title: Trolox3

city: Nijmegen

first: Werner

last: Koopman

state: GLD

address: Geert Grooteplein 26-28

department: 286 Biochemistry

institute: Radboud University Nijmegen Medical Centre

description: Cells culture in the presence of Trolox (0.5 mM, 96 hours)

hyb_protocol: 17 hours at 45 degrees in Affymetrix hybridization oven at 60 rpm,washing and staining in  Fluidics station 450 using stain cocktails: SAPE and antibody solution, (protocol FS450_0001)

scan_protocol: GeneChip scanner 3000 7G

data_processing:
Quantile normalization, with RMA, GC correction and median polish, log2 values from Partek Genomic Suite 6.5
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: 5120-C cells

label_protocol: GeneChip WT Terminal Labeling Kit

growth_protocol: Cells were cultured as described in: Distelmaier et al., Cytometry A 73A:129-138, 2008

extract_protocol: Rneasy column purification

treatment_protocol: Cells were treated with vehicle or Trolox as described in: Koopman et al., Biochim. Biophys. Acta 1777:853-859, 2008

value: 5120-C primary human skin fibroblasts

value: TROLOX


title: Wildtype strain grown in glucose, rep 1

status: Public on Jul 15 2012

type: RNA

city: Ottawa

first: Linda

middle: J

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

country: Canada

institute: Agriculture & Agri-Food Canada (AAFC)

description: Gene expression in wild-type yeast grown in glucose

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Custom Yeast Oligo Microarrays (G2509F) for 17 hours at 65°C in a rotating Robbins Model 400 hybridization oven (Robbins Scientific) and an Agilent Rotator Rack. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then a 10 seconds Acetonitrile Wash (Agilent) followed by a 30 seconds Stabilization and Drying Solution wash (Agilent).

scan_protocol: Slides were scanned immediately after washing using a GenePix 4200A (Molecular Devices) using only the cy3 channel, scanning each each array individually (scan area 2088 x 3112 pixels). Scan resolution 10 µm, lines to average= 1, focus position 0µm. Laser set at 100% and PMT between 330 and 370 according to strength of the individual array.

data_processing: The scanned images were analyzed with GenePix 6.0 (Molecular Devices) using default parameters to obtain background subtracted. To generate the normalized data, we have performed a global median intensity standardization manually to correct for position and scale for the arrays. Features flagged in GenePix as absent or non-uniform outliers were excluded.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: wild type yeast, no treatment

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis Protocol version 5.7 (Agilent) according to the manufacturer's instructions, except using half of the reagents amount in step 2, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Overnight cultures were diluted to 0.05 at OD 600nm in fresh YPD or YEP-Xylose and incubated at 30ºC to an optical density of 0.6 (OD600nm).

extract_protocol: Total RNA was extracted from yeast cells using TRI reagent (Sigma) as per the manufacturers protocol, followed by RNAeasy column purification (QIAGEN, Valencia, CA). The RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were grown in either 2% YEP-Glucose or YEP-Xylose till at mid-log phase

tag: strain


title: P.falciparum 3D7_schizonts_control_TP1_30mins post treatment

city: Singapore

first: Ramya

last: Ramadoss

address: 60 Nanyang Drive, 04n-18, School of Biological Sciences

country: Singapore

institute: Nanyang Technological University, School of Biological Sciences

hyb_protocol: Microarray hybridizations were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Scanning as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

data_processing: Data processing as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, Normalization and subsequent filtering for quality control were carried out using NOMAD database (http://derisilab.ucsf.edu). Spots were considered of good quality when they were unflagged and had a median intensity greater than the local background plus 2 times the standard deviation of the background for each dye channel. The values presented in the sample data represent log2-transformed ratios of the measurement in the sample channel (Cy5) divided by the corresponding measurement in the reference channel (Cy3, P. falciparum RNA reference pool).

organism: Plasmodium falciparum 3D7

source_name: P.falciparum 3d7 strain (in-vitro) untreated_control

label_protocol: Labeling carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.

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

value: lab strain 3d7

tag: culture type

value: in-vitro culture

tag: time point

tag: time post-treatment

source_name: P. falciparum 3d7 RNA reference pool

value: Lab Strain 3D7

tag: sample type

value: mix of several samples collected across the 48-hour intraerythrocytic life cycle


title: Female-SPI+E2-fed-pool3

city: Little rock

first: Kartik

last: Shankar

state: AR

address: 1120 Marshall Street, Slot 512-20B

department: Pharmacology and Toxicology

country: USA

institute: University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center

description: osteogenic  gene expression

hyb_protocol: Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94C. aRNAs were hybridized to an individual Affymetrix GeneChip Porcine arrays (N = 3/treatment) for 16 h at 45C in the hybridization oven set at 60 rpm.

scan_protocol: The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.

data_processing: CEL files were generated using GCOS and utilized for analysis using GeneSpring Gx v 7.3. RMA normalization was utilized to generated values using GeneSpring v 7.3.

label: biotin

organism: Rattus norvegicus

label_protocol: First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA  reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions

growth_protocol: Female casein control diet fed rats compared rats fed control diet with 17 beta estrodial, soy protein isolate diet and combination of 17 beta estrodial with soy protein isolate from PND21 to PND34

extract_protocol: Total bone RNA was isolated from the casein diet control, control diet with 17 beta estrodial, soy protein isolate and combination 17 beta estrodial with soy protein isolate fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion

treatment_protocol: Bone tissues after aspiration of bone marrow were collected from rats at sacrifice and flash frozen in liquid nitrogen

tag: gender

value: female

tag: age

value: postnatal day 34

tag: tissue

value: bone

tag: diet

value: combination of 17 beta estrodial with soy protein isolate (SPI+E2)


title: Female-SPI+E2-fed-pool2

description: osteogenic  gene expression


title: Wildtype strain grown in glucose, rep 3


title: Female-SPI+E2-fed-pool1

description: osteogenic gene expression


title: Trolox2

country: Netherlands

organism: Homo sapiens

tag: cell line

tag: treatment


title: Trolox1


title: Calcium ionophore_A23187 treatment/Timepoint 2_1 hour post treatment

type: genomic

data_processing: Data processing as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, Normalization and subsequent filtering for quality control were carried out using NOMAD database (http://derisilab.ucsf.edu). Spots were considered of good quality when they were unflagged and had a median intensity greater than the local background plus 2 times the standard deviation of the background for each dye channel. The values presented in the sample data represent log2-transformed ratios of the measurement in the sample channel (Cy3) divided by the corresponding measurement in the reference channel (Cy5, Untreated P. falciparum parasites).

molecule: genomic DNA

organism: Plasmodium falciparum

source_name: P. falciparum parasites (in-vitro) treated with A23187

extract_protocol: Total genomic DNA extracted using phenol-chlorofom method as previously described : Mackinnon, M.J. et al. Comparative transcriptional and genomic analysis of Plasmodium falciparum field isolates. PLoS Pathog 5, e1000644 (2009)

value: lab strain DD2

value: 1 hr

source_name: Untreated P. falciparum parasites (in-vitro)


title: Calcium ionophore_ionomycin treatment/Timepoint 2_1 hour post treatment

source_name: P. falciparum parasites (in-vitro) treated with ionomycin


title: Female-E2-fed-pool2

description: osteogenic  gene expression

value: 17 beta estrodial (E2)


title: Calcium ionophore_ionomycin treatment/Timepoint 4_4 hour post treatment

value: 4 hr


title: Vehicle1

description: Cells culture in the presence of vehicle DMSO (96 hours)

value: DMSO


title: Female-E2-fed-pool1

description: osteogenic  gene expression


title: Vehicle2


title: Female-SPI-fed-pool3

description: osteogenic  gene expression

source_name: Female-SPI-fed

value: soy protein isolate (SPI)


title: Female-E2-fed-pool3

description: osteogenic  gene expression


title: Female-CAS-fed-pool3

description: osteogenic gene expression

source_name: Female-CAS-fed

value: casein diet control (CAS)


title: Female-SPI-fed-pool1

description: osteogenic  gene expression


title: Female-CAS-fed-pool2

description: osteogenic  gene expression


title: Vehicle3

value: 5120-C primary human skin fibroblasts


title: Female-SPI-fed-pool2

description: osteogenic  gene expression


title: Female-CAS-fed-pool1

description: osteogenic gene expression


title: MDA-MB-435-Parental_1_Rep 1

status: Public on Jul 14 2012

city: Guangzhou

first: Mengfeng

last: Li

state: Guangdong

address: 74# zhongshan 2 Rd.

department: Zhongshan school of medicine

country: China

institute: Sun Yat-sen University

description: MDA-MB-435 primary cells cultured from parental tumor explants within No.1 mouse replicate 1, after 30 days inoculation.

hyb_protocol: Hybridization was performed by the Shanghai Biochip Corporation (http://www.shbiochip.com/) following the standard Agilent protocol.

scan_protocol: Scanning was performed by the Shanghai Biochip Corporation (http://www.shbiochip.com/) following the standard Agilent protocol.

data_processing: Data normalization and transformation were performed using GeneSpring GX 11 (Agilent) by the Shanghai Biochip Corporation.

source_name: parental MDA-MB-435 from No.1 mouse primary explants

label_protocol: Labeling was performed by the Shanghai Biochip Corporation (http://www.shbiochip.com/) following the standard Agilent protocol.

growth_protocol: The MDA-MB-435 breast cancer cells were cultured in complete DMEM medium and supplied with 10% FBS.

extract_protocol: Total RNA was isolated using mirVanaTM miRNA isolation kit (Ambion, Austin, TX) following supplier’s protocol.

treatment_protocol: MDA-MB-435 cells were injected into the mammary fat pads of BALB/C nude mice. After 30 days, the animals were sacrificed, pulmonary metastatic nodules were isolated and minced, and cell culture was established using the obtained explants.

tag: cell type

value: parental cells cultured from primary explant


title: MDA-MB-435-metastasis_1_Rep 1

description: MDA-MB-435 primary cells cultured from pulmonary metastatic nodules within No.1 mouse replicate 1, after 30 days inoculation.

source_name: metastatic MDA-MB-435 from No.1 mouse pulmonary metastatic nodules

value: metastatic cells cultured from pulmonary metastatic nodules


title: MDA-MB-435-Parental_2_Rep 2

description: MDA-MB-435 primary cells cultured from parental tumor explants within No.2 mouse replicate 2, after 30 days inoculation.

source_name: parental MDA-MB-435 from No.2 mouse primary explants


title: MDA-MB-435-metastasis_2_Rep 1

description: MDA-MB-435 primary cells cultured from pulmonary metastatic nodules within No.2 mouse replicate 1, after 30 days inoculation.

source_name: metastatic MDA-MB-435 from No.2 mouse pulmonary metastatic nodules


title: MDA-MB-435-metastasis_1_Rep 2

description: MDA-MB-435 primary cells cultured from pulmonary metastatic nodules within No.1 mouse replicate 2, after 30 days inoculation.


title: MDA-MB-435-Parental_2_Rep 1

description: MDA-MB-435 primary cells cultured from parental tumor explants within No.2 mouse replicate 1, after 30 days inoculation.


title: MDA-MB-435-metastasis_2_Rep 2

description: MDA-MB-435 primary cells cultured from pulmonary metastatic nodules within No.2 mouse replicate 2, after 30 days inoculation.


title: MDA-MB-435-Parental_1_Rep 2

description: MDA-MB-435 primary cells cultured from parental tumor explants within No.1 mouse replicate 2, after 30 days inoculation.


title: P.falciparum 3D7_schizonts_extracellular calcium chelation _EGTA+Ionomycin Treatment_TP2_1hr

source_name: P.falciparum 3d7 strain (in-vitro) treated with EGTA+ionomycin

value: lab strain 3d7

value: in-vitro culture


title: adult on TG section, biological rep2

city: Kuopio

first: Antti

middle: Juhani

last: Kurronen

address: Neulaniementie 2

department: A.I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

description:
A_TG_2.CEL
Gene expression data from adult mouse eGFP astrocytes after 22 h incubation on APdE9-transgenic mouse brain section

hyb_protocol: cRNA were hybridized on GeneChip Mouse Genome 430 2.0 array with 2-Cycle method following the manufacturer's protocol at Biomedicum Genomics (BMGen), Finland.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner following the manufacturer's protocol at Biomedicum Genomics (BMGen), Finland.

data_processing: The data were analyzed with GeneSpring GX 11.0 and was preprocessed with the robust multichip algorithm (RMA), normalized per chip to the median.

organism: Mus musculus

source_name: adult mouse astrocytes on tg APdE9 brain section

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

growth_protocol: For the adult astrocyte cultures, hippocampi and cortices were isolated from 6-8-week-old C57Bl/6j  wild-type and tg eGFP mice and the tissue was suspended in DMEM/F12 (3:1, Gibco BRL, NY, USA) containing 10 % heat-inactivated fetal bovine serum (Gibco BRL) and 100 U / ml penicillin-streptomycin (Gibco BRL). The cells were treated with Percoll (Sigma-Aldrich, St.Louis, USA) and plated onto poly-L-lysine coated flasks in DMEM/F12 (3:1) containing 10 % heat-inactivated fetal bovine serum, 100 U / ml penicillin-streptomycin and G5 supplement (Gibco BRL). Before the experiments the glial cell cultures were shaken to remove microglia at 200 rpm for 2 h. For the neonatal astrocyte cultures, hippocampi and cortices were isolated from 2-day-old wild-type and eGFP mice according to the protocol described above, except that the culture medium was DMEM (+4500mg/l glucose, + L-glutamine, -pyruvate, Gibco BRL) without G5 supplement and the isolation method included no Percoll treatment. Standard anti-GFAP (1:500; Dako Cytomation, Glostrup, Denmark) immunocytochemistry was used to determine the purity of astrocyte cultures. The cells were  incubated with biotinylated goat anti-rabbit IgG (1:200 dilution; Vector Laboratories, CA) secondary antibody and Vectastain ABC Elite kit was used (Vector Laboratories) according to manufacturer’s protocol.  Hydroxen peroxide (H2O2) and nickel enhanced diaminobenzidine (Ni-DAB) was added to detect the immunoreactivity. Three fields per well and at least three wells per cell type were analyzed for the percentage of Ni-DAB stained cells of all cellular profiles in the field. Adult and neonatal astrocyte cultures both contained on average 99.6 % ± 0.6 % anti-GFAP immunoreactive astrocytes. Anti-Iba (2 µg/ml; Wako, Germany) and anti-CD11b (1:500 dilution; Serotec, UK) antibodies were used to detect possible microglial cells. The cultures contained less than 0.4 % of microglial cells in all experiments.

extract_protocol: RibopureTM Kit (Ambion, Applied Biosystems, USA) was used for the total mRNA isolation according to the manufacturer’s instructions.

treatment_protocol: Tg APdE9 / wild-type mouse brain section incubated with neonatal (age 3 d) or adult (age 6-8 wks) mouse eGFP expressing astrocytes (4 x 105 cells / well), n=6. The mouse brain sections used were prepared from tg APdE9 mouse line (created by co-injection of chimeric mouse/human APPSwe and PS1-dE9 vectors, both controlled by their own mouse prion protein promoter element [APdE9 mice (Jankowsky et al. 2004) provided by Prof. Heikki Tanila] and their wild type C57Bl/6j littermates. Before the mRNA isolation process, the samples were pooled (n=3). The purity of the samples was checked with FACS (FACSCalibur, Becton Dickinson, USA) using the analyzing program CellQuestTM version 3.3 (Becton Dickinson, USA). After 22 h incubation the culture medium was removed from the wells and the brain sections with cultured eGFP astrocytes were incubated with 1 x trypsin-EDTA (500 µl /well) for up to 15 min at 37° C.  Partial detachment (at this point, the astrocytes should not lose the grip completely) of the astrocytes from the underlying brain section was monitored with a standard light microscope. After the incubation the brain sections with cultured astrocytes were carefully removed into small petri dishes filled with FBS-containing culture medium to inactivate the trypsin.  Subsequently, the brain sections were immediately examined with fluorescence microscope (Olympus IX-71, Japan). The eGFP astrocytes were separated from the underlying brain section using a special suction hose, which was a modified version from suction hoses typically used for the microinjection techniques. In the other end of the tube there is a pipet tip as a mouthpiece, in the middle of the tube a 0.22 µm filter and in the other end a stretched glass capillary (prepared with a Bunsen burner). The green fluorescent eGFP astrocytes were picked up gently from the underlying brain section (without breaking the brain tissue) using wavelength 468 nm of the fluorescence microscope and simultaneous light microscopy.

tag: developmental stage

value: adult

value: 6-8 wks

value: astrocyte

tag: incubation on brain section

value: APdE9-transgenic (TG)


title: adult on WT section, biological rep3

description:
A_WT_3.CEL
Gene expression data from adult mouse eGFP astrocytes after 22 h incubation on wild-type mouse brain section

source_name: adult mouse astrocytes on wt brain section

value: Wild type (WT)


title: adult on WT section, biological rep2

description:
A_WT_2.CEL
Gene expression data from adult mouse eGFP astrocytes after 22 h incubation on wild-type mouse brain section


title: adult on TG section, biological rep3

description:
A_TG_3.CEL
Gene expression data from adult mouse eGFP astrocytes after 22 h incubation on APdE9-transgenic mouse brain section


title: neonatal on TG section, biological rep3

description:
nn_TG_3.CEL
Gene expression data from neonatal mouse eGFP astrocytes after 22 h incubation on APdE9-transgenic mouse brain section

source_name: neonatal mouse astrocytes on tg APdE9 brain section

value: neonatal

value: 3 d


title: neonatal on TG section, biological rep1

description:
nn_TG_1.CEL
Gene expression data from neonatal mouse eGFP astrocytes after 22 h incubation on APdE9-transgenic mouse brain section


title: neonatal on WT section, biological rep1

description:
nn_WT_1.CEL
Gene expression data from neonatal mouse eGFP astrocytes after 22 h incubation on wild-type mouse brain section

source_name: neonatal mouse astrocytes on wt brain section


title: adult on TG section, biological rep1

description:
A_TG_1.CEL
Gene expression data from adult mouse eGFP astrocytes after 22 h incubation on APdE9-transgenic mouse brain section


title: adult on WT section, biological rep1

description:
A_WT_1.CEL
Gene expression data from adult mouse eGFP astrocytes after 22 h incubation on wild-type mouse brain section


title: neonatal on WT section, biological rep2

description:
nn_WT_2.CEL
Gene expression data from neonatal mouse eGFP astrocytes after 22 h incubation on wild-type mouse brain section


title: v-myb-L34A-HAER, biological rep3

city: Prague

first: Vladimir

last: Cermak

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics, Czech Academy of Sciences

description: Gene expression data from chicken neural crest cells expressing v-Myb-L3,4A-HAER.

hyb_protocol: Fragmented and labelled aRNA (12,5 ug) was hybridized for 16 hr at 45°C on GeneChip Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite (version 6.4) using Affymetrix default annotation and GC-RMA as normalization method.

organism: Gallus gallus

source_name: Chicken neural crest cells expressing v-Myb-L3,4A-HAER

label_protocol: Biotinylated aRNA was prepared from 100 ng total RNA according to GeneChip 3'IVT Express Kit manual

growth_protocol: Chicken embryo neural tubes (stage 10-13 hh) were explanted on collagen coated dishes in a medium containing retroviral particles. After 3 days the explant mass was removed and only cells emigrated from explants were left for further cultivation.

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

treatment_protocol: 200 nM 4-OH-tamoxifen for 4 hours

tag: genetic background

value: Brown Leghorn

tag: transfection


title: TesticularTissue_4mg.kg.day_dinitrobenzene_rat1

city: Sophia Antipolis

first: Sophie

last: Ludwig

address: 355 Rue Dostoievski BP 153

department: Toxicology Research

country: France

institute: Bayer Cropscience

description:
ST4M3823
Gene expression in testes of rat treated 4 days with 4 mg/kg/day dinitrobenzene.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >15.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55µL of 2x GEx Hybridization Buffer HI-RPM was then added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4131F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) , 1 minute with 37°C GE Wash buffer 2 (Agilent), 10 seconds with acetonitrile and 30 seconds with Stabilization and Drying Solution, and then dried immediately.

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

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.1.1  (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014879_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.
Ratio (treated/control) calculations and extraction of differentially expressed genes (probes) were then performed using GeneSpring software version 10.0.2 (Agilent Technologies). For normalization per array, the 75th percentile of the signal values taken from each microarray was used as the normalizing reference. Per gene normalization was based on calculating fold expression levels relative to the median of the control animals.

source_name: Testicular tissue, 4 mg/kg/day dinitrobenzene

label_protocol: Labeled cRNA targets were prepared using a Low RNA Input Linear Amplification Kit according to the One-Color Microarray-Based Gene Expression Analysis protocol provided by the manufacturer (Agilent Technologies). The resulting labeled cRNAs were purified using an RNeasy Mini Kit to remove unlabeled products and quantified by absorbance at 260nm. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from individual control and treated testicular samples using RNeasy Mini kits (Qiagen, CA) in accordance with the manufacturer's instructions.

treatment_protocol: Dinitrobenzene was administered to rats at a daily dose of 0, 0.1, 1, and 4 mg/kg body weight, for 4 consecutive days. At necropsy, testes were excised from each rat, and trimmed free of fat and connective tissue. Left testis was then decapsulated, and flash-frozen in liquid nitrogen prior to storing at -80°C until transcriptomic analyses.

value: Wistar

value: male

value: 7-8 weeks

value: testis

value: dinitrobenzene

tag: dinitrobenzene dosage

value: 4 mg/kg/day


title: neonatal on TG section, biological rep2

description:
nn_TG_2.CEL
Gene expression data from neonatal mouse eGFP astrocytes after 22 h incubation on APdE9-transgenic mouse brain section

tag: strain


title: v-myb-L34A-HAER, biological rep2

value: Chicken neural crest cells expressing v-Myb-L3,4A-HAER


title: v-myb-L34A-N118D-HAER, biological rep3

description: Gene expression data from chicken neural crest cells expressing v-Myb-L3,4A-N118D-HAER.

source_name: Chicken neural crest cells expressing v-Myb-L3,4A-N118D-HAER


title: TesticularTissue_1mg.kg.day_dinitrobenzene_rat9

description:
ST3M3821
Gene expression in testes of rat treated 4 days with 1 mg/kg/day dinitrobenzene.

source_name: Testicular tissue, 1 mg/kg/day dinitrobenzene

value: 1 mg/kg/day


title: TesticularTissue_1mg.kg.day_dinitrobenzene_rat8

description:
ST3M3815
Gene expression in testes of rat treated 4 days with 1 mg/kg/day dinitrobenzene.


title: TesticularTissue_4mg.kg.day_dinitrobenzene_rat5

description:
ST4M3828
Gene expression in testes of rat treated 4 days with 4 mg/kg/day dinitrobenzene.


title: neonatal on WT section, biological rep3

description:
nn_WT_3.CEL
Gene expression data from neonatal mouse eGFP astrocytes after 22 h incubation on wild-type mouse brain section


title: TesticularTissue_4mg.kg.day_dinitrobenzene_rat9

description:
ST4M3837
Gene expression in testes of rat treated 4 days with 4 mg/kg/day dinitrobenzene.


title: TesticularTissue_4mg.kg.day_dinitrobenzene_rat7

description:
ST4M3835
Gene expression in testes of rat treated 4 days with 4 mg/kg/day dinitrobenzene.


title: TesticularTissue_4mg.kg.day_dinitrobenzene_rat4

description:
ST4M3826
Gene expression in testes of rat treated 4 days with 4 mg/kg/day dinitrobenzene.


title: TesticularTissue_4mg.kg.day_dinitrobenzene_rat2

description:
ST4M3824
Gene expression in testes of rat treated 4 days with 4 mg/kg/day dinitrobenzene.


title: v-myb-L34A-N118D-HAER, biological rep2

value: Chicken neural crest cells expressing v-Myb-L3,4A-N118D-HAER


title: TesticularTissue_4mg.kg.day_dinitrobenzene_rat6

description:
ST4M3829
Gene expression in testes of rat treated 4 days with 4 mg/kg/day dinitrobenzene.


title: v-myb-L34A-HAER, biological rep1


title: v-myb-L34A-N118D-HAER, biological rep1


title: TesticularTissue_1mg.kg.day_dinitrobenzene_rat5

description:
ST3M3812
Gene expression in testes of rat treated 4 days with 1 mg/kg/day dinitrobenzene.


title: TesticularTissue_4mg.kg.day_dinitrobenzene_rat8

description:
ST4M3836
Gene expression in testes of rat treated 4 days with 4 mg/kg/day dinitrobenzene.


title: TesticularTissue_1mg.kg.day_dinitrobenzene_rat10

description:
ST3M3822
Gene expression in testes of rat treated 4 days with 1 mg/kg/day dinitrobenzene.


title: TesticularTissue_4mg.kg.day_dinitrobenzene_rat3

description:
ST4M3825
Gene expression in testes of rat treated 4 days with 4 mg/kg/day dinitrobenzene.


title: TesticularTissue_1mg.kg.day_dinitrobenzene_rat7

description:
ST3M3814
Gene expression in testes of rat treated 4 days with 1 mg/kg/day dinitrobenzene.


title: TesticularTissue_1mg.kg.day_dinitrobenzene_rat4

description:
ST3M3811
Gene expression in testes of rat treated 4 days with 1 mg/kg/day dinitrobenzene.


title: TesticularTissue_1mg.kg.day_dinitrobenzene_rat6

description:
ST3M3813
Gene expression in testes of rat treated 4 days with 1 mg/kg/day dinitrobenzene.


title: Mycelia ΔhapX, MM-Fe2(SO4)3, replicate 2

city: Cordoba

first: David

last: Turrá

address: Campus de Rabanales

country: Spain

institute: University of Cordoba

description: Mycelia shifted for 10 hour to minimal medium without 50 μM Fe2(SO4)3

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 110 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Fusarium oxysporum custom Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k 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 9.1 (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: Fusarium oxysporum

source_name: Mycelia, MM-Fe2(SO4)3, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the One-Color Microarray-Based Gene Expression Analysis v 6.5 kit (Agilent) according to the manufacturer's instructions.

growth_protocol: freshly obtained microconidia were germinated for 16 hours in iron depleted minimal medium (MM).

extract_protocol: Total RNA was extracted from F. oxysporum mycelia following previously reported protocols (Chomczynski and Sacchi, 1987).

treatment_protocol: Mycelia were harvested by filtration, washed three times in sterile ddH2O, and transferred for 10 hours to fresh minimal medium with or without 50 μM Fe2(SO4)3.

tag: iron

value: absent

tag: genotype/variation

value: ΔhapX


title: Mycelia ΔhapX, MM-Fe2(SO4)3, replicate 1

source_name: Mycelia, MM-Fe2(SO4)3, replicate 1


title: Mycelia ΔhapX, MM-Fe2(SO4)3, replicate 3

source_name: Mycelia, MM-Fe2(SO4)3, replicate 3


title: TesticularTissue_1mg.kg.day_dinitrobenzene_rat2

description:
ST3M3809
Gene expression in testes of rat treated 4 days with 1 mg/kg/day dinitrobenzene.


title: D1994A_01

type: protein

city: Philadelphia

first: Jason

last: Covy

state: PA

address: 3620 Hamilton Walk

institute: University of Pennslyvania

description: Protoarray substrate phosphorylation by the kinase LRRK2

hyb_protocol: Purified proteins are printed in duplicate on a nitrocellulose-coated glass slide.  No further hybridization steps are required after the labeling protocol.

scan_protocol: Dried slides were exposed to a PhosphorImager plate (Amersham Biosciences, Piscataway, NJ, USA), and scanned on a Storm 840 (Molecular Dynamics, Inc., Sunnyvale, CA, USA) at 50 microns

data_processing: Data was analyzed with ProtoArray Prospector v3.0 software (Invitrogen)

molecule: other

source_name: Recombinant LRRK2 protein (9705-2527) with D1994A mutation

label_protocol: Recombinant G2019S or D1994A  glutathione-S-transferase (GST)-LRRK2 (970-2527) (Invitrogen) was diluted to 50nM in 20mM Tris (pH 7.5), 10mM MgCl2, 1mM EGTA, 1mM Na3VO4, 5mM beta-glycerophosphate, 2mM DTT, 0.02% polysorbate 20, and 10 mCi /mL of  [gamma- 33P]ATP (33 nM final concentration) in a total volume of 120uL. Slides were overlayed with buffer alone, or buffer containing G2019S or D1994A LRRK2, then covered with a coverslip and placed in a 50 mL conical tube for 1 h at 30oC. Afterwards, slides were washed with 0.5% SDS buffer and water followed by centrifugation.

extract_protocol: Proteins (clones selected from Invitrogen’s Ultimate ORF™ Collection*) are expressed as N-terminal GST fusion proteins using a baculovirus expression system in insect cells. All proteins are purified under nondenaturing conditions and printed at 4°C to preserve native protein structure before being spotted in duplicate on glass slides.

tag: mutation


title: TesticularTissue_1mg.kg.day_dinitrobenzene_rat3

description:
ST3M3810
Gene expression in testes of rat treated 4 days with 1 mg/kg/day dinitrobenzene.


title: Mycelia ΔhapX, MM+Fe2(SO4)3, replicate 3

description: Mycelia shifted for 10 hour to minimal medium with 50 μM Fe2(SO4)3

source_name: Mycelia, MM+Fe2(SO4)3, replicate 3

value: present


title: TesticularTissue_1mg.kg.day_dinitrobenzene_rat1

description:
ST3M3808
Gene expression in testes of rat treated 4 days with 1 mg/kg/day dinitrobenzene.


title: TesticularTissue_0.1mg.kg.day_dinitrobenzene_rat9

description:
ST2M3806
Gene expression in testes of rat treated 4 days with 0.1 mg/kg/day dinitrobenzene.

source_name: Testicular tissue, 0.1 mg/kg/day dinitrobenzene

value: 0.1 mg/kg/day


title: TesticularTissue_0.1mg.kg.day_dinitrobenzene_rat10

description:
ST2M3807
Gene expression in testes of rat treated 4 days with 0.1 mg/kg/day dinitrobenzene.


title: TesticularTissue_0.1mg.kg.day_dinitrobenzene_rat7

description:
ST2M3799
Gene expression in testes of rat treated 4 days with 0.1 mg/kg/day dinitrobenzene.


title: Mycelia wt, MM+Fe2(SO4)3, replicate 3

value: wt


title: TesticularTissue_0.1mg.kg.day_dinitrobenzene_rat5

description:
ST2M3797
Gene expression in testes of rat treated 4 days with 0.1 mg/kg/day dinitrobenzene.


title: Mycelia ΔhapX, MM+Fe2(SO4)3, replicate 2

source_name: Mycelia, MM+Fe2(SO4)3, replicate 2


title: Mycelia wt, MM-Fe2(SO4)3, replicate 2


title: Mycelia ΔhapX, MM+Fe2(SO4)3, replicate 1

source_name: Mycelia, MM+Fe2(SO4)3, replicate 1


title: G2019S_01

source_name: Recombinant LRRK2 protein (9705-2527) with G2019S mutation


title: Mycelia wt, MM-Fe2(SO4)3, replicate 1


title: TesticularTissue_0.1mg.kg.day_dinitrobenzene_rat3

description:
ST2M3795
Gene expression in testes of rat treated 4 days with 0.1 mg/kg/day dinitrobenzene.


title: TesticularTissue_0.1mg.kg.day_dinitrobenzene_rat6

description:
ST2M3798
Gene expression in testes of rat treated 4 days with 0.1 mg/kg/day dinitrobenzene.


title: TesticularTissue_0.1mg.kg.day_dinitrobenzene_rat4

description:
ST2M3796
Gene expression in testes of rat treated 4 days with 0.1 mg/kg/day dinitrobenzene.


title: Mycelia wt, MM+Fe2(SO4)3, replicate 2


title: TesticularTissue_0.1mg.kg.day_dinitrobenzene_rat8

description:
ST2M3805
Gene expression in testes of rat treated 4 days with 0.1 mg/kg/day dinitrobenzene.


title: Mycelia wt, MM-Fe2(SO4)3, replicate 3


title: TesticularTissue_0.1mg.kg.day_dinitrobenzene_rat2

description:
ST2M3794
Gene expression in testes of rat treated 4 days with 0.1 mg/kg/day dinitrobenzene.


title: TesticularTissue_0.1mg.kg.day_dinitrobenzene_rat1

description:
ST2M3793
Gene expression in testes of rat treated 4 days with 0.1 mg/kg/day dinitrobenzene.


title: G2019S_02


title: Mycelia wt, MM+Fe2(SO4)3, replicate 1


title: TesticularTissue_0mg.kg.day_dinitrobenzene_rat8

description:
ST1M3791
Gene expression in testes of control rat treated 4 days with vehicle.

source_name: Testicular tissue, 0 mg/kg/day dinitrobenzene

value: vehicle control

value: 0 mg/kg/day


title: CGH S. japonicum Geographical Strains 7

city: Brisbane

first: Geoffrey

last: Gobert

address: 300 Herston Rd

country: Australia

institute: QIMR

description: Sample 7

hyb_protocol: Fluorescently labelled cRNA plus unlabelled Cot-1 DNA (1µg/µl) was used for hybridisation to the microarray. An Oligo aCGH Hybridization Kit (Agilent; Cat. No. 5188-5220) was loaded onto the microarray, locked into an Agilent SureHyb Chamber, and hybridised at 65C for 24h in a rotor hybridisation-oven at 15rpm. Microarray slides were disassembled and washed in low stringency buffer for 5min (Oligo aCGH Wash Buffer 1) and then a high stringency buffer for 1min (Oligo aCGH Wash Buffer 2)

scan_protocol: Microarrays were scanned with an Agilent DNA Microarray Scanner (G2565BA) at 5um resolution and 100% PMT (both Red & Green channels) sensitivity. Automatic outliner flagging was used and the resulting list filtered on the basis of p-value.

data_processing: The images from the DNA Microarray Scanner were extracted using Feature Extraction (v10.5) by applying the profile "Agilent HD_CGH" and the protocol "CGH_105_Dec08".  Automatic outliner flagging was used and the resulting list filtered on the basis of p-value generated. Feature-extracted data was analyzed and visualized using GENESPRING (version 11; Agilent Technologies). Microarray data were normalised using a normalisation scenario for 'Agilent FE two-color', which includes LOWESS Normalization. Data sets were further analyzed using published procedures based on two-color experiments and ProcessedSignal values were determined using Feature Extraction software and GeneSpring microarray software, including aspects of the signal to noise ratio, spot morphology and homogeneity. ProcessedSignal represents the signal after localized background subtraction and includes corrections for surface trends. Features were deemed 'Absent' when the processed signal intensity was less than twice the value of the processed signal error value. Features were deemed 'Marginal' when the measured intensity was at a saturated value or if there was a substantial amount of variation in the signal intensity within the pixels of a particular feature. Features that were neither absent nor marginal were deemed 'Present'. Data points were included only if they were present or marginal, and probes or contigs were retained if at least half of the data points were 'Present'. Differential probe hybridisation was statistically evaluated as a p-value and a cut-off value of ˜0.01 in at least 4 of 8 hybridisations used as the confidence level.

organism: Schistosoma japonicum

source_name: adult male_Chinese

label_protocol: A Genomic DNA ULS Labeling Kit (Cat. No. 5190-0419, Agilent) was used for the amplification and incorporation of fluorescent dyes (Cy3- and Cy5-CTP), with a starting amount of 500ng gDNA. Genomic DNA Purification Module (Cat. No. 5190-0418, Agilent) was used for labelled dye removal and labelled genomic DNA purification.

growth_protocol: Oncomelania hupensis hupensis snails, infected with SjC (Anhui isolate), were imported from the National Institute of Parasitic Diseases-CDC, Shanghai. O. hupensis quadrasi snails, harbouring SjP (Sorsogon isolate, Luzon), were maintained at the Queensland Institute of Medical Research (QIMR). ARC Swiss mice were infected percutaneously with 40 SjC or SjP cercariae shed from snails and adult worms perfused 6 weeks after challenge. After perfusion, male and femaleworms were separated, washed in chilled phosphate buffered saline (PBS), and stored in liquid nitrogen.

extract_protocol: PrepEase Genomic DNA Isolation Kits (USB, Cleveland, USA) were used to isolate genomic DNA (g DNA) from maleand femaleSjC and SjP. DNA quality and quantity were assessed using the Nanodrop system (Thermo Scientific Wilmington, USA). Two separate biologically replicate DNA samples were isolated from maleand femaleSjC and SjP.

treatment_protocol: Cot-1 DNA, also referred to as competitive DNA, is the double-stranded portion of a sheared genomic sample where the majority of repetitive elements (intragenic regions) are re-associated but single and low-copy elements remain single stranded. Cot-1 DNA was prepared from SjC and SjP DNA samples. In brief, gDNA (100µg, 1:1 mixture of SjC and SjP DNAs) in 400µl ddH2O was sonicated for 1-2 min. Samples were then checked on an agarose gel for the required average fragment size of 400bp. NaCl (5M) was added to each sample to obtain a final concentration of 0.3 M. Aliquots of the samples were incubated as follows: denature at 95°C for 3min; cool to 65°C for 2-5 seconds and then put on ice. S1 nuclease ssDNA digestion Kits (Promega, Madison, USA) were used to isolate double stranded DNA. After digestion, ~80% of the gDNA was retained, representing the repetitive, non-coding regions of the genome.

value: Chinese (SjC, Anhui isolate)

value: adult (7 week post cercarial challenge)

source_name: adult male_Philippine

value: Philippine (SjP, Sorsogon isolate)


title: CGH S. japonicum Geographical Strains 6

description: Sample 6

source_name: adult female_Philippine

value: female

source_name: adult female_Chinese


title: CGH S. japonicum Geographical Strains 8

description: Sample 8

value: male


title: Tear + P. aeruginosa antigens

city: Berkeley

first: James

last: Mun

state: CA

address: 688 Minor Hall

department: Vision Science

institute: UC Berkeley

hyb_protocol: The resultant biotinylated cRNA was fragmented and then hybridized to the GeneChip miRNA Array. The arrays were washed and stained using the Affymetrix Model 450 Fluidics Station.

scan_protocol: Gene chips were scanned using the Affymetrix Model 3000 scanner.

data_processing: Expression values were generated using Microarray Suite (MAS) v5.0 software. Each sample and hybridization underwent a quality control evaluation, including cRNA amplification of >4-fold, precentage of probe sets reliably detecting between 40% and 60% present call.

source_name: Human corneal epithelial cells exposed to Tear for 16h + 3 h with P. aeruginosa antgiens

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

growth_protocol: Telomerase-immortalized human corneal epithelial cells were grown on 96 well plates in serum-free KGM medium (Lonza, Walkersville, MD) to 70-90% confluency in 37oC incubator with 5% CO2.

extract_protocol: Total RNA was extracted with Rneasy Kit (Qiagen, Valencia, CA)

treatment_protocol: Human corneal epithelial cells were incubated in either 40 ul of fresh human tear fluid or high calcium KGM without antibiotics for 16 hours before extraction or before incubation with P. aeruginosa antigens for 3 h then extraction.

value: telomerase-immortalized human corneal epithelial cells


title: TesticularTissue_0mg.kg.day_dinitrobenzene_rat5

description:
ST1M3783
Gene expression in testes of control rat treated 4 days with vehicle.

value: Wistar

value: 7-8 weeks

value: testis


title: Media

source_name: Human corneal epithelial cells exposed to Media only for 16h


title: TesticularTissue_0mg.kg.day_dinitrobenzene_rat4

description:
ST1M3782
Gene expression in testes of control rat treated 4 days with vehicle.


title: TesticularTissue_0mg.kg.day_dinitrobenzene_rat2

description:
ST1M3780
Gene expression in testes of control rat treated 4 days with vehicle.


title: Tear

source_name: Human corneal epithelial cells exposed to human tear only for 16h


title: MCF_7_374a Rep_2

description: MCF-7 with miR-374a precursor stably transduced, replicate 2; 1.5μg/mL puromycin selection for 10 days.

growth_protocol: The MCF-7 breast cancer cells were cultured in complete DMEM medium and supplied with 10% FBS.

extract_protocol: Total RNA was isolated using the RNeasy RNA isolation kit (Qiagen) following the supplier's protocol.

treatment_protocol: pMSCV-miR-374a or empty vector was co-transfected with the pIK packaging plasmid in 293FT cells by using the standard calcium phosphate transfection method. Thirty-six hours after the co-transfection, supernatants were collected and incubated with cells to be infected for 24 hours in the presence of polybrene (2.5 μg/mL).  Following infection, puromycin (1.5μg/mL) was used to select stably transduced cells for 10 days.

value: breast cancer cells

tag: transduction

value: miR-374a precursor


title: CGH S. japonicum Geographical Strains 1

description: Sample 1

tag: gender


title: MCF_7_374a Rep_1

description: MCF-7 with miR-374a precursor stably transduced, replicate 1; 1.5μg/mL puromycin selection for 10 days.


title: MCF_7_vector Rep_1

description: MCF-7 with retroviral vector stably transduced, replicate 1; 1.5μg/mL puromycin selection for 10 days.

value: vector control


title: TesticularTissue_0mg.kg.day_dinitrobenzene_rat7

description:
ST1M3785
Gene expression in testes of control rat treated 4 days with vehicle.

tag: age


title: TesticularTissue_0mg.kg.day_dinitrobenzene_rat3

description:
ST1M3781
Gene expression in testes of control rat treated 4 days with vehicle.

tag: tissue


title: CGH S. japonicum Geographical Strains 5

description: Sample 5


title: TesticularTissue_0mg.kg.day_dinitrobenzene_rat1

description:
ST1M3778
Gene expression in testes of control rat treated 4 days with vehicle.


title: CGH S. japonicum Geographical Strains 3

description: Sample 3


title: CGH S. japonicum Geographical Strains 4

description: Sample 4


title: MCF_7_vector Rep_2

description: MCF-7 with retroviral vector stably transduced, replicate 2; 1.5μg/mL puromycin selection for 10 days.


title: TesticularTissue_0mg.kg.day_dinitrobenzene_rat6

description:
ST1M3784
Gene expression in testes of control rat treated 4 days with vehicle.


title: Media + P.aeruginosa antigens

source_name: Human corneal epithelial cells exposed to Media for 16h + 3 h with P. aeruginosa antgiens


title: CGH S. japonicum Geographical Strains 2

description: Sample 2


title: colon_norm_4

status: Public on Jul 13 2012

city: Galway

first: Paul

last: Geeleher

address: University Road

department: Mathematics

country: Ireland

institute: National University of Ireland, Galway

description: norm

hyb_protocol: Array hybridization and scanning were performed at the functional  genomics and high throughput screening facility at the National Centre for Biomedical  Engineering Science, NUI Galway.

scan_protocol: All the microarray slides were scanned by using an Agilent microarray scanner (G2565BA) according to the manufacturers user guide for appropriate settings and data was extracted by using Agilent feature extraction software (www.agilent.com/chem/fe). A feature extraction is the process by which information from probe features is extracted from microarray scan data, allowing us to measure gene expression in our experiment. Then, the raw and feature extraction data were given to an expert statistician for further analysis.

data_processing: Quantile normalized log2 intensity ratios, generated using R version 2.13.1 and the data were normalized using the normalizeBetweenArrays() function from the limma package (version 3.6.9). Control probes were omitted from the quantile normalization.

label_protocol: We labelled the IP DNA with fluorescent dye, cyanine 3 and reference (R) DNA with cyanine 5 and co-hybridized to the Agilent microarrays.

extract_protocol: For each sample of interest, 5 µg of purified genomic DNA (extracted using DNAeasy kit) was suspended in 250 µl of PBS. By using a Branson digital sonifier model 150, output power of was set up to number 3 and DNA was carefully sheared to 5 cycles with 10 seconds on and 10 seconds off. After that, the final volume was checked with a pipette and if necessary PBS was added to get a final volume of 250 µl. Then, 50 µl of sheared samples was transferred to a new 1.5 ml tube and stored at -20 C and this was termed as Reference (R) sample. The remaining 200 µl was used to immunoprecipitate the methylated DNA and this was termed (IP) sample. This IP sample was then added into 50 µl of antibody/magnetic bead mixture prepared as above. Then, 250 µl of 2X IP buffer was added to give a total volume of 500 µl and the tube was placed overnight on a tube rotator at 4 C.

tag: disease state

value: healthy

tag: sample type

value: input DNA

value: immunoprecipitated DNA

tag: antibody

tag: antibody vendor

value: Eurogentec


title: colon_UC_4

description: UC

value: ulcerative colitis


title: colon_norm_3

description: norm


title: colon_UC_3

description: UC


title: 529594A10 - L1-sgs2_R1 vs L1-sgs2-vcs_R1

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: Identify the transcript overlap and specificity between the PTGS and decapping/exoribonuclease pathways b identifying transcripts that are significantly changed in double mutants versus single mutants, and transcripts that are commonly changed among the single and double mutants compared to WT.

hyb_protocol: L1-sgs2-vcs_R1 Cy5 / L1-sgs2_R1 Cy3 : 30pmol.

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing:
For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.
We used the arrays with 73228 probes but we didn't exploit all the probe. Indeed half of the probes are "no gene" probes.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seedling - Media=Bouturage media  hygrometry=50%  Temperature=21C  Light=16h jour; 8h nuit

treatment_protocol: no treatment

tag: ecotype

value: Columbia

value: mutant (l1/vcs/sgs2)

tag: dev.stage (boyes et al. plant cell 2001)

extract_protocol: L1/sgs2 Repet1:3ug. (Qiagen_RNeasy.pdf)

value: mutant (l1/sgs2)


title: colon_UC_5

description: UC


title: 529594A03 - L1_R1 vs L1-sgs2_R1

hyb_protocol: L1-sgs2_R1 Cy5 / L1_R1 Cy3 : 30pmol.

extract_protocol: L1 Repet1:3ug. (Qiagen_RNeasy.pdf)

value: mutant (l1)


title: 529594A06 - L1-sgs2-vcs_R1 vs L1_R1

hyb_protocol: L1_R1 Cy5 / L1-sgs2-vcs_R1 Cy3 : 30pmol.


title: colon_norm_5

description: norm


title: colon_norm_2

description: norm


title: 529594A09 - L1-sgs2-vcs_R1 vs L1-sgs2_R1

hyb_protocol: L1-sgs2_R1 Cy5 / L1-sgs2-vcs_R1 Cy3 : 30pmol.


title: colon_UC_1

description: UC


title: 529594A04 - L1-sgs2_R1 vs L1_R1

hyb_protocol: L1_R1 Cy5 / L1-sgs2_R1 Cy3 : 30pmol.


title: 529594A05 - L1_R1 vs L1-sgs2-vcs_R1

hyb_protocol: L1-sgs2-vcs_R1 Cy5 / L1_R1 Cy3 : 30pmol.


title: 529594A01 - L1_R1 vs L1-vcs_R1

hyb_protocol: L1-vcs_R1 Cy5 / L1_R1 Cy3 : 30pmol.

extract_protocol: L1/vcs Repet1:3ug. (Qiagen_RNeasy.pdf)

value: mutant (l1/vcs)


title: 529594A02 - L1-vcs_R1 vs L1_R1

hyb_protocol: L1_R1 Cy5 / L1-vcs_R1 Cy3 : 30pmol.


title: 529591A08 - sgs3_R1 vs sgs3-xrn4_R1

hyb_protocol: sgs3-xrn4_R1 Cy5 / sgs3_R1 Cy3 : 30pmol.

value: mutant (xrn4-5/sgs3-11)

extract_protocol: sgs3-11 Repet1:3ug. (Qiagen_RNeasy.pdf)

value: mutant (sgs3-11)


title: 529594A08 - L1-vcs_R1 vs L1-sgs2-vcs_R1

hyb_protocol: L1-sgs2-vcs_R1 Cy5 / L1-vcs_R1 Cy3 : 30pmol.


title: colon_UC_2

description: UC


title: colon_norm_1

description: norm


title: 529591A03 - Col0_R1 vs xrn4_R1

hyb_protocol: xrn4_R1 Cy5 / Col0_R1 Cy3 : 30pmol.

extract_protocol: xrn4-5 Repet1:3ug. (Qiagen_RNeasy.pdf)

value: mutant (xrn4-5)

extract_protocol: Col0 Repet1:3ug. (Qiagen_RNeasy.pdf)

value: WT(Col)


title: 529591A11 - xrn4_R1 vs sgs3-xrn4_R1

hyb_protocol: sgs3-xrn4_R1 Cy5 / xrn4_R1 Cy3 : 30pmol.


title: 529594A07 - L1-sgs2-vcs_R1 vs L1-vcs_R1

hyb_protocol: L1-vcs_R1 Cy5 / L1-sgs2-vcs_R1 Cy3 : 30pmol.


title: 529591A06 - sgs3_R1 vs Col0_R1

hyb_protocol: Col0_R1 Cy5 / sgs3_R1 Cy3 : 30pmol.


title: 529591A07 - sgs3-xrn4_R1 vs sgs3_R1

hyb_protocol: sgs3_R1 Cy5 / sgs3-xrn4_R1 Cy3 : 30pmol.


title: 529591A05 - Col0_R1 vs sgs3_R1

hyb_protocol: sgs3_R1 Cy5 / Col0_R1 Cy3 : 30pmol.


title: 529588A09 - sgs3-xrn4_R2 vs xrn4_R2

hyb_protocol: xrn4_R2 Cy5 / sgs3-xrn4_R2 Cy3 : 30pmol.

extract_protocol: xrn4-5 Repet2:3ug. (Qiagen_RNeasy.pdf)


title: 528995A07 - L1-sgs2-vcs_R2 vs L1-vcs_R2

hyb_protocol: L1-vcs_R2 Cy5 / L1-sgs2-vcs_R2 Cy3 : 30pmol.

extract_protocol: L1/vcs Repet2:3ug. (Qiagen_RNeasy.pdf)


title: 529588A05 - xrn4_R2 vs Col0_R2

hyb_protocol: Col0_R2 Cy5 / xrn4_R2 Cy3 : 30pmol.

extract_protocol: Col0 Repet2:3ug. (Qiagen_RNeasy.pdf)


title: 529591A04 - xrn4_R1 vs Col0_R1

hyb_protocol: Col0_R1 Cy5 / xrn4_R1 Cy3 : 30pmol.


title: 529588A10 - xrn4_R2 vs sgs3-xrn4_R2

hyb_protocol: sgs3-xrn4_R2 Cy5 / xrn4_R2 Cy3 : 30pmol.


title: 528995A04 - L1-sgs2_R2 vs L1_R2

hyb_protocol: L1_R2 Cy5 / L1-sgs2_R2 Cy3 : 30pmol.

extract_protocol: L1 Repet2:3ug. (Qiagen_RNeasy.pdf)

extract_protocol: L1/sgs2 Repet2:3ug. (Qiagen_RNeasy.pdf)


title: 529588A06 - Col0_R2 vs sgs3_R2

hyb_protocol: sgs3_R2 Cy5 / Col0_R2 Cy3 : 30pmol.

extract_protocol: sgs3-11 Repet2:3ug. (Qiagen_RNeasy.pdf)


title: 529588A08 - sgs3_R2 vs sgs3-xrn4_R2

hyb_protocol: sgs3-xrn4_R2 Cy5 / sgs3_R2 Cy3 : 30pmol.


title: 528995A10 - L1-sgs2_R2 vs L1-sgs2-vcs_R2

hyb_protocol: L1-sgs2-vcs_R2 Cy5 / L1-sgs2_R2 Cy3 : 30pmol.


title: 528995A09 - L1-sgs2-vcs_R2 vs L1-sgs2_R2

hyb_protocol: L1-sgs2_R2 Cy5 / L1-sgs2-vcs_R2 Cy3 : 30pmol.


title: 529588A07 - sgs3_R2 vs Col0_R2

hyb_protocol: Col0_R2 Cy5 / sgs3_R2 Cy3 : 30pmol.


title: 529591A10 - sgs3-xrn4_R1 vs xrn4_R1

hyb_protocol: xrn4_R1 Cy5 / sgs3-xrn4_R1 Cy3 : 30pmol.


title: 529591A01 - Col0_R1 vs sgs3-xrn4_R1

hyb_protocol: sgs3-xrn4_R1 Cy5 / Col0_R1 Cy3 : 30pmol.


title: 528995A06 - L1-sgs2-vcs_R2 vs L1_R2

hyb_protocol: L1_R2 Cy5 / L1-sgs2-vcs_R2 Cy3 : 30pmol.


title: 529588A01 - Col0_R2 vs sgs3-xrn4_R2

hyb_protocol: sgs3-xrn4_R2 Cy5 / Col0_R2 Cy3 : 30pmol.

tag: genotype/variation:


title: 529588A02 - sgs3-xrn4_R2 vs Col0_R2

hyb_protocol: Col0_R2 Cy5 / sgs3-xrn4_R2 Cy3 : 30pmol.


title: 529588A03 - sgs3-xrn4_R2 vs sgs3_R2

hyb_protocol: sgs3_R2 Cy5 / sgs3-xrn4_R2 Cy3 : 30pmol.


title: 528995A02 - L1-vcs_R2 vs L1_R2

hyb_protocol: L1_R2 Cy5 / L1-vcs_R2 Cy3 : 30pmol.


title: 529591A02 - sgs3-xrn4_R1 vs Col0_R1

hyb_protocol: Col0_R1 Cy5 / sgs3-xrn4_R1 Cy3 : 30pmol.


title: 528995A03 - L1_R2 vs L1-sgs2_R2

hyb_protocol: L1-sgs2_R2 Cy5 / L1_R2 Cy3 : 30pmol.


title: 528995A05 - L1_R2 vs L1-sgs2-vcs_R2

hyb_protocol: L1-sgs2-vcs_R2 Cy5 / L1_R2 Cy3 : 30pmol.


title: 528995A01 - L1_R2 vs L1-vcs_R2

hyb_protocol: L1-vcs_R2 Cy5 / L1_R2 Cy3 : 30pmol.


title: 528995A08 - L1-vcs_R2 vs L1-sgs2-vcs_R2

hyb_protocol: L1-sgs2-vcs_R2 Cy5 / L1-vcs_R2 Cy3 : 30pmol.


title: 529588A04 - Col0_R2 vs xrn4_R2

hyb_protocol: xrn4_R2 Cy5 / Col0_R2 Cy3 : 30pmol.


title: OUMS-36 cells treated with heat stress at 41°C and cultured for 0 h

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: MAS5.0 using GeneChip Analysis Suite.

source_name: Human normal fibroblast cell line OUMS-36, heat stress, 0 h

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3’ IVT Express Kit (Affymetrix).

extract_protocol: Total RNA was extracted from cells using an RNeasy Total RNA Extraction kit (Qiagen), and treated with DNase I (Qiagen) for 15 min at room temperature to remove residual genomic DNA. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies), producing RIN values between 9.8 and 10.

treatment_protocol: OUMS-36 cells, a human normal fibroblast cell line, were cultured at 37°C. The cells were treated with heat stress at 41°C for 30 min, followed by incubation for 0 h at 37°C. Non-heat-stressed cells served as the control.

tag: cell line

tag: developmental stage

value: embryo

tag: case history

value: normal

tag: life span

value: finite

tag: morphology

value: fibroblast-like

tag: treatment

value: heat stress

tag: time after treatment

value: 0 h


title: OUMS-36 cells treated with heat stress at 41°C and cultured for 1 h

source_name: Human normal fibroblast cell line OUMS-36, heat stress, 1 h

treatment_protocol: OUMS-36 cells, a human normal fibroblast cell line, were cultured at 37°C. The cells were treated with heat stress at 41°C for 30 min, followed by incubation for 1 h at 37°C. Non-heat-stressed cells served as the control.

value: 1 h


title: OUMS-36 cells (control)

source_name: Human normal fibroblast cell line OUMS-36, untreated

treatment_protocol: OUMS-36 cells, a human normal fibroblast cell line, were cultured at 37°C. The cells were treated with heat stress at 41°C for 30 min, followed by incubation for 0, 1, or 3 h at 37°C. Non-heat-stressed cells served as the control.


title: Rectal Colon Biopsy_SD241297_PIBD [GP2339_93_M_PID_SS373979]

city: Stevenage

first: Fiona

middle: M

last: Kelly

state: HERTS

address: GunnelsWood Road

department: Biopharm R&D

country: United Kingdom

institute: GlaxoSmithKline

description: Sample name: GP2339_93_M_PID_SS373979

hyb_protocol: The fragmented and labeled cDNA was hybridized to U133plus2.0 GeneChips® in accordance with the Affymetrix protocol (Affymetrix, Santa Clara, CA, USA,)

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and fluorescence intensity for each feature of the array was obtained by using GeneChip® Operating Software (Affymetrix, Santa Clara, CA, USA).

data_processing: Samples were separated into separate technical batches and balanced for disease and gender. Each pair of biopsies was allocated to the same batch. Within each batch, samples were randomised.  The chip quality was assessed using Microarray Gene Chip Operating Suite 5 (MAS5) normalised data (normalised to a target intensity of 150) and Principle Component Analysis (PCA) performed in Umetrics SIMCA-P+ 11.5For statistical analysis of gene expression, all probe sets were normalised using the Rosetta Resolver version 5.1 group processing pipeline 15. The normalised data set was imported to SAS version 9.1, the data from two biopsies per donor averaged and the statistically analysed using a linear mixed models. The data set was modelled for disease group, gender, technical batches and the disease:gender interaction and estimates of fold change and P values between disease groups determined. A final intensity threshold was applied (keep genes >25 intensity in any disease group) to the data to remove genes with low detection levels. (Weng L. Rosetta error model for gene expression analysis.Bioinformatics. 2006 May 1;22(9):1111-21. Epub 2006 Mar 7.)

label: Biotin

source_name: Rectal Colon Biopsy

label_protocol: 50ng of total RNA was processed to Biotin-labeled cDNA using the NuGEN Ovation™ RNA Amplification System.

extract_protocol: Total RNA was extracted from rectal biopsy samples that had been preserved in RNAlater (Ambion, Applied Biosystems, Warrington, UK) using a Polytron type homogeniser (YellowLine DI 25 Basic) and 1ml TriZol reagent (Invitrogen, Paisley, UK). RNA was purified using RNeasy mini-columns (Qiagen, Valencia, CA) including on-column DNAse-1 step and elution in water

treatment_protocol: Subjects underwent sigmoidoscopy without bowel preparation. Biopsies were obtained using endoscopic biopsy forceps and immersed in formalin for histopathology or RNAlater for RNA extraction and gene expression analysis.

value: Rectal Colon Biopsy

tag: gender

value: M

tag: subject identifier

tag: disease

value: PIBD

tag: batch


title: Rectal Colon Biopsy_SD52932_HV [GP2339_90_F_CTL_SS102995]

description: Sample name: GP2339_90_F_CTL_SS102995

tag: tissue

value: F

value: HV


title: Rectal Colon Biopsy_SD241300_PIBD [GP2339_88_F_PID_SS373986]

description: Sample name: GP2339_88_F_PID_SS373986


title: OUMS-36 cells treated with heat stress at 41°C and cultured for 3 h

source_name: Human normal fibroblast cell line OUMS-36, heat stress, 3 h

treatment_protocol: OUMS-36 cells, a human normal fibroblast cell line, were cultured at 37°C. The cells were treated with heat stress at 41°C for 30 min, followed by incubation for 3 h at 37°C. Non-heat-stressed cells served as the control.

value: 3 h


title: Hs68 cells (control)

source_name: Human skin normal fibroblast cell line Hs68, untreated

treatment_protocol: Hs68 cells, a human skin normal fibroblast cell line, were cultured at 37°C. The cells were treated with heat stress at 41°C for 30 min, followed by incubation for 0, 1, or 3 h at 37°C. Non-heat-stressed cells served as the control.

value: male

value: newborn

value: foreskin


title: Rectal Colon Biopsy_SD52949_HV [GP2339_86_F_CTL_SS103029]

description: Sample name: GP2339_86_F_CTL_SS103029


title: Hs68 cells treated with heat stress at 41°C and cultured for 3 h

source_name: Human skin normal fibroblast cell line Hs68, heat stress, 3 h

treatment_protocol: Hs68 cells, a human skin normal fibroblast cell line, were cultured at 37°C. The cells were treated with heat stress at 41°C for 30 min, followed by incubation for 3 h at 37°C. Non-heat-stressed cells served as the control.


title: Hs68 cells treated with heat stress at 41°C and cultured for 1 h

source_name: Human skin normal fibroblast cell line Hs68, heat stress, 1 h

treatment_protocol: Hs68 cells, a human skin normal fibroblast cell line, were cultured at 37°C. The cells were treated with heat stress at 41°C for 30 min, followed by incubation for 1 h at 37°C. Non-heat-stressed cells served as the control.


title: Rectal Colon Biopsy_SD241315_PIBS [GP2339_87_F_PIS_SS374016]

description: Sample name: GP2339_87_F_PIS_SS374016

value: PIBS


title: Rectal Colon Biopsy_SD241302_PIBD [GP2339_91_M_PID_SS373990]

description: Sample name: GP2339_91_M_PID_SS373990


title: Rectal Colon Biopsy_SD52948_HV [GP2339_94_M_CTL_SS103026]

description: Sample name: GP2339_94_M_CTL_SS103026


title: Rectal Colon Biopsy_SD241306_PINIBS [GP2339_95_M_PIN_SS373998]

description: Sample name: GP2339_95_M_PIN_SS373998

value: PINIBS


title: Rectal Colon Biopsy_SD52941_HV [GP2339_78_F_CTL_SS103013]

description: Sample name: GP2339_78_F_CTL_SS103013


title: Rectal Colon Biopsy_SD241294_PIBD [GP2339_81_F_PID_SS373974]

description: Sample name: GP2339_81_F_PID_SS373974


title: Rectal Colon Biopsy_SD241319_HV [GP2339_89_F_CTL_SS374024]

description: Sample name: GP2339_89_F_CTL_SS374024


title: Rectal Colon Biopsy_SD241309_PINIBS [GP2339_96_M_PIN_SS374003]

description: Sample name: GP2339_96_M_PIN_SS374003


title: Rectal Colon Biopsy_SD241290_PIBD [GP2339_85_M_PID_SS373965]

description: Sample name: GP2339_85_M_PID_SS373965


title: Rectal Colon Biopsy_SD241305_PINIBS [GP2339_92_F_PIN_SS373996]

description: Sample name: GP2339_92_F_PIN_SS373996


title: Rectal Colon Biopsy_SD241312_PIBS [GP2339_84_M_PIS_SS374009]

description: Sample name: GP2339_84_M_PIS_SS374009


title: Rectal Colon Biopsy_SD52941_HV [GP2339_82_F_CTL_SS103012]

description: Sample name: GP2339_82_F_CTL_SS103012


title: Rectal Colon Biopsy_SD241314_PIBS [GP2339_79_F_PIS_SS374014]

description: Sample name: GP2339_79_F_PIS_SS374014


title: Rectal Colon Biopsy_SD52946_HV [GP2339_74_F_CTL_SS103022]

description: Sample name: GP2339_74_F_CTL_SS103022


title: Rectal Colon Biopsy_SD241310_PINIBS [GP2339_73_M_PIN_SS374006]

description: Sample name: GP2339_73_M_PIN_SS374006


title: Rectal Colon Biopsy_SD241297_PIBD [GP2339_83_M_PID_SS373980]

description: Sample name: GP2339_83_M_PID_SS373980


title: Rectal Colon Biopsy_SD241300_PIBD [GP2339_77_F_PID_SS373985]

description: Sample name: GP2339_77_F_PID_SS373985


title: Rectal Colon Biopsy_SD241310_PINIBS [GP2339_75_M_PIN_SS374005]

description: Sample name: GP2339_75_M_PIN_SS374005


title: Rectal Colon Biopsy_SD241306_PINIBS [GP2339_72_M_PIN_SS373997]

description: Sample name: GP2339_72_M_PIN_SS373997


title: Hs68 cells treated with heat stress at 41°C and cultured for 0 h

source_name: Human skin normal fibroblast cell line Hs68, heat stress, 0 h

treatment_protocol: Hs68 cells, a human skin normal fibroblast cell line, were cultured at 37°C. The cells were treated with heat stress at 41°C for 30 min, followed by incubation for 0 h at 37°C. Non-heat-stressed cells served as the control.

value: normal


title: Rectal Colon Biopsy_SD52930_HV [GP2339_71_M_CTL_SS102991]

description: Sample name: GP2339_71_M_CTL_SS102991


title: Rectal Colon Biopsy_SD241319_HV [GP2339_76_F_CTL_SS374023]

description: Sample name: GP2339_76_F_CTL_SS374023


title: Rectal Colon Biopsy_SD52932_HV [GP2339_69_F_CTL_SS102994]

description: Sample name: GP2339_69_F_CTL_SS102994


title: Rectal Colon Biopsy_SD52946_HV [GP2339_70_F_CTL_SS103023]

description: Sample name: GP2339_70_F_CTL_SS103023


title: Rectal Colon Biopsy_SD241296_PIBD [GP2339_65_F_PID_SS373978]

description: Sample name: GP2339_65_F_PID_SS373978


title: Rectal Colon Biopsy_SD241314_PIBS [GP2339_66_F_PIS_SS374013]

description: Sample name: GP2339_66_F_PIS_SS374013


title: Rectal Colon Biopsy_SD52938_HV [GP2339_68_M_CTL_SS103007]

description: Sample name: GP2339_68_M_CTL_SS103007


title: Rectal Colon Biopsy_SD241305_PINIBS [GP2339_63_F_PIN_SS373995]

description: Sample name: GP2339_63_F_PIN_SS373995


title: Rectal Colon Biopsy_SD241292_PIBD [GP2339_62_F_PID_SS373970]

description: Sample name: GP2339_62_F_PID_SS373970


title: Rectal Colon Biopsy_SD241292_PIBD [GP2339_64_F_PID_SS373969]

description: Sample name: GP2339_64_F_PID_SS373969


title: Rectal Colon Biopsy_SD52930_HV [GP2339_67_M_CTL_SS102990]

description: Sample name: GP2339_67_M_CTL_SS102990


title: Rectal Colon Biopsy_SD241320_HV [GP2339_61_F_CTL_SS374025]

description: Sample name: GP2339_61_F_CTL_SS374025


title: LD.3_3.1h

city: Aarhus

first: Lene

middle: Nagstrup

last: Conley

state: Denmark

address: Langelandsgade 140

department: Department of Chemistry

country: Denmark

institute: University of Aarhus

hyb_protocol: The labelled and purified reference samples were mixed and divided into aliquots before combining it with a labelled sample. Each of the labelled samples were co-hybridized with an aliquot of the labelled reference sample and a hybridization blocker containing polydA (Invitrogen Corporation, CA, USA) and Yeast tRNA (Invitrogen Corporation, CA, USA) to 27k pig oligonucleotide microarrays (GEO accession: GPL5972) using a Discovery XT hybridisation station (Ventana Discovery Systems, Tucson, AZ, USA). Chip Prep-2 was transferred from 4 ºC to room temperature 1 hour before use. ChipSpread was prepared by mixing equal volumes of ChipSpread A (20 mg/mL BSA, 4x SSC, 0.5 mg/mL sodium azide) and B (formamide; 2 mg/mL SDS) followed by incubation at room temperature for 1 hour before use. Labels were printed, trimmed and placed on the slides. The Chip Map reagents (Chip Prep-1, -2 and - 3) were mixed by inversion; the caps were removed and the reagents were placed in the Discovery. The slides were placed in the machine and the run was initiated. The slides were covered with 2.5 mL ChipSpread when the message appeared and the machine used app. 1.5 hours for pre-hybridization of the slides. The Chiphybe80 was mixed and 200 µL were added to the sample (<20 µL) followed by careful mixing. The sample mixtures were heated at 90°C for 3 minutes in a PCR machine carefully mixed by pipetting. The "button" on the machine was pressed to prepare the slides for hybridization. When prompted to, the samples were applied to the slides which were hybridized at 48 ºC for 6 hours. Oil was wiped from the backside of the slides using a clean-room napkin and the slides were placed in the slide-holder from the High Throughput Wash Station (Telechem, cat.no. HTW) placed in a mTub filled with RiboWash. If processing more than 20 slides, an equal number of slides were placed in two slide-holders and continued in parallel. The slide-holder was transferred to a HTW filled with RiboWash and washed for 2 min with magnetic stirring at 700 rpm. The HTW was refilled with RiboWash and the wash was repeated. The slide-holder was dipped in 2x SSC filled in a mTub (200 mL 20x SSC, Elga H2O + 1800 mL water). The slide-holder was then transferred to a HTW filled with 2x SSC and washed for 2 min with magnetic stirring at 700 rpm followed by refill of the HTW with 2x SSC and repetition of the wash. The slide-holder was dipped 10 times in 0.1x SSC filled in a mTub (5 mL 20x SSC, Elga H2O + 995 mL water) and the holder was left submerged in 0.1x SSC. The slides were transferred to a mBox slide holder placed in a mTub filled with Elga H2O. Arrays were dried by centrifugation (at 300 x g for 4 min placed in a mBox).

scan_protocol: Scanner: ScanArray Express HT system (Perkin Elmer), 5 µm resolution, 100 % laser power and PMT adjusted individually for each channel. Image analysis software: GenePix Pro (version 6.0.1.27, Molecular Devices) using FeatureType = Irregular Filled and BackgroundSubtraction = MorphologicalClosingFollowedByOpening

data_processing: Statistical analysis was carried out in the R computing environment (version 2.9.0 for Linux) using the package Linear Models for Microarray Analysis (Limma, version 2.18.0) which is part of the Bioconductor project. The log2-transformed median intensity ratios of Alexa-647 to Alexa-555 (not background corrected) were first normalized within-slide using the loess method and subsequently normalized between arrays using the scale method, both as implemented in Limma. The individual spots were weighted by a spot binary weight matrix where spots flagged by GenePix as non-detectable were given a weight of zero and a sum of the spot weights were calculated for each probe across the 39 microarrays in the four groups (control, T0, T1, and T3). Probes with a sum of 4 or less in any of the four groups were excluded from further analysis together with the control spots. A linear model including array quality weights was fitted to the normalized data set which subsequently was subjected to an empirical Bayes method to determine differentially expressed genes between the samples of high skatole level and samples of low skatole level. The false discovery rate (FDR) was taken into consideration using the method of Benjamini and Hochberg as implemented in Limma and an adjusted P-value below 0.05 was considered significant.

organism: Sus scrofa

label_protocol: Total-RNA was extracted from each sample and DNase treated using RNeasy Maxi Kit (Qiagen) following the enclosed protocols. Quantities were measured using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, DE, USA) and qualities were examined by the 28S:18S rRNA ratio using the RNA 6000 Nano LabChip Kit on 2100 Bioanalyzer (Agilent Technologies, CA, USA). Alexa Flour-labeled cDNA was synthesized from 20 µg of total-RNA using Superscript Plus Direct cDNA Labeling System (Invitrogen) and purified using the NucleoSpin 96 Extract II PCR Clean-up kit (Macherey-Nagel, Düren, Germany) following the enclosed protocols. Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the cDNA reactions. "Green" spike-in RNA was added to the common reference samples and "red" spike-in RNA was added to the samples.

extract_protocol: RNeasy Maxi Kit with DNase treatment following the enclosed protocol (Qiagen).

treatment_protocol: Ran on a treadmill until exhausted. Biopsy was taken 1 hour after exercise t=1_hour

tag: breed

value: Crossbreed between Danish Landrace x Danish Yorkshire sows and Duroc boars

value: sow

tag: weight

value: approx. 91 kg

value: longissimus dorsi

tag: animal id

tag: litter


title: Rectal Colon Biopsy_SD241309_PINIBS [GP2339_60_M_PIN_SS374004]

description: Sample name: GP2339_60_M_PIN_SS374004


title: LD.9_4.3h

treatment_protocol: Ran on a treadmill until exhausted. Biopsy was taken 3 hours after exercise t=3_hours


title: LD.4_4.3h


title: LD.10_3.1h


title: Rectal Colon Biopsy_SD241312_PIBS [GP2339_59_M_PIS_SS374010]

description: Sample name: GP2339_59_M_PIS_SS374010


title: Rectal Colon Biopsy_SD52949_HV [GP2339_55_F_CTL_SS103028]

description: Sample name: GP2339_55_F_CTL_SS103028


title: Rectal Colon Biopsy_SD241320_HV [GP2339_57_F_CTL_SS374026]

description: Sample name: GP2339_57_F_CTL_SS374026


title: LD.1_2.0h

treatment_protocol: Ran on a treadmill until exhausted. Biopsy was taken immediately after exercise t=0_hours


title: Rectal Colon Biopsy_SD241294_PIBD [GP2339_58_F_PID_SS373973]

description: Sample name: GP2339_58_F_PID_SS373973


title: Rectal Colon Biopsy_SD241302_PIBD [GP2339_54_M_PID_SS373989]

description: Sample name: GP2339_54_M_PID_SS373989


title: LD.9_3.1h


title: Rectal Colon Biopsy_SD241290_PIBD [GP2339_56_M_PID_SS373966]

description: Sample name: GP2339_56_M_PID_SS373966


title: LD.7_3.1h


title: LD.3_2.0h


title: LD.1_4.3h


title: LD.9_1.control

treatment_protocol: No treatment


title: Rectal Colon Biopsy_SD52938_HV [GP2339_52_M_CTL_SS103006]

description: Sample name: GP2339_52_M_CTL_SS103006


title: LD.8_3.1h


title: LD.1_1.control


title: LD.6_3.1h


title: LD.9_2.0h


title: LD.4_1.control


title: LD.4_3.1h


title: Rectal Colon Biopsy_SD52948_HV [GP2339_51_M_CTL_SS103027]

description: Sample name: GP2339_51_M_CTL_SS103027


title: Rectal Colon Biopsy_SD52947_HV [GP2339_47_F_CTL_SS103025]

description: Sample name: GP2339_47_F_CTL_SS103025


title: LD.4_2.0h


title: LD.5_1.control


title: LD.7_4.3h


title: Rectal Colon Biopsy_SD241296_PIBD [GP2339_53_F_PID_SS373977]

description: Sample name: GP2339_53_F_PID_SS373977


title: Rectal Colon Biopsy_SD86374_PIBS [GP2339_50_M_PIS_SS161483]

description: Sample name: GP2339_50_M_PIS_SS161483


title: LD.3_1.control


title: LD.6_2.0h


title: Rectal Colon Biopsy_SD241321_HV [GP2339_48_F_CTL_SS374027]

description: Sample name: GP2339_48_F_CTL_SS374027


title: LD.7_1.control


title: Rectal Colon Biopsy_SD52945_HV [GP2339_45_F_CTL_SS103021]

description: Sample name: GP2339_45_F_CTL_SS103021


title: Rectal Colon Biopsy_SD241295_PIBD [GP2339_44_F_PID_SS373976]

description: Sample name: GP2339_44_F_PID_SS373976


title: LD.2_2.0h


title: Rectal Colon Biopsy_SD52947_HV [GP2339_42_F_CTL_SS103024]

description: Sample name: GP2339_42_F_CTL_SS103024


title: LD.8_4.3h


title: LD.2_3.1h


title: LD.7_2.0h


title: Rectal Colon Biopsy_SD86374_PIBS [GP2339_49_M_PIS_SS161484]

description: Sample name: GP2339_49_M_PIS_SS161484


title: LD.1_3.1h


title: LD.3_4.3h


title: Rectal Colon Biopsy_SD241299_PIBD [GP2339_37_F_PID_SS373983]

description: Sample name: GP2339_37_F_PID_SS373983


title: Rectal Colon Biopsy_SD241303_PIBD [GP2339_41_M_PID_SS373992]

description: Sample name: GP2339_41_M_PID_SS373992


title: LD.5_3.1h


title: Rectal Colon Biopsy_SD241293_PIBD [GP2339_39_F_PID_SS373972]

description: Sample name: GP2339_39_F_PID_SS373972


title: Rectal Colon Biopsy_SD52943_HV [GP2339_40_M_CTL_SS103016]

description: Sample name: GP2339_40_M_CTL_SS103016


title: LD.6_4.3h


title: LD.8_2.0h


title: Rectal Colon Biopsy_SD241313_PIBS [GP2339_43_F_PIS_SS374012]

description: Sample name: GP2339_43_F_PIS_SS374012


title: LD.5_2.0h


title: LD.10_4.3h


title: Rectal Colon Biopsy_SD241318_HV [GP2339_34_M_CTL_SS374022]

description: Sample name: GP2339_34_M_CTL_SS374022


title: LD.5_4.3h


title: Rectal Colon Biopsy_SD52933_HV [GP2339_46_F_CTL_SS102997]

description: Sample name: GP2339_46_F_CTL_SS102997


title: Rectal Colon Biopsy_SD241316_PIBS [GP2339_35_M_PIS_SS374017]

description: Sample name: GP2339_35_M_PIS_SS374017


title: Rectal Colon Biopsy_SD52928_PIBS [GP2339_33_F_PIS_SS102986]

description: Sample name: GP2339_33_F_PIS_SS102986


title: Rectal Colon Biopsy_SD241313_PIBS [GP2339_38_F_PIS_SS374011]

description: Sample name: GP2339_38_F_PIS_SS374011


title: LD.6_1.control


title: Rectal Colon Biopsy_SD241293_PIBD [GP2339_36_F_PID_SS373971]

description: Sample name: GP2339_36_F_PID_SS373971


title: LD.8_1.control


title: Rectal Colon Biopsy_SD52950_HV [GP2339_31_F_CTL_SS103030]

description: Sample name: GP2339_31_F_CTL_SS103030


title: Rectal Colon Biopsy_SD52933_HV [GP2339_30_F_CTL_SS102996]

description: Sample name: GP2339_30_F_CTL_SS102996


title: Rectal Colon Biopsy_SD241322_HV [GP2339_27_F_CTL_SS374029]

description: Sample name: GP2339_27_F_CTL_SS374029


title: Rectal Colon Biopsy_SD241308_PINIBS [GP2339_29_F_PIN_SS374001]

description: Sample name: GP2339_29_F_PIN_SS374001


title: Rectal Colon Biopsy_SD241304_PINIBS [GP2339_32_M_PIN_SS373993]

description: Sample name: GP2339_32_M_PIN_SS373993


title: LD.10_1.control


title: Rectal Colon Biopsy_SD241318_HV [GP2339_26_M_CTL_SS374021]

description: Sample name: GP2339_26_M_CTL_SS374021


title: Rectal Colon Biopsy_SD241301_PIBD [GP2339_25_M_PID_SS373987]

description: Sample name: GP2339_25_M_PID_SS373987


title: LD.10_2.0h


title: BF.4_2.0h

data_processing: Statistical analysis was carried out in the R computing environment (version 2.9.0 for Linux) using the package Linear Models for Microarray Analysis (Limma, version 2.18.0) which is part of the Bioconductor project. The log2-transformed median intensity ratios of Alexa-647 to Alexa-555 (not background corrected) were first normalized within-slide using the loess method and subsequently normalized between arrays using the scale method, both as implemented in Limma. The individual spots were weighted by a spot binary weight matrix where spots flagged by GenePix as non-detectable were given a weight of zero and a sum of the spot weights were calculated for each probe across the 37 microarrays in the four groups (control, T0, T1, and T3). Probes with a sum of 4 or less in any of the four groups were excluded from further analysis together with the control spots. A linear model including array quality weights was fitted to the normalized data set which subsequently was subjected to an empirical Bayes method to determine differentially expressed genes between the samples of high skatole level and samples of low skatole level. The false discovery rate (FDR) was taken into consideration using the method of Benjamini and Hochberg as implemented in Limma and an adjusted P-value below 0.05 was considered significant.

label_protocol: Total-RNA was extracted from each sample using mirVana miRNA Isolation Kit from Ambion following the enclosed protocols. Quantities were measured using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, DE, USA) and qualities were examined by the 28S:18S rRNA ratio using the RNA 6000 Nano LabChip Kit on 2100 Bioanalyzer (Agilent Technologies, CA, USA). Alexa Flour-labeled cDNA was synthesized from 20 µg of total-RNA using Superscript Plus Direct cDNA Labeling System (Invitrogen) and purified using the NucleoSpin 96 Extract II PCR Clean-up kit (Macherey-Nagel, Düren, Germany) following the enclosed protocols. Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the cDNA reactions. "Green" spike-in RNA was added to the common reference samples and "red" spike-in RNA was added to the samples.

treatment_protocol: Ran on a treadmill until exhausted. Biopsy was taken immediately after exercise t=0_hour

value: Biceps femoris


title: BF.6_2.0h

extract_protocol: mirVana miRNA Isolation Kit from Ambion following the enclosed protocols


title: BF.5_1.control


title: LD.2_4.3h


title: Rectal Colon Biopsy_SD52935_HV [GP2339_24_M_CTL_SS103000]

description: Sample name: GP2339_24_M_CTL_SS103000

value: Rectal Colon Biopsy


title: Rectal Colon Biopsy_SD241317_PIBS [GP2339_23_F_PIS_SS374020]

description: Sample name: GP2339_23_F_PIS_SS374020


title: Rectal Colon Biopsy_SD241317_PIBS [GP2339_22_F_PIS_SS374019]

description: Sample name: GP2339_22_F_PIS_SS374019


title: BF.3_1.control


title: BF.7_3.1h


title: BF.9_4.3h

hyb_protocol: The labelled and purified reference samples were mixed and divided into aliquots before combining it with a labelled sample. Each of the 36 labelled samples were co-hybridized with an aliquot of the labelled reference sample and a hybridization blocker containing polydA (Invitrogen Corporation, CA, USA) and Yeast tRNA (Invitrogen Corporation, CA, USA) to 27k pig oligonucleotide microarrays (GEO accession: GPL5972) using a Discovery XT hybridisation station (Ventana Discovery Systems, Tucson, AZ, USA). Chip Prep-2 was transferred from 4 ºC to room temperature 1 hour before use. ChipSpread was prepared by mixing equal volumes of ChipSpread A (20 mg/mL BSA, 4x SSC, 0.5 mg/mL sodium azide) and B (formamide; 2 mg/mL SDS) followed by incubation at room temperature for 1 hour before use. Labels were printed, trimmed and placed on the slides. The Chip Map reagents (Chip Prep-1, -2 and - 3) were mixed by inversion; the caps were removed and the reagents were placed in the Discovery. The slides were placed in the machine and the run was initiated. The slides were covered with 2.5 mL ChipSpread when the message appeared and the machine used app. 1.5 hours for pre-hybridization of the slides. The Chiphybe80 was mixed and 200 µL were added to the sample (<20 µL) followed by careful mixing. The sample mixtures were heated at 90°C for 3 minutes in a PCR machine carefully mixed by pipetting. The "button" on the machine was pressed to prepare the slides for hybridization. When prompted to, the samples were applied to the slides which were hybridized at 48 ºC for 6 hours. Oil was wiped from the backside of the slides using a clean-room napkin and the slides were placed in the slide-holder from the High Throughput Wash Station (Telechem, cat.no. HTW) placed in a mTub filled with RiboWash. If processing more than 20 slides, an equal number of slides were placed in two slide-holders and continued in parallel. The slide-holder was transferred to a HTW filled with RiboWash and washed for 2 min with magnetic stirring at 700 rpm. The HTW was refilled with RiboWash and the wash was repeated. The slide-holder was dipped in 2x SSC filled in a mTub (200 mL 20x SSC, Elga H2O + 1800 mL water). The slide-holder was then transferred to a HTW filled with 2x SSC and washed for 2 min with magnetic stirring at 700 rpm followed by refill of the HTW with 2x SSC and repetition of the wash. The slide-holder was dipped 10 times in 0.1x SSC filled in a mTub (5 mL 20x SSC, Elga H2O + 995 mL water) and the holder was left submerged in 0.1x SSC. The slides were transferred to a mBox slide holder placed in a mTub filled with Elga H2O. Arrays were dried by centrifugation (at 300 x g for 4 min placed in a mBox).


title: Rectal Colon Biopsy_SD52943_HV [GP2339_20_M_CTL_SS103017]

description: Sample name: GP2339_20_M_CTL_SS103017

value: M


title: BF.7_2.0h


title: Rectal Colon Biopsy_SD241308_PINIBS [GP2339_17_F_PIN_SS374002]

description: Sample name: GP2339_17_F_PIN_SS374002


title: Rectal Colon Biopsy_SD52931_HV [GP2339_21_M_CTL_SS102993]

description: Sample name: GP2339_21_M_CTL_SS102993


title: Rectal Colon Biopsy_SD241307_PINIBS [GP2339_19_M_PIN_SS374000]

description: Sample name: GP2339_19_M_PIN_SS374000


title: BF.3_3.1h


title: BF.5_3.1h


title: Rectal Colon Biopsy_SD241298_PIBD [GP2339_18_M_PID_SS373981]

description: Sample name: GP2339_18_M_PID_SS373981

value: PIBD


title: BF.2_1.control


title: BF.9_3.1h


title: BF.9_2.0h


title: Rectal Colon Biopsy_SD241307_PINIBS [GP2339_14_M_PIN_SS373999]

description: Sample name: GP2339_14_M_PIN_SS373999


title: Rectal Colon Biopsy_SD52950_HV [GP2339_16_F_CTL_SS103031]

description: Sample name: GP2339_16_F_CTL_SS103031

value: F


title: BF.5_2.0h


title: Rectal Colon Biopsy_SD241299_PIBD [GP2339_15_F_PID_SS373984]

description: Sample name: GP2339_15_F_PID_SS373984


title: Rectal Colon Biopsy_SD52935_HV [GP2339_12_M_CTL_SS103001]

description: Sample name: GP2339_12_M_CTL_SS103001

value: HV


title: BF.8_4.3h


title: Rectal Colon Biopsy_SD241291_PIBD [GP2339_13_M_PID_SS373968]

description: Sample name: GP2339_13_M_PID_SS373968


title: BF.8_3.1h


title: Rectal Colon Biopsy_SD241295_PIBD [GP2339_08_F_PID_SS373975]

description: Sample name: GP2339_08_F_PID_SS373975


title: BF.6_3.1h


title: BF.10_2.0h


title: BF.8_2.0h


title: Rectal Colon Biopsy_SD241316_PIBS [GP2339_11_M_PIS_SS374018]

description: Sample name: GP2339_11_M_PIS_SS374018


title: BF.4_1.control


title: BF.10_4.3h


title: BF.1_1.control


title: Rectal Colon Biopsy_SD241321_HV [GP2339_06_F_CTL_SS374028]

description: Sample name: GP2339_06_F_CTL_SS374028


title: BF.3_4.3h


title: BF.7_1.control


title: Rectal Colon Biopsy_SD52931_HV [GP2339_10_M_CTL_SS102992]

description: Sample name: GP2339_10_M_CTL_SS102992


title: Rectal Colon Biopsy_SD241301_PIBD [GP2339_02_M_PID_SS373988]

description: Sample name: GP2339_02_M_PID_SS373988


title: Rectal Colon Biopsy_SD241304_PINIBS [GP2339_07_M_PIN_SS373994]

description: Sample name: GP2339_07_M_PIN_SS373994


title: Rectal Colon Biopsy_SD52928_PIBS [GP2339_09_F_PIS_SS102987]

description: Sample name: GP2339_09_F_PIS_SS102987


title: BF.1_2.0h


title: Rectal Colon Biopsy_SD241298_PIBD [GP2339_01_M_PID_SS373982]

description: Sample name: GP2339_01_M_PID_SS373982


title: BF.6_1.control


title: BF.2_2.0h


title: Rectal Colon Biopsy_SD241303_PIBD [GP2339_04_M_PID_SS373991]

description: Sample name: GP2339_04_M_PID_SS373991


title: Rectal Colon Biopsy_SD52945_HV [GP2339_05_F_CTL_SS103020]

description: Sample name: GP2339_05_F_CTL_SS103020


title: BF.7_4.3h


title: Rectal Colon Biopsy_SD241291_PIBD [GP2339_03_M_PID_SS373967]

description: Sample name: GP2339_03_M_PID_SS373967


title: Rectal Colon Biopsy_SD86373_IBS-C [GP602R_173_53_SS161482]

description: Sample name: GP602R_173_53_SS161482

value: IBS-C


title: BF.4_3.1h


title: BF.3_2.0h


title: BF.10_3.1h


title: Rectal Colon Biopsy_SD86373_IBS-C [GP602R_172_61_SS161481]

description: Sample name: GP602R_172_61_SS161481


title: Rectal Colon Biopsy_SD86367_IBS-D [GP602R_169_3_SS161470]

description: Sample name: GP602R_169_3_SS161470

value: IBS-D


title: Rectal Colon Biopsy_SD86367_IBS-D [GP602R_168_11_SS161469]

description: Sample name: GP602R_168_11_SS161469


title: Rectal Colon Biopsy_SD86372_IBS-C [GP602R_165_107_SS161480]

description: Sample name: GP602R_165_107_SS161480


title: BF.5_4.3h


title: BF.4_4.3h


title: BF.8_1.control


title: Rectal Colon Biopsy_SD86372_IBS-C [GP602R_164_108_SS161479]

description: Sample name: GP602R_164_108_SS161479


title: Normal brain_nb-005

city: Beijing

first: Wei

last: Zhang

address: No.6 Tiantan Xili, Dongcheng District

department: Glioma Center, Department of Neurosurgery

institute: Beijing Tiantan Hospital, Capital Medical University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol with Illumina BeadReader

data_processing: The data were background subtracted and normalized using quantile normalization with Illumina BeadStudio software v3.1

source_name: Human normal brain

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total RNA was extracted with mirVana miRNA Isolation kit (Ambion, Austin, TX) according to the manufacturer’s protocol. Quality control was performed with NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Houston, TX).

tag: patient population

value: Chinese

value: brain

tag: disease state


title: Glioblastoma_gbm-0612

source_name: Human glioblastoma

value: primary glioblastoma multiform (brain tumor)

tag: tumor grade

value: WHO grade 4

tag: patient age

tag: patient gender

value: male


title: Normal brain_nb-002

value: normal


title: Normal brain_nb-001


title: Rectal Colon Biopsy_SD86369_IBS-C [GP602R_159_81_SS161474]

description: Sample name: GP602R_159_81_SS161474


title: BF.9_1.control

value: Crossbreed between Danish Landrace x Danish Yorkshire sows and Duroc boars

value: sow


title: Rectal Colon Biopsy_SD86371_IBS-C [GP602R_163_26_SS161478]

description: Sample name: GP602R_163_26_SS161478


title: BF.2_3.1h

value: approx. 91 kg


title: Rectal Colon Biopsy_SD86366_IBS-D [GP602R_156_25_SS161467]

description: Sample name: GP602R_156_25_SS161467


title: BF.6_4.3h

value: Biceps femoris


title: Rectal Colon Biopsy_SD86371_IBS-C [GP602R_162_45_SS161477]

description: Sample name: GP602R_162_45_SS161477

value: Rectal Colon Biopsy


title: Glioblastoma_gbm-0609

value: female


title: Normal brain_nb-004


title: Normal brain_nb-003


title: Glioblastoma_gbm-0606


title: BF.2_4.3h


title: Rectal Colon Biopsy_SD86365_IBS-D [GP602R_155_52_SS161466]

description: Sample name: GP602R_155_52_SS161466


title: Rectal Colon Biopsy_SD52957_IBS-D [GP602R_149_31_SS161433]

description: Sample name: GP602R_149_31_SS161433


title: Rectal Colon Biopsy_SD86369_IBS-C [GP602R_158_76_SS161473]

description: Sample name: GP602R_158_76_SS161473


title: Rectal Colon Biopsy_SD52980_IBS-C [GP602R_145_60_SS161425]

description: Sample name: GP602R_145_60_SS161425


title: Glioblastoma_gbm-0604


title: Rectal Colon Biopsy_SD52980_IBS-C [GP602R_146_54_SS161426]

description: Sample name: GP602R_146_54_SS161426


title: Glioblastoma_gbm-0594


title: Rectal Colon Biopsy_SD52957_IBS-D [GP602R_152_27_SS161436]

description: Sample name: GP602R_152_27_SS161436


title: Rectal Colon Biopsy_SD86366_IBS-D [GP602R_157_41_SS161468]

description: Sample name: GP602R_157_41_SS161468


title: Rectal Colon Biopsy_SD86365_IBS-D [GP602R_154_70_SS161465]

description: Sample name: GP602R_154_70_SS161465


title: Rectal Colon Biopsy_SD52956_IBS-D [GP602R_142_22_SS161430]

description: Sample name: GP602R_142_22_SS161430

value: M


title: Glioblastoma_gbm-0593


title: Rectal Colon Biopsy_SD52956_IBS-D [GP602R_143_8_SS161431]

description: Sample name: GP602R_143_8_SS161431


title: Glioblastoma_gbm-0588


title: Glioblastoma_gbm-0597


title: Glioblastoma_gbm-0570


title: Glioblastoma_gbm-0573


title: Glioblastoma_gbm-0575


title: Glioblastoma_gbm-0549


title: Glioblastoma_gbm-0557


title: Rectal Colon Biopsy_SD52977_IBS-C [GP602R_137_129_SS161421]

description: Sample name: GP602R_137_129_SS161421

value: F


title: Glioblastoma_gbm-0525


title: Rectal Colon Biopsy_SD52977_IBS-C [GP602R_139_120_SS161423]

description: Sample name: GP602R_139_120_SS161423


title: Glioblastoma_gbm-0547


title: Rectal Colon Biopsy_SD86337_IBS-C [GP602R_135_7_SS161419]

description: Sample name: GP602R_135_7_SS161419


title: Glioblastoma_gbm-0527


title: Rectal Colon Biopsy_SD86336_IBS-D [GP602R_134_123_SS161418]

description: Sample name: GP602R_134_123_SS161418


title: Rectal Colon Biopsy_SD86336_IBS-D [GP602R_133_134_SS161417]

description: Sample name: GP602R_133_134_SS161417


title: Rectal Colon Biopsy_SD86337_IBS-C [GP602R_136_12_SS161420]

description: Sample name: GP602R_136_12_SS161420


title: Rectal Colon Biopsy_SD52989_IBS-C [GP602R_128_109_SS103109]

description: Sample name: GP602R_128_109_SS103109


title: Rectal Colon Biopsy_SD52990_IBS-C [GP602R_129_136_SS103110]

description: Sample name: GP602R_129_136_SS103110


title: Rectal Colon Biopsy_SD52989_IBS-C [GP602R_127_116_SS103108]

description: Sample name: GP602R_127_116_SS103108


title: Rectal Colon Biopsy_SD52990_IBS-C [GP602R_130_131_SS103111]

description: Sample name: GP602R_130_131_SS103111


title: Rectal Colon Biopsy_SD52988_IBS-C [GP602R_126_19_SS103107]

description: Sample name: GP602R_126_19_SS103107


title: Glioblastoma_gbm-0454


title: Glioblastoma_gbm-0464


title: Glioblastoma_gbm-0451


title: Glioblastoma_gbm-0504


title: Rectal Colon Biopsy_SD52988_IBS-C [GP602R_125_20_SS103106]

description: Sample name: GP602R_125_20_SS103106


title: Rectal Colon Biopsy_SD52987_IBS-C [GP602R_124_135_SS103105]

description: Sample name: GP602R_124_135_SS103105


title: Glioblastoma_gbm-0444


title: Glioblastoma_gbm-0442


title: Glioblastoma_gbm-0512


title: Glioblastoma_gbm-0439


title: Glioblastoma_gbm-0436


title: Glioblastoma_gbm-0409


title: Rectal Colon Biopsy_SD52987_IBS-C [GP602R_123_125_SS103104]

description: Sample name: GP602R_123_125_SS103104


title: Rectal Colon Biopsy_SD52985_IBS-C [GP602R_120_35_SS103101]

description: Sample name: GP602R_120_35_SS103101


title: Rectal Colon Biopsy_SD52985_IBS-C [GP602R_119_28_SS103100]

description: Sample name: GP602R_119_28_SS103100


title: Rectal Colon Biopsy_SD52982_IBS-C [GP602R_113_79_SS103094]

description: Sample name: GP602R_113_79_SS103094


title: Rectal Colon Biopsy_SD52983_IBS-C [GP602R_115_98_SS103096]

description: Sample name: GP602R_115_98_SS103096


title: Rectal Colon Biopsy_SD52982_IBS-C [GP602R_114_87_SS103095]

description: Sample name: GP602R_114_87_SS103095


title: Glioblastoma_gbm-0401


title: Glioblastoma_gbm-0437


title: Glioblastoma_gbm-0380


title: Glioblastoma_gbm-0377


title: Rectal Colon Biopsy_SD52986_IBS-C [GP602R_121_2_SS103102]

description: Sample name: GP602R_121_2_SS103102


title: Rectal Colon Biopsy_SD52984_IBS-C [GP602R_117_57_SS103098]

description: Sample name: GP602R_117_57_SS103098


title: Glioblastoma_gbm-0419


title: Rectal Colon Biopsy_SD52983_IBS-C [GP602R_116_100_SS103097]

description: Sample name: GP602R_116_100_SS103097


title: Glioblastoma_gbm-0371


title: Glioblastoma_gbm-0370


title: Glioblastoma_gbm-0373


title: Glioblastoma_gbm-0375


title: Glioblastoma_gbm-0349


title: Glioblastoma_gbm-0366


title: Rectal Colon Biopsy_SD52981_IBS-C [GP602R_112_39_SS103093]

description: Sample name: GP602R_112_39_SS103093


title: Rectal Colon Biopsy_SD52975_IBS-C [GP602R_100_85_SS103081]

description: Sample name: GP602R_100_85_SS103081


title: Rectal Colon Biopsy_SD52974_IBS-D [GP602R_98_97_SS103079]

description: Sample name: GP602R_98_97_SS103079


title: Rectal Colon Biopsy_SD52981_IBS-C [GP602R_111_47_SS103092]

description: Sample name: GP602R_111_47_SS103092


title: Glioblastoma_gbm-0346


title: Glioblastoma_gbm-0324


title: Glioblastoma_gbm-0345


title: Glioblastoma_gbm-0342


title: Rectal Colon Biopsy_SD52975_IBS-C [GP602R_99_80_SS103080]

description: Sample name: GP602R_99_80_SS103080


title: Rectal Colon Biopsy_SD52974_IBS-D [GP602R_97_101_SS103078]

description: Sample name: GP602R_97_101_SS103078


title: Glioblastoma_gbm-0311


title: Glioblastoma_gbm-0308


title: Rectal Colon Biopsy_SD52973_IBS-D [GP602R_96_14_SS103077]

description: Sample name: GP602R_96_14_SS103077


title: Rectal Colon Biopsy_SD52972_IBS-D [GP602R_94_72_SS103075]

description: Sample name: GP602R_94_72_SS103075


title: Glioblastoma_gbm-0292


title: Rectal Colon Biopsy_SD52973_IBS-D [GP602R_95_1_SS103076]

description: Sample name: GP602R_95_1_SS103076


title: Rectal Colon Biopsy_SD52971_IBS-D [GP602R_92_96_SS103073]

description: Sample name: GP602R_92_96_SS103073


title: Glioblastoma_gbm-0306


title: Rectal Colon Biopsy_SD52972_IBS-D [GP602R_93_78_SS103074]

description: Sample name: GP602R_93_78_SS103074


title: Glioblastoma_gbm-0335


title: Glioblastoma_gbm-0264


title: Glioblastoma_gbm-0287


title: Rectal Colon Biopsy_SD52970_IBS-D [GP602R_89_34_SS103070]

description: Sample name: GP602R_89_34_SS103070


title: Rectal Colon Biopsy_SD52968_IBS-D [GP602R_86_58_SS103067]

description: Sample name: GP602R_86_58_SS103067


title: Rectal Colon Biopsy_SD52969_IBS-D [GP602R_88_68_SS103069]

description: Sample name: GP602R_88_68_SS103069


title: Rectal Colon Biopsy_SD52969_IBS-D [GP602R_87_67_SS103068]

description: Sample name: GP602R_87_67_SS103068


title: Glioblastoma_gbm-0242


title: Glioblastoma_gbm-0240


title: Rectal Colon Biopsy_SD52970_IBS-D [GP602R_90_48_SS103071]

description: Sample name: GP602R_90_48_SS103071


title: Glioblastoma_gbm-0238


title: Rectal Colon Biopsy_SD52967_IBS-D [GP602R_84_86_SS103065]

description: Sample name: GP602R_84_86_SS103065


title: Glioblastoma_gbm-0255


title: Glioblastoma_gbm-0225


title: Rectal Colon Biopsy_SD52967_IBS-D [GP602R_83_89_SS103064]

description: Sample name: GP602R_83_89_SS103064


title: Rectal Colon Biopsy_SD52968_IBS-D [GP602R_85_65_SS103066]

description: Sample name: GP602R_85_65_SS103066


title: Rectal Colon Biopsy_SD52965_IBS-D [GP602R_79_137_SS103060]

description: Sample name: GP602R_79_137_SS103060


title: Rectal Colon Biopsy_SD52963_IBS-D [GP602R_76_93_SS103057]

description: Sample name: GP602R_76_93_SS103057


title: Rectal Colon Biopsy_SD52965_IBS-D [GP602R_80_121_SS103061]

description: Sample name: GP602R_80_121_SS103061