title: Acute_Bleo_5xIC50_t=24 (n=2)

description: 0_acuut Bleo 5xIC50 t=24_5 vs Bleo IC50 t=24_3 gl12964191

tag: cell line

tag: cell type

value: human microvascular endothelial cell line


title: SEQC NB patient 465

status: Public on Oct 21 2014

type: RNA

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

hyb_protocol: Hybridization was performed following the manufacturer's protocol. In brief, 1650 ng of Cy3-labeled cRNA was hybridized on 4x44K custom microarrays using Agilent's High-RPM Gene Expression Hyb Kit. Hybridization was performed for 17 hours at 65°C in a rotating hyb oven at 10 rpm according the company's recommendations.

scan_protocol: After washing, scanning was performed at an Agilent scanner G2505C according to the manufacturer's protocol.

data_processing: Resulting TIFF-images were processed using Agilent's Feature Extraction software Version 9.5.1.

molecule: total RNA

organism: Homo sapiens

source_name: neuroblastoma

label_protocol: Labeling was performed according to Agilent's recommentdations. In brief, 1µg total of tumor RNA was linearily amplified and labeled with Cy3 using Agilent's one-color Quick Amp Labeling Kit following the instructions of the protocol.

extract_protocol: 30-60mg of snap-frozen neuroblastoma specimen was cryo-sectioned and were homogenized in TRIzol reagent (Invitrogen, Karlsruhe, Germany) using the FastPrep FP120 cell disruptor (Qbiogene, Inc, Carlsbad, CA, USA).Total RNA was isolated following the TRIzol protocol (Invitrogen) and RNA integrity was assessed using the 2100 Bioanalyzer (Agilent, Waldbronn, Germany). Only samples with an RNA Integrity Number >7.5 were taken for further analysis.

treatment_protocol: All neuroblastoma samples of this set were obtained prior to any cytotoxic treatment and were snap-frozen immediately after surgery. Prior to RNA extraction tumor cell content was checked by a pathologist and only samples with >60% tumor content were processed further.

tag: tissue

value: Neuroblastoma

tag: dataset

tag: Sex

value: F

tag: age at diagnosis

tag: mycn status

tag: high risk

tag: inss stage

tag: class label

tag: progression

tag: death from disease


title: SEQC NB patient 464

value: M


title: SEQC NB patient 463


title: SEQC NB patient 461


title: SEQC NB patient 453


title: SEQC NB patient 455


title: Senescence Day 3, replicate 3

status: Public on Oct 22 2014

city: Poznan

first: Agnieszka

last: Zmienko

address: Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

description: Biological replicate 3 of 3. Samples collected 3 days after senescence induction by placing the leaves in the dark.

hyb_protocol: All of the hybridization, washing and drying steps were performed in A4x44k Quad Chambers in an HS 4800 Pro (Tecan) automatic hybridization station according to the manufacturer’s guidelines regarding Agilent microarrays treatment. A Gene Expression Hybridization Kit (Agilent) and Gene Expression Wash Buffer Kit solutions (Agilent) were used for the hybridization and washing steps, respectively.

scan_protocol: The intensity data were collected with 4200AL GenePix scanner and GenePix Pro 6.1 software at 5 µm resolution, at green and red channel. Each microarray was scanned twice with auto PMT adjusted at low (0.01 %) or high (1%) spot saturation levels.

data_processing: The scans were processed with GenePix Pro 6.1 software using morphological opening background method. Intensity data were analyzed with R/Bioconductor limma package. Background was subtracted (offset 10) and the scans with low and high intensity were merged with mergeScansRG function. Loess within-array normalization and Aquantile between-array normalization was applied.

organism: Hordeum vulgare

source_name: primary leaf-Dark-Day 3

label_protocol: Labeled cRNA samples were prepared from 200 ng RNA each, using Quick Amp Labeling Kit (Agilent). The labeling efficiency was monitored with Nanodrop 2000.

growth_protocol: Seedlings were grown for 7 days in soil under controlled conditions (day/night 16/8 h, 23 °C, light intensity 150 μmol m-2 s-1, 60% humidity).

extract_protocol: Samples from 3 biological replicates (independent cultivations) were obtained, and each sample was a pool of ~15 plants. Total RNA was extracted from frozen barley leaves with spin-columns (RNeasy Plant Mini Kit, QIAGEN) and DNase-digested with TURBO DNA-free kit (Ambion) according to the manufacturers’ standard protocols. RNA quality was determined using Nanodrop 2000 and 2100 Bioanalyzer (Agilent). All of the samples used for the study were pure (A260/A280 ≥ 1.9; A260/A230 ≥ 2) and showed no visible signs of degradation.

treatment_protocol: The senescence process was induced by placing the seedlings in the dark. Leaves were collected at day 0 (before senescence induction) day 3, day 5, day 7, day 10 and day 12, and the samples were named accordingly

tag: variety

value: Nagrad

source_name: pooled RNA from all samples


title: SEQC NB patient 449


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title: SEQC NB patient 258


title: 5hmC ESC (IVT)

type: genomic

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

description: 5hmC of ESCs

hyb_protocol: Hybridization was performed according to the distributors (Agilent Technologies) protocol.

scan_protocol: Scanning was done according to the distributors (Agilent Technologies) protocol.

data_processing: Logarithmic values were calculated from the raw data and the Cy5 signal was compared to the Cy3 measurement.

molecule: genomic DNA

organism: Mus musculus

source_name: WT ES immunoprecipitated 5hmC

label_protocol: Labeling was done with Cy3 and Cy5, according to the distributors (Agilent Technologies) protocol.

growth_protocol: ES cells were grown following standard experimental protocols.

extract_protocol: DNA was extracted by standard methods.

value: embryonic stem cell

source_name: WT ES genomic DNA


title: 5mC MBD

description: 5mC of ESCs

source_name: WT ES MBD precipitated methylated cytosine


title: SEQC NB patient 259


title: SEQC NB patient 260


title: 5hmC ESC

description: 5hmC of ESCs


title: SEQC NB patient 266


title: Huh7.5_1

city: Seoul

first: Jun-Seok

last: Lee

address: 39-1 Hawolgok-dong Seungbuk-gu

country: South Korea

institute: Korea Institute of Science and Technology (KIST)

description:
SAMPLE 1
Control cell line

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each Human HT12 expression v.4 bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).

scan_protocol: Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual. Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions

data_processing: The quality of hybridization and overall chip performance were monitored by visual inspection of both internal quality control checks and the raw scanned data. Raw data were extracted using the software provided by the manufacturer (Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)). Probes signal value was transformed by logarithm and normalized by quantile method.All data analysis of differentially expressed genes was conducted using R 2.15.3 (www.r-project.org).

label: biotin

source_name: Hepatic carcinoma cell line

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

growth_protocol: Huh 7.5 cells were maintianed in DMEM (High Glucose) supplemented with 10% Fetal Bovine Serum and 1% Pennicillin/Streptomycin., APC140 cells were maintianed in DMEM (High Glucose) supplemented with 10% Fetal Bovine Serum, 1X NEAA, 1% Pennicillin/Streptomycin and 0.5g/l geneticin. Passage frequency was three times per week.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. For quality control, RNA purity and integrity were evaluated by denaturing gel electrophoresis, OD 260/280 ratio, and analyzed on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: No additional chemicals/genetic materials treated except normal growth media

tag: hcv replicon

value: negative control


title: APC140_4

description:
SAMPLE 4
HCV2a replicon expressed Huh7.5 cell line


title: SEQC NB patient 255


title: SEQC NB patient 254


title: APC140_3

description:
SAMPLE 3
HCV2a replicon expressed Huh7.5 cell line


title: Huh7.5_2

description:
SAMPLE 2
Control cell line


title: SEQC NB patient 257


title: SEQC NB patient 253


title: SEQC NB patient 245


title: SEQC NB patient 241


title: SEQC NB patient 249


title: SEQC NB patient 248


title: SEQC NB patient 247


title: SEQC NB patient 246


title: SEQC NB patient 251


title: L1CAM overexpressing cells, biological replicate 1

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

country: Italy

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit, P/N 900720

scan_protocol: gene chip scanner 3000 7G

data_processing: The data were pre-processed with AGCC (Affymetrix) and Expression Console 1.1 using RMA

source_name: lECs_L1CAM overexpression

label_protocol: GeneChip WT Sense Target Labeling and Control Reagents, P/N 900652

growth_protocol: ECs were seeded on plates coated with glutaraldehyde-crosslinked gelatin and cultured in complete medium [MCDB131 medium (Gibco) supplemented with 20% FBS (Invitrogen), 2 mM L-Glutamine (Lonza), 1 mM Na-pyruvate (Gibco), 100 μg/ml heparin (Sigma), 50 μg/ml EC growth supplement (ECGS) obtained from calf brain] for 4 days to reach confluence.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (QIAGEN). Quality control of the RNA samples was performed using an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Mouse lung-derived EC (lECs), kindly provided by E. Dejana (Milan, Italy), were stably transfected with a pcDNA3.1/Hygro(-) vector containing mouse LICAM full length or with and empty  pcDNA3.1/Hygro(-) vector as control.

tag: strain background

tag: organ

value: lung

value: endothelium

value: lung endothelial cells (lECs)

tag: transfected with

tag: genotype/variation

value: L1CAM overexpression


title: SEQC NB patient 252


title: SEQC NB patient 243


title: L1CAM overexpressing cells, biological replicate 2

tag: cell type

value: pcDNA3.1/Hygro(-) vector containing mouse LICAM full length


title: SEQC NB patient 250

tag: tissue


title: SEQC NB patient 244

tag: dataset


title: SEQC NB patient 242

tag: Sex


title: SEQC NB patient 239

tag: age at diagnosis


title: lEC cells, biological replicate 2

source_name: lECs_vector control

value: empty  pcDNA3.1/Hygro(-) vector

value: vector control


title: SEQC NB patient 238

tag: mycn status


title: L1CAM overexpressing cells, biological replicate 3


title: lEC cells, biological replicate 3


title: SEQC NB patient 237

tag: high risk


title: Contorl2-Et

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

description: Gene expression data from LNCaP cells treated with vehicle (ethanol) after transfected with siControl

hyb_protocol: The samples were hybridized to Human Gene 1.0 ST microarrays according to standardized protocols from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with ver 1.1.1 of Affymetrix Expression Console software using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

source_name: prostate cancer

label_protocol: Total RNA was labeled employing the Affymetrix GeneChip Whole Transcript (WT) Terminal Labeling kit according to the manufacturer’s instructions

growth_protocol: LNCaP cells were cultures in RPMI 1640 containing 10% FBS.  Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol: Total RNAs were extracted using ISOGEN (Nippon gene) according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with each siRNA 48 h before hormone treatment. Cells were treated with vehicle or DHT (10 nM).

tag: cell line

value: LNCaP

tag: knockdown

value: siControl

tag: treatment

value: Vehicle


title: SEQC NB patient 240

tag: inss stage

tag: class label

tag: progression

tag: death from disease


title: Control2-DHT

description: Gene expression data from LNCaP cells treated with DHT 10 nM after transfected with siControl

value: DHT 10 nM


title: siCTBP2-Et

description: Gene expression data from LNCaP cells treated with vehicle (ethanol) after transfected with siCTBP2


title: SEQC NB patient 235

value: Neuroblastoma


title: SEQC NB patient 234

value: F


title: SEQC NB patient 304

value: M


title: siCTBP2-DHT

description: Gene expression data from LNCaP cells treated with DHT 10 nM after transfected with siCTBP2


title: SEQC NB patient 233


title: lEC cells, biological replicate 1

tag: strain background

tag: organ


title: siFOXP1-Et

description: Gene expression data from LNCaP cells treated with vehicle (ethanol) after transfected with siFOXP1


title: SiFOXA1-DHT

description: Gene expression data from LNCaP cells treated with DHT 10 nM after transfected with siFOXA1


title: SEQC NB patient 231


title: SiFOXA1-Et

description: Gene expression data from LNCaP cells treated with vehicle (ethanol) after transfected with siFOXA1


title: SEQC NB patient 236


title: SEQC NB patient 232


title: 059-1

city: Durham

first: Holly

middle: K

last: Dressman

state: NC

address: 101 Science Drive

department: IGSP

country: USA

institute: Duke

hyb_protocol: Targets were hybridized to the Human U133A 2.0 GeneChip (Affymetrix, Santa Clara, CA).  Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Hu133 2.0  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: We are most interested in parsimonious models for estimating radiation exposure from gene expression.  In order to obtain short gene lists, we utilized a two-step model building procedure.  First, we selected genes with absolute correlation to dose greater than 0.3.  Second, those genes were fed into an elastic net regression model to build the predictor.  Elastic net is a penalized regression technique which automatically drops out unimportant variables.  In order to control for overfitting, we utilized leave-one-out cross-validation.  Graphs show results on held out (out-of-bag) samples.  Cross-validation was carried out on both steps of the model building.

source_name: TBI

label_protocol: 500 ng of total RNA was amplified according to the MessageAmp Premier protocol (Ambion).  Affymetrix GeneChip analysis was performed according to the manufacturer’s instructions,

extract_protocol: Blood was collected in PAXgene fluid and total RNA was extracted using the RNeasy Protect Animal Blood Kit or Human Blood kit.  RNA was beta globin reduced using Ambion Human GLOBINclear kit for the human studies.  RNA was purified using the Qiagen RNEasy Mini Kit.  All total RNA samples were assessed for quality using a NanoDrop ND8000 Spectrophotometer for absorbance ratios, and the Agilent Bioanalyzer 2100 for RIN scores.

treatment_protocol:
For the Ex Vivo samples, healthy consented adult donor was randomly assigned to a radiation group and labeled with the target dose of 0 cGy, 150 cGy, 300 cGy, or 600 cGy.  In addition to the radiation exposures, the samples were also treated with either no treatment, GCSF, or LPS at time points 6 hours and 24 hours.  Radiation expire times from the Cs137 irradiator were calculated to achieve target doses specific for tubes filled with blood and inserted in the roaring test tube holder.  The dose rate was 480 cGy/min for the duration of the study. The healthy donors were enrolled to participate in this study following a protocol to collect PB samples that was previously approved by the Duke University Institutional Review Board.
For the TBI samples, adult patients, ages 21 to 66, were evaluated at the Duke University Adult Bone Marrow Transplantation Program enrolled in a Duke IRB-approved protocol to collect PB prior to and post TBI conditioning.  With approval from the Duke University Institutional Review Board (IRB), between 5-12 mL of peripheral blood was collected from consented patients prior to and 6 hours following TBI with 150-200 cGy as part of their pre-transplantation conditioning.  All patients receiving non-myeloablative conditioning were treated with 200 cGy of TBI from a linear accelerator at a dose rate of 20 cGy/min. All patients who underwent TBI-based myeloablative allogeneic or autologous stem-cell transplantation received radiation fractionated at 150 cGy per fraction at 20 cGy/min. All patients had PB collected (50 ml) prior to and 6 hours following exposure to either 200 cGy or 150 cGy radiation treatment.  The dose exposure for TBI patients used in this study were 0 cGy, 150 cGy, 450 cGy and 1050 cGy at 0, 6, 30 and 78 hours post irradiation.   Total RNA was extracted and assayed on the Affymetrix platform.

tag: source type

value: blood

tag: dose

tag: time

tag: subject number

tag: condition/tp dx

value: AML

tag: gender

value: Female


title: Control1-Et


title: Control1-DHT


title: siFOXP1-DHT

description: Gene expression data from LNCaP cells treated with DHT 10 nM after transfected with siFOXP1


title: SEQC NB patient 230

tag: tissue

tag: dataset

tag: Sex

tag: age at diagnosis

tag: mycn status


title: SEQC NB patient 228

tag: high risk

tag: inss stage


title: SEQC NB patient 229

tag: class label

tag: progression


title: 047-3

tag: treatment

value: Male

tag: chemo before tp

value: high dose araC + mitoxantrone


title: 023-1

tag: source type

value: etoposide, ARA-C and Mitoxantrone


title: SEQC NB patient 223

tag: death from disease


title: SEQC NB patient 226


title: 023-3

tag: dose

tag: time


title: SEQC NB patient 225


title: SEQC NB patient 227


title: SEQC NB patient 222


title: SEQC NB patient 224


title: 021-p

tag: subject number

tag: condition/tp dx

value: high-dose ARA-C times eight doses, Idarubicin


title: 039-3

value: Scleroderma

tag: gender

value: SCOT


title: SEQC NB patient 221

tag: tissue

tag: dataset


title: 040-3

value: 7+3 re-indurction then Mitozantrone and VP-16 consolidation


title: SEQC NB patient 220

tag: Sex

tag: age at diagnosis


title: 057-3

value: MDS

value: seven days of Ara-C and three days of daunorubicin


title: SEQC NB patient 219

tag: mycn status

tag: high risk


title: 038-3

value: ALL

value: AraC/etoposide x 3 cycles


title: SEQC NB patient 217

value: Neuroblastoma

tag: inss stage

tag: class label


title: 047-1

tag: treatment


title: SEQC NB patient 218

tag: progression


title: SEQC NB patient 216


title: 032-p

tag: source type

tag: chemo before tp

value: High dose ara C with amonafide


title: SEQC NB patient 215

value: M

tag: death from disease


title: 051-1

value: blood

tag: dose

tag: time

value: FLAG/IDA induction chemotherapy with CR achieved, high dose cytarabine #1


title: 025-p

tag: subject number

tag: condition/tp dx

value: AML

value: Female

value: ARA-C and Clofaribine


title: 057-7

tag: gender

value: Male


title: 024-p


title: SEQC NB patient 214

tag: tissue

tag: dataset

value: F


title: 014-3

value: Mantle Cell Lymphoma

value: R-CHOP


title: SEQC NB patient 210

tag: Sex

tag: age at diagnosis


title: 030-3

value: recurrent disease treated into CR2 (unknown chemo regimen)


title: SEQC NB patient 209

tag: mycn status

tag: high risk


title: SEQC NB patient 211

tag: inss stage

tag: class label


title: SEQC NB patient 256

tag: progression


title: 023-7

tag: source type

tag: treatment

value: etoposide, ARA-C and Mitoxantrone


title: SEQC NB patient 212

tag: death from disease


title: 025-1

tag: dose

tag: chemo before tp


title: 010-3

tag: time

tag: subject number


title: SEQC NB patient 213


title: 030-1

tag: condition/tp dx

tag: gender


title: SEQC NB patient 207

tag: tissue

tag: dataset


title: 055-1

value: Follicular Lymphoma

value: CVP-R x 6


title: SEQC NB patient 208

tag: Sex

tag: age at diagnosis


title: 055-3


title: 015-p

value: Scleroderma


title: SEQC NB patient 202

value: Neuroblastoma

tag: mycn status

tag: high risk


title: 003-p

value: SCOT


title: SEQC NB patient 206

value: M

tag: inss stage

tag: class label


title: 054-3

tag: source type

value: blood

value: ALL

value: A Randomized, Double-Blind, Placebo-Controlled Trial to Evaluate Palifermin (rHuKGF) in the Reduction of Acute Graft Versus Host Disease in Subjects with Hematologic Malignancies Undergoing Allogeneic Marrow/PBPC Transplantation). Palifermin/placebo 4.7 mg daily x3 14 mg iv


title: 003-3

tag: treatment


title: SEQC NB patient 204

tag: progression

tag: death from disease


title: 027-3

tag: dose

tag: chemo before tp

value: patient began late intensification phase with Doxorubicin, Vincristine, Dexamethasone, Cyclophosphamide, Cytarabine then maintenance chemo with  6-MP, MTX, Prednisone, Vincristine


title: SEQC NB patient 203


title: SEQC NB patient 201


title: 019-3

tag: time

tag: subject number

value: AML

value: Female

value: High-dose ARA-C


title: SEQC NB patient 200


title: 008-3

tag: condition/tp dx

tag: gender

value: Ara-C and Idarubicin  then 4 cycles of high dose ARA-C


title: SEQC NB patient 199

tag: tissue

tag: dataset


title: SEQC NB patient 195

tag: Sex

value: F

tag: age at diagnosis


title: SEQC NB patient 196

tag: mycn status

tag: high risk


title: SEQC NB patient 205

tag: inss stage

tag: class label


title: SEQC NB patient 198


title: 039-p

tag: source type

tag: treatment


title: 044-p

value: MAL

value: Male

value: eight cycles of hyper CVAD


title: 004-1

value: Precursor B-Lymphoblastic Lymphoma / Leukemia

value: Second cycle of high-dose ARA-C/MTX


title: SEQC NB patient 194

value: Neuroblastoma

tag: progression

tag: death from disease


title: 014-p

tag: dose

value: Mantle Cell Lymphoma

tag: chemo before tp

value: R-CHOP


title: SEQC NB patient 197


title: 042-3

value: blood

tag: time

tag: subject number

value: reinduction of therapy with Gemcitabine and Mitoxantrone


title: SEQC NB patient 193


title: 012-p

tag: condition/tp dx

tag: gender

value: high-dose ARA-C plus Oblimersen


title: 060-7

value: CML


title: 046-p

value: Non-Hodgkins

value: high-dose ARA-C


title: SEQC NB patient 190

tag: tissue

tag: dataset

value: M


title: 006-7

value: ALL

value: Female

value: HIDAC chemotherapy


title: SEQC NB patient 192

tag: Sex

tag: age at diagnosis


title: SEQC NB patient 188

value: F

tag: mycn status

tag: high risk


title: SEQC NB patient 189

tag: inss stage

tag: class label


title: 001-p

tag: source type

tag: treatment

value: Burkitt's Lymphoma / Burkitt Cell Leukemia

value: Male

value: CALGB 9251


title: 022-1

value: Scleroderma

value: SCOT


title: 015-1

value: R-CHOP


title: SEQC NB patient 191

value: Neuroblastoma

tag: progression

tag: death from disease


title: 039-1

value: blood

tag: dose

tag: chemo before tp


title: SEQC NB patient 186


title: SEQC NB patient 187


title: SEQC NB patient 185


title: 011-p

tag: time

tag: subject number


title: SEQC NB patient 183


title: 009-p

tag: condition/tp dx

value: MDS

tag: gender

value: one cycle of Vidaza


title: SEQC NB patient 184

tag: tissue

tag: dataset


title: 001-3


title: 017-3


title: 005-1

value: Diffuse Large B-Cell Lymphoma

value: R-ICE times two cycles


title: SEQC NB patient 180

tag: Sex

tag: age at diagnosis


title: 018-1


title: SEQC NB patient 178

value: M

tag: mycn status

tag: high risk


title: 017-1


title: SEQC NB patient 181

tag: inss stage

tag: class label


title: 004-3

tag: source type

tag: treatment

value: Precursor B-Lymphoblastic Lymphoma / Leukemia

value: Second cycle of high-dose ARA-C/MTX


title: SEQC NB patient 179

tag: progression

tag: death from disease


title: 024-7

tag: dose

value: AML

value: Female

tag: chemo before tp

value: high dose ARA-C


title: 042-p

tag: time

tag: subject number

value: reinduction of therapy with Gemcitabine and Mitoxantrone


title: 040-p

tag: condition/tp dx

tag: gender

value: 7+3 re-indurction then Mitozantrone and VP-16 consolidation


title: 004-p

value: Male


title: 040-7


title: SEQC NB patient 176

tag: tissue

tag: dataset


title: SEQC NB patient 182

tag: Sex

tag: age at diagnosis


title: SEQC NB patient 175

value: F

tag: mycn status

tag: high risk


title: SEQC NB patient 170

tag: inss stage

tag: class label


title: 004-7

tag: source type

tag: treatment


title: SEQC NB patient 174

tag: progression

tag: death from disease


title: SEQC NB patient 172


title: SEQC NB patient 173


title: SEQC NB patient 165


title: 047-7

tag: dose

tag: chemo before tp

value: high dose araC + mitoxantrone


title: 042-1_2

tag: time

tag: subject number


title: 041-1

tag: condition/tp dx

tag: gender

value: araC, daunorubicin and etoposide


title: 057-1

value: blood

value: seven days of Ara-C and three days of daunorubicin


title: 060-1

value: CML


title: SEQC NB patient 163

tag: tissue

value: Neuroblastoma

tag: dataset


title: 037-p

value: ALL

value: CVAD with Gleevec 400mg x14 days/cycle


title: SEQC NB patient 164

tag: Sex

value: M

tag: age at diagnosis


title: SEQC NB patient 171

tag: mycn status

tag: high risk


title: SEQC NB patient 167

tag: inss stage

tag: class label


title: 041-p

tag: source type

tag: treatment


title: 006-3

value: HIDAC chemotherapy


title: 005-3_2

value: Diffuse Large B-Cell Lymphoma

value: R-ICE times two cycles


title: SEQC NB patient 169

tag: progression

tag: death from disease


title: SEQC NB patient 166


title: 013-p

tag: dose

value: AML

tag: chemo before tp

value: Reinduced with mitoxantrone and etoposide


title: 008-p

tag: time

tag: subject number

value: Female

value: hyper CVAD induction chemo


title: SEQC NB patient 168

value: F


title: 035-3

tag: condition/tp dx

tag: gender

value: Male


title: 035-1


title: SEQC NB patient 159

tag: tissue

tag: dataset


title: 019-p

value: High-dose ARA-C


title: 059-7

value: blood


title: SEQC NB patient 158

tag: Sex

tag: age at diagnosis


title: SEQC NB patient 160

tag: mycn status

tag: high risk


title: SEQC NB patient 162

tag: inss stage

tag: class label


title: SEQC NB patient 161


title: 005-p

tag: source type

tag: treatment


title: 041-3

value: araC, daunorubicin and etoposide


title: 010-1


title: SEQC NB patient 151

tag: progression

tag: death from disease


title: SEQC NB patient 157


title: 014-1

tag: dose

value: Mantle Cell Lymphoma

tag: chemo before tp

value: SCOT


title: SEQC NB patient 150

value: Neuroblastoma


title: SEQC NB patient 152


title: 020-p

tag: time

tag: subject number

value: CLL

value: two more full cycles (8 doses) of Flavopyridol through Campath


title: 037-3

tag: condition/tp dx

value: ALL

tag: gender

value: CVAD with Gleevec 400mg x14 days/cycle


title: 024-3

value: ARA-C and Clofaribine


title: SEQC NB patient 149

tag: tissue

tag: dataset


title: 020-1


title: 054-1

value: A Randomized, Double-Blind, Placebo-Controlled Trial to Evaluate Palifermin (rHuKGF) in the Reduction of Acute Graft Versus Host Disease in Subjects with Hematologic Malignancies Undergoing Allogeneic Marrow/PBPC Transplantation). Palifermin/placebo 4.7 mg daily x3 14 mg iv


title: SEQC NB patient 153

tag: Sex

tag: age at diagnosis


title: SEQC NB patient 154

value: M

tag: mycn status

tag: high risk


title: 030-7

value: AML

value: Female

value: recurrent disease treated into CR2 (unknown chemo regimen)


title: SEQC NB patient 156

tag: inss stage

tag: class label


title: SEQC NB patient 148


title: 002-p

tag: source type

tag: treatment

value: Male

value: High-dose ARA-C times two cycles


title: 025-3

value: blood

value: high dose ARA-C


title: SEQC NB patient 145

tag: progression

tag: death from disease


title: SEQC NB patient 139

value: F


title: 003-1

tag: dose

value: Scleroderma

tag: chemo before tp

value: SCOT


title: SEQC NB patient 144

value: Neuroblastoma


title: 013-1

tag: time

tag: subject number

value: Reinduced with mitoxantrone and etoposide


title: 049-3

tag: condition/tp dx

value: MDS

tag: gender

value: cycle two ATGAM/Cyclosporin then sarted Exjade


title: SEQC NB patient 146

tag: tissue

tag: dataset


title: 015-3


title: SEQC NB patient 155

tag: Sex

tag: age at diagnosis


title: 038-1

value: ALL

value: AraC/etoposide x 3 cycles


title: SEQC NB patient 140

tag: mycn status

tag: high risk


title: 024-1


title: SEQC NB patient 142

tag: inss stage

tag: class label


title: 041-7

tag: source type

tag: treatment

value: araC, daunorubicin and etoposide


title: SEQC NB patient 137

value: M

tag: progression

tag: death from disease


title: SEQC NB patient 147


title: SEQC NB patient 143


title: SEQC NB patient 138


title: 023-p

tag: dose

value: AML

tag: chemo before tp

value: etoposide, ARA-C and Mitoxantrone


title: SEQC NB patient 141


title: 040-1

tag: time

tag: subject number

value: Female

value: 7+3 re-indurction then Mitozantrone and VP-16 consolidation


title: 036-p

value: blood

tag: condition/tp dx

tag: gender

value: ARA-C and Mitoxantrone x3d


title: SEQC NB patient 136

tag: tissue

tag: dataset


title: SEQC NB patient 135

tag: Sex

tag: age at diagnosis


title: SEQC NB patient 177

value: F

tag: mycn status

tag: high risk


title: SEQC NB patient 132

tag: inss stage

tag: class label


title: 150cGy-GCSF24-h5

source_name: ex vivo

tag: source type

tag: treatment

value: GCSF

value: Healthy

value: Male


title: SEQC NB patient 133

value: Neuroblastoma

tag: progression

tag: death from disease


title: SEQC NB patient 131


title: SEQC NB patient 130


title: 150cGy-LPS24-h2

tag: dose

value: LPS

tag: chemo before tp


title: 150cGy-LPS24-h3

tag: time

tag: subject number


title: 600cGy-GCSF6-h2

tag: condition/tp dx

tag: gender


title: SEQC NB patient 134

tag: tissue

tag: dataset


title: 0cGy-LPS6-h7


title: 0cGy-LPS24-h2


title: 0cGy-noTRT24-h5


title: SEQC NB patient 127

tag: Sex

tag: age at diagnosis


title: 0cGy-LPS6-h6


title: 300cGy-GCSF6-h3


title: SEQC NB patient 125

tag: mycn status

tag: high risk


title: 0cGy-GCSF24-h2


title: SEQC NB patient 128

tag: inss stage

tag: class label


title: SEQC NB patient 126


title: SEQC NB patient 129


title: 600cGy-GCSF6-h3

tag: source type

tag: treatment


title: SEQC NB patient 124

tag: progression

tag: death from disease


title: SEQC NB patient 123


title: 600cGy-LPS24-h5

tag: dose

tag: chemo before tp


title: 600cGy-noTRT6-h2

tag: time

tag: subject number


title: 600cGy-LPS6-h3

tag: condition/tp dx

tag: gender


title: SEQC NB patient 122

tag: tissue

tag: dataset


title: SEQC NB patient 121

tag: Sex

tag: age at diagnosis


title: 018-p

value: Scleroderma

value: SCOT


title: SEQC NB patient 119

tag: mycn status

tag: high risk


title: SEQC NB patient 120

tag: inss stage

tag: class label


title: 300cGy-GCSF6-h2

tag: source type

tag: treatment


title: 300cGy-LPS24-h3


title: 300cGy-noTRT6-h9


title: 300cGy-GCSF24-h2


title: 300cGy-LPS6-h4


title: 300cGy-noTRT24-h2


title: SEQC NB patient 115

tag: progression

tag: death from disease


title: SEQC NB patient 116


title: SEQC NB patient 114


title: SEQC NB patient 117


title: 150cGy-noTRT24-h5

tag: dose

tag: chemo before tp


title: SEQC NB patient 118


title: SEQC NB patient 111


title: SEQC NB patient 113


title: SEQC NB patient 110


title: 150cGy-GCSF24-h2

tag: time

tag: subject number


title: 150cGy-LPS24-h6

tag: condition/tp dx

tag: gender


title: 0cGy-noTRT6-h2


title: SEQC NB patient 108

tag: tissue

tag: dataset


title: SEQC NB patient 109

tag: Sex

tag: age at diagnosis


title: SEQC NB patient 112

tag: mycn status

tag: high risk


title: 0cGy-noTRT24-h2


title: SEQC NB patient 106

tag: inss stage

tag: class label


title: SEQC NB patient 107


title: 0cGy-LPS6-h3

tag: source type

tag: treatment


title: 150cGy-LPS6-h5


title: SEQC NB patient 105

tag: progression

tag: death from disease


title: 0cGy-LPS24-h3

tag: dose

tag: chemo before tp


title: 600cGy-noTRT6-h3

tag: time

tag: subject number


title: SEQC NB patient 104


title: 0cGy-GCSF24-h3

tag: condition/tp dx

tag: gender


title: SEQC NB patient 103

tag: tissue

tag: dataset


title: 600cGy-GCSF6-h7


title: SEQC NB patient 101

tag: Sex

tag: age at diagnosis


title: 600cGy-LPS6-h2


title: SEQC NB patient 102

tag: mycn status

tag: high risk


title: 600cGy-LPS24-h2


title: 300cGy-noTRT24-h3


title: 300cGy-noTRT6-h8


title: SEQC NB patient 100

tag: inss stage

tag: class label


title: 300cGy-LPS6-h7

tag: source type

tag: treatment


title: SEQC NB patient 099

tag: progression

tag: death from disease


title: 300cGy-GCSF24-h3

tag: dose

tag: chemo before tp


title: SEQC NB patient 095


title: SEQC NB patient 097


title: 300cGy-LPS24-h2

tag: time

tag: subject number


title: 150cGy-noTRT6-h3

tag: condition/tp dx

tag: gender


title: 150cGy-noTRT24-h6


title: SEQC NB patient 096

tag: tissue

tag: dataset


title: SEQC NB patient 094

tag: Sex

tag: age at diagnosis


title: 150cGy-LPS24-h9


title: SEQC NB patient 093

tag: mycn status

tag: high risk


title: 150cGy-GCSF6-h9


title: SEQC NB patient 098

tag: inss stage

tag: class label


title: SEQC NB patient 092


title: SEQC NB patient 091


title: 150cGy-GCSF24-h3

tag: source type

tag: treatment


title: 300cGy-GCSF6-h8


title: Foetal placenta Day 24, A vs.R, Biol. Rep. 3

city: Valencia

first: M. Desemparats

last: Saenz-de-Juano

state: Valencia

address: Camino de Vera s/n

department: Animal Science

country: Spain

institute: Universidad Politécnica Valencia

description: Biological Replicate 3 of 3, 24-day-old foetal placentas A vs.R

hyb_protocol: Hibridization was done using Agilent Gene Expression Hybridization Kit, following manufacturer's instructions. After 17 hours at 65ºC, hybridised slides were washed  were washed sequential.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.10.1.1). Normalization with the locally weighted linear regression (LOWESS) algorithm and identification of differentially expressed transcripts was achieved using the Limma package in R.

organism: Oryctolagus cuniculus

source_name: foetal placenta

label_protocol: Total RNA (100 ng) was labelled using QuickAmp Labelling Kit (Agilent Technologies) following manufacturer's instructions. Excess dye was removed with the QIAquick PCR purification kit  RNAeasy Mini Kit (QIAGEN) and dye incorporation and concentration were determined using the microarray setting on the Nanodrop 1000.

extract_protocol: Total RNA was extracted using TRIZOL reagent, following manufacter's instructions.

tag: line

value: Line R

value: Line A


title: SEQC NB patient 089

value: M

tag: progression

tag: death from disease


title: SEQC NB patient 090


title: 150cGy-LPS6-h6

tag: dose

tag: time

tag: chemo before tp


title: Foetal placenta Day 24, A vs.R, Biol. Rep. 2

description: Biological Replicate 2 of 3, dye-swap, 24-day-old foetal placentas A vs.R


title: Foetal placenta Day 14, A vs.R, Biol. Rep. 4

description: Biological Replicate 4 of 4, 14-day-old foetal placentas A vs.R


title: 0cGy-LPS6-h2

tag: subject number

tag: condition/tp dx

tag: gender


title: SEQC NB patient 088

tag: tissue

tag: dataset

tag: Sex


title: 0cGy-noTRT24-h3


title: 0cGy-LPS24-h7


title: 0cGy-GCSF24-h4


title: Foetal placenta Day 14, A vs.R, Biol. Rep. 2

description: Biological Replicate 2 of 4, dye swap,14-day-old foetal placentas A vs.R


title: Foetal placenta Day 24, A vs.R, Biol. Rep. 1

description: Biological Replicate 1 of 3, 24-day-old foetal placentas A vs.R


title: SEQC NB patient 085

tag: age at diagnosis

tag: mycn status

tag: high risk


title: SEQC NB patient 087

tag: inss stage

tag: class label


title: Foetal placenta Day 14, A vs.R, Biol. Rep. 1

description: Biological Replicate 1 of 4, 14-day-old foetal placentas A vs.R

tag: line


title: 0cGy-noTRT6-h3

tag: source type

tag: treatment


title: 600cGy-noTRT6-h4

tag: dose


title: Foetal placenta Day 14, A vs.R, Biol. Rep. 3

description: Biological Replicate 3 of 4, 14-day-old foetal placentas A vs.R


title: SEQC NB patient 084

tag: progression

tag: death from disease


title: WT_mice_intestine_pool

city: Tianjin

first: Rongcun

last: Yang

state: Tianjin

address: 94 Weijin Road

department: Immunology

institute: School of Medicine, Nankai University

description: Gene expression data from WT C57BL/6 mice intestine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were preprocessed using the RMA algorithm and differentially expressed genes were identified as the ones with a fold change (FC) between the 2 pooled samples greater than 2 or less than -2 and with a P present/absent call in the higherly expressed sample.

source_name: Total RNAs evenly pooled from 5 WT mice, including 2 male and 3 female mice, with the age of 6 wk and had been maintained in the specific pathogen free (SPF) environment since born

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

growth_protocol: Mice with C57BL/6 genetic background were maintained in the same SPF environment and when experiment begun, 5 WT (2 male and 3 female) and 5 KO (also 2 male and 3 female) mice of 6 wk old were sacrificed humanely following the rules concerning laboratory animals of Nankai University.

extract_protocol: Trizol extraction of total RNA from the prepared mouse gut epithelial cells was performed according to the manufacturer's instructions.

treatment_protocol: Mice intestines were cut longitudinally and washed in cold PBS and then were cut into 2 cm long fragments and shaken in a 15 mL conical tube containing PBS with 30 mM EDTA and a pH of 7.4 for 5 min. This procedure was repeated at least 4 times. The result primary product was collected and then suffered from immune cells exclusion using magnetic activated cell sorting (MACS) to filtered out CD4, CD8 cells, B cells, dendritic cells and macrophages. The final product was murine gut epithelial cells.

value: intestine epithelial cell

tag: strain

tag: genotype

value: WT

tag: age

value: 6 wk old


title: SEQC NB patient 083

tag: tissue


title: SEQC NB patient 086

tag: dataset


title: Patient 121

city: Nashville

first: Jing

last: Zhu

state: TN

institute: Vanderbilt University

hyb_protocol: Standard Affymetrix protocols for hybridization to the Affy HGU133 2.0 plus array were used.

scan_protocol: GeneChip Scanner was used for scanning and generating the raw .CEL files.

data_processing: MAS5 algorithm implemented in 'affy' package (Version 1.16.0) of Bioconductor was performed in R (Version 2.6.2) for data normalization.

source_name: Vanderbilt University Medical Center

label_protocol: Standard Affymetrix protocols were used.

extract_protocol: RNA was extracted using the Qiagen RNeasy kit.

tag: dfs_event (disease free survival)

value: 0 (no recurrence)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

value: 0 (no death)

tag: dss_time (disease specific survival time, months)


title: SEQC NB patient 082

tag: Sex

tag: age at diagnosis

tag: mycn status

tag: high risk

tag: inss stage


title: KO_mice_intestine_pool

description: Gene expression data from KO C57BL/6 mice intestine

source_name: Total RNAs evenly pooled from 5 KO mice, including 2 male and 3 female mice, with the age of 6 wk and had been maintained in the specific pathogen free (SPF) environment since born

value: lrrc19 gene KO


title: Patient 122


title: PBMC_active TB_T10_rep1

city: Chung-Li

first: Julia

middle: Tzu-Ya

last: Weng

address: 135 Yuan-Tung Road

department: Department of Computer Science and Engineering

country: Taiwan

institute: Yuan Ze University

description: Taiwanese Han

hyb_protocol: Fluorescent targets were hybridized to the Phalanx Human OneArray v6.1 with Phalanx hybridization buffer using Phalanx Hybridization System.

scan_protocol: The scanned images were analyzed with Agilent Scanner and processing by GenePix software 4.1 to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Data were analyzed with the Rosetta Resolver System software (Rosetta Biosoftware, USA). The Rosetta Resolver System Error Model was used to calculate the normalized intensities, CV, log2 ratio and p-value (differential expressed). Briefly, probes whose flags were -50 within all arrays were excluded; replicated probes within one chip were averaged; intensities were normalized by median scaling and taking the mean intensities.

source_name: peripheral blood mononuclear cell, active TB

label_protocol: Cyanine-5 (Cy5) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was isolated from peripheral blood mononuclear cells (PMBC). The quality of RNA was determined by an optical density (OD) 260/280 ratio ≥1.8, and OD 260/230 ratio ≥1.5 on a spectrophotometer, in addition to the intensity of the 18S and 28S rRNA bands on a 1% formaldehyde-agarose gel. RNA quantity was detected by a spectrophotometer. RNA integrity was examined on an Agilent Bioanalyzer. RNA with an RNA integrity number (RIN) ≥7.0 and 28S/18S >0.7 was subjected to microarray analysis.

tag: disease state

value: active TB


title: PBMC_active TB_T11_rep1

description: Taiwanese Han


title: Patient 119


title: PBMC_active TB_T10_rep2

description: Taiwanese Han


title: Patient 117

value: 1 (death from cancer)


title: Patient 120


title: 600cGy-LPS6-h8

tag: source type

value: blood

tag: dose

tag: treatment

tag: time

tag: subject number

tag: condition/tp dx

value: Healthy

tag: gender

tag: chemo before tp


title: 600cGy-LPS24-h10

value: Male


title: PBMC_active TB_T11_rep2

description: Taiwanese Han


title: SEQC NB patient 081

source_name: neuroblastoma

tag: tissue

value: Neuroblastoma

tag: dataset

tag: class label

tag: progression

tag: death from disease


title: SEQC NB patient 080

tag: Sex

value: F

tag: age at diagnosis

tag: mycn status


title: PBMC_active TB_T09_rep2

description: Taiwanese Han

tag: disease state


title: 600cGy-GCSF6-h4

tag: source type

value: GCSF


title: 600cGy-GCSF24-h5

tag: dose


title: Patient 118

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: Patient 115


title: 300cGy-noTRT24-h9

tag: treatment

tag: time

tag: subject number

tag: condition/tp dx

tag: gender

value: Female


title: SEQC NB patient 079

tag: tissue

tag: dataset

tag: high risk

tag: inss stage

tag: class label

tag: progression


title: Patient 116


title: 300cGy-noTRT6-h10

tag: source type

tag: chemo before tp


title: PBMC_active TB_T09_rep1

description: Taiwanese Han

tag: disease state


title: SEQC NB patient 077

tag: Sex

tag: age at diagnosis

tag: mycn status

tag: death from disease


title: SEQC NB patient 078


title: SEQC NB patient 076


title: PBMC_active TB_T08_rep2

description: Taiwanese Han


title: Patient 114

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: 300cGy-LPS24-h8

tag: dose

tag: treatment

value: LPS

tag: time

tag: subject number

tag: condition/tp dx

tag: gender


title: 300cGy-LPS6-h10

tag: source type


title: Patient 113


title: SEQC NB patient 075

tag: tissue

tag: dataset

tag: high risk

tag: inss stage

tag: class label

tag: progression


title: PBMC_active TB_T08_rep1

description: Taiwanese Han

tag: disease state


title: 300cGy-GCSF24-h10

tag: chemo before tp


title: 300cGy-GCSF6-h10


title: SEQC NB patient 073

tag: Sex

tag: age at diagnosis

tag: mycn status

tag: death from disease


title: PBMC_active TB_T07_rep2

description: Taiwanese Han


title: SEQC NB patient 074

value: M


title: Patient 111

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: Patient 108

source_name: University of Alabama at Birmingham


title: 150cGy-noTRT6-h7

tag: source type

tag: dose

tag: treatment

tag: time

tag: subject number

tag: condition/tp dx

tag: gender


title: 150cGy-noTRT24-h10


title: PBMC_active TB_T07_rep1

description: Taiwanese Han

tag: disease state


title: SEQC NB patient 072

tag: tissue

tag: dataset

tag: high risk

tag: inss stage

tag: class label

tag: progression


title: PBMC_active TB_T06_rep2

description: Taiwanese Han


title: Patient 106

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)


title: PBMC_active TB_T02_rep2

description: Taiwanese Han


title: 150cGy-LPS6-h10

tag: chemo before tp


title: PBMC_active TB_T06_rep1

description: Taiwanese Han


title: SEQC NB patient 070

tag: Sex

tag: age at diagnosis

tag: mycn status

tag: death from disease


title: SEQC NB patient 071


title: Patient 112

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: 150cGy-LPS24-h10

tag: source type

tag: dose

tag: treatment

tag: time

tag: subject number

tag: condition/tp dx

tag: gender


title: Patient 109


title: Patient 110


title: 150cGy-GCSF24-h8


title: PBMC_latent TB_L31_rep2

description: Taiwanese Han

source_name: peripheral blood mononuclear cell, latent TB infection

tag: disease state

value: latent TB infection


title: PBMC_active TB_T02_rep1

description: Taiwanese Han


title: Patient 107

tag: dfs_event (disease free survival)


title: 150cGy-GCSF6-h8


title: SEQC NB patient 069

tag: tissue

tag: dataset

tag: high risk

tag: inss stage

tag: class label

tag: progression


title: 0cGy-noTRT6-h8

tag: chemo before tp


title: SEQC NB patient 068

tag: Sex

tag: age at diagnosis

tag: mycn status

tag: death from disease


title: Patient 105

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: SEQC NB patient 067


title: 0cGy-noTRT24-h9

tag: source type

tag: dose

tag: treatment

tag: time

tag: subject number

tag: condition/tp dx

tag: gender


title: Patient 103

tag: dfs_event (disease free survival)


title: Patient 101


title: 0cGy-LPS6-h9


title: SEQC NB patient 066

tag: tissue

tag: dataset

tag: high risk

tag: inss stage

tag: class label

tag: progression


title: PBMC_latent TB_L30_rep2

description: Taiwanese Han

tag: disease state


title: SEQC NB patient 064

tag: Sex

tag: age at diagnosis

tag: mycn status

tag: death from disease


title: SEQC NB patient 065


title: PBMC_latent TB_L30_rep1

description: Taiwanese Han


title: 0cGy-LPS24-h10

tag: source type

tag: dose

tag: treatment

tag: chemo before tp


title: Patient 104

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: 0cGy-GCSF6-h6

tag: time

tag: subject number

tag: condition/tp dx

tag: gender


title: Patient 99

tag: dfs_event (disease free survival)


title: Patient 102


title: SEQC NB patient 063

tag: tissue

tag: dataset

tag: high risk

tag: inss stage

tag: class label

tag: progression


title: PBMC_latent TB_L29_rep1

description: Taiwanese Han

tag: disease state


title: SEQC NB patient 062

tag: Sex

tag: age at diagnosis

tag: mycn status

tag: death from disease


title: PBMC_latent TB_L28_rep1

description: Taiwanese Han


title: 0cGy-GCSF24-h7

tag: source type

tag: dose

tag: treatment

tag: chemo before tp


title: 600cGy-noTRT6-h5

tag: time

tag: subject number

tag: condition/tp dx

tag: gender


title: PBMC_latent TB_L29_rep2

description: Taiwanese Han


title: PBMC_latent TB_L28_rep2

description: Taiwanese Han


title: SEQC NB patient 060

tag: tissue

tag: dataset

tag: high risk


title: SEQC NB patient 061

tag: inss stage

tag: class label

tag: progression


title: Patient 98

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: 600cGy-noTRT6-h8

tag: source type

tag: dose


title: PBMC_latent TB_L27_rep2

description: Taiwanese Han

tag: disease state


title: 600cGy-noTRT6-h6

tag: treatment

tag: time

tag: chemo before tp


title: Patient 100


title: PBMC_latent TB_L31_rep1

description: Taiwanese Han


title: PBMC_latent TB_L27_rep1

description: Taiwanese Han


title: PBMC_latent TB_L24_rep2

description: Taiwanese Han


title: SEQC NB patient 058

tag: Sex

tag: age at diagnosis

tag: mycn status

tag: death from disease


title: 600cGy-noTRT6-h9

tag: subject number

tag: condition/tp dx

tag: gender


title: Patient 97

tag: dfs_event (disease free survival)


title: Patient 96

tag: dfs_time (disease free survival time, months)


title: 600cGy-noTRT24-h8


title: 600cGy-noTRT24-h10


title: PBMC_latent TB_L24_rep1

description: Taiwanese Han


title: SEQC NB patient 057

tag: tissue

tag: dataset

tag: high risk

tag: inss stage

tag: class label

tag: progression


title: Patient 94

value: 1 (cancer recurrence)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: Patient 93


title: PBMC_latent TB_L22_rep1

description: Taiwanese Han

tag: disease state


title: SEQC NB patient 059

tag: Sex

tag: age at diagnosis


title: 600cGy-noTRT24-h9

tag: source type

tag: dose

tag: treatment

tag: time

tag: chemo before tp


title: 600cGy-noTRT24-h7

tag: subject number

tag: condition/tp dx

tag: gender


title: Patient 95

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)


title: SEQC NB patient 056

tag: tissue

tag: dataset

tag: mycn status

tag: high risk

tag: inss stage

tag: class label

tag: death from disease


title: PBMC_latent TB_L22_rep2

description: Taiwanese Han

tag: disease state


title: 600cGy-LPS6-h5

tag: source type

tag: dose


title: SEQC NB patient 054

tag: Sex

tag: age at diagnosis

tag: progression


title: PBMC_healthy_C20_rep1

description: Taiwanese Han

source_name: peripheral blood mononuclear cell, healthy control

value: healthy control


title: SEQC NB patient 052


title: SEQC NB patient 053


title: Patient 91

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: PBMC_healthy_C15_rep1

description: Taiwanese Han


title: PBMC_healthy_C15_rep2

description: Taiwanese Han


title: SEQC NB patient 051


title: Patient 90

tag: dfs_event (disease free survival)

value: 0 (no recurrence)


title: PBMC_healthy_C20_rep2

description: Taiwanese Han


title: Patient 89

tag: dfs_time (disease free survival time, months)

value: 0 (no death)


title: 600cGy-LPS6-h10

tag: treatment

tag: time

tag: subject number

tag: condition/tp dx

tag: gender

tag: chemo before tp


title: 600cGy-LPS24-h6


title: Patient 92


title: PBMC_healthy_C14_rep2

description: Taiwanese Han


title: 600cGy-LPS6-h7


title: Patient 88


title: SEQC NB patient 055

tag: tissue

tag: dataset

tag: mycn status

tag: high risk

tag: inss stage

tag: class label

tag: death from disease


title: 600cGy-LPS6-h4

tag: source type

tag: dose


title: SEQC NB patient 050

tag: Sex

tag: age at diagnosis

tag: progression


title: PBMC_healthy_C9_rep2

description: Taiwanese Han

tag: disease state


title: 600cGy-LPS24-h7

tag: treatment

tag: time

tag: subject number


title: 600cGy-LPS24-h9

tag: condition/tp dx

tag: gender

tag: chemo before tp


title: Patient 86

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: PBMC_healthy_C14_rep1

description: Taiwanese Han


title: PBMC_healthy_C9_rep1

description: Taiwanese Han


title: SEQC NB patient 047

tag: tissue

tag: dataset

tag: mycn status

tag: high risk

tag: inss stage

tag: class label

tag: death from disease


title: Patient 85


title: Patient 87


title: SEQC NB patient 048

tag: Sex

tag: age at diagnosis

tag: progression


title: PBMC_healthy_C8_rep2

description: Taiwanese Han

tag: disease state


title: SEQC NB patient 049


title: 600cGy-LPS24-h8

tag: source type

tag: dose

tag: treatment

tag: time

tag: subject number

tag: condition/tp dx

tag: gender


title: 600cGy-GCSF6-h5

tag: chemo before tp


title: Patient 84

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: PBMC_healthy_C8_rep1

description: Taiwanese Han


title: PBMC_healthy_C2_rep2

description: Taiwanese Han


title: Patient 83


title: PBMC_healthy_C2_rep1

description: Taiwanese Han


title: SEQC NB patient 043

tag: tissue

tag: dataset

tag: mycn status

tag: high risk

tag: inss stage

tag: class label

tag: death from disease


title: Patient 81


title: SEQC NB patient 044

tag: Sex

tag: age at diagnosis

tag: progression


title: SEQC NB patient 046


title: SEQC NB patient 045


title: PBMC_healthy_C1_rep2

description: Taiwanese Han

tag: disease state


title: Patient 80


title: 600cGy-GCSF6-h6

tag: source type

tag: dose

tag: treatment

tag: time

tag: subject number

tag: condition/tp dx

tag: gender


title: Patient 82

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: 600cGy-GCSF6-h10

tag: chemo before tp


title: 600cGy-GCSF6-h8


title: 600cGy-GCSF24-h7


title: 600cGy-GCSF24-h10


title: SEQC NB patient 040

tag: tissue

tag: dataset

tag: mycn status

tag: high risk

tag: inss stage

tag: class label

tag: death from disease


title: SEQC NB patient 042

tag: Sex

tag: age at diagnosis

tag: progression


title: Patient 77


title: PBMC_healthy_C1_rep1

description: Taiwanese Han

tag: disease state


title: Patient 79


title: Patient 76


title: SEQC NB patient 039


title: 600cGy-GCSF24-h9

tag: source type

tag: dose

tag: treatment

tag: time

tag: subject number

tag: condition/tp dx

tag: gender


title: 300cGy-noTRT6-h7

tag: chemo before tp


title: Patient 78

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: SEQC NB patient 041

tag: tissue

tag: dataset

tag: mycn status

tag: high risk

tag: inss stage

tag: class label

tag: death from disease


title: SEQC NB patient 037

tag: Sex

tag: age at diagnosis

tag: progression


title: SEQC NB patient 038


title: 300cGy-noTRT6-h4

tag: source type

tag: dose

tag: treatment

tag: time

tag: subject number

tag: condition/tp dx


title: 600cGy-GCSF24-h8

tag: gender

tag: chemo before tp


title: Patient 75

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: Patient 71


title: Patient 74


title: SEQC NB patient 034

tag: tissue

tag: dataset

tag: mycn status

tag: high risk

tag: inss stage

tag: class label


title: SEQC NB patient 035

tag: Sex

tag: age at diagnosis

tag: progression

tag: death from disease


title: SEQC NB patient 033


title: Patient 72


title: 300cGy-noTRT24-h6

tag: source type

tag: dose

tag: treatment

tag: time

tag: subject number

tag: condition/tp dx


title: Patient 70

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: 300cGy-noTRT6-h5

tag: gender

tag: chemo before tp


title: SEQC NB patient 036

tag: tissue

tag: dataset

tag: mycn status

tag: high risk

tag: inss stage

tag: class label


title: 300cGy-noTRT6-h6

tag: source type

tag: dose


title: 300cGy-noTRT24-h7

tag: treatment

tag: time


title: 300cGy-noTRT24-h8

tag: subject number

tag: condition/tp dx


title: 300cGy-noTRT24-h10


title: SEQC NB patient 032

tag: Sex

tag: age at diagnosis

tag: progression

tag: death from disease


title: Patient 73

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: SEQC NB patient 031

tag: tissue

tag: dataset

tag: mycn status

tag: high risk


title: SEQC NB patient 030

tag: inss stage

tag: class label


title: 300cGy-LPS6-h6

tag: source type

tag: dose

tag: treatment

tag: time

tag: gender

tag: chemo before tp


title: SEQC NB patient 029

tag: Sex

tag: age at diagnosis

tag: progression

tag: death from disease


title: Patient 67

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: SEQC NB patient 027

tag: tissue

tag: dataset

tag: mycn status

tag: high risk


title: Patient 66


title: 300cGy-LPS6-h5

tag: source type

tag: dose

tag: subject number

tag: condition/tp dx


title: Patient 68


title: Patient 69


title: 300cGy-LPS6-h9

tag: treatment

tag: time

tag: gender

tag: chemo before tp


title: Patient 64


title: SEQC NB patient 026

tag: Sex

tag: age at diagnosis

tag: inss stage

tag: class label

tag: progression

tag: death from disease


title: Patient 65

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: SEQC NB patient 028

tag: tissue

tag: dataset

tag: mycn status

tag: high risk


title: Patient 62


title: 300cGy-LPS6-h8

tag: source type

tag: dose

tag: treatment

tag: time

tag: subject number

tag: condition/tp dx


title: SEQC NB patient 025

tag: Sex

tag: age at diagnosis

tag: inss stage

tag: class label


title: 300cGy-LPS24-h6

tag: gender

tag: chemo before tp


title: 300cGy-LPS24-h5


title: Patient 61

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: SEQC NB patient 023

tag: tissue

tag: dataset

tag: mycn status

tag: high risk

tag: progression

tag: death from disease


title: SEQC NB patient 022


title: 300cGy-LPS24-h9

tag: source type

tag: dose

tag: treatment

tag: time

tag: subject number

tag: condition/tp dx


title: SEQC NB patient 020

tag: Sex

tag: age at diagnosis

tag: inss stage

tag: class label


title: Patient 60

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: Patient 59


title: Patient 63


title: SEQC NB patient 024

tag: tissue

tag: dataset

tag: mycn status

tag: high risk


title: 300cGy-LPS24-h10

tag: source type

tag: dose

tag: gender

tag: chemo before tp


title: 300cGy-GCSF6-h5

tag: treatment

tag: time

tag: subject number

tag: condition/tp dx


title: Patient 58


title: Patient 57


title: SEQC NB patient 017

tag: Sex

tag: age at diagnosis

tag: inss stage

tag: class label

tag: progression

tag: death from disease


title: 300cGy-GCSF6-h9


title: Patient 55

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: SEQC NB patient 021

tag: tissue

tag: dataset

tag: mycn status

tag: high risk


title: SEQC NB patient 018


title: SEQC NB patient 016


title: Patient 54


title: SEQC NB patient 019


title: 300cGy-GCSF24-h7

tag: source type

tag: dose

tag: treatment

tag: time

tag: gender

tag: chemo before tp


title: 300cGy-GCSF6-h6

tag: subject number

tag: condition/tp dx


title: Patient 56


title: Patient 53


title: 300cGy-GCSF24-h8


title: 300cGy-GCSF24-h5


title: SEQC NB patient 014

tag: Sex

tag: age at diagnosis

tag: inss stage

tag: class label

tag: progression

tag: death from disease


title: 300cGy-GCSF6-h4


title: SEQC NB patient 015

tag: tissue

tag: dataset


title: 300cGy-GCSF24-h9


title: Patient 52

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: 150cGy-noTRT6-h4

tag: source type

tag: dose

tag: treatment

tag: time


title: Patient 51


title: Patient 50


title: 150cGy-noTRT6-h9

tag: subject number

tag: condition/tp dx

tag: gender

tag: chemo before tp


title: Patient 49


title: Patient 48


title: SEQC NB patient 012

tag: Sex

tag: age at diagnosis

tag: mycn status

tag: high risk

tag: inss stage

tag: class label


title: SEQC NB patient 010

tag: tissue

tag: dataset

tag: progression

tag: death from disease


title: SEQC NB patient 011


title: SEQC NB patient 013


title: 150cGy-noTRT6-h10

tag: source type

tag: dose


title: 150cGy-noTRT6-h8

tag: treatment

tag: time


title: SEQC NB patient 009


title: SEQC NB patient 008


title: 150cGy-noTRT24-h2

tag: subject number

tag: condition/tp dx


title: Patient 47

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: Patient 46


title: SEQC NB patient 007

tag: Sex

tag: age at diagnosis

tag: mycn status

tag: high risk


title: Patient 45


title: 150cGy-noTRT24-h3

tag: gender

tag: chemo before tp


title: Patient 44


title: 150cGy-noTRT24-h9


title: Patient 43


title: SEQC NB patient 001

tag: tissue

tag: dataset

tag: inss stage

tag: class label

tag: progression

tag: death from disease


title: SEQC NB patient 003


title: SEQC NB patient 004


title: SEQC NB patient 006


title: Patient 40


title: SEQC NB patient 002


title: 150cGy-LPS6-h4

tag: source type

tag: dose

tag: treatment

tag: time

tag: subject number

tag: condition/tp dx


title: Patient 42

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: 150cGy-LPS6-h8

tag: gender

tag: chemo before tp


title: Patient 39


title: 150cGy-noTRT24-h8


title: Patient 37


title: SEQC NB patient 005

tag: tissue

tag: dataset

tag: Sex

tag: age at diagnosis

tag: mycn status

tag: high risk


title: 150cGy-LPS6-h9

tag: source type

tag: dose


title: 150cGy-LPS24-h5

tag: treatment

tag: time


title: 150cGy-LPS6-h7

tag: subject number

tag: condition/tp dx


title: Patient 38

tag: dfs_event (disease free survival)

tag: dfs_time (disease free survival time, months)


title: Patient 36

tag: dss_event (disease specific survival)

tag: dss_time (disease specific survival time, months)


title: 150cGy-LPS24-h7

tag: gender

tag: chemo before tp


title: 150cGy-LPS24-h4


title: 150cGy-GCSF6-h5


title: Patient 41


title: 150cGy-LPS24-h8


title: Patient 34


title: Patient 35


title: 150cGy-GCSF6-h6


title: 150cGy-GCSF6-h4


title: Patient 33


title: 150cGy-GCSF6-h10


title: liver, allogeneic day5 rep.2

city: Tokyo

first: Masayuki

last: Fujino

address: Toyama, Shinjuku-ku, 1-23-1

institute: NIID

description: Gene expression after 5day in allografting liver

hyb_protocol: The purified labeled miRNA probes were hybridized to 8x15 K mouse miRNA microarrays (Agilent Technologies) in a rotating hybridization oven at 20 rpm for 20 hours at 55 °C. After hybridization, the arrays were washed in Gene Expression Wash Buffer 1 with Triton X-102 followed by Gene Expression Wash Buffer 2 with Triton X-102.

scan_protocol: All slides were immediately scanned at a resolution of 5 µm with Green-PMT XDR Hi 100%, Lo 5% using an Agilent DNA Microarray Scan (Agilent). The resulting images were quantified using Agilent’s Feature Extraction software program. The differentially expressed miRNAs were identified using a standard protocol developed for miRNA gene arrays. To increase the reliability of the data and ease of detection, miRNA species with a hybridization intensity <1.5 times the average hybridization intensity (mean) were excluded from the analysis.

data_processing: A miRNA clustering analysis was performed with the Hierarchical clustering algorithm provided in the Avadis, ArrayAssist 4.3 software package.

source_name: liver, allogeneic day5

label_protocol: One hundred ng of total RNA was dephosphorylated with calf intestinal alkaline phosphatase (Takara Bio Inc., Shiga, Japan), followed by denaturing with heat in the presence of dimethyl sulfoxide (SIGMA-Aldrich Co., St. Louis, MO). A cyanine dye, cyanine3-cytidine bisphosphate (Agilent), was then joined to the dephosphorylated single-stranded RNA using T4RNA ligase (Ambion). MicroBioSpin 6 columns (Bio-Rad Laboratories Inc., Hercules, CA) were used to remove any unincorporated cyanine dye from the samples.

growth_protocol: All mice were maintained under standard conditions and fed rodent food and water, in accordance with the guidelines of the Animal Use and Care Committee of the National Research Institute for Child Health and Development.

extract_protocol: Total RNA, including miRNA from RNAlater (Ambion, Austin, TX) immersed liver grafts, was isolated using the RNeasy Mini Kit and miRNeasy kit (QIAGEN Inc., Valencia, CA.), according to the manufacturer’s protocol. The quality and quantity of the RNA were evaluated using the NanoDrop 1000 (Thermo Scientific Inc., Waltham, MA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: B10.BR mice were used as donors and B10.D2 mice were used as recipients. Liver allo-transplantation surgery on the mice was performed in this combination. Three mice from each group were sacrificed, and the liver grafts were removed on days 5, 8, 14 and 100 after transplantation.

tag: strain

value: B10.BR (H2-Kk) mouse as donor and B10.D2 (H2-Kd) mouse for recipient

tag: tissue

value: liver

value: male


title: 150cGy-GCSF24-h7

value: blood


title: Patient 32

source_name: Nashville Veterans Affairs Medical Center


title: Patient 31


title: 150cGy-GCSF24-h10

value: Healthy


title: Patient 27


title: Patient 28

value: 1 (death from cancer)


title: liver, allogeneic day5 rep.3


title: Patient 26


title: Patient 30


title: liver, allogeneic day5 rep.1


title: 0cGy-noTRT6-h5

value: Male


title: 0cGy-noTRT6-h7


title: Patient 29


title: liver, allogeneic day100 rep.3

description: Gene expression after 100day in allografting liver

source_name: liver, allogeneic day100


title: Survivin-RNA (Cy3)

city: Santiago

first: Ulises

last: Urzua

address: Independencia 1027

department: Basic and Clinical Oncology

country: Chile

institute: University of Chile

hyb_protocol: Labeled test and reference cDNAs were cleaned up and made to 70 ul of a solution containing 25% formamide, 0.1% SDS and 3.5X SSC and 10 ug of salmon sperm DNA. Slides were place in closed hybridization chambers and incubated for 16-20 hrs in a water bath at 65°C. Washes in 2X SSC-0.1% SDS, 1X SSC, 0.2X SSC, and 0.05X SSC were performed sequentially, 1-min each

scan_protocol: Slides were quickly dried and scanned at 10-µm resolution in a ScanArray-Lite scanner (Perkin Elmer, MA). PMT gain was adjusted between 70-85% to obtain maximal signal intensities with minimal saturation.

data_processing: Array images were stored in TIFF format and extracted as GenePix result (gpr) files using GenePix Pro III software (Molecular Devices, CA).  Data was subjected to print-tip (local) Loess normalization and scale adjustment with the DNMAD tool (http://dnmad.bioinfo.cnio.es) and then filtered/imputed for missing values with the preP tool (http://prep.bioinfo.cnio.es/)

label_protocol: 15 µg of total RNA were primed with 1 µg of random hexamers plus 1 µg of oligo-dT at 75°C for 10 min, then reversed transcribed at 42°C for 2.5 h with 500 U SuperScript II (Invitrogen), and 0.5 mM each dATP, dCTP, dGTP, 0.2 mM dTTP, and 0.1 mM dUTP-Cy3 (or Cy5, when corresponded)

growth_protocol: Cells were cultured in DMEM medium supplemented with 10% FBS, 10,000 U/ml penicillin and 10 mg/ml streptomycin.

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

treatment_protocol: Cells were transiently transfected with Lipofectamine 2000 using 5 µg of each vector. Transfection efficiency was checked by epifluorescence microscopy : roughly 50%

tag: cell type

value: Human embryonic kidney (HEK293) cells

tag: tranfected

tag: transfected

value: pEGFP-survivin


title: 150cGy-GCSF24-h9

tag: source type

value: GCSF

value: Female


title: 150cGy-GCSF24-h6

tag: dose


title: 0cGy-noTRT6-h10

tag: treatment


title: liver, allogeneic day100 rep.2


title: liver, allogeneic day14 rep.3

description: Gene expression after 14day in allografting liver

source_name: liver, allogeneic day14


title: Patient 25


title: liver, allogeneic day100 rep.1


title: Patient 24


title: Survivin-RNA (Cy5)


title: Patient 23


title: liver, allogeneic day14 rep.2


title: liver, allogeneic day14 rep.1


title: 0cGy-noTRT6-h6

tag: time


title: liver, allogeneic day8 rep.3

description: Gene expression after 8day in allografting liver

source_name: liver, allogeneic day8


title: 0cGy-noTRT24-h8

tag: subject number


title: Patient 22


title: liver, allogeneic day8 rep.2


title: liver, allogeneic day8 rep.1


title: 0cGy-noTRT24-h7

tag: condition/tp dx


title: 0cGy-noTRT24-h10


title: Patient 17

tag: dfs_event (disease free survival)


title: 0cGy-LPS6-h10

value: LPS


title: Patient 18

tag: dfs_time (disease free survival time, months)


title: 0cGy-LPS6-h4


title: Patient 21

tag: dss_event (disease specific survival)


title: liver, syngeneic day5 rep.3

description: Gene expression after 5day in syngrafting liver

source_name: liver, syngeneic day5


title: Patient 20

tag: dss_time (disease specific survival time, months)


title: Patient 15


title: liver, syngeneic day5 rep.2

tag: gender


title: liver, syngeneic day5 rep.1


title: 0cGy-LPS24-h6

tag: chemo before tp


title: 0cGy-LPS6-h8


title: 0cGy-LPS24-h9


title: Patient 12


title: 0cGy-LPS24-h5


title: Patient 19


title: 0cGy-LPS6-h5


title: 0cGy-GCSF6-h2


title: Patient 13


title: 0cGy-GCSF6-h3


title: Patient 14


title: Patient 16


title: 0cGy-GCSF6-h7


title: Patient 10


title: 0cGy-LPS24-h8


title: Patient 9


title: 0cGy-GCSF6-h10


title: Patient 6


title: 0cGy-GCSF24-h6


title: 0cGy-GCSF24-h8


title: Patient 11


title: Patient 7


title: Patient 8


title: SUM159-P0 cells

city: Houston

first: Peijing

last: zhang

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

description: Control

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of six housekeeping genes: SNORD61, SNORD68, SNORD72, SNORD95, SNORD96A, RNU6-2.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR Green

source_name: SUM159 breast cancer cell lines

label_protocol: PCR assays were performed using the Human Apoptosis miScript miRNA PCR Array assay panel (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the miScript II Reverse Transcription Kits(SA Biosciences). Quantitative real-time PCR were performed (CFX96 instrument, Bio-Rad) with 40 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

tag: cell line

value: Parental breast cancer cell line


title: 0cGy-GCSF24-h10

source_name: ex vivo


title: Patient 5


title: SUM159-P2 cells

description: Test

source_name: Derived from SUM159 breast cancer cell lines

value: radioresistant breast cancer cell line


title: Patient 4


title: 0cGy-GCSF24-h9


title: Patient 2


title: Patient 3


title: Patient 1


title: NC8

status: Public on Oct 20 2014

city: TaiYuan

first: Zhifen

last: Liu

state: Shanxi

address: 85 Jiefang South Road

department: Psychiatry

institute: 1st hospital of Shanxi Medical University

hyb_protocol: 20 ug of Fragmented-labeled ds DNA were hybridized for for 16 hr at 45°C . Wash/Stain arrays with Affymetrix® Hybridization, Wash and Stain Kit using the FS450_0001 fluidics protocol.

scan_protocol: After hybridization and washing, processed slides were scanned with the Affymetrix GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA).

data_processing: All gene level files were imported into Affymetrix Expression Console (version 1.2.1) and normalized by the quantile method. Combat Software was used to adjust the normalized intensity to remove batch effects.

source_name: demographically-matched controls

label_protocol: Labeling of fragmented ds cDNA  according to the standard Affymetrix protocol  (GeneChip® Eukaryotic Double Strand Whole Transcript Protocol, Affymetrix).

growth_protocol: Peripheral blood (10 ml) was obtained just before breakfast .

extract_protocol: Total RNA was isolated using TRIZol according to the manufacturer's instructions.

treatment_protocol: Mononuclear cells were isolated within 1 h by density-gradient centrifugation and stored in Trizol  at − 80 °C.

tag: blood

value: peripheral blood

tag: average age

value: 6 female/6 male


title: NC10


title: NC9


title: NC11


title: NC3


title: NC7


title: NC4


title: NC12


title: NC2


title: Human prostate tumor cp12

city: Boston

first: Carmen

last: Priolo

state: MA

address: 1 Blackfan Circle

institute: Brigham and Women's Hospital

hyb_protocol: Performed at the Dana-Farber Cancer Institute Microarray Core and the protocols can be found at http://macf-web.dfci.harvard.edu/index.php?option=com_content&task=category&sectionid=5&id=20&Itemid=88

scan_protocol: Performed at the Dana-Farber Cancer Institute Microarray Core and the protocols can be found at http://macf-web.dfci.harvard.edu/index.php?option=com_content&task=category&sectionid=5&id=20&Itemid=89

data_processing: Dchip was used to generate the .txt files containing SNP genotype calls. GISTIC was applied to identify significantly altered regions.

source_name: Human prostate tumor

label_protocol: Performed at the Dana-Farber Cancer Institute Microarray Core and the protocols can be found at http://macf-web.dfci.harvard.edu/index.php?option=com_content&task=category&sectionid=5&id=20&Itemid=87

extract_protocol: AllPrep DNA/RNA Micro kit, Qiagen Inc.

tag: tissue

value: prostate cancer


title: NC5


title: Human prostate tumor cp11


title: ND 7

source_name: the patient in the first edisode of MDD

value: 5 female/5 male


title: NC1


title: Human prostate tumor cp89


title: Human prostate tumor cp10


title: Human prostate tumor cp88


title: NC6


title: ND 9


title: Human prostate tumor cp14


title: ND 8


title: Human prostate tumor cp13


title: Human prostate tumor cp9


title: ND 6


title: Human prostate tumor cp64


title: Human prostate tumor cp66


title: Human prostate tumor cp87


title: Human prostate tumor cp63


title: Human prostate tumor cp65


title: Human prostate tumor cp86


title: Human prostate tumor cp62


title: 0cGy-noTRT24-h6


title: ND 5


title: Human prostate tumor cp85


title: ND 4


title: Human prostate tumor cp61


title: ND 10


title: ND 3


title: ND 2


title: ND 1


title: Human prostate tumor cp84


title: Human prostate tumor cp67


title: Human prostate tumor cp56


title: Human prostate tumor cp81


title: Human prostate tumor cp53


title: Human prostate tumor cp83


title: Human prostate tumor cp50


title: Human prostate tumor cp51


title: Human prostate tumor cp52


title: Human prostate tumor cp80


title: Human prostate tumor cp8


title: Human prostate tumor cp60


title: Human prostate tumor cp79


title: Human prostate tumor cp77


title: Human prostate tumor cp76


title: Human prostate tumor cp75


title: Human prostate tumor cp49


title: Human prostate tumor cp4


title: Human prostate tumor cp54


title: Human prostate tumor cp78


title: Human prostate tumor cp3


title: Human prostate tumor cp71


title: Human prostate tumor cp70


title: ΔpacC 8 hr time point vs wild type 8 hr time point

city: Manchester

first: Margherita

last: Bertuzzi

address: Core Technology Facility, 46 Grafton Street

department: Institute for Inflammation and Repair

country: United Kingdom

institute: University of Manchester

hyb_protocol: The A. fumigatus oligonucleotide slides version 3 were used for microarray hybridization (http://pfgrc.tigr.org/slide_html/microarray_descriptions.shtml). Briefly, hybridizations were incubated for 18 h at 42°C. Post hybridization washes included (twice each) 55°C in 2X SSC, 0.1% SDS, RT in 0.1X SSC, 0.1% SDS and RT 0.1X SSC.

scan_protocol: After washing, slides were scanned with a GenePix 4000b scanner using GenePix Pro 3.0 software. PMT gains were changed in order to generate images with red:green ratios of as close to 1:1 as possible. Images were saved as .TIF files and TIGR Spotfinder (Saeed et al, 2003) was used to quantitate fluorescent intensities. Poor quality spots were identified manually and flagged. After Spotfinder analysis, results were exported as TIGR software compatible MEV files following local background subtraction.

data_processing:
The phase- or strain-specific comparative analysis of gene expression datasets was conducted in Genespring GX 11.02 (Agilent). Normalized log2 expression ratios were filtered on expression level and differentially regulated transcripts were defined as having log2 (Cy5/Cy3) greater than the arbitrary thresholds of ± 1.5.
In all the AvsB.mev raw data files, A=ch1=Cy5 and B=ch2=Cy3.

label: Cy5, Cy3

organism: Aspergillus fumigatus

source_name: BALs, leukopenic mice infected with ΔpacC, 8 hours post-infection

label_protocol: cDNA synthesis and labeling were performed as per JCVI PFGRC SOP m007 as described previously (McDonagh et al., 2008)(http://pfgrc.jcvi.org/index.php/microarray/protocols.html) Briefly, cDNA were generated using Invitrogen Superscript II, incorporating aminoallyl-dUTP. cDNA Samples were labeled with Cy3 or Cy5 during a 2 hour room temperature incubation followed by purification with a Qiagen PCR purification column to remove unbound dye.

extract_protocol: Bronchoalveolar lavage fluid (BAL) samples were centrifuged at 14000 rpm for 5 min and the pellet was washed with 500 μl ice cold H2O to lyse host cells. Seven BALs were pooled, resuspended in 450 μl ME-RLC buffer (QIAGEN) and ground in liquid nitrogen with a pestle and mortar. RNA was then extracted using RNeasy® Kit (QIAGEN). A reference RNA sample was extracted from A. fumigatus ATCC46645 conidia harvested from an ACM plate. Conidia were washed thoroughly with sterile water, quickly frozen in liquid nitrogen, and disrupted by grinding. Total RNA extraction was performed using the filamentous fungi protocol of the Rneasy mini Kit (Qiagen). Quality of RNA used for microarray analysis was checked by Nanodrop ND-1000 Spectrophotometer. Only RNA with an A260/280 and an A260/230 ratio > 1.9 was used for the experiments.

treatment_protocol:
[immunosuppression mice] CD1 mice were housed in individually vented cages and anaesthetized by halothane inhalation and infected by intranasal instillation of spore suspensions. Mice were rendered leukopenic by administration of cyclophosphamide (150 mg/kg, intraperitoneal) on days -3, -1, +2 and every subsequent third day, and a single subcutaneous dose of hydrocortisone acetate (112.5 mg/kg) administered on day -1.
[spores preparation] A. fumigatus spores were harvested into sterile water from cultures grown on solid Aspergillus Complete Media for 5 days and spore suspensions were filtered using Miracloth. Conidial suspensions were spun for 10 min at 4000 rpm, washed twice with sterile water. Following enumeration, spores were resuspended to the appropriate concentration in sterile saline.
[infection] Leukopenic male CD1 mice (n = 7) were infected via the intranasal route with 1×10e8 conidia in 40 μl of saline solution. Viable counts from administered inocula were determined, following serial dilution, by growth for 24 - 48 hr on ACM. Bronchoalveolar lavages (BALs) were performed using three 0.5 ml aliquots of pre-warmed sterile saline. BALs were snap frozen immediately following harvesting using liquid nitrogen.

tag: strain

tag: genotype/variation

value: ΔpacC

tag: time point

value: 8 hours

label: Cy3, Cy5

source_name: BALs, leukopenic mice infected with ATCC46645, 8 hours post-infection

value: WT


title: ΔpacC 4 hr time point vs wild type 4 hr time point

source_name: BALs, leukopenic mice infected with ΔpacC, 4 hours post-infection

value: 4 hours

source_name: BALs, leukopenic mice infected with ATCC46645, 4 hours post-infection


title: ΔpacC 16 hr time point vs wild type 16 hr time point

source_name: BALs, leukopenic mice infected with ΔpacC, 16 hours post-infection

value: 16 hours

source_name: BALs, leukopenic mice infected with ATCC46645, 16 hours post-infection


title: ΔpacC 12 hr time point vs wild type 12 hr time point

source_name: BALs, leukopenic mice infected with ΔpacC, 12 hours post-infection

value: 12 hours

source_name: BALs, leukopenic mice infected with ATCC46645, 12 hours post-infection


title: ΔpacC 16 hr time point vs ΔpacC 0 hrs

source_name: ΔpacC spores, 0 hours

treatment_protocol:
[immunosuppression mice] N/A
[spores preparation] A. fumigatus spores were harvested into sterile water from cultures grown on solid Aspergillus Complete Media for 5 days and spore suspensions were filtered using Miracloth. Conidial suspensions were spun for 10 min at 4000 rpm, washed twice with sterile water. Conidia were  quickly frozen in liquid nitrogen, and disrupted by grinding.
[infection] N/A

value: 0 hours


title: Human prostate tumor cp68


title: Human prostate tumor cp69


title: Human prostate tumor cp47


title: Human prostate tumor cp44


title: Human prostate tumor cp45


title: Human prostate tumor cp43


title: Human prostate tumor cp24


title: Human prostate tumor cp41


title: Wild type 16 hr time point vs wild type 0 hrs

source_name: ATCC46645 spores, 0 hours


title: Human prostate tumor cp42


title: Human prostate tumor cp23


title: ΔpacC 4 hr time point vs ΔpacC 0 hrs


title: Wild type 12 hr time point vs wild type 0 hrs


title: Human prostate tumor cp40


title: ΔpacC 8 hr time point vs ΔpacC 0 hrs


title: Human prostate tumor cp38


title: Human prostate tumor cp37


title: Human prostate tumor cp48


title: ΔpacC 12 hr time point vs ΔpacC 0 hrs


title: Human prostate tumor cp36


title: Wild type 8 hr time point vs wild type 0 hrs


title: Human normal prostate cp19

source_name: Human normal prostate

value: normal prostate


title: Human prostate tumor cp39


title: Human normal prostate cp31


title: Wild type 4 hr time point vs wild type 0 hrs


title: Gtf2i(+/Δex2) vs. WT(+/+)  Cortex replicate 3

city: Barcelona

first: Victoria

last: Campuzano

address: Dr Aiguader, 88

department: CEXS

institute: Universitat Pompeu Fabra

description: Cortex Replicate 3

hyb_protocol: Three biological replicate experiments were hybridized following the manufacturer’s instructions (SSC wash Agilent 60-mer oligo microarray processing protocol, Version 4.1, April 2004), each comparing Gtf2i+/Δex2 verus wild type cortex tissues. Thus, three microarray hybridizations were processed.

scan_protocol: Fluorescent images were obtained with the Agilent G2565BA Microarray Scanner System (Agilent Technologies) and TIFF images were quantified with the use of the Spot program (http://experimental.act.cmis.csiro.au/Spot/index.php) under the R environment (http://www.r-project.org).

data_processing:
The original raw data file (i.e. Agilent feature extraction files) are not available. The modified raw data files are provided along with the file contents description (raw_data_readme.txt available on Series records).

The resulting raw values were filtered and an intensity cut-off was applied, selecting those points with a foreground median/background median >3 in at least one channel.  A series of programs, collectively packaged as Array File Maker 4.0 (AFM), were use to manipulate and manage DNA microarray data (Breitkreutz, Jorgensen et al. 2001). AFM 4.0, Quantarray Data Handler 3.0, and Array Database 1.0 can be downloaded at the Tyers Lab Home Page [http://www.mshri.on.ca/tyers/] and are copyrighted against commercial gain.

source_name: Gtf2i(+/Δex2) Cortex

label_protocol: 500 ng of total RNA were reverse transcribed, amplified, labelled by in vitro transcription using the Low Input Linear Amplification Kit (Agilent 5184-3523), and hybridized following the manufacturer’s instructions (SSC wash Agilent 60-mer oligo microarray processing protocol, Version 4.1, April 2004).

growth_protocol: Cortex were fresh dissected from adult, 16 weeks old animals. Dissected tissues were directly frozen in liquid Nitrogen until RNA extraction

extract_protocol:
Total RNA extracted using Trizol following manufacturer's instructions. RNA quantification was performed through a Nanodrop spectrophotometer.
Starting material: 500 ng of Total RNA
Quality Control: The quality of every RNA sample were tested by nanochip analysis on the Agilent Bioanalyzer and by measuring the A260/A280 and A260/A230 ratios.  All samples have a minimum RIN score of at least 7.0 , an OD (A260/A280) ratio value >1.8 and an OD (A260/A230) ratio>1.5.

tag: strain background

value: mixed background (98.4%  C57BL/6J , 1.6% 129Sv/CD1)

tag: age

value: 16 weeks old

value: Cortex

source_name: WT (+/+) Cortex


title: Gtf2i(+/Δex2) vs. WT(+/+)  Cortex replicate 2

description: Cortex Replicate 2


title: Gtf2i(+/Δex2) vs. WT(+/+)  Cortex replicate 1

description: Cortex Replicate 1


title: Human normal prostate cp17


title: Human normal prostate cp29


title: Human normal prostate cp18


title: adenocarcinoma 17d

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: Pooled DNA (fresh/frozen) of different organs of non-cancer individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent G2505B micro-array scanner. Image data acquisition was performed in feature extraction software v10.5 (Agilent Technologies) using the Agilent CGH-105_Dec08 protocol with default settings

data_processing: Median Signal intensity minus median Background intensity; excluding negative values. To overcome potential wave bias due to differences in GC-content of the different chromosomal regions, a smoothing algorithm was applied on our dataset as described by van de Wiel et al, Bioinformatics 2009; 25(9):1099-1104.

source_name: Colorectal tissue, m-FCM sorted nuclei

label_protocol: DNA labeling protocol according to Enzo Life Sciences.

extract_protocol: Multiple haematoxylin-eosin stained cryostatic sections were used as references to increase the epithelian cell component. DAPI stained nuclei suspentions were prepared and measured by multiparameter FACS 440-Sorted. DNA was extracted using Archive Pure DNA kit (5 Prime), amplified with Enzo Bioscore Screening and Amplification kit and Whole Genome Amplification kit WGA2 (Sigma-Aldrich) and purified with QIAquick Purification kit (Qiagen).

value: Colorectal tissue, m-FCM sorted nuclei

tag: ploidy status

value: diploid

value: M

source_name: Fresh/frozen DNA pool from different organs of non-cancer individuals

value: M/F


title: adenocarcinoma 16a

value: aneuploid

value: Fresh/frozen DNA pool from different organs of non-cancer individuals


title: adenocarcinoma 17a


title: adenocarcinoma 15d

value: F


title: adenocarcinoma 16d


title: Human prostate tumor cp15

source_name: Human prostate tumor

value: prostate cancer


title: Human prostate tumor cp16


title: adenocarcinoma 15a


title: adenocarcinoma 13a


title: Human prostate tumor cp25


title: Human normal prostate cp28


title: adenocarcinoma 14d


title: adenocarcinoma 13d


title: adenocarcinoma 12d


title: adenocarcinoma 14a


title: adenocarcinoma 11a


title: adenocarcinoma 12a


title: adenocarcinoma 11d


title: adenocarcinoma 10a


title: adenocarcinoma 10d


title: adenocarcinoma 9a


title: adenocarcinoma 8a


title: adenocarcinoma 8d


title: adenocarcinoma 9d


title: adenocarcinoma 6a


title: adenocarcinoma 6d


title: adenocarcinoma 7a


title: adenocarcinoma 1a


title: adenocarcinoma 5a


title: adenocarcinoma 7d


title: adenocarcinoma 4a


title: adenocarcinoma 2a


title: adenocarcinoma 4d


title: adenocarcinoma 3d


title: adenocarcinoma 2d


title: adenocarcinoma 3a


title: adenocarcinoma 5d