title: AC02-1287-04

description: Blood gene expression data from ASD

tag: diagnosis

value: CONTROL

tag: gender

value: Black

tag: allergies

tag: developmental/speech disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: genetic testing

value: tylenol

tag: cerebral palsy

tag: seizure


title: A-0111-P1

status: Public on Sep 01 2012

type: RNA

city: Boston

first: Sek Won

last: Kong

state: MA

address: 300 Longwood Avenue

department: Informatics Program

country: USA

institute: Boston Children's Hospital

description: Blood gene expression data from ASD

hyb_protocol: The cRNA was quantified (using A260) and fragmented. Fragmented cRNA was hybridized on the GeneChips according to the manufacturer's standard protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000 at 2.5 μm resolution.

data_processing: The data were analyzed with Probe Logarithmic Intensity Error (PLIER) estimation method using Affymetrix Power Tools version 1.10.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Blood

label_protocol: A total of 1 ug RNA was processed using established Affymetrix protocols for the generation of biotin-labeled cRNA.

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

value: PDD-NOS

value: male

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: ethnicity

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: neurological disorder

value: yes (GERD)

tag: autoimmune disorder

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

value: flouride

tag: other diseases


title: DPM_Aorta_E2_4hr_rep1,2

first: Gavin

middle: R.

last: Schnitzler

address: 800 Washington St. Box 80

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed.  The chips are transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.

data_processing:
Raw microarray data was normalized using the GCRMA method (considering all samples with the same name as a group), and differential expression analyzed using Limma with array quality weighting. The relevant references are: Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004;3:Article3, and Ritchie ME, Diyagama D, Neilson J, et al. Empirical array quality weights in the analysis of microarray data. BMC Bioinformatics. 2006;7:261. Three contrasts were performed: DPM_E2-DPM_Veh (estrogen response in DPM), WT_E2-WT_Veh (estrogen response in WT), and (DPM_E2-DPM_Veh)-(WT_E2-WT_Veh) (differential estrogen response between DPM and WT).
Columns 2 through 5 in the log2FC_results table are normalized relative log2 expression level coefficients, calculated by Limma for all replicate samples of the same characteristics. Columns 6 through 11 are the results of Limma contrast fits for the indicated contrasts:  DPM_E2-DPM_Veh (estrogen response in DPM), WT_E2-WT_Veh (estrogen response in WT), and (DPM_E2-DPM_Veh)-(WT_E2-WT_Veh) (differential estrogen response between DPM and WT). The first column in each pair is the log2 fold change in the contrast. For (WT_E2-WT_Veh), for example this would be equal to the column 4 coefficent - the column 5 coefficient. The second column in each pair is the P.value assigned to the contrast (probability that a contrast of that magnitude would arise by chance).

organism: Mus musculus

source_name: DPM Aorta +E2 4hr

label_protocol: RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.  The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.  The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using magnetic particles. The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not routinely be carried forward in the analysis. Should this occur, investigators would be notified and asked how they would like to proceed.  The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.

growth_protocol: Transgenic disrupting peptide mice (DPM) express the Estrogen Receptor (ER) alpha amino acids 176-253 peptide under CMV promoter control. This peptide blocks interactions between ER and striatin, which inhibits rapid non-genomic signaling by ER to cellular kinases. 12-14 week old female WT and DPM mice (4 mice per sample) were overiectomized, and 1 week later aortas were harvested for ex vivo treatment.

extract_protocol: Total RNA from 4 aortas per sample was collected using TRIzol (InVitrogen) and the RNeasy kit (Qiagen).

treatment_protocol: Aortas were treated + 10 nM beta-estradiol (E2) or + EtOH vehicle (Veh) for 4 hrs ex vivo.

tag: background strain

tag: genotype/variation

value: DPM


title: WT_Aorta_Veh_4hr_rep1-3

source_name: WT Aorta +Veh (ctrl) 4hr

value: wild type


title: Ewing sarcoma E51 4756083018_R004_C010

type: genomic

city: Nashville

first: Scott

last: Borinstein

address: 2200 Pierce Ave

institute: Vanderbilt University

description:
4756083018_R004_C010
Bisulfite Treated DNA

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Primary Tumor Sample

label_protocol: Standard Illumina Protocol

growth_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit, then bisulfite treated with EZ DNA Methyation-Gold kit according to standard instructions

extract_protocol: Standard Illumina Protocol

tag: sample group

tag: tissue

value: primary Ewing sarcoma tumor


title: Ewing sarcoma E38 4756083018_R003_C003

description:
4756083018_R003_C003
Bisulfite Treated DNA


title: LMP1 lymphoma cell-low expression

city: Pittsburgh

first: Kathy

last: Shair

state: PA

address: 5117 Centre Avenue

department: UPMC Hillman Cancer Center

institute: University of Pittsburgh

description: Biological replicate 1 of 1

hyb_protocol: Agilent Gene Expression Hybridization Kit

scan_protocol: Agilent DNA Microarray Scanner with Sure Scan High Resolution Technology for scanning

data_processing: Genespring GX

source_name: negative lymphoma

label_protocol: Agilent Quick Amp Labeling Kit was used for labeling

growth_protocol: Primary lymphocytes were freshly harvested from the spleen of 6 month old transgenic mice. Primary splenic lymphoma cells were passaged in SCID mice by i.p. injection, and freshly harvested from the spleen upon enlargement.

extract_protocol: Total RNA was extracted using Qiagen's RNeasy Plus kit and DNaseI treated (DNA-free kit, Ambion) according to manufacturer's protocol.

treatment_protocol: Primary splenic B cells were immunoaffinity isolated using CD19 positive selection (Stemcell Technologies).  Expression of transgenes were verified by RT-PCR or western blotting. RNA integrity was assessed on an Agilent 2100 Bioanalyzer (RIN range: 8.5 - 10).

tag: cell type

value: lymphoma

tag: lmp1 expression

value: low

source_name: Balb/c negative pool

value: lymphocyte

tag: strain

value: Balb/c


title: A-0108-P1

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: allergies

tag: developmental/speech disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

value: yes (chronic diarrhea, chronic endocolitis)

tag: genetic testing

value: pentasa endocolitis

tag: cerebral palsy

tag: seizure


title: Exposed, replicate 5

city: Göteborg

first: Erik

last: Kristiansson

address: Chalmers Tvärgata 3

department: Department of Mathematical Sciences

country: Sweden

institute: Chalmers University of Technology

hyb_protocol: Fifteen micrograms of the biotin-labeled cRNA were fragmented to strands between 35 and 200 bases in length, 10 micrograms of which were hybridized onto the GeneChip® Rat Genome 230 2.0 Array overnight in the GeneChip® Hybridisation 6400 oven using standard procedures. The arrays were washed and then stained in a GeneChip® Fluidics Station 450.

scan_protocol: Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software.

data_processing: The microarray data was analyzed in the statistical language R 2.8.1 using the Bioconductor package. Preprocessing was performed using robust multi-array average from the rma package.

organism: Rattus norvegicus

source_name: Liver, exposed

label_protocol: The microarray experiments were performed at the Swegene Centre for Integrative Biology at Lund University (SCIBLU). In short, 5µg total RNA was processed following the GeneChip® Expression 3′-Amplification Reagents One-cycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) to produce double-stranded cDNA. This was used as a template to generate biotin-targeted cRNA following the manufacturer’s specifications.

extract_protocol: Liver samples were removed from the storage in liquid nitrogen and homogenized using the TissueLyser (Qiagen, Hilden, Germany). Total RNA was extracted with the RNeasy®Plus Mini Kit (Qiagen, Hilden, Germany). RNA quality and quantity were assessed by spectrophotometric measurements (Nanodrop 1000, NanoDrop Technologies, USA) and potential RNA degradation was measured with RNA StdSens Analysis Kit and Experion (Experion™ Electrophoresis Station, Bio-Rad Laboratories, Hercules, CA).

value: Sprague-Dawley

value: liver

tag: treatment

value: exposed


title: Negative lymphoma cell

description: Biological replicate 1 of 3

source_name: LMP1 lymphoma

tag: genotype/variation

value: negative


title: A-0105-P1

description: Blood gene expression data from ASD

value: PDD-NOS

value: male

value: Caucasian

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: neurological disorder

tag: autoimmune disorder

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

tag: other diseases


title: A-0101-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

value: Non-Hispanic

tag: allergies

tag: developmental/speech disorder

value: yes

value: yes (Febrile Seizures)

value: depapote


title: LMP1/2A lymphocyte, experimental replicate 2

description: Experimental replicate 2 of 2

tag: genotype/variation

tag: cell type

tag: strain


title: LMP1 lymphoma cell-high expression

description: Biological replicate 2 of 3

value: lymphoma

tag: lmp1 expression

value: high


title: Control, replicate 4

source_name: Liver, control

tag: tissue

tag: treatment

value: control


title: Control, replicate 5


title: Exposed, replicate 4


title: A-0096-P1

description: Blood gene expression data from ASD

tag: hours (minutes since last caloric intake)

tag: chronic diseases

value: yes (motor coordination issues)

tag: neurological disorder

tag: psychiatric disorder

value: yes (anxiety)

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

value: Amoxicillin, Cortef

tag: cerebral palsy

tag: seizure


title: LMP1 lymphoma cell-medium expression

description: Biological replicate 3 of 3

tag: genotype/variation

value: medium

value: lymphocyte

value: Balb/c


title: LMP1 lymphocyte, experimental replicate 2

description: Experimental replicate 2 of 2

tag: cell type


title: Ewing sarcoma E63 4756083018_R004_C006

description:
4756083018_R004_C006
Bisulfite Treated DNA

tag: sample group

value: primary Ewing sarcoma tumor


title: A-0095-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: PDD-NOS

tag: gender

value: male

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: allergies

tag: developmental/speech disorder

value: yes (Developmental Coordination Disorder)

value: yes (Diagnosed Gastroesophageal reflux from ages 1-2 years old)

tag: mri

tag: medications/vitamin names

tag: other diseases


title: Ewing sarcoma E38 4756083018_R004_C009

description:
4756083018_R004_C009
Bisulfite Treated DNA

tag: tissue


title: A-0094-P1

description: Blood gene expression data from ASD

value: Caucasian

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

tag: chronic diseases

value: yes (global)

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

value: Flouride


title: Exposed, replicate 3

tag: strain

value: Sprague-Dawley

tag: gender

value: liver

tag: treatment

value: exposed


title: Ewing sarcoma E63 4756083018_R004_C011

description:
4756083018_R004_C011
Bisulfite Treated DNA

tag: sample group


title: Ewing sarcoma E55 4756083018_R004_C005

description:
4756083018_R004_C005
Bisulfite Treated DNA


title: Ewing sarcoma E47 4756083018_R004_C004

description:
4756083018_R004_C004
Bisulfite Treated DNA


title: Control, replicate 3

value: control


title: A-0091-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: allergies

tag: developmental/speech disorder

tag: mri

tag: cerebral palsy

tag: seizure


title: Ewing sarcoma E39 4756083018_R004_C003

description:
4756083018_R004_C003
Bisulfite Treated DNA

tag: tissue


title: negative littermate lymphocyte, experimental replicate 2

description: Experimental replicate 2 of 2

source_name: negative littermate

tag: genotype/variation

value: negative littermate

tag: cell type


title: LMP2A lymphocyte, experimental replicate 2

description: Experimental replicate 2 of 2

value: lymphocyte


title: LMP1/2A lymphocyte, experimental replicate 1

description: Experimental replicate 1 of 2

value: Balb/c


title: A-0090-P1

description: Blood gene expression data from ASD

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: medications/vitamin names

tag: other diseases


title: Ewing sarcoma E31 4756083018_R004_C002

description:
4756083018_R004_C002
Bisulfite Treated DNA

tag: sample group

value: primary Ewing sarcoma tumor


title: LMP2A lymphocyte, experimental replicate 1

description: Experimental replicate 1 of 2

tag: strain


title: Exposed, replicate 2

tag: gender

tag: treatment


title: A-0088-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: PDD-NOS

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: allergies

tag: developmental/speech disorder

value: yes (anxiety)

tag: mri

tag: cerebral palsy

tag: seizure


title: Control, replicate 2

value: male

tag: tissue


title: A-0086-P1

description: Blood gene expression data from ASD

value: ASPERGER'S DISORDER

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct


title: Control, replicate 1

tag: strain

tag: gender

tag: treatment


title: negative littermate lymphocyte, experimental replicate 1

description: Experimental replicate 1 of 2

tag: genotype/variation

tag: cell type


title: NT (+P), biological rep2

city: Los Baños

first: Rico

last: Gamuyao

state: Laguna

address: College

department: Plant Breeding, Genetics, and Biotechnology Division

country: Philippines

institute: International Rice Research Institute

description:
Gene expression data from non-transgenic rice grown in P-fertilized soil
Gamuyao_H

hyb_protocol: ATLAS Biolabs GmbH (Germany)

scan_protocol: ATLAS Biolabs GmbH (Germany)

data_processing: Signal calculated by GeneChip Operating System (GCOS) 1.4 c/o ATLAS Biolabs GmbH (Germany)

organism: Oryza sativa

source_name: non-transgenic IR64 rice_P-fertilized soil

label_protocol: ATLAS Biolabs GmbH (Germany)

growth_protocol: IR64 35S::OsPSTOL1 plants and the corresponding Null segregants were under greenhouse conditions.

extract_protocol: Total root RNA was extracted using Trizol according to the instructions from the manufacturer (Invitrogen) with modifications. The RNA was re-precipitated by adding 2.5x volume absolute ethanol and one-tenth volume 3M NaOAc (pH 5.2), washed twice (70% and 100% ethanol), air-dried, and dissolved in RNase-free water before treatment with RNase-free DNase I (Promega).

treatment_protocol: Plants were grown in pots with P-deficient and P-fertilized soil conditions. Root samples were collected, frozen in liquid nitrogen, stored temporarily at -80 °C and used later for RNA extraction.

value: null segregants (non-transgenic)

tag: age

value: mid-tillering stage

tag: grown in

value: P-fertilized soil conditions

value: root


title: Ewing sarcoma E23 4756083018_R004_C001

description:
4756083018_R004_C001
Bisulfite Treated DNA

tag: sample group

tag: tissue


title: Exposed, replicate 1

value: Sprague-Dawley


title: LMP1 lymphocyte, experimental replicate 1

description: Experimental replicate 1 of 2


title: Ewing sarcoma E39 4756083018_R005_C009

description:
4756083018_R005_C009
Bisulfite Treated DNA


title: pmr5 mutant without treatment, biologcal rep 1

city: San Francisco

first: Bradley

middle: Robert

last: Dotson

state: CA

address: 55 Boardman Place Apt C

department: Plant and Microbial Biology

institute: University of California at Berkeley

description: Gene expression data from 3 week old rosettes of pmr5 mutant plants

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45Â°C on GeneChip ATH1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner 2500.

data_processing: Log2 (expression values) were extracted using robust multi-array analysis (RMA) implemented in the function rma() in the Bioconductor software package affy.

organism: Arabidopsis thaliana

source_name: pmr5 mutant 3 week old rosettes, without treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA.

growth_protocol: The plants were grown at 22°C with 14 hrs photoperiod

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

treatment_protocol: no treatment before collection

tag: genotype

value: pmr5 mutant

value: rosette

value: 3 wk

tag: genetic background


title: A-0078-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: ethnicity

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: mri

tag: medications/vitamin names

value: Adderall

tag: cerebral palsy

tag: seizure

tag: other diseases


title: Ewing sarcoma E62 4756083018_R003_C011

description:
4756083018_R003_C011
Bisulfite Treated DNA

tag: sample group

tag: tissue

value: primary Ewing sarcoma tumor


title: NT (+P), biological rep1

description:
Gene expression data from non-transgenic rice grown in P-fertilized soil
Gamuyao_G

tag: genotype/variation

tag: age

tag: grown in


title: A-0076-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: PDD-NOS

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

value: yes (Developmental Coordination Disorder)

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct


title: A-0074-A1

description: Blood gene expression data from ASD

value: male

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

value: yes (Chronic Gastroesophageal Reflux (GERD))

tag: mri

tag: medications/vitamin names

value: Allegra, topical acne medication

tag: cerebral palsy

tag: seizure


title: pmr5 mutant without treatment, biologcal rep 3

tag: genotype

tag: tissue

tag: age

tag: genetic background


title: T (+P), biological rep2

description:
Gene expression data from transgenic rice grown in P-fertilized soil
Gamuyao_F

source_name: transgenic IR64 rice with 35S::OsPSTOL1_P-fertilized soil

tag: genotype/variation

value: IR64 35S::OsPSTOL1 transgenic plant

value: mid-tillering stage

tag: grown in


title: T (+P), biological rep1

description:
Gene expression data from transgenic rice grown in P-fertilized soil
Gamuyao_E

value: P-fertilized soil conditions

value: root


title: Ewing sarcoma E50 4756083018_R007_C004

description:
4756083018_R007_C004
Bisulfite Treated DNA

tag: sample group


title: pmr5 mutant without treatment, biologcal rep 2

value: pmr5 mutant


title: NT (‒P), biological rep2

description:
Gene expression data from non-transgenic rice grown in P-deficient soil
Gamuyao_D

source_name: non-transgenic IR64 rice_P-deficient soil

value: null segregants (non-transgenic)

value: heading stage

value: P-deficient soil conditions


title: Col-0 without treatment, biological rep 3

description: Gene expression data from 3 week old rosettes of wild type Col-0 plants

source_name: Col-0 3 week old rosettes, without treatment

value: wild type

value: rosette

value: 3 wk


title: Ewing sarcoma E62 4756083018_R003_C006

description:
4756083018_R003_C006
Bisulfite Treated DNA

value: primary Ewing sarcoma tumor


title: A-0070-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

tag: gender

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: ethnicity

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

value: yes (Motor Delay)

value: yes (Siezure/ convulsion)

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

value: Trilectol

value: yes

tag: other diseases


title: NT (‒P), biological rep1

description:
Gene expression data from non-transgenic rice grown in P-deficient soil
Gamuyao_C

tag: age

tag: tissue


title: A-0068-P1

description: Blood gene expression data from ASD

value: male

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

value: yes (global)

tag: neurological disorder

tag: psychiatric disorder

tag: mri

tag: medications/vitamin names

value: B12 injections, geutotrione, kelatur, tetrahydrobiopterine

tag: cerebral palsy

tag: seizure


title: A-0072-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: PDD-NOS

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: gastrointestinal disorder

value: resperdal


title: Col-0 without treatment, biological rep 2

tag: genotype

tag: tissue

tag: age

tag: genetic background


title: T (‒P), biological rep2

description:
Gene expression data from transgenic rice grown in P-deficient soil
Gamuyao_B

source_name: transgenic IR64 rice with 35S::OsPSTOL1_ P-deficient soil

tag: genotype/variation

value: IR64 35S::OsPSTOL1 transgenic plant

value: heading stage

tag: grown in

value: P-deficient soil conditions

value: root


title: Ewing sarcoma E50 4756083018_R003_C010

description:
4756083018_R003_C010
Bisulfite Treated DNA

tag: sample group

value: primary Ewing sarcoma tumor


title: T (‒P), biological rep1

description:
Gene expression data from transgenic rice grown in P-deficient soil
Gamuyao_A


title: Ewing sarcoma E46 4756083018_R003_C004

description:
4756083018_R003_C004
Bisulfite Treated DNA


title: Ewing sarcoma E54 4756083018_R003_C005

description:
4756083018_R003_C005
Bisulfite Treated DNA


title: A-0060-P1

description: Blood gene expression data from ASD

value: ASPERGER'S DISORDER

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

value: yes (adhd/add)

value: yes (Celiac Disease)

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

value: Ritalin LA, Wellbutrin

tag: other diseases


title: Ewing sarcoma E30 4756083018_R003_C002

description:
4756083018_R003_C002
Bisulfite Treated DNA

tag: tissue


title: Ewing sarcoma E22 4756083018_R003_C001

description:
4756083018_R003_C001
Bisulfite Treated DNA


title: Ewing sarcoma E71 4756083018_R004_C007

description:
4756083018_R004_C007
Bisulfite Treated DNA


title: A-0065-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

tag: gender

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: ethnicity

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

tag: gastrointestinal disorder

value: Cingular

tag: cerebral palsy

tag: seizure


title: Ewing sarcoma E71 4756083018_R002_C012

description:
4756083018_R002_C012
Bisulfite Treated DNA

tag: sample group


title: unc-37(e262) A-class, biological rep3

first: William

middle: Clay

last: Spencer

state: TN

address: 465 21st Ave S

department: Cell & Developmental Biology

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

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

data_processing: Data were normalized using quantile normalization and Robust Multiarray analysis (RMA) summarization using RMAExpress.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans larvae at L2 stage

label_protocol: Samples were amplified and labeled using a 2-round IVT protocol (modified from the Affymetrix small-sample protocol).

growth_protocol: Animals were grown at 25C on 150 mm 8P plates inoculated with the E. coli strain Na22

extract_protocol: poly(A) RNA was isolated from wildtype and unc-37(e262) A-class motor neurons as described (Von Stetina, et al. 2007).

tag: cell type

value: A-class motor neurons

tag: developmental stage

tag: genotype/variation


title: Ewing sarcoma E49 4756083018_R006_C004

description:
4756083018_R006_C004
Bisulfite Treated DNA


title: Ewing sarcoma E49 4756083018_R002_C010

description:
4756083018_R002_C010
Bisulfite Treated DNA


title: Col-0 without treatment, biological rep 1

tag: genotype

value: wild type

value: rosette

tag: age

value: 3 wk

tag: genetic background


title: wildtype A-class, biological rep3


title: A-0055-A1

description: Blood gene expression data from ASD

source_name: Blood

value: male

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

value: yes (global)

tag: neurological disorder

tag: psychiatric disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: other diseases


title: A-0058-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: PDD-NOS

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

value: yes (Coordination issues)

tag: gastrointestinal disorder

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure


title: A-0053-P1

description: Blood gene expression data from ASD

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

value: yes (reflux)


title: lymph node metastasis patient 065, cancer, Homogenized

city: Tokyo

first: Ken

last: Miyaguchi

address: 5-45, Yushima 1, Bunkyo-ku

country: Japan

institute: Tokyo Medical and Dental University

description: Hybridized to 250K_Sty

hyb_protocol: Using Genome-Wide Human SNP Sty assay kit (Affymetrix), DNA was prepared and was hybridized to each array according to the manufacturer's instructions.

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

data_processing: Copy number analysis was performed using Genotyping Console software v4.0 (Affymetrix).

label: Biotin

source_name: surgically resected material

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from surgical materials using the QIAamp DNA Mini Kit (Qiagen) for tumor tissue. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

treatment_protocol: Surgically resected tissue was frozen and stored in -80 C freezer. Frozen tissue was manually homogenized prior to extraction of genomic DNA.

value: female

tag: source tissue

value: tongue

tag: Stage

tag: metastasis

value: lymph node metastasis

tag: tissue

value: oral squamous cell carcinoma tumor from tongue

tag: individual

value: patient 065


title: unc-37(e262) A-class, biological rep2

tag: cell type

tag: developmental stage

tag: genotype/variation


title: no lymph node metastasis patient 063, cancer, Homogenized

description: Hybridized to 250K_Sty

tag: gender

value: lower gingiva

value: oral squamous cell carcinoma tumor from lower gingiva

value: patient 063


title: A-0050-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

tag: age at blood drawing (months)

tag: race

value: Unknown

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

value: Multivitamin w/ Fluoride

tag: other diseases


title: no lymph node metastasis patient 064, cancer, Homogenized

description: Hybridized to 250K_Sty

tag: source tissue

tag: Stage

tag: metastasis

tag: tissue

tag: individual

value: patient 064


title: Ewing sarcoma E77 4756083018_R008_C012

description:
4756083018_R008_C012
Bisulfite Treated DNA

tag: sample group

value: primary Ewing sarcoma tumor


title: unc-37(e262) A-class, biological rep1

tag: cell type

value: A-class motor neurons

tag: developmental stage

tag: genotype/variation


title: A-0057-P1

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

value: male

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: ethnicity

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

value: yes (mild mental retardation, mixed language disorder)

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

value: 16p13.1 amplification

value: 40 mg Stratera, 1mg Tenex (x2day)

tag: cerebral palsy

tag: seizure


title: A-0052-P1

description: Blood gene expression data from ASD

value: PDD-NOS

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

tag: other diseases


title: wildtype A-class, biological rep2

tag: cell type

tag: developmental stage

tag: genotype/variation


title: Ewing sarcoma E77 4756083018_R002_C008

description:
4756083018_R002_C008
Bisulfite Treated DNA

tag: sample group

tag: tissue


title: EWS Cell line A673 5-AZA treated, replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: EWS Cell line A673 5-AZA treated

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

growth_protocol: Cell lines grown in media per manufactuers recommendations

extract_protocol: RNA isolated with Trizol followed by Rneasy

treatment_protocol: 5-AZA treatment per protocol

tag: cell line

tag: treatment

value: 5-AZA treated


title: no lymph node metastasis patient 061, cancer, Homogenized

description: Hybridized to 250K_Sty

tag: gender

tag: source tissue

value: tongue

tag: Stage

tag: metastasis

value: oral squamous cell carcinoma tumor from tongue

tag: individual

value: patient 061


title: no lymph node metastasis patient 060, cancer, Homogenized

description: Hybridized to 250K_Sty

value: patient 060


title: no lymph node metastasis patient 066, cancer, Homogenized

description: Hybridized to 250K_Sty

value: patient 066


title: no lymph node metastasis patient 062, cancer, Homogenized

description: Hybridized to 250K_Sty

value: patient 062


title: wildtype A-class, biological rep1


title: A-0044-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

tag: age at blood drawing (months)

tag: race

value: Asian

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

value: yes (moderate)

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

value: Miralax

tag: cerebral palsy

tag: seizure


title: EWS Cell line SK-N-MC, 5-AZA treated, replicate 2

source_name: EWS Cell line SK-N-MC, 5-AZA treated

tag: cell line

value: SK-N-MC

tag: treatment


title: no lymph node metastasis patient 059, cancer, Homogenized

description: Hybridized to 250K_Sty

tag: gender

value: female

tag: source tissue

value: buccal mucosa

tag: Stage

tag: metastasis

tag: tissue

value: oral squamous cell carcinoma tumor from buccal mucosa

tag: individual

value: patient 059


title: Ewing sarcoma E69 4756083018_R002_C007

description:
4756083018_R002_C007
Bisulfite Treated DNA

source_name: Primary Tumor Sample

tag: sample group

value: primary Ewing sarcoma tumor


title: Ewing sarcoma E69 4756083018_R008_C011

description:
4756083018_R008_C011
Bisulfite Treated DNA


title: Ewing sarcoma E61 4756083018_R002_C011

description:
4756083018_R002_C011
Bisulfite Treated DNA


title: A-0042-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: male

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: ethnicity

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

value: yes (pica)

tag: ct

tag: mri

tag: medications/vitamin names

tag: other diseases


title: EWS Cell line SK-ES-1, 5-AZA treated, replicate 2

source_name: EWS Cell line SK-ES-1, 5-AZA treated

tag: cell line

tag: treatment

value: 5-AZA treated


title: EWS Cell line SK-N-MC, mock treated, replicate 1

source_name: EWS Cell line SK-N-MC, mock treated

value: mock treated


title: EWS Cell line A673 mock treated, replicate 2

source_name: EWS Cell line A673 mock treated


title: EWS Cell line A673, 5-AZA treated, replicate 2

source_name: EWS Cell line A673, 5-AZA treated


title: EWS Cell line SK-ES-1, mock treated, replicate 2

source_name: EWS Cell line SK-ES-1, mock treated


title: no lymph node metastasis patient 057, cancer, Homogenized

description: Hybridized to 250K_Sty

tag: gender

tag: source tissue

value: tongue

tag: Stage

tag: metastasis

tag: tissue

value: oral squamous cell carcinoma tumor from tongue

tag: individual

value: patient 057


title: no lymph node metastasis patient 058, cancer, Homogenized

description: Hybridized to 250K_Sty

value: patient 058


title: Ewing sarcoma E61 4756083018_R002_C006

description:
4756083018_R002_C006
Bisulfite Treated DNA

tag: sample group


title: Ewing sarcoma E45 4756083018_R002_C004

description:
4756083018_R002_C004
Bisulfite Treated DNA


title: no lymph node metastasis patient 056, cancer, Homogenized

description: Hybridized to 250K_Sty

value: patient 056


title: A-0031-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: PDD-NOS

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

value: yes (expressive language disorder)

tag: psychiatric disorder

value: yes (adhd)

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

value: adderall, clonidine

tag: cerebral palsy

tag: seizure


title: A-0032-P1

description: Blood gene expression data from ASD

value: ASPERGER'S DISORDER

tag: gender

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

value: yes (adhd/add)

tag: ct

tag: mri

tag: medications/vitamin names

value: Concerta

tag: other diseases


title: A-0034-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: male

tag: age at blood drawing (months)

tag: race

value: Mixed (Caucasian, Black)

tag: ethnicity

value: Hispanic

tag: hours (minutes since last caloric intake)

value: yes (vertigo)

value: yes (megacolon)

value: 3q26.3-27 amplification

value: Miralax


title: EWS Cell line A673, mock treated, replicate 1

source_name: EWS Cell line A673, mock treated

tag: cell line

tag: treatment

value: mock treated


title: lymph node metastasis patient 055, cancer, Homogenized

description: Hybridized to 250K_Sty

tag: source tissue

value: lower gingiva

tag: Stage

tag: metastasis

value: lymph node metastasis

tag: tissue

value: oral squamous cell carcinoma tumor from lower gingiva

tag: individual

value: patient 055


title: A-0030-P1

description: Blood gene expression data from ASD

tag: gender

value: Caucasian

value: Non-Hispanic

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

value: yes (non-verbal)

tag: neurological disorder

value: yes (Seizure disorder)

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

value: fluvoxamine

tag: cerebral palsy

tag: seizure

value: yes


title: no lymph node metastasis patient 054, cancer, Homogenized

description: Hybridized to 250K_Sty

value: male

tag: source tissue

value: tongue

value: oral squamous cell carcinoma tumor from tongue

value: patient 054


title: A-0028-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: ct

tag: mri

tag: medications/vitamin names

tag: other diseases


title: no lymph node metastasis patient 053, cancer, Homogenized

description: Hybridized to 250K_Sty

tag: gender

value: buccal mucosa

tag: Stage

tag: metastasis

tag: tissue

value: oral squamous cell carcinoma tumor from buccal mucosa

tag: individual

value: patient 053


title: no lymph node metastasis patient 052, cancer, Homogenized

description: Hybridized to 250K_Sty

value: patient 052


title: Ewing sarcoma E37 4756083018_R002_C003

description:
4756083018_R002_C003
Bisulfite Treated DNA

tag: sample group

value: primary Ewing sarcoma tumor


title: Ewing sarcoma E29 4756083018_R002_C002

description:
4756083018_R002_C002
Bisulfite Treated DNA


title: Ewing sarcoma E21 4756083018_R002_C001

description:
4756083018_R002_C001
Bisulfite Treated DNA


title: A-0025-P1

description: Blood gene expression data from ASD

value: ASPERGER'S DISORDER

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

value: yes (adhd/add)

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

value: Concerta, Straterra

tag: cerebral palsy

tag: seizure


title: EWS Cell line SK-ES-1, 5-AZA treated, replicate 1

tag: cell line

tag: treatment

value: 5-AZA treated


title: EWS Cell line SK-N-MC, mock treated, replicate 2

value: SK-N-MC

value: mock treated


title: Ewing sarcoma E70 4756083018_R003_C007

description:
4756083018_R003_C007
Bisulfite Treated DNA


title: no lymph node metastasis patient 051, cancer, Homogenized

description: Hybridized to 250K_Sty

tag: gender

value: female

tag: source tissue

value: pterygopalatine fossa

tag: Stage

tag: metastasis

value: oral squamous cell carcinoma tumor from pterygopalatine fossa

value: patient 051


title: EWS Cell line SK-N-MC, 5-AZA treated, replicate 1


title: EWS Cell line SK-ES-1, mock treated, replicate 1


title: no lymph node metastasis patient 049, cancer, Homogenized

description: Hybridized to 250K_Sty

value: male

value: tongue

tag: tissue

value: oral squamous cell carcinoma tumor from tongue

tag: individual

value: patient 049


title: no lymph node metastasis patient 047, cancer, Homogenized

description: Hybridized to 250K_Sty

value: buccal mucosa

value: oral squamous cell carcinoma tumor from buccal mucosa

value: patient 047


title: Ewing sarcoma E70 4756083018_R001_C012

description:
4756083018_R001_C012
Bisulfite Treated DNA

tag: sample group

value: primary Ewing sarcoma tumor


title: A-0023-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: ethnicity

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

value: yes (mild mental retardation)

tag: neurological disorder

value: yes (Siezure/ convulsion (Tremors))

value: yes (Ulcerative colitis)

tag: ct

tag: mri

tag: medications/vitamin names

value: Colazol, Prevacid

value: yes

tag: other diseases


title: no lymph node metastasis patient 048, cancer, Homogenized

description: Hybridized to 250K_Sty

tag: gender

tag: source tissue

value: lower gingiva

tag: Stage

tag: metastasis

value: oral squamous cell carcinoma tumor from lower gingiva

value: patient 048


title: A-0022-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: PDD-NOS

value: male

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

value: Miralax (glycolax)

tag: cerebral palsy

tag: seizure


title: Syn2U

city: Worcester

first: Timothy

middle: P

last: Fitzgibbons

address: 55 Lake Avenue North

department: Molecular Medicine

institute: University of Massachusetts Medical School

description: control culture treated with scrambled shRNA

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip® WT Terminal Labeling and Hybridization User Manual)

scan_protocol: Affymetrix® GeneChip® Scanner 3000 with GCOS/AGCC software according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual)

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

source_name: primary culture,hippocampal neurons

label_protocol: Ambion WT Expression Kit, Affymetrix WT Terminal Labeling Kit

extract_protocol: thermally eluted from polyU Sepharose

tag: tissue

value: hippocampus

value: embryo

tag: treatment

value: scrambled shRNA


title: Ewing sarcoma E59 4756083018_R001_C011

description:
4756083018_R001_C011
Bisulfite Treated DNA

tag: sample group

value: primary Ewing sarcoma tumor


title: Ewing sarcoma E59 4756083018_R008_C005

description:
4756083018_R008_C005
Bisulfite Treated DNA


title: Ewing sarcoma E76 4756083018_R001_C008

description:
4756083018_R001_C008
Bisulfite Treated DNA


title: Syn1U


title: Ewing sarcoma E68 4756083018_R001_C007

description:
4756083018_R001_C007
Bisulfite Treated DNA


title: SG11U

description: culture treated with Gld2 shRNA

value: Gld2 shRNA


title: A-0008-P1

description: Blood gene expression data from ASD

value: AUTISM

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: ethnicity

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: ct

tag: mri

tag: medications/vitamin names


title: A-0006-P1

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: other diseases


title: SG12U

description: culture treated with Gld2 shRNA

tag: tissue

tag: treatment


title: Ewing sarcoma E60 4756083018_R001_C006

description:
4756083018_R001_C006
Bisulfite Treated DNA

tag: sample group


title: A-0010-P1

description: Blood gene expression data from ASD

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: cerebral palsy

tag: seizure


title: no lymph node metastasis patient 043, cancer, Homogenized

description: Hybridized to 250K_Sty

tag: gender

tag: source tissue

value: floor of mouth

tag: Stage

tag: metastasis

value: oral squamous cell carcinoma tumor from floor of mouth

tag: individual

value: patient 043


title: A-0021-P1

description: Blood gene expression data from ASD

tag: diagnosis

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

value: yes (add)

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

value: 7q21 amplification

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

value: Straterra

tag: other diseases


title: no lymph node metastasis patient 045, cancer, Homogenized

description: Hybridized to 250K_Sty

tag: gender

value: female

value: lower gingiva

tag: tissue

value: oral squamous cell carcinoma tumor from lower gingiva

value: patient 045


title: A-0016-P1

description: Blood gene expression data from ASD

value: male

tag: age at blood drawing (months)

tag: race

value: Mixed (Caucasian, Asian)

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

value: yes (mild mental retardation)

tag: cerebral palsy

tag: seizure


title: no lymph node metastasis patient 041, cancer, Homogenized

description: Hybridized to 250K_Sty

tag: source tissue

value: tongue

tag: Stage

tag: metastasis

value: oral squamous cell carcinoma tumor from tongue

tag: individual

value: patient 041


title: no lymph node metastasis patient 039, cancer, Homogenized

description: Hybridized to 250K_Sty

value: patient 039


title: no lymph node metastasis patient 046, cancer, Homogenized

description: Hybridized to 250K_Sty

value: patient 046


title: no lymph node metastasis patient 040, cancer, Homogenized

description: Hybridized to 250K_Sty

value: patient 040


title: Ewing sarcoma E52 4756083018_R001_C005

description:
4756083018_R001_C005
Bisulfite Treated DNA

tag: sample group

value: primary Ewing sarcoma tumor


title: Ewing sarcoma E44 4756083018_R001_C004

description:
4756083018_R001_C004
Bisulfite Treated DNA


title: Ewing sarcoma E36 4756083018_R001_C003

description:
4756083018_R001_C003
Bisulfite Treated DNA


title: Ewing sarcoma E28 4756083018_R001_C002

description:
4756083018_R001_C002
Bisulfite Treated DNA


title: Water Control-Recovery, biological replicate 16

city: Providence

first: Sara

last: Pacheco

state: RI

address: 70 Ship Street, Room 510

department: Pathology and Lab Medicine

institute: Brown University

description: messenger RNA

hyb_protocol: Followed manufacturer's instructions.

scan_protocol: Followed manufacturer's instructions.

data_processing: The probe cell intensity data from the Affymetrix GeneChips was normalized and annotated following previously published methods (Pacheco, Houseman et al. 2011 (PMID 21674046)). The linear models of microarray analysis (LIMMA) procedure (Smyth, Yang et al. 2003) (R package limma) was used to fit a linear regression model for each transcript on the Affymetrix GeneChip Array for each pair of treatment and controls. The p-values were adjusted for multiple comparisons with the qvalue package in R (Storey 2002) and the log2 expression ratios were transformed into fold change values.

source_name: sperm, water, recovery

label_protocol: Followed manufacturer's instructions.

extract_protocol:
Sperm isolation protocol: The cauda epididymides were punctured repeatedly with 30 or 26 gauge needles and put into micro-centrifuge tubes containing 1 mL phosphate-buffered saline (PBS). The samples were incubated in a water bath at 37°C for 10 minutes to aid sperm diffusion from the tissue. The tubes were spun for 3 minutes at 300 xg to pellet the epididymal pieces and the supernatant containing sperm were put into a new tube. The tube was spun for an additional 5 minutes at 2000 xg to pellet the sperm and the supernatant was removed. One mL of lysis buffer (0.15 M ammonium chloride, 10 mM potassium bicarbonate, 0.1 mM EDTA) was added to the sperm pellet, incubated on the bench top for 30 seconds and spun at 16,100 xg for 1 minute. The pellet was washed with 1 mL of PBS and spun at 16,100 xg for 1 minute.

RNA was extracted from the fresh sperm using the mirVana miRNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA), which separated the RNA into large and small fractions, per manufacturer’s instructions.

tag: strain

value: Fischer 344

value: sperm

tag: treatment

value: water

tag: recovery

value: yes


title: A-0001-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: PDD-NOS

tag: gender

value: Caucasian

value: Non-Hispanic

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

value: yes (anxiety)

tag: gastrointestinal disorder

value: yes (reflux)

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

tag: other diseases


title: A-0041-P1

description: Blood gene expression data from ASD

value: male

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

value: yes (mixed language disorder)

value: 16p13.1 amplification

tag: cerebral palsy

tag: seizure


title: Water Control-Recovery, biological replicate 19

description: messenger RNA

tag: strain

tag: tissue

tag: treatment

tag: recovery


title: Ewing sarcoma E44 4756083018_R008_C009

description:
4756083018_R008_C009
Bisulfite Treated DNA

tag: sample group


title: Water Control-Recovery, biological replicate 20

description: messenger RNA


title: Water Control-Recovery, biological replicate 17

description: messenger RNA


title: no lymph node metastasis patient 036, cancer, Homogenized

description: Hybridized to 250K_Sty

tag: gender

value: female

tag: source tissue

value: lower gingiva

tag: Stage

tag: metastasis

value: oral squamous cell carcinoma tumor from lower gingiva

tag: individual

value: patient 036


title: TL01-YMG-rep4

city: shanghai

first: hang

last: wu

address: Huashan Road

country: China

institute: sjtu

description: Gene expression at TL01 cultured in YMG medium

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

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

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

organism: Streptomyces hygroscopicus subsp. jinggangensis TL01

source_name: TL01, YMG, rep4

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

growth_protocol: Strain 5008 and TL01 were pre-cultured at 30°C for 48 h in 50 ml TSB liquid medium plus 1 % yeast extract in 250 ml shaking flasks with reciprocal shaking (220 rpm). 0.5 ml of each culture was inoculated 50 ml laboratory fermentation medium Yeast extract-Malt extract-Glucose (YMG) and  50 ml rice-peanut cake based industrial (IND) fermentation medium in three 250 ml shaking flasks. The batch cultures were incubated at 37°C for 48 h (220 rpm).

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

treatment_protocol: The mycelia was collected from the fermentation medium by centrifugation at 12,000 rpm for 5 min, resuspended in 1 mL TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US), and broken in a precellys homogenizer (6,500 rpm, 1×30 s; Peqlab) with glass beads (150–212 μm, Sigma). Cell debris was removed by centrifugation at 12,000 rpm for 5 min, and the extracted supernatants were stored at -80°C.

tag: cell type

value: Mycelia

tag: cultured medium

value: Yeast extract-Malt extract-Glucose


title: TL01-IND-rep4

description: Gene expression at TL01 cultured in IND medium

source_name: TL01, IND, rep4

value: rice-peanut cake based industrial fermentation medium


title: TL01-IND-rep2

source_name: TL01, IND, rep2


title: TL01-IND-rep3

source_name: TL01, IND, rep3


title: TL01-IND-rep1

source_name: TL01, IND, rep1


title: lymph node metastasis patient 038, cancer, Homogenized

description: Hybridized to 250K_Sty

source_name: surgically resected material

value: tongue

value: lymph node metastasis

value: oral squamous cell carcinoma tumor from tongue

value: patient 038


title: no lymph node metastasis patient 034, cancer, Homogenized

description: Hybridized to 250K_Sty

value: patient 034


title: Water Control-Recovery, biological replicate 13

description: messenger RNA

value: Fischer 344

value: sperm

value: water

value: yes


title: no lymph node metastasis patient 033, cancer, Homogenized

description: Hybridized to 250K_Sty

value: male

value: floor of mouth

value: oral squamous cell carcinoma tumor from floor of mouth

value: patient 033


title: no lymph node metastasis patient 035, cancer, Homogenized

description: Hybridized to 250K_Sty

value: female

value: patient 035


title: Water Control-Recovery, biological replicate 14

description: messenger RNA


title: Water Control-Recovery, biological replicate 15

description: messenger RNA


title: Water Control-Recovery, biological replicate 11

description: messenger RNA


title: Water Control-Recovery, biological replicate 12

description: messenger RNA


title: Ewing sarcoma E20 4756083018_R001_C001

description:
4756083018_R001_C001
Bisulfite Treated DNA

value: primary Ewing sarcoma tumor


title: TL01-YMG-rep2

source_name: TL01, YMG, rep2

value: Mycelia

value: Yeast extract-Malt extract-Glucose


title: TL01-YMG-rep3

source_name: TL01, YMG, rep3


title: lymph node metastasis patient 032, cancer, Homogenized

description: Hybridized to 250K_Sty

value: tongue

value: lymph node metastasis

value: patient 032


title: PBL 4756083018_R007_C008

description:
4756083018_R007_C008
Bisulfite Treated DNA

source_name: Peripheral Blood Leucocytes

value: PBL

value: Peripheral Blood Leucocyte


title: PBL 4398482045_G1

description:
4398482045_G1
Bisulfite Treated DNA


title: PBL 4428661019_G2

description:
4428661019_G2
Bisulfite Treated DNA


title: TL01-YMG-rep1

source_name: TL01, YMG, rep1


title: Ewing sarcoma E13 4398482045_H2

description:
4398482045_H2
Bisulfite Treated DNA

source_name: Primary Tumor Sample


title: HD-Recovery, biological replicate 20

description: messenger RNA

source_name: sperm, HD, recovery

value: Fischer 344

value: sperm


title: 5008-IND-rep4

description: Gene expression at 5008 cultured in IND medium

organism: Streptomyces hygroscopicus subsp. jinggangensis 5008

value: rice-peanut cake based industrial fermentation medium


title: HD-Recovery, biological replicate 19

description: messenger RNA

value: yes


title: 5008-IND-rep3


title: Ewing sarcoma E12 4398482045_G2

description:
4398482045_G2
Bisulfite Treated DNA


title: Ewing sarcoma E13 4398482027_H1

description:
4398482027_H1
Bisulfite Treated DNA


title: HD-Recovery, biological replicate 16

description: messenger RNA


title: 5008-IND-rep2


title: 5008-YMG-rep3

description: Gene expression at 5008 cultured in YMG medium


title: no lymph node metastasis patient 031, cancer, Homogenized

description: Hybridized to 250K_Sty

value: male

value: oral squamous cell carcinoma tumor from tongue

value: patient 031


title: HD-Recovery, biological replicate 18

description: messenger RNA


title: 5008-IND-rep1


title: no lymph node metastasis patient 028, cancer, Homogenized

description: Hybridized to 250K_Sty

value: female

value: patient 028


title: HD-Recovery, biological replicate 15

description: messenger RNA


title: HD-Recovery, biological replicate 17

description: messenger RNA


title: no lymph node metastasis patient 030, cancer, Homogenized

description: Hybridized to 250K_Sty

value: lower gingiva

value: oral squamous cell carcinoma tumor from lower gingiva

value: patient 030


title: no lymph node metastasis patient 027, cancer, Homogenized

description: Hybridized to 250K_Sty

value: tongue

value: patient 027


title: lymph node metastasis patient 025, cancer, Homogenized

description: Hybridized to 250K_Sty

value: lymph node metastasis

value: patient 025


title: no lymph node metastasis patient 026, cancer, Homogenized

description: Hybridized to 250K_Sty

value: patient 026


title: no lymph node metastasis patient 024, cancer, Homogenized

description: Hybridized to 250K_Sty

value: patient 024


title: 5008-YMG-rep4

value: Mycelia

value: Yeast extract-Malt extract-Glucose


title: Ewing sarcoma E12 4398482027_G1

description:
4398482027_G1
Bisulfite Treated DNA

value: primary Ewing sarcoma tumor


title: S53 4428661019_F1

description:
4428661019_F1
Bisulfite Treated DNA

source_name: hMSC Primary Culture

value: mesenchymal stem cell


title: HD-Recovery, biological replicate 13

description: messenger RNA

value: Fischer 344

value: sperm

value: yes


title: Ewing sarcoma E10 4398482027_F1

description:
4398482027_F1
Bisulfite Treated DNA


title: no lymph node metastasis patient 029, cancer, Homogenized

description: Hybridized to 250K_Sty

value: female

value: oral squamous cell carcinoma tumor from tongue

value: patient 029


title: S53 4398482027_F2

description:
4398482027_F2
Bisulfite Treated DNA


title: 5008-YMG-rep1


title: S52 4398482027_Ewing sarcoma E2

description:
4398482027_E2
Bisulfite Treated DNA


title: Ewing sarcoma E10 4398482045_F2

description:
4398482045_F2
Bisulfite Treated DNA


title: Ewing sarcoma E76 4756083018_R007_C012

description:
4756083018_R007_C012
Bisulfite Treated DNA


title: 5008-YMG-rep2


title: Water Control-Recovery, biological replicate 10

description: messenger RNA

value: water


title: HD-Recovery, biological replicate 11

description: messenger RNA


title: Ewing sarcoma E9 4398482027_Ewing sarcoma E1

description:
4398482027_E1
Bisulfite Treated DNA


title: no lymph node metastasis patient 022, cancer, Homogenized

description: Hybridized to 250K_Sty

value: male

value: lower gingiva

value: oral squamous cell carcinoma tumor from lower gingiva

value: patient 022


title: S52 4428661019_Ewing sarcoma E1

description:
4428661019_E1
Bisulfite Treated DNA


title: Water Control-Recovery, biological replicate 8

description: messenger RNA


title: Water Control-Recovery, biological replicate 9

description: messenger RNA


title: HD-Recovery, biological replicate 12

description: messenger RNA


title: no lymph node metastasis patient 021, cancer, Homogenized

description: Hybridized to 250K_Sty

value: patient 021


title: no lymph node metastasis patient 018, cancer, Homogenized

description: Hybridized to 250K_Sty

value: tongue

value: patient 018


title: Water Control-Recovery, biological replicate 6

description: messenger RNA


title: Water Control-Recovery, biological replicate 5

description: messenger RNA


title: Water Control-Recovery, biological replicate 7

description: messenger RNA


title: S51 4428661019_D1

description:
4428661019_D1
Bisulfite Treated DNA


title: Ewing sarcoma E7 4398482045_D2

description:
4398482045_D2
Bisulfite Treated DNA


title: Ewing sarcoma E9 4398482045_Ewing sarcoma E2

description:
4398482045_E2
Bisulfite Treated DNA


title: no lymph node metastasis patient 023, cancer, Homogenized

description: Hybridized to 250K_Sty

value: patient 023


title: no lymph node metastasis patient 020, cancer, Homogenized

description: Hybridized to 250K_Sty

value: patient 020


title: no lymph node metastasis patient 019, cancer, Homogenized

description: Hybridized to 250K_Sty

value: buccal mucosa

value: oral squamous cell carcinoma tumor from buccal mucosa

value: patient 019


title: Copper-treated MTF-1 ChIP

city: Waltham

first: Hillel

last: Sims

address: 415 South Street

department: Biology

institute: Brandeis University

description: MTF-1 ChIP of copper-treated S2 cells, biological reps 1-3.

hyb_protocol: Labeled samples were hybridized to the Affymetrix GeneChip Drosophila Tiling 2.0R Array and processed using the Affymetrix Hybridization Protocol.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G.

data_processing: Data was quantile normalized and analyzed with the Affymetrix Tiling Analysis Software (TAS) and visualized using the Integrated Genome Browser (IGB). Signal and p-value statistics were reported in BAR files.

organism: Drosophila melanogaster

source_name: MTF-1 ChIP DNA from Drosophila S2 cells, copper

label_protocol: Input and ChIP samples were random primed and amplified in the presence of 1 to 5 dUTP to dTTP. 7.5 µg of DNA was fragmented by APE1 and UDG, followed by biotinylated ddATP labeling to the ends of the fragments.

growth_protocol: S2 cells were grown in Schneider's medium with 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol: One 6-well plate with 2 x 10^6 S2 cells/well were used for each condition. After cells adhered, media was aspirated and 3mls of fresh media with 500 uM Cu, 50 uM Cd or water (non-treated) was added to each well. After 4hrs, cells were crosslinked adding formaldehyde to 11% for 15 minutes. Cells were then washed twice with 0.1M Tris 7.5 in 1X PBS followed by resuspension in 1X PBS 0.5% Triton X-100 on ice for 10 minutes. Nuclei were pelleted and resuspended in lysis buffer (1X PBS, 50mM Hepes, 2mM EDTA, 1% Triton, 0.1% SDS, 0.2mg/ml RNase A, protease inhibitor) and 2% sarkosyl. Samples were sonicated for thirty seconds with single-second pulse intervals. Samples were pelleted and further sonicated till the majority of DNA was sheared to approximately 500bp. ChIP using an MTF-1 antibody was carried out essentially as described in Marr et al. (2006) Coactivator cross-talk specifies transcriptional output. Genes & development 20(11):1458-1469 (PMID 16751183). The MTF-1 antibody (non-commercial) was raised against the N-terminal region (amino acids 1-113) and an internal acidic-rich region (amino acids 406-540) of MTF-1 fused to GST.

treatment_protocol: Cells were treated with 500 µM copper, 50 µM cadmium, or water in media for 4 hours.

value: copper

tag: chip antibody

source_name: Input DNA from Drosophila S2 cells, copper


title: no lymph node metastasis patient 017, cancer, Homogenized

description: Hybridized to 250K_Sty

value: female

value: patient 017


title: Cadmium-treated MTF-1 ChIP

description: MTF-1 ChIP of cadmium-treated S2 cells, biological reps 1-3.

source_name: MTF-1 ChIP DNA from Drosophila S2 cells, cadmium

value: cadmium

source_name: Input DNA from Drosophila S2 cells, cadmium

extract_protocol: One 6-well plate with 2 x 10^6 S2 cells/well were used for each condition. After cells adhered, media was aspirated and 3mls of fresh media with 500 uM Cu, 50 uM Cd or water (non-treated) was added to each well. After 4hrs, cells were crosslinked adding formaldehyde to 11% for 15 minutes. Cells were then washed twice with 0.1M Tris 7.5 in 1X PBS followed by resuspension in 1X PBS 0.5% Triton X-100 on ice for 10 minutes. Nuclei were pelleted and resuspended in lysis buffer (1X PBS, 50mM Hepes, 2mM EDTA, 1% Triton, 0.1% SDS, 0.2mg/ml RNase A, protease inhibitor) and 2% sarkosyl. Samples were sonicated for thirty seconds with single-second pulse intervals. Samples were pelleted and further sonicated till the majority of DNA was sheared to approximately 500bp.


title: S51 4398482027_D2

description:
4398482027_D2
Bisulfite Treated DNA

value: mesenchymal stem cell


title: Non-treated MTF-1 ChIP

description: MTF-1 ChIP of untreated S2 cells, biological reps 1-3.

source_name: MTF-1 ChIP DNA from Drosophila S2 cells, untreated

source_name: Input DNA from Drosophila S2 cells, untreated


title: no lymph node metastasis patient 016, cancer, Homogenized

description: Hybridized to 250K_Sty

value: male

value: floor of mouth

value: oral squamous cell carcinoma tumor from floor of mouth

value: patient 016


title: Ewing sarcoma E7 4398482027_D1

description:
4398482027_D1
Bisulfite Treated DNA

value: primary Ewing sarcoma tumor


title: lymph node metastasis patient 015, cancer, Homogenized

description: Hybridized to 250K_Sty

value: upper gingiva

value: lymph node metastasis

value: oral squamous cell carcinoma tumor from upper gingiva

value: patient 015


title: Ewing sarcoma E4 4398482045_C2

description:
4398482045_C2
Bisulfite Treated DNA


title: M7 4428661019_C1

description:
4428661019_C1
Bisulfite Treated DNA


title: Water Control-Recovery, biological replicate 3

description: messenger RNA

source_name: sperm, water, recovery

value: Fischer 344

value: sperm

value: water

value: yes


title: M7 4398482027_C2

description:
4398482027_C2
Bisulfite Treated DNA


title: HD-Recovery, biological replicate 10

description: messenger RNA


title: no lymph node metastasis patient 014, cancer, Homogenized

description: Hybridized to 250K_Sty

value: buccal mucosa

value: oral squamous cell carcinoma tumor from buccal mucosa

value: patient 014


title: HD-Recovery, biological replicate 9

description: messenger RNA


title: Water Control-Recovery, biological replicate 2

description: messenger RNA


title: Water Control-Recovery, biological replicate 1

description: messenger RNA


title: HD-Recovery, biological replicate 5

description: messenger RNA


title: lymph node metastasis patient 006, cancer, Homogenized

description: Hybridized to 250K_Sty

value: patient 006


title: HD-Recovery, biological replicate 8

description: messenger RNA


title: no lymph node metastasis patient 010, cancer, Homogenized

description: Hybridized to 250K_Sty

value: male

value: tongue

value: oral squamous cell carcinoma tumor from tongue

value: patient 010


title: no lymph node metastasis patient 007, cancer, Homogenized

description: Hybridized to 250K_Sty

value: patient 007


title: no lymph node metastasis patient 013, cancer, Homogenized

description: Hybridized to 250K_Sty

value: female

value: patient 013


title: no lymph node metastasis patient 011, cancer, Homogenized

description: Hybridized to 250K_Sty

value: lower gingiva

value: oral squamous cell carcinoma tumor from lower gingiva

value: patient 011


title: lymph node metastasis patient 008, cancer, Homogenized

description: Hybridized to 250K_Sty

value: lymph node metastasis

value: patient 008


title: no lymph node metastasis patient 009, cancer, Homogenized

description: Hybridized to 250K_Sty

value: patient 009


title: Ewing sarcoma E4 4398482027_C1

description:
4398482027_C1
Bisulfite Treated DNA

value: primary Ewing sarcoma tumor


title: no lymph node metastasis patient 005, cancer, Homogenized

description: Hybridized to 250K_Sty

value: patient 005


title: HD-Recovery, biological replicate 7

description: messenger RNA

value: Fischer 344

value: sperm

value: yes


title: Ewing sarcoma E2 4398482045_B2

description:
4398482045_B2
Bisulfite Treated DNA


title: Ewing sarcoma E1 4398482027_A1

description:
4398482027_A1
Bisulfite Treated DNA


title: Ewing sarcoma E1 4398482045_A2

description:
4398482045_A2
Bisulfite Treated DNA


title: Ewing sarcoma E8 4398482006_C2

description:
4398482006_C2
Bisulfite Treated DNA


title: Ewing sarcoma E3 4398482006_H1

description:
4398482006_H1
Bisulfite Treated DNA


title: Ewing sarcoma E2 4398482027_B1

description:
4398482027_B1
Bisulfite Treated DNA


title: HD-Recovery, biological replicate 14

description: messenger RNA


title: HD-Recovery, biological replicate 6

description: messenger RNA


title: TSC22D4 Knockdown Mouse Liver 1 + 2 (pool)

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

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

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of Mouse430_2 -type from Affymetrix. A Custom CDF Version 12 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

source_name: Liver, excized after 1 week of knockdown

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

growth_protocol: Mice were fed ad libitum and sacrificed in the morning.

extract_protocol: RNeasy Mini Kit (Quiagen)

treatment_protocol: Adenovirus mediated shRNA knockdown of TSC22D4 in the liver

tag: genotype/variation


title: Reference Mouse Liver 5 + 6 (pool)

value: Adenovirus mediated shRNA control

value: Liver, excized 1 week after injection with shRNAcontrol adenovirus


title: HD-Recovery, biological replicate 4

description: messenger RNA


title: TSC22D4 Knockdown Mouse Liver 3 + 4 (pool)

value: Adenovirus mediated shRNA knockdown of TSC22D4

value: Liver, excized after 1 week of knockdown


title: Ewing sarcoma E8 4398482051_C1

description:
4398482051_C1
Bisulfite Treated DNA


title: TSC22D4 Knockdown Mouse Liver 5 + 6 (pool)


title: no lymph node metastasis patient 003, cancer, Homogenized

description: Hybridized to 250K_Sty

value: male

value: patient 003


title: Reference Mouse Liver 1 + 2 (pool)


title: Ewing sarcoma E11 4398482051_D1

description:
4398482051_D1
Bisulfite Treated DNA


title: HD-Recovery, biological replicate 2

description: messenger RNA


title: HD-Recovery, biological replicate 1

description: messenger RNA


title: HD-Recovery, biological replicate 3

description: messenger RNA


title: Water Control, biological replicate  20

description: messenger RNA

source_name: sperm, water

value: water

value: no


title: Reference Mouse Liver 3 + 4 (pool)


title: Ewing sarcoma E3 4398482025_H2

description:
4398482025_H2
Bisulfite Treated DNA


title: lymph node metastasis patient 002, cancer, Homogenized

description: Hybridized to 250K_Sty

source_name: surgically resected material

value: tongue

value: oral squamous cell carcinoma tumor from tongue

value: patient 002


title: Ewing sarcoma E11 4398482006_D2

description:
4398482006_D2
Bisulfite Treated DNA


title: lymph node metastasis patient 001, cancer, Homogenized

description: Hybridized to 250K_Sty

value: lymph node metastasis

value: patient 001


title: MG63_cell line

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc.

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: osteosarcoma cell line

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: OS Cell lines were cultured as recommended by the suppliers

extract_protocol: Total RNA extracted using IsoGen lysis buffer following manufacturer's instructions.

tag: cell line

tag: tissue/cell type

value: osteosarcoma


title: HsOS-1_cell line


title: MNNG/HOS_cell line

value: MNNG/HOS


title: SK-ES-1 4756083018_R002_C009

description:
4756083018_R002_C009
Bisulfite Treated DNA

source_name: EWS Cell Line


title: Water Control, biological replicate  19

description: messenger RNA

value: Fischer 344

value: sperm


title: Water Control, biological replicate  18

description: messenger RNA


title: HuO3N1_cell line


title: SK-ES-1 4398482045_E1

description:
4398482045_E1
Bisulfite Treated DNA


title: Water Control, biological replicate  16

description: messenger RNA


title: SK-ES-1 4398482025_C2

description:
4398482025_C2
Bisulfite Treated DNA


title: SaOS2_cell line


title: SK-ES-1 4428661019_E2

description:
4428661019_E2
Bisulfite Treated DNA


title: Water Control, biological replicate  15

description: messenger RNA


title: Water Control, biological replicate  17

description: messenger RNA


title: 1_nebulin_+/+ [mRNA]

description: quadriceps RNA of mouse WT1 with both nebulin alleles

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of Mouse430_2 -type from Affymetrix. A Custom CDF Version 13 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

source_name: mouse WT1 wild type

extract_protocol: RNA was isolated from quadriceps using Trizol®-Reagent (Gibco brl). and Qiagen RNeasy Kit

value: nebulin +/+

value: quadriceps


title: 2_nebulin_+/+ [mRNA]

description: quadriceps RNA of mouse WT2 with both nebulin alleles

source_name: mouse WT2 wild type


title: 3_nebulin_+/+ [mRNA]

description: quadriceps RNA of mouse WT3 with both nebulin alleles

source_name: mouse WT3 wild type


title: HuO9N2_cell line


title: NOS1_cell line


title: SK-ES-1 4398482006_C1

description:
4398482006_C1
Bisulfite Treated DNA


title: OS67_biopsy_sample

source_name: osteosarcoma biopsy sample

tag: age

value: F

tag: subtype

value: Osteoblastic

value: Tibia

value: proximal

tag: chemotherapeutic response

value: Poor


title: Ewing sarcoma E6 4398482006_B2

description:
4398482006_B2
Bisulfite Treated DNA

source_name: Primary Tumor Sample

tag: tissue

value: primary Ewing sarcoma tumor


title: Ewing sarcoma E6 4398482051_B1

description:
4398482051_B1
Bisulfite Treated DNA


title: HD, biological replicate 20

description: messenger RNA

source_name: sperm, HD

tag: strain

tag: treatment

tag: recovery

value: no


title: Water Control, biological replicate  14

description: messenger RNA

value: water


title: SK-N-MC 4756083018_R001_C009

description:
4756083018_R001_C009
Bisulfite Treated DNA

tag: sample group

value: SK-N-MC


title: 1_nebulin_+/- [mRNA]

description: quadriceps RNA of mouse HZ1 with one nebulin allele

source_name: mouse HZ1 heterozygous

value: nebulin +/-


title: 2_nebulin_+/- [mRNA]

description: quadriceps RNA of mouse HZ2 with one nebulin allele

source_name: mouse HZ2 heterozygous


title: U2_cell line


title: 3_nebulin_+/- [mRNA]

description: quadriceps RNA of mouse HZ3 with one nebulin allele

source_name: mouse HZ3 heterozygous


title: Water Control, biological replicate  12

description: messenger RNA


title: OS52_biopsy_sample

tag: gender

value: M

value: Chondroblastic

value: Femur

value: distal


title: OS64_biopsy_sample

value: osteosarcoma

value: Humerus

value: Good


title: SK-N-MC 4428661019_D2

description:
4428661019_D2
Bisulfite Treated DNA


title: SK-N-MC 4398482045_D1

description:
4398482045_D1
Bisulfite Treated DNA


title: Water Control, biological replicate  13

description: messenger RNA

value: Fischer 344

value: sperm


title: Water Control, biological replicate  11

description: messenger RNA


title: HD, biological replicate 18

description: messenger RNA


title: OS51_biopsy_sample

value: Osteoblastic


title: HD, biological replicate 19

description: messenger RNA


title: OS65_biopsy_sample

value: Tibia

value: proximal


title: SK-N-MC 4398482025_B2

description:
4398482025_B2
Bisulfite Treated DNA


title: tni (Replicate 2)

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: tni (Replicate 2)

hyb_protocol: 1650ng of cy3 labeled samples were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: The normalization was done using GeneSpring GX 11.5 Software. Recommended 75th Percentile Shift Normalization.

source_name: tni mutant

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Long day conditions (16hrs light 8 hrs dark)

extract_protocol: RNeasy Plant Mini Kit (Qiagen, Germany)

tag: ecotype

value: 1-3 mm 5th leaf

value: tni mutant


title: HD, biological replicate 16

description: messenger RNA

value: no


title: OS50_biopsy_sample

value: Poor


title: SK-N-MC 4398482006_B1

description:
4398482006_B1
Bisulfite Treated DNA

extract_protocol: Standard Illumina Protocol

value: SK-N-MC


title: Col-0 (Replicate 2)

description: Col-0 (Replicate 2)

source_name: wild type

value: wild type


title: OS49_biopsy_sample

value: M

value: Pelvis


title: Col-0 (Replicate 1)

description: Col-0 (Replicate 1)


title: Ewing sarcoma E5 4398482051_A1

description:
4398482051_A1
Bisulfite Treated DNA

value: primary Ewing sarcoma tumor


title: OS48_biopsy_sample

value: F

value: osteosarcoma

value: Metatarsal


title: OS46_biopsy_sample

value: Fibroblastic

value: distal

value: Good


title: Ewing sarcoma E5 4398482006_A2

description:
4398482006_A2
Bisulfite Treated DNA


title: A673 4756083018_R008_C008

description:
4756083018_R008_C008
Bisulfite Treated DNA


title: HD, biological replicate 14

description: messenger RNA

value: Fischer 344

value: sperm


title: HD, biological replicate 13

description: messenger RNA


title: tni (Replicate 1)

description: tni (Replicate 1)

value: 1-3 mm 5th leaf


title: A673 4428661019_H2

description:
4428661019_H2
Bisulfite Treated DNA


title: HD, biological replicate 15

description: messenger RNA


title: HD, biological replicate 17

description: messenger RNA


title: OS45_biopsy_sample

value: Osteoblastic

value: Femur


title: A673 4428661019_C2

description:
4428661019_C2
Bisulfite Treated DNA


title: OS38_biopsy_sample


title: OS44_biopsy_sample

value: Tibia

value: proximal


title: OS36_biopsy_sample

value: Poor


title: A673 4398482025_A2

description:
4398482025_A2
Bisulfite Treated DNA


title: A673 4398482045_H1

description:
4398482045_H1
Bisulfite Treated DNA


title: A673 4398482006_A1

description:
4398482006_A1
Bisulfite Treated DNA


title: OS32_biopsy_sample

value: M


title: OS35_biopsy_sample


title: 30-A2-2-6 CTCF

city: Bethesda

first: Junfang

last: Zhang

state: MD

address: 37 Convent Dr.

department: NCI-CCR

institute: NIH

description: myeloid leukemia cell line with virus integration in Mml1`

hyb_protocol: A total of 3 µg of labeled ChIP and input DNA was cohybridized to the chip for 40 hours at 65°C

scan_protocol: scanned on an Agilent Scanner with Agilent Scan Control 7.0 software

data_processing: Data was extracted with Feature Extraction 9.1 software and analyzed using ChIP Analytics 1.3 software (Agilent).

label_protocol: A total of 2.5 µg of amplified DNA was labeled with Cy3 (input) or Cy5 (IP) dUTP (PerkinElmer Life and Analytical Sciences) using the CGH labeling kit (Invitrogen).

growth_protocol:
Tumor cell were cultured in Dulbecco modified Eagle medium with 10% (v/v) fetal bovine serum
Tumor cell were cultured in Dulbecco modified Eagle medium with 10% (v/v) fetal bovine serum
The murine myeloid cell line M1 was maintained in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum (Invitrogen). All tumor cell lines were cultured in Dulbecco modified Eagle medium with 10% (v/v) fetal bovine serum.

extract_protocol: Chromatin immunoprecipitation assays was conducted as previously described (Paul, Bies et al. 2010). Cells were fixed in 0.8% formaldehyde for 6 minutes at room temperature. After lysis, samples were sonicated to a size range of 200 to 1000 bp. Chromatin (150-200 µg) was immunoprecipitated with antibodies for H3K4me3 (Abcam, ab8580), H3K4me1 (Abcam, ab8895), H3K9/14Ac (Upstate, 06-599), CTCF (Abcam, ab70303), H3K9me3 (Abcam, ab8898), H3K27me3 (Upstate,17-622),or rabbit IgG (Sigma-Aldrich, 15006). A 10% aliquot was removed as an input fraction. ChIP DNA and input DNA were amplified using WGA2 kit (Sigma-Aldrich).

treatment_protocol: For cell differentiation, M1 cells were seeded at a density of 1-2 x 105 cells / ml in medium containing interleukin-6 (IL-6) for 4-5 days.

tag: c-myb expression

value: Yes

tag: antibody

value: CTCF


title: 30-C-19 CTCF

description: myeloid leukemia cell line with virus integration in Mml1

value: Tumor 30-C-19

source_name: 30-C-19 Input


title: HD, biological replicate 11

description: messenger RNA

value: no


title: 30-3-14 CTCF


title: Water Control, biological replicate 9

description: messenger RNA

value: water


title: Water Control, biological replicate 10

description: messenger RNA


title: Water Control, biological replicate 8

description: messenger RNA


title: HD, biological replicate 12

description: messenger RNA


title: 30-C-18 CTCF

value: Tumor 30-C-18

source_name: 30-C-18 Input


title: 30-2-7 CTCF

description: myeloid leukemia cell line with virus integration in Mml3


title: Water Control, biological replicate 6

description: messenger RNA

source_name: sperm, water


title: OS28_biopsy_sample

value: osteosarcoma


title: OS27_biopsy_sample

value: F


title: A673 4398482045_C1

description:
4398482045_C1
Bisulfite Treated DNA

data_processing: BeadStudio software v3.2


title: OS26_biopsy_sample

value: Telangiectatic


title: Water Control, biological replicate 7

description: messenger RNA

value: Fischer 344

value: sperm


title: Fusobacterium nucleatum in 33% blood

city: Oklahoma City

first: Justin

last: Merritt

state: OK

address: 975 NE 10th St BRC364

department: Oral Biology

institute: University of Oklahoma Health Sciences Center

description: Standard 49 format custom GeneChip.

hyb_protocol: The hybridization and washing procedures were performed similarly as recommended in the GeneChip® Expression Analysis Technical Manual with some minor modifications. The hybridization buffer consisted of 1x MES buffer (100 mM morpholineethanesulfonic acid [MES], 1M NaCl, 20 mM EDTA, 0.01% Tween-20), 50 pM B2 control oligo, 0.1 mg/mL herring sperm DNA, 0.5 mg/mL BSA, and the fragmented, labeled cDNA in a total volume of 200 µL. The hybridization solution was then loaded into the microarray cartridge and mixed for 16 hr at 60 rpm and 47°C in an Affymetrix hybridization oven. After the incubation period, the hybridization solution was removed and the array was washed and stained in the Affymetrix Fluidics Station 450 using a slightly modified script of the standard wash script file “ProkGE-WS2v3-450”, which increased the wash stringency from 45°C to 47°C. The staining solution consisted of 3 different MES buffers each in a 600 µL total volume. The first consisted of 1x MES buffer, 2 mg/mL BSA, and 10 µg/mL streptavidin, the second consisted of 1x MES buffer, 2 mg/mL BSA, 0.1 mg/mL goat IgG, and 5 µg/mL biotin anti-streptavidin, and the third solution consisted of 1x MES buffer, 2 mg/mL BSA, and 10 µg/mL streptavidin-phycoerythrin (Molecular Probes, Eugene, OR).

scan_protocol: The GeneChips® were scanned at 570 nM using an Affymetix 7G laser scanner.

data_processing: Analysis of signal intensities was performed using GeneChip® Operating Software (GCOS) ver. 1.4, and gene expression data were compared using the GCOS batch analysis function. Normalization procedures are performed directly by the software using a script designed by Affymetrix and provided with the F. nucleatum custom array. This eliminates user bias during the normalization procedure.

organism: Fusobacterium nucleatum subsp. nucleatum ATCC 25586

source_name: Fusobacterium nucleatum, 33% blood

label_protocol: 32 µL of fragmented cDNA was labeled with the BioArray terminal labeling kit (Enzo, New York, NY) in a total volume of 50 µL containing 10 µL 5x buffer, 5 µL 10x CoCl2, and 2 µL terminal deoxynucleotide transferase. The reaction was incubated at 37°C for 60 min.

growth_protocol: Cells were first grown to stationary phase in Columbia broth, which was then used as a starter culture to inoculate SDM cultures. Stationary phase cells were diluted 1:200 in 20 mL of SDM and grown 16 hrs overnight to early log phase (OD600 0.3 – 0.5). The following day, the 9% and 33% sheep blood was added to some cultures before incubating anaerobically for 3h at 37°C.

extract_protocol: Briefly, the cell pellets were resuspended in chilled Tris-EDTA buffer on ice and transferred to a 2-ml screw-cap tube containing 500 μl 0.1-mm silica beads. 900μl of preheated acidic phenol (pH 4.3) and 140μl of 10% sodium dodecyl sulfate were immediately added to the mixture and submitted to two consecutive 30-s homogenization cycles with a FastPrep-24 system set at a speed of 6.0 M/s, followed by acidic phenol-chloroform extraction and isopropyl alcohol precipitation. After treatment with RNase-free DNase, RNA was further purified over RNeasy spin columns. The resulting RNA integrity was confirmed by the presence of clearly defined rRNA bands in agarose gels.

treatment_protocol: Cells were harvested by centrifugation and lysed using a beat-beater.

tag: blood


title: M1+IL-6 CTCF

description: M1 cells treated with IL-6 for 5 days

source_name: M1+IL-6 CTCF

growth_protocol:
M1cells were seeded in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum and treated with interleukin-6 (IL-6) for5 days
M1cells were seeded in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum and treated with interleukin-6 (IL-6) for5 days
The murine myeloid cell line M1 was maintained in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum (Invitrogen). All tumor cell lines were cultured in Dulbecco modified Eagle medium with 10% (v/v) fetal bovine serum.

value: No

source_name: M1+IL-6 Input


title: Fusobacterium nucleatum in 9% blood

description: Standard 49 format custom GeneChip.

source_name: Fusobacterium nucleatum, 9% blood


title: Fusobacterium nucleatum in 0% blood

description: Standard 49 format custom GeneChip.

source_name: Fusobacterium nucleatum, 0% blood


title: M1 CTCF

description: untreated myeloblastic M1 cells

source_name: M1 CTCF

growth_protocol:
M1 was maintained in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum
M1 was maintained in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum
The murine myeloid cell line M1 was maintained in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum (Invitrogen). All tumor cell lines were cultured in Dulbecco modified Eagle medium with 10% (v/v) fetal bovine serum.

value: Myeloid M1

source_name: M1 Input


title: 30-3-14 H3K9me3


title: Water Control, biological replicate 3

description: messenger RNA


title: Water Control, biological replicate 4

description: messenger RNA


title: OS20_biopsy_sample

source_name: osteosarcoma biopsy sample

value: Chondroblastic

value: Femur

value: distal


title: 30-C-18 H3K9me3

value: Tumor  30-C-18


title: OS25_biopsy_sample

value: M

value: Osteoblastic

value: Pelvis

value: Poor


title: OS17_biopsy_sample

value: Humerus

value: proximal

value: Good


title: Water Control, biological replicate 5

description: messenger RNA

value: water

value: no


title: OS18_biopsy_sample

value: F

value: osteosarcoma

value: Telangiectatic


title: OS13_biopsy_sample


title: M1 H3K9me3

description: untreated myeloblastic M1 cells

source_name: M1 H3K9me3

value: Myeloid M1

value: Yes


title: M1+IL6 H3K9me3

description: M1 cells treated with IL-6 for 5 days

source_name: M1+IL6 H3K9me3

value: No

source_name: M1+IL6 Input


title: OS03_biopsy_sample

value: Femur

value: distal


title: 30-3-14 H3K27me3


title: M1+IL6 H3K27me3

description: M1 cells treated with IL-6 for 5 days

source_name: M1+IL6 H3K27me3


title: 30-C-18 H3K27me3

value: Tumor  30-C-18


title: HD, biological replicate 9

description: messenger RNA

source_name: sperm, HD

value: Fischer 344

value: sperm


title: Water Control, biological replicate 1

description: messenger RNA


title: HD, biological replicate 10

description: messenger RNA


title: HD, biological replicate 8

description: messenger RNA


title: M1 H3K27me3 rep1

description: untreated myeloblastic M1 cells

source_name: M1 H3K27me3 rep1


title: M1 H3K27me3 rep2

description: untreated myeloblastic M1 cells

source_name: M1 H3K27me3 rep2


title: Water Control, biological replicate 2

description: messenger RNA


title: biological replicate 5: 72h DFO 20µM+FAC 20µM

city: RENNES

first: DOYARD

last: Mathilde

address: rue Henri Le Guilloux

country: France

institute: INSERM

description:
gene expression after 72h of DFO 20µM+FAC 20µM treatment
267_3.txt
DFO+FAC_5

hyb_protocol: 1,65μg of each sample cRNA were hybridized using in situ Gene Expression Hybridization kit on Agilent Human Whole Genome Microarrays 4 × 44 K at 60°C, during 17h at 10rpm in the dark.

scan_protocol: Slides were scanned with the dynamic autofocus G2565BA Agilent scanner. Probe feature information was extracted using the Agilent Feature Extraction software v.10.7.

data_processing: Raw intensities were log2-transformed and normalized (median centering within and between arrays) with GeneSpring GX software v11.5.

label: Cy 3

label_protocol: Total RNA (350ng) were amplified and labelled using a One Color Agilent’s low RNA Imput Linear Amplification Kit PLUS according to the manufacturer protocol (Agilent).

growth_protocol: The osteoblast-like MG-63 cells were maintained in minimum essential medium supplemented with 10% fetal bovine serum, 2mM L-Glutamine, 1% non essential amino acids and 1% penicillin/streptomycin.

extract_protocol: Total RNAs were extracted using the SV Total RNA Isolation System (Promega®).

treatment_protocol: Ferric Ammonium Citrate and/or Desferioxamine were added or not during three days each day when cells reached confluence.

value: MG-63 osteoblastic cell line


title: HD, biological replicate 5

description: messenger RNA


title: 30-A2-2-6 H3K4me1


title: 30-2-7 H3K4me1


title: HD, biological replicate 7

description: messenger RNA


title: biological replicate 4: 72h DFO 20µM+FAC 20µM

description:
gene expression after 72h of DFO 20µM+FAC 20µM treatment
129_3.txt
DFO+FAC_4


title: HD, biological replicate 3

description: messenger RNA


title: RCS-L

city: College Park

first: Juan

last: Luo

address: RM1122, BLDG142, Animal & Avian Sciences

department: Animal & Avian Sciences

institute: University of Maryland

description: CGH in RCS-L

data_processing: The hybridization, normalization and segmentation analysis were performed by NimbleGen Systems Inc. (Madison, USA). A detailed description of their technical specifics can be found on http://www.nimblegen.com/products/lit/lit.html.Briefly, the segments with five or more probes having a mean log2 ratio greater than ±0.5 (0.5_5) were chosen as candidate CNVs.

organism: Gallus gallus

source_name: Genomic DNA from RCS-L red blood cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: Genomic DNA from 20μl red blood cells was extracted using the DNeasy bBlood & Tissue Mini Kit (Qiagen, USA).

value: RCS-L, moderate resistant to MD

tag: cell type

value: red blood cells

source_name: Genomic DNA from Red Junglefowl red blood cells

tag: reference

value: DNA from Red Junglefowl


title: biological replicate 3: 72h DFO 20µM+FAC 20µM

description:
gene expression after 72h of DFO 20µM+FAC 20µM treatment
266_3.txt
DFO+FAC_3

tag: cell line


title: L72-1

description: CGH in L72-1

hyb_protocol: The hybridization, normalization and segmentation analysis were performed by NimbleGen Systems Inc. (Madison, USA). A detailed description of their technical specifics can be found on http://www.nimblegen.com/products/lit/lit.html.

source_name: Genomic DNA from L72 red blood cells

value: L72, highly susceptible to MD


title: HD, biological replicate 4

description: messenger RNA

value: no


title: 30-3-14 H3K4me1


title: HD, biological replicate 2

description: messenger RNA


title: 2101_pool_s_3 with array type SUNFLOWER from Affymetrix

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

description: The aim of this project is to assess the possibility of implementing transcriptomic studies on sunflower plants grown in field assays. Data obtained from plants under drought in the glasshouse have already obtained. We intend to use these results as a template and see if the field offers the possibility of carrying these studies. In order to do so, treatment-effect as well as intra and inter-plot variability will be assessed.

hyb_protocol: labelled extract quantity: 10ug

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

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

organism: Helianthus annuus

label_protocol: labelling Biotin indirect, amplification=yes, ssDNA 5.5 ug.

growth_protocol: caulin leaf - - Plants were grown at INRA in Auzeville (Haute Garonne, France). They were sown on 7th May 2009 and the tissue used for the chip hybridizations was harvested on 30th July 2009, that is 85-day-long cultivation.

treatment_protocol: Name:ABSENCE OF IRRIGATION - environmental treatment - abiotic stress,water:time 30day .

tag: harvest date

tag: developmental stage

value: flowering stage (Boyes et al. Plant Cell 2001)

tag: condition

value: absence of irrigation


title: L72-2

description: CGH in L72-2

scan_protocol: The hybridization, normalization and segmentation analysis were performed by NimbleGen Systems Inc. (Madison, USA). A detailed description of their technical specifics can be found on http://www.nimblegen.com/products/lit/lit.html.


title: RCS-M

description: CGH in RCS-M

source_name: Genomic DNA from RCS-M red blood cells

value: RCS-M, moderate susceptible to MD


title: L63-2

description: CGH in L63-2

source_name: Genomic DNA from L63 red blood cells

value: L63, highly resistant to MD


title: 2915_pool_i_4 with array type SUNFLOWER from Affymetrix

treatment_protocol: Name:IRRIGATION - environmental treatment - hydrometry,tr_m,water:quantity 1 time 30day .  TR_M. Il correspond au ratio entre levapotranspiration réelle et levapotrnaspiration maximale. En étant un ratio, il ny a pas dunités. On nutilise pas water donc, en tant que facteur.

tag: age

value: irrigation


title: 30-C-18 H3K4me1

value: Tumor 30-C-18

value: Yes

source_name: 30-C-18 Input