title: UMA07166_rep1

description: A_4×44K_251485053224-1Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7166


title: UMA07151

status: Public on Nov 08 2011

type: RNA

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

country: USA

institute: University of North Carolina at Chapel Hill

description: A_4×44K_251485042800-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7151

hyb_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were analyzed with Agilent software.

data_processing: Data for both channels were Lowess-normalized using the University of North Carolina (UNC) microarray database, and then the log(2) ratio (test/reference) was taken.

molecule: total RNA

organism: Homo sapiens

source_name: Human Reference B

extract_protocol: Total RNA isolated by Stratagene.

tag: sample type

value: reference

tag: composition

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

source_name: Reduction Mammoplasty

extract_protocol: Qiagen RNeasy Kit.

tag: tissue

value: normal breast

tag: bmi


title: UMA07169

description: A_4×44K_251485051501-3Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7169

label_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).


title: UMA07168

description: A_4×44K_251485053222-3Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7168


title: UMA07165

description: A_4×44K_251485053221-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7165


title: Subject 10_t=30days_resveratrol

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: The Affymetrix GeneChip Human Gene 1.1 ST 24-array plate consists of 24 single Gene 1.1 ST arrays arranged into the standard 96 well plate format. For this experiment 20 arrays were used. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.16.0).

label: biotin

source_name: after 30 days intervention with resveratrol

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

growth_protocol: Ten healthy obese men (age 45–65 years; BMI 30-35 kg/m2) participated in a double-blind randomized cross-over study. Exclusion criteria were unstable body weight (weight gain or loss > 3 kg in the last three months), total body fat (%) < 25%, fasting plasma glucose > 6.1 mmol/l, hemoglobin < 7.8 mmol/l, engagement in programmed exercise > 2 hours total per week, impaired kidney and/ or hepatic function, first- or second-degree family member with type 2 diabetes mellitus, any medical condition requiring treatment and/or medication use, intake of dietary supplements except vitamins and minerals, unwilling to restrict high-resveratrol-containing foods, current alcohol consumption > 20 grams/day, participation in another biomedical study within 1 month before the first screening visit, a contraindication to MRI scanning. All subjects were informed about the nature of the study and written informed consent was obtained before study participation. The local Medical Ethical Committee of Maastricht University Medical Centre approved the study protocol.

extract_protocol: Skeletal muscle biopsies were taken in the morning of day 30 after an overnight fast. Biopsies were obtained from the vastus lateralis muscle under local anesthesia of the skin and fascia using the Bergström method with suction, cleaned from any visible fat and blood, immediately frozen in isopentane at its melting point, and stored at −80C until analysis.

treatment_protocol: The design of the study was a randomized cross-over design with two different treatments: placebo and resVida (150mg/day trans-resveratrol). Subjects were instructed to take the first supplement on the day after baseline measurements (d1) and the last supplement in the evening on day 29. In the morning of day 30, after a 36h in the respiration chamber, a muscle biopsy was taken, which was followed by the withdrawal of a fasting blood sample.

tag: ethnic background

value: Caucasian

tag: gender

value: male

tag: age

value: 45-65 years

value: vastus lateralis muscle


title: UMA07166

description: A_4×44K_251485053222-1Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7166


title: UMA07156

description: A_4×44K_251485042802-2Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7156


title: Subject 9_t=30days_placebo

source_name: after 30 days intervention with placebo


title: UMA07160

description: A_4×44K_251485053221-3Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7160


title: UMA07152

description: A_4×44K_251485048332-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7152


title: UMA07157

description: A_4×44K_251485053221-2Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7157


title: TLX1_VI

city: New York

first: Adolfo

last: Ferrando

state: NY

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

hyb_protocol: Affymetrix standard protocol.

scan_protocol: Affymetrix standard protocol.

data_processing: Array normalization was performed by DNAChip-Analyzer (dChip) by using Genepattern software

organism: Mus musculus

source_name: T-cell lymphoblastic tumor from TLX1 transgenic mouse

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

growth_protocol: Cells extracted from T-cell lymphoblastic tumor

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

treatment_protocol: No treatment

tag: strain

tag: cell type

value: T-cell lymphoblasts

tag: tlx1 status

value: TLX1 positive lymphoma

tag: genotype/variation

value: TLX1 transgenic


title: Subject 8_t=30days_placebo


title: TLX1_I


title: UMA07150

description: A_4×44K_251485042802-1Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7150


title: TLX1_V


title: TLX1_IV


title: TLX1_RUNX1_V

source_name: T-cell lymphoblastic tumor from TLX1 transgenic and RUNX heterozygous crossed mouse

value: TLX1 negative lymphoma


title: UMA07149

description: A_4×44K_251485048332-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7149


title: TLX1_III


title: UMA07148

description: A_4×44K_251485042800-3Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7148


title: TLX1_RUNX1_IV

value: TLX1 transgenic and RUNX heterozygous crossed


title: TLX1_II


title: Subject 7_t=30days_resveratrol


title: Subject 7_t=30days_placebo


title: TAL_LMO2_II

source_name: T-cell lymphoblastic tumor from Tal1-LMO2 double transgenic mouse

value: Tal1-LMO2 double transgenic


title: TLX1_RUNX1_I


title: Subject 6_t=30days_resveratrol


title: Subject 5_t=30days_resveratrol


title: Subject 5_t=30days_placebo


title: TAL_LMO2_I


title: UMA07144

description: A_4×44K_251485048333-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7144


title: UMA07142_rep1

description: A_4×44K_251485042709-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7142


title: UMA07143

description: A_4×44K_251485044720-1Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7143


title: TLX1_RUNX1_II


title: UMA07142

description: A_4×44K_251485044655-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7142


title: TLX1_RUNX1_III


title: UMA07140

description: A_4×44K_251485044721-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7140


title: TAL_LMO2_III


title: Subject 6_t=30days_placebo


title: ThPOK_III

source_name: T-cell lymphoblastic tumor from ThPOK transgenic mouse

value: ThPOK transgenic


title: Subject 4_t=30days_resveratrol


title: ThPOK_I


title: Subject 4_t=30days_placebo


title: ThPOK_II


title: TAL_I

source_name: T-cell lymphoblastic tumor from Tal1 transgenic mouse

value: Tal1 transgenic


title: UMA07138

description: A_4×44K_251485042805-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7138


title: Subject 3_t=30days_resveratrol


title: TAL_II


title: UMA07136

description: A_4×44K_251485048333-3Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7136


title: Pten_VI

source_name: T-cell lymphoblastic tumor from Pten knock out mouse

value: Pten knock out


title: Subject 3_t=30days_placebo


title: Subject 2_t=30days_resveratrol


title: E2A_IV

source_name: T-cell lymphoblastic tumor from rag E2A knock out mouse

value: rag E2A knock out


title: E2A_III


title: Subject 2_t=30days_placebo


title: Pten_V


title: Pten_III


title: Pten_II


title: UMA07131_rep1

description: A_4×44K_251485046987-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7131

value: reference


title: Pten_IV


title: UMA07135

description: A_4×44K_251485044721-3Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7135

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs


title: UMA07131

description: A_4×44K_251485044721-2Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7131

value: normal breast


title: pokemon_II

source_name: T-cell lymphoblastic tumor from Pokemon transgenic mouse

value: Pokemon transgenic


title: Subject 1_t=30days_placebo

value: Caucasian

value: male


title: UMA07130

description: A_4×44K_251485044721-1Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7130


title: T-lymphocytes, CD4_ healthy

city: Parma

first: Claudio

last: Casoli

address: Vicolo delle Asse 1

country: Italy

institute: GEMIB Laboratory

description: Healthy Purified_CD4+. Pool of six healthy donors.

data_processing:
Amplification signal was checked on each sample by SDS® software 2.3. Ct value was determined using auto-baseline and a threshold value of 0.2. Undetermined raw Ct values were set to 40.  The small non-coding MammU6 RNA was used  as housekeeping gene, while the RNA extracted from the pool of healthy donors was used as calibrator.The data were analyzed using Relative Quantification Manager 1.2 (Applied Biosystems) Software, based on the comparative Ct method (∆∆Ct). The software package automatically performs all deltadeltaCt-based fold-change calculations from the uploaded raw threshold cycle data.

The supplementary file contains the SDS 2.3 RQ Results.

label: FAM

source_name: CD4+ T-lymphocytes, healthy

label_protocol: A total of 100 ng of RNA from CD4+ T cells was reverse transcribed using the TaqMan® MicroRNA Reverse Transcription Kit in combination with the Megaplex™ RT Primers Pool A, which permits analysis of 377 human microRNAs of greatest interest to the research community (functionally defined and/or broadly/highly expressed) and an endogenous control. The thermal profile consisted of 40 cycles at 16°C for 2 minutes, 42°C for 1 minute and 50°C for 1 second followed by one step at 85°C for 5 minutes. The pre-amplification of the miRNA cDNA target (2,5 μl) was performed using TaqMan® PreAmp Master Mix Kit and Megaplex™ PreAmp Primers Pool A (Applied Biosystems). The thermal profile consisted of denaturation at 95°C for 10 minutes, one step at 55°C for 2 minutes followed by 2 minutes at 72°C, and 12 cycles at 95°C for 15 sec and 60°C for 4 minutes. According to manufacturer’s instructions, the preamplified cDNA product was mixed with the TaqMan® Universal PCR Master Mix, No AmpErase UNG, and loaded onto the TaqMan® MicroRNA Array A for PCR amplification. The following real-time PCR protocol was employed: 50°C for 2 minutes, 94.5°C for 10 minutes and 40 cycles at 97°C for 30 seconds and 59.7°C for 1 minute. All reactions (reverse transcription, preamplification and real-time PCR) were performed on a 7900HT Fast Real-Time PCR System (Applied Biosystems).

extract_protocol: Purified CD4+ T-lymphocytes were stored in RNAlater at -80°C or directly processed for miRNA extraction by the mirVana Isolation Kit (Ambion).

value: peripheral blood

value: CD4+ T-lymphocytes

tag: disease state

value: healthy


title: T-lymphocytes, CD4_donor_rgp120_mAbs

description: Healthy Purified_CD4+

source_name: CD4+ T-lymphocytes, rgp120+mAbs

tag: treatment

value: rgp120+mAbs exposure


title: T-lymphocytes, CD4_ donor_control

description: Healthy Purified_CD4+

source_name: CD4+ T-lymphocytes, untreated

value: untreated


title: T-lymphocytes, CD4_donor_rgp120

description: Healthy Purified_CD4+

source_name: CD4+ T-lymphocytes, rgp120

value: rgp120 exposure


title: pokemon_I

value: T-cell lymphoblasts

value: TLX1 negative lymphoma


title: Subject 1_t=30days_resveratrol

value: 45-65 years

value: vastus lateralis muscle


title: Pten_I

value: Pten knock out


title: UMA07129

description: A_4×44K_251485048333-2Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7129

value: reference


title: T-lymphocytes, CD4_donor_LAIgp120_mAbs

description: Healthy Purified_CD4+

source_name: CD4+ T-lymphocytes, HeLa-LAI+mAbs

value: HeLa-LAI+mAbs exposure


title: p53_II

source_name: T-cell lymphoblastic tumor from p53 knock out mouse

value: p53 knock out


title: p53_III


title: myb_I

source_name: T-cell lymphoblastic tumor from Cdkn2a knock out- Retroviral insertional mutagenesis mouse


title: LMO_I

source_name: T-cell lymphoblastic tumor from LMO1 transgenic mouse

value: LMO1 transgenic


title: LMO_III


title: LMO_II


title: T-lymphocytes, CD4_donor_LAIgp120

description: Healthy Purified_CD4+

source_name: CD4+ T-lymphocytes, HeLa-LAI

value: HeLa-LAI exposure


title: Nup98HoxD13_III

source_name: T-cell lymphoblastic tumor from Nup98HoxD13  transgenic mouse

value: Nup98HoxD13  transgenic


title: Nup98HoxD13_I


title: UMA07126

description: A_4×44K_251485048332-1Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7126

source_name: Human Reference B

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

source_name: Reduction Mammoplasty

value: normal breast


title: p53_I


title: UMA07113

description: A_4×44K_251485044720-3Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7113


title: pim1_ccnd3

value: Cdkn2a knock out- Retroviral insertional mutagenesis


title: Nup98HoxD13_II


title: myb_II


title: UMA07111

description: A_4×44K_251485042707-1Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7111


title: UMA07108

description: A_4×44K_251485042800-1Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7108


title: UMA07107

description: A_4×44K_251485042801-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7107


title: UMA07112

description: A_4×44K_251485042800-2Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7112


title: T-lymphocytes, Patient 18

source_name: CD4+ T-lymphocytes, MEU

value: peripheral blood

value: CD4+ T-lymphocytes

value: exposed to HIV-1

tag: stage of hiv infection

value: multiply exposed uninfected (MEU)


title: T-lymphocytes, Patient 16


title: T-lymphocytes, Patient 17


title: T-lymphocytes, Patient 14

source_name: CD4+ T-lymphocytes, naive

value: antiretroviral therapy naive


title: T-lymphocytes, Patient 13


title: T-lymphocytes, Patient 15


title: myc_mix_I

value: T-cell lymphoblasts

value: TLX1 negative lymphoma


title: mycras_mix_III


title: TLX1_RUNX1_VI

source_name: T-cell lymphoblastic tumor from TLX1 transgenic and RUNX heterozygous crossed mouse


title: UMA07106

description: A_4×44K_251485044720-2Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7106


title: Ikaros_III

source_name: T-cell lymphoblastic tumor from Ikaros Plastic  mouse

value: Ikaros Plastic


title: ras_I


title: UMA07105_rep1

description: A_4×44K_251485042805-3Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7105

value: reference


title: mycras_mix_II


title: myc_I


title: Ikaros_II


title: T-lymphocytes, Patient 12


title: myc_pure_II


title: Sec_Bcells_rep3

city: Manhasset

first: Thomas

middle: L

last: Rothstein

address: 350 Community Drive

department: Oncology and Cell Biology

institute: The Feinstien Institute for Medical Research

hyb_protocol: Labeled amplified material (750ng) was hybridized to Human whole genome HT12 arrays according to the manufacturer's instructions

scan_protocol: Micorarray scanning was done using a BeadStation array scanner

data_processing: Sample data analysis was done using Illumina's Genome Studio 2010.3 with quantile normalization

label: Cy3 streptavidin

source_name: Human Peripjheral Blood B cell subset

label_protocol: biotin UTP

growth_protocol: PBMCs were isolated from normal leukopacks using Ficoll gradient

extract_protocol: RNA was isolated using Qiagen Rneasy plus kit. RNA quantity was measured usind the Nanodro. RNA quality was determined using the Aglient bioanalyzer.

treatment_protocol: B cells were enriched using CD19+magnetic selection

value: normal

value: Sec b cell


title: UMA07104

description: A_4×44K_251485042714-3Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7104


title: Orc_Bcells_rep3

value: Orc b cell


title: Ikaros_I


title: UMA07105

description: A_4×44K_251485042714-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7105


title: T-lymphocytes, Patient 11


title: E2A_II

source_name: T-cell lymphoblastic tumor from E2A knock out mouse

value: E2A knock out


title: Orc_Bcells_rep2


title: Naïve_Bcells_rep3

value: Naïve b cell


title: UMA07101

description: A_4×44K_251485042802-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7101

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs


title: UMA07102

description: A_4×44K_251485048330-1Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7102

value: normal breast


title: T-lymphocytes, Patient 10


title: UMA07092

description: A_4×44K_251485042802-3Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7092


title: E2A_I


title: T-lymphocytes, Patient 09


title: UMA07090

description: A_4×44K_251485042803-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7090


title: Memory_Bcells_rep2

value: Memory b cell


title: T-lymphocytes, Patient 08

value: peripheral blood


title: T-lymphocytes, Patient 07

value: CD4+ T-lymphocytes


title: Memory_Bcells_rep3


title: olig2_LMO1_III

source_name: T-cell lymphoblastic tumor from olig1-LMO1 double transgenic mouse

value: olig1-LMO1 double transgenic


title: Memory_Bcells_rep1


title: olig2_LMO1_I


title: T-lymphocytes, Patient 06

source_name: CD4+ T-lymphocytes, LTNP

value: exposed to HIV-1

value: long-term non-progressor (LTNP)


title: olig2_LMO1_II

value: T-cell lymphoblasts


title: T-lymphocytes, Patient 05


title: UMA07089

description: A_4×44K_251485042803-2Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7089


title: Orc_Bcells_rep1


title: Naïve_Bcells_rep2


title: b_cat_I

source_name: T-cell lymphoblastic tumor from beta -catenin transgenic mouse

value: TLX1 negative lymphoma

value: beta -catenin transgenic


title: Sec_Bcells_rep2


title: UMA07077

description: A_4×44K_251485434103CAgilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7077

value: reference


title: b_cat_II


title: UMA07076

description: A_4×44K_251485334103BAgilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7076


title: Sec_Bcell_rep1

value: normal


title: T-lymphocytes, Patient 04


title: UMA07088_rep1

description: A_4×44K_251485042805-2Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7088


title: UMA07074

description: A_4×44K_251485042801-3Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7074


title: Naïve_Bcells_rep1


title: T-lymphocytes, Patient 02


title: T-lymphocytes, Patient 03


title: b_cat_III


title: T-lymphocytes, Patient 01


title: UMA07072

description: A_4×44K_251485042801-2Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7072


title: Hypoxia HeLa cells rep2

city: Madrid

first: eduardo

last: balsa

state: Madrid

address: Diego de león 62

department: Inmunologia

country: Spain

institute: Hospital de la Princesa

description: Gene expression of hypoxic 1% O2  6h HeLa cells

hyb_protocol: Cy3-labeled aRNA (1.65 g) was  hybridized for 17 hr at 65 C in a hybridization oven (G2545A, Agilent) set to  10 rpm in a final concentration of 13 GEx Hybridization Buffer HI-RPM,  according to manufacturer’s instructions (One-Color Microarray-Based  Gene Expression Analysis, Agilent Technologies).

scan_protocol: arrays were scanned at 5 m resolution on an Agilent DNA  Microarray Scanner (G2565BA, Agilent Technologies) using the default  settings for 4 3 44K format one-color arrays.

data_processing: standard Agilent proctocol

source_name: hypoxic 1% O2 6h HeLa cells

label_protocol: Then cDNA was converted to aRNA using T7 RNA polymerase,  which simultaneously amplifies target material and incorporates cyanine  3-labeled CTP.

extract_protocol: Total RNA was extracted using Ultraspec reagent (Biotecx, Houston, TX).

treatment_protocol: HeLa cells were culture either under normoxia or hypoxia (1% O2) for 6h.

tag: cell line

value: HeLa cells

value: 1 percent oxygen


title: UMA07073

description: A_4×44K_251485234102DAgilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7073


title: UMA07070

description: A_4×44K_251485134102BAgilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7070


title: UMA07075

description: A_4×44K_251485234103AAgilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7075


title: wild-type, passage 33 MEFs from mixed BL background 2

city: Bethesda

first: Ying

middle: E

last: Zhang

state: Maryland

address: 37 Convent Dr., Bldg.37, Rm.2056

department: LCMB/CCR

institute: National Cancer Institute, NIH

description: MEFs from a mix of 2 E14.5 embryos

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at the NCI-Frederick Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Data were processed using GeneSpringGX 11.5 software with guided workflow. Gene level expression were summarized after quantile normalized.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.mps
Notes : Created from guided workflow step : Filter on Probesets
Entity List :All Entities
Interpretation :All Samples
Experiment :Smurf2MEF
Percentile cut-off :20.0
Entities retained in which atleast 1 out of 8 sample values above cut-off
Technology : Affymetrix.ExonExprChip.MoGene-1_0-st-v1_na30_1_mm9_2009-12-08

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

growth_protocol: MEFs derived from day 11.5 mouse embryos, culturing in Dulbecco’s MEM supplemented with 10% fetal bovine serum and 100 units/ml penicillin-streptomycin.

extract_protocol: RNA was isolated from MEFs with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: not applicable

tag: passage

value: late

tag: genetic background

value: mixed 129SVJ/NIH Black Swiss (BL)

tag: genotype

value: wild-type

value: embryonic fibroblast


title: UMA07071

description: A_4×44K_251485234102CAgilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7071

tag: sample type

tag: composition

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

value: normal breast


title: Smurf2-/-, passage 33 MEFs from mixed BL background 2

description: MEFs from a mix of 3 E14.5 embryos


title: wild-type, passage 6 MEFs from mixed BL background 1

description: MEFs from a mix of 2 E14.5 embryos

value: early


title: pLKO-luc1 [HPBALL]

description: Gene expression data from T-ALL cell line

data_processing: Array normalization was performed by DNAChip-Analyzer (dChip) on Genepattern website.

source_name: HPBALL cell line

growth_protocol: HPBALL cell line were mantained in RPMI supplemented with 20%  FBS and 1% P/S

extract_protocol: Total RNA from duplicate experiments of HPBALL infected cells with pLKO-.1 Luc and pLKO.1 shTLX3 was extracted with the RNeasy kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: Lentiviral plasmids plKO.1 Luc and pLKO.1 shTLX3 and the correspondent packaging plasmids were transfected in HEK293T by using JetPEI transfection agent . The viral surnatant was collected 48 hrs after transfection, filtered and used to infect target cells. All the infections were performed by spinoculation of viral supernatants produced in HEK293T  cells. After infection, HPB-ALL cells were selected for 5 days in puromycin and ficolled the day before the experiments.

value: T-ALL cell line HPBALL

tag: infection

value: control


title: wild-type, passage 28 MEFs from C57B6 background 2

description: MEFs from a E14.5 Embryo


title: Normoxia HeLa cells rep2

description: Gene expression of normoxic HeLa cells

source_name: normoxic HeLa cells

value: normoxia


title: pLKO-shTLX3-1 [HPBALL]


title: pLKO-shTLX3-2 [HPBALL]


title: Normoxia HeLa cells rep1

description: Gene expression of normoxic HeLa cells


title: UMA07068

description: A_4×44K_251485048330-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7068

tag: tissue

tag: bmi


title: Smurf2-/-, passage 6 MEFs from mixed BL background 1

description: MEFs from a mix of 3 E14.5 embryos


title: pLKO-luc2 [HPBALL]


title: pLKO-shTLX1-2 [ALLSIL]

data_processing: Array normalization was performed by DNAChip-Analyzer (dChip).

source_name: ALLSIL cell line

growth_protocol: ALLSIL cell line were mantained in RPMI supplemented with 10%  FBS and 1% P/S

extract_protocol: Total RNA from duplicate experiments of ALLSIL infected cells with pLKO-.1 Luc and pLKO.1 shTLX1 was extracted with the RNeasy kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: Lentiviral plasmids plKO.1 Luc, pLKO.1-shTLX1 and the correspondent packaging plasmids were transfected in HEK293T by using JetPEI transfection agent. The viral surnatant was collected 48 hrs after transfection, filtered and used to infect target cells. All the infections were performed by spinoculation of viral supernatants produced in HEK293T  cells. After infection, ALL-SIL cells were selected for 5 days in puromycin and ficolled the day before the experiments.

value: T-ALL cell line ALLSIL


title: wild-type, passage 7 MEFs from C57B6 background 1

description: MEFs from a E14.5 Embryo


title: pLKO-shTLX1-1 [ALLSIL]


title: UMA07067

description: A_4×44K_251485034101DAgilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7067


title: Smurf2-/-, passage 28 MEFs from C57B6 background 2

description: MEFs from a E14.5 Embryo


title: UMA07063

description: A_4×44K_251485042805-1Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7063


title: pLKO-luc2 [ALLSIL]


title: Hypoxia HeLa cells rep1


title: UMA07065_rep1

description: A_4×44K_251485044749-3Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7065


title: UMA07065

description: A_4×44K_251485042714-1Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7065


title: UMA07064

description: A_4×44K_251485042803-1Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7064


title: monocyte_control_04

status: Public on Nov 07 2011

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

country: Germany

institute: Helmholtz Zentrum München

description: The fragmentation was checked by microcapillary electrophoresis on an Agilent 2100 bioanalyzer, and 20 μg of biotinylated cRNAs was hybridized to U133A GeneChips for 16 hours at 45°C with constant rotation.

hyb_protocol: All microarrays were processed in an Affymetrix GeneChip Fluidics Station 400. Following staining with streptavidin-conjugated phycoerythrin and washing cycles.

scan_protocol: Microarrays were scanned using the GeneArray Scanner (Agilent Technologies).

data_processing: Expression signals for each transcript and comparisons between different samples were calculated with the Affymetrix GeneChip software MAS5.0.

source_name: human peripheral blood monocytes

label_protocol: Following phenol-chloroform extraction, cDNA was used for in vitro transcription reaction using the T7 BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY) to produce biotinylated cRNA. Thereafter, the labeled cRNA was purified using RNeasy Mini Kit columns (Qiagen) and fragmented by incubation at 94°C for 30 minutes.

extract_protocol: Total RNA was extracted from the cells according to the manufacturer’s instructions using the RNeasy Protect Midi Kit (Qiagen, Hilden, Germany). Purity and integrity of the RNA was assessed on the Agilent 2100 bioanalyzer with the RNA 6000 Nano LabChip reagent set (Agilent Technologies, Böblingen, Germany). The RNA was quantified spectrophotometrically and then stored at −80°C.

tag: Species

value: Human, healthy;

tag: Cell Type

value: Monocytes;

tag: Pooled Matherial


title: Smurf2-/-, passage 7 MEFs from C57B6 background 1

description: MEFs from a E14.5 Embryo

tag: cell type


title: macrophage_untreated_03

description:
Differentiation was confirmed by phase contrast microscopy.
The fragmentation was checked by microcapillary electrophoresis on an Agilent 2100 bioanalyzer, and 20 μg of biotinylated cRNAs was hybridized to U133A GeneChips for 16 hours at 45°C with constant rotation.

source_name: human peripheral blood monocytes, M-CSF differntiated to macrophages

value: Human, healthy; Cell Type:Macrophages; M-CSF differntiated for 4 days; Pooled Material;


title: monocyte_control_03

tag: Pooled Material;


title: E9.5 RA-treated OFT region

city: Kashihara

first: Masahide

last: Sakabe

address: 840 Shijo-cho

department: Advanced Medical Research Center

country: Japan

institute: Nara Medical University

description: Gene expression data from RA-treated heart outflow tract region

hyb_protocol: Following fragmentation, cRNA were hybridized for 18 hr at 45C on GeneChip Mouse Genome 430 v2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneArray Scanner GCS3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Heart outflow tract region from mouse E9.5 embryos

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Heart outflow tract region were isolated from Control or Retinoic Acid (RA) treated E9.5 mouse embryos.

extract_protocol: RNA were purified using the Rneasy mini kit (Qiagen), according to manufacture's instructions.

treatment_protocol: OFT region were stabilized in RNAlater RNA stabilization reagent (Ambion), prior to total RNA preparation.

tag: strain

value: ICR

tag: developmental stage

value: heart OFT region

value: RA-treated


title: macrophage_untreated_04


title: monocyte_control_02

tag: Pooled Matherial;

tag: ApoE4 homozygote


title: macrophage_untreated_02

value: Human, healthy; Cell Type:Macrophages; ApoE4 homozygote; M-CSF differntiated for 4 days; Pooled Material;


title: macrophage_untreated_01

value: Macrophages;

tag: ApoE3 homozygote;

tag: M-CSF differntiated for 4 days;


title: OsGAMYB:SmGAMYB_rep2_dye swap

city: Nagoya

first: Koichiro

last: Aya

state: Aichi

address: Furo-cho, Chikusa-ku

department: Bioscience and Biotechnology Center

institute: Nagoya University

description: Dye swap of SmGAMYB_rep2

hyb_protocol: For microarray hybridization, 0.825 μg of cyanine-labeled cRNA were fragmented and hybridized with the rice 4x44K microarray RAP-DB (G2519F#15241) at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner using two-color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green PMT: XDR Hi 100%; XDR Lo 10%).

data_processing: Scanned tiff image files were analyzed with FeatureExtraction 9.5.1 (Agilent). Obtained background subtracted Signal intensities (gBGSubSignal) were normalized by variance stabilization (VSN) using R software (http://www.r-project.org/).

organism: Oryza sativa Japonica Group

source_name: Anther at the microspore stage

label_protocol: Two-color spike-mix was added to the RNA prior to labeling reaction. 0.4 μg of total RNA was amplified by using Quick Amp Labeling Kit (Agilent Technologies), in the presence of cyanine-3-CTP or cyanine-5-CTP according to the manufacturer’s protocol. The labeled cRNA was purified by RNeasy Mini Kit (QIAGEN) and quantified using NanoDrop ND-1000 UV-VIS spectrophotometer.

growth_protocol: All plants were grown in paddy field under normal conditions.

extract_protocol: Total RNA was extracted using Rneasy plant minikit (QIAGEN). The resulting RNA was quntified using NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop) and qulity-checked using Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: genotype

value: Vector control in gamyb mutant

tag: cultivator

value: Nipponbare

value: anther

value: OsGAMYB:SmGAMYB in gamyb mutant


title: pLKO-luc1 [ALLSIL]

tag: cell line


title: E9.5 WT OFT region

description: Gene expression data from WT heart outflow tract region

tag: treatment


title: OsGAMYB:SmGAMYB_rep1

description: Biological replicate 1 of 2 (SmGAMYB_rep1).

tag: tissue


title: OsGAMYB:PpGAMYB2_rep2

description: Biological replicate 2 of 2 (PpGAMYB2_rep2).

value: OsGAMYB:PpGAMYB2 in gamyb mutant


title: OsGAMYB:PpGAMYB2_rep1_dye swap

description: Dye swap of PpGAMYB2_rep1


title: OsGAMYB:PpGAMYB2_rep2_dye swap

description: Dye swap of PpGAMYB2_rep2


title: Cerebellum-Cicnull-4

city: Houston

first: Peng

last: Yu

state: TX

address: 1 Baylor Plaza

institute: BCM

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA normalization with Affymetrix Power Tools (APT) exon level

source_name: cerebellum, 28 days

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

value: mixed Swiss Webster (CD-1) background

value: Cic-L-null


title: OsGAMYB:SmGAMYB_rep2

description: Biological replicate 2 of 2 (SmGAMYB_rep2).


title: OsGAMYB:OsGAMYB_rep1

description: Biological replicate 1 of 2 (OsGAMYB_rep1).

value: OsGAMYB:OsGAMYB in gamyb mutant


title: OsGAMYB:PpGAMYB2_rep1

description: Biological replicate 1 of 2 (PpGAMYB2_rep1).


title: OsGAMYB:SmGAMYB_rep1_dye swap

description: Dye swap of SmGAMYB_rep1


title: OsGAMYB:OsGAMYB_rep1_dye swap

description: Dye swap of OsGAMYB_rep1


title: monocyte_control_01


title: OsGAMYB:OsGAMYB_rep2

description: Biological replicate 2 of 2 (OsGAMYB_rep2).


title: Cerebellum-Cicnull-2


title: Cerebellum-Cicnull-3


title: OsGAMYB:OsGAMYB_rep2_dye swap

description: Dye swap of OsGAMYB_rep2


title: T9862-42_iPSC

city: Los Angeles

first: Irina

last: Voineagu

state: CA

address: 695 Chrles E Young Dr

institute: UCLA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Log2 transformation and Quantile normalization uzing the R Lumi package

source_name: iPSC

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total RNA was isolated using the RNeasy Mini kit and RNase-Free DNase set (Qiagen), according to the protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: TS

tag: cell line of origin

value: fibroblasts from TS patient T9886

tag: differentiation state

value: iPSC


title: T9862-40_iPSC


title: Cerebellum-wildtype-4

value: wild-type


title: Cerebellum-Cicnull-1


title: T9862-35_iPSC


title: T7643-5_iPSC

value: fibroblasts from TS patient T7643


title: UMA07069

description: A_4×44K_251485034102AAgilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7069

source_name: Human Reference B

tag: sample type

value: reference

tag: composition

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

source_name: Reduction Mammoplasty

value: normal breast

tag: bmi


title: T7643-5_D3_neuronsKCl

source_name: neurons kept in 67mM KCl for 9h

value: neurons kept in 67mM KCl for 9h

tag: cell type

value: neurons


title: T7643-7_D2_neurospheres

source_name: neurospheres (at day 7 in suspension)

value: neurospheres (at day 7 in suspension)

value: neurospheres


title: T7643-7_iPSC


title: T7643-7_D2_neuronsKCl


title: T7643-7_D3_neuronsKCl


title: T9862-42_D2_neuronsKCl


title: T7643-7_D2_neurons

source_name: neurons at rest (day 45 of differentiation)


title: T7643-7_D3_neurospheres


title: T9862-5_iPSC


title: T9862-61_iPSC


title: T7643-5_D3_neurospheres


title: T9862_fibroblasts

source_name: fibroblasts

value: fibroblasts


title: T7643-7_D3_neurons

value: neurons at rest (day 45 of differentiation)


title: Cerebellum-wildtype-3

tag: strain

value: mixed Swiss Webster (CD-1) background


title: T7643-5_D3_neurons


title: Cerebellum-wildtype-2


title: Cerebellum-wildtype-1

data_processing: RMA normalization with Affymetrix Power Tools (APT) exon level summaries

extract_protocol: Trizol extraction with RNeasy cleanup


title: T9862-41_iPSC


title: T7643-5_D2_neurospheres


title: T7643-5_D2_neurons


title: T7643-32_D3_neuronsKCl


title: T7643-32_D2_neuronsKCl


title: T7643-5_D2_neuronsKCl


title: T7643-32_D3_neurospheres


title: T7643-32_D2_neurospheres


title: T7643-32_D2_neurons


title: NH2-6_iPSC

value: control

value: NHDF fibroblasts, line NH2


title: T7643-32_D3_neurons

value: TS


title: NH2-6_D3_neuronsKCl


title: NH2-6_D2_neurospheres


title: NH2-6_D3_neurons


title: T7643-3_iPSC


title: NH1-1_D3_neuronsKCl

value: NHDF fibroblasts, line NH1


title: NH1-1_D2_neurospheres


title: NH1-1_D3_neurons


title: NH2-6_D2_neurons


title: NH2-6_D2_neuronsKCl


title: NH1-1_D2_neurons


title: NH1-1_D2_neuronsKCl


title: NH1-1_D1_neurons


title: NH1-1_D3_neurospheres


title: NH1-1_iPSC

value: iPSC


title: IMR90_fibroblasts

value: IMR90 fibroblasts


title: NH2-6_D3_neurospheres


title: T7643-32_iPSC

value: fibroblasts from TS patient T7643


title: IM25-2_iPSC

value: IMR90 fibroblasts, line IM25


title: IM23-9_iPSC

value: IMR90 fibroblasts, line IM23


title: NHDF_fibroblasts

value: NHDF fibroblasts

value: NHDF


title: T7643_fibroblasts


title: IM23-9_D2_neurospheres


title: IM23-9_D1_neurons

value: neurons


title: IM23-9_D2_neurons


title: IM23-16_D1_neurons


title: IM23-16_iPSC


title: H9_ESC

source_name: ESC

value: not aplicable (H9- human ESC)

value: ESC


title: macrophage_untreated_07

tag: Species

value: Human Donors with Niemann-Pick type C disease; Cell Type:Macrophages; M-CSF differntiated for 4 days; Pooled Material;


title: macrophage_untreated_05

value: Human Donors with Niemann-Pick type C disease; Cell Type:Macrophages; ApoE3 homozygote; M-CSF differntiated for 4 days; Pooled Material;


title: IL-5+ memory Th2

city: Chiba-city

first: Yusuke

last: ENDO

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Immunology

institute: Chiba University

description:
Gene expression data from DO11.10 TCR Tg CD4+ T cells cultured 6 days in Th2 conditions and transferred into syngenic mice for 30 days.
EA690_01.CEL

hyb_protocol: RNA was hybridized to GeneChip Mouse Genome 430 2.0 Arrays from Affymetrix according to the manufacture's protocol.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Expression values were determined using GeneChip Operating Software (GCOS) v1.2 software.

source_name: primary CD4 T cells from spleen

label_protocol: Total RNA was extracted usin the IVT Labeling kit from Affymetrix.

growth_protocol: Splenic CD4 T cells were prepared using a magnetic cell sorter (AutoMACS; Miltenyi Biotec) yielding a purity of >98%. Where indicated, cells from DO11.10 TCR Tg mice were stimulated with an OVA peptide under Th2-culture conditions for 6 days in vitro. Th2 condtions; 25U/ml IL-2, 100U/ml IL-4.  These cells were transferred into syngenic BALB/c nu/nu recipient mice.  30 days after cell transfer, memory Th2 cells in the spleen were collected.

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

treatment_protocol: IL-5+ and IL-5- memory Th2 cells were separeted using Aria cell sorter, and were resuspendet in the Trizol solution (GibcoBRL).

value: BALB/c

value: spleen

value: CD4 T cell

tag: culture conditions

tag: genotype/variation


title: IL-5- memory Th2

description:
Gene expression data from DO11.10 TCR Tg CD4+ T cells cultured 6 days in Th2 conditions and transferred into syngenic mice for 30 days.
EA690_02.CEL


title: macrophage_untreated_06


title: H9_D2_neurons

value: control

value: neurons at rest (day 45 of differentiation)


title: H9_D2_neurospheres

value: neurospheres (at day 7 in suspension)

value: neurospheres


title: H9_D1_neurons


title: Atxn1 KO lung rep2

status: Public on Nov 06 2011

first: Hyojin

last: Kang

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Gene expression data from mouse lung tissues at P6

hyb_protocol: Affymetrix standard protocol

data_processing: The data were analyzed using Limma package in the Bioconductor R. The signal intensities were obtained and corrected for background by using Robust Multi-array Analysis (RMA) algorithm.

source_name: lung, Atxn1 knock-out

label_protocol: 100 ng of total RNA was subjected to the Affymetrix Gene ST labelling (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were maintained under the regulation of the Institutional Animal Care and Use Committee (IACUC) at Baylor College of Medicine

treatment_protocol: Lung tissues were dissected from P6 mice and quickly frozen with liquid nitrogen.

value: lung

value: Atxn1 -/-

tag: age


title: WT ctrl for Atxn1L KO rep2

source_name: lung, WT

value: WT


title: monocyte_control_07

value: Human Donors with Niemann-Pick type C disease; Cell Type:Monocytes; Pooled Material;


title: Atxn1L KO lung rep4

source_name: lung, Atxn1L knock-out

value: Atxn1L -/-


title: WT ctrl for Atxn1L KO rep4


title: Atxn1L KO lung rep3


title: WT ctrl for Atxn1L KO rep3


title: Atxn1 KO lung rep1


title: WT ctrl for Atxn1 KO rep1


title: WT ctrl for Atxn1 KO rep2


title: monocyte_control_05

source_name: human peripheral blood monocytes

value: Human

tag: Donors with Niemann-Pick type C disease;

tag: Cell Type

value: Monocytes;

tag: Pooled Material;


title: Jurkat Tat cells vs. Jurkat cells replicate 2

first: Siavash

middle: K

last: Kurdistani

address: 615 Charles E. Young Dr. South, 337

department: Biological Chemistry

institute: University of California Los Angeles

hyb_protocol: Hybridization onto the Whole Human Genome 4 x 44K Microarray (G4112F), washing, and scanning were carried out according to the manufacturer's instructions

scan_protocol: Agilent DNA Microarray Scanner

data_processing: Raw intensity data from resulting gene expression data were normalized by medium background-subtracted intensities between Cy5 and Cy3 channels followed by LOWESS normalization using Matlab.  Normalized log2 ratios of Jurkat-Tat cRNAs (Cy5) over Jurkat cRNAs (Cy3) were calculated and results from replicates were averaged.

source_name: Jurkat-Tat

label_protocol: cRNAs were generated from 250ng of total RNA and labeled with Cy3 (Jurkat) or Cy5 (Jurkat-Tat) using the Low Input Quick Amp Labeling Kit (Agilent)

growth_protocol: Jurkat-Tat cells were maintained in RPMI supplemented with 10% fetal bovine serum, 1%penicillin and streptomycin and 800 microg/ml of G418. Jurkat T cells were obtained from ATCC and cultured under standard tissue culture conditions.

extract_protocol: Total RNA was isolated from Jurkat and Jurkat-Tat cells using the RNeasy Mini kit (Qiagen).  according to manufacturer's instructions. Labeled cRNAs were hybridized to the Agilent Human whole-genome array according to Agilent protocol.

tag: expression

value: HIV Tat protein

tag: cell line

value: Jurkat

source_name: Jurkat


title: WT ctrl for Atxn1 KO rep3

tag: tissue

tag: genotype


title: monocyte_control_06

tag: pecies


title: Jurkat Tat cells vs Jurkat cells H3K9ac ChIP-chip

type: genomic

hyb_protocol: Hybridization onto the Human Promoter ChIP-on-chip microarray (244K) (G4489A), washing, and scanning were carried out according to the manufacturer's instructions

scan_protocol: The arrays were scanned using an Agilent DNA Microarray scanner.

data_processing: Data extraction and analyses were carried out using the Agilent Feature Extraction software (version 9.1.3.1) and Chip Analytics software (version 1.2). Probe signals were extracted with the Agilent Feature extraction software, normalized with Lowess normalization using the Chip Analytics software

molecule: genomic DNA

label_protocol: 2 μg of amplified material were labeled with Cy3 or Cy5 (PerkinElmer) using the Bioprime Labeling Kit (Invitrogen). DNA was mixed with 35 µl of random priming solution (Invitrogen Bioprime Kit) to a final volume of 75 µl, boiled for 5 min and quickly cooled in an ice-water bath for 5 min. The labeling reaction was completed with 60U Klenow, dNTPs (0.12 mM dATP, dGTP and dTTP and 0.06 mM dCTP), 1.28 mM Cy3 and Cy5 for IP from Jurkat cells and IP from Jurkat-Tat cells respectively, and incubated for 3h at 37°C. The labeled DNA was purified using Qiagen Qiaquick PCR purification Kit and the incorporation was measured with Nanodrop.

extract_protocol: Formaldehyde was added for 10 min at 37°C. After PBS washing, cross-linked cells were scraped from the plates and washed with 1 ml of PBS containing protease inhibitors (Roche). Cells were resuspended in 400 µl of Lysis buffer and incubated for 10 min on ice and immediately sonicated. 100 µl of the lysate were used for immunoprecipitation with anti-Histone H3 acetyl Lys9 antibody; After overnight reversal of crosslinking at 65°C, samples were treated with RNase A for 30 min at 37°C and subsequently purified using the Qiagen Qiaquick PCR purification Kit. 10 ng of each IP DNA were amplified using the WGA Kit (Sigma)(3).

tag: chip antibody

tag: chip antibody manufacturer

value: Upstate

tag: chip antibody catalog #


title: Atxn1 KO lung rep3


title: WT ctrl for Atxn1L KO rep1


title: Jurkat Tat cells vs. Jurkat cells replicate 1


title: Atxn1L KO lung rep2


title: Treated MCF-7 cell after 1 hr [C1_3rd replicate]

status: Public on Nov 05 2011

city: Gombak

first: Amid

last: Azura

state: Selangor

address: Jalan Gombak

department: Biotechnology Engineering

country: Malaysia

institute: IIUM,Gombak

description: Chip array was scanned by Affymetrix Microarray Suite/GCOS.

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned by Affymetrix Microarray Suite/GCOS at Research Instrument Laboratory Service, Petaling Jaya, Malaysia.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) using Affymetrix Microarray Suite/GCOS at Research Instrument Laboratory Service, Petaling Jaya, Malaysia.

data_processing: Raw data were processed with GeneSpringGX version 7.2 (Agilent Technologies, USA) for background correction and normalization. Data analysis and statistical evaluations were performed with ANOVA test. We defined a probeset as present when it had a P value <0.05 and the listed genes (p<0.05) were filter again with fold-change cutoff <2.00. Fold-change were performed between untreated cells and treated cells after 1 hr, and between treated cells after 48hrs and 1 hr. These criteria were suggested to narrow the list of genes to those significantly affected by TLE.

source_name: Treated MCF-7 cell after 1 hr

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: MCF-7 breast cancer cells were growth in 5 ml media (Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% heat-inactivated fetal bovine serum (FBS), 100 µg/ml streptomycin, 100 U/ml penicillin, in a 95% air, 5% CO2 atmosphere) in a T-25 flasks, allowed to grow until 60-80% confluent.

extract_protocol: RNA was isolated from untreated cells after 60-80% confluent. And RNA from treated MCF-7 cells was isolated after 1 hr and 48 hrs of treatment. The RNA isolation was performed using RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: MCF-7 cells at confluent level (approximately at exponential phase) was treated with 5.85µg/ml (IC50) TLE.

tag: treatment

value: tomato leaves extract

tag: time point

value: 1 hr


title: L2463

city: Leiden

first: Twinkal

middle: Chandubhai

last: Pansuriya

state: Zuid-Holland

address: Albinusdreef 2

department: Pathology

institute: LUMC

hyb_protocol: According to manufacturer’s protocol

scan_protocol: According to manufacturer’s protocol

data_processing:
Infinium Unsupervised clustering analysis was performed
25 using the Ward’s clustering algorithm based on Euclidian distance. The 2000 most variable CpG sites (excluding those on the X and Y chromosomes) were used in theclustering analysis.

label: C-Bio and A-DNP

source_name: Ollier enchondroma

label_protocol:
Bisulfite treatment was performed using EZ DNA Methylation™ Kit (Zymo
Research, Orange, CA)using 1ug of genomic DNA . Bisulphite converted DNA was then hybridized to Illumina HumanMethylation27 BeadChip (Illumina Inc., San Diego, CA) by following
manufacturer’s instructions.

extract_protocol: Genomic DNA from frozen tumors containing at least 80% of tumors cells, as estimated on haematoxylin using the Wizard Genomic DNA Purification Kit (Promega,Madison, WI), according to the manufacturer’s instructions.

tag: gender

value: Female

tag: disease

value: Ollier

tag: tumor

value: Enchondroma

value: with IDH1 mutation


title: L2100

value: Male

tag: age

tag: genotype/variation

value: without IDH1 or IDH2 mutation


title: Untreated MCF-7 cells [C0_3rd replicate]

source_name: Untreated MCF-7 cells

value: Untreated


title: MAF250

source_name: Maffucci enchondroma

value: Maffucci


title: L1598

source_name: Solitary enchondroma

value: Solitary enchondroma


title: L2357

value: without IDH1 or IDH2 mutation (R132G IDH1 mutation present in subpopulations)


title: Atxn1L KO lung rep1

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

value: lung

value: Atxn1L -/-

tag: strain


title: L1829


title: L2103a


title: Treated MCF-7 cell after 48 hrs [C3_3rd replicate]

source_name: Treated MCF-7 cell after 48 hrs

value: 48 hr


title: Untreated MCF-7 cells [B0_2nd replicate]


title: Treated MCF-7 cell after 1 hr [A1_1st replicate]


title: Treated MCF-7 cell after 48 hrs [B3_2nd replicate]


title: L1686


title: Treated MCF-7 cell after 48 hrs [A3_1st replicate]


title: summit/shoulder rep 2 13013B2 B

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

description:
This research was conducted in a 65 ha corn field located in eastern South Dakota.  The latitude and longitude values were 44o 10’ N and 96o 37’ W .  Elevation within the field ranged from 518 to 534 m. Broadcast fertilizer was applied to this field in the fall of 2007 and spring of 2008.  In the fall of 2007, 20 kg N ha-1, 23 kg P ha-1 ( 51.4 kg P2O5 ) and 36 kg K ha-1 (44.7 kg K2O) were applied.  In the following spring, 102 kg N ha-1 was applied.   In this field, a 97 day corn hybrid was planted in early May 2008.  During the growing season, precipitation was 8.91 cm and the growing degree days from planting to silage harvest were 984. Dominant soils were the Cubden (Aeric Calciaquoll), Wauby (Aquic Hapludoll), Kranzburg (Calcic Hapludoll), and Vienna (Calic Hapludoll).  Plant samples were collected on 18 July 2008.  Weather conditions at time of harvest was mostly sunny with a light wind and a temperature of about 26 C. There was a thunder storm on the evening preceeding harvest.
Channel 2 in the raw data file

hyb_protocol: 46,000-element microarray chip developed by the University of Arizona was hybridized using their protocol (International Microarray Workshop Handbook, 2009; Gardiner et al. 2005).

scan_protocol: Intensities based on fluorescence for each probe were visualized and quantified with a GenePix scanner9 and GenePix Pro software.

data_processing: GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were =0.05.  Quantile normalization with centering to normalize between hybridizations.

label: Alexa Fluor 555

organism: Zea mays

source_name: 306B2 R summit/shoulder 5: top 8 cm of the topmost fully expanded leaf of four plants grown on summit/shoulder plot 5 were harvested and pooled.

label_protocol: First strand cDNA synthesis was performed using 1900 ng total RNA and second strand cDNA synthesis was performed using the resulting first-strand cDNA sample to make double-stranded cDNA using the Aminoallyl Message Amp II kit7.  aRNA was synthesized using the resulting double-stranded cDNA. Technical replicates from each treatment were labeled with Alexa Fluor 647 or Alexa Fluor 555 dye. An Alexa Fluor 647-labeled sample from one treatment was mixed with an Alexa Fluor 555-labeled sample from another treatment.

extract_protocol: Total RNA was extracted using Trizol reagent5 and purified using Qiagen RNeasy MinElute cleanup kit6, following the manufacturer’s protocol.

treatment_protocol: 8 cm of the top most fully expanded leaf was harvested directly into liquid nitrogen and stored at -80 until RNA extraction.

value: leaf

tag: location

value: summit/shoulder


title: summit/shoulder rep 6   306E B

source_name: 3014E R backslope 3: top 8 cm of the topmost fully expanded leaf of four plants grown on backslope plot 3 were harvested and pooled.

growth_protocol: This research was conducted in a 65 ha corn field located in eastern South Dakota.  The latitude and longitude values were 44o 10’ N and 96o 37’ W .  Elevation within the field ranged from 518 to 534 m. Broadcast fertilizer was applied to this field in the fall of 2007 and spring of 2008.  In the fall of 2007, 20 kg N ha-1, 23 kg P ha-1 ( 51.4 kg P2O5 ) and 36 kg K ha-1 (44.7 kg K2O) were applied.  In the following spring, 102 kg N ha-1 was applied.   In this field, a 97 day corn hybrid was planted in early May 2008.  During the growing season, precipitation was 8.91 cm and the growing degree days from planting to silage harvest were 984. Dominant soils were the Cubden (Aeric Calciaquoll), Wauby (Aquic Hapludoll), Kranzburg (Calcic Hapludoll), and Vienna (Calic Hapludoll).  Plant samples were collected on 18 July 2008.  Weather conditions at time of harvest was mostly sunny with a light wind and a temperature of about 26 C. There was a thunder storm on the evening preceeding harvest.


title: backslope rep 3   3014E B

source_name: 13013E R summit/shoulder 3: top 8 cm of the topmost fully expanded leaf of four plants grown on summit/shoulder plot 3 were harvested and pooled.

value: backslope


title: L1251


title: Untreated MCF-7 cells [A0_1st replicate]


title: summit/shoulder rep 3 13013E B

source_name: 306E R summit/shoulder 6: top 8 cm of the topmost fully expanded leaf of four plants grown on summit/shoulder plot 6 were harvested and pooled.


title: summit/shoulder rep 5   306B2 B

source_name: 3014B4 R backslope 2: top 8 cm of the topmost fully expanded leaf of four plants grown on backslope plot 2 were harvested and pooled.


title: backslope rep 1   3014B1 B

source_name: 306B1 R summit/shoulder 4: top 8 cm of the topmost fully expanded leaf of four plants grown on summit/shoulder plot 4 were harvested and pooled.


title: backslope rep 2 3014B4 B

source_name: 13013B2 R summit/shoulder 2: top 8 cm of the topmost fully expanded leaf of four plants grown on summit/shoulder plot 2 were harvested and pooled.


title: Treated MCF-7 cell after 1 hr [B1_2nd replicate]

value: tomato leaves extract

value: 1 hr


title: L194


title: summit/shoulder rep 4 306B1 B

source_name: 13013B1 R summit/shoulder 1: top 8 cm of the topmost fully expanded leaf of four plants grown on summit/shoulder plot 1 were harvested and pooled.


title: L198


title: summit/shoulder rep 1 13013B1 B

source_name: 3014B1 R backslope 1: top 8 cm of the topmost fully expanded leaf of four plants grown on backslope plot 1 were harvested and pooled.


title: backslope rep 3  3014E R

description:
This research was conducted in a 65 ha corn field located in eastern South Dakota.  The latitude and longitude values were 44o 10’ N and 96o 37’ W .  Elevation within the field ranged from 518 to 534 m. Broadcast fertilizer was applied to this field in the fall of 2007 and spring of 2008.  In the fall of 2007, 20 kg N ha-1, 23 kg P ha-1 ( 51.4 kg P2O5 ) and 36 kg K ha-1 (44.7 kg K2O) were applied.  In the following spring, 102 kg N ha-1 was applied.   In this field, a 97 day corn hybrid was planted in early May 2008.  During the growing season, precipitation was 8.91 cm and the growing degree days from planting to silage harvest were 984. Dominant soils were the Cubden (Aeric Calciaquoll), Wauby (Aquic Hapludoll), Kranzburg (Calcic Hapludoll), and Vienna (Calic Hapludoll).  Plant samples were collected on 18 July 2008.  Weather conditions at time of harvest was mostly sunny with a light wind and a temperature of about 26 C. There was a thunder storm on the evening preceeding harvest.
Channel 1 in the raw data file

label: Alexa Fluor 647

source_name: 306E B summit/shoulder 6: top 8 cm of the topmost fully expanded leaf of four plants grown on summit/shoulder plot 6 were harvested and pooled.


title: backslope rep 2  3014B4 R

source_name: 306B2 B summit/shoulder 5: top 8 cm of the topmost fully expanded leaf of four plants grown on summit/shoulder plot 5 were harvested and pooled.


title: summit/shoulder rep 3  13013E R

source_name: 3014E B backslope3: top 8 cm of the topmost fully expanded leaf of four plants grown on backslope plot 3 were harvested and pooled.


title: A2780cis cisplatin-resistant ovarian cancer cell line_rep3

city: Kingston

first: Alexandria

last: Haslehurst

state: ON

address: Richardson Laboratory 88 Stuart St

country: Canada

institute: Queen's University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing Agilent 25X fragmentation buffer and Agilent 10X blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Microarrays 4x44K (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014850_D_F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw data was uploaded to GeneSpring 11.5.1 and normalized using default parameters (threshold raw signals to 1, percentile shift to 75, baseline to the median of all samples).

source_name: A2780cis ovarian cancer cell line (cisplatin-resistant)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Am Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer

growth_protocol: Cells were grown to 80% confluence in RPMI-1640 media with 1% Penicillin/Streptomycin, 10%FBS and 1% L-glutamine at 37degrees Celcius in 5% CO2. Cells were harvested following trypsinization. Cisplatin-resistant cell lines were maintained in media containing 1uM cisplatin.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini Kit following manufacturers protocol for extraction from animal cells. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: tissue of origin

value: Ovary


title: A2780cis cisplatin-resistant ovarian cancer cell line_rep4

tag: cell line


title: A2780cis cisplatin-resistant ovarian cancer cell line_rep1


title: summit/shoulder rep 2 13013B2 R

source_name: 3014B4 B backslope 2: top 8 cm of the topmost fully expanded leaf of four plants grown on backslope plot 2 were harvested and pooled.

tag: tissue


title: summit/shoulder rep 6 306E R

source_name: 13013E B summit/shoulder 3: top 8 cm of the topmost fully expanded leaf of four plants grown on summit/shoulder plot 3 were harvested and pooled.


title: L1684

source_name: Maffucci enchondroma

value: Female

value: Enchondroma


title: A2780cis cisplatin-resistant ovarian cancer cell line_rep5


title: A2780cis cisplatin-resistant ovarian cancer cell line_rep2


title: A2780 cisplatin-sensitive ovarian cancer cell line_rep6

source_name: A2780 ovarian cancer cell line (cisplatin-sensitive)


title: summit/shoulder rep 5  306B2 R

source_name: 13013B2 B summit/shoulder 2: top 8 cm of the topmost fully expanded leaf of four plants grown on summit/shoulder plot 2 were harvested and pooled.


title: A2780cis cisplatin-resistant ovarian cancer cell line_rep6


title: A2780 cisplatin-sensitive ovarian cancer cell line_rep5


title: A2780 cisplatin-sensitive ovarian cancer cell line_rep4


title: A2780 cisplatin-sensitive ovarian cancer cell line_rep1


title: A2780 cisplatin-sensitive ovarian cancer cell line_rep3


title: A2780 cisplatin-sensitive ovarian cancer cell line_rep2


title: summit/shoulder rep 4  306B1 R

source_name: 3014B1 B backslope 1: top 8 cm of the topmost fully expanded leaf of four plants grown on backslope plot 1 were harvested and pooled.


title: summit/shoulder rep 1  13013B1 R

source_name: 306B1 B summit/shoulder 4: top 8 cm of the topmost fully expanded leaf of four plants grown on summit/shoulder plot 4 were harvested and pooled.


title: Rice ZS97 at D2, biological rep1

city: wuhan

first: ding

middle: xi

last: peng

address: No.1,Shizishan Street Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

country: China

institute: Huazhong Agricultural University

description: Gene expression data from flag leaves after drought stress treatment at D2

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Oryza sativa Indica Group

source_name: Rice flag leaves after drought stress treatment at D2

value: flag leaves

tag: genotype

value: drought-sensitive indica cultivar

value: reproductive stage before flowering

tag: stress level


title: Rice ZS97 at D3, biological rep1

description: Gene expression data from flag leaves after drought stress treatment at D3

source_name: Rice flag leaves after drought stress treatment at D3


title: Rice ZS97 at D1, biological rep2

description: Gene expression data from flag leaves after drought stress treatment at D1

source_name: Rice flag leaves after drought stress treatment at D1


title: Rice ZS97 at D3, biological rep2


title: Rice ZS97 at D1, biological rep1


title: Rice ZS97 at D0, biological rep2

description: Gene expression data from flag leaves before drought stress treatment

source_name: Rice flag leaves before drought stress treatment


title: Rice ZS97 at D0, biological rep1


title: Rice ZS97 at D2, biological rep2


title: Rice IRAT109 at D3, biological rep2

value: drought-resistant japonica cultivar


title: Rice IRAT109 at D2, biological rep2


title: Rice IRAT109 at D1, biological rep1


title: Rice IRAT109 at D0, biological rep1


title: Rice IRAT109 at D1, biological rep2


title: backslope rep 1  3014B1 R

source_name: 13013B1 B summit/shoulder 1: top 8 cm of the topmost fully expanded leaf of four plants grown on summit/shoulder plot 1 were harvested and pooled.


title: Rice IRAT109 at D3, biological rep1


title: Rice IRAT109 at D2, biological rep1


title: U178 EGFR EGF minus rep2

city: LaJolla

first: Frank

last: Furnari

address: 9500 Gilman Drive

institute: Ludwig Institute

description: Gene expression data from U178-EGFR

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on human HG-U133A Affymetrix arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.  The comparison analysis was also performed to calculate the increased ratios (fold-change) after the stimulation of EGF in these cells.

source_name: U178 EGFR EGF minus rep2

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

growth_protocol: U87 and U178 cells engineered to express EGFR were serum starved for 24 h prior to stimulation.

treatment_protocol: U87 and U178 cells engineered to express EGFR were stimulated with or without 20 ng/mL of recombinant EGF for 3 h prior to sample collection.

tag: parental cell line


title: U87 EGFR EGF plus rep2

description: Gene expression data from U87-EGFR

source_name: U87 EGFR EGF plus rep2

value: EGF


title: MCPIP1_siRNA

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

hyb_protocol: Hybridization buffer was added to each labelled samples and denatured at 95C for 2min and then cooled. The samples were then hybridized to miRCURY LNA v.11 microarray at 56C for 16h in agilent hybridization oven rotated at 20 RPM. The following day, the slides were washed, dried, and scanned immediately.

scan_protocol: The miRNA arrays were scanned using a GenePix 4000B scanner (Molecular Devices), and data were analyzed using Array-Pro Analyzer Version 4.5 (Media Cybernetics).

data_processing: The signals across samples were normalized using a factor derived from the mean of the signal intensity of several house-keeping small RNAs.

source_name: HepG2 cells

label_protocol: A total of 1 ug of total RNA was used for each sample. MiRCURY™ LNA microRNA Power labeling Kit (Exiqon, Vedbaek, Denmark) was used following the manufacturers’ recommendations. Spike-ins (used as control probes) were added in equal amounts to each reaction and labeled.

extract_protocol: HepG2 cells were transfected with control siRNA or siRNA against MCPIP1. After transfection, total RNA was prepared using Trizol (Invitrogen).

tag: cell type

tag: sirna


title: Control_siRNA

value: Control


title: U178 EGFR EGF minus rep1

description: Gene expression data from U178-EGFR

source_name: U178 EGFR EGF minus rep1

tag: treatment


title: U178 EGFR EGF plus rep1

description: Gene expression data from U178-EGFR

source_name: U178 EGFR EGF plus rep1


title: U87 EGFR EGF plus rep1

description: Gene expression data from U87-EGFR

source_name: U87 EGFR EGF plus rep1


title: Ciona adult neural-complex spawning 2

city: Onnna, Kunigami

first: Takeshi

last: Kawashima

state: Okinawa

institute: Okinawa Institute of Science and Technology

description: This sample is extracted from a same individual with Sample4. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: quantile normalization

organism: Ciona intestinalis

source_name: Ciona adult nueral-complex spawning2

label_protocol: standard Agilent protocol

extract_protocol: All samples were saturated in RNAlater. RNA extraction: Trizol Reagent and Rneasy micro.

value: Neural Complex

value: spawning


title: Rice IRAT109 at D0, biological rep2


title: Ciona adult neural-complex under light 1

description: This sample is extracted from a same individual with Sample1. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

source_name: Ciona adult nueral-complex under light 1

value: light


title: Ciona adult neural-complex spawning 1

description: This sample is extracted from a same individual with Sample3. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

source_name: Ciona adult nueral-complex spawning1


title: Ciona adult ovary spawning 2

description: This sample is extracted from a same individual with Sample8. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

source_name: Ciona adult ovary spawning 2


title: U178 EGFR EGF plus rep2

description: Gene expression data from U178-EGFR

source_name: U178 EGFR EGF plus rep2


title: Ciona adult ovary spawning 1

description: This sample is extracted from a same individual with Sample7. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

source_name: Ciona adult ovary spawning 1


title: Ciona adult neural-complex under light 2

description: This sample is extracted from a same individual with Sample2. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

source_name: Ciona adult nueral-complex under light 2


title: U87 EGFR EGF minus rep2

description: Gene expression data from U87-EGFR

source_name: U87 EGFR EGF minus rep2


title: U87 EGFR EGF minus rep1

description: Gene expression data from U87-EGFR

source_name: U87 EGFR EGF minus rep1


title: Ciona adult ovary under light 2

description: This sample is extracted from a same individual with Sample6. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

source_name: Ciona adult ovary under light 1


title: Ciona adult ovary under light 1

description: This sample is extracted from a same individual with Sample5. This individual is mature adult of wild-type and was kept in fresh-sea water individually.


title: CD3+CD8+ rep2

city: New York

first: Alberto

last: Ambesi-Impiombato

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

description: Sorted T-Cell population CD3+CD8+

data_processing: Data was transformed to log2 scale and quantile normalized

source_name: T-Cell population CD3+CD8+

label_protocol: 10ng of RNA from each T-cell subset was amplified using the Ovation® PicoSL WTA System (Nugen), labeled by the EncoreTM BiotinIL Module (Nugen).  500 ng of RNA was amplified and biotinylated using the TotalPrep RNA Amplification Kit (Ambion).

extract_protocol: RNA isolation from sorted subsets of human thymocytes was performed in triplicate using the RNeasy micro kit (Qiagen) according to manufacturer's protocol

treatment_protocol: Thymus samples were obtained as surgical tissue discards from 3 pediatric patients (age from 7 days to 6 months) undergoing cardiac surgery at the New York Presbyterian Hospital. T-cell phenotype was confirmed by flow cytometry.

value: Thymus

tag: t-cell population


title: CD3+CD8+ rep1

description: Sorted T-Cell population CD3+CD8+


title: CD3+CD4+ rep2

description: Sorted T-Cell population CD3+CD4+

source_name: T-Cell population CD3+CD4+


title: CD3+CD8+ rep3

description: Sorted T-Cell population CD3+CD8+


title: DPCD3+ rep3

description: Sorted T-Cell population DPCD3+

source_name: T-Cell population DPCD3+


title: DPCD3+ rep2

description: Sorted T-Cell population DPCD3+


title: CD3+CD4+ rep1

description: Sorted T-Cell population CD3+CD4+


title: CD3+CD4+ rep3

description: Sorted T-Cell population CD3+CD4+


title: DPCD3- rep3

description: Sorted T-Cell population DPCD3-

source_name: T-Cell population DPCD3-


title: DPCD3+ rep1

description: Sorted T-Cell population DPCD3+


title: DPCD3- rep2

description: Sorted T-Cell population DPCD3-


title: DPCD3- rep1

description: Sorted T-Cell population DPCD3-


title: CD4ISP rep3

description: Sorted T-Cell population CD4ISP

source_name: T-Cell population CD4ISP


title: CD4ISP rep2

description: Sorted T-Cell population CD4ISP


title: CD4ISP rep1

description: Sorted T-Cell population CD4ISP


title: CD34+CD1a+ rep2

description: Sorted T-Cell population CD34+CD1a+

source_name: T-Cell population CD34+CD1a+


title: glucose-limited chemostat phenylalanine-3 (TV26)

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

description: Penicillium chrysogenum glucose-limited chemostat with L-phenylalanine as sole nitrogen source, wit a dilution rate of 0.03h-1.

hyb_protocol: Acquisition and quantification of array images were performed using Affymetrix GeneChip Operating Software (GCOS version 1.2). Before comparison, all arrays were globally scaled to a target value of 100 using the average signal from all gene features. To the 15,531 transcript features on the arrays, a filter was applied to extract 13,746 open reading frames of which there were 13,485 different genes. This discrepancy was due to several genes being represented more than once. To represent the variation in triplicate measurements, the coefficient of variation (S.D. divided by the mean) was calculated. When the genes were ranked according to increasing average intensity, the average coefficient of variation showed a sharp increase for the genes with the lowest expression. Therefore, all genes in which the average expression in all conditions was below 12 were removed from the dataset. Subsequently all remaining values below 12 were set to a value of 12. To assess differential expression, the Significance Analysis of Microarrays (SAM version 1.21) add-in to MicrosoftTM Excel was used for comparisons of replicate array experiments. SAM identifies genes with statistically significant changes in expression by assimilating a set of gene-specific t tests. Each gene is assigned a score on the basis of its change in gene expression relative to the standard deviation of repeated measurements for that gene. Genes with scores greater than a threshold are deemed potentially significant. The percentage of such genes identified by chance is the false discovery rate (FDR). To estimate the FDR, nonsense genes are identified by analyzing permutations of the measurements. The threshold can be adjusted to identify smaller or larger sets of genes, and FDRs are calculated for each set. Here internal SAM parameters for fold-change threshold and the false discovery rate values were set at 2 and 1% respectively.   The genes with significantly changed expression in one of the comparisons were arranged in groups via overlapping them in MicrosoftTM Excel.

scan_protocol: Scanning of the Affymetrix Genechip® microarrays was performed with The Affymetrix scanner 3000 following Affymetrix instructions

data_processing: Data were processed with the GeneChip® Operating Software version 1.2 (GCOS 1.2) using Affymetrix default analysis settings and global scaling as normalization method. Hybridization intensity scaled to 100 with GCOS 1.2.

label: Biotin

organism: Penicillium chrysogenum

source_name: Glucose-limited chemostat culture -0.03H-1

label_protocol: Double stranded cDNA synthesis was carried out using 10 µg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labelling using the GeneChip IVT labeling Kit (Affymetrix). Finally, labelled cRNA was purified (GeneChip Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridised to Affymetrix custom-made Penicillium chrysogenum GeneChip® microarrays (array code DSM_PENa520255F) at 45ºC for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.

growth_protocol: P.chrysogenum continuous cultures were performed with a filter sterilized carbon-limited defined mineral medium, having the following composition per liter: 0.8 g KH2PO4, 8.75 g Phenylalanine ((NH2)C9H9O2) or 5 g (NH4)2SO4, 3.8 g Na2SO4, 0.5 g MgSO4.7H2O, 7.5 g of glucose and 10 ml of trace element. The trace element solution contained 15 g.l-1 Na2EDTA.2H2O, 0.5 g.l-1 Cu2SO4.5H2O, 2 g.l-1 ZnSO4.7H2O, 2 g.l-1 MnSO4.H2O, 4 g.l-1 FeSO4.7H2O and 0,5 g.l-1 CaCl2.2H2O. KOH was added to set the medium pH at 5.5. P. chrysogenum was cultured in a 3 L bioreactor (Applikon, Schiedam, The Netherlands), with a working volume of 1.8 L and a dilution rate of 0.03h-1 at a pH of 6.5 as previously described in Harris DM, van der Krogt ZA, Klaassen P, Raamsdonk LM, Hage S, van den Berg MA, Bovenberg RA, Pronk JT, Daran JM Exploring and dissecting genome-wide gene expression responses of Penicillium chrysogenum to phenylacetic acid consumption and penicillinG production. BMC Genomics. 2009 10;10:75., with the exception of the employed antifoam. The BDH (10% vol/vol) antifoam (VWR International BV, Amsterdam, The Netherlands) was replaced by Silicone antifoam (Bluestar Silicone, Lyon, France).  Continuous cultures were assumed to be in steady-state after at least 5 volume changes and when culture dry weight and off gas CO2 analyses differed by less than 4% over two consecutive volume changes.

extract_protocol: 60 mL of culture broth was sampled and rapidly filtered over a glass fiber filter (Type A/E, Pall Life Sciences, East Hills, USA). The filter with mycelium was wrapped in aluminium foil, quenched in liquid nitrogen and stored at -80ºC until further use. For total RNA extraction, half of the pellet was grounded by mortar and pestle under constant cooling with liquid nitrogen. The powder was dissolved in 5 mL of Trizol reagent (Invitrogen) and 1 mL chloroform (Sigma) and mixed well. The two phases were separated by centrifugation (4600 g, 15 min). Total RNA was isolated using a phenol-chloroform extraction method, which consisted of two extraction steps in acid-phenol/chloroform/isoamyl alcohol (5:1, pH 4.8, Ambion, Foster City, USA), followed by a chloroform extraction step. Each time the phases were separated by centrifugation (4600 g, 15 min). Total RNA was precipitated for 30 min at -20ºC in 96% ethanol and 0.3 M sodium acetate. The RNA was collected by centrifugation at 23000 g for 15 min and dissolved in RNAse free H2O.

value: L-phenylalanine


title: CD34+CD1a- rep2

description: Sorted T-Cell population CD34+CD1a-

source_name: T-Cell population CD34+CD1a-


title: CD34+CD1a+ rep1

description: Sorted T-Cell population CD34+CD1a+


title: glucose-limited chemostat phenylalanine-2 (TV23)

treatment_protocol: 60 mL of culture broth was sampled and rapidly filtered over a glass fiber filter (Type A/E, Pall Life Sciences, East Hills, USA). The filter with mycelium was wrapped in aluminium foil, quenched in liquid nitrogen and stored at -80ºC until further use. For total RNA extraction, half of the pellet was grounded by mortar and pestle under constant cooling with liquid nitrogen. The powder was dissolved in 5 mL of Trizol reagent (Invitrogen) and 1 mL chloroform (Sigma) and mixed well. The two phases were separated by centrifugation (4600 g, 15 min). Total RNA was isolated using a phenol-chloroform extraction method, which consisted of two extraction steps in acid-phenol/chloroform/isoamyl alcohol (5:1, pH 4.8, Ambion, Foster City, USA), followed by a chloroform extraction step. Each time the phases were separated by centrifugation (4600 g, 15 min). Total RNA was precipitated for 30 min at -20ºC in 96% ethanol and 0.3 M sodium acetate. The RNA was collected by centrifugation at 23000 g for 15 min and dissolved in RNAse free H2O.


title: CD34+CD1a- rep3

description: Sorted T-Cell population CD34+CD1a-


title: glucose-limited chemostat (NH4)2SO4-2 (IS76)

description: Penicillium chrysogenum glucose-limited chemostat with (NH4)2SO4 as sole nitrogen source, wit a dilution rate of 0.03h-1.


title: CD34+CD1a+ rep3

description: Sorted T-Cell population CD34+CD1a+


title: L1977

hyb_protocol: Samples were hybridised according to the Agilent Oligonucleotide Array-based CGH for Genomic DNA Analysis manual for 8x15k arrays

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 10.7.1.1) was used for background subtraction and Linear normalization.

source_name: ollier

label_protocol: Samples were labeled according to the Agilent Oligonucleotide Array-based CGH for Genomic DNA Analysis manual for 8x15k arrays

extract_protocol: DNA was isolated using a Wizard® Genomic DNA Purification Kit from Promega following manufacturer's instructions

treatment_protocol: DNA was isolated from frozen tumor sections

tag: gender

value: male

source_name: Control genomic DNA (commercial source)

value: female


title: glucose-limited chemostat (NH4)2SO4-3 (IS80)


title: L2463


title: L2386


title: CD34+CD1a- rep1

description: Sorted T-Cell population CD34+CD1a-


title: L2218


title: L2280


title: L2102

source_name: Maffucci


title: glucose-limited chemostat (NH4)2SO4-1 (IS74)


title: WK03

city: Nashville

first: Kimryn

last: Rathmell

state: TN

address: 2220 Pierce Ave

department: Medicine

institute: Vanderbilt

description: Gene expression data from Human RCC sample

hyb_protocol: Tumor sample RNA and reference RNA were hybridized on Agilent Whole Human Genome 4x44k arrays by UNC Lineberger Comprehensive Cancer Center Genomics Core

scan_protocol: Agilent gene chips were scanned on an Agilent model C scanner by UNC Lineberger Comprehensive Cancer Center Genomics Core

data_processing: Data was retrieved from the UNC Microarray Database as LOWESS normalized, log2 of processed Red/Green signal (median), filter for 70% good data (Exclude if spot is not found in either channel, spot or spot background is a non-uniform outlier, spot or spot background is a non-uniform outlier for the population, spot is not a positive and significant signal in either channel, or Ch1 and 2 lowess normalized net (median) <10). Missing data was imputed with KNN (k=10) in SAM.  Each array was standard normalized (subtract the mean of the array and divide by the standard deviation). See GSE3538 et al. sample data were re-downloaded from the Stanford Microarray Database (http://smd.stanford.edu/) with Entrez ID annotation as log2 normalized ratios (median).  Raw data from remaining studies utilized Affymetrix arrays and were retrieved from GEO (http://www.ncbi.nlm.nih.gov/geo/). For the See GSE22541 et al. dataset, metastatic tumors were excluded.  Raw data files were imported into Partek Genomics Suite software, version 6.5 (Partek Inc., St. Louis, MO) using RMA normalization.  Each Affymetrix array type was imported separately and data was subsequently merged into one file containing only the overlapping probes.  Entrez IDs common to all datasets were identified using MergeMaid in R, and the Affymetrix data was merged with the Agilent datasets.  This combined dataset was imported into Partek, and batch effect from each source removed.    All reanalyzed data is linked to GSEnnnnn as GSEnnnnn_reanalysis.txt.

source_name: mRNA from Renal Clear Cell Carcinoma

label_protocol: Tumor sample RNA and reference RNA was labelled using the Agilent Two-Color Microarray-Based Gene Expression Analysis v 5.2 protocol by UNC Lineberger Comprehensive Cancer Center Genomics Core.

growth_protocol: Frozen RCCs were obtained through University of North Carolina - Chapel Hill's Tissue Procurement Facility

extract_protocol: RNA was extracted with a Qiagen RNeasy kit. RNA quality was determined using an Agilent LabChip Bioanalyzer. H&E was performed on tumor tissue samples to confirm clear cell or normal histopathology

tag: organism part

value: Kidney

tag: histology

value: Clear Cell

tag: biosource type

value: Frozen Sample

tag: biosource provider

value: University of North Carolina

source_name: Perou lab reference RNA

value: Cancer cell lines


title: T-ALL sample #52

description: sample collected in human clinical trial E2993 (Marks et al., 2009)

hyb_protocol: 500 ng of RNA was amplified and biotinylated using the TotalPrep RNA Amplification Kit (Ambion) and hybridized to the HumanHT-12 v4 Expression BeadChip (Illumina)

data_processing: Gene expression profiling data from 57 adult T-ALL patients were transfomed to log2 scale and normalized using quantile normalization without background subtraction

source_name: TALL lymphoblast sample 52

label_protocol: 10ng of RNA from each T-cell subset was amplified using the Ovation® PicoSL WTA System (Nugen), labeled by the EncoreTM BiotinIL Module (Nugen)

extract_protocol: RNA isolation from lymphoblast obtained from adult T-ALL patient samples was achieved using the RNeasy plus mini kit (Qiagen) according to manufacturer's protocol

treatment_protocol: Leukemic DNA and cryopreserved lymphoblast samples were provided by the Eastern Cooperative Oncology Group (ECOG). All samples were collected in clinical trial E2993(Marks et al., 2009) and informed consent to use leftover material for research purposes was obtained from all the patients at trial entry according to the declaration of Helsinki. T-cell phenotype was confirmed by flow cytometry

value: cryopreserved lymphoblast


title: WK06


title: L1685


title: L1684


title: T-ALL sample #53

source_name: TALL lymphoblast sample 53


title: L1686


title: WK05


title: L2205

description: L2205 was hybridised as gender matched


title: K25


title: WK04


title: K24


title: L1251


title: T-ALL sample #48

source_name: TALL lymphoblast sample 48


title: L1490


title: K22


title: K23


title: WK02


title: L1513


title: L0898

source_name: polystotic chondrosarcoma


title: K20


title: T-ALL sample #47

source_name: TALL lymphoblast sample 47


title: K19


title: L0172


title: T-ALL sample #45

source_name: TALL lymphoblast sample 45


title: K18


title: K21


title: L1083


title: T-ALL sample #49

source_name: TALL lymphoblast sample 49


title: K14


title: K17


title: L2392*

description: Note: this sample is previously uploaded under GEO accession number GSM564801. However, the current sample is normalized on a different dataset.

hyb_protocol: As per manufacturer's instructions.

scan_protocol: As per manufacturer's instructions.

data_processing:
For the expression array, unprocessed data were collected from BeadStudio and processed using variance-stabilizing transformation (vst) and robust spline normalization (rsn) with the Bioconductor package lumi. The processed data was analyzed using LIMMA (linear models for microarray data) analysis, which uses moderated t-test to detect differentially expressed genes between two groups by taking into account natural variance within these groups and correcting for multiple testing using false discovery rate indicating the number of differentially expressed genes between two groups.

Raw data file description: On the Illumina BeadChips, each sample is hybridized on 2 chips, which together compromise all probes per sample. There are four columns in each file. The first column represents the bead (there are approximately 30 replicate beads per probe on random positions on the Illumina BeadChip arrays, so the data that is generated is higly robust), the second the signal, and the other 2 the X and Y locations on the chip. These 2 raw files can be imported into BeadStudio, the program developed by Illumina for analyzing these data, or into R package beadarray.

source_name: Cartilage control

label_protocol: As per manufacturer's instructions.

extract_protocol: RNA was isolated using TRIzol reagent (Invitrogen), followed by RNA clean-up using the QIAGEN Rneasy mini kit (Qiagen GmbH, Hilden, Germany) according to manufacturers instructions. RNA concentration was measured spectrophotometrically and the fragment sizes were determined using RNA 6000 Nano Labchip kit.

value: articular cartilage

tag: sample type

value: control


title: T-ALL sample #44

source_name: TALL lymphoblast sample 44


title: K15


title: L2603*

description: Note: this sample is previously uploaded under GEO accession number GSM564802. However, the current sample is normalized on a different dataset.

value: cartilage


title: L1142*

description: Note: this sample is previously uploaded under GEO accession number GSM564795. However, the current sample is normalized on a different dataset.

source_name: Growth plate control

value: growth plate


title: K13


title: L1234*

description: Note: this sample is previously uploaded under GEO accession number GSM564796. However, the current sample is normalized on a different dataset.


title: K16


title: L2687*

description: Note: this sample is previously uploaded under GEO accession number GSM564793. However, the current sample is normalized on a different dataset.


title: K10


title: L2600*

description: Note: this sample is previously uploaded under GEO accession number GSM564794. However, the current sample is normalized on a different dataset.

value: rib cartilage


title: K12


title: K08


title: K07


title: L1829A

source_name: Solitary enchondroma

extract_protocol: Tumor samples were selected that contained more than 80% of tumor cells, as estimated on haematoxylin and eosin-stained frozen sections. RNA was isolated using TRIzol reagent (Invitrogen), followed by RNA clean-up using the QIAGEN Rneasy mini kit (Qiagen GmbH, Hilden, Germany) according to manufacturers instructions. RNA concentration was measured spectrophotometrically and the fragment sizes were determined using RNA 6000 Nano Labchip kit.

tag: disease

value: solitary enchondroma

tag: tumor

value: enchondroma

tag: idh1/2 mutations

value: yes


title: K09


title: L869

source_name: Solitary chondrosarcoma grade II

value: solitary chondrosarcoma

value: chondrosarcoma grade II


title: L784

value: no


title: J15

value: Kidney


title: L2280

source_name: Ollier chondrosarcoma grade I

value: Ollier chondrosarcoma

value: chondrosarcoma grade I


title: L1083

source_name: Ollier chondrosarcoma grade II


title: L1980d2


title: J11

value: Clear Cell

value: Frozen Sample

value: University of North Carolina


title: J12

value: Cancer cell lines


title: T-ALL sample #30

source_name: TALL lymphoblast sample 30

tag: tissue

value: cryopreserved lymphoblast


title: L813T


title: J10

source_name: mRNA from Renal Clear Cell Carcinoma


title: J13

source_name: Perou lab reference RNA


title: L286T


title: L2103b


title: T-ALL sample #28

source_name: TALL lymphoblast sample 28


title: J09


title: J07


title: K06


title: L2103a*

description: Note: this sample is previously uploaded under GEO accession number GSM564766. However, the current sample is normalized on a different dataset.

source_name: Ollier enchondroma

value: Ollier enchondroma


title: J08


title: J05


title: L1251*

description: Note: this sample is previously uploaded under GEO accession number GSM564767. However, the current sample is normalized on a different dataset.


title: J04


title: L206*

description: Note: this sample is previously uploaded under GEO accession number GSM564763. However, the current sample is normalized on a different dataset.


title: L1683*

description: Note: this sample is previously uploaded under GEO accession number GSM564765. However, the current sample is normalized on a different dataset.


title: L1081


title: J06


title: J03


title: L1975


title: L1977


title: L1630*

description: Note: this sample is previously uploaded under GEO accession number GSM564764. However, the current sample is normalized on a different dataset.


title: L1686*

description: Note: this sample is previously uploaded under GEO accession number GSM563897. However, the current sample is normalized on a different dataset.


title: Colo100.1_TOP_high

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

description:
ext110
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

source_name: Colon cancer stem cell culture

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: CSCs were cultured in modified neurobasal A medium containing N2 supplement (Invitrogen), Lipid Mixture-1 (Sigma), basic fibroblast growth factor (bFGF; 20 ng ml−1) and epidermal growth factor (EGF; 50 ng ml−1).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,

value: Colon CSC culture transduced with Wnt reporter construct

tag: cell fraction

value: high


title: J01


title: Colo100.1_TOP_low

description:
ext108
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).

value: low


title: G8


title: L1687


title: L1463


title: G4


title: G6


title: lm23_TOP_low

description:
ext249
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).


title: F1

description: Gene expression data from Human RCC sample


title: F6


title: J02