title: MCL27 Mantle Cell lymphoma methylation

city: Cambridge

first: Alan

middle: J

last: Watkins

address: Addenbrooke's Hospital

country: United Kingdom

institute: University of Cambridge

description: Mantle cell lymphoma used as comparison reference

hyb_protocol: Following hybridisation, single base extension of hybridised DNA using hapten labelled bases was performed.  Staining was then developed using immunochemical stains catalysed by the haptens, and the arrays washed

scan_protocol: The chips were scanned using the BeadArray™ Reader (Illumina) and the BeadScan™ software (Illumina) using the Infinium Methylation Scan setting. The scanned data was then analysed in GenomeStudio™ (Illumina) using the Methylation analysis module

data_processing: The scanned data bead file was spatially normalised to correct for background noise using the Smethillium algorithm (http://bioinfo-out.curie.fr/projects/smethillium) within the R environment (www.r-project.org).  Where multiple probes targeted different CpG loci relating to one gene, the probe predicted to have the greatest influence on gene expression (eg. at a transcriptional factor binding site, proximity to the promoters) was selected for analysis

label: Cy3, Cy5

source_name: MCL27 Mantle Cell lymphoma methylation

label_protocol: Bisulphite modified DNA was then amplified using the MSM master mix (Illumina) and incubated at 37oC for 22 hours.  Amplified DNA was then fragmented and hybridised to BeadChips in an Illumina Hybridisation Oven at 48oC for 18 hours

extract_protocol: genomic DNA extracted from frozen tissues was bisulphite modified using the EZ DNA Methylation Kit (Zymo Research Corporation)

treatment_protocol: 2μg genomic DNA extracted from frozen tissues with >70% tumour cells using Qiagen kit

tag: disease

value: Mantle cell lymphoma


title: 5 pooled F1 SED male gastrocnemius RNA 8 wks age 2

status: Public on Aug 30 2012

type: RNA

city: College Park

first: Stephen

last: Roth

state: MD

address: 2309 SPH Building

department: Kinesiology

country: USA

institute: University of Maryland

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at the University of Maryland School of Medicine Biopolymer-Genomics Core Facility

scan_protocol: Array scanning was performed with the GeneChip Scanner 3000 according to Affymetrix standard protocol

data_processing: The microarray gene expression data were imported from the probe cell intensity CEL files and the Affymetrix Expression Console software was used to calculate the summary measure of the probe level data.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: gastrocnemius muscle

label_protocol: Sense-strand cDNA was generated from total RNA using the Ambion WT Expression Kit and then was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling Kit

growth_protocol: F0 C57BL/6 mice were exposed to voluntary exercise or sedentary lifestyle and bred with like-exposed mates to produce an F1 generation. F1 mice of both ancestries were sedentary and sacrificed at 8 wk or bred with littermates to produce an F2 generation, which was also sedentary and sacrificed at 8 wk.

extract_protocol: Total RNA was extracted from powdered gastrocnemius muscle using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Germantown, MD). All samples were diluted to 98 ng/µl and pooled by generation and condition (5 pooled samples per array).

treatment_protocol: animals were either directly (F0) or indirectly through ancestry (F1, F2) exposed to exercise (EX) or sedentary (SED) lifestyle

tag: strain

tag: generation

tag: ancestry

value: SED

tag: Sex

value: male


title: 5 pooled F1 EX male gastrocnemius RNA 8 wks age 2

value: EX


title: 5 pooled F1 SED male gastrocnemius RNA 8 wks age 1


title: AH129-5, biological rep1

city: Beijing

first: Wei

last: Li

address: Beichen West Road

department: State key lab of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

description: Gene expression data from AH129-5

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

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

data_processing:
Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.
Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: ahES cell line AH129-5

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: ahES cells and ES cells were cultured in N2B27 medium plus 2i and LIF. MEF cells were cultured in DMEM plus 10% FBS. Round sperm were freshly isolated from testis.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: ahES cells and round sperm cells were G0/G1 phase haploid cells purified by FACS sorting

tag: genetic background

tag: cell type

value: G0/G1 stage androgenetic haploid embryonic stem cell

tag: cell line

value: ahES cell line AH129-5


title: AH129-N1,biological rep1

description: Gene expression data from AH-N1

source_name: ahES cell line AH129-N1

value: ahES cell line AH129-N1


title: MCL29 Mantle Cell lymphoma methylation

type: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: MCL29 Mantle Cell lymphoma methylation


title: 5 pooled F2 EX male gastrocnemius RNA 8 wks age 2


title: MCL24 Mantle Cell lymphoma methylation

source_name: MCL24 Mantle Cell lymphoma methylation


title: Knockout cre_ppar_beta_floxed_rep3

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

description: 8 weeks old mice, mixed genetic background (SV 129/C57BL/6)

hyb_protocol: Affymetrix Mouse Genome 430 2.0 arrays were hybridized with 11 microgramme of labeled, amplified cRNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol EukGeWS2v5_450)

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

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

source_name: pancreatic beta-cells

label_protocol: The synthesis of cRNA was performed using the MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification kits according to the manufacturers' protocols (Ambion, Austin, TX). Labeling, hybridization and scanning of the samples were performed as described by Affymetrix (www.affymetrix.com).

growth_protocol: Pancreas-specific knock-out animals were generated by breeding mice harbouring a floxed Ppar-beta (PPARbetafl/fl) to mice expressing the Cre transgene under the control of the Pdx1 promoter (Pdx1Cre).

extract_protocol: Total RNA from islets or pancreas was extracted by using guanidine thiocyanate (Sigma) according to the manufacturer’s recommendation.  RNA quality and quantity was assessed by NanoDrop®ND-1000 spectrophotometer and Aligent 2100 bio-analyzer.

treatment_protocol: Islet isolation was accomplished from 8 weeks-old mice by 100 mg of collagenase digestion (211U/mg) followed by purification through a Histopaque gradient. Islet perifusion was carried out by placing 30 islets into a perifusion chamber (Milipore) as describe previously (Gao N 2007).

tag: age

value: 8 weeks

tag: genotype

value: PPAR-beta deletion

value: pancreatic beta-cell


title: MCL25 Mantle Cell lymphoma methylation

source_name: MCL25 Mantle Cell lymphoma methylation


title: Knockout cre_ppar_beta_floxed_rep2


title: Knockout cre_ppar_beta_floxed_rep1


title: Control ppar_beta_floxed_rep3

value: control


title: MCL23 Mantle Cell lymphoma methylation

source_name: MCL23 Mantle Cell lymphoma methylation


title: NgR day5 Rep2 -12h Dox

city: Barcelona

first: Ana

last: Sevilla

state: Barcelona

address: Avda Diagonal 643. Edificio Malagef 4rd Floor, Faculty of Biology

department: Departamento de Biologia Celular, Fisiologia e Inmunologia

country: Spain

institute: Universidad de Barcelona

description: Gene Expression data from NgR day5 Rep2 -12h Dox

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Data was normalized using Robust Multichip Average (RMA) method using the Affymetrix Expression Console software

source_name: NgR day5 -12h Dox

label_protocol: Biotinylated cRNA were prepared with the GeneChip WT cDNA Synthesis and Amplification Kit

growth_protocol: rtTA-expressing ES cells Aniv15 were used for derivation of rescue clones and were maintained on primary mouse embryonic fibroblasts with mES media

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

treatment_protocol: NgRescue clone was grown in +Dox (1ug/ml) media; Dox withdrawal was performed for 5 days and at each day Dox was added for a pulse of 12h.

value: Embryonic Stem Cells

tag: genotype/variation

value: AINV15_Nanog_Rescue Clone


title: NgR day5 Rep1 -12h Dox

description: Gene Expression data from NgR day5 Rep1 -12h Dox


title: Control ppar_beta_floxed_rep2


title: MCL22 Mantle Cell lymphoma methylation

source_name: MCL22 Mantle Cell lymphoma methylation


title: NgR day3 Rep1 +12h Dox

description: Gene Expression data from NgR day3 Rep1 +12h Dox

source_name: NgR day3 +12h Dox


title: NgR day3 Rep2 +12h Dox

description: Gene Expression data from NgR day3 Rep2 +12h Dox


title: f271pan_1 with array type maize from Affymetrix

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

description: Four major QTL explaining lignin content and cell wall degradability variation have been identified in the F288 x F271 RIL progeny (Roussel et al., 2002, Maydica 47: 9-20). Gene expression has been considered as a way in identification of candidate gene underlying QTL. Five lines chosen for their allelic pattern at four main QTL were considered for expression studies, two lines with all four favorable alleles (RIL99, RIL54), two lines with the unfavorable allele at bin 6.06 QTL position (RIL39 , RIL71), and one line with the unfavorable allele at bin 9.02 QTL position (RIL118). The defavorable parent F271 was studied in complement and is the object of this last array. Expression studies will be investigated in ear internode at two stages (emerging tassel and early silking).

hyb_protocol: labelled extract quantity: 10ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Zea mays

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: ear internode - Crop field Irrigation was applied during a dry and hot summer to prevent water stress

treatment_protocol: no treatment

tag: developmental stage (boyes et al. plant cell 2001)

value: emerging tassel

tag: line

tag: tissue

value: ear internode


title: f271flo_2 with array type maize from Affymetrix

value: early silking


title: NgR day3 Rep3 +12h Dox

description: Gene Expression data from NgR day3 Rep3 +12h Dox


title: FL17 Follicular lymphoma methylation

description: Follicular lymphoma used as comparison reference

source_name: FL17 Follicular lymphoma methylation

value: Follicular lymphoma


title: NgR day5 Rep1 -Dox

description: Gene Expression data from NgR day5 Rep1 -Dox

source_name: NgR day5 -Dox


title: NgR day5 Rep3 -12h Dox

description: Gene Expression data from NgR day5 Rep3 -12h Dox


title: NgR day3 Rep3 -12h Dox

description: Gene Expression data from NgR day3 Rep3 -12h Dox

source_name: NgR day3 -12h Dox


title: FL20 Follicular lymphoma methylation

source_name: FL20 Follicular lymphoma methylation


title: NgR day5 Rep2 +12h Dox

description: Gene Expression data from NgR day5 Rep2 +12h Dox

source_name: NgR day5 +12h Dox


title: NgR day5 Rep3 -Dox

description: Gene Expression data from NgR day5 Rep3 -Dox


title: NgR day5 Rep3 +12h Dox

description: Gene Expression data from NgR day5 Rep3 +12h Dox


title: NgR day5 Rep1 +12h Dox

description: Gene Expression data from NgR day5 Rep1 +12h Dox


title: NgR day5 Rep2 -Dox

description: Gene Expression data from NgR day5 Rep2 -Dox


title: NgR day3 Rep2 -12h Dox

description: Gene Expression data from NgR day3 Rep2 -12h Dox


title: NgR day3 Rep3 -Dox

description: Gene Expression data from NgR day3 Rep3 -Dox

source_name: NgR day3 -Dox


title: NgR day3 Rep1 -12h Dox

description: Gene Expression data from NgR day3 Rep1 -12h Dox


title: FL21 Follicular lymphoma methylation

source_name: FL21 Follicular lymphoma methylation


title: FL14 Follicular lymphoma methylation

source_name: FL14 Follicular lymphoma methylation


title: Control ppar_beta_floxed_rep1

description: 8 weeks old mice, mixed genetic background (SV 129/C57BL/6)


title: f271pan_2 with array type maize from Affymetrix


title: f271flo_1 with array type maize from Affymetrix


title: FL16 Follicular lymphoma methylation

source_name: FL16 Follicular lymphoma methylation


title: FL13 Follicular lymphoma methylation

source_name: FL13 Follicular lymphoma methylation


title: NgR day1 Rep3 +12h Dox

description: Gene Expression data from NgR day1 Rep3 +12h Dox

source_name: NgR day1 +12h Dox


title: NgR day3 Rep2 -Dox

description: Gene Expression data from NgR day3 Rep2 -Dox


title: 8530 SMZL methylation

source_name: 8530 SMZL methylation

value: Splenic marginal zone lymphoma


title: NFRI 3145_0.6% AcOH No.2

city: Tsukuba

first: Toshihide

last: Nakamura

state: Ibaraki

address: 2-1-12 Kannondai

department: Applied Microbiology Division

country: Japan

institute: National Food Research Institute

hyb_protocol: At 45 degree for 16 hr

scan_protocol: GeneChip Scanner

data_processing: GeneChip Operating System (GCOS), ExpressionStat 5.0

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: NFRI 3145

label_protocol: According to the Affymetrix user's manual

extract_protocol: Hot phenol method

value: NFRI 3145

tag: stress tolerance

value: AcOH tolerant

tag: temperature

value: 30 degree

tag: treatment

value: 0.6% AcOH 30 min


title: NFRI 3145_0.6% AcOH No.1


title: C13 SMZL methylation

source_name: C13 SMZL methylation

tag: disease


title: C12 SMZL methylation

source_name: C12 SMZL methylation


title: NFRI 3145_0% AcOH No.2

tag: strain

value: 0% AcOH


title: NgR day1 Rep3 -12h Dox

description: Gene Expression data from NgR day1 Rep3 -12h Dox

source_name: NgR day1 -12h Dox


title: C9 SMZL methylation

source_name: C9 SMZL methylation


title: C8 SMZL methylation

source_name: C8 SMZL methylation


title: NgR day1 Rep2 -12h Dox

description: Gene Expression data from NgR day1 Rep2 -12h Dox


title: NgR day1 Rep1 -12h Dox

description: Gene Expression data from NgR day1 Rep1 -12h Dox


title: NgR day1 Rep2 +12h Dox

description: Gene Expression data from NgR day1 Rep2 +12h Dox


title: NgR day1 Rep1 +12h Dox

description: Gene Expression data from NgR day1 Rep1 +12h Dox


title: C7 SMZL methylation

source_name: C7 SMZL methylation


title: NgR day0 Rep2 +Dox

description: Gene Expression data from NgR day0 Rep2 +Dox

source_name: NgR day0 +Dox


title: NgR day1 Rep2 -Dox

description: Gene Expression data from NgR day1 Rep2 -Dox

source_name: NgR day1 -Dox


title: NgR day1 Rep1 -Dox

description: Gene Expression data from NgR day1 Rep1 -Dox


title: NBRC 0224_0.6% AcOH No.1

source_name: NBRC 0224

value: NBRC 0224

value: AcOH sensitive


title: NBRC 0224_0.6% AcOH No.2


title: NBRC 0224_0% AcOH No.2


title: C6 SMZL methylation

source_name: C6 SMZL methylation


title: NFRI 3145_0% AcOH No.1


title: NBRC 0224_0% AcOH No.1


title: NgR day1 Rep3 -Dox

description: Gene Expression data from NgR day1 Rep3 -Dox


title: NgR day3 Rep1 -Dox

description: Gene Expression data from NgR day3 Rep1 -Dox

source_name: NgR day3 -Dox


title: NgR day0 Rep3 +Dox

description: Gene Expression data from NgR day0 Rep3 +Dox


title: C5 SMZL methylation

source_name: C5 SMZL methylation


title: mouse embryonic stem cells. Strain CGR8

city: Valencia

first: Roque

last: Bort

address: Campanar 21

department: Unidad Hepatologia Experimental

institute: IIS La Fe

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45ºC on Affymetrix Mouse Gene 1.0ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the Affymetrix-recommended protocol.

data_processing: Data (.CEL files) were normalized using the robust multiarray algorithm (RMA). Thereupon, we employed a conservative probe-filtering step excluding probes not reaching a log2 expression value of 5 in at least one sample, which resulted in the selection of a total of 19621 probes from the original set of 28853. To identify genes differentially expressed between the different microarray study groups, we employed Linear Models for Microarray Data R-package.

source_name: mouse embryonic stem cells_strain CGR8

label_protocol: Total RNA (300 ng per sample) was labeled using the Affymetrix GeneChip WT cDNA Synthesis and Amplification kit according to the Affymetrix-recommended protocol.

growth_protocol: Glasgow Minimum Essential Medium (GMEM), 10% fetal bovine serum, 0.1 mM β-mercaptoethanol, 1× non-essential amino acids, 1x sodium pyruvate, 1x penicillin/streptomycin (Life-Technologies), 2 mM glutamine and 1000 U/ml  of recombinant leukemia inhibitor factor LIF (ES-GRO).

extract_protocol: Total RNA was extracted with RNeasy extraction kit (Qiagen). This RNA was measured and quality viability-analized with Agilent 2100 bioanalyzer. Samples had a RIN >9

tag: source cell type

value: mouse embryonic stem cells


title: cell clone number 1 from OKSM reprogrammed MEF

source_name: Isolated cell clone from MEF reprogrammed with Yamanaka's factor (OKSM)

value: Mouse Embryonic Fibroblast (MEF)

tag: infected with

value: Yamanaka's factor (OKSM)


title: mouse embryonic fibroblasts, p2

description: MEF

source_name: mouse embryonic fibroblasts_p2

growth_protocol: Dulbecco´s Modified Eagle´s Medium (DMEM), 10% fetal bovine serum, 1x penicillin/streptomycin (Life-Technologies)


title: cell clone number 2 from OKSM reprogrammed MEF


title: NFRI 3236  39 degree No.1

data_processing: GeneChip Operating System (GCOS)

source_name: NFRI 3236

value: NFRI 3236

value: heat tolerance

value: 39 degree


title: C4 SMZL methylation

source_name: C4 SMZL methylation


title: NFRI 3236  30 degree No.2


title: cell clone number 3 from OKS+F+G reprogrammed MEF

source_name: Isolated cell clone from MEF reprogrammed with Yamanaka's factor (OKS)+F+G

value: Yamanaka's factor (OKS) +FoxA2 (F)+Gata4 (G)


title: NFRI 3236  39 degree No.2


title: cell clone number 5 from OKS+F+G reprogrammed MEF


title: cell clone number 6 from OKS+F+G reprogrammed MEF


title: cell clone number 3 from OKSM reprogrammed MEF


title: PanOR probe vs gDNA

city: San Francisco

first: Eleanor

middle: Josephine

last: Clowney

state: CA

department: Anatomy

institute: UCSF

hyb_protocol: All labeling, hybridization, scanning, and data processing were performed by Nimblegen at Iceland facility

data_processing: Analysis included here is Nimblegen default peak-finder; our own analysis using MA2C with large sliding window produced similar results.

source_name: mouse genomic DNA

extract_protocol: panOR was generated by purifiaction of AT-rich mouse genomic DNA fragments amplified by Sigma WGA followed by two rounds of capture, elution and reamplification from a custom tiling array covering the mouse olfactory genome. Many lots of this probe were produced for DNA FISH and one lot was used for tiling array verification. Genomic DNA (used as input) was sonicated to the same size as the panOR probe.

tag: reference

value: mouse genomic DNA

source_name: panOR probe

tag: test

value: panOR probe


title: NFRI 3236  30 degree No.1


title: S288C  39 degree No.3

value: control strain


title: C2 SMZL methylation

source_name: C2 SMZL methylation

value: Splenic marginal zone lymphoma


title: C3 SMZL methylation

source_name: C3 SMZL methylation


title: S288C  39 degree No.2


title: C1 SMZL methylation

source_name: C1 SMZL methylation


title: S288C  39 degree No.1


title: cell clone number 2 from OKS+F+G reprogrammed MEF


title: cell clone number 1 from OKS+F+G reprogrammed MEF


title: S288C  30 degree No.3


title: PigDurocMaleGenomic_PigDurocFemaleGenomic_replicate3

first: Ben

last: Skinner

address: Tennis Court Road

department: Department of Pathology

hyb_protocol: Hybridisation and post-hybridisation washes followed Fiegler et al (2007) with the following modifications: 1µg Porcine Hybloc DNA (a Cot-1 equivalent - Applied Genetics Laboratories, Florida) was used as a competitor DNA with 0.15µg genomic DNA. Hybridisation was performed in a moist chamber for 48 hours. Fiegler,H., Redon,R. and Carter,N.P. (2007) Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes. Nat. Protocols, 2, 577–587.

scan_protocol: Each microarray slide was scanned using a GenePix Personal 4100A Scanner (Axon Instruments) at a 5µm resolution. Cy3 and Cy5 fluorescence intensities of each DNA spot was quantified in BlueFuse for Microarrays v3.2 (Blue-Gnome Ltd, Cambridge, UK).

data_processing: The Cy3/Cy5 fluorescence ratios were calculated and transformed into log2 values. The ratios were normalized using block median normalization for each of the sixteen blocks to account for any block-block variation. The results from the four experiments were exported from the software for further analysis using Inforsense 5.0.1. Each hybridization was treated as a separate experiment (i.e., the initial hybridization was treated as experiment 1 and the dye-swap hybridization was treated as experiment 2). Clones with a confidence score < 0.7 in each experiment were excluded. An average was taken of the log2 ratios for each clone across the experiments.

organism: Sus scrofa

source_name: Pig Duroc female gDNA

label_protocol:
DNA was labelled by random priming following the protocol of Fiegler et al (2007).
Fiegler,H., Redon,R. and Carter,N.P. (2007) Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes. Nat. Protocols, 2, 577–587.

growth_protocol: N/A - tissue from animal

extract_protocol: Side muscle was frozen at -20oC following slaughter. gDNA was extracted using a Qiagen Blood and Tissue kit following the manufacturers instructions.

tag: breed

value: Duroc

tag: gender

value: Female

tag: source

value: Fibroblast cell line 2-14

source_name: Pig Duroc male gDNA

growth_protocol: Cell lines were grown in standard culture conditions at 37oC in DMEM with L-glucose containing penicillin/streptomycin supplemented with foetal calf serum.

extract_protocol: gDNA was extracted from fibroblasts using a Qiagen Blood and Tissue kit following the manufacturers instructions.

value: Male

value: Side muscle


title: PigDurocMaleGenomic_PigDurocFemaleGenomic_replicate4


title: PigDurocMaleGenomic_PigDurocFemaleGenomic_replicate2


title: clostridium acetobutylicum ATCC 824 ccpA mutant transition phase (T)

city: Shanghai

first: Cong

last: Ren

address: 300 Feng Lin Road

institute: Institute of Plant Physiology and Ecology, SIBS, CAS.

description: ccpA mutant, 16h culture, transition phase

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit. Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Clostridium acetobutylicum

source_name: clostridium acetobutylicum, P2 medium, glucose and xylose as carbon source

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: The preinoculum and inoculum preparation were performed as described before (Ren, C. et al. 2010. Metab Eng 12:446-54). Clostridium acetobutylicum ATCC 824 and clostridium acetobutylicum ATCC 824 ccpA mutant were grown anaerobically in P2 medium at 37 ºC. The fermentations were carried out in BioFlo 110 bioreactors (New Brunswick Scientiﬁc, Edison, NJ) with 1.5 L working volume, in which pH was stabilized at ≥5.0 by adding 9% (w/v) aqueous ammonia and mixed sugars (40 g/L D-glucose and 20 g/L D-xylose) were used as carbon sources.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

value: ccpA mutant

tag: growth phase

value: transition phase (T)


title: clostridium acetobutylicum ATCC 824 ccpA mutant stationary phase (S)

description: ccpA mutant, 22h culture, stationary phase

tag: genotype/variation

value: stationary phase (S)


title: PigDurocMaleGenomic_PigDurocFemaleGenomic_replicate1

value: muscle gDNA


title: cell clone number 1 from OKS reprogrammed MEF

source_name: Isolated cell clone from MEF reprogrammed with Yamanaka's factor (OKS)

value: Mouse Embryonic Fibroblast (MEF)

value: Yamanaka's factor (OKS)


title: cell clone number 3 from OKS reprogrammed MEF


title: cell clone number 2 from OKS reprogrammed MEF


title: clostridium acetobutylicum ATCC 824 ccpA mutant middle exponential phase (M)

description: ccpA mutant, 11h culture, middle exponential phase

value: middle exponential phase (M)


title: clostridium acetobutylicum ATCC 824 stationary phase (S)

description: wild type, 12h culture, stationary phase

value: wild type


title: NFRI 3155  39 degree No.2

source_name: NFRI 3155

value: NFRI 3155

value: heat sensitive

value: 39 degree


title: S288C  30 degree No.2

value: control strain

value: 30 degree


title: NFRI 3155  39 degree No.1


title: clostridium acetobutylicum ATCC 824 ccpA mutant late exponential phase (L)

description: ccpA mutant, 14h culture, late exponential phase

value: late exponential phase (L)


title: NFRI 3155  30 degree No.2


title: BW25113-pCA24N-ghoS with 1 mM IPTG for 90min at 37C

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

hyb_protocol: Prepared hybridization cocktail for Single Probe Array (169 mini Format) with total 80 ul volume including 1X hybridization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labeled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Genome 2.0 Array, the hybridization was performed at 45°C, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

source_name: Planktonic cells

label_protocol: cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).”

extract_protocol: The overnight culture (0.2 ml) was used to inoculate 25 ml of fresh LB medium to reach a turbidity of 0.05 at 600 nm. 1 mM IPTG was added when turbidity reached 0.2 at 600 nm. Induction was continued for 90 min at 37°C with shaking (250 rpm), and the cells were harvested quickly by centrifuging at 13000 rpm for 1 min. After breaking the cells with a bead beater, the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).

tag: strains

value: E. coli K-12

value: 90 min with 1 mM IPTG

tag: medium

value: LB

tag: cell type

value: Planktonic cells

tag: temp


title: clostridium acetobutylicum ATCC 824 transition phase (T)

description: wild type, 12h culture, transition phase

value: transition phase (T)


title: NFRI 3155  30 degree No.1

tag: stress tolerance

tag: temperature


title: BW25113-pCA24N with 1 mM IPTG for 90min at 37C

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (169 mini Format) with total 80 ul volume including 1X hybridization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labeled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Genome 2.0 Array, the hybridization was performed at 45°C, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

tag: treatment


title: GEP_MCL29

description: Mutation is for IgH mutation and 7q deletion is tested by FISH

hyb_protocol: Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000

data_processing: Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value

source_name: Mantle cell lymphoma from lymph node

label_protocol: Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA

extract_protocol: RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)

tag: tumour

value: MCL


title: S288C  30 degree No.1

tag: strain


title: clostridium acetobutylicum ATCC 824 middle exponential phase (M)

description: wild type ,8h culture, middle exponential phase


title: GEP_MCL25


title: clostridium acetobutylicum ATCC 824 late exponential phase (L)

description: wild type, 10h culture, late exponential phase


title: GEP_MCL24


title: Custom_Oligo_2Kb_aCGH_SMZL21

hyb_protocol: Arrays were performed as per Agilent manufacturer's instructions. Briefly, array blocking was performed using Agilent 10X blocking agent, and labelled DNA suspended in Agilent 2x HiRPM Hybridization buffer. Samples were hybridized for 24hrs at 65 degrees. Washing was performed with 5 minutes in Agilent oligo aCGH wash buffer 1 at RT, and 1 minute in buffer 2 at 37 degrees.

scan_protocol: Scanning was perfomed in an Agilent High Resolution C scanner at 3 microns resolution.

data_processing: Data was analyzed using the Agilent Feature Extraction Software (v10.5) and visualized in Genomic Workbench Standard Edition (v5.0.14). Data was normalized using Lowess.

source_name: Spleen, SMZL patient

label_protocol: BioPrime aCGH labelling system (Invitrogen).

growth_protocol: Spleens were fresh frozen.

extract_protocol: Standard phenol-chloroform isoamyl alcohol extraction.

tag: tissue

value: spleen

tag: disease

value: splenic marginal zone lymphoma

source_name: Pooled PBMCs, 10 normal subjects

value: peripheral blood mononuclear cells

tag: sample type

value: reference


title: GEP_MCL23


title: Custom_Oligo_2Kb_aCGH_SMZL20


title: GEP_FL20

source_name: Follicular lymphoma from lymph node

value: FL


title: Ah129-NC1 vs 129Sv male mouse kidney

description: CGH analysis of AH129-NC1 cells VS. male mouse kidney

hyb_protocol: Hybridization was processing overnight at 42°C in Roche-NimbleGen hybridization system12.

scan_protocol: Arrays were scanned on an Roche-NimbleGen MS200 scanner.

data_processing: Arrays were processed using NimbleScan,which transformed image signal to digital signal, following using segMNT algorithm to analyse the normalized signal ratio.

source_name: ahES cell line Ah129-NC1

label_protocol: The sample labelling was using NimbleGen Dual-Color DNA Labeling Kit (05223547001).

growth_protocol: N2B27 + 2i + LIF

extract_protocol: The genomic DNA was extracted using Promega Genomic DNA Purification Kit (A1620).

treatment_protocol: FACS sorting G0/G1 stage cells

tag: genetic background

value: G0/G1 stage androgenetic haploid embryonic stem cell

tag: cell line

value: ahES cell line Ah129-NC1

source_name: 129/Sv male mouse kidney

growth_protocol: normal animal facility

value: male

value: kidney


title: Custom_Oligo_2Kb_aCGH_SMZL19


title: Custom_Oligo_2Kb_aCGH_SMZL17


title: GEP_MCL22


title: GEP_FL21


title: AH129-N1 vs 129Sv male mouse kidney

description: CGH analysis of AH129-N1 cells VS. male mouse kidney

source_name: ahES cell line AH129-N1

value: ahES cell line AH129-N1

tag: gender


title: GEP_FL16


title: Custom_Oligo_2Kb_aCGH_SMZL18


title: AH129-5 vs 129Sv male mouse kidney

description: CGH analysis of AH129-5 cells VS. male mouse kidney

source_name: ahES cell line AH129-5

value: ahES cell line AH129-5


title: GEP_FL17


title: Fe-NTA-induced rat RCC cell line 2

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

institute: Nagoya University

hyb_protocol: According to the manufacturer's protocol (Agilent Oligonucleotide Array-based CGH for Genomic DNA Analysis, Protocol Version 4.0, June 2006).

data_processing: Agilent Feature Extraction Software (v 9.5) was used for background subtraction and LOWESS normalization.

organism: Rattus norvegicus

source_name: Brown-Norway rat normal kidney

extract_protocol: Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).

value: Brown-Norway rat normal kidney

source_name: Fe-NTA induced renal cell carcinoma (RCC)


title: Custom_Oligo_2Kb_aCGH_SMZL16


title: SG-26 [Group B]

city: Washington

first: Timothy

last: McCaffrey

state: DC

address: 2300 I Street NW

department: Department of Biochemisty & Molecular Biology

institute: The George Washington University

hyb_protocol: Standard 18 hr hybridization with Affymetrix hybridization cocktail

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
RMA summarization in GeneSpring GX10. Unpaired t test p<0.05 with fold-change > 1.5-fold
RMA summarized raw signal value, and per gene normalized are both provided

source_name: whole blood

label_protocol: RNA (100 ng) was reverse transcribed with SuperScriptIII using random hexamers, cDNA was amplifed with Ovation RNA Amplification System v2 (NuGen). cDNA was cleaned and 3.75 ug was fragmented and labeled with FL-Ovation cDNA biotin module v2 kit (nuGen).

growth_protocol: NOT APPLICABLE

extract_protocol: blood collected into PaxGene tubes, frozen, and blood RNA extracted by PaxGene blood RNA isolation kit with on-column DNAse treatment

treatment_protocol: NOT APPLICABLE

tag: group

value: B

tag: breast cancer

value: Y

tag: low ejection fraction

value: N

tag: chemotherapy


title: GEP_FL14


title: Custom_Oligo_2Kb_aCGH_SMZL15


title: Eker rat RCC 1

scan_protocol: According to the manufacturer's protocol (Agilent Oligonucleotide Array-based CGH for Genomic DNA Analysis, Protocol Version 4.0, June 2006).

source_name: Eker rat normal kidney

tag: cell type

value: Eker rat normal kidney

source_name: Eker renal cell carcinoma (RCC)

value: Eker renal cell carcinoma (RCC)


title: NgR day0 Rep1 +Dox

description: Gene Expression data from NgR day0 Rep1 +Dox

source_name: NgR day0 +Dox

value: Embryonic Stem Cells

tag: genotype/variation

value: AINV15_Nanog_Rescue Clone


title: Fe-NTA-induced rat RCC cell line 1

label_protocol: According to the manufacturer's protocol (Agilent Oligonucleotide Array-based CGH for Genomic DNA Analysis, Protocol Version 4.0, June 2006).

value: Fe-NTA induced renal cell carcinoma (RCC)


title: SG-25 [Group B]


title: Fe-NTA-induced rat RCC 13


title: Custom_Oligo_2Kb_aCGH_SMZL14

value: spleen

value: splenic marginal zone lymphoma

value: peripheral blood mononuclear cells

value: reference


title: Custom_Oligo_2Kb_aCGH_SMZL13


title: SMZL_GEP_8530unmut_7qdel

source_name: Splenic marginal zone lymphoma with more than 70% tumour content

value: SMZL 7q deletion unmutated


title: SG-23 [Group B]


title: Fe-NTA-induced rat RCC 12


title: SMZL_GEP_C13mut

value: SMZL mutated


title: Custom_Oligo_2Kb_aCGH_SMZL12


title: SG-24 [Group B]


title: SG-21 [Group B]


title: SG-22 [Group B]


title: SMZL_GEP_8527mut


title: Custom_Oligo_2Kb_aCGH_SMZL9


title: SG-20 [Group B]


title: Fe-NTA-induced rat RCC 10


title: SMZL_GEP_8536mut


title: SMZL_GEP_C9mut_7qdel

value: SMZL 7q deletion mutated


title: SMZL_GEP_C8mut_7qdel


title: Custom_Oligo_2Kb_aCGH_SMZL11


title: Custom_Oligo_2Kb_aCGH_SMZL8


title: SG-19 [Group B]


title: Custom_Oligo_2Kb_aCGH_SMZL10


title: Fe-NTA-induced rat RCC 7


title: SMZL_GEP_C10mut_7qdel


title: Fe-NTA-induced rat RCC 11


title: SG-17 [Group B]


title: Fe-NTA-induced rat RCC 6


title: SMZL_GEP_C6mut_7qdel


title: Custom_Oligo_2Kb_aCGH_SMZL7


title: Fe-NTA-induced rat RCC 5


title: SMZL_GEP_C7unmut_7qdel


title: SG-18 [Group B]


title: Custom_Oligo_2Kb_aCGH_SMZL6


title: SG-16 [Group A]

value: A


title: Fe-NTA-induced rat RCC 8

value: Brown-Norway rat normal kidney


title: SMZL_GEP_C5mut


title: Fe-NTA-induced rat RCC 3


title: SG-13 [Group A]


title: Custom_Oligo_2Kb_aCGH_SMZL4


title: Fe-NTA-induced rat RCC 4


title: SG-15 [Group A]


title: Custom_Oligo_2Kb_aCGH_SMZL3


title: SMZL_GEP_C3mut


title: SMZL_GEP_C2mut


title: Fe-NTA-induced rat RCC 1


title: SG-14 [Group A]


title: Custom_Oligo_2Kb_aCGH_SMZL5


title: SMZL_GEP_C4mut


title: SG-12 [Group A]


title: SG-11 [Group C]

value: C


title: Fe-NTA-induced rat RCC 2


title: HTZ4CEL

city: Leipzig

first: Wolfgang

last: Enard

address: Deutscher Platz 6

country: Germany

institute: Max Planck Institute for evolutionary anthropology

description: control sample not depleted of miRNAs

hyb_protocol: standard Affy

scan_protocol: standard Affy

data_processing: Gene expression levels were extracted and summarized from the 9 Affymetrix CEL files using the MG-Mm430 Ensembl Custom CDF file (version 10) based on mouse Ensembl genes. We used the Rma algorithm (R-Bioconductor “affy” package) for background correction and quantile normalization of log2 transformed expression levels. Genes with expression levels above background were determined based on the Wilcoxon test, with the “mas5” function (R-Bioconductor “affy” package) and a cutoff of p<0.05. Among the 15,758 Ensembl genes present on the array, 12,198 were detectable with this criterion in at least one array and these were further analyzed. Student’s t-test was used to compare gene expression levels between the 9 samples.

source_name: Forebrain, E13.5, control

label_protocol: standard Affy

extract_protocol: RNAeasy

tag: Sex

value: male

value: brain

tag: brain region

value: dorsal telencephalon

tag: developmental stage

value: control


title: Liver_slimming_rep4

first: yanchang

last: wei

address: #1 Beichen West Rd

description: This sample is the fourth of four experimental biological replicates used in this experiment, each from separate animals.

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

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Raw signal intensities were normalized by the RMA method using NimbleScan v2.5. Low-intensity genes were filtered out (genes that had intensities >= 100 in 9 out of 9 samples were chosen for further analysis).

source_name: Liver cells, maternal slimming

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: At 16 weeks of age, mothers were mated with normal males in standard conditions to generate the F1 offspring.

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

treatment_protocol: Mothers slimming vs. control, mate with males in standard conditions, analyze the offspring's liver transcriptome through microarray analysis.

value: ICR

value: median lobe of liver

value: female

tag: generation

tag: treatment

value: enriched environment-induced maternal slimming


title: HTZ2CEL

description: control sample not depleted of miRNAs

tag: tissue

tag: strain


title: SMZL_GEP_C1unmut_7qdel

tag: tumour


title: HTZ3CEL

description: control sample not depleted of miRNAs


title: SG-8 [Group C]

value: N

value: Y


title: Liver_slimming_rep3

description: This sample is the third of four experimental biological replicates used in this experiment, each from separate animals.


title: SG-9 [Group C]


title: Custom_Oligo_2Kb_aCGH_SMZL2

value: spleen

tag: disease

value: splenic marginal zone lymphoma

value: peripheral blood mononuclear cells

tag: sample type

value: reference


title: Liver_control_rep5

description: This sample is the fifth of five control biological replicates used in this experiment, each from separate animals.

source_name: Liver cells, maternal control

tag: gender

value: mother fed standard diet


title: HUVEC cells, TNF and NOD, P7

city: Mannheim

first: Benito

last: Yard

address: Theodor-Kutzer-Ufer 1-3

institute: University hospital Mannheim

description:
TNFNOD_6
Gene expression data from human umbilical vein endothelial cells (HUVEC) treated with TNF-alpha with NOD.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000.

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of HGU133_2 -type from Affymetrix. A Custom CDF Version 11 with Entrez-based gene definitions was used to annotate the arrays. The raw fluorescence intensity values were normalized applying quantile normalization.

source_name: HUVEC cells treated with TNF-alpha and NOD

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

growth_protocol: HUVECs were isolated from fresh umbilical cords as described previously (Yard et al., 2004). The cells were grown in basal endothelial medium supplemented with 10% FBS and essential growth factors until they formed a confluent monolayer.

extract_protocol: Total RNA was isolated from these cultures using Trizol®-Reagent (Gibco-BRL).

treatment_protocol: Endothelial cell monolayers were stimulated for 24 hrs. with 10 ng/ml of TNF-α in the presence or absence of NOD (100 µM).

value: human umbilical vein endothelial cell (HUVEC)

value: TNF-alpha and N-octanoyl dopamine (NOD)


title: Custom_Oligo_2Kb_aCGH_SMZL1

first: Alan

last: Watkins

source_name: Spleen, SMZL patient

source_name: Pooled PBMCs, 10 normal subjects


title: SG-5 [Group D]

tag: group

value: D


title: DicerKO11CEL

description: sample depleted of miRNAs

source_name: Forebrain, E13.5, dicer knockout

value: male

value: brain

value: dicer knockout


title: SG-7 [Group C]

value: C

tag: breast cancer


title: Liver_slimming_rep1

description: This sample is the first of four experimental biological replicates used in this experiment, each from separate animals.

value: ICR

value: median lobe of liver


title: HTZ1CEL

description: control sample not depleted of miRNAs

value: female

value: dorsal telencephalon

value: control


title: HUVEC cells, TNF and NOD, P4vK

description:
TNFNOD_4
Gene expression data from human umbilical vein endothelial cells (HUVEC) treated with TNF-alpha with NOD.


title: DicerKO7CEL

description: sample depleted of miRNAs


title: Liver_slimming_rep2

description: This sample is the second of four experimental biological replicates used in this experiment, each from separate animals.

value: enriched environment-induced maternal slimming


title: HUVEC cells, TNF, P7

description:
TNF_5
Gene expression data from human umbilical vein endothelial cells (HUVEC) treated with TNF-alpha.

source_name: HUVEC cells treated with TNF-alpha

value: TNF-alpha


title: SG-4 [Group D]

value: Y

tag: low ejection fraction

value: N


title: Fe-NTA-induced rat RCC 9

value: Brown-Norway rat normal kidney

value: Fe-NTA induced renal cell carcinoma (RCC)


title: DicerKO10CEL

description: sample depleted of miRNAs


title: Liver_control_rep3

description: This sample is the third of five control biological replicates used in this experiment, each from separate animals.

value: mother fed standard diet


title: DicerKO9CEL

description: sample depleted of miRNAs


title: DicerKO5CEL

description: sample depleted of miRNAs


title: HUVEC cells, TNF, P4vK

description:
TNF_3
Gene expression data from human umbilical vein endothelial cells (HUVEC) treated with TNF-alpha.

value: human umbilical vein endothelial cell (HUVEC)


title: SG-3 [Group D]

value: D

tag: chemotherapy


title: HUVEC cells, TNF and NOD, P4

description:
TNFNOD_2
Gene expression data from human umbilical vein endothelial cells (HUVEC) treated with TNF-alpha with NOD.

tag: cell type

value: TNF-alpha and N-octanoyl dopamine (NOD)


title: Liver_control_MeDIP

description: MeDIP-chip of offspring from maternal control.

hyb_protocol: Hybridization was performed according to standard procedures by NimbleGen.

scan_protocol: Scanning was performed according to standard procedures by Nimblegen using NimbleScan.

data_processing: Arrays were processed using NimbleGen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: MeDIP DNA from liver tissues, maternal control

label_protocol: Labeling was performed according to standard procedures by NimbleGen.

extract_protocol:
Total genomic DNA was extracted using the Qiagen DNeasy kit (Qiagen) according to the manufacturer's instructions. DNA was sonicated to give fragments between 200bp and 1000bp.

1 ug of sonicated genomic DNA was used for immunoprecipitation using a mouse monoclonal anti-5-methylcytosine antibody (Diagenode). For this, DNA was heat-denatured at 94 °C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 uL primary antibody overnight at 4°C with rocking agitation in 400 uL immunoprecipitation buffer (0.5% BSA in PBS). To recover the immunoprecipitated DNA fragments, 200 uL of anti-mouse IgG magnetic beads were added and incubated for an additional 2 hours at 4 °C with agitation. After immunoprecipitation, a total of five immunoprecipitation washes were performed with ice-cold immunoprecipitation buffer. Washed beads were resuspended in TE buffer with 0.25% SDS and 0.25mg/mL proteinase K for 2 hours at 65 °C and then allowed to cool down to room temperature. MeDIP DNA were purified using Qiagen MinElute columns (Qiagen).

treatment_protocol: Mothers slimming vs. control, mate with males in standard conditions, analyze the offspring's liver methylome through microarray analysis.

value: pool of biological replicates

tag: medip antibody

value: mouse monoclonal antibody against 5-methylcytidine

tag: antibody vendor

value: Diagenode

tag: antibody catalog #

source_name: Input DNA from liver tissues, maternal control


title: SG-2 [Group D]


title: SG-1 [Group D]


title: Liver_slimming_MeDIP

description: MeDIP-chip of offspring from maternal slimming.

source_name: MeDIP DNA from liver tissues, maternal slimming

value: ICR

value: median lobe of liver

source_name: Input DNA from liver tissues, maternal slimming

extract_protocol: Total genomic DNA was extracted using the Qiagen DNeasy kit (Qiagen) according to the manufacturer's instructions. DNA was sonicated to give fragments between 200bp and 1000bp.


title: Liver_control_rep2

description: This sample is the second of five control biological replicates used in this experiment, each from separate animals.

value: male


title: Liver_control_rep1

description: This sample is the first of five control biological replicates used in this experiment, each from separate animals.


title: HUVEC cells, TNF, P4

description:
TNF_1
Gene expression data from human umbilical vein endothelial cells (HUVEC) treated with TNF-alpha.


title: Liver_control_rep4

description: This sample is the fourth of five control biological replicates used in this experiment, each from separate animals.

value: female


title: Urothelia_B3

status: Public on Aug 29 2012

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: .bed file contains gene-level normalized expression values

data_processing: Probesets flagged as cross-hybridizing were removed. Probesets were assigned to genes based on the GENCODE v10 annotation (July 2011). To normalize, we first classified each exon as constitutive, meaning present in all annotated isoforms, or not constitutive for each gene, reasoning these would be the most robust across celltypes. For genes with at least 4 constitutive probesets, only constitutive probesets were used to normalize. For all other genes, including all non-protein-coding genes, we sused all probesets that mapped to the gene. To normalize, we used Affymetrix Power Tools (APT) with the chipstream command “rma-bg, med-norm, pm-gcbg, med-polish”. This chipstream calls for an RMA normalization with gc-background correction using antigenomic background probes. We used an ComBat to correct for batch effects.

source_name: primary ureter cell culture of urothelial cells

label_protocol: 1ug of total RNA was labeled according to Standard Affymetrix WT protocol for Exon 1.0 ST arrays

growth_protocol: Cells were grown according to the approved ENCODE cell culture protocols.Specific protocol descriptions can be found at http://genome.ucsc.edu/ENCODE/cellTypes.html.

extract_protocol: total RNA was extracted from cell pellets using Trizol protocol


title: Osteobl_B2

hyb_protocol: Standard Affymetrix WT protocol for Exon 1.0 ST arrays

source_name: osteoblasts (NHOst)

value: osteoblasts (NHOst)


title: Stellate_B1

scan_protocol: Standard Affymetrix WT protocol for Exon 1.0 ST arrays

source_name: hepatic stellate cells, liver

value: hepatic stellate cells, liver


title: Urothelia_UT189_B2

source_name: primary ureter cell culture of urothelial cells, UT189 E.Coli treatment


title: Osteobl_B3


title: NHEK_B1

source_name: epidermal keratinocytes

value: epidermal keratinocytes


title: Melano_B3

source_name: epidermal melanocytes

value: epidermal melanocytes


title: SOX2 in NSC(Agilent-014707)_ slide2

city: Seoul

first: jihae

last: Seo

address: 11-1 Daehyun-Dong Seodaemun-Gu

department: Ewha research center for systems biology

country: South Korea

institute: Ewha womans university

hyb_protocol: Agilent aCGHarray hybridization protocol

scan_protocol: Agilent Technologies Scanner G2505B US45103026 Images were quantified using Agilent Feature Extraction Software.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: neural stem cell line REN cells

label_protocol: Cy5(Immunoprecipitated sample),Cy3(Genome DNA control)

extract_protocol: ChIP-v1_95_May07 (attached on the Series record)

tag: cell line

value: REN

value: immunoprecipitated

tag: antibody

value: control


title: Urothelia_UT189_B3

value: primary ureter cell culture of urothelial cells, UT189 E.Coli treatment


title: UCH-1_B2

source_name: chordoma

value: chordoma


title: Urothelia_B2

value: primary ureter cell culture of urothelial cells


title: ProgFib_B1

source_name: fibroblasts, Hutchinson-Gilford progeria syndrome


title: NHEK_B2


title: SOX2 in NSC(Agilent-014706)_ slide1


title: MCF-7_B1

source_name: mammary gland, adenocarcinoma

value: mammary gland, adenocarcinoma


title: Melano_B2


title: UCH-1_B1


title: Stellate_B2


title: Osteobl_B5


title: ProgFib_B2

value: fibroblasts, Hutchinson-Gilford progeria syndrome


title: Myometr_B1

source_name: myometrial cells

value: myometrial cells


title: Myometr_B2


title: Mel_2183_B1

source_name: Melanoma Cell line

value: Melanoma Cell line


title: MCF-7_Randomized_shRNA_control_B2

source_name: mammary gland, adenocarcinoma, grown with randomized shRNA


title: Medullo_B3

source_name: medulloblastoma (aka D721)

value: medulloblastoma (aka D721)


title: MCF-7_CTCF_shRNA_knockdown_B2

source_name: mammary gland, adenocarcinoma, CTCF knockdown using shRNA


title: MCF-7_Randomized_shRNA_control_B1

value: mammary gland, adenocarcinoma, grown with randomized shRNA


title: MCF-7_CTCF_shRNA_knockdown_B1

value: mammary gland, adenocarcinoma, CTCF knockdown using shRNA


title: Medullo_B2


title: MCF-7_vehicle_B2

source_name: mammary gland, adenocarcinoma, grown in Charcoal stripped hormone-free FBS


title: MCF-7_Randomized_shRNA_control_B3


title: MCF-7_vehicle_B1

value: mammary gland, adenocarcinoma, grown in Charcoal stripped hormone-free FBS


title: MCF-7_estrogen_B2

source_name: mammary gland, adenocarcinoma, grown with estradiol


title: Mel_2183_B2


title: Melano_B1


title: LNCaP_androgen_B2

source_name: prostate adenocarcinoma, grown with androgen


title: Medullo_B1


title: LNCaP_B1

source_name: prostate adenocarcinoma

value: prostate adenocarcinoma


title: K562_B4_V2

source_name: chronic myelogenous leukemia

value: chronic myelogenous leukemia


title: K562_NaBut_B3

source_name: chronic myelogenous leukemia, grown with sodium butyrate


title: MCF-7_estrogen_B1

value: mammary gland, adenocarcinoma, grown with estradiol


title: MCF-7_CTCF_shRNA_knockdown_B3


title: LNCaP_androgen_B1

value: prostate adenocarcinoma, grown with androgen


title: LNCaP_B2


title: K562_NaBut_B1

value: chronic myelogenous leukemia, grown with sodium butyrate


title: K562_NaBut_B4


title: MCF-7_Hypoxia_LacAcid_B2

source_name: mammary gland, adenocarcinoma, hypoxia, lactic acidosis


title: K562_NaBut_B2


title: K562_B3_V2


title: K562_B2_V2


title: K562_B1_V2


title: K562_B3


title: iPS_NIHi7_B2

source_name: induced pluripotent stem cell derived from skin fibroblast


title: iPS_CWRU1_B2

value: induced pluripotent stem cell derived from skin fibroblast


title: K562_B1


title: Huh-7_B2

source_name: hepatocellular carcinoma

value: hepatocellular carcinoma


title: K562_B2


title: HSMMtube_FSHD_B3

source_name: myotube from Facioscapulohumeral Muscular Dystrophy (FSHD) patient


title: iPS_NIHi11_B1


title: iPS_NIHi7_B1


title: HTR8svn_B1

source_name: trophoblast (HTR-8/SVneo) cell line,

value: trophoblast (HTR-8/SVneo) cell line,


title: iPS_NIHi11_B2


title: Huh-7.5_B1

source_name: hepatocellular carcinoma, hepatocytes selected for high levels of hepatitis C replication


title: iPS_CWRU1_B1


title: HTR8svn_B2


title: HUVEC_B1

source_name: umbilical vein endothelial cells

value: umbilical vein endothelial cells


title: Huh-7_B1


title: HSMMtube_FSHD_B2

value: myotube from Facioscapulohumeral Muscular Dystrophy (FSHD) patient


title: Huh-7.5_B2

value: hepatocellular carcinoma, hepatocytes selected for high levels of hepatitis C replication


title: HUVEC_B2


title: HSMMtube_FSHD_B1


title: HPDE6-E6E7_B1

source_name: pancreatic duct cells immortalized with E6E7 gene of HPV


title: HSMM_FSHD_B2

source_name: primary myoblast from Facioscapulohumeral Muscular Dystrophy (FSHD) patients


title: HSMM_FSHD_B3

value: primary myoblast from Facioscapulohumeral Muscular Dystrophy (FSHD) patients


title: Melano_B4

source_name: epidermal melanocytes

value: epidermal melanocytes


title: HSMM_FSHD_B1


title: HPDE6-E6E7_B2

value: pancreatic duct cells immortalized with E6E7 gene of HPV


title: HMEC_B1

source_name: mammary epithelial cells

value: mammary epithelial cells


title: HepG2_B3


title: HMEC_B2


title: HepG2_B2


title: HepG2_B1


title: Hepatocytes_B3

source_name: primary hepatocytes, liver

value: primary hepatocytes, liver


title: Hepatocytes_B1


title: HeLa-S3_IFNg4h_B2

source_name: cervical carcinoma, grown with interferon gamma


title: HeLa-S3_B1

source_name: cervical carcinoma

value: cervical carcinoma


title: HeLa-S3_IFNg4h_B1

value: cervical carcinoma, grown with interferon gamma


title: HeLa-S3_IFNa4h_B2

source_name: cervical carcinoma, grown with interferon alpha


title: H7_hESC_B3

source_name: embryonic stem cells

value: embryonic stem cells


title: HeLa-S3_B2


title: H9ES_B2


title: HEK293T_B2

source_name: embryonic kidney that expresses SV40 large T antigen


title: H1_hESC_B4


title: H1_hESC_B3


title: HeLa-S3_B3


title: H1_hESC_B1


title: H7_hESC_B1


title: HEK293T_B1

value: embryonic kidney that expresses SV40 large T antigen


title: HeLa-S3_IFNa4h_B1

value: cervical carcinoma, grown with interferon alpha


title: GM19240_B2

source_name: B-lymphocyte, lymphoblastoid

value: B-lymphocyte, lymphoblastoid


title: H9ES_B1


title: H9ES_B3


title: H1_hESC_B2


title: GM18507_B3


title: GM19238_B1


title: GM19240_B1


title: GM19239_B2


title: GM18507_B2


title: GM19238_B2


title: GM12892_B2


title: H7_hESC_B2


title: GM18507_B1


title: GM12891_B2


title: Gliobla_B3

source_name: glioblastoma (aka H54 and D54)

value: glioblastoma (aka H54 and D54)


title: GM12892_B1


title: GM12878_B2


title: Gliobla_B4


title: GM12878_B1


title: FibroP_AG20443_B2

source_name: fibroblasts taken from individuals with Parkinson's disease


title: FibroP_AG20443_B3

value: fibroblasts taken from individuals with Parkinson's disease


title: Gliobla_B1


title: GM12878_B3


title: FibroP_AG08396_B1


title: FibroP_AG08395_B2


title: GM12891_B1


title: FibroP_AG08395_B1


title: Colo829_B1

source_name: malignant melanoma

value: malignant melanoma


title: AoSMC_TGFb_B2

source_name: aortic smooth muscle cells, grwon with transforming growth factor beta


title: Fibrobl_B2

source_name: child fibroblast

value: child fibroblast


title: Colo829_B2


title: CLL_B2

source_name: chronic lymphocytic leukemia cell

value: chronic lymphocytic leukemia cell


title: FibroP_AG20443_B1


title: Fibrobl_B1


title: Astrocy_B1

source_name: astrocytes

value: astrocytes


title: FibroP_AG08396_B3


title: Gliobla_B2


title: CLL_B3


title: Chorion_B1

source_name: chorion cells (outermost of two fetal membranes)


title: FibroP_AG08395_B3


title: FibroP_AG08396_B2


title: GM19239_B1


title: Astrocy_B2


title: AoSMC_serum_free_media_B1

source_name: aortic smooth muscle cells, Grown with growth factors, then switched to media that contains no FBS


title: AoSMC_B2

source_name: aortic smooth muscle cells

value: aortic smooth muscle cells


title: AoSMC_TGFb_B1

value: aortic smooth muscle cells, grwon with transforming growth factor beta


title: AoSMC_B1


title: A549_B1

source_name: epithelial cell line, lung carcinoma

value: epithelial cell line, lung carcinoma


title: AoSMC_serum_free_media_B2

value: aortic smooth muscle cells, Grown with growth factors, then switched to media that contains no FBS


title: 8988T_B2

source_name: pancreas adenocarcinoma

value: pancreas adenocarcinoma


title: 8988T_B1


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-36

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

hyb_protocol: Labeled cDNA probes were hybridized in a head-to-head fashion, pretreated versus posttreated from the same individual, simultaneously to custom-made microarrays composed of ∼6,800 clones derived from the Prostate Expression DataBase, a public sequence repository of expressed sequence tag data derived from human prostate cDNA libraries.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 emissions using a GenePix 4000B fluorescent scanner (Axon Instruments)

data_processing: GenePix Pro 4.1 software was used to grid and extract image intensity data. Spots of poor quality as determined by visual inspection were removed from further analysis. Print tip-specific Loess normalization was performed in R using the Limma Bioconductor package,  using these settings: span=0.2, bc.method=subtract, offset=10.

label_protocol: cDNA was separately synthesized from 3 μg aRNA amplified from pretreated and posttreated specimens as described previously. To eliminate potential dye bias, we randomly alternated Cy3 and Cy5 labeling to pretreated and posttreated specimens across 31 samples.

extract_protocol: Total RNA was extracted from captured neoplastic epithelium using a Picopure RNA isolation kit according to the manufacturer's instructions (Arcturus). Extracted RNA underwent two rounds of amplification by a linear T7-RNA polymerase method developed by Eberwine et al. using a messageAMP aRNA kit (Ambion).

value: male

tag: age

tag: clinical stage

tag: surgical margin status

value: Positive

tag: nodal status at surgery

tag: gleason sum score (biopsy)

tag: gleason sum score (surgical)

tag: psa pre-chemotherapy

tag: psa post-chemotherapy

value: prostate needle biopsy tissue frozen in OCT blocks

value: neoplastic epithelium

value: prostatectomy tissue frozen in OCT blocks


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_KP-05

tag: gender

value: Negative

tag: tissue


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-02


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-03


title: Favorable Histology Wilms Tumor (WT00-095)

city: Chicago

first: Elizaebth

last: Perlman

state: IL

address: 2373 North Lincoln Avenue

institute: Northwestern University

hyb_protocol: The labeled, fragmented cRNA was hybridized to the Affymetrix HG - U133A oligonucleotide array for 16 hours at 45°C according to Affymetrix protocol. Staining was done in the GeneChip Fluidics Station using pre-programmed Affymetrix protocols.

scan_protocol: The arrays were scanned in an HP GeneArray Scanner.

data_processing: Data were normalized using robust multi-array average (RMA) method. The normalized value of each probeset for each tumor is provided in the attached excel spreadsheet All Normalized Data.

source_name: Pretreatment tumor tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated by Trizol (Invitrogen, Carlsbad, CA) extraction and treated with DNase I (Roche, Indianapolis, IN).

tag: Stage

value: II

tag: relapse

value: No


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_UW-09

tag: cell type


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_UW-01


title: A549_B2


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-04


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_KP-02


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_KP-01


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_KP-04


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_KP-03


title: Favorable Histology Wilms Tumor (WT00-099)

value: III

value: Yes


title: Favorable Histology Wilms Tumor (WT00-093)


title: Favorable Histology Wilms Tumor (WT00-097)

value: I


title: Favorable Histology Wilms Tumor (WT00-096)


title: Favorable Histology Wilms Tumor (WT00-091)


title: Favorable Histology Wilms Tumor (WT00-092)

value: IV


title: Favorable Histology Wilms Tumor (WT00-094)


title: Favorable Histology Wilms Tumor (WT00-089)


title: Favorable Histology Wilms Tumor (WT00-087)


title: Favorable Histology Wilms Tumor (WT00-009)


title: Favorable Histology Wilms Tumor (WT00-090)


title: Favorable Histology Wilms Tumor (WT00-098)


title: Favorable Histology Wilms Tumor (WT00-086)


title: Favorable Histology Wilms Tumor (WT00-088)


title: Favorable Histology Wilms Tumor (WT00-084)


title: Favorable Histology Wilms Tumor (WT00-085)


title: Favorable Histology Wilms Tumor (WT00-083)

value: V


title: Favorable Histology Wilms Tumor (WT00-007)


title: Favorable Histology Wilms Tumor (WT00-078)


title: Favorable Histology Wilms Tumor (WT00-076)


title: Favorable Histology Wilms Tumor (WT00-082)


title: Favorable Histology Wilms Tumor (WT00-081)


title: Favorable Histology Wilms Tumor (WT00-073)


title: Favorable Histology Wilms Tumor (WT00-071)


title: Favorable Histology Wilms Tumor (WT00-079)


title: Favorable Histology Wilms Tumor (WT00-069)


title: Favorable Histology Wilms Tumor (WT00-077)


title: Favorable Histology Wilms Tumor (WT00-068)


title: Favorable Histology Wilms Tumor (WT00-062)


title: Favorable Histology Wilms Tumor (WT00-060)


title: Favorable Histology Wilms Tumor (WT00-061)


title: Favorable Histology Wilms Tumor (WT00-074)


title: Favorable Histology Wilms Tumor (WT00-072)


title: Favorable Histology Wilms Tumor (WT00-064)


title: Favorable Histology Wilms Tumor (WT00-053)


title: Favorable Histology Wilms Tumor (WT00-065)


title: Favorable Histology Wilms Tumor (WT00-059)


title: Favorable Histology Wilms Tumor (WT00-063)


title: Favorable Histology Wilms Tumor (WT00-054)


title: Favorable Histology Wilms Tumor (WT00-067)


title: Favorable Histology Wilms Tumor (WT00-058)


title: Favorable Histology Wilms Tumor (WT00-051)


title: Favorable Histology Wilms Tumor (WT00-006)


title: Favorable Histology Wilms Tumor (WT00-050)


title: Favorable Histology Wilms Tumor (WT00-049)


title: Favorable Histology Wilms Tumor (WT00-004)


title: Favorable Histology Wilms Tumor (WT00-005)


title: Favorable Histology Wilms Tumor (WT00-047)


title: Favorable Histology Wilms Tumor (WT00-052)


title: Favorable Histology Wilms Tumor (WT00-044)


title: Favorable Histology Wilms Tumor (WT00-045)


title: Favorable Histology Wilms Tumor (WT00-039)


title: Favorable Histology Wilms Tumor (WT00-040)


title: Favorable Histology Wilms Tumor (WT00-036)


title: Favorable Histology Wilms Tumor (WT00-042)


title: Favorable Histology Wilms Tumor (WT00-033)


title: Favorable Histology Wilms Tumor (WT00-038)


title: Favorable Histology Wilms Tumor (WT00-301)


title: Favorable Histology Wilms Tumor (WT00-302)


title: Favorable Histology Wilms Tumor (WT00-046)


title: Favorable Histology Wilms Tumor (WT00-031)


title: Favorable Histology Wilms Tumor (WT00-032)


title: Favorable Histology Wilms Tumor (WT00-300)


title: Favorable Histology Wilms Tumor (WT00-003)


title: Favorable Histology Wilms Tumor (WT00-030)


title: Favorable Histology Wilms Tumor (WT00-029)


title: Favorable Histology Wilms Tumor (WT00-292)


title: Favorable Histology Wilms Tumor (WT00-294)


title: Favorable Histology Wilms Tumor (WT00-290)


title: Favorable Histology Wilms Tumor (WT00-297)


title: Favorable Histology Wilms Tumor (WT00-299)


title: Favorable Histology Wilms Tumor (WT00-291)


title: Favorable Histology Wilms Tumor (WT00-289)


title: snf1_N_1

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

hyb_protocol: Samples were hybridized with GeneChip yeast2 Arrays (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) by A GeneChip Fluidics Station FS-400 and GeneChip Scanner 3000 7G

data_processing: Probe Logarithmic Intensity Error (PLIER)

label_protocol: Labelling was done according to the Affymetrix GeneChip Expression Analysis Technical Manual.

growth_protocol: Chemostatcultivation on minimal media

extract_protocol: Total RNA was isolated from frozen cell pellets using FastRNA® Pro RED kit (QBiogene, Inc, USA)

treatment_protocol: biomass samples were taken at steadystate, cooled down imeediately and centrifuged with cooling, The cell prllets were frozen in liquid nitrogen

tag: strain

value: snf1 mutant


title: Favorable Histology Wilms Tumor (WT00-286)


title: Favorable Histology Wilms Tumor (WT00-278)


title: Favorable Histology Wilms Tumor (WT00-283)


title: ref_N_1

value: Reference


title: ref_N_2


title: snf1_C_1


title: ref_N_3


title: Favorable Histology Wilms Tumor (WT00-285)


title: snf1_C_3


title: Favorable Histology Wilms Tumor (WT00-273)


title: ref_C_2


title: snf1_N_3


title: ref_C_1


title: snf1_N_2


title: Favorable Histology Wilms Tumor (WT00-272)


title: Favorable Histology Wilms Tumor (WT00-277)


title: Favorable Histology Wilms Tumor (WT00-276)


title: ref_C_3


title: Nsnf1_N_2


title: Favorable Histology Wilms Tumor (WT00-027)


title: Nsnf1_N_1


title: Nsnf1_C_3


title: Favorable Histology Wilms Tumor (WT00-275)


title: Favorable Histology Wilms Tumor (WT00-288)


title: Nsnf1_N_3


title: Favorable Histology Wilms Tumor (WT00-268)


title: Nsnf1_C_1


title: Favorable Histology Wilms Tumor (WT00-265)


title: Favorable Histology Wilms Tumor (WT00-270)


title: Favorable Histology Wilms Tumor (WT00-269)


title: Nref_C_2


title: Nref_N_2


title: Nref_N_3


title: Nsnf1_C_2


title: Favorable Histology Wilms Tumor (WT00-264)


title: Favorable Histology Wilms Tumor (WT00-266)


title: Favorable Histology Wilms Tumor (WT00-267)


title: Favorable Histology Wilms Tumor (WT00-261)


title: Favorable Histology Wilms Tumor (WT00-255)


title: Nref_N_1


title: Nref_C_3


title: Favorable Histology Wilms Tumor (WT00-259)


title: Favorable Histology Wilms Tumor (WT00-262)


title: Thyroid-26N

city: Leiden

first: Jan

last: Oosting

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Illumina Beadstudio 2.3, Bioconductor BeadarraSNP

source_name: Thyroid tumor

label_protocol: DNA was prepared according to the standard Illumina protocol from 400 to 1000 ng of DNA

extract_protocol: DNA was isolated using an overnight digestion with proteinase K at 56 C. DNA was purified using the Promega Protein Precipitation solution.

treatment_protocol: The G0G1 vimentin-positive, keratin-negative stromal cell fractions and the vimentin-negative, keratin-positive tumour cells were flow-sorted using a FACSAria I flow-sorter at 40 psi with a 0.100 mm nozzle at a frequency of approximately 52.4 kHz in purity mode. The 488 nm and the 407 nm laser line were used for excitation.

tag: tumor type

value: PTC

tag: variant

value: HC

tag: fraction

value: keratin negative, vimentin positive (reference)

tag: dnaindex

tag: patient age


title: Nref_C_1


title: Favorable Histology Wilms Tumor (WT00-253)

tag: age


title: Thyroid-25T

value: keratin positive, vimentin negative (tumor)

value: vimentin-negative, keratin-positive tumour cell


title: Favorable Histology Wilms Tumor (WT00-252)


title: Thyroid-27N

value: tall cell

value: G0G1 vimentin-positive, keratin-negative stromal cell


title: Thyroid-26T


title: Favorable Histology Wilms Tumor (WT00-254)


title: Thyroid-27T


title: Favorable Histology Wilms Tumor (WT00-026)


title: Favorable Histology Wilms Tumor (WT00-263)


title: Favorable Histology Wilms Tumor (WT00-271)


title: Thyroid-24N


title: Thyroid-25N


title: Favorable Histology Wilms Tumor (WT00-251)


title: Favorable Histology Wilms Tumor (WT00-247)


title: Thyroid-23T

tag: variant:


title: Thyroid-24T


title: Favorable Histology Wilms Tumor (WT00-246)


title: Favorable Histology Wilms Tumor (WT00-249)


title: snf1_C_2


title: Thyroid-20T


title: Favorable Histology Wilms Tumor (WT00-245)


title: Favorable Histology Wilms Tumor (WT00-248)


title: Favorable Histology Wilms Tumor (WT00-243)


title: Favorable Histology Wilms Tumor (WT00-238)


title: Favorable Histology Wilms Tumor (WT00-240)


title: Thyroid-20N


title: Thyroid-21N


title: Thyroid-22T


title: Thyroid-21T


title: Favorable Histology Wilms Tumor (WT00-237)


title: Thyroid-23N


title: Thyroid-22N


title: Favorable Histology Wilms Tumor (WT00-244)


title: Favorable Histology Wilms Tumor (WT00-236)


title: Favorable Histology Wilms Tumor (WT00-234)


title: Thyroid-18T


title: Thyroid-19T


title: Thyroid-19N


title: Thyroid-17T


title: Favorable Histology Wilms Tumor (WT00-232)


title: Thyroid-18N


title: Thyroid-17N


title: Favorable Histology Wilms Tumor (WT00-242)


title: Thyroid-16T


title: Thyroid-16N


title: Favorable Histology Wilms Tumor (WT00-231)


title: Thyroid-15T

value: FVPC


title: Favorable Histology Wilms Tumor (WT00-230)


title: Favorable Histology Wilms Tumor (WT00-023)


title: Favorable Histology Wilms Tumor (WT00-229)


title: Favorable Histology Wilms Tumor (WT00-227)


title: Favorable Histology Wilms Tumor (WT00-223)


title: Favorable Histology Wilms Tumor (WT00-224)


title: Thyroid-15N


title: Favorable Histology Wilms Tumor (WT00-220)

value: II


title: Favorable Histology Wilms Tumor (WT00-222)

value: No


title: Thyroid-13N

value: FTC


title: Thyroid-14T


title: Thyroid-12N


title: Favorable Histology Wilms Tumor (WT00-225)


title: Favorable Histology Wilms Tumor (WT00-022)

value: III


title: Favorable Histology Wilms Tumor (WT00-219)


title: Favorable Histology Wilms Tumor (WT00-250)


title: Thyroid-10N


title: Thyroid-13T


title: Favorable Histology Wilms Tumor (WT00-216)


title: Thyroid-10T


title: Favorable Histology Wilms Tumor (WT00-214)


title: Thyroid-12T


title: Thyroid-11T


title: Thyroid-14N


title: Thyroid-9T


title: Favorable Histology Wilms Tumor (WT00-212)


title: Thyroid-11N


title: Thyroid-9N


title: Favorable Histology Wilms Tumor (WT00-215)

value: I


title: Favorable Histology Wilms Tumor (WT00-211)


title: Thyroid-8T2


title: Favorable Histology Wilms Tumor (WT00-213)


title: Thyroid-8N


title: Thyroid-7T


title: Thyroid-7N


title: Favorable Histology Wilms Tumor (WT00-210)


title: Thyroid-6T


title: Favorable Histology Wilms Tumor (WT00-021)


title: Thyroid-8T1


title: Favorable Histology Wilms Tumor (WT00-207)

value: Yes


title: Favorable Histology Wilms Tumor (WT00-206)


title: Thyroid-4T

value: FTC/ FVPC


title: Favorable Histology Wilms Tumor (WT00-020)


title: Thyroid-5N


title: Thyroid-6N


title: Favorable Histology Wilms Tumor (WT00-209)


title: Favorable Histology Wilms Tumor (WT00-204)

value: IV


title: Favorable Histology Wilms Tumor (WT00-203)


title: Thyroid-5T


title: Thyroid-3N


title: Favorable Histology Wilms Tumor (WT00-198)


title: Thyroid-3T


title: Favorable Histology Wilms Tumor (WT00-195)


title: Favorable Histology Wilms Tumor (WT00-205)


title: Favorable Histology Wilms Tumor (WT00-193)


title: Thyroid-2T


title: Favorable Histology Wilms Tumor (WT00-196)


title: Thyroid-2N


title: Favorable Histology Wilms Tumor (WT00-002)


title: Thyroid-4N


title: Favorable Histology Wilms Tumor (WT00-192)


title: Favorable Histology Wilms Tumor (WT00-019)


title: Favorable Histology Wilms Tumor (WT00-190)


title: Thyroid-1N


title: Favorable Histology Wilms Tumor (WT00-191)


title: Favorable Histology Wilms Tumor (WT00-189)


title: Favorable Histology Wilms Tumor (WT00-178)


title: Favorable Histology Wilms Tumor (WT00-183)


title: Favorable Histology Wilms Tumor (WT00-186)


title: Favorable Histology Wilms Tumor (WT00-187)


title: Favorable Histology Wilms Tumor (WT00-179)


title: Favorable Histology Wilms Tumor (WT00-177)


title: Thyroid-1T


title: Favorable Histology Wilms Tumor (WT00-171)


title: Favorable Histology Wilms Tumor (WT00-185)


title: Favorable Histology Wilms Tumor (WT00-018)


title: Favorable Histology Wilms Tumor (WT00-188)


title: Favorable Histology Wilms Tumor (WT00-175)


title: Favorable Histology Wilms Tumor (WT00-172)


title: Favorable Histology Wilms Tumor (WT00-184)


title: Favorable Histology Wilms Tumor (WT00-167)


title: Favorable Histology Wilms Tumor (WT00-166)


title: Favorable Histology Wilms Tumor (WT00-173)


title: Favorable Histology Wilms Tumor (WT00-170)


title: Favorable Histology Wilms Tumor (WT00-016)


title: Favorable Histology Wilms Tumor (WT00-158)


title: Favorable Histology Wilms Tumor (WT00-160)


title: Favorable Histology Wilms Tumor (WT00-180)


title: Favorable Histology Wilms Tumor (WT00-168)


title: Favorable Histology Wilms Tumor (WT00-153)


title: Favorable Histology Wilms Tumor (WT00-163)

value: V


title: Favorable Histology Wilms Tumor (WT00-154)


title: Favorable Histology Wilms Tumor (WT00-152)


title: Favorable Histology Wilms Tumor (WT00-156)


title: Favorable Histology Wilms Tumor (WT00-151)


title: Favorable Histology Wilms Tumor (WT00-155)


title: Favorable Histology Wilms Tumor (WT00-015)


title: Favorable Histology Wilms Tumor (WT00-146)


title: Favorable Histology Wilms Tumor (WT00-150)


title: Favorable Histology Wilms Tumor (WT00-149)


title: Favorable Histology Wilms Tumor (WT00-142)


title: Favorable Histology Wilms Tumor (WT00-147)


title: Favorable Histology Wilms Tumor (WT00-141)


title: Favorable Histology Wilms Tumor (WT00-144)


title: Favorable Histology Wilms Tumor (WT00-133)


title: Favorable Histology Wilms Tumor (WT00-145)


title: Favorable Histology Wilms Tumor (WT00-139)


title: Favorable Histology Wilms Tumor (WT00-129)


title: Favorable Histology Wilms Tumor (WT00-135)


title: Favorable Histology Wilms Tumor (WT00-128)


title: Favorable Histology Wilms Tumor (WT00-127)


title: Favorable Histology Wilms Tumor (WT00-130)


title: Favorable Histology Wilms Tumor (WT00-140)


title: Favorable Histology Wilms Tumor (WT00-131)


title: Favorable Histology Wilms Tumor (WT00-013)


title: Favorable Histology Wilms Tumor (WT00-118)


title: Favorable Histology Wilms Tumor (WT00-120)


title: Favorable Histology Wilms Tumor (WT00-123)


title: Favorable Histology Wilms Tumor (WT00-122)


title: Favorable Histology Wilms Tumor (WT00-119)


title: Favorable Histology Wilms Tumor (WT00-115)


title: Favorable Histology Wilms Tumor (WT00-124)


title: Favorable Histology Wilms Tumor (WT00-121)


title: Favorable Histology Wilms Tumor (WT00-136)


title: Favorable Histology Wilms Tumor (WT00-113)


title: Favorable Histology Wilms Tumor (WT00-111)


title: Favorable Histology Wilms Tumor (WT00-114)


title: Favorable Histology Wilms Tumor (WT00-108)


title: Favorable Histology Wilms Tumor (WT00-110)


title: Favorable Histology Wilms Tumor (WT00-010)


title: Favorable Histology Wilms Tumor (WT00-105)


title: Favorable Histology Wilms Tumor (WT00-103)


title: Favorable Histology Wilms Tumor (WT00-104)


title: Favorable Histology Wilms Tumor (WT00-112)


title: Favorable Histology Wilms Tumor (WT00-106)


title: Favorable Histology Wilms Tumor (WT00-001)


title: Stat5b untreated rep1

city: PHILADELPHIA

first: Adam

last: Ertel

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

hyb_protocol: The resultant fragmented and labeled cDNA was added to the hybridization cocktail in accordance with the NuGEN™ guidelines for hybridization onto Affymetrix GeneChip® arrays. Hybridization was run for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridization Oven 640.  Following hybridization, the array was washed and stained on the GeneChip® Fluidics Station 450.

scan_protocol: Arrays were inserted into the Affymetrix autoloader carousel and scanned using the GeneChip® Scanner 3000

data_processing: Raw intensity files from the Affymetrix Human Gene 1.0 ST GeneChip arrays were processed using Affymetrix Expression Console version 1.1.   Gene-level expression measurements were computed using the iterPLIER algorithm on the “core” probesets and exported with annotation release 30, dated November 9th, 2009.

source_name: MCF7 human breast cancer cell line expressing exogenous Stat5b

label_protocol: Amplified single-stranded cDNA was fragmented and labeled using the Encore™ cDNA Biotin Module. The enzymatically and chemically fragmented product (50-100 nt) was labeled via the attachment of biotinylated nucleotides onto the 3'-end of the fragmented cDNA.

growth_protocol: MCF7 human breast cancer cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 2mM L-glutamine, and 50 IU/ml penicillin-50ug/ml streptomycin.

extract_protocol: RNA was harvested using the Qiagen RNeasy Kit following the recommended protocol.

treatment_protocol: MCF7 cells were infected with adenovirus expressing Stat5a or Stat5b for 90 min in serum free media and cultured for an additional 24 hr in regular growth media.  Cells were serum-starved 16 hr prior to treatment with prolactin for 4 hr in serum-free media.

tag: cell line

value: MCF7 human breast cancer

tag: exogenous protein expression

tag: hormone treatment

value: untreated


title: Stat5b prolactin rep1

source_name: MCF7 human breast cancer cell line expressing exogenous Stat5b, treated with 10nM human prolactin for 4 hours

value: prolactin


title: Stat5b prolactin rep2


title: brain5+

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

hyb_protocol: According to the standard operating procedures of the ImmGen consortium (www.immgen.org)

data_processing: RMA background correction, normalized and summarization using aroma.affymetrix software, CDF MoGene-1.0-st-v1,r3 and core probes only.

source_name: CD103+ memory T cells from brain

growth_protocol: Memory cells were generated by adoptively transferring 10,000 naïve OT-I cells into B6 mice prior to intranasal infection with VSV-OVA. Memory cells were analyzed on day 20 post infection.

extract_protocol: The RNA was extacted using Trizol according to the standard operating procedures of the ImmGen consortium

treatment_protocol: Sorted OT-I cells from the brain and spleen of mice on day 20 post infection

value: Brain

tag: sort


title: brain4+

scan_protocol: According to the standard operating procedures of the ImmGen consortium (www.immgen.org)


title: spleen5-

source_name: CD103- memory T cells from spleen

label_protocol: According to the standard operating procedures of the ImmGen consortium (www.immgen.org)

value: Spleen


title: brain1+


title: spleen2-


title: spleen1-


title: brain3+


title: Stat5b untreated rep2


title: brain1-

source_name: CD103- memory T cells from brain


title: spleen4-


title: brain3-


title: IDE2+FGF2b

city: Farmington

first: Todd

middle: James

last: Jensen

state: CT

address: 263 Farmington Avenue   MC3501

department: Center for Vascular Biology

institute: University of Connecticut Health Center

description: Replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina BeadStudio

source_name: Embryonic Stem Cells

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

growth_protocol: Cells were maintained in GMEM medium supplemented with 1X PenStrep, 1X Pyruvate, 10% FCS, B-Mercaptoethanol, 2uM L-Glutamine, and CHO-LIF Conditioned Medium on 35mm Plates until differentiation began

extract_protocol: RNA was extracted with Trizol reagent, followed by DNase I treatment with Ambion Turbo DNASE. Treated RNA was assessed and quantified with nanodrop spectrophotometer.

treatment_protocol: Cells were cultured in differentiation medium containing 1uM IDE2 for the first 6 days, IDE2+FGF2 and IDE2+FGF10 conditions were then switched to differentiation medium containing either 500ng/ml of FGF2 or 25ng/ml of FGF10 for 5 days. IDE2 only condition continued differentiation in medim containing 1uM for all 11 days.  Differentiation medium was comprised of Iscoves Medium and Ham F12 medium with additional supplements including N2, B27, 1% FCS, 1X PenStrep, 2uM L-Glutamine, 1-Thioglycerol and Ascorbic Acid.

tag: differentiation medium

value: 1uM IDE2 and then 500ng/ml of FGF2


title: IDE2b

description: Replicate 2

value: 1uM IDE2


title: brain2+

tag: tissue


title: spleen3-


title: Stat5a untreated rep1

source_name: MCF7 human breast cancer cell line expressing exogenous Stat5a


title: Stat5a untreated rep3


title: Stat5b untreated rep3


title: Stat5b prolactin rep3


title: IDE2+FGF10a

description: Replicate 1

value: 1uM IDE2 and then 25ng/ml of FGF10


title: IDE2+FGF10b

description: Replicate 2


title: brain2-


title: Stat5a untreated rep2


title: Stat5a prolactin rep1

source_name: MCF7 human breast cancer cell line expressing exogenous Stat5a, treated with 10nM human prolactin for 4 hours


title: IDE2+FGF2a

description: Replicate 1


title: IDE2a

description: Replicate 1


title: ES Undiff b

description: Replicate 2


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-31

tag: gender

value: male

tag: clinical stage

tag: surgical margin status

value: Negative

tag: nodal status at surgery

tag: gleason sum score (biopsy)

tag: gleason sum score (surgical)

tag: psa pre-chemotherapy

tag: psa post-chemotherapy

value: prostate needle biopsy tissue frozen in OCT blocks

value: neoplastic epithelium

value: prostatectomy tissue frozen in OCT blocks


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_UW-10

tag: cell type


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-32

tag: age


title: Stat5a prolactin rep2


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_UW-03

value: Positive


title: Stat5a prolactin rep3


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-10


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-25


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-22


title: HUF1-p5-2

city: Beaverton

first: James

middle: Anthony

last: Byrne

state: OR

address: 505 NW 185th Ave

department: Reproductive Sciences

institute: ONPRC

description:
HUF1-p5-2
Untreated human skin fibroblasts (HUF1).
Cells are derived from a skin biopsy.

hyb_protocol: Following fragmentation, 3.75ug of single-strand cDNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays in the Affymetrix GeneChip Hybridization Oven 640 using standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001). GeneChips were washed in the Affymetrix Fluidics Station 450.

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

data_processing: Each CEL file was uploaded to GeneSifter (VisX Labs, Seattle, WA) using the Advanced Upload Method and normalized using the Affymetrix Microarray Analysis Suite (MAS) 5.0 algorithm. Data from control HUF cells was used as a baseline control to compare the replicates of HUF cells with or without BAY11 and hESCs.

source_name: HUF1 skin fibroblasts, untreated

label_protocol: 100ng of total RNA was amplified using NuGEN Ovation RNA Amplification System V2. Biotinylated cDNA were prepared according to the NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single-strand cDNA.

growth_protocol:
In vitro Culture of Human Embryonic Stem Cells-H9: H9 embryonic stem cells (hESC) (UCLA Broad Stem Cell Research Center-Stem Cell Core) were cultured in standard ESC conditions as published [26]. Briefly, hESC medium consisting of DMEM/F12 supplemented with 20% Knockout Serum ment (KSR), 1x Glutamax, 1x non-essential amino acids, 100 IU/mL Penicillin-Streptomycin (all from Invitrogen), 1x beta-mercaptoethanol (Millipore, Billerica, MA), and 10ng/mL recombinant human basic fibroblast growth factor (bFGF, Globalstem, Rockville, MD).

In vitro Culture of Primary Human Skin Cells: The human skin-derived (HUF1) primary cell line used in this study was obtained from a 4mm adult skin punch biopsy and cultured as described [26]. Briefly, all human biopsy-derived cells were cultured in complete DMEM/F12 media consisting of Dulbecco's Modified Eagle Medium Nutrient Mixture F-12 (DMEM/F12) supplemented with 10% fetal bovine serum (FBS), 1x MEM non-essential amino acids, 1x Glutamax, and 100 IU/ml penicillin-streptomycin (all from Invitrogen/Gibco, Grand Island, NY, USA) and maintained at 37°C in a 5% CO2 incubator. Culture media was changed every two days. Cells were allowed to expand to 80-90% confluency before passaging with 0.05% trypsin-EDTA (Invitrogen) and replating at a 1:3 ratio. A large bank of early passage HUF1 cells was cryopreserved in culture media supplemented with 10% dimethyl sulphoxide (DMSO, Sigma-Aldrich, St Louis, MO, USA). All research adhered to National Academy of Sciences guidelines.

extract_protocol: Total RNA was purified from each replicate using the RNeasy Mini Kit (Qiagen, Valencia, CA, http://www1.qiagen.com) according to the manufacturer's instructions.

treatment_protocol:
Synthetic mRNA Transfection: All work was done in strict RNase-free conditions. Synthetic mRNA was thawed on ice and then quickly diluted before degradation. Synthetic mRNA was diluted using Opti-MEM basal media (Invitrogen) with 100ng/µL synthetic mRNA diluted 5x and RNAiMAX (Invitrogen), with 5µL of RNAiMAX per microgram of RNA (1.2µg total synthetic mRNA and thus 6µL RNAiMAX), was diluted 10x. The synthetic mRNA was diluted into 48µL of Opti-MEM and 6µL of RNAiMAX was diluted into 54µL of Opti-MEM for the 10x dilution. Each dilution was separate, and the tube was flicked 5-6 times to mix. The two dilutions were then pooled, mixed again by 6 tube flicks, and then incubated at room temperature for 15 minutes. This mixture was then added directly into fibroblast culture media, without antibiotics as required by protocol. The cells were left to incubate with the synthetic mRNA for 4 hours, after which the media was d with fresh BAY11 or BX795 along with B18R all in standard fibroblast media.

25,000 passage 5 HUF cells were plated across four wells in a 24-well plate in standard DMEM/FBS media without antibiotics. 12 hours later, the cells were incubated with 1µM BAY11 + 200ng/mL B18R over two wells whereas the other two wells received just B18R at 200ng/mL final concentration. The final volume was 500µL in each well. After 24 hours incubation, the cells were then transfected with the modified synthetic mRNA as detailed above. This was done everyday for 3 days, and after the last incubation period of 24 hours, the cells were harvested for mRNA using Roche's High Pure RNA Isolation Kit according to the manufacturer's instructions. hESCs and control fibroblasts were harvested in the same manner.

value: skin fibroblasts

tag: treatment


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_UW-05


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_UW-11


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-19


title: HUF1-p4-plus-SynRNA-plus-BAY11-2

description:
HUF1-p4-plus-SynRNA-plus-BAY11-2
Human skin fibroblasts (HUF1) treated with OCT4 synthetic mRNA and BAY11.
Cells are derived from a skin biopsy.

source_name: HUF1 skin fibroblasts, OCT4 synthetic mRNA and BAY11

tag: cell line

value: OCT4 synthetic mRNA and BAY11


title: HUF1-p5-1

description:
HUF1-p5-1
Untreated human skin fibroblasts (HUF1).
Cells are derived from a skin biopsy.


title: ES Undiff a

description: Replicate 1


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-34


title: HUF1-p4-plus-SynRNA-plus-BAY11-1

description:
HUF1-p4-plus-SynRNA-plus-BAY11-1
Human skin fibroblasts (HUF1) treated with OCT4 synthetic mRNA and BAY11.
Cells are derived from a skin biopsy.


title: hESC-H9-p29-2

description:
hESC-H9-p29-2
Untreated human embryonic stem cells (H9).
Cells are derived from a blastocyst.

source_name: H9 embryonic stem cells, untreated

value: human embryonic stem cells


title: HUF1-p4-plus-SynRNA-1

description:
HUF1-p4-plus-SynRNA-1
Human skin fibroblasts (HUF1) treated with OCT4 synthetic mRNA.
Cells are derived from a skin biopsy.

source_name: HUF1 skin fibroblasts, OCT4 synthetic mRNA

value: OCT4 synthetic mRNA


title: H1299 siM

city: Beijing

first: Lei

last: Zhao

address: School of Medicine,Tsinghua University

institute: Tsinghua University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays scanned using a confocal scanner LuxScanTM 10K/A (CapitalBio),and the data of obtained images were extracted with the LuxScan3.0 software (CapitalBio).

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.

source_name: H1299 cells transfected by hMOF siRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: H1299 and A549 cell lines were grown in DMEM medium supplemented with 10% fetal bovine serum (FBS) and cultured in a humidified atmosphere in an incubator at 37°C with 5% CO2.

extract_protocol: Total RNA were extracted by Trizol reagent.

treatment_protocol: H1299 and A549 cells were transfected with siRNA using Lipofectamine 2000 reagent.

tag: source tissue

value: lung

value: control siRNA


title: hESC-H9-p29-1

description:
hESC-H9-p29-1
Untreated human embryonic stem cells (H9).
Cells are derived from a blastocyst.


title: H1299 NC

source_name: H1299 cells transfected by scramble siRNA


title: HUF1-p4-plus-SynRNA-2

description:
HUF1-p4-plus-SynRNA-2
Human skin fibroblasts (HUF1) treated with OCT4 synthetic mRNA.
Cells are derived from a skin biopsy.


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-24


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-16


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-07


title: A549 NC

source_name: A549 cells transfected by scramble siRNA

value: hMOF siRNA


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-13


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-23


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-28


title: A549 siM

source_name: A549 cells transfected by hMOF siRNA


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-15


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-08


title: Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_6082-14


title: Total RNA from tomato fruit 7 days post breaker

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

institute: University of Oxford

description: Total RNAs from Solanum lycopersicum cv. Micro-Tom 7 days post breaker

hyb_protocol: The samples were hybridised in the standard way, 16hrs at 45C and stainned with the Affymetix hyb wash and stain kit.

scan_protocol: Standard Affymetrix scanning protocol.

data_processing: The data were analyzed with Bioconductor affy package, using for background correction - RMA, normalization - quantiles, summarization - median polish. The default probe groupping was used.

organism: Solanum lycopersicum

source_name: breaker +7 days fruit

label_protocol: GeneChip 3' IVT Express kit. the user manual is P/N 702646 Rev.1

growth_protocol: Plants were grown in pots with soil in a growth chamber having a photoperiod of 16/8h day/night, a thermoperiod 23/ 18ºC  day/night and humidity of 40%.

extract_protocol: Total RNA was extracted from Solanum lycopersicum cv. Micro-Tom using a phenol chloroform procedure.

value: Whole tomato fruit 7 days post breaker

tag: genotype

value: Solanum lycopersicum cv. Micro-Tom

tag: developmental stage

value: breaker +7 days fruit