title: H2AZ ChIP in Suz12 KO ES cells using anti H2AZ antibody (Abcam ab4174)

description: Chip-chip in Suz12 KO mouse ES cells for H2AZ

source_name: Input DNA from Suz12 KO ES cells

value: Suz12 KO

value: embryonic stem cells

source_name: H2AZ ChIP DNA from Suz12 KO ES Cells


title: Foxp3- p.yoelii 5d (47)

status: Public on Apr 16 2012

type: RNA

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: Foxp3- p.yoelii 5d (47)

hyb_protocol: 1.6 µg labeled cRNA was hybridized to microarrays for 16h at 68°C and scanned using the Agilent DNA Microarray Scanner.

scan_protocol: Microarrays were scanned using the Agilent Scanner System. Data extractions were performed using Feature Extraction Software 10.7.1 (Agilent) with default patrameters of the GE1_107_Sep09 extraction protocol

data_processing: log2 transformed, median normalized to all samples, signal intensity expressed as relative to median signal intensity of all samples

molecule: total RNA

organism: Mus musculus

source_name: CD4+CD25-Foxp3- T cells isolated from Plasmodium yoelii infected Foxp3/eGFP BALB/c mice 5 days post infection by FACS

label_protocol: 500ng of total RNA were applied for Cy3-labelling reaction using the one color Quick Amp Labeling protocol (Agilent Technologies; Waldbronn, Germany).

extract_protocol: RNAeasy

tag: strain

value: BALB/c

tag: tissue

value: Spleen


title: H2AZ ChIP in Ring1B KO ES cells using anti H2AZ antibody (Abcam ab4174)

type: genomic

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

description: Chip-chip in Ring1B KO mouse ES cells for the histone variant H2AZ

hyb_protocol: Samples were hybridized according to standard protocol (http://www.nimblegen.com/products/lit/NG_ChIP-chip_Guide_v6p2.pdf)

scan_protocol: Arrays were scanned on MS 200 Microarray scanner as per manufacturer's instructions. Separate TIFF images were created for Cy3 and Cy5 at 2μM resolution.

data_processing: The mean signal intensity of the 4 replicate probes, on each array was taken. Loess normalization was used within arrays to correct for the dye bias, and scale normalization was used, within replicates group, to control inter array variability. The log enrichment for each group was calculated by dividing the mean of log2 input intensities by the mean of log2 ChIP enriched intensities.

molecule: genomic DNA

source_name: Input DNA from Ring1B KO ES cells

label_protocol: 1.0 µg of amplified ChIP DNA or Input DNA was directly labeled by Klenow random priming with Cy3/Cy5 nonamers as per manufacturer's instructions (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Cells were grown on mitomycin C treated primary embryonic fibroblasts (PEFs) derived from E12.5 mouse embryos, in DMEM (Invitrogen) supplemented with 15% foetal calf serum (FCS, Hyclone), 1,000 units/ml LIF, non-essential amino acids, sodium pyruvate, 2-mercaptoethanol, L-glutamine, and Penicillin/Streptomycin. ESCs were trypsinized and the PEFs allowed to re-attach to the tissue culture plastic for 2x 30 minutes in LIF-containing medium, before preparation of chromatin, and nuclear extracts from ESCs.

extract_protocol: ChIP was performed overnight (o/n) with 3 μg H2A.Z antibody and 90 μg chromatin. For polycomb ChIPs; 10 μg Ring1B or EZH2 antibody was incubated with 450 μg chromatin o/n. ChIP and input chromatin was decrosslinked at 65 ° C for 6 hours, RNase A at 37° C for 1 hour, then with Proteinase K at 55° C for 2 hours. The DNA samples were purified using the Qiagen DNA purification kit. Native ChIP for H3K27me3 was described in (Eskeland R, et al. 2010. Mol Cell 38(3) 452-464). 10ng of purified DNA (ChIP and Input) was amplified using the WGA2 kit from sigma (WGA2-50RXN) accoring to manufacturers instructions.

tag: fraction

value: Input DNA

tag: genotype/variation

value: Ring1B KO

tag: cell type

source_name: H2AZ ChIP DNA from Ring1b KO ES Cells

tag: antibody vendor

value: Abcam

tag: antibody catalog#

tag: antibody

value: ChIP DNA

value: Ring1b KO


title: EZH2 ChIP in Ring1B KO ES Cells using anti EZH2 antibody (Millipore 07-689)

description: Chip-chip in Ring1B KO mouse ES cells for EZH2

source_name: EZH2 ChIP DNA from Ring1b KO ES Cells

value: Millipore


title: H3K27me3 ChIP in Ring1B deficient ES Cells using anti H3K27me3 antibody (Millipore, 07-449)

description: Chip-chip in Ring1B KO mouse ES cells for the histone modifcation H3K27me3

source_name: H3K27me3 ChIP DNA from Ring1B KO ES Cells


title: H2AZ ChIP in Eed KO ES cells using anti H2AZ antibody (Abcam ab4174)

description: Chip-chip in Eed KO mouse ES cells for H2AZ

source_name: Input DNA from Eed KO ES cells

value: Eed KO

source_name: H2AZ ChIP DNA from Eed KO ES cells


title: A06_C

city: Tromsø

first: Chris

last: Fenton

address: Thor Knutsen vg 6

department: Microarray

country: Norway

institute: UITO

description: non-irradiated

hyb_protocol: Labelled probes were hybridized to a NimbleGen oligo arrays (12x135K) with the Roche NimbleGen hybridization system for 16 hours at 42°C and washed according to the manufacturer's protocol.

scan_protocol: The microarray slides were scanned with an Axon GenePix 4000B scanner (Molecular Devices Inc., USA) and features were extracted by using the NimbleScan v2.5 software.

data_processing: Normalization was carried out using quantile normalization (Bolstad et al. 2003).  For the purpose  of finding differentially expressed genes an empirical Bayes analysis using the LIMMA package was applied (Smyth 2004). The significance was determined at the 0.05 level corrected for false discovery rate (FDR) using the Benjamini-Hochberg method (Benjamini & Hochberg 1995). Principal component analysis (PCA) was carried out on the data in order to visualize the data structure and look for potential outlier samples (Gidsehaug et al. 2004). The differentially expressed genes were annotated by Protein Analysis THrough Evolutionary Relationships (PANTHER; http://www.panther.org/). Gene SetEnrichment Analysis (GSEA) was performed using the R statistical package (http://www.broad.mit.edu/gsea/ ).

organism: Homo sapiens

source_name: fibroblasts

label_protocol: Prior to probe generation 1 micro gram total RNA was amplified with the Ambion®MessageAmpTM II aRNA Amplification Kit (Applied Biosystems Inc., USA). RNA samples were transcribed to cDNA using the Invitrogen Superscript cDNA Synthesis Kit (InvitrogenTM, USA). cDNA was Cy3-labelled with the NimbleGen One-Color DNA Labeling Kit and according to the manufacturer’s protocol (Roche NimbleGen, Germany).

growth_protocol: Human CAFs were harvested from freshly resected non-small lung cell carcinoma (NSCLC) tumor tissues. Tumors from eight patients with an average age of 58 years (range 44-71) were included in this study. The Regional Ethical Committee (REK-Nord) approved the study, and all patients provided written informed consent.  Fibroblasts from tumors were isolated and characterized following standard procedures. Briefly, tumor resections were collected and cut into 1–1.5 mm3 pieces. Enzymatic digestion of tissues was carried out for 1.5 hrs in 10 mL DMEM/HAM‘S F-12 containing bacterial collagenase (Cat. #C-9407, Sigma-Aldrich, St. Louis, MO, USA) at a final concentration of 0.8 mg/mL. Digested tissue was spun down to eliminate collagenase, and resuspended in fresh growth medium (DMEM/HAM‘S F-12 supplemented with 10% FBS). Pure fibroblast cultures were obtained by selective cell detachment from the primary culture mix, and by further cell propagation in the presence of 10% FBS.  Cells were used for experiments after the second passage (2-3 weeks).

extract_protocol: Disruption and homogenization of cells were performed in lysis buffer using the MagNa Lyser Instrument (Roche Applied Science, Germany) and according to the manufacturer’s protocol. Subsequently, total RNA was isolated with the MagNa Pure Compact Instrument and the MagNa Pure Compact RNA Isolation Kit (Roche Applied Science, Germany). RNA was quantified by measuring absorbance at 260 nm, and RNA purity was determined by the ratios OD260nm/280nm and OD230/280nm using the NanoDrop instrument (NanoDrop® ND-1000, Wilmington, USA).

treatment_protocol: Adherent CAFs cultured in flasks were irradiated at RT with high energy photons produced by a Varian clinical linear-accelerator, delivered as single doses of 6, 12 and 18 Gy. Standard parameters for dose delivery was depth 30 mm, beam quality 15 MV, dose-rate 6 Gy/min and field size 20 x 20 cm. Radiation-doses were confirmed to be correct within an acceptable ± 4% by Thermo-Luminescent Dosimeters (TLDs) (Stathakis et al. 2006).

value: cancer-associated fibroblasts (CAFs)

tag: treatment

value: non-irradiated


title: Foxp3+p.yoelii 5d (44)

description: Foxp3+p.yoelii 5d (44)

source_name: CD4+CD25+Foxp3+ regulatory T cells isolated from Plasmodium yoelii infected Foxp3/eGFP BALB/c mice 5 days post infection by FACS


title: KLF2∆/∆ with LPS rep1

city: Cleveland

first: Patrick

last: Leahy

state: OH

address: 2103 Cornell Rd

department: Cancer Center

country: USA

institute: Case Western Res. U.

description: Gene expression data from K2∆/∆ peritoneal macrophages treated with 100ng/ml LPS for 6hours

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse gene array ST 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using  the Affymetrix GeneScanner 3000.

data_processing: Scanned images were converted to numerical values using Affymetrix Expression Console (EC) software ver1.1.  RMA was used to normalize data across all samples in the study.

label: biotin

source_name: K2∆/∆ peritoneal macrophages treated with 100ng/ml LPS for 6hours_rep1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: After 72 hours of thioglycolate injection, total cell suspension from peritoneal cavity were collected. These cells were seeded on 100mm tissue culture plates. Cells were allowed to attach for 4 hours and unattached cells were removed by washing with cell culture medium. These cells were placed in humidified incubator for additional 24 hours before LPS treatment.

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

treatment_protocol: LPS was diluted to final concentration of 100ng/ml in culture medium and this medium was placed on peritoneal macrophages derived from LysM Cre/Cre and KLF2∆/∆ mice for 6hours.

value: Thioglycolate elucidated primary peritoneal macrophages

tag: genotype

tag: age

value: 8 weeks


title: LysMCre/Cre with LPS rep1

description: Gene expression data from LysMCre/Cre peritoneal macrophages treated with 100ng/ml LPS for 6hours

source_name: LysMCre/Cre peritoneal macrophages treated with 100ng/ml LPS for 6hours_rep1

value: LysMCre/Cre


title: A12_R

description: irradiated

value: non-small lung cell carcinoma (NSCLC) tumor

value: irradiated


title: Foxp3- p.yoelii 3d (46)

description: Foxp3- p.yoelii 3d (46)

source_name: CD4+CD25-Foxp3- T cells isolated from Plasmodium yoelii infected Foxp3/eGFP BALB/c mice 3 days post infection by FACS


title: EZH2 ChIP in WT ES Cells using anti EZH2 antibody (Millipore 07-689)

description: Chip-chip in WT mouse ES cells for EZH2

source_name: Input DNA from WT ES cells

value: WT

value: embryonic stem cells

source_name: EZH2 ChIP DNA from WT ES Cells


title: A09_R

description: irradiated


title: Foxp3- WT (45)

description: Foxp3- WT (45)

source_name: CD4+CD25-Foxp3- T cells isolated from non-infected Foxp3/eGFP BALB/c mice by FACS

value: BALB/c

value: Spleen


title: Ring1B ChIP in WT ES cells using anti Ring1B antibody (MBL D139-3)

description: Chip-chip in WT mouse ES cells for Ring1B

value: Input DNA

source_name: Ring1B ChIP DNA from WT ES Cells

value: MBL


title: KLF2∆/∆ with LPS rep3

source_name: K2∆/∆ peritoneal macrophages treated with 100ng/ml LPS for 6hours_rep3


title: H2AZ ChIP in WT ES cells using anti H2AZ antibody (Abcam ab4174)

description: Chip-chip in WT mouse ES cells for the histone variant H2AZ

source_name: H2AZ ChIP DNA from WT ES Cells

value: Abcam

value: ChIP DNA


title: H3K27me3 ChIP in WT ES Cells using anti H3K27me3 antibody (Millipore, 07-449)

description: Chip-chip in WT mouse ES cells for the histone modifcation H3K27me3

source_name: H3K27me3 ChIP DNA from WT ES Cells

value: Millipore


title: LysMCre/Cre with LPS rep2

source_name: LysMCre/Cre peritoneal macrophages treated with 100ng/ml LPS for 6hours_rep2


title: KLF2∆/∆ with LPS rep2

source_name: K2∆/∆ peritoneal macrophages treated with 100ng/ml LPS for 6hours_rep2


title: A05_R

description: irradiated


title: A02_C

description: non-irradiated


title: A11_C

description: non-irradiated


title: LysMCre/Cre with LPS rep3

source_name: LysMCre/Cre peritoneal macrophages treated with 100ng/ml LPS for 6hours_rep3


title: A10_C

description: non-irradiated


title: Foxp3+WT (40)

description: Foxp3+WT (40)

source_name: CD4+CD25+Foxp3+ regulatory T cells isolated from Foxp3/eGFP BALB/c mice by FACS


title: LUFA soil control [28]

city: Amsterdam

first: Dick

last: Roelofs

state: Noord-Holland

address: De Boelelaan 1085

department: Animal Ecology

country: Netherlands

institute: VU University

description: Raw data file: Sarray06.txt

hyb_protocol: 300 ng of Cy3-labeled or Cy5-labeled cRNA (specific activity >8.0 pmol dye/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Custom Gene Expression Microarrays with 8 - 15 k format (GPL7150) for 17 hours at 65°C in a rotating Agilent hybridization oven (10 rpm)  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), washed in acetonitril for 10 seconds, then dried immediately by air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Red&Green and PMT is set to 100%, XDR Hi 100%, XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE2-v5_95 and Grid: 016342_D_F_20070323) to obtain mean Red or Green intensities and median Red or Green background intesities. In limma, edwards method for background correction was used (offset = 30), and global loess normalizion (MAANOVA) was done.

organism: Folsomia candida

source_name: total RNA from 10 animals

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 500 ng total RNA using the Quick Amp Labeling Kit, two-color (Agilent Technologies) according to the manufacturer's guidelines with a slight modification where the transcription (labeling) reactions were done in half the volume, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cultures were first age synchronized before exposure to soil: 20 adult animals were incubated per container; containing a plaster of Paris base mixed with charcoal, to lay eggs for 2 days. The incubation conditions were 20°C, 75% RH and 12:12 hour dark:light cycle

extract_protocol: Total RNA was extracted from all animals (~30) per jar, using SV Total RNA isolation System (Promega).

treatment_protocol: Approximately 10 animals, 23 d old, were exposed for four days in glass jars containing ~25 g of soil (both field soils and control soils at 50% water holding capacity) Exposure was done at same conditions as incubation. After exposure the animals were extracted from soil with tap water via floatation, put in 1.5 mL tubes and frozen in liquid N2.

tag: soil

value: LUFA soil control

tag: concentration

value: control


title: A01_R

description: irradiated

source_name: fibroblasts

value: cancer-associated fibroblasts (CAFs)


title: LUFA soil control [29]

description: Raw data file: Sarray07.txt


title: VH Soil NOEC rep4

description: Raw data file: Sarray08.txt

value: LUFA soil with vlagheide soil

value: NOEC


title: V703

city: Cleveland Heights

first: Peter

last: Scacheri

address: 10900 Euclid Ave; BRB 647

institute: Case Western Reserve University

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: All microarray data were processed in a single batch using the Affymetrix Expression Console software, obtaining gene level expression data using core probe sets (the highest confidence level probe sets, associated with BLAT alignments of mRNA with annotated full-length CDS regions) using median normalization and the PLIER (probe logarithmic intensity error estimation) algorithm to obtain expression values for 16,952 genes. Genes located on Y, random, and the mitochondrial chromosomes were excluded.

source_name: Colon Cancer Cell Line

label_protocol: Affymetrix standard protocol

growth_protocol: Primary cell lines were revived from -80C, passaged twice after initial plating, and harvested for RNA after no more than a total of 20 passages at 60-80% confluence.

extract_protocol: Normal colon crypts were isolated from surgical specimens of colon excised past the normal margin of tumors. Specimens were verified by microscopy to be free of any cancer cells.  Samples were washed in cold PBS, placed in cold DMEM+10%FBS, and then transported from the operating room to the laboratory within 8 hours of surgery.  Extraction of colonic crypts was performed by EDTA fractionation.  Briefly, colon mucosa was first dissected from each sample taking care to maintain tissue integrity.  The mucosa was then cut into thin strips, gently agitated in cell dissociation buffer (Invitrogen Cat. No.13151-014) for 30 minutes at 4*C, rinsed in cold PBS, and then agitated in fresh buffer for 30 minutes. The tissue strips were then rapidly pipetted until the solution became cloudy due to the release of crypts from the mucosa.  Mucosa strips were removed from the solution and discarded.  The remaining solution was examined microscopically for the presence of viable, intact crypts free of contaminating debris.

value: Colon Cancer Cell Line


title: HMC-1_exosome_RNA_1 vs. HMC-1_cell_RNA_1

city: Gothenburg

first: Karin

last: Ekström

address: Medicinaregatan 1G

country: Sweden

institute: Krefting Research Centre

description: miRCURY™ LNA array (v9.2)

hyb_protocol: The Hy3™-labelled exosome samples and a Hy5™-labeled mast cells were mixed pair-wise and hybridized to the miRCURY™ LNA array (v9.2). The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan Systems, Inc. San Jose, CA).

scan_protocol: The miRCURY™ LNA array microarray slides were scanned by a ScanArray 4000 XL scanner (Packard Biochip Technologies, Billerica, MA ,USA) and the image analysis was carried out using the ImaGene 6.1.0 software (BioDiscovery, Inc, El Segundo, CA  USA).

data_processing: MicroRNA profiling of exosomes (Hy3) and donor HMC-1 cells (Hy5) using the miRCURY™ LNA array (v9.2). The quantified signals were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. MicroRNA with signals equal to or below the background signal in 2 or more of the 4 replicate measurements were identified as absent in that slide. The limit for a miRNA to be listed as detectable was set to signal intensities higher than 3 x background (3 x median Hy3 or Hy5 for the total slide). In addition, where signals were detected for <3 of the slides, they were considered unreliable and excluded from sets of detected miRNAs. The experiment was performed in triplicate samples. The signal was calculated as the mean value of the log2MeanRatio Hy3/Hy5 for the triplicates ± SD. MicroRNA that were detected in all three slides were considered as present, indicated as exo or cell in slide 1-3. Full results file containing the replicate data analysis is provided as a supplementary file on the Series record.

source_name: exosomes isolated from the supernatant of HMC-1 cells

label_protocol: Total RNA from the exosome and the HMC-1 cell samples were labelled with Hy3™ and Hy5™ fluorescent stain, respectively, using the miRCURY™ Hy3™/Hy5™ power labelling kit.

growth_protocol: Cell culture and exosome release  The human mast cell line HMC-1 (Dr Joseph Butterfield, Mayo Clinic, USA), was cultured in IMDM containing 10% depleted fetal bovine serum (FBS), 100 U ml-1 penicillin, 100 µg ml-1 streptomycin, 2 mM L-glutamine and 1.2 mM alpha-thioglycerol (all from Sigma-Aldrich). To eliminate exosomes present in serum, FBS was ultracentrifuged at 120 000 g for 90 min using a Ti70 rotor (Beckman optima LE-80k Ultracentrifuge). Peripheral blood mononuclear cells (PBMC) were prepared from peripheral blood of healthy subjects by Ficoll-Plaque density separation. The CD34 cells were obtained from the PBMC by positive isolation using magnetic separation according to the manufacturer’s instruction (Miltenyi Biotec, Germany). CD34 cells were cultured in IMDM (Sigma-Aldrich) containing 10% FBS, 100 U ml-1 penicillin, 100 µg ml-1 streptomycin, 2 mM L-glutamine and 1mM sodium pyruvate. The purity of the separations ranged between 60-85%, as analyzed by flow cytometry using antibody against CD34 (BD Biosciences) in combination with 7-AAD for viability. Exosomes were isolated according to Valadi et al., 2007. Briefly, cells were stimulated with 1 µM calcium ionophore (Sigma-Aldrich) for 30 min, centrifuged at 500 g for 10 min to eliminate cells and at 16 500 g for 20 min, followed by filtration through 0.22 µm filter to remove cell debris. Exosomes were pelleted by ultracentrifugation (Beckman Ti70 rotor) at 120 000 g for 70 min. For PKH67 transfer experiments, exosomes were washed once in a large volume PBS. For electron microscopy, the exosome pellet was diluted in a large volume PBS, filtrated through 0.1 µm filters and pelleted by ultracentrifugation. Exosomes were measured for their protein content using BCA™ Protein Assay Kit (Pierce). Cell viability was assessed using trypan blue exclusion or 7-AAD.

extract_protocol: Extraction of total RNA was performed using Trizol followed by Rneasy clean-up according to the manufacturer's instructions.

treatment_protocol: Growth under normal conditions

tag: cell line

value: HMC-1 cells

tag: total rna source

value: exosome

source_name: HMC-1 cells

value: whole cell


title: V503


title: HMC-1_exosome_RNA_3 vs. HMC-1_cell_RNA_3

description: miRCURY™ LNA array (v9.2)


title: HMC-1_exosome_RNA_2 vs. HMC-1_cell_RNA_2

description: miRCURY™ LNA array (v9.2)


title: V9M


title: V432


title: VH Soil NOEC rep3

description: Raw data file: Sarray07.txt


title: V8


title: LUFA soil control [31]

description: Raw data file: Sarray08.txt


title: VH Soil NOEC rep2

description: Raw data file: Sarray06.txt


title: V457


title: V9P


title: VH Soil NOEC rep1

description: Raw data file: Sarray05.txt


title: V481


title: LUFA soil control [26]

description: Raw data file: Sarray05.txt


title: VH Soil EC50 rep4

description: Raw data file: Sarray04.txt


title: Crypt143

source_name: Normal Colon Crypt control

value: Normal Colon Crypt


title: Crypt535


title: Crypt540


title: LUFA soil control [21]

description: Raw data file: Sarray03.txt


title: LUFA soil control [20]

description: Raw data file: Sarray02.txt


title: VH Soil EC50 rep3

description: Raw data file: Sarray03.txt


title: Crypt145


title: Crypt625


title: V400


title: VH Soil EC50 rep2

description: Raw data file: Sarray02.txt


title: LUFA soil control [18]

description: Raw data file: Sarray01.txt


title: LUFA soil control [23]

description: Raw data file: Sarray04.txt


title: W296A3

city: Moscow

first: Jill

middle: L

last: Johnson

state: ID

department: Biological Sciences

institute: University of Idaho

description:
Gene expression data mutant Hsp90
biological rep3

hyb_protocol: 5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Yeast Genome 2.0 Array, Platform GPL2529. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Array processing was performed on the Fluidics Station 450 (Affymetrix) using GeneChip Operating System (GCOS) software (ver. 1.2; Affymetrix)

data_processing:
The data were analyzed using R software and Bioconductor packages. Quality assurance of microarray data was completed using the affyQAReport function from the Bioconductor package affyQCReport.
The Linear Models for Microarray Data (LIMMA) package was used to perform differential expression analysis on the filtered gene list using a linear model on log2 signal values with an empirical Bayes correction to the variance.

organism: Saccharomyces cerevisiae

source_name: mutant Hsp90, exponential growth

label_protocol: 5µg of RNA was used to make cRNA using the Affymetrix One-Cycle Kit (Affymetrix, Santa Clara, CA)

growth_protocol: Yeast were grown in at 30° YPD overnight, and harvested at O.D.600=0.5

treatment_protocol: Yeast pellets were washed once with water


title: CD34+ cells vehicle treated 2hr 37deg rep6

city: San Diego

first: Dave

last: Robbins

state: CA

address: 3535 General Atomics Court Ste. 200

institute: Fate Therapeutics

hyb_protocol: Hybridization to the Human Genome U133 Plus 2.0 GeneChips and staining were performed following Affymetrix protocols in a GeneChip Hybridization Oven 645. Staining was performed following Affymetrix protocols in a GeneChip Fluidics Station 450.

scan_protocol: Scanning was performed using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix Expression Console 1.1 using Affymetrix default RMA analysis settings.

label: Biotin

source_name: Isolated CD34+ cells

label_protocol: Biotinylated aRNA were prepared according to the standard Ambion MessageAmp II Biotin enhanced protocol from 100ng total RNA using the two round manufacturer's protocol.

extract_protocol: PicoPure extraction of total RNA was performed according to Ambion's manufacturer’s protocol

treatment_protocol: 2 hour ex vivo incubation at 37 deg C with Vehicle (DMSO)

value: Umbilical cord blood


title: W296A1

description:
Gene expression data mutant Hsp90
biological rep1


title: VH Soil EC50 rep1

description: Raw data file: Sarray01.txt


title: W296A2

description:
Gene expression data mutant Hsp90
biological rep2


title: WT3

description:
Gene expression data WT cells
biological rep3

source_name: WT Hsp90, exponential growth

value: WT


title: CD34+ cells vehicle treated 2hr 37deg rep2

value: 2 hour ex vivo incubation at 37 deg C with Vehicle (DMSO)


title: CD34+ cells vehicle treated 2hr 37deg rep5


title: CD34+ cells vehicle treated 2hr 37deg rep4


title: VH Extr EC50 rep3

description: Raw data file: Earray07.txt

value: LUFA soil with vlagheide extract


title: VH Extr EC50 rep4

description: Raw data file: Earray08.txt


title: acetone control [15]

description: Raw data file: Earray08.txt

value: LUFA soil with acetone control


title: CD34+ cells vehicle treated 2hr 37deg rep7


title: CD34+ cells vehicle treated 2hr 37deg rep1


title: acetone control [12]

description: Raw data file: Earray06.txt


title: WT2

description:
Gene expression data WT cells
biological rep2


title: WT1

description:
Gene expression data WT cells
biological rep1


title: acetone control [13]

description: Raw data file: Earray07.txt


title: CD34+ cells vehicle treated 2hr 37deg rep3


title: CD34+ cells Prostaglandin treated 2hr 37deg rep6

treatment_protocol: 2 hour ex vivo incubation at 37 deg C with Prostaglandin (16,16-dmPGE2)


title: CD34+ cells Prostaglandin treated 2hr 37deg rep7

value: 2 hour ex vivo incubation at 37 deg C with Prostaglandin (16,16-dmPGE2)


title: VH Extr EC50 rep2

description: Raw data file: Earray06.txt


title: DMSO-preexposed MDEC at #63

city: Columbus

first: Pei-Yin

last: Hsu

address: BRT836, 460W 12th Ave

institute: OSU

description: Gene expression data from MDEC with 3wk DMSO preexposure

hyb_protocol: Hybridization was carried out with a microRNA microarray panel (OSU CCC ver 2.0). Hybridization signals were detected with Streptavidin-Alexa647 conjugate.

scan_protocol: GeneChips were scanned using the PerkinElmer ScanArray XL5K scanner  and images were quantified using the GenePix Pro software.

data_processing: Average values of the replicates spots of each miRNA were normalized and analyzed in BRB-Array Tools version 3.2.3.  After excluding negative values with hybridization intensity below background, normalization was performed by using the median normalization method and normalized to median array as reference.

source_name: mammosphere-derived epithelial cells from #63 patient

label_protocol: RNA was biotin-labeled during reverse transcription using random hexamers.

value: reduction mammoplasties

tag: patient

value: DMSO


title: DES-preexposed MDEC at #61

description: Gene expression data from MDEC with 3wk DES preexposure

source_name: mammosphere-derived epithelial cells from #61 patient

value: DES


title: DMSO-preexposed MDEC at #62

source_name: mammosphere-derived epithelial cells from #62 patient


title: DES-preexposed MDEC at #62


title: DES-preexposed MDEC at #63


title: CD34+ cells Prostaglandin treated 2hr 37deg rep5


title: Foxp3+p.yoelii 3d (43)

description: Foxp3+p.yoelii 3d (43)

source_name: CD4+CD25+Foxp3+ regulatory T cells isolated from Plasmodium yoelii infected Foxp3/eGFP BALB/c mice 3 days post infection by FACS

value: BALB/c

value: Spleen


title: acetone control [10]

description: Raw data file: Earray05.txt

value: control


title: CD34+ cells Prostaglandin treated 2hr 37deg rep4


title: CD34+ cells Prostaglandin treated 2hr 37deg rep2


title: VH Extr NOEC rep4

description: Raw data file: Earray04.txt

value: NOEC


title: CD34+ cells Prostaglandin treated 2hr 37deg rep1


title: CD34+ cells Prostaglandin treated 2hr 37deg rep3


title: CD34+ cells vehicle treated 1hr 4deg rep2

treatment_protocol: 1 hour ex vivo incubation at 4 deg C with Vehicle (DMSO)


title: DMSO-preexposed MDEC at #61


title: VH Extr NOEC rep3

description: Raw data file: Earray03.txt


title: VH Extr NOEC rep2

description: Raw data file: Earray02.txt


title: acetone control [5]

description: Raw data file: Earray03.txt


title: acetone control [7]

description: Raw data file: Earray04.txt


title: acetone control [2]

description: Raw data file: Earray01.txt


title: acetone control [4]

description: Raw data file: Earray02.txt


title: CD34+ cells vehicle treated 1hr 4deg rep3

value: 1 hour ex vivo incubation at 4 deg C with Vehicle (DMSO)


title: VH Extr EC50 rep1

description: Raw data file: Earray05.txt


title: CD34+ cells Prostaglandin treated 1hr 4deg rep2

treatment_protocol: 1 hour ex vivo incubation at 4 deg C with FT-1050 (16,16-dmPGE2)


title: CD34+ cells Prostaglandin treated 1hr 4deg rep1

value: 1 hour ex vivo incubation at 4 deg C with FT-1050 (16,16-dmPGE2)


title: CD34+ cells Prostaglandin treated 1hr 4deg rep3


title: CD34+ cells vehicle treated 1hr 4deg rep1


title: Au-NP Replicate3

city: Lexington

first: Olga

last: Tsyusko

state: KY

address: 1100 S. Limestone St

department: Plant and Soil Sciences

institute: University of Kentucky

hyb_protocol: Following Fragmentation, 13 microgram of cRNA were hybridized to Affymetrix C. elegans genome array for 16 hours. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The microarray chips were scanned using Affymetrix GCS 3000 7G scanner

data_processing: The data were normalized using RMA algorithm followed by quantile normalization implemented in Partek Genomics Suite 6.4 (Partek, Inc, St Louis, MO).

organism: Caenorhabditis elegans

source_name: whole worms wild type

label_protocol: Biotinylated cRNA was prepared from 2 microgram total RNA according to standard protocol in the Affymetrix GeneChip Expression Analysis Manual.

growth_protocol: C. elegans were maintained on NGM plates at 20 ⁰C. Age-synchronized nematodes at L3 stage were used for the experiment

extract_protocol: RNA was extracted from each of the replicates using Trizol (Invitrogen) followed by purification with Qiagen RNeasy Kit (Qiagen, Chatsworth, CA).  Repeated freeze-thaw cycles (at -80 and 37⁰C) were used to lyse the cells.

treatment_protocol: LC10 at 5.9 mg/L of 4-nm citrate coated Au-NP for 12 hrs in 50% K-medium, the exposure solutions were replaced with 50% K-medium and left for another 12 hrs.

value: gold nanoparticles

tag: developmental stage


title: AN culture 1 extract 3

city: Espoo

first: Kirsi

last: Bromann

address: Tietotie 2

department: TK402, Cell Factory

country: Finland

institute: VTT Technical Research Centre of Finland

description: AN1599 (PbcR) expressed under strong constitutive A.nidulans gpdA promoter, random integration of expression cassette

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).Preliminary data processing was performed by NimbleGen Systems Inc., Madison, WI, USA. Normalized data was further analyzed with ArrayStar software by DNAStar.

organism: Aspergillus nidulans

source_name: oe:AN1599 (PbcR)

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: FGSC A4 control samples were grown at 37°C for 22 hours, and oe:AN1599 (PbcR) samples for 26 hours in YES-medium supplemented with 3 % gelatin. pH values of cultures were monitored and samples collected at pH-values ranging from 5.76 to 5.94 indicating the early exponential growth phase.

extract_protocol: Total RNA was purified with Qiagen Plant Rneasy Kit from 100 uL of frozen wet mycelia, and DNA was removed by DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.

treatment_protocol: Mycelia were filtered and zap-frozen in liquid nitrogen prior to RNA extraction.

tag: culture batch

value: veA+;oe:AN1599 (PbcR)


title: VH Extr NOEC rep1

description: Raw data file: Earray01.txt


title: Control Replicate1

tag: strain


title: AN culture 2 extract 3


title: WT culture 2 extract 2

description: control wild type

source_name: FGSC A4 control

value: Glasgow wild type (veA+)


title: AN culture 2 extract 2


title: HMC-1_exosome_RNA_2

hyb_protocol: The experiment was performed by SweGene (http://www.lth.se/index.php?id=7789) according to Affymetrix guidelines. Briefly, a hybridisation cocktail was prepared with the biotinylated and fragmented cRNA, control oligonucleotide, herring sperm DNA, acetylated BSA, 4-morpholinepropanesulfonic acid (MES), Tween 20, and bacterial cRNA controls respectively. The hybridisation cocktail was heated to 99°C for 5 min and to 45°C for 5 min, and was briefly centrifuged before hybridization. The pre-wet GeneChipTM probe array cartridge was filled with the hybridisation cocktail and incubated on rotation, 60 rpm at 45°C for 16–18 h. The cartridge was then subjected to an automated washing procedure, using the GeneChipTM Fluidics Station 400 and with a non stringent wash buffer, containing saline, sodium, phosphate, EDTA (SSPE), Tween 20 and antifoam according to the Affymetrix manual. A final wash with the stringent buffer, containing MES-sodium salt and Tween 20 was performed. The probe array was then stained with a solution of acetylated BSA, streptavidin and R-phycoerythrin in stain buffer, containing sodium-MES and Tween 20 and antifoam, followed by non stringent wash buffer. A second stain was performed with a solution of acetylated BSA, normal goat IgG and biotinylated goat antistreptavidin antibody in stain buffer. A third staining step with streptavidin R-phycoerythrin was performed as described above, before a final one with non-stringent wash buffer at 30°C.

scan_protocol: The probe arrays were scanned with the Gene Array Scanner (Affymetrix, Inc. www.affymetrix.com) and controlled by the software GenChip Operating System 1.2 (GCOS; Affymtrix Inc.).

data_processing: The expression level Signals were scaled in GCOS 1.2 to give a median array intensity of 100. This was done to enable different arrays to be compared. The program Spotfire DecisionSite 8.2 (www.spotfire.com) was used for gene-profiling analysis, genes only present in exosomes and expression differences. For the network analysis to identify biological mechanisms, the program Ingenuity was used (www.ingenuity.com).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix). The experiment was performed by SweGene (http://www.lth.se/index.php?id=7789) according to the Affymetrix guidelines.

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

value: mast cell line HMC-1

value: exosome


title: AN culture 1 extract 2


title: AN culture 2 extract 1


title: Au-NP Replicate2


title: GFP Replicate B

status: Public on Apr 15 2012

city: Charlottesville

first: Steven

middle: C

last: Smith

state: VA

department: Urology

institute: University of Virginia

description: As a control for other samples transfected with GFP-RhoGDI2 fusion transgene, UM-UC-3 cells were cotransfected with GFP (empty vector) and pBABE PURO (for selection) and sorted by FACS as described before (Moissoglu et al. Cancer Res 2009. PMID:19276387). Two biological replicates were prepared, A and B, which are paired (prepared at the same times) as biological replicates A and B, respectively, of the GFP-RhoGDI2 experimental samples.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: RMA, using its standard settings as implemented in the Bioinformatics Suite commercially available as an add on for Matlab R2009B, (The Mathworks, Natick, MA).

source_name: UM-UC-3 bladder cancer cells, stably transfected with GFP (control), biological replicate B

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA.

growth_protocol: um-uc-3 (atcc# crl-1749) bladder cancer cells were stably transfected with gfp, sorted for expression of gfp by fluorescence activated cell sorting as described (moissoglu et al. cancer res 2009. pmid: 19276387). RNA was isolated for microarray hybridization from cells in log phase growth.

extract_protocol: Total RNA was extracted using an RNeasy kit, per manufacturer instructions (Qiagen, Valencia, CA, USA).

value: um-uc-3 (atcc# crl-1749)

value: bladder cancer cells

value: transfected with gfp


title: WT culture 2 extract 1

description: control wild type


title: WT culture 1 extract 1

description: control wild type


title: WT culture 2 extract 3

description: control wild type


title: WT culture 1 extract 3

description: control wild type


title: AN culture 1 extract 1


title: HMC-1_exosome_RNA_4


title: Control Replicate3


title: Control Replicate2


title: HMC-1_exosome_RNA_1


title: Italian discordant healthy twin, pair 23

city: Linköping

first: Fredrik

last: Barrenas

address: Sandbäcksgatan 7, level 2

department: Dept of Clinical and Experimental Medicine

institute: Linköping University Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation  in R

source_name: CD4+ T cells

label_protocol: 200 ng total RNA was used in the labeling reaction, using Illumina TotalPrep RNA Amplification Kit (Cat nr IL1791, Illumina Inc, USA).

extract_protocol: Cells were lysed in Qiazol, disrupted and homogenized with TissueRuptor (Qiagen), total RNA was isolated according to the miRNeasy Mini protocol (Qiagen).

treatment_protocol: Peripheral blood mononuclear cells were collected outside pollen season and challenged with birch or grass allergen (100 ug/ml) for 7 days, CD4+ T cells were isolated using a MACS® LS column and CD4+ microbeads.

tag: twin pair

tag: twin's disease state

value: Healthy

tag: stress

value: treated with allergen

value: CD4+ T cells (isolated from allergen-challenged PBMCs)


title: Italian discordant healthy twin, pair 10

tag: cell type


title: Italian discordant allergic twin, pair 21

value: Allergic


title: Italian discordant allergic twin, pair 10


title: GFPRhoGDI2 Replicate B

description: As a control for experimental samples transfected with and stably expressing a GFP-RhoGDI2 fusion transgene, UM-UC-3 cells were transfected with GFP (empty vector), selected using puromycin, and sorted by FACS as described before (Moissoglu et al. Cancer Res 2009. PMID:19276387). Two biological replicates were prepared, GFP Replicates A and B, which are paired (prepared at the same times) as biological replicates A and B, respectively, of the GFP-RhoGDI2 experimental samples.

source_name: UM-UC-3 bladder cancer cells, stably transfected with GFP-tagged RhoGDI2, biological replicate B

growth_protocol: um-uc-3 (atcc# crl-1749) bladder cancer cells were stably transfected with gfp-tagged rhogdi2, sorted for expression of gfp-rhogdi2 by fluorescence activated cell sorting as described (moissoglu et al. cancer res 2009. pmid: 19276387). RNA was isolated for microarray hybridization from cells in log phase growth.

tag: genotype/variation

value: transfected with gfp-tagged rhogdi2


title: GFP Replicate A

description: As a control for other samples transfected with GFP-RhoGDI2 fusion transgene, UM-UC-3 cells were cotransfected with GFP (empty vector) and pBABE PURO (for selection) and sorted by FACS as described before (Moissoglu et al. Cancer Res 2009. PMID:19276387).

source_name: UM-UC-3 bladder cancer cells, stably transfected with GFP (control), biological replicate A

growth_protocol: um-uc-3 (atcc# crl-1749) bladder cancer cells were stably transfected with gfp, sorted for expression of gfp by fluorescence activated cell sorting as described (moissoglu et al. cancer res 2009. pmid: 19276387).  RNA was isolated for microarray hybridization from cells in log phase growth.


title: GFPRhoGDI2 Replicate A

source_name: UM-UC-3 bladder cancer cells, stably transfected with GFP-tagged RhoGDI2, biological replicate A


title: Italian discordant allergic twin, pair 23


title: Italian discordant healthy twin, pair 12


title: HMC-1_exosome_RNA_3

source_name: exosomes isolated from the supernatant of HMC-1 cells


title: Italian discordant healthy twin, pair 21


title: Swedish discordant allergic twin, pair 39


title: Italian discordant allergic twin, pair 07


title: Italian discordant healthy twin, pair 13


title: Italian discordant allergic twin, pair 13


title: Italian discordant allergic twin, pair 12


title: WT culture 1 extract 2

description: control wild type


title: Italian discordant healthy twin, pair 07


title: MPXV_2

city: Berlin

first: Daniel

last: Bourquain

state: Berlin

address: Seestraße 10

department: Centre for Biological Threats and Special Pathogens 1

institute: Robert Koch Institute

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays (4x44K) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.5.1.1 ) was used to read out and process the microarray image files.

source_name: HeLa

label_protocol: 1 µg of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Agilent Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

extract_protocol: TRIzol® extraction, according to manufacturer's protocol

value: HeLa

tag: inoculum

value: monkeypox virus strain MSF#6


title: Discordant healthy twin, pair D, during season

label_protocol: 200 ng total RNA was used in the labeling reaction, performed using Ambion MessageAmp kit

extract_protocol: Cells were lysed in RLT Plus buffer. RNA was isolated using the AllPrep DNA/RNA kit (Qiagen).

treatment_protocol: Peripheral blood mononuclear cells were collected during pollen season and CD4+ T cells were isolated using a MACS® LS column and CD4+ microbeads.

value: D

value: CD4+ T cells

tag: collection time

value: CD4+ cells obtained during pollen season


title: NK_2

value: non-infected


title: Swedish discordant healthy twin, pair 32


title: WWOX Knockout mice, biological rep3

city: Smithville

first: C. Marcelo

last: Aldaz

address: POB 389

department: Molecular Carcinogenesis

institute: The University of TX M.D. Anderson Cancer Center

description:
KO7
Gene expression data from BK5-cre +; WWOX flox/flox

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix GeneChip Mouse Genome 430 2.0

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

data_processing: QC and data pre-processing were performed in R/Bioconductor using the simpleaffy package (version 2.10.31). In order to gather the statistics, we processed the CEL files using the RMA normalization algorithm.

source_name: Mammary gland epithelial organoids_WWOX Knockout

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

extract_protocol: Total RNA was isolated and purified using the TRIzol/RNeasy Kit (Qiagen) from mammary epithelial organoids.

tag: strain background

value: WWOX-KO, BK5-cre +; WWOX flox/flox

value: 8 weeks

tag: tissue

value: Mammary gland epithelial organoids


title: CPXV_2

value: cowpox virus strain Brighton Red


title: WWOX Wildtype mice, biological rep3

description:
WT3
Gene expression data from BK5-cre -; WWOX flox/flox

source_name: Mammary gland epithelial organoids_WWOX Wildtype

value: WWOX-WT, BK5-cre -; WWOX flox/flox

tag: age


title: WWOX Knockout mice, biological rep2

description:
KO6
Gene expression data from BK5-cre +; WWOX flox/flox


title: Discordant allergic twin, pair B, during season

value: B


title: Swedish discordant healthy twin, pair 39

value: Healthy


title: WWOX Knockout  mice, biological rep1

description:
KO5
Gene expression data from BK5-cre +; WWOX flox/flox


title: WWOX Wildtype mice, biological rep2

description:
WT2
Gene expression data from BK5-cre -; WWOX flox/flox


title: MPXV


title: WWOX Wildtype mice, biological rep1

description:
WT1
Gene expression data from BK5-cre -; WWOX flox/flox


title: Discordant allergic twin, pair A, during season

value: A


title: IHD-W_2

value: vaccinia virus strain IHD-W


title: Au-NP Replicate1

tag: treatment

value: gold nanoparticles


title: Discordant allergic twin, pair D, during season

value: Allergic


title: Swedish discordant allergic twin, pair 28

value: treated with allergen

value: CD4+ T cells (isolated from allergen-challenged PBMCs)


title: Swedish discordant healthy twin, pair 29


title: CPXV

tag: cell line

value: HeLa


title: Discordant allergic twin, pair C, during season

value: C

value: CD4+ T cells


title: Swedish discordant allergic twin, pair 29


title: Discordant healthy twin, pair C, during season

value: CD4+ cells obtained during pollen season


title: Discordant healthy twin, pair A, during season


title: control treated

city: Munich

first: Ivonne

last: Regel

address: Ismaninger Strasse 22

institute: Klinikum rechts der Isar

hyb_protocol: Hybridization to the Affymetrix Human Gene 1.0 ST Array according to Affymetrix protocol.

scan_protocol: According to Affymetrix protocol

data_processing: Our core facility did the data processing according to standardized methods of affymetrix. (The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.)

source_name: gastric cancer

label_protocol: One-Cycle cRNA labeling kit from Affymetrix

extract_protocol: Total RNA was isolated with RNeasy Mini Kit from Qiagen according to manufactures instructions

value: AGS


title: Discordant healthy twin, pair B, during season


title: Swedish discordant allergic twin, pair 20


title: LBH589 treated

treatment_protocol: AGS cells were treated with 100 nM LBH589 for 24h.

value: treated with 100 nM LBH589 for 24h.


title: IHD-W


title: Swedish discordant healthy twin, pair 28


title: Swedish discordant healthy twin, pair 20


title: brain of adult hGFAP-Cre:Cx43f/f SVEV mouse, rep_3

status: Public on Apr 14 2012

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: The transcriptomes of WT and Cx43 null brains from both C57Bl/6 and SVEV strains were profiled and compared at perinatal and adult time points to learn more about the strain dependence of the Cx43-null phenotype.

hyb_protocol: Alexa Fluor®_647-labeled cDNA was co-hybridized with a distinct Alexa Fluor®_555-labeled biological replica overnight at 50°C on a Duke MO36K mouse oligonucleotide array spotted with 36k Operon oligonucleotides V4.0. Hybridization design ("multiple yellow" strategy) described in Iacobas et al. Biochem Biophys Res Commun. 2006.

scan_protocol: After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNAs, each array was scanned WITH A 4000B scanner (MDS, Toronto, Canada)) and images were primarily analyzed with GenePixPro 6.0 (Axon Instruments, CA).

data_processing: Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Physiol Genomics 2005.

label: Alexa Fluor®_647

source_name: brain of adult conditional knockout (hGFAP-Cre:Cx43f/f) SVEV mouse

label_protocol: 20ug total RNA extracted from each heart were reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_647–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).

growth_protocol: Conditional knockout (hGFAP-Cre:Cx43f/f) mice on the C57Bl/6 and SVEV backgrounds used in this study were generated in Dr. Kenneth McCarthy’s laboratory (Wiencken-Barger et al, 2007) and housed at our animal facility at Albert Einstein College of Medicine. All studies used protocols approved by the Einstein Animal Care and Use Committee.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: Brain was removed and minced

value: SVEV

value: adult

value: brain


title: brain of adult wild type SVEV mouse, rep_3

source_name: brain of adult wild type SVEV mouse

value: wild type


title: NK

value: non-infected


title: brain of adult wild type SVEV mouse, rep_4

hyb_protocol: Alexa Fluor®_555-labeled cDNA was co-hybridized with a distinct Alexa Fluor®_647-labeled biological replica overnight at 50°C on a Duke MO36K mouse oligonucleotide array spotted with 36k Operon oligonucleotides V4.0. Hybridization design ("multiple yellow" strategy) described in Iacobas et al. Biochem Biophys Res Commun. 2006.

label: Alexa Fluor®_555

label_protocol: 20ug total RNA extracted from each heart were reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_555–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).


title: Swedish discordant allergic twin, pair 32


title: brain of adult wild type SVEV mouse, rep_2


title: brain of adult wild type SVEV mouse, rep_1


title: brain of E19 wild type SVEV mouse, rep_4

source_name: brain of E19 wild type SVEV mouse


title: brain of adult hGFAP-Cre:Cx43f/f SVEV mouse, rep_1


title: brain of E19 wild type SVEV mouse, rep_3


title: brain of adult hGFAP-Cre:Cx43f/f SVEV mouse, rep_4


title: brain of adult wild type C57Bl/6 mouse, rep_2

source_name: brain of adult wild type C57Bl/6 mouse


title: brain of adult hGFAP-Cre:Cx43f/f SVEV mouse, rep_2


title: brain of adult wild type C57Bl/6 mouse, rep_3


title: brain of adult hGFAP-Cre:Cx43f/f C57Bl/6 mouse, rep_4

source_name: brain of adult conditional knockout (hGFAP-Cre:Cx43f/f) C57Bl/6 mouse


title: brain of adult wild type C57Bl/6 mouse, rep_1


title: brain of E19 wild type SVEV mouse, rep_1


title: brain of adult hGFAP-Cre:Cx43f/f C57Bl/6 mouse, rep_3


title: brain of E19 hGFAP-Cre:Cx43f/f SVEV mouse, rep_1


title: brain of adult wild type C57Bl/6 mouse, rep_4


title: brain of E19 hGFAP-Cre:Cx43f/f SVEV mouse, rep_3


title: brain of E19 wild type C57Bl/6 mouse, rep_3

source_name: brain of E19 wild type C57Bl/6 mouse


title: brain of adult hGFAP-Cre:Cx43f/f C57Bl/6 mouse, rep_1


title: brain of E19 hGFAP-Cre:Cx43f/f C57Bl/6 mouse, rep_4

source_name: brain of conditional knockout (hGFAP-Cre:Cx43f/f) C57Bl/6 mouse


title: brain of E19 wild type C57Bl/6 mouse, rep_1


title: brain of E19 hGFAP-Cre:Cx43f/f SVEV mouse, rep_4


title: brain of E19 wild type SVEV mouse, rep_2


title: brain of E19 wild type C57Bl/6 mouse, rep_2


title: brain of E19 wild type C57Bl/6 mouse, rep_4


title: brain of E19 hGFAP-Cre:Cx43f/f C57Bl/6 mouse, rep_2


title: brain of E19 hGFAP-Cre:Cx43f/f SVEV mouse, rep_2


title: hESCs, biological rep3

city: Shanghai

first: Yu

last: Ma

address: 225 South Chongqing Road

country: China

institute: Institute of Health Sciences

description: Gene Expression data of human embryonic stem cells

hyb_protocol: Array hybridization was processed using GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and Fluidics Station 450 (Affymetrix) followed the manufacturer's instructions.

scan_protocol: Slids were scanned by GeneChip Scanner 3000 (Affymetrix) and Command Console Software 3.1 (Affymetrix) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: a line of human embryonic stem cells (SHhES2), rep3

label_protocol: Total RNA was labelled and purified by using GeneChip 3' IVT Express Kit of Affymetrix as the manufacturer's instructions.

growth_protocol: Normal and KS fibroblast cells were transduced by retrovirus coding hOCT4, hSOX2, hKLF4 and hC-MYC and replated the next day. In the 12th day, human embryonic stem cell-like colonies were picked and expanded on MEF in KO-DMEM medium with 20% Knockout Serum Replacement, 100 U/ml penicillin, 100 g/ml streptomycin, 0.1 mM beta-mercaptoethanol (Sigma), 2 mM L-glutamine, 1% non essential amino acid and 4 ng/ml bFGF.

extract_protocol: Total RNA was extracted by Trizol as the manufacturer's protocol and purified by QIAGEN RNeasy kit.

tag: karyotype

value: hESC

tag: disease state

value: control


title: brain of E19 hGFAP-Cre:Cx43f/f C57Bl/6 mouse, rep_3


title: hESCs, biological rep2

source_name: a line of human embryonic stem cells (SHhES2), rep2


title: brain of E19 hGFAP-Cre:Cx43f/f C57Bl/6 mouse, rep_1


title: hESCs, biological rep1

source_name: a line of human embryonic stem cells (SHhES2), rep1


title: N-iPSC-1, biological rep3

description: Gene Expression data of normal iPSCs

source_name: a line of iPSCs from normal fibroblast cells (N-iPSC-1), rep3

value: iPSC


title: N-iPSC-1, biological rep2

description: Gene Expression data of normal iPSCs

source_name: a line of iPSCs from normal fibroblast cells (N-iPSC-1), rep2


title: N-iPSC-1, biological rep1

description: Gene Expression data of normal iPSCs

source_name: a line of iPSCs from normal fibroblast cells (N-iPSC-1), rep1


title: KS-iPSC-4, biological rep2

description: Gene Expression data of KS iPSCs

source_name: the other line of iPSCs from KS fibroblast cells (KS-iPSC-4), rep2

value: 47, XXY

value: Klinefelter’s Syndrome


title: AV_Mouse430_2_--3

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

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

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

data_processing: Partek software used for RMA processing.

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

growth_protocol: All cells were grown in DMEM medium supplemented with 10% fetal bovine serum at 37oC in a 5% CO2 incubator. Cells at 80-85% confluence were trypsinized, washed with PBS and plated for each experiment.

treatment_protocol: The sorted cell subpopulations were based upon CD24, CD29 expression

value: breast cancer stem cells

tag: cell subpopulation


title: AV_Mouse430_2_++2


title: AV_Mouse430_2_--2


title: AV_Mouse430_2_--1


title: N-fs, biological rep3

description: Gene Expression data of normal fibroblast cells

source_name: fibroblast cells from normal person, rep3

value: fibroblast


title: CCCP 15min-rep2

city: Normal

first: Arunachalam Muthaiyan

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

state: IL

address: Julian Hall

institute: Illinois State University

description: Analysis used no CCCP treated RNA as control samples for comparison to the CCCP treated S. aureus RNA samples.

hyb_protocol: Arrays were blocked in 1% SDS, 5 X SSC and 1 mg/ml BSA at 42C for 1 h.  Arrays were then washed 2X for 5 min in 0.1X SSC and 2X for 30 sec in sterile double-distilled water.  Arrays were hybirdized to Cy-labeled cDNAs denatured at 05C in 10 mM EDTA for 5 min and mixed with 40 ul hybridization buffer (Ambion) before loading under a caverslip on the array and sealing in hybridization cassettes.  Hybridization was carried out at 47C for 18 h.  Afterwards, array slides were washed in 2X SSC, 0.5% SDS at 37C for 5 min, followed by stringency washes 2X in 0.1X SSC at 37C for 2.5 min each, and 2X in 0.1X SSC at room temperature for 2.5 min each.

scan_protocol: Arrays were scanned using an Axon 4000b, and images analyzed using GenePix 6.0.

data_processing: Array intensity data was log2-transformed, and normalized using the Lowess algorithm.  Statistical analysis was performed using a significance analysis of microarrays (SAM, MultiExperiment Viewer, ver. 4.0) unpaired contrast.  A d-statistic was calculated for each gene based on repeated permutations, and a false discovery rate FDR of 0.01 was used to assign a critical cutoff for significance.

organism: Staphylococcus aureus

label_protocol: Amino-allyl labeled cDNA was dried and then suspended in 0.1 M sodium carbonate (pH 9.3) and coupled with either Cy3 or Cy5 (swapped between balanced samples, N=4).  Uncoupled dye was removed by column purification (Qiagen).

growth_protocol: Cultures were initiated from overnight cultures in MHB into fresh MHB at 1:100 and grown to OD600=0.35.

extract_protocol: Samples were added to RNA Protect (Qiagen, Valencia, CA) and processed according to the manufacturer's instructions.  Cells were harvested by centrifugation (8,000 X g, 20 min, 4C) and then resuspended in 1 ml Trizol (Invitrogen, Carlsbad, CA) and processed in an FP120 FastPrep cell disruptor (MP Biomedicals, Irvine, CA).  Chloroform was subsequently added to the lysates, followed by centrifugation (16,000 X g, 15 min, 4C) and RNA was precipitated 1:1 (vol/vol) in 100% ethyl alcohol.  The RNA was then purified using the RNeasy™ kit (Qiagen) according to the manufacturer's instructions. Contaminating DNA was removed from purified RNA using DNAfree (Ambion, Austin, TX).  cDNA was produced using SuperScript II Reverse Transcriptase (Invitrogen) from 2 µg of total RNA combined with random hexamers, 0.25 mM deoxynucleoside triphosphate, and 0.25 mM aminoallyl-dUTP.

treatment_protocol: Cultures in MHB grown to OD600=0.35 were treated with telavancin(8 µg/ml final concentration), or vancomycin (10 /µg ml) or  CCCP (2 µg/ ml );  or enduracidin (1 µg ml) and incubated for an additional 15 min , and 60 min before sampling.

value: CCCP

tag: time

source_name: sample collected at OD600 at 0.35 without any treatment

value: untreated


title: FaDu_si

first: Olivier

last: Gires

address: Marchioninistr. 15

department: Head and Neck Research Dept

institute: University Clinics Munich

description: Gene expression of FaDu cells treated with EpCAM specific siRNA

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized for 17 hr at 65C on Agilent 4x44k Whole Human Genome Array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Agilent Technologies Scanner G2505B; Agilent Scanner protocol GE1-v5_95_Feb07; Scan resolution 5 µm; XDR Hi 100% XDR Lo 10%

data_processing: Data extraction was done using Agilent Feature Extraction Software. Control ControlType Features were removed from the scanner data and the arrays have been median scaled.

source_name: FaDu treated with EpCAM specific siRNA

label_protocol: Cy3 labeled cRNA were prepared according to the standard Agilent protocol from 500ng total RNA.

growth_protocol: FaDu cells were grown in RPMI media supplemented with 10% FCS and passaged three times per week up to 80-90% confluency

extract_protocol: Total RNA from transiently transfected cells was isolated using RNAeasy kit (Qiagen, Hilden Germany)

treatment_protocol: FaDu cells were transiently transfected with control-siRNA or EpCAM-siRNA as follows: (3 × 105 cells per well) were transfected with 100 nM target-specific siRNA or control siRNA using the MATra transfection reagent (IBA). Control: 5´-UCGUCCGUAUCAUUUCAAU-3´; EpCAM: 5´-UGCCAGUGUACUUCAGUUG-3´;

value: FaDu (ATCC HTB-43)


title: N-fs, biological rep2

source_name: fibroblast cells from normal person, rep2


title: KS-iPSC-1, biological rep3

description: Gene Expression data of KS iPSCs

source_name: a line of iPSCs from KS fibroblast cells (KS-iPSC-1), rep3


title: KS-iPSC-1, biological rep2

description: Gene Expression data of KS iPSCs

source_name: a line of iPSCs from KS fibroblast cells (KS-iPSC-1), rep2


title: AV_Mouse430_2_++3

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


title: KS-fs, biological rep3

description: Gene Expression data of KS fibroblast cells

source_name: fibroblast cells from a KS patient, rep 3


title: KS-fs, biological rep2

source_name: fibroblast cells from a KS patient, rep 2


title: KS-iPSC-4, biological rep3

description: Gene Expression data of KS iPSCs

source_name: the other line of iPSCs from KS fibroblast cells (KS-iPSC-4), rep3


title: KS-iPSC-1, biological rep1

description: Gene Expression data of KS iPSCs

source_name: a line of iPSCs from KS fibroblast cells (KS-iPSC-1), rep1


title: KS-iPSC-4, biological rep1

description: Gene Expression data of KS iPSCs

source_name: the other line of iPSCs from KS fibroblast cells (KS-iPSC-4), rep1


title: N-fs, biological rep1

source_name: fibroblast cells from normal person, rep1


title: AV_Mouse430_2_++1


title: KS-fs, biological rep1

source_name: fibroblast cells from a KS patient, rep 1


title: FaDu_csi

description: Gene expression of FaDu cells treated with non-specific siRNA

source_name: FaDu treated with non-specific siRNA


title: CCCP 15min-rep1

tag: strain


title: Control quadriceps muscle sample Sample79

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

institute: University of Stirling

description:
Control quadriceps muscle sample
gene expression in healthy human skeletal muscle

hyb_protocol: For the microarray study, 3.75ug of cDNA was fragmented and labeled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to hgu133aplus2 arrays.

scan_protocol: As per Affymetrix recommendations using Affymetrix equipment

data_processing: Raw chip data were analysed using MAS 5.0 with global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further analysis used the bioconductor suite (bioC 2.8  / R 2.13) and further data processing were performed by RMA.

source_name: quadriceps muscle biopsy healthy control

label_protocol: Reverse transcription of RNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100ng of total RNA was reverse transcribed as per the manufacturer’s protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. For the microarray study, 3.75ug of cDNA was fragmented and labeled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array (Affymetrix, USA) using protocols provided by Nugen Technologies Inc.

extract_protocol: Tissue was homogenised in Qiazol (Qiagen, UK) reagent using a Polytron PT1200E (Kinematica AG, Switzerland). Total RNA was extracted using miRNEasy columns (Qiagen, UK) as directed by the manufacturer with an on column DNAse digestion step.

treatment_protocol: Biopsies were harvested from human quadriceps muscle using a Bergstrom needle under suction

value: skeletal muscle

tag: condition

value: healthy control

tag: Sex

value: M

tag: bmi

tag: weightlossfromusual

tag: crp

tag: height(cm)

tag: currentwgt

tag: quadsstr(n/kg)

tag: stepsperday

tag: tumour

value: HC


title: Control quadriceps muscle sample Sample94

tag: tissue

tag: age


title: Control quadriceps muscle sample Sample99


title: brain of adult hGFAP-Cre:Cx43f/f C57Bl/6 mouse, rep_2

tag: genotype/variation

value: adult

value: brain


title: Control quadriceps muscle sample Sample75

value: F


title: Control quadriceps muscle sample Sample73


title: Post-op quadriceps muscle sample Sample65

description:
Post-op quadriceps muscle sample
gene expression in human skeletal muscle post tumour removal

source_name: quadriceps muscle biopsy post operative

value: cancer-free

value: Gastric


title: Control quadriceps muscle sample Sample100


title: Post-op quadriceps muscle sample Sample63

value: Oesophagus


title: Post-op quadriceps muscle sample Sample97

value: Pancreas


title: Post-op quadriceps muscle sample Sample62


title: Post-op quadriceps muscle sample Sample61


title: Post-op quadriceps muscle sample Sample92


title: Post-op quadriceps muscle sample Sample88


title: Pre-op quadriceps muscle sample Sample87

description:
Pre-op quadriceps muscle sample
gene expression in human skeletal muscle prior to tumour removal

source_name: quadriceps muscle biopsy pre operative

value: cancer


title: Pre-op quadriceps muscle sample Sample95


title: Post-op quadriceps muscle sample Sample68


title: Post-op quadriceps muscle sample Sample82


title: Post-op quadriceps muscle sample Sample84


title: Healthy control whole blood RNA CTRL15

first: Jeroen

last: Maertzdorf

address: Chariteplatz 1

institute: MPIIB

description: CTRL whole blood RNA

hyb_protocol: Quantity and labelling efficiency were verified before hybridization to human whole genome microarrays (Agilent Technologies)

scan_protocol: Scanned on an Agilent Scanner G2505B. Image analysis was performed with Feature Extraction software (version 6.1.1, Agilent Technologies).

data_processing: Agilent Feature Extraction Software (v 6.1.1) was used for background subtraction and LOWESS normalization.

source_name: Peripheral blood CTRL

label_protocol: RNA was labeled with the Fluorescent Linear Amplification Kit (Agilent Technologies) following manufacturer’s instructions.

extract_protocol: RNA was isolated from peripheral blood collected in PAXgene tubes.

tag: gender

value: Female

value: peripheral blood

tag: disease state

value: control

tag: subject


title: Healthy control whole blood RNA CTRL14

description: CTRL whole blood RNA


title: Post-op quadriceps muscle sample Sample70


title: Healthy control whole blood RNA CTRL16

description: CTRL whole blood RNA

value: Male


title: Post-op quadriceps muscle sample Sample64


title: Pre-op quadriceps muscle sample Sample34


title: Healthy control whole blood RNA CTRL12

description: CTRL whole blood RNA


title: Pre-op quadriceps muscle sample Sample24


title: Pre-op quadriceps muscle sample Sample12


title: Emwa1 inoculated pskr1-5 at 3 dpi, biological replicate 1

city: Sophia Antipolis

first: Harald

last: Keller

address: 400 route des Chappes

department: UMR-ISA

country: France

institute: INRA

description: mutant expression after infection

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Background adjustment, quantile normalization, and summarization of raw data were performed with the Affymetrix Power Tools APT1.14.4 software package.

organism: Arabidopsis thaliana

source_name: A. thaliana pskr1-5 Hpa-inoculated.

label_protocol: standard Affymetrix protocol

growth_protocol: Seeds from A. thaliana ecotype Wassilewskija (WS) were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.

extract_protocol: In two independent experiments, cotyledons from the ecotype Wassilewskija (Ws-4) wild-type or pskr1-5 mutant plants were treated with water, or inoculated with H. arabidopsidis to establish a compatible interaction. Total RNA was extracted from about 100 mg of these tissues according to a procedure described (Laroche-Raynal et al., Plant Science Letters 35, 139-146,1984).

treatment_protocol: For infection, 10-day-old plants were spray-inoculated to saturation with a spore suspension of 40,000 spores/ml (strain  Emwa1)

value: Cotyledons

tag: genotype

tag: genetic background

tag: infection

value: biotrophic oomycete downy mildew pathogen, Hyaloperonospora arabidopsidis strain  Emwa1


title: Pre-op quadriceps muscle sample Sample78

value: skeletal muscle

tag: condition

tag: Sex

tag: bmi


title: Healthy control whole blood RNA CTRL05

description: CTRL whole blood RNA


title: Healthy control whole blood RNA CTRL08

description: CTRL whole blood RNA


title: Pre-op quadriceps muscle sample Sample47

value: M

tag: weightlossfromusual

tag: crp

tag: height(cm)


title: Healthy control whole blood RNA CTRL11

description: CTRL whole blood RNA


title: Healthy control whole blood RNA CTRL04

description: CTRL whole blood RNA


title: Emwa1 inoculated pskr1-5 at 3 dpi, biological replicate 2

description: mutant expression after infection


title: water-treated pskr1-5, biological replicate 2

description: mutant expression in the absence of infection

source_name: A. thaliana pskr1-5 treated with water.


title: Healthy control whole blood RNA CTRL07

description: CTRL whole blood RNA


title: Pre-op quadriceps muscle sample Sample91

tag: currentwgt

tag: quadsstr(n/kg)

tag: stepsperday


title: Healthy control whole blood RNA CTRL01

description: CTRL whole blood RNA

tag: tissue


title: Healthy control whole blood RNA CTRL06

description: CTRL whole blood RNA


title: Pre-op quadriceps muscle sample Sample80

tag: age

tag: tumour


title: water-treated pskr1-5, biological replicate 1


title: Healthy control whole blood RNA CTRL03

description: CTRL whole blood RNA

tag: gender

tag: disease state


title: Pre-op quadriceps muscle sample Sample13


title: Pre-op quadriceps muscle sample Sample4


title: Healthy control whole blood RNA CTRL02

description: CTRL whole blood RNA

tag: subject


title: Healthy control whole blood RNA CTRL13

description: CTRL whole blood RNA


title: Healthy control whole blood RNA CTRL18

description: CTRL whole blood RNA


title: Tuberculosis whole blood RNA TB07

description: TB whole blood RNA

source_name: Peripheral blood TB

value: tuberculosis


title: Healthy control whole blood RNA CTRL17

description: CTRL whole blood RNA


title: Tuberculosis whole blood RNA TB08

description: TB whole blood RNA


title: Healthy control whole blood RNA CTRL10

description: CTRL whole blood RNA


title: Emwa1 inoculated wild type at 3 dpi, biological replicate 1

description: wild-type expression after infection

source_name: A. thaliana Wt Hpa-inoculated.

tag: genotype

value: wild type

tag: genetic background


title: Tuberculosis whole blood RNA TB05

description: TB whole blood RNA


title: Pre-op quadriceps muscle sample Sample20

tag: condition


title: Tuberculosis whole blood RNA TB06

description: TB whole blood RNA


title: Healthy control whole blood microRNA CTRL8

description: CTRL whole blood total microRNA

hyb_protocol: Quantity and labelling efficiency were verified before hybridization to human microRNA arrays (Agilent Technologies)

label_protocol: Total RNA was labeled with the Fluorescent Linear Amplification Kit (Agilent Technologies) following manufacturer’s instructions.

extract_protocol: Total RNA was isolated from peripheral blood collected in PAXgene tubes.


title: Healthy control whole blood microRNA CTRL5

description: CTRL whole blood total microRNA


title: Healthy control whole blood microRNA CTRL6

description: CTRL whole blood total microRNA


title: Tuberculosis whole blood RNA TB02

description: TB whole blood RNA


title: Healthy control whole blood microRNA CTRL7

description: CTRL whole blood total microRNA


title: Tuberculosis whole blood RNA TB04

description: TB whole blood RNA


title: Tuberculosis whole blood RNA TB01

description: TB whole blood RNA


title: Tuberculosis whole blood RNA TB03

description: TB whole blood RNA


title: Emwa1 inoculated wild type at 3 dpi, biological replicate 2

description: wild-type expression after infection

tag: infection


title: Healthy control whole blood microRNA CTRL3

description: CTRL whole blood total microRNA


title: Healthy control whole blood microRNA CTRL4

description: CTRL whole blood total microRNA


title: water-treated wild type, biological replicate 1

description: wild-type expression in the absence of infection

source_name: A. thaliana Wt treated with water.


title: Healthy control whole blood RNA CTRL09

description: CTRL whole blood RNA


title: water-treated wild type, biological replicate 2


title: RPW-24 I

city: Boston

first: Read

last: Pukkila-Worley

state: MA

address: 55 Fruit Street

department: Molecular Biology and Medicine

institute: Massachusetts General Hospital

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Data were analyzed with freely available GenePattern version 2.0 Software on the BROAD public Server using CEL files as input. Data were processed using ExpressionFileCreator with GC-RMA and quantile normalization.  Data were then preprocessed using MultiplotPreprocess (no replicate FC, no random data, no outlier elimination, but with Stats), analyzed using Multiplot and means calculated from 3 independent biological replicates were visualized with scatter plots. Probability of differential expression was calculated by Multiplot from 3 independent biological replicates per sample using student t-tests and a probability of ≤ 0.025 was considered significant.

label_protocol: RNA samples were prepared and hybridized to Affymetrix full-genome GeneChips for C. elegans at the Harvard Medical School Biopolymer Facility following previously described protocols and instructions from Affymetrix.

growth_protocol: N2 C. elegans animals were synchronized by hypochlorite treatment.  Arrested L1s were plated on 10 cm NGM plates seeded with E. coli OP50 and grown at 20°C until the late L4 larval stage.

extract_protocol: RNA was extracted using TRI Reagent (Molecular Research Center) according to the manufactures instructions and purified using an RNeasy column (Qiagen).

treatment_protocol: Animals were incubated for 15 hours at 15°C in 2 mL of liquid S-basal complete medium containing 70 μM RPW-24 or DMSO and supplemented with E. coli OP50.  The final concentration of DMSO in both samples was 1%.

tag: treatment

value: whole organism

tag: strain


title: RPW-24 G


title: Tuberculosis whole blood microRNA TB08

description: TB whole blood total microRNA


title: Sarcoidosis whole blood RNA SARC17

description: SARC whole blood RNA

source_name: Peripheral blood SARC

value: sarcoidosis


title: RPW-24 H


title: Sarcoidosis whole blood RNA SARC18

description: SARC whole blood RNA


title: DMSO I

source_name: DMSO I

value: DMSO


title: DMSO H

source_name: DMSO H


title: Tuberculosis whole blood microRNA TB07

description: TB whole blood total microRNA


title: DMSO G

source_name: DMSO G


title: enduracidin 60min-rep2

description: Analysis used no enduracidin treated RNA as control samples for comparison to the enduracidin treated S. aureus RNA samples.

value: enduracidin

tag: time

source_name: sample collected at OD600 at 0.35 without any treatment

value: untreated


title: Sarcoidosis whole blood RNA SARC15

description: SARC whole blood RNA


title: enduracidin 60min-rep3


title: Healthy control whole blood microRNA CTRL1

description: CTRL whole blood total microRNA


title: Sarcoidosis whole blood RNA SARC16

description: SARC whole blood RNA


title: Tuberculosis whole blood microRNA TB06

description: TB whole blood total microRNA


title: Sarcoidosis whole blood RNA SARC13

description: SARC whole blood RNA


title: Healthy control whole blood microRNA CTRL2

description: CTRL whole blood total microRNA


title: Tuberculosis whole blood microRNA TB03

description: TB whole blood total microRNA


title: Tuberculosis whole blood microRNA TB02

description: TB whole blood total microRNA


title: Sarcoidosis whole blood RNA SARC12

description: SARC whole blood RNA


title: Sarcoidosis whole blood RNA SARC14

description: SARC whole blood RNA


title: Tuberculosis whole blood microRNA TB04

description: TB whole blood total microRNA


title: enduracidin 15min-rep3


title: Sarcoidosis whole blood RNA SARC10

description: SARC whole blood RNA


title: enduracidin 60min-rep1


title: Tuberculosis whole blood microRNA TB05

description: TB whole blood total microRNA


title: vancomycin 60min-rep1

description: Analysis used no vancomycin treated RNA as control samples for comparison to the vancomycin treated S. aureus RNA samples.

value: vancomycin


title: Sarcoidosis whole blood RNA SARC09

description: SARC whole blood RNA


title: Sarcoidosis whole blood RNA SARC11

description: SARC whole blood RNA


title: telavancin 60min-rep2

description: Analysis used no telavancin treated RNA as control samples for comparison to the telavancin treated S. aureus RNA samples.

value: telavancin


title: Sarcoidosis whole blood microRNA SARC16

description: SARC whole blood total microRNA


title: telavancin 60min-rep3


title: Sarcoidosis whole blood RNA SARC07

description: SARC whole blood RNA

value: Female


title: Sarcoidosis whole blood microRNA SARC13

description: SARC whole blood total microRNA

value: peripheral blood


title: Sarcoidosis whole blood microRNA SARC17

description: SARC whole blood total microRNA


title: Sarcoidosis whole blood RNA SARC05

description: SARC whole blood RNA


title: Tuberculosis whole blood microRNA TB01

description: TB whole blood total microRNA


title: vancomycin 60min-rep2


title: Sarcoidosis whole blood microRNA SARC15

description: SARC whole blood total microRNA


title: vancomycin 60min-rep3


title: enduracidin 15min-rep1


title: telavancin 60min-rep1


title: Sarcoidosis whole blood microRNA SARC14

description: SARC whole blood total microRNA


title: enduracidin 15min-rep2


title: Sarcoidosis whole blood RNA SARC04

description: SARC whole blood RNA


title: Sarcoidosis whole blood RNA SARC06

description: SARC whole blood RNA


title: Sarcoidosis whole blood microRNA SARC12

description: SARC whole blood total microRNA


title: Sarcoidosis whole blood RNA SARC08

description: SARC whole blood RNA


title: telavancin 15min-rep3


title: telavancin 15min-rep2


title: Sarcoidosis whole blood microRNA SARC09

description: SARC whole blood total microRNA


title: telavancin 15min-rep1


title: Sarcoidosis whole blood RNA SARC03

description: SARC whole blood RNA


title: Sarcoidosis whole blood microRNA SARC04

description: SARC whole blood total microRNA


title: Sarcoidosis whole blood RNA SARC01

description: SARC whole blood RNA


title: group A, liver allograft wedge biopsie tacrolimus treatment 10

status: Public on Apr 13 2012

city: Vienna

first: Julia

last: Wilflingseder

address: Währinger Gürtel 18-20

department: Nephrology and Dialysis

country: Austria

institute: Medical University of Vienna

description:
liver tissue in RNAlater, stored at -80°C
Gene expression data from liver allografts after 15 min flushing with tacrolimus albumin solution

hyb_protocol: cDNA were hybridized for 18 hr at 45C on GeneChip Human ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 7G.

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

source_name: liver allograft

label_protocol: Total RNA (200 ng per sample) was amplified and labeled using the Applause WT-Amp ST and Encore Biotin Module kit (NuGEN, San Carlos, CA)

treatment_protocol: Group A was administered tacrolimus, 20ng/ml in 1500ml albumin solution ; and Group B was administered only albumin solution. Wedge biopsie of the allograft were harvested after 15 min flushing time.

value: liver allograft


title: Sarcoidosis whole blood RNA SARC02

description: SARC whole blood RNA

value: Male


title: group B, liver allograft wedge biopsie placebo treatment 3

description:
liver tissue in RNAlater, stored at -80°C
Gene expression data from liver allografts after 15 min flushing with albumin solution


title: group A, liver allograft wedge biopsie tacrolimus treatment 6

value: liver allografts after 15 min flushing with tacrolimus albumin solution


title: group A, liver allograft wedge biopsie tacrolimus treatment 9


title: group B, liver allograft wedge biopsie placebo treatment 4

value: liver allografts after 15 min flushing with albumin solution


title: group B, liver allograft wedge biopsie placebo treatment 5


title: group A, liver allograft wedge biopsie tacrolimus treatment 7


title: group A, liver allograft wedge biopsie tacrolimus treatment 5


title: group B, liver allograft wedge biopsie placebo treatment 6


title: group A, liver allograft wedge biopsie tacrolimus treatment 2


title: group A, liver allograft wedge biopsie tacrolimus treatment 3


title: group A, liver allograft wedge biopsie tacrolimus treatment 1


title: group A, liver allograft wedge biopsie tacrolimus treatment 8


title: group A, liver allograft wedge biopsie tacrolimus treatment 4


title: group B, liver allograft wedge biopsie placebo treatment 7


title: group B, liver allograft wedge biopsie placebo treatment 2


title: group B, liver allograft wedge biopsie placebo treatment 1


title: Hypocotyl_PIC_120min_wildtype_rep1

city: Hanover

first: Kathleen

last: Greenham

state: NH

address: 78 College St

institute: Dartmouth College

description: This sample is of wildtype 120min Picloram treated hypocotyls dissected over a 30min period.  Roughly 400 hypocotyls were pooled for this replicate #1.

hyb_protocol: Hybridization was performed according to NimbleGen standard protocol at the GeneChip Microarray Core facility at the University of California San Diego.

scan_protocol: Scanning was performed according to NimbleGen standard protocol at the GeneChip Microarray Core facility at the University of California San Diego.

data_processing: Annotation packages were built with pdInfoBuilder using raw data files (.xys) along with a Nimblegen microarray design file (.ndf).  The data was RMA normalized in oligo using the annotation package in R.  See www.R-project.org/  AND www.bioconductor.org/

label_protocol: Labeling was performed according to NimbleGen standard protocol at the GeneChip Microarray Core facility at the University of California San Diego.

growth_protocol:
Arabidopsis seedlings were grown on 0.5X MS medium on nylon mesh under long day (16L:8D) conditions for 5d and transferred to 5μM picloram or a DMSO control at ZT2 for 30min or 2hrs.
Hypocotyls were dissected following the experimental or control treatment.  Dissection time was limited to 30min.  Tissue was immediately frozen in liquid N2.

extract_protocol: Total RNA was extracted using Trizol reagent (Sigma) followed by additional phenol extraction and ethanol precipitation steps.  mRNA was amplified using the MessageAmp II aRNA Amplification kit (Ambion) and the manufacterer's protocol. Labeled cDNA was prepared from aRNA using the Superscript ds cDNA synthesis kit (Invitrogen).

tag: phenotype

value: normal

tag: ecotype


title: Hypocotyl_DMSO_120min_wildtype_rep3

description: This sample is of wildtype 120-min DMSO treated hypocotyls dissected over a 30min period.  Roughly 400 hypocotyls were pooled for this replicate #3.


title: Hypocotyl_PIC_120min_wildtype_rep3

description: This sample is of wildtype 120min Picloram treated hypocotyls dissected over a 30min period.  Roughly 400 hypocotyls were pooled for this replicate #3.


title: Hypocotyl_PIC_120min_wildtype_rep2

description: This sample is of wildtype 120min Picloram treated hypocotyls dissected over a 30min period.  Roughly 400 hypocotyls were pooled for this replicate #2.


title: Hypocotyl_PIC_30min_wildtype_rep3

description: This sample is of wildtype 30min Picloram treated hypocotyls dissected over a 30min period.  Roughly 400 hypocotyls were pooled for this replicate #3.


title: glutamine sensing - Slide 2

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Mutant vs Wild-type, Glutamine
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27314.gif
is_reverse: Yes

hyb_protocol: not provided

scan_protocol: not provided

data_processing: VALUE is Log (base 2) of the ratio of the medians

source_name: Arabidopsis thaliana Gsr1 mutant

label_protocol: not provided

extract_protocol: not provided

value: Gsr1 mutant

source_name: wild type Arabidopsis thaliana


title: Hypocotyl_DMSO_120min_wildtype_rep1

description: This sample is of wildtype 120-min DMSO treated hypocotyls dissected over a 30min period.  Roughly 400 hypocotyls were pooled for this replicate #1.


title: Hypocotyl_DMSO_120min_wildtype_rep2

description: This sample is of wildtype 120-min DMSO treated hypocotyls dissected over a 30min period.  Roughly 400 hypocotyls were pooled for this replicate #2.


title: Hypocotyl_PIC_30min_wildtype_rep2

description: This sample is of wildtype 30min Picloram treated hypocotyls dissected over a 30min period.  Roughly 400 hypocotyls were pooled for this replicate #2.


title: Hypocotyl_DMSO_30min_wildtype_rep2

description: This sample is of wildtype 30-min DMSO treated hypocotyls dissected over a 30min period.  Roughly 400 hypocotyls were pooled for this replicate #2.


title: Hypocotyl_DMSO_30min_wildtype_rep3

description: This sample is of wildtype 30-min DMSO treated hypocotyls dissected over a 30min period.  Roughly 400 hypocotyls were pooled for this replicate #3.


title: WAT_CD1d-/-_HFD_αGalCer_repl3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description: epididymal adipose tissue, CD1d knockout mouse, after 4 days on a high fat diet, injected intraperitoneally with α-galactosylceramide (αGalCer) on days 0 and 2, replicate 3

hyb_protocol: The Affymetrix GeneChip Mouse Gene 1.1 ST arrays are peg arrays arranged into the standard 96 well plate format. The 13 arrays that were used in this experiment were provided as subset of a 1x 16 array plate. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.18.1).

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

growth_protocol: Wildtype C57/BL6 and B6.129S6-Cd1d1/Cd1d2tm1spb/J (CD1d-/-, #008881) were purchased from the Jackson Laboratory and bred in our facility.

extract_protocol: Total RNA was prepared from adipose tissue using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Six week-old mice were placed on a high fat diet (HFD) on day 0 with intraperitoneal injection of α-galactosylceramide (αGalCer; 100 ng/g bodyweight) or vehicle (pyridine) on day 0 and day 2. Mice were killed on day 4  by cervical dislocation and epididymal white adipose tissue was removed.

tag: background strain

tag: genotype/variation

value: CD1d knockout

value: male

value: 6.5 weeks

value: epididymal adipose tissue


title: WAT_CD1d-/-_HFD_vehicle_repl2

description: epididymal adipose tissue, CD1d knockout mouse, after 4 days on a high fat diet, injected intraperitoneally with vehicle on days 0 and 2, replicate 2

tag: tissue


title: WAT_CD1d-/-_HFD_αGalCer_repl2

description: epididymal adipose tissue, CD1d knockout mouse, after 4 days on a high fat diet, injected intraperitoneally with α-galactosylceramide (αGalCer) on days 0 and 2, replicate 2

tag: age


title: Hypocotyl_5uMPic_2hr_mutant_rep3

description: This sample is of afb5-5 Picloram treated hypocotyls dissected over a 30min period.  Roughly 700 hypocotyls were pooled for this replicate #3.

growth_protocol:
Arabidopsis seedlings were grown on nylon mesh under long day (16L:8D) conditions for 5d and transferred to 5uM picloram or a DMSO control at ZT2 for 2hrs.
Hypocotyls were dissected following the 2hr treatment.  Dissection time was limited to 30min.  Tissue was immediately frozen in liquid N2.

extract_protocol: Total RNA was extracted using the Invitrogen PureLink RNA mini kit.

value: Resistant to Picloram


title: Hypocotyl_PIC_30min_wildtype_rep1

description: This sample is of wildtype 30min Picloram treated hypocotyls dissected over a 30min period.  Roughly 400 hypocotyls were pooled for this replicate #1.


title: WAT_CD1d-/-_HFD_αGalCer_repl1

description: epididymal adipose tissue, CD1d knockout mouse, after 4 days on a high fat diet, injected intraperitoneally with α-galactosylceramide (αGalCer) on days 0 and 2, replicate 1


title: WAT_CD1d-/-_HFD_vehicle_repl3

description: epididymal adipose tissue, CD1d knockout mouse, after 4 days on a high fat diet, injected intraperitoneally with vehicle on days 0 and 2, replicate 3


title: Hypocotyl_5uMPic_2hr_mutant_rep1

description: This sample is of afb5-5 Picloram treated hypocotyls dissected over a 30min period.  Roughly 700 hypocotyls were pooled for this replicate #1.


title: WAT_WT_HFD_αGalCer_repl3

description: epididymal adipose tissue, wild type mouse, after 4 days on a high fat diet, injected intraperitoneally with galactosylceramide (αGalCer) on days 0 and 2, replicate 3

value: wild type


title: Hypocotyl_5uMPic_2hr_mutant_rep2

description: This sample is of afb5-5 Picloram treated hypocotyls dissected over a 30min period.  Roughly 700 hypocotyls were pooled for this replicate #2.


title: WAT_WT_HFD_αGalCer_repl1

description: epididymal adipose tissue, wild type mouse, after 4 days on a high fat diet, injected intraperitoneally with α-galactosylceramide (αGalCer) on days 0 and 2, replicate 1


title: Hypocotyl_5uMPic_2hr_wildtype_rep1

description: This sample is of wildtype Picloram treated hypocotyls dissected over a 30min period.  Roughly 700 hypocotyls were pooled for this replicate #1.


title: WAT_WT_HFD_vehicle_repl2

description: epididymal adipose tissue, wild type mouse, after 4 days on a high fat diet, injected intraperitoneally with vehicle on days 0 and 2, replicate 2


title: mouse lung_bleo_day21_rep3

city: Los Angeles

first: ting

last: Xie

address: 127 San Vicente Blvd

department: Pulmonary

institute: Cedars-Sinai Medical Center

hyb_protocol: After labeling, RNA from each sample was hybridazed onto the microarray slides using the miRCURY™ LNA miRNA Array labeling kit according to the manufacture's instructions.

scan_protocol: Slides was scaned by GenePix 4000B scanner(Molecular Devices, Sunnyvale, CA), Data and images were acqusited using GenePix Pro 6.1(Molecular Devices, Sunnyvale, CA) according to the manufacture's instructions.

data_processing: thresholding: raw signal to 1.0, summarization: Treatment of on-chip replicates- The signal value of a probeset is the geometric mean of all its probes. normalization: lowess, ratio computation: Cy5/Cy3, lowess normalized, log transformation: log2, baseline transformation: didn’t do any.

source_name: mouse lung, bleomycin, day21

label_protocol: RNA from each sample was labeled with Cy5 and reference sample RNA labeled with Cy3 using the miRCURY™ LNA miRNA Array labeling kit according to the manufacture's instructions.

growth_protocol: All experiments were carried out using 8- to 12-week-old female C57BL/6J mice. All studies were conducted in accordance with NIH guidelines for the care and use of animals and with approval from the Duke University Animal Care and Use Committee.

extract_protocol: Total RNA from lung tissues was isolated using the mirVana miRNA Isolation kit (Ambion, Austin, TX) according to the manufacturer’s instructions.

treatment_protocol: Under anesthesia, 2.5 U/kg bleomycin dissolved in sterile PBS was administered via trachea as previously described. Lung tissues were harvested at the time point of day 0, 3, 7, 14, and 21 post bleomycin challenges.

tag: Sex

value: lung

source_name: Mouse Lung Total RNA


title: mouse lung_bleo_day21_rep2


title: WAT_WT_HFD_αGalCer_repl2

description: epididymal adipose tissue, wild type mouse, after 4 days on a high fat diet, injected intraperitoneally with galactosylceramide (αGalCer) on days 0 and 2, replicate 2

tag: gender


title: WAT_WT_HFD_vehicle_repl1

description: epididymal adipose tissue, wild type mouse, after 4 days on a high fat diet, injected intraperitoneally with vehicle on days 0 and 2, replicate 1


title: mouse lung_bleo_day21_rep1


title: Hypocotyl_DMSO_30min_wildtype_rep1

description: This sample is of wildtype 30-min DMSO treated hypocotyls dissected over a 30min period.  Roughly 400 hypocotyls were pooled for this replicate #1.


title: WAT_CD1d-/-_HFD_vehicle_repl1

description: epididymal adipose tissue, CD1d knockout mouse, after 4 days on a high fat diet, injected intraperitoneally with vehicle on days 0 and 2, replicate 1


title: WAT_WT_HFD_αGalCer_repl4

description: epididymal adipose tissue, wild type mouse, after 4 days on a high fat diet, injected intraperitoneally with galactosylceramide (αGalCer) on days 0 and 2, replicate 4


title: mouse lung_bleo_day14_rep2

source_name: mouse lung, bleomycin, day14


title: Hypocotyl_5uMPic_2hr_wildtype_rep2

description: This sample is of wildtype Picloram treated hypocotyls dissected over a 30min period.  Roughly 700 hypocotyls were pooled for this replicate #2.


title: WAT_WT_HFD_vehicle_repl3

description: epididymal adipose tissue, wild type mouse, after 4 days on a high fat diet, injected intraperitoneally with vehicle on days 0 and 2, replicate 3


title: Hypocotyl_5uMPic_2hr_wildtype_rep3

description: This sample is of wildtype Picloram treated hypocotyls dissected over a 30min period.  Roughly 700 hypocotyls were pooled for this replicate #3.


title: Hypocotyl_DMSO_2hr_mutant_rep1

description: This sample is of afb5-5 DMSO treated hypocotyls dissected over a 30min period.  Roughly 700 hypocotyls were pooled for this replicate #1.


title: Hypocotyl_DMSO_2hr_mutant_rep3

description: This sample is of afb5-5 DMSO treated hypocotyls dissected over a 30min period.  Roughly 700 hypocotyls were pooled for this replicate #3.


title: Hypocotyl_DMSO_2hr_mutant_rep2

description: This sample is of afb5-5 DMSO treated hypocotyls dissected over a 30min period.  Roughly 700 hypocotyls were pooled for this replicate #2.


title: Hypocotyl_DMSO_2hr_wildtype_rep3

description: This sample is of wildtype DMSO treated hypocotyls dissected over a 30min period.  Roughly 700 hypocotyls were pooled for this replicate #3.


title: mouse lung_bleo_day14_rep1


title: mouse lung_bleo_day7_rep3

source_name: mouse lung, bleomycin, day7