title: muscle stem cells at 12wks old, biological rep1

description: Adult MuSC_1


title: pTH5661_HK_8mer_1841

status: Public on Aug 01 2014

type: protein

city: Cincinnati

first: Matthew

middle: Tyson

last: Weirauch

state: OH

address: 3333 Burnet Avenue

country: USA

institute: Cincinnati Children's Hospital

hyb_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate. After a 2-h incubation at 37oC, 12.5 ml of the mix was added to 137.5 ml of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 μM zinc acetate/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20/50 mM zinc acetate and once with PBS/0.01% Triton-X 100/50 mM zinc acetate. Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 mM zinc acetate. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20/50 mM zinc acetate and once with PBS/50 mMzinc acetate.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 mM resolution.  Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low).  The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used.   Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing: We provide several scores for each 8-mer in each experiment. Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots. Please see the supplementary files on the platform record (GPL11260) to match the raw data files with the array probes.

molecule: protein

organism: synthetic construct

source_name: ceh-19_HK design

label_protocol: DBD sequences along with 50 amino acid residues on either side of the DBD in the native protein were cloned as SacI–BamHI fragments into pTH5325, a modified T7-driven GST expression vector, in most cases.  See paper supplemental web site (http://hugheslab.ccbr.utoronto.ca/supplementary-data/CisBP/) for exceptions.

tag: dbd

value: Homeobox

tag: platform_id_id design

value: HK

tag: dbd source organism


title: muscle stem cells at P0, biological rep2

type: RNA

city: Toyoake

first: Takahiko

last: Sato

state: Aichi

address: 1-98, Dengakugakubo, Kutsukakecho

country: Japan

institute: Fujita Health University

description: Neonatal MuSC_2

hyb_protocol: Hybridization was performed on GeneChip miRNA 2.0 arrays (Affymetrix) using standard protocols available at www.affymetrix.com. Standard Affymetrix protocols were also used for staining and washing of the arrays.

scan_protocol: Standard Affymetrix protocols was used for scanning of the arrays (available at www.affymetrix.com).

data_processing: Data files were analyzed with Affymetrix Expression Console (v.1.2.1.20) using RMA background correction and quantile normalization

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: GFP+RFP+ sorted cells_neonatal mice

label_protocol: biotinylated cRNA were prepared with FlashTag Biotin HSR labelling kit (Genisphere) according to manufacture's protocol.

growth_protocol: Pax3-GFP; MyoD-RFP expressing compound mice were prepared at neonatal, juvenile and adult stages.

extract_protocol: total RNA was extracted with miRNeasy Micro kit (QIAGEN) according to manufacture's protocol

treatment_protocol: diaphragmic skeletal muscle tissue were dissected and homogenized with collagenase to collect single cells by FACs Aria2 (BD).

tag: strain background

tag: genotype/variation

value: expressing Pax3-GFP; MyoD-primed RFP

tag: developmental stage

value: neonatal (P0)

tag: tissue

value: diaphragmic skeletal muscle tissue

tag: cell type

value: GFP+RFP+ sorted cells


title: muscle stem cells at P0, biological rep1

description: Neonatal MuSC_1


title: Adjacent normal tissue from patient 106

city: Beijing

first: Jiagen

last: Li

address: 17 Panjiayuannanli Chaoyang District

country: China

institute: Cancer Institute, CAMS

description: Adjacent normal tissue from patient 106

hyb_protocol: The labeled RNA was purified and hybridized to miRNA arrays according to the Agilent manufacturer's instructions.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.

data_processing: The miRNA array data were analyzed for data summarization, normalization and quality control by using the Percentile Shift (90th percentile) with GeneSpring software V11.5 (Agilent).

organism: Homo sapiens

source_name: Adjacent normal tissue from patient 106

label_protocol: The extracted RNA were labeled according to the Agilent manufacturer's instructions. Briefly, the miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (100 ng) was dephosphorylated and ligated with pCp-Cy3.

extract_protocol: Total RNA was extracted from the specimens using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000) and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

tag: tissue type

value: Adjacent normal tissue

tag: patient

value: patient 106


title: Adjacent normal tissue from patient 97

description: Adjacent normal tissue from patient 97

source_name: Adjacent normal tissue from patient 97

value: patient 97


title: Adjacent normal tissue from patient 101

description: Adjacent normal tissue from patient 101

source_name: Adjacent normal tissue from patient 101

value: patient 101


title: human foreskin SKPs sample 3

city: Toronto

first: Freda

last: Miller

state: ON

address: 555 University Avenue

country: Canada

institute: Hospital for Sick Children

description: Gene expression data from neonatal foreskin cultured as SKPs

hyb_protocol: Samples were hybridized with GeneChip Human Gene 2.0 ST Arrays (Affymetrix) and scanned at the HSC Microarray Facility.

scan_protocol: The hybridized microarray image was scanned with the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Raw probe intensity values were background corrected, normalized with quantile normalization, transformed into the log2 scale, and summarized into probesets using the Robust Multichip Analysis (RMA) algorithm at the gene level in the Affymetrix Expression Console program.

source_name: neonatal foreskin cultured as SKPs

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

growth_protocol: Epidermis was dissected from dermis following enzymatic digestion.  The dermis was cut into small pieces and further digested and filtered until single cells were isolated.  These cells were cultured in proliferation-promoting conditions as previously described.

extract_protocol: Trizol extraction of total RNA was performed with the RNeasy Mini Kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: Cells proliferated as spheres.  After one or two passages, spheres were placed in Trizol reagent.

value: dermis

value: neonatal foreskin cultured as SKPs


title: muscle stem cells at 2wks old, biological rep２

description: Juvenile MuSC_2

source_name: GFP+RFP+ sorted cells_juvenilel mice

value: juvenilel (2wks)


title: human foreskin SKPs sample 4


title: Adjacent normal tissue from patient 96

description: Adjacent normal tissue from patient 96

source_name: Adjacent normal tissue from patient 96

value: patient 96


title: pTH5656_ME_8mer_1637

source_name: FOXP1_ME design

extract_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate.

value: ME


title: pTH5656_ME_8mer_1694


title: human foreskin SKPs sample 2


title: human foreskin SKPs sample 1


title: human facial SKPs sample 2

description: Gene expression data from <2 year old facial skin cultured as SKPs

source_name: facial skin less than two years old cultured as SKPs


title: human facial SKPs sample 3

value: facial skin less than two years old cultured as SKPs


title: Cancer tissue from patient 97

description: Cancer tissue from patient 97

source_name: Cancer tissue from patient 97

value: Cancer tissue

tag: dataset

value: test

tag: age

tag: gender

value: female

tag: tobacco use

value: no

tag: alcohol use

tag: family history

value: negative

tag: tumor location

value: middle

tag: tumor grade

value: moderately

tag: t stage

tag: n stage

tag: tnm stage

value: III

tag: status

value: dead


title: Cancer tissue from patient 106

description: Cancer tissue from patient 106

source_name: Cancer tissue from patient 106

value: patient 106

value: male

value: yes

value: positive

value: lower

value: well

value: I

value: survival


title: human facial SKPs sample 4

value: dermis

value: facial skin less than two years old cultured as SKPs


title: pTH5654_HK_8mer_2007

source_name: ENSTNIG00000008122_HK design

tag: dbd

value: Homeobox

tag: platform_id_id design

value: HK

tag: dbd source organism


title: pTH5654_ME_8mer_1529

source_name: ENSTNIG00000008122_ME design

value: ME


title: Cancer tissue from patient 101

description: Cancer tissue from patient 101

source_name: Cancer tissue from patient 101

tag: tissue type

value: Cancer tissue

value: patient 101

value: test

value: negative


title: pTH5647_ME_8mer_1563

source_name: GSPATP00020286001_ME design


title: Cancer tissue from patient 96

description: Cancer tissue from patient 96

source_name: Cancer tissue from patient 96

tag: patient

value: patient 96

value: middle

value: moderately

value: III

value: dead


title: human facial SKPs sample 1

tag: tissue

tag: cell type


title: US 185

city: Milano

first: Elena

last: Landoni

address: Via Vanzetti 5

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

description: miRNA profile of archival plasma sample

hyb_protocol: Hybridization for 20 h at 55 °C on SurePrint G3 Human v16 miRNA 8x60K microarrays (G4870A) designed on miRBase 16.0 from Agilent Technologies. The arrays were washed in Agilent GE Wash Buffers, following the manufacturer’s instructions

scan_protocol: All slides were immediately scanned at 2 mm resolution using an Agilent DNA microarray scanner

data_processing: The resulting images were analyzed using Agilent’s Feature Extraction software v10.7. In the employed platform, each miRNA is targeted by one to 4 different probes and each probe is spotted 10 to 40 times on the array. Then, the total gene signal for each miRNA was obtained by summing the probe signals derived using the Agilent Feature Extraction software. Using this software, each probe is defined detected if its value is greater than 3 times its standard error, and each miRNA is defined as detected if at least one of the probes is detected. Summarized data were log2 transformed

source_name: plasma

label_protocol: 2.5 µl of total RNA was dephosphorylated at 37°C for 30 min with calf intestinal phosphatase and denatured using 100% DMSO at 100°C for  5 min, labeled with pCp-Cy3 using T4 ligase by incubation at 16°C for 1 hour

growth_protocol: Plasma samples used in this study belong to the human plasma collection of the Fenretinide Breast Cancer Prevention Trial and RNA was extracted from 350 µl of sample.

extract_protocol: Total RNA was extracted from plasma using the commercial column-based system Qiagen miRNeasy® Mini Kit (Qiagen, Valencia, CA, USA), slightly modified by Exiqon (Vedbaek, Denmark. The eluate was digested using 1 u/µl heparinase I (Sigma-Aldrich, St. Luis, MO, USA), in the presence of an RNase inhibitor, (RNAsin; Promega, Madison, WI, USA) for 1 hour at room temperature, and RNA was stored at −80 °C.

value: plasma

tag: plasmaid

tag: drawing year

tag: age at drawing

tag: time from surgery

tag: hemolysis score (hs)

tag: hs class

value: no hemolysis


title: US 154

description: miRNA profile of archival plasma sample


title: US 159

description: miRNA profile of archival plasma sample

value: hemolyzed


title: US 143

description: miRNA profile of archival plasma sample


title: US 167

description: miRNA profile of archival plasma sample


title: US 135

description: miRNA profile of archival plasma sample


title: US 130

description: miRNA profile of archival plasma sample


title: Adjacent normal tissue from patient 6

description: Adjacent normal tissue from patient 6

source_name: Adjacent normal tissue from patient 6

value: Adjacent normal tissue

value: patient 6


title: US 125

description: miRNA profile of archival plasma sample


title: pTH5644_HK_8mer_2006

source_name: Ptx1_HK design

value: Homeobox


title: E.albidus_experiment 2_Control_4d_rep1

city: Aveiro

first: Sara

last: Novais

address: Campus de Santiago, Department of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

description: E.albidus gene expression after 4 days under control conditions

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit . 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GEx hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-030589 Custom Gene Expression Array for Enchytraeus albidus 8x15k, for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um).

data_processing: Fluorescence intensity data was obtained with Feature Extraction (10.5.1.1) Software (Agilent Technologies) using default parameters (protocol GE1_105_Dec08 and Grid: 030589_D_F_20101007) to obtain background subtracted intensities. The gBGSubSignal column was used for further analysis and intensities inferior to 1 were excluded from the analysis.

organism: Enchytraeus albidus

source_name: Enchytraeus albidus, experiment 2, control, 4 days, replicate 1

label_protocol: Cyanine-3 (Cy3) 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 RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Isolation of total RNA from each replicate was performed through the Trizol extraction method (Invitrogen, Belgium). This RNA followed a DNAse treatment (Fermentas, Germany) and further purification steps consisting of phenol/chloroform extractions. The quantity and purity of the isolated RNA were measured spectrophotometrically with nanodrop (NanoDrop ND-1000 Spectrophotometer) and its integrity was checked on a denaturing formaldehyde agarose gel electrophoresis.

treatment_protocol: Ten adult worms with well developed clitellum were introduced in the test vessels, each containing 25 g moist soil (control or spiked with acetone). The worms were exposed for 2 days in experiment 1 and for 2, 4 and 8 days in experiment 2 (at 20ºC and a 16:8h photoperiod). Further, organisms were sampled directly from the cultures (CULT – 10 adult worms for each of the three biological replicates) at day 0 of experiment 1. Three and four biological replicates per treatment  were used respectively in experiment 1 and 2. At test end, animals of each replicate were carefully removed, rinsed in deionised water, stored in RNA later (Ambion, USA) containing criotubes and frozen in liquid Nitrogen. All the samples were stored at -80ºC till further analysis.

value: Whole body extracts

tag: developmental stage

value: Adult organisms with well developed clitellum


title: US 119

description: miRNA profile of archival plasma sample


title: pTH5644_ME_8mer_1522

source_name: Ptx1_ME design

value: ME


title: Cancer tissue from patient 6

description: Cancer tissue from patient 6

source_name: Cancer tissue from patient 6

value: Cancer tissue

tag: dataset

value: training

tag: age

tag: gender

value: male

tag: tobacco use

value: yes

tag: alcohol use

tag: family history

tag: tumor location

value: lower

tag: tumor grade

value: poorly

tag: t stage

tag: n stage


title: Cancer tissue from patient 7

description: Cancer tissue from patient 7

source_name: Cancer tissue from patient 7

tag: tissue type

tag: patient

value: patient 7

value: test

value: no

value: negative

value: middle

value: moderately

tag: tnm stage

value: III

tag: status


title: US 153

description: miRNA profile of archival plasma sample

tag: tissue

value: plasma

tag: plasmaid

tag: drawing year

tag: age at drawing

tag: time from surgery

tag: hemolysis score (hs)

value: no hemolysis


title: pTH5647_HK_8mer_1891

source_name: GSPATP00020286001_HK design

tag: dbd

tag: platform_id_id design

value: HK

tag: dbd source organism


title: pTH5643_ME_8mer_1493

source_name: T13C5.4_ME design

value: Homeobox

value: ME


title: pTH5643_HK_8mer_1509

source_name: T13C5.4_HK design


title: Cancer tissue from patient 4

description: Cancer tissue from patient 4

source_name: Cancer tissue from patient 4

value: Cancer tissue

value: patient 4

tag: dataset

tag: age

tag: gender

tag: tobacco use

tag: alcohol use

tag: family history

tag: tumor location

value: upper

value: II

value: dead


title: US 111

description: miRNA profile of archival plasma sample

tag: hs class

value: hemolyzed


title: pTH5634_HK_8mer_1503

source_name: Ci-FoxM_HK design


title: pTH5642_ME_8mer_1492

source_name: ZFHX2_ME design


title: US 191

description: miRNA profile of archival plasma sample

tag: tissue


title: US 102

description: miRNA profile of archival plasma sample

tag: plasmaid


title: Adjacent normal tissue from patient 94

description: Adjacent normal tissue from patient 94

source_name: Adjacent normal tissue from patient 94

tag: tissue type

value: Adjacent normal tissue

tag: patient

value: patient 94


title: Adjacent normal tissue from patient 92

description: Adjacent normal tissue from patient 92

source_name: Adjacent normal tissue from patient 92

value: patient 92


title: Adjacent normal tissue from patient 87

description: Adjacent normal tissue from patient 87

source_name: Adjacent normal tissue from patient 87

value: patient 87


title: pTH5634_ME_8mer_7669

source_name: Ci-FoxM_ME design


title: Adjacent normal tissue from patient 4

description: Adjacent normal tissue from patient 4

source_name: Adjacent normal tissue from patient 4


title: US 92

description: miRNA profile of archival plasma sample

source_name: plasma

tag: drawing year

tag: age at drawing

tag: time from surgery


title: US 101

description: miRNA profile of archival plasma sample

tag: hemolysis score (hs)


title: US 88

description: miRNA profile of archival plasma sample


title: pTH5642_HK_8mer_1508

source_name: ZFHX2_HK design

tag: dbd

tag: platform_id_id design

tag: dbd source organism


title: US 108

description: miRNA profile of archival plasma sample


title: Adjacent normal tissue from patient 91

description: Adjacent normal tissue from patient 91

source_name: Adjacent normal tissue from patient 91

value: patient 91


title: Cancer tissue from patient 94

description: Cancer tissue from patient 94

source_name: Cancer tissue from patient 94

tag: dataset

value: training

tag: age

tag: gender

value: male

value: no

value: negative

value: middle

tag: tumor grade

value: moderately

tag: t stage

tag: n stage

tag: tnm stage

tag: status

value: survival


title: Adjacent normal tissue from patient 7

description: Adjacent normal tissue from patient 7

source_name: Adjacent normal tissue from patient 7

tag: tissue type

value: patient 7


title: Cancer tissue from patient 92

description: Cancer tissue from patient 92

source_name: Cancer tissue from patient 92

value: Cancer tissue

tag: patient

tag: tobacco use

tag: alcohol use

tag: family history

tag: tumor location

value: poorly


title: US 84

description: miRNA profile of archival plasma sample

tag: tissue

value: plasma

tag: plasmaid

tag: drawing year

tag: age at drawing

tag: time from surgery

tag: hemolysis score (hs)

tag: hs class


title: US 85

description: miRNA profile of archival plasma sample

value: no hemolysis


title: US 86

description: miRNA profile of archival plasma sample

value: hemolyzed


title: pTH5566_ME_8mer_904

source_name: Smp_016180_ME design

tag: dbd

tag: platform_id_id design

value: ME

tag: dbd source organism


title: US 83

description: miRNA profile of archival plasma sample


title: US 112

description: miRNA profile of archival plasma sample


title: pTH5566_HK_8mer_1008

source_name: Smp_016180_HK design

value: HK


title: Cancer tissue from patient 91

description: Cancer tissue from patient 91

source_name: Cancer tissue from patient 91

tag: dataset

value: test

tag: age

tag: gender

value: yes

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

value: II

tag: status


title: US 70

description: miRNA profile of archival plasma sample

tag: tissue

tag: plasmaid


title: pTH5553_HK_8mer_1016

source_name: cad_HK design

value: Homeobox


title: Cancer tissue from patient 87

description: Cancer tissue from patient 87

source_name: Cancer tissue from patient 87

tag: tissue type

tag: patient

value: patient 87

value: male

tag: tobacco use

value: no

tag: alcohol use

tag: family history

tag: tumor location

value: well

value: III


title: pTH5553_ME_8mer_893

source_name: cad_ME design

tag: dbd

tag: platform_id_id design

tag: dbd source organism


title: Adjacent normal tissue from patient 79

description: Adjacent normal tissue from patient 79

source_name: Adjacent normal tissue from patient 79

value: Adjacent normal tissue

value: patient 79


title: pTH5561_HK_8mer_1007

source_name: NR2E1_HK design


title: Adjacent normal tissue from patient 76

description: Adjacent normal tissue from patient 76

source_name: Adjacent normal tissue from patient 76

value: patient 76


title: Adjacent normal tissue from patient 77

description: Adjacent normal tissue from patient 77

source_name: Adjacent normal tissue from patient 77

value: patient 77


title: pTH5552_ME_8mer_892

source_name: NK-like_4_ME design


title: pTH5561_ME_8mer_902

source_name: NR2E1_ME design


title: US 62

description: miRNA profile of archival plasma sample

source_name: plasma

value: plasma

tag: drawing year

tag: age at drawing

tag: time from surgery

tag: hemolysis score (hs)

tag: hs class


title: US 65

description: miRNA profile of archival plasma sample

value: hemolyzed


title: US 64

description: miRNA profile of archival plasma sample

value: no hemolysis


title: US 76

description: miRNA profile of archival plasma sample


title: Adjacent normal tissue from patient 74

description: Adjacent normal tissue from patient 74

source_name: Adjacent normal tissue from patient 74

value: patient 74


title: US 60

description: miRNA profile of archival plasma sample


title: pTH5552_HK_8mer_1015

source_name: NK-like_4_HK design

value: HK


title: US 57

description: miRNA profile of archival plasma sample


title: US 61

description: miRNA profile of archival plasma sample


title: pTH5548_HK_8mer_1001

source_name: hbx5-1_HK design


title: US 50

description: miRNA profile of archival plasma sample


title: Cancer tissue from patient 77

description: Cancer tissue from patient 77

source_name: Cancer tissue from patient 77

value: Cancer tissue

tag: dataset

value: test

tag: age

tag: gender

value: yes

value: negative

value: middle

tag: tumor grade

value: moderately

tag: t stage

tag: n stage

tag: tnm stage

tag: status

value: dead


title: pTH5547_HK_8mer_985

source_name: hbx10_HK design

value: Homeobox


title: pTH5548_ME_8mer_846

source_name: hbx5-1_ME design

value: ME


title: Cancer tissue from patient 74

description: Cancer tissue from patient 74

source_name: Cancer tissue from patient 74

tag: tissue type

tag: patient

value: male

tag: tobacco use

value: no

tag: alcohol use

tag: family history

value: positive

tag: tumor location

value: lower

value: III


title: US 42

description: miRNA profile of archival plasma sample

tag: tissue

value: plasma

tag: plasmaid

tag: drawing year

tag: age at drawing

tag: time from surgery

value: hemolyzed


title: US 44

description: miRNA profile of archival plasma sample

tag: hemolysis score (hs)

tag: hs class

value: no hemolysis


title: Adjacent normal tissue from patient 73

description: Adjacent normal tissue from patient 73

source_name: Adjacent normal tissue from patient 73

value: Adjacent normal tissue

value: patient 73


title: US 38

description: miRNA profile of archival plasma sample


title: US 39

description: miRNA profile of archival plasma sample


title: pTH5543_ME_8mer_822

source_name: gtaH_ME design

tag: dbd

value: GATA

tag: platform_id_id design

tag: dbd source organism


title: Adjacent normal tissue from patient 71

description: Adjacent normal tissue from patient 71

source_name: Adjacent normal tissue from patient 71

value: patient 71


title: Cancer tissue from patient 76

description: Cancer tissue from patient 76

source_name: Cancer tissue from patient 76

value: Cancer tissue

value: patient 76

tag: dataset

value: training

tag: age

tag: gender

value: yes

value: negative

value: middle

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

tag: status


title: US 37

description: miRNA profile of archival plasma sample

tag: tissue

tag: plasmaid


title: pTH5543_HK_8mer_980

source_name: gtaH_HK design

value: HK


title: pTH5539_ME_8mer_7668

source_name: srfA_ME design

value: SRF-TF

value: ME


title: Adjacent normal tissue from patient 61

description: Adjacent normal tissue from patient 61

source_name: Adjacent normal tissue from patient 61

tag: tissue type

tag: patient

value: patient 61


title: pTH5534_ME_8mer_812

source_name: gtaE_ME design


title: pTH5539_HK_8mer_981

source_name: srfA_HK design


title: US 30

description: miRNA profile of archival plasma sample

source_name: plasma

value: plasma

tag: drawing year

tag: age at drawing

tag: time from surgery

tag: hemolysis score (hs)


title: US 34

description: miRNA profile of archival plasma sample

tag: hs class


title: US 32

description: miRNA profile of archival plasma sample

value: hemolyzed


title: US 33

description: miRNA profile of archival plasma sample

value: no hemolysis


title: US 35

description: miRNA profile of archival plasma sample


title: Adjacent normal tissue from patient 52

description: Adjacent normal tissue from patient 52

source_name: Adjacent normal tissue from patient 52

value: Adjacent normal tissue

value: patient 52


title: US 25

description: miRNA profile of archival plasma sample


title: US 26

description: miRNA profile of archival plasma sample


title: US 29

description: miRNA profile of archival plasma sample


title: Adjacent normal tissue from patient 60

description: Adjacent normal tissue from patient 60

source_name: Adjacent normal tissue from patient 60

value: patient 60


title: Cancer tissue from patient 61

description: Cancer tissue from patient 61

source_name: Cancer tissue from patient 61

tag: dataset

value: test

value: female

tag: tobacco use

value: no

tag: alcohol use

tag: family history

tag: tumor location

value: upper

value: moderately

value: III

value: dead


title: Cancer tissue from patient 71

description: Cancer tissue from patient 71

source_name: Cancer tissue from patient 71

value: Cancer tissue

value: patient 71

value: training

tag: age

tag: gender

value: male

value: yes

value: negative

tag: tumor grade

tag: t stage

tag: n stage

value: II


title: plasma pool sample 008

first: Yang

state: Beijing

address: 38 Xueyuan Road, Beijing 100191, China

department: Department of Occupational and Environmental Health Science School of Public Health

institute: Peking University

description: Gene expression in human plasma after high exposure to hexavalent chromium

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

scan_protocol: Slides  were  scanned  by  Agilent  Microarray  Scanner(Cat#G2565BA，Agilent   technologies,  Santa  Clara,  CA,  US)and  Feature  Extraction  software  10.7  (Agilent   technologies, Santa Clara, CA, US)with default settings. Raw data were normalized by   Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA,   US).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid: 021827_D_F_20091031) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: human plasma, high hexavalent exposure

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

extract_protocol: Total RNA was extracted from plasma using a commercial column-based system following the manufacturer’s instructions with the following modiﬁcations (Qiagen miRNeasy Mini Kit, Qiagen, USA). An aliquot of 200μl of plasma per sample was transferred to a new microcentrifuge tube and 1000μl QIAzol. Total RNA was eluted by adding 50μL of RNase-free water to the membrane of the spin column and incubating for 1 min before centrifugation at 8000×g for 1 min at room temperature. The RNA was stored at -20℃ until needed.

treatment_protocol: Post-shift blood samples on fasting state were collected. A total of 15 mL venous blood was also collected in different types of vacuum blood collection tubes.  The EDTA2K anticoagulant blood samples were collected for miRNAs analysis. Plasma samples were obtained by centrifugation at 3500 rpm for 10 min to precipitate the cellular components of blood specimen for the next analysis. Subsequently, the plasma samples were stored at -80 °C until analysis.

tag: tissue

value: plasma from peripheral blood


title: US 21

description: miRNA profile of archival plasma sample

value: plasma

tag: plasmaid

value: no hemolysis


title: US 193

description: miRNA profile of archival plasma sample

tag: drawing year


title: US 19

description: miRNA profile of archival plasma sample

tag: age at drawing


title: US 16

description: miRNA profile of archival plasma sample

tag: time from surgery

value: hemolyzed


title: US 20

description: miRNA profile of archival plasma sample

tag: hemolysis score (hs)


title: US 11

description: miRNA profile of archival plasma sample

tag: hs class


title: Cancer tissue from patient 79

description: Cancer tissue from patient 79

source_name: Cancer tissue from patient 79

tag: tissue type

tag: patient

value: patient 79

tag: dataset

value: middle

value: poorly

tag: tnm stage

tag: status

value: survival


title: pTH5534_HK_8mer_993

source_name: gtaE_HK design

tag: dbd

value: GATA

tag: platform_id_id design

value: HK

tag: dbd source organism


title: US 6

description: miRNA profile of archival plasma sample


title: US 189

description: miRNA profile of archival plasma sample


title: Cancer tissue from patient 51

description: Cancer tissue from patient 51

source_name: Cancer tissue from patient 51

value: Cancer tissue

value: patient 51

value: test

tag: age

tag: gender

tag: tobacco use

tag: alcohol use

tag: family history

tag: tumor location

value: lower

tag: tumor grade

value: moderately

tag: t stage


title: Cancer tissue from patient 60

description: Cancer tissue from patient 60

source_name: Cancer tissue from patient 60

value: patient 60

value: training

value: male

value: yes

value: negative

tag: n stage

value: dead


title: Cancer tissue from patient 52

description: Cancer tissue from patient 52

source_name: Cancer tissue from patient 52

tag: tissue type

value: patient 52

value: well

value: I


title: Adjacent normal tissue from patient 51

description: Adjacent normal tissue from patient 51

source_name: Adjacent normal tissue from patient 51

value: Adjacent normal tissue

tag: patient


title: pTH5531_ME_8mer_816

source_name: gtaG_ME design

value: GATA

value: ME


title: plasma pool sample 006

tag: tissue

value: plasma from peripheral blood


title: Adjacent normal tissue from patient 49

description: Adjacent normal tissue from patient 49

source_name: Adjacent normal tissue from patient 49

value: patient 49


title: Cancer tissue from patient 73

description: Cancer tissue from patient 73

source_name: Cancer tissue from patient 73

value: Cancer tissue

value: patient 73

tag: dataset

value: poorly

tag: tnm stage

value: III

value: survival


title: US 3

description: miRNA profile of archival plasma sample

value: plasma

tag: plasmaid

tag: drawing year

tag: age at drawing

tag: time from surgery

tag: hemolysis score (hs)

tag: hs class

value: no hemolysis


title: Cancer tissue from patient 49

description: Cancer tissue from patient 49

source_name: Cancer tissue from patient 49

value: training

tag: age

tag: gender

value: male

tag: tobacco use

value: yes

tag: alcohol use

value: negative

value: lower

value: moderately

tag: status


title: US 9

description: miRNA profile of archival plasma sample

value: hemolyzed


title: US 2

description: miRNA profile of archival plasma sample


title: Adjacent normal tissue from patient 46

description: Adjacent normal tissue from patient 46

source_name: Adjacent normal tissue from patient 46

value: Adjacent normal tissue

value: patient 46


title: pTH5547_ME_8mer_840

source_name: hbx10_ME design

tag: dbd

value: Homeobox

tag: platform_id_id design

value: ME

tag: dbd source organism


title: plasma pool sample 007

tag: tissue

value: plasma from peripheral blood


title: plasma pool sample 005


title: pTH5525_HK_8mer_979

source_name: gtaC_HK design

value: GATA

value: HK


title: pTH5531_HK_8mer_994

source_name: gtaG_HK design


title: US 52

description: miRNA profile of archival plasma sample

source_name: plasma


title: pTH5516_ME_8mer_874

source_name: Bm_svp_alpha_ME design


title: pTH5525_ME_8mer_818

source_name: gtaC_ME design


title: plasma pool sample 003

description: Gene expression in human plasma after low exposure to hexavalent chromium

source_name: human plasma, low hexavalent exposure


title: Adjacent normal tissue from patient 45

description: Adjacent normal tissue from patient 45

source_name: Adjacent normal tissue from patient 45

tag: tissue type

tag: patient

value: patient 45


title: plasma pool sample 002


title: pTH5523_HK_8mer_999

source_name: hbx5-2_HK design


title: pTH5511_ME_8mer_1997

source_name: Gsc_ME design


title: Adjacent normal tissue from patient 42

description: Adjacent normal tissue from patient 42

source_name: Adjacent normal tissue from patient 42

value: patient 42


title: pTH5517_HK_8mer_977

source_name: bzpD_HK design


title: pTH5523_ME_8mer_838

source_name: hbx5-2_ME design


title: pTH5516_HK_8mer_1006

source_name: Bm_svp_alpha_HK design


title: pTH5517_ME_8mer_810

source_name: bzpD_ME design


title: plasma pool sample 001


title: pTH5509_ME_8mer_873

source_name: VDR_ME design


title: Cancer tissue from patient 46

description: Cancer tissue from patient 46

source_name: Cancer tissue from patient 46

value: Cancer tissue

tag: dataset

tag: family history

tag: tumor location

value: middle

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

value: II

value: survival


title: Cancer tissue from patient 42

description: Cancer tissue from patient 42

source_name: Cancer tissue from patient 42

value: training

tag: age

tag: gender

value: male

value: yes

value: negative

value: poorly

value: dead


title: Cancer tissue from patient 45

description: Cancer tissue from patient 45

source_name: Cancer tissue from patient 45

tag: tobacco use

tag: alcohol use

value: no

value: moderately


title: Adjacent normal tissue from patient 36

description: Adjacent normal tissue from patient 36

source_name: Adjacent normal tissue from patient 36

value: Adjacent normal tissue

value: patient 36


title: pTH5509_HK_8mer_1005

source_name: VDR_HK design

tag: dbd

value: HK


title: Col

type: SRA

city: Seattle

first: Christopher

middle: Joel

last: Hale

state: WA

address: 1959 NE Pacific St., HSC H-458

department: Pathology

institute: University of Washington

description:
Bisulfite-treated genomic DNA
genomic DNA isolated by phenol/chloroform and bisulfite treated; quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane

library_source: genomic

data_processing:
BS-seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics), allowing up to 2 mismatches and retaining only uniquely mapping reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Samples 1..6: Fixed step UCSC Genome Browser wiggle format files for each chromosome for each cytosine context (CG, CHG, or CHH where H=A,T,C) with each line representing the methylation level (#methylated cytosines sequenced/#total cytosines sequenced) in a 50bp bin.
Supplementary_files_format_and_content: Samples 7..8: Variable step UCSC Genome Browser wiggle format files for each chromosome for each cytosine context (CG, CHG, or CHH where H=A,T,C) with following tab-separated information: bp position and methylation level (#methylated cytosines sequenced/#total cytosines sequenced).
Supplementary_files_format_and_content: Sample 9: Variable step UCSC Genome Browser wiggle format files for each chromosome for each cytosine context (CG, CHG, or CHH where H=A,T,C) with each line representing the methylation level (#methylated cytosines sequenced/#total cytosines sequenced).

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 3-week old leaf

growth_protocol: All plants were grown at 22 degrees celsius in constant light.

extract_protocol:
phenol-chloroform extraction followed by bisulfite treatment
converted and fragmented genomic DNA library as described in Stroud et al., Cell 2013

tag: genotype/variation

value: wildtype

tag: ecotype

value: Columbia

tag: sample

value: leaf

value: 3-week old


title: pTH5508_ME_8mer_872

source_name: HR3_ME design

tag: platform_id_id design

value: ME

tag: dbd source organism


title: pTH5508_HK_8mer_1004

source_name: HR3_HK design


title: Cancer tissue from patient 36

description: Cancer tissue from patient 36

source_name: Cancer tissue from patient 36

tag: tissue type

value: Cancer tissue

tag: patient

tag: dataset

value: test

value: middle

value: III

tag: status

value: survival


title: US 1

description: miRNA profile of archival plasma sample

source_name: plasma

tag: tissue

value: plasma

tag: plasmaid

tag: drawing year

tag: age at drawing

tag: time from surgery

tag: hemolysis score (hs)

tag: hs class

value: no hemolysis


title: Saliva_01

city: daejeon

first: Jonglyul

last: Park

address: 52, Eoeun-dong, Yuseong-gu

department: Medical genomics

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: miRNA expression data from saliva

hyb_protocol: Following ligation, ligated miRNA were hybridized for 18 hr at 48℃ on miRNA 3.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: miRNA 3.0 array were scanned using the Affymetrix GeneChip scanner 3000

data_processing: The data were analyzed with Robust Multi-array average (RMA) using Affymetrix expression console 1.3

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

extract_protocol: Total RNA including miRNA was isolated from each body fluids by Qiagen Rneasy Mini Kit according to the manufacturer's instructions.

value: Saliva


title: Saliva_03

description: miRNA expression data from saliva


title: Saliva_02

description: miRNA expression data from saliva


title: Adjacent normal tissue from patient 32

description: Adjacent normal tissue from patient 32

source_name: Adjacent normal tissue from patient 32

value: patient 32


title: Adjacent normal tissue from patient 31

description: Adjacent normal tissue from patient 31

source_name: Adjacent normal tissue from patient 31

value: Adjacent normal tissue

value: patient 31


title: Vaginal_05

description: miRNA expression data from vagianl

value: Vaginal


title: Saliva_04

description: miRNA expression data from saliva


title: Adjacent normal tissue from patient 28

description: Adjacent normal tissue from patient 28

source_name: Adjacent normal tissue from patient 28

value: patient 28


title: pTH5511_HK_8mer_2004

source_name: Gsc_HK design

tag: dbd

value: Homeobox

value: HK


title: pTH5506_HK_8mer_2086

source_name: Dll_HK design


title: pTH5505_HK_8mer_1013

source_name: FGSG_09566T0_HK design


title: Saliva_05

description: miRNA expression data from saliva


title: Adjacent normal tissue from patient 27

description: Adjacent normal tissue from patient 27

source_name: Adjacent normal tissue from patient 27

value: patient 27


title: pTH5505_ME_8mer_891

source_name: FGSG_09566T0_ME design

value: ME


title: pTH5506_ME_8mer_1045

source_name: Dll_ME design


title: plasma pool sample 004

source_name: human plasma, low hexavalent exposure

value: plasma from peripheral blood


title: Vaginal_02

description: miRNA expression data from vagianl


title: Vaginal_03

description: miRNA expression data from vagianl


title: Vaginal_04

description: miRNA expression data from vagianl


title: Vaginal_01

description: miRNA expression data from vagianl


title: pTH5504_ME_8mer_1031

source_name: Post-2_ME design


title: Cancer tissue from patient 32

description: Cancer tissue from patient 32

source_name: Cancer tissue from patient 32

value: Cancer tissue

value: test

tag: age

tag: gender

value: male

tag: tobacco use

value: yes

tag: alcohol use

tag: family history

value: negative

tag: tumor location

tag: tumor grade

value: moderately

tag: t stage

tag: n stage

tag: tnm stage

value: dead


title: Semen_05

description: miRNA expression data from semen

tag: tissue

value: Semen


title: Cancer tissue from patient 28

description: Cancer tissue from patient 28

source_name: Cancer tissue from patient 28

tag: tissue type

tag: patient

tag: dataset

value: middle

value: III

tag: status

value: survival


title: Cancer tissue from patient 31

description: Cancer tissue from patient 31

source_name: Cancer tissue from patient 31

value: patient 31

value: no

value: II


title: Semen_04

description: miRNA expression data from semen


title: Cancer tissue from patient 27

description: Cancer tissue from patient 27

source_name: Cancer tissue from patient 27

value: patient 27

value: training

value: lower

value: well


title: pTH5503_ME_8mer_651

source_name: SHOX-like_ME design

value: Homeobox

tag: platform_id_id design

value: ME

tag: dbd source organism


title: Adjacent normal tissue from patient 26

description: Adjacent normal tissue from patient 26

source_name: Adjacent normal tissue from patient 26

value: Adjacent normal tissue

value: patient 26


title: pTH5501_ME_8mer_744

source_name: FOXG1_ME design

tag: dbd


title: pTH5504_HK_8mer_2085

source_name: Post-2_HK design

value: HK


title: Semen_03

description: miRNA expression data from semen


title: Semen_02

description: miRNA expression data from semen


title: Semen_01

description: miRNA expression data from semen


title: pTH5503_HK_8mer_1012

source_name: SHOX-like_HK design


title: Adjacent normal tissue from patient 25

description: Adjacent normal tissue from patient 25

source_name: Adjacent normal tissue from patient 25

value: patient 25


title: Blood_04

description: miRNA expression data from blood

value: Blood


title: Adjacent normal tissue from patient 13

description: Adjacent normal tissue from patient 13

source_name: Adjacent normal tissue from patient 13

value: patient 13


title: Adjacent normal tissue from patient 23

description: Adjacent normal tissue from patient 23

source_name: Adjacent normal tissue from patient 23

value: patient 23


title: Cancer tissue from patient 25

description: Cancer tissue from patient 25

source_name: Cancer tissue from patient 25

value: Cancer tissue

value: test

tag: age

tag: gender

value: female

value: positive

value: middle

value: poorly

value: III

value: dead


title: Cancer tissue from patient 26

description: Cancer tissue from patient 26

source_name: Cancer tissue from patient 26

value: male

tag: tobacco use

value: yes

tag: alcohol use

value: negative


title: Blood_05

description: miRNA expression data from blood


title: pTH5501_HK_8mer_761

source_name: FOXG1_HK design


title: pTH5492_HK_8mer_1594

source_name: R06F6.6_HK design

value: Homeobox


title: pTH5492_ME_8mer_735

source_name: R06F6.6_ME design

value: ME


title: pTH5491_ME_8mer_734

source_name: HOXC_ME design


title: Blood_03

description: miRNA expression data from blood


title: DFCs transfected with pEV and differentiated 2

city: Regensburg

first: Sandra

last: Viale Bouroncle

address: Franz-Josef-Strauß-Allee 11

country: Germany

institute: University Hospital Regensburg

description: Gene expression of DFCs after transfection with pEV and osteogenic differentiation with BMP2

hyb_protocol: Hybridization to Affymetrix oligonucleotide microarray Human Gene 1.1 ST array was carried out overnight with 1biotin-labeled cRNA in a hybridization oven 640

scan_protocol: GeneTitan scanner (Affymetrix)

data_processing: Affymetrix GeneChip Operating Software (GCOS) 1.4 and the Expression Console 1.1. Software

source_name: DFVs with pEV in differentiation medium

label_protocol: Double-stranded cDNA was prepared from 5 μg of total cellular RNA (cDNA synthesis kit, Affymetrix Santa Clara, CA, USA), in vitro transcribed using an IVT labeling kit, and the cRNA product purified using a GeneChip Sample Cleanup Module (Affymetrix). All procedures according to the Affymetrix protocol.

growth_protocol: Cell were grown in DMEM medium (PAA, Pasching, Austria) and 10 % serum at 37°C in 5% CO2

extract_protocol: Total RNAs were extracted using the RNeasy isolation kit (Qiagen,Hilden, Germany) and quality-controlled using the RNA 6000 Nano LabChip (Agilent Technologies, Santa Clara, CA, USA)

treatment_protocol: After 48 h transfection and subconfluence cells at passage 6 were grown 3 days in the BMP2(10ng/ml) supplemented Osteogenesis Differentiation medium

tag: cell type

value: dental progenitor/stem cells


title: Blood_01

description: miRNA expression data from blood

value: Blood


title: pTH5491_HK_8mer_1585

source_name: HOXC_HK design

value: HK


title: Cancer tissue from patient 13

description: Cancer tissue from patient 13

source_name: Cancer tissue from patient 13

value: patient 13

value: training

tag: family history

tag: tumor location

value: upper

tag: tumor grade

value: I


title: DFCs transfected with pDLX3 and differentiated 1

description: Gene expression of DFCs after transfection with pDLX3 and osteogenic differentiation with BMP2

source_name: DFVs with pDLX3 in differentiation medium


title: Cancer tissue from patient 23

description: Cancer tissue from patient 23

source_name: Cancer tissue from patient 23

value: Cancer tissue

value: patient 23

value: test

value: female

value: no

value: moderately

tag: t stage

tag: n stage

tag: tnm stage

value: II

value: survival


title: Adjacent normal tissue from patient 11

description: Adjacent normal tissue from patient 11

source_name: Adjacent normal tissue from patient 11

tag: tissue type

value: Adjacent normal tissue

tag: patient

value: patient 11


title: pTH5490_HK_8mer_1593

source_name: VENTX_HK design

value: Homeobox


title: Adjacent normal tissue from patient 12

description: Adjacent normal tissue from patient 12

source_name: Adjacent normal tissue from patient 12

value: patient 12


title: DFCs transfected with pDLX3 and differentiated 2

value: dental progenitor/stem cells


title: pTH5490_ME_8mer_733

source_name: VENTX_ME design

value: ME


title: DFCs transfected with pEV and differentiated 1


title: Adjacent normal tissue from patient 10

description: Adjacent normal tissue from patient 10

source_name: Adjacent normal tissue from patient 10

value: patient 10


title: pTH5486_ME_8mer_728

source_name: Cnox5_ME design


title: Blood_02

description: miRNA expression data from blood

tag: tissue

value: Blood


title: pTH5486_HK_8mer_1011

source_name: Cnox5_HK design

tag: platform_id_id design

value: HK


title: pTH5481_ME_8mer_852

source_name: mybE_ME design

tag: dbd source organism


title: Adjacent normal tissue from patient 9

description: Adjacent normal tissue from patient 9

source_name: Adjacent normal tissue from patient 9

value: patient 9


title: pTH5480_ME_8mer_850

source_name: mybA_ME design

tag: dbd


title: pTH5481_HK_8mer_1000

source_name: mybE_HK design


title: Cancer tissue from patient 11

description: Cancer tissue from patient 11

source_name: Cancer tissue from patient 11

value: Cancer tissue

tag: dataset

tag: age

value: male

value: yes

value: positive

value: lower

value: poorly

value: III

tag: status

value: dead


title: Cancer tissue from patient 10

description: Cancer tissue from patient 10

source_name: Cancer tissue from patient 10

value: training

tag: gender

tag: tobacco use

tag: alcohol use

value: middle

value: II

value: survival


title: Adjacent normal tissue from patient 297

description: Adjacent normal tissue from patient 297

source_name: Adjacent normal tissue from patient 297

value: Adjacent normal tissue

value: patient 297


title: Cancer tissue from patient 9

description: Cancer tissue from patient 9

source_name: Cancer tissue from patient 9

value: test

tag: family history

value: negative

tag: tumor location

value: moderately


title: Cancer tissue from patient 12

description: Cancer tissue from patient 12

source_name: Cancer tissue from patient 12

value: Cancer tissue

value: patient 12

value: no

tag: tumor grade

tag: t stage


title: Adjacent normal tissue from patient 290

description: Adjacent normal tissue from patient 290

source_name: Adjacent normal tissue from patient 290

value: patient 290


title: Adjacent normal tissue from patient 268

description: Adjacent normal tissue from patient 268

source_name: Adjacent normal tissue from patient 268

value: patient 268


title: pTH5479_ME_8mer_726

source_name: zen2_ME design

value: Homeobox

value: ME


title: Adjacent normal tissue from patient 217

description: Adjacent normal tissue from patient 217

source_name: Adjacent normal tissue from patient 217

value: patient 217


title: Adjacent normal tissue from patient 201

description: Adjacent normal tissue from patient 201

source_name: Adjacent normal tissue from patient 201

value: patient 201


title: Cancer tissue from patient 297

description: Cancer tissue from patient 297

source_name: Cancer tissue from patient 297

value: training

value: male

value: middle

value: well

tag: n stage

tag: tnm stage


title: Cancer tissue from patient 290

description: Cancer tissue from patient 290

source_name: Cancer tissue from patient 290

tag: tissue type

tag: patient

value: yes

value: lower

value: III

value: survival


title: pTH5477_HK_8mer_2003

source_name: NOT-like_D_HK design

tag: platform_id_id design

value: HK


title: pTH5480_HK_8mer_984

source_name: mybA_HK design

tag: dbd source organism


title: Cancer tissue from patient 268

description: Cancer tissue from patient 268

source_name: Cancer tissue from patient 268

value: Cancer tissue

value: test

value: positive

value: upper

value: moderately

value: II


title: pTH5477_ME_8mer_1996

source_name: NOT-like_D_ME design

tag: dbd

value: Homeobox

value: ME


title: pTH5479_HK_8mer_760

source_name: zen2_HK design


title: pTH5474_ME_8mer_1995

source_name: UNCX_ME design


title: Cancer tissue from patient 217

description: Cancer tissue from patient 217

source_name: Cancer tissue from patient 217

value: patient 217

tag: dataset

value: training

value: negative

value: dead


title: pTH5466_HK_8mer_1283

source_name: Mlxip_HK design

value: HLH


title: pTH5474_HK_8mer_2002

source_name: UNCX_HK design


title: pTH5464_ME_8mer_2510

source_name: Jdp2_ME design


title: HepG2_K7174 vs. HepG2_DMSO

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: HepG2 cells treated with K7174 at 20 microM, and harvested after 24 hr

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc.

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: HepG2 DMSO

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: HepG2 cells are maintained with DMEM containing 10% fetal bovine serum (Biowest) and 1% penicillin-streptomycin (Sigma).

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

treatment_protocol: K7174 was treated at 20 microM for 24 hr

tag: cell line

tag: agent

value: control DMSO

source_name: HepG2 K7174

value: GATA inhibitor K-7174


title: pTH5466_ME_8mer_408

source_name: Mlxip_ME design


title: pTH5465_HK_8mer_1347

source_name: Mitf_HK design


title: pTH5464_HK_8mer_2542

source_name: Jdp2_HK design


title: pTH5462_ME_8mer_443

source_name: Jund_ME design


title: Cancer tissue from patient 201

description: Cancer tissue from patient 201

source_name: Cancer tissue from patient 201

value: patient 201

tag: age

tag: gender

value: female

value: no

value: III

tag: status


title: pTH5462_HK_8mer_1289

source_name: Jund_HK design

value: HK


title: Adjacent normal tissue from patient 112

description: Adjacent normal tissue from patient 112

source_name: Adjacent normal tissue from patient 112

value: Adjacent normal tissue

value: patient 112


title: Cancer tissue from patient 117

description: Cancer tissue from patient 117

source_name: Cancer tissue from patient 117

value: Cancer tissue

value: patient 117

value: male

tag: tobacco use

value: yes

tag: alcohol use

tag: family history

value: middle

value: moderately


title: Cancer tissue from patient 112

description: Cancer tissue from patient 112

source_name: Cancer tissue from patient 112

value: test

value: negative

tag: tumor location

value: lower

tag: tumor grade

value: poorly

tag: t stage

value: survival


title: Adjacent normal tissue from patient 102

description: Adjacent normal tissue from patient 102

source_name: Adjacent normal tissue from patient 102

tag: tissue type

value: patient 102


title: Cancer tissue from patient 102

description: Cancer tissue from patient 102

source_name: Cancer tissue from patient 102

tag: patient

value: female

value: no

value: well

tag: n stage

tag: tnm stage

value: I

value: dead


title: Adjacent normal tissue from patient 117

description: Adjacent normal tissue from patient 117

source_name: Adjacent normal tissue from patient 117

value: Adjacent normal tissue


title: Adjacent normal tissue from patient 129

description: Adjacent normal tissue from patient 129

source_name: Adjacent normal tissue from patient 129

value: patient 129


title: Adjacent normal tissue from patient 234

description: Adjacent normal tissue from patient 234

source_name: Adjacent normal tissue from patient 234

value: patient 234


title: Adjacent normal tissue from patient 231

description: Adjacent normal tissue from patient 231

source_name: Adjacent normal tissue from patient 231

value: patient 231


title: pTH5459_ME_8mer_442

source_name: Crebzf_ME design

tag: dbd

tag: platform_id_id design

value: ME

tag: dbd source organism


title: pTH5457_ME_8mer_879

source_name: Npas2_ME design

value: HLH


title: pTH5450_HK_8mer_1345

source_name: Hes5_HK design

value: HK


title: pTH5459_HK_8mer_1288

source_name: Crebzf_HK design


title: pTH5438_ME_8mer_716

source_name: FGSG_01100T0_ME design

value: Homeobox


title: pTH5438_HK_8mer_1010

source_name: FGSG_01100T0_HK design


title: pTH5460_HK_8mer_1598

source_name: Cebpb_HK design


title: pTH5460_ME_8mer_373

source_name: Cebpb_ME design


title: pTH5450_ME_8mer_392

source_name: Hes5_ME design


title: pTH5457_HK_8mer_2159

source_name: Npas2_HK design


title: Cancer tissue from patient 231

description: Cancer tissue from patient 231

source_name: Cancer tissue from patient 231

value: Cancer tissue

tag: dataset

value: training

value: male

value: yes

value: negative

value: middle

value: moderately

value: II


title: Cancer tissue from patient 129

description: Cancer tissue from patient 129

source_name: Cancer tissue from patient 129

value: test

tag: age

value: no

value: well

value: dead


title: Cancer tissue from patient 234

description: Cancer tissue from patient 234

source_name: Cancer tissue from patient 234

value: patient 234

tag: gender

value: III

value: survival


title: Cancer tissue from patient 229

description: Cancer tissue from patient 229

source_name: Cancer tissue from patient 229

value: patient 229

value: lower

tag: status


title: Adjacent normal tissue from patient 229

description: Adjacent normal tissue from patient 229

source_name: Adjacent normal tissue from patient 229

value: Adjacent normal tissue


title: Cancer tissue from patient 228

description: Cancer tissue from patient 228

source_name: Cancer tissue from patient 228

value: Cancer tissue

value: patient 228

tag: tobacco use


title: Adjacent normal tissue from patient 228

description: Adjacent normal tissue from patient 228

source_name: Adjacent normal tissue from patient 228


title: pTH5437_ME_8mer_489

source_name: Optix_ME design

value: Homeobox

value: ME


title: Human Endometriotic tissue 6

city: Chicago

first: Diana

last: Monsivais

address: 750 N Lake Shore Dr

institute: Northwestern University

description: Human Endometriotic tissue

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: Raw signal intensities of each probe were obtained using data analysis software(Beadstudio; Illumina) and imported to the Lumi package of Bioconductor fordata transformation and normalization [1-3]. A/P call detection was performed based on detection p value. The probes with less than 0.01 were considered as valid signals. The data for these probes were normalized by quantile method. Differentially expressed genes were identified using an Analysis of Variance (ANOVA) model with empirical Bayesian variance estimation [4]. Initially, genes were identified as being differentially expressed on the basis of a statistically significant (raw p-value < 0.01 and 1.5-fold change (up or  down) in expression level in different treatment samples.       [1] Du, P, Kibbe, W. A, and Lin, S. M. (2008) lumi: a pipeline for processing Illumina microarray. Bioinformatics. 24(13):1547-8.  [2] Lin, S. M., Du, P, Huber, W, and Kibbe, W. A. (2008) Model-based variance-stabilizing transformation for Illumina microarray data.  Nucleic  Acids Res. 36(2):e11  [3] Du, P, Kibbe, W. A., and Lin, S. M. (2007) nuID: a universal naming scheme of oligonucleotides for illumina, affymetrix, andother microarrays. Biol Direct. 2:16.  [4] Wettenhall, J. M., and Smyth, G. K. (2004). limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics 20, 3705-3706.

label: Biotin

source_name: Human Endometriotic tissue

label_protocol: standard as recommended by illumina

extract_protocol: RNA was prepared from the cultured stromal cells according to RNeasy kit (Qiagen, Valencia, CA).

tag: tissure

value: Endometriotic tissue


title: pTH5437_HK_8mer_757

source_name: Optix_HK design

value: HK


title: pTH5465_ME_8mer_407

source_name: Mitf_ME design

value: HLH


title: Human Endometriotic tissue 2

description: Human Endometriotic tissue


title: Human Endometriotic tissue 5

description: Human Endometriotic tissue


title: pTH5432_ME_8mer_484

source_name: HB-1_ME design


title: Human Endometriotic tissue 1

description: Human Endometriotic tissue


title: Human Endometriotic tissue 4

description: Human Endometriotic tissue


title: pTH5432_HK_8mer_756

source_name: HB-1_HK design


title: Human Endometriotic tissue 3

description: Human Endometriotic tissue


title: Normal human endometrial tissue 6

description: Normal human endometrial tissue

source_name: Normal human endometrial tissue

value: normal endometrial tissue


title: Normal human endometrial tissue 4

description: Normal human endometrial tissue


title: Adjacent normal tissue from patient 246

description: Adjacent normal tissue from patient 246

source_name: Adjacent normal tissue from patient 246

value: patient 246


title: pTH5430_ME_8mer_482

source_name: RARG_ME design


title: Adjacent normal tissue from patient 249

description: Adjacent normal tissue from patient 249

source_name: Adjacent normal tissue from patient 249

value: patient 249


title: Adjacent normal tissue from patient 247

description: Adjacent normal tissue from patient 247

source_name: Adjacent normal tissue from patient 247

value: patient 247


title: Cancer tissue from patient 245

description: Cancer tissue from patient 245

source_name: Cancer tissue from patient 245

value: patient 245

value: test

value: male

value: yes

tag: alcohol use

tag: family history

value: negative

value: middle

value: moderately

value: dead


title: Cancer tissue from patient 249

description: Cancer tissue from patient 249

source_name: Cancer tissue from patient 249

value: Cancer tissue

value: training

tag: tumor location

tag: tumor grade

value: poorly

value: II

value: survival


title: Cancer tissue from patient 246

description: Cancer tissue from patient 246

source_name: Cancer tissue from patient 246

tag: tissue type

tag: t stage

value: III


title: Cancer tissue from patient 247

description: Cancer tissue from patient 247

source_name: Cancer tissue from patient 247

tag: patient

value: lower

tag: n stage


title: pTH5419_ME_8mer_617

source_name: gbfA_ME design

tag: dbd

value: UNKNOWN

value: ME


title: Adjacent normal tissue from patient 245

description: Adjacent normal tissue from patient 245

source_name: Adjacent normal tissue from patient 245

value: Adjacent normal tissue

value: patient 245


title: pTH5419_HK_8mer_919

source_name: gbfA_HK design

tag: platform_id_id design

value: HK


title: pTH5418_ME_8mer_648

source_name: gtaT_ME design

value: GATA

tag: dbd source organism


title: pTH5412_HK_8mer_928

source_name: mybI_HK design


title: pTH5410_ME_8mer_611

source_name: mybZ_ME design


title: Normal human endometrial tissue 5

description: Normal human endometrial tissue

value: normal endometrial tissue


title: pTH5412_ME_8mer_645

source_name: mybI_ME design


title: Normal human endometrial tissue 1

description: Normal human endometrial tissue


title: Adjacent normal tissue from patient 243

description: Adjacent normal tissue from patient 243

source_name: Adjacent normal tissue from patient 243

value: patient 243


title: Normal human endometrial tissue 2

description: Normal human endometrial tissue

source_name: Normal human endometrial tissue


title: pTH5430_HK_8mer_755

source_name: RARG_HK design


title: Normal human endometrial tissue 3

description: Normal human endometrial tissue


title: pTH5418_HK_8mer_922

source_name: gtaT_HK design


title: pTH5410_HK_8mer_931

source_name: mybZ_HK design


title: Adjacent normal tissue from patient 241

description: Adjacent normal tissue from patient 241

source_name: Adjacent normal tissue from patient 241

value: patient 241


title: Adjacent normal tissue from patient 239

description: Adjacent normal tissue from patient 239

source_name: Adjacent normal tissue from patient 239

value: patient 239


title: Adjacent normal tissue from patient 236

description: Adjacent normal tissue from patient 236

source_name: Adjacent normal tissue from patient 236

value: patient 236


title: pTH5409_HK_8mer_926

source_name: mybAA_HK design


title: Cancer tissue from patient 243

description: Cancer tissue from patient 243

source_name: Cancer tissue from patient 243

value: Cancer tissue

tag: dataset

value: training

value: male

value: yes

value: no

value: positive

value: moderately

tag: tnm stage


title: Cancer tissue from patient 241

description: Cancer tissue from patient 241

source_name: Cancer tissue from patient 241

tag: age

tag: gender

value: female

value: upper

value: II

value: survival


title: pTH5408_HK_8mer_934

source_name: mybQ_HK design

value: HK


title: pTH5408_ME_8mer_642

source_name: mybQ_ME design

value: ME


title: Cancer tissue from patient 239

description: Cancer tissue from patient 239

source_name: Cancer tissue from patient 239

tag: tobacco use

value: negative

value: lower

value: III

tag: status

value: dead


title: Cancer tissue from patient 236

description: Cancer tissue from patient 236

source_name: Cancer tissue from patient 236

value: Cancer tissue

value: patient 236

tag: alcohol use

value: poorly


title: Adjacent normal tissue from patient 223

description: Adjacent normal tissue from patient 223

source_name: Adjacent normal tissue from patient 223

value: Adjacent normal tissue

value: patient 223


title: Control4, biol rep2

city: Riyadh

first: Dilek

last: Colak

address: MBC03, PO Box 3354

department: Biostatistics, Epidemiology and Scientific Computing

country: Saudi Arabia

institute: KFSHRC

description: Gene expression data from normal control.

hyb_protocol: A hybridization cocktail was prepared according to Affymetrix's whole transcript sense target labeling protocols. The whole cocktail, including around 5.5 ug fragmented and labelled DNA, was hybridized on Human Exon 1.0 ST arrays.  GeneChips were washed in the Affymetrix automated fluidic station.

scan_protocol: GeneChips were scanned using the Affymetrix G7 3000 scanner.

data_processing:
The open source R/Bioconductor packages (Fred Hutchinson Cancer Research Center, Seattle, WA, USA) were employed to normalize the data by GC Robust Multi-array Average (GC-RMA) algorithm. Further analyses were performed using PARTEK Genomics Suite (Partek® software, Partek Inc., St. Louis, MO, USA.). We used MATLAB (The Math Works, Inc., Natic, MA) and PARTEK Genomics Suite for the statistical analysis.

Exons included in the analysis: core
Genome build: hg18

source_name: LCL, control

label_protocol: 1 ug total RNA was used as starting material. rRNA reduction, 1st cycle dscDNA, cRNA (by IVT), and 2nd cycle 1st strand cDNA synthesis, cRNA hydrolysis, fragmentation (5.5ug single strand DNA) and terminal labeling were all done according to the standard Affymetrix whole transcript sense target labeling protocols.

growth_protocol: EBV-transformed lymphoblast cell lines from patients, carriers, and unrelated normal controls, according to protocols approved by the institutional review board.

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

tag: cell type

value: cultured lymphoblastoid cells

tag: disease state

value: healthy


title: Adjacent normal tissue from patient 222

description: Adjacent normal tissue from patient 222

source_name: Adjacent normal tissue from patient 222

value: patient 222


title: pTH5409_ME_8mer_790

source_name: mybAA_ME design


title: Index1, biol rep1

description: Gene expression data from index patient.

source_name: LCL, affected

value: global developmental delay and autistic features


title: Carrier2, biol rep1

description: Gene expression data from carrier.

source_name: LCL, carrier

value: carrier of global developmental delay and autistic features


title: Index2, biol rep1


title: Carrier2, biol rep2

description: Gene expression data from carrier.


title: Index1, biol rep2


title: Control4, biol rep1


title: pTH5406_ME_8mer_522

source_name: gtaI_ME design

value: GATA


title: Control3, biol rep1


title: Control3, biol rep2


title: pTH5403_HK_8mer_944

source_name: E2F_HK design

value: HK


title: pTH5404_HK_8mer_936

source_name: hbx4_HK design

value: Homeobox


title: Carrier1, biol rep2

description: Gene expression data from carrier.


title: pTH5403_ME_8mer_520

source_name: E2F_ME design

value: ME


title: pTH5405_HK_8mer_939

source_name: hbx2_HK design


title: pTH5404_ME_8mer_609

source_name: hbx4_ME design


title: pTH5406_HK_8mer_935

source_name: gtaI_HK design


title: pTH5405_ME_8mer_525

source_name: hbx2_ME design


title: Adjacent normal tissue from patient 221

description: Adjacent normal tissue from patient 221

source_name: Adjacent normal tissue from patient 221

value: patient 221


title: Index2, biol rep2


title: Control1, biol rep2


title: Control1, biol rep1


title: Carrier1, biol rep1

description: Gene expression data from carrier.


title: Adjacent normal tissue from patient 220

description: Adjacent normal tissue from patient 220

source_name: Adjacent normal tissue from patient 220

value: patient 220


title: Cancer tissue from patient 223

description: Cancer tissue from patient 223

source_name: Cancer tissue from patient 223

value: training

value: male

value: yes

tag: family history

value: negative

tag: tumor location

value: lower

tag: tumor grade

value: well

value: III

value: dead


title: Cancer tissue from patient 222

description: Cancer tissue from patient 222

source_name: Cancer tissue from patient 222

tag: tissue type

value: Cancer tissue

tag: patient

value: patient 222

value: test

value: middle

value: moderately

tag: t stage

value: II


title: Cancer tissue from patient 221

description: Cancer tissue from patient 221

source_name: Cancer tissue from patient 221

value: no

tag: n stage


title: Cancer tissue from patient 220

description: Cancer tissue from patient 220

source_name: Cancer tissue from patient 220

value: survival


title: pTH5399_ME_8mer_637

source_name: gtaL_ME design

tag: dbd

value: GATA

tag: platform_id_id design

value: ME

tag: dbd source organism


title: pTH5366_ME_8mer_797

source_name: bzpS_ME design


title: DC_TSLP_6h_R5

city: London

first: Raphael

last: Zollinger

state: London

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute (QMUL)

description: Sorted Dendritic Cells from healthy human blood

hyb_protocol: Affymetrix Standard protocol

scan_protocol: Affymetrix Standard protocol

data_processing: Data normalised in R using default settinsg of GCRMA package

source_name: sample cultured during 6h with recombinant TSLP (Thymic Stromal Lymphopoietin at 20 ng/uL) (TSLP_6h)

label_protocol: Affymetrix double amplification

growth_protocol: After purification, cells where either lysed immediatlely or cultured for 6h in RPMI (Gibco) medium containing 10% FBS (Hyclone) at 37 degree Celsius and 5% CO2 containing environment.

extract_protocol: Qiagen Rneasy microkit with on-column DNAse digestion.

treatment_protocol: Treatment stimuli were given from the start of culture.

value: blood

value: dendritic cells


title: HpeG2 siNTT rep2

city: Taichung

first: Shih-Ya

last: Hung

address: 2 Yude Road

country: Taiwan

institute: China Medical University

description: Gene expression data from HepG2 transfected with siNTT for 120 hr

hyb_protocol: 3.5 ug of ss-cDNA were hybridized for 16 hr at 45C on Affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 Scanner with autoloader.

data_processing: The raw images were visually scanned for defects and proper grid alignment and converted into CEL files using the MAS5 Software Suite (Affymetrix).

source_name: cells transfected with siNTT for 120 hr

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 5.5 ug total cDNA (GeneChip WT PLUS Reagent kit, Affymetrix).

growth_protocol: Human hepatoma HepG2 cells were cultured in DMEM  with 10% fetal bovine serum  in a 5% CO2/95% air atmosphere at 37 °C. Media was replaced every 2 days and cells were passaged at preconfluent densities to maintain exponential growth.

extract_protocol: Total RNA was extracted using High Pure RNA Isolation Kit according to the manufacturer's protocol. RNA was quantified spectrophotometrically at 260 nm. Two microgram of total RNA was subjected to reverse transcription (RT).

treatment_protocol: HepG2 cells were seeded at an approximate density of 2.5 X 10^5 on 6-well dishes in 2 ml of DMEM supplemented with 10% fetal bovine serum.When cells were approximately 80 to 90% confluent, siRNA constructs were transfected using lipofectamine 2000 Reagent. Cells were harvested 120 hr after transfection by High Pure RNA Isolation Kit (Roche).

tag: disease

value: hepatocellular carcinoma

value: male

tag: tissue

value: liver

tag: age

value: 15 years adolescent


title: pTH5363_ME_8mer_799

source_name: stkA_ME design


title: HpeG2 siNTT rep1

tag: gender


title: pTH5366_HK_8mer_924

source_name: bzpS_HK design

value: HK


title: pTH5399_HK_8mer_948

source_name: gtaL_HK design


title: DC_TNF_6h_R2

source_name: sample cultured during 6h with recombinant TNF (Tumor necrosis factor at 20 ng/mL) (TNF_6h)


title: pTH5367_ME_8mer_796

source_name: mybV_ME design


title: pTH5362_ME_8mer_800

source_name: mybG_ME design


title: HpeG2 siCon rep2

description: Gene expression data from HepG2 transfected with siControl vector for 120 hr

source_name: cells transfected with siControl vector for 120 hr


title: HpeG2 siNTT rep3


title: pTH5367_HK_8mer_921

source_name: mybV_HK design


title: DC_TSLP_6h_R4


title: HpeG2 siCon rep1

description: Gene expression data from HepG2 transfected with siControl for 120 hr


title: Adjacent normal tissue from patient 215

description: Adjacent normal tissue from patient 215

source_name: Adjacent normal tissue from patient 215

value: Adjacent normal tissue

value: patient 215


title: DC_TNF_6h_R3


title: Cancer tissue from patient 219

description: Cancer tissue from patient 219

source_name: Cancer tissue from patient 219

value: Cancer tissue

value: patient 219

tag: dataset

value: test

value: female

tag: tobacco use

tag: alcohol use

value: positive

value: well

tag: tnm stage

tag: status

value: dead


title: Adjacent normal tissue from patient 219

description: Adjacent normal tissue from patient 219

source_name: Adjacent normal tissue from patient 219


title: Adjacent normal tissue from patient 218

description: Adjacent normal tissue from patient 218

source_name: Adjacent normal tissue from patient 218

value: patient 218


title: Cancer tissue from patient 218

description: Cancer tissue from patient 218

source_name: Cancer tissue from patient 218

value: yes

tag: family history

value: negative

tag: tumor location

value: lower

tag: tumor grade

value: poorly

value: III


title: pTH5363_HK_8mer_929

source_name: stkA_HK design

value: GATA


title: pTH5362_HK_8mer_933

source_name: mybG_HK design

value: HK


title: pTH5355_ME_8mer_806

source_name: gtaN_ME design

value: ME


title: DC_TSLP_6h_R3

source_name: sample cultured during 6h with recombinant TSLP (Thymic Stromal Lymphopoietin at 20 ng/uL) (TSLP_6h)

tag: tissue type

value: blood

tag: cell type

value: dendritic cells


title: DC_TNF_6h_R1


title: Cancer tissue from patient 216

description: Cancer tissue from patient 216

source_name: Cancer tissue from patient 216

value: Cancer tissue

tag: patient

value: patient 216

value: training

value: male

tag: t stage

tag: n stage


title: Cancer tissue from patient 215

description: Cancer tissue from patient 215

source_name: Cancer tissue from patient 215

value: patient 215

value: test

value: no

value: middle

value: moderately

value: survival


title: Adjacent normal tissue from patient 212

description: Adjacent normal tissue from patient 212

source_name: Adjacent normal tissue from patient 212

value: Adjacent normal tissue

value: patient 212


title: DC_TSLP_6h_R2


title: Adjacent normal tissue from patient 214

description: Adjacent normal tissue from patient 214

source_name: Adjacent normal tissue from patient 214

value: patient 214


title: pTH5355_HK_8mer_947

source_name: gtaN_HK design

tag: dbd

value: GATA

tag: platform_id_id design

value: HK

tag: dbd source organism


title: DC_Control_6h_R3

source_name: DC sample cultured during 6h with no additional stimulus than the medium (Control_6h)

value: blood


title: DC_TSLP_6h_R1

value: dendritic cells


title: HpeG2 siCon rep3

source_name: cells transfected with siControl vector for 120 hr

tag: disease

value: hepatocellular carcinoma

tag: gender

tag: tissue

value: liver

tag: age

value: 15 years adolescent


title: Cancer tissue from patient 214

description: Cancer tissue from patient 214

source_name: Cancer tissue from patient 214

value: Cancer tissue

tag: dataset

value: male

tag: tobacco use

value: yes

tag: alcohol use

value: negative

value: poorly

tag: tnm stage

value: III

value: dead


title: Adjacent normal tissue from patient 211

description: Adjacent normal tissue from patient 211

source_name: Adjacent normal tissue from patient 211

value: Adjacent normal tissue

value: patient 211


title: DC_Control_0h_R6

source_name: freshly purified sample (Control_0h)


title: DC_Control_6h_R4


title: DC_Control_0h_R5


title: DC_Control_6h_R1


title: DC_Control_6h_R2


title: pTH5349_HK_8mer_989

source_name: bzpH_HK design


title: pTH5347_ME_8mer_845

source_name: bzpQ_ME design

value: ME


title: DC_Control_0h_R4


title: pTH5343_ME_8mer_521

source_name: DDB_G0270590_ME design


title: pTH5347_HK_8mer_990

source_name: bzpQ_HK design


title: Adjacent normal tissue from patient 210

description: Adjacent normal tissue from patient 210

source_name: Adjacent normal tissue from patient 210

value: patient 210


title: Cancer tissue from patient 211

description: Cancer tissue from patient 211

source_name: Cancer tissue from patient 211

value: test

tag: family history

value: positive

tag: tumor location

value: middle

tag: tumor grade

tag: status


title: Adjacent normal tissue from patient 208

description: Adjacent normal tissue from patient 208

source_name: Adjacent normal tissue from patient 208

tag: tissue type

tag: patient

value: patient 208


title: Cancer tissue from patient 210

description: Cancer tissue from patient 210

source_name: Cancer tissue from patient 210

value: training

value: no

value: lower

value: well

tag: t stage

tag: n stage


title: Cancer tissue from patient 212

description: Cancer tissue from patient 212

source_name: Cancer tissue from patient 212

value: Cancer tissue

value: patient 212

value: male

value: yes


title: pTH5343_HK_8mer_974

source_name: DDB_G0270590_HK design

tag: dbd

tag: platform_id_id design

value: HK

tag: dbd source organism


title: pTH5349_ME_8mer_847

source_name: bzpH_ME design


title: Adjacent normal tissue from patient 207

description: Adjacent normal tissue from patient 207

source_name: Adjacent normal tissue from patient 207

value: Adjacent normal tissue

value: patient 207


title: pTH5346_HK_8mer_973

source_name: dimB_HK design


title: DC_Control_0h_R3

value: blood

tag: cell type

value: dendritic cells


title: pTH5337_ME_8mer_951

source_name: Egr1_ME design

value: ME


title: Adjacent normal tissue from patient 216

description: Adjacent normal tissue from patient 216

source_name: Adjacent normal tissue from patient 216

value: patient 216


title: pTH5346_ME_8mer_843

source_name: dimB_ME design


title: DC_Control_0h_R1

source_name: freshly purified sample (Control_0h)


title: pTH5337_HK_8mer_1502

source_name: Egr1_HK design


title: Cancer tissue from patient 208

description: Cancer tissue from patient 208

source_name: Cancer tissue from patient 208

value: test

tag: age

tag: gender

value: negative

value: III

value: dead


title: Adjacent normal tissue from patient 206

description: Adjacent normal tissue from patient 206

source_name: Adjacent normal tissue from patient 206

value: patient 206


title: pTH5324_ME_8mer_841

source_name: bzpO_ME design


title: Cancer tissue from patient 207

description: Cancer tissue from patient 207

source_name: Cancer tissue from patient 207

tag: dataset

value: training

tag: tobacco use

value: middle

value: poorly


title: pTH5334_ME_8mer_314

source_name: PsHNF3a_ME design


title: Adjacent normal tissue from patient 205

description: Adjacent normal tissue from patient 205

source_name: Adjacent normal tissue from patient 205

value: patient 205


title: Cancer tissue from patient 206

description: Cancer tissue from patient 206

source_name: Cancer tissue from patient 206

value: Cancer tissue

value: male

value: yes

tag: alcohol use

value: well

tag: tnm stage

value: II

value: survival


title: pTH5334_HK_8mer_753

source_name: PsHNF3a_HK design

value: HK


title: NOK cl1 AkataBX-1 cl3 p30 EBV-

city: Shreveport

first: Rona

middle: S.

last: Scott

state: LA

address: 1501 Kings Highway

department: Microbiology and Immunology

institute: Louisiana State University Health Sciences Center-Shreveport

description: NOK I1 cl3 p30

hyb_protocol: FFollowing fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Expression Console version 1.3 (MAS 5 algorithm) using Affymetrix default analysis settings and global scaling with a target intensity value of 500 as normalization method.

source_name: NOK EBV-

label_protocol: Biotinylated cRNA was prepared from 150 ng of total RNA using the Affymetrix GeneChip 3' IVT Express Kit.

growth_protocol: Human telomerase (hTERT)-immortalized normal oral keratinocytes (NOK, kindly gifted by Dr. Karl Munger) were grown in keratinocyte serum free media (KSFM) supplemented with human epidermal growth factor and bovine pituitary extract (Life Technologies) in a humidified CO2 incubator at 37oC. Cells were passaged once a week using trypsinization at a 1:4 split.

extract_protocol: RNA was extracted using Stat-60 (TEL-TEST) as per manufacturer's instructions.

treatment_protocol: Uninfected parental cells, vector control (pTVRF=PTURF), EBV-infected, and EBV-negative  transiently-infected clones were seeded at 1x10^6 cells in a T75 flask.  RNA was harvested 3 days after seeding using STAT60 (Teltest) following the recommended protocol.

value: hTert immortalized normal oral keratinocytes derived from gingiva

tag: infection

value: EBV-negative  transiently-infected clone cl3


title: pTH5333_ME_8mer_326

source_name: PREP/MEIS-like_ME design

value: Homeobox

value: ME


title: pTH5324_HK_8mer_991

source_name: bzpO_HK design


title: NOK cl1 AkataBX-1 cl4 p30 EBV-

description: NOK I1 cl4 p30

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

value: EBV-negative  transiently-infected clone cl4


title: NOK cl1 AkataBX-1 cl3 p29 EBV-

description: NOK I1cl3 p29


title: Cancer tissue from patient 205

description: Cancer tissue from patient 205

source_name: Cancer tissue from patient 205

tag: family history

value: negative

tag: tumor location

value: upper

tag: tumor grade

value: moderately


title: pTH5333_HK_8mer_752

source_name: PREP/MEIS-like_HK design


title: NOK cl1 AkataBX-1 cl1 p29 EBV-

description: NOK  I1cl1 p29

value: EBV-negative  transiently-infected clone cl1


title: Adjacent normal tissue from patient 148

description: Adjacent normal tissue from patient 148

source_name: Adjacent normal tissue from patient 148

tag: tissue type

value: Adjacent normal tissue

tag: patient

value: patient 148


title: NOK cl1 AkataBX-1 cl1 p30 EBV-

description: NOK I1cl1 p30


title: pTH5323_ME_8mer_778

source_name: bzpF_ME design


title: Adjacent normal tissue from patient 146

description: Adjacent normal tissue from patient 146

source_name: Adjacent normal tissue from patient 146

value: patient 146


title: Adjacent normal tissue from patient 142

description: Adjacent normal tissue from patient 142

source_name: Adjacent normal tissue from patient 142

value: patient 142


title: pTH5323_HK_8mer_975

source_name: bzpF_HK design


title: Cancer tissue from patient 146

description: Cancer tissue from patient 146

source_name: Cancer tissue from patient 146

value: Cancer tissue

value: training

value: male

value: yes

value: middle

value: poorly

tag: t stage

tag: n stage

tag: status

value: dead


title: Cancer tissue from patient 136

description: Cancer tissue from patient 136

source_name: Cancer tissue from patient 136

value: patient 136

value: test

value: female

value: no

value: lower

value: III


title: Adjacent normal tissue from patient 136

description: Adjacent normal tissue from patient 136

source_name: Adjacent normal tissue from patient 136

value: Adjacent normal tissue


title: NOK cl1 AkataBX-1 cl4 p32 EBV+

description: NOK EBV+ I1cl4 p32

source_name: NOK EBV+

value: hTert immortalized normal oral keratinocytes derived from gingiva

value: EBV-infected clone cl4


title: NOK cl1 AkataBX-1 cl4 p29 EBV-

description: NOK I1cl4 p29

value: EBV-negative  transiently-infected clone cl4


title: pTH5320_ME_8mer_792

source_name: bzpJ_ME design

tag: dbd

tag: platform_id_id design

value: ME

tag: dbd source organism


title: NOK cl1 AkataBX-1 cl4 p31 EBV+

description: NOK EBV+ I1cl4 p31

tag: cell type


title: NOK cl1 pTURF transfected p23

description: NOK pTVRF cl2 p23

source_name: NOK vector transfected

value: vector transfected


title: Cancer tissue from patient 142

description: Cancer tissue from patient 142

source_name: Cancer tissue from patient 142

value: Cancer tissue

value: patient 142

tag: dataset

value: training

tag: age

tag: gender

value: male

value: positive

value: upper

value: moderately


title: pTH5320_HK_8mer_976

source_name: bzpJ_HK design

value: HK


title: NOK cl1 pTURF transfected p24

description: NOK pTVRF cl2 p24


title: NOK cl1 uninfected p32

description: NOK UN cl5 p32

source_name: NOK uninfected

value: uninfected


title: Adjacent normal tissue from patient 134

description: Adjacent normal tissue from patient 134

source_name: Adjacent normal tissue from patient 134

value: patient 134


title: pTH5267_HK_8mer_1348

source_name: Bhlhe22_HK design

value: HLH


title: pTH5270_HK_8mer_1372

source_name: Neurog1_HK design


title: Adjacent normal tissue from patient 132

description: Adjacent normal tissue from patient 132

source_name: Adjacent normal tissue from patient 132

value: Adjacent normal tissue

value: patient 132


title: pTH5265_ME_8mer_2501

source_name: Usf2_ME design


title: TIG-7 cells infected with lentiviruses for sh-p53, rep2

city: Tokyo

first: Ryo

last: Otomo

address: 5-1-1 Tsukiji, Chuo-ku

department: Division of Refractory Cancer Research

institute: National Cancer Center Research Institute

description: Gene expression data from TIG-7 cells infected with lentiviruses for sh-p53

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45˚C on GeneChip Human Genome U133 plus 2.0 Array (Affymetrix). Arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Softwere version 1.4 (GCOS1.4, Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: Target cRNA was prepared from 5 μg of total RNA with a One-cycle cDNA Synthesis Kit and 3’-amplification Reagents for IVT Labeling (Affymetrix).

growth_protocol: TIG-7 cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10 % fetal bovine serum, 100 units/ml penicillin and 100 units/ml streptomycin at 37 ℃ in a 5 % CO2 incubator

extract_protocol: Total RNA was purified using an RNeasy kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: TIG-7 cells were infected with lentiviruses for the expression of shRNA against p53.

tag: tissue

value: lung

tag: developmental stage

value: fetal

tag: cell line

tag: genotype/variation

value: p53 knockdown


title: NOK cl1 uninfected p31

description: NOK UN cl5 31

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0

data_processing: The data were analyzed with Expression Console version 1.3 using Affymetrix (MAS5 algorithm) default analysis settings and global scaling with a target intensity value of 500 as normalization method.

value: hTert immortalized normal oral keratinocytes derived from gingiva

tag: infection


title: pTH5265_HK_8mer_2533

first: Matthew

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital

hyb_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate. After a 2-h incubation at 37oC, 12.5 ml of the mix was added to 137.5 ml of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 μM zinc acetate/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20/50 mM zinc acetate and once with PBS/0.01% Triton-X 100/50 mM zinc acetate. Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 mM zinc acetate. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20/50 mM zinc acetate and once with PBS/50 mMzinc acetate.

data_processing: We provide several scores for each 8-mer in each experiment. Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots. Please see the supplementary files on the platform record (GPL11260) to match the raw data files with the array probes.

source_name: Usf2_HK design


title: pTH5270_ME_8mer_285

source_name: Neurog1_ME design

value: ME


title: TIG-7 cells infected with lentiviruses for sh-p53, rep1


title: Adjacent normal tissue from patient 135

description: Adjacent normal tissue from patient 135

hyb_protocol: The labeled RNA was purified and hybridized to miRNA arrays according to the Agilent manufacturer's instructions.

data_processing: The miRNA array data were analyzed for data summarization, normalization and quality control by using the Percentile Shift (90th percentile) with GeneSpring software V11.5 (Agilent).

source_name: Adjacent normal tissue from patient 135

tag: tissue type

value: patient 135


title: pTH5267_ME_8mer_2488

source_name: Bhlhe22_ME design


title: Adjacent normal tissue from patient 131

description: Adjacent normal tissue from patient 131

source_name: Adjacent normal tissue from patient 131

tag: patient

value: patient 131


title: pTH5260_HK_8mer_1358

source_name: Hes7_HK design


title: Cancer tissue from patient 135

description: Cancer tissue from patient 135

source_name: Cancer tissue from patient 135

value: Cancer tissue

value: training

value: male

tag: tobacco use

value: yes

tag: alcohol use

tag: family history

value: negative

tag: tumor location

value: lower

tag: tumor grade

value: poorly

tag: t stage

tag: tnm stage

value: III

value: dead


title: pTH5259_ME_8mer_2489

source_name: Hes2_ME design

tag: dbd

value: HLH

tag: platform_id_id design

tag: dbd source organism


title: Cancer tissue from patient 134

description: Cancer tissue from patient 134

source_name: Cancer tissue from patient 134

value: patient 134

tag: dataset

value: test

tag: age

tag: gender

value: female

value: no

value: middle

value: moderately

tag: n stage

value: II

tag: status

value: survival


title: Intact TIG-7 cells, rep1

description: Gene expresion data from intact TIG-7 cells

source_name: Intact TIG-7 cells

tag: tissue

value: lung

tag: developmental stage

value: fetal

tag: cell line

tag: genotype/variation

value: control


title: pTH5260_ME_8mer_275

source_name: Hes7_ME design

value: ME


title: Intact TIG-7 cells, rep2

value: male


title: Cancer tissue from patient 131

description: Cancer tissue from patient 131

source_name: Cancer tissue from patient 131

tag: tissue type

value: Cancer tissue

tag: patient

value: patient 131

value: training

tag: tobacco use

value: yes

tag: alcohol use

tag: family history

value: negative

value: poorly


title: pTH5259_HK_8mer_1370

source_name: Hes2_HK design

tag: dbd

value: HLH

value: HK


title: HB1.A4-Nurr1

city: Suwon

first: Myung Ae

last: Lee

state: Gyeonggi-do

address: Woncheon-dong, Yeongtong-gu

institute: ajou univ school of medicine 607

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133A 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: GeneChip 3.0 software (Affymetrix) was used for scanning and for first pass analysis and generation of raw data cell intensity (.cel) files. Data were subsequently submitted to a relational database for quality control assessment to include RNA quality, GeneChip sensitivity, and process quality determinations. Hierarchical clustering was performed and several distinct functional clusters were identified, including a cluster of genes possessed Nurr1-binding elements in promoter region. Hierarchical clustering using hamming distance correlation of the list of differentially expressed genes was conducted using EisenSoftware (Eisen lab, Lawrence Berkeley National Lab).

source_name: Human Neural Stem cell line with Nurr1 overexpression

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 701021 Rev 5., Affymetrix).

growth_protocol: Immortalized hNSC lines were maintained and passaged on uncoated culture dishes in DMEM with 10% Fetal bovine serum. All cells transduced with pLPCX or pLPC-Nurr1 were maintained in the same culture condition.

extract_protocol: Total RNA was extracted according to the manufacturer’s protocol (Affymetrix).

treatment_protocol: The retroviral vector pLPCX encoding human Nurr1 gene was infected into the PA317 amphotropic packaging cell line. Human NSC lines were infected with a retrovirus encoding human Nurr1 or control. All studies were performed within one week after transduction of retrovirus to avoid shut-down of Nurr1 gene expression in human neural stem cell lines.

tag: cell type

value: Immortalized human neural stem cell

tag: treatment

value: Nurr1 overexpression


title: HB1.A4

source_name: Human Neural Stem cell line(Maternal transcript)


title: Cancer tissue from patient 132

first: Jiagen

address: 17 Panjiayuannanli Chaoyang District

institute: Cancer Institute, CAMS

description: Cancer tissue from patient 132

source_name: Cancer tissue from patient 132

extract_protocol: Total RNA was extracted from the specimens using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000) and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

value: patient 132

tag: dataset

value: test

value: no

tag: tumor location

value: middle

tag: tumor grade

value: moderately

tag: t stage

tag: tnm stage

value: III

value: dead


title: Adjacent normal tissue from patient 122

description: Adjacent normal tissue from patient 122

source_name: Adjacent normal tissue from patient 122

value: Adjacent normal tissue

value: patient 122


title: Adjacent normal tissue from patient 119

description: Adjacent normal tissue from patient 119

source_name: Adjacent normal tissue from patient 119

value: patient 119