title: GBM10_NT

status: Public on Sep 30 2015

type: RNA

city: Cleveland

first: Tyler

middle: E

last: Miller

state: Ohio

department: Stem Cell Biology and Regenerative Medicine

country: USA

institute: Cleveland Clinic Lerner Research Institute

scan_protocol: GeneTitan

data_processing: The HuGene 2.1 array covers > 30,000 coding transcripts and 11,000 long internegic noncoding transcripts. Raw intensity values were normalized by robust multiarray average (RMA) analysis as previously described (Irizarry et al., 2003) using the Bioconductor oligo R package (Carvalho and Irizarry, 2010). Using the raw gene expression values, fold changes for each gene were calculated between each pair of non-targeting (NT) and FTH1 or FTL shRNA condition.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: GBM10 GSCs

label_protocol: Microarray hybridization and processing were performed at the Case Western Reserve University Genomics Sequencing Core according to the manufacturer’s protocol using the GeneTitan multichannel instrument (Affymetrix). Biotinylated cDNA fragments were generated from 500 ng of total RNA, and 180 ng of cDNA was hybridized onto the HuGene 2.1 PEG array (Affymetrix).

growth_protocol: Glioblastoma (GBM) tissues were obtained from excess surgical materials from patients at Duke University or the Cleveland Clinic after review from a neuropathologist in accordance with an approved protocol by the Institutional Review Board. As previously described (Bao et al., 2006; Eyler et al., 2011; Flavahan et al., 2013; Hjelmeland et al., 2011; Lathia et al., 2010; Li et al., 2009; Venere et al., 2014; Yan et al., 2014), GBM stem cells (CSCs) and/or non-CSCs were derived immediately after dissociation or after transient xenograft passage (fewer than five passages) in immunocompromised mice using prospective sorting either via magnetic columns (MACS, CD133 microbeads, Miltenyi Biotec) or flow cytometry (FACS, CD133/2-APC, Miltenyi Biotec) followed by functional analysis. The cancer stem cell phenotype of CD133+ cells was confirmed by functional assays of stem cell marker expression, sphere formation by in vitro limiting dilution and secondary tumor initiation. CD133-negative cells did not share these properties and were used in matched assays as non-CSCs. For short-term in vitro expansion, CSCs were cultured in Neurobasal medium (NBM) with B27 (without vitamin A, Invitrogen), basic fibroblast growth factor (20ng/ml) and epidermal growth factor (20ng/ml), on Petri dishes.

extract_protocol: RNA was extracted from ~2x106 cells with TRIzol (Invitrogen), separated using Phase Lock Gel tubes (5 Prime), and purified using the miRNAeasy kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: A non-targeting (NT) control shRNA sequence that is not expressed in the human transcriptome (SCH002; Sigma-Aldrich), served as a negative control for off-target effects. FTH1 shRNAs: NM_002032, 5 sequences: TRCN0000029429-33 and FTL shRNAs: NM_000146, 5 sequences: TRCN0000029434-38. To produce lentivirus, plasmids were co-transfected with packaging vectors psPAX2 and pCI-VSVG (Addgene) into 293FT cells using Lipofectamine 2000 (Invitrogen) or Fugene HD transfection reagent (Promega). For lentiviral transduction, cells were plated on geltrex-coated tissue culture treated plates and infected with a MOI ratio of ~ 5 viral particles per cell. Knockdown efficiency of FTH1 and FTL shRNA sequences were confirmed with qRT-PCR and western blot. FTH1 shRNA TRCN0000029433 (sequence: 5’-GCCGAATCTTCCTTCAGGATA-3’) and FTL shRNA TRCN0000029434 (sequence: 5’-CTGGAGACTCACTTCCTAGAT-3’) were validated as the best shRNAs to be used as each exhibited highest knockdown efficiency and no off-target effects.

tag: cell line

value: GBM10 GSCs

tag: knockdown

value: NT


title: 3832_FTH1

hyb_protocol: Microarray hybridization and processing were performed at the Case Western Reserve University Genomics Sequencing Core according to the manufacturer’s protocol using the GeneTitan multichannel instrument (Affymetrix). Biotinylated cDNA fragments were gene

source_name: 3832 GSCs

value: 3832 GSCs


title: 387_FTH1

source_name: 387 GSCs

value: 387 GSCs


title: GBM10_FTH1


title: 4121_FTL

source_name: 4121 GSCs

value: 4121 GSCs

value: FTL


title: JQ1_G07

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description: Gene expression in JQ1 treated cells

hyb_protocol: According to the standard Affymetrix protocol

data_processing: The data was analyzed using robust multi-array average (RMA) analysis using the Qlucore Omic Explorer

label: biotin

source_name: MDAMB231 cells, JQ1, 48h, replicate 3

label_protocol: Biotinylated cDNA fragments were prepared according to the standard Affymetrix protocol

growth_protocol: The human breast cancer cell line MDAMB231 was maintained in RPMI 1640 medium  supplemented with 10% fetal bovine serum (FBS) (Invitrogen) at 37°C, under a humidified atmosphere of 5% carbon dioxide.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: MDAMB231 cells were treated with 1 µM JQ1 or 3.17 µM mocetinostat or with the combination of both for 48 hours

tag: cell type

value: breast cancer


title: MGCD_B05

description: Gene expression in JQ1+MGCD treated cells

scan_protocol: According to the standard Affymetrix protocol

source_name: MDAMB231 cells, MGCD, 48h, replicate 3


title: GBM10_FTL


title: VEH_A05

description: Gene expression in MGCD treated cells

source_name: MDAMB231 cells, DMSO, 48h, replicate 2


title: 3691_NT

source_name: 3691 GSCs

value: 3691 GSCs


title: 3832_FTL


title: 3832_NT


title: 4121_NT


title: 3691_FTH1


title: 387_NT


title: MGCD_G05

source_name: MDAMB231 cells, MGCD, 48h, replicate 1


title: 387_FTL


title: VEH_D09

description: Gene expression in MGCD treated cells

source_name: MDAMB231 cells, DMSO, 48h, replicate 3


title: JQ1_D07

description: Gene expression in JQ1 treated cells

source_name: MDAMB231 cells, JQ1, 48h, replicate 2


title: 4121_FTH1


title: Vegetative conditions repA

city: Groningen

first: Wout

last: Overkamp

address: Nijenborgh 7

country: Netherlands

institute: Rijksuniversiteit Groningen, Department of Molecular Genetics

hyb_protocol: Hybridization was performed as described by Lulko et al., 2005 (Lulko, A.T., Buist, G., Kok, J., and Kuipers, O.P. (2007). Transcriptome Analysis of Temporal Regulation of Carbon Metabolism by CcpA in Bacillus subtilis Reveals Additional Target Genes. J. Mol. Microbiol. Biotechnol. 12, 82–95.)

scan_protocol: Slides were scanned using a confocal laser scanner (Genepix autoloader AL4200, Molecular Devices Ltd., Sunnyvale, USA).

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described (15, 18, 49). Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of the sigF mutant strain over the wild-type strain were calculated for sporulating and vegetative conditions. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: wildtype biological replicate #1

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences

growth_protocol: See colum 'Growth' under the SAMPLES section

extract_protocol: For RNA isolation, cells were broken using 500 mg of glass beads, 500 μl of phenol-chloroform, 30 μl of 3 M sodium acetate, and 15 μl of 20% sodium dodecyl sulfate. RNAs were isolated using the High Pure RNA isolation kit (Roche, Mannheim, Germany) according to the manufacturer's instructions. After a quality check of the isolated RNA using a Agilent Bioanalyzer 2100 with RNA 6000 LabChips (Agilent Technologies, the Netherlands), 20 μg of total RNA was used for cDNA synthesis and incorporation of aminoalyl-dUTP using SuperscriptIII reverse transcriptase  Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from four replicate cultures.

treatment_protocol: Harvested cultures were quickly centrifuged for 2 min at 6,000 × g, and frozen in liquid nitrogen.

tag: genotype/variation

value: wildtype

tag: growth

value: cells were grown in TY medium and samples for RNA isolation were taken at OD 1.5

source_name: sigF mutant biological replicate #1


title: VEH_H09

description: Gene expression in MGCD treated cells

source_name: MDAMB231 cells, DMSO, 48h, replicate 1


title: MGCD_H07

source_name: MDAMB231 cells, MGCD, 48h, replicate 2


title: JQ1_E05

description: Gene expression in JQ1 treated cells

source_name: MDAMB231 cells, JQ1, 48h, replicate 1


title: MGCD_JQ1_A07

description: Gene expression in DMSO treated cells

source_name: MDAMB231 cells, JQ1+MGCD, 48h, replicate 1


title: 3691_FTL


title: Vegetative conditions repC

source_name: wildtype biological replicate #2

source_name: sigF mutant biological replicate #2


title: MGCD_JQ1_H05

description: Gene expression in DMSO treated cells

source_name: MDAMB231 cells, JQ1+MGCD, 48h, replicate 3


title: MGCD_JQ1_B09

description: Gene expression in DMSO treated cells

source_name: MDAMB231 cells, JQ1+MGCD, 48h, replicate 2


title: Sporulating conditions repC

value: cells were grown in DSM medium until 2 hours after the transition point between the exponential and stationary growth phase.


title: CRC_16

city: seoul

first: SeungHyun

last: Jung

state: seoul

address: catholic university, medical college, banpo-dong

department: Department of Biochemistry

country: South Korea

institute: Catholic University of Korea

description:
Formalin-fixed paraffin-embedded (FFPE) tissue
17_S10-38712

hyb_protocol: Dye-labeled miRNA was purified using Micro Bio-Spin 6 column (Bio-Rad). Labeled RNA was applied on the miRNA array with a hybridization buffer. Array slide were incubated for 20 hours at 55°C in a hybridization oven (Agilent). After hybridization, slides were washed sequentially.

scan_protocol: The arrays were scanned using Agilent microarray scanner.

data_processing:
Raw data were generated from scanned images of Agilent array data using Agilent Feature Extraction Software 10.7.3.1.
Normalized signal intensity: The feature intensities were transferred to digital data and Log2 transformed by using Feature Extraction software on default setting. (Protocol is miRNA_107_Sep09, Grid is 031181_D_F_20121224).

source_name: Colorectal cancer tissue

label_protocol: Agilent Human miRNA Microarray Kit was used for miRNA expression profiling. MiRNA array experiments were conducted according to the manufacturer's instructions. In brief, 100 ng of total RNA from each sample was dephosphorylated and ligated with pCp-Cy3 dye.

extract_protocol: Formalin-fixed paraffin-embedded tissue sections (thickness 15 µm) were deparaffinized with xylene, washed with ethanol and then dried. Tumor cell rich areas (>70% of tumor cells) were selected and microdissected under a microscope. Total RNA was extracted using the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Life technologies) following manufacturer's instructions.

tag: tissue

value: Colon

tag: lymph node metastasis

value: Positive


title: CRC_14

description:
Formalin-fixed paraffin-embedded (FFPE) tissue
12_S08-17652


title: CRC_12

description:
Formalin-fixed paraffin-embedded (FFPE) tissue
18_S09-36216


title: CRC_03

description:
Formalin-fixed paraffin-embedded (FFPE) tissue
07_S12-5218

value: Negative


title: CRC_11

description:
Formalin-fixed paraffin-embedded (FFPE) tissue
13_S09-33607


title: CRC_10

description:
Formalin-fixed paraffin-embedded (FFPE) tissue
14_S09-7798


title: CRC_15

description:
Formalin-fixed paraffin-embedded (FFPE) tissue
15_S10-10927


title: Vegetative conditions repB


title: CRC_08

description:
Formalin-fixed paraffin-embedded (FFPE) tissue
11_S12-9007


title: U87 lysate 6Gy RT at 16hr replicate2

type: protein

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

description: protein lysate

hyb_protocol: 5 serial dilutions of lysates were arrayed on nitrocellulose‐coated slides, probed with (172 phosphorylated and non- phosphorylated) antibodies. Samples were probed with antibodies by a tyramide amplification approach (Dako CSA) and visualized by DAB colorimetric reaction.

scan_protocol: Slides were scanned on a flatbed scanner to produce 16-bit tiff images.  Spots from tiff images were identified and the density was quantified by Array-Pro Analyzer software.

data_processing: Relative protein levels for each sample were determined by interpolation of each dilution curves from the standard curve antibody slide. All the data points were normalized for protein loading and transformed to a linear value. Linear values were transformed to Log2 value and then median‐centered for hierarchical cluster analysis.

label: DAB

molecule: protein

source_name: U87-GBM cell line

growth_protocol: U251, U87  (National Cancer Institute Frederick Tumor Repository) human GBM cell lines were grown in Dulbecco's Modified Eagle Medium (DMEM) (Invitrogen, Carlsbad, CA) with 10% fetal bovine serum (FBS), and maintained at 37°C, 5% CO2.

extract_protocol: Treated GBM cell (U251,U87)  lysates were prepared  in  RPPA lysis buffer [1% Triton X-100, 50 nmol/L Hepes (pH 7.4), 150 nmol/L NaCl, 1.5 nmol/L MgCl2, 1 mmol/L EGTA, 100 nmol/L NaF, 10 nmol/L NaPPi, 10% glycerol, 1 nmol/L phenylmethylsulfonyl fluoride, 1 nmol/L Na3VO4, and aprotinin 10 μg/mL) as described elsewhere, and sent to RPPA Core Facility, MD Andersen Cancer Center, Houston, TX for RPPA analysis.

treatment_protocol: Tumor lysates were prepared from GBM tumor cells (U251and U87)  and  tumors grown orthotopically in nude mice treated with indicated doses (Gy) of radiation treatment .

tag: treatment

value: 6Gy RT at 16hr


title: CRC_05

description:
Formalin-fixed paraffin-embedded (FFPE) tissue
05_S12-2191


title: CRC_07

description:
Formalin-fixed paraffin-embedded (FFPE) tissue
04_S12-15170


title: CRC_09

description:
Formalin-fixed paraffin-embedded (FFPE) tissue
08_S12-5265


title: U87 lysate 6Gy RT at 6hr replicate2

description: protein lysate

label_protocol: tyramide amplification approach (Dako CSA) and visualized by DAB colorimetric reaction.

value: 6Gy RT at 6hr


title: CRC_01

description:
Formalin-fixed paraffin-embedded (FFPE) tissue
06_S12-2434


title: CRC_04

description:
Formalin-fixed paraffin-embedded (FFPE) tissue
10_S12-7035


title: Sporulating conditions repA


title: Sporulating conditions repB


title: CRC_02

description:
Formalin-fixed paraffin-embedded (FFPE) tissue
03_S12-13502


title: CRC_13

description:
Formalin-fixed paraffin-embedded (FFPE) tissue
16_S10-18683


title: U87lysate 2Gy RT at 16hr replicate2

description: protein lysate

value: 2Gy RT at 16hr


title: U87lysate 6Gy RT at 1hr replicate1

description: protein lysate

value: 6Gy RT at 1hr


title: U87 lysate 6Gy RT at 6hr replicate1

description: protein lysate


title: Control U87 replicate2

description: protein lysate


title: U87 lysate 6Gy RT at 1hr replicate2

description: protein lysate


title: U87 lysate 2Gy RT at 1hr replicate2

description: protein lysate

value: 2Gy RT at 1hr


title: CRC_06

description:
Formalin-fixed paraffin-embedded (FFPE) tissue
09_S12-6248


title: U251 lysate 6Gy RT at 16hr replicate2

description: protein lysate

source_name: U251-GBM cell line


title: U251 lysate 2Gy RT at 16hr replicate2

description: protein lysate


title: U87 lysate 2Gy RT at 6hr replicate1

description: protein lysate

value: 2Gy RT at 6hr


title: U87 lysate 2Gy RT at 16hr replicate1

description: protein lysate


title: Control U87 replicate1

description: protein lysate


title: U87 lysate 2Gy RT at 1hr replicate1

description: protein lysate


title: U87 lysate 6Gy RT at 16hr replicate1

description: protein lysate


title: U251 lysate 2Gy RT at 1hr replicate2

description: protein lysate


title: U251 lysate 6Gy RT at 1hr replicate2

description: protein lysate


title: U251 lysate 2Gy RT at 16hr replicate1

description: protein lysate


title: U251 lysate 2Gy RT at 6hr replicate1

description: protein lysate


title: U87 lysate 2Gy RT at 6hr replicate2

description: protein lysate


title: U251 lysate 2Gy RT at 6hr replicate2

description: protein lysate


title: Control U251 replicate2

description: protein lysate


title: U251 lysate 6Gy RT at 16hr replicate1

description: protein lysate


title: U251 lysate 2Gy RT at 1hr replicate1

description: protein lysate


title: Control U251 replicate1

description: protein lysate


title: U251 lysate 6Gy RT at 6hr replicate2

description: protein lysate


title: U251 lysate 6Gy RT at 6hr replicate1

description: protein lysate


title: U251 lysate 6Gy RT at 1hr replicate1

description: protein lysate


title: DMVEC 1

city: Oslo

first: Krisztina

last: Szoke

address: Sognsvannsveien 20.

country: Norway

institute: Institute of Immunology and Norwegian Center for Stem Cell Research, Oslo University Hospital, Rikshospitalet

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation by Illumina`s GenomeStudio software V2011.1, Gene Expression module V1.9.0.

source_name: skin

label_protocol: Biotin-labeled cRNA was synthesized from 500ng total RNA using the Illumina® TotalPrep™-96 RNA Amplification Kit (Ambion).

growth_protocol: Cells were cultured in EGM-2 medium and maintained at 37 degrees in an atmosphere of 5% CO2 in humid air.

extract_protocol: Total RNA was extracted using RNAqueous-4PCR Kit (Applied Biosystems) according to the manufacturer`s protocol and treated with Dnase I. The integrity of the RNA samples was assessed by Agilent 2100 Bioanalyser.

treatment_protocol: No treatment was applied prior to preparation of the samples.

value: skin


title: DMVEC 2

description: replicate 3


title: HUVEC 1

description: replicate 3

source_name: umbilical vein

value: umbilical vein


title: ECFC 2

description: replicate 3

source_name: peripheral blood

value: peripheral blood


title: HFE145_control3

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

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

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

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 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 using spectrophotometer (Nanodrop, ND-1000)

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

value: VTRNA1-1 ASO


title: HUVEC 2

description: replicate 3


title: HUVEC 3

description: replicate 3


title: ECFC 1

description: replicate 3


title: HAOEC_α-MSH_exp2_12h_rep2

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

country: Italy

institute: Centro Cardiologico Monzino IRCCS

description:
6991001100_K
Technical replicate 2.

scan_protocol: Standard Illumina scanning protocol for iSCAN.

data_processing: Raw data were imported in the R software version 2.15.2 and analyzed with the lumi package from the Bioconductor Suite version 2.11. Variance stabilizing transformation (VST) was applied and transformed data were then normalized by robust spline normalization (RSN).

source_name: Human aortic endothelial cells, α-MSH, 12h

label_protocol: RNA was used to generate biotinylated, linearly amplified RNA (cRNA) by Total Prep RNA Amplification Kit (Life Technologies), according to manufacturer's manual.

growth_protocol: HAOEC were placed in a T 75 plastic flask at a density of 2500 cells/cm2 with EBM2 media plus supplements. All experiments were performed at cell passage 4-6.

extract_protocol: Total RNA was extracted using the RNAdvance cell v2 kit (Agencourt) following recommended manufacturer's instructions. Then, total RNA was treated with DNase Turbo (Life Technologies) as described by the manufacturer's protocol. RNA quantification and purity were evaluated by micro-volume spectrophotometry using an Infinite 200 PRO plate reader (Tecan). The quality and integrity of the total RNA were checked by the RNA 6000 Nano Assay kit in a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: HAOEC were seeded in a culture-insert on a flat clean surface until their attachment (Ibidi GmbH). Than, HAOEC were treated with 10 nM α-MSH or medium alone.

value: aortic endothelial cells

tag: gender

value: female

tag: age

value: 54 years

tag: race

value: Hispanic

value: α-MSH stimulation

tag: time point


title: HFE145_knockdown3

value: nc886 ASO


title: HAOEC_Control_exp3_6h_rep2

description:
6991001100_G
Technical replicate 2.

source_name: Human aortic endothelial cells, control, 6h

value: medium control


title: HAOEC_Control_exp1_12h_rep2

description:
6991001100_H
Technical replicate 2.

source_name: Human aortic endothelial cells, control, 12h


title: ECFC 3

description: replicate 3


title: AT-EC 1

description: replicate 3

source_name: adipose tissue

value: adipose tissue


title: HAOEC_Control_exp2_6h_rep2

description:
6991001100_I
Technical replicate 2.


title: HFE145_control1


title: DMVEC 3

description: replicate 3


title: HFE145_knockdown2


title: AT-EC 3

description: replicate 3


title: HAOEC_Control_exp1_6h_rep2

description:
6991001100_L
Technical replicate 2.


title: HFE145_control2


title: HAOEC_α-MSH_exp2_6h_rep2

description:
6991001100_J
Technical replicate 2.

source_name: Human aortic endothelial cells, α-MSH, 6h


title: HAOEC_Control_exp2_12h_rep2

description:
6991001100_F
Technical replicate 2.


title: HAOEC_Control_exp3_12h_rep2

description:
6991001100_C
Technical replicate 2.


title: HFE145_knockdown1


title: HAOEC_α-MSH_exp3_12h_rep2

description:
6991001100_B
Technical replicate 2.


title: HAOEC_α-MSH_exp1_6h_rep2

description:
6991001100_D
Technical replicate 2.


title: AT-EC 2

description: replicate 3


title: HAOEC_α-MSH_exp1_12h_rep2

description:
6991001100_A
Technical replicate 2.


title: HAOEC_α-MSH_exp3_6h_rep2

description:
6991001100_E
Technical replicate 2.


title: HAOEC_Control_exp1_0.5h_rep2

description:
6898376001_I
Technical replicate 2.

source_name: Human aortic endothelial cells, control, 0.5h


title: HAOEC_Control_exp2_3h_rep2

description:
6898376001_G
Technical replicate 2.

source_name: Human aortic endothelial cells, control, 3h


title: HAOEC_α-MSH_exp3_12h_rep1

description:
6991001074_F
Technical replicate 1.


title: HAOEC_Control_exp3_6h_rep1

description:
6991001074_L
Technical replicate 1.


title: HAOEC_α-MSH_exp3_3h_rep2

description:
6898376001_F
Technical replicate 2.

source_name: Human aortic endothelial cells, α-MSH, 3h


title: HAOEC_α-MSH_exp1_3h_rep2

description:
6898376001_K
Technical replicate 2.


title: HAOEC_Control_exp1_12h_rep1

description:
6991001074_B
Technical replicate 1.


title: HAOEC_α-MSH_exp3_6h_rep1

description:
6991001074_C
Technical replicate 1.


title: HAOEC_α-MSH_exp3_0.5h_rep2

description:
6898376001_J
Technical replicate 2.

source_name: Human aortic endothelial cells, α-MSH, 0.5h


title: HAOEC_Control_exp2_0.5h_rep2

description:
6898376001_L
Technical replicate 2.


title: HAOEC_Control_exp1_3h_rep2

description:
6898376001_C
Technical replicate 2.


title: HAOEC_α-MSH_exp2_12h_rep1

description:
6991001074_I
Technical replicate 1.


title: HAOEC_α-MSH_exp1_0.5h_rep2

description:
6898376001_D
Technical replicate 2.


title: HAOEC_Control_exp2_6h_rep1

description:
6991001074_H
Technical replicate 1.


title: HAOEC_Control_exp3_0.5h_rep2

description:
6898376001_A
Technical replicate 2.


title: HAOEC_α-MSH_exp1_12h_rep1

description:
6991001074_K
Technical replicate 1.


title: HAOEC_α-MSH_exp2_3h_rep2

description:
6898376001_H
Technical replicate 2.


title: HAOEC_Control_exp3_12h_rep1

description:
6991001074_D
Technical replicate 1.


title: HAOEC_Control_exp1_6h_rep1

description:
6991001074_J
Technical replicate 1.


title: HAOEC_Control_exp2_12h_rep1

description:
6991001074_A
Technical replicate 1.


title: HAOEC_α-MSH_exp1_6h_rep1

description:
6991001074_E
Technical replicate 1.


title: HAOEC_Control_exp1_0.5h_rep1

description:
6991001065_H
Technical replicate 1.


title: HAOEC_α-MSH_exp2_0.5h_rep1

description:
6991001065_L
Technical replicate 1.


title: HAOEC_Control_exp2_3h_rep1

description:
6991001065_I
Technical replicate 1.


title: HAOEC_α-MSH_exp2_6h_rep1

description:
6991001074_G
Technical replicate 1.


title: HAOEC_Control_exp3_3h_rep2

description:
6898376001_E
Technical replicate 2.


title: HAOEC_α-MSH_exp3_0.5h_rep1

description:
6991001065_K
Technical replicate 1.


title: HAOEC_α-MSH_exp2_0.5h_rep2

description:
6898376001_B
Technical replicate 2.


title: HAOEC_α-MSH_exp3_3h_rep1

description:
6991001065_J
Technical replicate 1.


title: HAOEC_α-MSH_exp1_3h_rep1

description:
6991001065_G
Technical replicate 1.


title: replicate1 U87 lysate 2Gy RT at 16hr

description: protein lysate

source_name: U87-GBM cell line/xenograft

extract_protocol: The lysates were prepared  in  RPPA lysis buffer [1% Triton X-100, 50 nmol/L Hepes (pH 7.4), 150 nmol/L NaCl, 1.5 nmol/L MgCl2, 1 mmol/L EGTA, 100 nmol/L NaF, 10 nmol/L NaPPi, 10% glycerol, 1 nmol/L phenylmethylsulfonyl fluoride, 1 nmol/L Na3VO4, and aprotinin 10 μg/mL


title: replicate1 U87lysate 6Gy RT at 1hr

description: protein lysate


title: replicate1 U87 lysate 6Gy RT at 16hr

description: protein lysate

value: 6Gy RT at 16hr


title: replicate2 U87 lysate 2Gy RT at 1hr

description: protein lysate


title: replicate1 U87 lysate 6Gy RT at 6hr

description: protein lysate

value: 6Gy RT at 6hr


title: replicate2 U87 lysate 2Gy RT at 6hr

description: protein lysate


title: replicate2 Control U87

description: protein lysate

value: control


title: replicate2 U87 lysate 6Gy RT at 1hr

description: protein lysate

value: 6Gy RT at 1hr


title: replicate2 U87lysate 2Gy RT at 16hr

description: protein lysate

value: 2Gy RT at 16hr


title: replicate2 U87 lysate 6Gy RT at 16hr

description: protein lysate


title: replicate2 U87 lysate 6Gy RT at 6hr

description: protein lysate


title: replicate1 U87 lysate 2Gy RT at 1hr

description: protein lysate

value: 2Gy RT at 1hr


title: replicate1 U87 lysate 2Gy RT at 6hr

description: protein lysate

value: 2Gy RT at 6hr


title: replicate2 U251 lysate 6Gy RT at 16hr

description: protein lysate

source_name: U251-GBM cell line/xenogrft


title: replicate2 U251 lysate 6Gy RT at 1hr

description: protein lysate


title: replicate2 U251 lysate 6Gy RT at 6hr

description: protein lysate


title: replicate1 Control U87

description: protein lysate


title: replicate2 U251 lysate 2Gy RT at 16hr

description: protein lysate


title: HAOEC_Control_exp3_3h_rep1

description:
6991001065_E
Technical replicate 1.


title: HAOEC_Control_exp2_0.5h_rep1

description:
6991001065_C
Technical replicate 1.


title: MEFs, growing 1

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

description: Gene expression growing MEFs

hyb_protocol: 1.5 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 Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°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 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: Data were analysed with the Bioconductor package Limma, using loess normalisation.

organism: Mus musculus

source_name: MEF passgage 2, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were grown in DMEM media, containing 10% FBS and 1% penicillin/streptomycin

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen) in accordance with the manufacturers instructions.

treatment_protocol: Three independent MEF cultures were passaged every 3–4 days from passage 1 until the onset of replicative senecence at passage 7. RNA from each biological replicate was then pooled prior to gene expression analyses

value: Mouse embryonic fibroblasts


title: HAOEC_Control_exp3_0.5h_rep1

description:
6991001065_D
Technical replicate 1.


title: MEFs, growing 2

description: Gene expression growing MEFs

source_name: MEF passgage 2, replicate 2


title: MEFs, replicative senescence 2

description: Gene expression senescent MEFs

source_name: MEF passgage 7, replicate 2


title: HAOEC_Control_exp1_3h_rep1

description:
6991001065_F
Technical replicate 1.


title: HAOEC_α-MSH_exp1_0.5h_rep1

description:
6991001065_A
Technical replicate 1.


title: replicate2 U251 lysate 2Gy RT at 6hr

description: protein lysate


title: MEFs, replicative senescence 1

description: Gene expression senescent MEFs

source_name: MEF passgage 7, replicate 1


title: replicate2 U251 lysate 2Gy RT at 1hr

description: protein lysate


title: HAOEC_α-MSH_exp2_3h_rep1

description:
6991001065_B
Technical replicate 1.


title: replicate2 Control U251

description: protein lysate


title: Holstein breed - Cow No.12

type: genomic

city: Mexicali

first: RICARDO

last: SALOMON

state: Baja California

address: De la Normal street S/N and Blvd. Benito Juárez Col. Insurgentes Este

department: Engineering Institute

country: Mexico

institute: Autonomous University of Baja California

description: Hybridized to 648K

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Affymetrix® GeneChip® Command Console® Software (AGCC)

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software. Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Affymetrix Power Tools APT and PennCNV algorithm.
Primary data description:  Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; LogR Ratio (LRR); B-allele Frequency (BAF).

molecule: genomic DNA

organism: Bos taurus

source_name: Bovine blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from blood using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: breed

value: Holstein

value: Female

value: blood


title: Holstein breed - Cow No.11

description: Hybridized to 648K


title: replicate1 U251 lysate 6Gy RT at 6hr

description: protein lysate


title: Holstein breed - Cow No.10

description: Hybridized to 648K


title: replicate1 U251 lysate 2Gy RT at 16hr

description: protein lysate


title: replicate1 U251 lysate 6Gy RT at 1hr

description: protein lysate


title: replicate1 U251 lysate 2Gy RT at 6hr

description: protein lysate


title: replicate1 U251 lysate 2Gy RT at 1hr

description: protein lysate


title: Holstein breed - Cow No.9

description: Hybridized to 648K


title: Holstein breed - Cow No.8

description: Hybridized to 648K


title: Holstein breed - Cow No.7

description: Hybridized to 648K


title: Holstein breed - Cow No.6

description: Hybridized to 648K


title: Holstein breed - Cow No.5

description: Hybridized to 648K


title: Holstein breed - Cow No.4

description: Hybridized to 648K


title: Holstein breed - Cow No.3

description: Hybridized to 648K


title: Holstein breed - Cow No.2

description: Hybridized to 648K


title: Holstein breed - Cow No.1

description: Hybridized to 648K


title: S. japonicum infected pooled mice plasma Replicate 2 (I2)

city: Shanghai

first: Lihui

last: Zhu

state: Shanghai

address: 800 Dongchuang Road

department: School of Agriculture and Biology

country: China

institute: Shanghai Jiaotong University

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

data_processing:
Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor.
Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs were identified through Fold Change filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

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

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

value: plasma

tag: status

value: 25d post S. japonicum infection

tag: Sex

value: Male


title: hMADS-cells_adipo-differentiation_day15

city: Vienna

first: Michael

last: Karbiener

address: Benatzkygasse 2-6 / G

department: Global Pathogen Safety

country: Austria

institute: Takeda

description:
data for sample was generated from 2 independent biological replicates, each of which was analyzed in technical duplicates; pairs of hybridizations with identical RNA, but reverse dye assignment (dye swap) are specified by the first three digits of the names of the raw data files
d15

hyb_protocol: Shortly before hybridization, microarrays were washed in 0.2% SDS (3 times, 2 min each) and ddH2O (4 times, 1 min each), then incubated in prehybridization buffer (5x SSC, 0.1% SDS, 1% BSA) at 42°C for 45 min, again washed with ddH2O (five times, 30 sec each), finally dipped in isopropanol, and dried by immediate centrifugation. Immediately before applying the labeled cDNA samples to the microarray, the samples were heated at 95°C for 3 min, snap cooled on ice for 30 sec and centrifuged for 1 min at maximum speed. The sample was pipetted onto the microarray surface, and a rectangular coverslip was gradually lowered, distributing the sample across the spotted area of the microarray. Hybridization was performed by incubation at 42°C for 16-20 h. Subsequently, microarrays were submerged in wash buffer I (2x SSC, 0.1% SDS, preheated to 42°C) for 2 min, leading to separation of the microarray and the coverslip. Three washing steps (each 5 min at room temperature with gentle rotation) were performed using wash buffer I (2x SSC, 0.1% SDS, preheated to 30°C), wash buffer II (1x SSC), and wash buffer III (0.5xSSC). Finally, the microarray was dipped into ddH2O and dried by immediate centrifugation.

scan_protocol: Scanning of microarrays was performed with a GenePix 4000B microarray scanner (Axon Instruments) at 10 µm resolution using GenePix Pro 4.1 software (Axon Instruments).

data_processing: GenePix Pro 4.1 was used to filter out spots of suboptimal quality prior to further analysis. High intensity spots were filtered out if more than 10% of spot pixels were saturated in either of the two channels. Inhomogenity of spots was estimated by comparing (for either of the two channels) the median of pixel intensities to the mean; if the difference was greater than 20%, the spot was considered as inhomogenous and thus filtered out. Low intensity spots were defined by two distinct approaches: (i) if the sum of the medians/means of the pixel intensities in both channels was lower than 300, or (ii) if not more than 55 percent of the pixels within a spot had intensities higher than the intensity of the surrounding background plus one standard deviation of the background pixels. Subsequently, the filtered raw data was background corrected (by estimation and subtraction of local background), normalized by global mean and dye-swap pairs using ArrayNorm (PMID: 15073026), which was also used to merge biological replicates. Finally, features detecting the same transcript were combined by averaging and the data was exported as text-file containing log2 transformed ratios of gene expression.

source_name: hMADS cells, 15 days after induction of adipocyte differentiation

label_protocol: Concentration of total RNA samples was determined by UV/VIS photospetrometry on a NanoDrop-1000 device, and aliquots of 20 µg total RNA in 16.5 µL RNase-free H2O were prepared. For reverse transcription (RT), 2 µL random primers (3 mg/ml, lifetechnologies # 48190-011) were added to the RNA sample, followed by incubation at 70°C for 10 min and snap-freezing on ice for 30 sec. Subsequently, the following agents were added to complete the RT reactions: 0.6 µL aminoallyl-dNTP mix (25 mM dATP, 25 mM dCTP, 25 mM dGTP, 15mM dTTP (all lifetechnologies #10297-018), 10mM aminoallyl-dUTP (Sigma #A0410)), 6 µL 5x first strand buffer, 3 µL 0.1 M DTT, 2 µL SuperScript II Reverse Transcriptase (all lifetechnologies #18064-014). After mixing, RT reactions were incubated at 42°C for ~18 h. RNA was then hydrolyzed by adding 10 µL 1  M NaOH and 10 µL 0.5 M EDTA, followed by incubation at 65°C for 15 min. Subsequently, pH was neutralized by adding 10 µL 1 M HCl. To remove unincorporated aminoallyl-dUTP, reactions were purified based on the QIAquick PCR purification kit (QIAGEN #28106). Briefly, 300 µL of buffer PB were added to each sample before transfer to a QIAquick column and centrifugation (13000 x rcf, 1 min). Flowthrough was discarded and the cDNA (captured in the column matrix) was washed twice by addition of 750 µL phosphate wash buffer (5 mM potassium phosphate (prepared from 1M potassium phosphate buffer, pH 8.5), 80% EtOH) and subsequent centrifugation and discarding of flowthrough as above. Finally, the column matrix was dried by additional centrifugation for 1 min at maximum speed, and elution of purified cDNA was performed with 60 µL 4 mM potassium phosphate (diluted from 1M potassium phosphate buffer, pH 8.5). Samples were dried completely in a SpeedVac for 45 min and then resuspended in 4.5 µL of 0.1 M Na2CO3 buffer. To label the samples with fluorescent dyes, 4.5 µL of Cy5 or Cy3 NHS-ester (GE healthcare #PA25001 and #PA23001, one aliquot dissolved in 73 µL DMSO and stored at -80°C) were added and the samples were mixed and incubated at room temperature in the dark for 1 h. To remove uncoupled NHS-ester dyes, labeled cDNA samples were purified using the QIAquick PCR purification kit (QIAGEN #28106) according to the manufacturer’s instructions. After elution of the purified labeled cDNA in 60 µL Buffer EB, samples were again completely dried in a SpeedVac for 45 min. Subsequently, samples were resuspended in 24 µL hybridization buffer (50% N,N-Dimethylformamide (Sigma #D4551), 5xSSC, 0.1% SDS) and 1 µL human COT-1 DNA (lifetechnologies #15279-011, 20µg/µL, prepared according to the manufacturer’s instructions) as well as 1 µL poly(A)-DNA (20µg/µL, lifetechnologies primer service) were added to block nonspecific hybridization.

growth_protocol: For experiments, hMADS-2 cells (Rodriguez et al., 2005, PMID: 15867092) were used. Medium for proliferation of hMADS cells was termed Medium I and consisted of (DMEM 1 g/l Glc (Lonza #BE12-707F), 2mM L-Gln (Invitrogen/ Gibco #25030-024), 10mM HEPES (Invitrogen/ Gibco #15630-056), 100ug/ml Normocin (InVivogen #ant-nr-2), 10% FBS (Pan-Biotech, # P30-3300, lot.no. P250330), supplemented with 2.5 ng/mL human Fibroblast Growth Factor 2 (hFGF2, Sigma #F0291). In this medium, hMADS cells had population doubling times of 48-96 h (depending on the passage number, i.e. the replicative age of cells). At densities in the range of 50–80% of optical confluence, passaging of cells was performed at passaging ratios between 1:2 and 1:4, depending on the actual population doubling time. Cells were cultivated in 100 mm dishes (Greiner Bio-One #664160), with 10 ml Medium I per dish, at 37°C in a humidified atmosphere with 5% CO2. For passaging, old medium was aspirated and cells were washed with Phosphate Buffered Saline (PBS, Invitrogen / Gibco #10010015) before incubation with 0.05% Trypsin with EDTA in PBS (Invitrogen / Gibco #15400054; 1mL per 100 mm dish) for 3–5 min at 37°C. Subsequently, Trypsin was inactivated by addition of Medium I (prewarmed to 37°C), and the cell suspension was transferred to new culture dishes according to the desired passaging ratio.

extract_protocol: Cells were harvested with TRIzol reagent (lifetechnologies, Catalog number 15596-026). Total RNA was isolated according to the manufacturer's instructions and dissolved in RNase-free H2O.

treatment_protocol: hMADS cells were grown to confluence in Medium I, designated day -2. Two days later (day 0), adipocyte differentiation was induced by changing the medium to Medium II, consisting of DMEM(1 g/L Glc, Lonza Lonza #BE12-707F)/ Ham’s F12 (Lonza # BE12-615F) (50:50), 2mM L-Gln (Invitrogen/ Gibco #25030-024), 10mM HEPES (Invitrogen/ Gibco #15630-056), 100 µg/mL Normocin (InVivogen #ant-nr-2), 860 nM human insulin (Sigma #I9278), 10 µg/mL apo-transferrin (Sigma #T2252), 0.2 nM T3 (Sigma #T6397), 100 nM rosiglitazone (Cayman Chemicals / BRL49653), 100 µM IBMX (Sigma #I7018) and 1 µm Dexamethasone (Sigma #D4902). 10 ml Medium II were used for 1 100mm dish. Medium was replaced 3 days later by “Medium III”, which was identical to Medium II except that IBMX an Dexamethasone were omitted. Subsequently, Medium III was replaced every 2-3 days.

tag: differentiation stage

value: terminal stage of adipocyte differentiation (15 days post induction)

source_name: proliferating hMADS cells

value: undifferentiated, proliferating cells


title: adipo-d3_siSNEV_vs_siC_rep2

description: Biological replicate 2, cells harvested at day 3 after induction of adipocye differentiation

data_processing: GenePix Pro 4.1 was used to filter out spots of suboptimal quality prior to further analysis. High intensity spots were filtered out if more than 20% of spot pixels were saturated in either of the two channels. Inhomogenity of spots was estimated by comparing (for either of the two channels) the median of pixel intensities to the mean; if the difference was greater than 20%, the spot was considered as inhomogenous and thus filtered out. Low intensity spots were defined by two distinct approaches: (i) if the sum of the medians/means of the pixel intensities in both channels was lower than 700, or (ii) if not more than 55 percent of the pixels within a spot had intensities higher than the intensity of the surrounding background plus one standard deviation of the background pixels. Subsequently, the filtered raw data was background corrected (by estimation and subtraction of local background), normalized by global mean and dye-swap pairs using ArrayNorm (PMID: 15073026). Finally, features detecting the same transcript were combined by averaging and the data was exported as text-file containing log2 transformed ratios of gene expression.

source_name: ASCs, transfected with siRNA targeting SNEV

label_protocol: Concentration of total RNA samples was determined by UV/VIS photospetrometry on a NanoDrop-1000 device, and aliquots of 15 µg total RNA in 16.5 µL RNase-free H2O were prepared. For reverse transcription (RT), 2 µL random primers (3 mg/ml, lifetechnologies # 48190-011) were added to the RNA sample, followed by incubation at 70°C for 10 min and snap-freezing on ice for 30 sec. Subsequently, the following agents were added to complete the RT reactions: 0.6 µL aminoallyl-dNTP mix (25 mM dATP, 25 mM dCTP, 25 mM dGTP, 15mM dTTP (all lifetechnologies #10297-018), 10mM aminoallyl-dUTP (Sigma #A0410)), 6 µL 5x first strand buffer, 3 µL 0.1 M DTT, 2 µL SuperScript II Reverse Transcriptase (all lifetechnologies #18064-014). After mixing, RT reactions were incubated at 42°C for ~18 h. RNA was then hydrolyzed by adding 10 µL 1  M NaOH and 10 µL 0.5 M EDTA, followed by incubation at 65°C for 15 min. Subsequently, pH was neutralized by adding 10 µL 1 M HCl. To remove unincorporated aminoallyl-dUTP, reactions were purified based on the QIAquick PCR purification kit (QIAGEN #28106). Briefly, 300 µL of buffer PB were added to each sample before transfer to a QIAquick column and centrifugation (13000 x rcf, 1 min). Flowthrough was discarded and the cDNA (captured in the column matrix) was washed twice by addition of 750 µL phosphate wash buffer (5 mM potassium phosphate (prepared from 1M potassium phosphate buffer, pH 8.5), 80% EtOH) and subsequent centrifugation and discarding of flowthrough as above. Finally, the column matrix was dried by additional centrifugation for 1 min at maximum speed, and elution of purified cDNA was performed with 60 µL 4 mM potassium phosphate (diluted from 1M potassium phosphate buffer, pH 8.5). Samples were dried completely in a SpeedVac for 45 min and then resuspended in 4.5 µL of 0.1 M Na2CO3 buffer. To label the samples with fluorescent dyes, 4.5 µL of Cy5 or Cy3 NHS-ester (GE healthcare #PA25001 and #PA23001, one aliquot dissolved in 73 µL DMSO and stored at -80°C) were added and the samples were mixed and incubated at room temperature in the dark for 1 h. To remove uncoupled NHS-ester dyes, labeled cDNA samples were purified using the QIAquick PCR purification kit (QIAGEN #28106) according to the manufacturer’s instructions. After elution of the purified labeled cDNA in 60 µL Buffer EB, samples were again completely dried in a SpeedVac for 45 min. Subsequently, samples were resuspended in 24 µL hybridization buffer (50% N,N-Dimethylformamide (Sigma #D4551), 5xSSC, 0.1% SDS) and 1 µL human COT-1 DNA (lifetechnologies #15279-011, 20µg/µL, prepared according to the manufacturer’s instructions) as well as 1 µL poly(A)-DNA (20µg/µL, lifetechnologies primer service) were added to block nonspecific hybridization.

growth_protocol: ASCs were isolated according to the protocol of Wolbank et al., 2009 (PMID: 19125642) and maintained in DMEM (4.5g/l glucose) supplemented with 4mM L-Glutamine , 10%FCS, 1 ng/ml βFGF at 37°C and 5% CO2.

extract_protocol: At day 3 after induction of adipocyte differentiation, cells were harvested with TRIzol reagent (life technologies). Total RNA was isolated according to the manufacturer's instructions and dissolved in RNase-free H2O.

treatment_protocol: 14000 cells were seeded in 1.9 cm2 plate 48 hours prior to siRNA transfection. 50nM SNEV siRNA and control siRNA were introduced into cells by using DharmaFECT1 transfection reagent (Dharmacon) according to the manufacturer instruction. Adipogenic differentiation was induced by replacing the growth medium with fresh DMEM supplemented with 50mM 3-Isobutyl-1-methylxanthine (Sigma) 100µM Dexamethasone (Sigma), 50 µM hydrocortisone (Sigma), and 6mM Indomethacin (Sigma).

tag: differentiation

value: early adipocyte differentiation

source_name: ASCs, transfected with control siRNA


title: hMADS-cells_adipo-differentiation_day1

description:
data for sample was generated from 2 independent biological replicates, each of which was analyzed in technical duplicates; pairs of hybridizations with identical RNA, but reverse dye assignment (dye swap) are specified by the first three digits of the names of the raw data files
d1

source_name: hMADS cells, 1 day after induction of adipocyte differentiation

value: early adipocyte differentiation (1 day post induction)


title: hMADS-cells_2-day-post-confluence_day0

description:
data for sample was generated from 2 independent biological replicates, each of which was analyzed in technical duplicates; pairs of hybridizations with identical RNA, but reverse dye assignment (dye swap) are specified by the first three digits of the names of the raw data files
d0

source_name: hMADS cells, 2-day post confluence

value: before start of differentiation, 2-day post confluence


title: hMADS-cells_adipo-differentiation_day5

description:
data for sample was generated from 2 independent biological replicates, each of which was analyzed in technical duplicates; pairs of hybridizations with identical RNA, but reverse dye assignment (dye swap) are specified by the first three digits of the names of the raw data files
d5

source_name: hMADS cells, 5 days after induction of adipocyte differentiation

value: early adipocyte differentiation (5 days post induction)


title: hMADS-cells_confluent_day-2

description:
data for sample was generated from 2 independent biological replicates, each of which was analyzed in technical duplicates; pairs of hybridizations with identical RNA, but reverse dye assignment (dye swap) are specified by the first three digits of the names of the raw data files
d-2

source_name: hMADS cells, confluent stage

value: before start of differentiation, confluent stage


title: S. japonicum infected pooled mice plasma Replicate 1 (I1)

description: the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual

scan_protocol: the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).


title: hMADS-cells_adipo-differentiation_day10

description:
data for sample was generated from 2 independent biological replicates, each of which was analyzed in technical duplicates; pairs of hybridizations with identical RNA, but reverse dye assignment (dye swap) are specified by the first three digits of the names of the raw data files
d10

source_name: hMADS cells, 10 days after induction of adipocyte differentiation

value: late stage of adipocyte differentiation (10 days post induction)


title: hMADS-cells_adipo-differentiation_day2

description:
data for sample was generated from 2 independent biological replicates, each of which was analyzed in technical duplicates; pairs of hybridizations with identical RNA, but reverse dye assignment (dye swap) are specified by the first three digits of the names of the raw data files
d2

source_name: hMADS cells, 2 days after induction of adipocyte differentiation

value: early adipocyte differentiation (2 days post induction)


title: adipo-d3_siSNEV_vs_siC_rep1

description: Biological replicate 1, cells harvested at day 3 after induction of adipocye differentiation


title: Control pooled mice plasma Replicate 2 (C2)

source_name: control pooled mice plasma

value: control uninfected


title: Control pooled mice plasma Replicate 1 (C1)


title: RCH_156_v4_new

city: Leeds

first: Chulin

last: Sha

address: Woodhouse Lane

department: School of Mole&Cell Biology

country: United Kingdom

institute: University of Leeds

description: 6 month follow up

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Arrays were scanned on a BeadArray reader

data_processing: The data were normalised using lumi package in R

source_name: Biopsy

label_protocol: Standard Illumina label protocol

extract_protocol: Total RNA was extracted from 5mm paraffin sections using the Ambion RecoverAll kit standard protocol, with the exception of a 16-hour protease digestion. These were routinely collected tissue samples and no attempt was made to standardise fixation or processing protocols

value: DLBCL

value: Diffuse Large B-cell Lymphoma

value: R-CHOP

value: no


title: RCH_149_v4_new

description: 6 month follow up

value: unknown


title: RCH_154_v4_new

description: 6 month follow up


title: RCH_155_v4_new

description: 6 month follow up


title: RCH_146_v4_new

description: 6 month follow up


title: RCH_148_v4_new

description: 6 month follow up


title: RCH_153_v4_new

description: 6 month follow up


title: RCH_152_v4_new

description: 6 month follow up


title: RCH_147_v4_new

description: 6 month follow up


title: RCH_142_v4_new

description: 6 month follow up


title: RCH_150_v4_new

description: 6 month follow up


title: RCH_151_v4_new

description: 6 month follow up


title: RCH_141_v4_new

description: 6 month follow up


title: RCH_140_v4_new

description: 6 month follow up


title: RCH_139_v4_new

description: 6 month follow up


title: RCH_135_v4_new

description: 6 month follow up


title: RCH_144_v4_new

description: 6 month follow up


title: RCH_137_v4_new

description: 6 month follow up


title: RCH_136_v4_new

description: 6 month follow up


title: RCH_143_v4_new

description: 6 month follow up


title: RCH_145_v4_new

description: 6 month follow up


title: RCH_134_v4_new

description: 6 month follow up

value: yes


title: RCH_138_v4_new

description: 6 month follow up

value: BL


title: RCH_133_v4_new

description: 6 month follow up


title: RCH_132_v4_new

description: 6 month follow up


title: wild-type molar epithelia at E13.5, biologial replicate 4

city: Helsinki

first: Maria

last: Jussila

state: Helsinki

address: Viikinkaari 9

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

description: mandibular molar epithelia of 5 embryos of identical genotype pooled together

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute  • Transfer 200μl of hybridization solution to each array, then tape holes • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Probes were re-annotated using CustomCDF annotations. Data were quantile normalized and summarized by using RMA-package as applied in statistical environment R.

source_name: molar epithelia, wild-type

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Mandibular molar epithelia dissected from day E13.5 mouse embryos

extract_protocol: K14-cre43;Foxi3-floxed were identified manually, and confirmed together with wild-type embryos by genotyping after sample collection. Molar epithelium was separated enzymatically by dispase. Epithelia of both mandibular molars of each embryo were frozen on dry-ice and stored in -80°C. Molar epithelia of five embryos were pooled together at the time of RNA extraction. RNA was extracted using the RNeasy mini kit (Qiagen, Hilden, Germany).

value: mandibular molar epithelium

tag: genotype


title: RCH_131_v4_new

description: 6 month follow up


title: RCH_130_v4_new

description: 6 month follow up


title: RCH_128_v4_new

description: 6 month follow up


title: Foxi3 cKO molar epithelia at E13.5, biologial replicate 4

source_name: molar epithelia, Foxi3 cKO


title: RCH_125_v4_new

description: 6 month follow up


title: RCH_126_v4_new

description: 6 month follow up


title: wild-type molar epithelia at E13.5, biologial replicate 3


title: RCH_127_v4_new

description: 6 month follow up


title: RCH_129_v4_new

description: 6 month follow up


title: replicate1 U251 lysate 6Gy RT at 16hr

description: protein lysate

source_name: U251-GBM cell line/xenogrft

tag: cell line

value: 6Gy RT at 16hr


title: wild-type molar epithelia at E13.5, biologial replicate 2


title: replicate1 Control U251

description: protein lysate

value: control


title: Dox(+) - siDrosha

city: Chuo-ku

first: Mitsuhiro

last: Machitani

state: Tokyo

address: 5-1-1 Tsukiji

country: Japan

institute: National Cancer Center Research Institute

hyb_protocol: The samples were hybridized for 18 hr on GeneChip miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The normalization of RMA was performed using Affymetrix Expression Console Software.

source_name: HeLa-shDicer cells treated with siDrosha and Dox

label_protocol: Biotinylated samples were prepared using FlashTag Biotin HSR RNA labeling Kit for Affymetrix GeneChip miRNA Arrays according the the user manual.

growth_protocol: Hela-shDicer cells, which inducibly express shDicer by Dox treatment, were cultured in Dox-containing medium.

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

treatment_protocol: The cells were transfected with siControl or siAgp2. After 48 h incubation, total RNA was extracted using Isogen (Nippongen).

value: HeLa cells inducibly expressing shDicer under control of Doxycycline (HeLa-shDicer cells)

tag: agent

value: Dox

value: siDrosha


title: Dox(-) - siDrosha

source_name: HeLa-shDicer cells treated with siDrosha and without Dox

value: no Dox

tag: genotype/variation


title: RCH_123_v4_new

description: 6 month follow up


title: Foxi3 cKO molar epithelia at E13.5, biologial replicate 3


title: Foxi3 cKO molar epithelia at E13.5, biologial replicate 2


title: wild-type molar epithelia at E13.5, biologial replicate 1


title: RCH_122_v4_new

description: 6 month follow up


title: RCH_120_v4_new

description: 6 month follow up


title: RCH_119_v4_new

description: 6 month follow up


title: Dox(-) - siControl

source_name: HeLa-shDicer cells treated without Dox

value: siControl


title: Dox(-) - siAgo2

source_name: HeLa-shDicer cells treated with siAgo2 and without Dox


title: Dox(+) - siAgo2

source_name: HeLa-shDicer cells treated with siAgo2 and Dox


title: RCH_124_v4_new

description: 6 month follow up


title: Foxi3 cKO molar epithelia at E13.5, biologial replicate 1


title: RCH_116_v4_new

description: 6 month follow up


title: RCH_118_v4_new

description: 6 month follow up


title: RCH_117_v4_new

description: 6 month follow up


title: RCH_113_v4_new

description: 6 month follow up


title: RCH_121_v4_new

description: 6 month follow up


title: RCH_111_v4_new

description: 6 month follow up


title: RCH_103_v4_new

description: 6 month follow up


title: RCH_112_v4_new

description: 6 month follow up


title: RCH_114_v4_new

description: 6 month follow up


title: RCH_110_v4_new

description: 6 month follow up


title: RCH_104_v4_new

description: 6 month follow up


title: RCH_115_v4_new

description: 6 month follow up


title: RCH_109_v4_new

description: 6 month follow up


title: RCH_108_v4_new

description: 6 month follow up


title: RCH_107_v4_new

description: 6 month follow up


title: RCH_105_v4_new

description: 6 month follow up


title: RCH_106_v4_new

description: 6 month follow up


title: RCH_98_v4_new

description: 6 month follow up


title: RCH_100_v4_new

description: 6 month follow up


title: RCH_102_v4_new

description: 6 month follow up


title: RCH_95_v4_new

description: 6 month follow up


title: RCH_96_v4_new

description: 6 month follow up


title: RCH_97_v4_new

description: 6 month follow up


title: RCH_99_v4_new

description: 6 month follow up


title: RCH_101_v4_new

description: 6 month follow up


title: RCH_93_v4_new

description: 6 month follow up


title: RCH_94_v4_new

description: 6 month follow up


title: RCH_92_v4_new

description: 6 month follow up


title: RCH_91_v4_new

description: 6 month follow up


title: RCH_89_v4_new

description: 6 month follow up


title: RCH_86_v4_new

description: 6 month follow up


title: RCH_87_v4_new

description: 6 month follow up


title: RCH_88_v4_new

description: 6 month follow up


title: RCH_90_v4_new

description: 6 month follow up


title: RCH_83_v4_new

description: 6 month follow up


title: RCH_85_v4_new

description: 6 month follow up


title: RCH_84_v4_new

description: 6 month follow up


title: RCH_82_v4_new

description: 6 month follow up


title: RCH_81_v4_new

description: 6 month follow up


title: RCH_77_v4_new

description: 6 month follow up


title: RCH_80_v4_new

description: 6 month follow up


title: RCH_78_v4_new

description: 6 month follow up


title: RCH_76_v4_new

description: 6 month follow up


title: RCH_79_v4_new

description: 6 month follow up


title: N_adequate_9_placenta

city: Setagaya

first: Kazuhiko

last: Nakabayashi

department: Department of Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development

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

scan_protocol: Arrays were imaged using the Illumina's iScan system using standard recommended scanner setting

data_processing:
The intensity files (.idat), produced by the Illumina iScan system, were processed using Illumina GenomeStudio V2011.2 (Methylation Analysis Module v1.9.0) using Normalization to Internal Controls and Background Subtraction options. The average beta values were corrected using ComBat, an Empirical Bayes method-based statistical tool , to remove array-batch effects.
Unmethylated and methylated signal intensities

label: Cy3, Cy5

source_name: placenta (chorionic villi)

label_protocol: Standard Illumina labelling protocol

extract_protocol: Genomic DNA extracted using QIAamp DNA Mini Kit (Qiagen)

value: Male

tag: health state

value: Normal

tag: maternal gestational weight gain (g)


title: N_excessive_3_placenta


title: N_excessive_2_placenta


title: RCH_74_v4_new

description: 6 month follow up

value: DLBCL


title: RCH_75_v4_new

description: 6 month follow up

value: Diffuse Large B-cell Lymphoma


title: N_excessive_1_placenta


title: N_excessive_4_placenta

value: Female


title: N_adequate_7_placenta


title: N_excessive_5_placenta


title: N_adequate_5_placenta


title: N_adequate_8_placenta


title: N_adequate_4_placenta


title: N_adequate_1_placenta


title: N_adequate_3_placenta


title: N_adequate_2_placenta


title: N_adequate_6_placenta


title: CGH: Bert_v_Bert

city: Saint Paul

first: Robert

middle: M

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

hyb_protocol: Genomic DNA were hybridized to the microarray according to the manufacturer instructions (NimbleGen CGH User Guide Ver 9.1)

scan_protocol: Slides were scanned on the NimbleGen MS 200 Scanner (Roche/NimbleGen, Madison,WI) according to the array manufacturer instructions (NimbleGen CGH User Guild Ver 9.1)

data_processing: Data was analyzed using the Roche NimbleGen DEVA software.

organism: Glycine max

source_name: soybean line Bert-MN-01

label_protocol: 500 ng of genomic DNA was labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide Ver 9.1.

growth_protocol: single plant leaf tissue

extract_protocol: Genomic DNA samples were isolated using the Qiagen Plant DNeasy protocol

tag: tissue

value: single plant leaf tissue


title: RCH_72_v4_new

description: 6 month follow up

tag: treatment

value: R-CHOP

value: no


title: CGH: WPT_0391-1-6_v_Bert

source_name: transformed soybean plant WPT_0391-1-6


title: CGH: Williams_v_Wm82

source_name: soybean line Williams

value: Williams

source_name: soybean line Wm82-ISU-01


title: CGH: WPT_0384-1-1_v_Bert

source_name: transformed soybean plant WPT_0384-1-1


title: N_insufficient_5_placenta

tag: gender


title: N_insufficient_4_placenta


title: CGH: WPT_0389-2-2_v_Bert

source_name: transformed soybean plant WPT_0389-2-2


title: RCH_70_v4_new

description: 6 month follow up

tag: age


title: RCH_69_v4_new

description: 6 month follow up


title: CGH: WPT_0301-3-13_v_Wm82

source_name: transformed soybean plant WPT_0301-3-13


title: N_insufficient_3_placenta


title: RCH_67_v4_new

description: 6 month follow up

source_name: Biopsy


title: CGH: WPT_0312-5-126_v_Bert

source_name: transformed soybean plant WPT_0312-5-126


title: RCH_68_v4_new

description: 6 month follow up

value: BL


title: RCH_66_v4_new

description: 6 month follow up

value: unknown


title: RCH_73_v4_new

description: 6 month follow up


title: RCH_65_v4_new

description: 6 month follow up


title: RCH_62_v4_new

description: 6 month follow up


title: RCH_63_v4_new

description: 6 month follow up


title: HMRN_59_v4_new

value: CODOX-M/IVAC


title: N_insufficient_2_placenta


title: RCH_61_v4_new

description: 6 month follow up


title: FGR_excessive_3_placenta

value: Fetal growth restriction


title: RCH_64_v4_new

description: 6 month follow up


title: HMRN_58_v4_new

value: Burkitt lymphoma

value: COP/COPAD/COPADM

value: yes


title: HMRN_60_v4_new


title: HMRN_57_v4_new_rep


title: N_insufficient_1_placenta


title: HMRN_57_v4_new


title: TCPSD

city: Boulder

first: Kristi

middle: S

last: Anseth

state: CO

address: 3415 Colorado Ave

institute: University of Colorado - Boulder

hyb_protocol: Processed samples was then hybridized to a GeneChip Porcine Gene 1.0 ST array in the GeneChip® Hybridization Oven 645 with rotation at 60 rpm for 16 hr at 45°C. The arrays are washed and stained using FS450_0002 protocol.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: Transcription Analysis Console (Affymetrix) and Expression Console (Affymetrix)  using the Robust Multi-array Average (RMA) approach

organism: Sus scrofa

source_name: valvular interstitial cells cultured on tissue culture polystyrene, replicate D

label_protocol: Following the manufacturer’s protocol, 150 ng of starting total RNA was converted to cDNA with the GeneChip® WT PLUS Reagent Kit (Affymetrix). First, in vitro transcription is performed using the this kit to generate cRNA. The cRNA was then converted to single strand cDNA in second cycle. Last, the cDNA was fragmented and end-labeled with biotin.

growth_protocol: VICs were isolated from aortic valve leaflets of fresh porcine hearts (Hormel). A fraction of these freshly isolated cells were immediately flash-frozen in TriReagent (Sigma-Aldrich) to serve as the freshly isolated VIC control. The remaining cells were re-suspended in growth media composed of Media 199 (Life Technologies) supplemented with 15% fetal bovine serum (FBS, Life Technologies), 1% penicillin-streptomycin and 0.5 μg/mL fungizone. These VICs were grown to ~80% confluency on TCPS prior to use in experimental conditions.

extract_protocol: RNA was isolated from VICs 48 h after seeding or encapsulating using TriReagent (Sigma-Aldrich) according to the manufacturer’s instructions. Two sequential extractions with 1-bromo-3-chloropropane (Sigma-Aldrich) were followed by precipitation with 2-propanol (Sigma-Aldrich). RNA pellets were washed twice with 75% ethanol (Sigma-Aldrich) and re-suspended in water.

treatment_protocol: valvular interstitial cells were cultured in 2D or 3D PEG hydrogel systems and were compared to culture on tissue culture polystyrene and freshly isolated cells

value: aortic valve

tag: cell type

value: VIC

tag: culture conditions

value: tissue culture polystyrene

tag: culture time

value: 2 days


title: FGR_adequate_4_placenta

value: Male


title: TCPSC

source_name: valvular interstitial cells cultured on tissue culture polystyrene, replicate C


title: RCH_71_v4_new

description: 6 month follow up

value: DLBCL

value: Diffuse Large B-cell Lymphoma


title: HMRN_56_v4_new


title: FGR_adequate_5_placenta

value: Female


title: FGR_excessive_2_placenta


title: HMRN_55_v4_new

value: Diffuse Large B-cell Lymphoma MYC rearranged

value: R-CHOP


title: FGR_adequate_3_placenta


title: HMRN_52_v4_new


title: FGR_adequate_2_placenta


title: FGR_excessive_1_placenta


title: TCPSB

source_name: valvular interstitial cells cultured on tissue culture polystyrene, replicate B


title: FC

source_name: freshly isolated valvular interstitial cells, replicate C

value: freshly isolated (not cultured)


title: HMRN_53_v4_new

value: BL


title: FGR_insufficient_2_placenta


title: FB

source_name: freshly isolated valvular interstitial cells, replicate B


title: 3DC

source_name: valvular interstitial cells cultured within 3D PEG hydrogel substrate, replicate C

value: 3D PEG hydrogel substrate


title: FGR_excessive_4_placenta

value: Fetal growth restriction


title: FGR_insufficient_3_placenta


title: H3 + H4

city: Burley-in-Wharfedale

first: David

middle: Edwin

last: Iles

state: West Yorkshire

address: 50 Hall Drive

institute: Omics Ltd.

description: ChIP-chip spermatozoal chromatin anti-H3 + anti-H4

hyb_protocol: Labelled DNAs were precipitated with 0.1 volume 5 M NaCl and 1 volume isopropanol. ChIP and input DNAs were quantified and pooled in 43 μl hybridization buffer (NimbleGen Hybridization Kit, LS; Roche-Nimlegen; Cat. No. 05583934001); 41 μl volumes were hybridized for 20 hours at 42C to Nimblegen 2.1M arrays in a NimbleGen Hybridization System 4. Slides were washed in Nimblegen Wash buffers I, II and III according to manufacturer's instructions.

scan_protocol: Slides were scanned using a GenePix 4000B Microarray Scanner according to manufacturer's instructions.

data_processing:
Data were collected and processed using NimbleScan software as outlined in the Nimblegen Arrays User's Guide described at http://www.flychip.org.uk/protocols/chip/NimblegenBioPrime.php.
scaled log2 ratios (Cy5/Cy3)

organism: Drosophila melanogaster

source_name: H3+H4 ChIP DNA

label_protocol: Random primers were annealed to 1 μg denatured DNA templates and extended by Klenow fragment incorporating Cy3- or Cy5-dCTP at the Flychip Microarray Facility (http://www.flychip.org.uk/protocols/chip/NimblegenBioPrime.php) using a Bioprime DNA Labeling System (Invitrogen; Cat. No. 18094-011).

extract_protocol: For each ChIP replicate, 10E6 frozen spermatozoa were thawed at room temperature, washed in cold PBS and fixed in 100 μl 1% formaldehyde in PBS at room temperature for 10 minutes. Crosslinking was quenched by the addition of 400 μl 0.125 M glycine in PBS and incubation at 4C for 5 minutes. Cells were washed twice in 500 µl ice-cold PBS and incubated for 1 hour at room temperature in 500 µl lysis buffer A (10mM DTT, 10 mM HEPES pH8, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100, 10mM DTT, 0.5% (w/v) SDS and protease inhibitors (10 mg/ml aprotinin, 5 mg/ml leupeptin, and 0.5 mM PMSF)). The DTT was quenched by the addition of N-ethylmaleimide to a final concentration of 5 mM and the cells were resuspended in 100 µl lysis buffer B (10 mM HEPES pH8, 200 mM NaCl, 0.5 mM EGTA, 1 mM EDTA, 0.01% Triton X-100 and protease inhibitors), pelleted and resuspended in 100 μl IP buffer (25 mM Tris pH8, 150 mM NaCl, 2 mM EDTA, 1%Triton X-100 and 7.5% glycerol) with 0.25% SDS and protease inhibitors. Chromatin was sheared to approximately 500 bp fragments by sonication on ice using a MEM Soniprep 150 sonicator at 6 micron amplitude for 5 cycles of 20 seconds sonication and 40 seconds cooling. Lysates were diluted in four volumes IP buffer and cleared by centrifugation. For each IP, a 10 μl suspension of Protein G Dynabeads (pre-absorbed with BSA and herring sperm DNA) was incubated in 500 μl 100 mM sodium phosphate pH8, 0.5% BSA containing 5 µg ChIP-grade antibody (or 5 µg goat anti-rabbit IgG antibody for mock IPs) at 4C with rotation for 2 hours. The Dynabeads were washed in IP buffer and resuspended in 490 μl cleared lysate along with 25 μg sonicated herring sperm DNA. Reactions were incubated at 4C with rotation for 4 hours. Immune complexes were recovered, suspended in 500 μl buffer 1 (20 mM Tris-HCl pH8, and 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS and protease inhibitors) and incubated on ice for 10 minutes before being washed twice in 500 μl buffer 2 (20 mM Tris-HCl pH8, 500 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS and protease inhibitors) for 10 minutes at 4C with rotation and once in 500 μl buffer 3 (10 mM Tris-HCl pH8, 0.25 M LiCl, 1% sodium deoxycholate, 1 mM EDTA, and 1% NP40) for 10 minutes at 4C with rotation. Finally, the beads were washed twice in ice-cold TNE buffer (10 mM Tris pH8, 1 mM EDTA, 50 mM NaCl). Chromatin was eluted from the beads in 50 μl 1% SDS, 0.1 M NaHCO3 pH10.1 at room temperature with rotation for 15 minutes. Eluates were transferred to fresh non-stick tubes, the procedure was repeated and the eluates were pooled. To each pooled eluate, 4 μl 5 M NaCl and 5 µl 0.2 M EDTA were added and eluates were incubated overnight at 55C. The pH of the eluates was adjusted to 8.3 by the addition of 4 μl 2 M Tris pH6.5. Residual RNAs were removed by the addition of 1 µl 10 mg/ml RNase A followed by incubation at 37C for 30 minutes, and proteins were removed by the addition of 1 μl 10 mg/ml proteinase K and incubation at 55C for 4 hours. Input DNA was extracted from the sonicated chromatin of 2 x 10E6 cells in 200 μl IP buffer by the addition of 10 µl 3 M sodium acetate pH7 and 10 µl 10 % SDS, followed by overnight incubation at 55C. Residual RNAs and proteins were removed as before. DNAs were recovered using a GeneluteTM PCR Clean-Up kit (Sigma-Aldrich) and quantified using a PicoGreen dsDNA Quant-iT(TM) kit (Invitrogen) according to manufacturers’ instructions. DNAs of input, IP and mock samples were amplified in two steps; firstly, DNA was amplified using a GenomePlex Single Cell kit (WGA4; Sigma-Aldrich), and secondly, the DNA was re-amplified using a GenomePlex Re-amplification Kit (WGA3; Sigma-Aldrich) according to the manufacturer’s instructions.

value: mature spermatozoa

tag: chip antibody

value: anti-H3 + anti-H4

source_name: H3H4 input DNA

value: none, input DNA


title: FGR_insufficient_4_placenta

source_name: placenta (chorionic villi)


title: 3DD

source_name: valvular interstitial cells cultured within 3D PEG hydrogel substrate, replicate D

value: aortic valve


title: HMRN_51_v4_new

value: Burkitt lymphoma

value: CODOX-M/IVAC

value: yes


title: H4

description: ChIP-chip spermatozoal chromatin anti-H4

source_name: H4 ChIP DNA

value: rabbit polyclonal anti-histone H4; Abcam ab10158

source_name: H4 input DNA


title: mock_swap

description: ChIP-chip spermatozoal chromatin non-specific antibody

source_name: mock input DNA

source_name: mock ChIP DNA

value: goat polyclonal anti-rabbit IgG; Thermo Scientific 31210


title: FGR_insufficient_5_placenta


title: FGR_adequate_1_placenta


title: 3DB

source_name: valvular interstitial cells cultured within 3D PEG hydrogel substrate, replicate B

value: VIC

value: 2 days


title: mock


title: H3K36me3

description: ChIP-chip spermatozoal chromatin anti-H3K36me3

source_name: H3K36me3 ChIP DNA

value: rabbit polyclonal anti-histone H3K36me3; Abcam ab9050

source_name: H3K36me3 input DNA


title: HMRN_54_v4_new

source_name: Biopsy

value: Burkitt lymphoma - HIV associated


title: H3K36me3_swap


title: HMRN_50_v4_new

value: DLBCL


title: H3

description: ChIP-chip spermatozoal chromatin anti-H3

source_name: H3 ChIP DNA

value: rabbit polyclonal anti-histone H3; Cell Signaling #2650

source_name: H3 input DNA


title: HMRN_49_v4_new

value: Diffuse Large B-cell Lymphoma MYC rearranged


title: HMRN_48_v4_new_rep

value: BL

value: Diffuse Large B-cell Lymphoma

value: no


title: H3K27me3_swap

description: ChIP-chip spermatozoal chromatin anti-H3K27me3

source_name: H3K27me3 input DNA

value: mature spermatozoa

value: none, input DNA

source_name: H3K27me3 ChIP DNA

value: rabbit polyclonal anti-histone H3K27me3; Abcam ab6002


title: 2DB

source_name: valvular interstitial cells cultured on 2D PEG hydrogel substrate, replicate B

value: aortic valve

value: 2D PEG hydrogel substrate


title: 2DC

source_name: valvular interstitial cells cultured on 2D PEG hydrogel substrate, replicate C


title: HMRN_46_v4_new

description: relapse sample

value: Burkitt lymphoma

value: yes


title: 2DD

source_name: valvular interstitial cells cultured on 2D PEG hydrogel substrate, replicate D

value: VIC


title: HMRN_48_v4_new

value: CODOX-M/IVAC


title: HMRN_43_v4_new_rep

value: unknown


title: HMRN_44_v4_new


title: HMRN_47_v4_new


title: HMRN_43_v4_new


title: H3K27me3


title: HMRN_45_v4_new


title: FGR_insufficient_1_placenta

source_name: placenta (chorionic villi)

value: Female

value: Fetal growth restriction


title: H3K9me3

description: ChIP-chip spermatozoal chromatin anti-H3K9me3

source_name: H3K9me3 ChIP DNA

value: rabbit polyclonal anti-histone H3K9me3; Abcam ab8898

source_name: H3K9me3 input DNA


title: H3K9me3_swap


title: HMRN_40_v4_new

value: DLBCL


title: HMRN_38_v4_new


title: y2

city: Lausanne

first: Romano

last: Regazzi

address: Rue du Bugnon 9

department: DNF

country: Switzerland

institute: University of Lausanne

description: [Y2array512, control](normalized)

hyb_protocol: Hybridization was performed in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Scanner.

data_processing:
Data was extracted using Agilent Feature Extraction software. Raw intensity extraction and probe flagging was done according to the following Rules. All probes were regarded as present, marginal (background is not uniform or it is a population outlier) or absent (feature is not positive or significant, not uniform, not above background, saturated or is a population outlier). Probes flagged as absent were excluded from the fold change analysis and are not shown in the matrix.
Normalization was performed using the AgilentGeneSpring GX v11.5.1. Raw intensity values less than 5 are reset to 5.

organism: Rattus norvegicus

source_name: pancreatic islets_3 months

label_protocol: Arraystar RNA Flash Labeling Kit was used for sample labeling

extract_protocol: Wistar male rats were euthanised with CO2. Pancreatic islets were extracted via collagenase digestion. RNA was isolated with miRNeasy kit (Qiagen, Hombrechtikon, Switzerland).

tag: strain

value: wistar

value: male

value: 3 months

value: pancreatic islets


title: HMRN_30_v4_new

value: BL

value: Diffuse Large B-cell Lymphoma MYC rearranged

value: R-CHOP


title: HMRN_39_v4_new


title: 12m

description: [12marray212, condition](normalized)

source_name: pancreatic islets_12 months

value: 12 months


title: HMRN_34_v4_new


title: HMRN_42_v4_new


title: HMRN_29_v4_new

value: Burkitt lymphoma

value: COP/COPAD/COPADM


title: HMRN_33_v4_new

value: yes


title: o2

description: [02array512, condition](normalized)


title: y1

description: [Y1array91214, control](normalized)


title: HMRN_37_v4_new


title: HMRN_31_v4_new


title: y3

description: [Y3array512, control](normalized)


title: HMRN_41_v4_new

value: Diffuse Large B-cell Lymphoma

value: CODOX-M/IVAC

value: no


title: HMRN_32_v4_new


title: HMRN_36_v4_new

value: unknown


title: HMRN_27_v4_new

value: Burkitt Lymphoma


title: FD

source_name: freshly isolated valvular interstitial cells, replicate D

value: aortic valve

value: VIC

value: freshly isolated (not cultured)


title: HMRN_25_v4_new

value: Burkitt lymphoma - HIV associated


title: HMRN_24_v4_new


title: HMRN_19_v4_new

value: DLBCL

value: DLBCL - HIV+


title: HMRN_23_v4_new

value: Diffuse Large B-cell Lymphoma MYC rearranged


title: HMRN_20_v4_new


title: HMRN_35_v4_new

value: R-CHOP


title: HMRN_21_v4_new

value: BL


title: HMRN_28_v4_new

value: Burkitt lymphoma


title: HMRN_22_v4_new


title: HMRN_26_v4_new


title: o1

description: [01array512, condition](normalized)

value: wistar

value: male

value: 12 months

value: pancreatic islets


title: HMRN_15_v4_new

value: CODOX-M/IVAC

value: yes


title: LY_8_v4_new


title: HMRN_18_v4_new


title: LY_7_v4_new

value: Burkitt Lymphoma


title: HMRN_12_v4_new

value: COP/COPAD/COPADM


title: HMRN_11_v4_new


title: HMRN_13_v4_new


title: HMRN_17_v4_new


title: LY_5_v4_new


title: LY_4_v4_new

value: Diffuse Large B-cell Lymphoma

value: no


title: HMRN_16_v4_new

value: unknown


title: HMRN_10_v4_new


title: HMRN_9_v4_new

value: DLBCL


title: LY_1_v4_new


title: LY_3_v4_new


title: LY_2_v4_new


title: HMRN_71_v4_rep


title: HMRN_14_v4_new


title: HMRN_70_v4_rep

description: replicate sample


title: HMRN_67_v4_rep

description: replicate sample


title: HMRN_69_v4_rep

description: replicate sample


title: HMRN_66_v4_rep

description: replicate sample


title: HMRN_65_v4_rep

description: replicate sample


title: LY_6_v4_new


title: HMRN_64_v4_rep

description: replicate sample


title: HMRN_62_v4_rep

description: replicate sample


title: HMRN_62_v4_rep_2

description: replicate sample


title: HMRN_63_v4_rep

description: replicate sample


title: HMRN_57_v4_rep

description: replicate sample


title: HMRN_59_v4_rep

description: replicate sample


title: HMRN_55_v4_rep_2

description: relapse&replicate sample


title: HMRN_68_v4_rep

description: replicate sample


title: HMRN_60_v4_rep

description: replicate sample


title: HMRN_54_v4_rep

description: replicate sample


title: HMRN_55_v4_rep

description: relapse&replicate sample


title: HMRN_61_v4_rep

description: replicate sample


title: HMRN_50_v4_rep

description: replicate sample

value: Burkitt lymphoma - HIV associated


title: HMRN_56_v4_rep_2

description: replicate sample

value: Diffuse Large B-cell Lymphoma MYC rearranged


title: HMRN_53_v4_rep

description: replicate sample


title: HMRN_56_v4_rep

description: replicate sample


title: HMRN_51_v4_rep_2

description: replicate sample


title: HMRN_45_v4_rep

description: replicate sample


title: HMRN_51_v4_rep_3

description: replicate sample


title: HMRN_46_v4_rep

description: replicate sample

value: R-CHOP


title: HMRN_51_v4_rep

description: replicate sample


title: HMRN_58_v4_rep

description: replicate sample

value: BL


title: HMRN_48_v4_rep

description: replicate sample


title: HMRN_47_v4_rep

description: replicate sample

value: Burkitt lymphoma


title: HMRN_50_v4_rep_2

description: replicate sample


title: HMRN_43_v4_rep

description: replicate sample


title: HMRN_44_v4_rep

description: replicate sample


title: HMRN_49_v4_rep

description: replicate sample


title: LY_42_v4_rep

description: replicate sample


title: LY_41_v4_rep

description: replicate sample


title: LY_39_v4_rep

description: replicate sample


title: LY_37_v4_rep

description: replicate sample


title: LY_36_v4_rep

description: replicate sample


title: LY_34_v4_rep

description: replicate sample


title: LY_40_v4_rep

description: replicate sample


title: LY_38_v4_rep

description: replicate sample


title: LY_33_v4_rep

description: replicate sample


title: LY_32_v4_rep

description: replicate sample


title: LY_28_v4_rep

description: replicate sample


title: LY_31_v4_rep

description: replicate sample


title: LY_24_v4_rep_2

description: replicate sample


title: LY_29_v4_rep

description: replicate sample


title: LY_25_v4_rep

description: replicate sample


title: LY_26_v4_rep

description: replicate sample


title: LY_24_v4_rep

description: replicate sample


title: LY_27_v4_rep

description: replicate sample


title: LY_23_v4_rep

description: replicate sample


title: LY_22_v4_rep

description: replicate sample


title: LY_21_v4_rep

description: replicate sample


title: LY_19_v4_rep

description: replicate sample


title: LY_15_v4_rep

description: replicate sample


title: LY_20_v4_rep

description: replicate sample


title: LY_17_v4_rep

description: replicate sample


title: LY_16_v4_rep

description: replicate sample


title: LY_14_v4_rep

description: replicate sample


title: LY_18_v4_rep

description: replicate sample


title: LY_12_v4_rep

description: replicate sample


title: LY_13_v4_rep

description: replicate sample


title: LY_9_v4_rep

description: replicate sample


title: LY_11_v4_rep

description: replicate sample


title: LY_8_v4_rep

description: replicate sample


title: LY_10_v4_rep

description: replicate sample


title: LY_7_v4_rep

description: replicate sample


title: LY_35_v4_rep

description: replicate sample


title: LY_4_v4_rep

description: replicate sample


title: LY_6_v4_rep

description: replicate sample


title: LY_3_v4_rep

description: replicate sample


title: LY_2_v4_rep

description: replicate sample


title: LY_1_v4_rep

description: replicate sample


title: HMRN_49_v4_old

description: replicate sample from GSE32918


title: HMRN_53_v4_old

description: replicate sample from GSE32918


title: LY_5_v4_rep

description: replicate sample


title: yng_09

hyb_protocol: The hybridization used miRNA Complete Labeling and Hyb Kit according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565A) using one color scan setting for 8x15k array slides (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 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were log2 transformed and  normalized by Quantile method.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using miRNA Complete Labeling and Hyb Kit according to the manufacturer's instructions.

value: wistar

value: 3 months


title: yng_11

value: male


title: LY_30_v4_rep

description: replicate sample

value: EPOCH


title: yng_13

value: pancreatic islets


title: old_10

value: 12 months


title: old_02


title: old_16


title: old_04


title: HMRN_129_v4_old

description: replicate sample from GSE32918

value: yes


title: HMRN_47_v4_old

description: replicate sample from GSE32918


title: HMRN_107_v4_old

description: replicate sample from GSE32918


title: HMRN_64_v4_old

description: replicate sample from GSE32918

value: R-CHOP then CODOX-M/IVAC


title: HMRN_8_v4_old

description: replicate sample from GSE32918


title: HMRN_52_v4_rep

description: replicate sample

value: CODOX-M/IVAC


title: HMRN_74_v4_old

description: replicate sample from GSE32918


title: HMRN_76_v4_old

description: replicate sample from GSE32918


title: HMRN_112_v4_old

description: replicate sample from GSE32918


title: HMRN_172_v4_old

description: replicate sample from GSE32918


title: HMRN_42_v4_old

description: replicate sample from GSE32918

value: Diffuse Large B-cell Lymphoma

value: CODOX-M/IVAC x1 then R-CHOP

value: no


title: HMRN_64_v4_old_rep

description: replicate sample from GSE32918


title: DPSC-vector

city: Guangzhou

first: Pengfei

last: Liu

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences

description: gene expression in human dental pulp stem cells after infected with retrovirus containing blank pMX vector for 48 hours

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: human dental pulp stem cells infected with retrovirus containing blank pMX vector

extract_protocol: Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent to a 3.5 cm diameter dish, and passing the cell lysate several times through a pipette. The protocol includes Phase Separation, RNA Precipitation, RNA Wash, and Redissolving the RNA.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Normal human impacted third molar was collected from patient after giving informed consent. the dental pulp was isolated and further digested in a solution of 3 mg/mL collagenase type I for 1 hour at 37℃. Single-cell suspensions were obtained by passing the digested tissues through a 70-mm cell strainer (BD).Cell suspensions of dental pulp were seeded into 6-well plate and cultured with Alpha-Minimum Essential Medium (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco), 100 U/mL penicillin, and 0.1g/mL streptomycin (Hyclone) at 37℃ under 5% CO2 condition.

value: dental pulp


title: DPSC-SOX2

description: gene expression in human dental pulp stem cells after infected with retrovirus containing pMX-SOX2 vector for 48 hours

source_name: human dental pulp stem cells infected with retrovirus containing pMX-SOX2 vector


title: primary tumor_stage 3_#3

city: Changsha

first: xiayu

last: li

state: Hunan

address: Yuelu district, Tongzipo road #138

department: department of gastroenterology

institute: Xiangya third hospital

hyb_protocol: Chips with labeled samples were hybridized at 56°C for overnight in a heat-shrunk hybridization bag (Phalanx), and then washed using a miRCURY LNA™ washing buffer kit (Exiqon).

scan_protocol: Slides were scanned using a Genepix 4000B laser scanner (Axon, New York) and fluorescent intensities were extracted from the generated images by Genepix Pro 6.0 software (Axon).

data_processing: The repeatability of the microarray within each class ( normal, stage1,2,3 and 4) were examined by correlation analysis. Only those data with over 50% of intra-class correlation coefficient greater than 0.8 were selected for further analysis(Chen et al., 2007). Data filter: > 50% of the arrays and gene signal > 50 were selected. Normalization was done using per chip median normalization and median array method(Liu et al.,2004) .RVM F-test was applied to screen the dynamic differentially expressed miRNA for the normal and different TNM group(Wright et al., 2003).

source_name: colorectal primary tumor, stage 3

label_protocol: 1 μg total RNA was labeled using a miRCURY LNA™ microRNA Hy3/Hy5 power labeling kit (Exiqon).

extract_protocol: On average, 100-150mg of flash frozen sample tissue were prepared for the extraction of total RNA. TRIZOL Reagent (Invitrogen ) were used to extract total RNA according to manufacturer's protocol

value: colorectal primary tumor

tag: histology

value: G1,Well differentiated

tag: Sex

value: Female

tag: Stage


title: primary tumor_stage 3_#2


title: primary tumor_stage 4_#2

source_name: colorectal primary tumor, stage 4

value: G2,Moderately differentiated


title: primary tumor_stage 4_#1

value: Male


title: primary tumor_stage 3_#4

value: G3,Poorly differentiated


title: primary tumor_stage 3_#5


title: primary tumor_stage 3_#1


title: primary tumor_stage 2_#3

source_name: colorectal primary tumor, stage 2


title: primary tumor_stage 2_#4


title: primary tumor_stage 4_#4


title: primary tumor_stage 4_#5


title: primary tumor_stage 2_#5


title: primary tumor_stage 4_#3


title: primary tumor_stage 2_#1


title: primary tumor_stage 2_#2


title: primary tumor_stage 1_#4

source_name: colorectal primary tumor, stage 1


title: primary tumor_stage 1_#5


title: BL cell line-4

city: Madrid

first: Miguel

middle: R

last: Campanero

address: Calle Arturo Duperier 4

department: Instituto de Investigaciones Biomedicas Alberto Sols

country: Spain

institute: Consejo Superior de Investigaciones Cientificas

description: Biological replicate 1 of 5. BL cell line Mutu-I harvested in exponential phase of growth

hyb_protocol: Each of the 5 BL samples was mixed with the control pool and hybridized over night at 42ºC on Capital Bio 22K oligonucleotide arrays (Capitalbio V2.0). After hybridization, slides were washed following standard protocols.

scan_protocol: The arrays were scanned using a Capital Bio Luxscan 10K Scanner. From the raw tiff image the data was extracted using the software supplied with the scanner (Luxscan3 software)

data_processing: The analysis has been carried out on R statistical framework using the packages “marray” and “limma” for both stages of this analysis: preprocessing and quality control of the data and detection of differently expressed genes.    Data Pre-processing  All the arrays intensities, these are: sample, control, sample background and control background, were visualized to asset possible background irregularities. Background intensities were not homogeneous throughout the microarrays grids and the level of these intensities also varied between microarrays. To eliminate this effect and to make the 5 microarrays comparable, the following transformations have been applied:    1. Background correction. Method: subtraction.  2. Within array normalization. Method: print-tip normalization.  3. Between array normalization. Method: MAD scale transformation.    Statistical analysis  Lineal models as implemented by the “limma” package to find genes differentially expressed between the conditions were used.

source_name: BL cell line Mutu-I, harvested in their exponential growth phase

label_protocol: The RNA of the LCL cell lines X50-7, IB-4 and Dana were pooled in equimolar amount and labeled in Cy-3 as a universal control. The RNA from each BL cell line was labeled in Cy-5. All samples were labeled using the Ambion Aminoallyl Labeling kit, starting from 1 µg of total RNA.

growth_protocol: All cell lines were grown at 37ºC, 5% CO2 in RPMI supplemented with 10% FCS, 2mM glutamine, 100U/ml penicillin, and 100µg/ml streptomycin

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

tag: cell line

value: PMID:2165133; Epstein-Barr virus positive

source_name: Pool of 3 LCL cell lines harvested in their exponential growth phase

value: Pool of Epstein-Barr virus positive cell lines X50-7 (PMID:3027963), IB-4 (PMID:6253674) and Dana (PMID:9001242)


title: BL cell line-2

description: Biological replicate 1 of 5. BL cell line BL2 harvested in exponential phase of growth

source_name: BL cell line BL2, harvested in their exponential growth phase

value: PMID:6271555; Epstein-Barr virus negative


title: BL cell line-1

description: Biological replicate 1 of 5. BL cell line Akata, harvested in exponential phase of growth

source_name: BL cell line, Akata, harvested in their exponential growth phase

value: PMID:1647567; Epstein-Barr virus positive


title: primary tumor_stage 1_#1


title: primary tumor_stage 1_#2


title: primary tumor_stage 1_#3


title: distant normal_stage 4_#3

description: matched distant normal mucosa come from the same patient marked with identical sample name(I,II,III and IV stands for TNM stage 1,2,3 and 4,respectively, ca stands for tumor, n stands for normal mucosa);sample name with identical stage and number represent the same patient(for example, I-n-2 and I-ca-2 represent the normal mucosa and tumor from patient #2 of stage I,respectively).

source_name: colorectal distant normal mucosa, stage 4

value: colorectal distant normal mucosa

value: Normal mucosa


title: distant normal_stage 4_#4