title: T regs from mouse homozygous for SHP-1 knockout, biological rep 2

city: Charlottesville

first: David

last: Mullins

state: VA

address: 345 Crispell Dr. Rm G525

department: Microbiology

institute: University of Virginia

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16hr on the Affymetrix Mouse 2.0 GeneChip and processed in an Affymetrix Fluidics Station, per manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Hewlett Packard GeneArray Laser Scanner system

data_processing: Data were analyzed with DNAStar ArrayStar 3.0.2 build 38 using global scaling normalization.

label_protocol: Biotin-labeled cRNA was generated using the Affymetrix GeneChip IVT Labeling kit, per manufacturer's instructions, using 10ug of aRNA

growth_protocol: CD4+CD25+ T cells were isolated from lymph nodes (combined inguinal, axillary, brachial, cervical, lumbar, sacral, renal and pancreatic nodes unless otherwise indicated) of 17-19 day old mice using the Regulatory T cell Isolation kit (Miltenyi Biotec; Auburn, CA) according to the manufacturer’s protocol

extract_protocol: Total RNA extraction was performed using the Arcturus PicoPuire kit, per manufacturer's instructions; aRNA was generated and amplified using the Arcturus RiboAmp kit, per manufacturer's instructions, from 20ng of total RNA.

treatment_protocol: Cells were not treated or cultured after harvest

tag: cell type

value: T reg (CD4+CD25+) cells

tag: strain

value: BALB/c

tag: genotype/variation

value: homozygous (me) for SHP-1 knockout (motheaten phenotype)


title: Tissue_F63_MDA_U133A

status: Public on Aug 13 2010

type: RNA

city: Woburn

first: Christos

last: Hatzis

state: MA

address: 400 West Cummings Park, Suite 5350

country: USA

institute: Nuvera Biosciences

description: FL1203 F63.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A or Plus2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX.

data_processing: Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.  CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html). MAS5.0 signal intensity for each array was log2 transformed and scaled to a reference distribution of 1322 breast cancer specific genes.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: tissue from breast tumor excision

label_protocol: A single-round of T7 amplification was used to generate biotin-labeled cRNA for hybridization.  At least 1 ug of RNA was used for cRNA synthesis.

extract_protocol: Total RNA was extracted from fresh frozen breast cancer tissue using Qiagen RNeasy columns.

tag: tissue

value: breast cancer

tag: patient id

tag: lab

value: MDA

tag: array platform_id


title: T regs from mouse homozygous for SHP-1 knockout, biological rep 3

middle: W

organism: Mus musculus


title: Tissue_F59_MDA_U133A


title: T regs from mouse homozygous for SHP-1 knockout, biological rep 1


title: Chemostat_HDF_03

city: Espoo

first: Mikko

middle: Ilari

last: Arvas

address: Tietotie 2

department: Cell Factory

country: Finland

institute: VTT Technical Research Centre of Finland

description: Spare intergenic expression tiling of T. reesei chemostat cultivations

hyb_protocol: Standard Nimblegen expression, carried out by Nimblegen.

data_processing:
The expression values for all probes with a given GC% in a given
experiment were divided by the median expression value of the intergenic probes in that experiment.

organism: Trichoderma reesei

source_name: Chemostat growth rate D=0.03, high density

growth_protocol:
Growth was done as in:
Transcriptional monitoring of steady state and effects of anaerobic phases in chemostat cultures of the filamentous fungus Trichoderma reesei
doi-link: 10.1186/1471-2164-7-247 Rautio, Jari; Smit, Bart; Wiebe, Marilyn; Penttilä, Merja; Saloheimo, Markk BMC Genomics. Online journal. Vol. 7: article number 247 (2006), 15 p.

Inoculum was prepared by transferring 1 × 108 spores into a 1.5 l conical flask containing 500 ml growth medium (lactose 20 g l-1). The culture was grown for approximately 72 h at 28°C with shaking at 200 rpm and then 200 or 500 ml were transferred to a bioreactor (Braun Biostat CT2-DCU3 or CT5-2, B. Braun Biotech International GmbH, Meisungen, Germany) along with sufficient medium to give total final volumes of 2 or 5 l respectively. Cultivations in the bioreactors were carried out at 28°C, with aeration of 0.5 vvm (volumes of air per volume of liquid per minute) and stirring at 800 rpm. The pH was maintained at 4.8 ± 0.1 using 1 M NaOH. Approximately 0.2% v/v (final concentration) polypropylene glycol (mixed molecular weights; [39]) was used as an antifoam agent. Nitrogen, oxygen and carbon dioxide were monitored online by measuring peak areas at M/z = 24, 32 and 44 with an OmniStar mass specrometer (Pfeiffer Vacuum, Germany).

For lactose limited chemostat culture, the feed was started immediately after CO2 production stopped at the end of the batch phase, approximately 50 h after inoculation. The feed was supplied at constant rate to maintain a dilution rate of 0.03 h-1 for 5 to 6 residence times (R). The high cell density was achieved by increasing the lactose concentration of the growth medium from 20 g/L to 80 g/L.

extract_protocol: Samples were homogenised with FastPrep cell homogenizer (ThermoSavant, Dreirich, Germany) using 6 m/s for 45 s. RNA was extracted from the homogenate with Total RNA kit (A&A Biotechnolgies, Gnydia, Poland). Quality and quantity of RNA was monitored by absorbance measurement at A260 (DNA Quant, Pharmacia, Uppsala, Sweden) and Agilent Bioanalyser and RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Samples (20 – 50 ml) were withdrawn from the fermentor via a sterilisable port. Two times five mL aliquots were immediately filtered using glass-fibre filter disks (Whatman GF/B 47 mm ∅, Kent, UK). The biomass was immediately washed with 20 ml sterile, demineralised water, after which the biomass was removed to liquid nitrogen and stored at -80°C for further analysis.  These samples were also frozen in liquid nitrogen and stored at -80°C until analysed.

tag: Strain


title: Chemostat_HDF_01

scan_protocol: Standard Nimblegen expression, carried out by Nimblegen.

growth_protocol:
Growth was done as in:
Transcriptional monitoring of steady state and effects of anaerobic phases in chemostat cultures of the filamentous fungus Trichoderma reesei
doi-link: 10.1186/1471-2164-7-247 Rautio, Jari; Smit, Bart; Wiebe, Marilyn; Penttilä, Merja; Saloheimo, Markku BMC Genomics. Online journal. Vol. 7: article number 247 (2006), 15 p.

Inoculum was prepared by transferring 1 × 108 spores into a 1.5 l conical flask containing 500 ml growth medium (lactose 20 g l-1). The culture was grown for approximately 72 h at 28°C with shaking at 200 rpm and then 200 or 500 ml were transferred to a bioreactor (Braun Biostat CT2-DCU3 or CT5-2, B. Braun Biotech International GmbH, Meisungen, Germany) along with sufficient medium to give total final volumes of 2 or 5 l respectively. Cultivations in the bioreactors were carried out at 28°C, with aeration of 0.5 vvm (volumes of air per volume of liquid per minute) and stirring at 800 rpm. The pH was maintained at 4.8 ± 0.1 using 1 M NaOH. Approximately 0.2% v/v (final concentration) polypropylene glycol (mixed molecular weights; [39]) was used as an antifoam agent. Nitrogen, oxygen and carbon dioxide were monitored online by measuring peak areas at M/z = 24, 32 and 44 with an OmniStar mass specrometer (Pfeiffer Vacuum, Germany).

For lactose limited chemostat culture, the feed was started immediately after CO2 production stopped at the end of the batch phase, approximately 50 h after inoculation. The feed was supplied at constant rate to maintain a dilution rate of 0.03 h-1 for 5 to 6 residence times (R). The high cell density was achieved by increasing the lactose concentration of the growth medium from 20 g/L to 80 g/L.


title: Chemostat_D06_03

source_name: Chemostat growth rate D=0.06

label_protocol: Standard Nimblegen expression, carried out by Nimblegen.

growth_protocol:
Growth was done as in:
Transcriptional monitoring of steady state and effects of anaerobic phases in chemostat cultures of the filamentous fungus Trichoderma reesei
doi-link: 10.1186/1471-2164-7-247 Rautio, Jari; Smit, Bart; Wiebe, Marilyn; Penttilä, Merja; Saloheimo, Markku BMC Genomics. Online journal. Vol. 7: article number 247 (2006), 15 p.

Inoculum was prepared by transferring 1 × 108 spores into a 1.5 l conical flask containing 500 ml growth medium (lactose 20 g l-1). The culture was grown for approximately 72 h at 28°C with shaking at 200 rpm and then 200 or 500 ml were transferred to a bioreactor (Braun Biostat CT2-DCU3 or CT5-2, B. Braun Biotech International GmbH, Meisungen, Germany) along with sufficient medium to give total final volumes of 2 or 5 l respectively. Cultivations in the bioreactors were carried out at 28°C, with aeration of 0.5 vvm (volumes of air per volume of liquid per minute) and stirring at 800 rpm. The pH was maintained at 4.8 ± 0.1 using 1 M NaOH. Approximately 0.2% v/v (final concentration) polypropylene glycol (mixed molecular weights; [39]) was used as an antifoam agent. Nitrogen, oxygen and carbon dioxide were monitored online by measuring peak areas at M/z = 24, 32 and 44 with an OmniStar mass specrometer (Pfeiffer Vacuum, Germany).

For lactose limited chemostat culture, the feed was started immediately after CO2 production stopped at the end of the batch phase, approximately 50 h after inoculation. The feed was supplied at constant rate to maintain a dilution rate of 0.06 h-1 for 5 to 6 residence times (R).


title: Chemostat_HDF_02


title: MDG 014 - breast - non-cancer

city: Oslo

first: Vilde

middle: Drageset

last: Haakensen

address: Montebello

department: Dept of Genetics

country: Norway

institute: The Norwegian Radium Hospital

description: 031105_MDG014_251239126218_S01_Green_A01_GE2-SSPE_91_2.txt

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (Surehyb enables/SSPE)

scan_protocol: Agilent scanner (Agilent Technologies, Santa Clara, CA)

data_processing: Feature Extraction 9.1.3.1 software and lowess normalization was used.

source_name: Biopsy from area with some mammographic density

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit Protocol

extract_protocol: RNeasy Mini protocol, Qiagen, Valencia, CA

value: breast

tag: clinical characteristic/disease status

value: area with some mammographic density

source_name: Universal reference

tag: reference source

value: Stratagene, LaJolla, CA


title: Chemostat_D06_02


title: MDG 013 - breast - non-cancer

description: 161106_MDG013_251239137995_S01_GE2-SSPE_91_2.txt


title: Chemostat_D06_01


title: MDG 042 - breast - non-cancer

description: 081105_MDG042_251239126088_S01_Green_A01_GE2-SSPE_91_2.txt


title: S.pombe_mis4+_25°C_rep2

city: Bordeaux

first: Sonia

last: Dheur

address: 1, Rue Camille Saint-Saëns

department: Université Bordeaux 2

country: France

institute: IBGC CNRS UMR5095

description: Gene expression data from G1-arrested cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Yeast Genome 2.0 microarrays. Microarrays were washed and stained in an Affymetrix Fluidics Station 450.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G System.

data_processing: The data processing (background correction, normalization and probe summarization) was performed using the RMA algorithm with the Stratagene ArrayAssist Expression Software.

organism: Schizosaccharomyces pombe

source_name: S. pombe, mis4+ at 25°C

label_protocol: Biotinylated cRNA were prepared from 5 ug total RNA using the GeneChip One-Cycle Target Labelling Kit from Affymetrix

growth_protocol: Cells bearing ura4+-pREP2-res1 were grown in cycling conditions at 25°C in EMM2 containing 20 mg thiamine to repress expression of the C-terminal fragment of Res1.

extract_protocol: Total RNA was extracted using standard hot phenol method followed by a DNAse I treatment and a cleanup step on a QIAGEN RNeasy mini Kit column

treatment_protocol: Cells were harvested, washed and inoculated into fresh EMM2 without thiamine at a density of 3x105 cells/ml. Cell proliferation ceased after seven doublings. Once arrested, cells were shifted to 37°C for 2 hours.

tag: genotype

value: h- ura4+-pREP2-res1 mis4+

tag: temperature

tag: biological replicate


title: MDG 010 - breast - non-cancer

description: 220507_MDG010_251239152528_S01_GE2-SSPE_91_2.txt


title: MDG 037 - breast - non-cancer

description: 030107-mdg037_251239125947_S01_GE2-SSPE_91_2.txt


title: MDG 012 - breast - non-cancer

description: 220507_MDG012_251239152514_S01_GE2-SSPE_91_2.txt


title: MDG 008 - breast - non-cancer

description: 221107_MDG008_251239138041_S01_GE2-SSPE_91_2.txt


title: Tissue_F38_MDA_U133A


title: T regs from mouse heterozygous for SHP-1 knockout, biological rep 1

value: heterozygous (he) for SHP-1 knockout


title: T regs from mouse heterozygous for SHP-1 knockout, biological rep 2


title: T regs from WT mouse, biological rep 2

source_name: T regs from WT mouse

value: wt


title: Tissue_F13_MDA_U133A


title: Tissue_F13_MDA_PLUS2

description: U133 plus 2.0_80_FL_250_03_18_08.CEL


title: Tissue_F19_MDA_PLUS2

description: U133 plus 2.0_80_FL_251_03_18_08.CEL


title: MDG 011 - breast - non-cancer

description: 200407_MDG011_251239138761_S01_GE2-SSPE_91_2.txt


title: Tissue_F35_MDA_U133A


title: Tissue_F55_MDA_U133A

description: FL1202 F55.CEL


title: MDG 009 - breast - non-cancer

description: 101007_MDG009_251239138055_S01_GE2-SSPE_91_2.txt


title: healthy control 7

type: protein

city: Stanford

first: Persis

middle: P

last: Wadia

state: CA

address: 269 W Campus Drive, CCSR 2210

department: Medicine

institute: Stanford University

description: serum IgG antibodies

hyb_protocol: 1. Add 5 ml serum diluted (1:500) in PBST Probing Buffer at the indented numeral end of the 4-chamber incubation tray without touching the array surface. Allow the serum to flow across the array surface. Avoid pipetting serum directly onto the array surface. 2. Incubate the tray for 90 minutes at 4ºC on a shaker set at 50 rpm (circular shaking). 3. Aspirate the serum using vacuum or pipette as described on the previous page (Step 5). 4. Wash each array with 5 ml PBST Probing Buffer with gentle shaking on a shaker set at 50 rpm for 5 minutes at room temperature. Aspirate the PBST Probing Buffer as described on the previous page (Step 5). 5. Repeat Step 4 four more times using fresh PBST Probing Buffer each time to obtain a total of 5 wash steps. 6. During the wash steps, mix 2.5 μl Alexa Fluor® 647 goat anti-human IgG antibody (secondary antibody) with 5 ml PBST Probing Buffer per array to obtain a final antibody concentration of 1 μg/ml. Store on ice until use. 7. Add 5 ml Alexa Fluor® 647 antibody solution from Step 6 to the incubation tray at the indented numeral end of the tray without touching the array surface. Allow the solution to flow across the array surface. Avoid pipetting solution directly onto the array surface. 8. Incubate the tray for 90 minutes at 4ºC on a shaker set at 50 rpm (circular shaking). 9. Aspirate the antibody solution. 10. Wash each array with 5 ml PBST Probing Buffer with gentle shaking on a shaker set at 50 rpm for 5 minutes at room temperature. Aspirate the PBST Probing Buffer. 11. Repeat Step 10 four more times using fresh PBST Probing Buffer each time to obtain a total of 5 wash steps. 12. Proceed immediately to Drying the Microarray.

scan_protocol: The scanning time for each array is ~7-8 minutes. 1. Start the appropriate array acquisition and analysis software on the computer connected to the fluorescence microarray scanner. 2. Open the microarray enclosure on the scanner. 3. Place the ProtoArray® Microarray in the holder such that the nitrocellulosecoated side of the array faces the laser source and barcode on the array is closest to the outside of the instrument. 4. Close the microarray enclosure on the scanner. 5. Set the following settings to image the microarray: • Wavelength: 635 nm • PMT Gain: 600 • Laser Power: 100% • Pixel Size: 10 μm • Lines to Average: 1.0 • Focus Position: 0 μm 6. Preview the microarray. Adjust settings, if needed. Scan the microarray in detail and include the barcode for record 7. Save the image to a suitable location as ‘multi-image TIFF’ file. Remove the microarray from the scanner. 8. Proceed to downloading lot-specific information available on the ProtoArray® Central Portal, next page. GenePix® Pro microarray data acquisition software. Adjust the subarray grid to ensure the grid is in proper location for each subarray. After the grid is properly adjusted and all features are aligned, utilize the automatic spot finding functionalities of the image acquisition software program, if desired. Then, acquire the pixel intensity data for each feature by clicking the Analyze button in GenePix® Pro, and save/export the results as a .GPR (GenePix® Results) file.

data_processing: VALUE = Signal - Background

label: Alexa Fluor 647

molecule: protein

source_name: serum from healthy control

label_protocol: Add 5 ml Alexa Fluor® 647 (secondary) antibody solution to the incubation tray at the indented numeral end of the tray without touching the array surface. Allow the solution to flow across the array surface. Avoid pipetting solution directly onto the array surface

extract_protocol:
1. Draw 4.5 mL of blood into red top tubes
2. Let stand for 30 minutes until clot is formed
3. Centrifuge the tube for 5 minutes at 2000g using a swing-out rotor or other non-desk top centrifuge
4. Transfer (pipette) the clear supernatant (serum) carefully without disturbing the clot, to a 5 mL labeled cryotube

tag: patient

value: patient B9


title: Tissue_F19_MDA_U133A


title: T regs from WT mouse, biological rep 4


title: LVS vs LVS WT 4

city: Chapel Hill

first: Tom

last: Kawula

state: NC

address: 119 Manning Drive

department: Microbiology and Immunology

institute: University of North Carolina-Chapel Hill

description: WT LVS Cy3 vs WT LVS Cy5

hyb_protocol: Slide was hybridized for 16hr at 42 in MAUI Hybridization with volume of 50ul in solution of See protocol, and blocked in See protocol. After hybridization, the slide was washed with See protocol. Protocol obtained the Institute for Genomic Research modified for personal use, primarily in the hybridization chamber type and the method of spinning down the slides for drying.

scan_protocol: All slides were scanned to a CR value within 0.05 of 1.00 and then spots aligned to annotation file

data_processing: Slide was scanned and results file obtained from GenePixPro and then converted to .mev file for normalization in MIDAS.  In MIDAS, files were subjected to LOWESS normalization and Standard Deviation Regularization.

organism: Francisella tularensis

source_name: WT LVS

label_protocol: Protocol provided by the Institute for Genomic Research at the J.C. Venter Institute for use with their microarrays. We adapted this protocol for our personal use, though not many changes were made.

growth_protocol: Broth cultures grown to early mid-log phase in Chamberlains media pH 6.3 to harvest RNA.

extract_protocol: This is the standard lab protocol for RNA extraction from whole-bug Francisella

value: LVS


title: T regs from mouse heterozygous for SHP-1 knockout, biological rep 3


title: LVS vs LVS WT 2

description: WT LVS Cy3 vs WT LVS Cy5


title: Mouse_Cortex_Ethanol_2

city: New Haven

first: Kazue

last: Hashimoto-Torii

state: CT

address: 333 Cedar St.

institute: Yale University

hyb_protocol: Samples were hybridized according to Affymetrix protocols

scan_protocol: Standard Affymetrix scan protocol for gene expression profiling

data_processing: Data were processed (RMA) using Partek Genomics Suite.

label_protocol: standard Affymetrix 3’ IVT labeling protocol

extract_protocol: total RNA was extracted using Qiagen RNeasy Mini kit

tag: agent

value: Ethanol


title: MDG 007 - breast - cancer

description: 071107_MDG007_251239138173_S01_GE2-SSPE_91_2.txt

source_name: Biopsy from breast tumor

value: breast tumor


title: Chemostat_D03_03

source_name: Chemostat growth rate D=0.03

growth_protocol:
Growth was done as in:
Transcriptional monitoring of steady state and effects of anaerobic phases in chemostat cultures of the filamentous fungus Trichoderma reesei
doi-link: 10.1186/1471-2164-7-247 Rautio, Jari; Smit, Bart; Wiebe, Marilyn; Penttilä, Merja; Saloheimo, Markku BMC Genomics. Online journal. Vol. 7: article number 247 (2006), 15 p.

Inoculum was prepared by transferring 1 × 108 spores into a 1.5 l conical flask containing 500 ml growth medium (lactose 20 g l-1). The culture was grown for approximately 72 h at 28°C with shaking at 200 rpm and then 200 or 500 ml were transferred to a bioreactor (Braun Biostat CT2-DCU3 or CT5-2, B. Braun Biotech International GmbH, Meisungen, Germany) along with sufficient medium to give total final volumes of 2 or 5 l respectively. Cultivations in the bioreactors were carried out at 28°C, with aeration of 0.5 vvm (volumes of air per volume of liquid per minute) and stirring at 800 rpm. The pH was maintained at 4.8 ± 0.1 using 1 M NaOH. Approximately 0.2% v/v (final concentration) polypropylene glycol (mixed molecular weights; [39]) was used as an antifoam agent. Nitrogen, oxygen and carbon dioxide were monitored online by measuring peak areas at M/z = 24, 32 and 44 with an OmniStar mass specrometer (Pfeiffer Vacuum, Germany).

For lactose limited chemostat culture, the feed was started immediately after CO2 production stopped at the end of the batch phase, approximately 50 h after inoculation. The feed was supplied at constant rate to maintain a dilution rate of 0.03 h-1 for 5 to 6 residence times (R).


title: MDG 004 - breast - non-cancer

description: 071107_MDG004_251239138792_S01_GE2-SSPE_91_2.txt


title: healthy control 5

description: serum IgG antibodies

value: patient B3


title: T regs from WT mouse, biological rep 1


title: healthy control 2

description: serum IgG antibodies

value: patient B2


title: MDG 006 - breast - cancer

description: 101007_MDG006_251239138787_S01_GE2-SSPE_91_2.txt


title: healthy control 1

description: serum IgG antibodies

value: patient 134


title: healthy control 6

description: serum IgG antibodies

value: patient 7


title: LVS vs LVS WT 1

description: WT LVS Cy3 vs WT LVS Cy5


title: Fat body vs Brain and Disc

status: Public on Aug 12 2010

city: Bloomington

first: Brian

middle: R.

last: Calvi

state: IN

department: Biology

institute: Indiana University

description: This is the average value for two biological replicate experiments. Individual values for each independent experiment is provided in the supplementary file.

hyb_protocol: Methods were as described (Bogart et al., 2006) and details can be found at (https://dgrc.cgb.indiana.edu/microarrays/support/protocols.html).

scan_protocol: Hybridized arrays were scanned by GenePix 4100A (Axon Instruments, Union City, CA).

data_processing: The data was extracted with Axon GenePix Pro 5 image analysis software. The spot sizes and intensities quantified by the software and automatically flagged spot qualities were followed manual examination. Abnormal shape spots or spots with high local background or spots that were quantified due to false intensity caused by dust were flagged bad and discarded. The normalization of the intensity values from the two channels was performed using global normalizations. After normalizations data points with background subtracted median intensity signals <60% than two standard deviations (SD) above the overall background intensity in both channels were discarded. Further data analyses were performed using data analysis software Acuity 4 (Axon) and Microsoft Excel. Data points were averaged from replicate spots and inconsistent data points were removed manually.

organism: Drosophila melanogaster

source_name: fat body

label_protocol: Total RNA was reverse transcribed and fluorescently labeled with Cy3 (Amersham) using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, Austin, TX 78744), according to the manufacturer’s instructions.

extract_protocol: Drosophila adults yw67C23 strain were put on food for 6 hours, and the resulting population of 70-75 hours old larvae (feeding-stage 3rd instar) were used for hand dissection of fat body tissues.

tag: extraction method

value: hand dissected

value: fat body

tag: developmental stage

value: 3rd instar larvae collected 70-75 hours after egg laying

tag: genome/variation

value: wild-type

tag: cell cycle status

value: Endocycling tissue

source_name: brain-disc

label_protocol: Total RNA was reverse transcribed and fluorescently labeled with Cy5 (Amersham) using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, Austin, TX 78744), according to the manufacturer’s instructions.

extract_protocol: Drosophila adults yw67C23 strain were put on food for 6 hours, and the resulting population of 70-75 hours old larvae (feeding-stage 3rd instar) were used for hand dissection of brain-disc complexes.

value: brain-disc complexes

value: Mitotic cycling tissue


title: LVS vs LVS iclR deletion 2

description: WT LVS Cy3 vs LVS iclR deletion Cy5 slide 2

tag: strain

source_name: LVS iclR deletion


title: MDG 002 - breast - cancer

description: 101007_MDG002_251239138786_S01_GE2-SSPE_91_2.txt

tag: tissue

value: breast

value: Stratagene, LaJolla, CA


title: Chemostat_D03_01

description: Spare intergenic expression tiling of T. reesei chemostat cultivations


title: Mouse_Cortex_Control_2

value: Control


title: Mouse_Cortex_Control_1


title: LVS vs LVS iclR deletion 1

description: WT LVS Cy3 vs LVS iclR deletion Cy5

value: LVS


title: healthy control 3

description: serum IgG antibodies

value: patient B157


title: T regs from WT mouse, biological rep 3

tag: cell type

value: T reg (CD4+CD25+) cells

value: BALB/c

tag: genotype/variation

value: wt


title: Salivary gland vs Brain and Disc

description: This is the average value for three biological replicate experiments. Individual values for each independent experiment is provided in the supplementary file.

data_processing: The data was extracted with Axon GenePix Pro 5 image analysis software. The spot sizes and intensities quantified by the software and automatically flagged spot qualities were followed manual examination. Abnormal shape spots or spots with high local background or spots that were quantified due to false intensity caused by dust were flagged bad and discarded. The normalization of the intensity values from the two channels was performed using global normalizations. After normalizations data points with background subtracted median intensity signals <60% than two standard deviations (SD) above the overall background intensity in both channels were discarded.  Further data analyses were performed using data analysis software Acuity 4 (Axon) and Microsoft Excel.  Data points were averaged from replicate spots and inconsistent data points were removed manually.

source_name: salivary glands

extract_protocol: Drosophila adults yw67C23 strain were put on food for 6 hours, and the resulting population of 70-75 hours old larvae (feeding-stage 3rd instar) were used for hand dissection of salivary gland tissues.

value: salivary gland


title: Chemostat_D03_02


title: Type 2 Diabetes 02

city: Nashville

first: Britney

last: Grayson

state: TN

address: MCN T-3219, 1161 21st Ave South

institute: Vanderbilt University School of Medicine

description: type 2 diabetes cohort sample 02

hyb_protocol: Arrays were treated with 0.2% SDS and soaked in prehybridization solution (1% BSA, 5XSSC and 0.1%SDS) for 45 minutes at 55°C. Dye-labeled samples were mixed 1:1 with hybridization solution (50% formamide, 10X SSC, 0.2% SDS) and 1ul polyA RNA. Each sample was heatshocked at 100°C for 2 minutes, loaded onto the array and hybridized at 42°C for 16 hours. Arrays were washed in descending concentrations of 1: 2X SSC, 0.1% SDS; 2: 1X SSC; 3: 0.1x SSC.

scan_protocol: Arrays were scanned into the GenePix Pro4.1 Software using a 400B scanner (Axon Instruments, Union City, CA).

data_processing: Data presented here are single channel medians. Intensity values were normalized to whole array intensity sum=10,000

source_name: peripheral blood

label_protocol: 5 µg of total RNA were primed with 6 µl of Oligo dT at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 400 U SuperScript III RTase (Invitrogen), and 200um dATP, 200um dGTP, 200um dCTP, 51um dTTP and 149um AAdUTP. Samples were treated with RNAse H and cleaned with Qiagen PCR-cleanup kit. Samples were coupled to Cy3 or Cy5 dye (Amersham) in a 0.1M sodium bicarbonate buffer, incubated for 1h.

extract_protocol: For human samples, blood was drawn into a PaxGene tube and RNA extracted per manufacterer's protocol. For cell line, RNA was extracted using Trizol per manufacturer's instruction.

tag: disease state

value: Type 2 Diabetes

value: peripheral blood

tag: age (yr)

tag: gender

value: female

source_name: Cell line

tag: cell line

value: Jurkat T cell


title: Mouse_Cortex_Ethanol_1

value: Ethanol


title: Type 2 Diabetes 07

description: type 2 diabetes cohort sample 07


title: healthy control 4

description: serum IgG antibodies

value: patient 256


title: Coronary Artery Disease 03

description: coronary artery disease cohort sample 03

value: Coronary Artery Disease

value: male


title: Type 2 Diabetes 01

description: type 2 diabetes cohort sample 01


title: Type 2 Diabetes 04

description: type 2 diabetes cohort sample 04


title: Coronary Artery Disease 04

description: coronary artery disease cohort sample 04


title: Coronary Artery Disease 05

description: coronary artery disease cohort sample 05


title: Metabolic Syndrome 05

description: metabolic syndrome cohort sample 05

value: Metabolic Syndrome


title: Type 2 Diabetes 06

description: type 2 diabetes cohort sample 06


title: Metabolic Syndrome 06

description: metabolic syndrome cohort sample 06


title: Type 2 Diabetes 08

description: type 2 diabetes cohort sample 08


title: Coronary Artery Disease 02

description: coronary artery disease cohort sample 02


title: Type 2 Diabetes 05

description: type 2 diabetes cohort sample 05


title: MDG 001 - breast - cancer

description: 091007_MDG001_251239138783_S01_GE2-SSPE_91_2.txt

value: breast

tag: clinical characteristic/disease status

value: breast tumor

tag: reference source

value: Stratagene, LaJolla, CA


title: Coronary Artery Disease 06

description: coronary artery disease cohort sample 06


title: Type 2 Diabetes 03

description: type 2 diabetes cohort sample 03

value: unknown


title: Rheumatoid Arthritis 03

description: rheumatoid arthritis cohort sample 03

value: Rheumatoid Arthritis


title: Metabolic Syndrome 02

description: metabolic syndrome cohort sample 02


title: Rheumatoid Arthritis 05

description: rheumatoid arthritis cohort sample 05


title: Rheumatoid Arthritis 06

description: rheumatoid arthritis cohort sample 06


title: Rheumatoid Arthritis 04

description: rheumatoid arthritis cohort sample 04


title: Metabolic Syndrome 04

description: metabolic syndrome cohort sample 04


title: Metabolic Syndrome 03

description: metabolic syndrome cohort sample 03


title: Rheumatoid Arthritis 02

description: rheumatoid arthritis cohort sample 02


title: Rheumatoid Arthritis 01

description: rheumatoid arthritis cohort sample 01


title: Control 09

description: control cohort sample 09

value: Control


title: Control 08

description: control cohort sample 08


title: Control 07

description: control cohort sample 07


title: Control 05

description: control cohort sample 05


title: Control 06

description: control cohort sample 06


title: Control 04

description: control cohort sample 04


title: Control 01

description: control cohort sample 01


title: Metabolic Syndrome 01

description: metabolic syndrome cohort sample 01


title: Control 03

description: control cohort sample 03


title: Control 02

description: control cohort sample 02


title: LVS vs LVS iclR deletion 3

description: WT LVS Cy3 vs LVS iclR deletion Cy5

value: LVS


title: NasalPolyp_aCRSp9

city: Rochester

first: Douglas

middle: A

last: Plager

state: MN

address: 200 First Street SW

department: Dermatology

institute: Mayo Clinic Rochester

hyb_protocol: Hybridizations to Affymetrix GeneChip® Human Exon 1.0 ST Arrays were performed overnight at 45 °C.

scan_protocol: Arrays were washed, stained with phycoerythrin-labeled streptavidin, and scanned in the Affymetrix GeneChip® Scanner.

data_processing: The resulting image files were analyzed using Affymetrix Microarray Suite 5.1 to generate .CEL files containing the probe level intensities and the x, y coordinates of each probe on the array. The 39 exon array .CEL files were imported using Partek® Genomics Suite™ software (Partek Incorporated, St. Louis, MO) and normalized using default RMA settings.  Transcript expression levels were calculated using the well-established “core” set of exons for 21,980 distinct genes.  Comparisons between sample groups were performed using GeneSpring GX 9.0 software (Silicon Genetics, Redwood City, CA).  Molecular network analyses of the identified differentially transcribed genes used Ingenuity Pathways Analysis software (Ingenuity Systems, Mountain View, CA).

source_name: nasosinus tissue

label_protocol: Following the Affymetrix GeneChip® Whole Transcript Sense Target Labeling Assay (Affymetrix, Santa Clara, CA), total RNA was depleted of ribosomal RNA and converted into double-stranded cDNA using random hexamers tagged with a T7 promoter sequence.  This cDNA was used as template for T7 RNA Polymerase amplification into antisense cRNA.  The cRNA was converted into single-stranded sense DNA with incorportated dUTP, fragmented at the dUTP sites, and end-labeled with biotin.

growth_protocol: Not applicable

extract_protocol: After removal from RNAlater, each specimen was frozen in liquid nitrogen, placed in ice-cold TRIzol (Invitrogen, Carlsbad, CA), and immediately shattered and homogenized with a Polytron homogenizer (Brinkmann Instruments, Westbury, NY).  Total RNA was isolated according to the manufacturer’s protocol for TRIzol and further purified using the RNeasy Mini kit (Qiagen, Valencia, CA).

treatment_protocol: Nasosinus tissue was immediately placed in 4 mL of room temperature RNAlater (Ambion) for 2 minutes with occasional mixing, transported on ice, held overnight at 4 °C, and placed at -20 °C until total RNA isolation.

value: Asthmatic Chronic Rhinosinusitis with Nasal Polyps

value: polyp


title: NasalPolyp_aCRSp1


title: NasalMucosa(inflamed)_aCRSm5

value: inflamed mucosa


title: NasalMucosa_Normal4

value: Normal

value: mucosa


title: NasalPolyp_aCRSp6


title: NasalMucosa_Normal7


title: NasalMucosa(inflamed)_aCRSm9


title: NasalMucosa_AR3

value: Allergic Rhinitis


title: NasalMucosa_Normal5


title: NasalMucosa_Normal12


title: NasalMucosa(inflamed)_aCRSm2

value: Asthmatic Chronic Rhinosinusitis (no nasal polyps)


title: NasalMucosa_Normal8


title: NasalMucosa(inflamed)_aCRSm8


title: NasalPolyp_aCRSp11


title: NasalMucosa_Normal11


title: NasalPolyp_aCRSp7


title: NasalMucosa(inflamed)_aCRSm11


title: NasalMucosa_Normal3


title: NasalPolyp_aCRSp4


title: NasalPolyp_aCRSp3


title: NasalPolyp_aCRSp8


title: NasalMucosa(inflamed)_aCRSm7


title: NasalMucosa(inflamed)_aCRSm4


title: NasalMucosa_Normal6


title: NasalMucosa_Normal10


title: NasalMucosa(inflamed)_aCRSm3


title: NasalMucosa_Normal1


title: NasalMucosa_AR4


title: NasalMucosa(inflamed)_aCRSm6


title: NasalPolyp_aCRSp5


title: NasalMucosa_AR1


title: NasalMucosa-Polyp_aCRSm12

value: mucosa-polyp


title: NasalMucosa_Normal13


title: NasalMucosa_Normal2


title: NasalMucosa_Normal9


title: NasalPolyp_aCRSp10


title: Coronary Artery Disease 01

description: coronary artery disease cohort sample 01

value: Coronary Artery Disease

value: peripheral blood

value: male

value: Jurkat T cell


title: NasalMucosa(inflamed)_aCRSm1


title: Sample M, replicate 2

city: Durham

first: Dawn

last: Kernagis

address: 2100 Erwin Rd

department: Pathology

institute: Duke University Medical Center

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
M2

hyb_protocol: Hybridization targets were prepared from 2ug tRNA and hybridized according to standard Affymetric protocol.

scan_protocol: Arrays were scanned on the Affyemtrix GeneChip scanner. Probe set expression values, percent present, and 3'/5' probe set ratios for actin and GAPDH were calculated using the Affymetrix Microarray Analysis Suite v5.0.

data_processing: Expression data is RMA normalized (log2 transformed). The RMA normalization was conducted using Affymetrix Expression Console software.

source_name: Breast tumor core needle biopsy

label_protocol: Biotin labeled according to standard Affymetrix protocol

extract_protocol: Total RNA was extracted using a kit-based method (Rneasy, Qiagen, Valencia, CA)

treatment_protocol: Core needle biopsies ontained from breast cancer excisions following patient consent.

value: M

value: Breast tumor

tag: tumor grade

tag: er status

value: ER Positive

tag: pr status

value: PR Positive


title: Sample Q, replicate 1

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
Q1

tag: patient

value: Q

value: ER Negative


title: Sample P, replicate 1

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
P1

value: P

value: PR Negative


title: Sample N, replicate 1

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
N1

value: N


title: Sample P, replicate 2

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
P2


title: NasalMucosa(inflamed)_aCRSm10

value: Asthmatic Chronic Rhinosinusitis with Nasal Polyps

value: inflamed mucosa


title: Sample N, replicate 3

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
N3


title: Sample O, replicate 2

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
O2

value: O


title: Sample L, replicate 2

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
L2

value: L


title: Sample M, replicate 1

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
M1


title: Sample R, replicate 1

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
R1

value: R


title: Sample L, replicate 3

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
L3


title: Sample M, replicate 3

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
M3


title: Sample Q, replicate 2

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
Q2


title: Sample O, replicate 1

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
O1


title: Sample N, replicate 2

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
N2


title: Sample R, replicate 2

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
R2


title: NasalMucosa_AR2

value: Allergic Rhinitis

value: mucosa


title: Sample K, replicate 2

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
K2

value: K


title: Sample J, replicate 3

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
J3

value: J


title: Sample K, replicate 1

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
K1

value: Breast tumor


title: Sample J, replicate 2

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
J2

value: ER Positive


title: Sample L, replicate 1

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
L1

value: PR Positive


title: liver_leucine_rep3

city: Calgary

first: Lindsay

middle: K

last: Eller

state: AB

address: 2500 University Dr. NW

department: Faculty of Kinesiology

country: Canada

institute: University of Calgary

hyb_protocol: As per Affymetrix protocol (Whole Transcript Sense Target Labeling Assay Manual for Rat Gene 1.0 ST Array available at www.affymetrix.com)

scan_protocol: The chip scanned as per Affymetrix protocol using an Affymetrix Fluidics 450 scan station.

data_processing: The data was analyzed using Affymetrix Expression Console (algorithm-name: rma-gene-default, algorithm-version: 1.0, algorithm-param-quantification-name: med-polish).

organism: Rattus norvegicus

source_name: liver from leucine fed rats

growth_protocol: 12 week old rats were provided one of 3 ad libitium diets for 8 weeks.  Diets were prepared with 10% (by kcal) of either casein, leucine, or dairy protein.

extract_protocol: Total RNA was extracted from liver using Trizol Reagent (Invitrogen, Carlsbad, CA) and purified using the Qiagen RNeasy Miniprep (Qiagen, Mississauga, ON, Canada).  RNA was quantified using Ribogreen and RT performed using the Omniscript RT Kit as per manufacturers directions (Qiagen, Mississauga, ON, Canada).

treatment_protocol: Rats were over-anaesthetized with isoflurane and killed via aortic cut.  Liver was excised and submerged in liquid nitrogen immediately.  Liver was stored at -80˚C until analysis.

value: liver

tag: diet

value: leucine

tag: age

value: 20 weeks

value: Diet-induced obese Sprague-Dawley

value: male


title: liver_leucine_rep2

label_protocol: As per Affymetrix protocol (Whole Transcript Sense Target Labeling Assay Manual for Rat Gene 1.0 ST Array available at www.affymetrix.com)


title: LSK SRF-null 3

city: Villejuif

first: Virginie

last: PENARD

address: 39 rue Camille Desmoulins

department: Institut Gustave Roussy

institute: INSERM U985

description: Gene expression data from LSK cells SRF KO

hyb_protocol: 3,75 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Affymetrix MOE430A. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip 3000 7G Scanner

data_processing: The data were analyzed with GeneChip Operating Software 1.4

source_name: LSK cells SRF KO 3

label_protocol: 30 ng of total RNA were amplified and labeled using the NuGen Ovation RNA Amplification System V2 followed by the FL-Ovation cDNA Biotin Module V2 according to manufacturer’s protocol. (NuGEN Technologies Inc.).

growth_protocol: Srf flx/flx mice were crossed with the polyinosine-polycytidine (pIpC)-inducible Mx1-Cre recombinase mouse line. Induction was performed on 6 weeks-old mice by three intra-peritoneal (IP) injections of 200 µg/dose pIpC (Invivogen) every 2 days and mice were analyzed 35 days after the last injection.

extract_protocol: Total RNAs were collected from invalidated or not 105 LSKs (n=3 per genotype) using the RNeasy micro kit (Qiagen)  according to manufacturer’s protocol

treatment_protocol: FACS-sorted LSK (Lin-Sca1+c-Kit+) cells were isolated from pIpC-treated Srf flx/flx ;Mx1-Cre and Srf+/+;Mx1-Cre pooled animals

value: sorted LSK cells

value: SRF KO


title: liver_dairy_rep2

source_name: liver from dairy fed rats

value: dairy


title: LSK SRF-null 2

source_name: LSK cells SRF KO 2


title: liver_leucine_rep1


title: Sample I, replicate 3

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
I3

value: I


title: Sample J, replicate 1

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
J1


title: liver_dairy_rep4


title: liver_leucine_rep4


title: Sample I, replicate 2

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
I2


title: liver_dairy_rep1


title: liver_casein_rep2

source_name: liver from casein fed rats

value: casein


title: Sample I, replicate 1

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
I1


title: aldosterone 8 hours, biological rep2

city: Boston

first: Lakshmanan

last: Iyer

address: 136 Harrison Ave

department: Neuroscience

institute: Tufts University

description: gene expression data from ex vivo treated mouse aortas

hyb_protocol: cRNA was hybridized to the mouse430A2 Genome Array. GeneChips were washed and stained following standard Affymetrix Protocols.

scan_protocol: GeneChips were scanned using Affimetrix Chip Scanner.

data_processing: Data was normallized using GCRMA protocol in bioconductor.

source_name: mouse aorta treated with aldosterone for 8 hours

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

growth_protocol: Wild type C57Bl6 male mice were treated with spironolactone (20 mg/kg/day, an MR antagonist) for 5 days by Sub-cutaneous pellet.

extract_protocol: Trizol extraction of total RNA was performed followed by purification with the RNeasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Aortas were harvested and treated ex vivo in organ culture in DMEM (Gibco).

value: aorta

tag: hormone treatment

value: aldosterone

tag: time of treatment

value: 8 hours


title: Sample H, replicate 3

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
H3

value: H

value: ER Negative

value: PR Negative


title: liver_casein_rep4

tag: tissue

tag: strain


title: liver_dairy_rep3


title: liver_casein_rep1


title: LSK SRF-null 1

source_name: LSK cells SRF KO 1

tag: cell type

tag: genotype/variation


title: Sample H, replicate 4

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
H4

tag: disease state

value: Breast tumor


title: LSK control 2

description: Gene expression data from LSK cells SRF wt

source_name: LSK cells SRF wt 2

value: SRF wt


title: LSK control 3

source_name: LSK cells SRF wt 3


title: aldosterone 8 hours, biological rep3

tag: gender


title: liver_casein_rep3

value: liver


title: vehicle 8 hours, biological rep1

source_name: mouse aorta treated with vehicle for 8 hours

value: vehicle


title: vehicle 8 hours, biological rep3


title: vehicle 4 hours, biological rep2

source_name: mouse aorta treated with vehicle for 4 hours

value: 4 hours


title: vehicle 8 hours, biological rep2

value: male


title: Sample G, replicate 2

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
G2

value: G


title: aldosterone 8 hours, biological rep1


title: Sample G, replicate 1

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
G1


title: Sample G, replicate 3

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
G3


title: Sample H, replicate 1

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
H1


title: aldosterone 4 hours, biological rep2

source_name: mouse aorta treated with aldosterone for 4 hours


title: aldosterone 4 hours, biological rep1


title: Smc1_KD_Day5_Rep1

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Biological replicate 1 of 2.

hyb_protocol: Agilent (mouse 4x44k) expression arrays were hybridized according to our lab’s method, which differs slightly from the Agilent standard hybridization protocol. The hybridization cocktail consisted of 825 ng / 1.65 ug cy-dye labeled cRNA for each sample, Agilent hybridization blocking components, and fragmentation buffer. The hybridization cocktails were fragmented at 60°C for 30 minutes, and then Agilent 2X hybridization buffer was added to the cocktail prior to application to the array. The arrays were then hybridized for 16 hours at 60°C in an Agilent rotor oven set to maximum speed.

scan_protocol: Arrays were scanned using an Agilent scanner G2565BA and the data was extracted using Agilent’s Feature Extraction software v10.1.1.1.

data_processing: Data was extracted using Agilent’s Feature Extraction software v10.1.1.1 set to the default two-color gene expression protocol.

source_name: Embyonic stem cells

label_protocol: Cy-dye labeled cRNA samples were prepared using Agilent’s QuickAmp sample labeling kit. Input was 1 µg total RNA. Briefly, first and second strand cDNA are generated using MMLV-RT enzyme and an oligo-dT based primer. In vitro transcription is performed using T7 RNA polymerase and either cyanine 3-CTP or cyanine 5-CTP, creating a direct incorporation of dye into the cRNA.

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: V6.5 embryonic stem cells

tag: treatment

value: shRNA knockdown of Smc1


title: Nipbl_KD_Day5

value: shRNA knockdown of Nipbl


title: Sample F, replicate 3

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
F3

value: F

value: ER Positive


title: Sample H, replicate 2

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
H2


title: Med12_KD_Day5_Rep2

description: Biological replicate 2 of 2.

value: shRNA knockdown of Med12


title: c-Cbl +/+ MEP

first: Chozha Vendan

last: Rathinam

address: 300 Cedar St

department: Immunobiology

institute: Yale School Of Medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: MEP

label_protocol: Biotinylated cRNA was prepared using TotalPrep RNA Amplification kit (Applied Biosystems)

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen, Valencia, CA)

tag: genetic background

tag: genotype

value: c-Cbl +/+

value: MEP CD34-CD16/32-Lineage-c-Kit+Sca1-


title: vehicle 4 hours, biological rep3

value: aorta


title: c-Cbl A/- MEP

value: c-Cbl A/-


title: c-Cbl A/- GMP

source_name: GMP

value: GMP CD34+CD16/32+Lineage-c-Kit+Sca1-


title: vehicle 4 hours, biological rep1


title: Smc1_KD_Day5_Rep2

description: Biological replicate 2 of 2.


title: aldosterone 2 hours, biological rep3

source_name: mouse aorta treated with aldosterone for 2 hours

value: aldosterone

value: 2 hours


title: aldosterone 4 hours, biological rep3


title: Med12_KD_Day5_Rep1

description: Biological replicate 1 of 2.


title: LSK control 1

source_name: LSK cells SRF wt 1

value: sorted LSK cells

value: SRF wt


title: Sample F, replicate 1

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
F1

source_name: Breast tumor core needle biopsy

value: Breast tumor

tag: tumor grade

value: PR Negative


title: Sample F, replicate 2

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
F2

tag: er status


title: aldosterone 2 hours, biological rep2

value: male


title: aldosterone 2 hours, biological rep1


title: c-Cbl +/+ CMP

source_name: CMP

value: CMP CD34+CD16/32-Lineage-c-Kit+Sca1-


title: vehicle 2 hours, biological rep1

source_name: mouse aorta treated with vehicle for 2 hours

value: vehicle


title: c-Cbl +/+ GMP


title: Sample E, replicate 1

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
E1

value: E

value: ER Negative

tag: pr status


title: Sample E, replicate 2

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
E2

tag: patient


title: liver_feno_WT_rep6

first: hyewon

last: kang

address: 75 Fransis street

institute: Brigham & Women's Hospital

hyb_protocol: 20ug of cRNA was used for hybridization according to the Affymetrix GeneChip Manual,  45℃, overnight.

scan_protocol: GeneChips were scanned on an Affymetrix Model 3000 7G scanner with autoloader.

data_processing: CEL files were loaded and analyzed in dChip.  It was first normalized using an invariant normalization function. Normalized intensity values for individual genes expression were filtered out if a strong signal for the gene was not detected on greater than 30% of the GeneChips.  Fold changes (Pctp-/- vs wild type) of at least 1.2 were considered to be significant for P < 0.05 by two-tailed Student’s t-Test.

label: Biotin

source_name: Liver, 0.2% fenofibrate (wt/wt) supplemented diet, wild type, 7 days

label_protocol: Biotinylated cRNA was prepared according to the Affymetrix GeneChip Manual (rev 4.0) from 8ug total RNA.

growth_protocol: Mice lacking phosphatidylcholine transfer protein (PC-TP) and wild type littermate controls on FVB/NJ background were maintained in a standard rodent diet 5001 (LabDiets) until 8 weeks of age.

extract_protocol: Total RNA was extracted from liver using Trizol according to the manufacturer's instructions.

treatment_protocol: At 8 weeks of age, a diet including 0.2% fenofibrate (wt/wt) was provided to mice for 7days.  Then, mice were sacrified at age 9 weeks.

value: Wild type FVB

value: Liver

value: 9 weeks old

value: Male


title: Sample E, replicate 3

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
E3


title: vehicle 2 hours, biological rep3

value: aorta


title: c-Cbl +/+ MPP

source_name: MPP

value: c-Cbl +/+

value: MPP CD34+Flt3+Lineage-c-Kit+Sca1+


title: c-Cbl A/- CMP

value: c-Cbl A/-


title: c-Cbl A/- MPP


title: vehicle 2 hours, biological rep2

value: 2 hours


title: c-Cbl A/- STHSC

source_name: STHSC

value: STHSC CD34+Flt3-Lineage-c-Kit+Sca1+


title: liver_feno_WT_rep5


title: liver_feno_WT_rep4


title: c-Cbl A/- LTHSC

source_name: LTHSC

value: LTHSC CD34-Flt3-Lineage-c-Kit+Sca1+


title: c-Cbl +/+ STHSC


title: Sample D, replicate 2

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
D2

value: D

value: Breast tumor

value: ER Positive

value: PR Positive


title: c-Cbl -/- LTHSC

value: c-Cbl -/-


title: Sample C, replicate 3

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
C3

value: C


title: Sample D, replicate 1

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
D1


title: c-Cbl +/+ LTHSC


title: Sample C, replicate 2

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
C2


title: liver_feno_WT_rep1

value: Wild type FVB


title: liver_feno_WT_rep2

value: Liver