title: Daoy_0.25h_EGF_rep3

description: replicate 3

source_name: 0.25 h, EGF, rep 3


title: Daoy_0.25h_SHH_rep3

status: Public on Jul 31 2014

type: RNA

city: Berlin

first: Christoph

last: Wierling

address: Ihnestr. 73

department: Department Vertebrate Genomics

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: replicate 3

hyb_protocol: To perform whole genome expression analysis HumanHT-12 v4 chips were incubated with biotin labeled cRNA for 18h at 58°C in a hybridization oven under humidity controlled conditions. After hybridization the Illumina® Sentrix BeadChips were washed using buffers provided by the kit. 2.5 µl (1mg/ml) of Streptavidin-Cy3 (per Chip) diluted in 2.5 ml Blocking buffer were incubated on a Chip for 10 min under gentle shaking to allow binding of cRNA to gene specific probes. After washing, Illumina® Sentrix BeadChips were dried and and scanned.

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi package in R.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: 0.25 h, SHH, rep 3

label_protocol: 500 ng of total RNA in 11 µl RNase free water served as starting material for the generation of biotin-labeled cRNA with the Illumina® TotalPrepTM RNA amplification kit following supplier instructions. cRNA was cleaned up with cRNA filter cartridges before use for subsequent hybridization on Illumina® Sentrix BeadChips.

growth_protocol: Daoy cells (ATCC: HTB-186) were cultivated in Dulbecco’s modified Eagle’s medium (DMEM, Gibco/Invitrogen) with 10% (v/v) fetal bovine serum (FBS, Gibco/Invitrogen).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen, 74104) according to the manufacturer's protocol. Quantity and purity of RNA were determined by measuring the optical density at 260 and 280 nm with an UV/Vis Spectrophotometer (Thermo Scientific, Nanodrop 1000) and BioAnalyzer 2100 (Agilent Technologies Deutschland GmbH).

treatment_protocol: Hyperconfluent Daoy cells were pre-starved for 24 h in serum-reduced DMEM medium containing 0.5% (v/v) FBS before adding Sonic Hedgehog conditioned medium (Shh-N) or EGF (5 ng/ml) for stimulation. Total RNA was obtained at 14 different time points 24 h after EGF stimulation.

tag: cell line

value: Daoy cells (ATCC:HTB-186)

tag: treatment

value: SHH

tag: timepoint


title: WT fibroblasts from co-culture with tumor cells, Rep B

city: Cambridge

first: Marc

last: Mendillo

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute for Biomedical Research

description: Gene Expression after 72 hours in the presence or absence of coculture

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: 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.

organism: Mus musculus

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: In vitro cultured in DMEM with 10% FCS

extract_protocol: Qiagen RNeasy kit

treatment_protocol: For profiling of cancer cells, MEFs were treated with 10 μg/ml mitomycin C for 2h before co-culture.

tag: cell type

value: Mouse Embryonic Fibroblasts

tag: genotype


title: Daoy_0.25h_control_rep3

description: replicate 3

source_name: 0.25 h, control, rep 3

value: control


title: TwinL3_liver

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

hyb_protocol: Agilent one color protocol; Microarrays were washed the following day according to the supplemental Agilent protocol “Preventing Ozone-Related Problems”.  Slides were washed in GE Wash Buffer 1 at room temperature for 1 min, followed by GE Wash Buffer 2 at 37ºC for 1 min, acetonitrile wash at room temperature for 1 min, and Stabilizing and Drying Solution wash at room temperature for 30 s.

scan_protocol: Microarrays were kept in the dark until scanned at 5 μm at both 10 and 100 PMT (Agilent G2505 B Microarray Scanner).  Agilent Feature Extraction Software (v9.5) formed a composite of the two scans and calculated parameters for Extended Dynamic Range.

data_processing: Normalized signal intensity provided was done by data standardization of the median (JMP Genomics, V6.0).

organism: Micropterus salmoides

source_name: male liver

label_protocol: Agilent one color protocol for Cy3

extract_protocol: STAT60 protocol for total RNA

tag: gender

value: male

tag: tissue

value: liver

tag: location

value: Twin Lake


title: WT fibroblasts, Rep A

source_name: WT fibroblasts, Rep A


title: STL4_liver

value: Steiger Lake


title: Daoy_0h_SHH_rep3

description: replicate 3

source_name: 0 h, SHH, rep 3

value: 0 h


title: Hansenula polymorpha DL1-L Cd, rep2

city: Daejeon

first: Min Jeong

last: Sohn

address: 52 Eoeun-dong, Yuseong-gu

department: Protein therapeutics research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

hyb_protocol: Hybridization was performed using the 3DNA™ Submicro® EX Expression Array Detection Kit (Genisphere, Hatfield, PA, USA) according to the manufacturer's instructions as described previously (Oh et al.).

scan_protocol: The hybridized slides were scanned with the ScanArray 5000 scanner (Axon, Foster City, CA, U.S.A.).

data_processing:
Using GenePixTM Pro 4.0 (Axon) software, spot intensity was quantified for each channel and transferred to a Microsoft Excel spreadsheet. All arrays were analyzed using Quintet, an R-based unified cDNA microarray data analysis system with GUI (Choe et al., 2005).
Choe, J.-K., T.-H. Chung, S. Park, H. G. Cho, and C.-G. Hur. 2005. An open source microarray data analysis system with GUI: Quintet. In Slezak D. et al., (Eds) RSFDGrC 2005, LNAI 3642, pp. 392-401, Springer-Verlag Berling Heidelberg.

organism: Ogataea angusta

source_name: DL1-L, control

label_protocol: The labeling of target cDNAs was performed using the 3DNA™ Submicro® EX Expression Array Detection Kit (Genisphere, Hatfield, PA, USA) as described previously (Oh et al.).

extract_protocol:
Isolation of RNA and cDNA synthesis were carried out as described in Oh et al., 2004.
Oh, K.S., Kwon, O., Oh, Y.W., Sohn, M.J., Jung, S., Kim, Y.K., Kim, M.-G., Rhee, S.K., Gellissen, G., and Kang, H.A. (2004) Fabrication of a partial genome microarray of the methylotrophic yeast Hansenula polymorpha: Optimization and evaluation of transcript profiling. J. Microbiol. Biotechnol. 14, 1239-1248.

tag: strain

value: wild-type

tag: medium

value: YPD

source_name: DL1-L, 0.6mM Cd

value: cadmium stress


title: Daoy_0h_control_rep3

description: replicate 3

source_name: 0 h, control, rep 3


title: CalhG3_testis

source_name: testis

value: testis

value: Lake Calhoun


title: WT fibroblasts from co-culture with tumor cells, Rep A


title: tumor cells, Rep B

source_name: tumor cells, Rep B

value: D2A1 tumor cells

value: not applicable


title: Hsf1 null fibroblasts from co-culture with tumor cells, Rep A


title: tumor cells, Rep A

source_name: tumor cells, Rep A


title: STG4_testis


title: tumor cells from co-culture with Hsf1 null fibroblasts, Rep B


title: Daoy_48h_SHH+EGF_rep2

description: replicate 2

source_name: 48 h, SHH+EGF, rep 2

value: SHH+EGF


title: Daoy_48h_control_rep2

description: replicate 2

source_name: 48 h, control, rep 2

value: Daoy cells (ATCC:HTB-186)


title: Daoy_36h_SHH+EGF_rep2

description: replicate 2

source_name: 36 h, SHH+EGF, rep 2


title: STG1_testis


title: Daoy_36h_EGF_rep2

description: replicate 2

source_name: 36 h, EGF, rep 2

value: EGF


title: Daoy_36h_SHH_rep2

description: replicate 2

source_name: 36 h, SHH, rep 2

value: SHH


title: tumor cells from co-culture with WT fibroblasts, Rep B


title: Daoy_36h_control_rep2

description: replicate 2

source_name: 36 h, control, rep 2

value: control


title: tumor cells from co-culture with Hsf1 null fibroblasts, Rep A


title: TwinG3_testis

value: male


title: TwinG5_testis


title: STG3_testis


title: CalhG5_testis


title: TwinG2_testis


title: male-activated1

city: Easter Bush

first: Sunil

last: Nandi

state: Midlothian

address: University of Edinburgh

department: Developmental Biology

country: United Kingdom

institute: The Roslin Institute

description: gene expression in LPS-activated male

hyb_protocol: Hybridised on ChiGene 1.0 ST .

scan_protocol: GeneChip Scanner 3000 7G .

data_processing:
Analysed with GeneChip® Command Console® Software (AGCC), applying RMA normalisation to the CEL files.
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Chicken
program-name = Expression Console
program-version = 1.2.1.20

organism: Gallus gallus

source_name: female_LPS-activated macrophage cells

label_protocol: Ambion WT labelling kit .

growth_protocol: Fertilised chicken eggs were incubated at 38C with rocking.

extract_protocol: RNA was extracted using RNABee, following the manufacturer's instructions.

treatment_protocol: Cells were cultured in standard medium or with LPS to activate the macrophages.

tag: developmental stage

value: newly-hatched; 1-3 days old

value: Macrophages

tag: cell status

value: LPS-activated


title: CalhG2_testis


title: male-activated3

description: gene expression in LPS-activated male


title: TwinG4_testis

value: Twin Lake


title: STG5_testis

value: Steiger Lake


title: CalhG4_testis


title: male-resting1

description: gene expression in resting male

source_name: female_resting macrophage cells

value: resting


title: male-resting3

description: gene expression in resting male


title: Daoy_24h_control_rep2

description: replicate 2

source_name: 24 h, control, rep 2


title: Daoy_24h_SHH+EGF_rep2

description: replicate 2

source_name: 24 h, SHH+EGF, rep 2


title: Daoy_18h_SHH+EGF_rep2

description: replicate 2

source_name: 18 h, SHH+EGF, rep 2


title: TwinG6_testis


title: Daoy_24h_SHH_rep2

description: replicate 2

source_name: 24 h, SHH, rep 2


title: tumor cells from co-culture with WT fibroblasts, Rep A


title: female-activated3

description: gene expression in LPS-activated female

source_name: male_LPS-activated macrophage cells

value: female


title: Daoy_18h_EGF_rep2

description: replicate 2

source_name: 18 h, EGF, rep 2


title: TwinG1_testis

source_name: testis

value: testis


title: Daoy_24h_EGF_rep2

description: replicate 2

source_name: 24 h, EGF, rep 2


title: male-resting2

description: gene expression in resting male


title: female-activated2

description: gene expression in LPS-activated female


title: male-activated2

description: gene expression in LPS-activated male


title: Ecoli_WT_100uM_KCN_Sample4_TechRep2

city: Logan

first: Daniel

middle: R

last: Hyduke

state: UT

address: 4105 Old Main Hill ENGR 402S

department: Biological Engineering

institute: Utah State University

description: Cells were grown in MOPS media/0.5% glucose and aerobic conditions and treated with KCN

hyb_protocol: Samples were hybridized as specified in the Corning UltraGAPS manual. Slides were blocked and washed as specified in the Corning UltraGAPS manual

scan_protocol: Slides were scanned immediately after washing with a Virtek/BioRad scanner.

data_processing: Quantification of the scans were performed with ImaGene (Version 6.0.1; BioDiscovery; El Segundo, CA; www.biodiscovery.com); with the results presented in the associated text files. The normalized data VALUE was generated using LOWESS normalization with rank invariant selection, as implemented in lcDNA (receptor.seas.ucla.edu/lcDNA; Hyduke DR, Rohlin L, Kao KC, Liao JC. 2003 A software package for cDNA microarray data normalization and assessing confidence intervals. OMICS 7(3):227-234.)

organism: Escherichia coli

source_name: Control

label_protocol: Samples were directly labeled by direct incorporation of labeled dCTP.

growth_protocol: Cells aerobically grown to mid-log phase in MOPS/0.5% glucose at 37C and ~250 RPM.

extract_protocol: RNA extracted by hot phenol choloroform folled by Qiagen RNA Midi column.

treatment_protocol: Untreated

source_name: KCN

treatment_protocol: Treated with 100 uM KCN for 5 minutes before harvesting


title: Ecoli_WT_100uM_KCN_Sample2_TechRep1


title: Ecoli_WT_100uM_KCN_Sample3_TechRep2


title: Daoy_18h_SHH_rep2

description: replicate 2

source_name: 18 h, SHH, rep 2


title: Ecoli_WT_100uM_KCN_Sample1_TechRep2


title: Ecoli_WT_100uM_KCN_Sample3_TechRep1


title: STG2_testis


title: CalhG1_testis

value: Lake Calhoun


title: Ecoli_WT_100uM_KCN_Sample4_TechRep1


title: Daoy_18h_control_rep2

description: replicate 2

source_name: 18 h, control, rep 2


title: CalhG7_testis


title: Ecoli_WT_100uM_KCN_Sample2_TechRep2


title: Ecoli_WT_100uM_KCN_Sample1_TechRep1


title: Daoy_12h_SHH+EGF_rep2

description: replicate 2

source_name: 12 h, SHH+EGF, rep 2


title: female-resting3

description: gene expression in resting female

source_name: male_resting macrophage cells


title: female-activated1

description: gene expression in LPS-activated female


title: Daoy_12h_EGF_rep2

description: replicate 2

source_name: 12 h, EGF, rep 2


title: STG6_testis


title: CalhG8_testis


title: female-resting1

description: gene expression in resting female


title: Daoy_12h_SHH_rep2

description: replicate 2

source_name: 12 h, SHH, rep 2


title: TwinG8_testis


title: female-resting2

description: gene expression in resting female


title: Daoy_10.5h_SHH+EGF_rep2

description: replicate 2

source_name: 10.5 h, SHH+EGF, rep 2


title: dermal lymphatic endothelial cells_adrenomedullin__15 min_replicate 3

city: Chapel Hill

first: Kathleen

last: Caron

state: NC

address: 111 Mason Farm Drive

institute: UNC-Chapel HIll

description:
pool of human cell line RNA
Biological replicate 3 of 3

hyb_protocol: Cyanine-5 labeled cell line cRNA was co-hybridized to Agilent G4112A Whole Human Genome 44K oligonucleotide arrays with equimolar amounts of Cyanine-3 labeled UHRR. Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.  After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Axon Instruments GenePix 4000b scanner and processed using Agilent FeatureExtractor 9.1.3.1.

data_processing: Microarray data were normalized via the loess local intensity normalization and probes were filtered for features having a normalized intensity of < 30 aFU in either channel. Probes were removed if < 70% of the data were present across all samples. Missing data points were imputed using the k nearest-neighbors algorithm (k = 10). 31992 probes passed these filters, and were subsequently used for analysis. Scripts written in the R Statistical Language and Environment (R; Version 2.2.1, build r36812, release date 2005-12-20.) and Perl (ActiveState Perl 5.8.1, build 807, release date 2003-11-6) were used to standardize (μ = 0, σ = 1) each sample in the data set.

source_name: Human lymphatic endothelial cells

label_protocol: 500 ng of UHRR or cell line total RNA labeled with Cy-3 or Cy-5, respectively (Perkin Elmer) and amplified using the Low Input RNA Amplification Kit (Agilent) as described by the manufacturer.

growth_protocol: Human adult (HMVECdLyAd-Der, Lonza) were cultered to 90% confluency on a 10 cm plate in EGM-2MV media (Lonza) at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was extracted using an RNeasy kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: HMVECdLyAd-Der were serum starved overnight in RPMI with 0.5% FBS, washed with HBSS and treated with either vehicle (0.1% BSA in water) or 10 nM adrenomedullin (AM) for 15 minutes, 1 hour, or 24 hours.

tag: cell line id

value: HMVECdLyAd-Der

value: lymphatic endothelial cells

tag: passage day

tag: time of treatment (hours)

tag: compound

value: adrenomedullin

tag: passage

source_name: Stratagene UHRR reference

tag: sample type

value: Stratagene UHRR reference


title: HT1080-2

city: Seattle

first: David

middle: W.

last: Russell

state: WA

address: 1959 NE Pacific St

department: Medicine

institute: University of Washington

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The expression levels of target genes were determined by using the lumi 1.14.0 software package

source_name: HT1080 cell line

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

growth_protocol: HT1080 cells were grown 37⁰C in 5% CO2 in Dulbecco's modified Eagle's medium containing 4 g glucose/liter (Invitrogen), 10% heat-inactivated fetal bovine serum, 100 U/ml penicillin, 100 μg/ml streptomycin, and 1.25 μg/ml amphotericin and harvested at confluence.

extract_protocol: Total RNA was extracted from cells using Qiagen's RNeasy Mini Kit as described by the manufacturer.

tag: cell line


title: TwinG7_testis


title: HT1080-1

description: replicate 1


title: HT1080-3

description: replicate 3


title: Daoy_12h_control_rep2

description: replicate 2

source_name: 12 h, control, rep 2

value: Daoy cells (ATCC:HTB-186)

tag: treatment

tag: timepoint


title: DMP_C2

hyb_protocol: Silurana tropicalis microarrays were manufactured with Agilent Sure Print Technology in Fall 2011.  RNA labeling, microarray hybridization, and microarray analysis were performed according to Agilent’s One-Color Microarray-Gene Based Expression Analysis protocol (May 2010) using an Agilent kit (Agilent, Mississauga, ON, CAN).  After hybridization for 17 hours, microarray slides were washed and scanned using Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology and raw expression data along with tif images were extracted by the Feature Extraction Software 10.7.3.1.

data_processing: Normalized signal intensity provided here is Quantile Normalization (JMP Genomics, V6.0).

organism: Xenopus tropicalis

source_name: eggs

extract_protocol: RNA was extracted using the E.Z.N.A total RNA kit (VWR International, Mississauga, ON, CA).  RNA quantity was measured using the NanoDrop ND2000 (Thermo Scientific) prior to DNase treatment for real-time PCR and RNA integrity was evaluated according to Agilent 2100 Bioanalyzer protocol (Agilent, Mississauga, ON, CAN).

value: eggs

tag: agent


title: MMP_XH2

scan_protocol: After hybridization for 17 hours, microarray slides were washed and scanned using Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology and raw expression data along with tif images were extracted by the Feature Extraction Software 10.7.3.1.

value: MMP


title: DMP_MH8

value: DMP


title: CalhG6_testis

tag: gender

value: male


title: MMP_C9


title: dermal lymphatic endothelial cells_control_15 min_replicate 3

tag: cell type

value: vehicle control


title: Daoy_10.5h_EGF_rep2

description: replicate 2

source_name: 10.5 h, EGF, rep 2

value: EGF


title: Daoy_10.5h_control_rep2

description: replicate 2

source_name: 10.5 h, control, rep 2

value: control


title: STG8_testis

source_name: testis

tag: tissue

tag: location

value: Steiger Lake


title: Daoy_9h_EGF_rep2

description: replicate 2

source_name: 9 h, EGF, rep 2

value: 9 h


title: MMG1_testis

value: Medicine Lake


title: Daoy_10.5h_SHH_rep2

description: replicate 2

source_name: 10.5 h, SHH, rep 2

value: SHH


title: dermal lymphatic endothelial cells_control_15 min_replicate 1

description:
pool of human cell line RNA
Biological replicate 1 of 3


title: Daoy_9h_SHH+EGF_rep2

description: replicate 2

source_name: 9 h, SHH+EGF, rep 2

value: SHH+EGF


title: dermal lymphatic endothelial cells_control_15 min_replicate 2

description:
pool of human cell line RNA
Biological replicate 2 of 3

value: HMVECdLyAd-Der


title: DMP_C1


title: DCHP_LM11

value: DCHP


title: MMG5_testis

value: testis


title: STG7_testis


title: PMG7_testis

value: Prior Lake


title: MMG8_testis


title: PMG9_testis


title: Daoy_9h_SHH_rep2

description: replicate 2

source_name: 9 h, SHH, rep 2

value: Daoy cells (ATCC:HTB-186)


title: Daoy_9h_control_rep2

description: replicate 2

source_name: 9 h, control, rep 2


title: DCHP_SC2

value: eggs


title: DMP_MH9


title: dermal lymphatic endothelial cells_adrenomedullin__24 hour_replicate 1

value: lymphatic endothelial cells

value: adrenomedullin

value: Stratagene UHRR reference


title: DMP_MH13

value: DMP


title: PMG3_testis

value: male


title: dermal lymphatic endothelial cells_adrenomedullin__24 hour_replicate 2


title: dermal lymphatic endothelial cells_adrenomedullin__15 min_replicate 2


title: MMP_XH1

value: MMP


title: Daoy_7.5h_SHH+EGF_rep2

description: replicate 2

source_name: 7.5 h, SHH+EGF, rep 2


title: dermal lymphatic endothelial cells_control_24 hour_replicate 3

value: vehicle control


title: dermal lymphatic endothelial cells_adrenomedullin__24 hour_replicate 3


title: dermal lymphatic endothelial cells_adrenomedullin__15 min_replicate 1


title: DMP_C6


title: Daoy_7.5h_control_rep2

description: replicate 2

source_name: 7.5 h, control, rep 2

value: control


title: dermal lymphatic endothelial cells_control_24 hour_replicate 1


title: Daoy_7.5h_EGF_rep2

description: replicate 2

source_name: 7.5 h, EGF, rep 2

value: EGF


title: PMG2_testis


title: MMG4_testis

value: Medicine Lake


title: dermal lymphatic endothelial cells_adrenomedullin__1 hour_replicate 4

description:
pool of human cell line RNA
Biological replicate 4 of 4


title: DMP_MH11


title: PMG6_testis


title: MMG2_testis


title: dermal lymphatic endothelial cells_control_24 hour_replicate 2


title: dermal lymphatic endothelial cells_adrenomedullin__1 hour_replicate 3

description:
pool of human cell line RNA
Biological replicate 3 of 4


title: PMG1_testis


title: Daoy_6h_SHH_rep2

description: replicate 2

source_name: 6 h, SHH, rep 2

value: SHH

value: 6 h


title: Daoy_6h_SHH+EGF_rep2

description: replicate 2

source_name: 6 h, SHH+EGF, rep 2

value: SHH+EGF


title: MMP_XH6


title: Daoy_6h_EGF_rep2

description: replicate 2

source_name: 6 h, EGF, rep 2


title: dermal lymphatic endothelial cells_control_1 hour_replicate 3

source_name: Human lymphatic endothelial cells

value: HMVECdLyAd-Der

source_name: Stratagene UHRR reference


title: dermal lymphatic endothelial cells_adrenomedullin__1 hour_replicate 2

description:
pool of human cell line RNA
Biological replicate 2 of 4


title: MMG3_testis

value: testis


title: dermal lymphatic endothelial cells_control_1 hour_replicate 4


title: MMP_C6

source_name: eggs


title: DCHP_SC6


title: Daoy_4.5h_SHH+EGF_rep2

description: replicate 2

source_name: 4.5 h, SHH+EGF, rep 2

value: Daoy cells (ATCC:HTB-186)


title: MMP_C7

value: eggs


title: Daoy_7.5h_SHH_rep2

description: replicate 2

source_name: 7.5 h, SHH, rep 2


title: DMP_C3


title: DCHP_LM12

value: DCHP


title: PML5_liver

source_name: male liver

value: liver

value: Prior Lake


title: Daoy_4.5h_EGF_rep2

description: replicate 2

source_name: 4.5 h, EGF, rep 2


title: dermal lymphatic endothelial cells_control_1 hour_replicate 2

value: lymphatic endothelial cells

value: Stratagene UHRR reference


title: Daoy_4.5h_SHH_rep2

description: replicate 2

source_name: 4.5 h, SHH, rep 2


title: MML5_liver

value: male


title: MML1_liver


title: Daoy_6h_control_rep2

description: replicate 2

source_name: 6 h, control, rep 2


title: dermal lymphatic endothelial cells_adrenomedullin__1 hour_replicate 1

description:
pool of human cell line RNA
Biological replicate 1 of 4

value: adrenomedullin


title: DCHP_LM5


title: PML7_liver


title: DCHP_SC3


title: MML8_liver


title: dermal lymphatic endothelial cells_control_1 hour_replicate 1

value: vehicle control


title: DCHP_SC8


title: MMP_XH3

value: MMP


title: MML7_liver

value: Medicine Lake


title: MML6_liver


title: PML8_liver


title: DCHP_LM9


title: MMP_C4


title: High 9

data_processing: Normalized signal intensity provided here is LOESS Normalization (JMP Genomics, V6.0).

source_name: embryo stage 12 to 46

value: embryo stage 12 to 46

value: sodium arsenate

tag: dose

value: High


title: Daoy_3h_SHH+EGF_rep2

description: replicate 2

source_name: 3 h, SHH+EGF, rep 2

value: SHH+EGF

value: 3 h


title: Daoy_3h_EGF_rep2

description: replicate 2

source_name: 3 h, EGF, rep 2

value: Daoy cells (ATCC:HTB-186)

value: EGF


title: Daoy_4.5h_control_rep2

description: replicate 2

source_name: 4.5 h, control, rep 2

value: control


title: Daoy_3h_SHH_rep2

description: replicate 2

source_name: 3 h, SHH, rep 2

value: SHH


title: MML3_liver

value: liver


title: Control 8

tag: developmental stage

value: Control


title: PML9_liver

value: Prior Lake


title: R7-0.5uM_retinoic_acid_6_hrs 3

city: London

first: Peter

middle: Christian

last: Kloehn

state: Greater London

address: Queen Square

department: MRC Prion Unit

institute: UCL Institute of Neurology

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430 GeneChip  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol EukGE-WS2v5_450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GS3000.

data_processing: The data were analyzed with R package affy (using Robust Multiarray Averaging (RMA) method as normalization method) and limma for differential expression analysis.

source_name: Neuro2a cell clone

label_protocol: Total RNA was labeled with 3' IVT Express Kit (Affymetrix) according to the specification of the manufacturer

growth_protocol: Cells were maintained in OPTIMEM, 10% fetal calf serum and 1% Penicillin/Streptavidin according to Klohn et al. (2003) Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11666-71. PMID: 14504404

extract_protocol: total RNA was extracted using RNease kit (Qiagen) according to the specification of the manufacturer

treatment_protocol: No treatment

tag: clone

tag: prions susceptibility

value: prion-resistant revertant

value: R7-retinoic acid (0.5 microM, 1 in 10k dilution of 5mM stock), treatment for 6 hours


title: Daoy_1.5h_EGF_rep2

description: replicate 2

source_name: 1.5 h, EGF, rep 2


title: Daoy_3h_control_rep2

description: replicate 2

source_name: 3 h, control, rep 2


title: Daoy_1.5h_SHH+EGF_rep2

description: replicate 2

source_name: 1.5 h, SHH+EGF, rep 2


title: R7-0.5uM_DMSO_(1_in_10000)_6_hrs 3

value: R7-vehicle DMSO (1 in 10k dilution), treatment for 6 hours


title: R7-0.5uM_retinoic_acid_6_hrs 1


title: R7-0.5uM_DMSO_(1_in_10000)_6_hrs 2


title: Daoy_1.5h_SHH_rep2

description: replicate 2

source_name: 1.5 h, SHH, rep 2


title: Control 9


title: PML6_liver

value: male


title: R19-subconfluent-rep2

value: intermediate susceptible


title: Low 4

value: embryo stage 12 to 46

value: Low


title: PML2_liver


title: R19-subconfluent-rep3


title: R7-0.5uM_DMSO_(1_in_10000)_6_hrs 1


title: Control 5


title: Daoy_1.5h_control_rep2

description: replicate 2

source_name: 1.5 h, control, rep 2


title: High 8

value: sodium arsenate

value: High


title: R17-subconfluent-rep2


title: Low 6


title: Daoy_1h_SHH+EGF_rep2

description: replicate 2

source_name: 1 h, SHH+EGF, rep 2

value: SHH+EGF

value: 1 h


title: Daoy_1h_SHH_rep2

description: replicate 2

source_name: 1 h, SHH, rep 2

value: Daoy cells (ATCC:HTB-186)


title: Patient 22 in group SynSa3

type: genomic

city: Stanford

first: Joanna

last: Przybyl

address: 300 Pasteur Drive

department: Department of Pathology

institute: Stanford University

description: aCGH profile in metastatic tumor sample

hyb_protocol: Labeled samples were hybridized to SurePrint G3 Human CGH 4x180K whole-genome microarrays (G4449A)  (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s protocol.

scan_protocol: The microarray slides were scanned using the Agilent G2565A DNA Microarray Scanner (Agilent Technologies, SantaClara, CA, USA).

data_processing:
Image analysis was done using the Feature Extraction V10.10.1.1 software (Agilent Technologies, SantaClara, CA, USA).  aCGH data were analyzed using Agilent Genomic Workbench 7.0.4.0. software (Agilent Technologies, SantaClara, CA, USA). The ADM-2 algorithm was applied to identify DNA copy number aberrations (CNAs). Aberration Filter:  ( Minimum Number of Probes for Amplification >= 500 AND Minimum Avg. Absolute Log Ratio for Amplification >= 0.25 ) OR ( Minimum Number of Probes for Deletion >= 500  AND Minimum Avg. Absolute Log Ratio for Deletion >= 0.25 )
Normalized log2 ratio (Cy5/Cy3), ADM-2 alogrithm, threshold 6.0, calculated by the Agilent Genomic Workbench 7.0.4.0. software.

molecule: genomic DNA

source_name: tumor sample

label_protocol: 1ug of genomic DNA was labeled using Cy5 dye, and 1ug reference female DNA was labeled using Cy3 dye, according to manufacturer's recommendations. Male and female Megapool Reference DNA (catalog no. EA-100M and EA-100F) (KREATECH Diagnostics) were used for the aCGH experiments.

growth_protocol: not applicable

extract_protocol: Genomic DNA was extracted from the frozen tumor specimens using High Pure PCR Template Preparation Kit (Roche).

treatment_protocol: not applicable

tag: histosubtype

value: synovial sarcoma

tag: age at diagnosis [years]

value: Male

source_name: Reference DNA

tag: reference

value: Pooled genomic DNA from 100 healthy individuals


title: High 6


title: R19-subconfluent-rep1


title: R17-subconfluent-rep3


title: R17-subconfluent-rep1


title: Daoy_1h_EGF_rep2

description: replicate 2

source_name: 1 h, EGF, rep 2

value: EGF


title: Daoy_0.5h_EGF_rep2

description: replicate 2

source_name: 0.5 h, EGF, rep 2


title: High 5

source_name: embryo stage 12 to 46


title: Daoy_0.5h_SHH+EGF_rep2

description: replicate 2

source_name: 0.5 h, SHH+EGF, rep 2


title: PD112-subconfluent-rep2

value: prion-susceptible


title: PD112-subconfluent-rep1


title: PD112-subconfluent-rep3


title: Low 8


title: Daoy_1h_control_rep2

description: replicate 2

source_name: 1 h, control, rep 2

value: control


title: Patient 20 in group SynSa3

description: aCGH profile in metastatic tumor sample

value: Female


title: Control 10

value: Control


title: High 4


title: NN2a-subconfluent-rep3

value: resistant


title: High 10


title: Daoy_0.5h_SHH_rep2

description: replicate 2

source_name: 0.5 h, SHH, rep 2

value: SHH


title: NN2a-subconfluent-rep1


title: Patient 21 in group SynSa3

description: aCGH profile in metastatic tumor sample


title: Daoy_0.25h_EGF_rep2

description: replicate 2

source_name: 0.25 h, EGF, rep 2


title: NN2a-subconfluent-rep2

source_name: Neuro2a cell clone


title: Daoy_0.25h_SHH+EGF_rep2

description: replicate 2

source_name: 0.25 h, SHH+EGF, rep 2


title: Daoy_0.5h_control_rep2

description: replicate 2

source_name: 0.5 h, control, rep 2


title: Patient 19 in group SynSa3

description: aCGH profile in metastatic tumor sample


title: ATCC-subconfluent-rep3

value: ATCC


title: Patient 18 in group SynSa3

description: aCGH profile in metastatic tumor sample


title: Patient 17 in group SynSa3

description: aCGH profile in metastatic tumor sample


title: Low 5

value: embryo stage 12 to 46

value: Low


title: Daoy_0.25h_SHH_rep2

description: replicate 2

source_name: 0.25 h, SHH, rep 2


title: Patient 15 in group SynSa3

description: aCGH profile in metastatic tumor sample


title: ATCC-subconfluent-rep1


title: Control 6


title: Patient 13 in group SynSa3

description: aCGH profile in metastatic tumor sample


title: Patient 16 in group SynSa3

description: aCGH profile in metastatic tumor sample


title: Patient 14 in group SynSa3

description: aCGH profile in metastatic tumor sample


title: Low 7

value: sodium arsenate


title: R33-subconfluent-rep3


title: ATCC-subconfluent-rep2


title: Daoy_0.25h_control_rep2

description: replicate 2

source_name: 0.25 h, control, rep 2


title: Daoy_0h_SHH_rep2

description: replicate 2

source_name: 0 h, SHH, rep 2

value: 0 h


title: Angelica archangelica replicate 1 & 2

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Plenty Road

department: School of Science

country: Australia

institute: RMIT University

hyb_protocol: The SDA slides were pre-hybridized for 45 min at 42°C in a pre-warmed solution containing 5X standard saline citrate (SSC), 0.1% sodium dodecyl sulphate (SDS), 1% bovine serum albumin (BSA) and 25% formamide. The slides were rinsed twice with sterile MilliQ water and immediately dried with an air gun.   The biotin-labelled targets (dried to 16 μL) were added to 17.5 μL of fresh 2X Hybridization buffer (250 μL of formamide, 250 μL of 10X SSC, 10 μL of 10% SDS), 0.5 μL of 5 μg/μL Human Cot1 DNA (Sigma-Aldrich, St Louis, MO), 0.5 μL of 10 mg/mL Poly A (Sigma-Aldrich) and 0.5 μL of 10 mg/mL salmon sperm DNA (Sigma-Aldrich). The mixture was denatured at 100°C for 2 min and immediately applied onto the array under a 22 × 25-mm lifter slip (Grale Scientific, Victoria, Australia). The slides were then placed in waterproof, humidified hybridization chambers (Corning Incorporated Life Sciences) and incubated overnight in a 42°C water bath. Following hybridization, the slides were washed twice for 5 min in 500 mL Wash buffer 1 (1X SSC with 0.1% SDS), once for 5 min in 500 mL Wash buffer 3 (0.1X SSC with 0.1% SDS), and once for 5 min in 500 mL Wash buffer 4 (0.1X SSC). Subsequently the slides were transferred to 500 mL of 6X SSPE-T buffer (0.9 M NaCl, 0.06 M NaH2PO4.H2O, 0.006 M EDTA, 0.005% Triton X-100, pH 7.4) without allowing them to dry.   The biotinylated DNA targets bound on the array were then labelled with fluorescent FluoroLink™ streptavidin-labelled Cy3 dye (Amersham Pharmacia, UK) using a biotin–streptavidin system. Briefly, 200 μL of a Detection solution (0.5 µL of 0.8 µg/µL streptavidin-labelled Cy3, 0.8 µl of 25 µg/µL BSA, made to 200 µL with 6X SSPE-T) was applied directly onto the array surface and a 22 × 25-mm lifter slip was placed over it to evenly distribute the solution on the array. The slides were placed in hybridization chambers, wrapped in aluminum foil and incubated at 37oC for 1 h in the dark. Finally, the slides were washed thrice in 6X SSPE-T for 5 min and rinsed with sterile MilliQ water before being dried with an air gun. All hybridizations were performed with six technical replicates (corresponding to six sub-arrays) and two biological replicates, resulting in 12 data points for each array feature.

scan_protocol: Slides were scanned with a ScanArray Gx (PerkinElmer Life and Analytical Sciences, Downers Grove, IL) microarray scanner in conjunction with the supplied software. The slides were scanned with a resolution of 5 µm at 532 nm (Cy3, green laser) and at 55% photomultiplicator (PMT) gain whilst keeping background noise low. The scanned array was quantified using PerkinElmer ScanArray Express software v 2.0. The program individually quantified the signal intensity at each probe and normalized the data using the adaptive circle and LOWESS functions.

data_processing: Probes which did not hybridize were automatically flagged by the scanning software and labelled as ‘bad’. The values of all Bad features (signal to noise ratio (SNR) value of less than 5 in more than half of the  technical replications) have been converted to Zero . Manual flagging was used to remove spots displaying inconsistent hybridization such as ‘donut’ spots. ‘Good’ probes were accepted as having a mean ‘signal to noise ratio’ (SNR) value of greater than 5 in more than half of the technical replications. The signal intensities and flag values of the two biological replicates were compared and average signal intensities were calculated for only those features that were flagged ‘Good’ in both the replicates. The values of features that had a ‘Bad’ flag in either or both the replicates were converted to zero. Data analysis included subtracting the background from median signal intensity for each feature, log2 transformation and combining technical replicates by taking average.

label: Biotin/Steptavidin

organism: Angelica archangelica

source_name: Angelica archangelica

label_protocol: The preparation of targets in all cases involved the double digestion of 0.5 μg of gDNA with AluI and HaeIII, and purification using Qiaquick® PCR Purification Kit (Qiagen Inc.). Biotin-11-dUTP was then incorporated into restriction digested gDNA fragments using the Biotin DecaLabel™ DNA Labeling Kit (Fermentas, ON, Canada) following the manufacturer’s guidelines. However, the incubation time was increased to 20 h, the reaction stopped with 1 µl 0.5M EDTA, pH 8.0 and labelled gDNA fragments were purified using Qiaquick® PCR Purification Kit.

growth_protocol: fresh or preserved leaf samples were obtained

extract_protocol: Genomic DNA was extracted using Qiagen Plant Mini Kit as per manufacturer guidelines

tag: family

value: Apiaceae

tag: order

value: Apiales

value: leaves


title: Achellia millefolium replicate 1 & 2

organism: Achillea millefolium

source_name: Achillea millefolium

value: Asteraceae

value: Asterales


title: Camellia sinensis replicate 1 & 2

organism: Camellia sinensis

source_name: Camellia sinensis

value: Theaceae

value: Ericales


title: Patient 12 in group SynSa3

description: aCGH profile in metastatic tumor sample

source_name: tumor sample

value: synovial sarcoma

value: Male

source_name: Reference DNA

value: Pooled genomic DNA from 100 healthy individuals


title: Ilex paraguariensis replicate 1 & 2

organism: Ilex paraguariensis

source_name: Ilex paraguariensis

value: Aquifoliaceae

value: Aquifoliales


title: Coffee arabica replicate 1 & 2

organism: Coffea arabica

source_name: Coffea arabica

value: Rubiaceae

value: Gentianales


title: Daoy_0h_control_rep2

description: replicate 2

source_name: 0 h, control, rep 2

tag: cell line

value: Daoy cells (ATCC:HTB-186)

value: control


title: Patient 11 in group SynSa3

description: aCGH profile in metastatic tumor sample


title: Leonurus cardiaca replicate 1 & 2

organism: Leonurus cardiaca

source_name: Leonurus cardiaca

value: Lamiaceae

value: Lamiales


title: Sambuscus nigra replicate 1 & 2

organism: Sambucus nigra

source_name: Sambucus nigra

value: Adoxaceae

value: Dipsacales


title: R7-subconfluent-rep2

value: prion-resistant revertant


title: R7-subconfluent-rep1


title: Daoy_36h_SHH+EGF_rep1

description: replicate 1

source_name: 36 h, SHH+EGF, rep 1

tag: treatment

value: SHH+EGF


title: R7-subconfluent-rep3

source_name: Neuro2a cell clone


title: R33-subconfluent-rep2

value: resistant


title: Daoy_48h_SHH+EGF_rep1

description: replicate 1

source_name: 48 h, SHH+EGF, rep 1

tag: timepoint


title: R33-subconfluent-rep1


title: Schrophularia nodosa replicate 1 & 2

organism: Scrophularia nodosa

source_name: Scrophularia nodosa

value: Scrophulariaceae

value: leaves


title: Daoy_48h_control_rep1

description: replicate 1

source_name: 48 h, control, rep 1


title: Patient 8 in group SynSa3

description: aCGH profile in metastatic tumor sample

value: synovial sarcoma

value: Male


title: R5-subconfluent-rep2


title: Daoy_36h_control_rep1

description: replicate 1

source_name: 36 h, control, rep 1


title: Vitex agnus-custus replicate 1 & 2

organism: Vitex agnus-castus

source_name: Vitex agnus-castus


title: Patient 9 in group SynSa3

description: aCGH profile in metastatic tumor sample

value: Pooled genomic DNA from 100 healthy individuals


title: Patient 7 in group SynSa3

description: aCGH profile in metastatic tumor sample


title: Withania somnifera replicate 1 & 2

organism: Withania somnifera

source_name: Withania somnifera

value: Solanaceae

value: Solanales


title: Patient 10 in group SynSa3

description: aCGH profile in metastatic tumor sample

organism: Homo sapiens

value: Female


title: Daoy_36h_EGF_rep1

description: replicate 1

source_name: 36 h, EGF, rep 1

value: Daoy cells (ATCC:HTB-186)

value: EGF


title: R5-subconfluent-rep1

organism: Mus musculus


title: Daoy_36h_SHH_rep1

description: replicate 1

source_name: 36 h, SHH, rep 1

value: SHH


title: R5-subconfluent-rep3


title: Rehmannia glutinosa replicate 1 & 2

organism: Rehmannia glutinosa

source_name: Rehmannia glutinosa

value: Phrymaceae

value: Lamiales


title: Forsythia suspensa replicate 1 & 2

organism: Forsythia suspensa

source_name: Forsythia suspensa

value: Oleaceae


title: Patient 6 in group SynSa3

description: aCGH profile in metastatic tumor sample

source_name: tumor sample

source_name: Reference DNA


title: Patient 4 in group SynSa3

description: aCGH profile in metastatic tumor sample


title: Patient 5 in group SynSa3

description: aCGH profile in metastatic tumor sample


title: Daoy_24h_SHH+EGF_rep1

description: replicate 1

source_name: 24 h, SHH+EGF, rep 1


title: Symptum spp - replicate 1 & 2

description: Symptum spp

organism: Symphytum

source_name: Symphytum

value: Boraginaceae


title: R2-subconfluent-rep2

value: prion-resistant revertant


title: R2-subconfluent-rep1


title: Daoy_24h_control_rep1

description: replicate 1

source_name: 24 h, control, rep 1

value: control


title: Daoy_24h_SHH_rep1

description: replicate 1

source_name: 24 h, SHH, rep 1


title: Daoy_24h_EGF_rep1

description: replicate 1

source_name: 24 h, EGF, rep 1


title: Patient 2 in group SynSa3

description: aCGH profile in metastatic tumor sample


title: Daoy_18h_EGF_rep1

description: replicate 1

source_name: 18 h, EGF, rep 1


title: Patient 1 in group SynSa3

description: aCGH profile in metastatic tumor sample


title: Patient 26 in group SynSa2

description: aCGH profile in primary tumor sample


title: Digitalis purpurea - replicate 1 & 2

organism: Digitalis purpurea

source_name: Digitalis purpurea

value: Plantaginaceae


title: R2-subconfluent-rep3

source_name: Neuro2a cell clone


title: Daoy_18h_SHH_rep1

description: replicate 1

source_name: 18 h, SHH, rep 1


title: Daoy_18h_SHH+EGF_rep1

description: replicate 1

source_name: 18 h, SHH+EGF, rep 1

value: SHH+EGF


title: Lycium barbarum - replicate 1 & 2

organism: Lycium barbarum

source_name: Lycium barbarum

value: leaves


title: S7-subconfluent-rep2

value: prion-susceptible


title: Codonopsis spp - replicate 1 & 2

organism: Codonopsis

source_name: Codonopsis

value: Campanulaceae

value: Asterales


title: Taraxacum officinale - replicate 1 & 2

organism: Taraxacum officinale

source_name: Taraxacum officinale

value: Asteraceae


title: Tracheospermum jasminoides - replicate 1 & 2

organism: Trachelospermum jasminoides

source_name: Trachelospermum jasminoides

value: Apocynaceae

value: Gentianales


title: Patient 25 in group SynSa2

description: aCGH profile in primary tumor sample

value: synovial sarcoma

value: Male

value: Pooled genomic DNA from 100 healthy individuals


title: S7-subconfluent-rep1


title: Daoy_12h_EGF_rep1

description: replicate 1

source_name: 12 h, EGF, rep 1

value: Daoy cells (ATCC:HTB-186)

value: EGF


title: Patient 24 in group SynSa2

description: aCGH profile in primary tumor sample

source_name: tumor sample

value: Female


title: Gardenia jasminoides - replicate 1 & 2

organism: Gardenia jasminoides

source_name: Gardenia jasminoides

value: Rubiaceae


title: PD88-subconfluent-rep1


title: PD88-subconfluent-rep2


title: Patient 22 in group SynSa2

description: aCGH profile in primary tumor sample

source_name: Reference DNA


title: PD88-subconfluent-rep3


title: Patient 23 in group SynSa2

description: aCGH profile in primary tumor sample


title: Daoy_18h_control_rep1

description: replicate 1

source_name: 18 h, control, rep 1

value: control


title: Valeriana officinalis - replicate 1 & 2

organism: Valeriana officinalis

source_name: Valeriana officinalis

value: Valerianaceae

value: Dipsacales


title: PK1-subconfluent-rep3


title: Impatiens mix - replicate 1 & 2

description: Impatiens mix

organism: Impatiens

source_name: Impatiens

value: Balsaminaceae

value: Ericales

value: leaves


title: Daoy_12h_SHH+EGF_rep1

description: replicate 1

source_name: 12 h, SHH+EGF, rep 1

value: SHH+EGF


title: Patient 21 in group SynSa2

description: aCGH profile in primary tumor sample


title: Tetrapanax papyriferus - replicate 1 & 2

organism: Tetrapanax papyrifer

source_name: Tetrapanax papyriferus

value: Araliaceae

value: Apiales


title: Patient 3 in group SynSa3

description: aCGH profile in metastatic tumor sample


title: Daoy_12h_SHH_rep1

description: replicate 1

source_name: 12 h, SHH, rep 1

value: SHH


title: PK1-subconfluent-rep1

source_name: Neuro2a cell clone

value: prion-susceptible


title: Daoy_10.5h_EGF_rep1

description: replicate 1

source_name: 10.5 h, EGF, rep 1


title: Patient 18 in group SynSa2

description: aCGH profile in primary tumor sample

value: synovial sarcoma


title: PK1-subconfluent-rep2


title: Cornus spp - replicate 1 & 2

description: Cornus spp

organism: Cornus

source_name: Cornus

value: Cornaceae

value: Cornales


title: Daoy_10.5h_SHH+EGF_rep1

description: replicate 1

source_name: 10.5 h, SHH+EGF, rep 1

value: Daoy cells (ATCC:HTB-186)


title: Patient 17 in group SynSa2

description: aCGH profile in primary tumor sample

value: Male

value: Pooled genomic DNA from 100 healthy individuals


title: Daoy_12h_control_rep1

description: replicate 1

source_name: 12 h, control, rep 1

value: control


title: 20m-wt3

city: Lawrence

first: Xinkun

last: Wang

state: KS

address: 2099 Constant Ave

department: Genomics Facility

institute: The University of Kansas

description: total RNA extracted from homogenized hippocampus

hyb_protocol: Following fragmentation, cRNA were hybridized onto the Affymetrix GeneChip Mouse Genome 430 2.0 arrays using  the standard Affymetrix protocol . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Wild type mouse hippocampus at 20 month

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

extract_protocol: Qiagen RNeasy Mini kit was used for the total RNA extraction according to the manufacturer's instructions.

tag: strain

tag: genotype

value: Wild type

tag: age

value: Hippocampus


title: Patient 16 in group SynSa2

description: aCGH profile in primary tumor sample

tag: gender

value: Female


title: Daoy_10.5h_SHH_rep1

description: replicate 1

source_name: 10.5 h, SHH, rep 1


title: Patient 15 in group SynSa2

description: aCGH profile in primary tumor sample


title: 20m-wt1

tag: tissue


title: Platycodon grandiflorus - replicate 1 & 2

organism: Platycodon grandiflorus

source_name: Platycodon grandiflorus

value: Campanulaceae

value: Asterales


title: Tester - replicate 1 & 2

description: 67 asterids pool

organism: asterids

source_name: asterids pool

value: leaves


title: Patient 19 in group SynSa2

description: aCGH profile in primary tumor sample

organism: Homo sapiens

source_name: tumor sample


title: Driver - replicate 1 & 2

description: 104 non-asterid angiosperms and non-anigiosperm pool

organism: Embryophyta


title: Lonicera japonica - replicate 1 & 2

organism: Lonicera japonica

source_name: Lonicera japonica

value: Caprifoliaceae

value: Dipsacales


title: Patient 14 in group SynSa2

description: aCGH profile in primary tumor sample

source_name: Reference DNA


title: Daoy_10.5h_control_rep1

description: replicate 1

source_name: 10.5 h, control, rep 1


title: Daoy_9h_EGF_rep1

description: replicate 1

source_name: 9 h, EGF, rep 1

value: EGF

value: 9 h


title: Patient 13 in group SynSa2

description: aCGH profile in primary tumor sample

value: synovial sarcoma


title: 20m-Tg2

organism: Mus musculus

source_name: Transgenic mouse hippocampus at 20 month

value: Glud1 Tg


title: Patient 11 in group SynSa2

description: aCGH profile in primary tumor sample


title: Daoy_9h_SHH+EGF_rep1

description: replicate 1

source_name: 9 h, SHH+EGF, rep 1

value: SHH+EGF


title: Patient 12 in group SynSa2

description: aCGH profile in primary tumor sample


title: 20m-wt2


title: Daoy_9h_control_rep1

description: replicate 1

source_name: 9 h, control, rep 1

value: Daoy cells (ATCC:HTB-186)


title: 14m-wt3

source_name: Wild type mouse hippocampus at 14.5 month


title: 20m-Tg3

source_name: Transgenic mouse hippocampus a 20 month


title: Patient 10 in group SynSa2

description: aCGH profile in primary tumor sample

value: Male


title: 20m-Tg1


title: Daoy_9h_SHH_rep1

description: replicate 1

source_name: 9 h, SHH, rep 1

value: SHH


title: 14m-wt1


title: Daoy_7.5h_SHH+EGF_rep1

description: replicate 1

source_name: 7.5 h, SHH+EGF, rep 1


title: S7-subconfluent-rep3

source_name: Neuro2a cell clone

value: prion-susceptible


title: Patient 9 in group SynSa2

description: aCGH profile in primary tumor sample

value: Pooled genomic DNA from 100 healthy individuals


title: Daoy_7.5h_EGF_rep1

description: replicate 1

source_name: 7.5 h, EGF, rep 1


title: Patient 8 in group SynSa2

description: aCGH profile in primary tumor sample


title: Daoy_7.5h_control_rep1

description: replicate 1

source_name: 7.5 h, control, rep 1

value: control


title: Daoy_7.5h_SHH_rep1

description: replicate 1

source_name: 7.5 h, SHH, rep 1


title: 14m-Tg2

source_name: Transgenic mouse hippocampus at 14.5 month

value: Hippocampus


title: 9m-wt3

source_name: Wild type mouse hippocampus at 9 month

value: Wild type


title: Patient 7 in group SynSa2

description: aCGH profile in primary tumor sample

source_name: tumor sample


title: 14m-Tg3

source_name: Transgenic mouse hippocampus a 14.5 month


title: 14m-wt2


title: 14m-Tg1


title: Daoy_6h_SHH+EGF_rep1

description: replicate 1

source_name: 6 h, SHH+EGF, rep 1

value: 6 h


title: Patient 6 in group SynSa2

description: aCGH profile in primary tumor sample

source_name: Reference DNA


title: 9m-wt2


title: Patient 3 in group SynSa2

description: aCGH profile in primary tumor sample

value: Female


title: genomic DNA from leukemic blast 8359018137_RO6CO2

city: Stockholm

first: Ying

last: Qu

state: Stockholm

address: Hälsovagen 7

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institute

description: leukemic blast

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: The raw data was processed by GenomeStudio (QIAGEN) by standard protocol.

label: Cy5 and Cy35

source_name: leukemic blast (MNC)

label_protocol: Standard Illumina Protocol

extract_protocol: DNA and RNA was extracted by TRIzol ( Invitrogen) or ALLPrep ( QIAGEN ) according to the standard instructions. Sample quanlity were tested by Genomic DNA ScreenTape.

tag: sample id

tag: age at diagnosis in years

tag: batch

tag: cell type

value: leukemic blast


title: Daoy_6h_control_rep1

description: replicate 1

source_name: 6 h, control, rep 1


title: Daoy_6h_EGF_rep1

description: replicate 1

source_name: 6 h, EGF, rep 1


title: Daoy_6h_SHH_rep1

description: replicate 1

source_name: 6 h, SHH, rep 1


title: Patient 1 in group SynSa2

description: aCGH profile in primary tumor sample

tag: histosubtype


title: 9m-Tg3

source_name: Transgenic mouse hippocampus a 9 month


title: Patient 4 in group SynSa2

description: aCGH profile in primary tumor sample

tag: age at diagnosis [years]


title: 9m-Tg2

source_name: Transgenic mouse hippocampus at 9 month


title: 9m-Tg1


title: Patient 5 in group SynSa2

description: aCGH profile in primary tumor sample

tag: reference


title: Patient 2 in group SynSa2

description: aCGH profile in primary tumor sample


title: genomic DNA from leukemic blast 8359018152_RO6CO2

description: leukemic blast


title: Daoy_4.5h_EGF_rep1

description: replicate 1

source_name: 4.5 h, EGF, rep 1


title: Patient 15 in group SynSa1

description: aCGH profile in primary tumor sample


title: genomic DNA from leukemic blast 8359018137_RO5CO2

description: leukemic blast


title: genomic DNA from leukemic blast 8359018152_RO5CO2

description: leukemic blast


title: 4m-wt3

source_name: Wild type mouse hippocampus at 4.5 month


title: genomic DNA from leukemic blast 8363800026_RO6CO2

description: leukemic blast


title: 9m-wt1


title: genomic DNA from leukemic blast 8363800026_RO5CO2

description: leukemic blast


title: Patient 16 in group SynSa1

description: aCGH profile in primary tumor sample


title: Daoy_4.5h_SHH+EGF_rep1

description: replicate 1

source_name: 4.5 h, SHH+EGF, rep 1


title: Daoy_4.5h_control_rep1

description: replicate 1

source_name: 4.5 h, control, rep 1


title: 4m-wt2


title: Patient 14 in group SynSa1

description: aCGH profile in primary tumor sample


title: Daoy_4.5h_SHH_rep1

description: replicate 1

source_name: 4.5 h, SHH, rep 1


title: Daoy_3h_SHH+EGF_rep1

description: replicate 1

source_name: 3 h, SHH+EGF, rep 1

value: 3 h


title: Patient 13 in group SynSa1

description: aCGH profile in primary tumor sample


title: genomic DNA from leukemic blast 8363800011_RO5CO2

description: leukemic blast


title: 4m-wt1


title: 4m-Tg3

source_name: Transgenic mouse hippocampus a 4.5 month


title: Daoy_3h_EGF_rep1

description: replicate 1

source_name: 3 h, EGF, rep 1

value: EGF


title: Patient 11 in group SynSa1

description: aCGH profile in primary tumor sample

source_name: tumor sample


title: genomic DNA from leukemic blast 8363800011_RO6CO2

description: leukemic blast


title: genomic DNA from leukemic blast 8359018152_RO4CO2

description: leukemic blast


title: genomic DNA from leukemic blast 8363800026_RO4CO2

description: leukemic blast


title: 4m-Tg2

source_name: Transgenic mouse hippocampus at 4.5 month


title: Patient 10 in group SynSa1

description: aCGH profile in primary tumor sample

source_name: Reference DNA


title: Daoy_3h_SHH_rep1

description: replicate 1

source_name: 3 h, SHH, rep 1


title: Daoy_1.5h_SHH+EGF_rep1

description: replicate 1

source_name: 1.5 h, SHH+EGF, rep 1


title: 4m-Tg1


title: genomic DNA from leukemic blast 8363800011_RO4CO2

description: leukemic blast

source_name: leukemic blast (MNC)


title: Daoy_3h_control_rep1

description: replicate 1

source_name: 3 h, control, rep 1


title: Patient 8 in group SynSa1

description: aCGH profile in primary tumor sample


title: 10d-wt4

source_name: Wild type mouse hippocampus at 10 day


title: Daoy_1.5h_EGF_rep1

description: replicate 1

source_name: 1.5 h, EGF, rep 1


title: Patient 9 in group SynSa1

description: aCGH profile in primary tumor sample


title: genomic DNA from leukemic blast 8359018137_RO4CO2

description: leukemic blast


title: Patient 7 in group SynSa1

description: aCGH profile in primary tumor sample


title: 10d-wt3


title: 10d-wt2


title: Daoy_1.5h_control_rep1

description: replicate 1

source_name: 1.5 h, control, rep 1


title: Patient 6 in group SynSa1

description: aCGH profile in primary tumor sample


title: genomic DNA from leukemic blast 8363800026_RO3CO2

description: leukemic blast


title: genomic DNA from leukemic blast 8359018137_RO3CO2

description: leukemic blast


title: 10d-wt1


title: genomic DNA from leukemic blast 8359018152_RO3CO2

description: leukemic blast


title: Patient 5 in group SynSa1

description: aCGH profile in primary tumor sample


title: 10d-Tg3

source_name: Transgenic mouse hippocampus a 10 day


title: Patient 2 in group SynSa1

description: aCGH profile in primary tumor sample


title: genomic DNA from leukemic blast 8363800011_RO3CO2

description: leukemic blast


title: 10d-Tg2

source_name: Transgenic mouse hippocampus at 10 day


title: Patient 1 in group SynSa1

description: aCGH profile in primary tumor sample


title: Patient 3 in group SynSa1

description: aCGH profile in primary tumor sample


title: Daoy_1h_SHH+EGF_rep1

description: replicate 1

source_name: 1 h, SHH+EGF, rep 1

value: 1 h


title: 10d-Tg1


title: Daoy_1h_EGF_rep1

description: replicate 1

source_name: 1 h, EGF, rep 1


title: Daoy_0.5h_SHH+EGF_rep1

description: replicate 1

source_name: 0.5 h, SHH+EGF, rep 1


title: Daoy_1h_SHH_rep1

description: replicate 1

source_name: 1 h, SHH, rep 1


title: Daoy_1h_control_rep1

description: replicate 1

source_name: 1 h, control, rep 1


title: genomic DNA from leukemic blast 8363800026_RO2CO2

description: leukemic blast


title: Daoy_0.5h_EGF_rep1

description: replicate 1

source_name: 0.5 h, EGF, rep 1


title: genomic DNA from leukemic blast 8359018137_RO1CO2

description: leukemic blast


title: genomic DNA from leukemic blast 8359018137_RO2CO2

description: leukemic blast


title: Daoy_0.5h_control_rep1

description: replicate 1

source_name: 0.5 h, control, rep 1


title: genomic DNA from leukemic blast 8359018152_RO2CO2

description: leukemic blast


title: genomic DNA from leukemic blast 8359018152_RO6CO1

description: leukemic blast


title: genomic DNA from leukemic blast 8363800011_RO1CO2

description: leukemic blast


title: Daoy_0.25h_EGF_rep1

description: replicate 1

source_name: 0.25 h, EGF, rep 1


title: Daoy_0.25h_SHH_rep1

description: replicate 1

source_name: 0.25 h, SHH, rep 1


title: Patient 20 in group SynSa3 [transcriptome]

description: Gene expression in metastatic/recurrent tumor sample

hyb_protocol: Gene expression analysis was performed using Human Gene Expression 4x44K v2 microarrays (G4845A) according to the one-color microarray-based expression analysis protocol (Agilent Technologies).

data_processing: Image analysis was done using the Feature Extraction V10.10.1.1 software (Agilent Technologies, SantaClara, CA, USA). Microarray data were analyzed using Gene Spring GX default workflow parameters for Agilent one-color expression experiments (Agilent Technologies, SantaClara, CA, USA).

source_name: tumor sample

label_protocol: Total RNA (25ng) was reverse transcribed into cDNA by incorporating a T7 oligo-dT promoter primer prior to the generation of fluorescent cRNA using an Agilent LowInput Quick Amp Labeling Kit (Agilent Technologies, SantaClara, CA, USA).

extract_protocol: Total RNA of sufficient integrity and purity was obtained from 57 tumor specimens using the miRNeasy Mini Kit (Qiagen) with optional DNase treatment using RNase-free DNase Set (Qiagen). RNA quality was checked using Bio-Rad Experion system (Bio-Rad Laboratories).

value: synovial sarcoma


title: genomic DNA from leukemic blast 8363800011_RO2CO2

description: leukemic blast

source_name: leukemic blast (MNC)


title: Patient 21 in group SynSa3 [transcriptome]


title: Patient 22 in group SynSa3 [transcriptome]


title: Daoy_0.25h_SHH+EGF_rep1

description: replicate 1

source_name: 0.25 h, SHH+EGF, rep 1


title: Daoy_0.25h_control_rep1

description: replicate 1

source_name: 0.25 h, control, rep 1


title: Daoy_0h_SHH_rep1

description: replicate 1

source_name: 0 h, SHH, rep 1

value: 0 h


title: genomic DNA from leukemic blast 8359018137_RO6CO1

description: leukemic blast


title: Patient 19 in group SynSa3 [transcriptome]


title: RCC 13

city: Bronx

first: Yiting

last: Yu

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ,Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details.

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing:
Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background.PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167.)
normalized log2 (HpaII/MspI) ratios included in Series supplementary files RCC_hg18_ratio-p1.txt and RCC_hg18_ratio-p2.txt

source_name: histologically verified CCRCC tumor samples 13

label_protocol: Random 9-mers pre-labeled with either Cy5 or Cy3

extract_protocol: Genomic DNA was isolated as per dialysis tubing method. in summary, genomic DNA was isolated from cell lysates (0.1 M Tris-HCL pH 8.0; 10 mM EDTA pH 8.0 and 1% SDS), digested overnight at 50C on Proteinase K, follow by several organic extractions (TE-saturated phenol and Phenol-Chloroform-Isoamyl alcohol), DNA was purified and concentrated by ethanol precipitation and resuspended in LOTE pH 7.5 (3 mM Tris-Hcl and 0.2 mM EDTA).

treatment_protocol: Samples were collected under IRB protocol approved by the Albert Einstein College of Medicine. Kidney samples were obtained from living allograft donors and surgical nephrectomies and from left-over portions of diagnostic kidney biopsies. Tissue was placed into RNALater and manually microdissected at 4oC for the tubular compartment. We used Zeiss steromicroscope under 60x magnification for the microdissection.

value: clear cell renal cell cancer tumor

tag: restriction enzyme

value: MspI representation of genomic DNA

value: HpaII representation of genomic DNA


title: RCC 12

source_name: histologically verified CCRCC tumor samples 12


title: Daoy_0h_control_rep1

description: replicate 1

data_processing: The data were normalised using quantile normalisation with lumi package in R.

source_name: 0 h, control, rep 1

value: Daoy cells (ATCC:HTB-186)


title: RCC 10

source_name: histologically verified CCRCC tumor samples 10


title: genomic DNA from leukemic blast 8363800026_RO6CO1

description: leukemic blast

value: Male


title: SH-SY5Y cell 12h

city: Beijing

first: li

last: juan

address: East Street Fengtai District

country: China

institute: Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology

description: miRNA expression data from  SH-SY5Y cells at 12h

hyb_protocol: Following labeling, 21.5 ul of biotin-labeled RNA was hybridized for 16 hr at 48C on Affymetrix miRNA 2.0 Arrays. The miRNA 2.0 Arrays were washed and stained in the Affymetrix Fluidics Station 450 using fludics script FS450_0003.

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

data_processing: Data files were analyzed with Affymetrix miRNAQCtool using RMA background correction and quantile normalization (Default settings).Since the miRNA 2.0 array covers 131 organisms, we sorted out Human only.

source_name: SH-SY5Y cell 12h

label_protocol: A total of 1000ng of total RNA was labelled using the Genisphere HSR labelling Kit.

growth_protocol: Human neuroblastoma cell line, SH-SY5Y cells were cultured in Dulbecco's modiﬁed Eagle's medium/F-12 (DMEM/F-12, Invitrogen), supplemented with 10% fetal bovine serum (FBS) (Gibco) at 37℃ with 5% CO2

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

treatment_protocol: SH-SY5Y cells were infected with HEV71 at 1 multiplicity of infection. After 1h incubation, the cells were washed with PBS and refed with 2% containing medium. The adherent cells were harvested after 6 and 12 hours post-infection.

value: human neuroblastoma


title: RCC 11

source_name: histologically verified CCRCC tumor samples 11


title: Patient 17 in group SynSa3 [transcriptome]


title: Daoy_0.5h_SHH_rep1

description: replicate 1

hyb_protocol: To perform whole genome expression analysis HumanHT-12 v4 chips were incubated with biotin labeled cRNA for 18h at 58°C in a hybridization oven under humidity controlled conditions. After hybridization the Illumina® Sentrix BeadChips were washed using buffers provided by the kit. 2.5 µl (1mg/ml) of Streptavidin-Cy3 (per Chip) diluted in 2.5 ml Blocking buffer were incubated on a Chip for 10 min under gentle shaking to allow binding of cRNA to gene specific probes. After washing, Illumina® Sentrix BeadChips were dried and and scanned.

source_name: 0.5 h, SHH, rep 1

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen, 74104) according to the manufacturer's protocol. Quantity and purity of RNA were determined by measuring the optical density at 260 and 280 nm with an UV/Vis Spectrophotometer (Thermo Scientific, Nanodrop 1000) and BioAnalyzer 2100 (Agilent Technologies Deutschland GmbH).

value: SHH


title: Patient 18 in group SynSa3 [transcriptome]


title: RCC 9

source_name: histologically verified CCRCC tumor samples 9


title: HEV71-infected SH-SY5Y cell 12h

description: miRNA expression data from HEV71-infected SH-SY5Y cells at 12h

source_name: HEV71-infected SH-SY5Y cell 12h


title: SH-SY5Y cell  6h

description: miRNA expression data from  SH-SY5Y cells at 6h

source_name: SH-SY5Y cell  6h


title: genomic DNA from leukemic blast 8359018137_RO5CO1

description: leukemic blast


title: RCC 8

source_name: histologically verified CCRCC tumor samples 8


title: genomic DNA from leukemic blast 8359018152_RO4CO1

description: leukemic blast


title: genomic DNA from leukemic blast 8359018152_RO5CO1

description: leukemic blast


title: genomic DNA from leukemic blast 8363800026_RO5CO1

description: leukemic blast


title: Patient 15 in group SynSa3 [transcriptome]


title: Patient 13 in group SynSa3 [transcriptome]


title: Daoy_1.5h_SHH_rep1

description: replicate 1

source_name: 1.5 h, SHH, rep 1


title: RCC 7

source_name: histologically verified CCRCC tumor samples 7


title: Patient 14 in group SynSa3 [transcriptome]

source_name: tumor sample


title: RCC 6

source_name: histologically verified CCRCC tumor samples 6


title: genomic DNA from bone marrow CD34+ cells 8363800026_RO1CO1

description: normal bone marrow progenitor cells

source_name: normal bone marrow progenitor cells

value: normal bone marrow progenitor cells


title: genomic DNA from bone marrow CD34+ cells 8363800011_RO2CO1

description: normal bone marrow progenitor cells


title: Nymph (N) biological replicate 2, technical repeat

city: Pretoria

first: Christian

last: Stutzer

state: Gauteng

address: Lynnwood road

department: Biochemistry

country: South Africa

institute: University of Pretoria

description:
N2R
Technical replicate of biological replicate 2. Nymph, harvested after 7 days post infestation.

hyb_protocol: Hybridization was performed at 65oC for 17 hours. Prior to scanning, each slide was washed, rinsed and dried in Stabilization and Drying Solution (Agilent Technologies, USA). Following a drying step, slides were scanned with the GenePixTM 4000B microarray laser scanner (Molecular devices Inc., USA). Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on a 4000B microarray laser scanner (Molecular devices Inc., USA). Images were quantified using GenePix Pro feature extraction software (v6.0, Axon Molecular Devices, USA).

data_processing: Images were quantified using GenePix Pro feature extraction software (v6.0, Axon Molecular Devices, USA). Normalization within slides was performed using the Limma package in R (http://CRAN.R-project.org), employing the locally weighted scatterplot smoothing (LOWESS) technique, followed by Gquantile normalization between slides. The Limma package also was used to calculate the fold change between each group pair-wise comparison, to identify significantly differentially expressed transcripts with p-values adjusted for multiple comparisons false discovery rates.

organism: Rhipicephalus microplus

source_name: Nymph

label_protocol: 3 µg of high quality DNaseI-treated total RNA was used for cDNA synthesis using 500 U SuperscriptTM III (InvitrogenTM life technologies, USA), a poly-dT primer (250 pmol), random nanomers (775 pmol) and 5 mM each dATP, dTTP, dGTP, with 5 mM aminoallyl dUTP for Cyanine 3-dCTP/Cyanine 5-dCTP dye coupling. DNA was primed at 70°C for 10 min, then reversed transcribed at 42°C for 16 h.

growth_protocol: R. microplus (Mozambique strain) larvae, hatched at 25oC (75-85% humidity), were allowed to feed on Holstein-Friesian cattle.

extract_protocol: Total RNA was isolated according to manufacturer’s guidelines for TRI REAGENT.

value: mixed

value: day 7

value: Mozambique

tag: developmental stage

value: nymph

value: whole body

source_name: [reference] pooled life stages day 4, 5, 7, 13 and 15 and tissues at day 20

value: mixed for life stages, female for adult tissues


title: Patient 12 in group SynSa3 [transcriptome]


title: HEV71-infected SH-SY5Y cell 6h

description: miRNA expression data from HEV71-infected SH-SY5Y cells at 6h

source_name: HEV71-infected SH-SY5Y cell 6h

tag: cell line


title: Patient 11 in group SynSa3 [transcriptome]


title: genomic DNA from bone marrow CD34+ cells 8359018152_RO1CO1

description: normal bone marrow progenitor cells


title: genomic DNA from bone marrow CD34+ cells 8359018137_RO1CO1

description: normal bone marrow progenitor cells


title: Nymph (N) biological replicate 2

description:
N2
Biological replicate 2 of 2. Nymph, harvested after 7 days post infestation.

value: life stages day 4, 5, 7, 13 and 15 and tissues at day 20


title: Nymph (N) biological replicate 1, technical repeat

description:
N1R
Technical replicate of biological replicate 1. Nymph, harvested after 7 days post infestation.


title: RCC 5

source_name: histologically verified CCRCC tumor samples 5


title: RCC 4

source_name: histologically verified CCRCC tumor samples 4


title: Patient 9 in group SynSa3 [transcriptome]

value: synovial sarcoma


title: genomic DNA from leukemic blast 5729917034_RO3CO2

description: leukemic blast

source_name: leukemic blast (MNC)

value: Female

value: leukemic blast


title: Patient 10 in group SynSa3 [transcriptome]


title: genomic DNA from leukemic blast 5729917034_RO2CO2

description: leukemic blast


title: RCC 3

source_name: histologically verified CCRCC tumor samples 3

value: clear cell renal cell cancer tumor

value: MspI representation of genomic DNA


title: Nymph (N) biological replicate 1

description:
N1
Biological replicate 1 of 2. Nymph, harvested after 7 days post infestation.


title: genomic DNA from bone marrow CD34+ cells 8363800026_RO2CO1

description: normal bone marrow progenitor cells


title: RCC 2

source_name: histologically verified CCRCC tumor samples 2

value: HpaII representation of genomic DNA


title: Larvae (L) biological replicate 2

description:
L2
Biological replicate 2 of 2. Larvae, harvested after 4 days post infestation.

source_name: Larvae

value: day 4

value: larvae


title: genomic DNA from leukemic blast 5729917034_RO1CO2

description: leukemic blast


title: Larvae (L) biological replicate 2, technical repeat

description:
L2R
Technical replicate of biological replicate 2. Larvae, harvested after 4 days post infestation.


title: Patient 8 in group SynSa3 [transcriptome]

value: Male


title: genomic DNA from bone marrow CD34+ cells 8363800011_RO1CO1

description: normal bone marrow progenitor cells

value: normal bone marrow progenitor cells


title: genomic DNA from leukemic blast 8363800011_RO6CO1

description: leukemic blast


title: control 12

source_name: control microdissectedproximal tubules from non-tumor part of nephrectomy sample 12

value: control microdissected proximal tubules from non-tumor part of nephrectomy samples


title: control 13

source_name: control microdissectedproximal tubules from non-tumor part of nephrectomy sample 13


title: genomic DNA from leukemic blast 5729917034_RO6CO1

description: leukemic blast


title: Patient 7 in group SynSa3 [transcriptome]


title: RCC 1

source_name: histologically verified CCRCC tumor samples 1


title: control 11

source_name: control microdissectedproximal tubules from non-tumor part of nephrectomy sample 11


title: control 10

source_name: control microdissectedproximal tubules from non-tumor part of nephrectomy sample 10


title: genomic DNA from leukemic blast 5729917034_RO4CO1

description: leukemic blast


title: Larvae (L) biological replicate 1, technical repeat

description:
L1R
Technical replicate of biological replicate 1. Larvae, harvested after 4 days post infestation.

value: mixed


title: genomic DNA from leukemic blast 5729917034_RO5CO1

description: leukemic blast


title: Patient 5 in group SynSa3 [transcriptome]

source_name: tumor sample


title: control 9

source_name: control microdissectedproximal tubules from non-tumor part of nephrectomy sample 9


title: Patient 4 in group SynSa3 [transcriptome]


title: control 7

source_name: control microdissectedproximal tubules from non-tumor part of nephrectomy sample 7


title: control 8

source_name: control microdissectedproximal tubules from non-tumor part of nephrectomy sample 8


title: Patient 3 in group SynSa3 [transcriptome]


title: genomic DNA from leukemic blast 5729917060_RO2CO2

description: leukemic blast


title: genomic DNA from leukemic blast 5729917060_RO1CO2

description: leukemic blast


title: Larvae (L) biological replicate 1

description:
L1
Biological replicate 1 of 2. Larvae, harvested after 4 days post infestation.

value: Mozambique

source_name: [reference] pooled life stages day 4, 5, 7, 13 and 15 and tissues at day 20


title: Patient 2 in group SynSa3 [transcriptome]


title: control 6

source_name: control microdissectedproximal tubules from non-tumor part of nephrectomy sample 6


title: Patient 6 in group SynSa3 [transcriptome]


title: Patient 24 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample


title: Patient 25 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample


title: genomic DNA from leukemic blast 5729917060_RO6CO1

description: leukemic blast


title: genomic DNA from leukemic blast 5729917034_RO3CO1

description: leukemic blast


title: Patient 23 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample


title: control 5

source_name: control microdissectedproximal tubules from non-tumor part of nephrectomy sample 5


title: control 3

source_name: control microdissectedproximal tubules from non-tumor part of nephrectomy sample 3


title: control 4

source_name: control microdissectedproximal tubules from non-tumor part of nephrectomy sample 4


title: Patient 21 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample


title: Patient 1 in group SynSa3 [transcriptome]


title: genomic DNA from leukemic blast 5729917060_RO5CO1

description: leukemic blast

source_name: leukemic blast (MNC)


title: control 2

source_name: control microdissectedproximal tubules from non-tumor part of nephrectomy sample 2


title: control 1

source_name: control microdissectedproximal tubules from non-tumor part of nephrectomy sample 1


title: Patient 22 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample


title: Patient 20 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample


title: Patient 19 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample


title: Patient 16 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample


title: genomic DNA from leukemic blast 5729917060_RO2CO1

description: leukemic blast


title: genomic DNA from leukemic blast 5729917060_RO4CO1

description: leukemic blast


title: genomic DNA from leukemic blast 5729917060_RO1CO1

description: leukemic blast


title: Patient 12 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample


title: Patient 17 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample


title: Patient 18 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample


title: Patient 13 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample


title: genomic DNA from leukemic blast 5729917045_RO5CO2

description: leukemic blast


title: Patient 10 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample


title: genomic DNA from leukemic blast 5729917060_RO3CO1

description: leukemic blast


title: genomic DNA from leukemic blast 5729917045_RO4CO2

description: leukemic blast


title: genomic DNA from leukemic blast 5729917034_RO2CO1

description: leukemic blast


title: Patient 8 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample


title: Patient 7 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample


title: genomic DNA from leukemic blast 5729917045_RO3CO2

description: leukemic blast


title: Patient 6 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample


title: female, fadrozole-injected, LPS-activated, pool 1

description: 3241_2057M_Nandi_3328_Fsr8LPS.rma-gene-full

hyb_protocol: Hybridised on ChiGene 1.0 ST

scan_protocol: GeneChip Scanner 3000 7G

data_processing:
Analysed with GeneChip® Command Console® Software (AGCC), applying RMA normalisation to the CEL files
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = ChiGene-1_0-st
program-name = Expression Console
program-version = 1.1.2800.29167

organism: Gallus gallus

source_name: fadrozole-treated female_activated

label_protocol: Ambion WT labelling kit

extract_protocol: RNA was extracted using RNABee, following the manufacturer's instructions

treatment_protocol: At day 3 of incubation eggs were injected with either 100ul PBS (control) or 100ul PBS containing 1mg fadrozole.

value: female

value: embryos after formation of gonad into ovary/testis

value: chicken embryos

value: day 13

tag: injected with

value: 1mg fadrozole at day 3 of development

value: LPS-activated macrophages


title: Patient 4 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample

value: synovial sarcoma


title: Patient 5 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample

value: Female


title: Patient 1 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample


title: genomic DNA from leukemic blast 5729917045_RO3CO1

description: leukemic blast

value: leukemic blast


title: genomic DNA from leukemic blast 5729917045_RO5CO1

description: leukemic blast


title: genomic DNA from leukemic blast 5729917045_RO6CO2

description: leukemic blast


title: genomic DNA from leukemic blast 5729917045_RO6CO1

description: leukemic blast


title: male, fadrozole-injected, LPS-activated, pool 2

description: 3240_2057M_Nandi_3327_MF9LPS.rma-gene-full

source_name: fadrozole-treated male_activated

value: male


title: genomic DNA from leukemic blast 5729917034_RO6CO2

description: leukemic blast


title: genomic DNA from leukemic blast 5729917045_RO1CO2

description: leukemic blast


title: genomic DNA from leukemic blast 5729917045_RO2CO2

description: leukemic blast


title: Patient 16 in group SynSa1 [transcriptome]

description: Gene expression in primary tumor sample


title: female, fadrozole-injected, non-activated, pool 2

description: 3238_2057M_Nandi_3325_Fsr9C.rma-gene-full

source_name: fadrozole-treated female

value: non-activated macrophages


title: Patient 11 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample


title: male, fadrozole-injected, LPS-activated, pool 1

description: 3239_2057M_Nandi_3326_MF8LPS.rma-gene-full


title: genomic DNA from leukemic blast 5729917045_RO2CO1

description: leukemic blast


title: genomic DNA from leukemic blast 5729917034_RO5CO2

description: leukemic blast


title: genomic DNA from leukemic blast 5729917034_RO4CO2

description: leukemic blast


title: Patient 14 in group SynSa1 [transcriptome]

description: Gene expression in primary tumor sample


title: genomic DNA from bone marrow CD34+ cells 5729917060_RO6CO2

description: normal bone marrow progenitor cells

source_name: normal bone marrow progenitor cells


title: female, fadrozole-injected, non-activated, pool 1

description: 3237_2057M_Nandi_3324_Fsr8C.rma-gene-full


title: Patient 13 in group SynSa1 [transcriptome]

description: Gene expression in primary tumor sample


title: genomic DNA from leukemic blast 5729917045_RO1CO1

description: leukemic blast


title: genomic DNA from bone marrow CD34+ cells 5729917060_RO4CO2

description: normal bone marrow progenitor cells


title: genomic DNA from leukemic blast 5729917045_RO4CO1

description: leukemic blast


title: genomic DNA from leukemic blast 5729917034_RO1CO1

description: leukemic blast


title: genomic DNA from bone marrow CD34+ cells 5729917060_RO3CO2

description: normal bone marrow progenitor cells


title: male, fadrozole-injected, non-activated, pool 1

description: 3235_2057M_Nandi_3322_M F8 C.rma-gene-full

source_name: fadrozole-treated male


title: Patient 11 in group SynSa1 [transcriptome]

description: Gene expression in primary tumor sample

source_name: tumor sample


title: Patient 12 in group SynSa1 [transcriptome]

description: Gene expression in primary tumor sample


title: genomic DNA from bone marrow CD34+ cells 5729917060_RO5CO2

description: normal bone marrow progenitor cells


title: male, fadrozole-injected, non-activated, pool 2

description: 3236_2057M_Nandi_3323_MF9 C.rma-gene-full


title: female, fadrozole-injected, LPS-activated, pool 2

description: 3242_2057M_Nandi_3329_Fsr9LPS.rma-gene-full


title: male, PBS-injected, LPS-activated, pool 2

description: 3232_2057M_Nandi_3319_M C9LPS.rma-gene-full

source_name: control male_activated

value: 100ul PBS as control at day 3 of development


title: female, PBS-injected, LPS-activated, pool 2

description: 3234_2057M_Nandi_3321_F C9LPS.rma-gene-full

source_name: control female_activated


title: Vaginal secretion05

city: daejeon

first: Jonglyul

last: Park

address: 52, Eoeun-dong, Yuseong-gu

department: Medical genomics

description:
Vaginal secretion
Sample15

hyb_protocol: Amplified DNA was hybridized on the Infinium HumanMethylation 450 BeadChip (Illumina), following the Illumina Infinium HD Methylation protocol.

scan_protocol: The arrays were imaged using the Illumina HiScan SQ scanner, and image processing and extraction of intensity data were performed according to Illumina’s instructions.

data_processing: Each methylation signal was used to compute the β value, which is a quantitative measure of DNA methylation ranging from 0 (for completely unmethylated cytosines) to 1 (for completely methylated cytosines) (Bibikova et al., 2006).

label: Cy5 and Cy3

source_name: Vaginal secretion

label_protocol: standard Illumina protocol

extract_protocol: Genomic DNA (1 µg) from each sample was bisulfite converted using the EZ DNA methylation kit (Zymo Research), and 200 ng of the converted DNA was used for amplification.

tag: sample type

value: Vaginal secretion


title: female, PBS-injected, LPS-activated, pool 1

description: 3233_2057M_Nandi_3320_F C8LPS.rma-gene-full


title: Patient 8 in group SynSa1 [transcriptome]

description: Gene expression in primary tumor sample

value: Male


title: Vaginal secretion06

description:
Vaginal secretion
Sample16


title: Patient 9 in group SynSa1 [transcriptome]

description: Gene expression in primary tumor sample


title: Patient 10 in group SynSa1 [transcriptome]

description: Gene expression in primary tumor sample


title: male, PBS-injected, LPS-activated, pool 1

description: 3231_2057M_Nandi_3318_M C8LPS.rma-gene-full


title: Patient 9 in group SynSa2 [transcriptome]

description: Gene expression in primary tumor sample


title: Patient 6 in group SynSa1 [transcriptome]

description: Gene expression in primary tumor sample


title: Patient 7 in group SynSa1 [transcriptome]

description: Gene expression in primary tumor sample


title: female, PBS-injected, non-activated, pool 2

description: 3230_2057M_Nandi_3317_F C9C.rma-gene-full

source_name: control female


title: Vaginal secretion03

description:
Vaginal secretion
Sample13


title: Patient 5 in group SynSa1 [transcriptome]

description: Gene expression in primary tumor sample


title: male, PBS-injected, non-activated, pool 2

description: 3228_2057M_Nandi_3315_M C9C.rma-gene-full

source_name: control male


title: Vaginal secretion01

description:
Vaginal secretion
Sample11


title: female, PBS-injected, non-activated, pool 1

description: 3229_2057M_Nandi_3316_F C8C.rma-gene-full


title: Patient 4 in group SynSa1 [transcriptome]

description: Gene expression in primary tumor sample


title: male, PBS-injected, non-activated, pool 1

description: 3227_2057M_Nandi_3314_M C8C.rma-gene-full


title: Vaginal secretion02

description:
Vaginal secretion
Sample12


title: Patient 3 in group SynSa1 [transcriptome]

description: Gene expression in primary tumor sample


title: Patient 1 in group SynSa1 [transcriptome]

description: Gene expression in primary tumor sample


title: Patient 2 in group SynSa1 [transcriptome]

description: Gene expression in primary tumor sample


title: Saliva04

description:
Saliva
Sample10

source_name: Saliva

value: Saliva


title: Saliva03

description:
Saliva
Sample9


title: IE2 vs C2

description: compare gene expression profiles of control cells

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy and the lowess normalized log2 ratio (test/control) of each slide.

source_name: SH-SY5Y cells infected with HEV71 after transfected with miR-1246 inhibitor

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, GE Healthcare Cat. No. PA 55021/PA 53021) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. The amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

extract_protocol: Stably treated cells and control cells were harvest, and total RNA was extracted with Trizol Reagent (Invitrogen) and ethanol precipitation

treatment_protocol: SH-SY5Y cells were transfected wtih miR-1246 inhibitor and negtive control respectively using HiPerFect Transfection Reagent according to the manufacturer’s instructions. Then the cells were infected with HEV71 after transfection. After 12 hours infection, the cells were harvested to microarray analysisAll experiments were done in duplication. At 12 h post-infection, adherent cells were harvested.

value: human neuroblastoma

source_name: SH-SY5Y cells transfected with Negtive control

tag: system

value: human neuroblastoma cell line


title: IE1 vs C1


title: Saliva01

description:
Saliva
Sample7


title: Blood06

description:
Blood
Sample6

source_name: Blood

value: Blood


title: HCT116_miR-204 0730

status: Public on Jul 30 2014

city: WUXI

first: zhaohui

last: Huang

state: Jiangsu

address: 200 Huihe Road

department: Wuxi Oncology Institute

institute: the Affiliated Hospital of Jiangnan University

description: Gene expression after 48 hours after transfection with miR-204-5p

hyb_protocol: Hybridization was performed in Agilent’s SureHyb Hybridization Chambers using Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) according to the manufacturer's instructions. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) .

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (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.

source_name: Cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using Agilent Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HCT116 cells were cultured in McCoy's 5a supplemented with 10% fetal bovine serum. The cultures were incubated at 37C in a humidified incubator with 5% CO2.

extract_protocol: After propagation for 48 hours, total RNA was extracted from HCT116 cells using TRIzol reagent

treatment_protocol: HCT116 cells were seeded in 6-cm2 tissue culture plates and transfected with the miR-204-5p mimic or negative control (NC) using Lipofectamine 2000

value: colorectal cancer

tag: treatment

value: transfection with miR-204-5p


title: Blood-Volunteer5

city: Saint Genes Champanelle

first: Celine

last: BOBY

address: Centre INRA Auvergne-Rhône-Alpes

country: France

institute: INRA

hyb_protocol: After purification (Qiagen RNeasy Mini Kit), 825 ng of Cy3 and Cy5 labeled cRNA were hybridized onto G4845A Human GE 4x44K v2 microarray (Agilent, USA) with hybridization buffer (Agilent Gene Expression Hybridization Kit) according to the manufacturer’s instructions. After 17h of hybridization, slides were washed with the Gene Expression Wash Pack.

scan_protocol: Microarrays were scanned with Agilent G2505 scanner.

data_processing: Data were extracted with Feature Extraction 10.7 software (Agilent, USA) using Lowess normalization (no background subtraction).

source_name: blood sample at the beginning of the study (time 0)

label_protocol: 50 ng of total RNA extracted were amplified and fluorescently labelled to produce Cy5 or Cy3 cRNA using the Low Input Quick Amp Labeling two colors Kit (Agilent, USA) in the presence of spike-in two colors control.

extract_protocol: Total RNA was isolated from blood by means of the RiboPure-Blood kit (Ambion, Austin, TX, USA) in accordance with the manufacturer’s instructions.

treatment_protocol: At baseline and after 8 weeks of flavanol supplementation freshly collected blood was added to RNALater® (Ambion, Austin, TX, USA) and stored at -80°C.

tag: biological sources

value: blood

tag: mof supplementation

tag: age

tag: cigarettes/day

tag: years of smoking

tag: height (m)

tag: weight (kg)

tag: bmi (kg/m2)

tag: sys bp (mm hg)

tag: dia bp (mm hg)

tag: heart rate (beats/min)

source_name: blood samples after 8 weeks of MOF supplementation

value: 8 weeks


title: Saliva02

description:
Saliva
Sample8


title: Blood-Volunteer6

tag: gender


title: Blood-Volunteer2


title: Oct4 GFP Positive, biological rep 1

city: New Brunswick

first: John

last: Langenfeld

state: NJ

address: One Robert Wood Johnson Place

department: Surgery

institute: Rutgers-RWJMS

description: Gene expression data from H1299 cells Postive for Oct4 promoter/GFP

hyb_protocol: The labelled a RNA was hybridized at 50 degree C for 16 hrs

scan_protocol: DNA microarrays (human onearray version 4.2) were scanned using GenePix 4000B Scanner.

data_processing: The normalized (dChip)  signal inentsity values were compared for differential expression.

source_name: H1299 cells transfected with stable Oct4 promoter/GFP reporter vectors

label_protocol: Cy3 labelled a RNA was prepared according to the standard microarray labelling protocol from 1 ug total RNA.

growth_protocol: H1229 lung cancer cell lines were cultured in DMEM (Sigma Aldrich) with 5% fetal bovine serum for 24 hrs.

extract_protocol: Total RNA was extarcted using RNeasy mini kit (QIAgen) according to the manufacturer's instructions.

treatment_protocol: H1299 cells were stably transfected with the Oct4 promoter/GFP or Nestin promoter/GFP reporter vectors.

tag: cell line


title: Blood-Volunteer7


title: Blood-Volunteer4


title: HCT116_NC 0730

description: Gene expression after 48 hours after transfection with the negative control

tag: tissue

value: control


title: Blood05

description:
Blood
Sample5

tag: sample type


title: Blood-Volunteer1


title: Oct4 GPF Negative, biological rep 1

description: Gene expression data from H1299 cells negative for Oct4/GFP

source_name: H1299 cells negative for Oct4 promoter/GFP reporter vectors


title: Blood-Volunteer3


title: H520_control

city: Miaoli County

first: Shih Sheng

last: Jiang

address: No. 35 Keyan Road, Zhunan County

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: We used GeneSpringGX 11 for quantile normalization. The base of log transformation applied to the quamtile normalization was 2.

source_name: Human lung squamous cell carcinoma cell line H520, scrambled control siRNAs.

label_protocol: Biotinylated cRNA were prepared with the TargetAmp Nano-G Bioti- aRNA Labeling kit (Epicentre) for Illumina arrays.

extract_protocol: Total RNA was extracted with QIAGEN RNeasy mini kit according to  protocol provided in the kit by the  manufacturer. Quality control was performed with Agilent Bioanalyser.

value: control siRNA


title: 24 h post 5 cGy + 2 Gy radiation, biological rep3 (Agilent)

city: Hefei

first: Wei

last: Han

state: Anhui

address: #155 Shushanghu Road

institute: Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences

description:
microRNA expression data from AG 1522 human fibroblasts 24 h after 5 cGy + 2 Gy X-ray radiation (12 h interval).
AG_5p2Gy_24h_3

hyb_protocol: 100 ng Cy3-labeled RNA using the miRNA Complete Labeling and Hyb Kit (Agilent technologies, Santa Clara, CA, US) in the Hybridization Oven (Agilent technologies, Santa Clara, CA, US) at 55℃，20 rpm for 20 h according to the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA, US) using the Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: The raw data were normalized with quantile normalization to ensure comparability across samples.

source_name: Human skin fibroblast AG 1522 cells, first exposed to 5 cGy then followed by 2 Gy X-ray radiation with 12 h interval, 24 h after the final radiation

growth_protocol: Human skin fibroblast AG 1522 cells were cultured in modified α-MEM (Hyclone, Logan, US) supplemented with 20% fetal bovine serum (FBS) (Hyclone, Logan, US), 1% penicillin/streptomycin, 1% glutamine and 1% non-essential amino acids mix (Sigma-Aldrich, St. Louis, US). All cultures were grown in a humidified 5% CO2 atmosphere at 37℃. Prior to treatment, the confluence of cells obatined to 100%.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Then small molecular RNA was extracted using the mirVana miRNA Isolation Kit (Ambion, Austin, TX, US) following the manufacturer’s instructions.

treatment_protocol: The miRNA profiles for the 5 cGy5 cGy irradiation at 12 h after irradiation were examined.For the 2 Gy irradiation at 24 h after irradiation were examined.For the (5 cGy + 2 Gy) groups exposed to 5 cGy (priming dose) and then followed by 2 Gy (challenge dose), 24 h after application of the challenging dose were examined.

tag: cell type

value: skin fibroblast

value: 5 cGy followed by 2 Gy X-ray radiation

tag: time


title: 24 h post 5 cGy + 2 Gy radiation, biological rep2 (Agilent)

description:
microRNA expression data from AG 1522 human fibroblasts 24 h after 5 cGy + 2 Gy X-ray radiation (12 h interval).
AG_5p2Gy_24h_2

label_protocol: 100 ng Cy3-labeled RNA using the miRNA Complete Labeling and Hyb Kit (Agilent technologies, Santa Clara, CA, US) in the Hybridization Oven (Agilent technologies, Santa Clara, CA, US) at 55℃，20 rpm for 20 h according to the manufacturer’s instructions.

tag: treatment


title: LK2_control

source_name: Human lung squamous cell carcinoma cell line LK2, scrambled control siRNAs.