title: Surgery 2-PBS-12 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 12 H post infection


title: Surgery 3-MAA-30 min (data for dynamic bayesian analysis)

status: Public on Oct 03 2012

type: RNA

city: College Station

first: Leslie

middle: Garry

last: Adams

state: TX

address: 402 Raymond Stotzer Blvd.

department: Veterinary Pathobiology

country: USA

institute: Texas A&M University

hyb_protocol: cDNA from bovine experimental samples (i.e. from MAP and MAA infected and PBS control loops) were co-hybridized against cDNA generated from the bovine reference RNA sample 13K bovine 70mer oligoarray.  Prior to hybridization, the microarrays were denatured by exposing to steam from boiling water for three seconds, UV cross-linked and then immersed in pre-hybridization buffer [5X sodium chloride, sodium citrate buffer (SSC), 0.1% sodium dodecyl sulfate (SDS) (Ambion, Austin, TX), 1% bovine serum albumin (BSA)] at 42ºC for a minimum of 45 min followed by four washes in RNase-, DNase-free, distilled water, immersion in 100% isopropanol for 10 seconds, and dried by centrifugation. Slides were hybridized at 42ºC for approximately 40 hours in a dark humid chamber (Corning, Corning, NY) and washed for 10 min at 42ºC with low stringency buffer [1 X SSC, 0.2% SDS] followed by two 5-min washes in a higher stringency buffer [0.1 X SSC, 0.2% SDS and 0.1 X SSC] at room temperature in dark with mild agitation.

scan_protocol: Immediately after washing, the slides were scanned using a commercial laser scanner (GenePix 4100; Axon Instruments Inc., Foster City, CA). Scans were performed using the autoscan feature with the percent saturated pixels set at 0.03%

data_processing: log2 ratio of experiment/reference channel.  Prior to computing the ratio, we performed global scaling across all arrays and then a Lowess correction on an array basis.

molecule: total RNA

organism: Bos taurus

source_name: Ileal mucosa inoculated with MAA, tissue collected at 30 min post infection

label_protocol: Total RNA was reverse transcribed using Superscript III reverse transcriptase (Invitrogen, Carlsbad, CA) and labeled with amino-allyl-UTP (Ambion, Austin, TX).  Cy3 (Reference)  and Cy5 (Experimental, i.e. PBS, MAp or MAA inoculated loop) dye esters were covalently linked to the amino-allyl group by incubating the samples with the dye esters in 0.1M sodium carbonate buffer.

growth_protocol: Mycobacterium avium subsp. paratuberculosis (ATCC 19698 from American Type Culture Collection, Manassas, VA),  was grown aerobically in 7H9 broth (Difco Laboratories, Detroit, MI) supplemented with 2.5% (vol/vol) glycerol (Sigma Chemical Co., St. Louis, MO), oleic acid-albumin-dextrose-catalase (Difco Laboratories, Detroit, MI), 0.05% Tween 80 (Sigma Chemical Co., MO), and 2 mg of Mycobactin J (Allied Monitor, Inc., Fayette, MO.).  Mycobacterium avium subsp. avium (ATCC 35716 from American Type Culture Collection, Manassas, VA) was grown in 7H9 broth supplemented with 2.5% (vol/vol) glycerol, oleic acid-albumin-dextrose-catalase and 0.05% Tween 80.

extract_protocol: Total RNA was extracted after dissection of the ileal loops obtained at 30 min and at 1, 2, 4, 8, and 12 hours post-infection.  A 6 mm biopsy punch was used to collect tissue pieces of Peyer’s patch from the excised loop. The mucosa of the samples were immediately dissected, the tissue pieces finely minced with a scalpel blade, and two biopsy punches (0.1 mg of tissue) transferred to 1 ml of Trizol reagent (Molecular Research Center, Cincinnati, OH).  Tissues were further disrupted with an RNase, DNase free plastic disposable pestle.  The RNA extraction was performed using the recommended protocol from the manufacturer. The resultant RNA pellet was re-suspended in DEPC-treated water (Ambion, Austin, TX).  Genomic DNA was removed by RNase-free DNase I treatment (DNA-free, Ambion) according to the manufacture’s instructions, and samples were stored at −80ºC until used. The quality of the RNA was initially assessed by measurement of the lambda 260/280 ratio and agarose gel electrophoresis. RNA concentration was quantified by measuring absorbance at lambda 260nm using a NanoDrop® ND-1000 (NanoDrop, Wilmington, DW), and the RNA quality was determined using a Nano-Chip® on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Samples were characterized by distinct 18S and 28S rRNA peaks and RNA size distribution. Ten micrograms of RNA was used as starting material for each array.  Reference RNA was a pool of Madin-Darby bovine kidney and  bovine B lymphocyte cell lines and fresh bovine brain cortex and cerebellum.  Total RNA was isolated from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines (American Type Culture Collection, Manassas, VA) and fresh bovine brain cortex and cerebellum collected from surgery calves following euthanasia at the conclusion of each experiment.  Cell lines were grown in 150 cm2 cell culture flasks with Eagle’s minimum essential medium (E-MEM) (ATCC) supplemented with 10% heat-inactivated fetal bovine serum (HI-FBS). Tissues were homogenized in ice-cold Tri-reagent® (Ambion, Austin, TX). RNA concentration and quality from each sample was determined before and after pooling the samples. Total RNA isolated from three samples was pooled together in equal amounts, aliquoted and stored at −80ºC until needed.

treatment_protocol: Cows were infected (ligated ileal loops) with PBS, a virulent strain of Mycobacterium avium (subsp. paratuberculosis) or an avirulent M. avium strain (subsp. avium) for 30 min, 1h, 2h, 4h, 8h, or 12h. The experiment was performed in quadruplicate (except for the avirulent infections at 2 and 8 hours, which were performed three times each). Post-infection, RNA was collected, processed, and then hybridized to custom bovine gene expression arrays, each of which represented 13,258 transcripts spotted in duplicate.  There were therefore 70 arrays in total.

tag: male calf

tag: 3 to 6 weeks of age

tag: outbred

tag: distal ileum

source_name: reference RNA

tag: A mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

tag: cell lines were purchased from the American Type Culture Collection (ATCC), fresh bovine brain and cerebellum was collected from surgery calves immediately following euthanasia by barbituate overdose at the conclusion of bovine ligated ileal loop surgery.


title: Surgery 2-MAP-12 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 12 H post infection


title: Surgery 2-MAP-2 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 2 H post infection


title: Surgery 3-PBS-1 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 1H post infection


title: Surgery 2-PBS-2 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 2 H post infection


title: Surgery 2-PBS-8 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 8 H post infection


title: Surgery 2-MAA-12 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected at 12 H post infection


title: Surgery 2-MAA-4 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected 4 H post infection


title: Surgery 2-MAP-30 min (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 30 min post infection


title: Surgery 3-PBS-30 min (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 30 min post infection


title: Surgery 3-MAP-1 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 1H post infection


title: Surgery 2-MAA-2 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected 2 H post infection


title: Surgery 2-MAA-1 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected at 1H post infection


title: Surgery 2-MAA-30 min (data for dynamic bayesian analysis)


title: Surgery 2-PBS-4 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 4 H post infection


title: Surgery 2-MAP-1 h (data for dynamic bayesian analysis)


title: Surgery 2-PBS-1 h (data for dynamic bayesian analysis)


title: Surgery 2-PBS-30 min (data for dynamic bayesian analysis)


title: Surgery 1-MAP-8 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 8 H post infection


title: Hepa1_DEM_rep2

city: Sendai

first: Masayuki

last: Yamamoto

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

country: Japan

institute: Tohoku University Graduate School of Medicine

hyb_protocol: 1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2539.

data_processing: The data were analyzed using GeneSpring GX software (Agilent).  Normalization was performed usig Percentile Shift.

organism: Mus musculus

source_name: Hepa1 DEM

label_protocol: 500 ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.

growth_protocol: The mouse hepatoma cell line Hepa1c1c7 was cultured in DMEM supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin.   The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted from liver tissues using Isogen (Nippon Gene).

tag: cell line


title: Surgery 1-PBS-12 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 12 H post infection


title: Hepa1_DEM_rep1


title: Surgery 1-MAA-12 h (data for dynamic bayesian analysis)

source_name: reference RNA


title: Hepa1_DMSO_rep2

source_name: Hepa1 DMSO


title: Hepa1_DMSO_rep1


title: Surgery 1-MAA-4 h (data for dynamic bayesian analysis)


title: Surgery 1-MAP-2 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 2 H post infection


title: Surgery 1-PBS-2 h (data for dynamic bayesian analysis)


title: Surgery 1-MAP-4 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 4 H post infection


title: Med.Dose.12

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

hyb_protocol: Agilent Mouse G4846A  Microarrays (containing approximately 40,000 probes) were hybridized with 250 ng Cy5-labelled liver RNA and 250 ng Cy3-labelled Universal Mouse Reference RNA (Stratagene, CA, USA), used as a common reference on all arrays.  Arrays were incubated for 17 hours at 65 ºC in Agilent hybridization solution and washed according to manufacturer’s instructions.

scan_protocol: Arrays were scanned scanned on an Agilent G2505B scanner. Data were acquired using Agilent Feature Extraction software version 10.7.3.1

data_processing: The log2 of the ratio (sample(Cy5)/reference(Cy3)), using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R.

source_name: lung of mice

label_protocol: Individual 250 ng aliquots of RNA from each sample were amplified and labelled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent, (5184-3523)).

extract_protocol: RNA was isolated using the TRIzol reagent (Invitrogen Canada Inc., Burlington, ON, Canada), and further purified using RNeasy Mini Kits (Qiagen Inc., Mississauga, ON, Canada).  RNA was quantified using UV spectrophotometer, and quality was confirmed using the Agilent 2100 Bioanalyzer and RNA 6000 NanoLab Chip Kit (Agilent Technologies Canada Inc., Mississauga, ON, Canada).

tag: sampleID

tag: tissue

value: Part of lung

tag: age

value: 25 week

tag: gender

value: Male

tag: genotype/variation

value: transgenic mouse strain 40.6

tag: exposure

value: 28 days, daily

tag: time post exposure

value: 3 days

tag: dosage

value: 50 mg/kg/day BaP

source_name: universal mouse reference total RNA

extract_protocol: Unknown: Material was purchased as total RNA (universal mouse reference total RNA (Stratagene, CA, USA))

tag: catalog#

tag: vendor

value: Stratagene, La Jolla, CA, USA

tag: sample type

value: Total RNA derived from 11 mouse cell lines


title: Surgery 1-PBS-4 h (data for dynamic bayesian analysis)

tag: male calf

tag: 3 to 6 weeks of age


title: Surgery 1-PBS-8 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 8 H post infection

tag: outbred

tag: distal ileum


title: Surgery 1-MAA-1 h (data for dynamic bayesian analysis)

tag: A mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

tag: cell lines were purchased from the American Type Culture Collection (ATCC), fresh bovine brain and cerebellum was collected from surgery calves immediately following euthanasia by barbituate overdose at the conclusion of bovine ligated ileal loop surgery.


title: Med.Dose.13

tag: sampleID


title: High.Dose.18

tag: tissue

value: 75 mg/kg/day BaP


title: Surgery 1-PBS-1 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 1H post infection


title: Surgery 1-MAP-1 h (data for dynamic bayesian analysis)


title: High.Dose.16

tag: age


title: Control.1

tag: gender


title: Control.4

tag: genotype/variation


title: Low.Dose.9

tag: exposure

value: 25 mg/kg/day BaP


title: Low.Dose.6

tag: time post exposure


title: High.Dose.20

tag: dosage


title: Control.5

tag: catalog#


title: Surgery 1-MAA-30 min (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected at 30 min post infection


title: Surgery 1-MAP-30 min (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 30 min post infection


title: Surgery 1-PBS-30 min (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 30 min post infection


title: High.Dose17

tag: vendor


title: Low.Dose.8

tag: sample type


title: Med.Dose.15


title: Surgery 4-MAA-12 h (data for classical analysis)

data_processing: Arrays were normalized by scaling against the average reference intensity value (i.e., average across all 70 arrays), normalized by global mean, and then log transformed before statistical analyses were performed. Signals flagged as “bad” by GenePix were removed across all arrays in order to ensure that subsequent analyses for each time point were comparable. Pairwise comparisons of averaged signal values and Student’s t test were performed using GeneSifter software (VizX Labs, Seattle, WA). A fold-change of at least 1.5-fold and a p value of 0.05 or less was expected for a difference in signal to be considered statistically significant. All possible individual pairwise comparisons between controls and infections (38 comparisons each for 30 min, 1h, 4h, and 12h post-infection, and 34 comparisons each for 2h and 87hr post-infection) were also performed using Spotfire DecisionSite software (Spotfire, Inc., Somerville, MA).  Genes were further filtered using these various comparisons in order to ensure biological relevance (i.e., that observed differences were not the result of random variation between uninfected animals) and consistency (i.e., reproducibility across experiments). Because a relatively high level of variation between PBS-infected animals was observed (R2 values ranged from 6.2 to 9.1), the following criteria were used:  1. Biological relevance was determined as alterations between baseline and experiment (e.g., PBS-infected versus MAP-infected animals) that were at least 50% greater (on average) than the fold-change observed between any two baseline samples (i.e., PBS-infected versus PBS infected).   2. Consistency was defined as an average fold-change of at least 1.5 between each control (separately) and the four (or three) experimental replicates.

source_name: Ileal mucosa inoculated with MAA, tissue collected at 12 H post infection

tag: male calf


title: Surgery 4-MAP-12 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 12 H post infection

tag: 3 to 6 weeks of age


title: Control.2


title: Surgery 4-MAP-8 h (data for classical analysis)

tag: outbred


title: Low.Dose.7


title: Surgery 4-MAP-4 h (data for classical analysis)

tag: distal ileum


title: Surgery 4-PBS-8 h (data for classical analysis)

tag: A mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.


title: Low.Dose.10


title: Control.3


title: Med.Dose.14


title: High.Dose.19


title: Surgery 4-MAA-8 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected 8 H post infection

tag: cell lines were purchased from the American Type Culture Collection (ATCC), fresh bovine brain and cerebellum was collected from surgery calves immediately following euthanasia by barbituate overdose at the conclusion of bovine ligated ileal loop surgery.


title: thoracic aorta from non-transgenic littermate, replicate 2

city: Iowa City

first: Henry

last: Keen

state: IA

department: Pharmacology

institute: University of Iowa

description: thoracic aorta from mulitple mice, pooled

hyb_protocol: The hybridization procedures were performed at the University of Iowa DNA Core facility using protocols recommended by the manufacturer (Affymetrix).

scan_protocol: The scanning of the arrays was performed at the University of Iowa DNA Core facility using protocols recommended by the manufacturer (Affymetrix).

data_processing: Affymetrix Power Tools (APT, release apt-1.12.0) was used to process the microarray data files (i.e., *.CEL files) and to normalize the data according to the RMA (robust multiarray average) algorithm to generate gene-level (i.e., transcript) signal values.

label: biotin

source_name: thoracic aorta

label_protocol: A one-step amplification and labeling procedure (Affymetrix) starting with approximately 3-5 ug of total RNA was used to generate biotin-labeled RNA fragments.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA) and was purified using a column-based procedure following a standard protocol.

value: thoracic aorta

tag: genotype

value: non-transgenic

tag: strain


title: thoracic aorta from transgenic mouse with DN PPAR gamma (P467L mutation) targeted to vascular smooth muscle, replicate 3

tag: tissue

value: PPAR gamma P467L


title: Surgery 4-PBS-12 h (data for classical analysis)


title: Surgery 4-MAA-2 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected 2 H post infection


title: Surgery 4-PBS-4 h (data for classical analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 4 H post infection


title: Surgery 4-PBS-2 h (data for classical analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 2 H post infection

source_name: reference RNA


title: Surgery 4-MAP-2 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 2 H post infection


title: thoracic aorta from transgenic mouse with DN PPAR gamma (P467L mutation) targeted to vascular smooth muscle, replicate 2


title: Surgery 4-MAA-4 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected 4 H post infection


title: thoracic aorta from non-transgenic littermate, replicate 1


title: thoracic aorta from transgenic mouse with DN PPAR gamma (P467L mutation) targeted to vascular smooth muscle, replicate 1


title: Surgery 4-MAA-1 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected at 1H post infection


title: Surgery 4-MAP-1 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 1H post infection


title: Surgery 4-PBS-1 h (data for classical analysis)


title: Surgery 4-MAA-30 min (data for classical analysis)


title: ROSI 1 week Ly6Clo monocyte #1

city: New York

first: Emmanuel

last: GAUTIER

address: 1425 Madison ave

institute: Mount Sinai School of Medecine

description: Rosi Ly6Clo #1

hyb_protocol: as described in Grabner R, 2009

scan_protocol: as described in Grabner R, 2009

data_processing: All arrays were analysed with ArrayAssist (Stratagene). We used GC-RMA, and then compared the two subsets within each treatment using an unpaired T test with asymptotic P value computation and Benjamini-Hochburg correction.

source_name: blood

label_protocol: RNA amplification, direct labeling, hybridization, and slide scanning were carried out as described in Grabner R, 2009, with slight modifications. We enhanced the in vitro transcription-time from 4 h to 64 h and added fresh nucleotides and T7 polymerase alternating every 8 h and 16 h.

extract_protocol: Sorted samples were pelleted and immediately resuspended in TRIzol (Invitrogen, Carlsbad, CA) and stored at -80˚C until RNA isolation. RNA was isolated with RNeasy Micro-RNA isolation kit (Qiagen, Valencia, CA).

tag: gender

value: male

tag: monocyte subtype

tag: treatment

value: Rosiglitazone (Rosi)


title: Surgery 4-MAP-30 min (data for classical analysis)


title: ROSI 1 week Ly6Clo monocyte #2

description: Rosi Ly6Clo #2


title: CTRL 1 week Ly6Clo monocyte #2

description: Ly6Clo #2

value: control


title: Surgery 4-PBS-30 min (data for classical analysis)


title: Surgery 3-MAP-12 h (data for classical analysis)


title: Surgery 3-MAP-4 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 4 H post infection


title: Surgery 3-MAA-12 h (data for classical analysis)


title: Surgery 3-MAP-8 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 8 H post infection


title: CTRL 1 week Ly6Clo monocyte #4

description: Ly6Clo #4


title: CTRL 1 week Ly6Chi monocyte #1

description: Ly6Chi #1


title: CTRL 1 week Ly6Chi monocyte #4

description: Ly6Chi #4


title: ROSI 1 week Ly6Clo monocyte #3

description: Rosi Ly6Clo #3


title: CTRL 1 week Ly6Clo monocyte #1

description: Ly6Clo #1


title: ROSI 1 week Ly6Chi monocyte #3

description: Rosi Ly6Chi #3


title: ROSI 1 week Ly6Chi monocyte #2

description: Rosi Ly6Chi #2


title: Surgery 3-PBS-12 h (data for classical analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 12 H post infection


title: Surgery 3-MAA-4 h (data for classical analysis)


title: CTRL 1 week Ly6Chi monocyte #2

description: Ly6Chi #2


title: Surgery 3-MAA-8 h (data for classical analysis)


title: CTRL 1 week Ly6Clo monocyte #3

description: Ly6Clo #3


title: ROSI 1 week Ly6Chi monocyte #1

description: Rosi Ly6Chi #1


title: Surgery 3-PBS-8 h (data for classical analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 8 H post infection


title: Surgery 3-PBS-4 h (data for classical analysis)


title: 48w PDGFC+0.06% peretinoin-5

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

institute: Kanazawa University

description: Gene expression data from PDGF-C transgenic mouse treated with peretinoin

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: 48w PDGFC+0.06% peretinoin

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

extract_protocol: RNeasy Mini Kit (QIAGEN) for total RNA was performed according to the manufacturer's instructions.

value: Pdgf-c Tg

tag: genotype/variation

value: PDGF-C transgenic mice

tag: age

value: liver


title: CTRL 1 week Ly6Chi monocyte #3

description: Ly6Chi #3


title: Surgery 1-MAP-12 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 12 H post infection


title: Surgery 3-MAA-2 h (data for classical analysis)


title: 48w PDGFC+0.06% peretinoin-4


title: Surgery 3-PBS-2 h (data for classical analysis)


title: Surgery 3-MAP-2 h (data for classical analysis)


title: 48w PDGFC+0.06% peretinoin-2


title: Surgery 3-MAP-1 h (data for classical analysis)


title: Surgery 2-MAA-12 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected at 12 H post infection


title: Surgery 3-MAA-30 min (data for classical analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected at 30 min post infection


title: 48w PDGFC+0.06% peretinoin-1


title: 20w PDGFC+0.06% peretinoin-5

source_name: 20w PDGFC+0.06% peretinoin


title: Surgery 3-PBS-1 h (data for classical analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 1H post infection


title: Surgery 2-MAP-12 h (data for classical analysis)


title: Surgery 3-MAA-1 h (data for classical analysis)


title: 20w PDGFC+0.06% peretinoin-3


title: 48w PDGFC+0.06% peretinoin-3


title: Surgery 3-MAP-30 min (data for classical analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 30 min post infection


title: Erb1 vs. GFP 388828

city: Houston

first: Philip

last: Jonsson

address: Department of Biology and Biochemistry – NSM Center for Nuclear Receptors and Cell Signaling 3605 Cullen Blvd, Science & Engineering Research Center Bldg 545

institute: University of Houston

hyb_protocol: Hybridization was performed at 42 °C for at least 40 hours after pooling of samples for each array. Subsequent to hybridization the slides were washed in three SDS/SSC wash buffers of stepwise lower stringency.

scan_protocol: Slides were scanned using an Axon GenePix 4400A (MDS Analytical Technologies) to obtain TIFF files.

data_processing: Manual processing of data was carried out in GenePix Pro 6.1 to identify possible major issues. Subsequent analysis was carried out in the R environment using the following packages: Bioconductor bundle, Limma, Aroma, KTH. Print-tip lowess was used for normalization and empirical Bayes t-test for statistical analysis. Cut-offs set as described in article.

organism: Homo sapiens

source_name: PC3 cells, prostate adenocarcinoma

label_protocol: Labeling was carried out with aminoallyl-modified dUTP incorporated during cDNA synthesis using Superscript III (Invitrogen). Incubation with Cy3 or Cy5 monoreactive NHS-ester dured 30 min.

extract_protocol: RNA extraction was performed with TRIzol reagent (Invitrogen Carlsbad, CA) and chloroform extraction according to the manufacturer’s protocol.

tag: transfection

tag: cell line

value: GFP


title: 20w PDGFC+0.06% peretinoin-4


title: Surgery 2-PBS-12 h (data for classical analysis)

source_name: reference RNA


title: 48w PDGFC tumor-5

description: Gene expression data from PDGF-C transgenic mouse

source_name: 48w PDGFC tumor


title: Erb1 vs. GFP 388831


title: Surgery 3-PBS-30 min (data for classical analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 30 min post infection


title: Erb2 vs. GFP 390046


title: Erb1 vs. GFP 388829


title: 20w PDGFC+0.06% peretinoin-2


title: Erb1 vs. GFP 388826


title: Surgery 2-MAA-8 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected 8 H post infection


title: Erb2 vs. GFP 355121


title: 20w PDGFC+0.06% peretinoin-1


title: 48w PDGFC tumor-3


title: 48w PDGFC tumor-4


title: Erb1 vs. GFP 355112


title: Erb1 vs. GFP 355111


title: Erb2 vs. GFP 355120


title: Erb2 vs. GFP 390042


title: Surgery 2-MAP-8 h (data for classical analysis)


title: 48w PDGFC-5

source_name: 48w PDGFC


title: Surgery 2-PBS-8 h (data for classical analysis)


title: Surgery 2-MAA-4 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected 4 H post infection


title: LNK_Young_2

city: Philadelphia

first: Wei

last: Tong

state: PA

address: 316A Abramson Bldg., 3615 Civic Center Blvd.

department: Pediatrics

institute: Children's Hospital of Philadelphia, and University of Pennsylvania School of Medicine

description: Gene expression data from young Lnk-/- BM, biological replicate 2

hyb_protocol: Following fragmentation, cRNA were hybridized on Mouse Gene 1.0ST Array. GeneChips were washed and stained in the Tecan HS400 Hyb Station.

scan_protocol: GeneChips were scanned using the Axon GenePix 4000B scanner.

data_processing: The data were analyzed with the RMA method implemented by the affy package of R/Bioconductor

source_name: CD150+CD48-LSK bone marrow HSCs

label_protocol: Biotinylated cRNA were prepared according to NuGEN Pico protocol from 50 ng total RNA.

growth_protocol: None. Freshly isolated bone marrow hematopoietic stem cells.

extract_protocol: Trizol extraction of total RNA was performed according to QIAGEN miRNeasy instructions

tag: developmental stage

value: adult

value: Young

value: Lnk-/-

value: bone marow

tag: cell type

value: CD150+CD48-LSK HSCs


title: Surgery 2-MAP-4 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 4 H post infection

tag: male calf

tag: 3 to 6 weeks of age


title: LNK_Old_4

description: Gene expression data from old Lnk-/- BM, biological replicate 4

value: Old


title: LNK_Young_1

description: Gene expression data from young Lnk-/- BM, biological replicate 1


title: WT_Young_3

description: Gene expression data from young WT BM, biological replicate 3

value: WT


title: 48w PDGFC-4


title: LNK_Old_3

description: Gene expression data from old Lnk-/- BM, biological replicate 3


title: LNK_Young_3

description: Gene expression data from young Lnk-/- BM, biological replicate 3


title: LNK_Old_2

description: Gene expression data from old Lnk-/- BM, biological replicate 2


title: WT_Young_2

description: Gene expression data from young WT BM, biological replicate 2


title: LNK_Old_1

description: Gene expression data from old Lnk-/- BM, biological replicate 1


title: Surgery 2-MAA-2 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected 2 H post infection

tag: outbred

tag: distal ileum


title: WT_Young_1

description: Gene expression data from young WT BM, biological replicate 1


title: Surgery 2-PBS-4 h (data for classical analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 4 H post infection

tag: A mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

tag: cell lines were purchased from the American Type Culture Collection (ATCC), fresh bovine brain and cerebellum was collected from surgery calves immediately following euthanasia by barbituate overdose at the conclusion of bovine ligated ileal loop surgery.


title: 48w PDGFC-1

tag: strain


title: 48w PDGFC tumor-1

tag: tissue


title: 48w PDGFC tumor-2


title: WT_Old_4

description: Gene expression data from old WT BM, biological replicate 4

tag: genotype


title: 48w PDGFC-3


title: Surgery 2-MAP-2 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 2 H post infection


title: WT_Old_3

description: Gene expression data from old WT BM, biological replicate 3


title: 48w PDGFC-2


title: Surgery 2-PBS-2 h (data for classical analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 2 H post infection


title: WT_Old_1

description: Gene expression data from old WT BM, biological replicate 1


title: WT_Old_2

description: Gene expression data from old WT BM, biological replicate 2


title: 20w PDGFC-5

source_name: 20w PDGFC


title: Surgery 2-MAP-1 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 1H post infection


title: Surgery 2-PBS-1 h (data for classical analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 1H post infection


title: Surgery 2-MAA-1 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected at 1H post infection


title: 48w WT-4

description: Gene expression data from non transgenic mouse C57/B6 control

source_name: 48w WT

value: wild type


title: 20w PDGFC-2


title: 20w PDGFC-3


title: Surgery 2-MAP-30 min (data for classical analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 30 min post infection

source_name: reference RNA


title: Surgery 2-PBS-30 min (data for classical analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 30 min post infection


title: WT_Notch_Tum-2

city: Montréal

first: Lothar

last: Vassen

state: Quebec

address: 110, avenue des Pins Ouest

department: Hematopoiesis and Cancer

institute: IRCM

hyb_protocol: Samples were hybridized with [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Arrays and scanned using a GeneArray Scanner at the Génome Québec INNOVATION centre of the McGill University, Montréal, QC, Canada

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Data was processed using the AltAnalyze_V.2.0.3 Win32 software

source_name: thymocytes

label_protocol: Target RNA was reverse transcribed into cDNA using a NuGEN Ovation Pico RNA Kit and in-vitro transcription was performed to generate biotin-labeled cRNA. cRNA was labeled with streptavidin-phycoerythrin.

extract_protocol: Quiagen micro-RNA kit was used

treatment_protocol: Overall procedure: Gfi1f/f (WT_Tum) or Mx1Cre+Gfi1f/f  (KO_Tum) or Gfi1f/f Notch tg  (WT_Notch_Tum) or Mx1Cre+Gfi1f/f Notch tg  (Notch_KO_Tum)Mice were injected with di-Nitriso-N-Ethylurea (ENU) and observed for emergence of mediastinal using ultarsound. Upon emergence of a growing mediastinal tumor, mice were injected with pIpC, which induces deletion of Gfi1 in MxCre+ tg mice. About 2-3 weeks after pIpC injection, tumor cells were explanted.

value: wt

tag: protocol

value: transformed by Notch1-CT and ENU


title: KO_Notch_Tum-2

value: Gfi1 KO


title: Surgery 2-MAA-30 min (data for classical analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected at 30 min post infection


title: Surgery 1-MAA-12 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected at 12 H post infection


title: 20w PDGFC-1


title: Gfi1KO_thymocytes-1

value: untreated


title: 20w PDGFC-4


title: Gfi1KO_thymocytes-2


title: 48w WT-2


title: Gfi1KO_ENU_Tum-2

value: ENU transformed


title: WT_Notch_Tum-1


title: WT_ENU_Tum-3


title: Gfi1KO_ENU_Tum-1


title: Gfi1KO_irr-3

value: irradiated


title: WT_ENU_Tum-1


title: KO_Notch_Tum-1


title: WT_ENU_Tum-2


title: Gfi1KO_ENU_Tum-3


title: WT_thymocytes-2


title: Gfi1KO_irr-2


title: WT_thymocytes-1


title: Surgery 1-MAP-8 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 8 H post infection


title: Surgery 1-PBS-12 h (data for classical analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 12 H post infection


title: Papillary renal cell carcinoma type 2 II33 Tumor tissue

city: Erlangen

first: Sven

last: Wach

address: Glueckstrasse 6

department: Dept. of Urology

country: Germany

institute: University Hospital, Friedrich-Alexander-University Erlangen-Nuernberg

description:
TU_II33
miRNA gene expression from papillary RCC type 2 tissue

hyb_protocol: Affymetrix GeneChip miRNA Procedure (FluidicsScript 450-0003, Hyb. 48°C)

scan_protocol: Affymetrix-3000 7G

data_processing: Data files were analyzed with Partek genomics suite (v.6.5) using RMA background correction and quartile normalization

source_name: papillary type 2 renal cell carcinoma

label_protocol: FlashTag RNA Labeling with Genisphere RNA Labeling Kit

growth_protocol: Primary renal cell carcinoma samples from radical nephrectomy specimens.

extract_protocol: RNA was prepared by proteinase K digestion of formalin-fixed tissue samples followed by RNA precipitation. Epicentre MasterPure Complete DNA & RNA Purification Kit was used according to the manufacturer's instructions

tag: tissue source

value: radical nephrectomy specimen II33

tag: tissue type

value: tumor

tag: rcc subtype

value: papillary RCC type 2

tag: sample type

value: FFPE tissue


title: Papillary renal cell carcinoma type 2 II99 Tumor tissue

description:
TU_II99
miRNA gene expression from papillary RCC type 2 tissue

value: radical nephrectomy specimen II99


title: Papillary renal cell carcinoma type 2 II93 Tumor tissue

description:
TU_II93
miRNA gene expression from papillary RCC type 2 tissue

value: radical nephrectomy specimen II93


title: Surgery 1-MAA-4 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected 4 H post infection


title: 48w WT-1

tag: genotype/variation

tag: age

value: liver


title: 20w WT-4

source_name: 20w WT


title: 20w WT-3


title: Surgery 1-MAP-12 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 12 H post infection


title: Surgery 1-MAP-4 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 4 H post infection


title: Gfi1KO_irr-1


title: Surgery 1-PBS-8 h (data for classical analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 8 H post infection


title: Papillary renal cell carcinoma type 2 II30 Tumor tissue

description:
TU_II30
miRNA gene expression from papillary RCC type 2 tissue

value: radical nephrectomy specimen II30


title: Papillary renal cell carcinoma type 2 II22 Tumor tissue

description:
TU_II22
miRNA gene expression from papillary RCC type 2 tissue

value: radical nephrectomy specimen II22


title: 20w WT-2


title: Papillary renal cell carcinoma type 1 I95 Tumor tissue

description:
TU_I95
miRNA gene expression from papillary RCC type 1 tissue

source_name: papillary type 1 renal cell carcinoma

value: radical nephrectomy specimen I95

value: papillary RCC type 1


title: WT_irr-3

value: wt


title: 20w WT-5

value: wild type


title: 20w WT-1


title: Papillary renal cell carcinoma type 2 II98 Tumor tissue

description:
TU_II98
miRNA gene expression from papillary RCC type 2 tissue

value: radical nephrectomy specimen II98


title: WT_irr-2


title: WT_irr-1


title: Surgery 1-PBS-4 h (data for classical analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 4 H post infection


title: Papillary renal cell carcinoma type 1 I89 Tumor tissue

description:
TU_I89
miRNA gene expression from papillary RCC type 1 tissue

value: radical nephrectomy specimen I89


title: Papillary renal cell carcinoma type 2 II29 Tumor tissue

description:
TU_II29
miRNA gene expression from papillary RCC type 2 tissue

value: radical nephrectomy specimen II29


title: Surgery 1-PBS-2 h (data for classical analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 2 H post infection


title: Surgery 1-MAP-2 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 2 H post infection


title: Papillary renal cell carcinoma type 1 I15 Tumor tissue

description:
TU_I15
miRNA gene expression from papillary RCC type 1 tissue

value: radical nephrectomy specimen I15


title: 48w WT-3

source_name: 48w WT


title: Papillary renal cell carcinoma type 1 I93 Tumor tissue

description:
TU_I93
miRNA gene expression from papillary RCC type 1 tissue

value: radical nephrectomy specimen I93


title: Clear cell renal cell carcinoma 138 Tumor tissue

description:
TU_cc138
miRNA gene expression from clear cell RCC tissue

source_name: clear cell renal cell carcinoma

value: radical nephrectomy specimen 138

value: tumor

value: clear cell RCC


title: Clear cell renal cell carcinoma 182 Tumor tissue

description:
TU_cc182
miRNA gene expression from clear cell RCC tissue

value: radical nephrectomy specimen 182

value: FFPE tissue


title: Clear cell renal cell carcinoma A551 Tumor tissue

description:
TU_ccA551
miRNA gene expression from clear cell RCC tissue

value: radical nephrectomy specimen A551


title: Clear cell renal cell carcinoma 22A6 Tumor tissue

description:
TU_cc22A6
miRNA gene expression from clear cell RCC tissue

value: radical nephrectomy specimen 22A6


title: Clear cell renal cell carcinoma 17A5 Tumor tissue

description:
TU_cc17A5
miRNA gene expression from clear cell RCC tissue

value: radical nephrectomy specimen 17A5


title: Papillary renal cell carcinoma type 1 I13 Tumor tissue

description:
TU_I13
miRNA gene expression from papillary RCC type 1 tissue

value: radical nephrectomy specimen I13


title: Surgery 1-PBS-30 min (data for classical analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 30 min post infection

source_name: reference RNA


title: Clear cell renal cell carcinoma 16A4 Tumor tissue

description:
TU_cc16A4
miRNA gene expression from clear cell RCC tissue

value: radical nephrectomy specimen 16A4


title: Surgery 1-PBS-1 h (data for classical analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 1H post infection


title: Papillary renal cell carcinoma type 1 I84 Tumor tissue

description:
TU_I84
miRNA gene expression from papillary RCC type 1 tissue

value: radical nephrectomy specimen I84

value: papillary RCC type 1


title: Surgery 1-MAA-1 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected at 1H post infection


title: Surgery 1-MAP-30 min (data for classical analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 30 min post infection


title: Surgery 1-MAP-1 h (data for classical analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 1H post infection


title: Papillary renal cell carcinoma type 1 I01 Tumor tissue

description:
TU_I01
miRNA gene expression from papillary RCC type 1 tissue

value: radical nephrectomy specimen I01


title: tga3-2 Inf 32 vs. tga3-2 Mock 32, rep2

city: Norwich

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

country: United Kingdom

institute: The Genome Analysis Centre

hyb_protocol: The microarray experiments were carried out using the CATMA (version 4) microarray (Allemeersh et al., 2005; http://www.catma.org). Labelled samples were hybridized to slides overnight at 42oC. Following hybridization, slides were washed.

scan_protocol: Slides were scanned using an Affymetrix 428 array scanner at 532nm (Cy3) and 635nm (Cy5). Scanned data were quantified using ImaGene 7.5.0 software (BioDiscovery, Inc.).

data_processing: The data from each time point were normalized and fit to a linear model using the R Bioconductor package limmaGUI (Wettenhall and Smyth, 2004). Raw data was first adjusted using a PrintTip (local) lowess transformation. Data was then scaled to normalize between arrays. A least squares method was then used to fit the data to a linear model. In each time series, genes were selected as differentially expressed if the p-value adjusted by Benjamini and Hochberg's false discovery rate method was less than 0.05 for a moderated t-test of the log2 relative expression at one or more time points.

organism: Arabidopsis thaliana

source_name: tga3-2, infected, 32 hpi

label_protocol: Cy3- and Cy5-labelled cDNA probes were prepared by reverse transcribing 5µg of aRNA with Cy3- or Cy5-dCTP (GE Healthcare) and a modified dNTP mix (10mM each dATP, dGTP and dTTP; 2mM dCTP) using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen), with the inclusion of RNase inhibitor (RNaseOUT, Invitrogen) and DTT. Labelled probes were purified using QiaQuick PCR Purification columns (Qiagen), freeze-dried, and resuspended in 50µl hybridization buffer (25% formamide, 5xSSC, 0.1% SDS, 0.5µg/µl yeast tRNA [Invitrogen]).

growth_protocol: Arabidopsis plants Col-0 were grown under a 16:8 hr light:dark cycle at 20°C, 60% humidity and light intensity of 100 μmol photons.m-2.s-1. Arabidopsis seed was stratified for three days in 0.1% agar at 4°C before sowing onto Arabidopsis soil mix (Scotts Levingtons F2s compost:sand:fine grade vermiculite in a ratio of 6:1:1).

extract_protocol: Total RNA was isolated from four individual leaves from each sampled time point (arbitrarily labelled as biological replicates A, B, C and D) using TRIzol reagent (Invitrogen), purified with RNeasy columns (Qiagen) and amplified using the MessageAmp II aRNA Amplification kit (Ambion) in accordance with the kit protocol with a single round of amplification.

treatment_protocol: Botrytis cinerea strain pepper was sub-cultured on sterile tinned apricot halves in Petri dishes two weeks prior to use of the spores. Sub-cultures were incubated in the dark at 25°C. Spore inoculums were prepared by harvesting spores in water, filtration through glass wool to remove hyphae and suspension in half-strength sterile grape juice (Tesco's Own) to a concentration of 1 x 10^5 spores/ml. Leaf 7 from each plant was detached and placed on a bed of 0.8% agar in a propagator tray. Half of the leaves were inoculated with 5-7 (depending on the size of the leaf) 10 μl droplets of B. cinerea inoculum so that droplets were evenly spaced over the leaf. The remaining leaves were mock-inoculated with 5-7 10 μl droplets of sterile half-strength grape juice. Trays were covered with lids and kept under the same conditions as for plant growth, except the relative humidity was raised to 90%. Single infected and control leaves were sampled at 16, 24 and 32 hpi. Whole leaf samples were snap frozen in liquid nitrogen at the time of harvesting and stored at -80°C.

value: tga3-2 mutant

tag: treatment

value: infected with Botrytis cinerea

tag: hours post-infection

source_name: tga3-2, mock, 32 hpi

value: mock infected


title: tga3-2 Inf 32 vs. tga3-2 Mock 32, rep1


title: tga3-2 Mock 32 vs. tga3-2 Inf 32, rep2


title: tga3-2 Inf 32 vs. WT-Inf 32, rep2

source_name: WT, infected, 32 hpi

tag: ecotype

value: wild type


title: tga3-2 Mock 32 vs. tga3-2 Inf 32, rep1


title: Papillary renal cell carcinoma type 2 II99 Normal tissue

description:
NO_II99
miRNA gene expression data from corresponding normal tissue

source_name: normal (non-malignant) tissue

value: radical nephrectomy specimen II99

value: normal (non-malignant)


title: Papillary renal cell carcinoma type 2 II98 Normal tissue

description:
NO_II98
miRNA gene expression data from corresponding normal tissue

value: radical nephrectomy specimen II98


title: Papillary renal cell carcinoma type 2 II93 Normal tissue

description:
NO_II93
miRNA gene expression data from corresponding normal tissue

value: radical nephrectomy specimen II93


title: Papillary renal cell carcinoma type 2 II38 Normal tissue

description:
NO_II38
miRNA gene expression data from corresponding normal tissue

value: radical nephrectomy specimen II38

value: FFPE tissue


title: Marilyn.Foxp3-/- activated and TGFβ-experienced  biological replicate 3

city: Framingham

first: Duncan

last: Howie

state: MA

address: 49 New York Avenue

institute: Genzyme Corporation/Sir William Dunn School of Pathology Oxford University

description:
Foxp3KO_T3
A0050895
Marilyn.Foxp3-/- activated and TGFβ-experienced

hyb_protocol: Hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven.  Arrays were washed and stained on an Affymetrix FS450 Fluidics station

scan_protocol: The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Arrays were further pre-processed in the Affymetrix Expression Console software version 1.2 which was used to normalize CEL files using the quantile normalization method and the data was summarized data at gene level by using the Robust Multichip Analysis (RMA) algorithm . All further data analysis was performed in MP Genomics software version 5.1. Batch normalization was performed across two studies for the Foxp3CD2 cells.(biological replicates 4 and 5 repeated in second study)
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

label_protocol: biotin-labeled sense strand cDNA was prepared from 30µg cRNA generated from 1µg total RNA per sample using a modified Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay (Affymetrix, Inc.).Intermediate cRNA and resulting cDNA yields were quantified by spectrophotometry.  Fragmentation and labeling of cDNA was performed using 5 µg for Exon Arrays.

extract_protocol: Total RNA was isolated from the frozen cell pellets by Asuragen, Inc., according to the company’s standard operating procedure for automated isolation on a KingFisher magnetic particle separator

treatment_protocol: Cultured splenocytes were used to generate highly purified populations of Marilyn.Foxp3hCD2 activated (HY) and TGFB-induced (HYT) cells sorted as CD4+hCD2+ and CD4+hCD2-  and Marilyn.Foxp3-/- activated and TGFB-experienced (but Foxp3-) cells sorted as CD4+CD2

value: spleen

tag: cell type

value: TGFB

tag: study #


title: Marilyn.Foxp3-/- activated Untreated biological replicate 3

description:
Foxp3KO_UT3
A0050894
Marilyn.Foxp3-/- activated Untreated

value: UT


title: Papillary renal cell carcinoma type 2 II33 Normal tissue

description:
NO_II33
miRNA gene expression data from corresponding normal tissue

value: radical nephrectomy specimen II33


title: Marilyn.Foxp3-/- activated and TGFβ-experienced  biological replicate 2

description:
Foxp3KO_T2
A0050893
Marilyn.Foxp3-/- activated and TGFβ-experienced


title: Papillary renal cell carcinoma type 2 II30 Normal tissue

description:
NO_II30
miRNA gene expression data from corresponding normal tissue

value: radical nephrectomy specimen II30


title: Marilyn.Foxp3-/- activated and TGFβ-experienced  biological replicate 1

description:
Foxp3KO_T1
A0050891
Marilyn.Foxp3-/- activated and TGFβ-experienced


title: tga3-2 Inf 32 vs. WT-Inf 32, rep1


title: AFX platform, lab 2, tumor, colon adenocarcinoma, biological rep 2

city: Urbana

first: Chieh-Chun

last: Chen

state: Illinois

address: 1206 West Gregory Drive

department: Bioengineering

institute: University of illinois

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.
AFX_2_T2

hyb_protocol: 20 µg of cRNA was hybridized to each individual microarray (HG-U133-Plus-2.0). The microarrays were hybridized for 16 hours at 45°C, stained, and washed according to an Affymetrix protocol (EukGE-WS2v4) using an Affymetrix fluidics station.

scan_protocol: GeneChips were scanned using the Affymetrix scanner.

data_processing: The CEL file data were analyzed with BioConductor to generate probeset level data using the justPlier() function. Probe-level data were quantile normalized before PLIER summarization per test site (10 arrays). An offset value of 16 was then added to each probeset-level data point.

source_name: Sample type T (Tumor, colon adenocarcinoma)

label_protocol: 5 µg of total RNA was used to synthesize cRNA for each sample.

extract_protocol: Colorectal adenocarcinomas and matched normal colonic RNA sample were purchased from Oncomatrix, Inc., San Diego, CA.

value: Tumor, colon adenocarcinoma

tag: lab


title: AFX platform, lab 2, tumor, colon adenocarcinoma, biological rep 5

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.
AFX_2_T5


title: WT-Inf 32 vs. tga3-2 Inf 32, rep1


title: Marilyn.Foxp3-/- activated Untreated biological replicate 1

description:
Foxp3KO_UT1
A0050890
Marilyn.Foxp3-/- activated Untreated


title: AFX platform, lab 2, tumor, colon adenocarcinoma, biological rep 4

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.
AFX_2_T4


title: tga3-2 Inf 24 vs. tga3-2 Mock 24, rep2

source_name: tga3-2, infected, 24 hpi

source_name: tga3-2, mock, 24 hpi


title: Marilyn.Foxp3hCD2 activated (CD4+hCD2+) and TGFB-induced (HYT) biological replicate 5

description:
T_pos_5
A0052726
Marilyn.Foxp3hCD2 activated  and TGFβinduced (HYT)

value: marilynfoxp3hCD2 (Transgenic mice)


title: WT-Inf 32 vs. tga3-2 Inf 32, rep2

value: tga3-2 mutant


title: Papillary renal cell carcinoma type 2 II29 Normal tissue

description:
NO_II29
miRNA gene expression data from corresponding normal tissue

value: radical nephrectomy specimen II29


title: AFX platform, lab 2, matched normal colon tissue, biological rep 4

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.
AFX_2_N4

source_name: Sample type N (Normal, matched normal colon tissue)

value: Normal, matched normal colon tissue


title: Marilyn.Foxp3hCD2 activated (CD4+hCD2+) and TGFB-induced (HYT) biological replicate 4

description:
T_pos_4
A0050886
Marilyn.Foxp3hCD2 activated  and TGFβinduced (HYT)


title: tga3-2 Inf 24 vs. tga3-2 Mock 24, rep1

value: infected with Botrytis cinerea

value: mock infected


title: Marilyn.Foxp3hCD2 activated (CD4+hCD2+) and TGFB-induced (HYT) biological replicate 3

description:
T_pos_3
H0040284
Marilyn.Foxp3hCD2 activated  and TGFβinduced (HYT)


title: Marilyn.Foxp3-/- activated Untreated biological replicate 2

description:
Foxp3KO_UT2
A0050892
Marilyn.Foxp3-/- activated Untreated


title: Surgery 1-MAA-30 min (data for classical analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected at 30 min post infection

tag: male calf

tag: 3 to 6 weeks of age

tag: outbred

tag: distal ileum

tag: A mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

tag: cell lines were purchased from the American Type Culture Collection (ATCC), fresh bovine brain and cerebellum was collected from surgery calves immediately following euthanasia by barbituate overdose at the conclusion of bovine ligated ileal loop surgery.


title: AFX platform, lab 2, matched normal colon tissue, biological rep 5

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.
AFX_2_N5

tag: tissue


title: AFX platform, lab 2, tumor, colon adenocarcinoma, biological rep 3

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.
AFX_2_T3


title: Papillary renal cell carcinoma type 2 II22 Normal tissue

description:
NO_II22
miRNA gene expression data from corresponding normal tissue

tag: tissue source

value: radical nephrectomy specimen II22

tag: tissue type

value: normal (non-malignant)


title: Marilyn.Foxp3hCD2 activated (CD4+hCD2+) and TGFB-induced (HYT) biological replicate 2

description:
T_pos_2
H0040281
Marilyn.Foxp3hCD2 activated  and TGFβinduced (HYT)

tag: genotype


title: tga3-2 Mock 24 vs. tga3-2 Inf 24, rep2

tag: genotype/variation


title: AFX platform, lab 2, tumor, colon adenocarcinoma, biological rep 1

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.
AFX_2_T1


title: tga3-2 Mock 24 vs. tga3-2 Inf 24, rep1

tag: treatment


title: Papillary renal cell carcinoma type 1 I93 Normal tissue

description:
NO_I93
miRNA gene expression data from corresponding normal tissue

value: radical nephrectomy specimen I93

tag: sample type


title: Papillary renal cell carcinoma type 1 I15 Normal tissue

description:
NO_I15
miRNA gene expression data from corresponding normal tissue

value: radical nephrectomy specimen I15


title: Papillary renal cell carcinoma type 1 I13 Normal tissue

description:
NO_I13
miRNA gene expression data from corresponding normal tissue

value: radical nephrectomy specimen I13

value: FFPE tissue


title: Marilyn.Foxp3hCD2 activated (CD4+hCD2-) and TGFB-induced (HYT) biological replicate 5

description:
T_neg_5
A0052727
Marilyn.Foxp3hCD2 activated  and TGFβinduced (HYT)

value: spleen

value: TGFB


title: Papillary renal cell carcinoma type 1 I10 Normal tissue

description:
NO_I10
miRNA gene expression data from corresponding normal tissue

value: radical nephrectomy specimen I10


title: Marilyn.Foxp3hCD2 activated (CD4+hCD2+) and TGFB-induced (HYT) biological replicate 1

description:
T_pos_1
H0040278
Marilyn.Foxp3hCD2 activated  and TGFβinduced (HYT)


title: Papillary renal cell carcinoma type 1 I01 Normal tissue

description:
NO_I01
miRNA gene expression data from corresponding normal tissue

value: radical nephrectomy specimen I01


title: Marilyn.Foxp3hCD2 activated (CD4+hCD2-) and TGFB-induced (HYT) biological replicate 3

description:
T_neg_3
H0040285
Marilyn.Foxp3hCD2 activated  and TGFβinduced (HYT)


title: tga3-2 Inf 24 vs. WT-Inf 24, rep1

tag: hours post-infection

source_name: WT, infected, 24 hpi

tag: ecotype

value: wild type


title: Clear cell renal cell carcinoma A3 Normal tissue

description:
NO_ccA3
miRNA gene expression data from corresponding normal tissue

value: radical nephrectomy specimen A3


title: AFX platform, lab 1, tumor, colon adenocarcinoma, biological rep 4

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.
AFX_1_T4

value: Tumor, colon adenocarcinoma


title: AFX platform, lab 1, tumor, colon adenocarcinoma, biological rep 3

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.
AFX_1_T3


title: Marilyn.Foxp3hCD2 activated (CD4+hCD2-) and TGFB-induced (HYT) biological replicate 4

description:
T_neg_4
A0050888
Marilyn.Foxp3hCD2 activated  and TGFβinduced (HYT)

tag: cell type

value: marilynfoxp3hCD2 (Transgenic mice)

tag: study #


title: WT-Inf 24 vs. tga3-2 Inf 24, rep2

value: tga3-2 mutant


title: AFX platform, lab 2, matched normal colon tissue, biological rep 2

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.
AFX_2_N2

value: Normal, matched normal colon tissue

tag: lab


title: AFX platform, lab 1, tumor, colon adenocarcinoma, biological rep 5

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.
AFX_1_T5


title: tga3-2 Inf 16 vs. tga3-2 Mock 16, rep1

source_name: tga3-2, infected, 16 hpi

value: infected with Botrytis cinerea

source_name: tga3-2, mock, 16 hpi

value: mock infected


title: tga3-2 Inf 16 vs. tga3-2 Mock 16, rep2


title: tga3-2 Inf 24 vs. WT-Inf 24, rep2


title: Marilyn.Foxp3hCD2 activated (CD4+hCD2-) and TGFB-induced (HYT) biological replicate 2

description:
T_neg_2
H0040282
Marilyn.Foxp3hCD2 activated  and TGFβinduced (HYT)


title: AFX platform, lab 2, matched normal colon tissue, biological rep 3

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.
AFX_2_N3


title: AFX platform, lab 2, matched normal colon tissue, biological rep 1

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.
AFX_2_N1


title: WT-Inf 24 vs. tga3-2 Inf 24, rep1


title: Clear cell renal cell carcinoma 138 Normal tissue

description:
NO_cc138
miRNA gene expression data from corresponding normal tissue

value: radical nephrectomy specimen 138

value: normal (non-malignant)


title: AFX platform, lab 1, tumor, colon adenocarcinoma, biological rep 1

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.
AFX_1_T1


title: tga3-2 Mock 16 vs. tga3-2 Inf 16, rep2


title: Marilyn.Foxp3hCD2 activated (CD4+hCD2-) and TGFB-induced (HYT) biological replicate 1

description:
T_neg_1
H0040279
Marilyn.Foxp3hCD2 activated  and TGFβinduced (HYT)


title: AFX platform, lab 1, tumor, colon adenocarcinoma, biological rep 2

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.
AFX_1_T2


title: Marilyn.Foxp3hCD2 activated (HY)(Untreated) biological replicate 5

description:
UT_5
A0052725
Marilyn.Foxp3hCD2 activated (HY)(Untreated)

value: UT


title: Clear cell renal cell carcinoma 22A6 Normal tissue

description:
NO_cc22A6
miRNA gene expression data from corresponding normal tissue

value: radical nephrectomy specimen 22A6


title: Clear cell renal cell carcinoma 17A5 Normal tissue

description:
NO_cc17A5
miRNA gene expression data from corresponding normal tissue

value: radical nephrectomy specimen 17A5

value: FFPE tissue


title: tga3-2 Mock 16 vs. tga3-2 Inf 16, rep1


title: Clear cell renal cell carcinoma 16A4 Normal tissue

description:
NO_cc16A4
miRNA gene expression data from corresponding normal tissue

value: radical nephrectomy specimen 16A4


title: AFX platform, lab 1, matched normal colon tissue, biological rep 4

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.
AFX_1_N4


title: AFX platform, lab 1, matched normal colon tissue, biological rep 5

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.
AFX_1_N5


title: AFX platform, lab 1, matched normal colon tissue, biological rep 2

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.
AFX_1_N2


title: thoracic aorta from transgenic mouse with DN PPAR gamma (P467L mutation) targeted to vascular smooth muscle (exon) rep 4

description: thoracic aorta from one mouse, not pooled

data_processing:
Affymetrix Power Tools (APT, release apt-1.12.0) was used to process the microarray data files (i.e., *.CEL files) and to normalize the data according to the RMA (robust multiarray average) algorithm to generate gene-level (i.e., transcript) signal values.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm9.extended.mps

source_name: thoracic aorta

label_protocol: A kit (NuGen, San Carlos, CA) was used to implement a two-step amplification procedure starting with approximately 50 ng of total RNA to generate biotin-labeled RNA fragments.

growth_protocol: not applicable

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA) and was purified using a column-based kit (Purelink RNA, Invitrogen, Carlsbad, CA) following the manufacturer’s protocol.

treatment_protocol: not applicable

value: thoracic aorta

value: PPAR gamma P467L

tag: strain


title: Marilyn.Foxp3hCD2 activated (HY)(Untreated) biological replicate 1

description:
UT_1
H0040277
Marilyn.Foxp3hCD2 activated (HY)(Untreated)

value: spleen


title: Marilyn.Foxp3hCD2 activated (HY)(Untreated) biological replicate 2

description:
UT_2
H0040280
Marilyn.Foxp3hCD2 activated (HY)(Untreated)


title: AFX platform, lab 1, matched normal colon tissue, biological rep 1

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006 [PMID: 17160039]
AFX_1_N1


title: Marilyn.Foxp3hCD2 activated (HY)(Untreated) biological replicate 3

description:
UT_3
H0040283
Marilyn.Foxp3hCD2 activated (HY)(Untreated)


title: Marilyn.Foxp3hCD2 activated (HY)(Untreated) biological replicate 4

description:
UT_4
A0050885
Marilyn.Foxp3hCD2 activated (HY)(Untreated)


title: TC/CP, replicate 2

city: Bologna

first: Andrea

last: Grilli

state: Italy

address: v. di Barbiano 1/10

department: Laboratory of Experimental Oncology

country: Italy

institute: Rizzoli Orthopaedic Institute

description:
cell line referred as TC/CP
20100122_3_TC71_CIPbis_Plus2.0_(HG-U133_Plus_2).CEL

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 7G.

data_processing: The data were analyzed with Bioconductor affy package, using RMA algorithm for normalization and summarization.

source_name: Ewing's Sarcoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cells were maintained in standard medium (Iscove Modified Dulbecco’s medium, IMDM, plus 10% fetal bovine serum, FBS).

extract_protocol: Total RNA was extracted by the TRIzol extraction kit (Invitrogen). Quality and quantity of RNA samples were assessed with NanoDrop analysis (NanoDrop Technologies) and/or with an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells resistant to anti-IGF-1R HAb AVE1642, TKI NVP-AEW541 and to HAb anti-IGF-1R  Figitumumab (CP-751,871) were obtained from TC-71 cell line by exposure to increasing concentrations of the anti-IGF-1R HAb AVE1642 (up to 10 ug/ml), to the TKI NVP-AEW541 (up to 5 µM) or to the HAb CP-751,871 for six months.

tag: cell line

value: TC/CP

tag: cell line resistance

value: stably resistant to IGF-1R Hab CP-751,871


title: tga3-2 Inf 16 vs. WT-Inf 16, rep1

source_name: WT, infected, 16 hpi

value: wild type


title: tga3-2 Inf 16 vs. WT-Inf 16, rep2

value: tga3-2 mutant


title: thoracic aorta from transgenic mouse with DN PPAR gamma (P467L mutation) targeted to vascular smooth muscle (exon) rep 5


title: thoracic aorta from transgenic mouse with DN PPAR gamma (P467L mutation) targeted to vascular smooth muscle (exon) rep 6


title: AFX platform, lab 1, matched normal colon tissue, biological rep 3

description:
MAQC colon tumor samples used in Lin G, He X, Ji H, Shi L, Davis R and Zhong S, Nature Biotechnology, October, 2006.
AFX_1_N3

value: Normal, matched normal colon tissue


title: TC/AVE, replicate 2

description:
cell line referred as TC/AVE
20090617_TC-AVE(2)_Plus2.0_(HG-U133_Plus_2).CEL

value: TC/AVE

value: stably resistant to IGF-1R Hab AVE1642 Hab


title: thoracic aorta from transgenic mouse with DN PPAR gamma (P467L mutation) targeted to vascular smooth muscle (exon) rep 3


title: thoracic aorta from transgenic mouse with DN PPAR gamma (P467L mutation) targeted to vascular smooth muscle (exon) rep 7


title: TC/AEW, replicate 2

description:
cell line referred as TC/AEW
20090617_TC-AEW(2)_Plus2.0_(HG-U133_Plus_2).CEL

value: TC/AEW

value: stably resistant to IGF-1R TKI NVP-AEW541


title: WT-Inf 16 vs. tga3-2 Inf 16, rep2

value: infected with Botrytis cinerea


title: TC/AVE, replicate 1

description:
cell line referred as TC/AVE
20090617_TC-AVE_Plus2.0_(HG-U133_Plus_2).CEL


title: thoracic aorta from transgenic mouse with DN PPAR gamma (P467L mutation) targeted to vascular smooth muscle (exon) rep 1


title: TC/CP, replicate 1

description:
cell line referred as TC/CP
20100122_2_TC71_CIP_Plus2.0_(HG-U133_Plus_2).CEL


title: WT-Inf 16 vs. tga3-2 Inf 16, rep1


title: thoracic aorta from transgenic mouse with DN PPAR gamma (P467L mutation) targeted to vascular smooth muscle (exon) rep 2


title: TC-71, sample 3

description:
cell line referred as TC-71
TC71_2010.CEL

value: no IGF-1R drugs resistant


title: TC/AEW, replicate 1

description:
cell line referred as TC/AEW
20090617_TC-AEW_Plus2.0_(HG-U133_Plus_2).CEL


title: thoracic aorta from non-transgenic littermate (exon) rep5

value: non-transgenic


title: thoracic aorta from non-transgenic littermate (exon) rep 4


title: thoracic aorta from non-transgenic littermate (exon) rep 1


title: thoracic aorta from non-transgenic littermate (exon) rep 2


title: whole saliva from normal control No.2 _no treatment_rep2

city: Guangzhou

first: Zijun

last: Xie

address: No.106,zhongshan 2nd round

country: China

institute: Guangdong General Hospital

description: microRNA expression of whole saliva from healthy control No.2

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

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

source_name: whole saliva from normal control No.2 _no treatment_replicate2

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

extract_protocol: using the mirVana PARIS kit (Ambion, USA).1.0ml of saliva was distributed equally to 2 microcentrifuge tubes.that is to say, each microcentrifuge tube contains 500μL of saliva. 2)200μL of 2x denaturing solution was added to each tube. 3) Add 1ml of  Acid-Phenol:Chloroform to each tube, and vortex for 30–60 sec to mix.4) Centrifuge for 5 min at maximum speed (≥10,000 x g) at room temp to separate the mixture into aqueous and organic phases. After centrifugation, the interphase should be compact; if it is not, repeat the centrifugation.6) Carefully remove the aqueous (upper) phase without disturbing the lower phase or the interphase, and transfer it to a fresh tube. 7) Add 1.25 volumes 100% ethanol to the aqueous phase, and mix thoroughly. 8) For each sample, place a Filter Cartridge into one of the Collection Tubes. Pipet the lysate/ethanol mixture onto the Filter Cartridge. And apply the mixture in successive applications to the same filter. Centrifuge for ~30 sec or until the mixture has passed through the filter. Discard the flow-through, and repeat until all of the lysate/ethanol mixture is through the filter. Save the Collection Tube for the washing steps. 9) Wash the filter with 700 μL miRNA Wash Solution 1.10) Wash the filter twice with 500 μL Wash Solution 2/3.11)Tissue RNAs were eluted in 200μL of preheated nuclease-free water(95℃)，and saliva RNAs were eluted in 30μL of preheated nuclease-free water(95℃).

treatment_protocol: Subjects were asked to refrain from eating, drinking, smoking, and oral hygiene procedures for at least 2 hours before the collection. To stimulate glandular salivary flow, subjects received a 2% citric acid solution for application to the bilateral posterior lateral surfaces of the tongue with a cotton swab for 5 s every 30 s. The citric acid stimulation continued at 30-second intervals during the entire collection procedure. Up to 5 mL of saliva from each subject was collected in a 50-mL centrifuge tube. A total of 2 mL of saliva was removed from the tube as a whole saliva sample. The remaining 3 mL of saliva samples was centrifuged at 3,000 × g for 15 min at 4C to spin down exfoliated cells, and the supernatant was transferred into microcentrifuge tubes followed by a second centrifugation at 12,000 × g for 10 min at 4C to completely remove cellular components. Samples were stored at -80C until use. The procedure mentioned above must be finished within 2 h

value: whole saliva

tag: gender

value: male

tag: age

tag: disease state

value: healthy


title: whole saliva from esophageal cancer patient No.7 _before treatment_rep7

description: microRNA expression of whole saliva from esophageal cancer patient No.7

source_name: whole saliva from esophageal cancer patient No.7 _before treatment_replicate7

tag: tissue

value: esophageal cancer


title: whole saliva from esophageal cancer patient No.1 _before treatment_rep1

description: microRNA expression of whole saliva from esophageal cancer patient No.1

source_name: whole saliva from esophageal cancer patient No.1 _before treatment_replicate1

value: female


title: whole saliva from esophageal cancer patient No.2 _before treatment_rep2

description: microRNA expression of whole saliva from esophageal cancer patient No.2

source_name: whole saliva from esophageal cancer patient No.2 _before treatment_replicate2


title: thoracic aorta from non-transgenic littermate (exon) rep 3

description: thoracic aorta from one mouse, not pooled

value: thoracic aorta


title: TC-71, sample 2

description:
cell line referred as TC-71
TC71_2009.CEL


title: progesterone PROG replicate 1

city: Woodville South

first: Grant

last: Buchanan

state: South Australia

address: 28 Woodville Road

department: Surgery

country: Australia

institute: Basil Hetzel Institute for Translational Health Research, University of Adelaide

description: PROG replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed in Illumina Bead Studio using using Rank Invariant normalization. Subsequent data corrections and gene analyses were performed in R/Bioconductor.

source_name: ZR-75-1 cells

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

growth_protocol: ZR-75-1 cells were maintained in RPMI 1640 medium containing 10% fetal bovine serum.

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: Plated 1.5x10e5 cells/well in 6-well dishes for 48h in phenol red-free RPMI 1640 containing 10% hormone stripped FCS and treated for 16h with 10nM E2 or 10nM DHT alone or in combination, or equivalent vehicle (ethanol).

value: progesterone


title: SD_Wing

type: genomic

city: Duluth

first: Matthew

last: Slattery

state: MINNESOTA

address: 1035 University Drive, SMed 219

institute: University of Minnesota Medical School

description: Sd-GFP wing disc ChIP, replicates 1-3

hyb_protocol: Hybridization Cocktail (for 1 reaction): DNA (around 60 ul); Control Oligo B2 (3.3 ul); 2X Hybridization Buffer (110 ul); DMSO (15.4 ul); Water (31.3 ul), for a total of 220 ul volume per sample.  Boil 5 min at 99 C Cool to room temperature.  Hybridizations are done in the core facility as per the Affy protocol.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
ChIP-chip data were generated using Affymetrix Drosophila tiling array 2.0 and are subjected to the analysis using MAT (model based analysis of tiling arrays; Johnson et al, 2006). In MAT, all Control and IP samples corresponding to the same experiment are analyzed together.  We specified the MAT parameters Bandwidth, MaxGap and Minprobe parameters to be 200, 100 and 10 respectively. We used non-redundant dm3 BPMAP file and self generated Repeat Library files available for download at http://liulab.dfci.harvard.edu/MAT/Download.htm.  Peaks were called at 5% FDR.
additional results files:
YKI_Wing_FDR5.bed
YKI_Eye-antenna_FDR5.bed
SD_Wing_FDR5.bed
SD_Eye-antenna_FDR5.bed
Wing_SD-YKI_overlap.bed-peak+tss_distance+fbid.txt
Eye-antenna_SD-YKI_overlap.bed-peak+tss_distance+fbid.txt
All .wig files (YKI_Wing_MAT.wig; YKI_Eye-antenna_MAT.wig; SD_Wing_MAT.wig; SD_Eye-antenna_MAT.wig) were generated by MAT software (Johnson et al, PNAS, 2006) and contain MAT score (enrichment relative to input DNA) for each probe.  YKI_Wing_FDR5.bed, YKI_Eye-antenna_FDR5.bed, SD_Wing_FDR5.bed, and SD_Eye-antenna_FDR5.bed contain peaks called by MAT at 5% FDR. The files 'Wing_SD-YKI_overlap.bed-peak+tss_distance+fbid.txt' and 'Eye-antenna_SD-YKI_overlap.bed-peak+tss_distance+fbid.txt' contain called binding regions, distance to the nearest transcription start site, and genes contained within the nearest transcription unit for SD peaks that overlap with a YKI peak in the indicated tissue (wing or eye-antenna).

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Wing imaginal disc ChIP; Sd-GFP (CA07575) strain; GFP antibody

label_protocol: ChIP and Input DNA amplified using Sigma Whole Genome Amplifcation kit (WGA4).  After amplification, labeling proceeds as follows: Use the Bioprime DNA labeling Kit from Invitrogen, 20 ul of DNA (around 300ng/ul of PCR-purified DNA) 20 ul of 2.5X Random Primers solution.  Boil at 95C for 5 min, return to ice.  Add 5ul of 10X dnTP+U and 3ul of water, flick mix, spin.  Add 2ul of Klenow.  Incubate 2.5 hours at 37C, then add 5ul of stop buffer.  Purify using PCR purification kit, elute in 30 ul of buffer.  Quantify the amount of DNA using the Nanodrop spectrophotometer, and use 7.5 ug of DNA for susequent reaction. Use the Affymetrix double-stranded DNAlabeling kit to label DNA.  Prepare labeling mix -- 10X cDNA fragmentation buffer UDG, 10 U/ul APE1, 100 U/ul Nuclease-free H2O up to 48ul.  Incubate 1 hour at 37 C.  Boil at 93C for 2 min, let stand on ice for at least 2 min.  Label the fragmented double-stranded DNA with 5X TdT buffer (12ul) TdT (2ul) 5mM DNA labeling reagent (1ul).  Add the 15ul Mix to the DNA samples.  Incubate 60 min at 37C, 10 min at 70C and at least 2min on ice.

growth_protocol: Wandering 3rd instar larvae were manually removed from Drosophila culture. Larvae were inverted in PBS to expose imaginal discs. Imaginal discs dissected off after fixation.

extract_protocol: Third instar larvae were dissected in Serum Free Media (Gibco) and fixed for 20 minutes at room temperature in 1.8% formaldehyde, 50mM HEPES, 1mM EDTA, 0.5mM EGTA, 100mM NaCl. After quenching (0.125M Glycine, 1xPBS, 0.01% Triton) the fixed tissue was washed first in Buffer A (10mM HEPES, 10mM EDTA, 0.5mM EGTA, 0.25% Triton, 1mM PMSF), then in Buffer B (10mM HEPES, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.01% Triton, 1mM PMSF), for 10 minutes at 4C.  Imaginal discs were then dissected off the cuticles in Buffer B.  Discs were sonicated in Buffer C (10mM HEPES, 1mM EDTA, 0.5mM EGTA, 1mM PMSF, plus complete protease inhibitor cocktail (Roche)) on ice/EtOH.  Soluble chromatin was transferred to new tubes after centrifugation.  Fresh chromatin, precleared with protein G sepharose beads (Roche), was incubated overnight at 4C with antibody in RIPA buffer (140mM NaCl, 10mM HEPES, 1mM EDTA, 1% Glycerol, 1% Triton X-100, 0.1% DOC, 1mM PMSF).  Antibody-chromatin complexes were pulled down with protein G sepharose beads for 3 hours at 4C.  Bound beads were washed 4-times in RIPA buffer (as above plus 0.1mg/mL ssDNA) and once in TE.  Chromatin was eluted twice in Elution Buffer (1% SDS, 0.1M NaHCO3).  20ug Proteinase K was added, and samples were incubated for 3 hours at 55C, then 65C overnight.  DNA was purified via phenol-chloroform extraction and ethanol precipitation.

tag: developmental stage

value: wing imaginal disc

tag: antibody

value: anti-GFP

tag: antibody vendor

value: Abcam

tag: antibody catalog number

tag: antibody lot number


title: medroxyprogesterone acetate MPA replicate 4

description: MPA replicate 4

tag: treatment

value: medroxyprogesterone acetate


title: estradiol +  E2 replicate 4

description: E2 replicate 4

value: estradiol +


title: SD_Eye-antenna

description: Sd-GFP eye-antenna disc ChIP, replicates 1-3

source_name: Eye-antenna imaginal disc ChIP; Sd-GFP (CA07575) strain; GFP antibody

value: eye-antenna imaginal disc


title: progesterone PROG replicate 4

description: PROG replicate 4


title: 5a-dihydrotestosterone  DHT replicate 3

description: DHT replicate 3


title: YKI_Eye-antenna

description: Yki eye-antenna disc ChIP, replicates 1-3

source_name: Eye-antenna imaginal disc ChIP; yw strain; Yki antibody

value: yw

value: anti-Yki

tag: antibody provider

value: Duojia Pan Lab


title: estradiol + medroxyprogesterone acetate E2+MPA replicate 2

description: E2+MPA replicate 2

value: estradiol + medroxyprogesterone acetate


title: whole saliva from normal control No.1 _no treatment_rep1

description: microRNA expression of whole saliva from healthy control No.1

source_name: whole saliva from normal control No.1 _no treatment_replicate1

value: whole saliva


title: whole saliva from esophageal cancer patient No.5 _before treatment_rep5

description: microRNA expression of whole saliva from esophageal cancer patient No.5

source_name: whole saliva from esophageal cancer patient No.5 _before treatment_replicate5

value: male


title: whole saliva from esophageal cancer patient No.3 _before treatment_rep3

description: microRNA expression of whole saliva from esophageal cancer patient No.3

source_name: whole saliva from esophageal cancer patient No.3 _before treatment_replicate3


title: whole saliva from normal control No.3 _no treatment_rep3

description: microRNA expression of whole saliva from healthy control No.3

source_name: whole saliva from normal control No.3 _no treatment_replicate3

value: healthy


title: whole saliva from esophageal cancer patient No.4 _before treatment_rep4

description: microRNA expression of whole saliva from esophageal cancer patient No.4

source_name: whole saliva from esophageal cancer patient No.4 _before treatment_replicate4

value: esophageal cancer


title: whole saliva from esophageal cancer patient No.6 _before treatment_rep6

description: microRNA expression of whole saliva from esophageal cancer patient No.6

source_name: whole saliva from esophageal cancer patient No.6 _before treatment_replicate6


title: TC-71, sample 1

description:
cell line referred as TC-71
TC71_2005.CEL

value: no IGF-1R drugs resistant


title: estradiol + progesterone E2+PROG replicate 1

description: E2+PROG replicate 1

value: estradiol + progesterone


title: Lo PMX biological replicate 3

last: Hammons

address: 421 Curie Blvd

institute: University of Pennsylvania

hyb_protocol: Hybridization was for 16-18 hours overnight at 45°C. Washing and staining was done on an Affymetrix 450 series fluidics machine.

scan_protocol: Chips were scanned in an Affymetrix Gene Chip Scanner 3000.

data_processing: Cel files were imported into Partek Genomics Suite v6.5 where RMA was applied.

source_name: EA.hy 926 cells in Lo media treated with 0.5uM PMX for 48 hours

label_protocol: Affymetrix Terminal Labeling kit from Ambion

growth_protocol: EA.hy 926 cells were adapted to growth under low folate conditions in Medium 199, which contains 23nM of folic acid, supplemented with 10% FCS, non-essential amino acids, gentamycin, penicillin G, and fungizone to generate Lo cells. Parallel cultures of EA.hy 926 cells were grown under standard folate concentrations for that cell line in Medium 199 supplemented with 4mg/L (9uM) folic acid and supplemented as above to generate Hi cells.

extract_protocol: Total RNA was isolated using the RNeasy kit from Qiagen.

treatment_protocol: Cells were grown to confluence and media was changed. After 24 hours the cells were treated with 0.5uM PMX for 48 hours.

value: EA.hy 926

tag: folate

value: Lo (low)


title: Lo PMX biological replicate 2


title: vehicle VC replicate 3

description: VC replciate 3

value: vehicle


title: estradiol + progesterone E2+PROG replicate 3

description: E2+PROG replicate 3


title: 5a-dihydrotestosterone  DHT replicate 1

description: DHT replicate 1


title: estradiol + progesterone E2s+PROG replicate 1

description: E2s+PROG replicate 1


title: Hi PMX biological replicate 1

source_name: EA.hy 926 cells in Hi media treated with 0.5uM PMX for 48 hours

value: Hi (normal)


title: estradiol + progesterone E2+PROG replicate 4

description: E2+PROG replicate 4


title: YKI_Wing

description: Yki wing disc ChIP, replicates 1-3

source_name: Wing imaginal disc ChIP; yw strain; Yki antibody

value: wing imaginal disc

source_name: Wing imaginal disc ChIP; yw strain


title: medroxyprogesterone acetate MPA replicate 1

description: MPA replicate 1

value: medroxyprogesterone acetate


title: 5a-dihydrotestosterone  DHT replicate 2

description: DHT replicate 2


title: Lo PMX biological replicate 1


title: Lo Control biological replicate 1

source_name: EA.hy 926 cells in Lo media


title: Lo Control biological replicate 3


title: medroxyprogesterone acetate MPA replicate 2

description: MPA replicate 2


title: Lo Control biological replicate 2


title: Hi PMX biological replicate 2


title: estradiol +  E2 replicate 3

description: E2 replicate 3

value: estradiol +


title: estradiol + progesterone E2s+PROG replicate 4

description: E2s+PROG replicate 4


title: Hi PMX biological replicate 3


title: Hi Control biological replicate 3

source_name: EA.hy 926 cells in Hi media


title: estradiol + medroxyprogesterone acetate E2+MPA replicate 3

description: E2+MPA replicate 3


title: vehicle VC replicate 4

description: VC replicate 4


title: Hi Control biological replicate 1


title: OT-I Day 5 IL2 rep3

city: Miami

first: Thomas

middle: R

last: Malek

state: FL

address: 1600 NW 10th Avenue

department: Microbiology/Immunology

institute: University of Miami

description: FACS purified Treg subsets

hyb_protocol: Biotinylated cRNA was hybridized to Affymetrix Gene  ST1.0  arrays

scan_protocol: Image analysis was performed using the Affymetrix Command Console Software (AGCC).

data_processing: Resulting data were normalized with the RMA method using Affymetrix Power Tools package version 1.10.2. Multi-group comparisons of the transformed data of 3 independent biological replicates were performed using ANOVA applying the Benjamini Hochberg correction for false positives.

source_name: OT-I Day 5 IL2

label_protocol: 50 ng RNA was used in a single round of linear RNA probe amplification and labeling using NuGEN Ovation Pico WTA system, WT-Ovation Exon module and Encore Biotin Module (NuGEN, San Carlos, CA, USA)

extract_protocol: Total RNA was isolated using TRizol and further purified with RNAeasy Minikit (QIAGEN).

treatment_protocol: OT-I T cells were purified and 500,00 cells were adoptively transferred into congenic syngenic mice. 24 hours later mice were immunization with ovalbumin (10 μg) and LPS (10 μg). 24 hr later some mice received agonist IL-2/anti-IL2 (1.5 μg mouse IL-2/15 μg Jes-6.1). 3 and 5 days after immunization, the activated OT-I T cells were purifed by FACS and RNA was perpared for genome wide expression analysis using Affymetrix Mouse Gene ST1.0 arrays

value: OT-I TCR transgenic Rag1-/- C57BL/6

value: female

value: 8-10 weeks

tag: immunized with

value: ovalbumin and LPS

tag: treated with

value: IL-2 using an agonists IL-2/anti-IL-2 complexes (IL2/Jes-6.1)

tag: cell type

value: Splenic OT-I CD8+ T cells


title: 5a-dihydrotestosterone  DHT replicate 4

description: DHT replicate 4

source_name: ZR-75-1 cells

tag: cell line


title: Hi Control biological replicate 2


title: estradiol + 5a-dihydrotestosterone  E2+DHT replicate 1

description: E2+DHT replicate 1

value: estradiol + 5a-dihydrotestosterone


title: OT-I Day 3 IL2 rep1

description: FACS purified Treg subsets

source_name: OT-I Day 3 IL2

tag: strain


title: OT-I Day 5 rep2

description: FACS purified Treg subsets

source_name: OT-I Day 5

tag: gender


title: OT-I Day 5 IL2 rep1

description: FACS purified Treg subsets

tag: age


title: OT-I Day 5 IL2 rep2

description: FACS purified Treg subsets


title: estradiol + 5a-dihydrotestosterone  E2+DHT replicate 3

description: E2+DHT replicate 3


title: OT-I Day 3 IL2 rep3

description: FACS purified Treg subsets


title: OT-I Day 5 rep1

description: FACS purified Treg subsets


title: OT-I Day 3 IL2 rep2

description: FACS purified Treg subsets


title: estradiol + medroxyprogesterone acetate E2+MPA replicate 4

description: E2+MPA replicate 4

value: estradiol + medroxyprogesterone acetate


title: estradiol + progesterone E2+PROG replicate 2

description: E2+PROG replicate 2


title: OT-I Day 3 rep2

description: FACS purified Treg subsets

source_name: OT-I Day 3


title: progesterone PROG replicate 3

description: PROG replicate 3

value: progesterone


title: estradiol +  E2 replicate 2

description: E2 replicate 2


title: OT-I Day 3 rep1

description: FACS purified Treg subsets


title: OT-I Day 5 rep3

description: FACS purified Treg subsets


title: progesterone PROG replicate 2

description: PROG replicate 2


title: estradiol + 5a-dihydrotestosterone  E2+DHT replicate 2

description: E2+DHT replicate 2


title: vehicle VC replicate 1

description: VC replicate 1


title: medroxyprogesterone acetate MPA replicate 3

description: MPA replicate 3


title: OT-I Day 3 rep3

description: FACS purified Treg subsets


title: estradiol + progesterone E2s+PROG replicate 3

description: E2s+PROG replicate 3

value: estradiol + progesterone


title: estradiol + progesterone E2s+PROG replicate 2

description: E2s+PROG replicate 2


title: estradiol + medroxyprogesterone acetate E2+MPA replicate 1

description: E2+MPA replicate 1


title: G. hirsutum G.30

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

description:
gossypium  - harvest date: 28-04-07
In this study we characterized the fiber transcriptomes of the two species, Gossypium hirsutum and Gossypium barbadense that were parental genotypes of a RIL mapping population used previously for phenotypic QTL and expression QTL mapping., We used 454 deep pyrosequencing to characterize cDNAs from developing fibers at two key developmental time-points; 10 and 22 days post anthesis. A unigene set was assembled and annotated, and differential digital gene expression was assessed from the different time-point and genotype representations of the reads within assembled contigs. As a complementary approach, we conducted microarray-based hybridization profiling using the cotton Affymetrix gene chip and labeled cDNAs from fibers at 11 dpa and for the same two genotypes and compared differentially expressed genes identified by the two platforms. The 454 unigenes were also mined for the presence of microsatellite repeats and SNPs that will be useful markers for mapping and marker-assisted selection in cotton improvement.

hyb_protocol: labelled extract quantity: 10ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Gossypium hirsutum

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: seed - Grown in soil in temperature controlled glasshouse with natural lighting. 30oC day, 22oC night cycle

treatment_protocol: no treatment

tag: variety

value: Guazuncho 2

value: fiber

value: 11 dpa


title: G. barbadense V.2

organism: Gossypium barbadense

tag: tissue


title: G. hirsutum G.29


title: Subject 73 medium treated CD8 T cells at 72 hour rep1

city: St. Louis

first: Guangyong

last: Peng

state: MO

address: 1100 S Grand Blvd.

department: Internal Medicine

institute: Saint Louis University

data_processing: The data were normalised using quantile normalisation with Partek Genomics Suite

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

value: Naïve T cells

tag: subject

value: medium treated

tag: time

value: 72 hour


title: Subject 73 medium treated CD8 T cells at 48 hour rep1

value: 48 hour


title: KD2/3(A) cells, with Vav2 and Vav3 reexpressed using lentivirus, biological rep3, Exp 2

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

hyb_protocol: Mouse Gene 1.0 ST arrays (Affymetrix) under standard conditions

scan_protocol: Affymetrix system

data_processing: Upon microarray hybridization, the raw data was normalized, filtered and analyzed with the Bioconductor software (www.bioconductor.com) using the Affy and Siggenes applications.

source_name: breast cancer cell line

label_protocol: Total RNA was quantified using 6000 Nano Chips (Agilent Technologies, Santa Clara, CA) and used (2.3 μg/sample) to generated labeled cRNA probes according to the manufacturer’s instructions (Affymetrix).

growth_protocol: All cells were incubated at 37ºC with 5% CO2. 4T1 cells were cultured in Roswell Park Memorial Institute (RPMI) media supplemented with 10% fetal calf serum (FCS), penicillin (10 μg/ml), and streptomycin (100 μg/ml).

extract_protocol: Total cellular RNA was extracted from three independent exponential cultures of the appropriate cell lines using the RNAeasy kit (Qiagen)

treatment_protocol: Exponentially growing conditions

tag: transducer


title: estradiol + 5a-dihydrotestosterone  E2+DHT replicate 4

description: E2+DHT replicate 4


title: Subject 36 Treg treated CD8 T cells at 72 hour rep1

value: Treg treated


title: Clone A, 4T1 cells transduced with lentivirus encoding shRNAs to mouse Vav2 and Vav3 transcripts, biological rep5, Exp 2


title: Subject 36 medium treated CD8 T cells at 24 hour rep1

value: 24 hour


title: G. barbadense V.1


title: Subject 36 medium treated CD8 T cells at 4 hour rep1

value: 4 hour


title: KD2/3(A) cells, with Vav2 and Vav3 reexpressed using lentivirus, biological rep1, Exp 2


title: vehicle VC replicate 2

description: VC replicate 2

value: vehicle


title: Subject 73 medium treated CD8 T cells at 4 hour rep1


title: Subject 73 Treg treated CD8 T cells at 8 hour rep1

value: 8 hour


title: Subject 36 medium treated CD8 T cells at 48 hour rep1


title: Subject 36 Treg treated CD8 T cells at 48 hour rep1


title: Subject 36 medium treated CD8 T cells at 0 hour rep1

value: 0 hour


title: Subject 36 Treg treated CD8 T cells at 24 hour rep1


title: Clone A, 4T1 cells transduced with lentivirus encoding shRNAs to mouse Vav2 and Vav3 transcripts, biological rep6, Exp 2


title: KD2/3(A) cells, with Vav2 and Vav3 reexpressed using lentivirus, biological rep2, Exp 2


title: Subject 73 Treg treated CD8 T cells at 0 hour rep1


title: Subject 36 Treg treated CD8 T cells at 8 hour rep1


title: Subject 36 medium treated CD8 T cells at 8 hour rep1


title: Subject 36 Treg treated CD8 T cells at 0 hour rep1


title: Clone A, 4T1 cells transduced with lentivirus encoding shRNAs to mouse Vav2 and Vav3 transcripts, biological rep4, Exp 2


title: Clone A, 4T1 cells transduced with lentivirus encoding shRNAs to mouse Vav2 and Vav3 transcripts, biological rep2, Exp 1


title: estradiol +  E2 replicate 1

description: E2 replicate 1

value: estradiol +


title: Subject 73 Treg treated CD8 T cells at 24 hour rep1


title: Clone B, 4T1 cells transduced with lentivirus encoding shRNAs to mouse Vav2 and Vav3 transcripts, biological rep1, Exp 1


title: Subject 36 medium treated CD8 T cells at 72 hour rep1

source_name: Subject 36 nedium treated CD8 T cells at 72 hour


title: Clone A, 4T1 cells transduced with lentivirus encoding shRNAs to mouse Vav2 and Vav3 transcripts, biological rep3, Exp 1


title: Subject 73 medium treated CD8 T cells at 24 hour rep1


title: Subject 36 Treg treated CD8 T cells at 4 hour rep1


title: Clone B, 4T1 cells transduced with lentivirus encoding shRNAs to mouse Vav2 and Vav3 transcripts, biological rep3, Exp 1


title: TG kidney, rep1

status: Public on Oct 02 2012

city: Cardiff

first: David

middle: Allan

last: Carter

state: Cardiff

address: Museum Avenue

department: School of Biosciences

institute: Cardiff University

description: Ex-vivo kidney

hyb_protocol: Following fragmentation, 20 µg of cRNA was hybridized for 18h at 45C on an Affymetrix rat RG_U34A GeneChip array. GeneChips were then washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.

data_processing: Data were analysed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default settings and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Rattus norvegicus

source_name: TG kidney

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1oµg total RNA.

growth_protocol: Pups were kept on a 14:10 light:dark cycle, lights on 05.00h and sampled at 12.00h.

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

treatment_protocol: Kidneys were stored at -80C prior to RNA extraction

tag: strain background

value: Sprague-Dawley

tag: genotype/variation

value: pEgr-1/d4EGFP transgenic rats (Slade,J.P. et al, 2002)

value: 6 days postnatal

value: kidney

tag: sampling time

value: mid-day


title: 4T1 cells harboring the empty pLKO.1puro lentiviral vector, biological rep1, Exp 1

tag: vector

value: empty pLKO.1puro lentiviral vector


title: Subject 73 Treg treated CD8 T cells at 48 hour rep1

value: Naïve T cells

tag: treatment


title: Subject 73 Treg treated CD8 T cells at 4 hour rep1


title: Clone A, 4T1 cells transduced with lentivirus encoding shRNAs to mouse Vav2 and Vav3 transcripts, biological rep1, Exp 1


title: Subject 73 Treg treated CD8 T cells at 72 hour rep1


title: TG kidney, rep2

description: Ex-vivo kidney


title: Subject 73 medium treated CD8 T cells at 0 hour rep1

value: medium treated


title: WT kidney, rep2

description: Ex-vivo kidney

source_name: WT kidney

value: wild type


title: 4T1 cells harboring the empty pLKO.1puro lentiviral vector, biological rep2, Exp 1


title: Clone B, 4T1 cells transduced with lentivirus encoding shRNAs to mouse Vav2 and Vav3 transcripts, biological rep2, Exp 1


title: Subject 73 medium treated CD8 T cells at 8 hour rep1