title: Npl3 Replicate 2

city: Göttingen

first: Klaus

last: Jung

address: Humboldtallee 32

department: Medical Statistics

country: Germany

institute: University Medical Center Göttingen

hyb_protocol: Yeast microarrays (Y6.4k6; University Health Network Microarray Centre, Toronto, Canada) were pre-hybridized at 55°C for 30 min in 5 x SSC, 0.1 % SDS and 1 % bovine serum albumin and rinsed 5 times with water. The slides were dried by spinning them for 3 min at 1500 rpm. Labelled probes were supplemented with 3 μl of yeast tRNA (10 mg/ml) and 3 μl of denatured salmon sperm DNA (10 mg/ml). Probes were concentrated in a speed vac to a final volume of 26 μl and supplemented with 4 μl 2% bovine serum albumin and 10 μl 20 x SSC before they were spotted onto a microarray slide. The hybridization was carried out for 16 h at 55°C in a hybridization chamber. After removal of the HybriSlipTM Hybridization Cover (Sigma-Aldrich) the slides were washed with agitation three times in 1x SSC buffer containing 0.1 % SDS, two times with 1 x SSC buffer and once in ddH2O. Arrays were dried by centrifugation.

scan_protocol: Fluorescence intensities were monitored by using the scanner ScanArray Express (PerkinElmer Life Sciences) using ScanArray Express, Microarray Analysis System 4.0.0.4.

data_processing: quantile normalization of median signales using the R-package limma

label_protocol: The RNA probes from RNA Co-immunoprecipitations were qualitatively analyzed by ExperionTM (Biorad). One microgram of RNA from lysate was amplified using the Message AmpTM II aRNA Amplification kit (Ambion). 4 μg of an RNA sample was transcribed into Cy5 labeled cDNA using the AmershamTM CyScribeTM cDNA Post-labelling kit (GE Healthcare). Unincorporated nucleotides were removed following the manufacturer's protocol of illustraTM CyScribeTMGFXTM Purification kit (GE Healthcare).

growth_protocol: Yeast cells were grown at 25°C in selective medium to a density of 4 x 10^7 cells/ml.

extract_protocol: Yeast cells were grown at 25°C in selective medium to a density of 4 x 107 cells/ml. The cells were collected, washed with 1 x TBS and resuspended in RNA-IP buffer (25 mM Tris-HCl, pH 7.5, 100 mM KCl, 0,2% (v/v) Triton X-100, 0,2 mM PMSF, 5 mM DTT, 10 units RiboLockTM RNase Inhibitor (Thermo Scientific)). One cell pellet volume of glass beads, 1,5 volumes of RNA-IP buffer supplemented with protease inhibitor cocktails (Sigma and Roche) were added. Cells were lysed by vigorous vortexing for 25 sec and 4m/s using the FastPrep®-24 instrument (MP Biomedicals). For DNaseI digestion 800 µl lysate was incubated with 15 µl (40 Kunitz units) DNaseI (Qiagen) at 30°C for 30 min. The co-immunoprecipitation experiments were performed at 4°C for 3 h by incubating lysates with 20 µl of Protein G sepharose beads (Amersham Biosciences) conjugated to monoclonal c-myc (9E10)-antibody (Santa Cruz) or GFP-Trap®-beads (ChromoTek). The beads were washed five times with RNA-IP buffer and the RNA was eluted in 100 µl DEPC-treated ddH2O during incubation at 65°C for 10 min. The RNA eluate was purified via phenol-chloroform extraction followed by an ethanol precipitation. The RNA was finally eluted in 10 µl of DEPC-treated ddH2O. 100 µl of the lysate was collected as an input control before co-immunoprecipitation and wasand was purified via phenol-chloroform extraction followed by an ethanol precipitation and eluted in 10-20 µl  in parallel to the eluate (co-immunoprecipitated RNA) to obtain a total input sample for Microarray analyses. RNA co-immunoprecipitations were performed in two independent experiments each for myc-tagged Gbp2, Hrb1 and Npl3.

tag: probe

value: lysate

tag: co-ip

value: eluate


title: Control-10dayStress-1dayRest [BL6_C10-95_1d_heart]

status: Public on Dec 04 2013

type: RNA

city: Seattle

first: Ji-Hoon

last: Cho

state: WA

address: 401 Terry Avenue North

country: USA

institute: Institute for Systems Biology

description: Gene expression after 10day-stress and 1day-rest, control mouse heart tissue

hyb_protocol: The labeled antisense cRNAs were purified and hybridized to microarrays. The hybridization was carried out for 16 h at 45°C.

scan_protocol: The arrays were washed and scanned using an Agilent scanner.

data_processing: The scanned images of the arrays were converted and imported into the Institute for Systems Biology’s Systems Biology Experiment Analysis System (SBEAMS) for array data normalization and further analyses.

molecule: total RNA

organism: Mus musculus

source_name: Heart tissue, 10day-stress, 1day-rest, rep3

label_protocol: Total RNA was reverse transcribed and followed by generation of cDNAs. The resulting cDNAs were transcribed and labeled with cyanine 3-CTP.

extract_protocol: Total RNA was isolated from individual mouse heart samples by homogenization in TRIzol reagent per the manufacturer’s protocol (Invitrogen, Gran Island, NY). The quality and quantity of the RNA samples were evaluated using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Waltham, MA) and Agilent 2100 BioAnalyzer (Agilent, Santa Clara, CA).

treatment_protocol: The experimental animals were kept in a wire mesh box inside the aggressor´s cage for 6 hours a day for either 5 or 10 consecutive days.  Animals were randomly assigned to aggressors cages.  Each subject mouse was randomly placed 3-5 times within the home cage of an aggressor mouse and received bites/attacks for up to 2 min (or until 10 attacks/bites occurred, whichever came first.  Each day the stress procedure occurred at different times and different resident mice were used for each aggressor.  Body weight and temperature of the experimental mice were measured every day prior the beginning of the social defeat period and the return to their home cages.   Control mice were kept inside of the wired mesh boxes inside of a large cage without any aggressor.

tag: strain

tag: tissue

value: heart tissue


title: Control-10dayStress-1dayRest [BL6_C10-94_1d_heart]

source_name: Heart tissue, 10day-stress, 1day-rest, rep2


title: Grb1 Replicate 1

organism: Saccharomyces cerevisiae


title: Gbp2 Replicate 2


title: Grb1 Replicate 2


title: Gbp2 Replicate 1


title: Npl3 Replicate 1


title: pancreas_Sel1L1knockout_rep2

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.24.2).

label: biotin

source_name: pancreas, inducible Sel1L1 knockout

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: The Sel1ltm1e(KOMP)Wtsi (Sel1Lflox/+) ES cells on the C57BL/6N background were purchased from the KOMP Repository Project (ID CSD44577, UC Davis, http://www.knockoutmouse.org/martsearch/project/44577). Exon 6 of Sel1L gene was flanked with two loxP sites (floxed). The lacZ-neo cassette was deleted by crossing the animals onto the βActin-FLPe deleter mice on the C57BL/6J background (JAX 003800). The resulting Sel1Lflox/+ animals were intercrossed to generate Sel1Lflox/flox mice. The Sel1Lflox/flox mice were then crossed with actin-promoter driven estrogen receptor-Cre fusion protein transgenic (ERCre) mice on the C57BL/6J background (JAX 004781). The last stage of cross generated fl/fl;ERCre+ and the control cohort fl/fl;ERCre- littermates at 1:1 ratio.

extract_protocol: To extract RNA from pancreas, mice were anesthetized and pancreas tissues were perfused locally with RNAlater reagent (Qiagen). Tissues were then excised and soaked in RNAlater on ice for stabilization. Total RNA was extracted using Trizol and RNA miniprep kit (Sigma RTN350) with DNaseI digestion (Roche).

treatment_protocol: Tamoxifen (Sigma T5648) was dissolved in sunflower oil at 5 mg/ml. Age-matched littermates at the age of 8-20 weeks were injected intraperitoneally with tamoxifen at the volume of 5 μl/g body weight daily for three consecutive days.

tag: strain/background

tag: genotype/variation

value: inducible Sel1L1 knockout

value: pancreas


title: pancreas_Sel1L1knockout_rep3


title: pancreas_Sel1L1knockout_rep4


title: pancreas_Sel1L1knockout_rep1


title: pancreas_wildtype_rep4

source_name: pancreas, wild type

value: wild type


title: EVCT, treated, biological rep4

city: PARIS

first: Severine

middle: Aude

last: Degrelle

address: 4 avenue de l'Observatoire

country: France

institute: INSERM UMRS-1139

description: Gene expression data from EVCT rosiglitazone treated

hyb_protocol: 20 µg of fragmented cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000. Expression values were generated with Microarray Suite v5.0 (MAS5, Affymetrix)

data_processing: MAS 5.0

organism: Homo sapiens

source_name: EVCT cultured during 24H with rosiglitazone

label_protocol: Total RNA were extracted from EVCT by Trizol (Invitrogen) followed by purification using RNeasy Mini kit (Quiagen). Integrity and purity of RNA were checked on Bioanalyzer 2100 with RNA 6000 LabChip kit (Agilent Biotechnologies)

growth_protocol: EVCT were isolated by trypsin and purified on percoll gradient, then plated onto matrigel coated Petri dishes in DMEM/F12 10% FBS, cultured for 24h and then with or without rosiglitazone treatment for an additional 24 h period.

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

treatment_protocol: EVCT pellets were then snap-frozen and stored at -80°C until RNA extraction.

tag: cell type

value: extravillous cytotrophoblasts

tag: treatment

value: rosiglitazone


title: pancreas_wildtype_rep1


title: EVCT, treated, biological rep2


title: pancreas_wildtype_rep3


title: EVCT, control, biological rep2

description: Gene expression data from EVCT control

source_name: EVCT cultured 48h


title: EVCT, treated, biological rep1


title: EVCT, treated, biological rep3


title: EVCT, control, biological rep4

description: Gene expression data from EVCT control


title: EVCT, control, biological rep3

description: Gene expression data from EVCT control


title: BL6_C5-129_1d_heart

description: BL6_C5-127_1d_heart_miRNA_Hy3_v_BL6_C5-129_1d_heart_miRNA_Hy5.csv

hyb_protocol: Labeled samples were hybridized to Exiqon 5th generation miRCURY LNA microRNA array according to the manufacturer's protocol.

scan_protocol: After hybridization, the slides were washed and scanned with a scanner from Agilent (Santa Clara, CA).

data_processing: Scanned data was processed using AnalyzerDG software. For the preprocessing of two-channel microarray data in each experimental group,  Hy3 and Hy5 (high energy scanned) intensities were concatenated, normalized using LOWESS (within-array normalization) and normalized using the quantile method (between-array normalization).

source_name: Control_heart_tissue, C5R1

label_protocol: Total RNA from the heart tissue was labeled with either Hy3 or Hy5 dye with labeling kits from Exiqon then hybridized at 56°C for 16 h.

value: Control_heart_tissue, C5R1


title: pancreas_wildtype_rep2


title: Gene expression in wild-type IDH1/2 anaplastic glioma (sample no. 426)

city: Sendai

first: Masayuki

last: Kanamori

state: Miyagi

address: 1-1 Seiryo-cho

department: Neurosurgery

country: Japan

institute: Tohoku University, Graduate School of Medicine

hyb_protocol: 1.65 ug of Cy3-labeled cRNA was fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2539.

data_processing: The data were normalized to the 75th percentile. The data were analyzed using GeneSpring GX software (Agilent).

source_name: anaplastic glioma, surgically excised, wild-type IDH1/2

label_protocol: 500 ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.

growth_protocol: Gliomas were surgically excised.

extract_protocol: Total RNA was extracted from cells using Isogen (Nippon Gene). RNA was further purified using an RNeasy Mini Kit (Qiagen).

treatment_protocol: Tumor specimens  were immediately snap-frozen in liquid nitrogen and stored at -80˚C until the extraction of RNA.

value: glioma

tag: glioma type

value: anaplastic oligoastrocytoma

value: wild-type IDH1/2


title: Gene expression in wild-type IDH1/2 anaplastic glioma (sample no. 494)

value: anaplastic oligodendroglioma


title: Gene expression in wild-type IDH1/2 anaplastic glioma (sample no. 10-3)

value: anaplastic astrocytoma


title: Gene expression in wild-type IDH1/2 anaplastic glioma (sample no. 11-1)


title: EVCT, treated, biological rep5


title: EVCT, control, biological rep5

description: Gene expression data from EVCT control


title: EVCT, control, biological rep1

description: Gene expression data from EVCT control


title: Gene expression in IDH1 mutated anaplastic glioma (sample no. 113)

source_name: anaplastic glioma, surgically excised, mutated IDH1

value: mutated IDH1


title: Gene expression in wild-type IDH1/2 anaplastic glioma (sample no. 401)


title: Gene expression in IDH1 mutated anaplastic glioma (sample no. 148)


title: Gene expression in IDH1 mutated anaplastic glioma (sample no. 645)


title: Negative control rep3

city: Majadahonda

first: Laura

last: Sanz

state: Madrid

address: Joaquín Rodrigo 2

department: Molecular Immunology

country: Spain

institute: Hospital Puerta de Hierro

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials in a GeneChip® Hybridization Oven 640

scan_protocol: Affymetrix GeneChip® 3000 scanner

data_processing: The CEL files generated from the scanning were converted to gene expression signals using RMA Algorithm in Affymetrix® Expression Console

label: SAPE

source_name: Primary pericytes

label_protocol: cDNA was labeled with Affymetrix WT terminal Labeling kit

growth_protocol: HBVP were cultured in Pericyte Medium with 2% FBS, pericyte grorth supplement and penicillin/streptomycin (all from ScienceCell, Carlsbad, CA, USA).

extract_protocol: Total RNA was extracted using a Qiagen RNeasy Micro kit according to manufacturer´s instructions.

treatment_protocol: Cells were incubated 24h in 24w-plates, prior to stimulation with Lipopolysaccharide (LPS) from Escherichia coli 026:B6 (Sigma-Aldrich, Manchester, UK) at a concentration of 1 microgram/ml for 4h.

value: Brain


title: LPS treatment rep2

value: LPS at a concentration of 1 microgram/ml for 4h


title: Gene expression in wild-type IDH1/2 anaplastic glioma (sample no. 649)


title: Gene expression in IDH1 mutated anaplastic glioma (sample no. 517)


title: LPS treatment rep3


title: MSC rep3

source_name: Mesenchymal stem cells

growth_protocol: MSC were cultured in DMEM supplemented with heat-inactivated 10% fetal bovine serum (FBS), 2 mM L-glutamine, and penicillin/streptomycin (all from Invitrogen Life Technologies, Carlsbad, CA, USA). HBVP were cultured in Pericyte Medium with 2% FBS, pericyte grorth supplement and penicillin/streptomycin (all from ScienceCell, Carlsbad, CA, USA).

treatment_protocol: Cells were incubated 24h in 24w-plates.

value: Umbilical cord


title: dentate gyrus-granule cell layer-30daysRunning, repAT3

first: Jeremy

last: Miller

address: 615 Westlake Ave N

institute: Allen Institute for Brain Science

description: Gene expression data from 10- to 11-week-old C57BL/6 male mice

hyb_protocol: 15μg of biotinylated aRNA was fragmented and hybridized to Affymetrix MG-U74Av2 arrays.

scan_protocol: Gene chips were scanned following the manufactures protocol.

data_processing: Initial data analysis and normalization were done using the Affymetrix Expression Console using two algorithms: Robust Multichip Analysis (RMA) and Probe Logarithmic Intensity Error Estimation (PLIER) using the minus mismatch option (-MM).  Note that an additional filtering step to remove the effect of running was performed in the larger cross-species study, using ComBat (www.bu.edu/jlab/wp-assets/ComBat).

source_name: Outer granule cell layer from a mouse allowed access to running wheel for 30 days

label_protocol: 5ng total RNA starting material was amplified using the MessageAmp aRNA Kit (Ambion Inc, Austin, TX).  This method utilizes reverse transcription with T7 RNA Polymerase.  The first and second rounds of the kit were performed per the manual, with an additional third round identical to the second round except that the in vitro transcription step utilized the Enzo BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was purified from the laser captured tissue using the Absolutely RNA Nanoprep Kit (Stratagene, La Jolla, CA), and RNA yield was assessed using the RiboGreen RNA Quantitation Reagent (Molecular Probes Inc, Eugene, OR).  RNA from three groups of animals (no running, 4 days of running, 30 days of running), consisting of 3 animals each, was isolated independently and amplified separately.

treatment_protocol: Brains were quickly removed, flash-frozen in OCT mounting medium in a dry ice-isopentantane slurry, and stored at -80C until use.  12μm thin cryostat sections were stained with cresyl violet, rapidly dehydrated through xylenes, and stored until use a vacuum dessicator.  An Arcturus PixCell II machine (Arcturus, Mountain View, CA) was used to isolate 2-3 cell thick bands from both the inner and outer portions of the dentate granule cell layer.

tag: age

value: 10-11 week old

tag: Sex

value: male

value: brain

tag: region

value: dentate gyrus-granule cell layer

tag: animal


title: Negative control rep2


title: LPS treatment rep1


title: dentate gyrus-subgranular zone-30daysRunning, repAT3

source_name: Subgranular zone (inner granule cell layer) from a mouse allowed access to running wheel for 30 days

value: dentate gyrus-subgranular zone


title: Gene expression in IDH1 mutated anaplastic glioma (sample no. 366)


title: HBVP rep1


title: Gene expression in IDH1 mutated anaplastic glioma (sample no. 362)


title: HBVP rep3


title: Negative control rep1


title: dentate gyrus-granule cell layer-4daysRunning, repA42

source_name: Outer granule cell layer from a mouse allowed access to running wheel for 4 days


title: dentate gyrus-subgranular zone-30daysRunning, repAT2


title: dentate gyrus-subgranular zone-30daysRunning, repAT1


title: dentate gyrus-subgranular zone-4daysRunning, repA42

source_name: Subgranular zone (inner granule cell layer) from a mouse allowed access to running wheel for 4 days


title: dentate gyrus-granule cell layer-30daysRunning, repAT2


title: MSC rep1


title: dentate gyrus-granule cell layer-0daysRunning, repA03

source_name: Outer granule cell layer from a control mouse


title: dentate gyrus-subgranular zone-4daysRunning, repA43


title: dentate gyrus-granule cell layer-4daysRunning, repA43


title: dentate gyrus-granule cell layer-0daysRunning, repA01


title: HBVP rep2


title: dentate gyrus-subgranular zone-0daysRunning, repA02

source_name: Subgranular zone (inner granule cell layer) from a control mouse


title: dentate gyrus-granule cell layer-4daysRunning, repA41


title: dentate gyrus-subgranular zone-4daysRunning, repA41


title: T3M-1_wildtype_GFPsorted_triplicate

city: Bunkyo-ku

first: Mizuo

last: Ando

state: Tokyo

address: 7-3-1 Hongo

department: Otolaryngology-Head and Neck Surgery

institute: The University of Tokyo

description: Gene expression 2days after retroviral infection

hyb_protocol: Cy3-labelled cRNA hybridized to SurePrint G3 Human GE v2 8x60K Microarray with Gene Expression Hybridization Kit (Agilent) and Gene Expression Wash Pack (Agilent) according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters. The data were log2-transformed, and normalized by percentile shift-75%. In the matrix file, mean values were calculated for each biological triplicate.

source_name: Cell line, wildtype infected, GFP-sorted

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the one-color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was prepared using the RNeasy mini kit (Qiagen) following the manufacturer's recommendations.

tag: cell line

tag: histology

value: squamous cell carcinoma


title: dentate gyrus-granule cell layer-0daysRunning, repA02


title: T3M-1_mock_GFPsorted_triplicate

source_name: Cell line, mock infected, GFP-sorted


title: dentate gyrus-subgranular zone-0daysRunning, repA01


title: dentate gyrus-subgranular zone-0daysRunning, repA03


title: T3M-1_mutant_GFPsorted_triplicate

source_name: Cell line, mutant infected, GFP-sorted


title: EtOH treated NALM6 cells, exp35, pool 2

status: Public on Dec 03 2013

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

description:
Gene expression profile of 6 hours ethanol treated NALM6 preB-ALL cells, polysome profiling, pool 2, with mRNA potentially engaged in translation initiation, experiment 35.
Reagent: Ambion
Experiment: exp35

hyb_protocol: Target samples were hybridized to Human Exon 1.0 ST v2 microarrays according to the manufacturer's protocols in an Affymetrix hybridization oven.

scan_protocol: Microarrays were scanned in an Affymetrix 3000 scanner.

data_processing: Raw data was preprocessed using the GCRMA method (option GSB.adjust set to FALSE). For transcript probe set definition, a custom CDF package was used, that was based on a complete re-alignment of the Exon microarray oligo-probes and annotation to Ensembl version 67.

source_name: NALM6 precursor B-ALL cell line, ethanol, pool 2

label_protocol: Target RNA was labeled by addition of biotin-linked deoxynucleotides with terminal deoxynucleotidyl transferase according to the manufacturer's (Affymetrix) protocols. Washing and staining was performed in an Affymetrix 450S fluidics station.

growth_protocol: T-ALL CCRF-CEM-C7H2 and PreB-ALL NALM6 cells were cultured in RPMI 1640 supplemented with 10% fetal calf serum and 2mM L-glutamine at 37C, 5% carbon-dioxide and saturated humidity.

extract_protocol: Total RNA was extracted using the TRIZOL protocol according to the manufacturer's protocol, depleted of ribosomal RNA and transcribed into cDNA using T7-promoter-tagged hexamer primers. Antisense RNA was produced by T7-polymerase and transcribed into cDNA using random priming in the presence of dUTP which was used to enzymatically fragment the cDNA. The protocol for sample processed with Ambion reagents was identical to the one before (using Affymetrix reagents) with the exception that the ribosomal RNA depletion step was omitted, because specifically designed hexamere primer were used in the Ambion protocol, that preferentially do not bind to, and thus amplify, ribosomal RNA.

treatment_protocol: Cells were treated in 3 independent experiments for 6 hours either with 100nM dexamethasone (a synthetic glucocorticoid) or 0.1% ethanol as empty carrier control.

value: NALM6 precursor B-ALL

value: ethanol

tag: pool


title: GC treated NALM6 cells, exp35, pool 3

description:
Gene expression profile of 6 hours dexamethasone treated NALM6 preB-ALL cells, polysome profiling, pool 3, polysome bound RNA, engaged in translation, experiment 35.
Reagent: Ambion
Experiment: exp35

source_name: NALM6 precursor B-ALL cell line, dexamethasone, pool 3

value: dexamethasone


title: EtOH treated NALM6 cells, exp23, pool 3

description:
Gene expression profile of 6 hours ethanol treated NALM6 preB-ALL cells, polysome profiling, pool 3, polysome bound RNA, engaged in translation, experiment 23.
Reagent: Affymetrix
Experiment: exp23

source_name: NALM6 precursor B-ALL cell line, ethanol, pool 3


title: EtOH treated NALM6 cells, exp26, pool 3

description:
Gene expression profile of 6 hours ethanol treated NALM6 preB-ALL cells, polysome profiling, pool 3, polysome bound RNA, engaged in translation, experiment 26.
Reagent: Affymetrix
Experiment: exp26


title: GC treated NALM6 cells, exp26, pool 1

description:
Gene expression profile of 6 hours dexamethasone treated NALM6 preB-ALL cells, polysome profiling, pool 1, non-translated RNA, experiment 26.
Reagent: Affymetrix
Experiment: exp26

source_name: NALM6 precursor B-ALL cell line, dexamethasone, pool 1


title: GC treated NALM6 cells, exp23, pool 3

description:
Gene expression profile of 6 hours dexamethasone treated NALM6 preB-ALL cells, polysome profiling, pool 3, polysome bound RNA, engaged in translation, experiment 23.
Reagent: Affymetrix
Experiment: exp23


title: GC treated NALM6 cells, exp26, pool 2

description:
Gene expression profile of 6 hours dexamethasone treated NALM6 preB-ALL cells, polysome profiling, pool 2, with mRNA potentially engaged in translation initiation, experiment 26.
Reagent: Affymetrix
Experiment: exp26

source_name: NALM6 precursor B-ALL cell line, dexamethasone, pool 2


title: GC treated C7H2 cells, exp9, pool 2

description:
Gene expression profile of 6 hours dexamethasone treated C7H2 T-ALL cells, polysome profiling, pool 2, with mRNA potentially engaged in translation initiation, experiment 9.
Reagent: Affymetrix
Experiment: exp9

source_name: CCRF-CEM-C7H2 T-ALL cell line, dexamethasone, pool 2

value: CCRF-CEM-C7H2 T-ALL


title: EtOH treated NALM6 cells, exp26, pool 2

description:
Gene expression profile of 6 hours ethanol treated NALM6 preB-ALL cells, polysome profiling, pool 2, with mRNA potentially engaged in translation initiation, experiment 26.
Reagent: Affymetrix
Experiment: exp26


title: EtOH treated NALM6 cells, exp26, pool 1

description:
Gene expression profile of 6 hours ethanol treated NALM6 preB-ALL cells, polysome profiling, pool 1, non-translated RNA, experiment 26.
Reagent: Affymetrix
Experiment: exp26

source_name: NALM6 precursor B-ALL cell line, ethanol, pool 1


title: GC treated C7H2 cells, exp13, pool 1

description:
Gene expression profile of 6 hours dexamethason treated C7H2 T-ALL cells, polysome profiling, pool 1, non-translated RNA, experiment 13.
Reagent: Affymetrix
Experiment: exp13

source_name: CCRF-CEM-C7H2 T-ALL cell line, dexamethasone, pool 1


title: EtOH treated NALM6 cells, exp23, pool 2

description:
Gene expression profile of 6 hours ethanol treated NALM6 preB-ALL cells, polysome profiling, pool 2, with mRNA potentially engaged in translation initiation, experiment 23.
Reagent: Affymetrix
Experiment: exp23


title: GC treated NALM6 cells, exp23, pool 2

description:
Gene expression profile of 6 hours dexamethasone treated NALM6 preB-ALL cells, polysome profiling, pool 2, with mRNA potentially engaged in translation initiation, experiment 23.
Reagent: Affymetrix
Experiment: exp23


title: GC treated NALM6 cells, exp26, pool 3

description:
Gene expression profile of 6 hours dexamethasone treated NALM6 preB-ALL cells, polysome profiling, pool 3, polysome bound RNA, engaged in translation, experiment 26.
Reagent: Affymetrix
Experiment: exp26


title: EtOH treated NALM6 cells, exp23, pool 1

description:
Gene expression profile of 6 hours ethanol treated NALM6 preB-ALL cells, polysome profiling, pool 1, non-translated RNA, experiment 23.
Reagent: Affymetrix
Experiment: exp23


title: GC treated NALM6 cells, exp35, pool 2

description:
Gene expression profile of 6 hours dexamethasone treated NALM6 preB-ALL cells, polysome profiling, pool 2, with mRNA potentially engaged in translation initiation, experiment 35.
Reagent: Ambion
Experiment: exp35


title: EtOH treated C7H2 cells, exp10, pool 2

description:
Gene expression profile of 6 hours ethanol treated C7H2 T-ALL cells, polysome profiling, pool 2, with mRNA potentially engaged in translation initiation, experiment 10.
Reagent: Affymetrix
Experiment: exp10

source_name: CCRF-CEM-C7H2 T-ALL cell line, ethanol, pool 2


title: EtOH treated C7H2 cells, exp13, pool 3

description:
Gene expression profile of 6 hours ethanol treated C7H2 T-ALL cells, polysome profiling, pool 3, polysome bound RNA, engaged in translation, experiment 13.
Reagent: Affymetrix
Experiment: exp13

source_name: CCRF-CEM-C7H2 T-ALL cell line, ethanol, pool 3


title: GC treated C7H2 cells, exp10, pool 2

description:
Gene expression profile of 6 hours dexamethasone treated C7H2 T-ALL cells, polysome profiling, pool 2, with mRNA potentially engaged in translation initiation, experiment 10.
Reagent: Affymetrix
Experiment: exp10


title: GC treated NALM6 cells, exp35, pool 1

description:
Gene expression profile of 6 hours dexamethasone treated NALM6 preB-ALL cells, polysome profiling, pool 1, non-translated RNA, experiment 35.
Reagent: Ambion
Experiment: exp35


title: GC treated C7H2 cells, exp13, pool 3

description:
Gene expression profile of 6 hours dexamethasone treated C7H2 T-ALL cells, polysome profiling, pool 3, polysome bound RNA, engaged in translation, experiment 13.
Reagent: Affymetrix
Experiment: exp13

source_name: CCRF-CEM-C7H2 T-ALL cell line, dexamethasone, pool 3


title: EtOH treated C7H2 cells, exp13, pool 1

description:
Gene expression profile of 6 hours ethanol treated C7H2 T-ALL cells, polysome profiling, pool 1, non-translated RNA, experiment 13.
Reagent: Affymetrix
Experiment: exp13

source_name: CCRF-CEM-C7H2 T-ALL cell line, ethanol, pool 1


title: GC treated NALM6 cells, exp23, pool 1

description:
Gene expression profile of 6 hours dexamethasone treated NALM6 preB-ALL cells, polysome profiling, pool 1, non-translated RNA, experiment 23.
Reagent: Affymetrix
Experiment: exp23


title: EtOH treated NALM6 cells, exp35, pool 3

description:
Gene expression profile of 6 hours ethanol treated NALM6 preB-ALL cells, polysome profiling, pool 3, polysome bound RNA, engaged in translation, experiment 35.
Reagent: Ambion
Experiment: exp35


title: EtOH treated C7H2 cells, exp13, pool 2

description:
Gene expression profile of 6 hours ethanol treated C7H2 T-ALL cells, polysome profiling, pool 2, with mRNA potentially engaged in translation initiation, experiment 13.
Reagent: Affymetrix
Experiment: exp13


title: GC treated C7H2 cells, exp13, pool 2

description:
Gene expression profile of 6 hours dexamethasone treated C7H2 T-ALL cells, polysome profiling, pool 2, with mRNA potentially engaged in translation initiation, experiment 13.
Reagent: Affymetrix
Experiment: exp13


title: EtOH treated NALM6 cells, exp35, pool 1

description:
Gene expression profile of 6 hours ethanol treated NALM6 preB-ALL cells, polysome profiling, pool 1, non-translated RNA, experiment 35.
Reagent: Ambion
Experiment: exp35


title: EtOH treated C7H2 cells, exp10, pool 3

description:
Gene expression profile of 6 hours ethanol treated C7H2 T-ALL cells, polysome profiling, pool 3, polysome bound RNA, engaged in translation, experiment 10.
Reagent: Affymetrix
Experiment: exp10


title: EtOH treated C7H2 cells, exp9, pool 2

description:
Gene expression profile of 6 hours ethanol treated C7H2 T-ALL cells, polysome profiling, pool 2, with mRNA potentially engaged in translation initiation, experiment 9.
Reagent: Affymetrix
Experiment: exp9


title: dentate gyrus-granule cell layer-30daysRunning, repAT1

description: Gene expression data from 10- to 11-week-old C57BL/6 male mice

source_name: Outer granule cell layer from a mouse allowed access to running wheel for 30 days


title: donor2_CD34p_d7_TCP

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

hyb_protocol: See Affymetrix protocols

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the Affymetrix Power Tools (APT) Software Package. Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

source_name: Hematopoietic stem and progenitor cells from umbilical cord blood

label_protocol: biotin

growth_protocol: CD34+ cells were isolated from fresh umbilical cord blood after written consent according to the guidelines specifically approved by the Ethic Committee of RWTH Aachen University (Permit Number: EK187/08) using  the CD34 Micro Bead Kit on a MiniMACS system (Miltenyi Biotec GmbH, Bergisch-Gladbach, Germany). Cells were cultured in StemSpan serum free expansion medium (Stem Cell Technologies, Grenoble, France) supplemented with 10 µg/mL heparin (ratiopharm, GmbH, Ulm, Germany), 20 ng/mL thrombopoietin (TPO; PeproTech GmbH, Hamburg, Germany), 10 ng/mL stem cell factor (SCF; PeproTech), 10 ng/mL fibroblast growth factor 1 (FGF1; PeproTech). Culture was either performed on tissue culture plastic (TCP) or on a confluent layer of mesenchymal stromal cells (MSCs; passage 3 to 6). After seven days, CD34+ and CD34- fractions were again separated as described above.

extract_protocol: RNeasy kit (Qiagen)

tag: donor

value: CD34+ fraction

tag: passage

value: 7d on TCP


title: ZebrafishEmbryos_GoM_48-96

city: New York

first: Rui

last: Xiao

state: NY

address: 630 West 168th Street

department: Anesthesiology

institute: Columbia University

description: ZebrafishEmbryos_GoM250_48-96, Saced at 192 hpf

hyb_protocol: Processed according to the manufacturer's protocol in Lousiana State University Health and Science Center-Shreveport

data_processing: The data were analyzed with R/bioconductor platform. Results were standardized with RMA (Robust Multiarray Average) method.

organism: Danio rerio

growth_protocol: Adult zebrafish were bred the night before exposure date and the embryos were transferred into new containers (plastic storage container) with fresh, aerated, 28°C egg medium.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (QIAGEN).

treatment_protocol: ZFE were exposed to 250mg of emulsions that had been “buttered” on the bottom of cups, to which 30 ZFE and 100 ml of zebrafish medium were added. ZFE were exposed from 0-48, 48-96 or 96-192 hr post-fertilization  (hpf). Developmental changes and mortality were assessed at 192 hr for all groups. RNA samples collected from 0-48 and 48-96 hpf-exposed and control groups were hybridized to Affymetrix zebrafish microarrays.

value: ZebrafishEmbryos

value: Gulfport 250mg oil emulsion~48-96hpf

value: 192 hours post fertilization (hpf)


title: donor3_CD34p_d7_TCP


title: ZebrafishEmbyos_GP250~48-96_96

description: ZebrafishEmbyos, Gulfport 250mg oil emulsion~48-96hpf, Sac 96hpf

scan_protocol: Processed according to the manufacturer's protocol in Lousiana State University Health and Science Center-Shreveport

source_name: ZebrafishEmbyos, GP250~48-96, Sac 96hpf

treatment_protocol: ZFE were exposed continuously for 48 hours to 250mg of emulsions that had been “buttered” on the bottom of cups, to which 30 ZFE and 100 ml of zebrafish medium were added. ZFE were exposed from 0-48, 24-72 or 48-96 hr post-fertilization. RNA samples collected from all exposed and control groups were hybridized to Affymetrix zebrafish microarrays. We extracted RNA from all 30 ZFE in each cup for microarray analysis.

value: Zebrafish embyos

value: 96 hours post fertilization


title: ZebrafishEmbryos_GoM_0-48

description: ZebrafishEmbryos_GoM250_0-48, Saced at 192 hpf

label_protocol: Processed according to the manufacturer's protocol in Lousiana State University Health and Science Center-Shreveport

value: Gulfport  250mg oil emulsion~0-48hpf


title: GC treated C7H2 cells, exp10, pool 1

description:
Gene expression profile of 6 hours dexamethasone treated C7H2 T-ALL cells, polysome profiling, pool 1, non-translated RNA, experiment 10.
Reagent: Affymetrix
Experiment: exp10


title: donor3_CD34p_d0

value: freshly isolated


title: donor1_CD34p_d0


title: donor1_CD34m_d7_TCP

value: CD34- fraction


title: donor3_CD34m_d7_TCP


title: donor2_CD34p_d0


title: ZebrafishEmbryos_Control

description: ZebrafishEmbryos_Control, Saced at 192 hpf

value: control


title: donor2_CD34m_d7_TCP


title: donor1_CD34p_d7_TCP


title: GC treated C7H2 cells, exp9, pool 3

description:
Gene expression profile of 6 hours dexamethasone treated C7H2 T-ALL cells, polysome profiling, pool 3, polysome bound RNA, engaged in translation, experiment 9.
Reagent: Affymetrix
Experiment: exp9


title: EtOH treated C7H2 cells, exp9, pool 3

description:
Gene expression profile of 6 hours ethanol treated C7H2 T-ALL cells, polysome profiling, pool 3, polysome bound RNA, engaged in translation, experiment 9.
Reagent: Affymetrix
Experiment: exp9


title: WT_EL4_ABX_18h (29-F-29)

city: Frederick

first: Amiran

last: Dzutsev

state: MD

address: 1050 Boyles Str

department: CIP

institute: NCI, NIH

description: ABX-treated_18h-post oxaliplatin

hyb_protocol: cRNA was  hybridized overnight in a hybridization oven on to MouseGene 1.0 ST array according to manual factory protocol. Posthybridization arrays were stained with florescence on a Genechip Fluidics Station 450 (Affymetrix) according to the respective manufacturers' instructions.

scan_protocol: Arrays were then scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data was analyzed with Partek Genomics Suite 6.6

source_name: mouse EL4 subcutaneous tumor

label_protocol: 300ng of total RNA was amplified into complement-strand RNA (cRNA) using WT expression kit according to the Invitrogen protocol.  Sense DNA was converted via RT reaction and labeled with biotin using Affymetrix labeling kits

extract_protocol: Total RNA was extracted using RNAeasy kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Mice that were either pre-treated for 3 weeks with antibiotics cocktail or left untreated  were injected in the flank subcutaneously with 5 x10^5 EL4  cells. Seven days after the tumor inoculation the mice were treated with intraperitoneal oxaliplatin injection (10 mg per kg body weight). Tumors were collected after 0, 6 and 18 hours post-oxaliplatin injection.

tag: abx treatment

value: ABX

tag: time (post-oxaliplatin)

value: EL4 subcutaneous tumor


title: WT_EL4_ABX_18h (28-F-28)

description: ABX-treated_18h-post oxaliplatin

tag: tissue


title: EtOH treated C7H2 cells, exp9, pool 1

description:
Gene expression profile of 6 hours ethanol treated C7H2 T-ALL cells, polysome profiling, pool 1, non-translated RNA, experiment 9.
Reagent: Affymetrix
Experiment: exp9


title: ZebrafishEmbyos_Control~96_rep2

description: ZebrafishEmbyos, Control, Sac 96hpf

source_name: ZebrafishEmbyos, Control, Sac 96hpf


title: MSC rep2

source_name: Mesenchymal stem cells

value: Umbilical cord


title: WT_EL4_ABX_18h (27-F-27)

description: ABX-treated_18h-post oxaliplatin


title: WT_EL4_ABX_18h (30-F-30)

description: ABX-treated_18h-post oxaliplatin


title: ZebrafishEmbyos_Control~96_rep1

description: ZebrafishEmbyos, Control, Sac 96hpf


title: ZebrafishEmbyos_GP250~0-48_48

description: ZebrafishEmbyos, Gulfport  250mg oil emulsion~0-48hpf, Sac 48hpf

source_name: ZebrafishEmbyos, GP250~0-48, Sac 48hpf

value: 48 hours post fertilization


title: GC treated C7H2 cells, exp10, pool 3

description:
Gene expression profile of 6 hours dexamethasone treated C7H2 T-ALL cells, polysome profiling, pool 3, polysome bound RNA, engaged in translation, experiment 10.
Reagent: Affymetrix
Experiment: exp10

value: dexamethasone


title: ZebrafishEmbyos_GP250~24-72_72

description: ZebrafishEmbyos, Gulfport 250mg oil emulsion~24-72hpf, Sac 72hpf

source_name: ZebrafishEmbyos, GP250~24-72, Sac 72hpf

value: 72 hours post fertilization


title: ZebrafishEmbyos_FM250~24-72_72

description: ZebrafishEmbyos, FortMorgan 250mg oil emulsion~24-72hpf, Sac 72hpf

source_name: ZebrafishEmbyos, FM250~24-72, Sac 72hpf


title: ZebrafishEmbyos_Control~72_rep3

description: ZebrafishEmbyos, Control, Sac 72hpf

source_name: ZebrafishEmbyos, Control, Sac 72hpf


title: ZebrafishEmbyos_Control~72_rep2

description: ZebrafishEmbyos, Control, Sac 72hpf


title: WT_EL4_H2O_18h (21-F-21)

description: H2O-treated_18h-post oxaliplatin


title: ZebrafishEmbyos_Control~72_rep1

description: ZebrafishEmbyos, Control, Sac 72hpf


title: WT_EL4_H2O_18h (23-F-23)

description: H2O-treated_18h-post oxaliplatin


title: ZebrafishEmbyos_PK250~24-72_72

description: ZebrafishEmbyos, PerdidoKey 250mg oil emulsion~24-72hpf, Sac 72hpf

source_name: ZebrafishEmbyos, PK250~24-72, Sac 72hpf


title: WT_EL4_H2O_18h (22-F-22)

description: H2O-treated_18h-post oxaliplatin


title: WT_EL4_ABX_6h (17-F-17)

description: ABX-treated_6h-post oxaliplatin


title: WT_EL4_ABX_6h (20-F-20)

description: ABX-treated_6h-post oxaliplatin


title: WT_EL4_H2O_18h (25-F-25)

description: H2O-treated_18h-post oxaliplatin


title: WT_EL4_H2O_18h (24-F-24)

description: H2O-treated_18h-post oxaliplatin


title: N060

type: protein

city: Boston

first: Joshua

middle: WK

last: Ho

state: MA

address: 41 Avenue Louis Pasteur

department: Department of Medicine

institute: Brigham and Women's Hospital

description: This array survey leukocyte surface CD markers

hyb_protocol: Briefly, duplicate patterns of anti-CD antibody spots were robotically arrayed onto nitrocellulose membrane coated glass slides (Schleicher and Schuell, Keene, NH), and blocked with skim milk (5% in PBS).

scan_protocol: Cells captured on antibody dots were imaged using a DotScan™ slide reader (Medsaic, NSW, Australia). The number of immobilized cells was proportional to the light scattered at each antibody spot. Binding of PBMCs to each antibody dot was monitored by light scatter and averaged between the duplicate spots on each slide.

data_processing: Data were normalized to a range of 0 to 10 with respect to the spot with the maximum binding density on each slide.

molecule: protein

source_name: Peripheral Blood Mononuclear Cells

label_protocol: No labeling

extract_protocol: PBMCs were fractionated from whole blood by Ficoll density gradient centrifugation, washed in PBS, then resuspended in PBS + 1 mM EDTA. A total of 4 × 106 PBMC in 300 mL were applied evenly to the antibody-arrayed nitrocellulose surface for 30 minutes, then unbound cells were gently washed off and the slides fixed in 4% formaldehyde in PBS.

tag: gender

value: M

value: Peripheral Blood Mononuclear Cells


title: ZebrafishEmbyos_Control~48

description: ZebrafishEmbyos, Control, Sac 48hpf

source_name: ZebrafishEmbyos, Control, Sac 48hpf


title: WT_EL4_ABX_6h (18-F-18)

description: ABX-treated_6h-post oxaliplatin


title: N058


title: N069.2


title: WT_EL4_ABX_6h (16-F16)

description: ABX-treated_6h-post oxaliplatin


title: WT_EL4_ABX_18h (26-F-26)

description: ABX-treated_18h-post oxaliplatin


title: WT_EL4_ABX_0h (10-F-10)

description: ABX-treated_0h-post oxaliplatin


title: N059


title: WT_EL4_ABX_6h (19-F-19)

description: ABX-treated_6h-post oxaliplatin


title: WT_EL4_ABX_0h (9-F-09)

description: ABX-treated_0h-post oxaliplatin


title: EtOH treated C7H2 cells, exp10, pool 1

description:
Gene expression profile of 6 hours ethanol treated C7H2 T-ALL cells, polysome profiling, pool 1, non-translated RNA, experiment 10.
Reagent: Affymetrix
Experiment: exp10

value: CCRF-CEM-C7H2 T-ALL

value: ethanol


title: N056


title: WT_EL4_H2O_6h (12-F12)

description: H2O-treated_6h-post oxaliplatin


title: WT_EL4_H2O_6h (11-F-11)

description: H2O-treated_6h-post oxaliplatin


title: WT_EL4_H2O_6h (14-F14)

description: H2O-treated_6h-post oxaliplatin


title: WT_EL4_H2O_6h (15-F-15)

description: H2O-treated_6h-post oxaliplatin


title: WT_EL4_H2O_6h (13-F13)

description: H2O-treated_6h-post oxaliplatin


title: N055


title: GC treated C7H2 cells, exp9, pool 1

description:
Gene expression profile of 6 hours dexamethasone treated C7H2 T-ALL cells, polysome profiling, pool 1, non-translated RNA, experiment 9.
Reagent: Affymetrix
Experiment: exp9

source_name: CCRF-CEM-C7H2 T-ALL cell line, dexamethasone, pool 1


title: N054


title: N053


title: WT_EL4_H2O_0h (5-F-05)

description: H2O-treated_0h-post oxaliplatin


title: WT_EL4_ABX_0h (7-F-07)

description: ABX-treated_0h-post oxaliplatin


title: WT_EL4_ABX_0h (6-F-06)

description: ABX-treated_0h-post oxaliplatin


title: N048


title: N050


title: N049

value: F


title: N052


title: N051


title: N046


title: N047


title: WT_EL4_ABX_0h (8-F-08)

description: ABX-treated_0h-post oxaliplatin


title: N045


title: WT_EL4_H2O_0h (1-F-01)

description: H2O-treated_0h-post oxaliplatin


title: WT_EL4_H2O_0h (4-F-04)

description: H2O-treated_0h-post oxaliplatin


title: BALB/c intestine FD MTHFR+/- biological rep2

city: Montreal

first: Daniel

last: Leclerc

state: Quebec

address: 4060 Ste-Catherine West

department: Medical Genetics, Room 242

country: Canada

institute: Montreal Children's Hospital

description: Gene expression data from dissected duodenum tissue

hyb_protocol: Following fragmentation and labeling,  1.856ug of ssDNA were hybridized for 17 hrs at 45C on GeneChip® Mouse Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with FlexArray using Affymetrix default analysis settings and APT as normalization method.

source_name: Intestine tissues from BALB/c mice with mild MTHFR deficiency fed with low folate diet

label_protocol: Labeled and fragmented ssDNAs were prepared according to the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay from 100ng of Total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay User guide P/N 701880 Rev. 5)

growth_protocol: After weaning, BALB/c Mthfr +/- mice and C57Bl/6 Mthfr +/- mice were fed with a control diet (CD, 2mg folate/kg) and a low folate diet (FD, 0.3mg folate/kg) for 1 year. Both diets contain succinylsulfanthiozole (1%) to prevent folate synthesis by intestine microbial biota.

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

treatment_protocol: Mice were sacrificed and intestines were removed to examine for tumour incidence under dissecting microscope. Normal intestines were frozen at -80 degree.

tag: strain

value: BALB/c

value: duodenum

tag: genotype

value: MTHFR+/-

value: folate deficient diet

value: female


title: WT_EL4_H2O_0h (3-F-03)

description: H2O-treated_0h-post oxaliplatin


title: BALB/c intestine FD MTHFR+/- biological rep4

tag: treatment


title: N044

tag: cell type


title: BALB/c intestine CD MTHFR+/+ biological rep4

source_name: Intestine tissues from wildtype BALB/c mice fed with control diet

value: MTHFR+/+

value: control diet


title: BALB/c intestine FD MTHFR+/- biological rep1


title: N043

tag: age


title: N041


title: N042


title: WT_EL4_H2O_0h (2-F-02)

description: H2O-treated_0h-post oxaliplatin

value: EL4 subcutaneous tumor


title: BALB/c intestine FD MTHFR+/- biological rep3


title: N039


title: N040


title: drosophilasmaug1_cycloheximidefraction1_rep2

city: Toronto

first: Jason

middle: Gardiner

last: Dumelie

state: Ontario

address: 1 King's College Circle

department: Biochemistry

institute: University of Toronto

description: This sample is RNA from fraction 1 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying and in which cycloheximide was added rather than puromycin as a control. It is the second of two biological replicates.

hyb_protocol: RNA was hybridized using the protocol described in the NimbleGen Array User’s Guide (Gene Expression Arrays, version 5.0)

scan_protocol: Microarrays were scanned using Genepix Pro software on a Molecular Devices GenePix 4000B or 4300A scanner and quantified using Nimblescan.

data_processing: Polysome microarrays were normalized using the Robust Multi-array Average (RMA) quantile method. We further normalized the data using Arabidopsis spike-in RNAs (see extract protocol).  The hybridization signals from the spike-in RNAs were utilized by appllying a linear transformation to each sample with the parameters, a and b, determined by fitting the linear function Y = aX+b using the spike-in signal, where X is the expression level of the spike-in RNAs in a specific sample, and Y is the mean expression level of the spike-in RNAs across all the samples. The genes significantly expressed in wild-type or smaug mutant embryos in each of pools 1, 2, 3 and 4 were separately determined using one class unpaired analysis in SAM (FDR<5%). We defined the genes significantly expressed in the wild-type and smaug mutant embryos as the union of the significantly expressed genes from the four fractions derived from that genotype. We then compared these two lists and defined their intersection as the list of genes significantly expressed in both wild-type and smaug mutant embryos, and restricted all the following analysis to the genes in this list.

organism: Drosophila melanogaster

source_name: smaug mutant Drosophila melanogastor embryos collected 0-2 hours after egg laying

label_protocol: RNA samples from polysome experiments were used to generate double stranded cDNA following the protocol described in the NimbleGen Array Users Guide (Gene Expression Arrays, version 5.0) using a primer mixture of random hexamer primers and anchored-oligo-dT primers and with the following change: all reagents were added at half of the volume and amount indicated in the user guide. Either Cy3 or Cy5-tagged random nonamers (as indicated for each sample) were used to label cDNAs using the Roche NimbleGen protocol.

growth_protocol: Embryos and flies were raised at 25 degrees

extract_protocol:
Embryos laid by wild-type or smaug1 homozygous mothers were collected 0-2 hours post-egglaying, dechorionated with 100% bleach and lysed in an equal volume of polysome lysis buffer (7.5 mM MgCl2, 500 mM NaCl, 25mM Tris pH 7.5, 2 mg/mL heparin, 0.5 mg/mL cycloheximide, 1 mM DTT, 50 U/mL RNasin, 1mM AEBSF, 2 ug/mL leupeptide, 2 mM benzamidine, 2 ug/mL pepstatin A). Lysed samples were diluted 1 in 12.5 in polysome lysis buffer and 30% triton was added to a final concentration of 1% and then spun at 6000xg for 10 minutes and the resulting supernatant was diluted in polysome lysis buffer supplemented with 1% Triton to an A260 of 12.5.
A 12 mL 15% to 45% linear sucrose gradient in 7.5 mM MgCl2, 500 mM NaCl, 50 mM Tris pH 7.5 was created using a BioComp Model 117 Gradient Mate gradient maker using a rotation angle of 80.5 degrees and a rotation speed of 18 rpm for 1 minute and 58 seconds. After chilling the polysome gradient on ice, 400 uL of diluted embryo extract was loaded onto the top of the gradient which was then spun at 36,000 rpm in a SW 41 Ti rotor for 2.5 hours. The gradients were then separated into four pools  (pool 1 contained the top 4 mL, pool 2 contained the next 2 mL, pool 3 contained the next 3 mL and pool 4 contained the last 3 mL and the pellet). In vitro transcribed Arabidopsis spike-in RNAs was then added to each fraction to be used in subsequent data normalization. 20% SDS, 0.5 M EDTA and 20 mg/mL proteinase K were added to each fraction to final concentrations of 0.8%, 0.01M and 0.128mg/mL, respectively and then incubated for 30 minutes at room temperature. Glycogen was then added to a final concentration of 80 ug/mL and samples were ethanol precipitated overnight and the resulting pellet was washed with 75% ethanol and resuspended in phenol saturated water. Following two phenol-chloroform extractions samples were precipitated by the addition of 7.5M LiCl to a final concentration of 1.5M and an overnight incubation at 4oC. The resulting pellet was washed with 75% ethanol, resuspended in water and ethanol precipitated in the presence of 80 ug/mL of glycogen and 0.3 M sodium acetate. The precipitate was then washed with 75% ethanol and resuspended in water.
Experiments that investigated changes in mRNA mobility due to puromycin included those samples starting in P (indicating addition of puromycin) and C (indicating cycloheximide addition negative control). In these experiments, smaug1 embryos were lysed in puromycin lysis buffer (50 mM Tris pH 7.5,2mM MgCl2, 500 mM KCl, 100uM GTP, 1mM DTT, 50U/ml RNasin, 1mM AEBSF, 2ug/mL leupeptide, 2mM benzamidine, 2ug/mL pepstatin A). The lysed samples were split in half and cycloheximide was added to one sample to a final concentration of 0.5 mg/mL and puromycin was added to the other sample to a final concentration of 2mM. Samples were left on ice for 20 minutes and then incubated at 30 degrees Celsius for 10 minutes. Both samples were then diluted 1 in 12.5 with polysome lysis buffer supplemented with either puromycin or cycloheximide and 30% triton was added to a final concentration of 1%. The samples were then spun at 6000xg for 10 minutes and the supernatant was diluted with polysome lysis buffer supplemented with either puromycin or cycloheximide to give an A260 of 12.5 and these diluted samples were then fractionated and microarrays were performed as described above. Each experiment was performed in duplicate.

tag: developmental stage

value: Embryos collected 0-2 hours after egg laying

tag: molecule

value: RNA in cycloheximide treated polysome gradient fraction 1


title: drosophilasmaug1_puromycinfraction4_rep2

description: This sample is RNA from fraction 4 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying and in which puromycin was added to cause the dissociation of ribosomes. It is the second of two biological replicates.

value: RNA in puromycin treated polysome gradient fraction 4


title: BALB/c intestine CD MTHFR+/+ biological rep2


title: BALB/c intestine CD MTHFR+/+ biological rep1


title: drosophilasmaug1_cycloheximidefraction3_rep2

description: This sample is RNA from fraction 3 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying and in which cycloheximide was added rather than puromycin as a control. It is the second of two biological replicates.

value: RNA in cycloheximide treated polysome gradient fraction 3


title: drosophilasmaug1_cycloheximidefraction2_rep2

description: This sample is RNA from fraction 2 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying and in which cycloheximide was added rather than puromycin as a control. It is the second of two biological replicates.

value: RNA in cycloheximide treated polysome gradient fraction 2


title: BALB/c intestine CD MTHFR+/+ biological rep3


title: Control 23 baseline premalignancy

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

description:
ch1 raw data file: MAL_251495013276_S01_CGH_107_Sep09_1_3.txt
ch2 raw data file: MAL_251495013276_S01_CGH_107_Sep09_1_3.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent G2505B micro-array scanner. Image data acquisition was performed in feature extraction software v9.5.1 (Agilent Technologies) using the Agilent CGH_107_Sep09 protocol with default settings

data_processing:
Median Signal intensity minus median Background intensity; excluding negative values. To overcome potential wave bias due to differences in GC-content of the different chromosomal regions, a smoothing algorithm was applied on our dataset as described by van de Wiel et al, Bioinformatics 2009; 25(9):1099-1104. We use the sex difference as an internal quality control measure to check for experiment errors.
Dual channel hybs were analysed as single channel and compared as listed above.  All raw data file designations are provided in the description field, and the files are available on the Series record (to avoid duplication).

molecule: genomic DNA

source_name: Bronchial tissue, AFB-visualized

label_protocol: DNA labeling protocol according to Enzo Life Sciences

extract_protocol: DNA isolation protocol as described by van Zeeburg et al, Cancer Res 2005; 65(4):1271-1276

value: bronchial

value: male

tag: case or control

value: control

source_name: blood, pooled DNA from 100 healthy individuals

tag: reference


title: drosophilasmaug1_cycloheximidefraction4_rep2

description: This sample is RNA from fraction 4 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying and in which cycloheximide was added rather than puromycin as a control. It is the second of two biological replicates.

value: RNA in cycloheximide treated polysome gradient fraction 4


title: N038

value: F

value: Peripheral Blood Mononuclear Cells


title: N037


title: N036


title: drosophilasmaug1_puromycinfraction3_rep2

description: This sample is RNA from fraction 3 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying and in which puromycin was added to cause the dissociation of ribosomes. It is the second of two biological replicates.

value: RNA in puromycin treated polysome gradient fraction 3


title: drosophilasmaug1_puromycinfraction2_rep2

description: This sample is RNA from fraction 2 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying and in which puromycin was added to cause the dissociation of ribosomes. It is the second of two biological replicates.

value: RNA in puromycin treated polysome gradient fraction 2


title: N034


title: drosophilasmaug1_puromycinfraction1_rep2

description: This sample is RNA from fraction 1 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying and in which puromycin was added to cause the dissociation of ribosomes. It is the second of two biological replicates.

value: RNA in puromycin treated polysome gradient fraction 1


title: N035


title: Control 24 baseline premalignancy

description:
ch1 raw data file: 11668_S01_CGH_107_Sep09_1_4.txt
ch2 raw data file: 11668_S01_CGH_107_Sep09_1_4.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

value: female


title: drosophilasmaug1_cycloheximidefraction1_rep1

description: This sample is RNA from fraction 1 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying and in which cycloheximide was added rather than puromycin as a control. It is the first of two biological replicates.


title: drosophilasmaug1_puromycinfraction3_rep1

description: This sample is RNA from fraction 3 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying and in which puromycin was added to cause the dissociation of ribosomes. It is the first of two biological replicates.


title: drosophilasmaug1_puromycinfraction4_rep1

description: This sample is RNA from fraction 4 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying and in which puromycin was added to cause the dissociation of ribosomes. It is the first of two biological replicates.


title: drosophilasmaug1_cycloheximidefraction3_rep1

description: This sample is RNA from fraction 3 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying and in which cycloheximide was added rather than puromycin as a control. It is the first of two biological replicates.

extract_protocol:
Embryos laid by wild-type or smaug1 homozygous mothers were collected 0-2 hours post-egglaying, dechorionated with 100% bleach and lysed in an equal volume of polysome lysis buffer (7.5 mM MgCl2, 500 mM NaCl, 25mM Tris pH 7.5, 2 mg/mL heparin, 0.5 mg/mL cycloheximide, 1 mM DTT, 50 U/mL RNasin, 1mM AEBSF, 2 ug/mL leupeptide, 2 mM benzamidine, 2 ug/mL pepstatin A). Lysed samples were diluted 1 in 12.5 in polysome lysis buffer and 30% triton was added to a final concentration of 1% and then spun at 6000xg for 10 minutes and the resulting supernatant was diluted in polysome lysis buffer supplemented with 1% Triton to an A260 of 12.5.
A 12 mL 15% to 45% linear sucrose gradient in 7.5 mM MgCl2, 500 mM NaCl, 50 mM Tris pH 7.5 was created using a BioComp Model 117 Gradient Mate gradient maker using a rotation angle of 80.5 degrees and a rotation speed of 18 rpm for 1 minute and 58 seconds. After chilling the polysome gradient on ice, 400 uL of diluted embryo extract was loaded onto the top of the gradient which was then spun at 36,000 rpm in a SW 41 Ti rotor for 2.5 hours. The gradients were then separated into four pools  (pool 1 contained the top 4 mL, pool 2 contained the next 2 mL, pool 3 contained the next 3 mL and pool 4 contained the last 3 mL and the pellet). In vitro transcribed Arabidopsis spike-in RNAs was then added to each fraction to be used in subsequent data normalization. 20% SDS, 0.5 M EDTA and 20 mg/mL proteinase K were added to each fraction to final concentrations of 0.8%, 0.01M and 0.128mg/mL, respectively and then incubated for 30 minutes at room temperature. Glycogen was then added to a final concentration of 80 ug/mL and samples were ethanol precipitated overnight and the resulting pellet was washed with 75% ethanol and resuspended in phenol saturated water. Following two phenol-chloroform extractions samples were precipitated by the addition of 7.5M LiCl to a final concentration of 1.5M and an overnight incubation at 4oC. The resulting pellet was washed with 75% ethanol, resuspended in water and ethanol precipitated in the presence of 80 ug/mL of glycogen and 0.3 M sodium acetate. The precipitate was then washed with 75% ethanol and resuspended in water.!Sample_extract_protocol_ch1 = Experiments that investigated changes in mRNA mobility due to puromycin included those samples starting in P (indicating addition of puromycin) and C (indicating cycloheximide addition negative control). In these experiments, smaug1 embryos were lysed in puromycin lysis buffer (50 mM Tris pH 7.5,2mM MgCl2, 500 mM KCl, 100uM GTP, 1mM DTT, 50U/ml RNasin, 1mM AEBSF, 2ug/mL leupeptide, 2mM benzamidine, 2ug/mL pepstatin A). The lysed samples were split in half and cycloheximide was added to one sample to a final concentration of 0.5 mg/mL and puromycin was added to the other sample to a final concentration of 2mM. Samples were left on ice for 20 minutes and then incubated at 30 degrees Celsius for 10 minutes. Both samples were then diluted 1 in 12.5 with polysome lysis buffer supplemented with either puromycin or cycloheximide and 30% triton was added to a final concentration of 1%. The samples were then spun at 6000xg for 10 minutes and the supernatant was diluted with polysome lysis buffer supplemented with either puromycin or cycloheximide to give an A260 of 12.5 and these diluted samples were then fractionated and microarrays were performed as described above. Each experiment was performed in duplicate.


title: drosophilasmaug1_cycloheximidefraction2_rep1

description: This sample is RNA from fraction 2 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying and in which cycloheximide was added rather than puromycin as a control. It is the first of two biological replicates.


title: Control 22 baseline premalignancy

description:
ch1 raw data file: MACF_251495027225_S01_CGH_107_Sep09_1_2.txt
ch2 raw data file: MACF_251495027225_S01_CGH_107_Sep09_1_4.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: Control 21 baseline premalignancy

description:
ch1 raw data file: US22502676_251495030514_S01_CGH_107_Sep09_1_4.txt
ch2 raw data file: US22502676_251495030514_S01_CGH_107_Sep09_1_3.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: N033

description: This array survey leukocyte surface CD markers


title: drosophilasmaug1_cycloheximidefraction4_rep1

description: This sample is RNA from fraction 4 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying and in which cycloheximide was added rather than puromycin as a control. It is the first of two biological replicates.


title: drosophilasmaug1_puromycinfraction1_rep1

description: This sample is RNA from fraction 1 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying and in which puromycin was added to cause the dissociation of ribosomes. It is the first of two biological replicates.


title: drosophilasmaug1_puromycinfraction2_rep1

description: This sample is RNA from fraction 2 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying and in which puromycin was added to cause the dissociation of ribosomes. It is the first of two biological replicates.


title: N028

value: M


title: Control 17 baseline premalignancy

description:
ch1 raw data file: MACF_251495027273_S01_CGH_107_Sep09_1_4.txt
ch2 raw data file: 11618_S01_CGH_107_Sep09_1_4.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: Control 18 baseline premalignancy

description:
ch1 raw data file: US22502676_251495030514_S01_CGH_107_Sep09_1_3.txt
ch2 raw data file: US22502676_251495030514_S01_CGH_107_Sep09_1_3.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: Control 20 baseline premalignancy

description:
ch1 raw data file: US22502676_251495030514_S01_CGH_107_Sep09_1_2.txt
ch2 raw data file: US22502676_251495030514_S01_CGH_107_Sep09_1_3.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: ChIP-chip with CHD8 Ab. replicate 2

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

institute: CABIMER

description: ChIP-on-Chip CHD8. Rep. 2

hyb_protocol: Hybridization and Washes were performed as described in the "Agilent Microarray Analysis of Methylated DNA Immunoprecipitation" protocol. Agilent document G4170-90012 Revision A, Version 1.1 of May 2010.  Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 5 µg (per slide). Hibridization at 20rpm for 40 hours. Volume: 490 µL. Temperature (ºC): 65. Microarray design: Agilent's Human custom G3 1M Microarray for analysis of methylated DNA fractions, Agilent Microarray Design ID 027505_D_F_20100602

scan_protocol: Scanned on an G2565C DNA microarray scanner (Agilent).

data_processing: Images were quantified using Agilent Feature Extraction Software (ver. 10.7).

label: Alexa Fluor5

label_protocol: Amount of nucleic acid labeled: 1.5 µg for each slide. Labeled with "BioPrime Total FFPE Genomic Labeling System" by following manufacturer (Invitrogen) instructions. Invitrogen manual for kit 100005223 Ver. A, 23 July 2009. Labeled samples are purified with silica-based PureLink spin columns (Invitrogen).

growth_protocol: Cells  were maintained in Dulbecco's modified Eagle's medium (DMEM). Medium was supplemented with 7% fetal bovine serum , 100 units/ml penicillin and 100 µg/ml streptomycin, and cells were cultivated in a 37°C incubator with 5% CO2.

extract_protocol: Standard protocols for chromatin immunoprecipitation were used. The following antibodies were used: anti-CHD8 (A301-224A, Bethyl Laboratories; Lot number A301-224-1), anti-H3K4me3 (ab8580, Abcam; Lot number 1054726) and anti-H3K4me2 (ab32356, Abcam; Lot number GR26908-5).

treatment_protocol: No specific treatment was applied.

tag: cell line

tag: antibody

tag: disease state

value: cervix carcinoma


title: drosophila_wildtypefraction4_rep1

description: This sample is RNA from fraction 4 of a polysome gradient using RNA extracted from Wild Type embryos collected 0-2 hours after egg-laying. It is the first of three biological replicates.

source_name: Wild Type Drosophila melanogastor embryos collected 0-2 hours after egg laying

value: W1118 Wild Type

value: Embryos collected 0-2 hours after egg laying

value: RNA in polysome gradient fraction 4


title: drosophila_wildtypefraction4_rep2

description: This sample is RNA from fraction 4 of a polysome gradient using RNA extracted from Wild Type embryos collected 0-2 hours after egg-laying. It is the second of three biological replicates.


title: drosophila_wildtypefraction4_rep3

description: This sample is RNA from fraction 4 of a polysome gradient using RNA extracted from Wild Type embryos collected 0-2 hours after egg-laying. It is the third of three biological replicates.


title: N027


title: N026.1


title: N025


title: ChIP-chip with 3mK4H3 Ab

description: ChIP-on-Chip 3mK4H3

value: anti-H3K4me3 (ab8580, Abcam; Lot number 1054726)


title: Control 19 baseline premalignancy

value: Pooled DNA from the blood of 100 healthy individuals


title: drosophila_wildtypefraction3_rep3

description: This sample is RNA from fraction 3 of a polysome gradient using RNA extracted from Wild Type embryos collected 0-2 hours after egg-laying. It is the third of three biological replicates.

value: RNA in polysome gradient fraction 3


title: ChIP-chip with 2mK4H3 Ab

description: ChIP-on-Chip 2mK4H3

value: anti-H3K4me2 (ab32356, Abcam; Lot number GR26908-5)


title: Control 15 baseline premalignancy

description:
ch1 raw data file: MACF_251495027224_S01_CGH_107_Sep09_1_2.txt
ch2 raw data file: MACF_251495027224_S01_CGH_107_Sep09_1_4.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

value: bronchial

value: male

value: control


title: Control 16 baseline premalignancy

description:
ch1 raw data file: MACF_251495027273_S01_CGH_107_Sep09_1_1.txt
ch2 raw data file: 11618_S01_CGH_107_Sep09_1_4.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: N024

value: Peripheral Blood Mononuclear Cells


title: drosophila_wildtypefraction2_rep1

description: This sample is RNA from fraction 2 of a polysome gradient using RNA extracted from Wild Type embryos collected 0-2 hours after egg-laying. It is the first of three biological replicates.

value: RNA in polysome gradient fraction 2


title: drosophila_wildtypefraction3_rep2

description: This sample is RNA from fraction 3 of a polysome gradient using RNA extracted from Wild Type embryos collected 0-2 hours after egg-laying. It is the second of three biological replicates.


title: drosophila_wildtypefraction3_rep1

description: This sample is RNA from fraction 3 of a polysome gradient using RNA extracted from Wild Type embryos collected 0-2 hours after egg-laying. It is the first of three biological replicates.


title: drosophila_wildtypefraction2_rep3

description: This sample is RNA from fraction 2 of a polysome gradient using RNA extracted from Wild Type embryos collected 0-2 hours after egg-laying. It is the third of three biological replicates.


title: ChIP-chip with CHD8 Ab. replicate 1

description: ChIP-on-Chip CHD8. Rep. 1

value: anti-CHD8 (A301-224A, Bethyl Laboratories; Lot number A301-224-1)


title: drosophila_wildtypefraction2_rep2

description: This sample is RNA from fraction 2 of a polysome gradient using RNA extracted from Wild Type embryos collected 0-2 hours after egg-laying. It is the second of three biological replicates.


title: Control 13 baseline premalignancy

description:
ch1 raw data file: US22502676_251495030514_S01_CGH_107_Sep09_1_1.txt
ch2 raw data file: US22502676_251495030514_S01_CGH_107_Sep09_1_3.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: drosophila_wildtypefraction1_rep2

description: This sample is RNA from fraction 1 of a polysome gradient using RNA extracted from Wild Type embryos collected 0-2 hours after egg-laying. It is the second of three biological replicates.

value: RNA in polysome gradient fraction 1


title: drosophila_wildtypefraction1_rep1

description: This sample is RNA from fraction 1 of a polysome gradient using RNA extracted from Wild Type embryos collected 0-2 hours after egg-laying. It is the first of three biological replicates.


title: drosophila_wildtypefraction1_rep3

description: This sample is RNA from fraction 1 of a polysome gradient using RNA extracted from Wild Type embryos collected 0-2 hours after egg-laying. It is the third of three biological replicates.


title: Control 14 baseline premalignancy

description:
ch1 raw data file: MACF_251495027225_S01_CGH_107_Sep09_1_3.txt
ch2 raw data file: MACF_251495027224_S01_CGH_107_Sep09_1_4.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

value: female


title: drosophila_smgfraction4_rep1

description: This sample is RNA from fraction 4 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying. It is the first of three biological replicates.


title: N022

description: This array survey leukocyte surface CD markers

value: F


title: drosophila_smgfraction4_rep2

description: This sample is RNA from fraction 4 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying. It is the second of three biological replicates.


title: N021


title: drosophila_smgfraction4_rep3

description: This sample is RNA from fraction 4 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying. It is the third of three biological replicates.


title: drosophila_smgfraction3_rep3

description: This sample is RNA from fraction 3 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying. It is the third of three biological replicates.


title: N020

value: M


title: drosophila_smgfraction3_rep2

description: This sample is RNA from fraction 3 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying. It is the second of three biological replicates.


title: Control 12 baseline premalignancy

description:
ch1 raw data file: 11667_S01_CGH_107_Sep09_1_1.txt
ch2 raw data file: 11667_S01_CGH_107_Sep09_1_1.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: drosophila_smgfraction2_rep3

description: This sample is RNA from fraction 2 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying. It is the third of three biological replicates.


title: N019


title: N018


title: drosophila_smgfraction1_rep3

description: This sample is RNA from fraction 1 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying. It is the third of three biological replicates.


title: Control 09 baseline premalignancy

description:
ch1 raw data file: MACF_251495027271_S01_CGH_107_Sep09_1_4.txt
ch2 raw data file: MACF_251495027271_S01_CGH_107_Sep09_1_2.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: drosophila_smgfraction1_rep2

description: This sample is RNA from fraction 1 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying. It is the second of three biological replicates.


title: N017


title: drosophila_smgfraction3_rep1

description: This sample is RNA from fraction 3 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying. It is the first of three biological replicates.


title: drosophila_smgfraction2_rep1

description: This sample is RNA from fraction 2 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying. It is the first of three biological replicates.


title: N016


title: drosophila_smgfraction2_rep2

description: This sample is RNA from fraction 2 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying. It is the second of three biological replicates.


title: Control 10 baseline premalignancy

description:
ch1 raw data file: MACF_251495027226_S01_CGH_107_Sep09_1_2.txt
ch2 raw data file: MACF_251495027271_S01_CGH_107_Sep09_1_2.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: Control 07 baseline premalignancy

description:
ch1 raw data file: MACF_251495027271_S01_CGH_107_Sep09_1_3.txt
ch2 raw data file: MACF_251495027271_S01_CGH_107_Sep09_1_2.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: Control 06 baseline premalignancy

description:
ch1 raw data file: MACF_251495027226_S01_CGH_107_Sep09_1_3.txt
ch2 raw data file: MACF_251495027271_S01_CGH_107_Sep09_1_2.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: Control 05 baseline premalignancy

description:
ch1 raw data file: MACF_251495027271_S01_CGH_107_Sep09_1_1.txt
ch2 raw data file: MACF_251495027271_S01_CGH_107_Sep09_1_2.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: N015

description: This array survey leukocyte surface CD markers


title: drosophila_smgfraction1_rep1

description: This sample is RNA from fraction 1 of a polysome gradient using RNA extracted from smg1 embryos collected 0-2 hours after egg-laying. It is the first of three biological replicates.


title: Control 11 baseline premalignancy

description:
ch1 raw data file: MACF_251495027225_S01_CGH_107_Sep09_1_1.txt
ch2 raw data file: MACF_251495027225_S01_CGH_107_Sep09_1_4.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: Jurkat_cancer cell line

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

hyb_protocol: Agilent standard protocol

scan_protocol: Agilent standard protocol

data_processing: The data were analyzed using the Gene Spring GX 11.5.1 software program (Agilent Technologies).The data processing was performed as follows; (i) Threshold raw signals were set to 1.0, (ii) Log base 2 transformation was performed, (iii) 90th percentile normalization was chosen as the normalized algorithm.

source_name: Human Acute T cell Leukemia

label_protocol: Agilent standard protocol

extract_protocol: Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacturer's instruction.

value: cancer cell line


title: CB-2_soma

source_name: Cord Blood cells

value: soma


title: CB-1_soma


title: HepG2_cancer cell line

source_name: Human hepatocellular Carcinoma


title: PBMN-2_soma

source_name: Peripheral Blood Mononuclear cells


title: MCF7_cancer cell line

source_name: Human Breast Adenocarcinoma


title: Control 03 baseline premalignancy

description:
ch1 raw data file: MACF_251495027248_S01_CGH_107_Sep09_1_2.txt
ch2 raw data file: 251495027247_251495027247_S01_CGH_107_Sep09_1_3.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: DP74_soma

source_name: Dental Pulp cells


title: PBMN-1_soma


title: 2102EP4D3_hEC

source_name: hEC

value: hEC


title: Control 08 baseline premalignancy

description:
ch1 raw data file: MAL_251495011797_S01_CGH_107_Sep09_1_3.txt
ch2 raw data file: MAL_251495011797_S01_CGH_107_Sep09_1_3.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: Control 02 baseline premalignancy

description:
ch1 raw data file: MACF_251495027248_S01_CGH_107_Sep09_1_3.txt
ch2 raw data file: 251495027247_251495027247_S01_CGH_107_Sep09_1_3.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: N013


title: 711C1(p14)_undiff_hiPS

source_name: undifferentiated hiPS

tag: method

value: Sendai virus

tag: cell origin

value: CB CD34+  (donor a)

tag: transduction

value: OSKM


title: NTERA2 cloneD1_hEC


title: 711A6(p13)_undiff_hiPS


title: Control 04 baseline premalignancy

description:
ch1 raw data file: MACF_251495027226_S01_CGH_107_Sep09_1_1.txt
ch2 raw data file: MACF_251495027271_S01_CGH_107_Sep09_1_2.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

tag: tissue


title: HDF-1388_soma

source_name: Human Dermal Fibroblast cells


title: 711A1(p12)_undiff_hiPS


title: 665A1(p17)_undiff_hiPS

value: CB CD34+  (donor b)


title: 703B1(p17)_undiff_hiPS

value: PBMN abT (donor x)


title: N007

source_name: Peripheral Blood Mononuclear Cells

tag: gender


title: N008


title: Control 01 baseline premalignancy

description:
ch1 raw data file: MACF_251495027273_S01_CGH_107_Sep09_1_2.txt
ch2 raw data file: MACF_251495027273_S01_CGH_107_Sep09_1_4.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

value: bronchial

value: male


title: Case 12 baseline premalignancy

description:
ch1 raw data file: 11618_S01_CGH_107_Sep09_1_2.txt
ch2 raw data file: 11618_S01_CGH_107_Sep09_1_4.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

value: case


title: 622G1(p19)_undiff_hiPS

value: PBMN abT (donor y)


title: 622E1(p18)_undiff_hiPS


title: N006

value: Peripheral Blood Mononuclear Cells


title: N011


title: 610B1(p14)_undiff_hiPS

value: Episomal plasmid


title: N005


title: 665A7(p18)_undiff_hiPS


title: 610A2(P14)_undiff_hiPS


title: Case 10 baseline premalignancy

description:
ch1 raw data file: MACF_251495027273_S01_CGH_107_Sep09_1_3.txt
ch2 raw data file: MACF_251495027273_S01_CGH_107_Sep09_1_4.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

value: female


title: 606B1(P13)_undiff_hiPS


title: Case 08 baseline premalignancy

value: Pooled DNA from the blood of 100 healthy individuals


title: Case 09 baseline premalignancy


title: 703A1(p17)_undiff_hiPS


title: 606A1(p14)_undiff_hiPS


title: N003

value: M


title: N014


title: Case 07 baseline premalignancy

description:
ch1 raw data file: MACF_251495027272_S01_CGH_107_Sep09_1_3.txt
ch2 raw data file: MACF_251495027272_S01_CGH_107_Sep09_1_3.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: Case 06 baseline premalignancy

description:
ch1 raw data file: MACF_251495027272_S01_CGH_107_Sep09_1_2.txt
ch2 raw data file: 11618_S01_CGH_107_Sep09_1_4.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: 604A3(P14)_undiff_hiPS


title: 604B1(p13)_undiff_hiPS


title: 604A1(P14)_undiff_hiPS


title: N002


title: 585B1(p16)_undiff_hiPS


title: N001

value: F


title: Case 11 baseline premalignancy


title: 454E2(p46)_undiff_hiPS


title: 451F3(p41)_undiff_hiPS


title: 585A1(p16)_undiff_hiPS


title: a066


title: 404C2(p44)_undiff_hiPS

value: Fibro (HDF1388)


title: 414C2(p55)_undiff_hiPS


title: Case 05 baseline premalignancy

description:
ch1 raw data file: MACF_251495027248_S01_CGH_107_Sep09_1_2.txt
ch2 raw data file: MACF_251495027248_S01_CGH_107_Sep09_1_4.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: 409B2(p52)_undiff_hiPS


title: a065


title: a067


title: a068


title: Case 04 baseline premalignancy

description:
ch1 raw data file: MACF_251495027272_S01_CGH_107_Sep09_1_4.txt
ch2 raw data file: MACF_251495027272_S01_CGH_107_Sep09_1_3.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: N023


title: Liver Transgenic S2 WD Hybrid 5 HE013061T2D80

city: West Vancouver

first: Dionne

last: Sakhrani

state: BC

address: 4160 Marine Drive

institute: Fisheries and Oceans Canada

hyb_protocol: Hybridization followed the procedures at http://web.uvic.ca/grasp/microarray (Genisphere Array 50 Protocol).

scan_protocol: Fluorescence images were collected at 10μm resolution using a ScanArray microarray scanner (Perkin Elmer). The same laser power (95%) and photomultiplier tube (PMT) settings were used for all slides (Cy3 PMT 75, Cy5 PMT 68).  Fluorescence intensity data were extracted from TIF images using QuantArray version 3.0 software (Perkin Elmer).

data_processing: Data transformation (setting background corrected values <0.01 to 0.01 and Lowess normalization) and analysis were performed in GeneSpring GX 7.3.1 software (Agilent Technologies).  Spots with expression intensity below the 20th percentile were excluded and only entities where at least 100 percent of the samples in any 1 out of the 6 genotypes that have values above the cutoff were used in the analysis.

organism: Oncorhynchus mykiss

source_name: Liver Wild pool

label_protocol: Reverse transcriptase of 20ug of total RNA was performed following the SuperScript II Reverse Transcriptase protocol (Invitrogen).  Indirect labeling was performed on individual cDNA following the Array 50 kit protocol (Genisphere).

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

tag: strain

value: Wild pool

source_name: Liver Transgenic S2 WD Hybrid Individual 5

value: Growth Hormone Transgenic Strain 2 in Wild-Domestic hybrid


title: TKCB7-2(p42)_undiff_hiPS

value: Retrovirus


title: 246G1(p15)_undiff_hiPS

value: BJ

value: OSKM


title: TKCBV4-2(p82)_undiff_hiPS


title: a064


title: a063


title: 225C7(p14)_undiff_hiPS

value: Fibro (HDF1419)


title: DP31-4f1(p13)_undiff_hiPS


title: Liver Transgenic S2 WD Hybrid 4 HE013055T2D79

source_name: Liver Transgenic S2 WD Hybrid Individual 4


title: Liver Transgenic S2 WD Hybrid 3 HE013048T2D64

source_name: Liver Transgenic S2 WD Hybrid Individual 3


title: Case 02 baseline premalignancy

description:
ch1 raw data file: MACF_251495027224_S01_CGH_107_Sep09_1_1.txt
ch2 raw data file: MACF_251495027224_S01_CGH_107_Sep09_1_4.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

source_name: Bronchial tissue, AFB-visualized

value: bronchial


title: Case 03 baseline premalignancy

description:
ch1 raw data file: MACF_251495027273_S01_CGH_107_Sep09_1_1.txt
ch2 raw data file: MACF_251495027273_S01_CGH_107_Sep09_1_4.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

value: male

source_name: blood, pooled DNA from 100 healthy individuals


title: Liver Transgenic S2 WD Hybrid 2 HE013051T2D56

source_name: Liver Transgenic S2 WD Hybrid Individual 2


title: 1687-4f2(p12)_undiff_hiPS

value: Fibro (HDF1687)


title: 1503-4f1(p28)_undiff_hiPS

value: Fibro (HDF1503)


title: Case 01 baseline premalignancy

description:
ch1 raw data file: MACF_251495027272_S01_CGH_107_Sep09_1_1.txt
ch2 raw data file: MACF_251495027272_S01_CGH_107_Sep09_1_3.txt
Pooled DNA from the blood of 100 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

value: case


title: TKCBV5-6(p73)_undiff_hiPS


title: a061

description: This array survey leukocyte surface CD markers

value: Peripheral Blood Mononuclear Cells


title: a060


title: a059


title: Liver Transgenic S2 WD Hybrid 1 HE013053T2D47

source_name: Liver Transgenic S2 WD Hybrid Individual 1


title: a062


title: a058


title: Liver Transgenic S2 Wild 3 HE013046T2W61

source_name: Liver Transgenic S2 Wild Individual 3

value: Growth Hormone Transgenic Strain 2 in Wild


title: Liver Transgenic S2 Wild 4 HE013057T2W70

source_name: Liver Transgenic S2 Wild Individual 4


title: Liver Transgenic S2 Wild 2 HE013063T2W54

source_name: Liver Transgenic S2 Wild Individual 2


title: 1375-4f1(p10)_undiff_hiPS

value: Fibro (HDF1375)


title: 1377-4f1(p13)_undiff_hiPS

value: Fibro (HDF1377)


title: 1392-4f2(p19)_undiff_hiPS

value: Fibro (HDF1392)


title: 1488-4f1(p27)_undiff_hiPS

value: Fibro (HDF1488)


title: Liver Transgenic S2 Wild 5 HE013071T2W78

value: Wild pool

source_name: Liver Transgenic S2 Wild Individual 5


title: a057

value: F


title: DUCaP cells treated for 24 hours with R1881, experiment 3

hyb_protocol: Target samples were hybridized to Human Gene 1.0 ST v1 microarrays according to the manufacturer's protocols in a Affymetrix hybridization oven.

data_processing: Raw data was preprocessed using the GCRMA method. For transcript probe set definition a custom CDF package based on a complete re-alignment of the probe sequences to the genome and transcriptome (Ensembl version 68) was used; details on http://bioinfo.i-med.ac.at.

source_name: DUCaP

growth_protocol: Cells (LNCaP, VCaP, DuCaP) were grown on polylysine-coated (Sigma) petridishes in RPMI1640 supplemented with 10% charcoal-stripped FCS overnight.

extract_protocol: RNA was extracted using TRI-reagent (Sigma) according to the manufacturer`s protocol. After DNA digestion with DnaseI (Qiagen), RNA was purified using Rneasy kit (Qiagen).

treatment_protocol: Cells were cultured in the absence (EtOH) or presence of 1nM R1881 for 8 and 24 hours, respectively.

tag: date of experiment

tag: timepoint


title: DUCaP cells treated for 24 hours with EtOH, experiment 3

tag: treatment

value: EtOH


title: Liver Transgenic S2 Wild 1 HE013044T2W45

source_name: Liver Transgenic S2 Wild Individual 1


title: a056

tag: age

value: M

tag: cell type


title: Liver Transgenic S1 WD Hybrid 5 HE013045T1D37

source_name: Liver Transgenic S1 WD Hybrid Individual 5

value: Growth Hormone Transgenic Strain 1 in Wild-Domestic hybrid


title: DUCaP cells treated for 24 hours with R1881, experiment 2


title: a055


title: TIG120-4f1(p16)_undiff_hiPS

source_name: undifferentiated hiPS

value: Retrovirus

value: Fibro (TIG120)

value: OSKM


title: DUCaP cells treated for 24 hours with EtOH, experiment 2


title: Liver Transgenic S1 WD Hybrid 3 HE013067T1D13

source_name: Liver Transgenic S1 WD Hybrid Individual 3


title: a054

source_name: Peripheral Blood Mononuclear Cells


title: Liver Transgenic S1 WD Hybrid 4 HE013066T1D22

source_name: Liver Wild pool

source_name: Liver Transgenic S1 WD Hybrid Individual 4


title: TIG118-4f1(p10)_undiff_hiPS

value: Fibro (TIG118)


title: TIG121-4f4(p16)_undiff_hiPS

value: Fibro (TIG121)


title: DUCaP cells treated for 8 hours with R1881, experiment 2


title: DUCaP cells treated for 8 hours with EtOH, experiment 2


title: a052


title: a053


title: N012


title: DUCaP cells treated for 24 hours with R1881, experiment 1


title: TIG114-4f1(p21)_undiff_hiPS

value: Fibro (TIG114)


title: Liver Transgenic S1 Wild 5 HE013054T1W40

source_name: Liver Transgenic S1 Wild Individual 5

value: Growth Hormone Transgenic Strain 1 in Wild


title: TIG109-4f1(p20)_undiff_hiPS

value: Fibro (TIG109)


title: TIG107-3f1(p57)_undiff_hiPS

value: Fibro (TIG107)

value: OSK


title: Liver Transgenic S1 Wild 4 HE013052T1W32

source_name: Liver Transgenic S1 Wild Individual 4


title: Liver Transgenic S1 WD Hybrid 1 HE013065T1D5

source_name: Liver Transgenic S1 WD Hybrid Individual 1


title: DUCaP cells treated for 24 hours with EtOH, experiment 1


title: a051

value: Peripheral Blood Mononuclear Cells


title: TIG108-4f3(p16)_undiff_hiPS

value: Fibro (TIG108)

value: OSK(M)


title: a045


title: a046


title: DUCaP cells treated for 8 hours with R1881, experiment 1


title: a047


title: Liver Domestic 5 HE013058D35

value: Wild pool

source_name: Liver Domestic Individual 5

value: Domestic


title: a050

value: F


title: a049

value: M


title: a048


title: Liver Transgenic S1 Wild 1 HE013060T1W8

source_name: Liver Transgenic S1 Wild Individual 1


title: TIG107-4f1(p18)_undiff_hiPS

value: Retrovirus


title: 253G1(p32)_undiff_hiPS

value: Fibro (HDF1388)


title: 253G4(p30)_undiff_hiPS


title: TIG103-4f4(p8)_undiff_hiPS

value: Fibro (TIG103)

value: OSKM


title: Liver Transgenic S1 WD Hybrid 2 HE013056T1D6

source_name: Liver Transgenic S1 WD Hybrid Individual 2

value: Growth Hormone Transgenic Strain 1 in Wild-Domestic hybrid


title: Liver Transgenic S1 Wild 2 HE013070T1W24

source_name: Liver Transgenic S1 Wild Individual 2


title: 201B7(p18)_undiff_hiPS


title: Liver Domestic 4 HE013047D28

source_name: Liver Domestic Individual 4


title: DUCaP cells treated for 8 hours with EtOH, experiment 1

value: EtOH


title: Liver Transgenic S1 Wild 3 HE013059T1W31

source_name: Liver Transgenic S1 Wild Individual 3

value: Growth Hormone Transgenic Strain 1 in Wild


title: a044


title: VCaP cells treated for 24 hours with EtOH, experiment 3

source_name: VCaP


title: VCaP cells treated for 24 hours with R1881, experiment 3


title: Liver Domestic 3 HE013064D20

source_name: Liver Domestic Individual 3


title: VCaP cells treated for 8 hours with R1881, experiment 2


title: a043


title: VCaP cells treated for 24 hours with R1881, experiment 2


title: a042


title: VCaP cells treated for 8 hours with EtOH, experiment 1


title: 201B6(p25)_undiff_hiPS


title: VCaP cells treated for 8 hours with R1881, experiment 1


title: 201B2(p67)_undiff_hiPS


title: VCaP cells treated for 24 hours with EtOH, experiment 2


title: SA02(p32)_undiff_hES

source_name: undifferentiated hES

value: blastocyst


title: ES06(p43)_undiff_hES


title: a041


title: Liver Domestic 1 HE013068D3

source_name: Liver Domestic Individual 1


title: a039


title: a040


title: Liver Wild 4 HE013049W50

source_name: Liver Wild Individual 4

value: Wild


title: VCaP cells treated for 8 hours with EtOH, experiment 2


title: VCaP cells treated for 24 hours with EtOH, experiment 1


title: Liver Wild 5 HE013043W58

source_name: Liver Wild Individual 5


title: Liver Domestic 2 HE013062D19

source_name: Liver Wild pool

source_name: Liver Domestic Individual 2


title: Liver Wild 2 HE013042W10

source_name: Liver Wild Individual 2


title: Liver Wild 3 HE013069W25

source_name: Liver Wild Individual 3


title: ES03(p65)_undiff_hES


title: ES04(p74)_undiff_hES


title: H9(p40)_undiff_hES


title: Liver Wild 1 HE013050W9

source_name: Liver Wild Individual 1


title: a036

source_name: Peripheral Blood Mononuclear Cells


title: a037


title: a038


title: VCaP cells treated for 24 hours with R1881, experiment 1


title: LNCaP cells treated for 24 hours with R1881, experiment 3

source_name: LNCaP


title: KhES5(p47)_undiff_hES


title: LNCaP cells treated for 24 hours with EtOH, experiment 3


title: LNCaP cells treated for 8 hours with EtOH, experiment 2


title: H1(p49)_undiff_hES


title: a035