title: delta 7ECF vs WT rep3

city: Ithaca

first: John

middle: D.

last: Helmann

state: NY

address: 372 Wing Hall

department: Microbiology

institute: Cornell University

description: Alexa Fluor 555 (WT) / 647 (delta 7ECF)

hyb_protocol: Equal amounts (100-150 pmol) of labeled cDNA were combined plus hybridization buffer (2X = 50% formamide, 10X SSC, 0.1% SDS). cDNA mix was denatured at 95oC and hybridized 16-18 hours at 42oC to DNA microarray slides which had been prehybridized for at least 30 min at 42oC in 1% bovine serum albumin, 5X SSC (1X SSC is 0.15 M NaCl and 0.015 M sodium citrate), 0.1% sodium dodecyl sulfate (SDS), washed in water and dried. Following hybridization the slides were washed sequentially in: 2X SSC + 0.1% SDS for 5 min at 42oC, 2X SSC + 0.1% SDS for 5 min at room temperature, 2X SSC for 5 min at room temperature, 0.2X SSC for 5 min at room temperature, and finally dipped in water and spun until dry.

scan_protocol: Arrays were scanned using a GenePixTM 4000B array scanner (Axon Instruments, Inc.) Raw data files were produced from the scanned images using the GenePix Pro 4.0 software package (GPR files).

data_processing: Red/green fluorescence intensity values were normalized  using the GenePix Pro 4.0 software package such that the ratio of medians of all features was equal to 1

label: Alexa Fluor 555

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: WT

label_protocol: cDNA synthesis was performed using the SuperScriptTM Plus Indirect cDNA labeling System (Invitrogen) as per the manufacturer’s instructions using 20 microgram of total RNA. Total cDNA was labeled overnight with Alexa Fluor 555 or Alexa Fluor 647 (Invitrogen)

extract_protocol: The cell cultures were grown to an OD600 of 0.4 in LB broth with agitation. RNA isolation was performed using the RNeasy mini kit (Qiagen). RNA was subsequently DNase treated with TURBO DNA-freeTM (Ambion) and precipitated overnight. The RNA was dissolved in RNAse free water and quantified using a NanoDrop spectrophotometer (Nanodrop Tech. Inc., Wilmington, DE).

tag: genotype/variation

value: WT

label: Alexa Fluor 647

source_name: delta 7ECF

value: delta 7ECF


title: PL038

status: Public on Jul 21 2010

type: RNA

city: Marseille cedex 07

first: Stephanie

last: Devignot

address: Parc du Pharo BP60109

department: Virology

country: France

institute: IMTSSA

description: US22502694_251485022462_S01_GE1-v5_91_0806_1_3.txt

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome (4x44K) Oligo Microarrays (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), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set at 2 sensitivity levels : 10% and 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE1-v5_91_0806 and Grid: 014850_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Homo sapiens

source_name: DF: acute dengue fever

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification 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 and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

extract_protocol: RNA was prepared using the PaxGene Blood RNA Purification kit (PreAnalytix) following the manufacturer's recommendations. The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: tissue

value: whole blood

tag: severity

value: DF

tag: gender

value: female

tag: age (years)

tag: day of shock after onset of fever

tag: day of blood sampling after onset of fever

tag: day of infusion of plasma after onset of fever

value: not applicable

tag: dengue serotype

tag: immunological status

value: secondary

tag: tourniquet test

value: negative

tag: hepatomegaly

tag: platelet count

tag: hematocrit

tag: hemoconcentration (hematocrit >20%)

tag: white cells count

tag: neutrophil count

tag: lymphocyte count

tag: intensive monitoring

tag: infusion of crystalloid or colloid solution diluted in physiological saline

value: positive


title: PL017

description: US22502694_251485022476_S01_GE1-v5_91_0806_1_1.txt

source_name: DSS: acute dengue shock syndrome

tag: tissue

tag: severity

value: DSS

tag: gender

value: male

value: unknown


title: delta 7ECF vs WT rep3 dyeswap

country: USA

description: Alexa Fluor 555 (delta 7ECF) / 647 (WT)

tag: genotype/variation


title: delta 7ECF vs WT rep2

description: Alexa Fluor 555 (WT) / 647 (delta 7ECF)


title: PL026

description: US22502694_251485022461_S01_GE1-v5_91_0806_1_4.txt

tag: age (years)

tag: day of shock after onset of fever

tag: day of blood sampling after onset of fever

tag: day of infusion of plasma after onset of fever

value: positive (bolus)


title: delta 7ECF vs WT rep1

description: Alexa Fluor 555 (delta 7ECF) / 647 (WT)


title: PL029

description: US22502694_251485022461_S01_GE1-v5_91_0806_1_2.txt

tag: dengue serotype

tag: immunological status

tag: tourniquet test

tag: hepatomegaly


title: PL022

description: US22502694_251485022460_S01_GE1-v5_91_0806_1_1.txt

tag: platelet count

tag: hematocrit

tag: hemoconcentration (hematocrit >20%)

tag: white cells count


title: delta 7ECF vs delta MWX rep2

description: Alexa Fluor 555 (delta 7ECF) / 647 (delta MWX)

source_name: delta MWX

value: delta MWX


title: delta 7ECF vs delta MWX rep1


title: delta 7ECF vs delta MWX rep3 dyeswap

description: Alexa Fluor 555 (delta MWX) / 647 (delta 7ECF)


title: PL020

description: US22502694_251485022465_S01_GE1-v5_91_0806_1_2.txt

tag: neutrophil count

tag: lymphocyte count

tag: intensive monitoring

tag: infusion of crystalloid or colloid solution diluted in physiological saline


title: delta MWX vs WT rep3 dyeswap

description: Alexa Fluor 555 (delta MWX) / 647 (WT)

tag: genotype/variation


title: delta 7ECF vs delta MWX rep3


title: delta MWX vs WT rep3

description: Alexa Fluor 555 (WT) / 647 (delta MWX)


title: delta MWX vs WT rep1

description: Alexa Fluor 555 (WT) / 647 (delta MWX)


title: PL009

description: US22502694_251485022474_S01_GE1-v5_91_0806_1_3.txt

source_name: DHF: acute dengue hemorrhagic fever

tag: tissue

tag: severity

value: DHF

tag: gender

tag: age (years)

value: primary


title: PL005

description: US22502694_251485022475_S01_GE1-v5_91_0806_1_2.txt

tag: day of shock after onset of fever

tag: day of blood sampling after onset of fever

tag: day of infusion of plasma after onset of fever

tag: dengue serotype


title: delta MWX vs WT rep2

description: Alexa Fluor 555 (delta MWX) / 647 (WT)


title: PL004

description: US22502694_251485022460_S01_GE1-v5_91_0806_1_4.txt

tag: immunological status

tag: tourniquet test

tag: hepatomegaly

tag: platelet count


title: PL007

description: US22502694_251485022459_S01_GE1-v5_91_0806_1_3.txt

tag: hematocrit

tag: hemoconcentration (hematocrit >20%)

tag: white cells count

tag: neutrophil count


title: IMR90_0.5 h_control_rep1

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

hyb_protocol: 1.5 mg of cRNA (>9 pmol Cy3 per mg cRNA) was fragmented and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) using the Gene Expression Hybridization Kit as recommended by Agilent

scan_protocol: Slides were scanned immediately using the Agilent DNA Microarray Scanner (G2505B) and default parameters of Feature Extraction Software 9.1 (Agilent)

data_processing: Background corrected intensities were log2 transformed and median-normalized in BRB-ArrayTools, Version 3.7.0. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Lung fibroblast, control, 0.5 hr, rep1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 300 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer’s instructions

growth_protocol: Early passage human lung fibroblast cell strain IMR-90 (Coriell repository, NJ) was sub-cultured in Dulbecco’s modified Eagle’s medium (Gibco) and Ham’s F10 medium in a 1:1 mixture plus 15% fetal bovine serum. Young fibroblasts at population doubling <35 were used in all experiments.

extract_protocol: RNA was isolated using Ribopure (Ambion, Applied Biosytems), according to the manufacturer’s instructions

treatment_protocol: Cells were exposed to 0 (sham irradiated) or 50 cGy 4He ions (125 keV per micron) using the track segment mode of the 5.5-MV Singletron accelerator

tag: cell type

value: primary lung fibroblast


title: IMR90_0.5 h_bystander_rep2

source_name: Lung fibroblast, bystander, 0.5 hr, rep2


title: IMR90_0.5 h_bystander_rep4

source_name: Lung fibroblast, bystander, 0.5 hr, rep4


title: IMR90_0.5 h_bystander_rep3

source_name: Lung fibroblast, bystander, 0.5 hr, rep3


title: IMR90_0.5 h_control_rep2

source_name: Lung fibroblast, control, 0.5 hr, rep2


title: IMR90_0.5 h_control_rep4

source_name: Lung fibroblast, control, 0.5 hr, rep4


title: IMR90_0.5 h_bystander_rep1

source_name: Lung fibroblast, bystander, 0.5 hr, rep1


title: IMR90_0.5 h_alpha_rep2

source_name: Lung fibroblast, irradiated, 0.5 hr, rep2


title: IMR90_0.5 h_alpha_rep3

source_name: Lung fibroblast, irradiated, 0.5 hr, rep3


title: PL002

description: US22502694_251485022462_S01_GE1-v5_91_0806_1_4.txt

tag: tissue

tag: lymphocyte count

tag: intensive monitoring

tag: infusion of crystalloid or colloid solution diluted in physiological saline


title: IMR90_0.5 h_control_rep3

source_name: Lung fibroblast, control, 0.5 hr, rep3


title: IMR90_0.5 h_alpha_rep4

source_name: Lung fibroblast, irradiated, 0.5 hr, rep4


title: MD_Testes_expression_RED_rep2

city: Notre Dame

first: Dongyoung

last: Shin

state: IN

address: Galvin Science building

department: Biology

institute: Universoty of Notre Dame

description: This sample is of non drive strain, Red. It is the second of three T37 biological replicates used in this experiment, each from separate extracted testes

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Aedes aegypti

source_name: RED strain testes in pupal stage

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

growth_protocol: Aedes aegypti Red strain males were grown to early pupal stage at 26°C temperature, 80% humidity in 16 hour light/8 hour dark cycle.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) and the RNAlater reagent (Qiagen) and DNA was removed by DNase digestion with the RNase-Free DNase (Qiagen). RNA concentration was determined by NanoDrop (NanoDrop Technologies Inc.).

tag: strain

value: RED

tag: sex

tag: developmental stage

value: pupal stage

value: testes


title: MD_Testes_expression_RED_rep3

description: This sample is of non drive strain, Red. It is the third of three T37 biological replicates used in this experiment, each from separate extracted testes


title: MD_Testes_expression_RED_rep1

description: This sample is of non drive strain, Red. It is the first of three T37 biological replicates used in this experiment, each from separate extracted testes


title: MD_Testes_expression_T37_rep3

description: This sample is of meiotic drive strain, T37. It is the third of three T37 biological replicates used in this experiment, each from separate extracted testes

source_name: T37 strain testes in pupal stage

growth_protocol: Aedes aegypti T37 strain males were grown to early pupal stage at 26°C temperature, 80% humidity in 16 hour light/8 hour dark cycle.


title: IMR90_0.5 h_alpha_rep1

source_name: Lung fibroblast, irradiated, 0.5 hr, rep1


title: MACROPHAGES+THESC-CONDITIONED MEDIUM 2

city: Vermillion

first: Kathleen

middle: M

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

institute: University of South Dakota

description: Cells were grown in RPMI-1640 medium supplemented with 1% penicillin/streptomycin and 10% fetal bovine serum.

hyb_protocol: 10 micrograms of biotinylated cRNA were mixed with fragmentation buffer and heated to 94C for 20 min.  The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides, and hybridized for 18 hours at 37C.

scan_protocol: The slides were scanned in an Axon GenePix 4000B scanner.

data_processing: global median normalization, CodeLink Expression Analysis 5.0

source_name: CULTURED MONOCYTE CELL LINE (U-937) FROM ATCC DIFFERENTIATED INTO MACROPHAGES

label_protocol: Biotinylated cRNA were prepared using the MessageAmp II-Biotin Enhanced Kit from Ambion from 2 microgram total RNA starting material.

extract_protocol: The cultured U-937 monocytic cells were rinsed and TRI reagent (MRC) was added.  The cells were scraped into tubes and centrifuged in the presence of bromochloropropane and sodium acetate.  The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity was evaluated with the RNA 6000 NanoLabChip in an Agilent Bioanalyzer.

tag: cell line

value: U-937 monocytes

tag: passage

tag: treatment

value: 32 nM phorbol myristate acetate

tag: treatment duration

tag: secondary treatment

value: THESC conditioned medium serum starved

tag: secondary treatment duration


title: MD_Testes_expression_T37_rep2

description: This sample is of meiotic drive strain, T37. It is the second of three T37 biological replicates used in this experiment, each from separate extracted testes


city: Cambridge

first: Fatima

last: Al-Shahrour

state: MA

address: 7 Cambridge Center

department: Cancer program

institute: Broad Institute of MIT and Harvard

description: Gene expression data of HSC cells from MSI2-inducible mouse rep1

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix GCS 3000 7G scanner using Affymetrix standard protoco

data_processing: Signal normalization was performed by RMA method. RMA expression measure was computed using Bioconductor Affy package in R language (Bioconductor 2.5; R version 2.11.0)

label: biotin

organism: Mus musculus

source_name: Hematopoietic stem and progenitor cells (LineageLow, Sca1+, Kit+; LSK)

label_protocol: NuGen Ovation Biotin labeling system

growth_protocol: Hematopoietic stem and progenitors cells were isolated from rTA and MSI2-inducible mice using high-speed multiparameter flow cytometry.

extract_protocol: RNA was extracted using Qiagen RNeasy Micro Kit according to manufacturers instruction. The RNA was amplified using a linear amplification protocol (Nugen Ovation V2 amplification system)

treatment_protocol: The cells were treated with RLT lysis buffer (Qiagen) containing beta-mercaptoethanol to stabilize RNA.

value: Bone marrow cells

tag: genotype

value: MSI2-inducible mice


title: THESC ENDOMETRIAL CELLS VEHICLE+MACROPHAGE-CONDITIONED MEDIUM 1

description: Cells were grown in DMEM/F12 medium supplemented with 1% ITS+, 1% penicillin/streptomycin, and 500 ng/mL puromycin.  2% fetal bovine serum was also added to the medium from days 1-6.

source_name: CULTURED HUMAN ENDOMETRIAL CELL LINE (T-HESC) FROM ATCC

label_protocol: Biotinylated cRNA were prepared using the MessageAmp II-Biotin Enhanced Kit from Ambion from 1 microgram total RNA starting material.

extract_protocol: The cultured endometrial cells were rinsed and TRI reagent (MRC) was added.  The cells were scraped into tubes and centrifuged in the presence of bromochloropropane and sodium acetate.  The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity was evaluated with the RNA 6000 NanoLabChip in an Agilent Bioanalyzer.

value: telomerase immortalized human endometrial cell line (ATCC #CRL-4003)

value: vehicle 0.1% ethanol

tag: time course

value: 8 days

tag: serum starved

value: days 6-8

value: macrophage conditioned medium

tag: secondary time course

value: final 24 hours of 8 day treatment


description: Gene expression data of HSC cells from MSI2-inducible mouse rep2

tag: cell type


title: HSC cells from control rtTA mouse rep3

description: Gene expression data of HSC cells from control rtTA mouse rep3

value: control rtTA mouse


title: MACROPHAGES+THESC-CONDITIONED MEDIUM 1


title: MD_Testes_expression_T37_rep1

description: This sample is of meiotic drive strain, T37. It is the first of three T37 biological replicates used in this experiment, each from separate extracted testes

value: male

tag: tissue


title: MACROPHAGES CONTROL 3

value: serum starvation


title: THESC ENDOMETRIAL CELLS ESTRADIOL+PROGESTERONE 3

value: estradiol+progesterone

tag: dose

value: estradiol 10-8M medroxyprogesterone acetate 10-7M


title: THESC ENDOMETRIAL CELLS VEHICLE+MACROPHAGE-CONDITIONED MEDIUM 2


title: HSC cells from control rtTA mouse rep2

description: Gene expression data of HSC cells from control rtTA mouse rep2


title: MACROPHAGES CONTROL 1


title: THESC ENDOMETRIAL CELLS VEHICLE+MACROPHAGE-CONDITIONED MEDIUM 3


title: THESC ENDOMETRIAL CELLS ESTRADIOL+PROGESTERONE+MACROPHAGE-CONDITIONED MEDIUM 2


title: THESC ENDOMETRIAL CELLS ESTRADIOL+PROGESTERONE 2


title: THESC ENDOMETRIAL CELLS ESTRADIOL+PROGESTERONE 1


title: THESC ENDOMETRIAL CELLS ESTRADIOL+PROGESTERONE+MACROPHAGE-CONDITIONED MEDIUM 1


title: HSC cells from control rtTA mouse rep1

description: Gene expression data of HSC cells from control rtTA mouse rep1


title: MACROPHAGES+THESC-CONDITIONED MEDIUM 3


title: MACROPHAGES CONTROL 2


title: THESC ENDOMETRIAL CELLS ESTRADIOL+PROGESTERONE+MACROPHAGE-CONDITIONED MEDIUM 3


title: THESC ENDOMETRIAL CELLS CONTROL 3


title: 3.5 W/kg exposure group, biological rep1

status: Public on Jul 20 2010

city: Hangzhou

first: Guangdi

last: Chen

state: Zhejiang

address: 388 Yuhangtang

department: School of Medicine

country: China

institute: Zhejiang University

description:
Gene expression data from MCF-7 cells after exposure to RF EMF at SAR of 3.5 W/kg for 24 hours
3.5 W/kg-E1

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

scan_protocol: GeneChips were scanned using the GeneArray Scanner.

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 mean target intensity of each array was arbitrarily set to 500.

source_name: MCF-7 cells, RF EMF exposed at SAR of 3.5 W/kg for 24 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 20 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MCF-7 cells were grown in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum at 37°C in 5% humidified CO2.

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

treatment_protocol: MCF-7 cells were intermittently (5 min fields on/10 min fields off) exposed or sham-exposed to RF EMF for 24 h at an average SAR of 2.0 W/kg or a higher level of 3.5 W/kg.

value: Human breast cancer cell line, MCF-7

tag: stress

value: 1800 MHz RF-EMF

tag: rf-emf sar


title: 3.5 W/kg control group, biological rep2

description:
Gene expression data from MCF-7 cells after sham exposure for 24 hours
3.5 W/kg-C2

source_name: MCF-7 cells, RF EMF sham exposed for 24 hours

value: sham-exposure

value: control for 3.5 W/kg exposure group


title: THESC ENDOMETRIAL CELLS CONTROL 2


title: skin, 10days post-wounding, biological replicate2

city: Chicago

first: Zarema

middle: H

last: Arbieva

state: IL

address: 835 S. Wolcott A301

department: RRC

institute: UIC

hyb_protocol: 15 micrograms of fragmented cRNA were hybridized overnight at 45C, and washed and stained according to the EukGE-WS2v5_450 Affymetrix protocol.

scan_protocol: Arrays were scanned using Affymetyrix GeneChip Scanner 3000 7G.

data_processing: Hybridization intensities were normalized by quantiles and summarized using the RMA method. The S+ArrayAnalyzed statistical package (Insightful) was used for data transformation and subsequent statistical analysis.

source_name: skin, 10days post-wounding

label_protocol: Standard 3' IVT target labeling protocol (Affymetrix) starting with 5 micrograms of total RNA per labeling reaction.

extract_protocol: The RNeasy total RNA isolation protocol (Qiagen) was utilized.

treatment_protocol: 2mm biopsies were collected at defined time intervals after wounding  (6hrs, 12hrs, 24hrs, 3days, 5days, 7days, 10days) and from unwounded tissue.

tag: strain

value: Balb/c

tag: gender

value: female

tag: age

value: 6-8 weeks

value: skin

tag: time post-wound

value: 10 days


title: THESC ENDOMETRIAL CELLS CONTROL 1

tag: cell line

value: telomerase immortalized human endometrial cell line (ATCC #CRL-4003)

tag: passage

tag: treatment

value: vehicle 0.1% ethanol

value: 8 days

value: days 6-8


title: tongue, 10days post-wounding, biological replicate2

source_name: tongue, 10days post-wounding

value: mucosa (tongue)


title: skin, 10days post-wounding, biological replicate3


title: 2 W/kg exposure group, biological rep2

description:
Gene expression data from MCF-7 cells after exposure to RF EMF at SAR of 2.0 W/kg for 24 hours
2 W/kg-E2

source_name: MCF-7 cells, RF EMF exposed at SAR of 2.0 W/kg for 24 hours


title: tongue, 10days post-wounding, biological replicate1


title: tongue, 10days post-wounding, biological replicate3


title: 3.5 W/kg exposure group, biological rep2

description:
Gene expression data from MCF-7 cells after exposure to RF EMF at SAR of 3.5 W/kg for 24 hours
3.5 W/kg-E2


title: skin, 10days post-wounding, biological replicate1


title: 2 W/kg exposure group, biological rep1

description:
Gene expression data from MCF-7 cells after exposure to RF EMF at SAR of 2.0 W/kg for 24 hours
2 W/kg-E1


title: skin, 7days post-wounding, biological replicate1

source_name: skin, 7days post-wounding

value: 7 days


title: skin, 7days post-wounding, biological replicate3


title: 2 W/kg control group, biological rep1

description:
Gene expression data from MCF-7 cells after sham exposure for 24 hours
2 W/kg-C1

value: control for 2.0 W/kg exposure group


title: skin, 5days post-wounding, biological replicate3

source_name: skin, 5days post-wounding

value: 5 days


title: 2 W/kg control group, biological rep2

description:
Gene expression data from MCF-7 cells after sham exposure for 24 hours
2 W/kg-C2

value: Human breast cancer cell line, MCF-7


title: tongue, 7days post-wounding, biological replicate2

source_name: tongue, 7days post-wounding


title: skin, 5days post-wounding, biological replicate2


title: tongue, 7days post-wounding, biological replicate1


title: skin, 7days post-wounding, biological replicate2


title: Control vs. TBT exposed  individual B

city: Sapporo

first: Sorin

middle: Vasile

last: Sabau

address: 5-1-1-1 Minamisawa, Minamiku

country: Japan

institute: Tokai University

description: Experiment 2B:  mRNA from individual B that had been exposed to 100 nM TBT for 24 h was labeled with Cy5 (Cy5 target B). Equal amounts of mRNA derived from each of three control individuals  (exposed to 0.001% EtOH for 24 h) were mixed and then labeled with Cy3 (Cy3 target).

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent GenePix4000B scanner  (Axon Instruments) Images were quantified using GenePix Pro 4.0 microarray analysis software (Axon Instruments)

data_processing: GenePix Pro 4.0 was used for background subtraction and LOWESS normalization.

molecule: polyA RNA

organism: Ciona intestinalis

source_name: 100 nM TBT

label_protocol: Two micrograms of poly (A)+RNA was labeled with either Cy3 or Cy5 using an Agilent Fluorescent Linear Amplification Kit (Agilent Technologies)

growth_protocol: Ciona intestinalis were cultivated in Maizuru Bay, Kyoto, Japan, and provided through the National Bio-Resource Project (NBRP) of the MEXT, Japan.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The mRNA was then extracted using an mRNA purification kit (Amersham Biosciences, Piscataway, NJ) following the manufacturer’s protocol.

treatment_protocol: Ciona adults kept in a disposable plastic bag with 3 litter of filtered natural seawater were exposed to 100 nM TBT or to 0.001% ethanol as a control, for 24 h

value: 2 months

value: whole body (with removed tunic)


title: Control vs. TBT exposed  individual A

description: Experiment 2A:  mRNA from individual A that had been exposed to 100 nM TBT for 24 h was labeled with Cy5 (Cy5 target A). Equal amounts of mRNA derived from each of three control individuals  (exposed to 0.001% EtOH for 24 h) were mixed and then labeled with Cy3 (Cy3 target).


title: 3.5 W/kg control group, biological rep1

description:
Gene expression data from MCF-7 cells after sham exposure for 24 hours
3.5 W/kg-C1

value: sham-exposure

value: control for 3.5 W/kg exposure group


title: skin, 5days post-wounding, biological replicate1

value: Balb/c

value: female


title: Control vs. TBT exposed (3 pooled)

description: Experiment 1: Equal amounts of mRNA from three individuals after their exposure to 100 nM TBT or to 0.001% EtOH for 24 h were mixed. The mixed RNA samples were labeled either with Cy3 (EtOH) or with Cy5 (TBT) using Low RNA Fluorescent Linear Amplification Kit (Agilent Technologies)


title: tongue, 7days post-wounding, biological replicate3

value: 6-8 weeks


title: skin, 3days post-wounding, biological replicate3

source_name: skin, 3days post-wounding

value: skin

value: 3 days


title: tongue, 5days post-wounding, biological replicate3

source_name: tongue, 5days post-wounding


title: skin, 3days post-wounding, biological replicate2


title: tongue, 5days post-wounding, biological replicate2


title: tongue, 24hrs post-wounding, biological replicate2

source_name: tongue, 24hrs post-wounding

value: 24 hrs


title: skin, 3days post-wounding, biological replicate1


title: tongue, 24hrs post-wounding, biological replicate1


title: tongue, 24hrs post-wounding, biological replicate3


title: tongue, 3days post-wounding, biological replicate3

source_name: tongue, 3days post-wounding


title: tongue, 12hrs post-wounding, biological replicate2

source_name: tongue, 12hrs post-wounding

value: 12 hrs


title: skin, 24hrs post-wounding, biological replicate2

source_name: skin, 24hrs post-wounding


title: skin, 24hrs post-wounding, biological replicate1


title: tongue, 12hrs post-wounding, biological replicate3


title: skin, 12hrs post-wounding, biological replicate1

source_name: skin, 12hrs post-wounding


title: skin, 24hrs post-wounding, biological replicate3


title: tongue, 12hrs post-wounding, biological replicate1


title: tongue, 5days post-wounding, biological replicate1


title: tongue, 3days post-wounding, biological replicate2


title: skin, 6hrs post-wounding, biological replicate3

source_name: skin, 6hrs post-wounding

value: 6 hrs


title: skin, 12hrs post-wounding, biological replicate3


title: tongue, 3days post-wounding, biological replicate1

value: mucosa (tongue)


title: skin, 12hrs post-wounding, biological replicate2


title: skin, 6hrs post-wounding, biological replicate2


title: skin, 6hrs post-wounding, biological replicate1


title: tongue, 6hrs post-wounding, biological replicate3

source_name: tongue, 6hrs post-wounding


title: tongue, 6hrs post-wounding, biological replicate2


title: unwounded skin, biological replicate1

source_name: unwounded skin

value: 0 hr


title: unwounded skin, biological replicate3


title: tongue, 6hrs post-wounding, biological replicate1


title: unwounded skin, biological replicate2


title: unwounded tongue, biological replicate3

source_name: unwounded tongue


title: unwounded tongue, biological replicate1


title: Prostate cancer 49 Tumor tissue

city: Erlangen

first: Sven

last: Wach

address: Glueckstrasse 6

department: Dept. of Urology

country: Germany

institute: University Hospital, Friedrich-Alexander-University Erlangen-Nuernberg

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 49
Total RNA from FFPE tissue

hyb_protocol: Affymetrix GeneChip miRNA Procedure (FluidicsScript 450-0003, Hyb. 48°C)

scan_protocol: Affymetrix-3000 7G

data_processing: Data files were analyzed with Partek genomics suite (version 6.5) using RMA background correction and quartile normalization

source_name: Prostate cancer radical prostatectomy specimen 49

label_protocol: FlashTag RNA Labeling with Genisphere RNA Labeling Kit

extract_protocol: RNA was prepared by proteinase K digestion of formalin-fixed tissue samples followed by RNA precipitation. Epicentre MasterPure Complete DNA & RNA Purification Kit was used according to the manufacturer's instructions

treatment_protocol: Primary prostate cancer samples from thus far untreated patients after radical prostatectomy.

tag: specimen

tag: disease state

value: Primary prostate cancer

tag: tumor stage

tag: gleason score


title: Prostate cancer 35 Tumor tissue

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 35
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 35


title: Prostate cancer 36 Tumor tissue

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 36
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 36


title: Prostate cancer 33 Tumor tissue

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 33
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 33


title: B16F1 melanoma tumor grown in C57BL/6 wild-type mouse, irradiated, technical replicate 1

first: Sean

middle: Pravin

last: Pitroda

address: 5841 South Maryland Avenue, MC 1105

department: Radiation and Cellular Oncology

institute: The University of Chicago

description: Gene expression data from irradiated B16F1 melanoma tumor grown in C57BL/6 wild-type mouse.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner.

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 800.

source_name: Irradiated B16F1 melanoma tumor grown in C57BL/6 wild-type mouse

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: B16F1 murine melanoma cells were obtained from the American Type Culture Collection (Manassas, VA) and cultured in RPMI 1640 culture medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Atlanta Biologicals, Lawrenceville, GA), 100 units/ml penicillin and 100 mg/ml streptomycin (Invitrogen, Carlsbad, CA). Cell cultures were maintained at 37 deg C in a humidified environment containing 5% CO2. C57BL/6-NCr (C57BL/6 wild-type) mice were obtained from FCRI-Taconic (Germantown, NY). B6;129S-Tnfrsf1a[tm1Imx] Tnfrsf1b[tm1Imx]/J (TNFR1,2 -/-) breeding pairs were obtained from Jackson Laboratories (Bar Harbor, ME). Mice were 8-12 weeks of age when experimentation began. B16F1 cells (2x10^6 cells in 100 μl of phosphate-buffered saline) were injected subcutaneously into the right hind limbs of five to seven C57BL/6 and TNFR1,2 -/- mice. Tumor volume was determined by direct measurement with calipers and calculated by using the formula (length x width x depth/2). Tumors were permitted to grow to a volume of 268-478 mm3 after which mice were divided into treatment groups with equal mean tumor volumes.

extract_protocol: At the conclusion of each experiment, the animals were euthanized using CO2 followed by cervical dislocation in accordance with institutional guidelines. Tumors were excised five hours following treatment and snap frozen in liquid nitrogen. TRIzol extraction of total RNA was performed according to the manufacturer's instructions. Samples were pooled based on total RNA and analyzed in duplicate.

treatment_protocol: For radiation exposure, mice were restrained in plexiglass cages and all but the tumor-bearing hind limb was shielded with lead. A single dose of 20 Gray (Gy) was delivered using a Phillips orthovoltage X-ray generator operating at 250 kV and 15 mA.

value: whole melanoma tumor

tag: host strain

tag: host genotype

value: wild-type

value: irradiated


title: B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse, irradiated, technical replicate 1

description: Gene expression data from irradiated B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse.

source_name: Irradiated B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse

tag: tissue


title: B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse, untreated, technical replicate 2

description: Gene expression data from untreated B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse.

source_name: Untreated B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse

value: untreated


title: pRbp53_tumor2

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

description: RNA integrity tested with Bioanalyzer (Agilent)

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: RMA normalization, log2 transformed

source_name: skin tumor

label_protocol: Affymetrix protocol

extract_protocol: miRNeasy Mini Kit from QIAGEN

tag: genetic background

value: FVB

value: squamous cell carcinoma

tag: histological subtype

value: spindle cell carcinoma


title: B16F1 melanoma tumor grown in C57BL/6 wild-type mouse, irradiated, technical replicate 2


title: Prostate cancer 38 Tumor tissue

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 38
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 38


title: unwounded tongue, biological replicate2

value: Balb/c

value: female


title: Prostate cancer 39 Tumor tissue

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 39
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 39


title: Prostate cancer 41 Tumor tissue

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 41
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 41


title: B16F1 melanoma tumor grown in C57BL/6 wild-type mouse, untreated, technical replicate 1

description: Gene expression data from untreated B16F1 melanoma tumor grown in C57BL/6 wild-type mouse.

source_name: Untreated B16F1 melanoma tumor grown in C57BL/6 wild-type mouse


title: pRbp53_tumor3


title: Prostate cancer 50 Tumor tissue

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 50
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 50


title: B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse, irradiated, technical replicate 2


title: pRbp53_tumor4

value: mixed


title: B16F1 melanoma tumor grown in C57BL/6 wild-type mouse, untreated, technical replicate 2


title: Prostate cancer 29 Tumor tissue

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 29
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 29


title: B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse, untreated, technical replicate 1


title: Prostate cancer 31 Tumor tissue

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 31
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 31


title: pRbp53_tumor5


title: pRbp53_tumor1


title: p53_tumor6


title: p53_tumor5

value: poorly differentiated


title: Prostate cancer 28 Tumor tissue

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 28
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 28


title: Prostate cancer 26 Tumor tissue

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 26
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 26


title: Prostate cancer 27 Tumor tissue

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 27
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 27


title: Prostate cancer 7 Tumor tissue

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 7
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 7


title: p53_tumor4


title: p53_tumor3

value: undifferentiated


title: p53_tumor7


title: p53_tumor2


title: Prostate cancer 15 Tumor tissue

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 15
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 15


title: Prostate cancer 22 Tumor tissue

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 22
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 22


title: Prostate cancer 9 Tumor tissue

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 9
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 9


title: Prostate cancer 16 Tumor tissue

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 16
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 16


title: Control_skin_4

source_name: skin tissue

value: skin


title: Prostate cancer 50 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 50
Total RNA from FFPE tissue

value: normal control


title: Prostate cancer 1 Tumor tissue

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 1
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 1


title: Prostate cancer 5 Tumor tissue

description:
MiRNA gene expression from prostate cancer tissue
Tumor * 5
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 5


title: Control_skin_1

description: RNA integrity tested with Bioanalyzer (Agilent)


title: Synthetic Medium (Cy5) vs Minimal Medium (Cy3) replicate 2 [oligodT]

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

hyb_protocol: Samples were applied to microarrays enclosed in hybridization chambers (53°C water bath). After hybridization, slides were washed sequentially.

scan_protocol: Hybridized microarrays were scanned and gridded with a GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA)

data_processing: Normalized by background-subtracted mean-by-mean normalization of well measured spots, and statistically analyzed using a Bayesian analysis of gene expression levels with BAGEL software.

organism: Saccharomyces cerevisiae

source_name: cells

label_protocol: 2 µg of mRNA were primed with 0.5 µl of 100 µM MTP or Oligo-d(T) primer at 70°C for 10min, then reversed transcribed at 42°C for 2h in the presence of 400 U SuperScript II RTase (Invitrogen), and 0.8ul Amino-allyl dUTP/dNTP made from Sigma in mg aliquotes and dissolved in 20µl H2O-(DEPC) and mixed with 30µl of 100mM dATP, dTTP, dGTP, dCTP and 12µl 100mM dTTP;  25 µM Cy3/Cy5-label

growth_protocol: Saccharomyces cerevisiae S288c was grown in synthetic complete medium (SC) at 30°C shaking at 160 rpm until mid log phase (OD600=0.4). For nitrogen depletion, cells were collected and resuspended in an equal volume of minimal medium (MM) without amino acids or adenine and with limiting concentrations (0.025%) of ammonium sulfate. Cultures were harvested after 12h incubation, flash frozen in liquid nitrogen and stored at -80°C [25].

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

tag: environment condition

value: nitrogen poor

tag: primer type

value: oligodT

value: Nitrogen rich


title: p53_tumor1

source_name: skin tumor


title: Prostate cancer 39 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 39
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 39


title: Prostate cancer 36 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 36
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 36


title: Prostate cancer 41 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 41
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 41


title: Prostate cancer 49 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 49
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 49


title: p53_pRb_tumor_6

extract_protocol: RNeasy Fibrous Tissue Mini Kit (Qiagen)

tag: strain


title: p53_pRb_tumor_8


title: Control_skin_2


title: Control_skin_3


title: Prostate cancer 33 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 33
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 33


title: Prostate cancer 31 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 31
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 31


title: Synthetic Medium (Cy5) vs Minimal Medium (Cy3) replicate 1 [oligodT]


title: Minimal Medium (Cy5) vs Synthetic Medium (Cy3) replicate 2 [oligodT]


title: p53_pRb_tumor_7


title: Prostate cancer 38 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 38
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 38


title: p53_pRb_tumor_5


title: p53_pRb_tumor_3


title: p53_pRb_tumor_2


title: p53_pRb_tumor_4


title: Minimal Medium (Cy5) vs Synthetic Medium (Cy3) replicate 1 [oligodT]


title: p53_pRb_tumor_1


title: Prostate cancer 35 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 35
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 35


title: Prostate cancer 29 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 29
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 29


title: Prostate cancer 27 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 27
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 27


title: Prostate cancer 26 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 26
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 26


title: Prostate cancer 5 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 5
Total RNA from FFPE tissue


title: Prostate cancer 16 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 16
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 16


title: Prostate cancer 22 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 22
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 22


title: Prostate cancer 9 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 9
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 9


title: Prostate cancer 28 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 28
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 28


title: Prostate cancer 15 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 15
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 15


title: p53_tumor_7

description: RNA integrity tested with Bioanalyzer (Agilent)

source_name: skin tumor


title: p53_tumor_6


title: p53_tumor_2


title: p53_tumor_5


title: Prostate cancer 1 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 1
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 1


title: control_skin_4

source_name: skin tissue

tag: age

value: 2 months


title: p53_tumor_1


title: Prostate cancer 7 Normal tissue

description:
MiRNA gene expression data from corresponding normal tissue
Normal * 7
Total RNA from FFPE tissue

source_name: Prostate cancer radical prostatectomy specimen 7


title: control_skin_3


title: p53_tumor_3


title: control_skin_5


title: p53_tumor_4


title: control_skin_1


title: control_skin_2


title: 3364

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: H02_normoxic_Cy5 vs. HO1_hypoxic_Cy3

hyb_protocol: For Cy3 14 pmol and for Cy5 10 pmol incorporated dye was fragmented and resuspended in 55ul  2x GE hybridization buffer HI-RPM.The arrays were hybridized in microarray hybridization chambers (Agilent) overnight at 65ºC, rpm=10 for 17 hours.

scan_protocol: After washing the slides were scanned with a DNA microarray scanner (Agilent) and images were processed with the Feature Extraction Software version 9.1.1.1 (Agilent).

data_processing: The Agilent processed signal values (i.e., feature gProcessedSignal from Agilent Feature Extraction v9.1.1.1) were used for the data analysis. Base 2 log-ratios (Cy5/Cy3) were computed, and in case of multiple probes for the same Agilent ID, log-ratios were averaged. Control probes and probes with no signals flagged as positive and significant (by the Feature Extraction Software) were removed prior to analysis.

label_protocol: From 1 µg of cellular RNA, poly-A RNA was reversed transcribed using a poly dT-T7 primer. The resulting cDNA was immediately used for one round of amplification by T7 in vitro transcription reaction in the presence of Cyanine 5-CTP. The amplified and labeled RNA probes were purified separately with RNeasy purification columns (Qiagen, Belgium). Probes were verified for amplification yield and incorporation efficiency by measuring the RNA concentration at 280 nm and Cy5 incorporation at 650 nm using a Nanodrop spectrophotometer.

growth_protocol: HepG2 human hepatoblastoma cells were obtained from ATCC (HB-8065, Rockville, MD, USA). Cells were grown in a humidified incubator (20% O2, 5% CO2 at 37°C) in Williams Medium E (WEM, InVitrogen) supplemented with 10% fetal calf serum, 2 mM L-glutamine, 20 mU/ml insulin, 50 nM dexamethasone, 100 U/ml penicillin, 100 µg/ml streptomycin, 2.5 µg fungizone, 50 µg/ml gentamycin and 100 µg/ml vancomycin (=WEM-C).

extract_protocol: Samples in Trizol were homogenized in a Dounce homogenizer for RNA extraction. Thereafter, RNA was isolated with the RNeasy Kit (Qiagen, Chatsworth, CA) according to the manufacturer’s instructions. The quality of all RNA samples was monitored by measuring the 260/280 and 260/230 nm ratios with a NanoDrop spectrophotometer (NanoDrop Technologies, Centreville, DE) and by means of the Agilent 2100 BioAnalyzer (Agilent, Palo Alto, CA). Only RNA showing no signs of degradation or impurities (260/280 and 260/230 nm ratios, >1.8) was considered suitable for microarray analysis and used for labeling.

treatment_protocol: Cells were seeded at 3x106 in 75 cm² tissue culture flasks (n=4) at 20% O2 and were grown until 70% confluence (during five days, with medium refreshment every two days). After reaching near-confluence, cells were washed with buffer and medium was refreshed, 2 flasks were placed in a humidified incubator with hypoxic conditions (2% O2, 5% CO2 at 37°C), while the other flasks (n=2) remained in normoxic conditions (20% O2). Cells were cultured for 72hrs in these different oxygen conditions and after three days cells were harvested after trypsin treatment, mixed with Trizol (InVitrogen, Merelbeke, Belgium) and stored in -80°C for further analysis.

tag: exposure time

value: 72 hr

tag: condition

tag: dd

label_protocol: From 1 µg of cellular RNA, poly-A RNA was reversed transcribed using a poly dT-T7 primer. The resulting cDNA was immediately used for one round of amplification by T7 in vitro transcription reaction in the presence of Cyanine 3-CTP. The amplified and labeled RNA probes were purified separately with RNeasy purification columns (Qiagen, Belgium). Probes were verified for amplification yield and incorporation efficiency by measuring the RNA concentration at 280 nm and Cy3 incorporation at 550 nm using a Nanodrop spectrophotometer.


title: 3365

description: H04_normoxic_Cy5 vs. HO3_hypoxic_Cy3

tag: cell line

extract_protocol: Samples in Trizol were homogenized in a Dounce homogenizer for RNA extraction. Thereafter, RNA was isolated with the RNeasy Kit (Qiagen, Chatsworth, CA) according to the manufacturer’s instructions.  The quality of all RNA samples was monitored by measuring the 260/280 and 260/230 nm ratios with a NanoDrop spectrophotometer (NanoDrop Technologies, Centreville, DE) and by means of the Agilent 2100 BioAnalyzer (Agilent, Palo Alto, CA). Only RNA showing no signs of degradation or impurities (260/280 and 260/230 nm ratios, >1.8) was considered suitable for microarray analysis and used for labeling.


title: 3362

description: HO1_hypoxic_Cy5 vs. H02_normoxic_Cy3


title: 3363

description: HO3_hypoxic_Cy5 vs. H04_normoxic_Cy3


title: UM-PEL-1 xenografts, treated with PBS; material pooled from three mice

city: Miami

first: Kristopher

middle: A

last: Sarosiek

state: FL

address: 1580 NW 10th Ave

institute: University of Miami

description: UM-PEL-1 + PBS

hyb_protocol: cDNA was used to generate sense transcript cDNA used for hybridization on the Affymetrix Human Gene 1.0ST arrays.

scan_protocol: According to Affymetrix protocol.

data_processing: Image analysis was done using the Affymetrix Command Console Software (AGCC). Resulting CEL files were be imported into Partek software (Partek, Inc., St. Louis, MO) using median polish probeset summarization, GCRMA background correction and quantile normalization.

source_name: UM-PEL-1 tumor xenografts in NOD/SCID mice

label_protocol: RNA was amplified and labeled using NuGEN Ovation Pico WTA system, WT-Ovation Exon module and Encore Biotin Module (NuGEN, San Carlos, CA, USA).

growth_protocol: UM-PEL-1 cells, that were not cultured in vitro, were injected into the peritoneal cavities of NOD/SCID mice and grown for 3 days prior to treatment.

extract_protocol: RNA was isolated by TRIzol reagent according to the manufacturer's insturctions.

treatment_protocol: Mice were injected IP a single time with either PBS or bortezomib (0.3 mg/kg).  Cells were recovered from each of the three mice per treatment group after 24 hours and pooled.

tag: lymphoma type

value: Primary Effusion Lymphoma

tag: agent

value: PBS


title: UM-PEL-1 xenografts, treated with Bortezomib; material pooled from three mice

description: UM-PEL-1 + Bortezomib

value: Bortezomib


title: B-iPSCs_1 P4

status: Public on Jul 19 2010

type: genomic

first: Maria

middle: Eugenia

last: Figueroa

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

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

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

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

molecule: genomic DNA

source_name: B-iPSCs P4

label_protocol: Random priming with 9-mers pre-labeled with either Cy3 or Cy5 according to manufacturer's instructions using the NimbleGen Dual-Color DNA Labeling Kit (cat # 05223547001)

extract_protocol: Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)

tag: cell type

value: splenic B cell-derived iPSCs Passage #4

tag: fraction

value: MspI representation of genomic DNA

value: HpaII representation of genomic DNA


title: TTF-iPSCs_3 P4

source_name: TTF-iPSCs P4

value: Tail tip fibroblast-derived iPSCs Passage #4


title: B-iPSCs_3 P16

source_name: B-iPSCs P16

value: splenic B cell-derived iPSCs Passage #16


title: B-iPSCs_3 P4


title: B-iPSCs_1 P16


title: TTF-iPSCs_1 P16

source_name: TTF-iPSCs P16

value: Tail tip fibroblast-derived iPSCs Passage #16


title: TTF-iPSCs_3 P16


title: TTF-iPSCs_2 P4


title: B-iPSCs_2 P16


title: Gra-iPSCs_3 P4

source_name: Gra-iPSCs P4

value: Granulocyte-derived iPSCs Passage #4


title: TTF-iPSCs_2 P16


title: SMP-iPSCs_2 P4

source_name: SMP-iPSCs P4

value: Skeletal muscle precursor-derived iPSCs Passage #4


title: SMP-iPSCs_3 P4


title: Gra-iPSCs_2 P4


title: TTF-iPSCs_1 P4


title: Gra-iPSCs_1 P4


title: SMP-iPSCs_1 P4


title: WJ4_passage5_replicate1

city: Singapore

first: Woon-Khiong

last: Chan

email: dbscwk@nus.edu.sg, g0500139@nus.edu.sg

address: S2-05-19, 14 Science Drive 4

department: Biological Sciences

country: Singapore

institute: National University of Singapore

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit (Affymetrix) was used for the hybridization, wash and scan steps. 15 µg of fragmented cRNA probes were mixed with the Control Oligonucleotide B2 and Eukaryotic Hybridization Controls (bioB, bioC, bioD, cre) before application to the GeneChip Array. Hybridization was carried at 45 oC, 60 rpm for 16 hrs in the Hybridization Oven 640 (Affymetrix). Washing of the GeneChip Arrays was done on the Fluidics Station 450 (Affymetrix) with the Fluidics Script FS450_0001.

scan_protocol: Scanning was carried out with the GeneChip Scanner 3000. The scanned data was retrieved using the Affymetrix GeneChip Operating Software (GCOS) and inspected with the quality control parameters for image quality, presence of artifacts, grid alignment, border staining and hybridization controls.

data_processing: The Affymetrix GeneChip Human Genome U133 plus 2.0 Array CEL files were then imported into Expression Console (Affymetrix) for data processing. Quality control parameters were checked for the tabular report, signal distribution, and array comparisons. The performance report and signal detection calls for each GeneChip Array were analysed with the MAS 5.0 analysis. The expression summary file was generated with the RMA algorithm (parameters were RMA Background Correction to PM-only probes and quantile normalization). Two datasets analyses were performed. The first dataset contained the hESCs, hECCs, hWJSCs and hFC samples that were generated by our group. The second dataset contained a meta-analysis of the hWJSCs and hFC that were generated by our group and selected samples available from the public GEO database (human mesenchymal stem cells, umbilical vein endothelial cells, normal stroma, tumour stroma, fibroblast ).

source_name: WJ4, passage 5

label_protocol: The microarray experiment was carried out according to the manufacturer’s recommendations for the Affymetrix GeneChip Human Genome U133 plus 2.0 Array. The GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix) was used to perform the first-strand and second-strand synthesis reactions. First-strand synthesis was carried out with 3.5 µg sample RNA, poly-A RNA controls (Eukaryotic Poly-A RNA Control Kit, Affymetrix), and T7-Oligo(dT) Primer at 42 oC for 1 hr. The second-strand reaction was performed at 16 oC for 2 hrs. The double-stranded cDNA was purified with the GeneChip Sample Cleanup Module (Affymetrix). In vitro transcription to produce biotin-labeled cRNA was carried out with the GeneChip IVT Labeling Kit (Affymetrix) at 37 oC for 16 hrs. The adjusted cRNA yield was determined by the difference between the amount of cRNA measured after in vitro transcription and the starting amount of total RNA. 20 µg of purified biotin-labeled cRNA was then fragmented at 94oC for 35 min.

growth_protocol: Institutional Review Board (DSRB, National Healthcare Group) approval was given for collection of umbilical cords from human subjects by informed patient consent. hWJSCs were derived from 6 different umbilical cords using a method previously described by our group (Fong et al. 2007. Reprod Biomed Online 15:708-718). Primary cultures of hWJSCs were established in sterile plastic tissue culture flasks (BD, USA) in the presence of a culture medium comprised of DMEM (high glucose), 20% fetal bovine serum (FBS), glutamine, insulin-transferrin-selenium (ITS), bovine fibroblast growth factor (bFGF) and antimycotic-antibiotic solution (Invitrogen, USA). Once confluent, the hWJSCs were passaged by detachment and disassociation with trypsin, washed and re-seeded into new flasks in the presence of the same medium above. A karyotypically normal human embryonic stem cell line (hESC) (HES3, ESI Singapore Ltd.) and a variant hESC line (BG01V, SCRC-2002, ATCC) were cultured on mitomycin-C treated mouse embryonic fibroblasts (MEFs) in bulk culture medium (BCM) composed of KnockOut DMEM medium (Invitrogen) supplemented with 20% KO serum replacement, 0.1 mM ß mercaptoethanol, 1 mM glutamine, 0.1 nM nonessential amino acids, 50 units /ml penicillin, 50 µg/ml streptomycin, 1:200 dilution of ITS (insulin-transferrin-selenium) (Invitrogen) and 16 ng/ml bFGF (Chemicon). Three human embryonic carcinoma cell lines (hECC) (NCCIT, CRL-2073, ATCC), (NTERA-2 cl.D1, NT2D1; CRL-1973, ATCC), and GCT27C4 (kind gift from Dr Martin Pera) were cultured respectively in the following basal media RPMI 1640, High Glucose DMEM, and DMEM/F12 (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone) and L-glutamine (Invitrogen). A human fetal fibroblast cell line (hFC) (Detroit 551, D551; CCL-110, ATCC) was grown in DMEM supplemented with 10% fetal bovine serum (Hyclone) and L-glutamine (Invitrogen).

extract_protocol: Total RNA from the hESC and hWJSC cell lines were extracted with RNeasy Mini Kit (Qiagen). Total RNA from the hECC and human fibroblast cell lines was prepared according to the TRIzol reagent protocol (Invitrogen) and purified with the RNeasy MinElute Cleanup Kit (Qiagen). Total RNA yield was determined using Nanodrop™ 1000 (Thermo Fisher Scientific) while RNA integrity was evaluated with Bioanalyzer 2100 (Agilent Technologies).

value: Wharton's jelly stem cell line


title: WJ6_passage3_replicate1

source_name: WJ6, passage 3


title: WJ3_passage4_replicate2

source_name: WJ3, passage 4


title: WJ4_passage20_replicate1

source_name: WJ4, passage 20


title: WJ5_passage4_replicate2

source_name: WJ5, passage 4


title: WJ3_passage4_replicate1


title: WJ4_passage20_replicate2


title: WJ6_passage3_replicate2


title: WJ4_passage5_replicate2


title: WJ5_passage4_replicate1


title: WJ1_passage20_replicate2

source_name: WJ1, passage 20


title: WJ1_passage20_replicate1


title: WJ2_passage8_replicate2

source_name: WJ2, passage 8


title: WJ2_passage8_replicate1


title: WJ1_passage3_replicate1

source_name: WJ1, passage 3


title: WJ1_passage3_replicate2


title: D551_replicate1

value: fetal fibroblast cell line


title: B-iPSCs_2 P4


title: WJ6_passage3_replicate1


title: D551_replicate2


title: WJ4_passage5_replicate1


title: WJ3_passage4_replicate2


title: WJ3_passage4_replicate1


title: Strain a710 replicate 3 (one color)

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

institute: University of Wuerzburg

description: DNA isolated from the strain using Genomic Tip DNA isolation kit from Qiagen

hyb_protocol: The labelled DNA were mixed together with two volumes of hybridization buffer (Eurogentec, Belgium) and hybridized manually at 50°C

scan_protocol: The slides were scanned using a Scanarray HT scanner(Perkin Elmer) with settings to avoid more than 10% of the spots being saturated.

data_processing: Raw data generated after flagging for obvious cases of stray background and spots with a signal to noise ratio of less than 3 were further analyses using the R package limma.

organism: Neisseria meningitidis

source_name: DNA from Strain_a710

label_protocol: 4 µg of chromosomal DNA  with Cy3 dCTP using Klenow enzyme and random nonamers and the labelled DNA was precipitated and purified.

extract_protocol: Chromosomal DNA from the meningococcal strains were isolated using Genomic Tip 20/G (Qiagen, Germany).


title: Strain a710 replicate 2 (one color)


title: Strain a275 replicate 2 (one color)

source_name: DNA from Strain_a275


title: Strain a710 replicate 1 (one color)


title: Strain a153 replicate 2 (one color)

source_name: DNA from Strain_a153


title: Strain a153 replicate 3 (one color)


title: NT2D1_replicate2

value: embryonic carcinoma cell line


title: GCT27C4_replicate1


title: Strain a275 replicate 1 (one color)


title: WJ1_passage3_replicate2


title: NCCIT_replicate2

source_name: NCCIT


title: NCCIT_replicate1


title: NT2D1_replicate1


title: GCT27C4_replicate2


title: BG01V_replicate2

value: embryonic stem cell line


title: Strain a14 replicate 2 (one color)

source_name: DNA from Strain_a14


title: Strain a153 replicate 1 (one color)


title: Strain a14 replicate 1 (one color)


title: Strain 2135 replicate 2 (one color)

source_name: DNA from Strain_2135


title: Strain 2137 replicate 2 (one color)

source_name: DNA from Strain_2137


title: Strain 2137 replicate 1 (one color)


title: Strain 2135 replicate 1 (one color)


title: BG01V_replicate1


title: HES3_replicate2


title: HES3_replicate1


title: Skeletal muscle precursor-derived iPS cell Passage 4, biological rep 2

city: Charlestown

first: Toshihiro

last: Shioda

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

description:
JP 17
early-passage iPS cells, skeletal muscle precursor origin

hyb_protocol: Following fragmentation, biotinylated cRNA probe (25 ng/uL in 200 uL hybridizationconcktail) were hybridized for 17 hr at 45C on GeneChip mouse 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (protocol FS450_0001).

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

data_processing:
The data were analyzed with Affymetrix GeneChip Command Console (AGCC).
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console

source_name: Skeletal muscle precursor-derive iPS cell Passage 4, biological rep 2

label_protocol: Biotinylated cRNA probes were synthesized using the GeneChip Whole Transcript Sense Target Labeling Assay Kit (Affymetrix) following the manufacturer's instructions.

growth_protocol: iPS cells were cultured in the ES cell medium (DMEM with 15% FBS, L-Glutamin, penicillin-streptomycin, non-essential amino acids, beta-mercaptoethanol, and 1000 U/ml LIF) on irradiated MEF feeder cells.

extract_protocol: iPS cells grown on 35mm dishes were harvested when they reached about 50% confluency and preplated on non-gelatinized T25 flasks for 45 minutes to remove feeder cells. Cells were spun down and the pellet used for isolation of total RNA using the miRNeasy Mini Kit (QIAGEN) without DNase digestion. RNA was eluted from the columns using 50 ml RNase-free water or TE buffer, pH7.5 (10 mM Tris-HCl and 0.1 mM EDTA) and quantified using Nanodrop (Nanodrop Technologies).

treatment_protocol: Cells were passaged continuously from the original derivation up to 16 passages. Total RNA samples were prepared at passage 4.

value: mixed 129 and C57BL/6

value: iPS cells

tag: iPS origin

value: skeletal muscle precursor

tag: passage


title: Skeletal muscle precursor-derived iPS cell Passage 4, biological rep 3

description:
JP 18
early-passage iPS cells, skeletal muscle precursor origin

source_name: Skeletal muscle precursor-derive iPS cell Passage 4, biological rep 3


title: Skeletal muscle precursor-derived iPS cell Passage 4, biological rep 1

description:
JP 16
early-passage iPS cells, skeletal muscle precursor origin

source_name: Skeletal muscle precursor-derive iPS cell Passage 4, biological rep 1


title: Tail tip fibroblast-derived iPS cell Passage 4, biological rep 1

description:
JP 13
early-passage iPS cells, fibroblast origin

source_name: Tail tip fibroblast-derive iPS cell Passage 4, biological rep 1

value: tail tip fibroblast


title: B cell-derived iPS cell Passage 4, biological rep 3

description:
JP 12
early-passage iPS cells, B cell origin

source_name: B cell-derive iPS cell Passage 4, biological rep 3

value: splenic B cell


title: B cell-derived iPS cell Passage 4, biological rep 2

description:
JP 11
early-passage iPS cells, B cell origin

source_name: B cell-derive iPS cell Passage 4, biological rep 2


title: B cell-derived iPS cell Passage 4, biological rep 1

description:
JP 10
early-passage iPS cells, B cell origin

source_name: B cell-derive iPS cell Passage 4, biological rep 1


title: Tail tip fibroblast-derived iPS cell Passage 4, biological rep 3

description:
JP 15
early-passage iPS cells, fibroblast origin

source_name: Tail tip fibroblast-derive iPS cell Passage 4, biological rep 3


title: Granulocyte-derived iPS cell Passage 4, biological rep 3

description:
JP 9
early-passage iPS cells, granulocyte origin

source_name: Granulocyte-derive iPS cell Passage 4, biological rep 3

value: bone marrow granulocyte


title: Tail tip fibroblast-derived iPS cell Passage 4, biological rep 2

description:
JP 14
early-passage iPS cells, fibroblast origin

source_name: Tail tip fibroblast-derive iPS cell Passage 4, biological rep 2


title: SP Sty1-HA (treated with 0.5 mM H2O2 for 30min) ChIP-chip sample

first: Majid

last: Eshaghi

state: Singapore

address: Biopolis

department: Bilogical Investigation

institute: Genome Institute of Singapore

description: Schizosaccharomyces pombe Sty1-HA (treated with 0.5 mM H2O2 for 30min) cells Chip DNA vs Schizosaccharomyces pombe Sty1-HA (treated with 0.5 mM H2O2 for 30min) WCE DNA.

hyb_protocol: Samples were mixed with DIG Easy Hyb buffer (Roche) and Herring Sperm DNA (Invitrogen) before applying to MAUI mixer-slide assembly.  The slides were hybridized overnight for 16 hours at 42 degree Celsius under MAUI system (BioMicro). Hybridized slides were washed consecutively in 2x SSC/0.1% SDS for 1 min, 1x SSC for 4 min, 0.2x SSC for 4 min, and 0.05x SSC for 1 min, and then spin-dried before scanning.

scan_protocol: Microarray slides were scanned using the Axon genepix 4000B scanner at the resolution of 5 mirocon/ pixel at both red and green channels.  The data were acquired using the GAL file and normalized with the NimbleGen Scan software (NimbleGen Inc.).

data_processing: Analyses of ChIP-chip microarray data included identification of significantly enriched regions, prediction of occupancy patterns, and assignment to genomic features were done as describled in materials and metholds.

organism: Schizosaccharomyces pombe

source_name: Fission yeast cells

label_protocol: Chip genomic DNA was random-priming labeled with amino-allyl-dUTP (aa-dUTP) using the BioPrime DNA Labeling kit (Invitrogen Corporation, Carlsbad, CA) according the manufacture's instruction.  Labeled DNA was extracted with phenol/chloroform/isoamyl alcohol and precipitated with ethanol or siopropanol. The labeled DNA was then coupled with cyanine dyes Cy5 (Amersham, Buckinghamshire, UK)

growth_protocol: Yeast cells were cultured at 30 degree Celsius.

extract_protocol: Chip genomic DNA was extracted as described in materials and methods.

tag: Schizosaccharomyces pombe Sty1-HA (treated with 0.5 mM H2O2 for 30min) cells were cross-linked with formaldehyde and subjected to ChIP-chip experiment .

label_protocol: WCE DNA was random-priming labeled with amino-allyl-dUTP (aa-dUTP) using the BioPrime DNA Labeling kit (Invitrogen Corporation, Carlsbad, CA) according the manufacture's instruction.  Labeled DNA was extracted with phenol/chloroform/isoamyl alcohol and precipitated with ethanol or siopropanol. The labeled DNA was then coupled with cyanine dyes Cy3 (Amersham, Buckinghamshire, UK)

extract_protocol: WCE DNA of the cells were extracted as described in materials and methods.

tag: Reference DNA was obtained from whole cell extract (WCE)


title: SP Pcr1 deletion Sty1-HA (treated with 0.5 mM H2O2 for 30min) ChIP-chip sample

description: Schizosaccharomyces pombe Pcr1 deletion Sty1-HA (treated with 0.5 mM H2O2 for 30min) cells Chip DNA vs Schizosaccharomyces pombe Pcr1 deletion Sty1-HA (treated with 0.5 mM H2O2 for 30min) WCE DNA.

tag: Schizosaccharomyces pombe Pcr1 deletion Sty1-HA (treated with 0.5 mM H2O2 for 30min) cells were cross-linked with formaldehyde and subjected to ChIP-chip experiment .


title: Granulocyte-derived iPS cell Passage 4, biological rep 1

description:
JP 7
early-passage iPS cells, granulocyte origin

source_name: Granulocyte-derive iPS cell Passage 4, biological rep 1


title: SP Atf1 deletion Sty1-HA (treated with 0.5 mM H2O2 for 30min) ChIP-chip sample

description: Schizosaccharomyces pombe Atf1 deletion Sty1-HA (treated with 0.5 mM H2O2 for 30min) cells Chip DNA vs Schizosaccharomyces pombe Atf1 deletion Sty1-HA (treated with 0.5 mM H2O2 for 30min) WCE DNA.

tag: Schizosaccharomyces pombe Atf1 deletion Sty1-HA (treated with 0.5 mM H2O2 for 30min) cells were cross-linked with formaldehyde and subjected to ChIP-chip experiment .


title: Granulocyte-derived iPS cell Passage 4, biological rep 2

description:
JP 8
early-passage iPS cells, granulocyte origin

source_name: Granulocyte-derive iPS cell Passage 4, biological rep 2


title: Stat6ko_BMDM_+IL4

city: München

first: Silke

last: Huber

address: Goethestrasse 31

department: Institute for Immunology

institute: LMU Munich

description: Gene expression data from Stat6-deficient bone marrow derived macrophages cultured 24h with IL-4

hyb_protocol: 10µg labeled RNA in hybridization cocktail, heated 5 min 99°C, cool to 45°C, centrifuge, hybridization 17h over night at 45°C on mouse Gene ST

scan_protocol: Gene Scanner 3000 from Affymetrix

data_processing: Raw data analysis was performed with the Affymetrix Expression Console software, using RMA-sketch for normalization

source_name: Stat6-ko bone marrow derived macrophages cultured 24 h +IL-4

label_protocol: Gene Chip Whole Transcript Sense target labelling from Affymetrix using 200ng total RNA/Array

growth_protocol: Macrophages were differentiated from bone marrow cells for 7 days in the presence of 10% supernatant from the M-CSF producing fibroblast cell line L929.

extract_protocol: Total cellular RNA was isolated from sorted macrophages using a RNA isolation kit according to the manufacturer's instructions

treatment_protocol: After removal of nonadherent cells, macrophages were detachted with 5 mM EDTA, washed, counted and replated. Macrophages were cultured for 24h with medium (control) or in the presence of IL-4 (10 µg/mL).

tag: tissue

value: bone marrow

value: macrophages (BMDM)

tag: genome/variation


title: Stat6ko_BMDM_control

description: Gene expression data from Stat6-deficient bone marrow derived macrophages cultured in medium (control)

source_name: Stat6-ko bone marrow derived macrophages cultured in medium

tag: strain


title: SP Sty1-HA ChIP-chip sample

description: Schizosaccharomyces pombe Sty1-HA cells Chip DNA vs Schizosaccharomyces pombe Sty1-HA WCE DNA.

tag: Schizosaccharomyces pombe Sty1-HA cells were cross-linked with formaldehyde and subjected to ChIP-chip experiment .


title: SP Pcr1-HA (treated with 0.5mM H2O2 for 30min) ChIP-chip sample

description: Schizosaccharomyces pombe Pcr1-HA (treated with 0.5mM H2O2 for 30min) cells Chip DNA vs Schizosaccharomyces pombe Pcr1-HA (treated with 0.5mM H2O2 for 30min) WCE DNA.

tag: Schizosaccharomyces pombe Pcr1-HA (treated with 0.5mM H2O2 for 30min) cells were cross-linked with formaldehyde and subjected to ChIP-chip experiment .


title: BALBc_BMDM_+IL4

description: Gene expression data from BALB/c bone marrow derived macrophages cultured 24h with IL-4

source_name: BALB/c bone marrow derived macrophages cultured 24 h +IL-4

value: BALB/c

value: wild type


title: FDN.vs.Ctrl

description: DamID for FDN versus Control (unfused DamID)

hyb_protocol: Fragmented biotinylated DNA was hybridized on Affymetrix GeneChip® ENCODE 2.0R Arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).

scan_protocol: To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).

data_processing:
Raw data were processed and analysed using Model-based Analysis of Tiling arrays (MAT) (Johnson, et al. 2006)
*.bar files and *.bed files were generated by MAT and represent the MAT scores for each probe and the putative enriched genomic regions respectively.

source_name: FDN DamID DNA

label_protocol: For each sample 10-30 ng of genomic DNA was amplified using the Sigma WGA2 kit and subsequently fragmented and labeled according the the Affymetrix Chromatin Immunoprecipitation Assay Protocol.

growth_protocol: Polyclonal stable HeLa cell lines with integrated Dam, Dam-NIPP1 and Dam-NIPP-RATA  transgenes were generated and grown following standard cell culture procedures, using G418 as selective agent (also: see Vogel et al. 2007 as cited below)

extract_protocol: Genomic DNA was extracted from cells (Sigma GeneElute Mammalian Genomic DNA Minprep kit) and processed according to the DamID protocol published in (Vogel, M.J., Peric-Hupkes, D., and van Steensel, B. 2007. Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nature protocols 2(6): 1467-1478.)

treatment_protocol: no additional treatment

value: HeLa

source_name: unfused DamID (control)


title: RATA.vs.Ctrl

description: DamID for RATA (FDN mutant) versus Control (unfused DamID)

source_name: RATA DamID DNA


title: SP Pcr1-HA ChIP-chip sample

description: Schizosaccharomyces pombe Pcr1-HA cells Chip DNA vs Schizosaccharomyces pombe Pcr1_HA WCE DNA.

tag: Schizosaccharomyces pombe Pcr1-HA cells were cross-linked with formaldehyde and subjected to ChIP-chip experiment .


title: SP Atf1-HA (treated with 0.5 mM H2O2 for 30min) ChIP-chip sample

description: Schizosaccharomyces pombe Atf1-HA (treated with 0.5 mM H2O2 for 30min) cells Chip DNA vs Schizosaccharomyces pombe Atf1-HA (treated with 0.5 mM H2O2 for 30min) WCE DNA.

tag: Schizosaccharomyces pombe Atf1-HA (treated with 0.5 mM H2O2 for 30min) cells were cross-linked with formaldehyde and subjected to ChIP-chip experiment .


title: BALBc_BMDM_control

description: Gene expression data from BALB/c bone marrow derived macrophages cultured in medium (control)


title: SP Atf1-HA ChIP-chip sample

description: Schizosaccharomyces pombe Atf1-HA cells Chip DNA vs Schizosaccharomyces pombe Atf1_HA WCE DNA.

tag: Schizosaccharomyces pombe Atf1-HA cells were cross-linked with formaldehyde and subjected to ChIP-chip experiment .


title: B6CBA-B-iPSC-11 input, methyl-depleted

city: Baltimore

first: Akiko

last: Doi

state: MD

address: 855 N Wolfe St, Rangos 580

department: Medicine

institute: Johns Hopkins University School of Medicine

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

scan_protocol: Arrays were scanned on a GenePix 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 software (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

source_name: Input fraction from B6CBA-B-iPSC-11

label_protocol: 2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers for the input, methyl-depleted  (UT) fraction and Cy5 nonamers for the methyl-depleted (MD) fraction per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

extract_protocol: Genomic DNA (gDNA) were isolated using DNeasy kit (Qiagen) according to the manufacturer’s protocol. For each sample, 5 µg of genomic DNA was sheared into 1.6-3kb DNA size fragments, digested with McrBC, and fractionated on a 1% agarose gel alongside the sheared input, methyl-depleted  (UT) fraction to enrich for the methyl-depleted (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.

value: Blood-derived iPS cells

source_name: Methyl-depleted fraction from B6CBA-B-iPSC-11


title: 6678

description: Cells: HeLa-Tet-Off (Clontech)

hyb_protocol: 28 pmol Cy3 incorporated dye was fragmented and resuspended in hybridization buffer HI-RPM (Agilent Technologies). The arrays were hybridized in microarray hybridization chambers (Agilent Technologies) overnight at 65ºC, rpm=10 for 17 hours.

scan_protocol: After washing the slides were scanned with a DNA microarray scanner (Agilent Technologies) and images were processed with the Feature Extraction Software (Agilent Technologies).

data_processing: We use the Agilent processed signal values (i.e., feature gProcessedSignal) from Agilent Feature Extraction software and compute log2-intensities.  We remove Agilent control probes, as well as probes with signals below background on all arrays (absent spots). To decide whether a signal is significantly above background, we use the feature gIsPosAndSignif, also provided by the Agilent software. In case of multiple probes for the same Agilent ID, log2-intensities are averaged.

label_protocol: 1µg of sample was spiked with a set of 10 positive control transcripts (Agilent Technologies), converted to double stranded cDNA in a reverse transcription reaction, amplified and labeled with Cy3 in an in vitro transcription reaction according to the manufacturer's protocol (Agilent Technologies).

extract_protocol: HTO_parental was cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% FCS and 250 µg/ml geneticin, HTO_NIPP1wt and HTO_NIPP1m were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% FCS and 250 µg/ml geneticin, 200 µg/ml hygromycin and 50 ng/ml doxycyclin.  HTO_NIPP1wt and HTO_NIPP1m were cultured for 72 hours without doxycycline after which total RNA was isolated from all three cell lines using the Genelute Mammalian Total RNA Miniprep kit.

tag: cell line

value: HeLa-Tet-Off (Clontech)


title: B6CBA-BoneMarrow2 input, methyl-depleted

source_name: Input fraction from B6CBA-BoneMarrow2

tag: cell type

value: Bone marrow cells

source_name: Methyl-depleted fraction from B6CBA-BoneMarrow2


title: 6071

description: Cells: HeLa-Tet-Off (Clontech)


title: 6754

description: Cells: HeLa-Tet-Off (Clontech)


title: B6CBA-BoneMarrow1 input, methyl-depleted

source_name: Input fraction from B6CBA-BoneMarrow1

source_name: Methyl-depleted fraction from B6CBA-BoneMarrow1


title: B6CBA-F-iPSC-54 input, methyl-depleted

source_name: Input fraction from B6CBA-F-iPSC-54

value: Fibroblast-derived iPS cells

source_name: Methyl-depleted fraction from B6CBA-F-iPSC-54


title: B6CBA-B-iPSC-8 input, methyl-depleted

source_name: Input fraction from B6CBA-B-iPSC-8

source_name: Methyl-depleted fraction from B6CBA-B-iPSC-8


title: B6CBA-F-iPSC-56 input, methyl-depleted

source_name: Input fraction from B6CBA-F-iPSC-56

source_name: Methyl-depleted fraction from B6CBA-F-iPSC-56


title: B6CBA-F-iPSC-57 input, methyl-depleted

source_name: Input fraction from B6CBA-F-iPSC-57

source_name: Methyl-depleted fraction from B6CBA-F-iPSC-57


title: B6CBA-B-iPSC-12 input, methyl-depleted

source_name: Input fraction from B6CBA-B-iPSC-12

source_name: Methyl-depleted fraction from B6CBA-B-iPSC-12


title: B6129-Fibroblast2 input, methyl-depleted

source_name: Input fraction from B6129-Fibroblast2

value: Fibroblasts

source_name: Methyl-depleted fraction from B6129-Fibroblast2


title: B6129-Fibroblast1 input, methyl-depleted

source_name: Input fraction from B6129-Fibroblast1

source_name: Methyl-depleted fraction from B6129-Fibroblast1


title: Root SHR-GFP 6 day rep2

city: Tallahassee

first: Hongchang

last: Cui

address: 319 Stadium Dr.

department: Biological Science

institute: Florida State University

hyb_protocol: 6 ug of Cy5 and Cy3 labeled DNA were mixed and hybridized to the microarray following the procedure as recommended by Agilent co.

scan_protocol: The microarry was scanned at the default setting using an Agilent scanner G2565BA

data_processing: Data extraction from the scanned image were performed using the Agilent Feature Extraction software Version 9.0

organism: Arabidopsis thaliana

source_name: Roots of 6 days seedlings

label_protocol: DNA recovered from the ChIP samples was amplified using a random primed whole genome amplification method and the Cy5 and Cy3 dyes were introduced using an allyl-amino acid mediated labeling method

growth_protocol: Seeds were sterilized for 10 min using 50% bleach, and then were washed several times with sterile dH2O. Sow the seeds on a nylon membrane (Safar 03-100/40) that was placed on MS medium containing 1% agar and 1% sucrose. Place the plate vertically in a Percival with a scheme of 16 hr light/8hr dark illumination and 22C. Collect the roots after 6 days of germination.

extract_protocol: The root samples were fixed in 10x volume of 1% formaldhyde for 15 min under vacuum. To stop the fixation, add 2.5M glycine stcok solution to a final concentration of 0.1M. After thorough mixing, remove the solution and wash the tissues 3 times in 20x volume of 1XPBS buffer containing 5mM EDTA. After grounding the roots in liquid nitrogen, the root samples were suspended in 10x volume of extraction buffer (50mM Tris, 150 mM NaCl, 10% glycerol, 2mM EDTA, 1mM DTT and protease inhibitor cocktail). After filtration through 2 layers of miracloth, collect the flowthroguh and centrifuge at 1000xg for 10 min at 4C to collect the crude nuclei prpeparation, which was then subjected to sonication for 4 cycles of 10 sec at a power output of 40% using a Branson Sonifier D250. Centrifuge for 10 min at 12,000 rpm for 10 min to remove the debris and collect the supernant, which is the chromatin preparation. Chromatin Immunoprecipation was performed following the procedure as described in Cui et al, 2007. Science, 316: 421-425.

tag: genotype

value: Transgenic plants carrying the SHRpro::SHR-GFP construct in the shr-2 mutant, which is in the Columbia ecotype background.

tag: ecotype

value: Columbia

value: root

tag: age

value: 6 d

tag: antibody

value: anti-GFP

source_name: input DNA

tag: sample type

value: input DNA


title: Wild-type array 134

city: Stockholm

first: Pekka

middle: Juhani

last: Kohonen

address: Nobelsväg 13, Box 210

department: IMM Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

description: Wild-type control bursal B cell line DT40 was profiled with a custom-made filter array

hyb_protocol: The microarray membranes were prehybridized in Denhard’s hyb mix ( 12xSSC, 10xDenhard’s solution (0.2% BSA, 0.2% Ficoll, 0.2% polyvinylpyrolodone), 0.5% SDS, 100micrograms/ml ssDNA) and 7.5 microlitres d(A)40 (Amersham) for 2 h at 65°C. The labelled cDNA was added to the hybridisation mix and hybridised to the membranes over night at 65°C. The membranes were washed at 65°C 20 min in 1XSSC, 0.1% SDS, 2x10 min 0.3xSSC, 0.1xSDS and 0.1xSSC, 0.1%SDS.

scan_protocol: The radioactive signals were read using phosphoimager plates and a phosphoimage-reader Fluorescent Image Analyzer FLA-3000 (Fuji, Kanagawa, Japan). The scanning software supplied by the manufacturer with default settings was used for scanning producing a BAS image (*.img) file. Scanning resolution of 50 micro meters was used (the smallest available).

data_processing: AIDA image analyzer (v. 3.27) was used for acquiring the image data. Various approaches were used to filter bad-quality spots/probes for subsequent analyzes (Nera et al. 2006; Immunity; 24(3):283-93). Filtered values are indicated with NA. Maanova R/Biocondyuctor package was used to apply row-column-intensity wise detrending. Variance stabilizing transformation, using the vsn package, was carried out to transform the data (approximately to the log2 scale).

organism: Gallus gallus

source_name: ALV induced bursal cell line

label_protocol: Labelled cDNA was prepared using 0.5 micrograms mRNA, 0.5 micrograms dT(18)V (Eurogentech, Seraing, Belgium), incubated 10 min at 70°C, 0.5 microlitres RNasin (40 U/microlitres, Promega, Madison, WI, USA), 5.0 microlitres reaction buffer, 2.5 microlitres 0.1M DTT, 0.5 microlitres 20 mM dGTP dATP dTTP mix (Promega), 5.0 microlitres alpha-33P-dCTP (10 U/microlitres, Amersham Pharmacia Biotech Inc, Buckinghampshire, England), incubated 1 min at 37°C, 1microlitres Superscript II RT (Gibco BRL, Paisley, UK) and incubated 1.5h at 37°C. The mRNA was hydrolysed by 1microlitres 0.5 M EDTA, 1microlitres 10% SDS, 3microlitres 3N NaOH, incubated 30 min at 68°C and 1microlitres Tris-HCl (pH 8) and 3microlitres 2N HCl were added. The labelled cDNA was purified using MobiSpin S-300 columns (MobiTec, Göttingen, Denmark) according to manufacturers instructions.

growth_protocol: DT40 B cells were maintained in RPMI 1640 supplemented with 10% FCS, 1% chicken serum, 50 micromolar beta-mercaptoethanol, 2 micromolar L-glutamine, penicillin and streptomycin. The cells were cultured at +40 degrees Celsius with 5% CO2.

extract_protocol: The mRNA was isolated from the DT40 wt and Ikaros -/- cells using Trizol reagent (Life Technologies, Grand Island, NY, USA) and the Oligotex mRNA kit (Qiagen, Santa Clarita, California, USA) according to manufacturers instructions.

treatment_protocol: The Ikaros gene was disrupted by targeting vectors.

value: Bursal B cell


title: Root SHR-GFP 6 day rep1


title: B6129-Bl-iPSC-ABiPS input, methyl-depleted

source_name: Input fraction from B6129-Bl-iPSC-ABiPS

source_name: Methyl-depleted fraction from B6129-Bl-iPSC-ABiPS


title: B6129-Bl-iPSC-K02-2 input, methyl-depleted

source_name: Input fraction from B6129-Bl-iPSC-K02-2

source_name: Methyl-depleted fraction from B6129-Bl-iPSC-K02-2


title: B6CBA-Fibroblast1 input, methyl-depleted

source_name: Input fraction from B6CBA-Fibroblast1

source_name: Methyl-depleted fraction from B6CBA-Fibroblast1


description: hybridization of Pcr1 deletion strain treated with 0.5mM H2O2 at 120min time point and WT strain with no treatment (3rd repeat)

data_processing: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.  After background correction and removal of flagged values, features with low intensity (F/B<2 at either 635 or 532 channel) were removed.  Meidans of log base 2 expression ratios were given in the data table.

source_name: Fission yeast cells

label_protocol: Approximately 30 ug of total RNA was used to synthesize cDNA coupled with aa-dUTP by reverse transcriptase. Approximately 1.5 ug of cDNA was coupled with Cy5 fluorescence dye and purified through a Microcon YM-30. Cy5- and Cy3-labeled cDNA were pooled and hybridized to the spotted S. pombe oligonucleotide (oligo)-based DNA microarrays

growth_protocol: Yeast cells were cultured at 30 degree Celsius

extract_protocol: cDNA of the Pcr1 deletion strain treated with 0.5mM H2O2 at 120min time point generated from total RNA as described in materials and methods

tag: cDNA from Pcr1 deletion strain treated with 0.5mM H2O2 at 120min time point (3rd repeat)

source_name: cDNA from WT strain with no treatment

label_protocol: Approximately 30 ug of total RNA was used to synthesize cDNA coupled with aa-dUTP by reverse transcriptase. Approximately 1.5 ug of cDNA was coupled with Cy3 fluorescence dye and purified through a Microcon YM-30. Cy5- and Cy3-labeled cDNA were pooled and hybridized to the spotted S. pombe oligonucleotide (oligo)-based DNA microarrays

extract_protocol: total RNA of the WT cells were extracted as described in materials and methods

tag: Reference total RNA of the WT strain with no treatment


title: B6129-BoneMarrow1 input, methyl-depleted

source_name: Input fraction from B6129-BoneMarrow1

source_name: Methyl-depleted fraction from B6129-BoneMarrow1


title: Wild-type array 132


description: hybridization of Pcr1 deletion strain treated with 0.5mM H2O2 at 120min time point and WT strain with no treatment (2nd repeat)

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.

tag: cDNA from Pcr1 deletion strain treated with 0.5mM H2O2 at 120min time point (2nd repeat)


title: Ikaros deficient array 133

description: Ikaros deficient bursal B cell line DT40 was profiled with a custom-made filter array

value: Ikaros -/-


title: B6129-BoneMarrow2 input, methyl-depleted

source_name: Input fraction from B6129-BoneMarrow2

source_name: Methyl-depleted fraction from B6129-BoneMarrow2


title: B6129-Bl-iPSC-E3-1 input, methyl-depleted

source_name: Input fraction from B6129-Bl-iPSC-E3-1

source_name: Methyl-depleted fraction from B6129-Bl-iPSC-E3-1


title: B6CBA-Fibroblast2 input, methyl-depleted

source_name: Input fraction from B6CBA-Fibroblast2

source_name: Methyl-depleted fraction from B6CBA-Fibroblast2


description: hybridization of Pcr1 deletion strain treated with 0.5mM H2O2 at 120min time point and WT strain with no treatment (1st repeat)

tag: cDNA from Pcr1 deletion strain treated with 0.5mM H2O2 at 120min time point (1st repeat)


description: hybridization of Pcr1 deletion strain treated with 0.5mM H2O2 at 60min time point and WT strain with no treatment (3rd repeat)

extract_protocol: cDNA of the Pcr1 deletion strain treated with 0.5mM H2O2 at 60min time point generated from total RNA as described in materials and methods

tag: cDNA from Pcr1 deletion strain treated with 0.5mM H2O2 at 60min time point (3rd repeat)


title: Ikaros deficient array 131

source_name: ALV induced bursal cell line


description: hybridization of Pcr1 deletion strain treated with 0.5mM H2O2 at 60min time point and WT strain with no treatment (2nd repeat)

tag: cDNA from Pcr1 deletion strain treated with 0.5mM H2O2 at 60min time point (2nd repeat)


description: hybridization of Pcr1 deletion strain treated with 0.5mM H2O2 at 60min time point and WT strain with no treatment (1st repeat)

tag: cDNA from Pcr1 deletion strain treated with 0.5mM H2O2 at 60min time point (1st repeat)


title: 6067

description: Cells: HeLa-Tet-Off (Clontech)


description: hybridization of Pcr1 deletion strain treated with 0.5mM H2O2 at 30min time point and WT strain with no treatment (3rd repeat)

extract_protocol: cDNA of the Pcr1 deletion strain treated with 0.5mM H2O2 at 30min time point generated from total RNA as described in materials and methods

tag: cDNA from Pcr1 deletion strain treated with 0.5mM H2O2 at 30min time point (3rd repeat)


title: P. sojae strain P6954 - race 1: Treated - 12 Hours post inoculation - rep 3

city: Blacksburg

first: sucheta

last: Tripathy

state: VA

address: 1, Washington street

department: Virginia  Bioinformatics Institute

institute: Virginia Tech

description: Data was collected from the hypocotyl regions of Soybean plants at different time points

hyb_protocol: hybridization cocktail is prepared, including the fragmented target, probe array controls, BSA, and herring sperm DNA. It is then hybridized to the probe array during a 16-hour incubation(Affymetrix technical manual - 2004)

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000

data_processing: The data were analyzed with GCRMA suite from R package version 2.4.0. Background correction was using GCRMA followed by a modified quantile normalization routine where data from control chips are used to rank probes instead of averaging the probe values. Data was summarized using a memory efficient median polish method

organism: Phytophthora sojae

source_name: P.sojae strain P6954 - race 1: Treated - 12 Hours post inoculation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA. RNA is is first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction is carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling. The biotinylated cRNA targets are then cleaned up, fragmented, and hybridized to GeneChip expression arrays(Affymetrix Technical manual - 2004)

growth_protocol: P.sojae mycelia were cultured in V8 media at 25C for 2 days prior to inoculation onto Soybean hypocotyl.

extract_protocol: QIAGEN RNeasy Kit : As recommended by manufacturer

treatment_protocol: Agar plugs of P. sojae isolate P6954 (race 1) were transferred to Petri dishes containing V8 liquid medium and incubated at 25C. P6954 is genetically near-identical to P6947 (Forster et al, 1994) but unlike P6947, P6954 expresses Avr1b. After 2 days the mycelia were transferred to Petri dishes with water to wash excess V8 medium. Seedlings of highly-susceptible soybean cultivar Sloan were grown in the greenhouse with natural light for 9 days.After harvesting, seedling roots were washed gently to remove soil and then placed on moist cloth. Washed P. sojae mycelia were used to inoculate seedling hypocotyls: a small (~1 cm long) longitudinal slit was cut near the top half of the hypocotyls and the mycelia were placed inside the cut. After 3, 6 or 12 h, the tissue surrounding the infected hypocotyl slits. As a 0 h control, pure P6954 mycelial inocula were also harvested right after the wash step (no infection).  All samples were      transferred to liquid nitrogen and frozen at 80C.  The entire experiment was replicated three times. .

tag: strain

tag: time


title: P. sojae strain P6954 - race 1: Treated - 3 Hours post inoculation - rep 3

source_name: P.sojae strain P6954 - race 1: Treated - 3 Hours post inoculation

value: 3 h