title: Patient 5-mild

city: Bronx

first: Johanna

middle: Patricia

last: Daily

state: NY

address: 1301 Morris Park Avenue, Price Center

department: Medicine (Infectious Disease)

institute: Albert Einstein College of Medicine

hyb_protocol: Following fragmentation, 5.5 ug of sscDNA were hybridized for 17 hrs at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G7

data_processing: CEL files were analyzed using softward GenePattern; Robust Multi-array Average (RMA) procedure was used, and the data was quantile normalized with 28,132 gene-level probe sets. This gene list was thresholded to a minimum of 20 expression units (EU) and a maximum of 20000 EU. A filtered gene list of 3110 genes (linked as supplementary file on Series record) was generated by removing genes that varied less than 3 fold or 100 EU across the data set. Differentially abundant transcripts between the severe and mild clinical states for each paired sample were identified using a paired Student t-test of log2 transformed data.

source_name: Patient 5-mild

label_protocol: Biotinylated sscDNA were prepared according to the standard Ambion and Affymetrix protocols from 5.5 ug total sscDNA (The Ambion WT Expression Kit For Affymetrix GeneChip Whole Transcript (WT) Expression Manuals, 2009, Ambion and Affymetrix).

growth_protocol: 3mL of blood obtained from venipuncture was added to Tri_reagent BD (Molecular Researc Center).  The samples were immediately frozen at minus 80, and shipped in liquid nitrogen.

extract_protocol: The RNA sample was thawed at room temperature and extracted following manufacturers protocol. RIN were evaluated prior to sample hybridization and analysis.

treatment_protocol: The children were enrolled in a longitudinal study of severe malaria in Blantyre Malawi.  Human subjects approval was obtained prior to protocol initiation; consent was obtained for all samples.

tag: patient

value: Patient 5

value: blood

tag: age

value: 8 months

tag: malaria status

value: mild


title: Patient 4-mild

status: Public on Jan 11 2012

type: RNA

country: USA

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Patient 4-mild

value: Patient 4

tag: tissue

value: 23 months


title: G2AF

city: St Louis

first: Michael

middle: Sean

last: Behnke

state: MO

address: 660 S. Euclid Ave

department: Molecular Microbiology

institute: Washington University School of Medicine

hyb_protocol: Standard Affymetrix protocol with 5ug labeled cRNA.

scan_protocol: Standard Affymetrix protocol

data_processing: GeneSpring 7.2 RMA, Data transformation: Set measurements less than 0.01 to 0.01, Per Chip and Per Gene: Median Polishing

organism: Toxoplasma gondii

label_protocol: Affymetrix One Cycle: 3μg starting RNA - Standard One Cycle protocol

growth_protocol: Grown in human foreskin fibroblasts

extract_protocol: Parasites were purified from host cells and RNA was extracted using the Qiagen RNeasy kit (b-mercaptoethanol and DNase I treatment).

treatment_protocol: No treatment, standard growth for tachyzoite samples.   For bradyzoite samples, treatment with .3μM Cmpd1 for 48hrs.

tag: develpomental stage

value: tachyzoite

tag: treatment


title: FFA0005_BCM Mixed Dyslipidemia

type: genomic

city: houston

first: Ariel

last: Brautbar

address: 1 baylor plaza

institute: Baylor College of Medicine

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using GenomeStudio v2011.1 with Genotyping module 1.9.4 (Illumina).

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: Mixed dyslipidemia_fenofibric acid

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from peripheral blood

tag: disease state

value: Mixed dyslipidemia

value: peripheral blood

tag: percent change in apoc3 levels

tag: treatment group

value: fenofibric acid


title: A9SF


title: FFA0003_BCM Mixed Dyslipidemia


title: GT1-Fudr_c


title: Patient 5-severe

source_name: Patient 5-severe

value: severe


title: FFA0004_BCM Mixed Dyslipidemia


title: Patient 4-severe

source_name: Patient 4-severe


title: CTGara_c


title: GT1-Fudr_a


title: FFA0001_BCM Mixed Dyslipidemia


title: GT1-Fudr_b


title: CTGara_a


title: Patient 1-mild

source_name: Patient 1-mild

value: Patient 1


title: Patient 3-severe

source_name: Patient 3-severe

value: Patient 3

value: 42 months


title: Patient 2-mild

source_name: Patient 2-mild

value: Patient 2

value: 45 months


title: Patient 3-mild

source_name: Patient 3-mild


title: FFA0002_BCM Mixed Dyslipidemia


title: Patient 1-severe

source_name: Patient 1-severe


title: CTGara_b


title: 017286_Okusankichi

status: Public on Jan 10 2012

city: Tsukuba

first: Chikako

last: Nishitani

state: Ibaraki

country: Japan

institute: National Institutes of Fruit Tree Science

hyb_protocol: The labeled samples were hybridized to the oligoarray slides using Gene Expression Hybridization Kit (Agilent, Palo Alto, CA) as a hybridization buffer at 65°C for 17 h in a hybridization chamber. After hybridization, arrays were washed with Gene Expression Wash Buffer (Agilent, Palo Alto, CA) according to the manufacturer’s instructions.

scan_protocol: The dried slides were scanned by Agilent scanner. Raw data from scanning of the array was captured using Agilent Feature Extraction Ver. 9.5.3.1 or 10.7.1.1(with Linear & Lowess normalization).

data_processing: Normalization was performed by GeneSpring Ver. 7.3.1 (Agilent, Palo Alto, CA). Expression for each gene was calculated as the mean value of two to three biological replicates for all time points and the standard error of the mean. Per-chip and per-gene normalization was performed.

organism: Pyrus pyrifolia

source_name: 2009_Okusankichi flower 1 day before bloom

label_protocol: Reverse transcription of mRNA in the total RNA samples and composition of labeled cDNA was performed using Low RNA Input Linear Amplification Kit PLUS, One-Color (Agilent, Palo Alto, CA) according to the manufacturer’s instructions.

growth_protocol: Japanese pear trees (Pyrus pyrifolia Nakai cv. ‘Housui’) were managed according to standard orchard practices.

extract_protocol: Total RNAs were extracted from each sample using the method described in Wan et al. (1994). Isolated RNA was purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany) and the quality and purity were checked using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). RNA was ethanol precipitated and resuspended to 500 ng/μl.

treatment_protocol: Not treated.

tag: cultivar

value: Okusankichi

tag: day

tag: parthenocarpy

value: low


title: 017286_Taiheiyou

organism: Pyrus communis x Pyrus pyrifolia

source_name: 2009_Taiheiyo flower 1 day before bloom

value: La France x Okusankichi hybrid

value: high


title: 017286_Housui

source_name: 2009_Housui flower 1 day before bloom

value: Housui


title: Patient 2-severe

source_name: Patient 2-severe

value: blood


title: 017286_LaFrance

organism: Pyrus communis

source_name: 2009_LaFrance flower 1 day before bloom

value: La France


title: 017286_282-12

source_name: 2009_282-12 flower 1 day before bloom

value: La France x Housui hybrid


title: 017286_LeConte

organism: Pyrus hybrid cultivar

source_name: 2009_LeConte flower 1 day before bloom

value: Bartlett hybrid (Bartlett is one parent)


title: Intestine Wild type 8 hr calf 4

city: College Station

first: Leslie

middle: Garry

last: Adams

state: TX

address: 402 Raymond Stotzer Blvd.

department: Veterinary Pathobiology

institute: Texas A&M University

hyb_protocol: 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.  The arrays were then washed four times in RNase-, DNase-free, distilled water, immersed 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), washed for 10 min at 42ºC with low stringency buffer [1 X SSC, 0.2% SDS] and then washed twice for 5-min each wash in a higher stringency buffer [0.1 X SSC, 0.2% SDS and 0.1 X SSC] at room temperature with 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: The spots representing genes on the arrays were adjusted for background and normalized to internal controls using image analysis software (GenePixPro 4.0; Axon Instruments Inc.). Spots with fluorescent signal values below background were disregarded in all analyses. Samples were normalized against the bovine reference RNA signals across slides and within each slide.  Genes were considered as significantly altered if the average fold-change was at least 1.5, the adjusted p-value was less than 0.05, the alteration was reproducible across replicates, and the magnitude of difference between conditions was greater than 50% of the fold-change obtained for any two replicate controls.

organism: Bos taurus

source_name: Intestine, inoculated with Wild type (IR715), collected at 8 hr, calf 4

label_protocol: Briefly, cDNA from bovine experimental samples (i.e. from infected and control loops)  and cDNA generated from the bovine reference RNA sample were co-hybridized to the previously described custom 13K bovine 70-mer oligoarray. The cDNA was reverse-transcribed using Superscript III reverse transcriptase (Invitrogen, Carlsbad, CA) and labeled with amino-allyl-UTP (Ambion, Austin, TX).  Cy3 and Cy5 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: Derivatives of Salmonella enterica serotype Typhimurium strain ATCC 14028, IR715 and ZA21, were used in this study.  IR715 is a spontaneous naldixic acid resistant derivative and ZA21 is a previously described delta sipA sopABDE2 mutant.  Cultures were grown in Luria-Bertani (LB) broth [supplemented with appropriate antibiotics: naldixic acid (50 mg/l), kanamycin (100 mg/l), chloramphenicol (30 mg/l), and tetracycline (20 mg/l)]. To prepare the bacterial inoculum, wild type and mutant were cultured in LB broth for 18 hours at 37°C with shaking at 150 rpm in a shaking incubator (Model C24, New Brunswick Scientific, Edison, NJ).  The resultant cultures were diluted 1:100 in sterile LB broth and incubated as before for an additional 4 hours. Bacteria in the exponential phase of growth were then harvested by centrifugation for 15 min at 1,500 Xg and resuspended in fresh LB broth to obtain a final concentration of approximately 0.75 x 10e9 colony-forming units/ml (CFU)/ml. The bacterial concentration of the inoculum was confirmed by spreading serial 10-fold dilutions on agar plates containing the appropriate antibiotics.

extract_protocol: Total RNA was extracted after dissection of the ileal loops obtained at 15 min and 30 min and at 1, 2, 4, 8, and 12 hours post-infection.  A 6 mm biopsy punch was used to collect 8 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).  The RNA analyzed in all samples was of good to excellent quality (results not shown).  The average RNA intensity number (RIN) was 7.42 and the median was 7.7.  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.To generate the reference RNA (which was labeled with Cy3), 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: The bovine ligated ileal loop surgical procedure has been described. Briefly, the calves were fasted for 12 hours prior to the surgery.  Anesthesia was induced with propofol (Abbot Laboratories, Chicago, IL) followed by placement of an endotracheal tube and maintainance with isofluorane (Isoflo, Abbot Laboratories) for the duration of the experiment. A laparotomy was performed, the distal ileum was exposed, and 21 loops approximately 6 to 9 cm in length were ligated with umbilical tape, leaving 1 cm loops between them. Overnight bacterial cultures were grown as described above.  The ileal loops were inoculated by intralumenal injection of 3 ml of a suspension of S. Typhimurium strain IR715 or delta sipA sopABDE2 mutant (ZA21) in LB broth containing approximately 0.75 X 10e9 CFU/ml. Loops injected with sterile LB broth (3 ml) served as negative controls. The loops were replaced into the abdominal cavity until collected by excision.  At each of seven time points (15 min, 30 min, 1, 2, 4, 8, and 12 hours) three loops (one LB inoculated control loop, one wild type inoculated loop and one mutant inoculated loop) were excised.

tag: gender

value: male

value: 3 to 6 weeks

tag: genetic background

value: outbred

value: 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 line

value: Madin-Darby bovine kidney (MDBK)

value: bovine B lymphocyte (BL-3) c

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: Intestine Wild type 2 hr calf 4

source_name: Intestine, inoculated with Wild type (IR715), collected at 2 hr, calf 4

value: fresh bovine brain cortex and cerebellum


title: Intestine Neg Ctr 12 hr calf 4

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 12 hr, calf 4


title: Intestine Mutant 2 hr calf 4

source_name: Intestine, inoculated with Mutant (ZA21), collected at 2 hr, calf 4


title: Intestine Neg Ctr 2 hr calf 4

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 2 hr, calf 4


title: Intestine Mutant 12 hr calf 4

source_name: Intestine, inoculated with Mutant (ZA21), collected at 12 hr, calf 4


title: Intestine Mutant 8 hr calf 4

source_name: Intestine, inoculated with Mutant (ZA21), collected at 8 hr, calf 4


title: Intestine Wild type 12 hr calf 4

source_name: Intestine, inoculated with Wild type (IR715), collected at 12 hr, calf 4


title: Intestine Neg Ctr 8 hr calf 4

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 8 hr, calf 4


title: Intestine Wild type 4hr calf 4

source_name: Intestine, inoculated with Wild type (IR715), collected at 4hr, calf 4


title: Intestine Neg Ctr 4hr calf 4

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 4hr, calf 4


title: Intestine Mutant 1 hr calf 4

source_name: Intestine, inoculated with Mutant (ZA21), collected at 1 hr, calf 4


title: Intestine Wild type 1 hr calf 4

source_name: Intestine, inoculated with Wild type (IR715), collected at 1 hr, calf 4


title: Intestine Mutant 15 min calf 4

source_name: Intestine, inoculated with Mutant (ZA21), collected at 15 min, calf 4


title: Intestine Wild type 15 min calf 4

source_name: Intestine, inoculated with Wild type (IR715), collected at 15 min, calf 4


title: Intestine Wild type 30 min calf 4

source_name: Intestine, inoculated with Wild type (IR715), collected at 30 min, calf 4


title: Intestine Neg Ctr 15 min calf 4

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 15 min, calf 4


title: Intestine Neg Ctr 30 min calf 4

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 30 min, calf 4

source_name: reference RNA


title: Intestine Mutant 30 min calf 4

source_name: Intestine, inoculated with Mutant (ZA21), collected at 30 min, calf 4


title: Intestine Mutant 12 hr calf 3

source_name: Intestine, inoculated with Mutant (ZA21), collected at 12 hr, calf 3


title: Intestine Mutant 4hr calf 4

source_name: Intestine, inoculated with Mutant (ZA21), collected at 4hr, calf 4


title: Intestine Neg Ctr 1 hr calf 4

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 1 hr, calf 4


title: Intestine Neg Ctr 8 hr calf 3

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 8 hr, calf 3


title: FFA0019_BCM Mixed Dyslipidemia

source_name: Mixed dyslipidemia_fenofibric acid

value: Mixed dyslipidemia

value: peripheral blood

value: fenofibric acid


title: Intestine Neg Ctr 12 hr calf 3

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 12 hr, calf 3


title: Intestine Mutant 4hr calf 3

source_name: Intestine, inoculated with Mutant (ZA21), collected at 4hr, calf 3


title: Intestine Wild type 8 hr calf 3

source_name: Intestine, inoculated with Wild type (IR715), collected at 8 hr, calf 3


title: Intestine Mutant 2 hr calf 3

source_name: Intestine, inoculated with Mutant (ZA21), collected at 2 hr, calf 3


title: Intestine Wild type 1 hr calf 3

source_name: Intestine, inoculated with Wild type (IR715), collected at 1 hr, calf 3


title: Intestine Mutant 1 hr calf 3

source_name: Intestine, inoculated with Mutant (ZA21), collected at 1 hr, calf 3


title: Intestine Mutant 12 hr calf 2

source_name: Intestine, inoculated with Mutant (ZA21), collected at 12 hr, calf 2


title: Intestine Wild type 2 hr calf 3

source_name: Intestine, inoculated with Wild type (IR715), collected at 2 hr, calf 3


title: Intestine Neg Ctr 2 hr calf 3

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 2 hr, calf 3


title: Intestine Neg Ctr 15 min calf 3

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 15 min, calf 3


title: Intestine Wild type 15 min calf 3

source_name: Intestine, inoculated with Wild type (IR715), collected at 15 min, calf 3

source_name: reference RNA


title: Intestine Neg Ctr 4hr calf 3

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 4hr, calf 3


title: Intestine Wild type 12 hr calf 3

source_name: Intestine, inoculated with Wild type (IR715), collected at 12 hr, calf 3


title: Intestine Neg Ctr 1 hr calf 3

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 1 hr, calf 3


title: Intestine Mutant 15 min calf 3

source_name: Intestine, inoculated with Mutant (ZA21), collected at 15 min, calf 3


title: Intestine Mutant 30 min calf 3

source_name: Intestine, inoculated with Mutant (ZA21), collected at 30 min, calf 3


title: Intestine Neg Ctr 12 hr calf 2

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 12 hr, calf 2


title: Intestine Wild type 12 hr calf 2

source_name: Intestine, inoculated with Wild type (IR715), collected at 12 hr, calf 2


title: Intestine Neg Ctr 30 min calf 3

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 30 min, calf 3


title: Intestine Mutant 4hr calf 2

source_name: Intestine, inoculated with Mutant (ZA21), collected at 4hr, calf 2


title: Intestine Neg Ctr 4hr calf 2

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 4hr, calf 2


title: Intestine Wild type 4hr calf 3

source_name: Intestine, inoculated with Wild type (IR715), collected at 4hr, calf 3


title: Intestine Wild type 4hr calf 2

source_name: Intestine, inoculated with Wild type (IR715), collected at 4hr, calf 2


title: Intestine Wild type 30 min calf 3

source_name: Intestine, inoculated with Wild type (IR715), collected at 30 min, calf 3


title: Intestine Mutant 8 hr calf 2

source_name: Intestine, inoculated with Mutant (ZA21), collected at 8 hr, calf 2


title: Intestine Mutant 2 hr calf 2

source_name: Intestine, inoculated with Mutant (ZA21), collected at 2 hr, calf 2


title: Intestine Neg Ctr 8 hr calf 2

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 8 hr, calf 2


title: Intestine Neg Ctr 2 hr calf 2

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 2 hr, calf 2

source_name: reference RNA


title: Intestine Wild type 2 hr calf 2

source_name: Intestine, inoculated with Wild type (IR715), collected at 2 hr, calf 2


title: Intestine Wild type 8 hr calf 2

source_name: Intestine, inoculated with Wild type (IR715), collected at 8 hr, calf 2


title: Intestine Wild type 1 hr calf 2

source_name: Intestine, inoculated with Wild type (IR715), collected at 1 hr, calf 2


title: Intestine Mutant 30 min calf 2

source_name: Intestine, inoculated with Mutant (ZA21), collected at 30 min, calf 2


title: Intestine Mutant 1 hr calf 2

source_name: Intestine, inoculated with Mutant (ZA21), collected at 1 hr, calf 2


title: Intestine Mutant 15 min calf 2

source_name: Intestine, inoculated with Mutant (ZA21), collected at 15 min, calf 2


title: Intestine Mutant 12 hr calf 1

source_name: Intestine, inoculated with Mutant (ZA21), collected at 12 hr, calf 1


title: Intestine Wild type 15 min calf 2

source_name: Intestine, inoculated with Wild type (IR715), collected at 15 min, calf 2


title: Intestine Neg Ctr 30 min calf 2

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 30 min, calf 2


title: Intestine Wild type 30 min calf 2

source_name: Intestine, inoculated with Wild type (IR715), collected at 30 min, calf 2


title: Intestine Neg Ctr 4hr calf 1

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 4hr, calf 1


title: Intestine Mutant 2 hr calf 1

source_name: Intestine, inoculated with Mutant (ZA21), collected at 2 hr, calf 1


title: Intestine Neg Ctr 8 hr calf 1

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 8 hr, calf 1


title: Intestine Wild type 8 hr calf 1

source_name: Intestine, inoculated with Wild type (IR715), collected at 8 hr, calf 1


title: Intestine Mutant 8 hr calf 1

source_name: Intestine, inoculated with Mutant (ZA21), collected at 8 hr, calf 1


title: Intestine Neg Ctr 1 hr calf 2

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 1 hr, calf 2


title: Intestine Neg Ctr 12 hr calf 1

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 12 hr, calf 1

source_name: reference RNA


title: Intestine Mutant 4hr calf 1

source_name: Intestine, inoculated with Mutant (ZA21), collected at 4hr, calf 1


title: Intestine Neg Ctr 2 hr calf 1

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 2 hr, calf 1


title: Intestine Wild type 2 hr calf 1

source_name: Intestine, inoculated with Wild type (IR715), collected at 2 hr, calf 1


title: Intestine Mutant 15 min calf 1

source_name: Intestine, inoculated with Mutant (ZA21), collected at 15 min, calf 1


title: Intestine Wild type 30 min calf 1

source_name: Intestine, inoculated with Wild type (IR715), collected at 30 min, calf 1


title: Intestine Neg Ctr 15 min calf 2

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 15 min, calf 2


title: Intestine Mutant 1 hr calf 1

source_name: Intestine, inoculated with Mutant (ZA21), collected at 1 hr, calf 1


title: Intestine Wild type 15 min calf 1

source_name: Intestine, inoculated with Wild type (IR715), collected at 15 min, calf 1


title: Intestine Mutant 30 min calf 1

source_name: Intestine, inoculated with Mutant (ZA21), collected at 30 min, calf 1


title: Intestine Wild type 12 hr calf 1

source_name: Intestine, inoculated with Wild type (IR715), collected at 12 hr, calf 1


title: Intestine Neg Ctr 1 hr calf 1

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 1 hr, calf 1


title: Intestine Wild type 1 hr calf 1

source_name: Intestine, inoculated with Wild type (IR715), collected at 1 hr, calf 1


title: Intestine Neg Ctr 15 min calf 1

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 15 min, calf 1


title: Intestine Neg Ctr 30 min calf 1

source_name: Intestine, inoculated with Neg Ctr (LB), collected at 30 min, calf 1


title: Obese female child with FTO allele AA Ob_girl_65

city: Uppsala

first: Markus

last: Sällman Almén

address: Box 593

department: Dept. of Neuroscience

country: Sweden

institute: Uppsala Universitet

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina's iScan reader using standard recommended Illumina scanner settings

data_processing: Genomestudio2009.2 toghether with the methylumi and limma packages from Bioconductor. Probes with detection P-value>0.01 was removed from further analysis together with probes from the sex chromosomes.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from pheripheral whole blood using QiaGen Maxiprep kit

value: Female

value: whole blood

tag: weight

value: Obese

tag: fto-genotype

value: AA

tag: developmental stage

value: pre-adolescent


title: Obese female child with FTO allele TT Ob_girl_71

tag: tissue

value: TT


title: Obese female child with FTO allele AA Ob_girl_53


title: Obese female child with FTO allele TT Ob_girl_63


title: Obese female child with FTO allele TT Ob_girl_72


title: Obese female child with FTO allele TT Ob_girl_60


title: Intestine Wild type 4hr calf 1

source_name: Intestine, inoculated with Wild type (IR715), collected at 4hr, calf 1

tag: age


title: Obese female child with FTO allele TT Ob_girl_30


title: Obese female child with FTO allele AA Ob_girl_43


title: Obese female child with FTO allele AA Ob_girl_23


title: Obese female child with FTO allele AA Ob_girl_56


title: Obese female child with FTO allele TT Ob_girl_3


title: Obese female child with FTO allele TT Ob_girl_15


title: Obese female child with FTO allele AA Ob_girl_46


title: Obese female child with FTO allele TT Ob_girl_31


title: Obese female child with FTO allele AA Ob_girl_1


title: Obese female child with FTO allele TT Ob_girl_24


title: Obese female child with FTO allele AA Ob_girl_45


title: normal-weight female child with FTO allele AA N_girl_9

value: normal-weight


title: Obese female child with FTO allele TT Ob_girl_49


title: SJETV096

city: Memphis

first: Charles

middle: G

last: Mullighan

state: TN

address: 262 Danny Thomas Place, MS 342

department: Pathology

institute: St. Jude Children's Research Hospital

description: ETV6-RUNX1 B-precursor ALL

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

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

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 500.

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix One-Cycle protocol from 1 ug of total RNA

growth_protocol: No growth protocol. Cells were obtained from bone marrow or blood from children with acute lymphoblastic leukemia

extract_protocol: Trizol

tag: cell type

value: tumor cells obtained at diagnosis

tag: subtype


title: Obese female child with FTO allele TT Ob_girl_36


title: SJETV095

description: ETV6-RUNX1 B-precursor ALL


title: Obese female child with FTO allele AA Ob_girl_25


title: Obese female child with FTO allele TT Ob_girl_11


title: Obese female child with FTO allele AA Ob_girl_50


title: normal-weight female child with FTO allele AA N_girl_70


title: SJPHALL029

description: BCR-ABL1 B-precursor ALL


title: Obese female child with FTO allele AA Ob_girl_59


title: Intestine Mutant 8 hr calf 3

source_name: Intestine, inoculated with Mutant (ZA21), collected at 8 hr, calf 3

value: male

value: 3 to 6 weeks

source_name: reference RNA


title: normal-weight female child with FTO allele TT N_girl_7


title: normal-weight female child with FTO allele TT N_girl_58


title: normal-weight female child with FTO allele AA N_girl_57


title: normal-weight female child with FTO allele TT N_girl_42


title: normal-weight female child with FTO allele AA N_girl_26


title: normal-weight female child with FTO allele TT N_girl_44


title: normal-weight female child with FTO allele AA N_girl_38


title: normal-weight female child with FTO allele TT N_girl_40


title: normal-weight female child with FTO allele TT N_girl_6


title: normal-weight female child with FTO allele TT N_girl_17


title: normal-weight female child with FTO allele TT N_girl_19


title: normal-weight female child with FTO allele AA N_girl_62


title: normal-weight female child with FTO allele TT N_girl_47


title: normal-weight female child with FTO allele AA N_girl_8


title: normal-weight female child with FTO allele AA N_girl_4


title: normal-weight female child with FTO allele TT N_girl_54


title: SJETV071

description: ETV6-RUNX1 B-precursor ALL


title: normal-weight female child with FTO allele TT N_girl_29


title: normal-weight female child with FTO allele AA N_girl_16


title: genomic DNA from Normal PBL 204

city: Cincinnati

first: Scott

middle: M

last: Langevin

state: OH

address: 160 Panzeca Way, ML0056

department: Department of Environmental Health

institute: University of Cincinnati College of Medicine

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

source_name: genomic DNA from Normal PBL 204

extract_protocol: genomic DNA was extracted DNeasy blood and tissue kit according to standard instructions

value: Peripheral Blood


title: SJETV067

description: ETV6-RUNX1 B-precursor ALL


title: genomic DNA from Normal PBL 203

source_name: genomic DNA from Normal PBL 203


title: normal-weight female child with FTO allele TT N_girl_12


title: genomic DNA from Normal PBL 199

source_name: genomic DNA from Normal PBL 199


title: genomic DNA from Normal PBL 205

source_name: genomic DNA from Normal PBL 205


title: genomic DNA from Normal PBL 202

source_name: genomic DNA from Normal PBL 202


title: genomic DNA from Normal PBL 201

source_name: genomic DNA from Normal PBL 201


title: normal-weight female child with FTO allele AA N_girl_14


title: genomic DNA from Normal PBL 198

source_name: genomic DNA from Normal PBL 198


title: normal-weight female child with FTO allele AA N_girl_13


title: genomic DNA from Normal PBL 197

source_name: genomic DNA from Normal PBL 197


title: SJETV102

description: ETV6-RUNX1 B-precursor ALL


title: normal-weight female child with FTO allele AA N_girl_20


title: genomic DNA from Normal PBL 196

source_name: genomic DNA from Normal PBL 196


title: SJETV065

description: ETV6-RUNX1 B-precursor ALL


title: genomic DNA from Normal PBL 192

source_name: genomic DNA from Normal PBL 192


title: genomic DNA from Normal PBL 190

source_name: genomic DNA from Normal PBL 190


title: genomic DNA from Normal PBL 194

source_name: genomic DNA from Normal PBL 194


title: genomic DNA from Normal PBL 189

source_name: genomic DNA from Normal PBL 189


title: genomic DNA from Normal PBL 191

source_name: genomic DNA from Normal PBL 191


title: genomic DNA from Normal PBL 187

source_name: genomic DNA from Normal PBL 187


title: genomic DNA from Normal PBL 186

source_name: genomic DNA from Normal PBL 186


title: genomic DNA from Normal PBL 195

source_name: genomic DNA from Normal PBL 195


title: genomic DNA from Normal PBL 193

source_name: genomic DNA from Normal PBL 193


title: genomic DNA from Normal PBL 188

source_name: genomic DNA from Normal PBL 188


title: genomic DNA from Normal PBL 183

source_name: genomic DNA from Normal PBL 183


title: genomic DNA from Normal PBL 185

source_name: genomic DNA from Normal PBL 185


title: genomic DNA from Normal PBL 178

source_name: genomic DNA from Normal PBL 178


title: genomic DNA from Normal PBL 176

source_name: genomic DNA from Normal PBL 176


title: genomic DNA from Normal PBL 171

source_name: genomic DNA from Normal PBL 171


title: genomic DNA from Normal PBL 184

source_name: genomic DNA from Normal PBL 184


title: genomic DNA from Normal PBL 166

source_name: genomic DNA from Normal PBL 166


title: genomic DNA from Normal PBL 181

source_name: genomic DNA from Normal PBL 181


title: genomic DNA from Normal PBL 173

source_name: genomic DNA from Normal PBL 173


title: genomic DNA from Normal PBL 179

source_name: genomic DNA from Normal PBL 179


title: genomic DNA from Normal PBL 168

source_name: genomic DNA from Normal PBL 168


title: genomic DNA from Normal PBL 180

source_name: genomic DNA from Normal PBL 180


title: genomic DNA from Normal PBL 174

source_name: genomic DNA from Normal PBL 174


title: genomic DNA from Normal PBL 163

source_name: genomic DNA from Normal PBL 163


title: genomic DNA from Normal PBL 182

source_name: genomic DNA from Normal PBL 182


title: genomic DNA from Normal PBL 164

source_name: genomic DNA from Normal PBL 164


title: genomic DNA from Normal PBL 169

source_name: genomic DNA from Normal PBL 169


title: SJTALL027

description: T-lineage ALL

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis


title: genomic DNA from Normal PBL 172

source_name: genomic DNA from Normal PBL 172


title: genomic DNA from Normal PBL 177

source_name: genomic DNA from Normal PBL 177


title: genomic DNA from Normal PBL 167

source_name: genomic DNA from Normal PBL 167


title: genomic DNA from Normal PBL 175

source_name: genomic DNA from Normal PBL 175


title: genomic DNA from Normal PBL 170

source_name: genomic DNA from Normal PBL 170


title: genomic DNA from Normal PBL 165

source_name: genomic DNA from Normal PBL 165


title: genomic DNA from Normal PBL 159

source_name: genomic DNA from Normal PBL 159


title: genomic DNA from Normal PBL 160

source_name: genomic DNA from Normal PBL 160


title: genomic DNA from Normal PBL 162

source_name: genomic DNA from Normal PBL 162


title: genomic DNA from Normal PBL 158

source_name: genomic DNA from Normal PBL 158


title: genomic DNA from Normal PBL 154

source_name: genomic DNA from Normal PBL 154


title: genomic DNA from Normal PBL 153

source_name: genomic DNA from Normal PBL 153


title: genomic DNA from Normal PBL 139

source_name: genomic DNA from Normal PBL 139


title: genomic DNA from Normal PBL 149

source_name: genomic DNA from Normal PBL 149


title: genomic DNA from Normal PBL 143

source_name: genomic DNA from Normal PBL 143


title: genomic DNA from Normal PBL 155

source_name: genomic DNA from Normal PBL 155


title: genomic DNA from Normal PBL 144

source_name: genomic DNA from Normal PBL 144


title: genomic DNA from Normal PBL 150

source_name: genomic DNA from Normal PBL 150


title: genomic DNA from Normal PBL 148

source_name: genomic DNA from Normal PBL 148


title: genomic DNA from Normal PBL 145

source_name: genomic DNA from Normal PBL 145


title: SJTALL217

description: T-lineage ALL

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis


title: genomic DNA from Normal PBL 161

source_name: genomic DNA from Normal PBL 161


title: genomic DNA from Normal PBL 134

source_name: genomic DNA from Normal PBL 134


title: genomic DNA from Normal PBL 200

source_name: genomic DNA from Normal PBL 200


title: genomic DNA from Normal PBL 147

source_name: genomic DNA from Normal PBL 147


title: genomic DNA from Normal PBL 140

source_name: genomic DNA from Normal PBL 140


title: genomic DNA from Normal PBL 157

source_name: genomic DNA from Normal PBL 157


title: genomic DNA from Normal PBL 136

source_name: genomic DNA from Normal PBL 136


title: genomic DNA from Normal PBL 156

source_name: genomic DNA from Normal PBL 156


title: genomic DNA from Normal PBL 141

source_name: genomic DNA from Normal PBL 141


title: genomic DNA from Normal PBL 151

source_name: genomic DNA from Normal PBL 151


title: SJTALL220

description: T-lineage ALL


title: genomic DNA from Normal PBL 152

source_name: genomic DNA from Normal PBL 152


title: genomic DNA from Normal PBL 135

source_name: genomic DNA from Normal PBL 135


title: genomic DNA from Normal PBL 146

source_name: genomic DNA from Normal PBL 146


title: genomic DNA from Normal PBL 142

source_name: genomic DNA from Normal PBL 142


title: genomic DNA from Normal PBL 137

source_name: genomic DNA from Normal PBL 137


title: genomic DNA from Normal PBL 133

source_name: genomic DNA from Normal PBL 133


title: SJBALL051

description: B-precursor ALL with miscellaneous karyotype

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis


title: genomic DNA from Normal PBL 128

source_name: genomic DNA from Normal PBL 128


title: genomic DNA from Normal PBL 132

source_name: genomic DNA from Normal PBL 132


title: genomic DNA from Normal PBL 131

source_name: genomic DNA from Normal PBL 131


title: genomic DNA from Normal PBL 127

source_name: genomic DNA from Normal PBL 127


title: genomic DNA from Normal PBL 126

source_name: genomic DNA from Normal PBL 126


title: genomic DNA from Normal PBL 121

source_name: genomic DNA from Normal PBL 121


title: genomic DNA from Normal PBL 122

source_name: genomic DNA from Normal PBL 122


title: genomic DNA from Normal PBL 129

source_name: genomic DNA from Normal PBL 129


title: genomic DNA from Normal PBL 123

source_name: genomic DNA from Normal PBL 123


title: genomic DNA from Normal PBL 124

source_name: genomic DNA from Normal PBL 124


title: genomic DNA from Normal PBL 119

source_name: genomic DNA from Normal PBL 119


title: genomic DNA from Normal PBL 130

source_name: genomic DNA from Normal PBL 130


title: genomic DNA from Normal PBL 125

source_name: genomic DNA from Normal PBL 125


title: genomic DNA from Normal PBL 118

source_name: genomic DNA from Normal PBL 118


title: genomic DNA from Normal PBL 120

source_name: genomic DNA from Normal PBL 120


title: genomic DNA from Normal PBL 115

source_name: genomic DNA from Normal PBL 115


title: SJBALL039

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis


title: genomic DNA from Normal PBL 114

source_name: genomic DNA from Normal PBL 114


title: genomic DNA from Normal PBL 113

source_name: genomic DNA from Normal PBL 113


title: genomic DNA from Normal PBL 106

source_name: genomic DNA from Normal PBL 106


title: genomic DNA from Normal PBL 111

source_name: genomic DNA from Normal PBL 111


title: genomic DNA from Normal PBL 108

source_name: genomic DNA from Normal PBL 108


title: genomic DNA from Normal PBL 117

source_name: genomic DNA from Normal PBL 117


title: genomic DNA from Normal PBL 116

source_name: genomic DNA from Normal PBL 116


title: genomic DNA from Normal PBL 109

source_name: genomic DNA from Normal PBL 109


title: genomic DNA from Normal PBL 112

source_name: genomic DNA from Normal PBL 112


title: genomic DNA from Normal PBL 107

source_name: genomic DNA from Normal PBL 107


title: genomic DNA from Normal PBL 110

source_name: genomic DNA from Normal PBL 110


title: genomic DNA from Normal PBL 105

source_name: genomic DNA from Normal PBL 105


title: genomic DNA from Normal PBL 104

source_name: genomic DNA from Normal PBL 104


title: genomic DNA from Normal PBL 103

source_name: genomic DNA from Normal PBL 103


title: genomic DNA from Normal PBL 101

source_name: genomic DNA from Normal PBL 101


title: genomic DNA from Normal PBL 102

source_name: genomic DNA from Normal PBL 102


title: genomic DNA from Normal PBL 100

source_name: genomic DNA from Normal PBL 100


title: genomic DNA from Normal PBL 97

source_name: genomic DNA from Normal PBL 97


title: genomic DNA from Normal PBL 99

source_name: genomic DNA from Normal PBL 99


title: genomic DNA from Normal PBL 96

source_name: genomic DNA from Normal PBL 96


title: genomic DNA from Normal PBL 94

source_name: genomic DNA from Normal PBL 94


title: genomic DNA from Normal PBL 89

source_name: genomic DNA from Normal PBL 89


title: genomic DNA from Normal PBL 95

source_name: genomic DNA from Normal PBL 95


title: genomic DNA from Normal PBL 98

source_name: genomic DNA from Normal PBL 98


title: genomic DNA from Normal PBL 91

source_name: genomic DNA from Normal PBL 91


title: genomic DNA from Normal PBL 86

source_name: genomic DNA from Normal PBL 86


title: genomic DNA from Normal PBL 82

source_name: genomic DNA from Normal PBL 82


title: genomic DNA from Normal PBL 81

source_name: genomic DNA from Normal PBL 81


title: genomic DNA from Normal PBL 79

source_name: genomic DNA from Normal PBL 79


title: genomic DNA from Normal PBL 87

source_name: genomic DNA from Normal PBL 87


title: genomic DNA from Normal PBL 93

source_name: genomic DNA from Normal PBL 93


title: genomic DNA from Normal PBL 90

source_name: genomic DNA from Normal PBL 90


title: genomic DNA from Normal PBL 85

source_name: genomic DNA from Normal PBL 85


title: genomic DNA from Normal PBL 80

source_name: genomic DNA from Normal PBL 80


title: genomic DNA from Normal PBL 83

source_name: genomic DNA from Normal PBL 83


title: genomic DNA from Normal PBL 92

source_name: genomic DNA from Normal PBL 92


title: genomic DNA from Normal PBL 138

source_name: genomic DNA from Normal PBL 138


title: SJBALL101

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis


title: genomic DNA from Normal PBL 88

source_name: genomic DNA from Normal PBL 88


title: genomic DNA from Normal PBL 84

source_name: genomic DNA from Normal PBL 84


title: genomic DNA from Normal PBL 78

source_name: genomic DNA from Normal PBL 78


title: genomic DNA from Normal PBL 76

source_name: genomic DNA from Normal PBL 76


title: genomic DNA from Normal PBL 74

source_name: genomic DNA from Normal PBL 74


title: genomic DNA from Normal PBL 77

source_name: genomic DNA from Normal PBL 77


title: genomic DNA from Normal PBL 73

source_name: genomic DNA from Normal PBL 73


title: genomic DNA from Normal PBL 71

source_name: genomic DNA from Normal PBL 71


title: genomic DNA from Normal PBL 75

source_name: genomic DNA from Normal PBL 75


title: genomic DNA from Normal PBL 69

source_name: genomic DNA from Normal PBL 69


title: genomic DNA from Normal PBL 66

source_name: genomic DNA from Normal PBL 66


title: genomic DNA from Normal PBL 68

source_name: genomic DNA from Normal PBL 68


title: genomic DNA from Normal PBL 70

source_name: genomic DNA from Normal PBL 70


title: genomic DNA from Normal PBL 65

source_name: genomic DNA from Normal PBL 65


title: genomic DNA from Normal PBL 59

source_name: genomic DNA from Normal PBL 59


title: genomic DNA from Normal PBL 60

source_name: genomic DNA from Normal PBL 60


title: genomic DNA from Normal PBL 64

source_name: genomic DNA from Normal PBL 64


title: genomic DNA from Normal PBL 63

source_name: genomic DNA from Normal PBL 63


title: genomic DNA from Normal PBL 48

source_name: genomic DNA from Normal PBL 48


title: genomic DNA from Normal PBL 58

source_name: genomic DNA from Normal PBL 58


title: genomic DNA from Normal PBL 50

source_name: genomic DNA from Normal PBL 50


title: genomic DNA from Normal PBL 72

source_name: genomic DNA from Normal PBL 72


title: genomic DNA from Normal PBL 61

source_name: genomic DNA from Normal PBL 61


title: genomic DNA from Normal PBL 55

source_name: genomic DNA from Normal PBL 55


title: genomic DNA from Normal PBL 67

source_name: genomic DNA from Normal PBL 67


title: genomic DNA from Normal PBL 54

source_name: genomic DNA from Normal PBL 54


title: genomic DNA from Normal PBL 53

source_name: genomic DNA from Normal PBL 53


title: genomic DNA from Normal PBL 57

source_name: genomic DNA from Normal PBL 57


title: genomic DNA from Normal PBL 52

source_name: genomic DNA from Normal PBL 52


title: genomic DNA from Normal PBL 49

source_name: genomic DNA from Normal PBL 49


title: genomic DNA from Normal PBL 47

source_name: genomic DNA from Normal PBL 47


title: genomic DNA from Normal PBL 56

source_name: genomic DNA from Normal PBL 56


title: genomic DNA from Normal PBL 62

source_name: genomic DNA from Normal PBL 62


title: genomic DNA from Normal PBL 46

source_name: genomic DNA from Normal PBL 46


title: genomic DNA from Normal PBL 44

source_name: genomic DNA from Normal PBL 44


title: genomic DNA from Normal PBL 43

source_name: genomic DNA from Normal PBL 43


title: genomic DNA from Normal PBL 41

source_name: genomic DNA from Normal PBL 41


title: SJHYPER200

description: High hyperdiploid B-precursor ALL

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis


title: genomic DNA from Normal PBL 42

source_name: genomic DNA from Normal PBL 42


title: genomic DNA from Normal PBL 37

source_name: genomic DNA from Normal PBL 37


title: genomic DNA from Normal PBL 27

source_name: genomic DNA from Normal PBL 27


title: genomic DNA from Normal PBL 32

source_name: genomic DNA from Normal PBL 32


title: genomic DNA from Normal PBL 31

source_name: genomic DNA from Normal PBL 31


title: genomic DNA from Normal PBL 33

source_name: genomic DNA from Normal PBL 33


title: genomic DNA from Normal PBL 36

source_name: genomic DNA from Normal PBL 36


title: genomic DNA from Normal PBL 45

source_name: genomic DNA from Normal PBL 45


title: genomic DNA from Normal PBL 28

source_name: genomic DNA from Normal PBL 28


title: SJBALL096


title: genomic DNA from Normal PBL 39

source_name: genomic DNA from Normal PBL 39


title: genomic DNA from Normal PBL 21

source_name: genomic DNA from Normal PBL 21


title: genomic DNA from Normal PBL 38

source_name: genomic DNA from Normal PBL 38


title: genomic DNA from Normal PBL 34

source_name: genomic DNA from Normal PBL 34


title: genomic DNA from Normal PBL 25

source_name: genomic DNA from Normal PBL 25


title: genomic DNA from Normal PBL 29

source_name: genomic DNA from Normal PBL 29


title: genomic DNA from Normal PBL 20

source_name: genomic DNA from Normal PBL 20


title: genomic DNA from Normal PBL 24

source_name: genomic DNA from Normal PBL 24


title: genomic DNA from Normal PBL 35

source_name: genomic DNA from Normal PBL 35


title: genomic DNA from Normal PBL 19

source_name: genomic DNA from Normal PBL 19


title: genomic DNA from Normal PBL 22

source_name: genomic DNA from Normal PBL 22


title: SJHYPER147

description: High hyperdiploid B-precursor ALL

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis


title: genomic DNA from Normal PBL 30

source_name: genomic DNA from Normal PBL 30


title: SJHYPER132

description: High hyperdiploid B-precursor ALL


title: genomic DNA from Normal PBL 17

source_name: genomic DNA from Normal PBL 17


title: genomic DNA from Normal PBL 15

source_name: genomic DNA from Normal PBL 15


title: genomic DNA from Normal PBL 40

source_name: genomic DNA from Normal PBL 40


title: genomic DNA from Normal PBL 16

source_name: genomic DNA from Normal PBL 16


title: genomic DNA from Normal PBL 23

source_name: genomic DNA from Normal PBL 23


title: genomic DNA from Normal PBL 11

source_name: genomic DNA from Normal PBL 11


title: genomic DNA from Normal PBL 14

source_name: genomic DNA from Normal PBL 14


title: genomic DNA from Normal PBL 9

source_name: genomic DNA from Normal PBL 9


title: genomic DNA from Normal PBL 10

source_name: genomic DNA from Normal PBL 10


title: genomic DNA from Normal PBL 5

source_name: genomic DNA from Normal PBL 5


title: genomic DNA from Normal PBL 6

source_name: genomic DNA from Normal PBL 6


title: genomic DNA from Normal PBL 13

source_name: genomic DNA from Normal PBL 13


title: genomic DNA from Normal PBL 18

source_name: genomic DNA from Normal PBL 18


title: genomic DNA from Normal PBL 8

source_name: genomic DNA from Normal PBL 8


title: SJHYPER113

description: High hyperdiploid B-precursor ALL


title: SJHYPER114

description: High hyperdiploid B-precursor ALL


title: SJE2A029

description: TCF3-PBX1 B-precursor ALL


title: genomic DNA from Normal PBL 12

source_name: genomic DNA from Normal PBL 12


title: genomic DNA from Normal PBL 4

source_name: genomic DNA from Normal PBL 4


title: genomic DNA from Normal PBL 3

source_name: genomic DNA from Normal PBL 3


title: SJDOWN009

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis


title: genomic DNA from Normal PBL 7

source_name: genomic DNA from Normal PBL 7


title: genomic DNA from Normal PBL 2

source_name: genomic DNA from Normal PBL 2


title: genomic DNA from Normal PBL 1

source_name: genomic DNA from Normal PBL 1


title: SJHYPER098

description: High hyperdiploid B-precursor ALL


title: SJHYPER095

description: High hyperdiploid B-precursor ALL


title: SJDOWN013


title: SJE2A023

description: TCF3-PBX1 B-precursor ALL


title: cell line VE+N, biological rep 1

city: Milano

first: Costanza

last: Giampietro

address: Via Adamello 16

country: Italy

institute: Campus IFOM-IEO

description: SAMPLE 5

hyb_protocol: GeneChip Hybridization, Wash and Stain Kit (Affymetrix cat #900720) is used to prepare the Hybridization Cocktail . The kit contains mix for target dilution, DMSO at a final concentration of 7% and pre-mixed biotin-labelled control oligo B2 and bioB, bioC, bioD and Cre controls (Affymetrix cat #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM, respectively. These control oligos serve as positive controls for hybridization. Biotin-labeled sense targets were diluted in hybridization buffer at a concentration of 25 ng/ul and denatured at 99°C for 5 minutes. Hybridization cocktails were incubated at 45°C for 5 minutes and centrifuged at maximum speed for 1 minute prior to loading into the GeneChip® array cartridge.   Hybridizations were performed for 16 h at 45°C in a rotisserie oven at 60 RPM. Upon hybridization, GeneChip®  cartridges were washed and stained with GeneChip®  Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station 450 following the FS450_0007 standard protocol, including the following steps: (1) (wash) 10 cycles of 2 mixes/cycle with Wash Buffer A at 30°C; (2) (wash) 6 cycles of 15 mixes/cycle with Wash Buffer B at 50°C; (3) stain of the probe array for 5 min in SAPE solution at 35°C; (4) (wash) 10 cycles of 4 mixes/cycle with Wash Buffer A at 30°C; (5) stain of the probe array for 5 min in antibody solution at 35°C; (6) stain of the probe array for 5 min in SAPE solution at 35°C; (7) (final wash) 15 cycles of 4 mixes/cycle with Wash Buffer A at 35°C; (8) fill the probe array with Array Holding buffer. Load the cartridge into the GeneChip Scanner 3000 7G.

scan_protocol: GeneChip arrays are loaded in the Affymetrix GeneChip® Scanner3000 7G and scanned using default parameters. Affymetrix GeneChip® Command Console software (AGCC) was used to acquire GeneChip® images and generate .DAT and .CEL files, which were used for subsequent analysis under Partek Genomics Suite software.

data_processing: Data were analysed using Partek Genomics Suite v6.3 software (RMA algorithm).

organism: Mus musculus

source_name: ECs expressing VE+N cadherin

label_protocol: Concentration of totRNA is assessed using NanoDrop spectrophotometer and quality of totRNA is checked with an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA) to exclude sample degradation.  Biotin-labeled cDNA targets were synthesized starting from 150 ng of totRNA. Double stranded cDNA synthesis and related cRNA amplification was performed with Ambion® WT Expression Kit (Ambion, Austin, TX). cRNA was reverse transcribed to cDNA fragmented and terminal labeled with Affymetrix GeneChip® WT Teminal Labeling Kit (Affymetrix, Santa Clara, CA). All steps of the protocol were performed according to manufacturer’s specifications. Efficacy of fragmentation procedure was checked on Agilent Bioanalyzer 2100.  During target amplification, a set of Poly-A RNA Controls from B. subtilis (lys, phe, thr, and dap) are spiked in the totRNA sample and amplified along with the experimental sample. These Poly-A RNA Controls are pre-mixed at staggered concentrations to allow GeneChip® probe array users to assess the overall success of the assay. Poly-A RNA Controls final concentration in each target are lys 1:100,000, phe 1:50,000, thr 1:25,000 and dap 1:6,667.

growth_protocol: Culture medium was DMEM (GIBCO) with 20% FCS (HyClone), glutamine (2 mM, Sigma-Aldrich), penicillin/streptomycin (100 units/L, Sigma-Aldrich), sodium pyruvate (1mM, Sigma-Aldrich), heparin (100 μg/ml, from porcine intestinal mucosa; Sigma-Aldrich), and endothelial cell growth supplement (ECGS) (5 μg/ml, made from calf brain) (complete culture medium). Starving medium was (MCDB) 131 (GIBCO) with 1%BSA (EuroClone), glutamine (2 mM), penicillin/streptomycin (100 units/L) and sodium pyruvate (1mM). For all of the experiments, 50,000 cells/cm2 were seeded in complete culture medium (to reach confluence within 24 h) and cultured for 72 h (long confluent condition). Cells were then washed once with MCDB 131 and starved in MCDB 131 supplemented with 1% BSA (starving medium) for 18–20 h.

extract_protocol: Total RNA was extracted using commercial homogenization (QIAshredder) and purification (RNeasy Mini Kit) reagents (Qiagen).

tag: cell line source

value: embryonic stem cells

value: VE+N

value: Endothelial cells (ECs)

tag: genotype/variation

value: expressing VE- and N-cadherin


title: SJHYPER088

description: High hyperdiploid B-precursor ALL


title: cell line VE+N, biological rep 2

description: SAMPLE 6


title: 024595_LeConte_1DBF

source_name: 2010_LeConte  flower 1 day before bloom

tag: cultivar

value: Bartlett hybrid (Bartlett is one parent)

value: low


title: 024595_LaFrance_1DBF

source_name: 2010_LaFrance flower 1 day before bloom

value: La France

tag: day

value: high


title: cell line VE, biological rep 2

description: SAMPLE 4

source_name: ECs expressing VE cadherin

value: VE

value: expressing VE-cadherin


title: cell line VE, biological rep 1

description: SAMPLE 3


title: 024595_Okusankichi_1DBF

source_name: 2010_Okusankichi  flower 1 day before bloom

value: Okusankichi

tag: parthenocarpy


title: 024595_Taiheiyou_1DBF

source_name: 2010_Taiheiyo  flower 1 day before bloom

value: La France x Okusankichi hybrid


title: 024595_Housui_1DBF

source_name: 2010_Housui  flower 1 day before bloom

value: Housui


title: SJPHALL009

description: BCR-ABL1 B-precursor ALL

value: tumor cells obtained at diagnosis


title: cell line N, biological rep 1

description: SAMPLE 1

source_name: ECs expressing N cadherin

value: N

value: expressing N-cadherin


title: 024595_282_12_1DBF

source_name: 2010_282_12 flower 1 day before bloom

value: La France x Housui hybrid


title: genomic DNA from Normal PBL 51

source_name: genomic DNA from Normal PBL 51

value: Peripheral Blood


title: cell line N, biological rep 2

description: SAMPLE 2

value: embryonic stem cells


title: BDC/NOD DN2-3 replicate 2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset id list mentioned above, and using the standard  RMA workflow (background adjustment, quantile normalization, median polish probeset summarization).

source_name: BDC/NOD DN2-3

label_protocol: standard Affymetrix protocol

extract_protocol: RNA by Trizol method

tag: strain background

value: NOD

value: BDC2.5 TCR tg

tag: gender

value: female

value: 4 weeks

tag: isolation/cell type

value: CD4 and CD8 complement-mediated depletion followed by FACS sorting of CD4-CD8-Lin-CD25+ thymocytes (DN2-3)


title: BDC/NOD DN2-3 replicate 1

value: male


title: NOD DN2-3 replicate 1

source_name: NOD DN2-3

value: non-Tg


title: BDC/B6g7 DN4 replicate 1

source_name: BDC/B6g7 DN4

value: CD4 and CD8 complement-mediated depletion followed by FACS sorting of CD4-CD8-Lin-CD44-CD25- thymocytes (DN4)


title: B6g7 DN2-3 replicate 2


title: BDC/B6g7 DN2-3 replicate 2

source_name: BDC/B6g7 DN2-3


title: NOD DN4 replicate 2

source_name: NOD DN4


title: B6g7 DN4 replicate 1

source_name: B6g7 DN4


title: BDC/NOD DN4 replicate 1

source_name: BDC/NOD DN4


title: B6g7 DN2-3 replicate 1


city: NEW YORK

first: Panagiotis

last: Ntziachristos

address: 522 FIRST AVENUE

department: PATHOLOGY

institute: NYU MEDICAL SCHOOL

description: Gene expression data from DP (CD4+/8+) cells from Notch1-IC over-expressing peripheral tumor (thymoma) Replicate 2

hyb_protocol: 10 mcg of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using Agilent GeneSpring GX10 program.

label_protocol: 100 ng total RNA converted to cRNA using Affymetrix GeneChip® 3' IVT cDNA Synthesis and in vitro transcription kit resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

extract_protocol: Rneasy (QIAGEN) according to manufacturer's protocol.

tag: genotype

value: T-ALL

tag: sample type

tag: genetic background

value: WT C57/BLACK6

value: DP (CD4+/8+) cells


title: BDC/NOD DN4 replicate 2


title: B6g7 DN4 replicate 2


title: NOD DN2-3 replicate 2


title: BDC/B6g7 DN4 replicate 2


description: Gene expression data from DP (CD4+/8+) cells from Notch1-IC over-expressing peripheral tumor (thymoma) Replicate 1


title: BDC/B6g7 DN2-3 replicate 1


title: NOD DN4 replicate 1


title: BDC/NOD DP 3h 500nM replicate 2

source_name: BDC/NOD DP 3h 500nM_BDC mimotope-loaded TCRa-/- splenocytes stimulation

treatment_protocol: B6/NOD thymocytes mixed-stimulation with BDCmimotope-loaded TCRa-/- splenocytes for 1, 3 or 7h

tag: background strain

value: BDC2.5 TCR tg, Rag-/-, H2b

value: 6-7 weeks

tag: isolation

value: double sort as Thy1.2+Dump-CD4+CD8+CD45.1+ (NOD) or CD45.2+ (B6)


title: BDC/NOD DP 7h 500nM replicate 3

source_name: BDC/NOD DP 7h 500nM_BDC mimotope-loaded TCRa-/- splenocytes stimulation


title: BDC/NOD DP 7h 500nM replicate 2


title: BDC/NOD DP 7h 500nM replicate 4


description: Gene expression data from DP (CD4+/8+) cells from Normal Thymus Replicate 2

source_name: DP (CD4+/8+) cells from Normal Thymus

value: WT

value: DP (CD4+/8+) cells from Notch1-IC over-expressing peripheral tumor (thymoma)


title: wt PBS3

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

description: Littermate wild-type and PKCz -/- male mice (32 weeks of age) were subjected to continuous infusion of angiotensin II (or PBS as a control) for 14 days, a well established model for the induction of cardiac hypertrohy

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 RMA using RMAExpress 1.0.5

source_name: wild-type male mice non-treated

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

extract_protocol: Extraction of total RNA was performed with RNeasy Qiagen Kit according to the manufacturer's instructions.

treatment_protocol: Angiotensin II dissolved in PBS was continuously and subcutaneously infused in mice at a rate of 432 microg/kg/day using Alzet osmotic minipumps implanted dorsally under isofluorane anesthesia as reported

tag: strain

tag: tissue

value: heart

value: wild-type

value: 32 weeks


title: BDC/NOD DP 3h 500nM replicate 1

tag: age


description: Gene expression data from DP (CD4+/8+) cells from Normal Thymus Replicate 1

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using Agilent GeneSpring GX10 program. N

tag: cell type


title: BDC/NOD DP 7h 500nM replicate 1


title: BDC/NOD DP 1h 500nM replicate 2

source_name: BDC/NOD DP 1h 500nM_BDC mimotope-loaded TCRa-/- splenocytes stimulation


title: BDC/B6 DP 3h 500nM replicate 2

source_name: BDC/B6 DP 3h 500nM_BDC mimotope-loaded TCRa-/- splenocytes stimulation


title: wt PBS5


title: BDC/B6 DP 3h 500nM replicate 1


title: genomic DNA from Normal PBL 26

source_name: genomic DNA from Normal PBL 26

value: Peripheral Blood


title: BDC/B6 DP 7h 500nM replicate 3

source_name: BDC/B6 DP 7h 500nM_BDC mimotope-loaded TCRa-/- splenocytes stimulation

value: 4 weeks


title: BDC/NOD DP 1h 500nM replicate 1


title: BDC/B6 DP 7h 500nM replicate 4


title: BDC/NOD DP 7h 5nM replicate 4

source_name: BDC/NOD DP 7h 5nM_BDC mimotope-loaded TCRa-/- splenocytes stimulation


title: BDC/B6 DP 7h 500nM replicate 1


title: KO PBS4

source_name: PKCZ -/- male mice non-treated

value: PKCZ -/-


title: KO PBS3

value: male


title: BDC/B6 DP 1h 500nM replicate 1

source_name: BDC/B6 DP 1h 500nM_BDC mimotope-loaded TCRa-/- splenocytes stimulation


title: wt Ang2

source_name: wild-type male mice angiotensin II treated


title: BDC/NOD DP 3h 5nM replicate 1

source_name: BDC/NOD DP 3h 5nM_BDC mimotope-loaded TCRa-/- splenocytes stimulation


title: BDC/NOD DP 7h 5nM replicate 3


title: BDC/B6 DP 7h 500nM replicate 2


title: BDC/B6 DP 1h 500nM replicate 2


title: BDC/NOD DP 3h 5nM replicate 2


title: KO PBS2


title: BDC/NOD DP 1h 5nM replicate 2

source_name: BDC/NOD DP 1h 5nM_BDC mimotope-loaded TCRa-/- splenocytes stimulation


title: BDC/NOD DP 1h 5nM replicate 1


title: wt Ang3


title: wt Ang4


title: BDC/B6 DP 7h 5nM replicate 2

source_name: BDC/B6 DP 7h 5nM_BDC mimotope-loaded TCRa-/- splenocytes stimulation


title: BDC/B6 DP 7h 5nM replicate 3


title: KO Ang3

source_name: PKCZ -/- male mice angiotensin II treated


title: BDC/B6 DP 7h 5nM replicate 4


title: BDC/B6 DP 3h 5nM replicate 2

source_name: BDC/B6 DP 3h 5nM_BDC mimotope-loaded TCRa-/- splenocytes stimulation


title: BDC/B6 DP 7h 5nM replicate 1


title: KO Ang4


title: BDC/B6 DP 3h 5nM replicate 1


title: BDC/B6 DP 1h 5nM replicate 2

source_name: BDC/B6 DP 1h 5nM_BDC mimotope-loaded TCRa-/- splenocytes stimulation


title: BDC/B6 DP 1h 5nM replicate 1


title: BDC/NOD DP 7h CTR replicate 3

source_name: BDC/NOD DP 7h CTR


title: BDC/NOD DP 7h CTR replicate 2


title: BDC/NOD DP 7h CTR replicate 1


title: BDC/NOD DP 7h CTR replicate 4


title: BDC/NOD DP 3h CTR replicate 2

source_name: BDC/NOD DP 3h CTR


title: BDC/B6 DP 7h CTR replicate 2

source_name: BDC/B6 DP 7h CTR


title: BDC/NOD DP 3h CTR replicate 1


title: BDC/B6 DP 7h CTR replicate 4


title: 6000 Rads 48hrs Replicate 3

city: Cambridge

first: Daniel

middle: Elger

last: Wagner

address: 9 Cambridge Center

institute: Whitehead Institute

description:
Raw data file: 6000Rads_48hr-rep3.txt
Biological Replicate 3 of 3.  Control animals vs. 48hr-irradiated animals

hyb_protocol: Agilent custom planarian 4x44,000 expression arrays were hybridized according manufacturer instructions and scanned using an Agilent DNA microarray scanner.

scan_protocol: Array images were quantified and statistical significance of differential expression was calculated using Agilent’s Feature Extraction Image Analysis software with the default two-color gene expression protocol.

data_processing: Agilent two-color arrays were within-array normalized by loess, followed by between-array quantile normalization of average intensities across channels (Aquantile).

organism: Schmidtea mediterranea

source_name: Whole animals

label_protocol: Cy3 and Cy5-labeled cRNA was prepared using a QuickAmp labeling kit (Agilent) starting with 1μg total RNA

growth_protocol: Animals were maintained at 20 degrees celsius.

extract_protocol: RNA was extracted using the standard Trizol method

treatment_protocol: RNA was harvested from control animals and from animals after exposure to 6,000 rads ionizing radiation

tag: stress

value: unirradiated

tag: time

value: irradiated (6,000 Rads)

value: 48 hours


title: BDC/B6 DP 7h CTR replicate 3

tag: genotype/variation


title: 6000 Rads 48hrs Replicate 1

description:
Raw data file: 6000Rads_48hr-rep1.txt
Biological Replicate 1 of 3.  Control animals vs. 48hr-irradiated animals


title: BDC/B6 DP 3h CTR replicate 2

source_name: BDC/B6 DP 3h CTR


title: 6000 Rads 12hrs Replicate 2

description:
Raw data file: 6000Rads_12hr-rep2.txt
Biological Replicate 2 of 3.  Control animals vs. 12hr-irradiated animals

value: 12 hours


title: 6000 Rads 24hrs Replicate 3

description:
Raw data file: 6000Rads_24hr-rep3.txt
Biological Replicate 3 of 3.  Control animals vs. 24hr-irradiated animals

value: 24 hours


title: 6000 Rads 48hrs Replicate 2

description:
Raw data file: 6000Rads_48hr-rep2.txt
Biological Replicate 2 of 3.  Control animals vs. 48hr-irradiated animals


title: 6000 Rads 6hrs Replicate 5

description:
Raw data file: 6000Rads_06hr-rep5.txt
Biological Replicate 5 of 5.  Control animals vs. 6hr-irradiated animals

value: 6 hours


title: 6000 Rads 24hrs Replicate 1

description:
Raw data file: 6000Rads_24hr-rep1.txt
Biological Replicate 1 of 3.  Control animals vs. 24hr-irradiated animals


title: 6000 Rads 6hrs Replicate 2

description:
Raw data file: 6000Rads_06hr-rep2.txt
Biological Replicate 2 of 5.  Control animals vs. 6hr-irradiated animals


title: 6000 Rads 12hrs Replicate 1

description:
Raw data file: 6000Rads_12hr-rep1.txt
Biological Replicate 1 of 3.  Control animals vs. 12hr-irradiated animals


title: 6000 Rads 6hrs Replicate 1

description:
Raw data file: 6000Rads_06hr-rep1.txt
Biological Replicate 1 of 5.  Control animals vs. 6hr-irradiated animals


title: 6000 Rads 6hrs Replicate 4

description:
Raw data file: 6000Rads_06hr-rep4.txt
Biological Replicate 4 of 5.  Control animals vs. 6hr-irradiated animals


title: BDC/B6 DP 3h CTR replicate 1

value: BDC2.5 TCR tg, Rag-/-, H2b


title: 6000 Rads 12hrs Replicate 3

description:
Raw data file: 6000Rads_12hr-rep3.txt
Biological Replicate 3 of 3.  Control animals vs. 12hr-irradiated animals


title: 6000 Rads 24hrs Replicate 2

description:
Raw data file: 6000Rads_24hr-rep2.txt
Biological Replicate 2 of 3.  Control animals vs. 24hr-irradiated animals


title: 6000 Rads 6hrs Replicate 3

description:
Raw data file: 6000Rads_06hr-rep3.txt
Biological Replicate 3 of 5.  Control animals vs. 6hr-irradiated animals


title: PBMC from pTOL group (W87_pTOL)

status: Public on Jan 09 2012

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

description: PBMC from pTOL group

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'frma' function of the Bioconductor package (v2.6) 'frma' in R.2.11.1

source_name: Peripheral blood mononuclear cells

label_protocol: Standard Affymetrix protocol

extract_protocol: RNA was extracted from peripheral blood using the TRIzol method (Invitrogen, Cergy Pontoise, France). Genomic DNA was removed by DNase treatment (Roche, Indianapolis, IN, USA). RNA quality and quantity was determined using an Agilent 2100 BioAnalyzer (Palo Alto, CA, USA). RNA was reverse transcribed into cDNA using polydT oligonucleotide and Maloney leukemia virus reverse transcription (Invitrogen).

treatment_protocol: Ficoll PBMC isolation from peripheral blood

tag: tolerance group

value: pTOL

tag: gender [0=male;1=female]

tag: months from transplant

value: PBMC


title: PBMC from pTOL group (W39_pTOL)

description: PBMC from pTOL group


title: PBMC from pTOL group (W63_pTOL)

description: PBMC from pTOL group


title: PBMC from pTOL group (W14_pTOL)

description: PBMC from pTOL group


title: PBMC from pNonTOL group (W41_pNonTOL)

description: PBMC from pNonTOL group

value: pNonTOL


title: PBMC from pTOL group (W1_pTOL)

description: PBMC from pTOL group


title: PBMC from pNonTOL group (W116_pNonTOL)

description: PBMC from pNonTOL group


title: PBMC from pTOL group (W5_pTOL)

description: PBMC from pTOL group


title: PBMC from pTOL group (W4_pTOL)

description: PBMC from pTOL group


title: PBMC from pTOL group (W9_pTOL)

description: PBMC from pTOL group


title: PBMC from pTOL group (W8_pTOL)

description: PBMC from pTOL group


title: PBMC from pTOL group (W20_pTOL)

description: PBMC from pTOL group


title: PBMC from pTOL group (W10_pTOL)

description: PBMC from pTOL group


title: PBMC from pNonTOL group (W89_pNonTOL)

description: PBMC from pNonTOL group


title: PBMC from pNonTOL group (W73_pNonTOL)

description: PBMC from pNonTOL group


title: PBMC from pNonTOL group (W40_pNonTOL)

description: PBMC from pNonTOL group


title: PBMC from pNonTOL group (W78_pNonTOL)

description: PBMC from pNonTOL group


title: PBMC from pNonTOL group (W19_pNonTOL)

description: PBMC from pNonTOL group


title: PBMC from pNonTOL group (W6_pNonTOL)

description: PBMC from pNonTOL group


title: PBMC from NonTOL group (W116_NonTOL)

description: PBMC from NonTOL group

value: NonTOL


title: PBMC from pNonTOL group (W66_pNonTOL)

description: PBMC from pNonTOL group


title: PBMC from pNonTOL group (W15_pNonTOL)

description: PBMC from pNonTOL group


title: PBMC from pNonTOL group (W38_pNonTOL)

description: PBMC from pNonTOL group


title: PBMC from NonTOL group (W112_NonTOL)

description: PBMC from NonTOL group


title: PBMC from pNonTOL group (W11_pNonTOL)

description: PBMC from pNonTOL group


title: PBMC from NonTOL group (W115_NonTOL)

description: PBMC from NonTOL group


title: PBMC from pNonTOL group (W85_pNonTOL)

description: PBMC from pNonTOL group


title: PBMC from pNonTOL group (W17_pNonTOL)

description: PBMC from pNonTOL group


title: 98.d28

type: protein

city: Irvine

first: David

middle: Huw

last: Davies

state: CA

address: Med Surge II

department: Medicine

institute: University of California Irvine

description:
References:
Baldi, P., and Hatfield, G.W. (2002). DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling. Cambridge University Press
Baldi, P., and Long, A.D. (2001). A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. Bioinformatics 17, 509-519.
Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 57, 289--300.
Hermanson, G., Chun, S., Felgner, J., Tan, X., Pablo, J., Nakajima-Sasaki, R., Molina, D.M., Felgner, P.L., Liang, X., and Davies, D.H. (2011). Measurement of antibody responses to Modified Vaccinia virus Ankara (MVA) and Dryvax((R)) using proteome microarrays and development of recombinant protein ELISAs. Vaccine 30, 614-625.
Long, A.D., Mangalam, H.J., Chan, B.Y., Tolleri, L., Hatfield, G.W., and Baldi, P. (2001). Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem 276, 19937-19944.

hyb_protocol: Human sera were used at 1/100 dilution in protein array blocking buffer (Whatman) containing E. coli lysate (Antigen Discovery Inc, Irvine CA) to a final concentration of 10mg/ml protein to block anti-E. coli antibodies.   Sera were preincubated at RT for 30 minutes with constant mixing prior to applying to the arrays in triplicate and incubating overnight at 4oC with gentle agitation.   After washing in TBS + 0.05% Tween 20% (T-TBS), biotinylated anti-human IgG (Jackson) was used as secondary antibody followed after washing in T-TBS by streptavidin-PBXL3 conjugate (Martek Biosciences), both at 1/200 in blocking buffer.

scan_protocol: After washing five times, slides were air dried by brief centrifugation and then scanned and analyzed using a Perkin Elmer ScanArray Express HT microarray scanner (PerkinElmer).   Fluorescence intensities were quantified from tiff images by using ProScanArray Express software (PerkinElmer).

data_processing: Data analysis was performed using the R (http://www.r-project.org) statistical software.   In order to stabilize the variance observed in microarray signals, the vsn normalization was implemented as part of the Bioconductor suite (www.bioconductor.org) to the quantified array intensities using the 'no DNA' spots (IVTT reactions lacking the template DNA) as normalization controls.  Inter-group comparisons were performed using a Bayes regularized t-test adapted from Cyber-T for protein arrays (Baldi and Hatfield, 2002; Baldi and Long, 2001).    To account for multiple comparison conditions, p-values were corrected by the Benjamini and Hochberg (pBH) method  to control the false discovery rate (Benjamini and Hochberg, 1995).    After correction, p-values < 0.05 were considered significant.  An individual was defined as a responder if the ratio of retransformed signal intensities before and after DVX vaccination (d28/d0) was >2.0 for 2 or more of 6 signature antigens (WR101/H3L, WR113/D8L, WR148, WR150/A27L, WR070/I1L, and WR118/D13L).  Seroprevalence rates on d0 and d28 were determined for each antigen based on a cut off defined as the averaged+2SD of the naïve take population (n=50).   Individuals positive for one or more of the 6 signature antigens were considered seropositive.

molecule: protein

source_name: serum

label_protocol: Biotinylated anti-human IgG (Jackson) was used as secondary antibody followed after washing in T-TBS by streptavidin-PBXL3 conjugate (Martek Biosciences), both at 1/200 in blocking buffer.

extract_protocol: serum samples

tag: donor id

tag: vaccination status

value: previoulsy vaccinated

tag: skin take

value: yes

tag: nih clinical trial #

tag: vaccine type

value: DVX

tag: vaccine dilution

value: undiluted


title: PBMC from NonTOL group (W88_NonTOL)

description: PBMC from NonTOL group


title: PBMC from NonTOL group (W85_NonTOL)

description: PBMC from NonTOL group


title: 95.d28

value: 1:5 dilution


title: 94.d28


title: 96.d28


title: PBMC from NonTOL group (W82_NonTOL)

description: PBMC from NonTOL group


title: 93.d28

value: 1:10 dilution


title: PBMC from NonTOL group (W89_NonTOL)

description: PBMC from NonTOL group


title: 92.d28


title: 97.d28


title: PBMC from NonTOL group (W73_NonTOL)

description: PBMC from NonTOL group


title: PBMC from NonTOL group (W78_NonTOL)

description: PBMC from NonTOL group


title: PBMC from NonTOL group (W72_NonTOL)

description: PBMC from NonTOL group


title: PBMC from NonTOL group (W41_NonTOL)

description: PBMC from NonTOL group


title: PBMC from NonTOL group (W108_NonTOL)

description: PBMC from NonTOL group


title: PBMC from NonTOL group (W75_NonTOL)

description: PBMC from NonTOL group


title: PBMC from NonTOL group (W81_NonTOL)

description: PBMC from NonTOL group


title: PBMC from NonTOL group (W65_NonTOL)

description: PBMC from NonTOL group


title: BDC/NOD DP 7h 5nM replicate 1

source_name: BDC/NOD DP 7h 5nM_BDC mimotope-loaded TCRa-/- splenocytes stimulation

tag: background strain

tag: gender

value: male

value: 4 weeks

tag: isolation

value: double sort as Thy1.2+Dump-CD4+CD8+CD45.1+ (NOD) or CD45.2+ (B6)


title: 91.d28


title: BDC/NOD DP 7h 5nM replicate 2

tag: age


title: PBMC from NonTOL group (W38_NonTOL)

description: PBMC from NonTOL group

tag: cell type


title: PBMC from NonTOL group (W40_NonTOL)

description: PBMC from NonTOL group


title: 90.d28


title: PBMC from NonTOL group (W66_NonTOL)

description: PBMC from NonTOL group


title: 89.d28


title: 88.d28


title: PBMC from NonTOL group (W22_NonTOL)

description: PBMC from NonTOL group


title: 86.d28


title: 85.d28


title: PBMC from NonTOL group (W17_NonTOL)

description: PBMC from NonTOL group


title: PBMC from NonTOL group (W19_NonTOL)

description: PBMC from NonTOL group


title: PBMC from NonTOL group (W15_NonTOL)

description: PBMC from NonTOL group


title: 84.d28


title: PBMC from NonTOL group (W6_NonTOL)

description: PBMC from NonTOL group


title: PBMC from NonTOL group (W11_NonTOL)

description: PBMC from NonTOL group


title: 83.d28


title: 82.d28


title: 79.d28


title: 81.d28


title: 80.d28


title: 78.d28


title: 87.d28


title: PBMC from TOL group (W79_TOL)

description: PBMC from TOL group

value: TOL


title: 76.d28


title: PBMC from TOL group (W129_TOL)

description: PBMC from TOL group


title: 77.d28


title: PBMC from TOL group (W37_TOL)

description: PBMC from TOL group


title: PBMC from TOL group (W127_TOL)

description: PBMC from TOL group


title: PBMC from TOL group (W111_TOL)

description: PBMC from TOL group


title: PBMC from TOL group (W120_TOL)

description: PBMC from TOL group


title: PBMC from TOL group (W113_TOL)

description: PBMC from TOL group


title: PBMC from TOL group (W64_TOL)

description: PBMC from TOL group


title: 98.d0


title: 74.d28


title: PBMC from TOL group (W87_TOL)

description: PBMC from TOL group


title: 97.d0


title: PBMC from TOL group (W63_TOL)

description: PBMC from TOL group


title: 75.d28


title: 96.d0


title: 95.d0


title: PBMC from TOL group (W39_TOL)

description: PBMC from TOL group


title: 94.d0


title: 91.d0


title: 92.d0


title: 93.d0


title: PBMC from TOL group (W10_TOL)

description: PBMC from TOL group


title: PBMC from TOL group (W14_TOL)

description: PBMC from TOL group


title: PBMC from TOL group (W18_TOL)

description: PBMC from TOL group


title: PBMC from TOL group (W20_TOL)

description: PBMC from TOL group


title: PBMC from TOL group (W5_TOL)

description: PBMC from TOL group


title: PBMC from TOL group (W9_TOL)

description: PBMC from TOL group


title: 88.d0


title: 89.d0


title: PBMC from TOL group (W4_TOL)

description: PBMC from TOL group


title: 87.d0


title: 85.d0


title: 84.d0


title: 83.d0


title: 81.d0


title: PBMC from TOL group (W1_TOL)

description: PBMC from TOL group


title: PBMC from TOL group (W8_TOL)

description: PBMC from TOL group


title: 90.d0


title: 78.d0


title: 79.d0


title: 80.d0


title: 75.d0


title: 76.d0


title: 74.d0


title: 82.d0


title: 72.d28

value: naïve

value: Undiluted Dryvax


title: 73.d28


title: 71.d28


title: 68.d28


title: 70.d28


title: 77.d0


title: 66.d28


title: 67.d28


title: 65.d28


title: 64.d28


title: PBMC from NonTOL group (W21_NonTOL)

description: PBMC from NonTOL group


title: 63.d28


title: 62.d28


title: Liver biopsy after immunosuppressive therapy W129PST

description: Liver biopsy after immunosuppressive therapy (AFFY_W129PST) with a TOL POST status

data_processing: Data processing cel files were normalized with 'gcrma' function of the Bioconductor package (v2.4) 'gcrma' in R.2.9.1

extract_protocol: For total RNA extraction cryopreserved liver tissue samples were homogenized in TRIzol reagent (Invitrogen, San Diego, CA, USA) using pestle and nuclease-free 1,5ml reaction tubes (Ambion). Total RNA was then extracted following the manufacturers guidelines and quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

tag: immunotolerance group

value: TOL POST


title: Liver biopsy after immunosuppressive therapy W20PST

description: Liver biopsy after immunosuppressive therapy (AFFY_W20PST) with a TOL POST status


title: Liver biopsy after immunosuppressive therapy W113PST

description: Liver biopsy after immunosuppressive therapy (AFFY_W113PST) with a TOL POST status


title: Liver biopsy after immunosuppressive therapy W111PST

description: Liver biopsy after immunosuppressive therapy (AFFY_W111PST) with a TOL POST status


title: 69.d28

tag: time


title: 60.d28


title: 59.d28


title: 61.d28


title: 58.d28


title: 54.d28


title: 56.d28


title: 53.d28


title: 55.d28


title: 57.d28


title: 52.d28


title: 50.d28


title: 49.d28


title: 48.d28


title: Liver biopsy sample :REJ member: BX.P27

description: liver sample with typical acute cellular rejection taking place during the immediate post-transplant period  BX.P27

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Bioconductor (v2.5) Lumi package.

source_name: Liver biopsy sample

label_protocol: Biotinylated cDNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit (Ambion)

tag: liver sample group

value: REJ

tag: demographic origin center

value: Hospital Clinic


title: Liver biopsy sample :HEPC member: BX.P28

description: liver sample with chronic hepatitis due to recurrent hepatitis C virus infection  BX.P28

value: HEPC


title: Liver biopsy sample :Cont member: BX.CONT.48

description: liver sample from non-transplanted patient undergoing surgery for colorectal liver metastases BX.CONT.48

value: Cont


title: Liver biopsy sample :Cont member: BX.CONT.57

description: liver sample from non-transplanted patient undergoing surgery for colorectal liver metastases BX.CONT.57


title: 51.d28


title: 47.d28


title: Liver biopsy sample :Non-TOL REJ member: BX.W108.R

description: Liver sample at the time of rejection  BX.W108.R

growth_protocol: Liver sample at the time of rejection

value: Non-TOL REJ


title: Liver biopsy sample :REJ member: BX.P25

description: liver sample with typical acute cellular rejection taking place during the immediate post-transplant period  BX.P25


title: Liver biopsy sample :REJ member: BX.P26

description: liver sample with typical acute cellular rejection taking place during the immediate post-transplant period  BX.P26


title: Liver biopsy sample :Cont member: BX.CONT.42

description: liver sample from non-transplanted patient undergoing surgery for colorectal liver metastases BX.CONT.42


title: 46.d28

value: yes


title: Liver biopsy sample :Cont member: BX.CONT.58

description: liver sample from non-transplanted patient undergoing surgery for colorectal liver metastases BX.CONT.58


title: Liver biopsy after immunosuppressive therapy W120PST

description: Liver biopsy after immunosuppressive therapy (AFFY_W120PST) with a TOL POST status


title: 45.d28

value: DVX


title: Liver biopsy sample :Cont-Tx member: BX.P29

description: liver sample from transplant recipient under maintenance immunosuppression with normal liver function and normal liver histology 1 year after transplantation BX.P29

value: Cont-Tx


title: 43.d28


title: 44.d28


title: Liver biopsy sample :TOL member: BX.W130.P

description: Liver biopsy before immunosuppressive therapy BX.W130.P


title: Liver biopsy sample :TOL member: BX.W61.P

description: Liver biopsy before immunosuppressive therapy BX.W61.P

value: University Tor Vergata Rome


title: Liver biopsy sample :TOL member: BX.W44.P

description: Liver biopsy before immunosuppressive therapy BX.W44.P


title: Liver biopsy sample :Non-TOL member: BX.W134.P

description: Liver biopsy before immunosuppressive therapy BX.W134.P

value: Non-TOL


title: Liver biopsy sample :Cont member: CT54

description: liver sample from non-transplanted patient undergoing surgery for colorectal liver metastases CT54


title: Liver biopsy sample :TOL member: BX.W135.P

description: Liver biopsy before immunosuppressive therapy BX.W135.P


title: Liver biopsy sample :TOL member: BX.W94.P

description: Liver biopsy before immunosuppressive therapy BX.W94.P


title: 41.d28

description:
References:
Baldi, P., and Hatfield, G.W. (2002). DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling. Cambridge University Press
Baldi, P., and Long, A.D. (2001). A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. Bioinformatics 17, 509-519.
Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 57, 289--300.
Hermanson, G., Chun, S., Felgner, J., Tan, X., Pablo, J., Nakajima-Sasaki, R., Molina, D.M., Felgner, P.L., Liang, X., and Davies, D.H. (2011). Measurement of antibody responses to Modified Vaccinia virus Ankara (MVA) and Dryvax((R)) using proteome microarrays and development of recombinant protein ELISAs. Vaccine 30, 614-625.
Long, A.D., Mangalam, H.J., Chan, B.Y., Tolleri, L., Hatfield, G.W., and Baldi, P. (2001). Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem 276, 19937-19944.


title: 40.d28


title: Liver biopsy sample :Cont-Tx member: BX.P30

description: liver sample from transplant recipient under maintenance immunosuppression with normal liver function and normal liver histology 1 year after transplantation BX.P30


title: 38.d28


title: 42.d28


title: 39.d28


title: Liver biopsy sample :Cont member: CT53

description: liver sample from non-transplanted patient undergoing surgery for colorectal liver metastases CT53


title: Liver biopsy sample :Cont member: CT19

description: liver sample from non-transplanted patient undergoing surgery for colorectal liver metastases CT19


title: Liver biopsy sample :Cont member: CT52

description: liver sample from non-transplanted patient undergoing surgery for colorectal liver metastases CT52


title: Liver biopsy sample :Cont-Tx member: BX.P20.FER

description: liver sample from transplant recipient under maintenance immunosuppression with normal liver function and normal liver histology 1 year after transplantation BX.P20.FER


title: Liver biopsy sample :REJ member: BX.P19.GIM

description: liver sample with typical acute cellular rejection taking place during the immediate post-transplant period  BX.P19.GIM


title: 31.d28


title: Liver biopsy sample :HEPC member: BX.P18.VIL

description: liver sample with chronic hepatitis due to recurrent hepatitis C virus infection  BX.P18.VIL


title: 32.d28


title: 34.d28


title: 33.d28


title: 36.d28


title: 35.d28


title: Liver biopsy sample :Cont member: CT17

description: liver sample from non-transplanted patient undergoing surgery for colorectal liver metastases CT17


title: 86.d0

value: previoulsy vaccinated

value: 1:5 dilution


title: 37.d28


title: Liver biopsy sample :Cont-Tx member: BX.P24.MOR

description: liver sample from transplant recipient under maintenance immunosuppression with normal liver function and normal liver histology 1 year after transplantation BX.P24.MOR


title: 30.d28


title: 29.d28


title: 28.d28


title: 27.d28


title: 26.d28


title: Liver biopsy sample :HEPC member: BX.P13.DEL

description: liver sample with chronic hepatitis due to recurrent hepatitis C virus infection  BX.P13.DEL


title: Liver biopsy sample :Non-TOL member: BX.W115.P

description: Liver biopsy before immunosuppressive therapy BX.W115.P


title: Liver biopsy sample :Non-TOL member: BX.W131.P

description: Liver biopsy before immunosuppressive therapy BX.W131.P


title: Liver biopsy sample :Non-TOL member: BX.W123.P

description: Liver biopsy before immunosuppressive therapy BX.W123.P


title: 25.d28


title: Liver biopsy sample :HEPC member: BX.P8.MOT

description: liver sample with chronic hepatitis due to recurrent hepatitis C virus infection  BX.P8.MOT


title: 24.d28


title: Liver biopsy sample :Non-TOL member: BX.W78.P

description: Liver biopsy before immunosuppressive therapy BX.W78.P


title: Liver biopsy sample :REJ member: BX.P6.CAM

description: liver sample with typical acute cellular rejection taking place during the immediate post-transplant period  BX.P6.CAM


title: Liver biopsy sample :Non-TOL REJ member: BX.W109.R

description: Liver sample at the time of rejection  BX.W109.R


title: 73.d0

description:
References:
Baldi, P., and Hatfield, G.W. (2002). DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling. Cambridge University Press
Baldi, P., and Long, A.D. (2001). A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. Bioinformatics 17, 509-519.
Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 57, 289--300.
Hermanson, G., Chun, S., Felgner, J., Tan, X., Pablo, J., Nakajima-Sasaki, R., Molina, D.M., Felgner, P.L., Liang, X., and Davies, D.H. (2011). Measurement of antibody responses to Modified Vaccinia virus Ankara (MVA) and Dryvax((R)) using proteome microarrays and development of recombinant protein ELISAs. Vaccine 30, 614-625.
Long, A.D., Mangalam, H.J., Chan, B.Y., Tolleri, L., Hatfield, G.W., and Baldi, P. (2001). Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem 276, 19937-19944.


title: Liver biopsy sample :Non-TOL member: BX.W116.P

description: Liver biopsy before immunosuppressive therapy BX.W116.P


title: 70.d0


title: 72.d0


title: Liver biopsy sample :Non-TOL member: BX.W82.P

description: Liver biopsy before immunosuppressive therapy BX.W82.P


title: Liver biopsy sample :HEPC member: BX.P7.POR

description: liver sample with chronic hepatitis due to recurrent hepatitis C virus infection  BX.P7.POR


title: 71.d0


title: 69.d0


title: Liver biopsy sample :HEPC member: BX.P11.RUB

description: liver sample with chronic hepatitis due to recurrent hepatitis C virus infection  BX.P11.RUB


title: 68.d0


title: Liver biopsy sample :Non-TOL REJ member: BX.W83.R

description: Liver sample at the time of rejection  BX.W83.R


title: Liver biopsy sample :Non-TOL member: BX.W109.P

description: Liver biopsy before immunosuppressive therapy BX.W109.P


title: Liver biopsy sample :Non-TOL member: BX.W89.P

description: Liver biopsy before immunosuppressive therapy BX.W89.P


title: Liver biopsy sample :Non-TOL member: BX.W66.P

description: Liver biopsy before immunosuppressive therapy BX.W66.P


title: 67.d0


title: 66.d0


title: 65.d0


title: 64.d0


title: Liver biopsy sample :Non-TOL REJ member: BX.W65.R

description: Liver sample at the time of rejection  BX.W65.R


title: Liver biopsy sample :Non-TOL member: BX.W88.P

description: Liver biopsy before immunosuppressive therapy BX.W88.P


title: 61.d0


title: 60.d0


title: 62.d0


title: Liver biopsy sample :Non-TOL REJ member: BX.W11.R

description: Liver sample at the time of rejection  BX.W11.R


title: 59.d0


title: 57.d0


title: Liver biopsy sample :Non-TOL member: BX.W65.P

description: Liver biopsy before immunosuppressive therapy BX.W65.P


title: Liver biopsy sample :Non-TOL member: BX.W11.P

description: Liver biopsy before immunosuppressive therapy BX.W11.P


title: Liver biopsy sample :HEPC member: BX.P5.MAS

description: liver sample with chronic hepatitis due to recurrent hepatitis C virus infection  BX.P5.MAS


title: 63.d0


title: Liver biopsy sample :Cont member: CT40

description: liver sample from non-transplanted patient undergoing surgery for colorectal liver metastases CT40


title: Liver biopsy sample :Non-TOL REJ member: BX.W6.R

description: Liver sample at the time of rejection  BX.W6.R


title: Liver biopsy sample :Non-TOL REJ member: BX.W38.R

description: Liver sample at the time of rejection  BX.W38.R


title: Liver biopsy sample :Non-TOL REJ member: BX.W40.R

description: Liver sample at the time of rejection  BX.W40.R


title: Liver biopsy sample :Non-TOL REJ member: BX.W17.R

description: Liver sample at the time of rejection  BX.W17.R


title: Liver biopsy sample :Non-TOL member: BX.W2.P

description: Liver biopsy before immunosuppressive therapy BX.W2.P


title: 56.d0

description:
References:
Baldi, P., and Hatfield, G.W. (2002). DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling. Cambridge University Press
Baldi, P., and Long, A.D. (2001). A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. Bioinformatics 17, 509-519.
Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 57, 289--300.
Hermanson, G., Chun, S., Felgner, J., Tan, X., Pablo, J., Nakajima-Sasaki, R., Molina, D.M., Felgner, P.L., Liang, X., and Davies, D.H. (2011). Measurement of antibody responses to Modified Vaccinia virus Ankara (MVA) and Dryvax((R)) using proteome microarrays and development of recombinant protein ELISAs. Vaccine 30, 614-625.
Long, A.D., Mangalam, H.J., Chan, B.Y., Tolleri, L., Hatfield, G.W., and Baldi, P. (2001). Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem 276, 19937-19944.


title: 55.d0


title: 58.d0


title: 54.d0


title: 53.d0


title: 51.d0


title: 52.d0


title: 49.d0


title: 50.d0


title: Liver biopsy sample :TOL member: BX.W120.P

description: Liver biopsy before immunosuppressive therapy BX.W120.P


title: 48.d0