol: Cultured in M5300+10%FBS containing 15%WEHI supernatant and 15%BHK supernatant.

extract_protocol: Total RNA was extracted from 1X10E5 cells using the RNeasy Micro Kit (Qiagen).

treatment_protocol: URE cells were infected with short-hairpin-containing pSIH1-H1-copGFP lentiviral vector (System Biosciences, Mountain View, CA) containing either nucleotide sequences targeting luciferase (shControl) or HLX (shHLX). URE cells were transduced with short-hairpin-containing lentivirus for Hlx knockdown study and then GFP-positive cells were sorted. After culture for several days, RNA was extracted from 1X10E5 cells by RNeasy Micro Kit (Qiagen).

tag: vector

value: luciferase control

tag: infection protocol

value: URE


title: URE-shControl-1

value: GFP+ URE cells infected with luciferase control shRNA


title: adult_KSL-HLX_expression_vector-3

description: Sorted Lin-Kit+Sca-1+ cells from wild-type FVB/nJ bone marrow infected with mouse HLX (pCAD-HLX-IRES-GFP) lentivirus, cultured for 2 days, then sorted for GFP+ cells

label_protocol: 3ng RNA was used for amplification of cDNA by Nugen Ovation pico WTA system following the manufacture’s protocol. labeling was performed by GeneChip WT terminal labeling kit (Affymetrix).

growth_protocol: Cells were cultured in Iscove’s modified Dulbecco’s medium (IMDM) containing FBS, mIL-3, mIL-6 and mSCF.

extract_protocol: GFP-positive cells were sorted 2days after transduction by FACS and RNA was extracted from 5,000 to 10,000 GFP-positive cells using the RNeasy Micro Kit (Qiagen).

treatment_protocol: Sorted Lin-Kit+Sca-1+ cells from young adult wild-type FVB/nJ bone marrow were infected with control (pCAD-IRES-GFP) or Hlx lentivirus (pCAD-IRES-GFP-Hlx) in  in Iscove’s modified Dulbecco’s medium (IMDM) containing FBS, mIL-3, mIL-6 and mSCF  in the presence of 8ug/ml polybrene. GFP-positive cells were sorted 2 days after transduction.

value: HLX

value: infected, GFP+, sorted adult bone marrow  Lin-Kit+Sca-1+ cells

tag: age

value: young adult

value: FVB/nJ


title: URE-shHLX-3

description: sorted GFP+ URE cells infected with shRNA directed against Hlx (shHlx)

value: shHLX

value: GFP+ URE cells infected with shRNA against Hlx


title: URE-shControl-2


title: adult_KSL-control_vector-3

description: Sorted Lin-Kit+Sca-1+ cells from wild-type FVB/nJ bone marrow infected with control (pCAD-IRES-GFP) lentivirus, cultured for 2 days, then sorted for GFP+ cells

value: control


title: URE-shHLX-2


title: URE-shHLX-1


title: adult_KSL-control_vector-2

source_name: Sorted Lin-Kit+Sca-1+ cells from wild-type FVB/nJ bone marrow infected with control (pCAD-IRES-GFP) lentivirus, cultured for 2 days, then sorted for GFP+ cells


title: A549_3h_TBS_v2

description: Gene expression after 3 hours with TBS


title: Wild-type MEFs 3

description: Wild-type MEFs

value: Wild-type

value: Cultured T antigen transformed Mouse Embrionic Fibroblasts


title: OT-2 tcr transgenic + HDAC7 deltaP transgenic, peptide-injected 3

city: Novato

first: Eric

last: Verdin

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

hyb_protocol: In accordance with manufacturer's reccomendation for Gene 1.0ST arrays

scan_protocol: Affymetrix GCS3000 scanner and the GCOS 1.4 data acquisition software

data_processing: .cel files were normalized using Expression Console RMA

source_name: Flow-sorted CD4/CD8 DP thymocytes, TCR transgenic and HDAC7 mutant transgenic, activated in vivo

label_protocol: Labeling was in accordance with Affymetrix WT labeling kit

growth_protocol: Mice were all between 3 and 6 weeks of age

extract_protocol: total RNA was extracted using Qiagen Rneasy Mini kit, with on-column DNAse digestion

value: CD4/CD8 DP thymocyte

tag: source tissue

value: thymus

value: OT-2 TCR transgenic

value: activation by i.p. injection of agonist peptide for OT-2 TCR, 3 hours prior to harvest.


title: OT-2 tcr transgenic + HDAC7 deltaP transgenic, peptide-injected 1


title: adult_KSL-HLX_expression_vector-1

source_name: Sorted Lin-Kit+Sca-1+ cells from wild-type FVB/nJ bone marrow infected with mouse HLX (pCAD-HLX-IRES-GFP) lentivirus, cultured for 2 days, then sorted for GFP+ cells


title: adult_KSL-HLX_expression_vector-2


title: OT-2 tcr transgenic + HDAC7 deltaP transgenic, peptide-injected 2


title: forebrain_stg_rep3_E12.5

status: Public on Sep 13 2012

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

country: Germany

institute: Ulm University

description: Gene expression data from embryonal forebrain at E12.5

hyb_protocol: according to Affymetrix Whole Transcript (WT) Sense Target Labeling Assay

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Affymetrix® Expression Console™ Software for normalization, BRB Array Tools for statistical analysis

source_name: embryo at E12.5 from control mice

growth_protocol: Two time-pregnant dams were sacirified 12 days after the vaginal plug was detected, and the embryos were prepared.

extract_protocol: Trizol (Qiazol) extraction of total RNA with subsequent column purification was performed according to the manufacturer's instructions.

treatment_protocol: Forebrains were prepared by removing the developing forebrain and mibrain from the palate. The forebrain was then separated from the main part of the thalamus by cutting it away at the ventromedial hypothalamic nucleus and the lateral habenular nuclei and removing the the developing skin and divided into halves. Freshly prepared forebrains were snap-frozen in liquid nitrogen. One half was used for RNA extraction, the other one for proteinextraction and assessment of luciferase activity.

value: forebrain

value: CD1/NMRI mixed background


title: forebrain_dtg_rep5_E12.5

source_name: embryo at E12.5 from transgenic mice

label_protocol: Whole Transcript (WT) Sense Target Labeling Assay


title: forebrain_dtg_rep4_E12.5


title: forebrain_stg_rep4_E12.5


title: CNE1 MTA1 silencing rep1

city: Guangzhou

first: Xiaoxia

last: Zhu

address: Department of Radiation Oncology,Nanfang Hospital, Southern Medical University

department: Department of Radiation Oncology

country: China

description: This sample is of nasopharyngeal carcinoma cell line CNE1 cells with MTA1 gene silencing.

hyb_protocol: Array hybridization using the NimbleGen Hybridization System was performed by KangChen Bio-tech Inc., Shanghai, China, following the standard operating protocol. See www.nimblegen.com.

scan_protocol: Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation)  was performed by KangChen Bio-tech Inc., Shanghai, China, following the standard operating protocol. See www.nimblegen.com.

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software.Genes that have values greater than or equal to lower cut-off: 100.0 in all samples were chosen for data analysis.

source_name: nasopharyngeal carcinoma cell line CNE1 cells with MTA1 silencing

label_protocol: ds-cDNA labeling with NimbleGen one-color DNA labeling kit was performed by KangChen Bio-tech Inc., Shanghai, China, following the standard operating protocol. See www.nimblegen.com.

growth_protocol: CNE1 and CNE1/MTA1-si cells were cultured in RPMI-1640 medium (Invitrogen, USA) supplemented with 10% fetal bovine serum (FBS) and maintained at 37ºC under a humidified 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an NanoDrop ND-1000 at KangChen Bio-tech Inc. (Shanghai, China).

value: MTA1 gene silencing


title: forebrain_stg_rep1_E12.5


title: forebrain_dtg_rep3_E12.5


title: adult_KSL-control_vector-1


title: CNE1 wild type rep1

institute: Nanfang Hospital, Southern Medical University

description: This sample is of wild-type nasopharyngeal carcinoma cell line CNE1 cells.

source_name: nasopharyngeal carcinoma cell line CNE1 cells wild type


title: forebrain_stg_rep5_E12.5


title: forebrain_dtg_rep2_E12.5


title: ICL010_NL_7h_1

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing:
Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol.
platform: x86_64-redhat-linux-gnu
arch: x86_64
os: linux-gnu
system: x86_64, linux-gnu
R version 2.12.2 (2011-02-25)
bioconductor packages: limma
Information on package: 'limma'
limma version: 3.6.9
limma date: 2010/12/01version
For the generation of the normalized data, the limma package was used. Background correction was performed (method=normexp, offset=1). Data was quantile normalized between arrays with the quantile normalization method and then log2 transformed.

source_name: Calu-3 cells, infected with A/NL/602/2009, 7h

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation.

growth_protocol: Calu-3 cells, a human lung adenocarcinoma cell line, were maintained in a 1:1 mixture of Dulbecco's Modified Eagle's Medium (DMEM) and Ham's F12 nutrient medium (DF12; Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum. All cells were grown at 37°C in an atmosphere of 5% CO2, with an antibiotic/antimycotic mixture (Invitrogen).

extract_protocol: At the time of sample collection, triplicate wells of mock-infected and influenza virus-infected Calu-3 monolayers were washed with 5 ml cold phosphate-buffered saline (PBS) and lysed directly with 1 ml of TRIzol (Invitrogen), according to the manufacturer's recommendations. The resulting lysates were stored at -80°C until further processing. All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 -fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer's recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for quantitative real-time PCR (qPCR) and microarray analyses.

treatment_protocol: For RNA isolation, Calu-3 cells were seeded in 6-well plates (1 x 10^6 cells/well) two days prior to infection. Immediately preceding infection, monolayers were washed twice with DMEM/F12 supplemented with 0.3% bovine serum albumin (DF12-BSA), and inoculated at an MOI of 3 in DF12-BSA for 50 minutes at 37°C. Mock-infected controls were inoculated with DF12-BSA only. Following inoculation, monolayers were washed once with DF12-BSA and incubated in DF12-BSA containing 0.5 μg/ml of TPCK-treated trypsin (Worthington Biochemical Corporation, Lakewood, NJ).

value: lung adenocarcinoma cells

value: infected with A/NL/602/2009 virus

tag: dosage

value: multiplicity of infection of 3.0

tag: time of sample collection

value: 7h post-infection


title: ICL010_NL_36h_2

source_name: Calu-3 cells, infected with A/NL/602/2009, 36h

tag: treatment

value: 36h post-infection


title: forebrain_stg_rep2_E12.5

tag: tissue

tag: strain


title: ICL010_NL_48h_1

source_name: Calu-3 cells, infected with A/NL/602/2009, 48h

value: 48h post-infection


title: ICL010_NL_3h_1

source_name: Calu-3 cells, infected with A/NL/602/2009, 3h

value: 3h post-infection


title: ICL010_NL_3h_3


title: forebrain_dtg_rep1_E12.5


title: ICL010_NL_48h_2


title: ICL010_NL_7h_3


title: ICL010_NL_7h_2


title: ICL010_NL_3h_2


title: ICL010_NL_48h_3


title: ICL010_NL_36h_3


title: ICL010_NL_30h_2

source_name: Calu-3 cells, infected with A/NL/602/2009, 30h

value: 30h post-infection


title: ICL010_NL_36h_1


title: ICL010_NL_30h_3


title: ICL010_NL_30h_1


title: ICL010_NL_24h_2

source_name: Calu-3 cells, infected with A/NL/602/2009, 24h

value: 24h post-infection


title: ICL010_NL_24h_1


title: ICL010_NL_18h_2

source_name: Calu-3 cells, infected with A/NL/602/2009, 18h

value: 18h post-infection


title: ICL010_NL_18h_3


title: ICL010_NL_24h_3


title: ICL010_NL_18h_1


title: SM015_4.4_Tnfrsf1a1/b_mock_d7_2

source_name: lung, Tnfrsf1a/1b KO, mock infected, day 7

extract_protocol: Lung tissue was removed from RNAlater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) TRIzol and stored at -80°C until RNA isolation. All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2-fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer's recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol:
Ten-week-old mice were infected by intranasal instillation of 10^5 PFU of SARS MA15 in 50 µl of PBS or mock-infected with PBS alone. At days 4 and 7 days post-infection, lungs were harvested.
Specific lobes of the lung from each animal were harvested and briefly rinsed in cold (4ºC) PBS. Following the RNAlater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNAlater. After a 4ºC incubation for overnight, samples were stored at -80ºC until further processing.

tag: strain/background

tag: genotype

value: Tnfrsf1a/1b KO

tag: gender

value: female

value: 10 weeks

value: lung

value: mock infected

value: day 7 post-infection


title: SM015_4.5_Tnfrsf1a1/b_mock_d7_3


title: SM015_4.1_Tnfrsf1a1/b_mock_d4_1

source_name: lung, Tnfrsf1a/1b KO, mock infected, day 4

value: day 4 post-infection


title: ICL010_NL_12h_2

source_name: Calu-3 cells, infected with A/NL/602/2009, 12h

tag: cell type

value: lung adenocarcinoma cells

value: 12h post-infection


title: SM015_4.3_Tnfrsf1a1/b_mock_d7_1


title: SM015_3.2_Tnfrsf1a1/b_MA15_d4_2

source_name: lung, Tnfrsf1a/1b KO, infected with SARS MA15 virus, day 4

value: infected with 10^5 PFU of SARS MA15 virus


title: ICL010_NL_12h_3

value: infected with A/NL/602/2009 virus

value: multiplicity of infection of 3.0


title: SM015_2.4_B6_mock_d7_2

source_name: lung, wild-type, mock infected, day 7

value: wild-type


title: ICL010_NL_12h_1


title: ICL010_NL_0h_3

source_name: Calu-3 cells, infected with A/NL/602/2009, 0h

value: 0h post-infection


title: ICL010_mock_7h_2

source_name: Calu-3 cells, mock infected, 7h

value: multiplicity of infection of 0

value: 7h post-infection


title: SM015_2.5_B6_mock_d7_3


title: SM015_3.5_Tnfrsf1a1/b_MA15_d7_3

source_name: lung, Tnfrsf1a/1b KO, infected with SARS MA15 virus, day 7


title: ICL010_mock_48h_3

source_name: Calu-3 cells, mock infected, 48h

value: 48h post-infection


title: ICL010_NL_0h_2


title: SM015_3.3_Tnfrsf1a1/b_MA15_d7_1

value: Tnfrsf1a/1b KO


title: SM015_3.4_Tnfrsf1a1/b_MA15_d7_2

value: female


title: SM015_2.3_B6_mock_d7_1

value: 10 weeks


title: SM015_4.2_Tnfrsf1a1/b_mock_d4_2

value: lung


title: ICL010_mock_7h_3

value: mock infected


title: SM015_3.1_Tnfrsf1a1/b_MA15_d4_1


title: ICL010_NL_0h_1


title: ICL010_mock_48h_2


title: ICL010_mock_7h_1


title: SM015_2.2_B6_mock_d4_2

source_name: lung, wild-type, mock infected, day 4


title: SM015_1.4_B6_MA15_d7_2

source_name: lung, wild-type, infected with SARS MA15 virus, day 7

value: day 7 post-infection


title: SM015_1.5_B6_MA15_d7_3


title: ICL010_mock_48h_1


title: ICL010_mock_3h_3

source_name: Calu-3 cells, mock infected, 3h

value: 3h post-infection


title: ICL010_mock_3h_2

value: lung adenocarcinoma cells


title: SM015_2.1_B6_mock_d4_1

value: day 4 post-infection


title: SM015_1.3_B6_MA15_d7_1

value: infected with 10^5 PFU of SARS MA15 virus


title: ICL010_mock_24h_3

source_name: Calu-3 cells, mock infected, 24h

value: 24h post-infection


title: SM015_1.1_B6_MA15_d4_1

source_name: lung, wild-type, infected with SARS MA15 virus, day 4


title: ICL010_mock_36h_2

source_name: Calu-3 cells, mock infected, 36h

value: 36h post-infection


title: SM020_4.3_ppp1r14c_mock_d7_1

source_name: lung, ppp1r14c KO, mock infected, day 7

value: ppp1r14c KO


title: ICL010_mock_24h_2


title: ICL010_mock_30h_2

source_name: Calu-3 cells, mock infected, 30h

value: 30h post-infection


title: SM020_4.1_ppp1r14c_mock_d4_1

source_name: lung, ppp1r14c KO, mock infected, day 4


title: SM020_4.4_ppp1r14c_mock_d7_2


title: ICL010_mock_36h_3

value: multiplicity of infection of 0


title: SM015_1.2_B6_MA15_d4_2

value: wild-type


title: ICL010_mock_30h_3


title: SM020_4.2_ppp1r14c_mock_d4_2


title: SM020_3.4_ppp1r14c_MA15_d7_2

source_name: lung, ppp1r14c KO, infected with SARS MA15 virus, day 7


title: SM020_4.5_ppp1r14c_mock_d7_3


title: SM020_3.5_ppp1r14c_MA15_d7_3


title: SM020_3.2_ppp1r14c_MA15_d4_2

source_name: lung, ppp1r14c KO, infected with SARS MA15 virus, day 4


title: SM020_3.1_ppp1r14c_MA15_d4_1


title: ICL010_mock_36h_1


title: ICL010_mock_18h_3

source_name: Calu-3 cells, mock infected, 18h

value: 18h post-infection


title: ICL010_mock_12h_3

source_name: Calu-3 cells, mock infected, 12h

value: 12h post-infection


title: SM020_2.3_B6_mock_d7_1

source_name: lung, wild-type, mock infected, day 7

value: female


title: ICL010_mock_18h_1


title: SM020_2.2_B6_mock_d4_2

value: 10 weeks


title: ICL010_mock_30h_1


title: ICL010_mock_3h_1


title: ICL010_mock_24h_1


title: ICL010_mock_18h_2


title: SM020_2.5_B6_mock_d7_3

value: lung


title: SM020_2.4_B6_mock_d7_2

value: mock infected


title: SM020_1.3_B6_MA15_d7_1

value: day 7 post-infection


title: ICL010_mock_12h_2


title: SM020_2.1_B6_mock_d4_1


title: ICL010_mock_0h_2

source_name: Calu-3 cells, mock infected, 0h

value: 0h post-infection


title: ICL010_mock_0h_1

value: lung adenocarcinoma cells


title: ICL010_Cal_48h_3

source_name: Calu-3 cells, infected with A/CA/04/2009, 48h

value: infected with A/CA/04/2009 virus

value: multiplicity of infection of 3.0

value: 48h post-infection


title: SM020_1.4_B6_MA15_d7_2

value: infected with 10^5 PFU of SARS MA15 virus


title: ICL010_mock_0h_3


title: SM020_1.5_B6_MA15_d7_3


title: ICL010_Cal_24h_3

source_name: Calu-3 cells, infected with A/CA/04/2009, 24h

value: 24h post-infection


title: SM020_1.2_B6_MA15_d4_2

value: day 4 post-infection


title: SM020_1.1_B6_MA15_d4_1


title: ICL010_Cal_48h_1


title: ICL010_Cal_48h_2


title: ICL010_Cal_24h_2


title: ICL010_Cal_12h_2

source_name: Calu-3 cells, infected with A/CA/04/2009, 12h


title: ICL010_Cal_0h_2

source_name: Calu-3 cells, infected with A/CA/04/2009, 0h


title: ICL010_Cal_24h_1


title: ICL010_Cal_0h_1


title: ICL010_Cal_12h_1


title: ICL010_Cal_12h_3


title: ICL010_Cal_0h_3


title: N417_SSEA-1+_2

city: Kitakyushu

first: Mitsuhiro

last: Suzuki

state: Fukuoka

address: 1-1 Iseigaoka, Yahatanisi-ku

department: Biochemistry

institute: University of Occupational and Environmental Health, Japan

hyb_protocol: Samples were hybridized using Agilent 10x blocking agent and 25x fragmentation buffer, and 2xGEx hybridization buffer according to the manufacturer's instructions for 17 hours at 65C.

scan_protocol: Slides were scanned on green dye channel, with 5 µm resolution (Agilent microarray scanner p/n G2505C) and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: Lung

label_protocol: 100 ng of total RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 100 ng of total RNA with an oligo-dT-T7 promoter primer and AffinityScript MT -RT. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP), and T7 polymerase. the antisense cRNA was then purified (QIAGEN RNeasy minikit) and spectrophotometrically quantified (NanoDrop ND-1000 UV-VIS Spectrophotometer) in order to determine the yield and specific activity of each reaction - μg cRNA yield and specific activity (pmol Cy3 per μg cRNA)

growth_protocol: N417 cells were cultured in RPMI1640-media supplemented with 10% fetal calf serum and iPS cells were cultured in DMEM-media with 10% knock-out serum,100 U/ml penicillin and 100 μg/ml streptomycin. Cells were maintained in a humidified incubator with 10% CO2 at 37°C.

extract_protocol: Total RNAs were prepared with QIAGEN RNeasy minikit according to manufacturer’s protocol.

treatment_protocol: SSEA-1 positive-N417 cells or SSEA-1/-3 double negative-N417 cells were isolated by FACS sorter (BD, AriaII) with anti-SSEA-1 antibody.

tag: sorted cells


title: ICL010_mock_12h_1

value: multiplicity of infection of 0


title: SM019_3.2_B6_mock_d7_1

value: wild-type


title: SM019_3.1_B6_mock_d4_3

source_name: lung, wild-type, mock infected, day 4


title: SM019_3.3_B6_mock_d7_2


title: N417_SSEA-1+_3


title: SM019_3.4_B6_mock_d7_3


title: N417_SSEA-1+_1


title: N417_SSEA-1/3DN_3


title: N417_SSEA-1/3DN_2


title: N417_SSEA-1/3DN_1


title: SM019_2.2_B6_MA15_d7_3

source_name: lung, wild-type, infected with SARS MA15 virus, day 7


title: SM019_2.4_B6_mock_d4_2


title: SM019_1.2_B6_MA15_d4_2

source_name: lung, wild-type, infected with SARS MA15 virus, day 4


title: iPS_253G1_2

source_name: Fibroblast

value: fibroblast


title: SM019_2.3_B6_mock_d4_1


title: SM019_1.4_B6_MA15_d7_1


title: SM019_1.1_B6_MA15_d4_1


title: iPS_253G1_3


title: SM019_2.1_B6_MA15_d7_2


title: iPS_253G1_1


title: IRF4-control_Th17_cells_42hr_rep2

city: South San Francisco

first: Smita

last: Agrawal

address: 1 DNA Way

department: Immunology

institute: Genentech Inc.

description: IRF4 +/- rep2

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

scan_protocol: Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 10.7.

data_processing:
The matrix data table was created by first log transforming the raw data and then filtering out all probes that showed a standard deviation of <0.25  across all samples as well as probes that do not have an associated entrez id. Agilent Feature Extraction software version 10.7 was used for background subtraction and LOWESS normalization.
The normalized data was then analyzed further using Partek Genomic Suite Version 6.6 by performing a 1-way ANOVA test between the IRF4 KO vs IRF4 Het samples. Data for the probes which showed a > 2-fold change (up or down) with a p-value <0.05 is presented in the 'Analyzed_data.txt' file (available on Series records). It is presented in ascending order of differential expression (Fold-Change) between the IRF4 KO vs IRF4 Het samples. The probeset ID, Gene Symbol, p-value of differential expression and Fold-Change between the IRF4 KO and IRF4 Het samples are indicated. Negative fold changes indicate down-regulation in IRF4 KO samples and positive fold changes indicate up-regulation.

label_protocol: Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).

growth_protocol: Naïve T- cells isolated from spleen were cultured on a-CD3 coated plates with 2.5 mg/ml a-CD28, 20 ng/ml IL-6, 20 ng/ml IL-23, 1 ng/ml hTGFb, 10 mg/ml a-IL4 and 10 mg/ml a-IFNg for 42 hrs

extract_protocol: Total RNA was isolated using Qiagen RNeasy kit following manufacturer's protocol and including on-column DNase-digestion. RNA was quantified using UV-spec Nanodrop and then profiled on Agilent Bioanalyzer.

tag: strain background

tag: genotype/variation

value: spleen

value: Naïve CD4+, CD62L hi, CD25 - T cells

tag: differentiation condition

tag: timepoint

value: 42 hrs

source_name: Stratagene's Universal Mouse Reference RNA (UMRR) cat # 740100

tag: sample type

value: Reference:pooled RNA from 11 tissues


title: colon_Runx1-KO_Cy5_15554

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

description:
raw data file: US22502676_251486810270_S01_GE2-v5_95_Feb07_1_4.txt
ko_4_Cy5

hyb_protocol: according to Agilent Gene Expression oligo microarrays protocol (version 5.0.1)

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 9.5.1).

data_processing:
Agilent Feature Extraction Software (v 9.5.1) Pre-processing of data, quality checks, and significance analysis were all performed as described in: Fijneman et al,Pla2g2a attenuates colon tumorigenesis in azoxymethane-treated C57BL/6 mice; expression studies reveal Pla2g2a target genes and pathways. Cell Oncol 2009; 31: 345-56.  Please see readme.txt on the Series record for additional details from the reference above.
Two-channel arrays were analyzed as single-channel; comparison/ratios were not considered in the analysis of the data.  Raw data are linked as supplementary files on the Series record and each applies to two GEO Sample records as indicated in the description field above.

source_name: Runx1  knockout

extract_protocol: total RNA was isolated according to manufacturer's protocol , Qiagen

value: Villin-Cre + / Runx1-floxed

value: C57BL/6 background

value: male

tag: age (days)


title: IRF4-mut_Th17_cells_42hr_rep2

description: IRF4 -/- rep2


title: IRF4-mut_Th17_cells_42hr_rep1

description: IRF4 -/- rep1


title: colon_Runx1-WT_Cy5_15478

description:
raw data file: US22502676_251486810270_S01_GE2-v5_95_Feb07_1_1.txt
wt_1_Cy5

source_name: Runx1 wild-type

label_protocol: according to Agilent Gene Expression oligo microarrays protocol (version 5.0.1)

value: Villin-Cre - / Runx1-floxed


title: IRF4-mut_Th17_cells_42hr_rep3

description: IRF4 -/- rep3


title: colon_Runx1-KO_Cy3_15514

description:
raw data file: US22502676_251486810270_S01_GE2-v5_95_Feb07_1_3.txt
ko_7_Cy3


title: colon_Runx1-KO_Cy5_15448

description:
raw data file: US22502676_251486810270_S01_GE2-v5_95_Feb07_1_2.txt
ko_2_Cy5


title: colon_Runx1-WT_Cy5_15507

description:
raw data file: US22502676_251486810270_S01_GE2-v5_95_Feb07_1_3.txt
wt_3_Cy5


title: colon_Runx1-KO_Cy3_15447

description:
raw data file: US22502676_251486810270_S01_GE2-v5_95_Feb07_1_1.txt
ko_5_Cy3


title: IRF4-control_Th17_cells_42hr_rep1

description: IRF4 +/- rep1


title: colon_Runx1-WT_Cy3_15550

description:
raw data file: US22502676_251486810270_S01_GE2-v5_95_Feb07_1_4.txt
wt_8_Cy3


title: colon_Runx1-WT_Cy3_15479

description:
raw data file: US22502676_251486810270_S01_GE2-v5_95_Feb07_1_2.txt
wt_6_Cy3