title: Aorta-APOE-deficient and vitamin E treatment-rep1

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

description: Gene expression data of aortas isolated from vitamin E-treated APOE-deficient mice

hyb_protocol: For hybridization, 15 µg of fragmented cRNA were incubated with the chip (Mouse Genome MG430 2.0 Array) in 200 µl of the hybrization solution in a Hybridization Oven 640 (Affymetrix) for 16 h at 45 °C. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual.

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

data_processing: The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v.1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 200.

source_name: Aortas isolated from vitamin E-treated APOE-deficient mice

label_protocol: Biotinylated cRNA was prepared according to the protocol of the manufacturer (Affymetrix; GeneChip Expression Analysis Technical Manual).

growth_protocol: The study was initiated with 4-6 week-old APOE-deficient mice on a B6 (C57BL/6J) background, and non-transgenic B6 controls. Mice had free access to food and water, and were fed a standard rodent chow containing 7 % fat and 0.15 % cholesterol (Ain 93-based diet). For atherosclerosis treatment, a group of APOE-deficient mice received treatment with the antioxidant vitamin E (2000 IU/kg diet) for 7 months. At an age of 32-34 weeks, aortas were isolated from three study groups (APOE-deficient, vitamin E-treated APOE-deficient, and nontransgenic B6 control mice), dissected free of fat, and immediately frozen in liquid nitrogen.

extract_protocol: Total aortic RNA was isolated with the RNeasy Midi kit according to the manufacturer`s instructions (Qiagen).

treatment_protocol: The study was performed with aortas isolated from three groups of mice (32-34 weeks of age), i.e. untreated APOE-deficient mice (APOE), APOE-deficient mice treated with vitamin E (2000 IU/kg diet) for 7 months (VitE), and B6 control mice (Cont).

value: aorta

tag: genetic background

tag: genotype

value: APOE-deficient

value: vitamin E

value: aortas from vitamin E-treated APOE-deficient mice


title: CL1-5 biological repeat 1

status: Public on Dec 11 2012

type: RNA

city: Taipei

first: Michael

last: Hsiao

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

description: Gene expression data from CL1-5

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

label: biotin

molecule: total RNA

organism: Homo sapiens

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: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were cultured in RPMI basal media supplemented with 10 % of fetal bovine serum and 1% penicillin/streptomycin.

tag: parental cell line

tag: cell type

value: Lung adenocarcinoma

tag: cell population

value: highly invasive


title: MEL_control_uninduced_rep2

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

country: USA

institute: National Institutes of Health

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

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

data_processing: Bioconductor/R (R 2.15.2); affy (1.36.0) and limma (3.14.1) packages; Mouse430_2_Mm_ENTREZG cdf (brainarray v.16.0)

organism: Mus musculus

source_name: MEL_control knockdown_uninduced

growth_protocol: Cells cultured in DMEM supplemented with 10% fetal bovine serum

extract_protocol: RNA was prepared from 2e6 cells using the Rneasy Plus Mini Kit (Qiagen). One microgram of RNA was reverse transcribed with random hexamers using the Superscript III first-strand synthesis system as suggested by the manufacturer (Invitrogen).

treatment_protocol: Uninduced MEL cells were differentiated by incubating 2.5e5 cells/ml with 1.5-2% DMSO; cells were stably transformed with either control or Ldb1 shRNA from Open Biosystems.

tag: strain background

value: BALB/c

value: Murine erythroidleukema (MEL) cells

tag: genotype/variation

value: control


title: E-group bone 1 week postsurgery rep2

city: Guangzhou

first: DaoZhang

last: Cai

state: GuangDong

department: Orthopaedics

country: China

institute: The Third Affiliated Hospital of Sun Yat-sen University

description: Gene expression proﬁles of subchondral bone at 1 week postsurgery

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60℃ for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Microarrays (G4131F) for 17 hours at 65℃ in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: subchondral bone,operation,1 week postsurgery

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Temperature 20-22℃, Humidity 55±5%, Specified rat pathogen free conditions, 12 hours light/dark cycle, Water ad libitum, Nutrients MF-Oriental Yeast-Japan, Housed in cages according to Chinese legislation.

extract_protocol: Total RNA of the subchondral bone was extracted using E.Z.N.A Total RNA Kit Ⅱ (Omega Bio-Tek, Inc., USA), according to the manufacturer's instructions, including a DNase digestion step. The quantity and quality of RNA were assessed using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technology, Rockland, DE) and the agarose gel electrophoresis.

treatment_protocol: Animals were equally divided into two groups: experimental group (E-Group) and sham-operated group (S-Group). The right knee joints of the E-Group rats underwent open surgery, involved in both medial meniscectomy and medial collateral ligament (MCL) transaction with micro-scissors. The right knee joints of the S-Group rats were carried out with a sham operation, via a similar incision, without operations of the medial meniscus and the medial collateral ligament. Animals were killed at 1, 2, and 4 weeks postsurgery. After exarticulation of the right knee joints of the rats, the femurs were fracted from the epiphyseal plate quickly, and the femoral condyles were frozen in liquid nitrogen until subchondral bone separation and total RNA extraction. The articular cartilage and epiphyseal plate tissue of the femur condyle sample were cleared away with a micro-electric burnish implement with drill to obtain subchondral bone.

tag: gender

value: male

tag: age

tag: tissue

value: subchondral bone

tag: treatment

value: medial meniscectomy and medial collateral ligament transection

tag: time

value: 1 week postsurgery

tag: strain

value: Sprague Dawley


title: Aorta-APOE-deficient and vitamin E treatment-rep2

tag: sample type


title: CL1-0 biological repeat 2

description: Gene expression data from CL1-0

value: poorly invasive


title: MEL_Ldb1KD_induced_rep3

source_name: MEL_Ldb1 shRNA knockdown_DMSO induced

value: Ldb1 shRNA knockdown

tag: induced with


title: MEL_Ldb1KD_uninduced_rep1

source_name: MEL_Ldb1 shRNA knockdown_uninduced


title: CL1-5 biological repeat 3

description: Gene expression data from CL1-5


title: MEL_Ldb1KD_induced_rep2


title: CL1-0 biological repeat 1

description: Gene expression data from CL1-0


title: CL1-0 biological repeat 3

description: Gene expression data from CL1-0


title: No Epilepsy, sample 3

city: Duarte

first: Charles

last: Wang

state: CA

address: 1710 Flower Ave

department: Functional Genomics Core

institute: City of Hope

hyb_protocol: Five micrograms of biotinylated fragmented cDNA were hybridized on Affymetrix HG-U133 plus 2.0 arrays for 20 hours at 45 C, GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Affymetrix GeneChip Scanner 300 7G was used to scan the GeneChips

data_processing: The data were analyzed with Partek Genomic Suite 6.5, RMA was used for probe level summarization and cross-array normalization

source_name: FFPE peritumoral sections

label_protocol: Biotin labeled cDNA were prepared using WT-Ovation FFPE RNA amplification system and FL-Ovation cDNA biotin module from NuGen

growth_protocol: Surgical resectioned tumors was fixed in formalin and embedded in parafim

extract_protocol: RNA was extracted using Qiagen Rneasy FFPE kit according to manufacture's protocol

treatment_protocol: Three to five sections of peritumoral tissue were obtained from FFPE blocks

value: Female

value: peritumoral cortex

tag: disease state

value: no epilepsy

tag: tumor type

value: oligodendroglioma


title: No Epilepsy, sample 4

value: Male

value: ganglioglioma


title: MEL_control_induced_rep3

source_name: MEL_control knockdown_DMSO induced


title: MEL_Ldb1KD_induced_rep1


title: CBR30-50_rep3

city: Wuhan

first: chunmei

last: wang

address: Hongshan district, No.1

institute: huazhong agriculture university

description: H. parasuis CBR30-50, replicate 3

hyb_protocol: Hybridization was performed using the Gene Expression Hybridization Kit (Agilent) according to the manufacturer’s instructions. Briefly, after fragmentation, 1 mg of cRNA was hybridized to the slide by incubating at 65°C with a 10rpm rotation for 17 h.

scan_protocol: The slides were scanned by the Agilent Microarray Scanner System with a resolution of 5 mm. The scanner used 100% and 10% post-translational modification and automatically combined the data from these two sources.

data_processing: Images analyzed using Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, USA). Raw data were normalized using the Quantile algorithm Gene Spring Software 11.0 (Agilent Technologies).

organism: Glaesserella parasuis

source_name: H. parasuis CBR30-50 with no cecropin B at OD600 >0.3 (12 h)

label_protocol: RNA was reverse-transcribed into cDNA, and then transcribed into cRNA. After purification, 4 mg of the cRNA was labeled with the amino-group reactive dye, Cy3 NHS ester (GE Healthcare, Waukesha, WI), and purified.

growth_protocol: Overnight cultures of H. parasuis SH0165, CBR30 or CBR30-50 were inoculated in the TSB medium and grown at 37°C and 180 rpm. Growth was measured at mid-log-phase.

extract_protocol: Total RNA of SH0165, CBR30, and CBR30-50 was extracted using TRIzol reagent (Invitrogen Corp., Carlsbad, CA, USA), and purified using the Qiagen RNeasy Mini Kit (Hilden, Germany).

treatment_protocol: Bacterial cultures were centrifuged for 5 min (2300 g at 4°C).


title: No Epilepsy, sample 5

value: astrocytoma


title: CBR30-50_rep2

description: H. parasuis CBR30-50, replicate 2


title: No Epilepsy, sample 1


title: control group_rep1

description: H. parasuis SH0165, replicate 1

source_name: H. parasuis SH0165 with no tilmicosin at OD600 >0.3 (12 h)


title: CBR30_rep3

description: H. parasuis CBR30, replicate 3

source_name: H. parasuis CBR30 with 30μg/mL cecropin B at OD600 >0.3 (20 h)


title: Epilepsy, sample 5

value: epilepsy


title: control group_rep3

description: H. parasuis SH0165, replicate 3


title: control group_rep2

description: H. parasuis SH0165, replicate 2


title: E-group bone 1 week postsurgery rep3


title: CBR30-50_rep1

description: H. parasuis CBR30-50, replicate 1


title: No Epilepsy, sample 2


title: MEL_control_induced_rep2

value: BALB/c

value: Murine erythroidleukema (MEL) cells


title: CBR30_rep2

description: H. parasuis CBR30, replicate 2


title: Healthy Living donor [H4-Glom-LD5]

status: Public on Dec 10 2012

city: Ann Arbor

first: Viji

last: Nair

address: 1152 West Medical Centre Dr.

institute: University of Michigan

description: Gene expression data from the glomeruli of human pre-transplant living donor control kidney

hyb_protocol: According to the Affymetrix Expression Analysis Technical Manual.

data_processing: The data were analyzed using GenePattern pipeline: RMA method and Human Entrez Gene custom CDF annotation version 10 was used for the normalization.  Each of the hybridization was normalized seperately and the VALUE column contains the batch-corrected data using Combat.

source_name: Kidney Biopsy from Human Healthy Living donor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, Affymetrix). GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

extract_protocol: Total RNA was isolated using the RNeasy mini kit from Qiagen, following the manufacturer’s instructions.

value: Glomeruli from kidney biopsy


title: Healthy Living donor [H4-Glom-LD9]

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.


title: MEL_control_induced_rep1

value: control


title: Healthy Living donor [H4-Glom-LD10]


title: Epilepsy, sample 2


title: CBR30_rep1

description: H. parasuis CBR30, replicate 1


title: Epilepsy, sample 3


title: Epilepsy, sample 1


title: IgA Nephropathy [H4-Glom-IgA3]

description: Gene Expression data from the glomeruli of human IgA Nephropathy kidney

data_processing:
The data were analyzed using GenePattern pipeline: RMA method and Human Entrez Gene custom CDF annotation version 10 was used for the normalization
Each of the hybridization was normalized seperately and the VALUE column contains the batch-corrected data using Combat

source_name: Kidney Biopsy from Human IgA Nephropathy

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

extract_protocol: Total RNA was isolated using Rneasy kit (Qiagen) following manufacturer's protocol


title: Healthy Living donor [H4-Glom-LD7]


title: IgA Nephropathy [H4-Glom-IgA27]


title: IgA Nephropathy [H4-Glom-IgA8]


title: Healthy Living donor [H4-Glom-LD8]


title: IgA Nephropathy [H4-Glom-IgA2]


title: IgA Nephropathy [H4-Glom-IgA25]


title: IgA Nephropathy [H4-Glom-IgA7]


title: IgA Nephropathy [H4-Glom-IgA9]


title: IgA Nephropathy [H4-Glom-IgA23]


title: IgA Nephropathy [H4-Glom-IgA5]


title: IgA Nephropathy [H4-Glom-IgA17]


title: IgA Nephropathy [H4-Glom-IgA1]


title: TET2 KD ES cells

city: Ann arbor

first: qiang

last: chen

state: Michigan

address: 1150 W. medical school road

institute: umich

description: Gene expression from TET2 KD mouse ES cells

hyb_protocol: Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations on a GeneTitan Instrument.

scan_protocol: Arrays were scanned on an Affymetrix GeneAtlas instrument

data_processing: Expression estimates were calculated by Affymetrix Expression Console (AGCC)

source_name: TET2 KD ES cells

label_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Biotinylated cRNA was generated from the cDNA reaction using the BioArray High Yield RNA Transcript Kit.

growth_protocol: Mouse ES cells were maintained on gelatin-coated dishes in Glasgow Minimum Essential medium (GMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum, 55 mM b-mercaptoethanol (GIBCO), 2mM L-glutamine, 0.1mM MEM non-essential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of ESGRO (Chemicon) under feeder-free conditions

extract_protocol: For expression microarray analysis comparing control KD and Tet2 KD mouse ES cells, 2 µg of total RNA purified from puromycin treated cells were reverse-transcribed into cDNA with a T7-(dT)24 primer from a custom kit (Life Technologies).

treatment_protocol: For Tet2 knockdown (KD), mouse ES cells were infected with lentiviruses with short-hairpin RNA (shRNA) specific for Tet2. All analyses were performed using Tet2-depleted ES cells that were treated with with puromycin for 72 hours. Lentiviruses with scramble RNA was used as a control. Short-hairpin RNA (shRNA) sequences were cloned into pMSCV-puro vector under the control of the U6 promoter.

value: TET2 KD

value: mouse ES cells


title: IgA Nephropathy [H4-Glom-IgA16]


title: IgA Nephropathy [H4-Glom-IgA6]


title: IgA Nephropathy [H4-Glom-IgA10]


title: IgA Nephropathy [H4-Glom-IgA13]


title: IgA Nephropathy [H4-Glom-IgA26]


title: IgA Nephropathy [H4-Glom-IgA22]


title: IgA Nephropathy [H4-Glom-IgA4]


title: Control KD ES cells

description: Gene expression from control KD mouse ES cells

source_name: control KD ES cells

value: control KD


title: Epilepsy, sample 4


title: Hypertensive nephropathy [H2-Glom-HT6]

description: Gene Expression data from the glomeruli of human Hypertensive nephropathy kidney

source_name: Kidney Biopsy from Human Hypertensive nephropathy


title: Hypertensive nephropathy [H2-Glom-HT25]


title: IgA Nephropathy [H4-Glom-IgA24]


title: IgA Nephropathy [H4-Glom-IgA21]


title: Hypertensive nephropathy [H2-Glom-HT2]


title: IgA Nephropathy [H4-Glom-IgA20]


title: IgA Nephropathy [H4-Glom-IgA18]


title: IgA Nephropathy [H4-Glom-IgA19]


title: Hypertensive nephropathy [H2-Glom-HT14]


title: IgA Nephropathy [H4-Glom-IgA14]


title: Hypertensive nephropathy [H2-Glom-HT15]


title: IgA Nephropathy [H4-Glom-IgA15]


title: Hypertensive nephropathy [H2-Glom-HT18]


title: Hypertensive nephropathy [H2-Glom-HT16]


title: Hypertensive nephropathy [H2-Glom-HT13]


title: IgA Nephropathy [H4-Glom-IgA12]


title: IgA Nephropathy [H4-Glom-IgA11]


title: Hypertensive nephropathy [H2-Glom-HT5]


title: Healthy Living donor [H1-Glom-LD3]


title: Hypertensive nephropathy [H2-Glom-HT1]


title: Healthy Living donor [H1-Glom-LD2]


title: Hypertensive nephropathy [H2-Glom-HT7]


title: Hypertensive nephropathy [H2-Glom-HT8]


title: Hypertensive nephropathy [H2-Glom-HT11]


title: Healthy Living donor [H1-Glom-LD4]


title: Hypertensive nephropathy [H2-Glom-HT4]


title: Hypertensive nephropathy [H2-Tub-HT6]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive nephropathy kidney

value: Tubulointerstitium from kidney biopsy


title: Hypertensive nephropathy [H2-Tub-HT8]


title: Hypertensive nephropathy [H2-Tub-HT5]


title: Hypertensive nephropathy [H2-Tub-HT7]


title: Hypertensive nephropathy [H2-Tub-HT4]


title: Hypertensive nephropathy [H2-Tub-HT3]


title: Hypertensive nephropathy [H2-Glom-HT12]


title: Hypertensive nephropathy [H2-Tub-HT9]


title: Healthy Living donor [H1-Glom-LD1]


title: Hypertensive nephropathy [H2-Tub-HT15]


title: Hypertensive nephropathy [H2-Tub-HT17]


title: Hypertensive nephropathy [H2-Tub-HT13]


title: Hypertensive nephropathy [H2-Tub-HT16]


title: Hypertensive nephropathy [H2-Tub-HT20]


title: Hypertensive nephropathy [H2-Tub-HT12]


title: Healthy Living donor [H7-Glom-LD990]


title: Healthy Living donor [H1-Tub-LD1]

description: Gene expression data from the tubulointerstitium of human pre-transplant living donor control kidney


title: Hypertensive nephropathy [H2-Tub-HT10]


title: Healthy Living donor [H7-Glom-LD992]


title: Hypertensive nephropathy [H2-Tub-HT1]


title: Healthy Living donor [H7-Glom-LD994]


title: Healthy Living donor [H7-Glom-LD989]


title: Healthy Living donor [H7-Glom-LD987]


title: Healthy Living donor [H1-Tub-LD2]


title: Hypertensive nephropathy [H2-Tub-HT14]


title: Healthy Living donor [H1-Tub-LD3]


title: Healthy Living donor [H7-Glom-LD985]


title: Healthy Living donor [H7-Glom-LD983]


title: Healthy Living donor [H7-Glom-LD988]


title: Healthy Living donor [H7-Glom-LD981]


title: Hypertensive nephropathy [H2-Tub-HT11]


title: Hypertensive nephropathy [H2-Tub-HT18]


title: Healthy Living donor [H7-Glom-LD984]


title: Healthy Living donor [H7-Glom-LD993]


title: Healthy Living donor [H7-Glom-LD980]


title: Healthy Living donor [H7-Glom-LD979]


title: Healthy Living donor [H7-Glom-LD978]


title: Healthy Living donor [H7-Glom-LD982]


title: Healthy Living donor [H7-Glom-LD976]


title: Healthy Living donor [H7-Glom-LD975]


title: Healthy Living donor [H7-Glom-LD974]


title: Healthy Living donor [H7-Tub-LD1184]


title: Healthy Living donor [H7-Tub-LD1183]


title: Healthy Living donor [H7-Tub-LD1175]


title: Healthy Living donor [H7-Tub-LD1180]


title: Healthy Living donor [H7-Tub-LD1182]


title: Healthy Living donor [H7-Tub-LD1177]


title: Healthy Living donor [H7-Tub-LD1170]


title: Healthy Living donor [H7-Tub-LD1179]


title: Healthy Living donor [H7-Tub-LD1172]


title: Healthy Living donor [H7-Tub-LD1168]


title: Healthy Living donor [H7-Tub-LD1169]


title: Healthy Living donor [H7-Tub-LD1171]


title: Healthy Living donor [H7-Tub-LD1173]


title: Healthy Living donor [H7-Tub-LD1166]


title: Healthy Living donor [H7-Tub-LD1174]


title: Healthy Living donor [H7-Tub-LD1164]


title: Healthy Living donor [H7-Tub-LD1178]


title: Healthy Living donor [H7-Tub-LD1165]


title: Uninfected cell Neg2, biological rep2

city: Lanzhou

first: Aijiang

last: Guo

state: Gansu

address: 1 Xujiaping Yanchangbu Chengguan District

institute: Lanzhou veterinary research institute, CAAS

description: Gene expression data from normal chicken cecal epithelia

hyb_protocol: Following fragmentation, cRNA probes (10 ug each) were hybridized with Affymetrix GeneChip Chicken Genome Array for 16 hr at 45 C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 30007G.

data_processing: The hybridization data were analyzed using dCHIP. An invariant set normalization procedure was performed to normalize the different arrays.

organism: Gallus gallus

source_name: Normal cecal epithelia

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (2 ug/probe) (see: Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Chickens infected with parasites and uninfected control chickens were raised in two separate rooms, and care and feeding were given by different workers to minimize potential cross-contaminations.

extract_protocol: Total RNA was isolated from samples using a Trizol RNA isolation kit according to the manufacturer's instructions.

treatment_protocol: Chickens were orally inoculated with sporulated oocysts, and euthanized at 4.5 d post-infection. Cecal epithelia from Infected and uninfected chickens were collected and stored in Trizol solution (Invitrogen) on ice. Parasite merozoites were collected at 5 d post-infection and also stored in the Trizol solution.

tag: infection


title: XY8

type: genomic

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

hyb_protocol: All arrays were washed and stained on an Affymetrix FS450 fluidics station.

scan_protocol: All arrays were scanned using an Affymetrix GeneChip 3000 7G scanner as per Affymetrix procedures.

data_processing: Genotype analysis was performed using Affymetrix Genotyping Console version 4.0 with the default settings.

molecule: genomic DNA

source_name: NPC biopsy

label_protocol: DNA was labelled according to Affymetrix standard protocol.

extract_protocol: 8 micron cryosections were transferred onto PALM membrane slides (P.A.L.M. Microlaser Technologies) and air dried on ice for about 1 minute. Slides were immersed for 2 minutes in cold 75% ethanol, tapped dry and stained for 30 seconds in cold haematoxylin and eosin (9:1) containing 1% NucleoGuard (AmpTec, Hamburg). Excess stain was tapped off and slides were washed in cold nuclease-free water for 30 seconds, cold 75% ethanol for 1 minute, cold 100% ethanol for 1 minute then air dried. Tumour cells for analysis were excised by laser microdissection and pressure catapulting using a PALM MicroBeam instrument and caught on PALM Adhesive Caps. A minimum of 200,000 µm2 of tissue was collected for each DNA extraction. DNA was extracted from microdissected cells by adding 100 µl of lysis buffer (10mM Tris-HCl, pH 8.0, 1mM EDTA, 1% Tween 20, 0.4 mg/ml proteinase K (Qiagen)) to the tube containing the captured cells and incubating inverted for 3hr at 55OC then 5min at 95 OC. 2 µl of linear polyacrylamide solution (GenElute, Sigma) were added and DNA was recovered by ethanol precipitation. The pellet was washed with 70% ethanol and air dried. The precipitated DNA was subject to whole genome amplification using a Genomiphi kit (GE Healthcare) according to the manufacturer’s instructions.

value: nasopharyngeal carcinoma


title: Infected cell T3, biological rep3

description: Gene expression data from chicken cecal epithelia infected with Eimeria tenella

source_name: cecal epithelia infected with parasites

value: Eimeria tenella


title: Uninfected cell Neg3, biological rep3


title: Infected cell T2, biological rep2


title: Parasite merozoites (Mzt)

description: Microarray signals using probes derived from parasite material (additional control)

organism: Eimeria tenella

source_name: Parasites from infected cecal epithelia


title: Uninfected cell Neg1, biological rep1


title: XY5


title: Hypertensive nephropathy [H2-Tub-HT2]


title: Infected cell T1, biological rep1


title: MMAH


title: XY6


title: 1836

hyb_protocol: All arrays were washed and stained on an Affymetrix FS450 fluidics station

source_name: blood from normal individual

label_protocol: DNA was subject to whole genome amplification using a Genomiphi kit (GE Healthcare) according to the manufacturer’s instructions and labelled according to Affymetrix standard protocol.

extract_protocol: Genomic DNA was extracted using Qiagen QIAamp blood kit.

value: normal control


title: immature oocytes [VG1_23]

city: Nantes

first: Raluca

last: TEUSAN

address: 1, rue gaston veil

country: France

institute: INSERM U915

description:
Sample name: VG1_23
Raw data file: 91_4.txt

hyb_protocol: RNA  samples  were hybridised  on  Whole  Human  Genome  Oligo  Microarray 4x44K  (Agilent Technologies: Two-Color  Microarray-162 Based  Gene  Expression  Analysis)

scan_protocol: Hybridized arrays were scanned using Agilent fluorescence scanner.

data_processing: Hybridization and background signals were measured using GenePix Pro 5.0 image analysis software (Axon Instruments).  For each microarray, Cy3 and Cy5 signal intensities were individually normalized to the median profile of all Cy3 or Cy5 signal intensities by Lowess

source_name: Cumulus cells

label_protocol: RNA  samples  were  prepared  according  to  the  Agilent  protocol  (Two-Color  Microarray-162 Based  Gene  Expression  Analysis)  and  hybridised  on  Whole  Human  Genome  Oligo  Microarray 4x44K  (Agilent Technologies).

extract_protocol: Total RNA  extraction  was  carried  out  using  the  Rneasy Micro Kit (Qiagen).  A DNase  step  was included  in  the  extraction  protocol  to  remove  residual  genomic  DNA  contamination.

value: Cumulus cells

tag: oocyte developmental competence

value: VG


title: MDIG


title: embryo of poor quality [E1_21]

description:
Sample name: E1_21
Raw data file: 91_3.txt

value: E


title: MKEC


title: XY23


title: MOUZ


title: Hypertensive nephropathy [H2-Tub-HT19]


title: immature oocytes [VG28_19]

description:
Sample name: VG28_19
Raw data file: 91_2.txt


title: embryo of poor quality [E3_22]

description:
Sample name: E3_22
Raw data file: 91_3.txt


title: blastocyst [B13_17]

description:
Sample name: B13_17
Raw data file: 91_1.txt

value: B


title: immature oocytes [VG28_20]

description:
Sample name: VG28_20
Raw data file: 91_2.txt


title: blastocyst [B31_18]

description:
Sample name: B31_18
Raw data file: 91_1.txt


title: C666

source_name: NPC cell line

extract_protocol: DNA was extracted from C666-1 cells using a DNeasy kit (Qiagen) according to the manufacturer’s instructions.


title: embryo of poor quality [E12_16]

description:
Sample name: E12_16
Raw data file: 89_4.txt


title: MKAV


title: 1906


title: embryo of poor quality [E19_15]

description:
Sample name: E19_15
Raw data file: 89_4.txt


title: 1834


title: HKC1


title: immature oocytes [VG23_13]

description:
Sample name: VG23_13
Raw data file: 89_3.txt


title: Amp_C666


title: blastocyst [B2_8]

description:
Sample name: B2_8
Raw data file: 88_4.txt


title: blastocyst [B41_14]

description:
Sample name: B41_14
Raw data file: 89_3.txt


title: XY16


title: 1680


title: HK6


title: HKC2


title: immature oocytes [VG16_10]

description:
Sample name: VG16_10
Raw data file: 89_1.txt


title: blastocyst [B7_11]

description:
Sample name: B7_11
Raw data file: 89_2.txt


title: blastocyst [B4_7]

description:
Sample name: B4_7
Raw data file: 88_4.txt


title: HKD1


title: immature oocytes [VG10_6]

description:
Sample name: VG10_6
Raw data file: 88_3.txt


title: HK4


title: 1635


title: immature oocytes [VG19_9]

description:
Sample name: VG19_9
Raw data file: 89_1.txt


title: blastocyst [B10_12]

description:
Sample name: B10_12
Raw data file: 89_2.txt


title: immature oocytes [VG8_5]

description:
Sample name: VG8_5
Raw data file: 88_3.txt


title: embryo of poor quality [E15_4]

description:
Sample name: E15_4
Raw data file: 88_2.txt


title: blastocyst [B12_2]

description:
Sample name: B12_2
Raw data file: 88_1.txt


title: embryo of poor quality [E38_3]

description:
Sample name: E38_3
Raw data file: 88_2.txt


title: Usi12_clone_mutp53

city: Hamburg

first: Genrich

last: Tolstonog

department: Department of Tumor Virology

country: Germany

institute: Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology

description:
SAMPLE 27
gene expression data from human U-251 MG cell line expressing p53 shRNA and ectopic mutp53R273H

hyb_protocol: performed by Source BioScience imaGenes (www.imagenes-bio.de)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent).

source_name: Usi12 cells stably transfected with pcDNA3-p53R273H vector

growth_protocol: The cells were maintained in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum (FCS).

extract_protocol: Total RNA was isolated from cells using peqGOLD TriFast (Peqlab) according to the manufacturer’s instructions. The quality and integrity of the total RNA was evaluated with the Agilent 2100 Bioanalyzer and the concentration was measured using a NanoDrop spectrophotometer.

treatment_protocol: Transient siRNA transfection was performed in 6-well cell culture plates using Oligofectamine (Invitrogen) according to manufacturer´s protocol.  The cells were incubated for 96 hours before RNA was extracted. To obtain clones with a stable reduction of p53 expression, cells were transfected either with 1.8 µg pSuper-p53/0.2 µg pCI-neo (Oligoengine), or 2 µg pENTR/H1-p53 using the NHDF Neo kit, program U20 (Amaxa AG). As control for off-target effects of the shRNA, cells were transfected with pENTR/H1-scr for the expression of scrambled shRNA.

tag: cell line

value: U-251 MG human glioblastoma cell line


title: SB-429_Bad_Quality

city: Charleston

first: Marion

last: Neely

state: SC

address: 331 Ft. Johnson Rd

department: NCCOS

institute: National Ocean Services

hyb_protocol: Agilent One- Color Microarray - Based Gene Expression Analysis (Low Input Quick Amp Labeling) Protocol

scan_protocol: Agilent G2505B Scanner, Agilent Scan Control software, eXtended Dynamic Range Scan Mode 5µm scan, XDR PMT: Hi 100%, Lo 10%

data_processing: Feature Extraction v 10.7.3.1, Protocol GE1_107_Sep09. Raw Intensity data was normalized using Bioconductor (http://www.bioconductor.org) to generate variance-stabilized normalization (VSN).

organism: Morone saxatilis

source_name: Ovary

extract_protocol: Qiagen Rneasy Mini with on column DNase digestion

tag: egg quality

value: Bad


title: Usi12A18_subclone

description:
SAMPLE 25
gene expression data from human U-251 MG cell line expressing p53 shRNA

scan_protocol: performed by Source BioScience imaGenes (www.imagenes-bio.de)

source_name: subclone derived from Usi12 clone


title: Usi12A8_subclone

description:
SAMPLE 26
gene expression data from human U-251 MG cell line expressing p53 shRNA

label_protocol: performed by Source BioScience imaGenes (www.imagenes-bio.de)


title: Usi12_clone_pCDNA3

description:
SAMPLE 28
gene expression data from human U-251 MG cell line expressing p53 shRNA

source_name: Usi12 cells stably transfected with empty pcDNA3 vector


title: blastocyst [B12_1]

description:
Sample name: B12_1
Raw data file: 88_1.txt

tag: cell type


title: SB-437_Good_Quality

label_protocol: Agilent One- Color Microarray - Based Gene Expression Analysis (Low Input Quick Amp Labeling) Protocol

value: Good


title: SB-399_Bad_Quality


title: SB-411_Good_Quality


title: SB-382_Good_Quality


title: Usi12_clone

description:
SAMPLE 24
gene expression data from human U-251 MG cell line expressing p53 shRNA

source_name: clone derived from human U-251 MG cell line by stable transfection with pSuper-p53/pCI-neo vectors (Oligoengine)


title: sh6_clone_mutp53

description:
SAMPLE 19
gene expression data from human U-251 MG cell line expressing p53 shRNA and ectopic mutp53R273H

source_name: sh6 cells stably transfected with pcDNA3-p53R273H vector


title: scr3_clone

description:
SAMPLE 16
gene expression data from human U-251 MG cell line expressing scrambled shRNA

source_name: clone derived from human U-251 MG cell line by stable transfection with pENTR/H1-scr vector


title: sh23_clone

description:
SAMPLE 23
gene expression data from human U-251 MG cell line expressing p53 shRNA

source_name: clone derived from human U-251 MG cell line by stable transfection with pENTR/H1-p53 vector


title: SB-94_Bad_Quality


title: SB-375_Bad_Quality


title: sh10_clone_mutp53

description:
SAMPLE 22
gene expression data from human U-251 MG cell line expressing p53 shRNA and ectopic mutp53R273H

source_name: sh10 cells stably transfected with pcDNA3-p53R273H vector


title: sh6_clone

description:
SAMPLE 17
gene expression data from human U-251 MG cell line expressing p53 shRNA


title: SB-74_Bad_Quality


title: sh6_clone_pCDNA3

description:
SAMPLE 18
gene expression data from human U-251 MG cell line expressing p53 shRNA

source_name: sh6 cells stably transfected with empty pcDNA3 vector


title: scr2_clone

description:
SAMPLE 15
gene expression data from human U-251 MG cell line expressing scrambled shRNA


title: sh10_clone_pCDNA3

description:
SAMPLE 21
gene expression data from human U-251 MG cell line expressing p53 shRNA

source_name: sh10 cells stably transfected with empty pcDNA3 vector


title: SB-251_Bad_Quality


title: SB-129_Bad_Quality


title: scr1_clone_sip53

description:
SAMPLE 14
gene expression data from human U-251 MG cell line expressing scrambled shRNA and transiently transfected with p53-specific siRNA

source_name: scr1 cells transiently transfected with p53-specific siRNA


title: sh10_clone

description:
SAMPLE 20
gene expression data from human U-251 MG cell line expressing p53 shRNA


title: SB-127_Good_Quality


title: SB-48_Good_Quality


title: SB-44_Good_Quality


title: SB-111_Bad_Quality


title: scr1_clone_scr

description:
SAMPLE 13
gene expression data from human U-251 MG cell line expressing scrambled shRNA and transiently transfected with scrambled siRNA

source_name: scr1 cells transiently transfected with scrambled siRNA


title: SB-58_Good_Quality


title: Skeletal muscle from obese male 20 after 8-week training

city: Toulouse

first: Nathalie

last: Viguerie

address: Avenue Poulhes

institute: INSERM

description: Labeling and hybridization qualities were verified with Agilent’s spike in kit.

hyb_protocol: 825 ng of Cy5 labelled probe was cohybridized the same amount of Cy3 labelled control probe. We used the Whole Human Genome Microarray Kit, 4x44K from Agilent with the gene expression hybridization kit according to the manufacturer’s protocol.

scan_protocol: Micro-arrays were scanned on a InnoScan 710A scanner (Innopsys, Carbonne, France, EU) and data were extracted with Mapix software version 5.5.0 (Innopsys).

data_processing: Features with a signal to background ratio strictly below 2 in both color as well as control spots were discarded. The data without background subtraction were normalized with the Lowess procedure and quantiles method by use of R. Value is the Log2 of normalized 635/ 532 value ratio.

source_name: mix of liver, adipose tissue and skeletal muscle

label_protocol: Total RNA quality was checked by capillary electrophoresis (Experion, BioRad) and quantified using Nanodrop ND-1000 Spectrophotometer (Labtech). Only good quality RNA extracts only were used for microarray hybridization. Fluorescent probes were obtained by amplifying and labelling 200ng of RNA with the low RNA input linear amplification kit (Agilent).

extract_protocol: Total RNA was purchased at Applied Biosystems/Ambion

value: mix of male and female

source_name: Human vastus lateralis muscle, trained (after training)

extract_protocol: Tissue was crushed in QIAzol (Qiagen) and total RNA was extracted with the RNeasy mini kit (Qiagen) according to manufacturer instructions.

value: after 8-week training

value: male

value: skeletal muscle


title: EXP260109_96h_scr

description:
SAMPLE 8
gene expression data from human U-251 MG cell transiently transfected with scrambled siRNA

source_name: human U-251 MG cells transiently transfected with scrambled siRNA


title: scr1_clone

description:
SAMPLE 12
gene expression data from human U-251 MG cell line expressing scrambled shRNA


title: Skeletal muscle from obese male 16 after 8-week training

description: Labeling and hybridization qualities were verified with Agilent’s spike in kit

value: mix of liver, adipose tissue and skeletal muscle


title: Skeletal muscle from obese male 25 after 8-week training


title: Skeletal muscle from obese male 8 after 8-week training


title: U251_sip53

description:
SAMPLE 11
gene expression data from human U-251 MG cells transiently transfected with p53-specific siRNA


title: U251_scr

description:
SAMPLE 10
gene expression data from human U-251 MG cells transiently transfected with p53-specific siRNA


title: Skeletal muscle from obese male 1 after 8-week training


title: EXP140209_96h_sip53

description:
SAMPLE 5
gene expression data from human U-251 MG cells transiently transfected with p53-specific siRNA


title: EXP260109_96h_sip53

description:
SAMPLE 9
gene expression data from human U-251 MG cells transiently transfected with p53-specific siRNA


title: EXP251108_96h_scr

description:
SAMPLE 6
gene expression data from human U-251 MG cell transiently transfected with scrambled siRNA


title: PTS mutant strain grown as a biofilm

city: Boston

first: laetitia

last: Houot

state: MA

address: 300 longwood av.

department: Infectious diseases

institute: children's Hospital Boston

description:
Analysis compare V. cholerae MO10 delta PTS mutant to wild type strain grown as surface-associated cells.
Sample 2

hyb_protocol: Before use, the microarrays were preincubated for 1 h at 42°C with buffer (5x SSC, 0.1% SDS, 1% BSA) passed through a 0.22 μm filtered.  Slides were rinsed with 2 L of distilled water and then with isopropyl alcohol before drying.  DNA microarrays were incubated in hybridization chambers (Corning) at 42°C for 18–20 h, then washed to remove unspecific hybridization (once with 2x SSC, 0.1% SDS for 5 min, twice with 0.1x SSC, 0.1% SDS for 6 min, twice with 0.1x SSC for 5 min).

scan_protocol: Hybridized arrays were scanned using a GenePixTM 4000B scanner (Axon Instruments).

data_processing:
Data analysis was carried out using GenPixTM Pro, version 4.0 and Genespring version 5.0.1 (Silicon Genetics). For each spot, the local fluorescence background was subtracted. Then, the mean values from each channel were normalized globally by locally weighted linear regression (Lowess). A Lowess curve was fit to the log-intensity versus log-ratio plot (Genespring default parameter). Normalised values were used to calculate the Cy3/Cy5 fluorescence ratios from experimental and biological repeats with all replicates combined. Data was compiled from 3 planktonic and 3 biofilm cultures each with a dye-swap replicate, thus providing 3 biological repeats within 6 technical repeats.
Genespring normalized+filtered data linked as supplementary file on Series record.  The normalized data before filtering are unavailable.

organism: Vibrio cholerae MO10

source_name: surface-associated cells

label_protocol: cDNA was labelled with Cy3 and Cy5 during synthesis from total RNA using Superscript III Kit (Invitrogen) as per the manufacturer's instructions. Samples purified using QIAGEN PCR purification kit before hybridization.

growth_protocol: Wild type and PTS mutant strains were grown statically in glass tubes  filled with 2 ml of minimal medium supplemented with glucose (0.5% wt/vol). After incubation for 24 hours at 27°C, planktonic cells were collected and used in planktonic cell analyses. The remaining surface-associated cells were gently dispersed in 2 ml 1x PBS with glass beads, collected, and used in biofilm cell analyses. Cells were pelleted by centrifugation at 4000 rpm for 15 min and incubated for 5 min in 200 μl lysosyme-TE buffer (400 μl/ ml).

extract_protocol: Total RNA was extracted with the RNeasy kit (Qiagen), and possible DNA contamination was removed by treating the samples with 1 μl DNase I for 15 min at 37°C (Promega). Total RNA was ethanol precipitated and resuspended in 20 μl RNase free water.

treatment_protocol: The PTS mutant was constructed by deleting a operon that encompasses the genes encoding VC0964 (EIIAglucose), VC0965 (EI) and VC0966 (HPr).

value: Delta PTS

value: wild type


title: Skeletal muscle from  obese male 17, control

source_name: Human vastus lateralis muscle, control (before training)

value: before training


title: SB-38_Good_Quality

source_name: Ovary


title: U251_subline1

description:
SAMPLE 2
gene expression data from human U-251 MG cell line derived subline

source_name: subline derived from human U-251 MG cell line


title: Skeletal muscle from  obese male 20, control


title: PTS mutant strain grown as planktonic cells

description:
Analysis compare V. cholerae MO10 delta PTS mutant to wild type strain grown as planktonic cells.
Sample 1

source_name: planktonic cells


title: EXP140209_96h_scr

description:
SAMPLE 4
gene expression data from human U-251 MG cell transiently transfected with scrambled siRNA


title: U251

description:
SAMPLE 1
gene expression data from human U-251 MG cells

source_name: human U-251 MG cells


title: U251_subline12

description:
SAMPLE 3
gene expression data from human U-251 MG cell line derived subline


title: Skeletal muscle from  obese male 25, control


title: kidney_Hemin_4

city: São Paulo

first: Hatylas

last: Azevedo

state: Sao Paulo

address: Doutor Arnaldo Avenue, 455

department: Pediatrics

country: Brazil

institute: University of São Paulo

description: Gene expression of kidney tissue extracted from mices submitted to treatment with the drug Hemin

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Mice Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95 Feb07 and Grid: 014868_D_F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: kidney, mices submitted to Hemin treatment, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: Total RNA was isolated from kidney samples using Trizol reagent (Life Technologies) and purified using RNeasy Spin Columns (Qiagen, USA). RNA quantity was determined using a Nanovue spectrophotometer (GE Healthcare, USA). The RNA quality was performed using a 2100 Bioanalyzer with an RNA 6000 Nano kit and Ladder (Agilent Technologies, USA), according to the manufacturer’s instructions.

treatment_protocol: Mice were anesthetized with Ketamine-Xylazine, a midline incision was made and both renal pedicles were cross-clamped for 45 minutes. During the procedure, animals were kept well hydrated with saline and at a constant temperature (~37oC) through a heating pad device. Subsequently, microsurgery clamps were removed, the abdomen closed and animals placed in single cages, warmed by indirect light until completely recovered from anesthesia. Animals were kept under adjustable conditions until sacrifice, namely 6 hours after renal reperfusion. In order to induce heme-oxygenase 1 (Hmox1) expression, mice received Hemin (Frontier Scientific, Canada) i.p., 25 mg/kg, 24 hours prior to surgery.

tag: surgery procedure

tag: protection maneuver against iri

value: Hemin


title: kidney_Hemin_2

source_name: kidney, mices submitted to Hemin treatment, replicate 2


title: kidney_Hemin_3

source_name: kidney, mices submitted to Hemin treatment, replicate 3


title: Skeletal muscle from  obese male 16, control

tag: gender


title: Skeletal muscle from  obese male 1, control


title: C2C12_GFP+DFO_rep2

city: Madison

first: David

middle: J.

last: Pagliarini

state: WI

address: 433 Babcock Dr.

department: Biochemistry

institute: University of Wisconsin-Madison

description: DFO 2

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Mouse 430 2.0 Arrays using standard Affymetrix procedures.

scan_protocol: GeneChips were scanned using the GCS 3000 from Affymetrix.

data_processing: Files were processed by dCHIP using model-based expression with mismatch probe background subtraction, quantile normalization and running median smoothing.

source_name: C2C12 mouse myotube, GFP adenovirus, DFO treatment

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

growth_protocol: C2C12 mouse myoblasts were maintained in high glucose DMEM with 10% fetal bovine serum (FBS) and 1 × penicillin-streptomycin at 37°C and 5% CO2. To induce differentiation, the myoblasts were grown to near confluence then switched to media containing 2% dialyzed FBS.

extract_protocol: Total RNA was extracted with an RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: After 3 days of differentiation, myotubes were infected with adenovirus containing overexpression constructs for either GFP or GFP-PGC-1α ± treatment with 100 µM DFO. The cells were then incubated for 3 days, after which RNA was extracted.

tag: morphology

value: myotube

tag: adenovirus overexpression construct

value: GFP

value: deferoxamine (DFO)


title: glomeruli from non diabetic DBA mouse 17

description: Gene expression data from non diabetic DBA mouse

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
The data were analyzed using ChipInspector which carries out significance analysis on the single probe level. Normalized probe set level data not provided for individual Sample records. ChipInspector gives the log2 based fold change ratio between two group samples for each gene
Entrez Gene IDs and Gene symbols and  Log base 2  fold change values
The following is from the ChipInspector Manual v2 (no probe set level output):
Initial to the significance calculation for a microarray experiment, the raw data is normalized  on the single probe level, i.e. the values are adjusted to improve consistency and reduce  bias. Each value of an array is multiplied by a constant to make the mean intensity the same  for each individual array.
Because values are calculated for the single probes, ChipInspector calculates differing fold  changes when compared to a probe-set-based analysis strategy.

source_name: glomeruli from nondiabetic littermate control mouse

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: DBA mice were fasted for 4 h and then given intraperitoneal injections of 40 mg/kg STZ or vehicle control daily for 5 consecutive days as described in Zhang H, et. al. Rosiglitazone reduces renal and plasma markers of oxidative injury and reverses urinary metabolite abnormalities in the amelioration of diabetic nephropathy. Am J Physiol Renal Physiol 2008;295:F1071-1081.

tag: tissue

value: glomeruli

value: non-diabetic

tag: genetic background

value: DBA


title: glomeruli from non diabetic DBA mouse 16

tag: strain


title: glomeruli from non diabetic DBA mouse 15


title: C2C12_GFP-PGC-1α+DFO_rep2

description: PGC+DFO 2

source_name: C2C12 mouse myotube, GFP-PGC-1α adenovirus, DFO treatment

tag: treatment


title: C2C12_GFP-PGC-1α_rep2

description: PGC 2

source_name: C2C12 mouse myotube, GFP-PGC-1α adenovirus


title: Skeletal muscle from  obese male 8, control

description: Labeling and hybridization qualities were verified with Agilent’s spike in kit.


title: C2C12_GFP+DFO_rep1

description: DFO 1


title: kidney_IPC+IRI_3

description: Gene expression of kidney tissue extracted from a mice model of renal Ischemia-reperfusion injury (IRI) submitted to ischemic pre-conditioning (IPC)

source_name: kidney, mices submitted to IRI and previous IPC, replicate 3

value: IPC+IRI

value: ischemic preconditioning (IPC)


title: C2C12_GFP-PGC-1α+DFO_rep1

description: PGC+DFO 1


title: C2C12_GFP-PGC-1α_rep1

description: PGC 1


title: Skeletal muscle from  obese male 3, control

source_name: mix of liver, adipose tissue and skeletal muscle

value: mix of male and female


title: Skeletal muscle from obese male 3 after 8-week training

source_name: Human vastus lateralis muscle, trained (after training)

value: after 8-week training


title: kidney_Hemin_1

source_name: kidney, mices submitted to Hemin treatment, replicate 1


title: Skeletal muscle from  obese male 18, control

treatment_protocol: control

value: male


title: Skeletal muscle from obese male 18 after 8-week training

value: skeletal muscle


title: glomeruli from non diabetic DBA mouse 12


title: glomeruli from non diabetic DBA mouse 10


title: kidney_IPC+IRI_2

source_name: kidney, mices submitted to IRI and previous IPC, replicate 2


title: glomeruli from Diabetic DBA-STZ mouse 9

description: Gene expression data from Diabetic DBA-STZ mouse

source_name: glomeruli from Diabetic  mouse

value: Diabetic

value: STZ


title: glomeruli from Diabetic DBA-STZ mouse 8


title: glomeruli from non diabetic DBA mouse 13


title: glomeruli from Diabetic DBA-STZ mouse 7


title: glomeruli from Diabetic DBA-STZ mouse 6


title: glomeruli from Diabetic DBA-STZ mouse 5


title: C2C12_GFP_rep2

description: GFP 2

source_name: C2C12 mouse myotube, GFP adenovirus


title: kidney_IPC+IRI_1

source_name: kidney, mices submitted to IRI and previous IPC, replicate 1


title: glomeruli from Diabetic DBA-STZ mouse 3


title: kidney_IPC+IRI_4

source_name: kidney, mices submitted to IRI and previous IPC, replicate 4


title: glomeruli from non diabetic DBA mouse 11


title: kidney_IRI+Hemin_4

description: Gene expression of kidney tissue extracted from a mice model of renal Ischemia-reperfusion injury (IRI) submitted to pre-treatment with the drug Hemin

source_name: kidney, mices submitted to IRI and previous treatment with Hemin, replicate 4

value: IRI


title: glomeruli from Diabetic DBA-STZ mouse 2


title: glomeruli from Diabetic DBA-STZ mouse 1


title: kidney_IRI+Hemin_3

source_name: kidney, mices submitted to IRI and previous treatment with Hemin, replicate 3


title: C2C12_GFP_rep1

description: GFP 1


title: AMC 2

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Canine 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Cel files were normalized using the GC-RMA algorithm as implemented in the Genedata Analyst Software Package.

label: Biotin

organism: Canis lupus familiaris

source_name: TZL

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix protocol from 2.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: Primary tumor samples - mechanical dissociation and 80uM filtered

extract_protocol: RNA was prepared using the RNEasy Minnii Kit and QIAshredder column (Qiagen, Valencia, CA)

tag: age at diagnosis

tag: breed

value: Golden Retriever

value: M

value: TZL

tag: grade

value: Low

tag: phenotype

value: T [T cell lymphoma]


title: glomeruli from Diabetic DBA-STZ mouse 4

value: glomeruli

tag: disease state


title: glomeruli from non diabetic BKS db/db  eNOS+/+ mouse 12

description: Gene expression data from non diabetic BKS db/db  eNOS+/+  glomeruli (20 weeks old)

value: non-diabetic

value: BKS

value: BKS db/db  eNOS+/+

tag: age

value: 20 wk


title: AMC 37


title: kidney_IRI+Hemin_2

source_name: kidney, mices submitted to IRI and previous treatment with Hemin, replicate 2

value: Hemin


title: kidney_IRI+Hemin_1

source_name: kidney, mices submitted to IRI and previous treatment with Hemin, replicate 1


title: AMC 20

value: F


title: kidney_IRI_4

description: Gene expression of kidney tissue extracted from a mice model of renal Ischemia-reperfusion injury (IRI)

source_name: kidney, mices submitted to ischemia-Reperfusion Injury (IRI), replicate 4


title: glomeruli from non diabetic BKS db/db  eNOS+/+ mouse 11

source_name: glomeruli from nondiabetic littermate control mouse


title: AMC 76

source_name: PTCL

value: Bichon Frise

value: PTCL

value: Intermediate


title: AMC 41

source_name: DLBCL

value: DLBCL

value: High

value: B [b cell lymphoma]


title: glomeruli from non diabetic BKS db/db  eNOS+/+ mouse 10


title: glomeruli from non diabetic BKS db/db  eNOS+/+ mouse 9


title: glomeruli from Diabetic BKS db/db eNOS -/- mouse 7

description: Gene expression data from Diabetic BKS db/db eNOS -/- glomeruli (20 weeks old)

value: Diabetic

value: BKS db/db eNOS -/-


title: AMC 48

value: Boxer

value: M


title: glomeruli from Diabetic BKS db/db eNOS -/- mouse 6

value: glomeruli


title: kidney_IRI_3

source_name: kidney, mices submitted to ischemia-Reperfusion Injury (IRI), replicate 3

value: IRI


title: glomeruli from Diabetic BKS db/db eNOS -/- mouse 4

value: BKS


title: kidney_IRI_2

source_name: kidney, mices submitted to ischemia-Reperfusion Injury (IRI), replicate 2


title: glomeruli from non-diabetic BKS db/db  eNOS+/+ mouse 8

value: non-diabetic

value: BKS db/db  eNOS+/+


title: glomeruli from Diabetic BKS db/db eNOS -/- mouse 5

value: 20 wk


title: glomeruli from Diabetic BKS db/db eNOS -/- mouse 3


title: glomeruli from Diabetic BKS db/db eNOS -/- mouse 2


title: kidney_IRI_1

source_name: kidney, mices submitted to ischemia-Reperfusion Injury (IRI), replicate 1


title: kidney_control_4

description: Gene expression of kidney tissue extracted from mices submitted to no surgical procedure or treatment

source_name: kidney, Control, replicate 4


title: glomeruli from Diabetic BKS db/db eNOS -/- mouse 1

source_name: glomeruli from Diabetic  mouse


title: kidney_control_3

source_name: kidney, Control, replicate 3


title: glomeruli from non diabetic BKS db/m  mouse m-9

description: Gene expression data from nondiabetic db/m glomeruli (24 weeks old)

value: BKS db/m

value: 24 wk


title: AMC 34

value: F

value: PTCL

value: T [T cell lymphoma]


title: AMC 73

value: Golden Retriever

value: DLBCL

value: High


title: glomeruli from non diabetic BKS db/m  mouse m-10


title: AMC 21

value: TZL

value: Low


title: kidney_control_2

source_name: kidney, Control, replicate 2


title: glomeruli from non diabetic BKS db/m  mouse m-8


title: glomeruli from non diabetic BKS db/m  mouse m-7


title: AMC 30

value: M


title: AMC 69

source_name: LBT

value: LBT


title: glomeruli from non diabetic BKS db/m  mouse m-6

value: glomeruli


title: EXP251108_96h_sip53

description:
SAMPLE 7
gene expression data from human U-251 MG cells transiently transfected with p53-specific siRNA

tag: cell line

value: U-251 MG human glioblastoma cell line


title: Skeletal muscle from obese male 17 after 8-week training

description: Labeling and hybridization qualities were verified with Agilent’s spike in kit

source_name: mix of liver, adipose tissue and skeletal muscle

value: mix of male and female

source_name: Human vastus lateralis muscle, trained (after training)

value: after 8-week training

value: male

value: skeletal muscle


title: glomeruli from Diabetic BKS  db/db mouse 5

description: Gene expression data from Diabetic db/db glomeruli (24 weeks old)

value: Diabetic

value: BKS

value: BKS  db/db

value: 24 wk


title: AMC 16

source_name: TZL

value: Golden Retriever

value: T [T cell lymphoma]


title: kidney_control_1

source_name: kidney, Control, replicate 1


title: AMC 23

source_name: MZL

value: MZL

value: B [b cell lymphoma]


title: AMC 22

source_name: BL

value: BL

value: High


title: glomeruli from Diabetic BKS  db/db mouse 4


title: Biological replicate 2 of 3: control embryos E. tarda infected

city: Leiden

first: Michiel

last: van der Vaart

address: Einsteinweg 55

department: IBL

country: Netherlands

institute: University of Leiden

hyb_protocol: The dual colour hybridization of the microarray chips was performed at the Microarray Department (MAD) of the University of Amsterdam (Amsterdam, The Netherlands) using the standard Agilent protocol.

scan_protocol: The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies. The arrays were scanned twice with 10% PMT and 100% PMT laser power.

data_processing: Microarray data was processed from raw data image files with Feature Extraction Software 9.5.3.1 (Agilent Technologies). The XDR function was used to extend the dynamic range. Processed data were subsequently imported into Rosetta Resolver 7.0 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. The Agilent Feature Extraction files contain the final log ratio data. The algorithms that were used to normalize the feature signal and calculate the log ratios are described in the Reference Guide for Agilent Feature Extraction Software v9.5. The standard settings as described for the GE2-v5_95 protocol in the Reference Guide were used. In order to calculate the normalized signal, the Rank Consistency Probes method was used and the Linear&LOWESSDyeNormFactor (= DyeNormalSignal/(BGSubSignal x LinearDyeNormFactor) was calculated as described on page 231 of the Reference Guide. The dye normalized signal was calculated as follows (page 232): DyeNormSignal = BGSubSignal x DyeNormFactor. The log10 ratio was subsequently calculated as follows (page 232): LogRatio = Log(rProcessedSignal/gProcessedSignal), where rProcessedSignal and gProcessedSignal are signals post dye normalization and post surrogate processing in the red and green channels, respectively. The surrogate values are calculated and used as the lowest limit of detection to replace the dye normalized signal when either the mean feature signal is less than the background signal or not significant when compared to the background signal, or when the mean signal is less than its background standard deviation (page 226).

organism: Danio rerio

source_name: D. rerio myd88-experiment CR

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 ug of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 or Cy5 dye (GE Healthcare) and column purified.

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: Single embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro-injected into the caudal vein with (1) 200 CFU of S. typhimurium SL1027 bacteria suspended in PBS (phosphate-buffered saline), (2)  mock-injected with PBS as a control, (3) 200 CFU of E. tarda bacteria suspended in PBS (phosphate-buffered saline), (4) mock-injected with PBS as a control . At 36 hpf (8 h post infection) three single embryos per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.

tag: sample type

value: The CR (common reference) was a mixture of all RNA samples from this microarray study. Separate CRs were made for the S. typhimurium, M. Marinum and E. tarda infection experiments

value: embryo

value: Ab

source_name: Wildtype Et 2

value: Wildtype; injected with E. tarda into the caudal vein at 28 hpf; RNA isolated at 8 h post injection

tag: infection

value: E. tarda

tag: genotype

value: wild type


title: Biological replicate 3 of 3: control embryos E. tarda infected

source_name: Wildtype Et 3


title: AMC 50

tag: gender

value: M

value: TZL

value: Low


title: glomeruli from Diabetic BKS  db/db mouse 3

value: glomeruli

value: Diabetic

value: BKS

value: BKS  db/db


title: Biological replicate 2 of 3: mutant embryos E. tarda infected

source_name: Myd88 mutant Et 2

value: MyD88 mutant; injected with E. tarda into the caudal vein at 28 hpf; RNA isolated at 8 h post injection

value: MyD88 mutant


title: AMC 15

value: Golden Retriever

value: F

value: LBT

value: T [T cell lymphoma]


title: ETS1_U251_rep3

description: Sample 26

data_processing: Tukey biweight-scaled log2 ratio GFF files were created by NimbleGen v2.6 software.

source_name: ETS1 ChIP DNA_U251 cells

extract_protocol: Cells were cultured in 15-cm diameter tissue culture dishes. At 80% confluence, cells were washed with warm PBS (pH 7.4) and were treated with DMEM supplemented with 1% formaldehyde (Sigma-Aldrich) for 10 min at room temperature. Crosslinking was stopped by adding 125 mM glycin (final concentration). Treated cells were washed twice with cold PBS, scraped in PBS and collected by centrifugation at 1350 x g at 4°C for 5 min. Cell pellets from two to five 15-cm dishes were pooled and resuspended in 5 ml lysis buffer 1 (140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100 in 50 mM HEPES-KOH, pH 7.5 supplemented with protease inhibitors (5 μg/ml leupeptin (Sigma-Aldrich), 1 μg/ml pepstatin (Sigma-Aldrich), 1% Trasylol (Bayer), 0.1 mg/ml Pefabloc SC (Biomol GmbH)) and incubated for 10 min on ice with gentle shaking. After centrifugation at 1350 x g at 4°C for 5 min, the supernatant was discarded and the pellet was resuspended in 5 ml lysis buffer 2 (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA in 10 mM Tris-HCl, pH 8.0 supplemented with protease inhibitors) and left shaking at room temperature for 10 min. Cells were pelleted by centrifugation at 1350 x g at 4°C for 5 min, the supernatant was discarded and the pellet was resuspended in 2-3 ml lysis buffer 3 (100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine in 10 mM Tris-HCl, pH 8.0 supplemented with protease inhibitors) or ChIP-SDS-lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % (w/v) SDS) and sonicated in 15 ml Falcon tubes for 15 minutes in a Bioruptor UCD-200 (Diagenode) with 30 second on/off cycles. After sonication, when lysis buffer 3 had been used Triton X-100 was added to the samples to a final concentration of 1% and debris was eliminated by centrifugation for 20 minutes at 20,000 x g at 4°C. Samples in ChIP-SDS-lysis buffer were centrifuged without addition of Triton X-100. 50 µl of the lysate was collected as input and after addition of 150 µl elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0) the crosslinks were reversed by incubation at 65°C overnight. 200 µl TE buffer and 8 µl 10 mg/ml RNAse A were added followed by 2 hours at 37°C. To remove proteins 300 mM CaCl2 in 10 mM Tris pH 8.0 and 4 µl 20 mg/ml proteinase K (Roche) were added and samples were incubated for at least 30 min at 50°C. DNA was purified by phenol-chloroform-isoamylalcohol (25:24:1; Biomol GmbH) extraction with subsequent precipitation with ethanol in the presence of 20 μg glycogen (Roche), washed with 70% ethanol, air-dried and dissolved in water. DNA size was estimated by agarose gel electrophoresis.  For immunoprecipitation (IP), anti-histone H3 lysine 4 trimethylation, anti-histone H3 lysine 9 acetylation, anti-RNA-Polymerase II, anti-RNA-Polymerase II CTD repeat YSPTSPS phospho S2, anti-RNA-Polymerase II CTD repeat YSPTSPS phospho S5, anti-p53, anti-SP1, and anti-ETS1 antibodies and Dynabeads Protein A or anti-mouse (Invitrogen) were used. Beads and antibodies were pre-incubated in blocking buffer (0.5% BSA in PBS) overnight at 4°C with shaking and washed three times in blocking buffer prior to IP. 100-200 µl sonicated lysate in lysis buffer 3 were used per IP and brought to 1 ml reaction volume by addition of IP buffer (100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1% Triton X-100 in 10 mM Tris-HCl, pH 8.0). In case of samples in ChIP-SDS-lysis buffer 100-200 µl sonicated lysate were diluted 1:10 in ChIP dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1 % (v/v) Triton X-100). The pre-incubated antibody/bead was added and samples were incubated overnight at 4°C with agitation. The next day beads were washed 3 x with IP buffer, 1 x in high salt wash buffer (500 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1% Triton X-100 in 10 mM Tris-HCl, pH 8.0), 1 x in RIPA buffer (500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate in 50 mM HEPES-KOH, pH 7.6) and 1 x in 50 mM NaCl in TE buffer. Protein-DNA complexes were eluted in 210 μl elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0) for 15 minutes at 65°C and supernatants were collected. Crosslinks reversal, RNAse A and proteinase K treatments and DNA purification were performed as described for the input samples.

treatment_protocol: non-treated cells were grown in 15-cm-diameter plates to 80% confluence

tag: cell type

value: human glioblastoma cells

tag: chip antibody

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody cat. #

source_name: input DNA_U251 cells


title: Biological replicate 3 of 3: mutant embryos E. tarda infected

value: The CR (common reference) was a mixture of all RNA samples from this microarray study. Separate CRs were made for the S. typhimurium, M. Marinum and E. tarda infection experiments

tag: tissue

value: embryo

tag: genetic background

value: Ab

source_name: Myd88 mutant Et 3

value: E. tarda


title: Biological replicate 1 of 3: control embryos E. tarda infected

source_name: Wildtype Et 1

value: Wildtype; injected with E. tarda into the caudal vein at 28 hpf; RNA isolated at 8 h post injection

value: wild type


title: AMC 62

tag: age at diagnosis

value: TZL

value: Low


title: glomeruli from Diabetic BKS  db/db mouse 2

source_name: glomeruli from Diabetic  mouse

value: glomeruli

value: Diabetic

value: BKS

tag: strain

value: BKS  db/db

value: 24 wk


title: ETS1_U251_rep2

description: Sample 25


title: AMC 63

tag: breed

value: Golden Retriever

value: F

value: MZL

tag: grade

value: B [b cell lymphoma]


title: ETS1_U251_rep1

description: Sample 24

value: human glioblastoma cells

value: Santa Cruz Biotechnology


title: glomeruli from Diabetic BKS db/db mouse 1

tag: disease state

value: BKS db/db


title: Biological replicate 3 of 3: control embryos PBS control for S. tarda

value: The CR (common reference) was a mixture of all RNA samples from this microarray study. Separate CRs were made for the S. typhimurium, M. Marinum and E. tarda infection experiments

value: embryo

value: Ab

source_name: Wildtype PBSet 3

value: Wildtype; mock-injected with buffer into the caudal vein at 28 hpf; RNA isolated at 8 h post injection

value: mock


title: Biological replicate 1 of 3: mutant embryos E. tarda infected

source_name: Myd88 mutant Et 1

value: MyD88 mutant; injected with E. tarda into the caudal vein at 28 hpf; RNA isolated at 8 h post injection

value: E. tarda

value: MyD88 mutant


title: SP1_U251_rep3

description: Sample 23

source_name: SP1 ChIP DNA_U251 cells

value: Upstate


title: AMC 68

source_name: NBNT

value: NBNT

value: Low

tag: phenotype

value: NBNT [non-T, non-B-cell lymphoma]


title: Biological replicate 1 of 3: control embryos PBS control for S. tarda

source_name: Wildtype PBSet 1

value: wild type


title: AMC 67

source_name: DLBCL

value: Rottweiler

value: F

value: DLBCL

value: High

value: B [b cell lymphoma]


title: AMC 40

value: Golden Retriever


title: SP1_U251_rep1

description: Sample 21

tag: cell line

value: human glioblastoma cells


title: glomeruli from non diabetic DBA mouse 14

source_name: glomeruli from nondiabetic littermate control mouse

value: glomeruli

value: non-diabetic

value: DBA


title: Biological replicate 3 of 3: mutant embryos PBS control for S. tarda

tag: sample type

value: The CR (common reference) was a mixture of all RNA samples from this microarray study. Separate CRs were made for the S. typhimurium, M. Marinum and E. tarda infection experiments

value: embryo

value: Ab

source_name: Myd88 mutant PBSet 3

value: MyD88 mutant; mock-injected with buffer into the caudal vein at 28 hpf; RNA isolated at 8 h post injection

value: mock


title: Biological replicate 2 of 3: control embryos PBS control for S. tarda

source_name: D. rerio myd88-experiment CR

source_name: Wildtype PBSet 2

value: Wildtype; mock-injected with buffer into the caudal vein at 28 hpf; RNA isolated at 8 h post injection

tag: infection


title: p53_U251_rep4

description: Sample 20

source_name: p53 ChIP DNA_U251 cells

value: Santa Cruz Biotechnology


title: AMC 43

source_name: MZL

value: Mastiff

value: MZL

value: Low


title: Biological replicate 2 of 3: mutant embryos PBS control for S. tarda

source_name: Myd88 mutant PBSet 2

tag: genotype

value: MyD88 mutant


title: AMC 36

source_name: TZL

tag: gender

value: M

value: TZL

value: T [T cell lymphoma]


title: p53_U251_rep2

description: Sample 18

tag: cell type

value: human glioblastoma cells

source_name: input DNA_U251 cells


title: Biological replicate 1 of 3: mutant embryos PBS control for S. tarda

source_name: Myd88 mutant PBSet 1


title: embryo of poor quality [E98_25]

description:
Sample name: E98_25
Raw data file: 74_1.txt

source_name: Cumulus cells

value: Cumulus cells

tag: oocyte developmental competence

value: E


title: p53_U251_rep3

description: Sample 19

tag: chip antibody

tag: chip antibody vendor


title: Biological replicate 2 of 3: control embryos S.typhimurium infected

value: The CR (common reference) was a mixture of all RNA samples from this microarray study. Separate CRs were made for the S. typhimurium, M. Marinum and E. tarda infection experiments

tag: tissue

source_name: Wildtype St 2

value: Wildtype; injected with S. typhimurium into the caudal vein at 28 hpf; RNA isolated at 8 h post injection

value: S. typhimurium

value: wild type


title: SP1_U251_rep2

description: Sample 22

value: Upstate

tag: chip antibody cat. #


title: AMC 35_1

tag: age at diagnosis

value: Labrador

value: F

value: DLBCL

value: High

value: B [b cell lymphoma]


title: embryo of poor quality [E97_38]

description:
Sample name: E97_38
Raw data file: 75_3.txt


title: AMC 75

source_name: LBT

value: Golden Retriever

value: LBT


title: Biological replicate 3 of 3: control embryos S.typhimurium infected

value: embryo

tag: genetic background

value: Ab

source_name: Wildtype St 3


title: AMC 25

tag: breed

value: M

value: TZL

value: Low

value: T [T cell lymphoma]


title: p53_U251_rep1

description: Sample 17

value: human glioblastoma cells

value: Santa Cruz Biotechnology


title: embryo of poor quality [E92_14]

description:
Sample name: E92_14
Raw data file: 72_3.txt

value: Cumulus cells

value: E


title: Biological replicate 1 of 3: control embryos S.typhimurium infected

value: The CR (common reference) was a mixture of all RNA samples from this microarray study. Separate CRs were made for the S. typhimurium, M. Marinum and E. tarda infection experiments

source_name: Wildtype St 1

value: Wildtype; injected with S. typhimurium into the caudal vein at 28 hpf; RNA isolated at 8 h post injection

value: S. typhimurium

value: wild type


title: AMC 35

value: Labrador

value: F

value: DLBCL

tag: grade

value: High

value: B [b cell lymphoma]


title: embryo of poor quality [E89_33]

description:
Sample name: E89_33
Raw data file: 75_1.txt


title: RNA-Pol-II-S2-P_p53-siRNA_rep2

description: Sample 15

source_name: RNA Pol II S2-P  ChIP DNA_p53-siRNA transfected U251 cells

treatment_protocol: cells were transfected with p53-siRNA using Oligofectamine (Invitrogen) and 96 hours later submitted to ChIP

tag: transfected with

value: RNA Pol II S2-P

value: Abcam

source_name: input DNA_p53-siRNA transfected U251 cells


title: embryo of poor quality [E74_37]

description:
Sample name: E74_37
Raw data file: 75_3.txt


title: Biological replicate 2 of 3: mutant embryos S.typhimurium infected

value: embryo

value: Ab

source_name: Myd88 mutant St 2

value: MyD88 mutant; injected with S. typhimurium into the caudal vein at 28 hpf; RNA isolated at 8 h post injection

value: MyD88 mutant


title: embryo of poor quality [E83_34]

description:
Sample name: E83_34
Raw data file: 75_1.txt

value: Cumulus cells


title: embryo of poor quality [E95_10]

description:
Sample name: E95_10
Raw data file: 72_1.txt

value: E


title: RNA-Pol-II-S5-P_p53-siRNA_rep2

description: Sample 16

source_name: RNA Pol II S5-P  ChIP DNA_p53-siRNA transfected U251 cells

value: human glioblastoma cells

value: RNA Pol II S5-P


title: H3K4me3_p53-siRNA_rep2

description: Sample 14

source_name: H3K4me3 ChIP DNA_p53-siRNA transfected U251 cells

value: ActiveMotif


title: AMC 71

source_name: DLBCL

value: Golden Retriever

value: M

tag: disease state

tag: phenotype


title: Biological replicate 3 of 3: mutant embryos S.typhimurium infected

source_name: D. rerio myd88-experiment CR

tag: sample type

value: The CR (common reference) was a mixture of all RNA samples from this microarray study. Separate CRs were made for the S. typhimurium, M. Marinum and E. tarda infection experiments

source_name: Myd88 mutant St 3

value: S. typhimurium


title: H3K9ac_p53-siRNA_rep2

description: Sample 13

source_name: H3K9ac ChIP DNA_p53-siRNA transfected U251 cells

tag: cell line

value: Millipore


title: embryo of poor quality [E68_9]

description:
Sample name: E68_9
Raw data file: 72_1.txt


title: AMC 74

value: DLBCL

value: High

value: B [b cell lymphoma]


title: Biological replicate 1 of 3: mutant embryos S.typhimurium infected

value: embryo

source_name: Myd88 mutant St 1

tag: infection

tag: genotype


title: AMC 70

source_name: BL

value: German Shepherd

tag: gender

value: F

value: BL


title: AMC 53

source_name: MZL

value: MZL

value: Low


title: RNA-Pol-II-S5-P_control-siRNA_rep2

description: Sample 12

source_name: RNA Pol II S5-P  ChIP DNA_control siRNA transfected U251 cells

treatment_protocol: cells were transfected with scrambled siRNA using Oligofectamine (Invitrogen) and 96 hours later submitted to ChIP

tag: cell type

value: human glioblastoma cells

value: scrambled control siRNA

value: Abcam

source_name: input DNA_control siRNA transfected U251 cells

value: control siRNA


title: RNA-Pol-II-S2-P_control-siRNA_rep2

description: Sample 11

source_name: RNA Pol II S2-P  ChIP DNA_control siRNA transfected U251 cells

tag: chip antibody

value: RNA Pol II S2-P


title: embryo of poor quality [E66_30]

description:
Sample name: E66_30
Raw data file: 74_3.txt

source_name: Cumulus cells

value: Cumulus cells

tag: oocyte developmental competence

value: E


title: Biological replicate 2 of 3: control embryos PBS control for S.typhimurium

value: The CR (common reference) was a mixture of all RNA samples from this microarray study. Separate CRs were made for the S. typhimurium, M. Marinum and E. tarda infection experiments

tag: tissue

value: Ab

source_name: Wildtype PBS 2

value: Wildtype; mock-injected with buffer into the caudal vein at 28 hpf; RNA isolated at 8 h post injection

value: mock

value: wild type


title: Biological replicate 3 of 3: control embryos PBS control for S.typhimurium

value: embryo

source_name: Wildtype PBS 3


title: AMC 77

value: Boxer

value: F

value: DLBCL

value: High

value: B [b cell lymphoma]


title: embryo of poor quality [E57_3]

description:
Sample name: E57_3
Raw data file: 71_2.txt


title: Biological replicate 3 of 3: mutant embryos PBS control for S.typhimurium

source_name: Myd88 mutant PBS 3

value: MyD88 mutant; mock-injected with buffer into the caudal vein at 28 hpf; RNA isolated at 8 h post injection

value: MyD88 mutant


title: H3K4me3_control-siRNA_rep2

description: Sample 10

source_name: H3K4me3 ChIP DNA_control siRNA transfected U251 cells

value: human glioblastoma cells

value: scrambled control siRNA

tag: chip antibody vendor

value: ActiveMotif

tag: chip antibody cat. #

value: control siRNA


title: AMC 26

tag: age at diagnosis

value: Golden Retriever

value: M


title: Biological replicate 2 of 3: mutant embryos PBS control for S.typhimurium

value: The CR (common reference) was a mixture of all RNA samples from this microarray study. Separate CRs were made for the S. typhimurium, M. Marinum and E. tarda infection experiments

tag: genetic background

value: Ab

source_name: Myd88 mutant PBS 2


title: Biological replicate 1 of 3: control embryos PBS control for S.typhimurium

source_name: Wildtype PBS 1

value: Wildtype; mock-injected with buffer into the caudal vein at 28 hpf; RNA isolated at 8 h post injection

value: mock

value: wild type


title: RNA-Pol-II-S5-P_p53-siRNA_rep1

description: Sample 8

source_name: RNA Pol II S5-P  ChIP DNA_p53-siRNA transfected U251 cells

value: RNA Pol II S5-P

value: Abcam

source_name: input DNA_p53-siRNA transfected U251 cells


title: RNA-Pol-II-S2-P_p53-siRNA_rep1

description: Sample 7

source_name: RNA Pol II S2-P  ChIP DNA_p53-siRNA transfected U251 cells

value: RNA Pol II S2-P


title: AMC 72

tag: breed

value: F

value: MZL

tag: grade

value: Low

value: B [b cell lymphoma]


title: H3K9ac_control-siRNA_rep2

description: Sample 9

source_name: H3K9ac ChIP DNA_control siRNA transfected U251 cells

value: human glioblastoma cells

tag: transfected with

value: scrambled control siRNA

value: Millipore


title: AMC 33

source_name: DLBCL

value: Rottweiler

tag: disease state

value: DLBCL

value: High

tag: phenotype


title: embryo of poor quality [E56_4]

description:
Sample name: E56_4
Raw data file: 71_2.txt

value: Cumulus cells

value: E


title: Biological replicate 1 of 3: mutant embryos PBS control for S.typhimurium

source_name: D. rerio myd88-experiment CR

tag: sample type

value: The CR (common reference) was a mixture of all RNA samples from this microarray study. Separate CRs were made for the S. typhimurium, M. Marinum and E. tarda infection experiments

value: embryo

value: Ab

source_name: Myd88 mutant PBS 1

value: MyD88 mutant; mock-injected with buffer into the caudal vein at 28 hpf; RNA isolated at 8 h post injection

value: mock

value: MyD88 mutant


title: embryo of poor quality [E49_23]

description:
Sample name: E49_23
Raw data file: 73_4.txt


title: embryo of poor quality [E53_20]

description:
Sample name: E53_20
Raw data file: 73_2.txt


title: embryo of poor quality [E24_29]

description:
Sample name: E24_29
Raw data file: 74_3.txt


title: embryo of poor quality [E30_26]

description:
Sample name: E30_26
Raw data file: 74_1.txt


title: H3K9ac_p53-siRNA_rep1

description: Sample 5

source_name: H3K9ac ChIP DNA_p53-siRNA transfected U251 cells

tag: cell line


title: RNA-Pol-II-S5-P_control-siRNA_rep1

description: Sample 4

source_name: RNA Pol II S5-P  ChIP DNA_control siRNA transfected U251 cells

value: RNA Pol II S5-P

value: Abcam

source_name: input DNA_control siRNA transfected U251 cells

value: control siRNA


title: embryo of poor quality [E16_24]

description:
Sample name: E16_24
Raw data file: 73_4.txt

source_name: Cumulus cells


title: blastocyst [B93_11]

description:
Sample name: B93_11
Raw data file: 72_2.txt

value: B


title: IMGUS_71

city: Heidelberg

first: Julia

last: Starmann

address: Im Neuenheimer Feld 460

department: Molecular Genetics

institute: German Cancer Research Center (DKFZ) and National Center for Tumor Diseases Heidelberg (NCT)

hyb_protocol: Hybridization is performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes. After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals are developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays are dried and scanned.

scan_protocol: Microarray scanning was done using a Beadstation array scanner, setting adjusted to a scaling factor of 1 and PMT settings at 430.

data_processing: Data processing was done using open source statistical tool lumi package from Bioconductor. Data extraction was done for all beads individually, and outliers are removed when > 2.5 MAD (median absolute deviation). All remaining data points are used for the calculation of the mean average signal for a given probe, and standard deviation for each probe was calculated. Finally data was transformed using quantile normalization.

label_protocol: Total RNA was prepared for hybridization on Illumina  human-6 v3 BeadChip arrays (Illumina) according to manufacturer’s recommendations. In brief, 300 ng/µl total RNA was used for cDNA synthesis, followed by the generation of biotin-labeled cRNA according to the MessageAmp II aRNA Amplification kit (Ambion).

growth_protocol: 44 human liver tissue surgical samples (normal n=13; steatosis n=19; steatohepatitis n=12, 8/2 cirrhotic/non-cirrhotic) obtained from patients undergoing liver surgery for HCC, other malignancy/metastatic disease, benign tumors of the liver and organ dedicated to transplantation. Virtually normal control samples in this cohort were taken from patients undergoing surgical resection of liver metastasis, but the surrounding liver tissue used for the molecular analyses was normal, non-tumorous liver tissue without detectable pathological changes. The samples were provided by the Biobank at the Medical University of Graz.

extract_protocol: Total RNA was isolated from the samples using TRI Reagent® (Molecular Research Center, Cincinnati, OH, USA) according to the manufacturer´s protocols. The RNA quality was analyzed using microcapillary electrophoresis (Agilent 2100 Bioanalyzer, Agilent Technologies, Böblingen, Germany). Only samples with RIN (RNA integrity number) of 5.0 or higher were subjected to gene expression array analysis.

treatment_protocol: No treatment

value: liver

tag: diagnosis

value: normal


title: embryo of poor quality [E20_19]

description:
Sample name: E20_19
Raw data file: 73_2.txt


title: IMGUS_70

value: steatosis


title: embryo of poor quality [E37_13]

description:
Sample name: E37_13
Raw data file: 72_3.txt


title: IMGUS_69


title: blastocyst [B99_18]

description:
Sample name: B99_18
Raw data file: 73_1.txt


title: RNA-Pol-II-S2-P_control-siRNA_rep1

description: Sample 3

source_name: RNA Pol II S2-P  ChIP DNA_control siRNA transfected U251 cells

value: human glioblastoma cells

value: scrambled control siRNA

value: RNA Pol II S2-P


title: H3K4me3_p53-siRNA_rep1

description: Sample 6

source_name: H3K4me3 ChIP DNA_p53-siRNA transfected U251 cells

value: ActiveMotif


title: blastocyst [B88_36]

description:
Sample name: B88_36
Raw data file: 75_2.txt

value: Cumulus cells


title: H3K4me3_control-siRNA_rep1

description: Sample 2


title: IMGUS_68


title: XY23

source_name: NPC biopsy

extract_protocol: 8 micron cryosections were transferred onto PALM membrane slides (P.A.L.M. Microlaser Technologies) and air dried on ice for about 1 minute. Slides were immersed for 2 minutes in cold 75% ethanol, tapped dry and stained for 30 seconds in cold haematoxylin and eosin (9:1) containing 1% NucleoGuard (AmpTec, Hamburg). Excess stain was tapped off and slides were washed in cold nuclease-free water for 30 seconds, cold 75% ethanol for 1 minute, cold 100% ethanol for 1 minute then air dried.  Tumour cells for analysis were excised by laser microdissection and pressure catapulting using a PALM MicroBeam instrument and caught on PALM Adhesive Caps. A minimum of 200,000 µm2 of tissue was collected for each DNA extraction. DNA was extracted from microdissected cells by adding 100 µl of lysis buffer (10mM Tris-HCl, pH 8.0, 1mM EDTA, 1% Tween 20, 0.4 mg/ml proteinase K (Qiagen)) to the tube containing the captured cells and incubating inverted for 3hr at 55OC then 5min at 95 OC. 2 µl of linear polyacrylamide solution (GenElute, Sigma) were added and DNA was recovered by ethanol precipitation. The pellet was washed with 70% ethanol and air dried. The precipitated DNA was subject to whole genome amplification using a Genomiphi kit (GE Healthcare) according to the manufacturer’s instructions.

value: nasopharyngeal carcinoma


title: H3K9ac_control-siRNA_rep1

description: Sample 1

value: Millipore


title: IMGUS_66


title: IMGUS_72


title: IMGUS_67


title: blastocyst [B87_35]

description:
Sample name: B87_35
Raw data file: 75_2.txt


title: XY16


title: MOUZ


title: XY8


title: blastocyst [B83_32]

description:
Sample name: B83_32
Raw data file: 74_4.txt


title: XY6


title: blastocyst [B79_17]

description:
Sample name: B79_17
Raw data file: 73_1.txt


title: IMGUS_49


title: blastocyst [B67_21]

description:
Sample name: B67_21
Raw data file: 73_3.txt


title: IMGUS_46


title: XY5


title: IMGUS_63


title: blastocyst [B64_1]

description:
Sample name: B64_1
Raw data file: 71_1.txt


title: blastocyst [B76_31]

description:
Sample name: B76_31
Raw data file: 74_4.txt


title: blastocyst [B63_5]

description:
Sample name: B63_5
Raw data file: 71_3.txt


title: IMGUS_39


title: IMGUS_38


title: MMAH


title: MKAV


title: blastocyst [B50_12]

description:
Sample name: B50_12
Raw data file: 72_2.txt


title: IMGUS_60


title: AMC 49

source_name: LBT

value: Labrador

tag: gender

value: F

value: LBT

value: High

value: T [T cell lymphoma]


title: blastocyst [B60_2]

description:
Sample name: B60_2
Raw data file: 71_1.txt

tag: cell type


title: blastocyst [B53_28]

description:
Sample name: B53_28
Raw data file: 74_2.txt


title: HKC2


title: HKD1


title: blastocyst [B47_22]

description:
Sample name: B47_22
Raw data file: 73_3.txt


title: IMGUS_61


title: MKEC


title: HKC1


title: MDIG


title: blastocyst [B61_6]

description:
Sample name: B61_6
Raw data file: 71_3.txt


title: blastocyst [B40_27]

description:
Sample name: B40_27
Raw data file: 74_2.txt


title: IMGUS_55


title: IMGUS_40


title: blastocyst [B101_39]

description:
Sample name: B101_39
Raw data file: 75_4.txt


title: blastocyst [B100_40]

description:
Sample name: B100_40
Raw data file: 75_4.txt


title: IMGUS_58


title: blastocyst [B96-80]

description:
Sample name: B96-80
Raw data file: 23_4.txt


title: MDA-MB-231-10-30 B

city: Houston

first: Xiang

last: Zhang

state: TX

address: One Baylor Plaza, BCM600

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

description: Affymetrix U133A_2

hyb_protocol: 10 ug cRNA hybridized using standard Affymetrix protocol

scan_protocol: Gene chip scanned using the Hewlett-Packard GeneArray Scanner G2500A

data_processing: Data normalized by RMA algorithm implemented by the Affy package of R program

source_name: MDA-MB-231 cell subpopulations in vitro

label_protocol: Biotin labeling with standard Affymetrix protocol

growth_protocol: DMEM regular medium + 0.2% serum, monolayer growth in plastic dishes

extract_protocol: Total RNA extracted using Dynabeads® mRNA Purification Kit with manufacturer's recommended protocol

treatment_protocol: With or without CXCL12 and IGF1 treatment (30 ng/ml and 10 ng/ml, respectively). Treatment last for 3 weeks.

value: MDA-MB-231 cell subpopulations in vitro

tag: treatment

value: Treated with IGF1 (10 ng/ml) and CXCL12 (30 ng/ml)


title: IMGUS_59

value: liver


title: IMGUS_29


title: IMGUS_30


title: IMGUS_50

value: normal


title: blastocyst [B87-80]

description:
Sample name: B87-80
Raw data file: 23_4.txt

tag: oocyte developmental competence

value: B


title: HK4


title: HK6


title: IMGUS_28

tag: tissue

value: steatosis


title: 1836

source_name: blood from normal individual

extract_protocol: Genomic DNA was extracted using Qiagen QIAamp blood kit.

value: normal control


title: embryo of poor quality [E95-80]

description:
Sample name: E95-80
Raw data file: 23_3.txt

extract_protocol: Total RNA  extraction  was  carried  out  using  the  Rneasy Micro Kit (Qiagen).  A DNase  step  was included  in  the  extraction  protocol  to  remove  residual  genomic  DNA  contamination.

value: E


title: MDA-MB-231-10-30 A

description: Affymetrix U133A_2


title: blastocyst [B88]

description:
Sample name: B88
Raw data file: 23_2.txt


title: IMGUS_62


title: IMGUS_27


title: IMGUS_25


title: blastocyst [B13b]

description:
Sample name: B13b
Raw data file: 23_3.txt


title: embryo of poor quality [E71-50]

description:
Sample name: E71-50
Raw data file: 23_2.txt


title: 1834


title: C666

source_name: NPC cell line

extract_protocol: DNA was extracted from C666-1 cells using a DNeasy kit (Qiagen) according to the manufacturer’s instructions.


title: MDA-MB-231-0-0 B

description: Affymetrix U133A_2

value: No IGF1 and CXCL12 treatment


title: Linalool_rep4

city: miki

first: kenji

last: gomi

state: kagawa

country: Japan

institute: Kagawa University

description: gene expression after 24 hr in linalool-treated rice leaf blades

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rice Oligo Microarrays for 17 hours at 65 ºC 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 ºC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides.

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

organism: Oryza sativa Japonica Group

source_name: Rice leaf blades treated with 10 μM linalool, replicate4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using an Agilent Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: Rice plants were grown from seed in growthchamber [25 ºC, 60 - 80% relative humidity (RH)].

extract_protocol: Total RNA from rice was extracted from leaf blades after each treatment using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Five-leaf-stage rice plants were treated with 10μM linalool for 1 day at 25 ºC.

tag: cultivar

value: Hinohikari

tag: leaf-stage

value: five-leaf

value: fifth-leaf blade

value: 10 μM linalool


title: MDA-MB-231-0-0 A

description: Affymetrix U133A_2


title: blastocyst [B100]

description:
Sample name: B100
Raw data file: 23_1.txt

value: Cumulus cells


title: Amp_C666

value: nasopharyngeal carcinoma


title: Linalool_rep3

source_name: Rice leaf blades treated with 10 μM linalool, replicate3


title: IMGUS_26


title: IMGUS_23


title: IMGUS_22


title: blastocyst [B87-65]

description:
Sample name: B87-65
Raw data file: 23_1.txt


title: embryo of poor quality [E39b]

description:
Sample name: E39b
Raw data file: 22_4.txt


title: embryo of poor quality [E71-80]

description:
Sample name: E71-80
Raw data file: 22_3.txt


title: blastocyst [B96-65]

description:
Sample name: B96-65
Raw data file: 22_3.txt


title: embryo of poor quality [E95-65]

description:
Sample name: E95-65
Raw data file: 22_4.txt


title: Linalool_rep2

source_name: Rice leaf blades treated with 10 μM linalool, replicate2


title: 1635


title: embryo of poor quality [E92]

description:
Sample name: E92
Raw data file: 22_2.txt


title: Mock_rep4

description: gene expression after 24 hr in mock-treated rice leaf blades

source_name: Rice leaf blades without treatment, replicate4


title: Linalool_rep1

source_name: Rice leaf blades treated with 10 μM linalool, replicate1


title: IMGUS_15

value: steatohepatitis


title: 1680


title: IMGUS_19


title: blastocyst [B61]

description:
Sample name: B61
Raw data file: 22_1.txt


title: IMGUS_9


title: 1906


title: IMGUS_8


title: IMGUS_17


title: embryo of poor quality [E38b]

description:
Sample name: E38b
Raw data file: 22_2.txt


title: Mock_rep1

source_name: Rice leaf blades without treatment, replicate1


title: Mock_rep2

source_name: Rice leaf blades without treatment, replicate2


title: Mock_rep3

source_name: Rice leaf blades without treatment, replicate3