title: 124 (20081249)

description: FreshFrozen


title: 125 (10011256)

status: Public on Feb 11 2016

type: RNA

city: Hoesholm

first: Anker

last: Hansen

address: Venlighedsvej 1

country: Denmark

institute: Medical Prognosis Institute A/S

description: FFPE

hyb_protocol: Affymetrix standardized protocol for U133p2 array

data_processing: R, affypackage, justRMA

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: NSCLC

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol

tag: Stage

value: Stage 1A

tag: tissue

value: NSCLC


title: HepG2 _24h_DMSO_3

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: HCC cells treated with DMSO

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of Hugene-2_0-st-type from Affymetrix. A Custom CDF Version 19 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

source_name: HCC cell line

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

growth_protocol: HepG2 cells were cultured in RPMI at 37°C in a 5% CO2 atmosphere.

extract_protocol: total RNA was extracted using the NucleoSpin RNA II kit (Machery-Nagel, Düren, Germany) according to the manufacturer's protocol

treatment_protocol: HepG2 cells were treated with DMSO (control) or Verteporfin (0.75 µM) for 24 hours followed by RNA isolation

tag: treatment

value: DMSO

tag: cell line


title: HepG2 _24h_Verte_1

description: HCC cells treated with Verteporfin

value: Verteporfin


title: 155 (20081553)

description: FreshFrozen

scan_protocol: Affymetrix standardized protocol for U133p2 array


title: HepG2 _24h_DMSO_1

description: HCC cells treated with DMSO


title: Pig 12, F4

city: bologna

first: PAOLO

middle: o

last: BOSI

state: BOLOGNA

address: Viale Fanin, 46

department: DISTAL

country: Italy

institute: UNIVERSITY OF BOLOGNA

description: Gene expression data from jejunum mucosa

hyb_protocol: Total mRNA was hybridized on  Affymetrix©Porcine Gene 1.1 ST array strips.  Affymetrix hybridization, wash, and stain Kit for WT Array Strips were used.

scan_protocol: Quantification of transcript expression on a GeneAtlas imaging station (Affymetrix).

data_processing: Performance quality tests of the arrays including the labelling, hybridization, scanning and background signals by a Robust Multichip Analysis were performed on the CEL files using Affymetrix Expression ConsoleTM.

organism: Sus scrofa

source_name: Pig 12, complex microbial association, jejunum mucosa

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

extract_protocol: Total mRNA was isolated, according to Qiagen RNeasy® Midi Kit protocol (Qiagen, Hilden, Germany). Purity and integrity evaluation was assessed just before analysis by Agilent Bioanalyzer 2100.

treatment_protocol:
animal protocol: Twelve piglets from sows [(Great York × Pietrain) × ‘Dalland’ cross] were obtained by caesarean delivery (CD) (day 0) and were divided over two microbiota association treatments, housed in separate clean, non-sterile rooms and balanced for BW and litter of origin. Piglets were housed in two pens per room suited with an automatic feeding system for supply of a moist diet.
Pigs received pasteurized sow colostrum at birth (d0), 2 mL of starter microbiota (10^7 CFU of each Lactob. Amylovorus (LAM), Clostr. glycolicum, and Parabacteroides spp.) on d1-d3 of age and either a placebo inoculant (simple association, SA) or an inoculant consisting of diluted feces of an adult sow (complex association, CA) on d3-d4 of age. On days 26-37 of age, jejunal loops were perfused for 8 h with either enterotoxigenic E. coli F4 (ETEC), F4 fimbriae (F4), LAM or saline (CTRL) and jejunal samples were obtained from each piglet immediately afterwards. For each loop in each subject, the jejunum tract was removed, opened,  washed in ice-cold PBS, and tissue sample was collected and immediately frozen in liquid nitrogen and stored at -80°C until use.

value: jejunum mucosa

tag: breed

value: (Great York x Pie) x 'Dalland' cross, litter 7

tag: diet

value: artificially fed

tag: weight

value: 9.80 kg live weight

value: F4 fimbriae


title: Pig 11, Lact. amylovorus

source_name: Pig 11, complex microbial association, jejunum mucosa

value: (Great York x Pie) x 'Dalland' cross, litter 6

value: 10.35 kg live weight

value: Lact. amylovorus


title: Pig 11, F4


title: Pig 11, ETEC

value: enterotoxigenic E. coli F4 (ETEC)


title: 255 (20092559)

description: FreshFrozen


title: 424 (20104245)

description: FreshFrozen


title: 135 (20091354)

description: FreshFrozen


title: 294 (20112943)

description: FreshFrozen


title: 409 (20104092)

description: FreshFrozen


title: 272 (20102722)

description: FreshFrozen


title: 469 (20104696)

description: FreshFrozen


title: 092 (20090920)

description: FreshFrozen


title: Pig 12, Lact. amylovorus


title: 10-751A_CAF

status: Public on Feb 12 2016

type: genomic

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

country: USA

institute: Fred Hutchinson Cancer Center

description: 10-751A_cancer-associated fibroblasts (CAF)

hyb_protocol: Standard Illumina Infinium HD protocol

scan_protocol: Standard Illumina Infinium HD protocol

data_processing: Intensity data were extracted in Genome studio version 1.9.4

label: c-bio; a-DNP

molecule: genomic DNA

label_protocol: Standard Illumina Infinium HD protocol

extract_protocol:
tissue: For the preparation of cancer-associated fibroblasts (CAF) and benign/normal associated fibroblasts (NAF), de-identified prostate tissue samples were collected at Vanderbilt University under local IRB approval through the NCI-funded Cooperative Human Tissue Network. CAF and NAF were isolated from cancer and normal tissue respectively, as previously described (PMID:11719442). CAF activity was validated using a tissue recombination bioassay in which CAF or NAF were recombined with initiated reporter epithelium (BPH-1) and grafted to the renal capsule of severe combined immunodeficient (SCID) mice. Cells were classified as CAF if they demonstrated the ability to induce tumorigenesis (defined grossly and histologically) in the epithelial cells under these conditions. Cells from benign sources were also checked to confirm that they did not induce tumor growth.
Genomic DNA was extracted from cells using the QIAamp DNA mini kit (Qiagen, Inc.) according to the manufacturer’s instructions.

tag: gender

value: male

tag: sample type

value: CAF

tag: cell type

tag: cancer (ca) benign (b)

value: Ca

tag: patient


title: Pig 10, F4

source_name: Pig 10, simple microbial association, jejunum mucosa


title: 254 (20092542)

description: FreshFrozen


title: Pig 11, Saline

value: saline


title: Pig 12, Saline


title: Pooled_Tissue_UK [12 - 1G]

city: Loughborough

first: Tim

last: Giles

address: College Road

country: United Kingdom

institute: University of Nottingham

description: Co-purified RNA and DNA

hyb_protocol: The arrays were conditioned by washing with 150 µl water for 20 minutes at 30°C followed by incubation with 500 µl of pre-hybridisation buffer (5x SSC (Life Technologies), 0.1% SDS (Sigma), 4x Denhardt's solution (Life Technologies)) for 30 minutes at 50°C.  10µl of the labelled DNA was added to 90µl hybridisation buffer (5x SSC, 1% SDS, 4x Denhardt's solution). The sample was denatured for 3 minutes at 95°C.  The sample was allowed to hybridise with the microarray for 30 minutes at 50°C at 550rpm.  The array was then washed with 150 µl Wash Buffer 1 (1x SSC, 0.2% SDS) for 20 minutes at 60°C at 550 rpm.  The array was then washed with 150 µl Wash Buffer 2 (0.1% SSC, 0.2% SDS) for 20 minutes at 60°C at 550 rpm. The array was then washed with 150 µl Wash Buffer 3 (0.1x SSC) for 20 minutes at 60°C at 550 rpm. This buffer was removed and a blocking solution (100µl) of 2% biotin-free milk (Marvel) in PBS containing 1% BSA (New England Biolabs) and 0.1% Tween20 was added and incubated for 60 minutes at 30°C at 300 rpm. The blocking solution was removed and replaced with a conjugation solution (Streptavidin Poly-Horse radish peroxidase (HRP), ThermoScientific) diluted 1:100 in the blocing solution and incubated at 15 minutes at 30°C at 300 rpm. Post-conjugation washes with Wash Buffers 1, 2 and 3 were performed again.  Following removal of Wash Buffer 3,  100 µl of the Tetramethylbenzidine couple with hydrogen peroxide (TMB/H2O2) staining solution (TrueBlue, Insight BioTechnology LTD) was added and incubated for 10 minutes at 25°C.

scan_protocol: The ArrayStrip was inserted into the ArrayMate (Alere) and the array image recorded.

data_processing: The recorded image was analysed using Alere's integrated Iconoclust software and analysis script. Iconoclust processes the signals and automatically normalises the signal value after an algorithm processes the average intensity of the spot and the local background noise.

organism: Rattus norvegicus

source_name: Pooled sample of liver, kidney and lung

label_protocol: Biotin labelling was performed using biotinylated primers to produce a product ready for hybridisation

extract_protocol: Automated nucleic acid extraction was performed on the samples using a QIAcube (Qiagen) and appropriate kit (cador Pathogen Mini Kit (Qiagen)), following partial homogenisation of each tissue sample.  The protocol Purification of Pathogen Nucleic Acids from Fluid Samples (Qiagen) was used.  This protocol is intended for the purification of viral RNA and DNA and the DNA of easy-to-lyse bacteria from fluid samples or pretreated tissue samples.

value: Pooled sample of liver, kidney and lung


title: Pooled_Tissue_Canada [1 - 4C]

description: Co-purified RNA and DNA

organism: Rattus rattus


title: Pooled_Tissue_Canada [1 - 4A]

description: Co-purified RNA and DNA


title: Pooled_Tissue_UK [11 - 4B]

description: Co-purified RNA and DNA


title: 106 (20081065) #2

description: FreshFrozen

value: Stage 1A

value: NSCLC


title: 402 (20104023)

description: FreshFrozen


title: Pig 9, Lact. amylovorus

source_name: Pig 9, simple microbial association, jejunum mucosa

value: (Great York x Pie) x 'Dalland' cross, litter 5

value: 8.51 kg live weight


title: 207 (20082079)

description: FreshFrozen


title: Pig 12, ETEC

value: jejunum mucosa

value: (Great York x Pie) x 'Dalland' cross, litter 7


title: Pooled_Tissue_UK [10 - 4G]

description: Co-purified RNA and DNA


title: 253 (20092535)

description: FreshFrozen


title: Pig 9, Saline

value: artificially fed


title: Pig 10, ETEC

value: 9.80 kg live weight


title: 105 (20081058)

description: FreshFrozen


title: Pooled_Tissue_UK [9 - 12E]

description: Co-purified RNA and DNA

organism: Apodemus sylvaticus


title: Pig 10, Lact. amylovorus

value: (Great York x Pie) x 'Dalland' cross, litter 6


title: 066 (20080662)

description: FreshFrozen


title: Pig 9, F4

value: F4 fimbriae


title: 474 (20104740)

description: FreshFrozen


title: Pig 9, ETEC


title: 016 (20090166)

description: FreshFrozen


title: 100 (20091002)

description: FreshFrozen


title: 151 (20081515)

description: FreshFrozen


title: Pooled_Tissue_UK [10 - 10G]

description: Co-purified RNA and DNA

organism: Mus musculus


title: Pooled_Tissue_UK [10 - 10F]

description: Co-purified RNA and DNA


title: Pig 8, Lact. amylovorus

source_name: Pig 8,complex microbial association, jejunum mucosa

value: (Great York x Pie) x 'Dalland' cross, litter 4

value: 7.86 kg live weight

value: Lact. amylovorus


title: Pooled_Tissue_UK [10 - 8A]

description: Co-purified RNA and DNA


title: Pig 8, F4


title: 017 (20090173)

description: FreshFrozen


title: 233 (20092337)

description: FreshFrozen


title: 125 (20081256)

description: FreshFrozen


title: 467 (20104672)

description: FreshFrozen


title: 106 (20081065)

description: FreshFrozen


title: 430 (20104306)

description: FreshFrozen


title: 109 (20081096)

description: FreshFrozen


title: 222 (20082222)

description: FreshFrozen


title: Pooled_Tissue_UK [9 - 4C]

description: Co-purified RNA and DNA


title: Pooled_Tissue_UK [9 - 3C]

description: Co-purified RNA and DNA


title: Pooled_Tissue_UK [8 - 12G]

description: Co-purified RNA and DNA


title: Pooled_Tissue_Canada [6 - 11D]

description: Co-purified RNA and DNA


title: Pig 7, Saline

source_name: Pig 7,complex microbial association, jejunum mucosa

value: (Great York x Pie) x 'Dalland' cross, litter 3

value: 9.24 kg live weight


title: 431 (20104313)

description: FreshFrozen


title: 074 (20080747) #2

description: FreshFrozen


title: Pig 7, Lact. amylovorus


title: 074 (20080747)

description: FreshFrozen


title: Pig 8, ETEC

value: enterotoxigenic E. coli F4 (ETEC)


title: 458 (20104580)

description: FreshFrozen


title: 450 (20104504)

description: FreshFrozen


title: Pooled_Tissue_Canada [4 - 11D]

description: Co-purified RNA and DNA

value: Pooled sample of liver, kidney and lung


title: 275 (20102753)

description: FreshFrozen

value: Stage 1A


title: Pig 8, Saline

value: saline


title: Pig 7, F4


title: Pig 7, ETEC


title: Pig 6, F4

source_name: Pig 6, simple microbial association, jejunum mucosa

value: 8.10 kg live weight


title: 292 (20112929)

description: FreshFrozen

value: NSCLC


title: 120 (20081201)

description: FreshFrozen


title: 127 (20081270)

description: FreshFrozen


title: Pig 6, Lact. amylovorus

value: jejunum mucosa


title: 133 (20091330)

description: FreshFrozen


title: Pooled_Tissue_Canada [4 - 5B]

description: Co-purified RNA and DNA


title: 460 (20104603)

description: FreshFrozen


title: Pooled_Tissue_Canada [6 - 3E]

description: Co-purified RNA and DNA


title: Pooled_Tissue_Canada [4 - 2H]

description: Co-purified RNA and DNA


title: 137 (20091378)

description: FreshFrozen


title: Pig 6, Saline


title: 154 (20081546)

description: FreshFrozen


title: 130 (20091309)

description: FreshFrozen


title: 270 (20102708)

description: FreshFrozen


title: 419 (20104191)

description: FreshFrozen


title: Pig 6, ETEC


title: 145 (20091453)

description: FreshFrozen


title: Pig 5, Lact. amylovorus

source_name: Pig 5, simple microbial association, jejunum mucosa

value: 6.61 kg live weight


title: Pooled_Tissue_Canada [3 - 6B]

description: Co-purified RNA and DNA


title: Pig 5, F4

value: artificially fed


title: Pooled_Tissue_Canada [3 - 2D]

description: Co-purified RNA and DNA


title: Pooled_Tissue_Canada [3 - 2C]

description: Co-purified RNA and DNA


title: Pooled_Tissue_Canada [4 - 2F]

description: Co-purified RNA and DNA


title: 123 (20081232)

description: FreshFrozen


title: Pooled_Tissue_Canada [3 - 3F]

description: Co-purified RNA and DNA


title: 435 (20114350)

description: FreshFrozen


title: Pooled_Tissue_Canada [2 - 12B]

description: Co-purified RNA and DNA


title: Pig 5, Saline


title: Pooled_Tissue_Canada [2 - 11H]

description: Co-purified RNA and DNA


title: 168 (20091682)

description: FreshFrozen


title: 031 (20100315)

description: FreshFrozen


title: 163 (20081638)

description: FreshFrozen


title: Pooled_Tissue_Canada [2 - 11E]

description: Co-purified RNA and DNA


title: Pig 5, ETEC


title: Pig 4, Lact. amylovorus

source_name: Pig 4,complex microbial association, jejunum mucosa

value: (Great York x Pie) x 'Dalland' cross, litter 2

value: 7.27 kg live weight


title: 146 (20091460)

description: FreshFrozen


title: 078 (20090784)

description: FreshFrozen


title: Pooled_Tissue_Canada [2 - 11B]

description: Co-purified RNA and DNA


title: Pig 4, F4

value: F4 fimbriae


title: 032 (20100322)

description: FreshFrozen


title: Pig 4, Saline


title: Pig 4, ETEC


title: 408 (20104085)

description: FreshFrozen


title: 122 (20081225)

description: FreshFrozen


title: 279 (20102791)

description: FreshFrozen


title: Pooled_Tissue_Canada [2 - 10G]

description: Co-purified RNA and DNA


title: DP10-c

city: Ghantou

first: Yang

last: Liu

state: Guangdong

address: No.22, Xingling Street, Jinping District

department: Department of Histology and Embryology

country: China

institute: Shantou University Medical College

description: we used passage-10 DP cells only

hyb_protocol: The samples were  hybridized on the miRCURY™ LNA Array (v.18.0)(Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

scan_protocol: Following the washing steps the slides were scanned using the Axon GenePix 4000B microarray scanner.Scanned images were  imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction

data_processing:
After low intensity miRNAs filtering, raw signal intensities are normalized in Median method. (miRNAs that intensities>=30 in all samples are chosen for calculating normalization factor)
Expressed data were normalized using the median. After normalization, differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR). The threshold value we used to screen up- and down-regulated miRNAs was a fold change >=1.50 and a P-value <=0.05.

source_name: cultured dermal papilla cell

label_protocol: The samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit(Exiqon, Vedbaek, Denmark).One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

growth_protocol: The DP was cultured in Dulbecco’s modified Eagle’s medium (Gibco) containing 10% fetal serum at 37°C in a humidified atmosphere containing 5% CO2. DP cells were cultivated continuously

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and an miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using a Nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA integrity was determined by gel electrophoresis.

value: scalp specimens

value: DP

tag: passage

value: Late passage (10)


title: Pooled_Tissue_Canada [2 - 10D]

description: Co-purified RNA and DNA


title: Pig 3, Lact. amylovorus

source_name: Pig 3,complex microbial association, jejunum mucosa

value: 8.11 kg live weight

value: Lact. amylovorus


title: DP10-b

description: we used passage-10 DP cells only


title: 071 (20080716)

description: FreshFrozen


title: DP10-a

description: we used passage-10 DP cells only


title: Pooled_Tissue_Canada [2 - 10C]

description: Co-purified RNA and DNA


title: Pig 3, F4


title: 208 (20082086)

description: FreshFrozen


title: DP4-c

description: we used passage-4 DP cells only

value: Early-passage (4)


title: 089 (20090890)

description: FreshFrozen


title: Pooled_Tissue_Canada [2 - 9B]

description: Co-purified RNA and DNA

value: Pooled sample of liver, kidney and lung


title: 239 (20092399)

description: FreshFrozen

value: Stage 1A


title: Pooled_Tissue_Canada [2 - 8G]

description: Co-purified RNA and DNA


title: Pig 3, ETEC

value: enterotoxigenic E. coli F4 (ETEC)


title: DP4-b

description: we used passage-4 DP cells only


title: Pig 2, Lact. amylovorus

source_name: Pig 2, simple microbial association, jejunum mucosa

value: 7.21 kg live weight


title: Pooled_Tissue_Canada [2 - 8E]

description: Co-purified RNA and DNA


title: Pig 3, Saline

value: saline


title: DP4-a

description: we used passage-4 DP cells only


title: 168 (20091682) #2

description: FreshFrozen

value: NSCLC


title: Pooled_Tissue_Canada [2 - 9H]

description: Co-purified RNA and DNA


title: 265 (20092658)

description: FreshFrozen


title: 451 (20104511)

description: FreshFrozen


title: Pig 2, F4

value: jejunum mucosa


title: Pig 2, ETEC

value: artificially fed


title: 262 (20092627)

description: FreshFrozen


title: 099 (20090999)

description: FreshFrozen


title: Pooled_Tissue_Canada [2 - 7F]

description: Co-purified RNA and DNA


title: Pooled_Tissue_Canada [2 - 8D]

description: Co-purified RNA and DNA


title: 277 (20102777)

description: FreshFrozen


title: Pooled_Tissue_Canada [2 - 6E]

description: Co-purified RNA and DNA


title: Pooled_Tissue_Canada [2 - 7A]

description: Co-purified RNA and DNA


title: 304 (20113049)

description: FreshFrozen


title: Pooled_Tissue_Canada [2 - 4E]

description: Co-purified RNA and DNA


title: Pooled_Tissue_Canada [2 - 4G]

description: Co-purified RNA and DNA


title: Pooled_Tissue_Canada [2 - 4H]

description: Co-purified RNA and DNA


title: Pig 2, Saline

value: (Great York x Pie) x 'Dalland' cross, litter 2


title: Pooled_Tissue_Canada [2 - 4D]

description: Co-purified RNA and DNA


title: Pig 1, F4

source_name: Pig 1, simple microbial association, jejunum mucosa

value: (Great York x Pie) x 'Dalland' cross, litter 1

value: 7.15 kg live weight


title: 260 (20092603)

description: FreshFrozen


title: Pig 10, Saline

value: (Great York x Pie) x 'Dalland' cross, litter 6

value: 9.80 kg live weight


title: 165 (20081652)

description: FreshFrozen


title: Pig 1, Saline


title: Pooled_Tissue_Canada [2 - 3C]

description: Co-purified RNA and DNA


title: 204 (20082048)

description: FreshFrozen


title: Pig 1, Lact. amylovorus


title: 472 (20104726)

description: FreshFrozen


title: Pig 1, ETEC


title: 014 (20090142)

description: FreshFrozen


title: Pooled_Tissue_Canada [2 - 2F]

description: Co-purified RNA and DNA


title: Capan1_Vector_trans2

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Six (6) micrograms of cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix GeneChip Primeview Human Gene Expression Array. Following hybridization, arrays were washed and stained using theAffymetrix Fluidics Station 450 system.

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

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.5.

source_name: Puromycin resistant Capan1 cells after transduction with MSCV-puro vector

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

growth_protocol: Capan1 cells were grown in IMDM/FCS medium according to ATCC specifications.

extract_protocol: Total RNA was extracted using Trizol and the PureLink RNA Mini kit (Lifesciences).

treatment_protocol: Capan1 cell were transduced with amphotropic retroviruses carrying either an MSCV-SV40-PuroR or MSCV-PROX1-PuroR, for 2.5 h. Three indeendent transductions were performed for each MSCV_puro and MSCV_PROX1_puro. Two days after transduction, the cells were incubated with 0.5 ug/mL puromycin and selected for 4 days. The selections was stopped after all the cells in the growth control (non-transduced Capan1) have died.

value: Human pancreatic ductal adenocarcinoma


title: 202 (20082024)

description: FreshFrozen

source_name: NSCLC


title: Pooled_Tissue_Canada [2 - 2A]

description: Co-purified RNA and DNA


title: Pooled_Tissue_Canada [2 - 3B]

description: Co-purified RNA and DNA


title: Pooled_Tissue_Canada [2 - 1B]

description: Co-purified RNA and DNA


title: 200 (20082000)

description: FreshFrozen


title: 013 (20090135)

description: FreshFrozen


title: Pooled_Tissue_Canada [2 - 1A]

description: Co-purified RNA and DNA


title: Pooled_Tissue_Canada [2 - 2C]

description: Co-purified RNA and DNA


title: Capan1_Prox1_trans2

source_name: Puromycin resistant Capan1 cells after transduction with MSCV-puro-Prox1


title: Capan1_Vector_trans3


title: 447 (20114473)

description: FreshFrozen


title: Capan1_Prox1_trans1


title: Pooled_Tissue_Canada [1 - 12D]

description: Co-purified RNA and DNA


title: Pooled_Tissue_Canada [1 - 12E]

description: Co-purified RNA and DNA


title: Pooled_Tissue_Canada [1 - 12H]

description: Co-purified RNA and DNA


title: Capan1_Vector_trans1


title: 228 (20082284)

description: FreshFrozen


title: Capan1_Prox1_trans3


title: 235 (20092351)

description: FreshFrozen


title: 266 (20092665)

description: FreshFrozen


title: LH118_tumor_FFPE sample

city: Madrid

first: Juan Ángel

last: Fresno Vara

state: Madrid

address: Paseo de la castellana 261

department: INGEMM

country: Spain

institute: Hospital La Paz

hyb_protocol: Hybridization, washing, staining and scanning of Affymetrix Human Genome U219 arrays were performed following the manufacturer's recommendations.

scan_protocol: standard Affymetrix protocol

data_processing: Scanned images (DAT files) were transformed into intensities (CEL files) by Gene Atlas Instrument Control 1.0.6 Software (Affymetrix). The raw intensity values were background corrected, log2 transformed, quartile normalized and summarized using RMA (Genomics Suite v.6.6, Partek).

source_name: primary tumor_Control

label_protocol: Since a significant part of RNA isolated from FFPE samples is not suitable for enzymatic reactions, we decided to use Pico Profiling, a novel method optimized for whole transcriptome amplification. 10 µg cDNA was subsequently fragmented by DNAseI and biotinylated by terminal transferase obtained from GeneChip Mapping 10Kv2 Assay Kit (Affymetrix).

extract_protocol: Selected FFPE tumour specimens were cut into serial sections with a thickness of 10 µm. RNA was then extracted with the RecoverAll Total Nucleic Acid Isolation Kit (Life Technologies).

treatment_protocol: Participants had to fulfill all the following criteria: a confirmed diagnosis of metastatic breast cancer; HER2 positive disease, as determined by 3+ immunohistochemistry or positive FISH; treatment with chemotherapy plus trastuzumab; stable disease or a complete response lasting at least 3 years. A control group was also created with patients who had had a progression within the first 12 months of first-line trastuzumab-based therapy.

tag: age (years)

value: primary tumor

tag: sample group

value: Control

tag: tumor size (t)

tag: lymph node status (n)

tag: tumor grade (g)

tag: er status

tag: pgr status


title: LH114_tumor_FFPE sample


title: LH117_tumor_FFPE sample

value: Tx

value: ND


title: Pooled_Tissue_Canada [1 - 12C]

description: Co-purified RNA and DNA

tag: tissue

value: Pooled sample of liver, kidney and lung


title: 245 (20092450)

description: FreshFrozen

tag: Stage

value: Stage 1A


title: LH116_tumor_FFPE sample


title: 039 (20100391)

description: FreshFrozen


title: LH113_tumor_FFPE sample

value: metastasis

value: Nx


title: 241 (20092412)

description: FreshFrozen

value: NSCLC


title: 232 (20092320)

description: FreshFrozen


title: Pooled_Tissue_Canada [1 - 12B]

description: Co-purified RNA and DNA


title: 258 (20092580)

description: FreshFrozen


title: LH112_tumor_FFPE sample


title: Pooled_Tissue_Canada [1 - 10E]

description: Co-purified RNA and DNA


title: Pooled_Tissue_Canada [1 - 11B]

description: Co-purified RNA and DNA


title: LH111_tumor_FFPE sample


title: Pooled_Tissue_Canada [1 - 9C]

description: Co-purified RNA and DNA


title: Pooled_Tissue_Canada [1 - 9B]

description: Co-purified RNA and DNA


title: Pooled_Tissue_Canada [1 - 8F]

description: Co-purified RNA and DNA


title: 069 (20080693)

description: FreshFrozen


title: LH108_tumor_FFPE sample


title: 453 (20104535)

description: FreshFrozen


title: Pooled_Tissue_Canada [1 - 8D]

description: Co-purified RNA and DNA


title: LH110_tumor_FFPE sample


title: 405 (20104054)

description: FreshFrozen


title: 457 (20104573)

description: FreshFrozen


title: LH106_tumor_FFPE sample


title: Pooled_Tissue_Canada [1 - 7B]

description: Co-purified RNA and DNA


title: Pooled_Tissue_Canada [1 - 5B]

description: Co-purified RNA and DNA


title: Pooled_Tissue_Canada [1 - 4H]

description: Co-purified RNA and DNA


title: LH107_tumor_FFPE sample


title: Pooled_Tissue_Canada [1 - 4G]

description: Co-purified RNA and DNA


title: LH109_tumor_FFPE sample


title: 263 (20092634)

description: FreshFrozen


title: LH103_tumor_FFPE sample


title: LH102_tumor_FFPE sample


title: LH105_tumor_FFPE sample


title: 464 (20104641)

description: FreshFrozen


title: 261 (20092610)

description: FreshFrozen


title: Pooled_Tissue_Canada [1 - 4D]

description: Co-purified RNA and DNA


title: 111 (20081119)

description: FreshFrozen


title: 223 (20082239)

description: FreshFrozen


title: 257 (20092573)

description: FreshFrozen


title: 117 (20081171)

description: FreshFrozen


title: LH101_tumor_FFPE sample


title: 080 (20090807)

description: FreshFrozen


title: LH104_tumor_FFPE sample


title: Pooled_Tissue_Canada [1 - 4E]

description: Co-purified RNA and DNA


title: LH042_tumor_FFPE sample

source_name: primary tumor_Long-HER

value: Long-HER (long-term responder)


title: 264 (20092641)

description: FreshFrozen


title: 004 (20080044)

description: FreshFrozen


title: LH039_tumor_FFPE sample


title: LH040_tumor_FFPE sample


title: LH038_tumor_FFPE sample


title: 459 (20104597)

description: FreshFrozen


title: LH037_tumor_FFPE sample


title: LH036_tumor_FFPE sample


title: 463 (20104634)

description: FreshFrozen


title: LH041_tumor_FFPE sample


title: LH035_tumor_FFPE sample


title: 118 (20081188)

description: FreshFrozen


title: 268 (20102685)

description: FreshFrozen


title: LH032_tumor_FFPE sample


title: 417 (20104177)

description: FreshFrozen


title: LH033_tumor_FFPE sample


title: 110 (20081102)

description: FreshFrozen


title: 244 (20092443)

description: FreshFrozen


title: 221 (20082215)

description: FreshFrozen


title: LH031_tumor_FFPE sample


title: LH028_tumor_FFPE sample


title: 234 (20092344)

description: FreshFrozen


title: 162 (20081621)

description: FreshFrozen


title: 067 (20080679)

description: FreshFrozen


title: 219 (20082192)

description: FreshFrozen


title: LH027_tumor_FFPE sample


title: LH024_tumor_FFPE sample


title: LH025_tumor_FFPE sample


title: LH030_tumor_FFPE sample


title: 288 (20112882)

description: FreshFrozen


title: 107 (20081072)

description: FreshFrozen


title: Heart FG4497, rep3

city: Boston

first: William

middle: James

last: Gibson

state: Massachusetts

address: 34 Fairfield St #1

institute: Harvard Medical School

description:
Fibrogen3
Gene expression data from the heart muscle of mice treated with the hypoxia-inducing compound FG-4497.
Biological replicate 3.

hyb_protocol: Tissue RNA was hybridized to Affymetrix Mouse Gene 1.0 ST arrays processed by the Dana Farber Core Facility.

scan_protocol: Arrays were scanned.

data_processing: The data were analyzed with GenePattern to create gct file using Affymetrix default analysis settings (RMA) with background correction and quantile normalization.

source_name: heart muscle of mice treated with FG-4497 (Fibrogen)

label_protocol: cDNA was made from 500 ng of total RNA by reverse transcription with random primers (StrataScript First Strand cDNA Synthesis Kit, Stratagene, La Jolla, CA, USA).

growth_protocol: Mice were fed ad libitum chow. All mice were back-crossed to C57BL/6.

extract_protocol: RNA was purified with TRIzol (Invitrogen, Carlsbad, CA, USA) from cells in culture or homogenized tissues prepared with a TissueLyser II.

treatment_protocol: Mice were treated with vehicle or the EglN inhibitor FG-4497 (50mg/kg intraperitoneal), and heart muscle was subsequently isolated.

tag: strain/background

tag: treatment

tag: genotype/variation

value: EglN1 WT

value: heart muscle


title: LH029_tumor_FFPE sample

tag: sample type


title: LH026_tumor_FFPE sample


title: LH023_tumor_FFPE sample


title: Heart FG4497, rep2

description:
Fibrogen2
Gene expression data from the heart muscle of mice treated with the hypoxia-inducing compound FG-4497.
Biological replicate 2.


title: Heart FG4497, rep1

description:
Fibrogen1
Gene expression data from the heart muscle of mice treated with the hypoxia-inducing compound FG-4497.
Biological replicate 1.


title: 144 (20091446)

description: FreshFrozen


title: Heart control, rep3

description:
FibControl3
Gene expression data from the heart muscle of mice harvested at the same time as their counterparts that were treated with the hypoxia-inducing compound FG-4497.
Biological replicate 3.

source_name: heart muscle of mice harvested at same time (control) as those treated with FG-4497

value: vehicle


title: Heart control, rep2

description:
FibControl2
Gene expression data from the heart muscle of mice harvested at the same time as their counterparts that were treated with the hypoxia-inducing compound FG-4497.
Biological replicate 2.


title: 307 (20113070)

description: FreshFrozen


title: LH022_tumor_FFPE sample


title: LH020_tumor_FFPE sample


title: 281 (20102814)

description: FreshFrozen


title: 087 (20090876) #2

description: FreshFrozen


title: Heart control, rep1

description:
FibControl1
Gene expression data from the heart muscle of mice harvested at the same time as their counterparts that were treated with the hypoxia-inducing compound FG-4497.
Biological replicate 1.


title: 090 (20090906)

description: FreshFrozen


title: LH019_tumor_FFPE sample


title: LH021_tumor_FFPE sample


title: LH018_tumor_FFPE sample


title: Quadriceps KO, rep2

description:
2245_Quad_KO
Gene expression data from the quadriceps muscle of mice with EglN1 Floxx genotype and skeletal-muscle Cre recombinase after inducing gene deletion.
Biological replicate 2.

source_name: mouse quadriceps muscle with EglN1 KO

treatment_protocol: To induce expression of Cre recombinase, mice were treated with tamoxifen for 3 days prior to harvesting tissues.

value: tamoxifen

value: EglN1 KO

value: quadriceps muscle


title: Quadriceps KO, rep3

description:
2266_Quad_KO
Gene expression data from the quadriceps muscle of mice with EglN1 Floxx genotype and skeletal-muscle Cre recombinase after inducing gene deletion.
Biological replicate 3.


title: Quadriceps KO, rep1

description:
2244_Quad_KO
Gene expression data from the quadriceps muscle of mice with EglN1 Floxx genotype and skeletal-muscle Cre recombinase after inducing gene deletion.
Biological replicate 1.


title: 262 (20092627) #2

description: FreshFrozen


title: 087 (20090876)

description: FreshFrozen


title: Quadriceps WT, rep2

description:
2272_Quad_Ctrl
Gene expression data from the quadriceps muscle of mice with EglN1 WT genotype and skeletal-muscle Cre recombinase after inducing Cre.
Biological replicate 2.

source_name: mouse quadriceps muscle with EglN1 WT


title: 448 (20114480)

description: FreshFrozen


title: SGBS preadipocytes with siRNA to a scrambled gene(control), with differentiation for 24hr, biological rep 2

city: Worcester

first: Michael

middle: P

last: Czech

state: MA

address: 373 Plantation St., Biotech II, Suite 100

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description:
Gene expression data from human SGBS preadipocytes with differentiation media for 24hr and siRNA to scrambled control
SGBS preadip Scr Diff+

hyb_protocol: 3.5 ug of cDNA were hybridized overnight at 45C for 16-18hrs to Affymetrix Human Gene 2.0 ST arrays. GeneChips were washed and stained on Affymetrix Fluidics 450 using FS450_0002 protocol.

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

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy

source_name: SGBS adipocytes

label_protocol: Targets were prepared using Ambion WT Expression Kit and Affymetrix GeneChip WT Terminal Labeling and Hybridization Mix according to the manufacturer's instructions

growth_protocol: Simpson Golabi Behmel Syndrome (SGBS) cells were cultured in DMEM/F12 media supplemented with 10% fetal bovine serum, 33 uM biotin, 17 uM pantothenic acid, 100 units/ml penicillin and 0.1 mg/ml streptomycin until full confluence.

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

treatment_protocol: Cells were washed with PBS before differentiation was stimulated with serum-free media containing rosiglitazone, dexamethasone, 3-isobutyl-1-methylxanthine, cortisol, transferrin, triiodotyronin, and human insulin.

tag: cell type


title: SGBS preadipocytes with siRNA to a scrambled gene(control), with differentiation for 24hr, biological rep 3

value: SGBS preadipocytes with differentiation media


title: 154 (20081546) #2

description: FreshFrozen


title: 164 (20081645)

description: FreshFrozen


title: 236 (20092368)

description: FreshFrozen


title: LH017_tumor_FFPE sample

value: primary tumor


title: Quadriceps WT, rep3

description:
2255_Quad_Ctrl
Gene expression data from the quadriceps muscle of mice with EglN1 WT genotype and skeletal-muscle Cre recombinase after inducing Cre.
Biological replicate 3.


title: LH016_tumor_FFPE sample


title: LH014_tumor_FFPE sample


title: Quadriceps WT, rep1

description:
2257_Quad_Ctrl
Gene expression data from the quadriceps muscle of mice with EglN1 WT genotype and skeletal-muscle Cre recombinase after inducing Cre.
Biological replicate 1.


title: SGBS preadipocytes with siRNA to a scrambled gene(control), with differentiation for 24hr, biological rep 1

description:
Gene expression data from human SGBS preadipocytes with differentiation media for 24hr and siRNAto scrambled control
SGBS preadip Scr Diff+


title: LH013_tumor_FFPE sample


title: Soleus WT, rep3

description:
2272_Sol_Ctrl
Gene expression data from the soleus muscle of mice with EglN1 WT genotype and skeletal-muscle Cre recombinase after inducing Cre.
Biological replicate 3.

source_name: mouse soleus muscle with EglN1 WT

value: soleus muscle


title: 285 (20102852)

description: FreshFrozen


title: LH011_tumor_FFPE sample

value: Control


title: SGBS preadipocytes with siRNA to a scrambled gene(control), without differentiation, biological rep 3

description:
Gene expression data from human SGBS preadipocytes with siRNA to scrambled control
SGBS preadip Scr Diff-

source_name: SGBS preadipocytes

value: SGBS preadipocytes without differentiation


title: 400 (20104009)

description: FreshFrozen


title: Soleus WT, rep2

description:
2257_Sol_Ctrl
Gene expression data from the soleus muscle of mice with EglN1 WT genotype and skeletal-muscle Cre recombinase after inducing Cre.
Biological replicate 2.


title: SGBS preadipocytes with siRNA to a scrambled gene(control), without differentiation, biological rep 2


title: Soleus WT, rep1

description:
2255_Sol_Ctrl
Gene expression data from the soleus muscle of mice with EglN1 WT genotype and skeletal-muscle Cre recombinase after inducing Cre.
Biological replicate 1.


title: LH006_tumor_FFPE sample


title: 305 (20113056)

description: FreshFrozen


title: 238 (20092382)

description: FreshFrozen


title: LH008_tumor_FFPE sample

value: ND


title: SGBS preadipocytes with siRNA to a scrambled gene(control), without differentiation, biological rep 1


title: 286 (20102869)

description: FreshFrozen

value: Stage 1A


title: Soleus KO, rep1

description:
2244_Sol_KO
Gene expression data from the soleus muscle of mice with EglN1 Floxx genotype and skeletal-muscle Cre recombinase after inducing gene deletion.
Biological replicate 1.

source_name: mouse soleus muscle with EglN1 KO


title: SGBS preadipocytes with siRNA to Tenomodulin, with differentiation for 24hr, biological rep 3

description:
Gene expression data from human SGBS preadipocytes with differentiation media for 24hr and siRNA to tenomodulin
SGBS preadip siTNMD Diff+


title: SGBS preadipocytes with siRNA to Tenomodulin, with differentiation for 24hr, biological rep 1


title: LH001_tumor_FFPE sample


title: Soleus KO, rep2

description:
2245_Sol_KO
Gene expression data from the soleus muscle of mice with EglN1 Floxx genotype and skeletal-muscle Cre recombinase after inducing gene deletion.
Biological replicate 2.


title: Soleus KO, rep3

description:
2266_Sol_KO
Gene expression data from the soleus muscle of mice with EglN1 Floxx genotype and skeletal-muscle Cre recombinase after inducing gene deletion.
Biological replicate 3.


title: 283 (20102838)

description: FreshFrozen


title: 259 (20092597)

description: FreshFrozen


title: SGBS preadipocytes with siRNA to Tenomodulin, without differentiation, biological rep 3

description:
Gene expression data from human SGBS preadipocytes with siRNA to tenomodulin
SGBS preadip siTNMD Diff-


title: LH002_tumor_FFPE sample


title: LH004_tumor_FFPE sample


title: SGBS preadipocytes with siRNA to Tenomodulin, with differentiation for 24hr, biological rep 2


title: LH003_tumor_FFPE sample


title: E8.75 Tbx5 KO;Nkx2-5 KO heart, biological rep2

city: SAN FRANCISCO

first: Benoit

middle: G.

last: Bruneau

address: 1650 OWENS STREET

institute: GLADSTONE INSTITUTES

description: Gene expression data from E8.75 Tbx5 KO;Nkx2-5 KO hearts

hyb_protocol: The labeled cDNA was hybridized to Mouse GeneChip Gene 1.0 ST microarrays (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned according to the protocol described in GeneChip Expression Analysis Technical Manual 702232 Rev.

data_processing: Affymetrix AGCC 3.2.2 was used for Data processing.

source_name: E8.75 Tbx5 KO;Nkx2-5 KO heart

label_protocol: RNA was amplified into cDNA using the NuGen Ovation kit followed by fragmentation and labeling using NuGEN Encore Biotin Module.

extract_protocol: Extraction of total RNA was performed using the ARCTURUS® PicoPure® RNA Isolation Kit.

value: dissected embryonic heart

tag: genotype

value: Tbx5 KO;Nkx2-5 KO

tag: age


title: SGBS preadipocytes with siRNA to Tenomodulin, without differentiation, biological rep 1


title: E8.75 Tbx5 KO;Nkx2-5 KO heart, biological rep3


title: E8.75 Tbx5 KO;Nkx2-5 KO heart, biological rep1


title: 423 (20104238)

description: FreshFrozen

value: NSCLC


title: SGBS preadipocytes with siRNA to Tenomodulin, without differentiation, biological rep 2


title: 129 (20091293)

description: FreshFrozen


title: LH015_tumor_FFPE sample

value: Long-HER (long-term responder)


title: 091 (20090913)

description: FreshFrozen


title: E8.75 Tbx5 KO heart, biological rep2

description: Gene expression data from E8.75 Tbx5 KO hearts

source_name: E8.75 Tbx5 KO heart

value: Tbx5 KO


title: E8.75 Tbx5 KO heart, biological rep3


title: E8.75 Nkx2-5 KO heart, biological rep3

description: Gene expression data from E8.75 Nkx2-5 KO hearts

source_name: E8.75 Nkx2-5 KO heart

value: Nkx2-5 KO


title: 248 (20092481)

description: FreshFrozen


title: E8.75 Nkx2-5 KO heart, biological rep2


title: CD45-Ter119-Itgav-Tie2-rep1

city: Stanford

first: Rahul

last: Sinha

state: CA

address: 265 Campus Drive

department: ISCBRM

institute: Stanford University School of Medicine

description: fore and hind limbs pooled litter

hyb_protocol: standard Affymetrix protocol

data_processing: Normalized Intenstity values were computed based on Gene Expression Commons Algorithum [ https://gexc.stanford.edu/]

source_name: wild-type, anterior posterior limb

label_protocol: Amplified cRNA was streptavidin-labeled, fragmented, and hybridized to Affymetrix 430-2.0 arrays as recommended by the manufacturer (Affymetrix, Santa Clara). Arrays were scanned with a Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1. software.

growth_protocol: Skeletal tissues were dissected from P3 GFP-labeled mice and dissociated by mechanical and enzymatic dissociation. Specifically, the tissue was placed in collagenase digestion buffer supplemented with DNase and incubated at 37oC for 40 minutes under constant agitation. After collagenase digestion and neutralization, undigested materials were gently triturated by repeated pipetting. Total dissociated cells were filtered through 40 m nylon mesh, pelleted at 200g at 4oC, resuspended in staining media (2% fetal calf serum in PBS), blocked with rat IgG and stained with fluorochrome-conjugated antibodies against CD45, Tie2, AlphaV integrin, CD105, Thy1.1, Thy 1.2, 6C3 and CD200 for fractionation by fluorescence activated-cell sorting.

extract_protocol: RNA was isolated with RNeasy Micro Kit (Qiagen, Germantown, MD) as per manufacturer’s instructions. RNA was twice amplified with a RiboAmp RNA amplification kit (Arcturus Engineering, Mountain View, CA).

value: postnatal day 3

value: fore and hind limbs

value: wild type


title: Low-gain Heifer 7

city: College Station

first: Bruna

middle: Rios Coelho

last: Alves

state: TX

address: 2471 TAMU - Department of Animal Sciences

department: Animal Sciences

institute: Texas A&M University

description: LG-Heifer 7

hyb_protocol: Input and methylated-enriched labeled DNA were co-hybridized to the array (2 µg each), using the Oligo aCGH/ChIP-on-chip Hybridization Kit (Agilent Technologies) at 65o C.

scan_protocol: The array was scanned using the G2505C Microarray Scanner (Agilent) Images were quantified using Agilent Feature Extraction Software (version 10.7).  A resolution of 5µm and extended dynamic range (XDR) of 0.05 were applied to obtain the signal intensities.

data_processing: The Chip Interactive Analysis application of the Agilent Genomic Workbench software (version 7.0) was used to analyze signal intensity data. Signal intensities were normalized according the Agilent Feature Extraction output, which applies the Lowess method.

label: Alexa Fluor® 647

organism: Bos taurus

label_protocol: Input (total) and methylated-enriched DNA (3 µg each) were labeled with Alexa Fluor® 555 and Alexa Fluor® 647, respectively, using the BioPrime® Plus Array CGH Genomic Labeling Module (Invitrogen) and following the manufacturer’s instructions.

growth_protocol: Heifers were fed, from 4.5 to 8.5 mo af age, for a targeted daily body weight gain of 1Kg/d (High-gain, HG) or 0.5 Kg/d (Low-gain, LG). Tissue from the hypothalamic arcuate nucleus was obtained at 8.5 mo of age.

extract_protocol: Genomic DNA was isolated by phenol-chloroform extraction followed by ethanol precipitation. Methylated-enriched DNA obtained from a methyl-CpG binding domain-based (MBD) protein assay.

tag: individual id

value: Heifer 7

tag: gender

value: Female

tag: nutritional schedules

value: targeted daily body weight gain of 0.5 Kg/d (Low-gain, LG)

value: Arcuate nucleus (hypothalamus)

tag: molecule subtype

value: Methylated-enriched DNA

label: Alexa Fluor® 555

value: input DNA


title: E8.75 WT heart, biological rep3

description: Gene expression data from E8.75 WT hearts

source_name: E8.75 WT heart

value: WT


title: Low-gain Heifer 8

description: LG-Heifer 8

value: Heifer 8


title: E8.75 Tbx5 KO heart, biological rep1

value: dissected embryonic heart


title: CD45-Ter119-ItgavlowTie2+rep2

description: fore and hind limbs pooled litter

scan_protocol: Arrays were scanned with a Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1. software.


title: E8.75 Nkx2-5 KO heart, biological rep1


title: CD45-Ter119-Itgav-Tie2-rep2

description: fore and hind limbs pooled litter


title: Low-gain Heifer 6

description: LG-Heifer 6

value: Heifer 6


title: High-gain Heifer 3

description: HG-Heifer 3

value: Heifer 3

value: targeted daily body weight gain of 1Kg/d (High-gain, HG)


title: CD45-Ter119-Itgav-Tie2-rep3

description: fore and hind limbs pooled litter


title: CD45-Ter119-ItgavlowTie2+rep1

description: fore and hind limbs pooled litter


title: E8.75 WT heart, biological rep2


title: High-gain Heifer 4

description: HG-Heifer 4

value: Heifer 4


title: genotype: Moneymaker - pathogen infection: infected - rep2

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: roots of greenhouse-grown tomato plant variety Moneymaker (susceptible to Pyranochaeta lycopersici) infected with Pyrenochaeta lycopersici (May still include original submitter created erros/discrepancies)

hyb_protocol: Affy-Eukaryotic Target Hybridization

scan_protocol: Affy-Array Scanning

data_processing: The MAS5.0 Normalization was performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org, Version: 2.12.1). The target value is 500 for all cases. The code was developed using R2.4.1 to 2.13.0, Bioconductor 1.9 to 2.12.1, and simpleaffy 2.8.0. to 2.28.0 The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html.

organism: Solanum lycopersicum

label_protocol: Affymetrix one-cycle target labeling

extract_protocol: NucleospinRNA Plant (Macherey-Nagel)

tag: germplasm name

value: Moneymaker

tag: pathogen susceptibility

value: susceptible

tag: infected with

value: Pyranochaeta lycopersici

tag: organism part

tag: development stage

value: 2 leaf expansion stage ('PO:0001052')

tag: growth media

value: vermiculite


title: Resc 3, replicate 3

city: Heidelberg

first: Roberta

last: Scognamiglio

state: BW

address: Im Neuenheimer Feld 280

department: Stem Cells and Cance

institute: DKFZ

description: Gene expression data from mouse ESCs

hyb_protocol: Hybridization performed on a Affymetrix Fluidics Station

scan_protocol: Array scanning and raw data processing were done using GCOS software (Affymetrix)

data_processing: CEL files were imported to R statistical package version 3.2.2 using R oligo package version 1.32.0. Microarray data was subjected to RMA normalization. Significance analysis was performed using the bioconductor package LIMMA version 3.2.15

source_name: ESCs treated for 60h with the 10058-F4 MYC inhibitor followed by 48h inhibitor withdrawal (rescue)

label_protocol: Biotin labelling of cRNA was performed utilizing the Affymetrix GeneChip IVT labelling kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: ESCs were routinely propagated on 0.1% gelatine-coated plates, without feeders or serum, in N2B27 medium (NDiff N2B27 base medium, Stem Cell Sciences Ltd, SCS-SF-NB-02) supplemented with the small-molecule inhibitors PD0325901 (Stemgent, 04-0006, 1 μM) and CHIR99021 (Stemgent, 04-0004, 3 μM), LIF (Millipore, ESG1106, 1.000 U/ml) and β-mercaptoethanol (Gibco, 31350-010, 0.05 mM). Cells were replated every three days following dissociation with StemPro® Accutase® (Gibco, A11105-01).

extract_protocol: Total RNA isolation was performed using ARCTURUS® PicoPure® RNA Isolation Kit (Life Technologies, Invitrogen) according to the manufacturer’s instructions. DNAse treatment was performed using RNAse-free DNAse Set (Qiagen).

treatment_protocol: In the samples treated with the small-molecule c-Myc inhibitor (MYCi), 10058-F4 (Calbiochem, 475956) was dissolved in 2i medium at a final concentration of 64 μM. As a control, DMSO alone was added at the same final volume as the inhibitor. The MYCi⇒Released (Resc) group was treated with 10058-F4 for 60h, followed by withdrawal of the inhibitor and culture in 2i medium for additional 48h.

value: mouse embryonic stem cells (ESCs)


title: Resc 1, replicate 1

description: Gene expression data from mouse ESCs


title: CD45-Ter119-ItgavlowTie2+rep3

description: fore and hind limbs pooled litter

value: postnatal day 3

tag: tissue

value: fore and hind limbs

value: wild type


title: genotype: Mogeor - pathogen infection: infected - rep1

description: roots of greenhouse-grown tomato plant variety Mogeor (resistant to Pyranochaeta lycopersici) infected with Pyrenochaeta lycopersici (May still include original submitter created erros/discrepancies)

value: Mogeor

value: resistant


title: Resc 2, replicate 2

description: Gene expression data from mouse ESCs


title: DMSO 3, replicate 3

description: Gene expression data from mouse ESCs

source_name: ESCs treated for 60h with DMSO (control)


title: Low-gain Heifer 5

description: LG-Heifer 5

value: Heifer 5

value: Female

value: targeted daily body weight gain of 0.5 Kg/d (Low-gain, LG)

value: Arcuate nucleus (hypothalamus)

value: Methylated-enriched DNA

value: input DNA


title: genotype: Moneymaker - pathogen infection: uninfected - rep1

description: roots of greenhouse-grown tomato plant variety Moneymaker (susceptible to Pyranochaeta lycopersici) mock-treated (May still include original submitter created erros/discrepancies)

value: Moneymaker


title: genotype: Moneymaker - pathogen infection: uninfected - rep2

value: susceptible


title: genotype: Mogeor - pathogen infection: uninfected - rep2

description: roots of greenhouse-grown tomato plant variety Mogeor (resistant to Pyranochaeta lycopersici) mock treated (May still include original submitter created erros/discrepancies)


title: E8.75 WT heart, biological rep1

value: dissected embryonic heart

value: WT


title: genotype: Mogeor - pathogen infection: infected - rep2

value: Pyranochaeta lycopersici

value: 2 leaf expansion stage ('PO:0001052')

value: vermiculite


title: DMSO 2, replicate 2

description: Gene expression data from mouse ESCs

value: mouse embryonic stem cells (ESCs)


title: genotype: Mogeor - pathogen infection: uninfected - rep1


title: genotype: Moneymaker - pathogen infection: infected - rep1


title: High-gain Heifer 2

description: HG-Heifer 2

value: Heifer 2

value: targeted daily body weight gain of 1Kg/d (High-gain, HG)


title: High-gain Heifer 1

description: HG-Heifer 1

value: Heifer 1


title: DMSO 1, replicate 1

description: Gene expression data from mouse ESCs


title: MYCi 1, replicate 1

description: Gene expression data from mouse ESCs

source_name: ESCs treated for 60h with the 10058-F4 MYC inhibitor


title: Vitamin A-sufficient NALT lymphocytes 10 days post-infection, replicate 2

hyb_protocol: Six (6) micrograms of cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix HT MG-430 PM array. Following hybridization, arrays were washed and stained using the GeneTitan system.

scan_protocol: HT MG-430PM arrays were scanned using the Affymetrix GeneTitan system.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Affymetrix Expression Console software v1.1.

source_name: NALT lymphocytes from vitamin A-sufficient mouse harvested day 10 post-infection with Sendai virus

label_protocol: Twenty (20) nanograms of total RNA were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module.

growth_protocol: Control and vitamin A-deficient mice (n=3 per group) were infected with 250 pfu Sendai virus. Nasal tissues were harvested at 10 days post-infection and combined for each group. Tissue was treated with collagenase (4 mg/mL in PBS) for 30 min at 37°C, then passed through a 70 µM cell strainer with a syringe plunger. Cell suspensions were layered onto a 40/75% discontinuous percoll gradient and centrifuged at 1000xg for 30 min. Lymphocytes were collected from the gradient interface (nasal-associated lymph tissue [NALT]) and washed 1x with PBS.

extract_protocol: RNA was extracted using the RNeasy Microkit (Qiagen) according to the manufacturer's protocol.

tag: strain/background

value: vitamin A sufficient

value: nasal-associated lymph tissue (NALT) lymphocytes

tag: treatment

value: Sendai virus infection

tag: timepoint

value: day 10 post-infection


title: Vitamin A-sufficient NALT lymphocytes 10 days post-infection, replicate 1

tag: genotype/variation

tag: cell type


title: Vitamin A-deficient NALT lymphocytes 10 days post-infection, replicate 1

source_name: NALT lymphocytes from vitamin A-deficient mouse harvested day 10 post-infection with Sendai virus

value: vitamin A deficient


title: Vitamin A-sufficient NALT lymphocytes 10 days post-infection, replicate 3


title: Vitamin A-deficient NALT lymphocytes 10 days post-infection, replicate 3


title: Control pancreas, rep3

hyb_protocol: Ten micrograms of cRNA were fragmented and then hybridized for 16 hr at 45C on an Affymetrix Mouse Genome 430 2.0 GeneChip array. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

source_name: Postnatal day 15 whole pancreas, control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix).

growth_protocol: Mice were housed and maintained in a controlled environment and all procedures were performed in accordance with St. Jude IACUC guidelines.

extract_protocol: Total RNA was extracted using Trizol and the PureLink RNA Mini kit (Life Sciences).

value: NMRI

value: whole pancreas

tag: age

value: postnatal day 15


title: Control pancreas, rep1


title: Control pancreas, rep2


title: oxMYB72_WCS417_3

city: Utrecht

first: Corné

last: Pieterse

address: Padualaan 8

department: Biology

country: Netherlands

institute: Utrecht University

hyb_protocol: cRNA labeling, hybridization, washing and scanning of Affymetrix Arabidopsis ATH1 GeneChips (Affymetrix) were performed according to Affymetrix OneCycle Lab protocols (Affymetrix, Santa Clara, CA, USA).

data_processing: Data were normalized using the Robust Multichip Average (RMA) expression measure in the Affypackage (Gautier et al., 2004).

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Roots of 19-day-old oxMYB72 seedlings, 2 days after WCS417 treatment

growth_protocol: Growth protocols as described in: Zamioudis, C., Hanson, J. and Pieterse, C.M.J. (2014). ß-Glucosidase BGLU42 is a MYB72-dependent key regulator of rhizobacteria-induced systemic resistance and modulates iron deficiency responses in Arabidopsis roots. New Phytologist 204: 368-379.  Seeds of Col-0, myb72-2 and oxMYB72 were surface sterilized and sown on 1 X Murashige and Skoog (MS) agar-solidified medium supplemented with 1% sucrose (Murashige & Skoog, 1962). After 2 d of stratification at 4°C, the Petri dishes were positioned vertically and transferred toa growth chamber (22°C; 12 h : 12 h light : dark; light intensity, 100 μmol/m2/s). Uniform 5-d-old seedlings were transferred to new plates containing agar-solidified Hoagland medium composed of KNO3 (5 mM), KH2PO4 (2 mM), Ca(NO3)2 (5 mM), MgSO4 (2 mM), KCl (50 μM), H3BO3 (50 μM), MnSO4 (10 μM), ZnSO4 (2 μM), CuSO4 (1.5 μM), (NH4)6Mo7O24 (0.075 μM) and MES (2.5 mM). The concentration of Fe(III)EDTA was adjusted to 50 μM and the pH of the medium to 5.8. Pseudomonas fluorescens WCS417 (now renamed into Pseudomonas simiae WCS417) was cultured at 28°C on King’s medium B (KB) agar plates supplemented with 50 μg/ml of rifampicin. After 24 h of growth, cells were collected in 10 mM MgSO4, washed twice by centrifugation for 5 min at 5000 g and finally resuspended in 10mM MgSO4. For in vitro assays, the bacterial titer was adjusted to the optical density at 600 nm (OD600) of 0.01 (10-E7 colony-forming units (CFU)/ml).

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen), according to the manufacturer’s instructions. RNA purity and integrity were confirmed using an RNA 6000 Nano Assay (Agilent Technologies, Waldbronn, Germany) and gel electrophoresis.

treatment_protocol: Treatment protocol as described in: Zamioudis, C., Hanson, J. and Pieterse, C.M.J. (2014). ß-Glucosidase BGLU42 is a MYB72-dependent key regulator of rhizobacteria-induced systemic resistance and modulates iron deficiency responses in Arabidopsis roots. New Phytologist 204: 368-379.  Ten microliters of bacterial suspension were then applied on each root of 17-d-old seedlings, immediately below the hypocotyl.

tag: genotype

value: 35S:FLAG-MYB72/myb72-2 (oxMYB72)

value: roots

tag: developmental stage

value: 19-day-old seedlings


title: Leghorn-ind5_RJF

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

description: Biological replicate 5 of 6 for Leghorn compared to Red Jungle Fowl reference

hyb_protocol: The Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol for enzymatic labeling from Agilent Technologies was followed for hybridization.

scan_protocol: Either an Agilent G2505B Scanner was used following the manufacturers protocol or a GenePix 4100A scanner was used with settings of 5 µm resolution, a saturation tolerance of 0.005% and PMT adjusted to a ratio of 1 ± 0.05

data_processing: Feature extraction was performed using either the Agilent Feature Extraction Software or the GenePix software. Images were processed using R-Bioconductor, Agilent Genomic Workbench version 5.0, and Nexus Copy Number software version 6.1. In R-Bioconductor, data was log2-transformed and normalized by Scale and Centering. Log2 ratios were calculated using each sample as the tester to the red jungle fowl as the reference. This normalized data was processed by the two softwares per the company protocols.

organism: Gallus gallus

source_name: whole blood

label_protocol: The Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol for enzymatic labeling from Agilent Technologies was followed for labeling.

extract_protocol: Genomic DNA was isolated from whole blood using the Wizard Genomic DNA extraction kit per the manufacturers protocol.

tag: strain

value: White Leghorn

value: whole blood

value: Red Jungle Fowl


title: Vitamin A-deficient NALT lymphocytes 10 days post-infection, replicate 2


title: MYCi 2, replicate 2

description: Gene expression data from mouse ESCs

value: mouse embryonic stem cells (ESCs)


title: Fayoumi-ind4_RJF

description: Biological replicate 4 of 6 for Fayoumi compared to Red Jungle Fowl reference

value: Fayoumi


title: oxMYB72_WCS417_2

scan_protocol: cRNA labeling, hybridization, washing and scanning of Affymetrix Arabidopsis ATH1 GeneChips (Affymetrix) were performed according to Affymetrix OneCycle Lab protocols (Affymetrix, Santa Clara, CA, USA).


title: Prox1-OE pancreas, rep3

source_name: Postnatal day 15 whole pancreas, Prox1 overexpressed


title: oxMYB72_WCS417_1

label_protocol: cRNA labeling, hybridization, washing and scanning of Affymetrix Arabidopsis ATH1 GeneChips (Affymetrix) were performed according to Affymetrix OneCycle Lab protocols (Affymetrix, Santa Clara, CA, USA).


title: Prox1-OE pancreas, rep2


title: RJF_Leghorn-ind6

description: Red Jungle Fowl reference compared to Biological replicate 6 of 6 for Leghorn


title: oxMYB72_Ctrl_2

source_name: Roots of untreated, 19-day-old oxMYB72 seedlings


title: RJF_lineB-pool5

description: Red Jungle Fowl reference compared to Biological replicate 5 of 6 for line B

value: Line B


title: Prox1-OE pancreas, rep1


title: RJF_lineA-pool5

description: Red Jungle Fowl reference compared to Biological replicate 5 of 6 for line A

value: Line A


title: 1104 hiPSC-CMs unstimulated

type: SRA

city: Milwaukee

first: Wenli

last: Li

state: Wisconsin

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: CM harvested 18 hours post stimulation

library_source: transcriptomic

data_processing:
two-step alignment approach for RNA-seq alignment. First, TopHat (v.2.0.3)  was used with the following settings: '-r 70 --mate-std-dec 90' for paired-end reads from Illumina RNA-seq; and ‘-r 200’ for single-end reads from Proton RNA-seq. Second, unmapped reads from step one were realigned with Bowtie2 [30] using the “–very-sensitive-local” method.
HTseq(v0.6) was used for calculating raw read counts of Proton RNA-seq
raw read counts for AmpliSeq was produced by the ampliSeqRNA plugin available for Ion TorrentTM sequencing platforms
Illumina RNA-seq data for UHRR (Agilent Universal Human Reference RNA) and HBRR (Ambion FirstChoice® Human Brain Reference Total RNA):GEO accession number: GSE49712
Proton RNA-seq data for above two reference RNA samples: GEO accession number: GSE46876
Genome_build: UCSC hg19

source_name: hiPSC cardiomyocytes

extract_protocol:
Total RNA was extracted per manufacturer’s recommendations using total RNA Purification 96-Well Kit (Norgen Biotek Corp.).
Proton RNA-seq libraries were prepared for sequencing using standard ribosomal RNA depletion method for Proton RNA-seq. For library preparation of AmpliSeq whole transcriptome a barcoded cDNA library is first generated with SuperScript® VILO™ cDNA Synthesis kit from 10ng of total RNA. Then cDNA is amplified using Ion AmpliSeq™ technology to accurately maintain expression levels of all targeted genes. Amplified cDNA Libraries were evaluated for quality and quantified using Agilent Bioanalyzer High sensitivity chip. Libraries were then diluted to 100pM and pooled equally, with eight individual samples per pool.

treatment_protocol: The hiPSC-CMs were stimulated with endothelin-1 (ET-1) to induce a hypertrophic response following our established CM hypertrophy protocol (Aggarwal et al., 2014. Plos One.)

tag: individual

value: derived cardiomyocytes (CMs) from hiPSC

value: without Endothelin stimulation


title: Leghorn-ind4_RJF

description: Biological replicate 4 of 6 for Leghorn compared to Red Jungle Fowl reference


title: 1156 hiPSC-CMs stimulated

description: CM harvested 18 hours post stimulation

value: with Endothelin stimulation


title: 1104 hiPSC-CMs stimulated

description: CM harvested 18 hours post stimulation

data_processing:
two-step alignment approach for RNA-seq alignment. First, TopHat (v.2.0.3)  was used with the following settings: '-r 70 --mate-std-dec 90' for paired-end reads from Illumina RNA-seq; and ‘-r 200’ for single-end reads from Proton RNA-seq. Second, unmapped reads from step one were realigned with Bowtie2 [30] using the “–very-sensitive-local” method.
HTseq(v0.6) was used for calculating raw read counts of Proton RNA-seq
raw read counts for AmpliSeq was produced by the ampliSeqRNA plugin available for Ion TorrentTM sequencing platforms
Illumina RNA-seq data for UHRR (Agilent Universal Human Reference RNA) and HBRR (Ambion FirstChoice® Human Brain Reference Total RNA):GEO accession number: GSE49712
Proton RNA-seq data for above two reference RNA samples: GEO accession number: GSE46876
Genome_build: UCSC hg19

Raw data files are not available for open access.^SAMPLE = GSM1931830
two-step alignment approach for RNA-seq alignment. First, TopHat (v.2.0.3)  was used with the following settings: '-r 70 --mate-std-dec 90' for paired-end reads from Illumina RNA-seq; and ‘-r 200’ for single-end reads from Proton RNA-seq. Second, unmapped reads from step one were realigned with Bowtie2 [30] using the “–very-sensitive-local” method.
HTseq(v0.6) was used for calculating raw read counts of Proton RNA-seq
raw read counts for AmpliSeq was produced by the ampliSeqRNA plugin available for Ion TorrentTM sequencing platforms
Illumina RNA-seq data for UHRR (Agilent Universal Human Reference RNA) and HBRR (Ambion FirstChoice® Human Brain Reference Total RNA):GEO accession number: GSE49712
Proton RNA-seq data for above two reference RNA samples: GEO accession number: GSE46876
Genome_build: UCSC hg19

Raw data files are not available for open access.^SAMPLE = GSM1931831
two-step alignment approach for RNA-seq alignment. First, TopHat (v.2.0.3)  was used with the following settings: '-r 70 --mate-std-dec 90' for paired-end reads from Illumina RNA-seq; and ‘-r 200’ for single-end reads from Proton RNA-seq. Second, unmapped reads from step one were realigned with Bowtie2 [30] using the “–very-sensitive-local” method.
HTseq(v0.6) was used for calculating raw read counts of Proton RNA-seq
raw read counts for AmpliSeq was produced by the ampliSeqRNA plugin available for Ion TorrentTM sequencing platforms
Illumina RNA-seq data for UHRR (Agilent Universal Human Reference RNA) and HBRR (Ambion FirstChoice® Human Brain Reference Total RNA):GEO accession number: GSE49712
Proton RNA-seq data for above two reference RNA samples: GEO accession number: GSE46876
Genome_build: UCSC hg19

Raw data files are not available for open access.


title: RJF_lineB-pool6

description: Red Jungle Fowl reference compared to Biological replicate 6 of 6 for line B


title: RJF_Fayoumi-ind3

description: Red Jungle Fowl reference compared to Biological replicate 3 of 6 for Fayoumi


title: 1156 hiPSC-CMs unstimulated

description: CM harvested 18 hours post stimulation

data_processing:
two-step alignment approach for RNA-seq alignment. First, TopHat (v.2.0.3)  was used with the following settings: '-r 70 --mate-std-dec 90' for paired-end reads from Illumina RNA-seq; and ‘-r 200’ for single-end reads from Proton RNA-seq. Second, unmapped reads from step one were realigned with Bowtie2 [30] using the “–very-sensitive-local” method.
HTseq(v0.6) was used for calculating raw read counts of Proton RNA-seq
raw read counts for AmpliSeq was produced by the ampliSeqRNA plugin available for Ion TorrentTM sequencing platforms
Illumina RNA-seq data for UHRR (Agilent Universal Human Reference RNA) and HBRR (Ambion FirstChoice® Human Brain Reference Total RNA):GEO accession number: GSE49712
Proton RNA-seq data for above two reference RNA samples: GEO accession number: GSE46876
Genome_build: UCSC hg19

Raw data files are not available for open access.


title: Fayoumi-ind6_RJF

description: Biological replicate 6 of 6 for Fayoumi compared to Red Jungle Fowl reference


title: Fayoumi-ind5_RJF

description: Biological replicate 5 of 6 for Fayoumi compared to Red Jungle Fowl reference


title: RJF_lineA-pool6

description: Red Jungle Fowl reference compared to Biological replicate 6 of 6 for line A


title: oxMYB72_Ctrl_3


title: oxMYB72_Ctrl_1


title: Leghorn-ind3_RJF

description: Biological replicate 3 of 6 for Leghorn compared to Red Jungle Fowl reference


title: myb72_WCS417_2

source_name: Roots of 19-day-old myb72-2 seedlings, 2 days after WCS417 treatment


title: RJF_Fayoumi-ind2

description: Red Jungle Fowl reference compared to Biological replicate 2 of 6 for Fayoumi


title: lineB-pool3_RJF

description: Biological replicate 4 of 6 for line B compared to Red Jungle Fowl reference


title: myb72_WCS417_1


title: myb72_Ctrl_2

source_name: Roots of untreated,19-day-old myb72-2 seedlings


title: myb72_WCS417_3


title: RJF_lineA-pool4

description: Red Jungle Fowl reference compared to Biological replicate 4 of 6 for line A


title: Col-0_WCS417_3

source_name: Roots of 19-day-old Col-0 seedlings, 2 days after WCS417 treatment


title: 22Rv1-Wildtype untransfected-2

city: Madison

first: Jordan

middle: Edmund

last: Bloom

state: WI

address: 1111 Highland Ave.

department: Medicine

institute: University of Wisconsin-Madison

hyb_protocol: Samples were hybridized with Human Transcriptome Array 2.0(Affymetrix) and scanned at the University of Wisconsin-Madison Biotechnology Center.

scan_protocol: Gene chips were post processed on the AFX Fluidics 450 Station, and Chips were scanned on the GC3000 G7 Scanner (Serial #50208130)

data_processing: Raw data were processed with the Affymetrix Command Console version 4.0.0.1567G (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with Transcriptome Analysis Console 3.0(Affymetrix). RMA expression value derived from Expression Console software; core-gene analysis.

source_name: 22Rv1 Cells- Wildtype

label_protocol: Single-stranded cDNA was generated from 15ug the total cRNA with the Affymetrix WT Plus Expression and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix), according to manufacturer's instructions.

growth_protocol: Cells were grown in DMEM medium supplemented with 10% fetal calf serum,200U/ml penicillin/streptomycin,1mM sodium pyruvate, and 0.1uM B-mercaptoethanol at 37C/5%CO2. Cells were harvested once they reached confluence in a T75 dish, harvested cells were centrifuged at 200gx5mins and then proceeded to RNA extraction

extract_protocol: RNA was extracted using the Reliaprep RNA cell miniprep system(Promega) according to manufacturer's instructions. Quality assessment was conducted using an Agilent RNA Nanochip and by a Nanodrop spectrophotometer (Thermo). Total RNA RIN values average 2.50

treatment_protocol: Cells were transfected using lipofectamine with shRNA against SSX2 (SAbiosciences) or scramble shRNA control, selection was maintained by 1mg/ml neomycin in the media

tag: ssx expression

value: High (wildtype)

tag: cell line


title: myb72_Ctrl_1


title: 22Rv1-scramble shRNA control-3

source_name: 22Rv1 Cells- shRNA scramble control

value: High (scramble control)


title: 22Rv1-scramble shRNA control-2


title: Col-0_WCS417_2


title: myb72_Ctrl_3


title: RJF_Leghorn-ind2

description: Red Jungle Fowl reference compared to Biological replicate 2 of 6 for Leghorn


title: lineB-pool1_RJF

description: Biological replicate 2 of 6 for line B compared to Red Jungle Fowl reference


title: RJF_Fayoumi-ind1

description: Red Jungle Fowl reference compared to Biological replicate 1 of 6 for Fayoumi


title: 22Rv1-scramble shRNA control-1


title: 22Rv1-Wildtype untransfected-3


title: lineA-pool3_RJF

description: Biological replicate 3 of 6 for line A compared to Red Jungle Fowl reference


title: 22Rv1-SSX2 Knockdown-3

source_name: 22Rv1 Cells-SSX2 Knockdown


title: Col-0_WCS417_1


title: 22Rv1-Wildtype untransfected-1


title: RJF_Leghorn-ind1

description: Red Jungle Fowl reference compared to Biological replicate 1 of 6 for Leghorn


title: lineB-pool2_RJF

description: Biological replicate 3 of 6 for line B compared to Red Jungle Fowl reference


title: Col-0_Ctrl_2

source_name: Roots of untreated,19-day-old Col-0 seedlings


title: Col-0_Ctrl_3


title: lineA-pool1_RJF

description: Biological replicate 2 of 6 for line A compared to Red Jungle Fowl reference


title: Col-0_Ctrl_1


title: 157T_NOD-_ER+_PR+_HER-

status: Public on Feb 10 2016

city: Bangalore

first: Neeraj

last: KUMAR

address: Indian Institute of Science Bangalore

department: MRDG

country: India

institute: Indian Institute of Science Bangalore

hyb_protocol: 750 ng of labelled cRNA each from normal and Tumor were mixed with blocking agent and fragmentation buffer followd by incubation at 65 °C for 30 min. This is followed by addition of 55 ul of 2x GEx Hybridization Buffer HI-RPM to stop the fragmentation reaction. Later 100 ul of the above mix were added to each array.

scan_protocol: Agilent Feature Extraction Software (10.5.1.1) was used for background subtraction and LOWESS normalization.

data_processing: normalized log10 ratio (Cy5/Cy3) tumor/normal

source_name: breast tissue

label_protocol: 200 ng of RNA each from normal and tumor samples were used. Labeling of the probes was done using the Low RNA Input Linear Amplification Kit (Agilent Technologies, USA). Briefly 200 ng of RNA were reverse transcribed using T7promoter attached Oligo-dT primers at 40 °C for 2 hrs followed by 65 °C for 15 min. This cDNA were transcribed using T7 polymerase with respective labelled nucleotides at 40 °C for 2hrs. This synthesized labelled cRNA were purified using RNeasy mini column.

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

value: normal breast tissues

value: tumor breast tissue

tag: patient id

tag: nod status

value: NOD-

tag: er status

value: ER+

tag: pr status

value: PR+

tag: her status

value: HER-

tag: er

tag: pr

tag: her

tag: size

tag: diag.

value: IDC - III with focal DCIS, and with infiltrating margins (both breasts)

tag: skin

value: Free

tag: dsm

tag: nodal status

value: No nodes identified

tag: last follow-up

value: Patient didn't turned up for adj treatment

tag: other relevant investigations

tag: follow-up period


title: 22Rv1-SSX2 Knockdown-2

tag: ssx expression

tag: cell line


title: 96T_NOD-_ER0_PR0_HER0

tag: tissue

tag: patient id

tag: nod status

value: IDC III  with infiltrating margins, and showing lymphocytic response.

tag: last follow-up notes

value: NAD (To continue with Tamoxifen)


title: 80T_NOD-_ER-_PR-_HER+

tag: er status

value: ER-

tag: pr status

value: PR-

tag: her status

value: HER+

tag: er

value: IDC - III with focal high grade DCIS, Margins fairly circumscribed, lymphocytic infiltration seen at the periphery

value: Close but free

value: NAD


title: 84T_NOD+_ER0_PR0_HER0

value: normal breast tissues

value: tumor breast tissue

value: NOD+

tag: pr

tag: her

tag: age

tag: size

tag: diag.

value: IDC-III, with infiltrating margins

value: involved

value: Advised RT, But patient didn't come further.


title: RJF_lineB-pool4

description: Red Jungle Fowl reference compared to Biological replicate 1 of 6 for line B

tag: strain

value: Red Jungle Fowl

value: whole blood

value: Line B


title: 22Rv1-SSX2 Knockdown-1


title: 75T_NOD+_ER+_PR+_HER-

value: ER+

value: PR+

value: HER-

value: IDC - III with focal high grade DCIS, and infiltrating margins

tag: skin

value: Free

tag: dsm

tag: nodal status

value: 4/10 metastases

tag: last follow-up

tag: other relevant investigations

tag: follow-up period


title: 93T_NOD-_ER-_PR+_HER+

tag: tissue

tag: patient id

tag: nod status

value: NOD-

value: ER-

value: HER+

value: IDC - III with focal DCIS, and with infiltrating margins

value: vertebra metastases


title: 70T_2NOD+_ER0_PR0_HER0

value: normal breast tissues

value: tumor breast tissue

tag: er status

tag: pr status

tag: her status

value: IDC - III with high grade extensive DCIS, and infiltrating margins

value: Involved

value: 2/10 metastases

tag: last follow-up notes

value: NAD


title: 150T_NOD+_ER+_PR+_HER-

value: NOD+

value: ER+

tag: er

tag: pr

tag: her

tag: age

value: IDC - III with margins focally infiltrative

value: Dermis shows involvement

value: 4/7 metastases

value: Patient discharged, didnt turn up further.


title: 159T_NOD-_ER+_PR-_HER-

value: NOD-

value: PR-

value: HER-

tag: size

tag: diag.

value: IDC-III with infiltrating margins

tag: skin

value: Free


title: 149T_NOD+_ER+_PR+_HER-

value: normal breast tissues

value: PR+

value: IDC-III

tag: dsm

tag: nodal status

value: 6/12 meta

tag: last follow-up


title: 233T_NOD+_ER+_PR+_HER-

tag: tissue

value: tumor breast tissue

value: DCIS high grade with focal area of invasion.

value: 11/11 node & 2/2 apical nodes free

tag: other relevant investigations

tag: follow-up period


title: 227T_NOD-_ER-_PR-_HER-

tag: patient id

tag: nod status

tag: er status

value: ER-

value: DCIS High grade (with one focus of invasion).

value: 15/15 Reactive

value: NAD


title: 268T_NOD-_ER-_PR+_HER+

tag: pr status

tag: her status

value: HER+

value: DCIS

value: 10/10 reactive


title: 58T_NOD-_ER-_PR+_HER+

value: NOD-

tag: er

tag: pr

value: IDC- III with infiltrating margins

tag: last follow-up notes

value: Blood in sputum


title: 135T_NOD-_ER+_PR+_HER+

value: normal breast tissues

value: ER+

tag: her

tag: age

tag: size

value: Mucinous carcinoma with neuro endocrine areas grade- III with infiltrating margins

value: Free

value: close to tumour

value: NAD(To continue with Letrozol)


title: lineA-pool2_RJF

description: Biological replicate 1 of 6 for line A compared to Red Jungle Fowl reference

tag: strain

value: Line A

value: whole blood

value: Red Jungle Fowl


title: 229T_NOD-_ER-_PR-_HER

value: tumor breast tissue

value: ER-

value: PR-

value: HER

tag: diag.

value: IDC III  with focal DCIS

tag: skin

tag: dsm

tag: nodal status

value: 3/15 shows Metastases


title: 193T_NOD+_ER-_PR+_HER-

tag: tissue

value: NOD+

value: PR+

value: HER-

value: IDC-III, margins fairly circumscrebed

value: 4/12 Metastases

tag: last follow-up

tag: other relevant investigations

value: Supraclavicular node metastses.

tag: follow-up period


title: 210T_NOD-_ER-_PR+_HER0

value: normal breast tissues

tag: patient id

tag: nod status

value: NOD-

tag: er status

tag: pr status

value: Cannot be evaluated

value: Residual DCIS tumour

value: Tumour present in dermis

value: 11/11 Free(Right), 1/12 metastases(left)


title: 78T_NOD+_ER-_PR-_HER+

value: tumor breast tissue

value: ER-

tag: her status

value: HER+

tag: er

tag: pr

value: 3x2 cms

value: IDC- III with focal high grade DCIS, margins infiltrating

value: Free

value: 3/10 metastases

tag: last follow-up notes

value: Pain in operated site

value: 7 months


title: 28T_NOD-_ER-_PR-_HER+

value: PR-

tag: her

tag: age

tag: size

value: IDC-III

value: Negative


title: 180T_NOD-_ER-_PR+_HER+

value: normal breast tissues

value: NOD-

value: PR+

tag: diag.

value: IDC -III, with infiltrating margisn and focal DCIS

tag: skin

tag: dsm


title: 82T_NOD-_ER+_PR+_HER+

tag: tissue

value: ER+

value: IDC-III with infiltrating margins, vasculat emboli present with deposits in fat

tag: nodal status

tag: last follow-up

value: Passed away in November 2010

value: Developed veribral and liver metastasis


title: 190T_NOD-_ER-_PR-_HER-

value: tumor breast tissue

tag: patient id

value: ER-

value: HER-

value: DCIS high grade

value: NAD

tag: other relevant investigations

tag: follow-up period


title: 136T_NOD+_ER+_PR+_HER-

tag: nod status

value: NOD+

tag: er status

tag: pr status

value: Neuro endocrine carcinoma- skin and margins fairly circumscribed, close to tumour but free

value: involved

value: 3/17 metastases

value: Plan for RT, But patient not willing for RT/CT


title: 166T_NOD-_ER+_PR+_HER-

value: normal breast tissues

value: NOD-

tag: her status

tag: er

tag: pr

value: IDC-III with infiltrating margins

value: Free

value: 10/10 reactive


title: 138T_NOD-_ER-_PR+_HER-

value: PR+

tag: her

tag: age

value: IDC - III with extensive DCIS, and with infiltrating margins

value: Close but free

value: 9/9 Free

tag: last follow-up notes


title: 57T-_NOD+_ER-_PR-_HER+

value: tumor breast tissue

value: ER-

value: PR-

value: HER+

tag: size

tag: diag.

value: IDC-III

tag: skin

value: 1/13 meta


title: 54T_NOD-_ER-_PR-_HER0

tag: tissue

value: Not done

value: IDC - III with focal DCIS, margins fairly circumscribed, with moderate lymphocytic infiltrate

tag: dsm

tag: nodal status


title: 303T_NOD-_ER-_PR-_HER-

value: normal breast tissues

tag: patient id

value: HER-

value: IDC-III with circumscribed margins.

value: 17/17 nodes free

tag: last follow-up

value: NAD

tag: other relevant investigations


title: 72T_NOD+_ER-_PR-_HER+

tag: nod status

value: NOD+

tag: er status

value: IDC -III, infiltrating margins were seen, Moderate Desmoplasia dermal lymphatic emboli were seen

value: Free

value: 15/22 meta apical nodes  adipose tissue

tag: follow-up period


title: 304T_NOD-_ER-_PR-_HER-

value: tumor breast tissue

value: NOD-

tag: pr status

tag: her status

tag: er

value: IDC-III with infiltrating margins. Moderate lymphocytic infiltrate seen, Dense Fibrosys


title: 194T_NOD-_ER+_PR-_HER+

value: ER+

value: PR-

value: HER+

tag: pr

tag: her

tag: age

value: IDC - III with focal DCIS

value: close, but free

value: Patient did not come further


title: 92T_NOD+_ER+_PR+_HER+

value: normal breast tissues

value: PR+

tag: size

tag: diag.

value: Involved. Stroma shows moderate desmoplasia

value: 4/10 metastases with PNS.

tag: last follow-up notes

value: Skeletal metastases

value: bone metastases & multiple skeletal metastases


title: 151T_NOD+_ER-_PR-_HER-

tag: tissue

value: NOD+

value: ER-

value: HER-

value: IDC-III

tag: skin

tag: dsm

value: 5/13 meta


title: 60T_NOD-_ER-_PR-_HER+

value: tumor breast tissue

tag: patient id

value: NOD-

value: IDC - III with infiltrating margin

value: Free

tag: nodal status

value: 3/3 Neg., 3/3 extra nodes free

tag: last follow-up

value: NAD


title: 244T_NOD-_ER-_PR-_HER+

value: normal breast tissues

tag: nod status

tag: er status

value: PR-

value: HER+

value: IDC - III with dense lymphoplasmacytic and focally infilterate  periphery around tumor cells.

value: 11/11 Free, Apical node- Free

tag: other relevant investigations


title: 171T_NOD-_ER-_PR-_HER-

tag: pr status

tag: her status

value: IDC with infiltrating margins, stroma shows moderate desmoplasia with areas of necrosis

value: 9/9 reactive

tag: follow-up period


title: 43T_NOD+_ER+_PR+_HER+

value: NOD+

value: ER+

value: PR+

tag: er

tag: pr

tag: her

value: ILC - III - Bilateral breast, with focal insitu lobular

value: Positive - of right breast

value: 7/7 metastases with perpheral nodal spread

value: Multiple skeletal lesions


title: 300T_NOD+_ER-_PR-_HER-

value: tumor breast tissue

value: ER-

value: HER-

tag: age

tag: size

value: 4x3x2( diffused gray white areas)

tag: diag.

value: IDC- III with infiltrating margins, vascular emboli present

value: Free

value: 2/15 nodes show metastasis


title: 179T_NOD-_ER-_PR-_HER-

tag: tissue

value: normal breast tissues

value: NOD-

value: PR-

value: IDC III  with focal DCIS and infiltrating margins, showing moderate lymphocytic response.

tag: skin

value: close to tumour, but free

tag: last follow-up notes

value: Advised CT/RT, Patient refused.


title: 59T_NOD-_ER-_PR-_HER+

tag: patient id

value: HER+

value: IDC-III with infiltrative margins

tag: dsm

tag: nodal status

value: 10/10 reactive


title: 155T_NOD+_ER+_PR+_HER+

tag: nod status

value: NOD+

tag: er status

value: ER+

value: PR+

value: IDC-III

value: 3/17 meta

tag: last follow-up


title: 46T_NOD-_ER-_PR-_HER+

value: tumor breast tissue

value: ER-

tag: pr status

tag: her status

value: IDC - III with focal DCIS, margins circumscribed, with moderate lymphocytic infiltrate

value: Very close to DSM

value: 8/8 free

value: NAD

tag: other relevant investigations


title: 61T_NOD0_ER+_PR+_HER+

value: normal breast tissues

tag: er

tag: pr

value: IDC -II with all margins free and dense fibrosis.

tag: follow-up period


title: 35T_NOD+_ER+_PR+_HER+

tag: her

tag: age

tag: size

value: IDC - III with focal DCIS

value: 5/11 metastases with perinodal spread

value: Pain in left side of chest, due to advanced disease. Advised palliative treatments.


title: 79T_NOD+_ER-_PR-_HER+

tag: tissue

value: PR-

value: HER+

tag: diag.

value: IDC-III with margins circumscribed

tag: skin

value: Free

value: 1 node +ve, 6/6 nodes -ve


title: 295T_NOD+_ER+_PR+_HER+

tag: patient id

value: NOD+

value: ER+

value: PR+

value: IDC-III with moderate lymphocytic response

tag: dsm

value: 15/26 nodes show metastases.

value: Passed away on 26/9/09


title: 160T_NOD+_ER-_PR-_HER+

value: tumor breast tissue

tag: nod status

value: ER-

value: IDC-III with infiltrating margins

tag: nodal status

value: 5/11 show metastasis

tag: last follow-up notes

value: NAD

value: Recurrence chest wall & Bone metastasis


title: 25T_NOD+_ER-_PR-_HER+

value: normal breast tissues

tag: er status

tag: pr status

value: PR-

value: Focal IDC with extensive high grade DCIS

value: 3/10 metastases with perinodal spread

tag: last follow-up


title: 235T_NOD+_ER+_PR+_HER+

tag: her status

value: HER+

tag: er

value: 2+, Advised FISH

value: IDC- III with focal DCIS and infiltrating margins

value: Free

value: 2/16 Metastases with perinodal spread.

tag: other relevant investigations


title: 251485053519-2_NOD+_ER-_PR+_HER-

value: NOD+

value: PR+

value: HER-

tag: pr

tag: her

value: IDC-III

value: POSITIVE

tag: follow-up period


title: 40T_NOD+_ER-_PR-_HER+

tag: tissue

value: tumor breast tissue

value: ER-

tag: age

tag: size

value: IDC - III with extensive DCIS, and with infiltrating margins

value: Involved

value: 4/8 metastases


title: 89T_NOD-_ER-_PR+_HER+

value: normal breast tissues

tag: patient id

value: NOD-

tag: diag.

value: IDC - III with infiltrating margins

tag: skin

value: involved, upper dermis with ulceration

value: Vomitings

value: Metastasis insternnum;She was Dead


title: 266T_NOD+_ER+_PR+_HER+

tag: nod status

value: ER+

value: HER+

value: IDC- III with infiltrating margins

value: Free

tag: dsm

tag: nodal status

value: 2/16 nodes show metastasis

value: NAD


title: 42T_NOD+_ER-_PR+_HER-

value: tumor breast tissue

value: NOD+

tag: er status

tag: pr status

value: PR+

value: HER-

value: IDC III with focal infiltrating margins

value: Very close to tumour

value: 4/10 lymph nodes show metastasis

tag: last follow-up notes

value: Chest wall recurrence


title: 132T_NOD+_ER+_PR+_HER+

value: normal breast tissues

tag: her status

tag: er

value: IDC-III with focal high grade DCIS and infiltrating margins - superior surgical margin shows involvement, other margins- free

value: 11/15 nodes show metastases.

tag: last follow-up


title: 277T_NOD-_ER-_PR-_HER+

value: NOD-

value: ER-

value: PR-

tag: pr

tag: her

value: IDC-III witn infiltrating margins, lymphatic emboli seen

tag: other relevant investigations


title: 267T_NOD-_ER-_PR-_HER+

tag: tissue

value: HER+

tag: age

value: IDC- III with infiltrating margins

value: Free

tag: follow-up period


title: 269T_NOD0_ER-_PR-_HER-

value: tumor breast tissue

tag: patient id

tag: size

tag: diag.

value: IDC-III , Areas of necrosis, lymphatic emboli seen.

value: Not removed

value: Advides RT, Patient did not come.


title: 68T_NOD+_ER-_PR+_HER+

tag: nod status

value: NOD+

value: PR+

value: IDC-III

tag: skin

tag: dsm

value: 3/10 meta


title: 236T_NOD-_ER-_PR-_HER-

value: normal breast tissues

tag: er status

tag: pr status

value: HER-

value: IDC -III with focal margins infiltrating predominantly circumscribed, lymphocytic response seen at the edge.

tag: nodal status

value: 9/9 Free

value: completed 3 cycles of 2nd line CT

value: Multiple liver masses.


title: 51T_NOD+_ER+_PR+_HER+

value: ER+

tag: her status

value: HER+

tag: er

value: 1/12 metastaic


title: 256T_NOD0_ER-_PR-_HER-

value: tumor breast tissue

value: ER-

value: PR-

tag: pr

value: IDC-III, large areas of necrosis

value: Free

value: 3/14 nodes metastasis

tag: last follow-up

tag: last follow-up notes

value: NAD

value: Bilateral carcinoma


title: 239T_NOD+_ER-_PR-_HER

tag: tissue

value: normal breast tissues

value: NOD+

value: HER

tag: her

value: IDC- III with infiltrating margins, inferia margins shows tumour.

value: 9/16 Metastases

value: No follow up after 11.10.10

tag: other relevant investigations


title: 238T_NOD-_ER-_PR-_HER-

tag: patient id

value: NOD-

value: HER-

tag: age

value: IDC- III with sqvamoid areas and infiltrating margins,moderate lymphocytic response

value: 7/7 Free, 2/2 apical nodes Free

value: Regular follow up,NAD

tag: follow-up period


title: 186T_NOD-_ER+_PR+_HER+

value: tumor breast tissue

tag: nod status

value: ER+

value: PR+

value: HER+

tag: size

tag: diag.

value: IDC- III with focal DCIS and infiltrating margins and moderate desmoplaria

value: NAD, To continue Litrazol


title: 164T_NOD+_ER-_PR-_HER-

value: normal breast tissues

tag: er status

value: ER-

value: PR-

value: IDC- III with infiltrating margins and moderate desmoplaria with focal DCIS

tag: skin

value: Free

tag: dsm

value: 2/14 metastases

value: Plan for RT, But didn't turn up.


title: 192T_NOD-_ER-_PR-_HER-

value: NOD-

tag: pr status

tag: her status

value: HER-

value: IDC-III with medullary like areas(Both breasts)

value: involved in Right

tag: nodal status

value: 11/11 Free(Right), 1/12 metastases(left)

value: NAD


title: 168T_NOD-_ER-_PR-_HER-

value: tumor breast tissue

tag: er

tag: pr

value: IDC-III stroma in minimal large area of necrosis

value: very close to tumour

value: 12/12 are reactive

tag: last follow-up


title: 254T_NOD-_ER-_PR-_HER-

tag: tissue

value: normal breast tissues

tag: her

value: IDC-III


title: 255T_NOD-_ER-_PR-_HER-

tag: patient id

value: ER-

value: PR-

value: IDC - III with margins fairly well circumscribed, stroma is minimal, larger areas of necrosis seen.

tag: last follow-up notes

value: Head ache/ Vomiting, Advised brain CT scan

tag: other relevant investigations

value: Brain metastasis


title: 173T_NOD+_ER-_PR-_HER-

tag: nod status

value: NOD+

tag: age

value: IDC-III with predominantly high grade DCIS

value: Free

value: 7/17 metsatasis

value: Planed second line CT, Inj Docetaxel & carboplatin

value: Recurent tumour

tag: follow-up period


title: 198T_NOD-_ER-_PR-_HER-

value: tumor breast tissue

value: NOD-

tag: er status

value: HER-

tag: size

tag: diag.

value: IDC- III with infiltrating margins and mild lymphocytic response.

value: NAD


title: 184T_NOD-_ER-_PR-_HER-

value: normal breast tissues

tag: pr status

value: IDC - III , fairly circumscribed with lymphocytic infiltrate, Medial margins shows a focal DCIS, Inferia of other margins are free

tag: skin

tag: dsm


title: 176T_NOD+_ER-_PR-_HER-

value: ER-

value: PR-

tag: her status

tag: er

value: IDC-III with infiltrative margins,Necrosis& emboli , high grade DCIS seen

tag: nodal status

value: 6/10 nodes show metas with peri nodal spread


title: 162T_NOD-_ER-_PR-_HER-

tag: tissue

tag: pr

value: IDC-III with infiltrative margins

value: Free but clode to tumour

value: 17/17 reactive changes

tag: last follow-up


title: 292T_NOD+_ER-_PR-_HER-

tag: patient id

value: NOD+

tag: her

value: Medullary carcinoma grade - III

value: Free

value: 8/10 show metastasis

tag: last follow-up notes

value: Passed away on August 2011

value: Brain metastases.


title: 45T_NOD-_ER-_PR-_HER-

value: tumor breast tissue

tag: nod status

value: NOD-

value: HER-

tag: age

value: IDC-III

value: Involved with ulcer

value: Very close to Tumour

value: 10/10 nodes free

tag: other relevant investigations


title: 67T_NOD+_ER-_PR-_HER-

value: normal breast tissues

tag: er status

value: ER-

value: PR-

tag: size

value: IDC- III moderate desmoplaria with focal DCIS

value: 7/11 metastases with Peri nodal spread.

value: Advised RT, Patient didn't come further

value: Severe pain and advanced disease

tag: follow-up period


title: LSK_R882H_rep2

city: Tokyo

first: Junji

last: Koya

address: 7-3-1, Hongo, Bunkyo-ku

country: Japan

institute: The University of Tokyo

hyb_protocol: 2 micrograms of cDNA were hybridized to the Agilent SurePrint G3 Mouse Gene Expression 8x60K (Agilent) by using Gene Expression Hybridization Kit (Agilent).

scan_protocol: Arrays were scanned using Agilent microarray scanner.

data_processing: The scanned images were analyzed with Agilent Feature Extraction 10 (Agilent). Genechip analysis was performed using GeneSpring GX 12.6 software (Agilent). The median shift normalization to the 75th percentile and baseline transformation using the median of all samples was applied. Data were filtered on expression 20-100 percentile and detected flags in the raw data at least 1 out of 9 samples.

source_name: DNMT3A R882H-transduced LSK cells derived from transplanted mice

label_protocol: Biotin labeling of fragmented cDNA was carried out by SureTag Complete DNA Labeling Kit (Agilent).

growth_protocol: C57BL/6 mice were maintained in specific-pathogen-free facility at The University of Tokyo.

extract_protocol: Total RNA was extracted by TaKaRa NucleoSpin RNA XS (Takara). Amplified cDNA was obtained from 3.67 ng of total RNA by using NuGen Ovation Pico WTA System V2 (NuGEN).

tag: strain/background

tag: cell type

value: murine LSK cells

tag: treatment

value: DNMT3A R882H-transduced


title: LSK_R882H_rep3


title: LSK_WT_rep1

source_name: DNMT3A wild-type-transduced LSK cells derived from transplanted mice

value: DNMT3A wild-type-transduced


title: LSK_R882H_rep1


title: LSK_WT_rep3


title: LSK_EV_rep3

source_name: empty vector-transduced LSK cells derived from transplanted mice

value: empty vector-transduced


title: Human Peripheral Blood T cells [Sample_40]

city: New Haven

first: Rakesh

last: Verma

state: CT

address: 333 Cedar St.

department: Yale Cancer Center

institute: Yale University

hyb_protocol: Samples were hybridized with GeneChip® Human Transcriptome Array 2.0 (Affymetrix) and scanned at the Yale Center for Genome Anlaysis (YCGA) Microarray Core Facility.

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

data_processing: Data on coding genes were analyzed using Genespring GX 12.5 platform. Data were imported via exon expression workflow employing RMA16 or PLIER16 (normalization) for analyzing the coding genes using the specific annotation support file for human transcriptome array 2.0 (as provided by Genespring GX).

source_name: Human Peripheral Blood T cells

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Not Applicable

extract_protocol: RNA was isolated from sorted peripheral blood T cells using RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

tag: gender

value: M

value: Peripheral Blood T cells

tag: agent

tag: time point

value: post


title: Human Peripheral Blood T cells [Sample_31]

tag: tissue

value: pre


title: LSK_EV_rep2


title: Human Peripheral Blood T cells [Sample_39]


title: LSK_EV_rep1


title: Human Peripheral Blood T cells [Sample_25]


title: Human Peripheral Blood T cells [Sample_24]


title: Human Peripheral Blood T cells [Sample_36]

value: F


title: LSK_WT_rep2


title: Human Peripheral Blood T cells [Sample_35]


title: Human Peripheral Blood T cells [Sample_30]


title: Human Peripheral Blood T cells [Sample_28]


title: Human Peripheral Blood T cells [Sample_33]


title: Human Peripheral Blood T cells [Sample_32]


title: Human Peripheral Blood T cells [Sample_37]


title: Human Peripheral Blood T cells [Sample_29]


title: Human Peripheral Blood T cells [Sample_34]