title: Her2, TUM061

source_name: Breast tumor sample from IHC defined Er- Her2+ subgroup


title: Her2, TUM059

status: Public on Jan 23 2015

type: RNA

city: PARIS

first: Thierry

last: Dubois

address: 26 rue d’Ulm

department: Recherche Center

country: France

institute: Institut Curie

description: Breast tumor sample from IHC defined Er- Her2+ subgroup

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data were analyzed using standard AffyCDF or Brainarray HGU133Plus2_Hs_ENTREZG version 13 custom chipset definition file. Data were normalized using GC-RMA. Batch and hybridization effects were corrected using a linear model in which they were treated as fixed effects. Samples with technical replicates were subsequently averaged.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Following RNA quality and quantity control, 2 µg of total RNA were amplified and labeled according to the Affymetrix one cycle synthesis target preparation protocol to hybridize Affymetrix U133 plus 2.0 chips, as described by the company.

growth_protocol: Tumor samples were obtained from patients treated at the hospital of Institut Curie (Biological Resource Center, Paris, France). Healthy samples were obtained from mammary plastic surgery. Cell lines were grown from the American Type Culture Collection (ATCC),

extract_protocol: Total RNA was extracted and purified from frozen tumor samples using the RNeasy Mini Kit (Qiagen) followed by the RNA clean up kit (Macherey Nagel), according to manufacturers’ instructions.

tag: hybridation batch


title: DNA from PB S40, SGA, no rhGH treatment

type: genomic

city: Kiel

first: Susanne

last: Bens

address: Arnold-Heller-Str.3 (Haus 10)

department: Institute of Human Genetics

country: Germany

institute: Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were scanned using the Illumina iScan

data_processing: GenomeStudio software (version 2011.1, Methylation module version 1.9.0)

label: Cy5 and Cy3

molecule: genomic DNA

source_name: peripheral blood (PB) cells from child born small for gestational age (SGA), no treatment

label_protocol: Standard Illumina Protocol

extract_protocol: various DNA extraction methods

tag: tissue

value: Peripheral Blood (PB)

tag: diagnosis

value: born small for gestational age (SGA)

tag: rhgh treatment

value: no treatment


title: Her2, TUM063


title: BA Luminal B, TUM102

description: Breast tumor sample from IHC defined Luminal B subgroup

value: Luminal B


title: DNA from PB S39, SGA, no rhGH treatment


title: DNA from PB S37, SGA, no rhGH treatment


title: BA Luminal A, TUM094

description: Breast tumor sample from IHC defined Luminal A subgroup

value: Luminal A


title: DNA from PB S38, SGA, no rhGH treatment


title: Her2, TUM058_repA


title: Her2, TUM062


title: BA Luminal A, TUM093

source_name: Breast tumor sample from IHC defined Luminal A subgroup


title: Her2, TUM060


title: TNBC, TUM056

description: Breast tumor sample from IHC defined Triple Negative subgroup

value: TNBC


title: TNBC, TUM054

source_name: Breast tumor sample from IHC defined Triple Negative subgroup


title: TNBC, TUM048_repA


title: TNBC, TUM051_repA


title: TNBC, TUM049


title: Her2, TUM057


title: Her2, TUM055


title: BA Luminal B, TUM107

source_name: Breast tumor sample from IHC defined Luminal B subgroup


title: BA Luminal A, TUM089


title: BA Luminal A, TUM092


title: TNBC, TUM051_repB


title: Her2, TUM046


title: TNBC, TUM053


title: TNBC, TUM045_repA


title: BA Luminal A, TUM088


title: Her2, TUM044


title: BA Luminal A, TUM087


title: TNBC, TUM043_repB


title: Her2, TUM047


title: TNBC, TUM050


title: Her2, TUM058_repB


title: Her2, TUM040


title: BA Luminal A, TUM086


title: TNBC, TUM048_repB


title: TNBC, TUM052


title: Her2, TUM042


title: Her2, TUM037


title: Her2, TUM038_repB


title: Her2, TUM035_repB


title: TNBC, TUM045_repB


title: TNBC, TUM043_repA


title: TNBC, TUM039


title: Her2, TUM041


title: Her2, TUM038_repA


title: Her2, TUM036


title: ko 28 day rep 2

city: Columbus

first: Kellie

middle: J.

last: Archer

state: OH

address: 1841 Neil Ave

department: Division of Biostatistics

country: USA

institute: Ohio State University

description:
Sample name: 5355492033_E
ko 28 day rep 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: GenomeStudioV2010.1 was used for processing the scanned images by applying background subtraction and quantile normalization to the bead-level data to obtain expression summaries and detection call p-values. Probes having a detection p-value <0.05 were considered present and absent otherwise. Because the detection call indicates whether expression can be reliably measured, probes called absent for all 12 arrays (N=20,355) were removed, leaving 24,926 probes for gene expression analysis.

organism: Mus musculus

source_name: total testicular RNA

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

growth_protocol: All the mice were kept in the same pathogen-free   animal room, and the mice have free access for food and water.

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

treatment_protocol: The animals were maintained untill they were 22 or 28 days old.Testicular  RNA was extracted from these mice, and microarray was conducted.

tag: age

value: 28 days old

tag: genotype/variation

value: ko

value: testicle


title: Her2, TUM035_repA


title: Prostate-41

first: Erica

middle: Hlavin

last: Bell

state: Ohio

address: 410 W 12th Ave

institute: The Ohio State University

hyb_protocol: Performed according to manufacturer's protocol

data_processing: Data processed using nSolver; a geometric mean was used to normalize miRNA expression

source_name: radical prostatectomy

label_protocol: nCounter Human miRNA Assay Kit

extract_protocol: Total RNA was exctracted by Qiagen miRNeasy FFPE kit

value: prostate cancer

tag: time to first recurrence

tag: positive lymph nodes

tag: d'amico risk classification

value: H

tag: stephensen risk classification

value: L

tag: gleason score

tag: time from rt to second biochemical recurrence (days)

tag: time from rt to last follow up-censored (days)


title: Prostate-39

scan_protocol: Performed according to manufacturer's protocol


title: Her2, TUM031


title: Prostate-43

value: H+


title: Prostate-42


title: ko 28 day rep 3

description:
Sample name: 5355492033_F
ko 28 day rep 3


title: Prostate-38


title: TNBC, TUM032_repB


title: Prostate-40


title: ko 28 day rep 1

description:
Sample name: 5355492033_D
ko 28 day rep 1


title: TNBC, TUM032_repA


title: TNBC, TUM034


title: TNBC, TUM030


title: TNBC, TUM033


title: TNBC, TUM029


title: wt 28 day rep 3

description:
Sample name: 5355492033_C
wt 28 day rep 3

value: wt


title: wt 28 day rep 1

description:
Sample name: 5355492033_A
wt 28 day rep 1


title: Prostate-35


title: Her2, TUM027


title: Her2, TUM026_repB


title: TNBC, TUM028_repB


title: Prostate-33


title: Prostate-37


title: ko 22 day rep 3

description:
Sample name: 5355492032_F
ko 22 day rep 3

value: 22 days old


title: wt 28 day rep 2

description:
Sample name: 5355492033_B
wt 28 day rep 2


title: TNBC, TUM028_repA


title: Prostate-36

value: I


title: Prostate-32


title: ko 22 day rep 1

description:
Sample name: 5355492032_D
ko 22 day rep 1


title: Prostate-34


title: TNBC, TUM025


title: wt 22 day rep 2

description:
Sample name: 5355492032_B
wt 22 day rep 2


title: TNBC, TUM023


title: wt 22 day rep 1

description:
Sample name: 5355492032_A
wt 22 day rep 1


title: wt 22 day rep 3

description:
Sample name: 5355492032_C
wt 22 day rep 3


title: TNBC, TUM024


title: ko 22 day rep 2

description:
Sample name: 5355492032_E
ko 22 day rep 2


title: Prostate-29


title: Prostate-31


title: Her2, TUM022


title: Prostate-30


title: Her2, TUM026_repA


title: Her2, TUM021_repA


title: Her2, TUM021_repB


title: Prostate-28


title: tumor_shMemo_rep1

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

description:
shMemo-1
xenograft tumors derived from human MDA-MB-231 shMemo pools, grown in NOD/SCID mice

hyb_protocol: Affymetrix GeneChip arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.

data_processing: Probesets were summarized and probeset-level values normalized with justRMA() function from R (version 2.10.0) / Bioconductor (version 2.5) package affy using the annotation from Netaffx (www.netaffx.com).

label: Biotin

source_name: shMemo tumor

label_protocol: RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix (GeneChip Whole Transcription Sense Target Labeling technical manual, Rev. 2).

growth_protocol: Tumors were collected 4 weeks post-injection into the second mammary fatpad of 6-8 week old NOD/SCID mice

extract_protocol: Tumors were collected and snap frozen in liquid nitrogen.  Samples were homogenized  using the Precellys-24 tissue homogenizer using 2mL tubes with metallic beads.  mRNA was purified using the FujiFilm Quickgene RNA tissue kit SII. cDNA synthesis and amplification was performed using GE Healthcare Ready-to-go You-Prime Frist-Strand Beads.

value: MDA-MB-231 derived tumor

value: shMemo


title: Her2, TUM020_repB

description: Breast tumor sample from IHC defined Er- Her2+ subgroup


title: Prostate-26


title: Prostate-27


title: tumor_shControl_rep3

description:
shLacZ-3
xenograft tumors derived from human MDA-MB-231 shControl pools, grown in NOD/SCID mice

source_name: shControl tumor

value: shLacZ


title: tumor_shMemo_rep2

description:
shMemo-2
xenograft tumors derived from human MDA-MB-231 shMemo pools, grown in NOD/SCID mice


title: Prostate-25


title: tumor_shMemo_rep3

description:
shMemo-3
xenograft tumors derived from human MDA-MB-231 shMemo pools, grown in NOD/SCID mice


title: Prostate-24


title: Her2, TUM019


title: Prostate-23


title: Her2, TUM020_repA


title: TNBC, TUM018_repB

description: Breast tumor sample from IHC defined Triple Negative subgroup


title: tumor_shControl_rep1

description:
shLacZ-1
xenograft tumors derived from human MDA-MB-231 shControl pools, grown in NOD/SCID mice


title: TNBC, TUM018_repA


title: Prostate-22


title: vestibualr organ at P90 of Igf1 +/+, biological rep 2

city: Sheffield

first: Marta

last: Milo

state: South Yorkshire

address: Western Bank

department: Biomedical Science

country: United Kingdom

institute: University of Sheffield

description: transcripts expression data from Igf1 -/- mouse vestibular organ at P90

hyb_protocol: Affymetrix GeneChip Mouse Gene 1.0 ST arrays were hybridized to 11 mg of labeled, amplified cDNA, washed, stained and scanned according to the protocol described in WT Sense Target Labeling Assay Manual

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: The data were analyzed with mmBGX (Turro et al, 2010) to quantify false positives and uncertainty of the measurements. mmBGX is a full hierarchical Bayesian method, where alternative matching of the probes are also considered and estimated of alternative splicing expression are provided. Gene expression estimated with mmBGX are posterior summaries for transcript that is associated with a measure of uncertainty (PROB) used to detect diﬀerential expression. The three biological replicates where combined into one summarised value using a hierarchical bayesian model.

source_name: Igf1 +/+ mouse vestibular organs 90 days old (P90)

label_protocol: 100ng of total RNA were amplified and labeled using the Whole Transcript (WT) Sense Target Labeling Protocol

growth_protocol: Igf1+/+ and Igf1-/- mice were studied at different time points (E18.5, P15 and P90) to follow their progression from embryonic stage to adult mice.

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

treatment_protocol: Mice were anesthetized with pentobarbiturate (Dolethal, Vetoquinol, Spain) and transcardially perfused with 4% paraformaldehyde in 0.1 M phosphate-buffered saline (PBS), pH7.5. The inner ear was dissected out.

value: vestibular organ

tag: genetic background

value: hybrid Mf1 with 129/sv background

tag: genotype


title: vestibualr organ at P90 of Igf1 -/-, biological rep 3

source_name: Igf1 -/- mouse vestibular organs 90 days old (P90)


title: tumor_shControl_rep2

description:
shLacZ-2
xenograft tumors derived from human MDA-MB-231 shControl pools, grown in NOD/SCID mice


title: Prostate-21


title: vestibualr organ at P90 of Igf1 +/+, biological rep 3


title: vestibualr organ at P90 of Igf1 -/-, biological rep 2


title: vestibualr organ at P90 of Igf1 +/+, biological rep 1


title: Prostate-20


title: TNBC, TUM017_repA


title: vestibualr organ at P15 of Igf1 +/+, biological rep 3

description: transcripts expression data from Igf1 -/- mouse vestibular organ at P15

source_name: Igf1 +/+ mouse vestibular organs 15day old (P15)


title: Prostate-19


title: vestibualr organ at P90 of Igf1 -/-, biological rep 1


title: TNBC, TUM017_repB


title: Her2, TUM016_repA


title: Her2, TUM016_repB


title: Her2, TUM015_repB


title: Her2, TUM015_repA


title: Prostate-18


title: Prostate-17


title: vestibualr organ at P15 of Igf1 +/+, biological rep 2


title: TNBC, TUM014


title: vestibualr organ at P15 of Igf1 +/+, biological rep 1


title: vestibualr organ at P15 of Igf1 -/-, biological rep 3

source_name: Igf1 -/- mouse vestibular organs 15day old (P15)


title: TNBC, TUM013_repA


title: DNA from PBMC P26, 4 days rhGH treatment

description:
P26_stimulated
IGF-1 generation test

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were scanned using the Illumina iScan.

data_processing: GenomeStudio software (version 2011.1, Methylation module version 1.9.0).

source_name: PBMCs, after rhGH treatment

label_protocol: Standard Illumina Protocol.

growth_protocol: None.

extract_protocol: DNeasy Blood and Tissue Kit (Qiagen).

treatment_protocol: 4 days of rhGH treatment during IGF-1 generation test.

tag: cell type

value: peripheral blood mononuclear cells

tag: treatment

value: recombinant human growth hormone

tag: patient


title: Prostate-16


title: TNBC, TUM013_repB

value: TNBC

tag: hybridation batch


title: Prostate-15

tag: diagnosis


title: Prostate-14


title: DNA from PBMC P25, 4 days rhGH treatment

description:
P25_stimulated
IGF-1 generation test


title: vestibualr organ at P15 of Igf1 -/-, biological rep 2

tag: tissue


title: vestibualr organ at P15 of Igf1 -/-, biological rep 1

tag: age


title: DNA from PBMC P24, 4 days rhGH treatment

description:
P24_stimulated
IGF-1 generation test


title: Prostate-13


title: DNA from PBMC P22, 4 days rhGH treatment

description:
P22_stimulated
IGF-1 generation test


title: DNA from PBMC P23, 4 days rhGH treatment

description:
P23_stimulated
IGF-1 generation test


title: vestibualr organ at E18.5 of Igf1 +/+, biological rep 3

description: transcripts expression data from Igf1 +/+ mouse vestibular organ at E18.5

source_name: Igf1 +/+ mouse vestibular organs at embrionic stage E18.5


title: TNBC, TUM011


title: vestibualr organ at E18.5 of Igf1 +/+, biological rep 1


title: Prostate-12


title: vestibualr organ at E18.5 of Igf1 +/+, biological rep 2


title: TNBC, TUM012


title: DNA from PBMC P21, 4 days rhGH treatment

description:
P21_stimulated
IGF-1 generation test


title: Prostate-11


title: DNA from PBMC P20, 4 days rhGH treatment

description:
P20_stimulated
IGF-1 generation test


title: TNBC, TUM010_repA


title: TNBC, TUM010_repB


title: DNA from PBMC P18, 4 days rhGH treatment

description:
P18_stimulated
IGF-1 generation test


title: vestibualr organ at E18.5 of Igf1 -/-, biological rep 3

description: transcripts expression data from Igf1 -/- mouse vestibular organ at E18.5

source_name: Igf1 -/- mouse vestibular organs at embrionic stage E18.5


title: DNA from PBMC P19, 4 days rhGH treatment

description:
P19_stimulated
IGF-1 generation test


title: TNBC, TUM008


title: Prostate-10


title: Her2, TUM009


title: Prostate-9


title: vestibualr organ at E18.5 of Igf1 -/-, biological rep 1


title: vestibualr organ at E18.5 of Igf1 -/-, biological rep 2


title: Prostate-8


title: DNA from PBMC P14, 4 days rhGH treatment

description:
P14_stimulated
IGF-1 generation test


title: TNBC, TUM007


title: Prostate-7


title: DNA from PBMC P17, 4 days rhGH treatment

description:
P17_stimulated
IGF-1 generation test


title: DNA from PBMC P15, 4 days rhGH treatment

description:
P15_stimulated
IGF-1 generation test


title: Prostate-6


title: TNBC, TUM006_repB


title: DNA from PBMC P16, 4 days rhGH treatment

description:
P16_stimulated
IGF-1 generation test


title: Prostate-5


title: DNA from PBMC P12, 4 days rhGH treatment

description:
P12_stimulated
IGF-1 generation test


title: Prostate-4


title: TNBC, TUM005


title: DNA from PBMC P13, 4 days rhGH treatment

description:
P13_stimulated
IGF-1 generation test


title: TNBC, TUM006_repA


title: TNBC, TUM004


title: Prostate-3


title: MicMa_267

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

institute: Fraunhofer Institute for Cell Therapy and Immunology

description: Expression analysis of 6 Basal-like breast cancer patient samples. Fresh frozen tumor biopsies from early breast cancer cases were collected from 920 patients included in the Oslo Micrometastasis (MicMa) Study -- Oslo I from various hospitals between 1995 and 1998 (Naume et al. "Presence of bone marrow micrometastasis is associated with different recurrence risk within molecular subtypes of breast cancer." Mol Oncol 2007, 1: 160-171; Wiedswang et al. "Detection of isolated tumor cells in bone marrow is an independent prognostic factor in breast cancer." J Clin Oncol 2003, 21: 3469-3478.). Expression was assessed by using an Agilent custom microarray (244K, nONCOchip). The custom array contains probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway by employing TAS (Kampa et al. "Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22". Genome Research, 14:331-42, 2004). In addition, the Agilent custom array interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe set 014850.

hyb_protocol: nONCOchip 1.0 arrays were proceed using the Agilent Hybridization Kit, Agilent Hybrization-Chambers and an commercial Hyb-Oven according to the manufacturer's protocol (Agilent One-Color Quick Amp Labeling Kit).

scan_protocol: Arrays were scanned using a GenePix 4200 Scanner and the GenePix Pro 6.1 Software (Molecular Devices) with following settings: laser power: 2.32-2.43, PMT: 400, resolution: 5µm, Focus: 1µm, Lines to Average: 2, Wavelength: 532nm, Filter: Standard Green.

data_processing: The data were analyzed with R (version 2.14.2) and BioConductor. Expression levels were quantile normalized and a linear model was fitted using the R package limma in order to identify differentially expressed probes. Reliable variance estimations were obtained by empirical Bayes moderated t-statistics. False discovery rate was controlled by Benjamini-Hochberg adjustment.

source_name: Fresh frozen tumor biopsies from early breast cancer cases (Oslo I study, subtype: Basal-like)

label_protocol: 1µg RNA were analyzed on nONCOchip 1.0 array according to the manufacturer's protocol (Agilent One-Color Quick Amp Labeling kit protocol) with the adaptation of using an N6 − T 7 primer instead of a polyT-T7 primer.

value: early breast cancer

tag: subtype

value: Basal-like

tag: sample


title: Prostate-2

value: prostate cancer

tag: time to first recurrence

tag: positive lymph nodes


title: Her2, TUM002_repB

source_name: Breast tumor sample from IHC defined Er- Her2+ subgroup


title: TNBC, TUM003


title: MicMa_185


title: DNA from PBMC P11, 4 days rhGH treatment

description:
P11_stimulated
IGF-1 generation test


title: MicMa_709


title: Her2, TUM002_repA


title: DNA from PBMC P10, 4 days rhGH treatment

description:
P10_stimulated
IGF-1 generation test


title: MicMa_067


title: TNBC, TUM001_repA


title: TNBC, TUM001_repB


title: Prostate-1

tag: d'amico risk classification

value: H

tag: stephensen risk classification


title: DNA from PBMC P8, 4 days rhGH treatment

description:
P8_stimulated
IGF-1 generation test


title: PAO1-wt [ChIP]

city: Karlsruhe

first: Andreas

last: Doetsch

address: Haid-und-Neu-Str. 9

department: Physiology and Biochemistry of Nutrition

institute: Max Rubner-Institute

hyb_protocol: The biotin-labeled DNA was hybridized to an Affymetrix P. aeruginosa genome chip as described previously (Dötsch et al., 2009, BMC Genomics 10:29)

scan_protocol: According to Affymetrix GeneChip protocol

data_processing:
Enrichment of hybridization signals was calculated with the Tiling Analysis Software (TAS, Affymetrix) from two independent DBP IPs compared to  independent control IP (bandwidth parameter was set to 150 bp). For each gene (PAO1 annotation taken from www.pseudomonas.com), the promoter region was defined as the sequence from -350 to -1 bp with respect to the ATG start codon, excluding overlap to upstream coding regions. Promoter enrichment was defined as the maximum enrichment found within the promoter region.
[results file descriptions] Bar files are labelled with "signal" or "pvalue" and contain the calculated enrichment or the p-value as calculated by the TAS software.

organism: Pseudomonas aeruginosa PAO1

label_protocol: Approximately 7.5 μg of amplified DNA from the control immunoprecipitation and the DNA-binding proteins (DBP) immunoprecipitations (IPs) were fragmented (to a size of 50~500 bp) and labeled using the GeneChip WT double stranded DNA terminal labeling kit (Affymetrix, Santa Clara, USA) according to the instructions of the manufacturer.

growth_protocol: Briefly, bacterial cells were grown in Luria-Bertani (LB) broth until early stationary phase (OD600 = 2.0).

extract_protocol: Cells were harvested by centrifugation, washed twice in ice-cold Tris-buffered saline (TBS, pH 7.6), and resuspended in 500 μl of lysis buffer (10 mM Tris-HCl, pH 8.0, 20% sucrose, 50 mM NaCl, 10 mM EDTA). Lysozyme (2.5 mg) was added and the cells were incubated for 30 min at 37°C. The DNA was sheared to an average size of 100~1000 base pairs by a series of pulsed sonication steps (Branson Sonicator S250 Analogue, 5 mm Standard tip, 6 times 60 s at 90% duty on Level 4). Insoluble material was removed by centrifugation at 13,000 g for 10 min and 850 μl of the cell extract supernatant from His-tagged or non-His-tagged control bacterial strain were mixed with 750 μl of immunoprecipitation (IP) buffer (50 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% (v/v) Triton X-100, 0.1% (m/v) sodium deoxycholate) and PMSF (phenylmethanesulfonyl fluoride, final concentration 1 mM) and incubated with 20 μl of protein G-Sepharose beads (Sigma) for 1 h at room temperature with gentle mixing. After removal of the Sepharose beads by gentle centrifugation, proteins were immunoprecipitated by adding 20 μl of protein G-Sepharose beads (Sigma) coupled to mouse anti-His monoclonal antibody (Novagen). The composite was incubated overnight at 4°C with gentle mixing. Samples were then washed twice with IP buffer, once with IP buffer containing 500 mM NaCl, once with washing buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5 % (v/v) Nonidet-P40, 0.5 % (m/v) sodium deoxycholate) and once with TE buffer (10 mM Tris-HCl, 1 mM EDTA , pH 7.5). Immunoprecipitated complexes were eluted by incubation of the beads with elution buffer (50 mM Tris-HCl, pH 7.5, 10 mM EDTA, 1% (m/v) SDS) at 65°C for 10 min. Forty μl of the immunoprecipitated samples were un-cross-linked by the addition of 32 μg Pronase and incubation for 2 h at 42°C and for 6 h at 65°C. DNA was purified using PCR Purification kit (Qiagen, Germany).

treatment_protocol: 1 mM H2O2 was added to treat the cultures for 10 min, then formaldehyde was added to a final concentration of 1%. After incubation at room temperature for 20 min, glycine was added to a final concentration of 0.5 M.

tag: plasmid

tag: treatments

value: 10 min 1mM H2O2

tag: chip antibody


title: PAO1-pUCP4203-2 [ChIP]

description: bar files contain enrichment and P-value for comparison of his-tagged strain versus non-tagged wild type

value: mouse anti-His monoclonal antibody (Novagen)


title: MicMa_042


title: human human fetal liver cells,  hematopoietic progenitor, rep 3 [set 2]

city: Los Angeles, CA

first: Hanna

last: Mikkola

state: CA

address: 615 Charles E Young Drive South

department: MCDB

institute: UCLA

hyb_protocol: used Affymetrix standard protocols.

scan_protocol: Scanner model is GCS 3000 7G. Image process used Affymetrix(r) GeneChip(r) Command Console(r) (AGCC) Software

data_processing: R package Limma provided through Bioconductor (v.2.8) was used for assessing differential expression (> 2-fold and p-value <0.05). Robust Multiarray Averaging was used to obtain absolute expression mRNA levels.

label_protocol: used Affymetrix standard protocols.

extract_protocol: RNA was purified from sorted using RNeasy Mini Kit (QIAGEN), according ot manufacturer's instructions.

value: 2nd trimester human fetal liver

value: hematopoietic progenitor enriched


title: MicMa_031


title: DNA from PBMC P9, 4 days rhGH treatment

description:
P9_stimulated
IGF-1 generation test


title: DNA from PBMC P4, 4 days rhGH treatment

description:
P4_stimulated
IGF-1 generation test


title: PAO1-pUCP4203-1 [ChIP]


title: human human fetal liver cells,  hematopoietic progenitor, rep 2 [set 2]


title: DNA from PBMC P7, 4 days rhGH treatment

description:
P7_stimulated
IGF-1 generation test


title: MicMa_132

description: Expression analysis of 5 Luminal B breast cancer patient samples. Fresh frozen tumor biopsies from early breast cancer cases were collected from 920 patients included in the Oslo Micrometastasis (MicMa) Study -- Oslo I from various hospitals between 1995 and 1998 (Naume et al. "Presence of bone marrow micrometastasis is associated with different recurrence risk within molecular subtypes of breast cancer." Mol Oncol 2007, 1: 160-171; Wiedswang et al. "Detection of isolated tumor cells in bone marrow is an independent prognostic factor in breast cancer." J Clin Oncol 2003, 21: 3469-3478.). Expression was assessed by using an Agilent custom microarray (244K, nONCOchip). The custom array contains probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway by employing TAS (Kampa et al. "Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22". Genome Research, 14:331-42, 2004). In addition, the Agilent custom array interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe set 014850.

source_name: Fresh frozen tumor biopsies from early breast cancer cases (Oslo I study, subtype: Luminal B)

value: Luminal B


title: MicMa_148


title: MicMa_091


title: MicMa_088


title: DNA from PBMC P3, 4 days rhGH treatment

description:
P3_stimulated
IGF-1 generation test


title: human human fetal liver cells,  hematopoietic progenitor enriched, rep 1 [set 2]


title: DNA from PBMC P1, 4 days rhGH treatment

description:
P1_stimulated
IGF-1 generation test


title: human fetal liver cells, hematopoietic stem cell enriched, rep 3 [set 2]

value: hematopoietic stem cell enriched


title: human fetal liver cells, hematopoietic progenitor enriched, rep 4

scan_protocol: Scanner model is GCS 3000 7G. Image process used Affymetrix(r) GeneChip(r) Command Console(r) (AGCC) Software.

source_name: human fetal liver_CD34+CD38+CD90-


title: DNA from PBMC P26, baseline

description:
P26_baseline
IGF-1 generation test

source_name: PBMCs, before rhGH treatment


title: Cornelia de Lange Syndrome aCGH expriment

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

description: Cornelia de Lange Syndrome patient blood as test sample

hyb_protocol: standard Agilent protocol

scan_protocol: Scanned on an Agilent G2600D scanner.

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: Cornelia de Lange Syndrome patient blood sample

label_protocol: standard Agilent protocol

growth_protocol: Peripheral blood samples were exsanguinated into an EDTA anticoagulant tube.

extract_protocol: DNA was extracted with the QIAamp DNA Blood Midi Kit (Qiagen, Duesseldorf, Germany) following the manufacturer’s instructions. Purified genomic DNA was resuspended in ddH2O for SNP-array analysis or in Tris-EDTA for other experiments, and DNA stocks were stored at -80℃.

value: Blood

tag: disease state

value: Cornelia de Lange Syndrome

source_name: Normal blood sample

value: normal


title: MicMa_085


title: MicMa_632

description: Expression analysis of 5 Luminal A breast cancer patient samples. Fresh frozen tumor biopsies from early breast cancer cases were collected from 920 patients included in the Oslo Micrometastasis (MicMa) Study -- Oslo I from various hospitals between 1995 and 1998 (Naume et al. "Presence of bone marrow micrometastasis is associated with different recurrence risk within molecular subtypes of breast cancer." Mol Oncol 2007, 1: 160-171; Wiedswang et al. "Detection of isolated tumor cells in bone marrow is an independent prognostic factor in breast cancer." J Clin Oncol 2003, 21: 3469-3478.). Expression was assessed by using an Agilent custom microarray (244K, nONCOchip). The custom array contains probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway by employing TAS (Kampa et al. "Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22". Genome Research, 14:331-42, 2004). In addition, the Agilent custom array interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe set 014850.

source_name: Fresh frozen tumor biopsies from early breast cancer cases (Oslo I study, subtype: Luminal A)

value: Luminal A


title: human fetal liver cells, hematopoietic progenitor enriched, rep 3

tag: cell type


title: DNA from PBMC P25, baseline

description:
P25_baseline
IGF-1 generation test

value: peripheral blood mononuclear cells

tag: treatment


title: human fetal liver cells, hematopoietic progenitor enriched, rep 2

source_name: human fetal liver_CD34+CD38-CD90-


title: MicMa_263


title: DNA from PBMC P2, 4 days rhGH treatment

description:
P2_stimulated
IGF-1 generation test

value: recombinant human growth hormone

tag: patient


title: MicMa_101


title: DNA from PBMC P23, baseline

description:
P23_baseline
IGF-1 generation test


title: human fetal liver cells, hematopoietic stem cell enriched, rep 3

source_name: human fetal liver_CD34+CD38-CD90+


title: human fetal liver cells, hematopoietic progenitor enriched, rep 1


title: MicMa_318

description: Expression analysis of 5 ERBB2 breast cancer patient samples. Fresh frozen tumor biopsies from early breast cancer cases were collected from 920 patients included in the Oslo Micrometastasis (MicMa) Study -- Oslo I from various hospitals between 1995 and 1998 (Naume et al. "Presence of bone marrow micrometastasis is associated with different recurrence risk within molecular subtypes of breast cancer." Mol Oncol 2007, 1: 160-171; Wiedswang et al. "Detection of isolated tumor cells in bone marrow is an independent prognostic factor in breast cancer." J Clin Oncol 2003, 21: 3469-3478.). Expression was assessed by using an Agilent custom microarray (244K, nONCOchip). The custom array contains probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway by employing TAS (Kampa et al. "Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22". Genome Research, 14:331-42, 2004). In addition, the Agilent custom array interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe set 014850.

source_name: Fresh frozen tumor biopsies from early breast cancer cases (Oslo I study, subtype: ERBB2)


title: MicMa_065


title: MicMa_122


title: human fetal liver cells, hematopoietic stem cell enriched, rep 1 [set 2]


title: DNA from PBMC P24, baseline

description:
P24_baseline
IGF-1 generation test


title: DNA from PBMC P20, baseline

description:
P20_baseline
IGF-1 generation test


title: DNA from PBMC P22, baseline

description:
P22_baseline
IGF-1 generation test


title: liver_NAFL and type 2 diabetes mellitus (T2DM)_12 weeks_rep1

city: Shanghai

first: Xiaolin

last: Liu

address: Chongqingnan road, 280

institute: School of Medicine, Shanghai Jiao Tong University

hyb_protocol: The pre-hybridization of ROA v1 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on ROA v1 in duplication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm PMT 10 ; 532nm PMT 10) and quantify the fluoresence intensity.

data_processing:
The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.
The Matrix value is normalized intensities. The pairwise comparison were performed by Rosetta Resolver® System error-weighted modeling to find significant diffrential expressed probes (log2 |Fold change| ≥ 1 and P < 0.05).

organism: Rattus norvegicus

source_name: liver, fed with high fat diet and injected with streptozocin, 12 weeks

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

extract_protocol: RNA extraction by Trizol method. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

tag: gender

value: male

tag: strain

value: SD

value: liver

tag: developmental stage

value: 18 weeks old


title: liver_NAFL and type 2 diabetes mellitus (T2DM)_12 weeks_rep3

tag: tissue


title: DNA from PBMC P19, baseline

description:
P19_baseline
IGF-1 generation test


title: human fetal liver cells, hematopoietic stem cell enriched, rep 1


title: DU145 xenograft in NOD/SCID mice_NVP-BEZ235 and taxotere_4 weeks

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on HG_U133_2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: CEL files were processed using GCRMA in R (version 2.6.2 (2008-02-08)), using packages downloaded from Bioconductor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Affymetrix GeneChip Expression Manual 701021 Rev.5)

growth_protocol: DU145 xenograft tumors were established by using early-passage cells and maintained in NOD.CB17-Prkdc(SCID) mice. For s.c. tumor development, 100 μL of collagen-embedded cells was injected s.c. into 5- to 8-week-old NOD.CB17-Prkdc(SCID) mice. The mice were observed for 3–5 months for appearance and development of tumors.

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

value: DU145 xenograft in NOD/SCID mice

tag: dose

value: 10 mg/kg, intravenous for taxotere, 12.5 mg/kg perorally for NVP_BEZ235

tag: schedule

value: once per week for taxotere and once per day for NVP_BEZ235


title: DU145 xenograft in NOD/SCID mice_NVP-BEZ235_4 weeks

value: 12.5 mg/kg, perorally

value: once per day


title: MicMa_079

tag: diagnosis

value: early breast cancer

tag: subtype

tag: sample


title: liver_NAFL and type 2 diabetes mellitus (T2DM)_12 weeks_rep2


title: liver_non-alcoholic fatty liver (NAFL)_rep3

source_name: liver, fed with high fat diet, 12 weeks


title: human fetal liver cells, hematopoietic stem cell enriched, rep 2

value: 2nd trimester human fetal liver

value: hematopoietic stem cell enriched


title: DNA from PBMC P21, baseline

description:
P21_baseline
IGF-1 generation test


title: MicMa_057


title: DNA from PBMC P17, baseline

description:
P17_baseline
IGF-1 generation test


title: liver_non-alcoholic fatty liver (NAFL)_rep2


title: DNA from PBMC P16, baseline

description:
P16_baseline
IGF-1 generation test


title: DNA from PBMC P18, baseline

description:
P18_baseline
IGF-1 generation test


title: human fetal liver cells, hematopoietic stem cell enriched, rep 2 [set 2]


title: MicMa_627

description: Expression analysis of 5 Normal-like breast cancer patient samples. Fresh frozen tumor biopsies from early breast cancer cases were collected from 920 patients included in the Oslo Micrometastasis (MicMa) Study -- Oslo I from various hospitals between 1995 and 1998 (Naume et al. "Presence of bone marrow micrometastasis is associated with different recurrence risk within molecular subtypes of breast cancer." Mol Oncol 2007, 1: 160-171; Wiedswang et al. "Detection of isolated tumor cells in bone marrow is an independent prognostic factor in breast cancer." J Clin Oncol 2003, 21: 3469-3478.). Expression was assessed by using an Agilent custom microarray (244K, nONCOchip). The custom array contains probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway by employing TAS (Kampa et al. "Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22". Genome Research, 14:331-42, 2004). In addition, the Agilent custom array interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe set 014850.

source_name: Fresh frozen tumor biopsies from early breast cancer cases (Oslo I study, subtype: Normal-like)

value: Normal-like


title: DNA from PBMC P15, baseline

description:
P15_baseline
IGF-1 generation test


title: MicMa_146


title: liver_non-alcoholic steatohepatitis (NASH)_rep3

source_name: liver, fed with methionine-choline-deficient diet, 8 weeks


title: liver_non-alcoholic steatohepatitis (NASH)_rep2


title: liver_non-alcoholic fatty liver (NAFL)_rep1


title: MicMa_451


title: DU145 xenograft in NOD/SCID mice_vehicle_4 weeks

value: 0 mg/kg, intravenous

value: once per week


title: DNA from PBMC P13, baseline

description:
P13_baseline
IGF-1 generation test

value: peripheral blood mononuclear cells


title: DNA from PBMC P14, baseline

description:
P14_baseline
IGF-1 generation test


title: DNA from PBMC P10, baseline

description:
P10_baseline
IGF-1 generation test


title: liver_non-alcoholic steatohepatitis (NASH)_rep1


title: liver_control_rep3

source_name: liver,control


title: MicMa_053


title: MicMa_034


title: MicMa_020


title: RP_66

description: Expression analysis of 5 normal patient samples. Breast tissue samples from breast reduction operations were provided from the Colosseum Clinic, Oslo in co-operation with Akershus University Hospital, Lørenskog and are referred to as normal tissue. Expression was assessed by using an Agilent custom microarray (244K, nONCOchip). The custom array contains probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway by employing TAS (Kampa et al. "Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22". Genome Research, 14:331-42, 2004). In addition, the Agilent custom array interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe set 014850.

value: normal patient


title: DNA from PBMC P12, baseline

description:
P12_baseline
IGF-1 generation test


title: liver_control_rep2

value: male


title: DNA from PBMC P11, baseline

description:
P11_baseline
IGF-1 generation test


title: DNA from PBMC P9, baseline

description:
P9_baseline
IGF-1 generation test


title: RP_46

source_name: Breast tissue samples from breast reduction operations


title: liver_control_rep1

value: SD


title: RP_45


title: CD141+ cDCs_culture_10 [9407205014_J]

status: Public on Jan 22 2015

city: Cleveland

first: Peter

middle: A

last: Wilkinson

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description: CD141+ cDCs_culture

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC).

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the quantified output data was conducted using the limma from the R statistical language and various software packages from Bioconductor.  Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

source_name: Sorted Cells

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: Gene expression was analyzed directly ex vivo for blood samples or after differentiation of cord blood CD34+ cells in MS5 stromal cell + Flt3l + SCF + GM-CSF culture

extract_protocol: Cells were washed twice with cold PBS and lysed with 100 µl of cold RLT buffer (QIAGEN, Germany) supplemented with 1% beta-mercaptoethanol (BM) (Sigma, St. Louis, MO USA), and transferred to 1.7 ml tubes with 250 µl of cold RLT/BM buffer and quickly stored at -80oC. The samples underwent nucleic acid isolation in a designated Pre-PCR room using Qiagen’s RNeasy Micro Kit and underwent DNase I treatment.  Total RNA concentrations were quantified using a NanoDrop 2000c spectrophotometer and quality was assessed using BioRad’s Experion automated electrophoresis system.  With each batch of samples a 500 ng HeLa RNA control and two water non-template negative controls were included.

treatment_protocol: Three dendritic cell subsets i.e. CD141+ cDCs, CD1c+ cDCs and CD303+ pDCs as well as classical monocytes (CD14+CD16-) were isolated either ex-vivo from blood samples or in vitro after differentiation of cord blood CD34+ cells in MS5 stromal cell + Flt3l + SCF + GM-CSF culture.

tag: sampleID

value: MS5 + Flt3l + SCF + GM-CSF

tag: donor

tag: cell subset

value: CD141+ cDC


title: DNA from PBMC P8, baseline

description:
P8_baseline
IGF-1 generation test


title: RP_38


title: CD1c+ cDCs_culture_7 [9407205014_E]

description: CD1c+ cDCs_culture

value: CD1c+ cDC


title: pDCs_culture_10 [9407205014_G]

value: pDC


title: CD141+ cDCs_culture_7 [9407205014_H]

description: CD141+ cDCs_culture


title: Monocytes_culture_9 [9407205014_B]

value: monocytes


title: pDCs_culture_8 [9407205014_C]


title: DNA from PBMC P4, baseline

description:
P4_baseline
IGF-1 generation test


title: CD141+ cDCs_culture_8 [9407205014_I]

description: CD141+ cDCs_culture


title: pDCs_culture_7 [9407205014_F]


title: CD141+ cDCs_culture_9 [9406915091_K]

description: CD141+ cDCs_culture


title: DNA from PBMC P7, baseline

description:
P7_baseline
IGF-1 generation test


title: CD1c+ cDCs_culture_10 [9406915091_D]

description: CD1c+ cDCs_culture


title: Monocytes_culture_8 [9406915091_G]


title: CD1c+ cDCs_culture_9 [9406915091_L]

description: CD1c+ cDCs_culture


title: DNA from PBMC P3, baseline

description:
P3_baseline
IGF-1 generation test


title: pDCs_culture_9 [9406915091_H]


title: RP_26


title: MicMa_083


title: CD1c+ cDCs_culture_8 [9406915091_C]

description: CD1c+ cDCs_culture


title: CD141+ cDCs_blood_6 [8363885026_A]

description: CD141+ cDCs_blood


title: pDCs_blood_3 [8363885022_H]


title: DNA from PBMC P1, baseline

description:
P1_baseline
IGF-1 generation test


title: DU145 xenograft in NOD/SCID mice_taxotere_4 weeks

value: DU145 xenograft in NOD/SCID mice

value: 10 mg/kg, intravenous


title: Monocytes_blood_2 [8363885012_H]


title: Monocytes_blood_5 [8363885016_A]


title: pDCs_blood_2 [8363885018_C]


title: Monocytes_culture_7 [9406915091_E]


title: Expression analysis in HFF cells residing in G0 phase, biological replicate 3

description: Expression analysis of long non-coding RNAs and mRNAs regulated by cyclins. HFF cells were synchronised by serum starvation and reside in G0 phase of mitotic cell cycle.

hyb_protocol: nONCOchip 2.0 arrays were processed using the Agilent Hybridization Kit, Agilent Hybrization-Chambers and the Agilent Hybridization Oven according to the manufacturer's protocol (Agilent One-Color Quick Amp Labeling Kit).

scan_protocol: Arrays were scanned using the Agilent High-Resolution Microarray Scanner according the manufacturer’s instructions with following settings: Profile: AgilentG3_GX_1Color, Channels: G, Scan region: Agilent HD (61x 21,6 mm), Resolution: 3µm double pass, Tiff: 20 bit, GPMT: 100%, XDR: no xdr. Quality control of the scans and extraction of result.tab.txtles were done using Agilent Feature Extraction Software. Result.tab.txtles were used for subsequent data analysis.

data_processing: Data was processed with R (version 3.0.1 2013-05-16). Raw expression levels were normalized (quantile normalization).

source_name: Human foreskin fibroblasts (HFF) in G0 phase of mitotic cell cycle

label_protocol: 1µg total RNA was analyzed on nONCOchip 2.0 array according to the manufacturer's protocol (Agilent One-Color Quick Amp Labeling kit protocol). Instead of the Oligo-dT/T7-primer delivered with the Quick Amp Labeling Kit, 120 pmol of a random N6/T7 primer synthesized by M.tab.txtion was used.

tag: cell line

value: HFF

tag: cell cycle


title: CD141+ cDCs_blood_1 [8363885012_E]

description: CD141+ cDCs_blood


title: DNA from PBMC P2, baseline

description:
P2_baseline
IGF-1 generation test

tag: cell type


title: Expression analysis in HFF cells residing in G1 phase, biological replicate 1

description: Expression analysis of long non-coding RNAs and mRNAs regulated by cyclins. HFF cells were synchronised by serum starvation and reside in G1 phase of mitotic cell cycle.

source_name: Human foreskin fibroblasts (HFF) in G1 phase of mitotic cell cycle


title: Expression analysis in HFF cells residing in G1 phase, biological replicate 3


title: CD141+ cDCs_blood_3 [8363885008_G]

description: CD141+ cDCs_blood

tag: treatment


title: pDCs_blood_6 [8363885011_L]


title: pDCs_blood_1 [8363885008_A]


title: CD1c+ cDCs_blood_6 [8363885008_C]

description: CD1c+ cDCs_blood


title: CD141+ cDCs_blood_4 [8363885011_J ]

description: CD141+ cDCs_blood


title: CD1c+ cDCs_blood_1 [8363885022_F]

description: CD1c+ cDCs_blood


title: Monocytes_blood_6 [8363885001_K]


title: Expression analysis in HFF cells residing in G0 phase, biological replicate 1


title: Expression analysis in HFF cells residing in G0 phase, biological replicate 2


title: Monocytes_blood_1 [8363885011_E]


title: CD1c+ cDCs_blood_3 [8363885004_F]

description: CD1c+ cDCs_blood


title: med16_1dpi_rep3

city: Gainesville

first: Zhonglin

last: Mou

state: FL

address: 981 Museum Road

department: Microbiology and Cell Science & Plant Molecular and Cellular  Biology

institute: University of Florida

description: raw_data_file: raw_data_20.txt

hyb_protocol: For each array, 1.65 μg of Cy3 or Cy5 labeled cRNA was fragmented and hybridized with rotation at 65°C for 17 hr.  Samples were hybridized to Arabidopsis 4 × 44k arrays (Agilent Technologies).  The arrays were washed according to the manufacturer’s protocol.

scan_protocol: The arrays were scanned on a G2505B scanner (Agilent Technologies).

data_processing:
Data were extracted using Feature Extraction 10.1.1.1 software (Agilent Technologies).
Data (individual signal intensity values) obtained from the microarray probes were background corrected using a normexp+offset method, in which a small positive offset (k = 50) was added to move the corrected intensities away from zero.  The resulting data were log transformed (using 2 as the base) and normalized between individual samples by scaling the individual log-transformed signal intensities so that all datasets had comparable lower quartile, median and upper quartile values.  After normalization, the Student’s t-test was performed considering a probe-by-probe comparison between different genotypes at the same time point using wild type (Col-0) as the reference sample and between different time points of the same genotype using the 0-hr sample as the reference.  In each comparison, a p-value and fold change (FC) were computed for each gene locus.  The gene expression fold changes were computed based on the normalized log-transformed signal intensity data.

organism: Arabidopsis thaliana

source_name: med8, infected, 1 day, replicate 3

label_protocol: cDNA was synthesized from 200 ng of total RNA and used as a template for in vitro transcription in the presence of T7 RNA Polymerase and cyanine labeled CTP’s using the Quick Amp Labeling kit (Agilent Technologies) according the manufacturer’s protocol.  The amplified, labeled complementary RNA (cRNA) was purified using the RNeasy Mini kit (Qiagen, Valencia, CA).

growth_protocol: Arabidopsis seeds were sown on autoclaved soil (Sunshine MVP, Sun Gro Horticulture, Agawam, MA) and vernalized at 4°C for 3 days.  Plants were germinated and grown at 23 to 25°C under a 16-hr-light/8-hr-dark regime.

extract_protocol: About 100 mg leaf tissues were ground into a fine powder in liquid nitrgen and resuspended in 500 μL 80°C water-saturated phenol and 500 μL 80°C extraction buffer (100 mM LiCl, 100 mM Tris pH 8.0, 10 mM EDTA, 1% SDS).  After brief vortexing and centrifugation at 14,000 rpm for 5 min, the aqueous phase was transferred to another cold tube containing 500 μL of 24:1 chloroform:isoamyl alcohol.  After vortexing and centrifugation, the aqueous phase was transferred to a DEPC-treated tube with 1/10 volume of 3 M NaOAc and 2 volume of 100% ethanol.  The tube was inverted to mix and placed at -80°C for 30 min and then spun at 14,000 rpm for 15 min.  After removing the supernatant, the pellet was washed with 80% ethanol, dried briefly, and resuspended in DEPC-treated water.

treatment_protocol: Sclerotinia sclerotiorum was cultured on minimal medium (1 g of NaOH, 3 g of DL-malic acid, 2 g of NH4NO3, 0.1 g of MgSO4x7H2O, and 39 g of Bacto-agar per liter) prior to inoculation to reduce the aggressiveness of the fungus for about 2 days at room temperature.  An agar plug (2 mm in diameter) containing the advancing edge of S. sclerotiorum mycelia was removed to inoculate Arabidopsis leaves.  One rosette leaf per plant was inoculated.  Leaf tissues were collected at the indicated time points for RNA extraction.

tag: time point

value: 1 day after Sclerotinia sclerotiorum infection

source_name: med16, infected, 1 day, replicate 3


title: med8_4dpi_rep1

description: raw_data_file: raw_data_24.txt

source_name: med16, infected, 4 day, replicate 1

value: 4 days after Sclerotinia sclerotiorum infection

source_name: med8, infected, 4 day, replicate 1


title: CD141+ cDCs_blood_2 [8363877100_I]

description: CD141+ cDCs_blood


title: CD1c+ cDCs_blood_4 [8363877084_E]

description: CD1c+ cDCs_blood


title: med16_1dpi_rep2

description: raw_data_file: raw_data_16.txt

source_name: med8, infected, 1 day, replicate 2

source_name: med16, infected, 1 day, replicate 2


title: pDCs_blood_4 [8363877100_B]


title: Col-0_1dpi_rep3

description: raw_data_file: raw_data_19.txt

source_name: elp2, infected, 1 day, replicate 3

source_name: Col-0, infected, 1 day, replicate 3


title: Expression analysis in HFF cells residing in G1 phase, biological replicate 2


title: elp2_4dpi_rep1

description: raw_data_file: raw_data_23.txt

source_name: Col-0, infected, 4 day, replicate 1

source_name: elp2, infected, 4 day, replicate 1


title: Col-0_0dpi_rep3

description: raw_data_file: raw_data_17.txt

source_name: elp2, infected, 0 day, replicate 3

value: 0 day after Sclerotinia sclerotiorum infection

source_name: Col-0, infected, 0 day, replicate 3


title: elp2_2dpi_rep1

description: raw_data_file: raw_data_21.txt

source_name: Col-0, infected, 2 day, replicate 1

value: 2 days after Sclerotinia sclerotiorum infection

source_name: elp2, infected, 2 day, replicate 1


title: CD1c+ cDCs_blood_2 [8363877084_D]

description: CD1c+ cDCs_blood

source_name: Sorted Cells


title: med16_0dpi_rep2

description: raw_data_file: raw_data_14.txt

source_name: med8, infected, 0 day, replicate 2

source_name: med16, infected, 0 day, replicate 2


title: Col-0_0dpi_rep2

description: raw_data_file: raw_data_13.txt

source_name: elp2, infected, 0 day, replicate 2

source_name: Col-0, infected, 0 day, replicate 2


title: med8_1dpi_rep1

description: raw_data_file: raw_data_12.txt

source_name: med16, infected, 1 day, replicate 1

source_name: med8, infected, 1 day, replicate 1


title: pDCs_blood_5 [8363885021_A]


title: med16_0dpi_rep3

description: raw_data_file: raw_data_18.txt

source_name: med8, infected, 0 day, replicate 3

source_name: med16, infected, 0 day, replicate 3


title: med8_0dpi_rep1

description: raw_data_file: raw_data_10.txt

source_name: med16, infected, 0 day, replicate 1

source_name: med8, infected, 0 day, replicate 1


title: Col-0_4dpi_rep3

description: raw_data_file: raw_data_7.txt

source_name: elp2, infected, 4day, replicate 3

source_name: Col-0, infected, 4 day, replicate 3


title: Col-0_1dpi_rep2

description: raw_data_file: raw_data_15.txt

source_name: elp2, infected, 1 day, replicate 2

source_name: Col-0, infected, 1 day, replicate 2


title: elp2_0dpi_rep1

description: raw_data_file: raw_data_9.txt

source_name: Col-0, infected, 0 day, replicate 1

source_name: elp2, infected, 0 day, replicate 1


title: med16_4dpi_rep3

description: raw_data_file: raw_data_8.txt

source_name: med8, infected, 4day, replicate 3

source_name: med16, infected, 4 day, replicate 3


title: CD141+ cDCs_blood_5 [8363877100_K]

description: CD141+ cDCs_blood

source_name: Sorted Cells


title: Col-0_4dpi_rep2

description: raw_data_file: raw_data_3.txt

source_name: elp2, infected, 4day, replicate 2

source_name: Col-0, infected, 4 day, replicate 2


title: med16_4dpi_rep2

description: raw_data_file: raw_data_4.txt

source_name: med8, infected, 4day, replicate 2

source_name: med16, infected, 4 day, replicate 2


title: med16_2dpi_rep3

description: raw_data_file: raw_data_6.txt

source_name: med8, infected, 2day, replicate 3

source_name: med16, infected, 2 day, replicate 3


title: med8_2dpi_rep1

description: raw_data_file: raw_data_22.txt

source_name: med16, infected, 2 day, replicate 1

source_name: med8, infected, 2 day, replicate 1


title: Col-0_2dpi_rep3

description: raw_data_file: raw_data_5.txt

source_name: elp2, infected, 2day, replicate 3

source_name: Col-0, infected, 2 day, replicate 3


title: Col-0_2dpi_rep2

description: raw_data_file: raw_data_1.txt

source_name: elp2, infected, 2day, replicate 2

source_name: Col-0, infected, 2 day, replicate 2


title: med16_2dpi_rep2

description: raw_data_file: raw_data_2.txt

source_name: med8, infected, 2day, replicate 2

source_name: med16, infected, 2 day, replicate 2


title: med16_4dpi_rep1

description: raw_data_file: raw_data_24.txt

source_name: med16, infected, 4 day, replicate 1

source_name: med8, infected, 4 day, replicate 1


title: Col-0_4dpi_rep1

description: raw_data_file: raw_data_23.txt

source_name: Col-0, infected, 4 day, replicate 1

source_name: elp2, infected, 4 day, replicate 1


title: med8_1dpi_rep3

description: raw_data_file: raw_data_20.txt

source_name: med8, infected, 1 day, replicate 3

source_name: med16, infected, 1 day, replicate 3


title: Col-0_2dpi_rep1

description: raw_data_file: raw_data_21.txt

source_name: Col-0, infected, 2 day, replicate 1

source_name: elp2, infected, 2 day, replicate 1


title: med16_2dpi_rep1

description: raw_data_file: raw_data_22.txt


title: elp2_1dpi_rep2

description: raw_data_file: raw_data_15.txt

source_name: elp2, infected, 1 day, replicate 2

source_name: Col-0, infected, 1 day, replicate 2


title: elp2_1dpi_rep3

description: raw_data_file: raw_data_19.txt

source_name: elp2, infected, 1 day, replicate 3

source_name: Col-0, infected, 1 day, replicate 3


title: med16_1dpi_rep1

description: raw_data_file: raw_data_12.txt

source_name: med16, infected, 1 day, replicate 1

source_name: med8, infected, 1 day, replicate 1


title: Col-0_1dpi_rep1

description: raw_data_file: raw_data_11.txt

source_name: Col-0, infected, 1 day, replicate 1

source_name: elp2, infected, 1 day, replicate 1


title: med8_1dpi_rep2

description: raw_data_file: raw_data_16.txt

source_name: med8, infected, 1 day, replicate 2

source_name: med16, infected, 1 day, replicate 2


title: elp2_0dpi_rep3

description: raw_data_file: raw_data_17.txt

source_name: elp2, infected, 0 day, replicate 3

source_name: Col-0, infected, 0 day, replicate 3


title: elp2_0dpi_rep2

description: raw_data_file: raw_data_13.txt

source_name: elp2, infected, 0 day, replicate 2

source_name: Col-0, infected, 0 day, replicate 2


title: med8_0dpi_rep3

description: raw_data_file: raw_data_18.txt

source_name: med8, infected, 0 day, replicate 3

source_name: med16, infected, 0 day, replicate 3


title: med8_4dpi_rep3

description: raw_data_file: raw_data_8.txt

source_name: med8, infected, 4day, replicate 3

source_name: med16, infected, 4 day, replicate 3


title: elp2_1dpi_rep1

description: raw_data_file: raw_data_11.txt


title: Col-0_0dpi_rep1

description: raw_data_file: raw_data_9.txt

source_name: Col-0, infected, 0 day, replicate 1

source_name: elp2, infected, 0 day, replicate 1


title: med8_0dpi_rep2

description: raw_data_file: raw_data_14.txt

source_name: med8, infected, 0 day, replicate 2

source_name: med16, infected, 0 day, replicate 2


title: med8_2dpi_rep3

description: raw_data_file: raw_data_6.txt

source_name: med8, infected, 2day, replicate 3

source_name: med16, infected, 2 day, replicate 3


title: elp2_4dpi_rep3

description: raw_data_file: raw_data_7.txt

source_name: elp2, infected, 4day, replicate 3

source_name: Col-0, infected, 4 day, replicate 3


title: elp2_4dpi_rep2

description: raw_data_file: raw_data_3.txt

source_name: elp2, infected, 4day, replicate 2

source_name: Col-0, infected, 4 day, replicate 2


title: elp2_2dpi_rep3

description: raw_data_file: raw_data_5.txt

source_name: elp2, infected, 2day, replicate 3

source_name: Col-0, infected, 2 day, replicate 3


title: Caco2, Au5nm_300µM, 72h, replicate 3

city: Varese (VA)

first: Marco

last: Fabbri

address: via dunant 5

country: Italy

institute: Università dell'Insubria

description: Gene expression of Caco2 exposed to Au5nm_300µM for 72h

scan_protocol: Scanned with the Agilent G2565BA Microarray Scanner (Agilent)

data_processing: The fluorescence intensities on scanned images were extracted and preprocessed by Agilent Feature Extraction Software (v10.5.1.1). The data are normilze by quantile normalization and log2 transformed.

growth_protocol: For the gene expression experiment, 250 000 and 90 000 Caco-2 cells were seeded in 2 ml complete cell culture medium, in a 6 well/plate (Falcon, Italy), for the 24 and 72 h exposures (5 and 30 nm AuNPs, 100 and 300 microM), respectively.  Cell lysates were stored at -80 ºC until the RNA extraction step was performed.

extract_protocol: At the end of treatment, the culture medium was removed. Cells were washed twice with PBS and harvested with 300 µL of RLT plus RNeasy lysis buffer. (Qiagen). Total RNA was purified from Caco-2 cells using the RNeasy Plus Mini Kit, following standard RNA isolation protocol (Qiagen).

value: colon carcinoma

tag: time


title: Caco2, Au5nm_100µM, 72h, replicate 2

description: Gene expression of Caco2 exposed to Au5nm_100µM for 72h


title: Caco2, Au5nm_100µM, 72h, replicate 3


title: med8_2dpi_rep2

description: raw_data_file: raw_data_2.txt

source_name: med8, infected, 2day, replicate 2

tag: strain

source_name: med16, infected, 2 day, replicate 2


title: med8_4dpi_rep2

description: raw_data_file: raw_data_4.txt

source_name: med8, infected, 4day, replicate 2

source_name: med16, infected, 4 day, replicate 2


title: Caco2, Solvent5nm, 72h, replicate 1

description: Gene expression of Caco2 exposed to Solvent5nm for 72h


title: Caco2, Au40nm_100µM, 72h, replicate 3

description: Gene expression of Caco2 exposed to Au40nm_100µM for 72h


title: Caco2, Solvent5nm, 72h, replicate 3


title: elp2_2dpi_rep2

description: raw_data_file: raw_data_1.txt

source_name: elp2, infected, 2day, replicate 2

source_name: Col-0, infected, 2 day, replicate 2


title: Caco2, Au5nm_300µM, 72h, replicate 2


title: Caco2, Au40nm_300µM, 72h, replicate 1

description: Gene expression of Caco2 exposed to Au40nm_300µM for 72h


title: Caco2, Solvent5nm, 72h, replicate 2


title: Caco2, Au40nm_300µM, 72h, replicate 2


title: Caco2, Au5nm_300µM, 72h, replicate 1


title: Caco2, Au40nm_300µM, 72h, replicate 3


title: Caco2, Au40nm_100µM, 72h, replicate 1


title: Caco2, Au40nm_100µM, 72h, replicate 2


title: Caco2, Solvent40nm, 72h, replicate 2

description: Gene expression of Caco2 exposed to Solvent40nm for 72h


title: Caco2, Control, 72h, replicate 2

description: Gene expression of Caco2 exposed to Control  for 72h

value: Control


title: Caco2, Au5nm_100µM, 72h, replicate 1


title: Caco2, Control, 72h, replicate 1


title: Caco2, Control, 72h, replicate 3


title: Caco2, Solvent40nm, 72h, replicate 3


title: Caco2, Solvent40nm, 72h, replicate 1


title: Caco2, Au5nm_300µM, 24h, replicate 1

description: Gene expression of Caco2 exposed to Au5nm_300µM for 24h


title: Caco2, Au5nm_300µM, 24h, replicate 3


title: Caco2, Solvent5nm, 24h, replicate 3

description: Gene expression of Caco2 exposed to Solvent5nm for 24h


title: Caco2, Au40nm_100µM, 24h, replicate 3

description: Gene expression of Caco2 exposed to Au40nm_100µM for 24h


title: Caco2, Au40nm_300µM, 24h, replicate 2

description: Gene expression of Caco2 exposed to Au40nm_300µM for 24h


title: Caco2, Au5nm_300µM, 24h, replicate 2


title: Caco2, Au5nm_100µM, 24h, replicate 2

description: Gene expression of Caco2 exposed to Au5nm_100µM for 24h


title: Caco2, Solvent40nm, 24h, replicate 1

description: Gene expression of Caco2 exposed to Solvent40nm for 24h


title: Caco2, Au40nm_300µM, 24h, replicate 1


title: Caco2, Solvent40nm, 24h, replicate 3


title: Caco2, Au5nm_100µM, 24h, replicate 1


title: Caco2, Au40nm_100µM, 24h, replicate 2


title: Caco2, Solvent5nm, 24h, replicate 2


title: Caco2, Solvent40nm, 24h, replicate 2


title: Caco2, Solvent5nm, 24h, replicate 1


title: Caco2, Au40nm_100µM, 24h, replicate 1


title: Caco2, Control, 24h, replicate 1

description: Gene expression of Caco2 exposed to Control  for 24h


title: Caco2, Au40nm_300µM, 24h, replicate 3


title: Caco2, Control, 24h, replicate 3


title: Caco2, Control, 24h, replicate 2


title: 786-O biological replicate 1

city: Halle (Saale)

first: Anja

last: Harder

address: Große Steinstr. 52

department: Cure NF Research Group

institute: Martin Luther University Halle-Wittenberg

description: gene expression data of 786-O cell line incubated during normoxia

hyb_protocol: Labeled cDNA was hybridized onto Human GeneChip 1.0 ST arrays (Affymetrix). The chips were stained and washed following standard procedure.

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

data_processing: Data analyses were performed using Partek Genomic Suite (Partek) software after Robust Multichip Average (RMA) normalization.

source_name: renal cell carcinoma

label_protocol: Fragmented cDNA was end-labeled using Affymetrix terminal labeling kit .

growth_protocol: 3 x 10^6 786-O VHL-negative and VHL-transfected cells were incubated for 24 h during normoxia or hypoxia conditions.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen),  reverse transcribed and amplified with the WT expression kit (Invitrogen) according to the manufacturer’s manual.

treatment_protocol: No treatment

tag: transfection

tag: condition

value: normoxia


title: 786-O biological replicate 2


title: 786-O VHL Hypoxia biological replicate 1

description: gene expression data of 786-O cells transfected with a VHL-overexpression vector incubated during hypoxia

value: VHL

value: hypoxia


title: 786-O Hypoxia biological replicate 2

description: gene expression data of 786-O cell line incubated during hypoxia


title: 786-O VHL biological replicate 2

description: gene expression data of 786-O cells transfected with a VHL-overexpression vector incubated during normoxia


title: e10.5 Eyes MUT, biological rep1

city: Cincinnati

first: Richard

last: Lang

state: Oh

address: 3333 Burnet Ave, 2447 TCHRF

department: Ophthalmology Research

institute: Cincinnati Children's Medical Center

description: Gene expression data from e10.5 mouse eye regions

hyb_protocol: The WT- Ovation Pico RNA Amplification System Version 1.0 (Nugen) is used to prepare target cDNA.  Then the WT-Ovation Exon Module v1.0 (NuGEN) is used to create sense-strand cDNA targets. Finally the FL-Ovation cDNA Biotin Module V2 (NuGEN) chemically fragments and labels the sense-strand cDNA targets.

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

data_processing: The data were analyzed with GeneSpring Affymetrix Software

source_name: Wls;LeCre mutant embryo eyes stage e10.5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using 1-20ng total RNA. The quality of the Total RNA is checked by the 2100 Agilent Bioanalyzer using the RNA 6000 Pico Assay.

growth_protocol: Genetically modified mice used in this study were Le-Cre (Ashery-Padan, et al, 2000) and Wls-conditional (Carpenter et al., 2010).  Embryonic time points were determined by 0.5 days after vaginal plug.

extract_protocol: Tissue was processed for RNA isolation using Qiagen Micro Kit to produce 20ng of totall RNA according to manufacture instructions.

treatment_protocol: Embryos were harvested in fresh, ice cold PBS, and eye regions were removed using the MC-2010 Micro-Cautery Instrument (Protech International, Inc.) and place in fresh RLT buffer from Qiagen Micro Rneasy Kit.  Samples from 2-4 embryos of the same genotype were combined to create a single sample containing 4-8 eye regions for RNA extraction.

tag: tissue

value: embryonic eye region

tag: genotype

value: Wls fl/fl ; Lecre +/-

tag: age

value: embryonic stage 10.5


title: e10.5 Eyes WT, biological rep4

source_name: WT Mouse embryo eye stage e10.5

value: wild type


title: e10.5 Eyes MUT, biological rep2


title: e10.5 Eyes WT, biological rep3


title: e10.5 Eyes MUT, biological rep3


title: 786-O VHL biological replicate 1


title: e10.5 Eyes MUT, biological rep4


title: 786-O VHL Hypoxia biological replicate 2


title: 786-O Hypoxia biological replicate 1


title: e10.5 Eyes WT, biological rep1


title: e10.5 Eyes WT, biological rep2


title: Caco2, Au5nm_100µM, 24h, replicate 3


title: HCC with adrenal gland metastasis PEM-09P primary

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

hyb_protocol: According to Agilent user guide.

scan_protocol: Dried array slides were scanned using the DNA Microarray Scanner (Agilent, Santa Clara, CA).

data_processing: Raw image files of the arrays were processed using Feature Extraction software 8.1 using default CGH parameters (Agilent, Santa Clara, CA). Spot values were normalized using the default linear-lowess normalization.

source_name: HCC with adrenal gland metastasis

label_protocol:
Cy5: Five micrograms of genomic DNA were digested with the restriction enzymes AluI and RsaI (10U/uL; Invitrogen, Carlsbad, CA). Digested DNA was purified using QIAprep Spin Miniprep Kit (QIAGEN, using the BioPrime Array CGH Genomic Labeling kit (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions in a volume of 50 µl with a modified dNTP mix containing 120 µM each of dATP, dGTP, and dCTP; 60 µM dTTP; Valencia, CA) and labeled and 60 µM Cy5-dUTP (GE Amersham, Piscataway, NJ). Tumor DNA was pooled, purified and concentrated to 79 µl using Vivaspin 500 concentrator (VS0122, 30k MWCO, Vivascience, Littleton, MA).
Cy3: Five micrograms of reference DNA of the opposite gender (human genomic DNA, Promega, San Luis Obispo, CA) were digested with the restriction enzymes AluI and RsaI (10U/uL; Invitrogen, Carlsbad, CA). Digested DNA was purified using QIAprep Spin Miniprep Kit (QIAGEN, Valencia, CA) and labeled using the BioPrime Array CGH Genomic Labeling kit (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions in a volume of 50 µl with a modified dNTP mix containing 120 µM each of dATP, dGTP, and dCTP; 60 µM dTTP; and 60 µM Cy3-dUTP (GE Amersham, Piscataway, NJ). Reference DNA was pooled, purified and concentrated to 79 µl using Vivaspin 500 concentrator (VS0122, 30k MWCO, Vivascience, Littleton, MA).

extract_protocol: Phenol/Chloroform Extraction Protocol: Genomic tumor cell DNA was isolated from microdissected fresh frozen clinical tumor samples using proteinaseK digestion (P2308, Sigma-Aldrich, St. Louis, MO) and subsequent Phenol/Chlororform extraction.

value: HCC tumor tissue

tag: gender

value: M

tag: pair

source_name: Female human genomic DNA, Promega, G152A

value: F

tag: sample type


title: Study Sample 16 (Cancer)

city: HAIDARI

first: NIKOLAOS

last: SIAFAKAS

state: ATHENS

address: 1, RIMINI STR.

department: CLINICAL MICROBIOLOGY

country: Greece

institute: ATTIKON UNIVERSITY HOSPITAL

description: miRNA profile

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 6th and 7th (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 17.0 and 19.0. The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria). Following hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes

scan_protocol: The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).

data_processing:
The quantified signals were background corrected (Normexp with offset value 10) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. Spike-in controls were added in various concentrations in both the Hy3™ and the Hy5™ labeling reactions to evaluate the labeling reaction, hybridization, and the performance of the array experiment.
Principal Component Analysis (PCA) was applied in order to explore the naturally arising sample classes based on the expression profile. A heat map diagram was produced that showed the results of a two-way hierarchical clustering of microRNAs and samples. The clustering was done using the complete-linkage method together with the euclidean distance measure. The statistical significance of the relative expression of miRNAs between the control and the study groups was determined using the Student's t-test. Furthermore, the Benjamini-Hochberg multiple testing adjustment method was applied to the p-values for the control of possible false positive results.
These 113 features refer to human miRNAs which were present in all study samples.

source_name: Peripheral Blood

label_protocol: 300ng of total RNA from both sample and reference were then labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark), following the procedure described by the manufacturer.

extract_protocol: Total RNA purification that contained miRNA was carried out using the RNeasy Protect Animal Blood kit (Qiagen), according to the manufacturer's instructions

treatment_protocol: 500μl of whole blood from each patient were drawn into an RNAprotect Animal Blood Tube (Qiagen, Hilden, Germany). Following gentle inversion, the tubes were incubated for 2h at ambient temperature, according to the manufacturer's instructions, in order to allow for efficient cell lysis. All tubes were then stored at -80˚C prior to RNA purification.

tag: disease state

value: Cancer

value: Whole Blood

value: Female


title: Study Sample 18 (Cancer)

description: miRNA profile

value: Male


title: med16_0dpi_rep1

description: raw_data_file: raw_data_10.txt

source_name: med16, infected, 0 day, replicate 1

value: 0 day after Sclerotinia sclerotiorum infection

source_name: med8, infected, 0 day, replicate 1


title: HCC with adrenal gland metastasis PEM-08M metastasis

value: adrenal gland metastasis

value: Female human genomic DNA, Promega, G152A


title: HCC with lung metastasis PEM-13P primary

source_name: HCC with lung metastasis


title: CC with lung metastasis PEM-11P primary

source_name: CC with lung metastasis

value: cholangiocarcinoma


title: Study Sample 17 (Cancer)

description: miRNA profile


title: HCC with adrenal gland metastasis PEM-07P primary


title: CC with lymph node metastasis PEM-06M metastasis

source_name: CC with lymph node metastasis

value: lymph node metastasis


title: HCC with lung metastasis PEM-13M metastasis

value: lung metastasis


title: CC with lymph node metastasis PEM-06P primary


title: HCC with adrenal gland metastasis PEM-07M metastasis


title: 35S-GR-HDG1 5d+Chx+Dex-8hrs rep3

city: Wageningen

first: Gabino

last: Sanchez-Perez

address: Droevendaalsesteeg 1

department: Bioscience

country: Netherlands

institute: Wageningen University

description:
Gene expression data from Arabidopsis 5 days seedlings 8 hrs after HDG1 induction
35S-HDG1_Chx+Dex_T8_3

hyb_protocol: Performed by NASC's International Affymetrix Service

data_processing: GeneChip intensities were background-corrected, normalized and summarized by RMA method (Irizarry et al., 2003), using the oligo package from Bioconductor.

source_name: Col seedlings 8h chx and dex induction 35S::GR-HDG1

growth_protocol: For each microarray sample, approximately 40 p35S::GR-HDG1 or wild-type Col-0 seeds were sown on a 55 µm nylon mesh on top of solid half-strength MS medium and grown for five days. The mesh was then transferred to a Petri dish containing 25 ml liquid half-strength MS medium with 10 µM DEX and/or 10 µM CHX and placed for 8 hours on a slowly shaking platform at 21˚C.

extract_protocol: Invitek RNA isolation Kit

treatment_protocol: The mesh was then transferred to a Petri dish containing 25 ml liquid half-strength MS medium with 10 µM DEX and/or 10 µM CHX and placed for 8 hours on a slowly shaking platform at 21˚C. All conditions were replicated in triplicate.

tag: cultivar

value: Seedlings 5 days

tag: genotype/variation

value: chx and dex


title: CC with lung metastasis PEM-11M metastasis


title: HCC with adrenal gland metastasis PEM-09M metastasis


title: 35S-GR-HDG1 5d+Chx+Dex-8hrs rep2

description:
Gene expression data from Arabidopsis 5 days seedlings 8 hrs after HDG1 induction
35S-HDG1_Chx+Dex_T8_2

scan_protocol: Performed by NASC's International Affymetrix Service


title: HCC/CC with lymph node metastasis PEM-04M metastasis

source_name: HCC/CC with lymph node metastasis


title: Angiosarcoma with lymph node metastasis PEM-03P primary

source_name: Angiosarcoma with lymph node metastasis

value: angiosarcoma tumor tissue


title: Angiosarcoma with lymph node metastasis PEM-03M metastasis


title: Colon adenocarcinoma with liver metastasis GIM-14M metastasis

value: liver metastasis

source_name: Male human genomic DNA, Promega, G147A

value: Male human genomic DNA, Promega, G147A


title: CC with lymph node metastasis PEM-02M metastasis

value: M


title: HCC/CC with lymph node metastasis PEM-04P primary

value: HCC/CC tumor tissue

value: F


title: HCC with adrenal gland metastasis PEM-08P primary

value: HCC tumor tissue


title: CC with lymph node metastasis PEM-02P primary


title: CC with lymph node metastasis PEM-01P primary


title: Study Sample 15 (Cancer)

description: miRNA profile

value: Cancer

value: Whole Blood


title: Study Sample 13 (Cancer)

description: miRNA profile

value: Male


title: Study Sample 11 (Cancer)

description: miRNA profile

value: Female


title: Study Sample 10 (Cancer)

description: miRNA profile


title: Colon adenocarcinoma with liver metastasis GIM-14P primary

value: colon adenocarcinoma tissue


title: CC with lymph node metastasis PEM-01M metastasis

value: Female human genomic DNA, Promega, G152A


title: Colon adenocarcinoma with liver metastasis GIM-13P primary


title: Study Sample 9 (Cancer)

description: miRNA profile


title: Study Sample 7 (Schizophrenia & Cancer)

description: miRNA profile

value: Schizophrenia and cancer


title: Study Sample 8 (Schizophrenia & Cancer)

description: miRNA profile


title: Study Sample 6 (Schizophrenia & Cancer)

description: miRNA profile


title: 35S-GR-HDG1 5d+Chx+Dex-8hrs rep1

description:
Gene expression data from Arabidopsis 5 days seedlings 8 hrs after HDG1 induction
35S-HDG1_Chx+Dex_T8_1

label_protocol: Performed by NASC's International Affymetrix Service


title: Colon adenocarcinoma with liver metastasis GIM-13M metastasis


title: Colon adenocarcinoma with liver metastasis GIM-12M metastasis


title: 35S-GR-HDG1 5d+Chx-8hrs rep2

description:
Gene expression data from Arabidopsis 5 days seedlings 8 hrs after HDG1 induction
35S-HDG1_chx_T8_2

source_name: Col seedlings 8h chx induction 35S::GR-HDG1

value: chx


title: Col_5d+Chx+Dex-8hrs rep2

description:
Gene expression data from Arabidopsis 5 days seedlings.
Col_Chx+Dex_T8_2

source_name: Col seedlings 8h chx and dex

value: Seedlings 5 days

value: wild-type


title: Colon adenocarcinoma with liver metastasis GIM-09P primary


title: Col_5d+Chx+Dex-8hrs rep3

description:
Gene expression data from Arabidopsis 5 days seedlings.
Col_Chx+Dex_T8_3

value: chx and dex


title: Colon adenocarcinoma with liver metastasis GIM-04P primary


title: Study Sample 5 (Schizophrenia & Cancer)

description: miRNA profile


title: Colon adenocarcinoma with liver metastasis GIM-09M metastasis

value: liver metastasis


title: Study Sample 4 (Schizophrenia & Cancer)

description: miRNA profile


title: Col_5d+Chx+Dex-8hrs rep1

description:
Gene expression data from Arabidopsis 5 days seedlings.
Col_Chx+Dex_T8_1


title: 35S-GR-HDG1 5d+Chx-8hrs rep1

description:
Gene expression data from Arabidopsis 5 days seedlings 8 hrs after HDG1 induction
35S-HDG1_chx_T8_1


title: Col_5d+Chx-8hrs rep2

description:
Gene expression data from Arabidopsis 5 days seedlings.
Col_chx_T8_2

source_name: Col seedlings 8h chx


title: Study Sample 3 (Schizophrenia & Cancer)

description: miRNA profile


title: 35S-GR-HDG1 5d+Dex-8hrs rep3

description:
Gene expression data from Arabidopsis 5 days seedlings 8 hrs after HDG1 induction
35S-HDG1_dex_T8_3

source_name: Col seedlings 8h dex induction 35S::GR-HDG1

value: dex


title: Col_5d+Chx-8hrs rep3

description:
Gene expression data from Arabidopsis 5 days seedlings.
Col_chx_T8_3


title: Col_5d+Chx-8hrs rep1

description:
Gene expression data from Arabidopsis 5 days seedlings.
Col_chx_T8_1


title: 35S-GR-HDG1 5d+Chx-8hrs rep3

description:
Gene expression data from Arabidopsis 5 days seedlings 8 hrs after HDG1 induction
35S-HDG1_chx_T8_3


title: Study Sample 2 (Schizophrenia & Cancer)

description: miRNA profile


title: Study Sample 1 (Schizophrenia & Cancer)

description: miRNA profile


title: 35S-GR-HDG1 5d+Dex-8hrs rep1

description:
Gene expression data from Arabidopsis 5 days seedlings 8 hrs after HDG1 induction
35S-HDG1_dex_T8_1


title: ATP syn Cf6 IR rep3

city: London

first: Ariana

middle: Pia

last: Gatt

address: London

institute: King's College London

description: Gene expression data from CNS tissue expressing ATP Cf6 RNAi in neurons

hyb_protocol: Hybridisations were performed using the Affymetrix Terminal Labelling kit on Drosophila Gene 1.0 ST Arrays (Affymetrix).

scan_protocol: Imaging of the arrays was performed using the Affymetrix GCS3000 microarray system.

data_processing: Data normalisation was processed using a Robust Multichip Average (RMA) algorithm and analysed using the Omics Explorer package (Qlucore). A false discovery rate (FDR) of 0.2% was used.

organism: Drosophila melanogaster

source_name: CNS tissue from nsybGal4/UAS-TFAM3M larvae

label_protocol: cRNA was prepared from 500ng of total RNA using the Ambion WT Expression kit  (Ambion).

growth_protocol: Larvae were grown on standard fly food at 25 degrees.

extract_protocol: For the microarray analysis the complete CNS from 10-15 wandering third instar larvae were dissected in PBS and placed into PBS on ice and then transferred into 100ul of lysis buffer from the Absolutely RNA Microprep kit (Stratagene) and vortexed for 5 seconds. Total RNA was then prepared using this kit. For each genotype RNA samples were prepared in triplicate and stored at -80oC.

treatment_protocol: One control and one experimental genotypes were used: Control (nsybGal4/+) and ATP Cf6 IR (nsybGal4>ATP Cf6 IR).

value: nsybGal4/ATPCf6 IR

value: CNS

tag: developmental stage

value: larvae


title: Colon adenocarcinoma with liver metastasis GIM-02P primary

value: F

value: M

value: Male human genomic DNA, Promega, G147A


title: Colon adenocarcinoma with liver metastasis GIM-02M metastasis


title: Colon adenocarcinoma with liver metastasis GIM-04M metastasis


title: ATP syn Cf6 IR rep2


title: Control Sample 6 (Schizophrenia)

description: miRNA profile

value: Schizophrenia

value: Whole Blood

value: Male


title: Control Sample 5 (Schizophrenia)

description: miRNA profile

value: Female


title: Colon adenocarcinoma with liver metastasis GIM-01P primary

value: colon adenocarcinoma tissue


title: Control Sample 4 (Schizophrenia)

description: miRNA profile


title: Control Sample 3 (Schizophrenia)

description: miRNA profile


title: ATP syn Cf6 IR rep1


title: Control Sample 2 (Schizophrenia)

description: miRNA profile


title: Col_5d+Dex-8hrs rep2

description:
Gene expression data from Arabidopsis 5 days seedlings.
Col_dex_T8_2

source_name: Col seedlings 8h dex


title: Control Sample 1 (Schizophrenia)

description: miRNA profile


title: Study Sample 12 (Cancer)

description: miRNA profile

value: Cancer


title: Colon adenocarcinoma with liver metastasis GIM-01M metastasis


title: Col_5d+Dex-8hrs rep3

description:
Gene expression data from Arabidopsis 5 days seedlings.
Col_dex_T8_3

value: Seedlings 5 days


title: N15

city: Jacksonville

last: Copland

state: Florida

address: 4500 San Pablo Rd

department: Cancer Research

institute: The Mayo Clinic, Jacksonville FL

hyb_protocol: The IVT products were column-purified, fragmented, and hybridized onto Affymetrix U133 Plus 2.0 GeneChips® at 45º C for 16 h.

scan_protocol: Subsequent to hybridization, the arrays were washed and stained with streptavidin-phycoerythrin, then scanned in an Affymetrix GeneChip® Scanner 3000 (Santa Clara, CA). All control parameters were confirmed to be within normal ranges before normalization and data reduction was initiated.

data_processing: Raw data was processed by MAS.5 (Affymetrix) and analyzed using GeneSpring GX10

source_name: normal thyroid

label_protocol: The RNA products were column-purified (Affymetrix) and then in vitro transcribed to generate biotin-labeled cRNA.

extract_protocol: RNA was extracted from flash frozen patient tissue samples (anaplastic thyroid carcinoma, matched normal thyroid tissue, and unmatched normal thyroid tissue) using TRIzol (Invitrogen) and chloroform (Sigma). All tumor samples are from the primary tumor site. RNA extracts were purified on Spin Chroma column (BD bioscience K1332-2). The 18S/28S bands were verified on a 1% agarose gel. RNA samples were shipped to Advanced Genomic Technology Center Gene Expression Core at the Mayo Clinic in Rochester, MN for further analysis. RNA quality was assessed by Agilent Bioanalyzer (Santa Clara, CA). Reverse transcription to second strand cDNA was generated from 100 ng of good quality total RNA.

tag: tissue type

value: normal thyroid

tag: matched/unmatched

value: unmatched


title: 35S-GR-HDG1 5d+Dex-8hrs rep2

description:
Gene expression data from Arabidopsis 5 days seedlings 8 hrs after HDG1 induction
35S-HDG1_dex_T8_2

tag: treatment


title: PBMC_mort_nonagenarian 81064

city: Tampere

first: Saara

last: Marttila

address: Biokatu 6

department: School of Medicine

country: Finland

institute: University of Tampere

description: Sample name: 81064

hyb_protocol: 1,500 ng of labeled cRNA was hybridized overnight according to the Illumina protocol.

scan_protocol: BeadScan

data_processing: The preprocessing, filtering and analysis of the data were performed with the Chipster v2.0 program (Kallio, M.A., et al. MBC Genomics 12, 507 (2011)). The lumi pipeline was used for data preprocessing and normalization. Array_Address_ID was used as a probe identifier, background correction was performed with the bgAdjust.affy package, and the data were log2-transformed and normalized with the quantile method.

source_name: Human PBMC

label_protocol: Labeled cRNA was prepared from 330 ng of total RNA using an Illumina TotalPrep RNA Amplification Kit (Ambion Inc., TX, USA) with overnight incubation according to the manufacturer's protocol.

growth_protocol: Freshly drawn blood, stored at -70 C until the analysis.

extract_protocol: RNA was purified using an miRNeasy mini kit (Qiagen, CA, USA) according to the manufacturer's protocol using on-column DNase digestion (AppliChem GmbH, Darmstadt, Germany).

treatment_protocol: Blood was collected to EDTA-containing tubes between 8 and 12 am. Leucocytes were separated with a density gradient and stored in RNAlater.

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

value: nonagenarian

tag: Sex

value: female

tag: status 31.1.2013 (1 died, 0 alive)

tag: follow_up_time in years_until 31.1.2013

tag: status 31.5.2014 (1 died, 0 alive)

tag: body mass index

tag: cf-dna level (µg/ml)

tag: frailty index

value: frail


title: PBMC_mort_nonagenarian 81074

description: Sample name: 81074

tag: age


title: Col_5d+Dex-8hrs rep1

description:
Gene expression data from Arabidopsis 5 days seedlings.
Col_dex_T8_1

tag: tissue

value: wild-type

value: dex


title: PBMC_mort_nonagenarian 81059

description: Sample name: 81059


title: PBMC_mort_nonagenarian 81019

description: Sample name: 81019


title: PBMC_mort_nonagenarian 81084

description: Sample name: 81084


title: PBMC_mort_nonagenarian 81136

description: Sample name: 81136


title: N12


title: N9


title: N18


title: N16

value: matched to T16


title: PBMC_mort_nonagenarian 28897

description: Sample name: 28897

value: pre-frail


title: PBMC_mort_nonagenarian 28861

description: Sample name: 28861


title: PBMC_mort_nonagenarian 28895

description: Sample name: 28895


title: PBMC_mort_nonagenarian 28868

description: Sample name: 28868


title: N3


title: PBMC_mort_nonagenarian 81018

description: Sample name: 81018


title: Study Sample 14 (Cancer)

description: miRNA profile

source_name: Peripheral Blood

tag: disease state

tag: sample type

tag: gender


title: N14

value: matched to T14


title: N5


title: PBMC_mort_nonagenarian 28812

description: Sample name: 28812


title: N11


title: N8


title: N6


title: PBMC_mort_nonagenarian 28816

description: Sample name: 28816


title: Colon adenocarcinoma with liver metastasis GIM-12P primary

value: M

tag: pair

source_name: Female human genomic DNA, Promega, G152A

value: F


title: N1

tag: tissue type


title: T10

source_name: Anaplastic Thyroid Carcinoma

value: anaplastic thyroid carcinoma (ATC)

tag: tissue subtype

value: subtype spindle/squamoid cell

tag: matched/unmatched


title: T12

value: subtype spindle cell


title: T6

value: subtype spindle/giant cell


title: T16

value: matched to N16


title: PBMC_mort_nonagenarian 28798

description: Sample name: 28798

tag: cell type


title: T14

value: matched to N14


title: PBMC_mort_nonagenarian 28778

description: Sample name: 28778

value: peripheral blood mononuclear cells (PBMCs)

tag: Sex

value: male

value: non-frail


title: PBMC_mort_nonagenarian 28782

description: Sample name: 28782

value: nonagenarian

value: female

tag: status 31.1.2013 (1 died, 0 alive)


title: PBMC_mort_nonagenarian 28806

description: Sample name: 28806

tag: follow_up_time in years_until 31.1.2013


title: T7

value: unmatched


title: T15

value: subtype squamoid/giant cell


title: PBMC_mort_nonagenarian 28760

description: Sample name: 28760

tag: status 31.5.2014 (1 died, 0 alive)

value: frail


title: T11

value: subtype squamoid cell


title: T8


title: PBMC_mort_nonagenarian 28726

description: Sample name: 28726

tag: body mass index


title: T2

value: subtype N/A


title: PBMC_mort_nonagenarian 28736

description: Sample name: 28736

tag: cf-dna level (µg/ml)


title: PBMC_mort_nonagenarian 28803

description: Sample name: 28803

tag: frailty index

value: pre-frail


title: PBMC_mort_nonagenarian 28720

description: Sample name: 28720

tag: age


title: T4

value: anaplastic thyroid carcinoma (ATC)


title: PBMC_mort_nonagenarian 28735

description: Sample name: 28735


title: AT/RT-like_INI1(+)_patient2

city: Taipei

first: Tsung-Han

last: Hsieh

address: No.250, Wusing St., Xinyi Dist., Taipei City 112, Taiwan (R.O.C.)

department: Institute of Microbiology and Immunology

country: Taiwan

institute: Taipei Medical University

description: Gene expression data from pediatic CNS AT/RT-like patient

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

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

data_processing: RMA through R based affymetrix module

source_name: AT/RT-like tumor,INI1(+),patient2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

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

tag: tumor site

value: cerebellum

tag: diagnosis

value: AT/RT-like


title: N2

value: normal thyroid


title: T1


title: PBMC_mort_nonagenarian 28777

description: Sample name: 28777


title: PBMC_mort_nonagenarian 28716

description: Sample name: 28716


title: PBMC_mort_nonagenarian 28752

description: Sample name: 28752


title: AT/RT_INI1(-)_patient6

description: Gene expression data from pediatic CNS AT/RT patient

source_name: AT/RT tumor,INI1(-),patient6

value: AT/RT


title: AT/RT_INI1(-)_patient7

source_name: AT/RT tumor,INI1(-),patient7


title: AT/RT_INI1(-)_patient4

source_name: AT/RT tumor,INI1(-),patient4


title: AT/RT_INI1(-)_patient3

source_name: AT/RT tumor,INI1(-),patient3


title: AT/RT_INI1(-)_patient5

source_name: AT/RT tumor,INI1(-),patient5


title: AT/RT_INI1(-)_patient2

source_name: AT/RT tumor,INI1(-),patient2


title: AT/RT_INI1(-)_patient1

source_name: AT/RT tumor,INI1(-),patient1


title: PBMC_mort_nonagenarian 28706

description: Sample name: 28706


title: PBMC_mort_nonagenarian 28704

description: Sample name: 28704


title: PBMC_mort_nonagenarian 28698

description: Sample name: 28698


title: PBMC_mort_nonagenarian 28667

description: Sample name: 28667


title: PBMC_mort_nonagenarian 28695

description: Sample name: 28695


title: PBMC_mort_nonagenarian 28657

description: Sample name: 28657


title: PBMC_mort_nonagenarian 28649

description: Sample name: 28649


title: PBMC_mort_nonagenarian 28629

description: Sample name: 28629


title: PBMC_mort_nonagenarian 28623

description: Sample name: 28623


title: PBMC_mort_nonagenarian 28647

description: Sample name: 28647


title: PBMC_mort_nonagenarian 28614

description: Sample name: 28614


title: PBMC_mort_nonagenarian 28622

description: Sample name: 28622


title: PBMC_mort_nonagenarian 28664

description: Sample name: 28664


title: HCC with lung metastasis, metastasis tumor PEM-22M

hyb_protocol: Labeled cRNA was hybridized onto Affymetix GeneChip HG-U133 Plus 2.0 Arrays.

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5.0

source_name: HCC with lung metastasis

label_protocol: RNA was amplified with two linear amplification steps by in vitro transcription using the MEGAscript T7 kit (Ambion, Austin, TX) followed by the labeling step using the BioArray HighYield RNA Transcript Labeling Kit T3 from Enzo Life Sciences (Farmingdale, NY).

growth_protocol: Enriched tumor endothelium was obtained by laser capture microdissection

extract_protocol: Total RNA was isolated using the PicoPure protocol (Arcturus, Mountain View, CA)

tag: tissue

value: tumor endothelium from lung metastasis

tag: disease state

value: HCC with lung metastasis


title: HCC with lung metastasis, metastasis tumor PEM-19M


title: HCC with lung metastasis, metastasis tumor PEM-20M


title: HCC with lung metastasis, metastasis tumor PEM-21M


title: PBMC_mort_nonagenarian 28615

description: Sample name: 28615

value: peripheral blood mononuclear cells (PBMCs)


title: HCC with lung metastasis, metastasis tumor PEM-18M


title: HCC with lung metastasis, metastasis tumor PEM-23M


title: AT/RT-like_INI1(+)_patient1

source_name: AT/RT-like tumor,INI1(+),patient1

tag: gender

value: male


title: PBMC_mort_nonagenarian 28592

description: Sample name: 28592

value: nonagenarian


title: HCC with lung metastasis, metastasis tumor PEM-17M


title: HCC with lung metastasis, metastasis tumor PEM-15M


title: HCC with lung metastasis, primary tumor PEM-13P

value: tumor endothelium from HCC tumor tissue