title: Knock-out mouse, Starved (S7)

hyb_protocol: Total RNA samples hybridized to the Affymetrix Hugene 1.0 st chip according to the protocols provided by the manufacturer

data_processing:
Probe intensities were extracted from Affymetrix CEL files and normalized using RMA and summarized at the transcript cluster level using the R/Bioconductor (http://bioconductor.org) oligo package.  Array quality control was performed to remove arrays that significantly differed in performance.  Significance testing was performed by fitting gene-wise linear models using the limma Bioconductor package.  Significance testing was performed using a moderated t-test, and comparisons of pre- (V0) and post-treatment (V1) individuals were performed using a moderated paired t-test.  Gene set analysis was performed using the MSigDB (http://www.pnas.org/content/102/43/15545.abstract) and libraries generated from the Halloran labs Pathogenesis Based Transcript (PBT; http://transplants.med.ualberta.ca/Nephlab/data/gene_lists.html) gene sets.  The PBTs represent the major biologic events in cellular graft rejection and were derived from experimental mouse kidney transplants, cultured cells and human kidney biopsies.  Gene sets were converted to HUGO gene symbols and analysis was executed using the limma romer function.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: Knock-out mouse, Starved

label_protocol: Follow protocols of Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix Genechip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA)

growth_protocol: Mice were bred in the barrier facility at the Albert Einstein College of Medicine's animal institute. Transgenic C57BL/6 mice for Albumin-Cre were purchased from Jackson Laboratory and bred with mice containing loxP sequences flanking exon 9A of the lamp2 gene. Multiple breedings were carried out initially to generate several lines of mice to avoid inter-breeding.

extract_protocol: Mice were euthanized by cervical dislocation and livers were dissected. A 1x1 mm piece of liver was stored at -80 degrees in RNAlater buffer (Qiagen). Mouse liver total RNA was extracted using Trizol and purified with Rneasy chromatography (Qiagen).

treatment_protocol: Mice were fed a standard chow diet (Lab Diet #5058). Where indicated, mice were starved for 24 hours with water ad libitum.

value: liver

tag: phenotype

value: chaperone-mediated autophagy (CMA) deficient


title: 73290-1

status: Public on Dec 31 2014

type: RNA

city: Wuhan

first: Yi

last: Huang

state: Hubei

address: No. 2 Xudong Second Road, Wuchang District

department: Rapeseed Genetics and Breeding

country: China

institute: Oil Crops Research Institute, Chinese Academy of Agricultural Sciences

description: A Brassica genomics resource was developed at the Plant Biotechnology Institute, National Research Council Canada (PBI-NRC) and Agriculture and Agri-Food Canada (AAFC) in collaboration with other institutes. About 95,418 unique sequences were assembled using 781,826 EST sequences mainly from three species: B. napus, B. rapa, and B. oleracea. These unique sequences were submitted to CombiMatrix for the development of a 35-40mer oligonucleotide microarray, for which probes were synthesized in situ onto electrodes on a microchip. The customized Combimatrix Brassica array comprised 90,500 probes and was called as 90K array.

hyb_protocol: 1. The pre-hybridization and hybridization procedures were performed precisely according to the protocol of CombiMatrix (www.combimatrix.com).   2. Cy5 dye-labeled RNA populations from individual tissue samples were hybridized to the 90K array and three biological replicates were performed.

scan_protocol: 1. Hybridized arrays were scanned using a LuxScan 10K Scanner (CapitalBio Corporation, Beijing, China) at 5 μm resolution, 100% laser power, and different PMT values to obtain a similar overall intensity between slides.   2. The scans were saved as TIF files.

data_processing: 1. Raw spot fluorescence intensities were collected using LuxScan version 2.0 (CapitalBio Corporation, Beijing, China) and saved as .txt file.   2. Samples that were originally negative after background subtraction and those with an overall signal intensity of less than 100 were filtered out.   3. Array features annotated as “Empty”, “Blank”, and internal controls were flagged and excluded from the analysis.  4. Twelve LSR files containing the raw probe intensity values were imported into R and the signal intensities were quantile normalization was performed to normalize between arrays using the R-package LIMMA [24] with a 5% false discovery rate (FDR<=0.05).   5. Probes with at least one missing value within triplicates were removed from subsequent analysis.   6. The background-corrected signal intensity of each probe on the array was combined by averaging three biological replicates.   7. A gene was considered to be differentially expressed when its fold-change in expression between two samples was larger than 1.5- or less than 0.67-fold.

molecule: total RNA

organism: Brassica napus

source_name: main inflorescence

label_protocol: 1. About 3.0 µg of total RNA for each sample was reverse transcribed into amino allyl-modified aRNA using a Message™ II aRNA Amplification Kit (Cat: 1753, Ambion, Austin, TX, USA), according to the manufacturer's protocol.   2. The quality of amplification was identified using agarose gel electrophoresis, and the aRNA yield was quantified using a NanoDrop® 1000 spectrophotometer.   3. The aRNA was selected as the template for fluorescent target preparation for microarray experiments.  4. About 5.0 µg of aRNA was labeled with mono-reactive NHS esters of Cy5 in the dark for 30 min at room temperature, and the samples were then purified and used as targets for hybridization.

growth_protocol: 1. Two elite Brassica napus L. lines, cv. Zhongshuang 11 (ZS11), which was used for genome sequencing, and 73290, which was used for re-sequencing, developed by the Rapeseed Biotechnology Breeding Unit, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences (Wuhan, China), were used to generate an F2:3 population harboring 183 offspring for QTL mapping of yield traits.    2. Subsequently, an F6 inbred line (RIL) population was obtained from the F2:3 population by single-seed-descendant. Nine lines with an extremely high number of PMIs and Nine with an extreme number were selected from the above F6 RIL population. Afterwards, ZS11, 73290, and the 18 extreme RIL lines were used for gene expression profiling analysis in the main inflorescence.

extract_protocol: 1. Using an RNeasy Mini Kit (Cat. 74124, Qiagen, Mississauga, ON) according to the manufacturer’s recommendations, total RNA of inflorescence primordia was extracted in biological triplicate, each consisting of three main inflorescence sections taken from three independent plants.   2. Trace amounts of DNA were removed using DNase I (Cat. 18068-015, Invitrogen, USA).   3. The RNA yield and purity were determined spectrophotometrically with a NanoDrop®1000 spectrophotometer (Thermo Fisher Scientific, USA), and the intactness of RNA was verified by electrophoresis on a 1% agarose gel with 1×TBE running buffer at 70 V for 40 min.   4. Purified total RNA was precipitated and re-suspended in DEPC-treated water to a final concentration of about 500 ng/µL.   5. For the extreme PMI lines, the total RNA of inflorescence primordia was extracted individually and pooled at equal concentrations within each extreme-PMI group. Nine lines were used for each biological replicate in the reverse transcription analysis.

treatment_protocol: 1. Seeds were sown on May 17, 2011 in the experimental station of Qinghai University (Xining, Qinghai Province, China).   2. Individual plants of each accession, which did not exhibit any obvious phenotypic differences, were reserved by eliminating potential false types at several developmental stages.  3. The development of the main inflorescence (MI) was observed under an anatomical microscope (OLympus, Japan). The inflorescence primordia of three to five plants for each accession was examined every three days under the microscope, beginning at the eighth leaf stage.   4. The main inflorescence primordia of five plants per line that were at the pistil-stamen primordia initiation stage of the first floral on the main inflorescence, were harvested in the morning, immediately frozen in nitrogen, and then kept at -80⁰С for total RNA isolation.

tag: parental line


title: S13WT

city: Sapporo

first: Hiroyuki

last: Yamaguchi

address: N5 K12 Jo Kita-ku

country: Japan

institute: Hokkaido University

description:
254821610001_1_2
Gene expression of Neochlamydia S13 at 24hr after amoebal incubation with Legionella infection
Neochlamydia S13 drafe genome sequence: DDBJ accession number BASK01000001-BASK01001342

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25x Agilent fragmentation buffer (2.2ul) and 55ul of 2x Agilent hybridization buffer for blocking fragmentation was added following the manufacturers instructions. On completion of the fragmentation reaction, 100ul of  the fragmentation mixture was hybridized to constamized Agilent Neochlamydia S13 genome oligo microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the custamized DNA Microarray Scanner  using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label: Cyanine 3 CTP

organism: Neochlamydia sp. S13

source_name: bacteria, amoebal (Acanthamoeba) endosymbiont

label_protocol: Purified RNAs (100ng) were amplified with T7 RNA polymerase, and cRNAs were also labeled with cyanine 3 CTP using a Low Input Quick Amp WT Labeling Kit (Agilent Technologies, Santa Clara, CA) according to manufacturer’s instructions.

growth_protocol: As described previously [Matsuo et al., Env Microbiol Rep, 4: 524-533, 2010], amoeba (Acanthamoeba) strain persistently infected withNeochlamydia S13 were isolated from  a soil sample, Sapporo, Japan. The amoeba was maintained in PYG broth [0.75% (w/v) peptone, 0.75% (w/v) yeast extract and 1.5% (w/v) glucose] at 30°C [5].

extract_protocol: Total RNA was extracted from either Neochlamydia S13-harboring amoebae with or without Legionella (JR32) infection (at 24h after the infection) using an RNeasy Mini kit (Qiagen, Valencia, CA) according to manufacturer’s instructions. Extracted RNA was treated with DNase (DNA-free; Ambion, Austin, TX).

treatment_protocol: Amoebae (5 × 105 cells) were infected with Legionella (5 × 105 CFU: colony-forming unit) at a multiplicity of infection (MOI) of 1 for 2 h at 30°C, and then uninfected bacteria were killed with 50 µg/ml gentamycin. After washing with PYG medium, the infected amoebae were incubated for up to 6 days.

tag: host

value: ameobae without Legionella infection


title: GLU, biological rep2

city: Dalian

first: Ying

last: Ge

address: 9 Western Section, Lvshun South Street

institute: Dalian Medical University

description:
GLU_r2
tumor bearing mice were treated with 10 mg/kg of glucose (GLU) by tail vein injection with the frequency of every 4 days. Mice were sacrificed on day 12 (D12) and tumor tissues were isolated.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized with Genechip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned with Genechip Scanner 3000

data_processing: The expression raw data was preprocessed using Robust Multichip Analysis (RMA) with quantile normalization and custom CDF file hgu133plus2hsentrezgcdf, v17.1.0

label: biotin

organism: Homo sapiens

source_name: tumor treated by GLU

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

growth_protocol: Tumor suppression effects of DSNs and TAX were investigated with tumor-bearing female BALB/c nude mice in JOINN Laboratories (Beijing, China). BALB/c nude mice were purchased from Vital River Laboratories (Beijing, China). Mice were subcutaneous injected with MCF-7 cells. After three weeks, the tumor bearing mice were sacrificed for further experiments. The tumor tissues were isolated and cut into pieces at about 2 mm3 under aseptic conditions. Around 4-5 weeks old mice were subcutaneously inoculated with tumor tissues on the right flank. Tumors were allowed to grow to about 50-100 mm3.

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

treatment_protocol: Mice bearing similar volume of tumors were chosen and divided into four groups randomly with 6 mice in each group. Mice from different groups were treated with 10 mg/kg of TAX, DSNs, equivalent BSNs or glucose (GLU) separately by tail vein injection with the frequency of every 4 days. Body weight and tumor size were measured every 3 days. Mice were sacrificed on day 12 (D12) and tumor tissues were isolated and frozen in liquid nitrogen immediately for RNA isolation

tag: treatment (of tumor-bearing female balb/c nude mice)

value: glucose

tag: tissue

value: tumor


title: CD14 fraction healthy person H6

city: Saarbrücken

first: Christina

last: Backes

address: Campus, Building E 2.1

department: Chair for Clinical Bioinformatics

country: Germany

institute: Saarland University

description: CD14 fraction healthy person H6

hyb_protocol: Hybridisations were performed in Agilent SureHyb chambers for 20 hours at 55C and washed according to manufacturer's instructions.

scan_protocol: Array-chips were scanned in a high resolution microarray scanner from Agilent Technologies using Scan Control 8.5.1 software, 3 microns resolution in double path mode.

data_processing: Signal intensity values were extracted from the raw data file using feature extraction software (Agilent Technologies). The gTotalProbeSignals were summed up to calculate the total expression value for each miRNA per sample. Quantile normalization was applied to normalize expression values across the arrays using the preprocessCore package of the programming language R. After that we log2-transformed the expression values.

source_name: CD14 cells

label_protocol: Total RNA samples were labelled using the Agilent miRNA Complete Labelling and Hybridisation Kit

extract_protocol: Total RNA including small RNAs was isolated using miRNeasy Micro Kit (Qiagen)  according to manufacturer’s instructions.

tag: disease state

value: healthy

tag: gender

value: female

tag: age

tag: cell type

value: CD14 cells


title: CD14 fraction healthy person H5

description: CD14 fraction healthy person H5

value: male


title: CD14 fraction healthy person H4

description: CD14 fraction healthy person H4


title: BSNs, biological rep2

description:
BSNs_r2
tumor bearing mice were treated with 10 mg/kg of blank solid lipid nanoparticles (BSNs) by tail vein injection with the frequency of every 4 days. Mice were sacrificed on day 12 (D12) and tumor tissues were isolated.

source_name: tumor treated by BSNs

value: blank solid lipid nanoparticles


title: GLU, biological rep1

description:
GLU_r1
tumor bearing mice were treated with 10 mg/kg of glucose (GLU) by tail vein injection with the frequency of every 4 days. Mice were sacrificed on day 12 (D12) and tumor tissues were isolated.


title: Knock-out mouse, Starved (S6)

city: New York

first: Bin

last: Ye

state: NY

address: 1301 Morris Park Ave

department: Genetics

country: USA

institute: Albert Einstein College of Medicine

scan_protocol: Affymetrix Gene Chip 3000 7G scanner, software AGCC v2.0

organism: Mus musculus


title: ZS11-1

value: Zhongshuang 11 (ZS11)


title: CD14 fraction healthy person H2

description: CD14 fraction healthy person H2


title: Knock-out mouse, Starved (S5)


title: S13WT_Lp

description:
254821610001_1_1
Gene expression of Neochlamydia S13 at 24hr after amoebal incubation without Legionella infection
Neochlamydia S13 drafe genome sequence: DDBJ accession number BASK01000001-BASK01001342

value: ameobae with Legionella infection


title: ZS11-2


title: CD14 fraction healthy person H1

description: CD14 fraction healthy person H1


title: Wild type mouse, Starved (3)

source_name: Wild type mouse, Starved

value: wild type


title: Knock-out mouse, Fed (F5)

source_name: Knock-out mouse, Fed


title: Wild type mouse, Starved (S4)


title: Knock-out mouse, Fed (F8)


title: Knock-out mouse, Fed (F6)


title: CD14 fraction healthy person H3

description: CD14 fraction healthy person H3


title: Cumulus Cells, Unprimed, replicate 3

city: Bar Harbor

first: Timothy

middle: Michael

last: Stearns

state: ME

address: 600 Main Street

department: Computational Sciences

institute: The Jackson Laboratory

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430v2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Average signal intensities for each probeset within arrays were calculated by the rma function provided within the affy package for R using a custom (Ensembl Transcript v13) CDF file (Dai et al., 2005; http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13.0.0/version.html).  The RMA method incorporates convolution background correction, sketch-quantile normalization, and summarization based on a multi-array model fit robustly using the median polish algorithm.

source_name: Cumulus Cells, Unprimed

label_protocol: Fragmented biotinylated aRNA were produced from 20ng Total RNA according to the standard protocol using the MessageAmp II aRNA Amplification Kit from Ambion for the first round of amplification and using the MessageAmp II Biotin Enhanced Kit from Ambion for the second round of amplification.

growth_protocol: Fresh samples of cumulus cells and mural granulosa cells were isolated from the ovaries of 22 day old mice

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Micro kit according to the manufacturers instructions.

treatment_protocol: Half of the mice were treated with 5 IU equine chorionic gonadotropin 44 hours before isolation of cumulus and mural granulosa cells

value: cumulus

tag: pmsg-stimulation

value: unprimed


title: Mural Cells, PMSG-Stimulated, replicate 3

source_name: Mural Cells, PMSG-Stimulated

value: mural

value: stimulated


title: Mural Cells, Unprimed, replicate 3

source_name: Mural Cells, Unprimed


title: CD14 fraction lung cancer patient L11

description: CD14 fraction lung cancer patient L11

value: Lung adenocarcinoma


title: CD14 fraction lung cancer patient L10

description: CD14 fraction lung cancer patient L10


title: Mural Cells, Unprimed, replicate 2


title: CD14 fraction lung cancer patient L6

description: CD14 fraction lung cancer patient L6


title: Cumulus Cells, PMSG-Stimulated, replicate 3

source_name: Cumulus Cells, PMSG-Stimulated


title: CD14 fraction lung cancer patient L4

description: CD14 fraction lung cancer patient L4


title: Cumulus Cells, Unprimed, replicate 2


title: CD14 fraction lung cancer patient L3

description: CD14 fraction lung cancer patient L3

value: squamous cell carcinoma


title: Mural Cells, PMSG-Stimulated, replicate 2


title: Wild type mouse, Fed (F4)

source_name: Wild type mouse, Fed

value: liver


title: CD14 fraction lung cancer patient L5

description: CD14 fraction lung cancer patient L5

value: small cell lung carcinoma


title: Cumulus Cells, PMSG-Stimulated, replicate 2


title: Wild type mouse, Fed (F2)


title: CD14 fraction lung cancer patient L2

description: CD14 fraction lung cancer patient L2


title: PAXGene blood healthy person H7

description: PAXGene blood healthy person H7

source_name: whole blood

value: whole blood


title: Mural Cells, Unprimed, replicate 1


title: Peripheral blood mononuclear cells, down syndrome, biological rep. 6, technical rep. 1 [CD7]

city: São José do Rio Preto

first: Érika

middle: Cristina

last: Pavarino

state: São Paulo

address: Avenida Brigadeiro Faria Lima, nº 5416 - UPGEM/Bloco U-6

department: Departamento de Biologia Molecular

country: Brazil

institute: Faculdade de Medicina de São José do Rio Preto (FAMERP)

description: down syndrome

data_processing:
The analysis was performed using the language and statistical platform R. Specifically, the HTqPCR bioconductor package was used to calculate the dCt, ddCt  and Fold-Change values, as well as to filter data. The Ct value was considered Undetermined or Unreliable if it was greater than 37 or whether the value was in the normal tails. The NA value was assigned to Undetermined values. The delta-Ct values were calculated using as control the genes 18S, GADPH, GUSB and HPRT1. The delta-delta-Ct and Fold-Change values were calculated using the down syndrome group as Target and control group as Calibrator.
Matrix non-normalized contains the raw data. Matrix Normalized contains 2^-deltaCt values. Fold Change contains 2^-(delta-deltaCt). All values were calculated in the R language

label: FAM

source_name: Peripheral blood mononuclear cells

label_protocol: Reverse transcription was performed from 1000 ng total RNA using High Capacity cDNA Reverse Transcription kit (Applied Biosystems). Quantitative real-time RCR were performed with one cycle for two minutes at 50°C, one cycle of 10 minutes at 94.5°C, and 40 cycles for three seconds at 95°C followed by 30 seconds at 60°C

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen)

treatment_protocol: Peripheral blood mononuclear cells were freshly isolated by Ficoll Paque Plus (Sigma-Aldrich)

tag: age (years)


title: Peripheral blood mononuclear cells, down syndrome, biological rep. 5, technical rep. 2 [CD5R]

description: down syndrome


title: Peripheral blood mononuclear cells, down syndrome, biological rep. 6, technical rep. 2 [CD7R]

description: down syndrome


title: Wild type mouse, Fed (F1)


title: Cumulus Cells, Unprimed, replicate 1


title: Cumulus Cells, PMSG-Stimulated, replicate 1


title: PAXGene blood healthy person H6

description: PAXGene blood healthy person H6

value: healthy


title: Peripheral blood mononuclear cells, down syndrome, biological rep. 4, technical rep. 1 [CD19]

description: down syndrome

value: female


title: Mural Cells, PMSG-Stimulated, replicate 1


title: Peripheral blood mononuclear cells, down syndrome, biological rep. 5, technical rep. 1 [CD5]

description: down syndrome


title: M1448-11

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 48 hours. Treated with CsA. Replicate 3.

hyb_protocol: Fragmented ssDNAs were hybridized to the standard arrays for 17h at 45°C; the arrays were  then  washed  and stained  using  the  fluidics  station  and  then  scanned  using  GeneChip Scanner  3000.  The  images  were  analyzed  using  Command  Console  and  comparison analyses were carried out according to the instructions provided by Affymetrix.

scan_protocol: Scanned using GeneChip Scanner 3000. The images were analyzed using Command Console and comparison analyses were carried out according to the instructions provided by Affymetrix.

data_processing: CEL files were processed in Bioconductor using the xps package. Expression data was summarized at the transcript level and normalized using RMA. Log2 transformation was applied to the expression data.

source_name: c-kit lineage negative cells derived from C57BL/6 mouse bone marrow at 48 hours. Treated with CsA.

label_protocol: ssDNA was prepared, fragmented and belled according to the Affymetrix protocol.

growth_protocol: lineage negative, cKIT positive progenitors were cultured in  IMDM (containing 200ng/ml mrFLT3-L (Stem cells), 10% heat-inactivated FCS (Life Technologies), streptomycin 100mg/ml and penicillin 100 U/ml) at 3x106 cells/ml. For culture of sorted progenitors, stem cell factor (SCF; 50ng/ml), IL-6 (20ng/ml) and IL-3 (10ng/ml; all R&D Systems) were added (referred to as HSC medium).

extract_protocol: Total  RNA  was  extracted  following  the  double  extraction  protocol:  RNA  isolation  by  acid guanidinium thiocyanate-phenol-chloroform extraction (Trizolitrogen) followed by a Qiagen RNeasy  clean-up  procedure.  RNA  purity  was  assessed  by  spectrophotometer  (Nanodrop):  260/280 and 260/230 ratios were evaluated.  If the 260/280 and 260/230 ratios are < of 1.8, RNA samples are ethanol precipitated. Total RNA integrity was assessed by Agilent Bioanalyzer and the  RNA  Integrity  Number  (RIN)  was  calculated  and  RIN  greater  than  9,  were  used  for microarray analysis.

treatment_protocol: 2µg/ml CsA or 0.2µg/ml FK506 (Cell signalling Technology) were added to the cell culture for 30 mins preceding the addition of Flt3-L were maintained throughout the culture.

tag: strain


title: ZS11-3


title: Wild type mouse, Starved (S3)


title: Peripheral blood mononuclear cells, down syndrome, biological rep. 4, technical rep. 2 [CD19R]

description: down syndrome


title: miR-34a tranfected UM-SCC-23  VS Control UM-SCC-23

first: YU

last: WANG

address: No.237 Luoyu Road

institute: Wuhan University

description: Lentivector clone pCDH-CMV-MCS-EF1-eGFP  and  Lenti‐miR‐34a was purchased by SBI. To make lentivirus, co-transfected the packaging mix and the lentivector clone using lipo2000 into 293t cell lines. Wait 48 hours, collect the supernatant and concentrate. Combine the virus with um-scc-23 cells repectively.Stable cell lines,um-scc-23 , transfected with  pCDH-CMV-MCS-EF1-eGFP-34a or pCDH-CMV-MCS-EF1-eGFP was obtained.

hyb_protocol: Cy5-dCTP for test samples and Cy3-dCTP for CONTROL samples labeled double-stranded cDNA dissolved in 80μl hybridization solution containing 3×SSC, 0.2%SDS, 5×Denhart’s, and 25% formamide. The slides were covered with a LifterSlip™ coverslip (Erie Company, Portsmouth, NH, USA) and hybridized in chamber at 42℃ for over night. After hybridization, slides were washed three times in 0.2% SDS, 2x SSC at 42℃ for 5 minutes and three times in 0.2 x SSC at room temperature for 5 minutes before signal scanning.

scan_protocol: the 22K Human Genome Array fluorescence intensities of Cy3 and Cy5 dyes at each spot were scanned and quantified by double tunnel laser scanning LuxScan 10KA (CapitalBio)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

source_name: Larynx squamous cell carcinoma transfected with pCDH-CMV-MCS-EF1-eGFP-miR-34a

label_protocol: 5µg of total RNA were primed with 1 µl of 100 µM primer containing T7 RNA polymerase promoter sequence at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U CbcScript (CapitalBio Corp, China), and synthesis of the second strand of cDNA at 16°C for 2 h in the presence of RNaseH and DNA Polymerase. cRNA was synthesized by T7 Enzyme Mix (CapitalBio Corp, China) with the template of cDNA. 2 µl of cRNA were primed with 1 µl random primer at 65°C for 10 min, then reversed transcribed at 25°C for 10 min and 37°C for 1.5h in the presence of CbcScript II (CapitalBio Corp, China). The Cy3- and Cy5-dCTP double-stranded cDNA was labeled using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China). And, Cy5-dCTP or Cy3-dCTP were added at a final concentration of 120µM each dATP, dGTP, and dTTP and 60µM dCTP and 40µM Cy5-dCTP for test samples (or Cy3-dCTP for reference samples), respectively.

growth_protocol: fadu and um-scc-23 cells were cultured in DMEM (high glucose) medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100ug/ml streptomycin in a humidified atmosphere of 5% CO2.

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

treatment_protocol: Cells were transfected with pCDH-CMV-MCS-EF1-eGFP  or Lenti‐miR‐34a via Packaging Lentivirus .The stable cell lines were selected by FCM after 96h post-transfection.

tag: cell lines

value: Larynx squamous cell carcinoma

tag: transfection construct

value: Lenti -pCDH-CMV-MCS-EF1-eGFP‐miR‐34a


title: M1447-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 48 hours. Untreated. Replicate 3.

source_name: c-kit lineage negative cells derived from C57BL/6 mouse bone marrow at 48 hours. Untreated.

value: lineage negative, cKIT positive progenitors


title: miR-34a tranfected FADU VS Control FADU

description: Lentivector clone pCDH-CMV-MCS-EF1-eGFP  and  Lenti‐miR‐34a was purchased by SBI. To make lentivirus, co-transfected the packaging mix and the lentivector clone using lipo2000 into 293t cell lines. Wait 48 hours, collect the supernatant and concentrate. Combine the virus with FADU  cells repectively.Stable cell lines,Fadu ,transfected with pCDH-CMV-MCS-EF1-eGFP-miR-34a or  pCDH-CMV-MCS-EF1-eGFP was obtained.

source_name: Oropharyngeal squamous cell carcinoma transfected with pCDH-CMV-MCS-EF1-eGFP-miR-34a

value: Fadu

value: Oropharyngeal squamous cell carcinoma


title: M1445-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 24 hours. Treated with CsA. Replicate 3.

source_name: c-kit lineage negative cells derived from C57BL/6 mouse bone marrow at 24 hours. Treated with CsA.


title: M1449-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 48 hours. Treated with FK506. Replicate 3.

source_name: c-kit lineage negative cells derived from C57BL/6 mouse bone marrow at 48 hours. Treated with FK506.


title: M1446-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 24 hours. Treated with FK506. Replicate 3.

source_name: c-kit lineage negative cells derived from C57BL/6 mouse bone marrow at 24 hours. Treated with FK506.


title: PAXGene blood healthy person H4

description: PAXGene blood healthy person H4


title: Peripheral blood mononuclear cells, down syndrome, biological rep. 3, technical rep. 2 [CD16-1R]

description: down syndrome

value: male


title: Peripheral blood mononuclear cells, down syndrome, biological rep. 3, technical rep. 1 [CD16-1]

description: down syndrome


title: PAXGene blood healthy person H5

description: PAXGene blood healthy person H5


title: M1444-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 24 hours. Untreated. Replicate 3.

source_name: c-kit lineage negative cells derived from C57BL/6 mouse bone marrow at 24 hours. Untreated.


title: Peripheral blood mononuclear cells, down syndrome, biological rep. 2, technical rep. 2 [CD15-2R]

description: down syndrome


title: Peripheral blood mononuclear cells, down syndrome, biological rep. 1, technical rep. 2 [CD11R]

description: down syndrome


title: Peripheral blood mononuclear cells, down syndrome, biological rep. 2, technical rep. 1 [CD15-2]

description: down syndrome


title: PAXGene blood healthy person H2

description: PAXGene blood healthy person H2


title: PAXGene blood healthy person H3

description: PAXGene blood healthy person H3


title: Peripheral blood mononuclear cells, control, biological rep. 6, technical rep. 2 [CC5R]

description: control


title: PAXGene blood lung cancer patient L10

description: PAXGene blood lung cancer patient L10


title: PAXGene blood healthy person H1

description: PAXGene blood healthy person H1


title: M1443-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 0 hours. Untreated. Replicate 3.

source_name: c-kit lineage negative cells derived from C57BL/6 mouse bone marrow at 0 hours. Untreated.


title: M1442-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 48 hours. Treated with FK506. Replicate 2.


title: HK vs KK, biolrep 1, techrep 2 dyeswap

city: Budapest

first: Endre

last: Sebestyén

address: Üllői út 26.

department: 1st Department of Pathology and Experimental Cancer Research

country: Hungary

institute: Semmelweis University

hyb_protocol: The cRNA of two biological replicates labeled with Cy3 or Cy5 (dye-swap) were hybridized to the Agilent 4X44K Barley Chip.

scan_protocol: Scanning was performed, using an Agilent High-Resolution Microarray Scanner. The detection of signal intensities and the grid adjustment were accomplished with the Agilent Feature Extraction Software.

data_processing: Intensity data were imported into the R 2.12.0 statistical programming language. Further analysis was carried out using the LIMMA package of BIOCONDUCTOR. Background correction was done using the normexp method. Normalization of data within arrays was done using the loess method, and to normalize the data between arrays, the quantile method was used. The duplicateCorrelation method of LIMMA was used for correcting the correlation between biological samples. The scripts used for data processing can be found here: https://github.com/razZ0r/hvcold

organism: Hordeum vulgare

source_name: barley, cold, no inhibitor

label_protocol: The RNA amplification and labeling procedure was done according to the manufacturer’s recommendations (Agilent).

growth_protocol: Seeds were germinated on sterile filter paper soaked in MQ water. Seedlings were grown under control conditions (20/20 °C (day/night), irraditaion: 16 hours per day, 208 μE/m2/s, 75 % RH) for 3 days.

extract_protocol: Two biological replicates with three technical replicates (each replicate consisted of five plants) were harvested. RNA was isolated using TRIzol reagent (Invitrogen) and the samples were DNase I treated and cleaned up with MinElute Kit (Qiagen) according to the manufacturer’s instructions. The RNA Integrity Number (RIN) of the samples was determined using the Agilent BioAnalyzer, and, equal amounts of RNA from the four technical replicates were pooled and used for cRNA amplification.

treatment_protocol: 3-day-old seedlings were pretreated with one of the following solutions: MQ water / Lanthanium (1 mM) / EGTA (10 mM) / mastoparan (10 μM) for 24 hours. Then half part of the plant population of each pretreatment group was placed in cold room (4/4 °C (day/night), irraditaion: 16 hours per day, 208 μE/m2/s, 75 % RH) for 24 hours. The other part of the populations remained under control conditions. Sampling was carried out at 24 hours after the beginning of cold treatment.

tag: cultivar

value: Nure

tag: inhibitor

tag: temperature

value: cold (4°C)

value: lower part (~1.5 cm) of the stem (hypocotyl and cotyledons)

value: 4 d

source_name: barley, normal temp, no inhibitor

value: normal


title: KK vs HK, biolrep 2, techrep 1


title: M1440-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 48 hours. Untreated. Replicate 2.


title: KK vs HK, biolrep 1, techrep 1


title: HK vs KK, biolrep 2, techrep 2 dyeswap


title: HK vs HM, biolrep 2, techrep 1

source_name: barley, cold, mastoparan

value: mastoparan


title: Peripheral blood mononuclear cells, down syndrome, biological rep. 1, technical rep. 1 [CD11]

description: down syndrome


title: PAXGene blood lung cancer patient L11

description: PAXGene blood lung cancer patient L11

value: Lung adenocarcinoma


title: Peripheral blood mononuclear cells, control, biological rep. 6, technical rep. 1 [CC5]

description: control


title: M1437-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 24 hours. Untreated. Replicate 2.


title: PAXGene blood lung cancer patient L6

description: PAXGene blood lung cancer patient L6


title: M1439-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 24 hours. Treated with FK506. Replicate 2.


title: KLa vs HLa, biolrep 2, techrep 1

source_name: barley, normal temp, lanthanum

value: lantanum

source_name: barley, cold, lantanum


title: HM vs HK, biolrep 2, techrep 2 dyeswap


title: PAXGene blood lung cancer patient L5

description: PAXGene blood lung cancer patient L5

value: small cell lung carcinoma

value: whole blood


title: M1436-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 0 hours. Untreated. Replicate 2.


title: Peripheral blood mononuclear cells, control, biological rep. 5, technical rep. 1 [CC21]

description: control


title: Peripheral blood mononuclear cells, control, biological rep. 5, technical rep. 2 [CC21R]

description: control


title: HK vs HM, biolrep 1, techrep 1


title: Peripheral blood mononuclear cells, control, biological rep. 4, technical rep. 2 [CC18R]

description: control

value: female


title: M1438-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 24 hours. Treated with CsA. Replicate 2.


title: PAXGene blood lung cancer patient L3

description: PAXGene blood lung cancer patient L3

value: squamous cell carcinoma


title: HLa vs KLa, biolrep 1, techrep 2 dyeswap


title: M1441-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 48 hours. Treated with CsA. Replicate 2.


title: Peripheral blood mononuclear cells, control, biological rep. 4, technical rep. 1 [CC18]

description: control


title: KLa vs HLa, biolrep 1, techrep 1


title: M1428-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 48 hours. Treated with FK506. Replicate 1.


title: PAXGene blood lung cancer patient L4

description: PAXGene blood lung cancer patient L4


title: M1425-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 24 hours. Treated with FK506. Replicate 1.


title: M1427-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 48 hours. Treated with CsA. Replicate 1.


title: KK vs KM, biolrep 2, techrep 1

source_name: barley, normal temp, mastoparan


title: Peripheral blood mononuclear cells, control, biological rep. 3, technical rep. 1 [CC17]

description: control


title: HM vs HK, biolrep 1, techrep 2 dyeswap


title: KM vs KK, biolrep 1, techrep 2 dyeswap


title: M1426-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 48 hours. Untreated. Replicate 1.


title: meningioma H659 rep1

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

description: using miRNA Complete Labeling and Hyb Kit (Agilent, Cat. No 5190-0456),  Cyanine 3-pcp

hyb_protocol: The expression profile of 1205 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations

scan_protocol: Array´s were scanned with the Agilent Scanner with default settings.

data_processing: Raw expression values were extracted using the Feature Extraction Software of Agilent. Raw signal intensities were quantile normalized for every comparison using only the relevant samples for the respective comparison: 1) Meningothelial vs Fibroblastic, 2) Meningothelial vs Transitional, 3) Fibroblastic vs Transitional, 4) Meningothelial vs WHO II, 5) Meningothelial vs WHO III, 6) Transitional vs WHO II, 7) Transitional vs WHO III, 8) Fibroblastic vs WHO II,   9) Fibroblastic vs WHO III,  10) WHO I vs WHO II, 11) WHO I vs WHO III,  12) WHO I vs WHO II+III, 13) WHO II vs WHO III

source_name: tumor tissue

extract_protocol: Total RNA including miRNAs was isolated using theQiagen miRNeasy Kit according to manufacturers recommendations.  RNA concentration was measured using NanoDrop2000 (ThermoScientific). RNA integrity was measured using the PicoRNA kit (Agilent) on a Bioanalyzer2100.

value: m

tag: who grade

value: WHO I

tag: histological subtype

value: fibroblastic meningioma


title: meningioma H2374 rep1

label_protocol: The expression profile of 1205 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations

value: f

value: WHO II

value: atypical meningioma


title: meningioma H2313 rep1

value: meningothelial meningioma


title: Peripheral blood mononuclear cells, control, biological rep. 2, technical rep. 2 [CC11R]

description: control

source_name: Peripheral blood mononuclear cells


title: KM vs KK, biolrep 2, techrep 2 dyeswap

value: Nure

value: lower part (~1.5 cm) of the stem (hypocotyl and cotyledons)


title: M1424-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 24 hours. Treated with CsA. Replicate 1.

value: lineage negative, cKIT positive progenitors


title: Peripheral blood mononuclear cells, control, biological rep. 2, technical rep. 1 [CC11]

description: control


title: meningioma H288 rep1

value: WHO III

value: anaplastic meningioma


title: M1423-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 24 hours. Untreated. Replicate 1.


title: KE vs KK, biolrep 1, techrep 2 dyeswap

source_name: barley, normal temp, EGTA

value: EGTA

value: normal

value: 4 d


title: KK vs KE, biolrep 2, techrep 1


title: KE vs KK, biolrep 2, techrep 2 dyeswap


title: KK vs KE, biolrep 1, techrep 1


title: Peripheral blood mononuclear cells, control, biological rep. 1, technical rep. 2 [CC10R]

description: control

value: male


title: Peripheral blood mononuclear cells, control, biological rep. 3, technical rep. 2 [CC17R]

description: control

value: female


title: meningioma H340 rep1

value: transitional meningioma


title: meningioma H2416 rep1

value: m

value: WHO I


title: meningioma H597 rep1

value: f


title: KK vs KM, biolrep 1, techrep 1

value: mastoparan


title: Peripheral blood mononuclear cells, control, biological rep. 1, technical rep. 1 [CC10]

description: control


title: meningioma H1904 rep1

value: fibroblastic meningioma


title: KLa vs KK, biolrep 2, techrep 2 dyeswap

value: lanthanum


title: meningioma H2395 rep1

value: WHO II

value: atypical meningioma


title: M1422-11

description: Bone marrow from C57BL/6 mouse will be depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit at time 0 hours. Untreated. Replicate 1.

value: lineage negative, cKIT positive progenitors


title: Thrombomodulin- DC TM treated sorted expt 4 biological rep2

city: Stanford

first: John

last: Morser

address: 269 Campus Drive

department: Hematology

institute: Stanford University

hyb_protocol: Used Affymetrix protocol  FS450-007

scan_protocol: Affymetrix Genechip Scanner 3000 7G

data_processing: The data were processed by  Affymetrix Genechip Command Console software with Affymetrix default analysis settings and RMA as normalization method.

source_name: TM- dendritic cells TM treated sorted

label_protocol: Affymetrix GeneChip ® Whole Transcript (WT) Sense Target Labeling

growth_protocol: Bone marrow cells isolated from Balb/c mice were differentiated into dendritic cells in the presence of 100 ng/ml GM-CSF (Takagi T, Taguchi O, Toda M, Ruiz DB, Bernabe PG, et al. (2011)  Am J Respir Crit Care Med 183: 31-42).  On day 6, DCs RNA was extracted from DCs. In some experiments TM+ and TM- dendritic cells were isolated by MACS before RNA isolation.  Populations were >93% pure.

extract_protocol: RNeasy from Qiagen according to manufacturer's instructions

treatment_protocol: Some samples were treated with 200 nM soluble human TM (Asahi) on day 4, before isolation of TM+ and TM- DCs on day 6.

tag: strain background

value: Balb/c

value: bone marrow derived dendritic cell


title: KK vs KLa, biolrep 1, techrep 1

value: Nure

value: lower part (~1.5 cm) of the stem (hypocotyl and cotyledons)


title: Thrombomodulin+ DC untreated sorted expt 4 biological rep2

source_name: TM+ dendritic cells control sorted


title: meningioma H444 rep1


title: PAXGene blood lung cancer patient L2

description: PAXGene blood lung cancer patient L2

source_name: whole blood

value: Lung adenocarcinoma

value: whole blood


title: Thrombomodulin+ DC TM treated sorted expt 4 biological rep2

source_name: TM+ dendritic cells TM treated sorted


title: Thrombomodulin- DC untreated sorted expt 4 biological rep2

source_name: TM- dendritic cells control sorted


title: meningioma H108 rep1

value: WHO III

value: anaplastic meningioma


title: Thrombomodulin- DC TM treated sorted expt 4 biological rep1


title: Thrombomodulin+ DC TM treated sorted expt 4 biological rep1


title: ShootApicalMeristem_9weeks_4°C_rep1 Beta_vulgaris_5

city: Reims

first: Claire

last: Hébrard

address: Camus Moulin de la Housse

country: France

institute: Unité de Recherche Vigne et Vins de Champagne

description: Gene expression after 9 weeks of vernalization (4°C)

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Beta vulgaris Oligo Microarrays (custom) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 033486_D_F_20110407) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Beta vulgaris

source_name: Shoot Apical Meristem, 9 weeks, 4°C

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling Kit, One color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Six biennial sugar beet genotypes (Beta vulgaris altissima) were germinated and grown during eight weeks at 22°C under a 16 h photoperiod (700 μM m-2 s-1).

extract_protocol: RNA was prepared using using Nucleospin® RNA Plant (Macherey-Nagel, Hoerdt, France) following the manufacturer's recommendations. The protocol includes lysis of plant tissues, and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Eight-weeks old sugar beet plantlets were placed during nine weeks at 4°C to mimic the vernalization process. Shoot apices were collected immediately after cold treatment, and differentiated tissues removed to isolate the shoot apical meristem, which was frozen in liquid nitrogen and stored at -80°C.

tag: genotype

value: shoot apical meristem

tag: capacity to bolt

value: high (=bolting sensitive)


title: ShootApicalMeristem_9weeks_4°C_rep1 Beta_vulgaris_7

tag: tissue

value: low (=bolting resistant)


title: meningioma H2382 rep1

tag: gender

value: m


title: meningioma H2358 rep1

tag: age

value: f

value: WHO I

value: meningothelial meningioma


title: KLa vs KK, biolrep 1, techrep 2 dyeswap

value: lanthanum

value: normal

value: 4 d


title: ShootApicalMeristem_9weeks_4°C_rep1 Beta_vulgaris_3


title: Thrombomodulin+ DC TM treated sorted expt 3 biological rep2

value: Balb/c

tag: cell type

value: bone marrow derived dendritic cell


title: Thrombomodulin- DC untreated sorted expt 4 biological rep1


title: VSMC SA001 day13 batch co_c

city: Basel

first: Tobias

last: Heckel

address: Grenzacherstr. 124

department: pRED

country: Switzerland

institute: Roche

description: VSMCs in vitro differentiated from HESC SA001 depleted with CD144 Microbeads and an autoMACSpro (Miltenyi Biotec) and cultivated in VSMC Expansion Medium on collagen coated wells (Biocoat, BD Bioscience). Total cultivation time starting from HESC plating is 13 days (day 13). It is the thrid of three wild-type  replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed following the standard operating protocol of NimbleGen Systems Inc., Madison, WI USA. See www.nimblegen.com.

scan_protocol: Scanning was performed on a NimbleGen MS200 Microarray Scanner at 2 μm pixel resolution following the standard operating protocol of NimbleGen Systems Inc., Madison, WI USA. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to background correction, quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.).

source_name: Human Embryonic Stem Cell line SA001 from Cellartis AB differentiated into Vascular Smooth Muscle Cells; batch co_c

label_protocol: Labeling was performed using 5 ug of total RNA input following the standard operating protocol of NimbleGen Systems Inc., Madison, WI USA. See www.nimblegen.com.

growth_protocol:
Primary endothelial and vascular smooth muscle cells were cultured at 37°C, 5% CO2 and 95% humidity in EGM2 medium (Lonza) until they reached a confluency of maximal 80%.
The Human Embryonic Stem Cell line SA001 (Cellartis AB) was cultured in Priming Medium, consisting N2B27 medium (1:1 mixture of DMEM:F12 (1:1) with Glutamax (Invitrogen) and Neurobasal media supplemented with N2 and B27 (all Invitrogen)) with 1 μM CP21R7 (Roche) and 25 ng/ml BMP4 (R&D Systems)
For differentiation into VSMCs, Human Embryonic Stem Cell line SA001 was cultured in VSMC Induction Medium consisting of N2B27 medium supplemented with 10ng/ml PDGF-BB and 2ng/ml Activin
For differentiation into VSMCs, Human Embryonic Stem Cell line SA001 was cultured in VSMC Expansion Medium consisting of  N2B27 with 2ug/ml Heparin and 2ng/ml ActivinA
For differentiation into ECs, Human Embryonic Stem Cell line SA001 was cultured in EC Induction Medium consisting of StemPro-34 SFM medium (Invitrogen) supplemented with 200ng/ml VEGF (PeproTech) and 2μM Forskolin (Sigma-Aldrich)
For differentiation into ECs, Human Embryonic Stem Cell line SA001 was cultured in EC Expansion Medium consisting of StemPro-34 SFM supplemented with 50 ng/ml VEGF

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) . DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA).

treatment_protocol: cells were flash frozen and stored at -80°C until RNA extraction

tag: phenotype


title: Thrombomodulin- DC TM treated sorted expt 3 biological rep2


title: ShootApicalMeristem_9weeks_4°C_rep1 Beta_vulgaris_4


title: ShootApicalMeristem_9weeks_4°C_rep1 Beta_vulgaris_2


title: ShootApicalMeristem_9weeks_4°C_rep1 Beta_vulgaris_1


title: meningioma H2460 rep1


title: VSMC SA001 day13 batch co_b

description: VSMCs in vitro differentiated from HESC SA001 depleted with CD144 Microbeads and an autoMACSpro (Miltenyi Biotec) and cultivated in VSMC Expansion Medium on collagen coated wells (Biocoat, BD Bioscience). Total cultivation time starting from HESC plating is 13 days (day 13). It is the second of three wild-type  replicates used in this experiment, each from separate cultures.

source_name: Human Embryonic Stem Cell line SA001 from Cellartis AB differentiated into Vascular Smooth Muscle Cells; batch co_b


title: VSMC SA001 day6 batch c

description: VSMCs in vitro differentiated from HESC SA001 depleted with CD144 Microbeads and an autoMACSpro (Miltenyi Biotec) and cultivated in VSMC Induction Medium on gelatin coated wells. Total cultivation time starting from HESC plating is 6 days (day 6). It is the third of three wild-type replicates used in this experiment, each from separate cultures.

source_name: Human Embryonic Stem Cell line SA001 from Cellartis AB differentiated into Vascular Smooth Muscle Cells; batch c


title: meningioma H841 rep1

value: transitional meningioma


title: meningioma H470 rep1


title: meningioma H695 rep1

value: fibroblastic meningioma


title: ShootApicalMeristem_9weeks_4°C_genotype5

type: genomic

description: Shoot Apical Meristem, 9 weeks, 4°C, genotype 5

hyb_protocol: DNA hybridization was conducted following Agilent Technologies instructions. Briefly, Cy5- and Cy3-labeled DNAs were pooled in ddH2O before addition of Hybridization mix (Agilent Technologies), incubation at 95°C for 3 min and then at 37°C for 30 min. Samples were loaded onto the arrays (1x244K) and hybridized at 67°C for 40 hours at 20 rpm in Agilent hybridization chambers. Arrays were then washed according to the protocol at room temperature.

scan_protocol: Microarray slides were scanned with G2505C scanner (Agilent Technologies) Raw signal data were extracted using Feature Extraction 10.7 software. Reproducibility and reliability of each single microarray was assessed using Quality Control report data (Feature Extraction, Agilent Technologies).

data_processing: Data normalization, performed by Feature Extraction software, was used to correct cyanine bias with the linear method: the mean signal of probes selected for quality criteria (signal above background, non-outlier and whose ranks are similar between the two dyes) allowed the normalization of all probes values. For each probe, Cy5/Cy3 log ratio was then calculated. Data filtering was based on Feature Extraction flag criteria: non outlier population; not saturated, uniform and significant Cy3 and Cy5 probe signal; Cy3 and Cy5 probe signal above background. A probe signal was considered as “well above background” if g/rBGSubSignal was greater than 2.6 g/rBG_SD. To pass the filtering, a probe needed to pass all flag criteria for all replicates of at least one experimental condition (bolting resistant or bolting sensitive).

molecule: genomic DNA

organism: Beta vulgaris subsp. vulgaris

label_protocol: For each sample, labeled DNA was generated according to Agilent Technologies recommendations. Briefly, approximately 500 ng of input control and immunoprecipitated (IP) methylated DNA were labeled using Genomic DNA Enzymatic Labeling Kit (Agilent Technologies). The use of random primers and the exo-Klenow fragment allowed the differential labeling of input control and IP methylated DNA with cyanine 3-labeled dUTP and cyanine 5-labeled dUTP respectively. Labeled DNA was purified using 30 kDa Amicon columns (Millipore, Molsheim, France). Quality control of synthesized labeled DNA was based on DNA and Cy5/Cy3 concentration measurement. For each sample, a yield of 2.5 µg of labeled DNA and a specific activity of 7-20 pmolCy5/gDNA and 18-25 pmolCy3/gDNA were chosen as quality minimum thresholds.

growth_protocol: Six biennial sugar beet genotypes (Beta vulgaris altissima) were germinated and grown during eight weeks at 22°C under a 16 h photoperiod (700 μM m-2 s-1).  Eight-weeks old sugar beet plantlets were then placed during nine weeks at 4°C to mimic the vernalization process. Shoot apices were collected immediately after cold treatment, and differentiated tissues removed to isolate the shoot apical meristem, which was frozen in liquid nitrogen and stored at -80°C.

extract_protocol: DNA was extracted using Plant DNAzol Reagent (InVitrogen, Cergy-Pontoise, France) according to the manufacturer’s recommendations. To avoid RNA contamination, 100 µg RNase A/mL Plant DNAzol was added at the beginning of the isolation procedure. DNA was precipitated at -20°C during at least 30 min using 96% ethanol (2.5v) and 3M Na-Acetate (pH 5.2, 0.1v). DNA were then washed using 70% ethanol, vacuum dried and solubilized in ultrapure water. Concentrations and purity of DNA were estimated using NanoDrop 1000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). DNA was sonicated using a VC 505 Vibra-Cell sonicator (Fisher Scientific, Illkirch, France) to obtain fragments ranging from 0.2 to 0.8 kb. Methylated DNA was immunoprecipitated according to Weng et al. (2009). Briefly, 11 µg of sonicated DNA were diluted in 250 µL of IP buffer 1X composed of 10 mM Na3PO4 (pH 7.0), 140 mM NaCl, 0.05% Triton X-100 and denaturated during 10 min in boiling water. After 10 min of ice cooling, 4 µg of DNA were kept at -20°C to be used as input control for microarray analysis. The 7 µg of DNA left were incubated overnight with 10 µg of mouse monoclonal anti-5mC antibodies (Eurogentec, Angers, France) on a rotator in a 4°C cold room. The DNA-antibodies mixture was coupled with Dynabeads Protein G (InVitrogen) during 2 hours at 4°C. Beads were washed 4 times with IP Buffer 1X using a magnetic rack (Invitrogen). Methylated DNA was eluted by digesting antibodies overnight with 100 µg of Proteinase K (Sigma-Aldrich, Saint-Quentin Fallavier, France) in 250 µL of a digestion buffer composed of 50 mM Tris (pH 8.0), 10 mM EDTA pH 8.0, 0.5% SDS at 50°C on a rotator. DNA was isolated with 1 phenol/chloroform/isoamyl alcohol (25:24:1) (v/v/v) and 2 chloroform/isoamyl alcohol (24:1) (v/v) extractions using phase lock gel heavy tubes (Eppendorf, Le Pecq, France) and ethanol precipitation. DNA pellets were solubilized in ultrapure water and concentrations were estimated using NanoDrop 1000 spectrophotometer (Thermo Scientific).

tag: fraction

value: Methylated DNA

source_name: Shoot Apical Meristem, 9 weeks, 4°C, replicate 1

value: input


title: KK vs KLa, biolrep 2, techrep 1

source_name: barley, normal temp, no inhibitor

value: Nure

value: lower part (~1.5 cm) of the stem (hypocotyl and cotyledons)


title: meningioma H83 rep1

value: WHO III

value: anaplastic meningioma


title: ShootApicalMeristem_9weeks_4°C_genotype7

description: Shoot Apical Meristem, 9 weeks, 4°C, genotype 7

value: shoot apical meristem

value: low (=bolting resistant)


title: VSMC SA001 day13 batch co_a

description: VSMCs in vitro differentiated from HESC SA001 depleted with CD144 Microbeads and an autoMACSpro (Miltenyi Biotec) and cultivated in VSMC Expansion Medium on collagen coated wells (Biocoat, BD Bioscience). Total cultivation time starting from HESC plating is 13 days (day 13). It is the first of three wild-type replicates used in this experiment, each from separate cultures.

source_name: Human Embryonic Stem Cell line SA001 from Cellartis AB differentiated into Vascular Smooth Muscle Cells; batch co_a


title: Thrombomodulin- DC untreated sorted expt 3 biological rep2


title: meningioma H2463 rep1

value: m

value: WHO I


title: DC TM treated unsorted expt 3 biological rep2

source_name: dendritic cells TM treated


title: DC untreated unsorted expt 3 biological rep2

source_name: dendritic cells control


title: VSMC SA001 day6 batch a

description: VSMCs in vitro differentiated from HESC SA001 depleted with CD144 Microbeads and an autoMACSpro (Miltenyi Biotec) and cultivated in VSMC Induction Medium on gelatin coated wells. Total cultivation time starting from HESC plating is 6 days (day 6). It is the first of three wild-type replicates used in this experiment, each from separate cultures.

source_name: Human Embryonic Stem Cell line SA001 from Cellartis AB differentiated into Vascular Smooth Muscle Cells; batch a


title: meningioma H442 rep1

source_name: tumor tissue

value: f


title: EC SA001 day14 batch 2.0

description: ECs in vitro differentiated from HESC SA001 enriched with CD144 Microbeads and an autoMACSpro (Miltenyi Biotec) and cultivated in EC Expansion Medium on human fibronectin (Sigma-Aldrich). Total cultivation time starting from HESC plating is 14 days (day 14). It is the third of three wild-type replicates used in this experiment, each from separate cultures.

source_name: Human Embryonic Stem Cell line SA001 from Cellartis AB differentiated into Endothelial Cells; batch 2.0


title: ShootApicalMeristem_9weeks_4°C_genotype3

description: Shoot Apical Meristem, 9 weeks, 4°C, genotype 3

value: high (=bolting sensitive)


title: Thrombomodulin+ DC TM treated sorted expt 3 biological rep1


title: EC SA001 day14 batch 1.8

description: ECs in vitro differentiated from HESC SA001 enriched with CD144 Microbeads and an autoMACSpro (Miltenyi Biotec) and cultivated in EC Expansion Medium on human fibronectin (Sigma-Aldrich). Total cultivation time starting from HESC plating is 14 days (day 14). It is the second of three wild-type replicates used in this experiment, each from separate cultures.

source_name: Human Embryonic Stem Cell line SA001 from Cellartis AB differentiated into Endothelial Cells; batch 1.8


title: Thrombomodulin+ DC untreated sorted expt 3 biological rep2

source_name: TM+ dendritic cells control sorted


title: Thrombomodulin+ DC untreated sorted expt 3 biological rep1


title: Thrombomodulin+ DC untreated sorted expt 4 biological rep1


title: meningioma H987 rep1


title: VSMC SA001 day6 batch b

description: VSMCs in vitro differentiated from HESC SA001 depleted with CD144 Microbeads and an autoMACSpro (Miltenyi Biotec) and cultivated in VSMC Induction Medium on gelatin coated wells. Total cultivation time starting from HESC plating is 6 days (day 6). It is the second of three wild-type replicates used in this experiment, each from separate cultures.

source_name: Human Embryonic Stem Cell line SA001 from Cellartis AB differentiated into Vascular Smooth Muscle Cells; batch b


title: ShootApicalMeristem_9weeks_4°C_genotype1

description: Shoot Apical Meristem, 9 weeks, 4°C, genotype 1


title: EC SA001 day10

description: ECs in vitro differentiated from HESC SA001 enriched with CD144 Microbeads and an autoMACSpro (Miltenyi Biotec) and cultivated in EC Expansion Medium on human fibronectin (Sigma-Aldrich). Total cultivation time starting from HESC plating is 10 days (day 10)

source_name: Human Embryonic Stem Cell line SA001 from Cellartis AB differentiated into Endothelial Cells


title: Thrombomodulin- DC TM treated sorted expt 3 biological rep1

source_name: TM- dendritic cells TM treated sorted


title: meningioma H2385 rep1

description: using miRNA Complete Labeling and Hyb Kit (Agilent, Cat. No 5190-0456),  Cyanine 3-pcp

value: WHO II

value: atypical meningioma


title: meningioma H1044 rep1


title: ShootApicalMeristem_9weeks_4°C_genotype4

description: Shoot Apical Meristem, 9 weeks, 4°C, genotype 4


title: EC SA001 day14 batch 1.7

description: ECs in vitro differentiated from HESC SA001 enriched with CD144 Microbeads and an autoMACSpro (Miltenyi Biotec) and cultivated in EC Expansion Medium on human fibronectin (Sigma-Aldrich). Total cultivation time starting from HESC plating is 14 days (day 14). It is the first of three wild-type replicates used in this experiment, each from separate cultures.

source_name: Human Embryonic Stem Cell line SA001 from Cellartis AB differentiated into Endothelial Cells; batch 1.7


title: ShootApicalMeristem_9weeks_4°C_genotype2

description: Shoot Apical Meristem, 9 weeks, 4°C, genotype 2


title: meningioma H311 rep1


title: EC SA001 day5

description: ECs in vitro differentiated from HESC SA001 enriched with CD144 Microbeads and an autoMACSpro (Miltenyi Biotec) and cultivated in EC Induction Medium on human fibronectin (Sigma-Aldrich). Total cultivation time starting from HESC plating is 5 days (day 5)


title: Primary melanoma_201

city: Lund

first: Göran

last: Jönsson

address: Scheelevägen 8

country: Sweden

institute: Lund University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using cubic spline normalisation. Features present in <80% of assays were discarded (presence defined as detection p‐value < 0.01), leaving 12,379 features for further analysis. After log2 transformation, the data were adjusted for plate by median centering each feature to zero.Reporters with standard deviation (SD) across the replicates of at least 0.3 in at least 50% of the replicated samples were excluded (n=3,447). Replicate samples were merged by average. Missing values have been imputed by k‐nearest neighbor imputation (k=10), using the R package impute. Using principal componenet analysis (PCA) the variation of  PC1 and PC3 were removed since these were strongly associated with technical variables. Hence, the processed data represent log(2) values adjusted for technical variation.

source_name: Primary melanoma

label_protocol: Standard Illumina labelling protocol

extract_protocol: RNA was extractedusing the FFPE Roche kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: melanoma

tag: mutation status

value: Sporadic

tag: thickness

tag: histology

value: NM

tag: clark

tag: number of replicates


title: meningioma H2419 rep1

value: meningothelial meningioma


title: Primary melanoma_202


title: Primary melanoma_203


title: Primary melanoma_200


title: meningioma H800 rep1


title: Primary melanoma_199

value: LMM


title: meningioma H693 rep1

value: transitional meningioma


title: meningioma H149 rep1


title: HESC SA001 day4

description: This sample is of HESC after 4 days of cultivation with priming medium and the GSK3 inhibitor CP21R7 (1 μM) + BMP4 (25 ng/ml)  (day 4)

source_name: Human Embryonic Stem Cell line SA001 from Cellartis AB


title: HESC SA001 day3

description: This sample is of HESC after 3 days of cultivation with priming medium and the GSK3 inhibitor CP21R7 (1 μM) + BMP4 (25 ng/ml)  (day 3)


title: Primary melanoma_197

value: SSM


title: Primary melanoma_198


title: Primary melanoma_196


title: DC untreated unsorted expt 3 biological rep1

value: Balb/c

value: bone marrow derived dendritic cell


title: HESC SA001 day1

description: This sample is of HESC after 1 day of cultivation with Rho-kinase inhibitor Y-27632 (10 μM) (day 1)


title: Thrombomodulin+ DC TM treated sorted expt 2 biological rep2

source_name: TM+ dendritic cells TM treated sorted


title: HPVSMC Lonza

description: This sample is of HPVSMC from one biological replicate used in this experiment.

source_name: Normal -(PASMC) Human pulmonary artery vascular smooth muscle cells    (primary cells)

value: normal-HPVSMC


title: Thrombomodulin- DC TM treated sorted expt 2 biological rep2


title: Thrombomodulin+ DC TM treated sorted expt 2 biological rep1


title: HESC SA001

description: This sample is of HESC at the time point of plating the cells (day 0)

value: normal-HESC


title: DC untreated unsorted expt 2 biological rep2


title: DC TM treated unsorted expt 3 biological rep1


title: DC TM treated unsorted expt 2 biological rep2


title: meningioma H2400 rep1

value: m


title: meningioma H429 rep1

value: WHO I

value: fibroblastic meningioma


title: meningioma H2280 rep1

value: f


title: Primary melanoma_194


title: Primary melanoma_195


title: Primary melanoma_193

value: Mucosal


title: Thrombomodulin- DC TM treated sorted expt 2 biological rep1


title: HSVEC Lonza

description: This sample is of HSVEC from one biological replicate used in this experiment.

source_name: Normal -(HSVEC) Human adult saphenous vein endothelial cells    (primary cells)

value: normal-HSVEC


title: HAVSMC Lonza

description: This sample is of HAVSMC  from one biological replicate used in this experiment.

source_name: Normal -(AoSMC) Human Aortic vascular smooth muscle cells  (primary cells)

value: normal-HAVSMC


title: DC untreated unsorted expt 2 biological rep1


title: Primary melanoma_192

value: melanoma


title: DC TM treated unsorted expt 2 biological rep1

source_name: dendritic cells TM treated


title: HAEC Lonza batch B

description: This sample is of HAEC. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Normal -(HAEC) Human Aortic Endothelial Cells (batch B)    (primary cells)

value: normal-HAEC


title: meningioma H989 rep1


title: meningioma H294 rep1


title: meningioma H2441 rep1

value: meningothelial meningioma


title: Primary melanoma_190

value: Sporadic


title: meningioma H450 rep1

value: WHO III

value: anaplastic meningioma


title: meningioma H12 rep1


title: Primary melanoma_191


title: HAEC Lonza batch A

description: This sample is of HAEC. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Normal -(HAEC) Human Aortic Endothelial Cells (batch A: AE)    (primary cells)


title: Primary melanoma_188

value: SSM


title: DC TM treated unsorted expt 1 biological rep3

value: Balb/c

value: bone marrow derived dendritic cell


title: meningioma H2343 rep1

source_name: tumor tissue

value: WHO II

value: atypical meningioma


title: HE vs HK, biolrep 2, techrep 2 dyeswap

source_name: barley, cold, EGTA

tag: cultivar

value: Nure

tag: inhibitor

value: EGTA

tag: temperature

value: cold (4°C)

value: lower part (~1.5 cm) of the stem (hypocotyl and cotyledons)

value: 4 d

source_name: barley, cold, no inhibitor


title: HE vs HK, biolrep 1, techrep 2 dyeswap


title: meningioma H2347 rep1

value: m

tag: who grade

value: WHO I

tag: histological subtype

value: fibroblastic meningioma


title: HAEC Lonza batch R

description: This sample is of HAEC. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Normal -(HAEC) Human Aortic Endothelial Cells (batch RNCB)    (primary cells)

value: normal-HAEC


title: HK vs HE, biolrep 2, techrep 1


title: DC TM treated unsorted expt 1 biological rep4

tag: strain background


title: DC untreated unsorted expt 1 biological rep4

source_name: dendritic cells control


title: DC TM treated unsorted expt 1 biological rep1


title: DC untreated unsorted expt 1 biological rep3


title: HK vs HE, biolrep 1, techrep 1

tag: tissue


title: Primary melanoma_187

value: melanoma

value: Sporadic

value: LMM


title: HLa vs HK, biolrep 2, techrep 2 dyeswap

source_name: barley, cold, lantanum

value: lantanum


title: Primary melanoma_189

value: Mucosal


title: DC TM treated unsorted expt 1 biological rep2

value: Balb/c

value: bone marrow derived dendritic cell


title: DC untreated unsorted expt 1 biological rep2


title: Primary melanoma_184


title: HESC SA001 day2

description: This sample is of HESC after 2 days of cultivation with priming medium and the GSK3 inhibitor CP21R7 (1 μM) + BMP4 (25 ng/ml)  (day 2)


title: meningioma H1915 rep1

tag: gender

value: WHO III

value: anaplastic meningioma


title: meningioma H857 rep1

tag: age

value: transitional meningioma


title: Primary melanoma_185

value: NM


title: Primary melanoma_186


title: Primary melanoma_183

value: SSM


title: HK vs HLa, biolrep 1, techrep 1

value: Nure

value: cold (4°C)

value: lower part (~1.5 cm) of the stem (hypocotyl and cotyledons)

value: 4 d


title: HK vs HLa, biolrep 2, techrep 1


title: Primary melanoma_182


title: Primary melanoma_181


title: meningioma H2314 rep1

value: f

value: WHO I


title: HM vs KM, biolrep 2, techrep 2 dyeswap

source_name: barley, cold, mastoparan

value: mastoparan

source_name: barley, normal temp, mastoparan

value: normal


title: meningioma H480 rep1

value: meningothelial meningioma


title: Thrombomodulin- DC  untreated sorted expt 3 biological rep1

source_name: TM- dendritic cells control sorted

tag: cell type


title: Primary melanoma_180

source_name: Primary melanoma

value: melanoma

value: Sporadic


title: DC untreated unsorted expt 1 biological rep1

value: Balb/c

value: bone marrow derived dendritic cell


title: FGF21KO.T3_2

city: Houston

first: Paul

last: Webb

address: 6670 Bertner Ave

department: Genomic Medicine

institute: Houston Methodist Research Institute

description: replicate 2

data_processing: Unmodified microarray data obtained from GenomeStudio (Illumina) was background-subtracted and quantile-normalized using the lumi package within R

source_name: Mouse Liver

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

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 within the kit. RNA quality was assessed with an Agilent Bioanalyzer.

treatment_protocol: Vehicle (DMSO) or T3 ( 1 mg/kg body weigh) were administrated daily by oral gavage for 3 days

value: Male

value: liver

tag: genotype

tag: treatment

value: T3 3-day

tag: genetic background


title: FGF21KO.T3_3

description: replicate 3


title: FGF21KO.DMSO_4

description: replicate 4

value: DMSO 3-day


title: FGF21KO.T3_1

description: replicate 1


title: KM vs HM, biolrep 2, techrep 1

value: Nure


title: meningioma H1116 rep1

value: fibroblastic meningioma


title: FGF21KO.T3_4

description: replicate 4


title: meningioma H833 rep1

value: transitional meningioma


title: KM vs HM, biolrep 1, techrep 1

value: lower part (~1.5 cm) of the stem (hypocotyl and cotyledons)

value: 4 d

value: cold (4°C)


title: Primary melanoma_179

tag: mutation status

tag: thickness

value: NM


title: meningioma H2287 rep1

value: f

value: WHO II

value: atypical meningioma


title: meningioma H1179 rep1

value: WHO III

value: anaplastic meningioma


title: Primary melanoma_178

value: melanoma

value: Sporadic

tag: histology

tag: clark


title: meningioma H691 rep1

value: WHO I


title: meningioma H2399 rep1


title: meningioma H302 rep1


title: HE vs KE, biolrep 1, techrep 2 dyeswap

tag: cultivar

value: EGTA

source_name: barley, normal temp, EGTA

value: normal


title: meningioma H1021 rep1

value: m


title: Primary melanoma_177

value: SSM

tag: number of replicates


title: HM vs KM, biolrep 1, techrep 2 dyeswap

value: Nure

tag: inhibitor

value: mastoparan

tag: temperature


title: WT.T3_4

description: replicate 4

value: Male

value: liver

value: Wild Type

value: T3 3-day


title: KE vs HE, biolrep 2, techrep 1

value: lower part (~1.5 cm) of the stem (hypocotyl and cotyledons)

value: 4 d

value: cold (4°C)


title: Primary melanoma_175

value: NM


title: HLa vs HK, biolrep 1, techrep 2 dyeswap

value: lantanum


title: HE vs KE, biolrep 2, techrep 2 dyeswap


title: KE vs HE, biolrep 1, techrep 1


title: FGF21KO.DMSO_3

description: replicate 3

value: DMSO 3-day


title: meningioma H2401 rep1

value: f

tag: who grade

value: WHO I

tag: histological subtype

value: meningothelial meningioma


title: HLa vs KLa, biolrep 2, techrep 2 dyeswap

tag: tissue

source_name: barley, normal temp, lanthanum

value: normal


title: FGF21KO.DMSO_1

description: replicate 1

tag: gender


title: WT.T3_3

description: replicate 3


title: Primary melanoma_176

value: melanoma

value: Sporadic

value: SSM


title: WT.T3_1

description: replicate 1

value: Male


title: FGF21KO.DMSO_2

description: replicate 2

value: liver


title: WT.T3_2

description: replicate 2

value: Wild Type


title: meningioma H975 rep1

tag: age


title: Primary melanoma_173

value: LMM


title: meningioma H90 rep1

value: fibroblastic meningioma


title: Primary melanoma_172


title: WT.DMSO_4

description: replicate 4


title: meningioma H249 rep1

value: WHO II

value: atypical meningioma


title: Primary melanoma_171

value: NM


title: Primary melanoma_170


title: Primary melanoma_169


title: meningioma H588 rep1

value: m

value: WHO III

value: anaplastic meningioma


title: WT.DMSO_3

description: replicate 3

value: DMSO 3-day


title: Primary melanoma_168


title: Primary melanoma_167


title: serum-Wilms-preCT-8 (comparison 3)

description:
US11153896_253118111388_S01_miRNA_1010_Sep10_1_1.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM355/1

data_processing: Raw expression values were extracted using the Feature Extraction Software of Agilent. Raw signal intensities were quantil normalized for every comparison; 1) Wilms serum pre CT vs controls 2) wilms serum post CT vs controls and 3) Wilms serum pre CT vs Wilms serum post CT

label: Cyanine 3

source_name: serum-Wilms-preCT

label_protocol: using miRNA Complete Labeling and Hyb Kit (Agilent, Cat. No 5190-0456),  Cyanine 3-pcp

extract_protocol: Total RNA including miRNAs was isolated using the protocol from Leidinger et al. with minor modifications. In detail 100µl serum sample, 250µl nuclease-free water (Life Technologies) and 750µl Trizol LS (Life Technologies) were mixed and incubated at RT for 5min. After addition of 1µl glycogen (20mg/ml) and 5µl 5mM cel spike-in control (Qiagen) and 200µl chloroform the solution was vortexed and incubated at RT for 3min followed by centrifugation at 4°C and 14 000rpm for 15min. The upper aqueous phase was transferred into a new tube and RNA was precipitated using 1.5Vol of 100% ethanol. The solution was added to a RNA binding column from the MinElute Cleanup Kit (Qiagen) and RNA was washed and purified using the buffer from the miRNeasy kit (Qiagen). Total RNA including miRNA was eluted in 15µl nuclease-free water and stored at -80°C. RNA concentration was measured using NanoDrop2000 (ThermoScientific). RNA integrity was measured using the Small RNA kit (Agilent) on a Bioanalyzer2100.

tag: individual

value: Wilms tumor patient

value: untreated

tag: sample type

value: serum


title: serum-Wilms-preCT-7 (comparison 3)

description:
US11153896_253118111388_S01_miRNA_1010_Sep10_2_1.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM341/1

tag: treatment


title: serum-Wilms-preCT-9 (comparison 3)

description:
US11153896_253118111385_S01_miRNA_1010_Sep10_2_4.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM357/1


title: Primary melanoma_166

value: nevus


title: WT.DMSO_1

description: replicate 1

tag: genotype

tag: genetic background


title: DNA methylation in FHC

city: Shinagawa-ku

first: Hideyuki

last: Takeshima

state: Tokyo

department: Institute for Advanced Life Sciences

institute: Hoshi University

description: Normal cells

hyb_protocol: Standard Illumina Protocol

scan_protocol: The array was scanned with an iScan System.

data_processing: The data were analyzed using GenomeStudio Methylation Module Software.

label: Cy5 and Cy3

source_name: Cell line

label_protocol: Standard Illumina Protocol

growth_protocol: Du145, PC3, MCF7, MDA-MB-231, and RKO were maintained in RPMI1640 medium.  HCT116 was maintained in McCoy's 5A medium.  RWPE1 was maintained in keratinocyte-SFM.  HMEC was maintained in mammary epithelial cell serum-free growth medium.  FHC was maintained in mixture of Ham's F12 and DMEM (1:1).

extract_protocol: Genomic DNA was extracted by standard phenol/chloroform method, and was quantified using a Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies).

tag: cell line

value: FHC


title: DNA methylation in RKO

description: Cancer cell line

value: RKO


title: serum-Wilms-preCT-6 (comparison 3)

description:
US11153896_253118111388_S01_miRNA_1010_Sep10_1_3.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM320/1


title: WT.DMSO_2

description: replicate 2

value: Male

value: liver


title: Experimental#3: Sca-1 pos treated rep 2

city: Chicago

first: Yuru

last: Liu

state: Illinois

address: 835 S. Wolcott Ave.

department: Pharmacology

institute: University of Illinois

description:
SAMPLE 11
replicate 2

data_processing: The data were normalised using quantile normalization using Bioconductor

source_name: Sca-1 pos treated

label_protocol: Standard Illumina labeling protocol

extract_protocol: RNA were isolated by Trizol and further purified with Qiagen Rneasy kit.

treatment_protocol: mice were injected via i.t. with P. aeruginosa, and type II cells were isolated from lungs and further separated into Sca-1+ and Sca-1- fractions.

tag: injection

value: P. aeruginosa

tag: time

value: lung

tag: cell type

value: alveolar type II cells

tag: cell population

value: Sca-1 pos treated


title: serum-Wilms-preCT-5 (comparison 3)

description:
US11153896_253118111159_S01_miRNA_1010_Sep10_1_4.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM315/1


title: Primary melanoma_165

value: melanoma

tag: mutation status

value: Sporadic

tag: thickness

tag: histology

value: NM

tag: clark

tag: number of replicates


title: Experimental#3: Sca-1 pos treated rep 1

description:
SAMPLE 10
replicate 1

tag: tissue


title: Experimental#2: Sca-1 neg treated rep 3

description:
SAMPLE 9
replicate 3

source_name: Sca-1 neg treated

value: Sca-1 neg treated


title: Primary melanoma_164


title: DNA methylation in HCT116

description: Cancer cell line


title: serum-Wilms-preCT-4 (comparison 3)

description:
US11153896_253118111159_S01_miRNA_1010_Sep10_1_1.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM301/1


title: Experimental#3: Sca-1 pos treated rep 3

description:
SAMPLE 12
replicate 3


title: serum-Wilms-preCT-3 (comparison 3)

description:
US11153896_253118111390_S01_miRNA_1010_Sep10_1_3.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM296/1


title: Experimental#2: Sca-1 neg treated  rep 2

description:
SAMPLE 8
replicate 2


title: Primary melanoma_163

value: SSM


title: serum-Wilms-preCT-2 (comparison 3)

description:
US11153896_253118111385_S01_miRNA_1010_Sep10_1_4.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM285/1

value: Wilms tumor patient


title: Experimental#2: Sca-1 neg treated rep 1

description:
SAMPLE 7
replicate 1


title: Primary melanoma_162


title: serum-Wilms-preCT-16 (comparison 3)

description:
US11153896_253118111390_S01_miRNA_1010_Sep10_2_1.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM396/1

value: untreated


title: Primary melanoma_161


title: Primary melanoma_160


title: serum-Wilms-preCT-15 (comparison 3)

description:
US11153896_253118111392_S01_miRNA_1010_Sep10_2_3.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM388/1

value: serum


title: Experimental#1: Sca-1 pos untreated rep 3

description:
SAMPLE 6
replicate 3

source_name: Sca-1 pos untreated

value: control

value: Sca-1 pos untreated


title: Primary melanoma_159


title: Primary melanoma_174


title: DNA methylation in HMEC

description: Normal cells

value: HMEC


title: DNA methylation in MDA-MB-231

description: Cancer cell line


title: serum-Wilms-preCT-14 (comparison 3)

description:
US11153896_253118111405_S01_miRNA_1010_Sep10_2_2.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM384/1


title: DNA methylation in MCF7

description: Cancer cell line


title: Experimental#1: Sca-1 pos untreated rep 2

description:
SAMPLE 5
replicate 2


title: Experimental#1: Sca-1 pos untreated rep 1

description:
SAMPLE 4
replicate 1


title: DNA methylation in PC3

description: Cancer cell line


title: serum-Wilms-preCT-13 (comparison 3)

description:
US11153896_253118111390_S01_miRNA_1010_Sep10_2_3.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM374/1


title: Control:  Sca-1 neg untreated rep 3

description:
SAMPLE 3
replicate 3

source_name: Sca-1 neg untreated

value: Sca-1 neg untreated


title: DNA methylation in Du145

description: Cancer cell line


title: Primary melanoma_158


title: Primary melanoma_157

value: LMM


title: serum-Wilms-preCT-12 (comparison 3)

description:
US11153896_253118111385_S01_miRNA_1010_Sep10_2_2.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM364/1


title: DNA methylation in RWPE1

description: Normal cells


title: serum-Wilms-preCT-11 (comparison 3)

description:
US11153896_253118111405_S01_miRNA_1010_Sep10_2_4.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM363/1


title: Primary melanoma_156


title: Control:  Sca-1 neg untreated rep 2

description:
SAMPLE 2
replicate 2


title: Primary melanoma_155


title: serum-Wilms-preCT-10 (comparison 3)

description:
US11153896_253118111160_S01_miRNA_1010_Sep10_1_1.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM362/1


title: 1444-12H_3090

city: Durham

first: Susan

middle: K.

last: Murphy

state: NC

address: B226 LSRC B Wing, Research Drive, Box 91012

department: Obstetrics and Gynecology

institute: Duke University Medical Center

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

scan_protocol: Arrays were imaged using HiScan using standard recommended Illumina scanner setting

data_processing:
Please note that raw data (beta values) was used for data analysis. Normalization or filtering was not performed since there was excellent correlation between the beta values for a substantial number of CpG sites and the methylation % for these same CpGs obtained by bisulfite pyrosequencing.  The beta values were taken directly from Illumina's Genome Studio  v2010.3 software.
The non_normalized.txt contains unmethylated and methylated signal intensities.

label: Cy3, Cy5

source_name: ovarian cancer

growth_protocol: Samples were embedded in optimal cutting temperature medium and stored at -80 degrees celsius prior to use. All sections were cut and mounted on slides to confirm ≥60% tumor content with ≤20% necrosis.

extract_protocol: DNA was extracted from frozen tissues using the AllPrep DNA/RNA/Protein Mini Kit (Qiagen).

tag: gender

value: female

tag: histologic type

value: serous


title: 1444-12G_3562

value: mucinous


title: Primary melanoma_153


title: Primary melanoma_152


title: Primary melanoma_154


title: serum-wilms-postCT-9 (comparison 3)

description:
US11153896_253118111385_S01_miRNA_1010_Sep10_2_3.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM357/2

source_name: serum-wilms-postCT

tag: individual

value: chemotherapy

tag: sample type


title: Control:  Sca-1 neg untreated rep 1

description:
SAMPLE 1
replicate 1

value: lung

value: alveolar type II cells


title: 1444-12F_1526


title: Exon3_T2

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina mouse-6 V2.0 expression BeadChip according to the manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina BeadArray Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the manufacturer's instructions.

data_processing: Array data processing was performed on Illumina BeadStudio software. We normalized gene expression data using quantile normalization and log2 transformation. To export to a data matrix, the Sample Gene Profile option of this software was used.

label: Biotin

source_name: Liver tumor

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 750 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion, Inc., Austin, TX). cRNA concentrations were determined using a spectrophotometer (Nanodrop, ND-1000).

extract_protocol: Total RNA was isolated from tissues with the mirVana RNA Isolation labeling kit (Ambion, Inc.) according to the manufacturer protocol. RNA quality and integrity were confirmed by the ExperionTM Automated Electrophoresis System (BIO-RAD).

tag: strain/background

tag: genotype

value: Ctnnb1 flox(ex3)/+

value: tumor


title: Primary melanoma_151

value: melanoma

value: Sporadic

value: NM


title: serum-Wilms-preCT-1 (comparison 3)

description:
US11153896_253118111160_S01_miRNA_1010_Sep10_1_3.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM265/1

value: Wilms tumor patient

tag: treatment

value: untreated

value: serum


title: Exon3_T1


title: Exon3_T3


title: WT_04

source_name: Normal liver control

value: wild-type

value: liver


title: 1444-12D_1774


title: Exon3_T4


title: WT_03


title: 1444-12E_3435

value: endometrioid


title: serum-wilms-postCT-8 (comparison 3)

description:
US11153896_253118111388_S01_miRNA_1010_Sep10_1_2.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM355/2


title: serum-wilms-postCT-7 (comparison 3)

description:
US11153896_253118111388_S01_miRNA_1010_Sep10_2_2.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM341/2


title: 1444-12B_1357

value: female


title: serum-wilms-postCT-6 (comparison 3)

description:
US11153896_253118111388_S01_miRNA_1010_Sep10_1_4.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM320/2


title: Primary melanoma_150


title: Primary melanoma_146


title: serum-wilms-postCT-5 (comparison 3)

description:
US11153896_253118111159_S01_miRNA_1010_Sep10_2_1.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM315/2


title: 1444-12C_NL

source_name: normal lymphocyte DNA

value: normal lymphocyte DNA


title: 1444-11H_3310

value: clear cell


title: Primary melanoma_144

value: Mucosal


title: Primary melanoma_143

value: SSM


title: serum-wilms-postCT-3 (comparison 3)

description:
US11153896_253118111159_S01_miRNA_1010_Sep10_1_3.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM296/2

value: chemotherapy


title: serum-wilms-postCT-4 (comparison 3)

description:
US11153896_253118111159_S01_miRNA_1010_Sep10_1_2.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM301/2


title: WT_01


title: 1444-12A_3423


title: Primary melanoma_145


title: 1444-11G_3018

value: serous


title: serum-wilms-postCT-2 (comparison 3)

description:
US11153896_253118111385_S01_miRNA_1010_Sep10_1_3.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM285/2


title: Primary melanoma_142


title: WT_02


title: Withaferin A treated Cells_rep2

city: Miami

first: Annalise

last: Smith

state: FL

address: 1580 NW 10th Avenue

department: Microbiology and Immunology

institute: University of Miami

description:
replicate 2
Sample 2 WA treated

hyb_protocol: Standard Illumina Hybridization protocol

scan_protocol: Standard Illumina Scanning protocol

data_processing: Each batch was individually Quantile normalized and log2 transformed to median of samples. The batch bias correction was done using the ComBat module on R/Bioconductor package

source_name: rat her-2/neu cells

growth_protocol: Rat her-2/neu expressing murine cells were grown in 20% FBS containing DMEM media with gentamicin and l-glutamine. All three individual replicates were completed at early passage numbers- passage 2,3 and 4

extract_protocol: Total RNA was extracted with Trizol followed by purifcation and DNase1 treatment using Qiagen miRNA easy mini kit following the manufacturers instructions. Two rounds of quality control was performed with Agilent Bioanalyzer

treatment_protocol: Cells were treated with 8μM of Withaferin A diluted in culture media for 6hrs

value: rat her-2/neu expressing murine cancer cells

tag: agent

value: Withaferin A


title: serum-wilms-postCT-16 (comparison 3)

institute: Saarland University

description:
US11153896_253118111390_S01_miRNA_1010_Sep10_2_2.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM396/2


title: Primary melanoma_141

value: melanoma


title: 1444-11C_1675


title: 1444-11F_3464

value: mucinous


title: Withaferin A treated Cells_rep1

description:
replicate 1
Sample 1 WA treated


title: serum-wilms-postCT-15 (comparison 3)

description:
US11153896_253118111392_S01_miRNA_1010_Sep10_2_4.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM388/2

value: Wilms tumor patient


title: Untreated Cells_rep3

description:
replicate 3
sample 3_untreated

value: Untreated


title: 1444-11D_3361


title: Primary melanoma_140

value: Sporadic


title: Withaferin A treated Cells_rep3

description:
replicate 3
Sample 3 WA treated


title: Untreated Cells_rep2

description:
replicate 2
sample 2_untreated


title: serum-wilms-postCT-14 (comparison 3)

description:
US11153896_253118111405_S01_miRNA_1010_Sep10_2_1.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM384/2

value: serum


title: 1444-11E_1504


title: serum-wilms-postCT-13 (comparison 3)

description:
US11153896_253118111390_S01_miRNA_1010_Sep10_2_4.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM374/2


title: 1444-11B_CpG

source_name: universally methylated DNA

value: unknown

value: universally methylated DNA


title: serum-wilms-postCT-12 (comparison 3)

description:
US11153896_253118111385_S01_miRNA_1010_Sep10_2_1.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM364/2


title: Primary melanoma_139

source_name: Primary melanoma

value: NM


title: Primary melanoma_138


title: Primary melanoma_137


title: serum-wilms-postCT-11 (comparison 3)

description:
US11153896_253118111405_S01_miRNA_1010_Sep10_2_3.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM363/2